pax_global_header00006660000000000000000000000064146761332020014516gustar00rootroot0000000000000052 comment=c520c7ee965a740bfc05f7610808eca0ce7307fa weblogo-3.8.0/000077500000000000000000000000001467613320200131645ustar00rootroot00000000000000weblogo-3.8.0/.coveragerc000066400000000000000000000002361467613320200153060ustar00rootroot00000000000000[run] omit = weblogo/seq_io/_nexus/Nodes.py weblogo/seq_io/_nexus/Trees.py weblogo/seq_io/_nexus/__init__.py weblogo/utils/deoptparse.py weblogo/_cgi.pyweblogo-3.8.0/.github/000077500000000000000000000000001467613320200145245ustar00rootroot00000000000000weblogo-3.8.0/.github/workflows/000077500000000000000000000000001467613320200165615ustar00rootroot00000000000000weblogo-3.8.0/.github/workflows/python-build.yml000066400000000000000000000021741467613320200217260ustar00rootroot00000000000000# This workflow will install the python package and dependencies, and run tests against a variety of Python versions name: Build on: push: branches: [ master ] pull_request: branches: [ master ] schedule: - cron: "0 13 * * *" # Every day at 1pm UTC (6am PST) jobs: build: runs-on: ubuntu-latest strategy: matrix: python-version: ['3.9', '3.10', '3.11', '3.12'] steps: - uses: actions/checkout@v3 - name: Set up Python ${{ matrix.python-version }} uses: actions/setup-python@v4 with: python-version: ${{ matrix.python-version }} - name: Install dependencies run: | sudo apt-get update sudo apt-get install -y ghostscript python -m pip install --upgrade pip if [ -f requirements.txt ]; then pip install -r requirements.txt; fi python -m pip install . - name: Test with pytest run: | python -m pytest - name: Lint with black and isort (run `make delint` to fix issues) run: | black --check . isort --check . - name: Lint with flake8 run: | flake8 . weblogo-3.8.0/.github/workflows/python-publish.yml000066400000000000000000000015411467613320200222720ustar00rootroot00000000000000# This workflows will upload a Python Package using Twine when a release is created # For more information see: https://help.github.com/en/actions/language-and-framework-guides/using-python-with-github-actions#publishing-to-package-registries name: Upload Python Package on: release: types: [created] jobs: deploy: runs-on: ubuntu-latest steps: - uses: actions/checkout@v3 - name: Set up Python uses: actions/setup-python@v4 with: python-version: '3.x' - name: Install dependencies run: | python -m pip install --upgrade pip pip install setuptools wheel twine - name: Build and publish env: TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }} TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }} run: | python setup.py sdist bdist_wheel twine upload dist/* weblogo-3.8.0/.gitignore000066400000000000000000000027051467613320200151600ustar00rootroot00000000000000# Customizations .DS_Store tmp junk devnotes.txt version.py version.html # Standard python .gitignore # https://github.com/github/gitignore/blob/master/Python.gitignore # Byte-compiled / optimized / DLL files __pycache__/ *.py[cod] *$py.class # C extensions *.so # Distribution / packaging .Python build/ develop-eggs/ dist/ downloads/ eggs/ .eggs/ lib/ lib64/ parts/ sdist/ var/ wheels/ *.egg-info/ .installed.cfg *.egg MANIFEST # PyInstaller # Usually these files are written by a python script from a template # before PyInstaller builds the exe, so as to inject date/other infos into it. *.manifest *.spec # Installer logs pip-log.txt pip-delete-this-directory.txt # Unit test / coverage reports htmlcov/ .tox/ .nox/ .coverage .coverage.* .cache nosetests.xml coverage.xml *.cover .hypothesis/ .pytest_cache/ # Translations *.mo *.pot # Django stuff: *.log local_settings.py db.sqlite3 # Flask stuff: instance/ .webassets-cache # Scrapy stuff: .scrapy # Sphinx documentation docs/_build/ # PyBuilder target/ # Jupyter Notebook .ipynb_checkpoints # IPython profile_default/ ipython_config.py # pyenv .python-version # celery beat schedule file celerybeat-schedule # SageMath parsed files *.sage.py # Environments .env .venv env/ venv/ ENV/ env.bak/ venv.bak/ # Spyder project settings .spyderproject .spyproject # Rope project settings .ropeproject # mkdocs documentation /site # mypy .mypy_cache/ .dmypy.json dmypy.json # Pyre type checker .pyre/weblogo-3.8.0/.readthedocs.yml000066400000000000000000000006511467613320200162540ustar00rootroot00000000000000# Read the Docs configuration file for Sphinx projects # See https://docs.readthedocs.io/en/stable/config-file/v2.html for details # Required version: 2 # Set the OS, Python version and other tools you might need build: os: ubuntu-22.04 tools: python: "3.12" # Build documentation in the "docs/" directory with Sphinx sphinx: configuration: docs/conf.py python: install: - requirements: requirements.txt weblogo-3.8.0/CITATION.cff000066400000000000000000000011211467613320200150510ustar00rootroot00000000000000cff-version: 1.2.0 preferred-citation: authors: - family-names: "Crooks" given-names: "Gavin" - family-names: "Hon" given-names: "Gary" - family-names: "Chandonia" given-names: "John-Marc" - family-names: "Brenner" given-names: "Steven" title: "WebLogo: A Sequence Logo Generator" type: article journal: "Genome Research" volume: 14 start: 1188 end: 1190 year: 2004 doi: 10.1101/gr.849004 version: 3.8 date-released: 2024-03-03 license: MIT url: "http://weblogo.threeplusone.com/" repository-code: "https://github.com/WebLogo/weblogo" weblogo-3.8.0/DEVELOPERS.txt000066400000000000000000000020141467613320200153720ustar00rootroot00000000000000 ================== DEVELOPING WEBLOGO ================== --------------------------------------------- Procedure to Build and Release new versions --------------------------------------------- 1. Make sure local repository is up to date. The WebLogo repository is https://github.com/WebLogo/weblogo git pull origin master 2. Update changelog (weblogo/htdocs/weblogo_changelog.txt) 3. Update manual.html with the latest --help text. 4. Rebuild examples. cd weblogo/htdocs/examples bash build_examples.sh 5. Run tests make test 6. Run webpage tests. ./weblogo --serve # then goto localhost:8080/test.html and try tests 7. Commit final changes. 8. Tag tag release on Github at https://github.com/WebLogo/weblogo/releases/new (creating a new release with autoupdate pypi and conda packages) 10. Update server: login to weblogo.threeplusone.com, weblogo directory and switch branches git checkout 3.x.x 11. Check server is working correctly. Run tests at weblogo.threeplusone.com/tests.html weblogo-3.8.0/LICENSE.txt000066400000000000000000000030261467613320200150100ustar00rootroot00000000000000The MIT Open Source License =========================== Parts of the code are covered by the MIT license. Please refer to individual source code files for further details. # Copyright (c) 2003-2004 The Regents of the University of California. # Copyright (c) 2005 Gavin E. Crooks # Copyright (c) 2006 David Ding # Copyright (c) 2006 Clare Gollnick # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS # IN THE SOFTWARE. weblogo-3.8.0/Makefile000066400000000000000000000031371467613320200146300ustar00rootroot00000000000000# top-level pyquil Makefile NAME = weblogo FILES = $(NAME) tests docs/conf.py setup.py USER = -i ~/.ssh/aws_kaiju.pem ec2-user HOST = weblogo.threeplusone.com DIR = /home/ec2-user/weblogo # Kudos: Adapted from Auto-documenting default target # https://marmelab.com/blog/2016/02/29/auto-documented-makefile.html help: @grep -E '^[a-zA-Z_-]+:.*?## .*$$' $(MAKEFILE_LIST) | awk 'BEGIN {FS = ":.*?## "}; {printf "\033[36m%-12s\033[0m %s\n", $$1, $$2}' test: ## Run unittests with current enviroment @python -m pytest cov: ## Report test coverage @python -m pytest --cov=weblogo --cov-report term-missing lint: ## Lint check python source @isort --check $(FILES) || echo "isort: FAILED!" @black --check --quiet $(FILES) || echo "black: FAILED!" @flake8 $(FILES) delint: ## Run isort and black to delint project @echo isort $(FILES) @echo black $(FILES) @echo types: ## Report type errors and untyped functions @mypy weblogo tests --ignore-missing-imports --follow-imports=skip --disallow-untyped-defs docs: ## Build documentation $(MAKE) -C docs html && open docs/_build/html/index.html examples: ## Build examples cd weblogo/htdocs/examples && ./build_examples.sh login: ## ssh into remote server ssh ${USER}@${HOST} sync: ## Sync remote server ssh ${USER}@${HOST} 'cd weblogo && git pull' reinstall: ## Reinstall weblogo on remote server # pip install needed to update versions with latest git tag ssh ${USER}@${HOST} 'cd weblogo && sudo pip3 install -e .' restart: ## Restart remote server ssh ${USER}@${HOST} 'sudo systemctl restart httpd.service' .PHONY: help .PHONY: docsweblogo-3.8.0/README.md000066400000000000000000000075771467613320200144630ustar00rootroot00000000000000# WebLogo: A Sequence Logo Generator WebLogo is a web based application designed to make the generation of sequence logos as easy and painless as possible. WebLogo can create output in several common graphics' formats, including the bitmap formats GIF and PNG, suitable for on-screen display, and the vector formats EPS and PDF, more suitable for printing, publication, and further editing. Additional graphics options include bitmap resolution, titles, optional axis, and axis labels, antialiasing, error bars, and alternative symbol formats. A sequence logo is a graphical representation of an amino acid or nucleic acid multiple sequence alignment. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. The width of the stack is proportional to the fraction of valid symbols in that position. > References > Crooks GE, Hon G, Chandonia JM, Brenner SE WebLogo: A sequence logo generator, Genome Research, 14:1188-1190, (2004) [Full Text ](http://www.ncbi.nlm.nih.gov/pmc/articles/PMC419797/) > Schneider TD, Stephens RM. 1990. Sequence Logos: A New Way to Display Consensus Sequences. Nucleic Acids Res. 18:6097-6100 ## Current Software Version 3.7 ## WebLogo 2 The legacy WebLogo 2 server can be found here. ## Installation To install with pip: ```sh $ pip install weblogo ``` To install with conda: ```sh $ conda install -c conda-forge weblogo ``` ## Development To install the development version of WebLogo, clone the github repository. ```sh $ git clone git clone https://github.com/WebLogo/weblogo.git weblogo ``` Please consult the developer notes, DEVELOPERS.txt and software license LICENSE.txt Outstanding bugs and feature requests are listed on the WebLogo issue tracker. ## Open Source License This package is distributed under the The MIT Open Source License Open Source License. Much of the code was written by Gavin E. Crooks, Gary Hon, Steven Brenner, John-Marc Chandonia, Liana Lareau, David Ding, Clare Gollnick and other contributors. ## Copyright Notice Copyright (c) 2006, The Regents of the University of California, through Copyright (c) 2006-2011, The Regents of the University of California, through Lawrence Berkeley National Laboratory (subject to receipt of any required approvals from the U.S. Dept. of Energy). All rights reserved. Parts of this software package are covered by the individual copyrights of the contributors. Please refer to individual source code files for further details. Notice: This software was developed under funding from the U.S. Department of Energy. As such, the U.S. Government has been granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, and perform publicly and display publicly. Beginning five (5) years after the date permission to assert copyright is obtained from the U.S. Department of Energy, and subject to any subsequent five (5) year renewals, the U.S. Government is granted for itself and others acting on its behalf a paid-up, nonexclusive, irrevocable, worldwide license in the Software to reproduce, prepare derivative works, distribute copies to the public, perform publicly and display publicly, and to permit others to do so. ## Disclaimer While no permanent records are kept of submitted sequences, we cannot undertake to guarantee that data sent to WebLogo remains secure. Moreover, no guarantees whatsoever are provided about data generated by WebLogo. ## Labels: bioinformatics, python, biology, science, visualization weblogo-3.8.0/cap.fa000066400000000000000000000036561467613320200142510ustar00rootroot00000000000000>aldB -18->4 attcgtgatagctgtcgtaaag >ansB 103->125 ttttgttacctgcctctaactt >araB1 109->131 aagtgtgacgccgtgcaaataa >araB2 147->169 tgccgtgattatagacactttt >cdd 1 107->129 atttgcgatgcgtcgcgcattt >cdd 2 57->79 taatgagattcagatcacatat >crp 1 115->137 taatgtgacgtcctttgcatac >crp 2 gaaggcgacctgggtcatgctg >cya 151->173 aggtgttaaattgatcacgttt >cytR 1 125->147 cgatgcgaggcggatcgaaaaa >cytR 2 106->128 aaattcaatattcatcacactt >dadAX 1 95->117 agatgtgagccagctcaccata >dadAX 2 32->54 agatgtgattagattattattc >deoP2 1 75->97 aattgtgatgtgtatcgaagtg >deoP2 2 128->150 ttatttgaaccagatcgcatta >fur 136->158 aaatgtaagctgtgccacgttt >gal 56->78 aagtgtgacatggaataaatta >glpACB (glpTQ) 1 54->76 ttgtttgatttcgcgcatattc >glpACB (glpTQ) 2 94->116 aaacgtgatttcatgcgtcatt >glpACB (glpTQ) 144->166 atgtgtgcggcaattcacattt >glpD (glpE) 95->117 taatgttatacatatcactcta >glpFK 1 120->142 ttttatgacgaggcacacacat >glpFK 2 95->117 aagttcgatatttctcgttttt >gut (srlA) 72->94 ttttgcgatcaaaataacactt >ilvB 87->109 aaacgtgatcaacccctcaatt >lac 1 (lacZ) 88->110 taatgtgagttagctcactcat >lac 2 (lacZ) 16->38 aattgtgagcggataacaattt >malEpKp1 110->132 ttgtgtgatctctgttacagaa >malEpKp2 139->161 TAAtgtggagatgcgcacaTAA >malEpKp3 173->195 TTTtgcaagcaacatcacgAAA >malEpKp4 205->227 GACctcggtttagttcacaGAA >malT 121->143 aattgtgacacagtgcaaattc >melR 52->74 aaccgtgctcccactcgcagtc >mtl 302->324 TCTTGTGATTCAGATCACAAAG >nag 156->178 ttttgtgagttttgtcaccaaa >nupG2 97->119 aaatgttatccacatcacaatt >nupG1 47->69 ttatttgccacaggtaacaaaa >ompA 166->188 atgcctgacggagttcacactt >ompR 161->183 taacgtgatcatatcaacagaa >ptsH A 316->338 Ttttgtggcctgcttcaaactt >ptsH B 188->210 ttttatgatttggttcaattct >rhaS (rhaB) 161->183 aattgtgaacatcatcacgttc >rot 1 (ppiA) 182->204 ttttgtgatctgtttaaatgtt >rot 2 (ppiA) 129->151 agaggtgattttgatcacggaa >tdcA 60->82 atttgtgagtggtcgcacatat >tnaL 73->95 gattgtgattcgattcacattt >tsx 2 146->168 gtgtgtaaacgtgaacgcaatc >tsx 1 107->129 aactgtgaaacgaaacatattt >uxuAB 165->187 TCTTGTGATGTGGTTAACCAAT weblogo-3.8.0/changelog.txt000066400000000000000000000000621467613320200156520ustar00rootroot00000000000000 See weblogolib/htdocs/weblogo_changelog.txt weblogo-3.8.0/docs/000077500000000000000000000000001467613320200141145ustar00rootroot00000000000000weblogo-3.8.0/docs/Makefile000066400000000000000000000011041467613320200155500ustar00rootroot00000000000000# Minimal makefile for Sphinx documentation # # You can set these variables from the command line. SPHINXOPTS = SPHINXBUILD = sphinx-build SOURCEDIR = . BUILDDIR = _build # Put it first so that "make" without argument is like "make help". help: @$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O) .PHONY: help Makefile # Catch-all target: route all unknown targets to Sphinx using the new # "make mode" option. $(O) is meant as a shortcut for $(SPHINXOPTS). %: Makefile @$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)weblogo-3.8.0/docs/_static/000077500000000000000000000000001467613320200155425ustar00rootroot00000000000000weblogo-3.8.0/docs/_static/qf.css000066400000000000000000000044301467613320200166630ustar00rootroot00000000000000/* Overide guzzle.css defaults. https://github.com/guzzle/guzzle_sphinx_theme/blob/master/guzzle_sphinx_theme/guzzle_sphinx_theme/static/guzzle.css_t */ body { background-color: #fff; font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-size: 15px; line-height: 1.4; } #left-column { overflow: hidden; } #right-column { float: left; } h1 > a, h2 > a, h3 > a, h4 > a, h5 > a, h6 > a { color: #990000; } h1, h2, h3, h4, h5, h6 { color: #990000; font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; text-shadow: gray 1px 1px 1px; } h1 { font-size: 38px; background-color: #eee; } h2 { font-size: 28px; } h3 { font-size: 24px; } h4 { font-size: 20px; } h5 { font-size: 18px; } div.clearer { clear: both; } .container-wrapper { padding: 0; position: relative; } div.related { display: none; } p { padding: 0; font-family: inherit; font-size: inherit; color: #333; } code { padding: 2px 0.7px !important; } code, pre, tt { font-size: 16px; } pre { background-color: #f7f7f7; border-color: #f7f7f7; } div.highlight { background-color: none !important; } .breadcrumb { margin-bottom: -20px; margin-top: -20px; } div.sphinxsidebar { word-wrap: break-word; position: absolute; overflow-y: scroll; top: 0; left: 0; bottom: 0; right: -20px; height: 100%; } div.sphinxsidebar p { padding: 0px 10px; color: #666; text-transform: uppercase; font-size: 12px; font-weight: bold; letter-spacing: 1px; } div.sphinxsidebar .sidebar-toc a { font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; } .sidebar-block h2 { display: none; } .text-logo { font-size: 22px; color: #990000; font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; font-weight: normal; background-color: #eee; text-shadow: gray 1px 1px 1px; } .text-logo:hover { color: #fff; } .admonition-title { font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; } @media print{ .rst-versions,footer,.wy-nav-side{ display:none } .wy-nav-content-wrap{ margin-left:0 } } .rst-versions{ position:fixed; bottom:0; left:0; width:300px; color:#fcfcfc; background:#1f1d1d; font-family: "Helvetica Neue", Helvetica, Arial, sans-serif; z-index:400 } weblogo-3.8.0/docs/_templates/000077500000000000000000000000001467613320200162515ustar00rootroot00000000000000weblogo-3.8.0/docs/_templates/readme.txt000066400000000000000000000000001467613320200202350ustar00rootroot00000000000000weblogo-3.8.0/docs/conf.py000066400000000000000000000126751467613320200154260ustar00rootroot00000000000000# Configuration file for the Sphinx documentation builder. import os import sys import guzzle_sphinx_theme from setuptools_scm import get_version # Hack for readthedocs sys.path.insert(0, os.path.abspath("..")) __version__ = get_version(root="..", relative_to=__file__) print("__version__", __version__) with open("./_templates/version.html", "w") as f: f.write('
v%s
' % __version__) html_theme_path = guzzle_sphinx_theme.html_theme_path() html_theme = "guzzle_sphinx_theme" html_title = "WebLogo Documentation" html_short_title = "WebLogo" # Custom sidebar templates, maps document names to template names. html_sidebars = { "**": ["logo-text.html", "version.html", "searchbox.html", "globaltoc.html"] } def setup(app): app.add_stylesheet("qf.css") # -- Project information ----------------------------------------------------- project = "WebLogo" copyright = "2004-2018, Gavin E. Crooks" author = "Gavin E. Crooks" version = __version__ release = __version__ # -- General configuration --------------------------------------------------- # If your documentation needs a minimal Sphinx version, state it here. # # needs_sphinx = '1.0' # Add any Sphinx extension module names here, as strings. They can be # extensions coming with Sphinx (named 'sphinx.ext.*') or your custom # ones. extensions = [ "sphinx.ext.autodoc", "sphinx.ext.todo", "sphinx.ext.coverage", "sphinx.ext.mathjax", "sphinx.ext.githubpages", "sphinx.ext.napoleon", "sphinx.ext.doctest", ] # Add any paths that contain templates here, relative to this directory. templates_path = ["_templates"] # The suffix(es) of source filenames. # You can specify multiple suffix as a list of string: # # source_suffix = ['.rst', '.md'] source_suffix = ".rst" # The master toctree document. master_doc = "index" # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. # # This is also used if you do content translation via gettext catalogs. # Usually you set "language" from the command line for these cases. language = None # List of patterns, relative to source directory, that match files and # directories to ignore when looking for source files. # This pattern also affects html_static_path and html_extra_path. exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"] # The name of the Pygments (syntax highlighting) style to use. pygments_style = None # -- Options for HTML output ------------------------------------------------- # The theme to use for HTML and HTML Help pages. See the documentation for # a list of builtin themes. # # html_theme = "sphinx_rtd_theme" # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. # # html_theme_options = {} # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ["_static"] # Custom sidebar templates, must be a dictionary that maps document names # to template names. # # The default sidebars (for documents that don't match any pattern) are # defined by theme itself. Builtin themes are using these templates by # default: ``['localtoc.html', 'relations.html', 'sourcelink.html', # 'searchbox.html']``. # # html_sidebars = {} # -- Options for HTMLHelp output --------------------------------------------- # Output file base name for HTML help builder. htmlhelp_basename = "WebLogodoc" # -- Options for LaTeX output ------------------------------------------------ latex_elements = { # The paper size ('letterpaper' or 'a4paper'). # # 'papersize': 'letterpaper', # The font size ('10pt', '11pt' or '12pt'). # # 'pointsize': '10pt', # Additional stuff for the LaTeX preamble. # # 'preamble': '', # Latex figure (float) alignment # # 'figure_align': 'htbp', } # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, # author, documentclass [howto, manual, or own class]). latex_documents = [ (master_doc, "WebLogo.tex", "WebLogo Documentation", "Gavin E. Crooks", "manual"), ] # -- Options for manual page output ------------------------------------------ # One entry per manual page. List of tuples # (source start file, name, description, authors, manual section). man_pages = [(master_doc, "weblogo", "WebLogo Documentation", [author], 1)] # -- Options for Texinfo output ---------------------------------------------- # Grouping the document tree into Texinfo files. List of tuples # (source start file, target name, title, author, # dir menu entry, description, category) texinfo_documents = [ ( master_doc, "WebLogo", "WebLogo Documentation", author, "WebLogo", "One line description of project.", "Miscellaneous", ), ] # -- Options for Epub output ------------------------------------------------- # Bibliographic Dublin Core info. epub_title = project # The unique identifier of the text. This can be a ISBN number # or the project homepage. # # epub_identifier = '' # A unique identification for the text. # # epub_uid = '' # A list of files that should not be packed into the epub file. epub_exclude_files = ["search.html"] # -- Extension configuration ------------------------------------------------- weblogo-3.8.0/docs/formatting.rst000066400000000000000000000002261467613320200170200ustar00rootroot00000000000000=============== Logo Formatting =============== .. contents:: :local: .. currentmodule:: weblogo .. automodule:: weblogo.logo_formatter :members: weblogo-3.8.0/docs/index.rst000066400000000000000000000044671467613320200157700ustar00rootroot00000000000000.. WebLogo documentation master file, created by sphinx-quickstart on Sat Nov 3 20:56:21 2018. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. WebLogo 3: Sequence Logos Redrawn =================================== WebLogo is software designed to make the generation of sequence logos easy and painless. A sequence logo is a graphical representation of an amino acid or nucleic acid multiple sequence alignment. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. In general, a sequence logo provides a richer and more precise description of, for example, a binding site, than would a consensus sequence. WebLogo features a web interface (http://weblogo.threeplusone.com), and a command line interface provides more options and control (http://weblogo.threeplusone.com/manual.html#CLI). These pages document the API. The main WebLogo webserver is located at http://weblogo.threeplusone.com Please consult the manual for installation instructions and more information: (Also located in the weblogolib/htdocs subdirectory.) http://weblogo.threeplusone.com/manual.html For help on the command line interface run .. code-block:: console weblogo --help To build a simple logo run .. code-block:: console weblogo < cap.fa > logo0.eps To run as a standalone webserver at localhost:8080 .. code-block:: console weblogo --serve Distribution and Modification ----------------------------- This package is distributed under the MIT Open Source License. Please see the LICENSE.txt file for details on copyright and licensing. The WebLogo source code can be downloaded from https://github.com/WebLogo/weblogo WebLogo requires Python 3.6 or 3.7. Generating logos in PDF or bitmap graphics formats require that the ghostscript program 'gs' be installed. Scalable Vector Graphics (SVG) format also requires the program 'pdf2svg'. .. contents:: :local: .. currentmodule:: weblogo .. toctree:: :maxdepth: 3 :caption: Contents: intro seq seq_io logo formatting * :ref:`genindex` * :ref:`modindex` weblogo-3.8.0/docs/intro.html000066400000000000000000000000001467613320200161230ustar00rootroot00000000000000weblogo-3.8.0/docs/intro.rst000066400000000000000000000007241467613320200160040ustar00rootroot00000000000000=========== WebLogo API =========== .. contents:: :local: .. currentmodule:: weblogo To create a logo in python code: .. code-block:: python >>> from weblogo import * >>> fin = open('cap.fa') >>> seqs = read_seq_data(fin) >>> logodata = LogoData.from_seqs(seqs) >>> logooptions = LogoOptions() >>> logooptions.title = "A Logo Title" >>> logoformat = LogoFormat(logodata, logooptions) >>> eps = eps_formatter(logodata, logoformat) weblogo-3.8.0/docs/logo.rst000066400000000000000000000002721467613320200156070ustar00rootroot00000000000000============================== Logo Data, Options, and Format ============================== .. contents:: :local: .. currentmodule:: weblogo .. automodule:: weblogo.logo :members: weblogo-3.8.0/docs/seq.rst000066400000000000000000000002431467613320200154350ustar00rootroot00000000000000======================= Alphabets and Sequences ======================= .. contents:: :local: .. currentmodule:: weblogo .. automodule:: weblogo.seq :members: weblogo-3.8.0/docs/seq_io.rst000066400000000000000000000002021467613320200161170ustar00rootroot00000000000000=========== Sequence IO =========== .. contents:: :local: .. currentmodule:: weblogo .. automodule:: weblogo.seq_io :members: weblogo-3.8.0/requirements.txt000066400000000000000000000002111467613320200164420ustar00rootroot00000000000000numpy scipy setuptools setuptools-scm # Testing pytest >= 4.6 pytest-cov tox flake8 mypy isort black # Docs sphinx guzzle_sphinx_theme weblogo-3.8.0/setup.cfg000066400000000000000000000003711467613320200150060ustar00rootroot00000000000000 # Make isort compatible with black [isort] profile = black # flake8 linter configuration [flake8] exclude = _nexus max-line-length = 88 extend-ignore = E203, E501, W503 # mypy type enforcement configuration [mypy] exclude=weblogo/seq_io/_nexus/ weblogo-3.8.0/setup.py000077500000000000000000000044531467613320200147070ustar00rootroot00000000000000#!/usr/bin/env python from setuptools import setup long_description = """ WebLogo (https://github.com/WebLogo/weblogo) is a tool for creating sequence logos from biological sequence alignments. It can be run on the command line, as a standalone webserver, as a CGI webapp, or as a python library. The main WebLogo webserver is located at http://weblogo.threeplusone.com Please consult the manual for installation instructions and more information: ./weblogo/htdocs/manual.html (Also located at http://weblogo.threeplusone.com/manual.html.) """ setup( name="weblogo", python_requires=">=3.9", install_requires=["numpy", "scipy", "setuptools"], use_scm_version=True, setup_requires=["setuptools_scm"], description="WebLogo3 : Sequence Logos Redrawn", long_description=long_description, license="MIT", maintainer="Gavin Crooks", maintainer_email="gec@threeplusone.com", url="https://github.com/WebLogo/weblogo", classifiers=[ "Development Status :: 5 - Production/Stable", "Intended Audience :: Science/Research", "License :: OSI Approved :: MIT License", "Topic :: Scientific/Engineering :: Bio-Informatics", "Programming Language :: Python", "Natural Language :: English", "Operating System :: OS Independent", "Topic :: Software Development :: Libraries", "Topic :: Software Development :: Libraries :: Python Modules", # Specify the Python versions you support here. In particular, ensure # that you indicate whether you support Python 2, Python 3 or both. "Programming Language :: Python :: 3", "Programming Language :: Python :: 3.9", "Programming Language :: Python :: 3.10", "Programming Language :: Python :: 3.11", "Programming Language :: Python :: 3.12", ], packages=[ "weblogo", "weblogo.seq_io", "weblogo.seq_io._nexus", "weblogo.utils", ], package_data={ "weblogo": [ "htdocs/*.*", "htdocs/img/*.*", "htdocs/examples/*.*", "template.eps", "data/*.*", ] }, entry_points={ "console_scripts": [ "weblogo = weblogo._cli:main", "transformseq = weblogo._transformseq:main", ], }, ) weblogo-3.8.0/tests/000077500000000000000000000000001467613320200143265ustar00rootroot00000000000000weblogo-3.8.0/tests/__init__.py000077500000000000000000000007221467613320200164430ustar00rootroot00000000000000# TODO: replace with direct calls to pkg_resources from typing import TextIO from weblogo.utils import resource_filename, resource_stream, resource_string def data_string(name: str) -> bytes: return resource_string(__name__, "data/" + name, __file__) def data_stream(name: str) -> TextIO: return resource_stream(__name__, "data/" + name, __file__) def data_filename(name: str) -> str: return resource_filename(__name__, "data/" + name, __file__) weblogo-3.8.0/tests/build_test.sh000077500000000000000000000111671467613320200170310ustar00rootroot00000000000000#!/bin/bash mkdir -p tmp echo "# Test weblogo by building logos with many different options." echo -n '.' weblogo < cap.fa > tmp/logo0.eps ||exit echo -n '.' weblogo --title "Default Logo with Title" < cap.fa > tmp/logo1.eps ||exit echo -n '.' weblogo --debug yes --fineprint "Default Logo with this fineprint and debug on" < cap.fa > tmp/logo2.eps ||exit echo -n '.' weblogo --debug no --fineprint "--debug no" --debug no < cap.fa > tmp/logo3.eps ||exit echo -n '.' weblogo --debug yes --fineprint "" --title "No fine print" --debug yes < cap.fa > tmp/logo4.eps ||exit echo -n '.' weblogo --debug yes --fineprint "No title" --title "" < cap.fa > tmp/logo5.eps ||exit echo -n '.' weblogo --debug yes --fineprint "--first-index -10" --first-index -10 < cap.fa > tmp/logo6.eps ||exit echo -n '.' weblogo --debug yes --fineprint " --first-index -10 --stacks-per-line 11 " --first-index -10 --stacks-per-line 11 < cap.fa > tmp/logo7a.eps ||exit echo -n '.' weblogo --debug yes --fineprint " --first-index -10 --stacks-per-line 8 " --first-index -10 --stacks-per-line 8 < cap.fa > tmp/logo7b.eps ||exit echo -n '.' weblogo --debug yes --fineprint " --first-index -10 --stacks-per-line 7 " --first-index -10 --stacks-per-line 7 < cap.fa > tmp/logo7c.eps ||exit echo -n '.' weblogo --debug yes --fineprint "Test fin and fout" --fin cap.fa --fout tmp/logo8.eps ||exit # Test Y Axis echo -n '.' weblogo --debug yes --fineprint "Custom yaxis label " --ylabel 'yaxis label' < cap.fa > tmp/logo9a.eps ||exit echo -n '.' weblogo --debug yes --fineprint "Custom units" --units 'nats' < cap.fa > tmp/logo9b.eps ||exit echo -n '.' weblogo --debug yes --fineprint "Override custom units with custom yaxis label." --ylabel 'yaxis label' --units nats < cap.fa > tmp/logo9c.eps ||exit echo -n '.' weblogo --debug yes --fineprint "Empty ylabel" --ylabel '' < cap.fa > tmp/logo9d.eps echo -n '.' weblogo --debug yes --fineprint "No Yaxis" --show-yaxis no < cap.fa > tmp/logo9e.eps ||exit # Test X Axis echo -n '.' weblogo --debug yes --format pdf --fineprint "Custom xaxis label " --xlabel 'xaxis label' < cap.fa > tmp/logo10a.pdf ||exit echo -n '.' weblogo --debug yes --format pdf --fineprint "Empty xlabel" --xlabel '' < cap.fa > tmp/logo10b.pdf ||exit echo -n '.' weblogo --debug yes --format pdf --fineprint "No Xaxis" --show-xaxis no < cap.fa > tmp/logo10c.pdf ||exit echo -n '.' weblogo --debug yes --format pdf --fineprint "No Xaxis, custom label" --xlabel "Custom xlabel" --show-xaxis no < cap.fa > tmp/logo10d.pdf ||exit # Test Formats echo -n '.' weblogo --debug no --fineprint "Format: eps" --format eps < cap.fa > tmp/logo11a.eps ||exit echo -n '.' weblogo --debug no --fineprint "Format: png" --size large --format png < cap.fa > tmp/logo11b.png ||exit echo -n '.' weblogo --debug no --fineprint "Format: png high res" --format png_print < cap.fa > tmp/logo11c.png ||exit echo -n '.' weblogo --debug no --fineprint "Format: pdf" --format pdf < cap.fa > tmp/logo11d.pdf ||exit echo -n '.' weblogo --debug no --fineprint "Format: jpeg" --size large --format jpeg < cap.fa > tmp/logo11e.jpeg ||exit echo -n '.' weblogo --debug no --fineprint "Format: EPS" --format EPS < cap.fa > tmp/logo11f.eps ||exit # Test Sizes echo -n '.' weblogo --debug no --format png_print --fineprint "default size" < cap.fa > tmp/logo12_default.png ||exit echo -n '.' weblogo --debug no --format png_print --fineprint "--size large" --size large < cap.fa > tmp/logo12_large.png ||exit echo -n '.' weblogo --debug no --format png_print --fineprint "--size medium" --size medium < cap.fa > tmp/logo12_medium.png ||exit echo -n '.' weblogo --debug no --format png_print --fineprint "--size small" --size small < cap.fa > tmp/logo12_small.png ||exit echo -n '.' weblogo --format pdf --fineprint "" > tmp/logo13.pdf << LimitString > GTTGTTGTTGTT > GTCGTCGTCGTC > GGGGGGGGGGGG > GGAGGAGGAGGA LimitString # Test unit options echo -n '.' weblogo --format pdf --fineprint "probability" --unit probability > tmp/logo14a.pdf < cap.fa ||exit echo -n '.' weblogo --format pdf --fineprint "bits" --unit bits > tmp/logo14b.pdf < cap.fa ||exit echo -n '.' weblogo --format pdf --fineprint "nats" --unit nats > tmp/logo14c.pdf < cap.fa ||exit echo -n '.' weblogo --format pdf --fineprint "kJ/mol" --unit kJ/mol \ > tmp/logo14d.pdf < cap.fa ||exit echo -n '.' weblogo --format pdf --fineprint "kT" --unit kT \ > tmp/logo14e.pdf < cap.fa ||exit echo -n '.' weblogo --format pdf --fineprint "kcal/mol" --unit kcal/mol \ > tmp/logo14f.pdf < cap.fa || exit echo -n '.' weblogo --format pdf --alphabet 'AGTC' > tmp/logo15.pdf < cap.fa || exit echo weblogo-3.8.0/tests/data/000077500000000000000000000000001467613320200152375ustar00rootroot00000000000000weblogo-3.8.0/tests/data/1CGP.pdb000077500000000000000000015441601467613320200164360ustar00rootroot00000000000000HEADER GENE-REGULATORY PROTEIN 12-AUG-91 1CGP 1CGP 2 COMPND CATABOLITE GENE ACTIVATOR PROTEIN COMPLEX WITH DNA 1CGP 3 COMPND 2 (CAP-DNA COMPLEX) 1CGP 4 SOURCE (ESCHERICHIA COLI) 1CGP 5 AUTHOR S.C.SCHULTZ,G.C.SHIELDS,T.A.STEITZ 1CGP 6 REVDAT 2 15-OCT-94 1CGPA 1 JRNL 1CGPA 1 REVDAT 1 31-JAN-94 1CGP 0 1CGP 7 JRNL AUTH S.C.SCHULTZ,G.C.SHIELDS,T.A.STEITZ 1CGP 8 JRNL TITL CRYSTAL STRUCTURE OF A CAP-DNA COMPLEX: THE DNA 1CGP 9 JRNL TITL 2 IS BENT BY 90 DEGREES 1CGP 10 JRNL REF SCIENCE V. 253 1001 1991 1CGPA 2 JRNL REFN ASTM SCIEAS US ISSN 0036-8075 038 1CGP 12 REMARK 1 1CGP 13 REMARK 1 REFERENCE 1 1CGP 14 REMARK 1 AUTH M.-C.VANEY,G.L.GILLILAND,J.G.HARMAN,A.PETERKOFSKY, 1CGP 15 REMARK 1 AUTH 2 I.T.WEBER 1CGP 16 REMARK 1 TITL CRYSTAL STRUCTURE OF A CAMP-INDEPENDENT FORM OF 1CGP 17 REMARK 1 TITL 2 CATABOLITE GENE ACTIVATOR PROTEIN WITH ADENOSINE 1CGP 18 REMARK 1 TITL 3 SUBSTITUTED IN ONE OF TWO CAMP-BINDING SITES 1CGP 19 REMARK 1 REF BIOCHEMISTRY V. 28 4568 1989 1CGP 20 REMARK 1 REFN ASTM BICHAW US ISSN 0006-2960 033 1CGP 21 REMARK 2 1CGP 22 REMARK 2 RESOLUTION. 3.0 ANGSTROMS. 1CGP 23 REMARK 3 1CGP 24 REMARK 3 REFINEMENT. 1CGP 25 REMARK 3 PROGRAM X-PLOR 1CGP 26 REMARK 3 AUTHORS BRUNGER 1CGP 27 REMARK 3 R VALUE 0.235 1CGP 28 REMARK 3 RMSD BOND DISTANCES 0.014 ANGSTROMS 1CGP 29 REMARK 3 RMSD BOND ANGLES 3.4 DEGREES 1CGP 30 REMARK 3 1CGP 31 REMARK 3 NUMBER OF PROTEIN ATOMS 3112 1CGP 32 REMARK 3 NUMBER OF DNA ATOMS 1262 1CGP 33 REMARK 4 1CGP 34 REMARK 4 THE SHEET STRUCTURE GIVEN BELOW HAS BEEN DESCRIBED BY THE 1CGP 35 REMARK 4 DEPOSITORS AS A *BETA ROLL*. THE STRANDS HAVE BEEN RENAMED 1CGP 36 REMARK 4 BY THE PROTEIN DATA BANK IN ORDER TO DESCRIBE THE SHEET 1CGP 37 REMARK 4 STRUCTURE CONSISTENT WITH DATA BANK SPECIFICATIONS. 1CGP 38 REMARK 4 THE FOLLOWING TABLE GIVES THE CORRESPONDING STRAND NAMES, 1CGP 39 REMARK 4 1CGP 40 REMARK 4 DEPOSITOR,S ORIGINAL PROTEIN DATA BANK 1CGP 41 REMARK 4 NAME NAME 1CGP 42 REMARK 4 1CGP 43 REMARK 4 1. BETA-1 STRAND 1 AA 1CGP 44 REMARK 4 2. BETA-2 STRAND 1 BA 1CGP 45 REMARK 4 3. BETA-3 STRAND 3 AA 1CGP 46 REMARK 4 4. BETA-4 STRAND 3 BA 1CGP 47 REMARK 4 5. BETA-5 STRAND 4 BA 1CGP 48 REMARK 4 6. BETA-6 STRAND 4 AA 1CGP 49 REMARK 4 7. BETA-7 STRAND 2 BA 1CGP 50 REMARK 4 8. BETA-8 STRAND 2 AA 1CGP 51 REMARK 4 1CGP 52 REMARK 4 THE BETA ROLL CONSISTS OF STRANDS BETA-1, BETA-8, BETA-3 1CGP 53 REMARK 4 AND BETA-6 ON ONE SIDE AND STRANDS BETA-2, BETA-7, BETA-4, 1CGP 54 REMARK 4 AND BETA-5 ON THE OTHER SIDE. 1CGP 55 REMARK 5 1CGP 56 REMARK 5 SITE *S1* CONSTITUTES THE RESIDUES WHICH INTERACT WITH 1CGP 57 REMARK 5 CYCLIC AMP. 1CGP 58 REMARK 6 1CGPA 3 REMARK 6 CORRECTION. CORRECT VOLUME NUMBER FOR JRNL REFERENCE. 1CGPA 4 REMARK 6 15-OCT-94. 1CGPA 5 SEQRES 1 A 205 VAL LEU GLY LYS PRO GLN THR ASP PRO THR LEU GLU TRP 1CGP 59 SEQRES 2 A 205 PHE LEU SER HIS CYS HIS ILE HIS LYS TYR PRO SER LYS 1CGP 60 SEQRES 3 A 205 SER THR LEU ILE HIS GLN GLY GLU LYS ALA GLU THR LEU 1CGP 61 SEQRES 4 A 205 TYR TYR ILE VAL LYS GLY SER VAL ALA VAL LEU ILE LYS 1CGP 62 SEQRES 5 A 205 ASP GLU GLU GLY LYS GLU MET ILE LEU SER TYR LEU ASN 1CGP 63 SEQRES 6 A 205 GLN GLY ASP PHE ILE GLY GLU LEU GLY LEU PHE GLU GLU 1CGP 64 SEQRES 7 A 205 GLY GLN GLU ARG SER ALA TRP VAL ARG ALA LYS THR ALA 1CGP 65 SEQRES 8 A 205 CYS GLU VAL ALA GLU ILE SER TYR LYS LYS PHE ARG GLN 1CGP 66 SEQRES 9 A 205 LEU ILE GLN VAL ASN PRO ASP ILE LEU MET ARG LEU SER 1CGP 67 SEQRES 10 A 205 ALA GLN MET ALA ARG ARG LEU GLN VAL THR SER GLU LYS 1CGP 68 SEQRES 11 A 205 VAL GLY ASN LEU ALA PHE LEU ASP VAL THR GLY ARG ILE 1CGP 69 SEQRES 12 A 205 ALA GLN THR LEU LEU ASN LEU ALA LYS GLN PRO ASP ALA 1CGP 70 SEQRES 13 A 205 MET THR HIS PRO ASP GLY MET GLN ILE LYS ILE THR ARG 1CGP 71 SEQRES 14 A 205 GLN GLU ILE GLY GLN ILE VAL GLY CYS SER ARG GLU THR 1CGP 72 SEQRES 15 A 205 VAL GLY ARG ILE LEU LYS MET LEU GLU ASP GLN ASN LEU 1CGP 73 SEQRES 16 A 205 ILE SER ALA HIS GLY LYS THR ILE VAL VAL 1CGP 74 SEQRES 1 B 205 VAL LEU GLY LYS PRO GLN THR ASP PRO THR LEU GLU TRP 1CGP 75 SEQRES 2 B 205 PHE LEU SER HIS CYS HIS ILE HIS LYS TYR PRO SER LYS 1CGP 76 SEQRES 3 B 205 SER THR LEU ILE HIS GLN GLY GLU LYS ALA GLU THR LEU 1CGP 77 SEQRES 4 B 205 TYR TYR ILE VAL LYS GLY SER VAL ALA VAL LEU ILE LYS 1CGP 78 SEQRES 5 B 205 ASP GLU GLU GLY LYS GLU MET ILE LEU SER TYR LEU ASN 1CGP 79 SEQRES 6 B 205 GLN GLY ASP PHE ILE GLY GLU LEU GLY LEU PHE GLU GLU 1CGP 80 SEQRES 7 B 205 GLY GLN GLU ARG SER ALA TRP VAL ARG ALA LYS THR ALA 1CGP 81 SEQRES 8 B 205 CYS GLU VAL ALA GLU ILE SER TYR LYS LYS PHE ARG GLN 1CGP 82 SEQRES 9 B 205 LEU ILE GLN VAL ASN PRO ASP ILE LEU MET ARG LEU SER 1CGP 83 SEQRES 10 B 205 ALA GLN MET ALA ARG ARG LEU GLN VAL THR SER GLU LYS 1CGP 84 SEQRES 11 B 205 VAL GLY ASN LEU ALA PHE LEU ASP VAL THR GLY ARG ILE 1CGP 85 SEQRES 12 B 205 ALA GLN THR LEU LEU ASN LEU ALA LYS GLN PRO ASP ALA 1CGP 86 SEQRES 13 B 205 MET THR HIS PRO ASP GLY MET GLN ILE LYS ILE THR ARG 1CGP 87 SEQRES 14 B 205 GLN GLU ILE GLY GLN ILE VAL GLY CYS SER ARG GLU THR 1CGP 88 SEQRES 15 B 205 VAL GLY ARG ILE LEU LYS MET LEU GLU ASP GLN ASN LEU 1CGP 89 SEQRES 16 B 205 ILE SER ALA HIS GLY LYS THR ILE VAL VAL 1CGP 90 SEQRES 1 C 31 G T C A C A C T T T T C G 1CGP 91 SEQRES 2 C 31 G C G A A A A G T G T G A 1CGP 92 SEQRES 3 C 31 C A T A T 1CGP 93 SEQRES 1 D 31 G T C A C A C T T T T C G 1CGP 94 SEQRES 2 D 31 G C G A A A A G T G T G A 1CGP 95 SEQRES 3 D 31 C A T A T 1CGP 96 FTNOTE 1 1CGP 97 FTNOTE 1 HIS A 159 - PRO A 160 OMEGA ANGLE = 215.267 1CGP 98 FTNOTE 1 PEPTIDE BOND DEVIATES SIGNIFICANTLY FROM TRANS CONFORMATION 1CGP 99 HET CMP A 1 25 CYCLIC AMP 1CGP 100 HET CMP B 2 25 CYCLIC AMP 1CGP 101 FORMUL 5 CMP 2(C10 H12 N5 O6 P1) 1CGP 102 HELIX 1 AA PRO A 9 CYS A 18 1 1CGP 103 HELIX 2 BA TYR A 99 PRO A 110 1 1CGP 104 HELIX 3 CA ILE A 112 GLY A 132 1 1CGP 105 HELIX 4 DA THR A 140 ALA A 151 1 1CGP 106 HELIX 5 EA THR A 168 VAL A 176 1 1CGP 107 HELIX 6 FA ARG A 180 GLU A 191 1 1CGP 108 HELIX 7 AB PRO B 9 CYS B 18 1 1CGP 109 HELIX 8 BB TYR B 99 PRO B 110 1 1CGP 110 HELIX 9 CB ILE B 112 GLU B 129 1 1CGP 111 HELIX 10 DB THR B 140 ALA B 151 1 1CGP 112 HELIX 11 EB THR B 168 VAL B 176 1 1CGP 113 HELIX 12 FB ARG B 180 GLU B 191 1 1CGP 114 SHEET 1 AA 4 HIS A 19 TYR A 23 0 1CGP 115 SHEET 2 AA 4 THR A 90 SER A 98 -1 1CGP 116 SHEET 3 AA 4 GLU A 34 ILE A 42 -1 1CGP 117 SHEET 4 AA 4 ASP A 68 ILE A 70 -1 1CGP 118 SHEET 1 BA 4 SER A 27 GLN A 32 0 1CGP 119 SHEET 2 BA 4 GLU A 77 ALA A 88 -1 1CGP 120 SHEET 3 BA 4 ALA A 48 LYS A 52 -1 1CGP 121 SHEET 4 BA 4 GLU A 58 LEU A 64 -1 1CGP 122 SHEET 1 CA 4 MET A 157 PRO A 160 0 1CGP 123 SHEET 2 CA 4 ASP A 161 ILE A 165 -1 1CGP 124 SHEET 3 CA 4 LYS A 201 VAL A 205 -1 1CGP 125 SHEET 4 CA 4 LEU A 195 HIS A 199 -1 1CGP 126 SHEET 1 AB 4 HIS B 19 TYR B 23 0 1CGP 127 SHEET 2 AB 4 THR B 90 SER B 98 -1 1CGP 128 SHEET 3 AB 4 GLU B 34 ILE B 42 -1 1CGP 129 SHEET 4 AB 4 ASP B 68 ILE B 70 -1 1CGP 130 SHEET 1 BB 4 SER B 27 GLN B 32 0 1CGP 131 SHEET 2 BB 4 GLU B 77 ALA B 88 -1 1CGP 132 SHEET 3 BB 4 ALA B 48 LYS B 52 -1 1CGP 133 SHEET 4 BB 4 GLU B 58 LEU B 64 -1 1CGP 134 SHEET 1 CB 4 MET B 157 PRO B 160 0 1CGP 135 SHEET 2 CB 4 ASP B 161 ILE B 165 -1 1CGP 136 SHEET 3 CB 4 LYS B 201 VAL B 205 -1 1CGP 137 SHEET 4 CB 4 LEU B 195 HIS B 199 -1 1CGP 138 SITE 1 S1A 20 ILE A 30 VAL A 49 LEU A 61 SER A 62 1CGP 139 SITE 2 S1A 20 TYR A 63 LEU A 64 GLY A 71 GLU A 72 1CGP 140 SITE 3 S1A 20 LEU A 73 ARG A 82 SER A 83 ALA A 84 1CGP 141 SITE 4 S1A 20 TRP A 85 VAL A 86 ARG A 123 LEU A 124 1CGP 142 SITE 5 S1A 20 GLN A 125 VAL A 126 THR A 127 SER B 128 1CGP 143 SITE 1 S1B 20 ILE B 30 VAL B 49 LEU B 61 SER B 62 1CGP 144 SITE 2 S1B 20 TYR B 63 LEU B 64 GLY B 71 GLU B 72 1CGP 145 SITE 3 S1B 20 LEU B 73 ARG B 82 SER B 83 ALA B 84 1CGP 146 SITE 4 S1B 20 TRP B 85 VAL B 86 ARG B 123 LEU B 124 1CGP 147 SITE 5 S1B 20 GLN B 125 VAL B 126 THR B 127 SER A 128 1CGP 148 CRYST1 138.000 152.600 76.000 90.00 90.00 90.00 C 2 2 21 16 1CGP 149 ORIGX1 1.000000 0.000000 0.000000 0.00000 1CGP 150 ORIGX2 0.000000 1.000000 0.000000 0.00000 1CGP 151 ORIGX3 0.000000 0.000000 1.000000 0.00000 1CGP 152 SCALE1 0.007246 0.000000 0.000000 0.00000 1CGP 153 SCALE2 0.000000 0.006553 0.000000 0.00000 1CGP 154 SCALE3 0.000000 0.000000 0.013158 0.00000 1CGP 155 ATOM 1 N PRO A 9 32.555 55.928 33.201 1.00 82.62 1CGP 156 ATOM 2 CA PRO A 9 31.300 56.105 32.474 1.00 82.25 1CGP 157 ATOM 3 C PRO A 9 30.441 54.837 32.272 1.00 81.70 1CGP 158 ATOM 4 O PRO A 9 30.717 53.724 32.761 1.00 80.50 1CGP 159 ATOM 5 CB PRO A 9 31.739 56.735 31.148 1.00 81.60 1CGP 160 ATOM 6 CG PRO A 9 33.025 57.434 31.456 1.00 81.77 1CGP 161 ATOM 7 CD PRO A 9 33.667 56.405 32.380 1.00 82.49 1CGP 162 ATOM 8 N THR A 10 29.403 55.045 31.429 1.00 80.95 1CGP 163 ATOM 9 CA THR A 10 28.528 54.017 30.858 1.00 78.09 1CGP 164 ATOM 10 C THR A 10 29.421 52.851 30.397 1.00 77.84 1CGP 165 ATOM 11 O THR A 10 29.233 51.665 30.651 1.00 77.16 1CGP 166 ATOM 12 CB THR A 10 27.762 54.735 29.696 1.00 76.00 1CGP 167 ATOM 13 OG1 THR A 10 27.021 55.812 30.270 1.00 73.16 1CGP 168 ATOM 14 CG2 THR A 10 26.838 53.811 28.943 1.00 76.54 1CGP 169 ATOM 15 H THR A 10 29.122 55.965 31.232 1.00 0.00 1CGP 170 ATOM 16 HG1 THR A 10 26.086 55.541 30.227 1.00 0.00 1CGP 171 ATOM 17 N LEU A 11 30.494 53.298 29.750 1.00 78.01 1CGP 172 ATOM 18 CA LEU A 11 31.625 52.524 29.280 1.00 78.45 1CGP 173 ATOM 19 C LEU A 11 32.029 51.324 30.137 1.00 77.79 1CGP 174 ATOM 20 O LEU A 11 32.040 50.195 29.640 1.00 78.36 1CGP 175 ATOM 21 CB LEU A 11 32.774 53.529 29.160 1.00 79.81 1CGP 176 ATOM 22 CG LEU A 11 33.797 53.479 28.042 1.00 80.69 1CGP 177 ATOM 23 CD1 LEU A 11 34.770 52.319 28.232 1.00 79.74 1CGP 178 ATOM 24 CD2 LEU A 11 33.017 53.438 26.729 1.00 80.99 1CGP 179 ATOM 25 H LEU A 11 30.496 54.249 29.526 1.00 0.00 1CGP 180 ATOM 26 N GLU A 12 32.285 51.521 31.437 1.00 75.90 1CGP 181 ATOM 27 CA GLU A 12 32.814 50.465 32.298 1.00 73.47 1CGP 182 ATOM 28 C GLU A 12 31.768 49.404 32.597 1.00 70.22 1CGP 183 ATOM 29 O GLU A 12 32.028 48.196 32.656 1.00 67.77 1CGP 184 ATOM 30 CB GLU A 12 33.311 51.085 33.587 1.00 76.42 1CGP 185 ATOM 31 CG GLU A 12 34.349 52.200 33.389 1.00 81.10 1CGP 186 ATOM 32 CD GLU A 12 35.652 51.820 32.661 1.00 84.42 1CGP 187 ATOM 33 OE1 GLU A 12 36.352 50.891 33.102 1.00 85.75 1CGP 188 ATOM 34 OE2 GLU A 12 35.977 52.487 31.665 1.00 85.97 1CGP 189 ATOM 35 H GLU A 12 32.002 52.364 31.856 1.00 0.00 1CGP 190 ATOM 36 N TRP A 13 30.541 49.899 32.743 1.00 68.38 1CGP 191 ATOM 37 CA TRP A 13 29.363 49.077 32.953 1.00 66.37 1CGP 192 ATOM 38 C TRP A 13 29.215 48.167 31.748 1.00 66.16 1CGP 193 ATOM 39 O TRP A 13 28.880 46.996 31.899 1.00 65.63 1CGP 194 ATOM 40 CB TRP A 13 28.130 49.987 33.124 1.00 65.28 1CGP 195 ATOM 41 CG TRP A 13 26.826 49.329 32.707 1.00 64.32 1CGP 196 ATOM 42 CD1 TRP A 13 26.175 48.459 33.532 1.00 64.89 1CGP 197 ATOM 43 CD2 TRP A 13 26.199 49.483 31.502 1.00 64.47 1CGP 198 ATOM 44 NE1 TRP A 13 25.134 48.052 32.847 1.00 64.56 1CGP 199 ATOM 45 CE2 TRP A 13 25.118 48.635 31.643 1.00 64.51 1CGP 200 ATOM 46 CE3 TRP A 13 26.391 50.187 30.340 1.00 65.01 1CGP 201 ATOM 47 CZ2 TRP A 13 24.202 48.474 30.634 1.00 64.95 1CGP 202 ATOM 48 CZ3 TRP A 13 25.473 50.032 29.328 1.00 65.40 1CGP 203 ATOM 49 CH2 TRP A 13 24.394 49.186 29.473 1.00 65.24 1CGP 204 ATOM 50 H TRP A 13 30.434 50.870 32.694 1.00 0.00 1CGP 205 ATOM 51 HE1 TRP A 13 24.398 47.527 33.225 1.00 0.00 1CGP 206 ATOM 52 N PHE A 14 29.379 48.735 30.555 1.00 66.97 1CGP 207 ATOM 53 CA PHE A 14 29.349 47.966 29.329 1.00 66.91 1CGP 208 ATOM 54 C PHE A 14 30.439 46.889 29.402 1.00 68.84 1CGP 209 ATOM 55 O PHE A 14 30.143 45.695 29.586 1.00 68.24 1CGP 210 ATOM 56 CB PHE A 14 29.533 48.979 28.162 1.00 63.74 1CGP 211 ATOM 57 CG PHE A 14 30.113 48.411 26.873 1.00 61.04 1CGP 212 ATOM 58 CD1 PHE A 14 29.349 47.596 26.058 1.00 58.64 1CGP 213 ATOM 59 CD2 PHE A 14 31.440 48.668 26.565 1.00 60.12 1CGP 214 ATOM 60 CE1 PHE A 14 29.928 47.044 24.941 1.00 57.10 1CGP 215 ATOM 61 CE2 PHE A 14 32.005 48.101 25.446 1.00 58.90 1CGP 216 ATOM 62 CZ PHE A 14 31.251 47.286 24.634 1.00 58.12 1CGP 217 ATOM 63 H PHE A 14 29.436 49.714 30.531 1.00 0.00 1CGP 218 ATOM 64 N LEU A 15 31.702 47.347 29.410 1.00 71.07 1CGP 219 ATOM 65 CA LEU A 15 32.885 46.492 29.348 1.00 74.00 1CGP 220 ATOM 66 C LEU A 15 32.976 45.328 30.308 1.00 75.64 1CGP 221 ATOM 67 O LEU A 15 33.565 44.293 29.970 1.00 76.82 1CGP 222 ATOM 68 CB LEU A 15 34.147 47.335 29.513 1.00 73.58 1CGP 223 ATOM 69 CG LEU A 15 34.622 48.059 28.268 1.00 73.87 1CGP 224 ATOM 70 CD1 LEU A 15 35.794 48.953 28.623 1.00 74.11 1CGP 225 ATOM 71 CD2 LEU A 15 35.025 47.042 27.205 1.00 73.61 1CGP 226 ATOM 72 H LEU A 15 31.833 48.317 29.444 1.00 0.00 1CGP 227 ATOM 73 N SER A 16 32.393 45.475 31.501 1.00 76.48 1CGP 228 ATOM 74 CA SER A 16 32.309 44.372 32.446 1.00 75.72 1CGP 229 ATOM 75 C SER A 16 31.644 43.125 31.871 1.00 74.45 1CGP 230 ATOM 76 O SER A 16 31.774 42.045 32.452 1.00 75.22 1CGP 231 ATOM 77 CB SER A 16 31.542 44.809 33.694 1.00 76.42 1CGP 232 ATOM 78 OG SER A 16 30.303 45.412 33.381 1.00 76.49 1CGP 233 ATOM 79 H SER A 16 32.134 46.370 31.809 1.00 0.00 1CGP 234 ATOM 80 HG SER A 16 30.489 46.302 33.068 1.00 0.00 1CGP 235 ATOM 81 N HIS A 17 30.896 43.199 30.769 1.00 71.48 1CGP 236 ATOM 82 CA HIS A 17 30.333 41.988 30.235 1.00 69.94 1CGP 237 ATOM 83 C HIS A 17 30.662 41.886 28.779 1.00 69.47 1CGP 238 ATOM 84 O HIS A 17 29.831 41.880 27.869 1.00 70.35 1CGP 239 ATOM 85 CB HIS A 17 28.825 41.902 30.402 1.00 68.45 1CGP 240 ATOM 86 CG HIS A 17 27.990 43.027 30.965 1.00 67.01 1CGP 241 ATOM 87 ND1 HIS A 17 26.699 43.226 30.747 1.00 65.83 1CGP 242 ATOM 88 CD2 HIS A 17 28.433 44.007 31.795 1.00 66.40 1CGP 243 ATOM 89 CE1 HIS A 17 26.368 44.295 31.420 1.00 66.71 1CGP 244 ATOM 90 NE2 HIS A 17 27.424 44.761 32.036 1.00 66.75 1CGP 245 ATOM 91 H HIS A 17 30.718 44.055 30.331 1.00 0.00 1CGP 246 ATOM 92 HD1 HIS A 17 26.131 42.750 30.107 1.00 0.00 1CGP 247 ATOM 93 HE2 HIS A 17 27.551 45.661 32.413 1.00 0.00 1CGP 248 ATOM 94 N CYS A 18 31.966 41.723 28.683 1.00 68.54 1CGP 249 ATOM 95 CA CYS A 18 32.686 41.571 27.449 1.00 68.19 1CGP 250 ATOM 96 C CYS A 18 33.850 40.685 27.810 1.00 68.99 1CGP 251 ATOM 97 O CYS A 18 34.449 40.846 28.873 1.00 69.50 1CGP 252 ATOM 98 CB CYS A 18 33.317 42.837 26.940 1.00 67.08 1CGP 253 ATOM 99 SG CYS A 18 32.222 44.082 26.249 1.00 66.60 1CGP 254 ATOM 100 H CYS A 18 32.515 41.746 29.502 1.00 0.00 1CGP 255 ATOM 101 N HIS A 19 34.229 39.781 26.906 1.00 69.89 1CGP 256 ATOM 102 CA HIS A 19 35.385 38.909 27.122 1.00 69.55 1CGP 257 ATOM 103 C HIS A 19 36.474 39.620 26.355 1.00 66.70 1CGP 258 ATOM 104 O HIS A 19 36.391 39.791 25.133 1.00 65.31 1CGP 259 ATOM 105 CB HIS A 19 35.256 37.525 26.507 1.00 73.16 1CGP 260 ATOM 106 CG HIS A 19 33.822 37.063 26.393 1.00 76.98 1CGP 261 ATOM 107 ND1 HIS A 19 32.846 37.673 25.717 1.00 79.38 1CGP 262 ATOM 108 CD2 HIS A 19 33.315 35.938 26.986 1.00 77.77 1CGP 263 ATOM 109 CE1 HIS A 19 31.764 36.966 25.887 1.00 80.49 1CGP 264 ATOM 110 NE2 HIS A 19 32.052 35.924 26.645 1.00 80.72 1CGP 265 ATOM 111 H HIS A 19 33.786 39.841 26.038 1.00 0.00 1CGP 266 ATOM 112 HD1 HIS A 19 32.886 38.480 25.156 1.00 0.00 1CGP 267 ATOM 113 HE2 HIS A 19 31.423 35.188 26.818 1.00 0.00 1CGP 268 ATOM 114 N ILE A 20 37.414 40.104 27.144 1.00 63.89 1CGP 269 ATOM 115 CA ILE A 20 38.533 40.890 26.658 1.00 62.38 1CGP 270 ATOM 116 C ILE A 20 39.588 39.915 26.107 1.00 61.22 1CGP 271 ATOM 117 O ILE A 20 40.004 38.979 26.796 1.00 60.75 1CGP 272 ATOM 118 CB ILE A 20 39.055 41.748 27.857 1.00 62.00 1CGP 273 ATOM 119 CG1 ILE A 20 37.898 42.407 28.650 1.00 61.90 1CGP 274 ATOM 120 CG2 ILE A 20 40.007 42.800 27.306 1.00 61.23 1CGP 275 ATOM 121 CD1 ILE A 20 36.909 43.345 27.939 1.00 60.60 1CGP 276 ATOM 122 H ILE A 20 37.362 39.914 28.102 1.00 0.00 1CGP 277 ATOM 123 N HIS A 21 39.997 40.019 24.843 1.00 59.48 1CGP 278 ATOM 124 CA HIS A 21 40.966 39.121 24.238 1.00 56.22 1CGP 279 ATOM 125 C HIS A 21 42.130 39.913 23.680 1.00 52.15 1CGP 280 ATOM 126 O HIS A 21 41.997 41.102 23.422 1.00 49.85 1CGP 281 ATOM 127 CB HIS A 21 40.258 38.321 23.144 1.00 59.23 1CGP 282 ATOM 128 CG HIS A 21 39.394 37.153 23.639 1.00 62.31 1CGP 283 ATOM 129 ND1 HIS A 21 38.375 36.548 23.026 1.00 63.45 1CGP 284 ATOM 130 CD2 HIS A 21 39.571 36.486 24.840 1.00 64.29 1CGP 285 ATOM 131 CE1 HIS A 21 37.944 35.565 23.796 1.00 64.18 1CGP 286 ATOM 132 NE2 HIS A 21 38.671 35.537 24.888 1.00 64.77 1CGP 287 ATOM 133 H HIS A 21 39.646 40.753 24.297 1.00 0.00 1CGP 288 ATOM 134 HD1 HIS A 21 38.055 36.753 22.117 1.00 0.00 1CGP 289 ATOM 135 HE2 HIS A 21 38.600 34.887 25.628 1.00 0.00 1CGP 290 ATOM 136 N LYS A 22 43.295 39.337 23.462 1.00 50.71 1CGP 291 ATOM 137 CA LYS A 22 44.441 40.103 22.998 1.00 52.57 1CGP 292 ATOM 138 C LYS A 22 44.867 39.562 21.641 1.00 51.78 1CGP 293 ATOM 139 O LYS A 22 45.107 38.363 21.494 1.00 53.47 1CGP 294 ATOM 140 CB LYS A 22 45.578 39.977 24.018 1.00 54.63 1CGP 295 ATOM 141 CG LYS A 22 45.097 40.577 25.339 1.00 59.90 1CGP 296 ATOM 142 CD LYS A 22 45.545 39.908 26.643 1.00 64.67 1CGP 297 ATOM 143 CE LYS A 22 46.872 40.430 27.225 1.00 69.13 1CGP 298 ATOM 144 NZ LYS A 22 48.018 40.013 26.427 1.00 73.56 1CGP 299 ATOM 145 H LYS A 22 43.410 38.372 23.536 1.00 0.00 1CGP 300 ATOM 146 1HZ LYS A 22 47.914 40.405 25.468 1.00 0.00 1CGP 301 ATOM 147 2HZ LYS A 22 48.043 38.976 26.363 1.00 0.00 1CGP 302 ATOM 148 3HZ LYS A 22 48.911 40.357 26.836 1.00 0.00 1CGP 303 ATOM 149 N TYR A 23 44.932 40.396 20.621 1.00 47.83 1CGP 304 ATOM 150 CA TYR A 23 45.313 40.009 19.285 1.00 44.35 1CGP 305 ATOM 151 C TYR A 23 46.730 40.418 18.956 1.00 45.13 1CGP 306 ATOM 152 O TYR A 23 47.054 41.578 19.198 1.00 47.02 1CGP 307 ATOM 153 CB TYR A 23 44.387 40.660 18.350 1.00 42.12 1CGP 308 ATOM 154 CG TYR A 23 43.073 39.954 18.345 1.00 42.02 1CGP 309 ATOM 155 CD1 TYR A 23 42.949 38.857 17.518 1.00 41.81 1CGP 310 ATOM 156 CD2 TYR A 23 42.043 40.430 19.126 1.00 41.14 1CGP 311 ATOM 157 CE1 TYR A 23 41.745 38.215 17.459 1.00 43.01 1CGP 312 ATOM 158 CE2 TYR A 23 40.837 39.792 19.073 1.00 41.84 1CGP 313 ATOM 159 CZ TYR A 23 40.709 38.696 18.238 1.00 43.59 1CGP 314 ATOM 160 OH TYR A 23 39.496 38.038 18.163 1.00 46.66 1CGP 315 ATOM 161 H TYR A 23 44.754 41.332 20.803 1.00 0.00 1CGP 316 ATOM 162 HH TYR A 23 39.456 37.524 17.349 1.00 0.00 1CGP 317 ATOM 163 N PRO A 24 47.627 39.599 18.425 1.00 44.53 1CGP 318 ATOM 164 CA PRO A 24 48.947 40.021 17.975 1.00 44.71 1CGP 319 ATOM 165 C PRO A 24 48.927 40.806 16.676 1.00 45.32 1CGP 320 ATOM 166 O PRO A 24 47.986 40.687 15.888 1.00 44.68 1CGP 321 ATOM 167 CB PRO A 24 49.691 38.734 17.860 1.00 44.98 1CGP 322 ATOM 168 CG PRO A 24 48.614 37.791 17.370 1.00 44.09 1CGP 323 ATOM 169 CD PRO A 24 47.457 38.163 18.275 1.00 44.62 1CGP 324 ATOM 170 N SER A 25 49.976 41.561 16.392 1.00 45.83 1CGP 325 ATOM 171 CA SER A 25 50.068 42.238 15.115 1.00 48.20 1CGP 326 ATOM 172 C SER A 25 49.933 41.236 13.982 1.00 47.59 1CGP 327 ATOM 173 O SER A 25 50.492 40.144 14.042 1.00 48.63 1CGP 328 ATOM 174 CB SER A 25 51.397 42.917 15.021 1.00 50.58 1CGP 329 ATOM 175 OG SER A 25 51.584 43.675 16.207 1.00 57.14 1CGP 330 ATOM 176 H SER A 25 50.702 41.695 17.032 1.00 0.00 1CGP 331 ATOM 177 HG SER A 25 52.277 44.311 16.007 1.00 0.00 1CGP 332 ATOM 178 N LYS A 26 49.105 41.634 13.020 1.00 47.73 1CGP 333 ATOM 179 CA LYS A 26 48.715 40.951 11.798 1.00 46.02 1CGP 334 ATOM 180 C LYS A 26 47.639 39.922 11.991 1.00 45.65 1CGP 335 ATOM 181 O LYS A 26 47.160 39.358 10.999 1.00 45.56 1CGP 336 ATOM 182 CB LYS A 26 49.873 40.257 11.113 1.00 45.43 1CGP 337 ATOM 183 CG LYS A 26 50.677 41.353 10.502 1.00 47.66 1CGP 338 ATOM 184 CD LYS A 26 51.825 40.808 9.693 1.00 51.73 1CGP 339 ATOM 185 CE LYS A 26 52.709 41.990 9.308 1.00 53.35 1CGP 340 ATOM 186 NZ LYS A 26 53.185 42.657 10.508 1.00 55.00 1CGP 341 ATOM 187 H LYS A 26 48.639 42.485 13.146 1.00 0.00 1CGP 342 ATOM 188 1HZ LYS A 26 53.670 41.948 11.096 1.00 0.00 1CGP 343 ATOM 189 2HZ LYS A 26 52.385 43.051 11.045 1.00 0.00 1CGP 344 ATOM 190 3HZ LYS A 26 53.845 43.418 10.258 1.00 0.00 1CGP 345 ATOM 191 N SER A 27 47.196 39.687 13.227 1.00 46.33 1CGP 346 ATOM 192 CA SER A 27 46.142 38.727 13.373 1.00 46.55 1CGP 347 ATOM 193 C SER A 27 44.901 39.326 12.740 1.00 47.14 1CGP 348 ATOM 194 O SER A 27 44.662 40.538 12.717 1.00 47.91 1CGP 349 ATOM 195 CB SER A 27 45.896 38.420 14.829 1.00 46.03 1CGP 350 ATOM 196 OG SER A 27 45.544 39.545 15.616 1.00 47.08 1CGP 351 ATOM 197 H SER A 27 47.540 40.147 14.013 1.00 0.00 1CGP 352 ATOM 198 HG SER A 27 46.309 40.117 15.663 1.00 0.00 1CGP 353 ATOM 199 N THR A 28 44.220 38.427 12.070 1.00 47.47 1CGP 354 ATOM 200 CA THR A 28 42.979 38.735 11.421 1.00 45.48 1CGP 355 ATOM 201 C THR A 28 41.913 38.364 12.459 1.00 45.61 1CGP 356 ATOM 202 O THR A 28 41.842 37.278 13.070 1.00 44.93 1CGP 357 ATOM 203 CB THR A 28 42.990 37.889 10.144 1.00 44.50 1CGP 358 ATOM 204 OG1 THR A 28 44.112 38.355 9.374 1.00 43.37 1CGP 359 ATOM 205 CG2 THR A 28 41.630 37.896 9.454 1.00 44.16 1CGP 360 ATOM 206 H THR A 28 44.538 37.503 12.073 1.00 0.00 1CGP 361 ATOM 207 HG1 THR A 28 44.220 37.737 8.651 1.00 0.00 1CGP 362 ATOM 208 N LEU A 29 41.103 39.382 12.706 1.00 46.26 1CGP 363 ATOM 209 CA LEU A 29 40.010 39.232 13.630 1.00 46.14 1CGP 364 ATOM 210 C LEU A 29 38.911 38.891 12.622 1.00 49.22 1CGP 365 ATOM 211 O LEU A 29 38.781 37.728 12.174 1.00 54.85 1CGP 366 ATOM 212 CB LEU A 29 39.716 40.549 14.376 1.00 42.49 1CGP 367 ATOM 213 CG LEU A 29 40.738 41.658 14.635 1.00 40.15 1CGP 368 ATOM 214 CD1 LEU A 29 40.227 42.498 15.784 1.00 40.42 1CGP 369 ATOM 215 CD2 LEU A 29 42.074 41.134 15.059 1.00 38.93 1CGP 370 ATOM 216 H LEU A 29 41.178 40.201 12.173 1.00 0.00 1CGP 371 ATOM 217 N ILE A 30 38.239 39.913 12.082 1.00 46.56 1CGP 372 ATOM 218 CA ILE A 30 37.107 39.698 11.212 1.00 42.70 1CGP 373 ATOM 219 C ILE A 30 37.593 39.286 9.854 1.00 43.38 1CGP 374 ATOM 220 O ILE A 30 38.615 39.791 9.413 1.00 40.61 1CGP 375 ATOM 221 CB ILE A 30 36.341 40.979 11.151 1.00 40.04 1CGP 376 ATOM 222 CG1 ILE A 30 35.747 41.249 12.482 1.00 39.25 1CGP 377 ATOM 223 CG2 ILE A 30 35.239 40.876 10.160 1.00 38.61 1CGP 378 ATOM 224 CD1 ILE A 30 35.221 42.664 12.612 1.00 40.07 1CGP 379 ATOM 225 H ILE A 30 38.639 40.803 12.107 1.00 0.00 1CGP 380 ATOM 226 N HIS A 31 36.918 38.345 9.228 1.00 47.51 1CGP 381 ATOM 227 CA HIS A 31 37.196 38.014 7.839 1.00 55.06 1CGP 382 ATOM 228 C HIS A 31 35.928 38.531 7.210 1.00 55.31 1CGP 383 ATOM 229 O HIS A 31 34.858 38.233 7.756 1.00 56.51 1CGP 384 ATOM 230 CB HIS A 31 37.174 36.556 7.426 1.00 60.87 1CGP 385 ATOM 231 CG HIS A 31 38.091 35.629 8.184 1.00 68.17 1CGP 386 ATOM 232 ND1 HIS A 31 38.433 35.601 9.484 1.00 71.79 1CGP 387 ATOM 233 CD2 HIS A 31 38.726 34.579 7.552 1.00 70.44 1CGP 388 ATOM 234 CE1 HIS A 31 39.236 34.570 9.654 1.00 73.37 1CGP 389 ATOM 235 NE2 HIS A 31 39.409 33.964 8.492 1.00 73.50 1CGP 390 ATOM 236 H HIS A 31 36.073 38.030 9.608 1.00 0.00 1CGP 391 ATOM 237 HD1 HIS A 31 38.198 36.227 10.210 1.00 0.00 1CGP 392 ATOM 238 HE2 HIS A 31 39.973 33.168 8.360 1.00 0.00 1CGP 393 ATOM 239 N GLN A 32 35.943 39.244 6.089 1.00 55.14 1CGP 394 ATOM 240 CA GLN A 32 34.693 39.676 5.507 1.00 55.80 1CGP 395 ATOM 241 C GLN A 32 33.988 38.426 5.047 1.00 54.64 1CGP 396 ATOM 242 O GLN A 32 34.660 37.442 4.744 1.00 56.22 1CGP 397 ATOM 243 CB GLN A 32 34.990 40.551 4.375 1.00 56.86 1CGP 398 ATOM 244 CG GLN A 32 33.794 41.089 3.696 1.00 60.17 1CGP 399 ATOM 245 CD GLN A 32 33.889 40.715 2.258 1.00 62.99 1CGP 400 ATOM 246 OE1 GLN A 32 33.404 39.662 1.854 1.00 65.65 1CGP 401 ATOM 247 NE2 GLN A 32 34.523 41.585 1.479 1.00 64.17 1CGP 402 ATOM 248 H GLN A 32 36.772 39.373 5.597 1.00 0.00 1CGP 403 ATOM 249 1HE2 GLN A 32 34.773 42.455 1.854 1.00 0.00 1CGP 404 ATOM 250 2HE2 GLN A 32 34.697 41.300 0.560 1.00 0.00 1CGP 405 ATOM 251 N GLY A 33 32.675 38.422 5.049 1.00 54.38 1CGP 406 ATOM 252 CA GLY A 33 31.954 37.234 4.692 1.00 54.57 1CGP 407 ATOM 253 C GLY A 33 31.602 36.431 5.935 1.00 55.94 1CGP 408 ATOM 254 O GLY A 33 30.625 35.690 5.845 1.00 56.98 1CGP 409 ATOM 255 H GLY A 33 32.201 39.244 5.265 1.00 0.00 1CGP 410 ATOM 256 N GLU A 34 32.287 36.493 7.099 1.00 56.93 1CGP 411 ATOM 257 CA GLU A 34 31.888 35.740 8.297 1.00 58.76 1CGP 412 ATOM 258 C GLU A 34 30.478 36.181 8.681 1.00 59.45 1CGP 413 ATOM 259 O GLU A 34 30.060 37.285 8.333 1.00 59.15 1CGP 414 ATOM 260 CB GLU A 34 32.676 36.037 9.580 1.00 61.21 1CGP 415 ATOM 261 CG GLU A 34 34.166 35.776 9.889 1.00 64.42 1CGP 416 ATOM 262 CD GLU A 34 34.727 36.501 11.152 1.00 65.73 1CGP 417 ATOM 263 OE1 GLU A 34 33.947 37.041 11.967 1.00 66.54 1CGP 418 ATOM 264 OE2 GLU A 34 35.958 36.531 11.318 1.00 63.82 1CGP 419 ATOM 265 H GLU A 34 33.066 37.083 7.164 1.00 0.00 1CGP 420 ATOM 266 N LYS A 35 29.710 35.387 9.415 1.00 59.79 1CGP 421 ATOM 267 CA LYS A 35 28.433 35.866 9.919 1.00 60.41 1CGP 422 ATOM 268 C LYS A 35 28.721 36.742 11.132 1.00 59.70 1CGP 423 ATOM 269 O LYS A 35 29.575 36.479 11.998 1.00 58.35 1CGP 424 ATOM 270 CB LYS A 35 27.487 34.709 10.335 1.00 62.10 1CGP 425 ATOM 271 CG LYS A 35 28.093 33.491 11.033 1.00 63.14 1CGP 426 ATOM 272 CD LYS A 35 28.451 32.401 10.018 1.00 64.10 1CGP 427 ATOM 273 CE LYS A 35 29.650 31.581 10.488 1.00 63.91 1CGP 428 ATOM 274 NZ LYS A 35 30.890 32.299 10.255 1.00 63.80 1CGP 429 ATOM 275 H LYS A 35 30.048 34.511 9.675 1.00 0.00 1CGP 430 ATOM 276 1HZ LYS A 35 30.836 33.243 10.691 1.00 0.00 1CGP 431 ATOM 277 2HZ LYS A 35 31.023 32.407 9.230 1.00 0.00 1CGP 432 ATOM 278 3HZ LYS A 35 31.687 31.768 10.661 1.00 0.00 1CGP 433 ATOM 279 N ALA A 36 28.041 37.867 11.123 1.00 59.43 1CGP 434 ATOM 280 CA ALA A 36 28.156 38.796 12.210 1.00 60.84 1CGP 435 ATOM 281 C ALA A 36 27.364 38.278 13.404 1.00 62.59 1CGP 436 ATOM 282 O ALA A 36 26.173 37.964 13.284 1.00 62.61 1CGP 437 ATOM 283 CB ALA A 36 27.610 40.125 11.772 1.00 60.78 1CGP 438 ATOM 284 H ALA A 36 27.432 38.079 10.388 1.00 0.00 1CGP 439 ATOM 285 N GLU A 37 28.024 38.175 14.557 1.00 64.42 1CGP 440 ATOM 286 CA GLU A 37 27.336 37.770 15.777 1.00 65.01 1CGP 441 ATOM 287 C GLU A 37 27.933 38.417 17.018 1.00 61.90 1CGP 442 ATOM 288 O GLU A 37 27.343 38.375 18.104 1.00 60.51 1CGP 443 ATOM 289 CB GLU A 37 27.404 36.251 15.934 1.00 70.08 1CGP 444 ATOM 290 CG GLU A 37 26.114 35.554 16.412 1.00 74.39 1CGP 445 ATOM 291 CD GLU A 37 25.378 34.770 15.313 1.00 75.96 1CGP 446 ATOM 292 OE1 GLU A 37 25.714 33.592 15.112 1.00 74.87 1CGP 447 ATOM 293 OE2 GLU A 37 24.471 35.336 14.676 1.00 77.60 1CGP 448 ATOM 294 H GLU A 37 28.995 38.285 14.555 1.00 0.00 1CGP 449 ATOM 295 N THR A 38 29.040 39.134 16.858 1.00 59.97 1CGP 450 ATOM 296 CA THR A 38 29.776 39.640 17.998 1.00 59.31 1CGP 451 ATOM 297 C THR A 38 30.226 41.053 17.666 1.00 56.47 1CGP 452 ATOM 298 O THR A 38 30.729 41.281 16.564 1.00 57.25 1CGP 453 ATOM 299 CB THR A 38 30.979 38.695 18.229 1.00 61.19 1CGP 454 ATOM 300 OG1 THR A 38 30.446 37.367 18.183 1.00 63.06 1CGP 455 ATOM 301 CG2 THR A 38 31.723 38.948 19.539 1.00 61.34 1CGP 456 ATOM 302 H THR A 38 29.372 39.404 15.984 1.00 0.00 1CGP 457 ATOM 303 HG1 THR A 38 31.144 36.768 17.899 1.00 0.00 1CGP 458 ATOM 304 N LEU A 39 29.994 41.966 18.599 1.00 51.59 1CGP 459 ATOM 305 CA LEU A 39 30.419 43.358 18.493 1.00 46.75 1CGP 460 ATOM 306 C LEU A 39 31.784 43.369 19.190 1.00 44.84 1CGP 461 ATOM 307 O LEU A 39 31.980 42.536 20.090 1.00 44.99 1CGP 462 ATOM 308 CB LEU A 39 29.455 44.282 19.254 1.00 44.25 1CGP 463 ATOM 309 CG LEU A 39 29.621 45.782 19.088 1.00 42.06 1CGP 464 ATOM 310 CD1 LEU A 39 28.833 46.192 17.873 1.00 41.77 1CGP 465 ATOM 311 CD2 LEU A 39 29.075 46.552 20.259 1.00 40.22 1CGP 466 ATOM 312 H LEU A 39 29.693 41.625 19.467 1.00 0.00 1CGP 467 ATOM 313 N TYR A 40 32.740 44.232 18.845 1.00 41.92 1CGP 468 ATOM 314 CA TYR A 40 34.018 44.300 19.527 1.00 40.23 1CGP 469 ATOM 315 C TYR A 40 34.244 45.704 19.994 1.00 38.53 1CGP 470 ATOM 316 O TYR A 40 33.596 46.583 19.442 1.00 38.88 1CGP 471 ATOM 317 CB TYR A 40 35.172 43.972 18.626 1.00 40.91 1CGP 472 ATOM 318 CG TYR A 40 35.073 42.594 18.005 1.00 43.09 1CGP 473 ATOM 319 CD1 TYR A 40 34.305 42.471 16.860 1.00 43.72 1CGP 474 ATOM 320 CD2 TYR A 40 35.715 41.501 18.569 1.00 42.64 1CGP 475 ATOM 321 CE1 TYR A 40 34.155 41.249 16.258 1.00 42.92 1CGP 476 ATOM 322 CE2 TYR A 40 35.573 40.271 17.964 1.00 43.06 1CGP 477 ATOM 323 CZ TYR A 40 34.794 40.172 16.821 1.00 43.73 1CGP 478 ATOM 324 OH TYR A 40 34.644 38.963 16.186 1.00 45.17 1CGP 479 ATOM 325 H TYR A 40 32.623 44.836 18.086 1.00 0.00 1CGP 480 ATOM 326 HH TYR A 40 34.166 39.093 15.361 1.00 0.00 1CGP 481 ATOM 327 N TYR A 41 35.112 45.991 20.954 1.00 38.29 1CGP 482 ATOM 328 CA TYR A 41 35.441 47.369 21.298 1.00 40.77 1CGP 483 ATOM 329 C TYR A 41 36.948 47.417 21.503 1.00 40.70 1CGP 484 ATOM 330 O TYR A 41 37.491 46.643 22.291 1.00 41.40 1CGP 485 ATOM 331 CB TYR A 41 34.714 47.832 22.585 1.00 42.74 1CGP 486 ATOM 332 CG TYR A 41 35.127 49.226 23.087 1.00 44.63 1CGP 487 ATOM 333 CD1 TYR A 41 36.283 49.388 23.841 1.00 44.59 1CGP 488 ATOM 334 CD2 TYR A 41 34.370 50.344 22.772 1.00 45.89 1CGP 489 ATOM 335 CE1 TYR A 41 36.686 50.638 24.259 1.00 45.74 1CGP 490 ATOM 336 CE2 TYR A 41 34.768 51.608 23.194 1.00 45.82 1CGP 491 ATOM 337 CZ TYR A 41 35.930 51.737 23.931 1.00 46.22 1CGP 492 ATOM 338 OH TYR A 41 36.366 52.976 24.340 1.00 48.29 1CGP 493 ATOM 339 H TYR A 41 35.542 45.244 21.422 1.00 0.00 1CGP 494 ATOM 340 HH TYR A 41 35.807 53.647 23.944 1.00 0.00 1CGP 495 ATOM 341 N ILE A 42 37.668 48.303 20.826 1.00 40.44 1CGP 496 ATOM 342 CA ILE A 42 39.120 48.322 20.906 1.00 40.78 1CGP 497 ATOM 343 C ILE A 42 39.537 48.957 22.200 1.00 42.28 1CGP 498 ATOM 344 O ILE A 42 39.390 50.168 22.336 1.00 44.34 1CGP 499 ATOM 345 CB ILE A 42 39.744 49.111 19.709 1.00 40.34 1CGP 500 ATOM 346 CG1 ILE A 42 39.265 48.513 18.380 1.00 39.64 1CGP 501 ATOM 347 CG2 ILE A 42 41.273 49.060 19.807 1.00 39.08 1CGP 502 ATOM 348 CD1 ILE A 42 39.835 49.101 17.081 1.00 39.45 1CGP 503 ATOM 349 H ILE A 42 37.219 48.948 20.234 1.00 0.00 1CGP 504 ATOM 350 N VAL A 43 40.063 48.175 23.125 1.00 44.52 1CGP 505 ATOM 351 CA VAL A 43 40.522 48.697 24.394 1.00 46.08 1CGP 506 ATOM 352 C VAL A 43 41.936 49.195 24.204 1.00 46.27 1CGP 507 ATOM 353 O VAL A 43 42.262 50.246 24.746 1.00 47.33 1CGP 508 ATOM 354 CB VAL A 43 40.452 47.598 25.436 1.00 47.40 1CGP 509 ATOM 355 CG1 VAL A 43 41.187 47.998 26.699 1.00 48.50 1CGP 510 ATOM 356 CG2 VAL A 43 38.977 47.343 25.763 1.00 47.91 1CGP 511 ATOM 357 H VAL A 43 40.270 47.247 22.909 1.00 0.00 1CGP 512 ATOM 358 N LYS A 44 42.809 48.518 23.478 1.00 47.27 1CGP 513 ATOM 359 CA LYS A 44 44.106 49.108 23.203 1.00 48.13 1CGP 514 ATOM 360 C LYS A 44 44.480 48.710 21.800 1.00 44.92 1CGP 515 ATOM 361 O LYS A 44 43.959 47.697 21.327 1.00 43.12 1CGP 516 ATOM 362 CB LYS A 44 45.128 48.595 24.212 1.00 53.58 1CGP 517 ATOM 363 CG LYS A 44 46.250 49.605 24.542 1.00 59.59 1CGP 518 ATOM 364 CD LYS A 44 47.477 49.650 23.599 1.00 63.46 1CGP 519 ATOM 365 CE LYS A 44 48.640 48.691 23.972 1.00 65.74 1CGP 520 ATOM 366 NZ LYS A 44 48.325 47.267 23.856 1.00 67.37 1CGP 521 ATOM 367 H LYS A 44 42.538 47.667 23.078 1.00 0.00 1CGP 522 ATOM 368 1HZ LYS A 44 48.027 47.064 22.880 1.00 0.00 1CGP 523 ATOM 369 2HZ LYS A 44 47.564 47.004 24.513 1.00 0.00 1CGP 524 ATOM 370 3HZ LYS A 44 49.172 46.706 24.079 1.00 0.00 1CGP 525 ATOM 371 N GLY A 45 45.318 49.480 21.124 1.00 42.61 1CGP 526 ATOM 372 CA GLY A 45 45.773 49.064 19.814 1.00 43.87 1CGP 527 ATOM 373 C GLY A 45 45.027 49.654 18.618 1.00 44.76 1CGP 528 ATOM 374 O GLY A 45 44.024 50.371 18.751 1.00 45.82 1CGP 529 ATOM 375 H GLY A 45 45.566 50.354 21.491 1.00 0.00 1CGP 530 ATOM 376 N SER A 46 45.614 49.365 17.444 1.00 43.21 1CGP 531 ATOM 377 CA SER A 46 45.184 49.858 16.159 1.00 43.28 1CGP 532 ATOM 378 C SER A 46 44.968 48.765 15.143 1.00 41.12 1CGP 533 ATOM 379 O SER A 46 45.789 47.874 14.949 1.00 41.33 1CGP 534 ATOM 380 CB SER A 46 46.219 50.806 15.604 1.00 47.50 1CGP 535 ATOM 381 OG SER A 46 46.453 51.923 16.466 1.00 54.46 1CGP 536 ATOM 382 H SER A 46 46.409 48.795 17.417 1.00 0.00 1CGP 537 ATOM 383 HG SER A 46 47.060 51.657 17.168 1.00 0.00 1CGP 538 ATOM 384 N VAL A 47 43.920 48.960 14.374 1.00 39.20 1CGP 539 ATOM 385 CA VAL A 47 43.390 48.035 13.406 1.00 35.07 1CGP 540 ATOM 386 C VAL A 47 43.187 48.690 12.021 1.00 35.40 1CGP 541 ATOM 387 O VAL A 47 42.977 49.902 11.922 1.00 34.54 1CGP 542 ATOM 388 CB VAL A 47 42.163 47.590 14.199 1.00 34.08 1CGP 543 ATOM 389 CG1 VAL A 47 40.850 47.770 13.467 1.00 33.67 1CGP 544 ATOM 390 CG2 VAL A 47 42.446 46.181 14.601 1.00 34.04 1CGP 545 ATOM 391 H VAL A 47 43.437 49.813 14.445 1.00 0.00 1CGP 546 ATOM 392 N ALA A 48 43.261 47.942 10.925 1.00 35.39 1CGP 547 ATOM 393 CA ALA A 48 42.982 48.461 9.599 1.00 35.07 1CGP 548 ATOM 394 C ALA A 48 41.832 47.675 9.027 1.00 36.21 1CGP 549 ATOM 395 O ALA A 48 41.809 46.439 9.049 1.00 35.53 1CGP 550 ATOM 396 CB ALA A 48 44.111 48.266 8.646 1.00 35.24 1CGP 551 ATOM 397 H ALA A 48 43.491 46.994 11.024 1.00 0.00 1CGP 552 ATOM 398 N VAL A 49 40.857 48.444 8.588 1.00 38.35 1CGP 553 ATOM 399 CA VAL A 49 39.642 47.943 7.974 1.00 38.66 1CGP 554 ATOM 400 C VAL A 49 39.931 47.908 6.476 1.00 38.06 1CGP 555 ATOM 401 O VAL A 49 40.209 48.957 5.885 1.00 38.79 1CGP 556 ATOM 402 CB VAL A 49 38.473 48.914 8.318 1.00 38.24 1CGP 557 ATOM 403 CG1 VAL A 49 37.201 48.478 7.629 1.00 37.09 1CGP 558 ATOM 404 CG2 VAL A 49 38.231 48.921 9.815 1.00 38.92 1CGP 559 ATOM 405 H VAL A 49 40.965 49.414 8.634 1.00 0.00 1CGP 560 ATOM 406 N LEU A 50 39.893 46.760 5.819 1.00 36.63 1CGP 561 ATOM 407 CA LEU A 50 40.130 46.701 4.402 1.00 37.21 1CGP 562 ATOM 408 C LEU A 50 39.268 45.735 3.607 1.00 38.12 1CGP 563 ATOM 409 O LEU A 50 38.639 44.832 4.147 1.00 38.68 1CGP 564 ATOM 410 CB LEU A 50 41.599 46.412 4.191 1.00 37.57 1CGP 565 ATOM 411 CG LEU A 50 42.429 45.502 5.040 1.00 38.59 1CGP 566 ATOM 412 CD1 LEU A 50 41.962 44.082 4.998 1.00 39.50 1CGP 567 ATOM 413 CD2 LEU A 50 43.829 45.558 4.466 1.00 40.22 1CGP 568 ATOM 414 H LEU A 50 39.629 45.961 6.313 1.00 0.00 1CGP 569 ATOM 415 N ILE A 51 39.128 45.955 2.302 1.00 40.53 1CGP 570 ATOM 416 CA ILE A 51 38.321 45.138 1.405 1.00 40.73 1CGP 571 ATOM 417 C ILE A 51 39.224 44.782 0.251 1.00 43.61 1CGP 572 ATOM 418 O ILE A 51 40.096 45.564 -0.122 1.00 40.47 1CGP 573 ATOM 419 CB ILE A 51 37.117 45.928 0.908 1.00 38.95 1CGP 574 ATOM 420 CG1 ILE A 51 37.548 47.198 0.215 1.00 38.25 1CGP 575 ATOM 421 CG2 ILE A 51 36.233 46.209 2.103 1.00 38.67 1CGP 576 ATOM 422 CD1 ILE A 51 36.444 48.235 0.014 1.00 39.80 1CGP 577 ATOM 423 H ILE A 51 39.630 46.715 1.927 1.00 0.00 1CGP 578 ATOM 424 N LYS A 52 39.059 43.589 -0.295 1.00 51.10 1CGP 579 ATOM 425 CA LYS A 52 39.917 43.105 -1.364 1.00 57.63 1CGP 580 ATOM 426 C LYS A 52 39.033 42.662 -2.528 1.00 61.79 1CGP 581 ATOM 427 O LYS A 52 37.868 42.273 -2.326 1.00 63.54 1CGP 582 ATOM 428 CB LYS A 52 40.722 41.893 -0.954 1.00 59.00 1CGP 583 ATOM 429 CG LYS A 52 41.153 41.724 0.483 1.00 62.48 1CGP 584 ATOM 430 CD LYS A 52 41.989 40.465 0.591 1.00 66.83 1CGP 585 ATOM 431 CE LYS A 52 41.202 39.143 0.478 1.00 71.21 1CGP 586 ATOM 432 NZ LYS A 52 40.579 38.860 -0.819 1.00 73.78 1CGP 587 ATOM 433 H LYS A 52 38.270 43.049 -0.093 1.00 0.00 1CGP 588 ATOM 434 1HZ LYS A 52 41.290 38.887 -1.578 1.00 0.00 1CGP 589 ATOM 435 2HZ LYS A 52 39.841 39.565 -1.013 1.00 0.00 1CGP 590 ATOM 436 3HZ LYS A 52 40.145 37.915 -0.793 1.00 0.00 1CGP 591 ATOM 437 N ASP A 53 39.556 42.748 -3.754 1.00 65.42 1CGP 592 ATOM 438 CA ASP A 53 38.864 42.280 -4.938 1.00 69.34 1CGP 593 ATOM 439 C ASP A 53 39.192 40.801 -5.116 1.00 70.06 1CGP 594 ATOM 440 O ASP A 53 40.276 40.358 -4.750 1.00 69.19 1CGP 595 ATOM 441 CB ASP A 53 39.318 43.037 -6.191 1.00 70.96 1CGP 596 ATOM 442 CG ASP A 53 38.420 42.766 -7.405 1.00 73.24 1CGP 597 ATOM 443 OD1 ASP A 53 37.302 43.294 -7.468 1.00 72.69 1CGP 598 ATOM 444 OD2 ASP A 53 38.844 42.000 -8.278 1.00 74.54 1CGP 599 ATOM 445 H ASP A 53 40.439 43.137 -3.824 1.00 0.00 1CGP 600 ATOM 446 N GLU A 54 38.293 40.036 -5.758 1.00 71.75 1CGP 601 ATOM 447 CA GLU A 54 38.452 38.604 -6.020 1.00 71.79 1CGP 602 ATOM 448 C GLU A 54 39.739 38.331 -6.770 1.00 70.43 1CGP 603 ATOM 449 O GLU A 54 40.281 37.242 -6.662 1.00 70.55 1CGP 604 ATOM 450 CB GLU A 54 37.329 38.010 -6.877 1.00 73.34 1CGP 605 ATOM 451 CG GLU A 54 35.928 38.621 -6.707 1.00 77.69 1CGP 606 ATOM 452 CD GLU A 54 35.690 39.893 -7.535 1.00 80.92 1CGP 607 ATOM 453 OE1 GLU A 54 36.601 40.334 -8.250 1.00 80.66 1CGP 608 ATOM 454 OE2 GLU A 54 34.581 40.434 -7.466 1.00 82.84 1CGP 609 ATOM 455 H GLU A 54 37.445 40.467 -5.970 1.00 0.00 1CGP 610 ATOM 456 N GLU A 55 40.289 39.260 -7.555 1.00 69.49 1CGP 611 ATOM 457 CA GLU A 55 41.582 39.006 -8.172 1.00 68.69 1CGP 612 ATOM 458 C GLU A 55 42.751 39.563 -7.328 1.00 66.15 1CGP 613 ATOM 459 O GLU A 55 43.813 39.922 -7.851 1.00 65.58 1CGP 614 ATOM 460 CB GLU A 55 41.583 39.614 -9.588 1.00 71.50 1CGP 615 ATOM 461 CG GLU A 55 40.389 39.289 -10.498 1.00 75.01 1CGP 616 ATOM 462 CD GLU A 55 40.003 37.810 -10.650 1.00 77.98 1CGP 617 ATOM 463 OE1 GLU A 55 39.196 37.309 -9.857 1.00 80.63 1CGP 618 ATOM 464 OE2 GLU A 55 40.467 37.171 -11.594 1.00 77.99 1CGP 619 ATOM 465 H GLU A 55 39.833 40.102 -7.709 1.00 0.00 1CGP 620 ATOM 466 N GLY A 56 42.554 39.719 -6.012 1.00 62.72 1CGP 621 ATOM 467 CA GLY A 56 43.599 40.073 -5.070 1.00 57.99 1CGP 622 ATOM 468 C GLY A 56 43.824 41.508 -4.616 1.00 55.02 1CGP 623 ATOM 469 O GLY A 56 44.304 41.679 -3.489 1.00 52.93 1CGP 624 ATOM 470 H GLY A 56 41.678 39.542 -5.629 1.00 0.00 1CGP 625 ATOM 471 N LYS A 57 43.547 42.564 -5.385 1.00 53.16 1CGP 626 ATOM 472 CA LYS A 57 43.925 43.906 -4.946 1.00 52.05 1CGP 627 ATOM 473 C LYS A 57 43.128 44.354 -3.723 1.00 48.32 1CGP 628 ATOM 474 O LYS A 57 41.938 44.077 -3.633 1.00 46.58 1CGP 629 ATOM 475 CB LYS A 57 43.769 44.854 -6.181 1.00 56.57 1CGP 630 ATOM 476 CG LYS A 57 43.996 46.399 -6.061 1.00 62.96 1CGP 631 ATOM 477 CD LYS A 57 45.254 46.890 -5.255 1.00 66.33 1CGP 632 ATOM 478 CE LYS A 57 45.460 48.415 -5.045 1.00 65.08 1CGP 633 ATOM 479 NZ LYS A 57 46.667 48.605 -4.249 1.00 64.75 1CGP 634 ATOM 480 H LYS A 57 43.105 42.425 -6.245 1.00 0.00 1CGP 635 ATOM 481 1HZ LYS A 57 47.462 48.115 -4.710 1.00 0.00 1CGP 636 ATOM 482 2HZ LYS A 57 46.527 48.206 -3.298 1.00 0.00 1CGP 637 ATOM 483 3HZ LYS A 57 46.900 49.615 -4.173 1.00 0.00 1CGP 638 ATOM 484 N GLU A 58 43.740 44.989 -2.743 1.00 45.20 1CGP 639 ATOM 485 CA GLU A 58 43.011 45.395 -1.572 1.00 44.30 1CGP 640 ATOM 486 C GLU A 58 43.240 46.844 -1.250 1.00 42.10 1CGP 641 ATOM 487 O GLU A 58 44.326 47.381 -1.472 1.00 42.50 1CGP 642 ATOM 488 CB GLU A 58 43.405 44.514 -0.395 1.00 45.28 1CGP 643 ATOM 489 CG GLU A 58 44.861 44.224 -0.071 1.00 47.29 1CGP 644 ATOM 490 CD GLU A 58 45.024 43.175 1.031 1.00 48.90 1CGP 645 ATOM 491 OE1 GLU A 58 44.991 41.979 0.732 1.00 49.19 1CGP 646 ATOM 492 OE2 GLU A 58 45.187 43.544 2.194 1.00 49.06 1CGP 647 ATOM 493 H GLU A 58 44.683 45.232 -2.814 1.00 0.00 1CGP 648 ATOM 494 N MET A 59 42.186 47.440 -0.732 1.00 40.67 1CGP 649 ATOM 495 CA MET A 59 42.120 48.842 -0.368 1.00 41.48 1CGP 650 ATOM 496 C MET A 59 41.723 49.026 1.079 1.00 40.76 1CGP 651 ATOM 497 O MET A 59 40.778 48.377 1.540 1.00 42.43 1CGP 652 ATOM 498 CB MET A 59 41.104 49.563 -1.248 1.00 42.67 1CGP 653 ATOM 499 CG MET A 59 40.532 50.860 -0.692 1.00 42.59 1CGP 654 ATOM 500 SD MET A 59 40.210 51.955 -2.070 1.00 46.09 1CGP 655 ATOM 501 CE MET A 59 41.666 52.960 -2.037 1.00 46.70 1CGP 656 ATOM 502 H MET A 59 41.416 46.871 -0.537 1.00 0.00 1CGP 657 ATOM 503 N ILE A 60 42.404 49.945 1.766 1.00 38.50 1CGP 658 ATOM 504 CA ILE A 60 42.133 50.248 3.162 1.00 35.20 1CGP 659 ATOM 505 C ILE A 60 41.001 51.252 3.157 1.00 35.08 1CGP 660 ATOM 506 O ILE A 60 40.993 52.258 2.449 1.00 34.77 1CGP 661 ATOM 507 CB ILE A 60 43.400 50.826 3.819 1.00 34.83 1CGP 662 ATOM 508 CG1 ILE A 60 44.394 49.704 3.981 1.00 34.52 1CGP 663 ATOM 509 CG2 ILE A 60 43.108 51.454 5.167 1.00 33.52 1CGP 664 ATOM 510 CD1 ILE A 60 45.735 50.292 4.361 1.00 33.83 1CGP 665 ATOM 511 H ILE A 60 43.007 50.534 1.254 1.00 0.00 1CGP 666 ATOM 512 N LEU A 61 39.985 50.886 3.907 1.00 33.90 1CGP 667 ATOM 513 CA LEU A 61 38.852 51.750 4.080 1.00 31.69 1CGP 668 ATOM 514 C LEU A 61 39.171 52.670 5.251 1.00 31.82 1CGP 669 ATOM 515 O LEU A 61 38.736 53.819 5.191 1.00 33.24 1CGP 670 ATOM 516 CB LEU A 61 37.589 50.919 4.349 1.00 29.04 1CGP 671 ATOM 517 CG LEU A 61 36.862 50.310 3.163 1.00 25.71 1CGP 672 ATOM 518 CD1 LEU A 61 35.708 49.453 3.580 1.00 23.29 1CGP 673 ATOM 519 CD2 LEU A 61 36.272 51.429 2.364 1.00 26.01 1CGP 674 ATOM 520 H LEU A 61 40.053 50.089 4.454 1.00 0.00 1CGP 675 ATOM 521 N SER A 62 39.885 52.247 6.312 1.00 32.24 1CGP 676 ATOM 522 CA SER A 62 40.268 53.129 7.426 1.00 32.71 1CGP 677 ATOM 523 C SER A 62 41.092 52.453 8.477 1.00 32.05 1CGP 678 ATOM 524 O SER A 62 41.149 51.230 8.567 1.00 30.26 1CGP 679 ATOM 525 CB SER A 62 39.092 53.710 8.200 1.00 33.59 1CGP 680 ATOM 526 OG SER A 62 38.247 52.637 8.576 1.00 36.78 1CGP 681 ATOM 527 H SER A 62 40.118 51.296 6.356 1.00 0.00 1CGP 682 ATOM 528 HG SER A 62 37.382 52.773 8.186 1.00 0.00 1CGP 683 ATOM 529 N TYR A 63 41.769 53.267 9.249 1.00 33.27 1CGP 684 ATOM 530 CA TYR A 63 42.449 52.716 10.385 1.00 36.62 1CGP 685 ATOM 531 C TYR A 63 41.469 53.090 11.471 1.00 39.78 1CGP 686 ATOM 532 O TYR A 63 40.867 54.167 11.442 1.00 42.23 1CGP 687 ATOM 533 CB TYR A 63 43.768 53.394 10.625 1.00 35.51 1CGP 688 ATOM 534 CG TYR A 63 44.771 53.189 9.515 1.00 35.07 1CGP 689 ATOM 535 CD1 TYR A 63 45.104 51.909 9.138 1.00 37.17 1CGP 690 ATOM 536 CD2 TYR A 63 45.357 54.269 8.900 1.00 34.84 1CGP 691 ATOM 537 CE1 TYR A 63 46.026 51.686 8.138 1.00 37.13 1CGP 692 ATOM 538 CE2 TYR A 63 46.280 54.059 7.895 1.00 35.96 1CGP 693 ATOM 539 CZ TYR A 63 46.596 52.765 7.526 1.00 36.42 1CGP 694 ATOM 540 OH TYR A 63 47.455 52.515 6.491 1.00 35.71 1CGP 695 ATOM 541 H TYR A 63 41.644 54.236 9.210 1.00 0.00 1CGP 696 ATOM 542 HH TYR A 63 47.623 53.340 6.030 1.00 0.00 1CGP 697 ATOM 543 N LEU A 64 41.233 52.173 12.378 1.00 42.98 1CGP 698 ATOM 544 CA LEU A 64 40.360 52.385 13.521 1.00 45.47 1CGP 699 ATOM 545 C LEU A 64 41.358 52.322 14.673 1.00 49.44 1CGP 700 ATOM 546 O LEU A 64 42.281 51.494 14.598 1.00 52.24 1CGP 701 ATOM 547 CB LEU A 64 39.372 51.250 13.650 1.00 44.25 1CGP 702 ATOM 548 CG LEU A 64 37.894 51.527 13.665 1.00 44.02 1CGP 703 ATOM 549 CD1 LEU A 64 37.355 51.732 12.279 1.00 43.59 1CGP 704 ATOM 550 CD2 LEU A 64 37.192 50.305 14.190 1.00 44.34 1CGP 705 ATOM 551 H LEU A 64 41.778 51.359 12.330 1.00 0.00 1CGP 706 ATOM 552 N ASN A 65 41.288 53.110 15.749 1.00 51.64 1CGP 707 ATOM 553 CA ASN A 65 42.292 53.015 16.811 1.00 52.81 1CGP 708 ATOM 554 C ASN A 65 41.537 52.758 18.106 1.00 52.29 1CGP 709 ATOM 555 O ASN A 65 40.313 52.553 18.066 1.00 50.83 1CGP 710 ATOM 556 CB ASN A 65 43.113 54.319 16.906 1.00 55.42 1CGP 711 ATOM 557 CG ASN A 65 43.745 54.803 15.590 1.00 57.62 1CGP 712 ATOM 558 OD1 ASN A 65 43.153 55.657 14.917 1.00 59.11 1CGP 713 ATOM 559 ND2 ASN A 65 44.890 54.337 15.089 1.00 56.37 1CGP 714 ATOM 560 H ASN A 65 40.493 53.649 15.909 1.00 0.00 1CGP 715 ATOM 561 1HD2 ASN A 65 45.367 53.601 15.532 1.00 0.00 1CGP 716 ATOM 562 2HD2 ASN A 65 45.223 54.820 14.296 1.00 0.00 1CGP 717 ATOM 563 N GLN A 66 42.189 52.679 19.265 1.00 52.30 1CGP 718 ATOM 564 CA GLN A 66 41.449 52.425 20.481 1.00 53.16 1CGP 719 ATOM 565 C GLN A 66 40.351 53.399 20.803 1.00 49.80 1CGP 720 ATOM 566 O GLN A 66 40.411 54.580 20.483 1.00 47.88 1CGP 721 ATOM 567 CB GLN A 66 42.373 52.353 21.672 1.00 58.60 1CGP 722 ATOM 568 CG GLN A 66 43.377 53.452 21.979 1.00 65.11 1CGP 723 ATOM 569 CD GLN A 66 44.310 53.020 23.124 1.00 69.06 1CGP 724 ATOM 570 OE1 GLN A 66 45.389 52.434 22.892 1.00 70.25 1CGP 725 ATOM 571 NE2 GLN A 66 43.881 53.254 24.374 1.00 68.95 1CGP 726 ATOM 572 H GLN A 66 43.160 52.615 19.249 1.00 0.00 1CGP 727 ATOM 573 1HE2 GLN A 66 42.985 53.631 24.496 1.00 0.00 1CGP 728 ATOM 574 2HE2 GLN A 66 44.484 53.023 25.109 1.00 0.00 1CGP 729 ATOM 575 N GLY A 67 39.334 52.839 21.425 1.00 47.37 1CGP 730 ATOM 576 CA GLY A 67 38.147 53.563 21.738 1.00 46.53 1CGP 731 ATOM 577 C GLY A 67 37.070 53.312 20.706 1.00 47.05 1CGP 732 ATOM 578 O GLY A 67 35.909 53.678 20.946 1.00 48.49 1CGP 733 ATOM 579 H GLY A 67 39.390 51.920 21.736 1.00 0.00 1CGP 734 ATOM 580 N ASP A 68 37.395 52.734 19.542 1.00 46.41 1CGP 735 ATOM 581 CA ASP A 68 36.397 52.489 18.513 1.00 45.08 1CGP 736 ATOM 582 C ASP A 68 35.738 51.143 18.594 1.00 42.72 1CGP 737 ATOM 583 O ASP A 68 36.318 50.171 19.068 1.00 43.16 1CGP 738 ATOM 584 CB ASP A 68 37.011 52.621 17.142 1.00 47.08 1CGP 739 ATOM 585 CG ASP A 68 37.392 54.061 16.798 1.00 49.82 1CGP 740 ATOM 586 OD1 ASP A 68 36.546 54.961 16.884 1.00 50.75 1CGP 741 ATOM 587 OD2 ASP A 68 38.550 54.274 16.435 1.00 50.72 1CGP 742 ATOM 588 H ASP A 68 38.327 52.532 19.319 1.00 0.00 1CGP 743 ATOM 589 N PHE A 69 34.482 51.109 18.249 1.00 38.75 1CGP 744 ATOM 590 CA PHE A 69 33.789 49.876 18.164 1.00 38.94 1CGP 745 ATOM 591 C PHE A 69 34.175 49.247 16.837 1.00 38.69 1CGP 746 ATOM 592 O PHE A 69 34.391 49.970 15.870 1.00 38.64 1CGP 747 ATOM 593 CB PHE A 69 32.337 50.171 18.208 1.00 43.46 1CGP 748 ATOM 594 CG PHE A 69 31.780 50.337 19.608 1.00 48.47 1CGP 749 ATOM 595 CD1 PHE A 69 31.401 49.208 20.326 1.00 49.62 1CGP 750 ATOM 596 CD2 PHE A 69 31.641 51.598 20.160 1.00 49.44 1CGP 751 ATOM 597 CE1 PHE A 69 30.897 49.337 21.601 1.00 50.47 1CGP 752 ATOM 598 CE2 PHE A 69 31.132 51.716 21.439 1.00 50.12 1CGP 753 ATOM 599 CZ PHE A 69 30.758 50.591 22.152 1.00 50.69 1CGP 754 ATOM 600 H PHE A 69 34.016 51.938 18.057 1.00 0.00 1CGP 755 ATOM 601 N ILE A 70 34.278 47.925 16.741 1.00 38.71 1CGP 756 ATOM 602 CA ILE A 70 34.561 47.213 15.502 1.00 38.87 1CGP 757 ATOM 603 C ILE A 70 33.372 46.269 15.387 1.00 40.50 1CGP 758 ATOM 604 O ILE A 70 32.980 45.705 16.411 1.00 39.80 1CGP 759 ATOM 605 CB ILE A 70 35.789 46.244 15.485 1.00 38.77 1CGP 760 ATOM 606 CG1 ILE A 70 37.114 46.749 16.067 1.00 38.58 1CGP 761 ATOM 607 CG2 ILE A 70 35.990 45.979 14.002 1.00 38.40 1CGP 762 ATOM 608 CD1 ILE A 70 38.256 45.685 16.085 1.00 35.91 1CGP 763 ATOM 609 H ILE A 70 34.044 47.391 17.535 1.00 0.00 1CGP 764 ATOM 610 N GLY A 71 32.771 46.060 14.210 1.00 43.50 1CGP 765 ATOM 611 CA GLY A 71 31.716 45.061 14.033 1.00 45.82 1CGP 766 ATOM 612 C GLY A 71 30.300 45.572 14.315 1.00 47.76 1CGP 767 ATOM 613 O GLY A 71 29.347 44.812 14.461 1.00 48.20 1CGP 768 ATOM 614 H GLY A 71 32.982 46.637 13.443 1.00 0.00 1CGP 769 ATOM 615 N GLU A 72 30.095 46.894 14.337 1.00 46.57 1CGP 770 ATOM 616 CA GLU A 72 28.779 47.462 14.615 1.00 44.86 1CGP 771 ATOM 617 C GLU A 72 27.728 47.110 13.594 1.00 45.05 1CGP 772 ATOM 618 O GLU A 72 26.620 46.726 13.948 1.00 45.10 1CGP 773 ATOM 619 CB GLU A 72 28.802 48.982 14.682 1.00 44.31 1CGP 774 ATOM 620 CG GLU A 72 29.289 49.739 13.450 1.00 43.11 1CGP 775 ATOM 621 CD GLU A 72 30.782 49.827 13.158 1.00 43.62 1CGP 776 ATOM 622 OE1 GLU A 72 31.627 49.274 13.864 1.00 41.22 1CGP 777 ATOM 623 OE2 GLU A 72 31.098 50.500 12.190 1.00 45.98 1CGP 778 ATOM 624 H GLU A 72 30.868 47.454 14.165 1.00 0.00 1CGP 779 ATOM 625 N LEU A 73 28.089 47.142 12.315 1.00 46.35 1CGP 780 ATOM 626 CA LEU A 73 27.127 47.030 11.234 1.00 48.56 1CGP 781 ATOM 627 C LEU A 73 26.232 45.801 11.134 1.00 50.64 1CGP 782 ATOM 628 O LEU A 73 25.325 45.784 10.292 1.00 51.70 1CGP 783 ATOM 629 CB LEU A 73 27.909 47.252 9.933 1.00 48.48 1CGP 784 ATOM 630 CG LEU A 73 27.959 48.662 9.287 1.00 49.68 1CGP 785 ATOM 631 CD1 LEU A 73 27.863 49.834 10.256 1.00 48.16 1CGP 786 ATOM 632 CD2 LEU A 73 29.294 48.732 8.598 1.00 49.76 1CGP 787 ATOM 633 H LEU A 73 29.039 47.232 12.109 1.00 0.00 1CGP 788 ATOM 634 N GLY A 74 26.406 44.777 11.978 1.00 52.78 1CGP 789 ATOM 635 CA GLY A 74 25.514 43.628 11.964 1.00 54.09 1CGP 790 ATOM 636 C GLY A 74 24.456 43.760 13.062 1.00 55.81 1CGP 791 ATOM 637 O GLY A 74 23.342 43.247 12.936 1.00 56.38 1CGP 792 ATOM 638 H GLY A 74 27.103 44.785 12.675 1.00 0.00 1CGP 793 ATOM 639 N LEU A 75 24.749 44.537 14.112 1.00 56.90 1CGP 794 ATOM 640 CA LEU A 75 23.898 44.719 15.274 1.00 56.30 1CGP 795 ATOM 641 C LEU A 75 22.486 45.070 14.963 1.00 57.21 1CGP 796 ATOM 642 O LEU A 75 21.612 44.770 15.753 1.00 58.52 1CGP 797 ATOM 643 CB LEU A 75 24.464 45.805 16.127 1.00 55.42 1CGP 798 ATOM 644 CG LEU A 75 23.729 46.293 17.325 1.00 55.42 1CGP 799 ATOM 645 CD1 LEU A 75 23.486 45.213 18.356 1.00 55.95 1CGP 800 ATOM 646 CD2 LEU A 75 24.588 47.380 17.885 1.00 57.64 1CGP 801 ATOM 647 H LEU A 75 25.578 45.059 14.090 1.00 0.00 1CGP 802 ATOM 648 N PHE A 76 22.264 45.717 13.844 1.00 58.29 1CGP 803 ATOM 649 CA PHE A 76 20.921 46.100 13.543 1.00 61.45 1CGP 804 ATOM 650 C PHE A 76 20.113 45.126 12.732 1.00 66.49 1CGP 805 ATOM 651 O PHE A 76 18.902 45.080 12.941 1.00 67.45 1CGP 806 ATOM 652 CB PHE A 76 20.987 47.427 12.876 1.00 59.68 1CGP 807 ATOM 653 CG PHE A 76 21.600 48.352 13.889 1.00 60.17 1CGP 808 ATOM 654 CD1 PHE A 76 20.959 48.593 15.076 1.00 61.41 1CGP 809 ATOM 655 CD2 PHE A 76 22.830 48.901 13.643 1.00 60.65 1CGP 810 ATOM 656 CE1 PHE A 76 21.564 49.383 16.025 1.00 62.84 1CGP 811 ATOM 657 CE2 PHE A 76 23.419 49.700 14.599 1.00 61.33 1CGP 812 ATOM 658 CZ PHE A 76 22.795 49.943 15.794 1.00 62.02 1CGP 813 ATOM 659 H PHE A 76 23.010 45.922 13.243 1.00 0.00 1CGP 814 ATOM 660 N GLU A 77 20.668 44.313 11.824 1.00 72.65 1CGP 815 ATOM 661 CA GLU A 77 19.790 43.426 11.060 1.00 77.19 1CGP 816 ATOM 662 C GLU A 77 20.303 41.986 11.105 1.00 77.82 1CGP 817 ATOM 663 O GLU A 77 21.455 41.645 10.797 1.00 78.66 1CGP 818 ATOM 664 CB GLU A 77 19.666 43.885 9.588 1.00 79.49 1CGP 819 ATOM 665 CG GLU A 77 18.352 43.424 8.902 1.00 83.80 1CGP 820 ATOM 666 CD GLU A 77 18.101 41.908 8.774 1.00 86.16 1CGP 821 ATOM 667 OE1 GLU A 77 18.802 41.261 7.989 1.00 87.78 1CGP 822 ATOM 668 OE2 GLU A 77 17.221 41.372 9.465 1.00 86.44 1CGP 823 ATOM 669 H GLU A 77 21.622 44.097 11.890 1.00 0.00 1CGP 824 ATOM 670 N GLU A 78 19.331 41.163 11.488 1.00 77.21 1CGP 825 ATOM 671 CA GLU A 78 19.500 39.746 11.680 1.00 77.11 1CGP 826 ATOM 672 C GLU A 78 20.054 39.023 10.463 1.00 75.80 1CGP 827 ATOM 673 O GLU A 78 19.497 39.083 9.371 1.00 73.61 1CGP 828 ATOM 674 CB GLU A 78 18.139 39.155 12.077 1.00 79.31 1CGP 829 ATOM 675 CG GLU A 78 18.162 38.101 13.204 1.00 81.55 1CGP 830 ATOM 676 CD GLU A 78 18.554 38.607 14.604 1.00 82.43 1CGP 831 ATOM 677 OE1 GLU A 78 19.761 38.668 14.900 1.00 82.48 1CGP 832 ATOM 678 OE2 GLU A 78 17.646 38.915 15.395 1.00 82.21 1CGP 833 ATOM 679 H GLU A 78 18.446 41.551 11.633 1.00 0.00 1CGP 834 ATOM 680 N GLY A 79 21.222 38.420 10.668 1.00 75.66 1CGP 835 ATOM 681 CA GLY A 79 21.801 37.515 9.690 1.00 74.59 1CGP 836 ATOM 682 C GLY A 79 22.694 38.121 8.623 1.00 73.59 1CGP 837 ATOM 683 O GLY A 79 22.696 37.673 7.474 1.00 73.03 1CGP 838 ATOM 684 H GLY A 79 21.739 38.647 11.466 1.00 0.00 1CGP 839 ATOM 685 N GLN A 80 23.524 39.101 8.963 1.00 72.38 1CGP 840 ATOM 686 CA GLN A 80 24.353 39.711 7.944 1.00 69.45 1CGP 841 ATOM 687 C GLN A 80 25.797 39.250 8.024 1.00 69.04 1CGP 842 ATOM 688 O GLN A 80 26.308 38.808 9.058 1.00 69.27 1CGP 843 ATOM 689 CB GLN A 80 24.266 41.214 8.090 1.00 67.34 1CGP 844 ATOM 690 CG GLN A 80 22.838 41.689 7.984 1.00 64.96 1CGP 845 ATOM 691 CD GLN A 80 22.794 43.179 7.845 1.00 64.72 1CGP 846 ATOM 692 OE1 GLN A 80 22.811 43.660 6.722 1.00 65.49 1CGP 847 ATOM 693 NE2 GLN A 80 22.753 43.967 8.908 1.00 63.83 1CGP 848 ATOM 694 H GLN A 80 23.585 39.409 9.885 1.00 0.00 1CGP 849 ATOM 695 1HE2 GLN A 80 22.702 43.540 9.788 1.00 0.00 1CGP 850 ATOM 696 2HE2 GLN A 80 22.818 44.931 8.752 1.00 0.00 1CGP 851 ATOM 697 N GLU A 81 26.457 39.326 6.883 1.00 67.84 1CGP 852 ATOM 698 CA GLU A 81 27.851 38.981 6.802 1.00 66.25 1CGP 853 ATOM 699 C GLU A 81 28.649 40.206 7.225 1.00 62.78 1CGP 854 ATOM 700 O GLU A 81 28.187 41.353 7.171 1.00 63.03 1CGP 855 ATOM 701 CB GLU A 81 28.184 38.589 5.366 1.00 70.77 1CGP 856 ATOM 702 CG GLU A 81 27.460 37.298 4.920 1.00 75.18 1CGP 857 ATOM 703 CD GLU A 81 27.663 36.825 3.467 1.00 76.88 1CGP 858 ATOM 704 OE1 GLU A 81 28.075 37.623 2.613 1.00 76.67 1CGP 859 ATOM 705 OE2 GLU A 81 27.388 35.641 3.198 1.00 77.86 1CGP 860 ATOM 706 H GLU A 81 26.034 39.730 6.105 1.00 0.00 1CGP 861 ATOM 707 N ARG A 82 29.864 39.970 7.687 1.00 58.59 1CGP 862 ATOM 708 CA ARG A 82 30.799 41.024 8.042 1.00 54.07 1CGP 863 ATOM 709 C ARG A 82 31.226 41.683 6.727 1.00 51.78 1CGP 864 ATOM 710 O ARG A 82 31.565 40.979 5.769 1.00 50.29 1CGP 865 ATOM 711 CB ARG A 82 32.001 40.422 8.758 1.00 52.07 1CGP 866 ATOM 712 CG ARG A 82 31.648 39.502 9.924 1.00 50.38 1CGP 867 ATOM 713 CD ARG A 82 32.207 39.871 11.279 1.00 48.93 1CGP 868 ATOM 714 NE ARG A 82 31.462 40.962 11.858 1.00 48.18 1CGP 869 ATOM 715 CZ ARG A 82 31.082 40.950 13.132 1.00 48.25 1CGP 870 ATOM 716 NH1 ARG A 82 31.392 39.965 13.980 1.00 48.74 1CGP 871 ATOM 717 NH2 ARG A 82 30.370 41.980 13.555 1.00 48.44 1CGP 872 ATOM 718 H ARG A 82 30.079 39.036 7.841 1.00 0.00 1CGP 873 ATOM 719 HE ARG A 82 31.231 41.737 11.305 1.00 0.00 1CGP 874 ATOM 720 1HH1 ARG A 82 31.959 39.200 13.676 1.00 0.00 1CGP 875 ATOM 721 2HH1 ARG A 82 31.114 40.041 14.936 1.00 0.00 1CGP 876 ATOM 722 1HH2 ARG A 82 30.165 42.710 12.904 1.00 0.00 1CGP 877 ATOM 723 2HH2 ARG A 82 30.095 42.034 14.513 1.00 0.00 1CGP 878 ATOM 724 N SER A 83 31.145 43.018 6.697 1.00 48.78 1CGP 879 ATOM 725 CA SER A 83 31.409 43.861 5.544 1.00 44.46 1CGP 880 ATOM 726 C SER A 83 32.828 44.081 5.065 1.00 42.61 1CGP 881 ATOM 727 O SER A 83 33.040 44.404 3.892 1.00 42.62 1CGP 882 ATOM 728 CB SER A 83 30.815 45.209 5.799 1.00 44.46 1CGP 883 ATOM 729 OG SER A 83 31.324 45.718 7.029 1.00 44.80 1CGP 884 ATOM 730 H SER A 83 30.814 43.463 7.500 1.00 0.00 1CGP 885 ATOM 731 HG SER A 83 30.739 45.397 7.740 1.00 0.00 1CGP 886 ATOM 732 N ALA A 84 33.825 43.893 5.907 1.00 38.57 1CGP 887 ATOM 733 CA ALA A 84 35.187 44.144 5.500 1.00 36.31 1CGP 888 ATOM 734 C ALA A 84 36.100 43.285 6.344 1.00 35.52 1CGP 889 ATOM 735 O ALA A 84 35.604 42.554 7.192 1.00 33.91 1CGP 890 ATOM 736 CB ALA A 84 35.473 45.589 5.734 1.00 36.71 1CGP 891 ATOM 737 H ALA A 84 33.684 43.524 6.806 1.00 0.00 1CGP 892 ATOM 738 N TRP A 85 37.395 43.234 6.095 1.00 37.20 1CGP 893 ATOM 739 CA TRP A 85 38.343 42.521 6.939 1.00 40.10 1CGP 894 ATOM 740 C TRP A 85 38.876 43.546 7.909 1.00 38.84 1CGP 895 ATOM 741 O TRP A 85 39.076 44.702 7.561 1.00 40.62 1CGP 896 ATOM 742 CB TRP A 85 39.587 41.968 6.219 1.00 42.89 1CGP 897 ATOM 743 CG TRP A 85 39.408 40.667 5.469 1.00 46.69 1CGP 898 ATOM 744 CD1 TRP A 85 39.893 39.461 5.918 1.00 48.56 1CGP 899 ATOM 745 CD2 TRP A 85 38.734 40.558 4.308 1.00 50.67 1CGP 900 ATOM 746 NE1 TRP A 85 39.510 38.578 5.028 1.00 49.09 1CGP 901 ATOM 747 CE2 TRP A 85 38.812 39.205 4.063 1.00 52.20 1CGP 902 ATOM 748 CE3 TRP A 85 38.080 41.428 3.469 1.00 55.80 1CGP 903 ATOM 749 CZ2 TRP A 85 38.209 38.704 2.935 1.00 56.59 1CGP 904 ATOM 750 CZ3 TRP A 85 37.482 40.921 2.332 1.00 57.59 1CGP 905 ATOM 751 CH2 TRP A 85 37.545 39.566 2.072 1.00 57.79 1CGP 906 ATOM 752 H TRP A 85 37.760 43.775 5.371 1.00 0.00 1CGP 907 ATOM 753 HE1 TRP A 85 39.887 37.680 4.935 1.00 0.00 1CGP 908 ATOM 754 N VAL A 86 39.163 43.141 9.117 1.00 37.34 1CGP 909 ATOM 755 CA VAL A 86 39.668 44.037 10.116 1.00 34.98 1CGP 910 ATOM 756 C VAL A 86 40.920 43.268 10.492 1.00 35.95 1CGP 911 ATOM 757 O VAL A 86 40.800 42.144 10.988 1.00 36.05 1CGP 912 ATOM 758 CB VAL A 86 38.566 44.098 11.185 1.00 33.45 1CGP 913 ATOM 759 CG1 VAL A 86 39.037 44.877 12.359 1.00 34.36 1CGP 914 ATOM 760 CG2 VAL A 86 37.351 44.808 10.654 1.00 32.21 1CGP 915 ATOM 761 H VAL A 86 39.121 42.182 9.314 1.00 0.00 1CGP 916 ATOM 762 N ARG A 87 42.115 43.733 10.189 1.00 38.34 1CGP 917 ATOM 763 CA ARG A 87 43.306 43.019 10.628 1.00 41.47 1CGP 918 ATOM 764 C ARG A 87 44.031 43.914 11.629 1.00 42.07 1CGP 919 ATOM 765 O ARG A 87 44.039 45.143 11.493 1.00 42.94 1CGP 920 ATOM 766 CB ARG A 87 44.172 42.661 9.389 1.00 45.29 1CGP 921 ATOM 767 CG ARG A 87 45.606 43.197 9.163 1.00 52.06 1CGP 922 ATOM 768 CD ARG A 87 46.479 42.533 8.068 1.00 56.26 1CGP 923 ATOM 769 NE ARG A 87 45.960 42.589 6.701 1.00 61.97 1CGP 924 ATOM 770 CZ ARG A 87 45.082 41.673 6.205 1.00 65.29 1CGP 925 ATOM 771 NH1 ARG A 87 44.569 40.672 6.956 1.00 65.20 1CGP 926 ATOM 772 NH2 ARG A 87 44.672 41.749 4.923 1.00 65.69 1CGP 927 ATOM 773 H ARG A 87 42.177 44.603 9.736 1.00 0.00 1CGP 928 ATOM 774 HE ARG A 87 46.249 43.325 6.121 1.00 0.00 1CGP 929 ATOM 775 1HH1 ARG A 87 44.834 40.563 7.913 1.00 0.00 1CGP 930 ATOM 776 2HH1 ARG A 87 43.917 40.035 6.549 1.00 0.00 1CGP 931 ATOM 777 1HH2 ARG A 87 44.997 42.476 4.319 1.00 0.00 1CGP 932 ATOM 778 2HH2 ARG A 87 44.025 41.074 4.572 1.00 0.00 1CGP 933 ATOM 779 N ALA A 88 44.587 43.355 12.700 1.00 42.63 1CGP 934 ATOM 780 CA ALA A 88 45.254 44.096 13.759 1.00 41.73 1CGP 935 ATOM 781 C ALA A 88 46.562 44.686 13.286 1.00 41.85 1CGP 936 ATOM 782 O ALA A 88 47.489 43.959 12.948 1.00 40.26 1CGP 937 ATOM 783 CB ALA A 88 45.538 43.167 14.928 1.00 40.98 1CGP 938 ATOM 784 H ALA A 88 44.605 42.382 12.745 1.00 0.00 1CGP 939 ATOM 785 N LYS A 89 46.686 46.001 13.226 1.00 44.40 1CGP 940 ATOM 786 CA LYS A 89 47.933 46.623 12.815 1.00 47.33 1CGP 941 ATOM 787 C LYS A 89 48.960 46.485 13.908 1.00 48.26 1CGP 942 ATOM 788 O LYS A 89 50.159 46.630 13.679 1.00 49.07 1CGP 943 ATOM 789 CB LYS A 89 47.826 48.108 12.585 1.00 49.80 1CGP 944 ATOM 790 CG LYS A 89 47.482 48.604 11.196 1.00 53.56 1CGP 945 ATOM 791 CD LYS A 89 47.902 50.066 11.056 1.00 55.79 1CGP 946 ATOM 792 CE LYS A 89 47.123 50.915 12.067 1.00 59.06 1CGP 947 ATOM 793 NZ LYS A 89 47.600 52.286 12.071 1.00 61.96 1CGP 948 ATOM 794 H LYS A 89 45.956 46.555 13.554 1.00 0.00 1CGP 949 ATOM 795 1HZ LYS A 89 47.489 52.685 11.117 1.00 0.00 1CGP 950 ATOM 796 2HZ LYS A 89 48.609 52.282 12.326 1.00 0.00 1CGP 951 ATOM 797 3HZ LYS A 89 47.066 52.850 12.761 1.00 0.00 1CGP 952 ATOM 798 N THR A 90 48.487 46.272 15.126 1.00 48.67 1CGP 953 ATOM 799 CA THR A 90 49.334 46.227 16.299 1.00 49.10 1CGP 954 ATOM 800 C THR A 90 48.720 45.253 17.271 1.00 48.93 1CGP 955 ATOM 801 O THR A 90 47.753 44.566 16.946 1.00 49.12 1CGP 956 ATOM 802 CB THR A 90 49.441 47.629 16.953 1.00 49.32 1CGP 957 ATOM 803 OG1 THR A 90 48.199 48.301 16.731 1.00 51.18 1CGP 958 ATOM 804 CG2 THR A 90 50.641 48.407 16.437 1.00 49.21 1CGP 959 ATOM 805 H THR A 90 47.546 46.036 15.266 1.00 0.00 1CGP 960 ATOM 806 HG1 THR A 90 47.928 48.107 15.825 1.00 0.00 1CGP 961 ATOM 807 N ALA A 91 49.291 45.196 18.458 1.00 49.09 1CGP 962 ATOM 808 CA ALA A 91 48.776 44.348 19.492 1.00 49.79 1CGP 963 ATOM 809 C ALA A 91 47.491 44.983 19.982 1.00 50.03 1CGP 964 ATOM 810 O ALA A 91 47.518 46.099 20.496 1.00 51.16 1CGP 965 ATOM 811 CB ALA A 91 49.787 44.302 20.597 1.00 51.70 1CGP 966 ATOM 812 H ALA A 91 50.017 45.804 18.686 1.00 0.00 1CGP 967 ATOM 813 N CYS A 92 46.372 44.316 19.857 1.00 50.85 1CGP 968 ATOM 814 CA CYS A 92 45.120 44.900 20.272 1.00 53.21 1CGP 969 ATOM 815 C CYS A 92 44.483 44.192 21.449 1.00 54.51 1CGP 970 ATOM 816 O CYS A 92 44.402 42.961 21.495 1.00 54.95 1CGP 971 ATOM 817 CB CYS A 92 44.132 44.887 19.127 1.00 53.03 1CGP 972 ATOM 818 SG CYS A 92 44.557 45.971 17.753 1.00 54.83 1CGP 973 ATOM 819 H CYS A 92 46.426 43.398 19.522 1.00 0.00 1CGP 974 ATOM 820 N GLU A 93 44.002 44.953 22.411 1.00 55.32 1CGP 975 ATOM 821 CA GLU A 93 43.288 44.368 23.517 1.00 55.08 1CGP 976 ATOM 822 C GLU A 93 41.899 44.690 23.031 1.00 52.34 1CGP 977 ATOM 823 O GLU A 93 41.577 45.875 22.957 1.00 51.16 1CGP 978 ATOM 824 CB GLU A 93 43.677 45.113 24.775 1.00 60.50 1CGP 979 ATOM 825 CG GLU A 93 44.240 44.136 25.806 1.00 66.87 1CGP 980 ATOM 826 CD GLU A 93 45.273 44.702 26.790 1.00 70.69 1CGP 981 ATOM 827 OE1 GLU A 93 46.416 44.959 26.371 1.00 72.35 1CGP 982 ATOM 828 OE2 GLU A 93 44.929 44.862 27.971 1.00 71.89 1CGP 983 ATOM 829 H GLU A 93 43.991 45.921 22.268 1.00 0.00 1CGP 984 ATOM 830 N VAL A 94 41.111 43.709 22.624 1.00 50.32 1CGP 985 ATOM 831 CA VAL A 94 39.795 43.928 22.044 1.00 50.17 1CGP 986 ATOM 832 C VAL A 94 38.719 43.281 22.903 1.00 48.98 1CGP 987 ATOM 833 O VAL A 94 38.834 42.114 23.274 1.00 48.26 1CGP 988 ATOM 834 CB VAL A 94 39.718 43.326 20.616 1.00 51.42 1CGP 989 ATOM 835 CG1 VAL A 94 38.375 43.662 19.986 1.00 51.45 1CGP 990 ATOM 836 CG2 VAL A 94 40.817 43.876 19.733 1.00 51.73 1CGP 991 ATOM 837 H VAL A 94 41.390 42.790 22.815 1.00 0.00 1CGP 992 ATOM 838 N ALA A 95 37.691 44.025 23.277 1.00 49.27 1CGP 993 ATOM 839 CA ALA A 95 36.580 43.524 24.069 1.00 50.84 1CGP 994 ATOM 840 C ALA A 95 35.593 42.841 23.135 1.00 53.56 1CGP 995 ATOM 841 O ALA A 95 35.510 43.310 21.993 1.00 54.83 1CGP 996 ATOM 842 CB ALA A 95 35.899 44.685 24.752 1.00 48.14 1CGP 997 ATOM 843 H ALA A 95 37.670 44.948 22.974 1.00 0.00 1CGP 998 ATOM 844 N GLU A 96 34.876 41.780 23.565 1.00 55.97 1CGP 999 ATOM 845 CA GLU A 96 33.872 41.095 22.745 1.00 58.45 1CGP1000 ATOM 846 C GLU A 96 32.523 40.881 23.422 1.00 59.11 1CGP1001 ATOM 847 O GLU A 96 32.563 40.242 24.491 1.00 60.53 1CGP1002 ATOM 848 CB GLU A 96 34.247 39.711 22.378 1.00 61.07 1CGP1003 ATOM 849 CG GLU A 96 35.546 39.381 21.725 1.00 67.12 1CGP1004 ATOM 850 CD GLU A 96 35.403 37.931 21.299 1.00 70.38 1CGP1005 ATOM 851 OE1 GLU A 96 35.713 37.054 22.113 1.00 71.33 1CGP1006 ATOM 852 OE2 GLU A 96 34.933 37.689 20.175 1.00 72.14 1CGP1007 ATOM 853 H GLU A 96 35.147 41.364 24.406 1.00 0.00 1CGP1008 ATOM 854 N ILE A 97 31.362 41.251 22.841 1.00 59.19 1CGP1009 ATOM 855 CA ILE A 97 30.015 41.068 23.433 1.00 59.08 1CGP1010 ATOM 856 C ILE A 97 29.203 40.319 22.403 1.00 59.61 1CGP1011 ATOM 857 O ILE A 97 29.370 40.545 21.200 1.00 60.17 1CGP1012 ATOM 858 CB ILE A 97 29.086 42.302 23.644 1.00 58.73 1CGP1013 ATOM 859 CG1 ILE A 97 29.853 43.467 24.122 1.00 61.17 1CGP1014 ATOM 860 CG2 ILE A 97 28.055 42.045 24.693 1.00 56.46 1CGP1015 ATOM 861 CD1 ILE A 97 30.241 44.304 22.887 1.00 64.60 1CGP1016 ATOM 862 H ILE A 97 31.427 41.619 21.930 1.00 0.00 1CGP1017 ATOM 863 N SER A 98 28.282 39.481 22.871 1.00 60.56 1CGP1018 ATOM 864 CA SER A 98 27.332 38.789 22.009 1.00 60.56 1CGP1019 ATOM 865 C SER A 98 26.380 39.859 21.494 1.00 59.45 1CGP1020 ATOM 866 O SER A 98 25.963 40.730 22.274 1.00 59.91 1CGP1021 ATOM 867 CB SER A 98 26.525 37.744 22.809 1.00 61.59 1CGP1022 ATOM 868 OG SER A 98 26.903 37.628 24.194 1.00 62.97 1CGP1023 ATOM 869 H SER A 98 28.182 39.348 23.835 1.00 0.00 1CGP1024 ATOM 870 HG SER A 98 26.407 36.917 24.619 1.00 0.00 1CGP1025 ATOM 871 N TYR A 99 25.981 39.832 20.228 1.00 57.95 1CGP1026 ATOM 872 CA TYR A 99 25.030 40.821 19.727 1.00 57.58 1CGP1027 ATOM 873 C TYR A 99 23.760 40.859 20.581 1.00 59.60 1CGP1028 ATOM 874 O TYR A 99 23.402 41.863 21.202 1.00 58.14 1CGP1029 ATOM 875 CB TYR A 99 24.681 40.501 18.265 1.00 53.56 1CGP1030 ATOM 876 CG TYR A 99 25.552 41.157 17.182 1.00 49.36 1CGP1031 ATOM 877 CD1 TYR A 99 26.580 42.062 17.453 1.00 47.44 1CGP1032 ATOM 878 CD2 TYR A 99 25.265 40.830 15.880 1.00 46.71 1CGP1033 ATOM 879 CE1 TYR A 99 27.301 42.638 16.423 1.00 44.98 1CGP1034 ATOM 880 CE2 TYR A 99 25.985 41.395 14.860 1.00 44.21 1CGP1035 ATOM 881 CZ TYR A 99 26.985 42.292 15.129 1.00 43.64 1CGP1036 ATOM 882 OH TYR A 99 27.621 42.871 14.057 1.00 41.19 1CGP1037 ATOM 883 H TYR A 99 26.425 39.207 19.610 1.00 0.00 1CGP1038 ATOM 884 HH TYR A 99 27.828 42.225 13.380 1.00 0.00 1CGP1039 ATOM 885 N LYS A 100 23.196 39.667 20.768 1.00 63.60 1CGP1040 ATOM 886 CA LYS A 100 21.984 39.447 21.550 1.00 66.77 1CGP1041 ATOM 887 C LYS A 100 22.077 40.035 22.943 1.00 67.31 1CGP1042 ATOM 888 O LYS A 100 21.107 40.479 23.559 1.00 68.14 1CGP1043 ATOM 889 CB LYS A 100 21.701 37.954 21.683 1.00 68.37 1CGP1044 ATOM 890 CG LYS A 100 21.264 37.195 20.406 1.00 72.67 1CGP1045 ATOM 891 CD LYS A 100 22.277 37.009 19.232 1.00 74.59 1CGP1046 ATOM 892 CE LYS A 100 23.532 36.157 19.540 1.00 75.93 1CGP1047 ATOM 893 NZ LYS A 100 23.209 34.769 19.855 1.00 76.32 1CGP1048 ATOM 894 H LYS A 100 23.636 38.913 20.339 1.00 0.00 1CGP1049 ATOM 895 1HZ LYS A 100 22.761 34.314 19.035 1.00 0.00 1CGP1050 ATOM 896 2HZ LYS A 100 22.547 34.746 20.657 1.00 0.00 1CGP1051 ATOM 897 3HZ LYS A 100 24.073 34.251 20.112 1.00 0.00 1CGP1052 ATOM 898 N LYS A 101 23.287 40.080 23.458 1.00 67.82 1CGP1053 ATOM 899 CA LYS A 101 23.441 40.572 24.787 1.00 68.92 1CGP1054 ATOM 900 C LYS A 101 23.580 42.072 24.694 1.00 67.51 1CGP1055 ATOM 901 O LYS A 101 22.982 42.767 25.520 1.00 66.26 1CGP1056 ATOM 902 CB LYS A 101 24.640 39.854 25.344 1.00 72.64 1CGP1057 ATOM 903 CG LYS A 101 24.553 39.474 26.837 1.00 76.47 1CGP1058 ATOM 904 CD LYS A 101 24.891 40.610 27.804 1.00 79.00 1CGP1059 ATOM 905 CE LYS A 101 26.221 41.178 27.324 1.00 81.52 1CGP1060 ATOM 906 NZ LYS A 101 26.891 42.029 28.264 1.00 82.94 1CGP1061 ATOM 907 H LYS A 101 24.081 39.910 22.920 1.00 0.00 1CGP1062 ATOM 908 1HZ LYS A 101 27.040 41.443 29.108 1.00 0.00 1CGP1063 ATOM 909 2HZ LYS A 101 26.312 42.848 28.530 1.00 0.00 1CGP1064 ATOM 910 3HZ LYS A 101 27.811 42.335 27.888 1.00 0.00 1CGP1065 ATOM 911 N PHE A 102 24.301 42.617 23.709 1.00 67.30 1CGP1066 ATOM 912 CA PHE A 102 24.427 44.068 23.577 1.00 67.71 1CGP1067 ATOM 913 C PHE A 102 23.039 44.695 23.418 1.00 69.05 1CGP1068 ATOM 914 O PHE A 102 22.731 45.733 24.026 1.00 69.08 1CGP1069 ATOM 915 CB PHE A 102 25.315 44.429 22.372 1.00 64.28 1CGP1070 ATOM 916 CG PHE A 102 25.760 45.892 22.338 1.00 61.35 1CGP1071 ATOM 917 CD1 PHE A 102 26.602 46.394 23.317 1.00 61.09 1CGP1072 ATOM 918 CD2 PHE A 102 25.316 46.721 21.329 1.00 59.19 1CGP1073 ATOM 919 CE1 PHE A 102 26.994 47.716 23.280 1.00 60.60 1CGP1074 ATOM 920 CE2 PHE A 102 25.716 48.039 21.306 1.00 58.57 1CGP1075 ATOM 921 CZ PHE A 102 26.555 48.544 22.276 1.00 59.69 1CGP1076 ATOM 922 H PHE A 102 24.828 42.031 23.132 1.00 0.00 1CGP1077 ATOM 923 N ARG A 103 22.166 44.004 22.671 1.00 69.44 1CGP1078 ATOM 924 CA ARG A 103 20.783 44.410 22.531 1.00 71.28 1CGP1079 ATOM 925 C ARG A 103 20.212 44.721 23.907 1.00 72.70 1CGP1080 ATOM 926 O ARG A 103 19.666 45.802 24.152 1.00 73.54 1CGP1081 ATOM 927 CB ARG A 103 19.964 43.302 21.899 1.00 72.57 1CGP1082 ATOM 928 CG ARG A 103 19.613 43.585 20.449 1.00 75.50 1CGP1083 ATOM 929 CD ARG A 103 20.706 43.180 19.468 1.00 77.72 1CGP1084 ATOM 930 NE ARG A 103 20.665 41.758 19.143 1.00 80.15 1CGP1085 ATOM 931 CZ ARG A 103 21.089 41.272 17.960 1.00 81.97 1CGP1086 ATOM 932 NH1 ARG A 103 21.619 42.036 16.990 1.00 82.54 1CGP1087 ATOM 933 NH2 ARG A 103 21.003 39.962 17.739 1.00 83.85 1CGP1088 ATOM 934 H ARG A 103 22.518 43.248 22.161 1.00 0.00 1CGP1089 ATOM 935 HE ARG A 103 20.327 41.129 19.814 1.00 0.00 1CGP1090 ATOM 936 1HH1 ARG A 103 21.694 43.026 17.108 1.00 0.00 1CGP1091 ATOM 937 2HH1 ARG A 103 21.906 41.617 16.129 1.00 0.00 1CGP1092 ATOM 938 1HH2 ARG A 103 20.638 39.361 18.451 1.00 0.00 1CGP1093 ATOM 939 2HH2 ARG A 103 21.277 39.583 16.856 1.00 0.00 1CGP1094 ATOM 940 N GLN A 104 20.488 43.818 24.852 1.00 74.61 1CGP1095 ATOM 941 CA GLN A 104 20.026 43.966 26.217 1.00 76.07 1CGP1096 ATOM 942 C GLN A 104 20.617 45.185 26.875 1.00 74.72 1CGP1097 ATOM 943 O GLN A 104 19.893 45.982 27.472 1.00 75.53 1CGP1098 ATOM 944 CB GLN A 104 20.378 42.728 27.037 1.00 79.34 1CGP1099 ATOM 945 CG GLN A 104 19.480 41.540 26.669 1.00 83.07 1CGP1100 ATOM 946 CD GLN A 104 19.912 40.190 27.234 1.00 84.06 1CGP1101 ATOM 947 OE1 GLN A 104 19.778 39.885 28.423 1.00 85.01 1CGP1102 ATOM 948 NE2 GLN A 104 20.451 39.342 26.366 1.00 84.55 1CGP1103 ATOM 949 H GLN A 104 21.024 43.036 24.613 1.00 0.00 1CGP1104 ATOM 950 1HE2 GLN A 104 20.536 39.630 25.431 1.00 0.00 1CGP1105 ATOM 951 2HE2 GLN A 104 20.725 38.472 26.712 1.00 0.00 1CGP1106 ATOM 952 N LEU A 105 21.908 45.399 26.738 1.00 73.07 1CGP1107 ATOM 953 CA LEU A 105 22.482 46.560 27.371 1.00 73.37 1CGP1108 ATOM 954 C LEU A 105 21.879 47.851 26.874 1.00 73.46 1CGP1109 ATOM 955 O LEU A 105 21.748 48.757 27.690 1.00 72.60 1CGP1110 ATOM 956 CB LEU A 105 23.977 46.592 27.154 1.00 74.60 1CGP1111 ATOM 957 CG LEU A 105 24.808 45.922 28.234 1.00 75.47 1CGP1112 ATOM 958 CD1 LEU A 105 24.625 44.427 28.123 1.00 75.39 1CGP1113 ATOM 959 CD2 LEU A 105 26.273 46.312 28.091 1.00 75.75 1CGP1114 ATOM 960 H LEU A 105 22.431 44.738 26.237 1.00 0.00 1CGP1115 ATOM 961 N ILE A 106 21.446 47.956 25.607 1.00 75.04 1CGP1116 ATOM 962 CA ILE A 106 20.813 49.183 25.088 1.00 77.10 1CGP1117 ATOM 963 C ILE A 106 19.530 49.546 25.852 1.00 78.41 1CGP1118 ATOM 964 O ILE A 106 19.365 50.696 26.292 1.00 77.77 1CGP1119 ATOM 965 CB ILE A 106 20.527 49.016 23.553 1.00 76.37 1CGP1120 ATOM 966 CG1 ILE A 106 21.854 48.982 22.789 1.00 75.86 1CGP1121 ATOM 967 CG2 ILE A 106 19.647 50.160 23.035 1.00 76.25 1CGP1122 ATOM 968 CD1 ILE A 106 21.725 48.616 21.301 1.00 75.24 1CGP1123 ATOM 969 H ILE A 106 21.690 47.218 25.005 1.00 0.00 1CGP1124 ATOM 970 N GLN A 107 18.654 48.543 26.033 1.00 78.80 1CGP1125 ATOM 971 CA GLN A 107 17.409 48.682 26.794 1.00 78.60 1CGP1126 ATOM 972 C GLN A 107 17.713 49.137 28.215 1.00 77.36 1CGP1127 ATOM 973 O GLN A 107 16.969 49.894 28.825 1.00 77.35 1CGP1128 ATOM 974 CB GLN A 107 16.663 47.357 26.899 1.00 80.12 1CGP1129 ATOM 975 CG GLN A 107 16.371 46.639 25.581 1.00 83.27 1CGP1130 ATOM 976 CD GLN A 107 15.207 47.184 24.763 1.00 85.09 1CGP1131 ATOM 977 OE1 GLN A 107 15.134 48.362 24.409 1.00 87.20 1CGP1132 ATOM 978 NE2 GLN A 107 14.242 46.346 24.408 1.00 85.08 1CGP1133 ATOM 979 H GLN A 107 18.881 47.687 25.605 1.00 0.00 1CGP1134 ATOM 980 1HE2 GLN A 107 14.310 45.402 24.646 1.00 0.00 1CGP1135 ATOM 981 2HE2 GLN A 107 13.496 46.748 23.918 1.00 0.00 1CGP1136 ATOM 982 N VAL A 108 18.800 48.616 28.761 1.00 76.29 1CGP1137 ATOM 983 CA VAL A 108 19.263 48.979 30.081 1.00 75.75 1CGP1138 ATOM 984 C VAL A 108 19.895 50.384 30.100 1.00 74.97 1CGP1139 ATOM 985 O VAL A 108 19.791 51.078 31.118 1.00 74.73 1CGP1140 ATOM 986 CB VAL A 108 20.221 47.831 30.495 1.00 77.23 1CGP1141 ATOM 987 CG1 VAL A 108 20.792 48.054 31.886 1.00 78.35 1CGP1142 ATOM 988 CG2 VAL A 108 19.436 46.519 30.532 1.00 77.58 1CGP1143 ATOM 989 H VAL A 108 19.268 47.912 28.270 1.00 0.00 1CGP1144 ATOM 990 N ASN A 109 20.616 50.864 29.081 1.00 73.39 1CGP1145 ATOM 991 CA ASN A 109 21.061 52.253 28.997 1.00 72.16 1CGP1146 ATOM 992 C ASN A 109 21.388 52.639 27.562 1.00 74.11 1CGP1147 ATOM 993 O ASN A 109 22.464 52.333 27.035 1.00 76.07 1CGP1148 ATOM 994 CB ASN A 109 22.344 52.616 29.786 1.00 68.22 1CGP1149 ATOM 995 CG ASN A 109 22.731 54.088 29.570 1.00 65.40 1CGP1150 ATOM 996 OD1 ASN A 109 23.892 54.480 29.611 1.00 63.78 1CGP1151 ATOM 997 ND2 ASN A 109 21.834 55.030 29.291 1.00 64.16 1CGP1152 ATOM 998 H ASN A 109 20.914 50.231 28.405 1.00 0.00 1CGP1153 ATOM 999 1HD2 ASN A 109 20.883 54.800 29.222 1.00 0.00 1CGP1154 ATOM 1000 2HD2 ASN A 109 22.175 55.950 29.249 1.00 0.00 1CGP1155 ATOM 1001 N PRO A 110 20.543 53.474 26.945 1.00 75.00 1CGP1156 ATOM 1002 CA PRO A 110 20.792 54.072 25.636 1.00 74.60 1CGP1157 ATOM 1003 C PRO A 110 22.108 54.805 25.400 1.00 73.47 1CGP1158 ATOM 1004 O PRO A 110 22.531 54.843 24.246 1.00 72.94 1CGP1159 ATOM 1005 CB PRO A 110 19.590 54.966 25.422 1.00 75.09 1CGP1160 ATOM 1006 CG PRO A 110 18.505 54.136 26.059 1.00 75.18 1CGP1161 ATOM 1007 CD PRO A 110 19.175 53.739 27.369 1.00 74.81 1CGP1162 ATOM 1008 N ASP A 111 22.853 55.336 26.381 1.00 73.52 1CGP1163 ATOM 1009 CA ASP A 111 24.071 56.076 26.068 1.00 74.25 1CGP1164 ATOM 1010 C ASP A 111 25.134 55.227 25.355 1.00 73.10 1CGP1165 ATOM 1011 O ASP A 111 25.881 55.802 24.545 1.00 72.69 1CGP1166 ATOM 1012 CB ASP A 111 24.670 56.711 27.355 1.00 76.30 1CGP1167 ATOM 1013 CG ASP A 111 25.819 57.729 27.148 1.00 77.88 1CGP1168 ATOM 1014 OD1 ASP A 111 25.801 58.524 26.193 1.00 76.97 1CGP1169 ATOM 1015 OD2 ASP A 111 26.750 57.718 27.962 1.00 79.41 1CGP1170 ATOM 1016 H ASP A 111 22.611 55.184 27.311 1.00 0.00 1CGP1171 ATOM 1017 N ILE A 112 25.232 53.890 25.507 1.00 70.06 1CGP1172 ATOM 1018 CA ILE A 112 26.205 53.208 24.661 1.00 66.85 1CGP1173 ATOM 1019 C ILE A 112 25.620 53.223 23.263 1.00 65.97 1CGP1174 ATOM 1020 O ILE A 112 26.382 53.648 22.398 1.00 67.31 1CGP1175 ATOM 1021 CB ILE A 112 26.537 51.718 24.974 1.00 64.46 1CGP1176 ATOM 1022 CG1 ILE A 112 25.481 51.024 25.780 1.00 63.67 1CGP1177 ATOM 1023 CG2 ILE A 112 27.914 51.727 25.614 1.00 63.04 1CGP1178 ATOM 1024 CD1 ILE A 112 24.252 50.608 24.955 1.00 62.93 1CGP1179 ATOM 1025 H ILE A 112 24.610 53.407 26.092 1.00 0.00 1CGP1180 ATOM 1026 N LEU A 113 24.327 52.934 22.976 1.00 63.53 1CGP1181 ATOM 1027 CA LEU A 113 23.865 52.958 21.587 1.00 63.36 1CGP1182 ATOM 1028 C LEU A 113 24.057 54.352 20.973 1.00 64.13 1CGP1183 ATOM 1029 O LEU A 113 24.327 54.504 19.782 1.00 64.18 1CGP1184 ATOM 1030 CB LEU A 113 22.395 52.564 21.467 1.00 61.44 1CGP1185 ATOM 1031 CG LEU A 113 21.845 52.523 20.023 1.00 61.17 1CGP1186 ATOM 1032 CD1 LEU A 113 22.588 51.545 19.117 1.00 59.55 1CGP1187 ATOM 1033 CD2 LEU A 113 20.409 52.113 20.115 1.00 61.07 1CGP1188 ATOM 1034 H LEU A 113 23.691 52.837 23.709 1.00 0.00 1CGP1189 ATOM 1035 N MET A 114 24.015 55.390 21.803 1.00 65.05 1CGP1190 ATOM 1036 CA MET A 114 24.395 56.714 21.350 1.00 65.57 1CGP1191 ATOM 1037 C MET A 114 25.884 56.785 21.023 1.00 65.25 1CGP1192 ATOM 1038 O MET A 114 26.187 57.078 19.862 1.00 65.82 1CGP1193 ATOM 1039 CB MET A 114 24.073 57.768 22.403 1.00 66.53 1CGP1194 ATOM 1040 CG MET A 114 22.584 58.011 22.506 1.00 66.70 1CGP1195 ATOM 1041 SD MET A 114 21.925 58.365 20.865 1.00 67.97 1CGP1196 ATOM 1042 CE MET A 114 22.402 60.065 20.773 1.00 66.67 1CGP1197 ATOM 1043 H MET A 114 23.616 55.250 22.683 1.00 0.00 1CGP1198 ATOM 1044 N ARG A 115 26.845 56.504 21.927 1.00 64.41 1CGP1199 ATOM 1045 CA ARG A 115 28.283 56.580 21.626 1.00 64.75 1CGP1200 ATOM 1046 C ARG A 115 28.668 55.826 20.353 1.00 61.51 1CGP1201 ATOM 1047 O ARG A 115 29.477 56.290 19.548 1.00 60.51 1CGP1202 ATOM 1048 CB ARG A 115 29.093 56.018 22.790 1.00 68.76 1CGP1203 ATOM 1049 CG ARG A 115 28.932 56.791 24.101 1.00 74.14 1CGP1204 ATOM 1050 CD ARG A 115 29.465 55.900 25.232 1.00 78.53 1CGP1205 ATOM 1051 NE ARG A 115 29.276 56.394 26.604 1.00 80.68 1CGP1206 ATOM 1052 CZ ARG A 115 30.278 56.892 27.348 1.00 81.19 1CGP1207 ATOM 1053 NH1 ARG A 115 31.528 56.979 26.890 1.00 81.49 1CGP1208 ATOM 1054 NH2 ARG A 115 30.022 57.277 28.593 1.00 80.93 1CGP1209 ATOM 1055 H ARG A 115 26.565 56.231 22.824 1.00 0.00 1CGP1210 ATOM 1056 HE ARG A 115 28.396 56.315 27.028 1.00 0.00 1CGP1211 ATOM 1057 1HH1 ARG A 115 31.748 56.638 25.975 1.00 0.00 1CGP1212 ATOM 1058 2HH1 ARG A 115 32.256 57.328 27.480 1.00 0.00 1CGP1213 ATOM 1059 1HH2 ARG A 115 29.108 57.126 28.968 1.00 0.00 1CGP1214 ATOM 1060 2HH2 ARG A 115 30.755 57.650 29.161 1.00 0.00 1CGP1215 ATOM 1061 N LEU A 116 28.014 54.686 20.132 1.00 58.11 1CGP1216 ATOM 1062 CA LEU A 116 28.191 53.845 18.958 1.00 54.84 1CGP1217 ATOM 1063 C LEU A 116 27.697 54.500 17.673 1.00 54.48 1CGP1218 ATOM 1064 O LEU A 116 28.426 54.616 16.677 1.00 53.09 1CGP1219 ATOM 1065 CB LEU A 116 27.447 52.534 19.190 1.00 51.15 1CGP1220 ATOM 1066 CG LEU A 116 27.691 51.392 18.238 1.00 49.41 1CGP1221 ATOM 1067 CD1 LEU A 116 27.797 50.121 19.042 1.00 49.61 1CGP1222 ATOM 1068 CD2 LEU A 116 26.585 51.307 17.215 1.00 48.99 1CGP1223 ATOM 1069 H LEU A 116 27.403 54.385 20.842 1.00 0.00 1CGP1224 ATOM 1070 N SER A 117 26.430 54.911 17.647 1.00 54.94 1CGP1225 ATOM 1071 CA SER A 117 25.852 55.535 16.478 1.00 54.22 1CGP1226 ATOM 1072 C SER A 117 26.602 56.802 16.158 1.00 53.87 1CGP1227 ATOM 1073 O SER A 117 26.782 57.119 14.990 1.00 56.21 1CGP1228 ATOM 1074 CB SER A 117 24.379 55.786 16.755 1.00 54.09 1CGP1229 ATOM 1075 OG SER A 117 23.822 54.505 17.043 1.00 55.07 1CGP1230 ATOM 1076 H SER A 117 25.800 54.740 18.385 1.00 0.00 1CGP1231 ATOM 1077 HG SER A 117 22.950 54.401 16.645 1.00 0.00 1CGP1232 ATOM 1078 N ALA A 118 27.132 57.516 17.132 1.00 53.29 1CGP1233 ATOM 1079 CA ALA A 118 27.982 58.652 16.831 1.00 53.23 1CGP1234 ATOM 1080 C ALA A 118 29.152 58.216 15.953 1.00 52.96 1CGP1235 ATOM 1081 O ALA A 118 29.386 58.772 14.871 1.00 51.88 1CGP1236 ATOM 1082 CB ALA A 118 28.526 59.230 18.113 1.00 53.81 1CGP1237 ATOM 1083 H ALA A 118 26.865 57.318 18.054 1.00 0.00 1CGP1238 ATOM 1084 N GLN A 119 29.814 57.133 16.395 1.00 53.25 1CGP1239 ATOM 1085 CA GLN A 119 30.958 56.591 15.681 1.00 53.90 1CGP1240 ATOM 1086 C GLN A 119 30.554 56.213 14.265 1.00 52.53 1CGP1241 ATOM 1087 O GLN A 119 31.188 56.669 13.315 1.00 53.79 1CGP1242 ATOM 1088 CB GLN A 119 31.540 55.365 16.445 1.00 55.69 1CGP1243 ATOM 1089 CG GLN A 119 32.202 55.757 17.796 1.00 57.96 1CGP1244 ATOM 1090 CD GLN A 119 33.127 54.775 18.534 1.00 58.35 1CGP1245 ATOM 1091 OE1 GLN A 119 33.242 53.579 18.268 1.00 58.29 1CGP1246 ATOM 1092 NE2 GLN A 119 33.862 55.281 19.511 1.00 58.12 1CGP1247 ATOM 1093 H GLN A 119 29.553 56.740 17.258 1.00 0.00 1CGP1248 ATOM 1094 1HE2 GLN A 119 33.768 56.235 19.697 1.00 0.00 1CGP1249 ATOM 1095 2HE2 GLN A 119 34.459 54.685 20.020 1.00 0.00 1CGP1250 ATOM 1096 N MET A 120 29.467 55.492 14.056 1.00 49.98 1CGP1251 ATOM 1097 CA MET A 120 29.027 55.211 12.705 1.00 47.27 1CGP1252 ATOM 1098 C MET A 120 28.729 56.495 11.911 1.00 46.79 1CGP1253 ATOM 1099 O MET A 120 28.972 56.567 10.704 1.00 47.38 1CGP1254 ATOM 1100 CB MET A 120 27.789 54.377 12.738 1.00 47.52 1CGP1255 ATOM 1101 CG MET A 120 27.801 53.113 13.564 1.00 48.15 1CGP1256 ATOM 1102 SD MET A 120 26.494 52.072 12.856 1.00 49.48 1CGP1257 ATOM 1103 CE MET A 120 25.007 52.838 13.427 1.00 50.58 1CGP1258 ATOM 1104 H MET A 120 29.002 55.157 14.852 1.00 0.00 1CGP1259 ATOM 1105 N ALA A 121 28.222 57.567 12.517 1.00 45.00 1CGP1260 ATOM 1106 CA ALA A 121 27.926 58.791 11.803 1.00 42.20 1CGP1261 ATOM 1107 C ALA A 121 29.190 59.424 11.285 1.00 41.25 1CGP1262 ATOM 1108 O ALA A 121 29.277 59.743 10.097 1.00 39.11 1CGP1263 ATOM 1109 CB ALA A 121 27.226 59.744 12.731 1.00 42.63 1CGP1264 ATOM 1110 H ALA A 121 27.922 57.487 13.441 1.00 0.00 1CGP1265 ATOM 1111 N ARG A 122 30.213 59.540 12.127 1.00 42.57 1CGP1266 ATOM 1112 CA ARG A 122 31.462 60.106 11.652 1.00 46.31 1CGP1267 ATOM 1113 C ARG A 122 32.034 59.233 10.569 1.00 46.02 1CGP1268 ATOM 1114 O ARG A 122 32.605 59.745 9.603 1.00 47.43 1CGP1269 ATOM 1115 CB ARG A 122 32.516 60.264 12.754 1.00 50.63 1CGP1270 ATOM 1116 CG ARG A 122 32.304 61.553 13.590 1.00 58.74 1CGP1271 ATOM 1117 CD ARG A 122 32.622 62.964 12.980 1.00 64.31 1CGP1272 ATOM 1118 NE ARG A 122 31.939 63.451 11.755 1.00 69.38 1CGP1273 ATOM 1119 CZ ARG A 122 30.616 63.765 11.644 1.00 71.57 1CGP1274 ATOM 1120 NH1 ARG A 122 29.760 63.617 12.678 1.00 73.02 1CGP1275 ATOM 1121 NH2 ARG A 122 30.120 64.246 10.485 1.00 69.82 1CGP1276 ATOM 1122 H ARG A 122 30.066 59.267 13.060 1.00 0.00 1CGP1277 ATOM 1123 HE ARG A 122 32.494 63.546 10.953 1.00 0.00 1CGP1278 ATOM 1124 1HH1 ARG A 122 30.096 63.284 13.559 1.00 0.00 1CGP1279 ATOM 1125 2HH1 ARG A 122 28.795 63.844 12.557 1.00 0.00 1CGP1280 ATOM 1126 1HH2 ARG A 122 30.742 64.434 9.730 1.00 0.00 1CGP1281 ATOM 1127 2HH2 ARG A 122 29.151 64.480 10.421 1.00 0.00 1CGP1282 ATOM 1128 N ARG A 123 31.816 57.921 10.677 1.00 44.05 1CGP1283 ATOM 1129 CA ARG A 123 32.252 57.035 9.614 1.00 42.05 1CGP1284 ATOM 1130 C ARG A 123 31.489 57.281 8.330 1.00 40.49 1CGP1285 ATOM 1131 O ARG A 123 32.131 57.382 7.276 1.00 40.06 1CGP1286 ATOM 1132 CB ARG A 123 32.097 55.577 10.054 1.00 42.15 1CGP1287 ATOM 1133 CG ARG A 123 33.226 55.193 11.008 1.00 41.64 1CGP1288 ATOM 1134 CD ARG A 123 32.882 54.004 11.878 1.00 38.75 1CGP1289 ATOM 1135 NE ARG A 123 33.817 53.979 12.973 1.00 37.37 1CGP1290 ATOM 1136 CZ ARG A 123 33.993 52.876 13.682 1.00 37.17 1CGP1291 ATOM 1137 NH1 ARG A 123 33.316 51.750 13.471 1.00 34.68 1CGP1292 ATOM 1138 NH2 ARG A 123 34.877 52.888 14.658 1.00 38.50 1CGP1293 ATOM 1139 H ARG A 123 31.501 57.553 11.531 1.00 0.00 1CGP1294 ATOM 1140 HE ARG A 123 34.312 54.787 13.204 1.00 0.00 1CGP1295 ATOM 1141 1HH1 ARG A 123 32.624 51.674 12.755 1.00 0.00 1CGP1296 ATOM 1142 2HH1 ARG A 123 33.518 50.977 14.069 1.00 0.00 1CGP1297 ATOM 1143 1HH2 ARG A 123 35.407 53.708 14.867 1.00 0.00 1CGP1298 ATOM 1144 2HH2 ARG A 123 35.000 52.046 15.180 1.00 0.00 1CGP1299 ATOM 1145 N LEU A 124 30.170 57.483 8.359 1.00 37.24 1CGP1300 ATOM 1146 CA LEU A 124 29.493 57.763 7.120 1.00 36.67 1CGP1301 ATOM 1147 C LEU A 124 30.100 59.015 6.520 1.00 38.15 1CGP1302 ATOM 1148 O LEU A 124 30.409 59.042 5.322 1.00 40.48 1CGP1303 ATOM 1149 CB LEU A 124 28.028 57.984 7.331 1.00 34.74 1CGP1304 ATOM 1150 CG LEU A 124 27.105 56.961 6.710 1.00 35.00 1CGP1305 ATOM 1151 CD1 LEU A 124 25.722 57.565 6.646 1.00 35.02 1CGP1306 ATOM 1152 CD2 LEU A 124 27.488 56.640 5.280 1.00 34.54 1CGP1307 ATOM 1153 H LEU A 124 29.677 57.349 9.192 1.00 0.00 1CGP1308 ATOM 1154 N GLN A 125 30.405 59.986 7.381 1.00 38.64 1CGP1309 ATOM 1155 CA GLN A 125 31.007 61.225 6.952 1.00 38.19 1CGP1310 ATOM 1156 C GLN A 125 32.360 61.016 6.295 1.00 34.62 1CGP1311 ATOM 1157 O GLN A 125 32.533 61.460 5.162 1.00 33.65 1CGP1312 ATOM 1158 CB GLN A 125 31.091 62.114 8.172 1.00 43.74 1CGP1313 ATOM 1159 CG GLN A 125 31.372 63.535 7.780 1.00 51.75 1CGP1314 ATOM 1160 CD GLN A 125 32.802 63.984 8.021 1.00 57.01 1CGP1315 ATOM 1161 OE1 GLN A 125 33.685 63.800 7.182 1.00 59.13 1CGP1316 ATOM 1162 NE2 GLN A 125 33.066 64.619 9.164 1.00 59.70 1CGP1317 ATOM 1163 H GLN A 125 30.125 59.885 8.318 1.00 0.00 1CGP1318 ATOM 1164 1HE2 GLN A 125 32.340 64.814 9.792 1.00 0.00 1CGP1319 ATOM 1165 2HE2 GLN A 125 34.002 64.862 9.317 1.00 0.00 1CGP1320 ATOM 1166 N VAL A 126 33.314 60.305 6.873 1.00 32.13 1CGP1321 ATOM 1167 CA VAL A 126 34.570 60.144 6.170 1.00 32.53 1CGP1322 ATOM 1168 C VAL A 126 34.448 59.210 4.976 1.00 31.96 1CGP1323 ATOM 1169 O VAL A 126 35.139 59.444 3.978 1.00 34.17 1CGP1324 ATOM 1170 CB VAL A 126 35.729 59.607 7.076 1.00 32.40 1CGP1325 ATOM 1171 CG1 VAL A 126 35.754 60.437 8.340 1.00 33.38 1CGP1326 ATOM 1172 CG2 VAL A 126 35.570 58.140 7.453 1.00 35.36 1CGP1327 ATOM 1173 H VAL A 126 33.172 59.990 7.786 1.00 0.00 1CGP1328 ATOM 1174 N THR A 127 33.621 58.159 4.947 1.00 30.54 1CGP1329 ATOM 1175 CA THR A 127 33.620 57.288 3.787 1.00 28.93 1CGP1330 ATOM 1176 C THR A 127 32.989 57.948 2.565 1.00 27.87 1CGP1331 ATOM 1177 O THR A 127 33.407 57.645 1.448 1.00 26.16 1CGP1332 ATOM 1178 CB THR A 127 32.910 55.987 4.159 1.00 29.06 1CGP1333 ATOM 1179 OG1 THR A 127 33.392 55.552 5.427 1.00 29.19 1CGP1334 ATOM 1180 CG2 THR A 127 33.192 54.919 3.109 1.00 29.62 1CGP1335 ATOM 1181 H THR A 127 33.074 57.921 5.725 1.00 0.00 1CGP1336 ATOM 1182 HG1 THR A 127 34.349 55.506 5.372 1.00 0.00 1CGP1337 ATOM 1183 N SER A 128 32.038 58.877 2.737 1.00 28.20 1CGP1338 ATOM 1184 CA SER A 128 31.500 59.645 1.628 1.00 29.90 1CGP1339 ATOM 1185 C SER A 128 32.612 60.500 1.048 1.00 31.78 1CGP1340 ATOM 1186 O SER A 128 32.756 60.612 -0.182 1.00 32.95 1CGP1341 ATOM 1187 CB SER A 128 30.373 60.563 2.079 1.00 29.81 1CGP1342 ATOM 1188 OG SER A 128 29.343 59.769 2.635 1.00 30.53 1CGP1343 ATOM 1189 H SER A 128 31.616 58.980 3.615 1.00 0.00 1CGP1344 ATOM 1190 HG SER A 128 29.672 59.452 3.490 1.00 0.00 1CGP1345 ATOM 1191 N GLU A 129 33.454 61.069 1.922 1.00 32.37 1CGP1346 ATOM 1192 CA GLU A 129 34.590 61.831 1.437 1.00 34.12 1CGP1347 ATOM 1193 C GLU A 129 35.554 60.979 0.617 1.00 33.17 1CGP1348 ATOM 1194 O GLU A 129 35.963 61.396 -0.460 1.00 32.03 1CGP1349 ATOM 1195 CB GLU A 129 35.283 62.430 2.618 1.00 36.98 1CGP1350 ATOM 1196 CG GLU A 129 36.486 63.254 2.219 1.00 43.36 1CGP1351 ATOM 1197 CD GLU A 129 37.133 63.869 3.445 1.00 48.25 1CGP1352 ATOM 1198 OE1 GLU A 129 36.488 64.741 4.032 1.00 50.32 1CGP1353 ATOM 1199 OE2 GLU A 129 38.255 63.484 3.814 1.00 50.85 1CGP1354 ATOM 1200 H GLU A 129 33.258 61.078 2.887 1.00 0.00 1CGP1355 ATOM 1201 N LYS A 130 35.936 59.779 1.060 1.00 33.26 1CGP1356 ATOM 1202 CA LYS A 130 36.784 58.898 0.275 1.00 32.32 1CGP1357 ATOM 1203 C LYS A 130 36.119 58.582 -1.053 1.00 30.81 1CGP1358 ATOM 1204 O LYS A 130 36.820 58.555 -2.064 1.00 30.93 1CGP1359 ATOM 1205 CB LYS A 130 37.060 57.615 1.056 1.00 35.29 1CGP1360 ATOM 1206 CG LYS A 130 38.101 56.650 0.448 1.00 38.56 1CGP1361 ATOM 1207 CD LYS A 130 38.602 55.606 1.466 1.00 41.57 1CGP1362 ATOM 1208 CE LYS A 130 40.135 55.663 1.637 1.00 42.01 1CGP1363 ATOM 1209 NZ LYS A 130 40.764 54.770 0.692 1.00 42.22 1CGP1364 ATOM 1210 H LYS A 130 35.707 59.552 1.983 1.00 0.00 1CGP1365 ATOM 1211 1HZ LYS A 130 40.199 54.755 -0.181 1.00 0.00 1CGP1366 ATOM 1212 2HZ LYS A 130 40.804 53.829 1.132 1.00 0.00 1CGP1367 ATOM 1213 3HZ LYS A 130 41.726 55.090 0.475 1.00 0.00 1CGP1368 ATOM 1214 N VAL A 131 34.816 58.364 -1.140 1.00 29.45 1CGP1369 ATOM 1215 CA VAL A 131 34.196 58.220 -2.440 1.00 29.60 1CGP1370 ATOM 1216 C VAL A 131 34.494 59.464 -3.256 1.00 30.68 1CGP1371 ATOM 1217 O VAL A 131 34.988 59.344 -4.371 1.00 31.46 1CGP1372 ATOM 1218 CB VAL A 131 32.686 58.034 -2.280 1.00 29.88 1CGP1373 ATOM 1219 CG1 VAL A 131 31.960 58.202 -3.620 1.00 29.94 1CGP1374 ATOM 1220 CG2 VAL A 131 32.441 56.646 -1.710 1.00 27.45 1CGP1375 ATOM 1221 H VAL A 131 34.299 58.193 -0.322 1.00 0.00 1CGP1376 ATOM 1222 N GLY A 132 34.283 60.650 -2.700 1.00 31.62 1CGP1377 ATOM 1223 CA GLY A 132 34.556 61.904 -3.380 1.00 34.57 1CGP1378 ATOM 1224 C GLY A 132 35.957 62.038 -3.957 1.00 36.08 1CGP1379 ATOM 1225 O GLY A 132 36.074 62.385 -5.130 1.00 35.73 1CGP1380 ATOM 1226 H GLY A 132 33.853 60.683 -1.821 1.00 0.00 1CGP1381 ATOM 1227 N ASN A 133 37.019 61.763 -3.199 1.00 38.18 1CGP1382 ATOM 1228 CA ASN A 133 38.399 61.812 -3.690 1.00 41.09 1CGP1383 ATOM 1229 C ASN A 133 38.638 60.861 -4.842 1.00 42.48 1CGP1384 ATOM 1230 O ASN A 133 39.177 61.280 -5.867 1.00 43.18 1CGP1385 ATOM 1231 CB ASN A 133 39.481 61.424 -2.684 1.00 43.23 1CGP1386 ATOM 1232 CG ASN A 133 39.496 62.239 -1.404 1.00 46.31 1CGP1387 ATOM 1233 OD1 ASN A 133 38.850 63.283 -1.275 1.00 47.04 1CGP1388 ATOM 1234 ND2 ASN A 133 40.207 61.745 -0.390 1.00 47.55 1CGP1389 ATOM 1235 H ASN A 133 36.814 61.620 -2.254 1.00 0.00 1CGP1390 ATOM 1236 1HD2 ASN A 133 40.682 60.901 -0.526 1.00 0.00 1CGP1391 ATOM 1237 2HD2 ASN A 133 40.193 62.269 0.436 1.00 0.00 1CGP1392 ATOM 1238 N LEU A 134 38.212 59.602 -4.731 1.00 43.20 1CGP1393 ATOM 1239 CA LEU A 134 38.374 58.653 -5.822 1.00 44.34 1CGP1394 ATOM 1240 C LEU A 134 37.728 59.168 -7.117 1.00 44.50 1CGP1395 ATOM 1241 O LEU A 134 38.293 59.129 -8.209 1.00 46.77 1CGP1396 ATOM 1242 CB LEU A 134 37.734 57.313 -5.454 1.00 44.83 1CGP1397 ATOM 1243 CG LEU A 134 38.196 56.527 -4.235 1.00 45.23 1CGP1398 ATOM 1244 CD1 LEU A 134 37.470 55.191 -4.172 1.00 44.85 1CGP1399 ATOM 1245 CD2 LEU A 134 39.683 56.289 -4.325 1.00 45.47 1CGP1400 ATOM 1246 H LEU A 134 37.737 59.326 -3.918 1.00 0.00 1CGP1401 ATOM 1247 N ALA A 135 36.508 59.665 -7.013 1.00 43.20 1CGP1402 ATOM 1248 CA ALA A 135 35.794 60.160 -8.164 1.00 40.94 1CGP1403 ATOM 1249 C ALA A 135 36.354 61.442 -8.724 1.00 39.89 1CGP1404 ATOM 1250 O ALA A 135 36.401 61.631 -9.931 1.00 39.67 1CGP1405 ATOM 1251 CB ALA A 135 34.347 60.416 -7.805 1.00 41.48 1CGP1406 ATOM 1252 H ALA A 135 36.064 59.637 -6.140 1.00 0.00 1CGP1407 ATOM 1253 N PHE A 136 36.746 62.346 -7.859 1.00 40.17 1CGP1408 ATOM 1254 CA PHE A 136 37.126 63.662 -8.296 1.00 41.64 1CGP1409 ATOM 1255 C PHE A 136 38.587 64.018 -8.457 1.00 43.66 1CGP1410 ATOM 1256 O PHE A 136 38.934 64.881 -9.276 1.00 45.03 1CGP1411 ATOM 1257 CB PHE A 136 36.547 64.685 -7.355 1.00 39.62 1CGP1412 ATOM 1258 CG PHE A 136 35.050 64.749 -7.209 1.00 38.10 1CGP1413 ATOM 1259 CD1 PHE A 136 34.223 64.460 -8.267 1.00 37.73 1CGP1414 ATOM 1260 CD2 PHE A 136 34.532 65.147 -5.996 1.00 38.63 1CGP1415 ATOM 1261 CE1 PHE A 136 32.860 64.577 -8.108 1.00 38.17 1CGP1416 ATOM 1262 CE2 PHE A 136 33.164 65.262 -5.843 1.00 39.09 1CGP1417 ATOM 1263 CZ PHE A 136 32.330 64.977 -6.902 1.00 38.76 1CGP1418 ATOM 1264 H PHE A 136 36.683 62.173 -6.904 1.00 0.00 1CGP1419 ATOM 1265 N LEU A 137 39.442 63.435 -7.628 1.00 45.50 1CGP1420 ATOM 1266 CA LEU A 137 40.817 63.874 -7.525 1.00 47.64 1CGP1421 ATOM 1267 C LEU A 137 41.818 62.912 -8.123 1.00 49.46 1CGP1422 ATOM 1268 O LEU A 137 41.776 61.723 -7.810 1.00 51.71 1CGP1423 ATOM 1269 CB LEU A 137 41.183 64.090 -6.067 1.00 46.99 1CGP1424 ATOM 1270 CG LEU A 137 40.648 65.267 -5.276 1.00 46.83 1CGP1425 ATOM 1271 CD1 LEU A 137 39.222 65.075 -4.822 1.00 47.84 1CGP1426 ATOM 1272 CD2 LEU A 137 41.471 65.362 -4.017 1.00 48.37 1CGP1427 ATOM 1273 H LEU A 137 39.202 62.613 -7.161 1.00 0.00 1CGP1428 ATOM 1274 N ASP A 138 42.761 63.380 -8.949 1.00 49.25 1CGP1429 ATOM 1275 CA ASP A 138 43.727 62.441 -9.471 1.00 48.96 1CGP1430 ATOM 1276 C ASP A 138 44.725 62.039 -8.370 1.00 47.67 1CGP1431 ATOM 1277 O ASP A 138 44.864 62.724 -7.349 1.00 45.41 1CGP1432 ATOM 1278 CB ASP A 138 44.395 63.081 -10.711 1.00 52.44 1CGP1433 ATOM 1279 CG ASP A 138 45.448 64.180 -10.600 1.00 55.53 1CGP1434 ATOM 1280 OD1 ASP A 138 45.732 64.661 -9.503 1.00 56.33 1CGP1435 ATOM 1281 OD2 ASP A 138 45.999 64.542 -11.648 1.00 56.77 1CGP1436 ATOM 1282 H ASP A 138 42.777 64.325 -9.189 1.00 0.00 1CGP1437 ATOM 1283 N VAL A 139 45.440 60.930 -8.574 1.00 45.66 1CGP1438 ATOM 1284 CA VAL A 139 46.358 60.336 -7.616 1.00 42.32 1CGP1439 ATOM 1285 C VAL A 139 47.222 61.341 -6.928 1.00 41.14 1CGP1440 ATOM 1286 O VAL A 139 47.310 61.272 -5.717 1.00 39.10 1CGP1441 ATOM 1287 CB VAL A 139 47.273 59.287 -8.288 1.00 42.26 1CGP1442 ATOM 1288 CG1 VAL A 139 48.288 58.674 -7.330 1.00 41.40 1CGP1443 ATOM 1289 CG2 VAL A 139 46.406 58.136 -8.748 1.00 43.50 1CGP1444 ATOM 1290 H VAL A 139 45.294 60.474 -9.428 1.00 0.00 1CGP1445 ATOM 1291 N THR A 140 47.820 62.288 -7.622 1.00 42.94 1CGP1446 ATOM 1292 CA THR A 140 48.629 63.265 -6.928 1.00 45.69 1CGP1447 ATOM 1293 C THR A 140 47.818 63.936 -5.830 1.00 46.04 1CGP1448 ATOM 1294 O THR A 140 48.242 63.955 -4.678 1.00 48.30 1CGP1449 ATOM 1295 CB THR A 140 49.134 64.306 -7.906 1.00 45.92 1CGP1450 ATOM 1296 OG1 THR A 140 49.681 63.595 -9.023 1.00 46.33 1CGP1451 ATOM 1297 CG2 THR A 140 50.109 65.272 -7.218 1.00 44.04 1CGP1452 ATOM 1298 H THR A 140 47.799 62.290 -8.599 1.00 0.00 1CGP1453 ATOM 1299 HG1 THR A 140 50.592 63.336 -8.855 1.00 0.00 1CGP1454 ATOM 1300 N GLY A 141 46.597 64.326 -6.144 1.00 44.80 1CGP1455 ATOM 1301 CA GLY A 141 45.760 64.980 -5.162 1.00 45.72 1CGP1456 ATOM 1302 C GLY A 141 45.383 64.021 -4.053 1.00 45.76 1CGP1457 ATOM 1303 O GLY A 141 45.468 64.373 -2.873 1.00 45.24 1CGP1458 ATOM 1304 H GLY A 141 46.235 64.124 -7.027 1.00 0.00 1CGP1459 ATOM 1305 N ARG A 142 45.013 62.799 -4.440 1.00 46.46 1CGP1460 ATOM 1306 CA ARG A 142 44.639 61.794 -3.465 1.00 46.35 1CGP1461 ATOM 1307 C ARG A 142 45.806 61.526 -2.525 1.00 46.91 1CGP1462 ATOM 1308 O ARG A 142 45.599 61.707 -1.326 1.00 48.12 1CGP1463 ATOM 1309 CB ARG A 142 44.215 60.511 -4.155 1.00 45.17 1CGP1464 ATOM 1310 CG ARG A 142 42.728 60.456 -4.455 1.00 45.40 1CGP1465 ATOM 1311 CD ARG A 142 42.384 59.091 -5.045 1.00 45.77 1CGP1466 ATOM 1312 NE ARG A 142 42.483 59.092 -6.495 1.00 45.50 1CGP1467 ATOM 1313 CZ ARG A 142 42.767 58.024 -7.266 1.00 45.93 1CGP1468 ATOM 1314 NH1 ARG A 142 43.011 56.786 -6.824 1.00 44.16 1CGP1469 ATOM 1315 NH2 ARG A 142 42.791 58.224 -8.578 1.00 46.95 1CGP1470 ATOM 1316 H ARG A 142 44.971 62.623 -5.402 1.00 0.00 1CGP1471 ATOM 1317 HE ARG A 142 42.293 59.934 -6.952 1.00 0.00 1CGP1472 ATOM 1318 1HH1 ARG A 142 43.003 56.587 -5.849 1.00 0.00 1CGP1473 ATOM 1319 2HH1 ARG A 142 43.245 56.058 -7.470 1.00 0.00 1CGP1474 ATOM 1320 1HH2 ARG A 142 42.593 59.143 -8.913 1.00 0.00 1CGP1475 ATOM 1321 2HH2 ARG A 142 43.000 57.483 -9.214 1.00 0.00 1CGP1476 ATOM 1322 N ILE A 143 47.035 61.228 -2.989 1.00 46.73 1CGP1477 ATOM 1323 CA ILE A 143 48.199 60.988 -2.140 1.00 46.25 1CGP1478 ATOM 1324 C ILE A 143 48.470 62.249 -1.317 1.00 48.85 1CGP1479 ATOM 1325 O ILE A 143 48.847 62.148 -0.139 1.00 49.96 1CGP1480 ATOM 1326 CB ILE A 143 49.470 60.618 -2.977 1.00 42.76 1CGP1481 ATOM 1327 CG1 ILE A 143 49.255 59.329 -3.710 1.00 41.51 1CGP1482 ATOM 1328 CG2 ILE A 143 50.664 60.373 -2.070 1.00 41.17 1CGP1483 ATOM 1329 CD1 ILE A 143 50.496 58.777 -4.425 1.00 41.78 1CGP1484 ATOM 1330 H ILE A 143 47.158 61.237 -3.946 1.00 0.00 1CGP1485 ATOM 1331 N ALA A 144 48.244 63.441 -1.882 1.00 49.92 1CGP1486 ATOM 1332 CA ALA A 144 48.415 64.690 -1.158 1.00 52.09 1CGP1487 ATOM 1333 C ALA A 144 47.554 64.729 0.111 1.00 54.48 1CGP1488 ATOM 1334 O ALA A 144 48.069 64.761 1.247 1.00 55.73 1CGP1489 ATOM 1335 CB ALA A 144 48.040 65.847 -2.068 1.00 50.77 1CGP1490 ATOM 1336 H ALA A 144 48.034 63.486 -2.835 1.00 0.00 1CGP1491 ATOM 1337 N GLN A 145 46.231 64.627 -0.096 1.00 55.65 1CGP1492 ATOM 1338 CA GLN A 145 45.260 64.585 0.983 1.00 56.66 1CGP1493 ATOM 1339 C GLN A 145 45.634 63.487 1.966 1.00 56.87 1CGP1494 ATOM 1340 O GLN A 145 45.516 63.718 3.168 1.00 58.02 1CGP1495 ATOM 1341 CB GLN A 145 43.871 64.325 0.418 1.00 58.27 1CGP1496 ATOM 1342 CG GLN A 145 43.107 65.614 0.139 1.00 61.59 1CGP1497 ATOM 1343 CD GLN A 145 42.136 66.050 1.247 1.00 63.20 1CGP1498 ATOM 1344 OE1 GLN A 145 41.070 66.583 0.961 1.00 63.75 1CGP1499 ATOM 1345 NE2 GLN A 145 42.340 65.899 2.547 1.00 64.40 1CGP1500 ATOM 1346 H GLN A 145 45.930 64.510 -1.021 1.00 0.00 1CGP1501 ATOM 1347 1HE2 GLN A 145 43.163 65.495 2.894 1.00 0.00 1CGP1502 ATOM 1348 2HE2 GLN A 145 41.618 66.212 3.122 1.00 0.00 1CGP1503 ATOM 1349 N THR A 146 46.107 62.321 1.512 1.00 56.45 1CGP1504 ATOM 1350 CA THR A 146 46.596 61.266 2.380 1.00 55.24 1CGP1505 ATOM 1351 C THR A 146 47.761 61.719 3.224 1.00 55.82 1CGP1506 ATOM 1352 O THR A 146 47.634 61.651 4.450 1.00 56.09 1CGP1507 ATOM 1353 CB THR A 146 46.980 60.054 1.518 1.00 55.02 1CGP1508 ATOM 1354 OG1 THR A 146 45.709 59.553 1.139 1.00 55.62 1CGP1509 ATOM 1355 CG2 THR A 146 47.832 58.965 2.162 1.00 54.08 1CGP1510 ATOM 1356 H THR A 146 46.020 62.122 0.554 1.00 0.00 1CGP1511 ATOM 1357 HG1 THR A 146 45.397 58.905 1.775 1.00 0.00 1CGP1512 ATOM 1358 N LEU A 147 48.849 62.240 2.668 1.00 55.92 1CGP1513 ATOM 1359 CA LEU A 147 49.977 62.571 3.512 1.00 59.41 1CGP1514 ATOM 1360 C LEU A 147 49.625 63.555 4.608 1.00 61.51 1CGP1515 ATOM 1361 O LEU A 147 49.930 63.373 5.792 1.00 60.99 1CGP1516 ATOM 1362 CB LEU A 147 51.096 63.074 2.618 1.00 59.21 1CGP1517 ATOM 1363 CG LEU A 147 51.714 61.998 1.711 1.00 59.68 1CGP1518 ATOM 1364 CD1 LEU A 147 53.182 62.267 1.616 1.00 58.86 1CGP1519 ATOM 1365 CD2 LEU A 147 51.645 60.599 2.302 1.00 59.85 1CGP1520 ATOM 1366 H LEU A 147 48.879 62.368 1.698 1.00 0.00 1CGP1521 ATOM 1367 N LEU A 148 48.760 64.455 4.177 1.00 65.28 1CGP1522 ATOM 1368 CA LEU A 148 48.141 65.415 5.054 1.00 69.09 1CGP1523 ATOM 1369 C LEU A 148 47.388 64.775 6.226 1.00 70.86 1CGP1524 ATOM 1370 O LEU A 148 47.673 65.021 7.394 1.00 71.35 1CGP1525 ATOM 1371 CB LEU A 148 47.188 66.239 4.246 1.00 70.61 1CGP1526 ATOM 1372 CG LEU A 148 46.896 67.590 4.812 1.00 72.26 1CGP1527 ATOM 1373 CD1 LEU A 148 47.983 68.513 4.264 1.00 72.36 1CGP1528 ATOM 1374 CD2 LEU A 148 45.470 68.042 4.481 1.00 73.54 1CGP1529 ATOM 1375 H LEU A 148 48.554 64.487 3.219 1.00 0.00 1CGP1530 ATOM 1376 N ASN A 149 46.414 63.930 5.952 1.00 74.02 1CGP1531 ATOM 1377 CA ASN A 149 45.623 63.312 6.999 1.00 78.53 1CGP1532 ATOM 1378 C ASN A 149 46.407 62.391 7.906 1.00 79.55 1CGP1533 ATOM 1379 O ASN A 149 46.151 62.318 9.116 1.00 81.28 1CGP1534 ATOM 1380 CB ASN A 149 44.500 62.495 6.419 1.00 82.10 1CGP1535 ATOM 1381 CG ASN A 149 43.515 63.305 5.601 1.00 85.44 1CGP1536 ATOM 1382 OD1 ASN A 149 43.452 64.540 5.628 1.00 86.72 1CGP1537 ATOM 1383 ND2 ASN A 149 42.730 62.595 4.795 1.00 87.58 1CGP1538 ATOM 1384 H ASN A 149 46.157 63.801 5.018 1.00 0.00 1CGP1539 ATOM 1385 1HD2 ASN A 149 42.874 61.629 4.761 1.00 0.00 1CGP1540 ATOM 1386 2HD2 ASN A 149 42.041 63.075 4.295 1.00 0.00 1CGP1541 ATOM 1387 N LEU A 150 47.359 61.640 7.356 1.00 78.75 1CGP1542 ATOM 1388 CA LEU A 150 48.167 60.757 8.167 1.00 77.72 1CGP1543 ATOM 1389 C LEU A 150 48.902 61.616 9.165 1.00 79.07 1CGP1544 ATOM 1390 O LEU A 150 48.905 61.268 10.337 1.00 78.98 1CGP1545 ATOM 1391 CB LEU A 150 49.159 60.017 7.331 1.00 76.80 1CGP1546 ATOM 1392 CG LEU A 150 48.609 59.100 6.283 1.00 75.84 1CGP1547 ATOM 1393 CD1 LEU A 150 49.779 58.572 5.479 1.00 75.29 1CGP1548 ATOM 1394 CD2 LEU A 150 47.760 58.015 6.924 1.00 75.47 1CGP1549 ATOM 1395 H LEU A 150 47.494 61.695 6.389 1.00 0.00 1CGP1550 ATOM 1396 N ALA A 151 49.416 62.786 8.764 1.00 80.92 1CGP1551 ATOM 1397 CA ALA A 151 50.068 63.737 9.665 1.00 82.48 1CGP1552 ATOM 1398 C ALA A 151 49.196 64.415 10.734 1.00 84.12 1CGP1553 ATOM 1399 O ALA A 151 49.585 65.396 11.379 1.00 83.75 1CGP1554 ATOM 1400 CB ALA A 151 50.720 64.812 8.816 1.00 82.00 1CGP1555 ATOM 1401 H ALA A 151 49.425 62.999 7.804 1.00 0.00 1CGP1556 ATOM 1402 N LYS A 152 47.994 63.892 10.938 1.00 86.83 1CGP1557 ATOM 1403 CA LYS A 152 47.069 64.337 11.952 1.00 89.56 1CGP1558 ATOM 1404 C LYS A 152 46.607 63.077 12.706 1.00 89.98 1CGP1559 ATOM 1405 O LYS A 152 46.017 63.163 13.783 1.00 90.74 1CGP1560 ATOM 1406 CB LYS A 152 45.912 65.061 11.236 1.00 91.68 1CGP1561 ATOM 1407 CG LYS A 152 45.049 65.966 12.121 1.00 94.47 1CGP1562 ATOM 1408 CD LYS A 152 45.862 67.146 12.710 1.00 96.04 1CGP1563 ATOM 1409 CE LYS A 152 45.137 67.977 13.800 1.00 95.79 1CGP1564 ATOM 1410 NZ LYS A 152 43.942 68.648 13.314 1.00 95.11 1CGP1565 ATOM 1411 H LYS A 152 47.667 63.194 10.341 1.00 0.00 1CGP1566 ATOM 1412 1HZ LYS A 152 43.293 67.942 12.913 1.00 0.00 1CGP1567 ATOM 1413 2HZ LYS A 152 44.211 69.326 12.573 1.00 0.00 1CGP1568 ATOM 1414 3HZ LYS A 152 43.468 69.151 14.091 1.00 0.00 1CGP1569 ATOM 1415 N GLN A 153 46.847 61.858 12.210 1.00 90.35 1CGP1570 ATOM 1416 CA GLN A 153 46.453 60.636 12.883 1.00 90.90 1CGP1571 ATOM 1417 C GLN A 153 47.331 60.410 14.110 1.00 91.14 1CGP1572 ATOM 1418 O GLN A 153 48.552 60.590 14.066 1.00 90.83 1CGP1573 ATOM 1419 CB GLN A 153 46.581 59.464 11.914 1.00 91.79 1CGP1574 ATOM 1420 CG GLN A 153 45.232 58.916 11.408 1.00 93.68 1CGP1575 ATOM 1421 CD GLN A 153 44.617 57.773 12.229 1.00 94.33 1CGP1576 ATOM 1422 OE1 GLN A 153 45.306 56.854 12.689 1.00 94.78 1CGP1577 ATOM 1423 NE2 GLN A 153 43.300 57.738 12.426 1.00 93.53 1CGP1578 ATOM 1424 H GLN A 153 47.410 61.769 11.421 1.00 0.00 1CGP1579 ATOM 1425 1HE2 GLN A 153 42.705 58.381 11.994 1.00 0.00 1CGP1580 ATOM 1426 2HE2 GLN A 153 42.998 57.047 13.063 1.00 0.00 1CGP1581 ATOM 1427 N PRO A 154 46.772 60.038 15.259 1.00 92.06 1CGP1582 ATOM 1428 CA PRO A 154 47.499 59.812 16.492 1.00 93.66 1CGP1583 ATOM 1429 C PRO A 154 48.577 58.743 16.415 1.00 95.85 1CGP1584 ATOM 1430 O PRO A 154 48.328 57.572 16.696 1.00 96.55 1CGP1585 ATOM 1431 CB PRO A 154 46.407 59.497 17.494 1.00 93.13 1CGP1586 ATOM 1432 CG PRO A 154 45.320 58.885 16.648 1.00 92.28 1CGP1587 ATOM 1433 CD PRO A 154 45.344 59.850 15.478 1.00 92.50 1CGP1588 ATOM 1434 N ASP A 155 49.759 59.174 15.992 1.00 97.82 1CGP1589 ATOM 1435 CA ASP A 155 50.991 58.388 15.932 1.00100.33 1CGP1590 ATOM 1436 C ASP A 155 51.999 59.225 15.193 1.00100.40 1CGP1591 ATOM 1437 O ASP A 155 53.181 58.890 15.199 1.00 99.69 1CGP1592 ATOM 1438 CB ASP A 155 50.906 57.023 15.174 1.00102.74 1CGP1593 ATOM 1439 CG ASP A 155 50.854 56.989 13.646 1.00104.93 1CGP1594 ATOM 1440 OD1 ASP A 155 51.916 57.000 13.005 1.00105.67 1CGP1595 ATOM 1441 OD2 ASP A 155 49.744 56.921 13.107 1.00106.40 1CGP1596 ATOM 1442 H ASP A 155 49.800 60.112 15.707 1.00 0.00 1CGP1597 ATOM 1443 N ALA A 156 51.507 60.251 14.490 1.00101.22 1CGP1598 ATOM 1444 CA ALA A 156 52.371 61.206 13.841 1.00102.73 1CGP1599 ATOM 1445 C ALA A 156 53.225 61.789 14.946 1.00103.63 1CGP1600 ATOM 1446 O ALA A 156 52.746 62.233 15.997 1.00103.00 1CGP1601 ATOM 1447 CB ALA A 156 51.577 62.328 13.206 1.00103.30 1CGP1602 ATOM 1448 H ALA A 156 50.546 60.351 14.339 1.00 0.00 1CGP1603 ATOM 1449 N MET A 157 54.504 61.583 14.692 1.00105.99 1CGP1604 ATOM 1450 CA MET A 157 55.566 62.052 15.553 1.00108.19 1CGP1605 ATOM 1451 C MET A 157 55.858 63.423 14.967 1.00109.11 1CGP1606 ATOM 1452 O MET A 157 55.575 63.710 13.798 1.00108.84 1CGP1607 ATOM 1453 CB MET A 157 56.822 61.176 15.443 1.00108.84 1CGP1608 ATOM 1454 CG MET A 157 56.618 59.664 15.639 1.00109.65 1CGP1609 ATOM 1455 SD MET A 157 55.753 58.791 14.295 1.00110.37 1CGP1610 ATOM 1456 CE MET A 157 57.126 58.337 13.274 1.00110.25 1CGP1611 ATOM 1457 H MET A 157 54.735 61.247 13.803 1.00 0.00 1CGP1612 ATOM 1458 N THR A 158 56.378 64.341 15.752 1.00110.62 1CGP1613 ATOM 1459 CA THR A 158 56.702 65.643 15.210 1.00112.29 1CGP1614 ATOM 1460 C THR A 158 58.160 65.548 14.770 1.00113.09 1CGP1615 ATOM 1461 O THR A 158 58.927 64.739 15.315 1.00113.56 1CGP1616 ATOM 1462 CB THR A 158 56.481 66.680 16.316 1.00112.78 1CGP1617 ATOM 1463 OG1 THR A 158 55.330 66.285 17.078 1.00112.57 1CGP1618 ATOM 1464 CG2 THR A 158 56.309 68.072 15.710 1.00113.27 1CGP1619 ATOM 1465 H THR A 158 56.563 64.172 16.697 1.00 0.00 1CGP1620 ATOM 1466 HG1 THR A 158 54.588 66.207 16.471 1.00 0.00 1CGP1621 ATOM 1467 N HIS A 159 58.577 66.296 13.758 1.00113.45 1 1CGP1622 ATOM 1468 CA HIS A 159 59.967 66.257 13.343 1.00114.49 1 1CGP1623 ATOM 1469 C HIS A 159 60.395 67.701 13.275 1.00114.38 1 1CGP1624 ATOM 1470 O HIS A 159 60.245 68.329 12.229 1.00114.70 1 1CGP1625 ATOM 1471 CB HIS A 159 60.110 65.579 11.956 1.00115.35 1 1CGP1626 ATOM 1472 CG HIS A 159 61.372 65.903 11.140 1.00116.05 1 1CGP1627 ATOM 1473 ND1 HIS A 159 61.581 66.998 10.401 1.00116.03 1 1CGP1628 ATOM 1474 CD2 HIS A 159 62.491 65.110 11.022 1.00116.35 1 1CGP1629 ATOM 1475 CE1 HIS A 159 62.765 66.905 9.847 1.00115.90 1 1CGP1630 ATOM 1476 NE2 HIS A 159 63.301 65.764 10.225 1.00116.47 1 1CGP1631 ATOM 1477 H HIS A 159 57.956 66.902 13.293 1.00 0.00 1 1CGP1632 ATOM 1478 HD1 HIS A 159 60.981 67.789 10.368 1.00 0.00 1 1CGP1633 ATOM 1479 HE2 HIS A 159 64.172 65.417 9.932 1.00 0.00 1 1CGP1634 ATOM 1480 N PRO A 160 61.097 68.233 14.266 1.00114.59 1 1CGP1635 ATOM 1481 CA PRO A 160 60.974 69.615 14.732 1.00115.04 1 1CGP1636 ATOM 1482 C PRO A 160 59.877 70.420 14.048 1.00115.48 1 1CGP1637 ATOM 1483 O PRO A 160 58.759 70.536 14.567 1.00115.40 1 1CGP1638 ATOM 1484 CB PRO A 160 62.380 70.194 14.530 1.00114.94 1 1CGP1639 ATOM 1485 CG PRO A 160 63.186 69.080 13.900 1.00114.79 1 1CGP1640 ATOM 1486 CD PRO A 160 62.484 67.854 14.470 1.00114.90 1 1CGP1641 ATOM 1487 N ASP A 161 60.189 70.869 12.829 1.00115.75 1CGP1642 ATOM 1488 CA ASP A 161 59.232 71.596 12.032 1.00115.75 1CGP1643 ATOM 1489 C ASP A 161 58.871 70.690 10.865 1.00114.17 1CGP1644 ATOM 1490 O ASP A 161 59.685 70.277 10.024 1.00113.04 1CGP1645 ATOM 1491 CB ASP A 161 59.853 72.916 11.579 1.00117.39 1CGP1646 ATOM 1492 CG ASP A 161 59.975 73.912 12.742 1.00118.51 1CGP1647 ATOM 1493 OD1 ASP A 161 58.949 74.344 13.295 1.00118.33 1CGP1648 ATOM 1494 OD2 ASP A 161 61.112 74.245 13.092 1.00119.06 1CGP1649 ATOM 1495 H ASP A 161 60.988 70.545 12.367 1.00 0.00 1CGP1650 ATOM 1496 N GLY A 162 57.620 70.273 11.058 1.00112.51 1CGP1651 ATOM 1497 CA GLY A 162 56.905 69.374 10.179 1.00110.03 1CGP1652 ATOM 1498 C GLY A 162 56.422 68.155 10.973 1.00107.83 1CGP1653 ATOM 1499 O GLY A 162 56.784 67.916 12.142 1.00108.18 1CGP1654 ATOM 1500 H GLY A 162 57.189 70.473 11.914 1.00 0.00 1CGP1655 ATOM 1501 N MET A 163 55.581 67.356 10.335 1.00104.18 1CGP1656 ATOM 1502 CA MET A 163 55.114 66.154 10.975 1.00100.54 1CGP1657 ATOM 1503 C MET A 163 55.938 65.045 10.403 1.00 98.43 1CGP1658 ATOM 1504 O MET A 163 56.525 65.166 9.327 1.00 96.90 1CGP1659 ATOM 1505 CB MET A 163 53.661 65.909 10.678 1.00101.11 1CGP1660 ATOM 1506 CG MET A 163 52.854 66.957 11.418 1.00102.28 1CGP1661 ATOM 1507 SD MET A 163 53.404 67.079 13.143 1.00103.45 1CGP1662 ATOM 1508 CE MET A 163 51.965 66.507 14.007 1.00102.62 1CGP1663 ATOM 1509 H MET A 163 55.430 67.480 9.374 1.00 0.00 1CGP1664 ATOM 1510 N GLN A 164 55.978 63.966 11.143 1.00 96.65 1CGP1665 ATOM 1511 CA GLN A 164 56.732 62.801 10.761 1.00 95.91 1CGP1666 ATOM 1512 C GLN A 164 55.757 61.642 10.888 1.00 92.36 1CGP1667 ATOM 1513 O GLN A 164 55.120 61.450 11.925 1.00 91.58 1CGP1668 ATOM 1514 CB GLN A 164 57.925 62.658 11.715 1.00 98.99 1CGP1669 ATOM 1515 CG GLN A 164 58.928 61.528 11.451 1.00101.55 1CGP1670 ATOM 1516 CD GLN A 164 60.223 61.644 12.254 1.00102.71 1CGP1671 ATOM 1517 OE1 GLN A 164 61.115 62.441 11.936 1.00103.29 1CGP1672 ATOM 1518 NE2 GLN A 164 60.398 60.854 13.307 1.00103.14 1CGP1673 ATOM 1519 H GLN A 164 55.491 63.909 11.985 1.00 0.00 1CGP1674 ATOM 1520 1HE2 GLN A 164 59.692 60.229 13.556 1.00 0.00 1CGP1675 ATOM 1521 2HE2 GLN A 164 61.246 60.957 13.785 1.00 0.00 1CGP1676 ATOM 1522 N ILE A 165 55.587 60.893 9.818 1.00 88.17 1CGP1677 ATOM 1523 CA ILE A 165 54.766 59.705 9.807 1.00 84.45 1CGP1678 ATOM 1524 C ILE A 165 55.655 58.649 9.184 1.00 83.28 1CGP1679 ATOM 1525 O ILE A 165 56.554 58.943 8.399 1.00 82.10 1CGP1680 ATOM 1526 CB ILE A 165 53.502 59.861 8.952 1.00 83.35 1CGP1681 ATOM 1527 CG1 ILE A 165 53.787 60.689 7.708 1.00 82.56 1CGP1682 ATOM 1528 CG2 ILE A 165 52.412 60.395 9.860 1.00 81.67 1CGP1683 ATOM 1529 CD1 ILE A 165 52.712 60.600 6.628 1.00 83.07 1CGP1684 ATOM 1530 H ILE A 165 56.079 61.111 9.001 1.00 0.00 1CGP1685 ATOM 1531 N LYS A 166 55.464 57.400 9.581 1.00 81.51 1CGP1686 ATOM 1532 CA LYS A 166 56.223 56.288 9.046 1.00 79.03 1CGP1687 ATOM 1533 C LYS A 166 55.109 55.539 8.340 1.00 76.83 1CGP1688 ATOM 1534 O LYS A 166 54.097 55.217 8.974 1.00 75.13 1CGP1689 ATOM 1535 CB LYS A 166 56.796 55.479 10.196 1.00 80.67 1CGP1690 ATOM 1536 CG LYS A 166 57.700 54.307 9.849 1.00 82.50 1CGP1691 ATOM 1537 CD LYS A 166 57.671 53.251 10.979 1.00 84.67 1CGP1692 ATOM 1538 CE LYS A 166 58.081 53.692 12.407 1.00 85.98 1CGP1693 ATOM 1539 NZ LYS A 166 59.513 53.919 12.565 1.00 87.67 1CGP1694 ATOM 1540 H LYS A 166 54.729 57.195 10.197 1.00 0.00 1CGP1695 ATOM 1541 1HZ LYS A 166 59.822 54.667 11.909 1.00 0.00 1CGP1696 ATOM 1542 2HZ LYS A 166 60.029 53.042 12.354 1.00 0.00 1CGP1697 ATOM 1543 3HZ LYS A 166 59.719 54.219 13.539 1.00 0.00 1CGP1698 ATOM 1544 N ILE A 167 55.229 55.363 7.027 1.00 75.15 1CGP1699 ATOM 1545 CA ILE A 167 54.268 54.612 6.230 1.00 73.54 1CGP1700 ATOM 1546 C ILE A 167 54.926 54.277 4.896 1.00 72.37 1CGP1701 ATOM 1547 O ILE A 167 55.504 55.110 4.205 1.00 72.75 1CGP1702 ATOM 1548 CB ILE A 167 52.932 55.426 6.025 1.00 72.71 1CGP1703 ATOM 1549 CG1 ILE A 167 52.005 54.587 5.184 1.00 72.37 1CGP1704 ATOM 1550 CG2 ILE A 167 53.156 56.768 5.371 1.00 72.78 1CGP1705 ATOM 1551 CD1 ILE A 167 50.537 55.004 5.198 1.00 72.27 1CGP1706 ATOM 1552 H ILE A 167 56.012 55.723 6.553 1.00 0.00 1CGP1707 ATOM 1553 N THR A 168 54.933 52.997 4.582 1.00 70.85 1CGP1708 ATOM 1554 CA THR A 168 55.548 52.522 3.358 1.00 71.10 1CGP1709 ATOM 1555 C THR A 168 54.828 52.979 2.111 1.00 70.36 1CGP1710 ATOM 1556 O THR A 168 53.607 53.176 2.190 1.00 70.66 1CGP1711 ATOM 1557 CB THR A 168 55.563 51.020 3.403 1.00 72.17 1CGP1712 ATOM 1558 OG1 THR A 168 54.206 50.596 3.605 1.00 73.33 1CGP1713 ATOM 1559 CG2 THR A 168 56.516 50.517 4.466 1.00 72.96 1CGP1714 ATOM 1560 H THR A 168 54.622 52.352 5.244 1.00 0.00 1CGP1715 ATOM 1561 HG1 THR A 168 53.673 51.337 3.908 1.00 0.00 1CGP1716 ATOM 1562 N ARG A 169 55.525 53.032 0.967 1.00 68.81 1CGP1717 ATOM 1563 CA ARG A 169 54.883 53.342 -0.298 1.00 67.30 1CGP1718 ATOM 1564 C ARG A 169 53.742 52.349 -0.511 1.00 67.01 1CGP1719 ATOM 1565 O ARG A 169 52.667 52.750 -0.951 1.00 68.91 1CGP1720 ATOM 1566 CB ARG A 169 55.856 53.241 -1.464 1.00 67.37 1CGP1721 ATOM 1567 CG ARG A 169 56.763 54.439 -1.725 1.00 69.28 1CGP1722 ATOM 1568 CD ARG A 169 57.868 54.638 -0.705 1.00 71.73 1CGP1723 ATOM 1569 NE ARG A 169 58.924 55.513 -1.192 1.00 74.69 1CGP1724 ATOM 1570 CZ ARG A 169 59.865 55.995 -0.367 1.00 77.73 1CGP1725 ATOM 1571 NH1 ARG A 169 59.895 55.693 0.941 1.00 78.77 1CGP1726 ATOM 1572 NH2 ARG A 169 60.815 56.791 -0.853 1.00 79.39 1CGP1727 ATOM 1573 H ARG A 169 56.500 52.889 1.011 1.00 0.00 1CGP1728 ATOM 1574 HE ARG A 169 58.961 55.755 -2.141 1.00 0.00 1CGP1729 ATOM 1575 1HH1 ARG A 169 59.228 55.059 1.327 1.00 0.00 1CGP1730 ATOM 1576 2HH1 ARG A 169 60.616 56.066 1.523 1.00 0.00 1CGP1731 ATOM 1577 1HH2 ARG A 169 60.831 57.026 -1.823 1.00 0.00 1CGP1732 ATOM 1578 2HH2 ARG A 169 61.512 57.162 -0.239 1.00 0.00 1CGP1733 ATOM 1579 N GLN A 170 53.914 51.071 -0.155 1.00 65.69 1CGP1734 ATOM 1580 CA GLN A 170 52.844 50.057 -0.141 1.00 64.75 1CGP1735 ATOM 1581 C GLN A 170 51.495 50.568 0.400 1.00 62.35 1CGP1736 ATOM 1582 O GLN A 170 50.477 50.686 -0.292 1.00 61.02 1CGP1737 ATOM 1583 CB GLN A 170 53.225 48.859 0.741 1.00 67.61 1CGP1738 ATOM 1584 CG GLN A 170 54.603 48.244 0.586 1.00 70.46 1CGP1739 ATOM 1585 CD GLN A 170 54.711 47.198 -0.509 1.00 71.56 1CGP1740 ATOM 1586 OE1 GLN A 170 54.564 47.428 -1.708 1.00 70.32 1CGP1741 ATOM 1587 NE2 GLN A 170 54.971 45.982 -0.065 1.00 74.27 1CGP1742 ATOM 1588 H GLN A 170 54.840 50.760 -0.081 1.00 0.00 1CGP1743 ATOM 1589 1HE2 GLN A 170 55.096 45.852 0.900 1.00 0.00 1CGP1744 ATOM 1590 2HE2 GLN A 170 54.989 45.255 -0.715 1.00 0.00 1CGP1745 ATOM 1591 N GLU A 171 51.515 50.907 1.686 1.00 59.89 1CGP1746 ATOM 1592 CA GLU A 171 50.362 51.391 2.410 1.00 57.12 1CGP1747 ATOM 1593 C GLU A 171 49.605 52.515 1.749 1.00 54.40 1CGP1748 ATOM 1594 O GLU A 171 48.404 52.422 1.502 1.00 51.38 1CGP1749 ATOM 1595 CB GLU A 171 50.843 51.827 3.738 1.00 58.52 1CGP1750 ATOM 1596 CG GLU A 171 50.934 50.730 4.733 1.00 61.47 1CGP1751 ATOM 1597 CD GLU A 171 49.689 50.740 5.587 1.00 63.05 1CGP1752 ATOM 1598 OE1 GLU A 171 48.662 50.206 5.186 1.00 62.59 1CGP1753 ATOM 1599 OE2 GLU A 171 49.750 51.304 6.671 1.00 66.08 1CGP1754 ATOM 1600 H GLU A 171 52.350 50.805 2.176 1.00 0.00 1CGP1755 ATOM 1601 N ILE A 172 50.346 53.571 1.424 1.00 52.20 1CGP1756 ATOM 1602 CA ILE A 172 49.770 54.725 0.760 1.00 51.29 1CGP1757 ATOM 1603 C ILE A 172 49.129 54.220 -0.515 1.00 49.88 1CGP1758 ATOM 1604 O ILE A 172 47.980 54.580 -0.765 1.00 49.13 1CGP1759 ATOM 1605 CB ILE A 172 50.839 55.790 0.434 1.00 51.81 1CGP1760 ATOM 1606 CG1 ILE A 172 51.394 56.344 1.750 1.00 52.05 1CGP1761 ATOM 1607 CG2 ILE A 172 50.229 56.924 -0.409 1.00 51.95 1CGP1762 ATOM 1608 CD1 ILE A 172 52.522 57.373 1.626 1.00 52.18 1CGP1763 ATOM 1609 H ILE A 172 51.306 53.525 1.598 1.00 0.00 1CGP1764 ATOM 1610 N GLY A 173 49.805 53.349 -1.259 1.00 48.64 1CGP1765 ATOM 1611 CA GLY A 173 49.228 52.696 -2.416 1.00 47.93 1CGP1766 ATOM 1612 C GLY A 173 47.837 52.148 -2.135 1.00 46.80 1CGP1767 ATOM 1613 O GLY A 173 46.875 52.493 -2.823 1.00 44.43 1CGP1768 ATOM 1614 H GLY A 173 50.746 53.180 -1.067 1.00 0.00 1CGP1769 ATOM 1615 N GLN A 174 47.720 51.384 -1.054 1.00 47.77 1CGP1770 ATOM 1616 CA GLN A 174 46.447 50.834 -0.613 1.00 48.64 1CGP1771 ATOM 1617 C GLN A 174 45.431 51.860 -0.139 1.00 48.53 1CGP1772 ATOM 1618 O GLN A 174 44.248 51.526 0.014 1.00 49.02 1CGP1773 ATOM 1619 CB GLN A 174 46.619 49.885 0.537 1.00 49.80 1CGP1774 ATOM 1620 CG GLN A 174 47.407 48.699 0.121 1.00 54.71 1CGP1775 ATOM 1621 CD GLN A 174 47.641 47.717 1.250 1.00 57.86 1CGP1776 ATOM 1622 OE1 GLN A 174 48.301 47.971 2.261 1.00 59.57 1CGP1777 ATOM 1623 NE2 GLN A 174 47.081 46.533 1.058 1.00 60.04 1CGP1778 ATOM 1624 H GLN A 174 48.558 51.134 -0.615 1.00 0.00 1CGP1779 ATOM 1625 1HE2 GLN A 174 46.566 46.440 0.236 1.00 0.00 1CGP1780 ATOM 1626 2HE2 GLN A 174 47.215 45.839 1.731 1.00 0.00 1CGP1781 ATOM 1627 N ILE A 175 45.876 53.059 0.226 1.00 46.96 1CGP1782 ATOM 1628 CA ILE A 175 44.979 54.095 0.703 1.00 44.38 1CGP1783 ATOM 1629 C ILE A 175 44.414 54.897 -0.449 1.00 43.98 1CGP1784 ATOM 1630 O ILE A 175 43.239 55.248 -0.526 1.00 45.09 1CGP1785 ATOM 1631 CB ILE A 175 45.743 55.004 1.687 1.00 43.89 1CGP1786 ATOM 1632 CG1 ILE A 175 46.185 54.190 2.920 1.00 44.00 1CGP1787 ATOM 1633 CG2 ILE A 175 44.851 56.166 2.094 1.00 43.43 1CGP1788 ATOM 1634 CD1 ILE A 175 46.918 54.913 4.080 1.00 41.84 1CGP1789 ATOM 1635 H ILE A 175 46.843 53.187 0.274 1.00 0.00 1CGP1790 ATOM 1636 N VAL A 176 45.303 55.229 -1.342 1.00 42.01 1CGP1791 ATOM 1637 CA VAL A 176 44.931 56.031 -2.447 1.00 41.39 1CGP1792 ATOM 1638 C VAL A 176 44.351 55.274 -3.609 1.00 42.54 1CGP1793 ATOM 1639 O VAL A 176 43.436 55.767 -4.242 1.00 43.86 1CGP1794 ATOM 1640 CB VAL A 176 46.179 56.781 -2.713 1.00 41.27 1CGP1795 ATOM 1641 CG1 VAL A 176 46.401 57.196 -4.145 1.00 43.71 1CGP1796 ATOM 1642 CG2 VAL A 176 46.030 57.980 -1.822 1.00 40.81 1CGP1797 ATOM 1643 H VAL A 176 46.228 54.949 -1.226 1.00 0.00 1CGP1798 ATOM 1644 N GLY A 177 44.843 54.099 -3.948 1.00 43.52 1CGP1799 ATOM 1645 CA GLY A 177 44.312 53.363 -5.069 1.00 43.84 1CGP1800 ATOM 1646 C GLY A 177 45.164 53.601 -6.297 1.00 44.59 1CGP1801 ATOM 1647 O GLY A 177 44.726 54.233 -7.255 1.00 47.50 1CGP1802 ATOM 1648 H GLY A 177 45.584 53.703 -3.458 1.00 0.00 1CGP1803 ATOM 1649 N CYS A 178 46.407 53.132 -6.246 1.00 43.46 1CGP1804 ATOM 1650 CA CYS A 178 47.347 53.209 -7.352 1.00 43.34 1CGP1805 ATOM 1651 C CYS A 178 48.524 52.306 -6.988 1.00 45.23 1CGP1806 ATOM 1652 O CYS A 178 48.575 51.866 -5.840 1.00 44.27 1CGP1807 ATOM 1653 CB CYS A 178 47.806 54.629 -7.520 1.00 42.62 1CGP1808 ATOM 1654 SG CYS A 178 48.619 55.145 -6.002 1.00 40.33 1CGP1809 ATOM 1655 H CYS A 178 46.753 52.785 -5.396 1.00 0.00 1CGP1810 ATOM 1656 N SER A 179 49.486 51.984 -7.871 1.00 47.74 1CGP1811 ATOM 1657 CA SER A 179 50.551 51.022 -7.567 1.00 48.49 1CGP1812 ATOM 1658 C SER A 179 51.691 51.578 -6.714 1.00 50.13 1CGP1813 ATOM 1659 O SER A 179 51.966 52.784 -6.840 1.00 51.04 1CGP1814 ATOM 1660 CB SER A 179 51.130 50.493 -8.877 1.00 48.56 1CGP1815 ATOM 1661 OG SER A 179 52.050 51.366 -9.529 1.00 48.15 1CGP1816 ATOM 1662 H SER A 179 49.531 52.452 -8.730 1.00 0.00 1CGP1817 ATOM 1663 HG SER A 179 51.629 52.176 -9.844 1.00 0.00 1CGP1818 ATOM 1664 N ARG A 180 52.474 50.771 -5.959 1.00 49.58 1CGP1819 ATOM 1665 CA ARG A 180 53.500 51.352 -5.084 1.00 49.65 1CGP1820 ATOM 1666 C ARG A 180 54.504 52.126 -5.899 1.00 50.19 1CGP1821 ATOM 1667 O ARG A 180 55.064 53.128 -5.470 1.00 50.39 1CGP1822 ATOM 1668 CB ARG A 180 54.318 50.339 -4.269 1.00 50.98 1CGP1823 ATOM 1669 CG ARG A 180 55.250 49.428 -5.060 1.00 53.19 1CGP1824 ATOM 1670 CD ARG A 180 56.537 48.892 -4.411 1.00 52.49 1CGP1825 ATOM 1671 NE ARG A 180 57.220 48.150 -5.464 1.00 52.23 1CGP1826 ATOM 1672 CZ ARG A 180 57.891 48.774 -6.443 1.00 52.46 1CGP1827 ATOM 1673 NH1 ARG A 180 58.088 50.090 -6.439 1.00 52.35 1CGP1828 ATOM 1674 NH2 ARG A 180 58.417 48.074 -7.439 1.00 52.66 1CGP1829 ATOM 1675 H ARG A 180 52.332 49.806 -5.992 1.00 0.00 1CGP1830 ATOM 1676 HE ARG A 180 57.158 47.174 -5.485 1.00 0.00 1CGP1831 ATOM 1677 1HH1 ARG A 180 57.720 50.650 -5.698 1.00 0.00 1CGP1832 ATOM 1678 2HH1 ARG A 180 58.597 50.524 -7.181 1.00 0.00 1CGP1833 ATOM 1679 1HH2 ARG A 180 58.334 47.079 -7.457 1.00 0.00 1CGP1834 ATOM 1680 2HH2 ARG A 180 58.934 48.538 -8.159 1.00 0.00 1CGP1835 ATOM 1681 N GLU A 181 54.612 51.673 -7.142 1.00 50.43 1CGP1836 ATOM 1682 CA GLU A 181 55.478 52.258 -8.116 1.00 53.22 1CGP1837 ATOM 1683 C GLU A 181 54.988 53.674 -8.313 1.00 53.87 1CGP1838 ATOM 1684 O GLU A 181 55.746 54.612 -8.054 1.00 54.21 1CGP1839 ATOM 1685 CB GLU A 181 55.390 51.498 -9.420 1.00 55.59 1CGP1840 ATOM 1686 CG GLU A 181 55.980 50.107 -9.370 1.00 59.55 1CGP1841 ATOM 1687 CD GLU A 181 55.034 48.964 -9.054 1.00 61.99 1CGP1842 ATOM 1688 OE1 GLU A 181 54.214 49.063 -8.139 1.00 63.82 1CGP1843 ATOM 1689 OE2 GLU A 181 55.147 47.956 -9.747 1.00 64.14 1CGP1844 ATOM 1690 H GLU A 181 53.997 50.991 -7.447 1.00 0.00 1CGP1845 ATOM 1691 N THR A 182 53.712 53.853 -8.677 1.00 54.25 1CGP1846 ATOM 1692 CA THR A 182 53.204 55.187 -8.939 1.00 53.85 1CGP1847 ATOM 1693 C THR A 182 53.254 56.096 -7.715 1.00 53.96 1CGP1848 ATOM 1694 O THR A 182 53.541 57.298 -7.793 1.00 53.09 1CGP1849 ATOM 1695 CB THR A 182 51.780 55.084 -9.476 1.00 52.38 1CGP1850 ATOM 1696 OG1 THR A 182 51.561 53.926 -10.292 1.00 50.70 1CGP1851 ATOM 1697 CG2 THR A 182 51.597 56.271 -10.383 1.00 53.12 1CGP1852 ATOM 1698 H THR A 182 53.121 53.085 -8.817 1.00 0.00 1CGP1853 ATOM 1699 HG1 THR A 182 51.995 54.079 -11.147 1.00 0.00 1CGP1854 ATOM 1700 N VAL A 183 53.055 55.463 -6.569 1.00 54.79 1CGP1855 ATOM 1701 CA VAL A 183 53.149 56.161 -5.309 1.00 55.89 1CGP1856 ATOM 1702 C VAL A 183 54.575 56.701 -5.206 1.00 56.88 1CGP1857 ATOM 1703 O VAL A 183 54.776 57.887 -4.966 1.00 56.33 1CGP1858 ATOM 1704 CB VAL A 183 52.785 55.171 -4.182 1.00 55.03 1CGP1859 ATOM 1705 CG1 VAL A 183 52.774 55.899 -2.852 1.00 54.50 1CGP1860 ATOM 1706 CG2 VAL A 183 51.404 54.577 -4.422 1.00 52.36 1CGP1861 ATOM 1707 H VAL A 183 52.780 54.523 -6.599 1.00 0.00 1CGP1862 ATOM 1708 N GLY A 184 55.590 55.902 -5.490 1.00 59.65 1CGP1863 ATOM 1709 CA GLY A 184 56.961 56.376 -5.473 1.00 64.97 1CGP1864 ATOM 1710 C GLY A 184 57.140 57.548 -6.426 1.00 68.20 1CGP1865 ATOM 1711 O GLY A 184 57.486 58.663 -6.015 1.00 70.18 1CGP1866 ATOM 1712 H GLY A 184 55.414 54.955 -5.641 1.00 0.00 1CGP1867 ATOM 1713 N ARG A 185 56.783 57.277 -7.676 1.00 70.07 1CGP1868 ATOM 1714 CA ARG A 185 56.860 58.209 -8.781 1.00 71.26 1CGP1869 ATOM 1715 C ARG A 185 56.383 59.607 -8.419 1.00 72.00 1CGP1870 ATOM 1716 O ARG A 185 57.058 60.600 -8.714 1.00 72.30 1CGP1871 ATOM 1717 CB ARG A 185 56.022 57.670 -9.904 1.00 72.91 1CGP1872 ATOM 1718 CG ARG A 185 56.639 57.953 -11.244 1.00 76.58 1CGP1873 ATOM 1719 CD ARG A 185 57.232 56.677 -11.796 1.00 78.97 1CGP1874 ATOM 1720 NE ARG A 185 56.157 55.805 -12.224 1.00 80.46 1CGP1875 ATOM 1721 CZ ARG A 185 56.374 54.642 -12.840 1.00 81.60 1CGP1876 ATOM 1722 NH1 ARG A 185 57.589 54.148 -13.102 1.00 81.85 1CGP1877 ATOM 1723 NH2 ARG A 185 55.307 53.945 -13.195 1.00 82.83 1CGP1878 ATOM 1724 H ARG A 185 56.441 56.374 -7.832 1.00 0.00 1CGP1879 ATOM 1725 HE ARG A 185 55.230 56.075 -12.057 1.00 0.00 1CGP1880 ATOM 1726 1HH1 ARG A 185 58.415 54.644 -12.837 1.00 0.00 1CGP1881 ATOM 1727 2HH1 ARG A 185 57.655 53.281 -13.595 1.00 0.00 1CGP1882 ATOM 1728 1HH2 ARG A 185 54.398 54.310 -12.995 1.00 0.00 1CGP1883 ATOM 1729 2HH2 ARG A 185 55.397 53.083 -13.693 1.00 0.00 1CGP1884 ATOM 1730 N ILE A 186 55.226 59.686 -7.745 1.00 73.28 1CGP1885 ATOM 1731 CA ILE A 186 54.662 60.957 -7.314 1.00 74.00 1CGP1886 ATOM 1732 C ILE A 186 55.247 61.489 -6.010 1.00 73.75 1CGP1887 ATOM 1733 O ILE A 186 55.346 62.708 -5.860 1.00 73.13 1CGP1888 ATOM 1734 CB ILE A 186 53.105 60.784 -7.251 1.00 73.77 1CGP1889 ATOM 1735 CG1 ILE A 186 52.637 60.778 -8.710 1.00 73.79 1CGP1890 ATOM 1736 CG2 ILE A 186 52.389 61.881 -6.452 1.00 73.64 1CGP1891 ATOM 1737 CD1 ILE A 186 51.128 60.709 -9.004 1.00 73.85 1CGP1892 ATOM 1738 H ILE A 186 54.709 58.865 -7.609 1.00 0.00 1CGP1893 ATOM 1739 N LEU A 187 55.682 60.676 -5.052 1.00 74.85 1CGP1894 ATOM 1740 CA LEU A 187 56.264 61.167 -3.809 1.00 76.64 1CGP1895 ATOM 1741 C LEU A 187 57.498 62.001 -4.174 1.00 79.10 1CGP1896 ATOM 1742 O LEU A 187 57.650 63.128 -3.702 1.00 78.40 1CGP1897 ATOM 1743 CB LEU A 187 56.579 59.928 -2.943 1.00 75.27 1CGP1898 ATOM 1744 CG LEU A 187 56.336 59.889 -1.425 1.00 74.08 1CGP1899 ATOM 1745 CD1 LEU A 187 54.941 60.333 -1.083 1.00 74.58 1CGP1900 ATOM 1746 CD2 LEU A 187 56.461 58.462 -0.929 1.00 73.39 1CGP1901 ATOM 1747 H LEU A 187 55.532 59.711 -5.153 1.00 0.00 1CGP1902 ATOM 1748 N LYS A 188 58.337 61.522 -5.104 1.00 83.30 1CGP1903 ATOM 1749 CA LYS A 188 59.504 62.259 -5.600 1.00 87.07 1CGP1904 ATOM 1750 C LYS A 188 59.039 63.553 -6.246 1.00 87.79 1CGP1905 ATOM 1751 O LYS A 188 59.674 64.578 -6.036 1.00 88.33 1CGP1906 ATOM 1752 CB LYS A 188 60.302 61.529 -6.685 1.00 89.51 1CGP1907 ATOM 1753 CG LYS A 188 61.111 60.285 -6.336 1.00 92.42 1CGP1908 ATOM 1754 CD LYS A 188 61.665 59.702 -7.649 1.00 94.15 1CGP1909 ATOM 1755 CE LYS A 188 62.126 58.240 -7.522 1.00 95.12 1CGP1910 ATOM 1756 NZ LYS A 188 62.480 57.675 -8.816 1.00 94.78 1CGP1911 ATOM 1757 H LYS A 188 58.134 60.624 -5.444 1.00 0.00 1CGP1912 ATOM 1758 1HZ LYS A 188 63.335 58.135 -9.188 1.00 0.00 1CGP1913 ATOM 1759 2HZ LYS A 188 61.701 57.807 -9.494 1.00 0.00 1CGP1914 ATOM 1760 3HZ LYS A 188 62.659 56.658 -8.712 1.00 0.00 1CGP1915 ATOM 1761 N MET A 189 57.969 63.563 -7.045 1.00 88.76 1CGP1916 ATOM 1762 CA MET A 189 57.418 64.783 -7.624 1.00 89.64 1CGP1917 ATOM 1763 C MET A 189 57.097 65.775 -6.511 1.00 89.74 1CGP1918 ATOM 1764 O MET A 189 57.480 66.943 -6.563 1.00 89.37 1CGP1919 ATOM 1765 CB MET A 189 56.178 64.404 -8.400 1.00 91.34 1CGP1920 ATOM 1766 CG MET A 189 56.113 65.011 -9.782 1.00 92.91 1CGP1921 ATOM 1767 SD MET A 189 55.145 63.983 -10.923 1.00 95.61 1CGP1922 ATOM 1768 CE MET A 189 56.410 63.280 -11.954 1.00 94.00 1CGP1923 ATOM 1769 H MET A 189 57.596 62.700 -7.323 1.00 0.00 1CGP1924 ATOM 1770 N LEU A 190 56.494 65.302 -5.433 1.00 91.16 1CGP1925 ATOM 1771 CA LEU A 190 56.241 66.118 -4.263 1.00 93.35 1CGP1926 ATOM 1772 C LEU A 190 57.525 66.483 -3.504 1.00 95.13 1CGP1927 ATOM 1773 O LEU A 190 57.499 67.417 -2.691 1.00 95.03 1CGP1928 ATOM 1774 CB LEU A 190 55.279 65.365 -3.361 1.00 93.70 1CGP1929 ATOM 1775 CG LEU A 190 53.868 65.079 -3.853 1.00 94.50 1CGP1930 ATOM 1776 CD1 LEU A 190 53.267 63.938 -3.051 1.00 94.38 1CGP1931 ATOM 1777 CD2 LEU A 190 53.026 66.337 -3.731 1.00 94.92 1CGP1932 ATOM 1778 H LEU A 190 56.147 64.387 -5.472 1.00 0.00 1CGP1933 ATOM 1779 N GLU A 191 58.644 65.751 -3.656 1.00 97.54 1CGP1934 ATOM 1780 CA GLU A 191 59.950 66.139 -3.098 1.00 98.97 1CGP1935 ATOM 1781 C GLU A 191 60.576 67.271 -3.915 1.00 99.54 1CGP1936 ATOM 1782 O GLU A 191 61.007 68.272 -3.327 1.00100.10 1CGP1937 ATOM 1783 CB GLU A 191 61.005 65.010 -3.091 1.00 99.32 1CGP1938 ATOM 1784 CG GLU A 191 60.873 63.942 -2.015 1.00100.87 1CGP1939 ATOM 1785 CD GLU A 191 62.165 63.198 -1.666 1.00101.44 1CGP1940 ATOM 1786 OE1 GLU A 191 62.928 63.709 -0.835 1.00101.05 1CGP1941 ATOM 1787 OE2 GLU A 191 62.385 62.103 -2.202 1.00101.67 1CGP1942 ATOM 1788 H GLU A 191 58.535 64.861 -4.040 1.00 0.00 1CGP1943 ATOM 1789 N ASP A 192 60.637 67.162 -5.264 1.00 98.69 1CGP1944 ATOM 1790 CA ASP A 192 61.119 68.216 -6.168 1.00 96.75 1CGP1945 ATOM 1791 C ASP A 192 60.314 69.457 -5.822 1.00 95.68 1CGP1946 ATOM 1792 O ASP A 192 60.868 70.475 -5.432 1.00 95.48 1CGP1947 ATOM 1793 CB ASP A 192 60.885 67.863 -7.659 1.00 97.01 1CGP1948 ATOM 1794 CG ASP A 192 61.690 66.695 -8.260 1.00 96.92 1CGP1949 ATOM 1795 OD1 ASP A 192 62.625 66.205 -7.619 1.00 96.67 1CGP1950 ATOM 1796 OD2 ASP A 192 61.378 66.277 -9.386 1.00 96.00 1CGP1951 ATOM 1797 H ASP A 192 60.349 66.300 -5.629 1.00 0.00 1CGP1952 ATOM 1798 N GLN A 193 58.992 69.376 -5.795 1.00 94.94 1CGP1953 ATOM 1799 CA GLN A 193 58.162 70.466 -5.312 1.00 95.11 1CGP1954 ATOM 1800 C GLN A 193 58.346 70.887 -3.841 1.00 95.42 1CGP1955 ATOM 1801 O GLN A 193 57.539 71.678 -3.353 1.00 95.68 1CGP1956 ATOM 1802 CB GLN A 193 56.714 70.106 -5.489 1.00 94.84 1CGP1957 ATOM 1803 CG GLN A 193 56.068 70.305 -6.823 1.00 94.19 1CGP1958 ATOM 1804 CD GLN A 193 54.613 69.950 -6.626 1.00 94.31 1CGP1959 ATOM 1805 OE1 GLN A 193 54.154 68.922 -7.100 1.00 95.19 1CGP1960 ATOM 1806 NE2 GLN A 193 53.831 70.710 -5.874 1.00 94.28 1CGP1961 ATOM 1807 H GLN A 193 58.549 68.555 -6.106 1.00 0.00 1CGP1962 ATOM 1808 1HE2 GLN A 193 54.232 71.480 -5.421 1.00 0.00 1CGP1963 ATOM 1809 2HE2 GLN A 193 52.894 70.441 -5.797 1.00 0.00 1CGP1964 ATOM 1810 N ASN A 194 59.310 70.401 -3.053 1.00 95.46 1CGP1965 ATOM 1811 CA ASN A 194 59.551 70.812 -1.671 1.00 97.55 1CGP1966 ATOM 1812 C ASN A 194 58.451 70.566 -0.639 1.00 97.61 1CGP1967 ATOM 1813 O ASN A 194 58.512 71.111 0.472 1.00 96.84 1CGP1968 ATOM 1814 CB ASN A 194 59.893 72.307 -1.624 1.00100.92 1CGP1969 ATOM 1815 CG ASN A 194 61.221 72.726 -2.232 1.00104.08 1CGP1970 ATOM 1816 OD1 ASN A 194 61.812 73.714 -1.796 1.00105.76 1CGP1971 ATOM 1817 ND2 ASN A 194 61.784 72.120 -3.270 1.00105.65 1CGP1972 ATOM 1818 H ASN A 194 59.933 69.752 -3.425 1.00 0.00 1CGP1973 ATOM 1819 1HD2 ASN A 194 61.340 71.404 -3.772 1.00 0.00 1CGP1974 ATOM 1820 2HD2 ASN A 194 62.678 72.439 -3.506 1.00 0.00 1CGP1975 ATOM 1821 N LEU A 195 57.451 69.712 -0.904 1.00 97.58 1CGP1976 ATOM 1822 CA LEU A 195 56.369 69.507 0.054 1.00 96.42 1CGP1977 ATOM 1823 C LEU A 195 56.571 68.249 0.873 1.00 95.40 1CGP1978 ATOM 1824 O LEU A 195 56.144 68.171 2.030 1.00 94.30 1CGP1979 ATOM 1825 CB LEU A 195 55.015 69.403 -0.648 1.00 97.04 1CGP1980 ATOM 1826 CG LEU A 195 54.445 70.607 -1.410 1.00 97.41 1CGP1981 ATOM 1827 CD1 LEU A 195 53.050 70.229 -1.895 1.00 97.84 1CGP1982 ATOM 1828 CD2 LEU A 195 54.367 71.855 -0.524 1.00 97.14 1CGP1983 ATOM 1829 H LEU A 195 57.510 69.095 -1.659 1.00 0.00 1CGP1984 ATOM 1830 N ILE A 196 57.176 67.216 0.295 1.00 94.71 1CGP1985 ATOM 1831 CA ILE A 196 57.442 66.039 1.082 1.00 94.24 1CGP1986 ATOM 1832 C ILE A 196 58.942 65.753 1.128 1.00 95.30 1CGP1987 ATOM 1833 O ILE A 196 59.655 65.938 0.138 1.00 95.01 1CGP1988 ATOM 1834 CB ILE A 196 56.606 64.853 0.477 1.00 92.83 1CGP1989 ATOM 1835 CG1 ILE A 196 56.572 63.763 1.519 1.00 93.06 1CGP1990 ATOM 1836 CG2 ILE A 196 57.200 64.227 -0.763 1.00 91.46 1CGP1991 ATOM 1837 CD1 ILE A 196 55.844 64.203 2.792 1.00 93.15 1CGP1992 ATOM 1838 H ILE A 196 57.490 67.268 -0.632 1.00 0.00 1CGP1993 ATOM 1839 N SER A 197 59.440 65.376 2.303 1.00 96.35 1CGP1994 ATOM 1840 CA SER A 197 60.818 64.938 2.463 1.00 97.18 1CGP1995 ATOM 1841 C SER A 197 60.704 63.446 2.778 1.00 97.63 1CGP1996 ATOM 1842 O SER A 197 59.954 63.099 3.705 1.00 98.28 1CGP1997 ATOM 1843 CB SER A 197 61.432 65.717 3.610 1.00 97.81 1CGP1998 ATOM 1844 OG SER A 197 61.310 67.115 3.363 1.00 99.40 1CGP1999 ATOM 1845 H SER A 197 58.873 65.427 3.102 1.00 0.00 1CGP2000 ATOM 1846 HG SER A 197 60.874 67.540 4.103 1.00 0.00 1CGP2001 ATOM 1847 N ALA A 198 61.389 62.539 2.066 1.00 97.58 1CGP2002 ATOM 1848 CA ALA A 198 61.176 61.108 2.263 1.00 97.26 1CGP2003 ATOM 1849 C ALA A 198 62.428 60.255 2.268 1.00 97.19 1CGP2004 ATOM 1850 O ALA A 198 63.440 60.608 1.657 1.00 97.66 1CGP2005 ATOM 1851 CB ALA A 198 60.275 60.529 1.172 1.00 96.38 1CGP2006 ATOM 1852 H ALA A 198 62.103 62.807 1.447 1.00 0.00 1CGP2007 ATOM 1853 N HIS A 199 62.329 59.141 3.007 1.00 97.20 1CGP2008 ATOM 1854 CA HIS A 199 63.356 58.106 3.081 1.00 96.52 1CGP2009 ATOM 1855 C HIS A 199 62.806 56.914 3.912 1.00 95.58 1CGP2010 ATOM 1856 O HIS A 199 63.408 56.582 4.936 1.00 96.47 1CGP2011 ATOM 1857 CB HIS A 199 64.597 58.783 3.721 1.00 97.40 1CGP2012 ATOM 1858 CG HIS A 199 65.900 57.999 3.706 1.00 97.90 1CGP2013 ATOM 1859 ND1 HIS A 199 66.406 57.273 4.702 1.00 98.06 1CGP2014 ATOM 1860 CD2 HIS A 199 66.775 57.953 2.648 1.00 97.60 1CGP2015 ATOM 1861 CE1 HIS A 199 67.550 56.783 4.294 1.00 97.93 1CGP2016 ATOM 1862 NE2 HIS A 199 67.759 57.195 3.061 1.00 98.26 1CGP2017 ATOM 1863 H HIS A 199 61.587 59.112 3.652 1.00 0.00 1CGP2018 ATOM 1864 HD1 HIS A 199 65.923 57.013 5.524 1.00 0.00 1CGP2019 ATOM 1865 HE2 HIS A 199 68.540 56.944 2.517 1.00 0.00 1CGP2020 ATOM 1866 N GLY A 200 61.701 56.212 3.587 1.00 93.24 1CGP2021 ATOM 1867 CA GLY A 200 61.156 55.146 4.444 1.00 90.85 1CGP2022 ATOM 1868 C GLY A 200 60.049 55.652 5.379 1.00 90.35 1CGP2023 ATOM 1869 O GLY A 200 59.006 55.029 5.569 1.00 89.36 1CGP2024 ATOM 1870 H GLY A 200 61.222 56.417 2.758 1.00 0.00 1CGP2025 ATOM 1871 N LYS A 201 60.312 56.779 6.036 1.00 91.57 1CGP2026 ATOM 1872 CA LYS A 201 59.340 57.527 6.837 1.00 92.47 1CGP2027 ATOM 1873 C LYS A 201 59.200 58.894 6.145 1.00 92.01 1CGP2028 ATOM 1874 O LYS A 201 60.154 59.335 5.478 1.00 93.51 1CGP2029 ATOM 1875 CB LYS A 201 59.845 57.752 8.262 1.00 94.06 1CGP2030 ATOM 1876 CG LYS A 201 60.999 58.755 8.384 1.00 96.04 1CGP2031 ATOM 1877 CD LYS A 201 61.324 59.035 9.832 1.00 98.38 1CGP2032 ATOM 1878 CE LYS A 201 62.445 60.065 9.963 1.00 99.28 1CGP2033 ATOM 1879 NZ LYS A 201 62.894 60.051 11.343 1.00 99.64 1CGP2034 ATOM 1880 H LYS A 201 61.227 57.125 6.011 1.00 0.00 1CGP2035 ATOM 1881 1HZ LYS A 201 63.260 59.099 11.556 1.00 0.00 1CGP2036 ATOM 1882 2HZ LYS A 201 62.084 60.244 11.964 1.00 0.00 1CGP2037 ATOM 1883 3HZ LYS A 201 63.642 60.755 11.492 1.00 0.00 1CGP2038 ATOM 1884 N THR A 202 58.096 59.610 6.239 1.00 89.76 1CGP2039 ATOM 1885 CA THR A 202 57.941 60.860 5.544 1.00 88.47 1CGP2040 ATOM 1886 C THR A 202 57.700 61.956 6.539 1.00 88.57 1CGP2041 ATOM 1887 O THR A 202 57.077 61.763 7.586 1.00 87.26 1CGP2042 ATOM 1888 CB THR A 202 56.754 60.826 4.568 1.00 88.44 1CGP2043 ATOM 1889 OG1 THR A 202 55.689 60.192 5.267 1.00 87.18 1CGP2044 ATOM 1890 CG2 THR A 202 57.078 60.133 3.246 1.00 88.48 1CGP2045 ATOM 1891 H THR A 202 57.383 59.360 6.847 1.00 0.00 1CGP2046 ATOM 1892 HG1 THR A 202 55.008 59.952 4.635 1.00 0.00 1CGP2047 ATOM 1893 N ILE A 203 58.250 63.108 6.189 1.00 89.49 1CGP2048 ATOM 1894 CA ILE A 203 58.030 64.319 6.941 1.00 89.15 1CGP2049 ATOM 1895 C ILE A 203 57.245 65.179 5.978 1.00 87.77 1CGP2050 ATOM 1896 O ILE A 203 57.689 65.583 4.893 1.00 86.46 1CGP2051 ATOM 1897 CB ILE A 203 59.363 64.998 7.342 1.00 90.74 1CGP2052 ATOM 1898 CG1 ILE A 203 60.007 64.208 8.487 1.00 92.08 1CGP2053 ATOM 1899 CG2 ILE A 203 59.124 66.431 7.811 1.00 91.02 1CGP2054 ATOM 1900 CD1 ILE A 203 60.871 62.954 8.170 1.00 93.16 1CGP2055 ATOM 1901 H ILE A 203 58.799 63.144 5.377 1.00 0.00 1CGP2056 ATOM 1902 N VAL A 204 56.018 65.353 6.421 1.00 87.05 1CGP2057 ATOM 1903 CA VAL A 204 55.045 66.106 5.666 1.00 87.85 1CGP2058 ATOM 1904 C VAL A 204 55.277 67.481 6.234 1.00 87.58 1CGP2059 ATOM 1905 O VAL A 204 55.234 67.645 7.464 1.00 87.68 1CGP2060 ATOM 1906 CB VAL A 204 53.599 65.618 5.963 1.00 88.83 1CGP2061 ATOM 1907 CG1 VAL A 204 52.555 66.471 5.251 1.00 89.20 1CGP2062 ATOM 1908 CG2 VAL A 204 53.439 64.206 5.435 1.00 89.93 1CGP2063 ATOM 1909 H VAL A 204 55.859 65.153 7.369 1.00 0.00 1CGP2064 ATOM 1910 N VAL A 205 55.617 68.431 5.357 1.00 87.29 1CGP2065 ATOM 1911 CA VAL A 205 55.814 69.805 5.805 1.00 86.60 1CGP2066 ATOM 1912 C VAL A 205 54.464 70.445 6.168 1.00 87.65 1CGP2067 ATOM 1913 O VAL A 205 53.392 69.828 6.231 1.00 87.86 1CGP2068 ATOM 1914 CB VAL A 205 56.534 70.707 4.710 1.00 85.62 1CGP2069 ATOM 1915 CG1 VAL A 205 57.935 70.186 4.414 1.00 84.81 1CGP2070 ATOM 1916 CG2 VAL A 205 55.709 70.755 3.436 1.00 84.56 1CGP2071 ATOM 1917 H VAL A 205 55.710 68.220 4.401 1.00 0.00 1CGP2072 TER 1918 VAL A 205 1CGP2073 HETATM 1919 P CMP A 1 30.904 44.446 10.242 1.00 30.87 1CGP2074 HETATM 1920 O1P CMP A 1 30.168 44.651 8.974 1.00 30.82 1CGP2075 HETATM 1921 O2P CMP A 1 30.287 43.676 11.335 1.00 31.62 1CGP2076 HETATM 1922 O5* CMP A 1 32.294 43.822 9.881 1.00 30.29 1CGP2077 HETATM 1923 C5* CMP A 1 33.292 44.587 9.225 1.00 30.38 1CGP2078 HETATM 1924 C4* CMP A 1 33.550 45.782 10.033 1.00 31.38 1CGP2079 HETATM 1925 O4* CMP A 1 34.507 46.673 9.455 1.00 32.86 1CGP2080 HETATM 1926 C3* CMP A 1 32.290 46.560 10.042 1.00 31.76 1CGP2081 HETATM 1927 O3* CMP A 1 31.358 45.853 10.849 1.00 31.66 1CGP2082 HETATM 1928 C2* CMP A 1 32.763 47.888 10.596 1.00 31.92 1CGP2083 HETATM 1929 O2* CMP A 1 33.037 47.825 12.004 1.00 30.86 1CGP2084 HETATM 1930 C1* CMP A 1 34.098 47.998 9.822 1.00 32.64 1CGP2085 HETATM 1931 N9 CMP A 1 33.907 48.851 8.618 1.00 34.98 1CGP2086 HETATM 1932 C8 CMP A 1 33.255 48.608 7.424 1.00 34.57 1CGP2087 HETATM 1933 N7 CMP A 1 33.236 49.633 6.612 1.00 34.57 1CGP2088 HETATM 1934 C5 CMP A 1 33.927 50.622 7.316 1.00 34.99 1CGP2089 HETATM 1935 C6 CMP A 1 34.259 51.956 7.009 1.00 35.83 1CGP2090 HETATM 1936 N6 CMP A 1 33.877 52.561 5.887 1.00 36.18 1CGP2091 HETATM 1937 N1 CMP A 1 34.957 52.630 7.921 1.00 35.63 1CGP2092 HETATM 1938 C2 CMP A 1 35.277 52.013 9.051 1.00 34.28 1CGP2093 HETATM 1939 N3 CMP A 1 35.034 50.792 9.473 1.00 32.61 1CGP2094 HETATM 1940 C4 CMP A 1 34.340 50.141 8.527 1.00 34.63 1CGP2095 HETATM 1941 H2* CMP A 1 33.611 48.577 12.194 1.00 0.00 1CGP2096 HETATM 1942 1H6 CMP A 1 33.439 52.013 5.153 1.00 0.00 1CGP2097 HETATM 1943 2H6 CMP A 1 33.955 53.560 5.756 1.00 0.00 1CGP2098 ATOM 1944 N PRO B 9 3.593 53.533 14.188 1.00 95.99 1CGP2099 ATOM 1945 CA PRO B 9 3.003 53.405 15.517 1.00 95.71 1CGP2100 ATOM 1946 C PRO B 9 3.983 54.182 16.381 1.00 94.82 1CGP2101 ATOM 1947 O PRO B 9 3.727 55.364 16.622 1.00 95.04 1CGP2102 ATOM 1948 CB PRO B 9 2.938 51.911 15.734 1.00 96.67 1CGP2103 ATOM 1949 CG PRO B 9 2.710 51.395 14.336 1.00 96.83 1CGP2104 ATOM 1950 CD PRO B 9 3.778 52.206 13.616 1.00 96.70 1CGP2105 ATOM 1951 N THR B 10 5.146 53.643 16.777 1.00 93.42 1CGP2106 ATOM 1952 CA THR B 10 6.193 54.445 17.397 1.00 92.31 1CGP2107 ATOM 1953 C THR B 10 6.484 55.537 16.358 1.00 92.64 1CGP2108 ATOM 1954 O THR B 10 6.634 56.717 16.672 1.00 93.13 1CGP2109 ATOM 1955 CB THR B 10 7.452 53.599 17.631 1.00 91.81 1CGP2110 ATOM 1956 OG1 THR B 10 7.095 52.211 17.619 1.00 91.33 1CGP2111 ATOM 1957 CG2 THR B 10 8.096 53.981 18.945 1.00 91.49 1CGP2112 ATOM 1958 H THR B 10 5.309 52.677 16.752 1.00 0.00 1CGP2113 ATOM 1959 HG1 THR B 10 7.925 51.742 17.758 1.00 0.00 1CGP2114 ATOM 1960 N LEU B 11 6.425 55.126 15.074 1.00 92.68 1CGP2115 ATOM 1961 CA LEU B 11 6.523 56.029 13.943 1.00 92.76 1CGP2116 ATOM 1962 C LEU B 11 5.471 57.110 14.013 1.00 93.10 1CGP2117 ATOM 1963 O LEU B 11 5.836 58.275 13.905 1.00 92.14 1CGP2118 ATOM 1964 CB LEU B 11 6.316 55.331 12.610 1.00 92.16 1CGP2119 ATOM 1965 CG LEU B 11 7.356 54.371 12.101 1.00 91.61 1CGP2120 ATOM 1966 CD1 LEU B 11 7.041 54.139 10.641 1.00 91.64 1CGP2121 ATOM 1967 CD2 LEU B 11 8.772 54.930 12.220 1.00 91.60 1CGP2122 ATOM 1968 H LEU B 11 6.377 54.168 14.909 1.00 0.00 1CGP2123 ATOM 1969 N GLU B 12 4.199 56.761 14.252 1.00 93.38 1CGP2124 ATOM 1970 CA GLU B 12 3.134 57.754 14.303 1.00 93.66 1CGP2125 ATOM 1971 C GLU B 12 3.420 58.761 15.393 1.00 92.14 1CGP2126 ATOM 1972 O GLU B 12 3.348 59.958 15.120 1.00 90.94 1CGP2127 ATOM 1973 CB GLU B 12 1.767 57.141 14.591 1.00 95.86 1CGP2128 ATOM 1974 CG GLU B 12 1.323 55.905 13.787 1.00 99.46 1CGP2129 ATOM 1975 CD GLU B 12 1.297 55.912 12.248 1.00101.70 1CGP2130 ATOM 1976 OE1 GLU B 12 1.497 56.955 11.604 1.00102.95 1CGP2131 ATOM 1977 OE2 GLU B 12 1.059 54.832 11.692 1.00102.88 1CGP2132 ATOM 1978 H GLU B 12 3.982 55.823 14.419 1.00 0.00 1CGP2133 ATOM 1979 N TRP B 13 3.821 58.282 16.577 1.00 91.27 1CGP2134 ATOM 1980 CA TRP B 13 4.205 59.140 17.696 1.00 91.41 1CGP2135 ATOM 1981 C TRP B 13 5.308 60.117 17.275 1.00 89.51 1CGP2136 ATOM 1982 O TRP B 13 5.260 61.323 17.578 1.00 88.73 1CGP2137 ATOM 1983 CB TRP B 13 4.714 58.303 18.900 1.00 94.14 1CGP2138 ATOM 1984 CG TRP B 13 5.389 59.152 19.993 1.00 97.57 1CGP2139 ATOM 1985 CD1 TRP B 13 4.678 60.076 20.734 1.00 98.80 1CGP2140 ATOM 1986 CD2 TRP B 13 6.733 59.142 20.327 1.00 98.97 1CGP2141 ATOM 1987 NE1 TRP B 13 5.557 60.649 21.532 1.00 99.59 1CGP2142 ATOM 1988 CE2 TRP B 13 6.783 60.124 21.314 1.00 99.35 1CGP2143 ATOM 1989 CE3 TRP B 13 7.888 58.473 19.959 1.00 99.49 1CGP2144 ATOM 1990 CZ2 TRP B 13 7.979 60.439 21.932 1.00 98.81 1CGP2145 ATOM 1991 CZ3 TRP B 13 9.084 58.795 20.579 1.00 98.80 1CGP2146 ATOM 1992 CH2 TRP B 13 9.124 59.765 21.553 1.00 98.50 1CGP2147 ATOM 1993 H TRP B 13 3.836 57.310 16.682 1.00 0.00 1CGP2148 ATOM 1994 HE1 TRP B 13 5.318 61.122 22.355 1.00 0.00 1CGP2149 ATOM 1995 N PHE B 14 6.334 59.571 16.616 1.00 86.03 1CGP2150 ATOM 1996 CA PHE B 14 7.435 60.354 16.109 1.00 83.11 1CGP2151 ATOM 1997 C PHE B 14 6.869 61.445 15.214 1.00 85.22 1CGP2152 ATOM 1998 O PHE B 14 7.006 62.637 15.511 1.00 86.23 1CGP2153 ATOM 1999 CB PHE B 14 8.381 59.449 15.331 1.00 77.28 1CGP2154 ATOM 2000 CG PHE B 14 9.490 60.266 14.719 1.00 72.29 1CGP2155 ATOM 2001 CD1 PHE B 14 10.504 60.753 15.507 1.00 70.69 1CGP2156 ATOM 2002 CD2 PHE B 14 9.434 60.559 13.382 1.00 70.69 1CGP2157 ATOM 2003 CE1 PHE B 14 11.464 61.550 14.944 1.00 69.62 1CGP2158 ATOM 2004 CE2 PHE B 14 10.406 61.351 12.835 1.00 69.61 1CGP2159 ATOM 2005 CZ PHE B 14 11.419 61.849 13.611 1.00 69.19 1CGP2160 ATOM 2006 H PHE B 14 6.369 58.600 16.532 1.00 0.00 1CGP2161 ATOM 2007 N LEU B 15 6.138 61.015 14.190 1.00 87.85 1CGP2162 ATOM 2008 CA LEU B 15 5.524 61.892 13.217 1.00 91.36 1CGP2163 ATOM 2009 C LEU B 15 4.675 62.967 13.878 1.00 93.38 1CGP2164 ATOM 2010 O LEU B 15 4.676 64.098 13.401 1.00 94.22 1CGP2165 ATOM 2011 CB LEU B 15 4.632 61.116 12.239 1.00 91.27 1CGP2166 ATOM 2012 CG LEU B 15 5.179 60.014 11.327 1.00 90.99 1CGP2167 ATOM 2013 CD1 LEU B 15 4.075 59.643 10.339 1.00 91.40 1CGP2168 ATOM 2014 CD2 LEU B 15 6.415 60.472 10.568 1.00 90.32 1CGP2169 ATOM 2015 H LEU B 15 6.004 60.057 14.108 1.00 0.00 1CGP2170 ATOM 2016 N SER B 16 3.984 62.699 14.987 1.00 95.39 1CGP2171 ATOM 2017 CA SER B 16 3.202 63.713 15.680 1.00 96.70 1CGP2172 ATOM 2018 C SER B 16 4.021 64.895 16.208 1.00 96.53 1CGP2173 ATOM 2019 O SER B 16 3.488 65.976 16.459 1.00 97.60 1CGP2174 ATOM 2020 CB SER B 16 2.461 63.035 16.825 1.00 98.19 1CGP2175 ATOM 2021 OG SER B 16 1.818 61.828 16.409 1.00100.28 1CGP2176 ATOM 2022 H SER B 16 3.899 61.765 15.266 1.00 0.00 1CGP2177 ATOM 2023 HG SER B 16 1.784 61.777 15.450 1.00 0.00 1CGP2178 ATOM 2024 N HIS B 17 5.329 64.745 16.425 1.00 95.39 1CGP2179 ATOM 2025 CA HIS B 17 6.154 65.862 16.868 1.00 94.15 1CGP2180 ATOM 2026 C HIS B 17 6.728 66.581 15.653 1.00 92.92 1CGP2181 ATOM 2027 O HIS B 17 7.325 67.663 15.743 1.00 92.62 1CGP2182 ATOM 2028 CB HIS B 17 7.286 65.355 17.751 1.00 94.95 1CGP2183 ATOM 2029 CG HIS B 17 6.801 64.750 19.064 1.00 96.53 1CGP2184 ATOM 2030 ND1 HIS B 17 7.073 65.099 20.326 1.00 96.64 1CGP2185 ATOM 2031 CD2 HIS B 17 5.957 63.662 19.123 1.00 96.83 1CGP2186 ATOM 2032 CE1 HIS B 17 6.425 64.268 21.119 1.00 96.90 1CGP2187 ATOM 2033 NE2 HIS B 17 5.760 63.407 20.383 1.00 96.92 1CGP2188 ATOM 2034 H HIS B 17 5.760 63.899 16.186 1.00 0.00 1CGP2189 ATOM 2035 HD1 HIS B 17 7.732 65.765 20.634 1.00 0.00 1CGP2190 ATOM 2036 HE2 HIS B 17 5.258 62.622 20.697 1.00 0.00 1CGP2191 ATOM 2037 N CYS B 18 6.527 65.980 14.491 1.00 91.76 1CGP2192 ATOM 2038 CA CYS B 18 7.027 66.498 13.255 1.00 91.51 1CGP2193 ATOM 2039 C CYS B 18 6.048 67.364 12.500 1.00 90.99 1CGP2194 ATOM 2040 O CYS B 18 4.856 67.478 12.756 1.00 90.34 1CGP2195 ATOM 2041 CB CYS B 18 7.483 65.331 12.413 1.00 92.28 1CGP2196 ATOM 2042 SG CYS B 18 8.960 64.644 13.192 1.00 93.12 1CGP2197 ATOM 2043 H CYS B 18 5.914 65.225 14.428 1.00 0.00 1CGP2198 ATOM 2044 N HIS B 19 6.646 68.101 11.587 1.00 91.56 1CGP2199 ATOM 2045 CA HIS B 19 5.958 69.158 10.870 1.00 92.43 1CGP2200 ATOM 2046 C HIS B 19 6.268 68.820 9.434 1.00 91.16 1CGP2201 ATOM 2047 O HIS B 19 7.452 68.842 9.071 1.00 91.41 1CGP2202 ATOM 2048 CB HIS B 19 6.550 70.539 11.259 1.00 94.71 1CGP2203 ATOM 2049 CG HIS B 19 7.442 70.473 12.509 1.00 97.83 1CGP2204 ATOM 2050 ND1 HIS B 19 8.776 70.490 12.618 1.00 99.17 1CGP2205 ATOM 2051 CD2 HIS B 19 6.959 70.243 13.780 1.00 99.18 1CGP2206 ATOM 2052 CE1 HIS B 19 9.102 70.266 13.875 1.00 99.27 1CGP2207 ATOM 2053 NE2 HIS B 19 7.998 70.096 14.565 1.00100.03 1CGP2208 ATOM 2054 H HIS B 19 7.593 67.921 11.395 1.00 0.00 1CGP2209 ATOM 2055 HD1 HIS B 19 9.410 70.467 11.873 1.00 0.00 1CGP2210 ATOM 2056 HE2 HIS B 19 7.923 69.585 15.403 1.00 0.00 1CGP2211 ATOM 2057 N ILE B 20 5.241 68.436 8.670 1.00 89.22 1CGP2212 ATOM 2058 CA ILE B 20 5.431 68.023 7.286 1.00 86.55 1CGP2213 ATOM 2059 C ILE B 20 5.394 69.220 6.345 1.00 85.09 1CGP2214 ATOM 2060 O ILE B 20 4.418 69.969 6.291 1.00 85.49 1CGP2215 ATOM 2061 CB ILE B 20 4.345 66.993 6.864 1.00 85.36 1CGP2216 ATOM 2062 CG1 ILE B 20 4.299 65.799 7.818 1.00 84.89 1CGP2217 ATOM 2063 CG2 ILE B 20 4.677 66.505 5.464 1.00 85.08 1CGP2218 ATOM 2064 CD1 ILE B 20 3.256 64.729 7.437 1.00 84.63 1CGP2219 ATOM 2065 H ILE B 20 4.318 68.513 8.999 1.00 0.00 1CGP2220 ATOM 2066 N HIS B 21 6.504 69.471 5.668 1.00 83.64 1CGP2221 ATOM 2067 CA HIS B 21 6.544 70.495 4.640 1.00 83.03 1CGP2222 ATOM 2068 C HIS B 21 6.500 69.774 3.312 1.00 81.13 1CGP2223 ATOM 2069 O HIS B 21 6.875 68.599 3.219 1.00 80.44 1CGP2224 ATOM 2070 CB HIS B 21 7.818 71.300 4.683 1.00 85.84 1CGP2225 ATOM 2071 CG HIS B 21 7.992 72.229 5.875 1.00 89.16 1CGP2226 ATOM 2072 ND1 HIS B 21 9.140 72.808 6.215 1.00 90.56 1CGP2227 ATOM 2073 CD2 HIS B 21 7.027 72.632 6.777 1.00 90.32 1CGP2228 ATOM 2074 CE1 HIS B 21 8.910 73.560 7.275 1.00 91.36 1CGP2229 ATOM 2075 NE2 HIS B 21 7.636 73.447 7.605 1.00 91.40 1CGP2230 ATOM 2076 H HIS B 21 7.288 68.898 5.838 1.00 0.00 1CGP2231 ATOM 2077 HD1 HIS B 21 10.007 72.595 5.791 1.00 0.00 1CGP2232 ATOM 2078 HE2 HIS B 21 7.184 73.962 8.311 1.00 0.00 1CGP2233 ATOM 2079 N LYS B 22 6.044 70.448 2.272 1.00 79.39 1CGP2234 ATOM 2080 CA LYS B 22 5.993 69.807 0.975 1.00 78.62 1CGP2235 ATOM 2081 C LYS B 22 7.082 70.474 0.139 1.00 75.23 1CGP2236 ATOM 2082 O LYS B 22 7.389 71.654 0.359 1.00 74.78 1CGP2237 ATOM 2083 CB LYS B 22 4.613 70.014 0.340 1.00 82.17 1CGP2238 ATOM 2084 CG LYS B 22 4.094 68.748 -0.359 1.00 85.30 1CGP2239 ATOM 2085 CD LYS B 22 3.559 68.967 -1.794 1.00 88.58 1CGP2240 ATOM 2086 CE LYS B 22 4.637 69.164 -2.885 1.00 89.56 1CGP2241 ATOM 2087 NZ LYS B 22 4.031 69.248 -4.211 1.00 90.54 1CGP2242 ATOM 2088 H LYS B 22 5.847 71.407 2.311 1.00 0.00 1CGP2243 ATOM 2089 1HZ LYS B 22 3.346 70.030 -4.218 1.00 0.00 1CGP2244 ATOM 2090 2HZ LYS B 22 3.537 68.358 -4.424 1.00 0.00 1CGP2245 ATOM 2091 3HZ LYS B 22 4.765 69.424 -4.928 1.00 0.00 1CGP2246 ATOM 2092 N TYR B 23 7.720 69.711 -0.750 1.00 70.12 1CGP2247 ATOM 2093 CA TYR B 23 8.785 70.198 -1.608 1.00 65.24 1CGP2248 ATOM 2094 C TYR B 23 8.519 69.616 -2.976 1.00 62.01 1CGP2249 ATOM 2095 O TYR B 23 8.299 68.410 -3.035 1.00 61.19 1CGP2250 ATOM 2096 CB TYR B 23 10.147 69.705 -1.146 1.00 64.61 1CGP2251 ATOM 2097 CG TYR B 23 10.580 70.167 0.243 1.00 64.71 1CGP2252 ATOM 2098 CD1 TYR B 23 10.167 69.497 1.384 1.00 64.86 1CGP2253 ATOM 2099 CD2 TYR B 23 11.404 71.258 0.379 1.00 63.83 1CGP2254 ATOM 2100 CE1 TYR B 23 10.574 69.905 2.642 1.00 64.41 1CGP2255 ATOM 2101 CE2 TYR B 23 11.815 71.660 1.638 1.00 64.37 1CGP2256 ATOM 2102 CZ TYR B 23 11.406 70.990 2.769 1.00 64.16 1CGP2257 ATOM 2103 OH TYR B 23 11.787 71.439 4.030 1.00 64.36 1CGP2258 ATOM 2104 H TYR B 23 7.509 68.754 -0.768 1.00 0.00 1CGP2259 ATOM 2105 HH TYR B 23 12.756 71.477 4.054 1.00 0.00 1CGP2260 ATOM 2106 N PRO B 24 8.471 70.375 -4.073 1.00 59.79 1CGP2261 ATOM 2107 CA PRO B 24 8.420 69.884 -5.444 1.00 59.50 1CGP2262 ATOM 2108 C PRO B 24 9.691 69.203 -5.940 1.00 60.21 1CGP2263 ATOM 2109 O PRO B 24 10.749 69.364 -5.333 1.00 60.35 1CGP2264 ATOM 2110 CB PRO B 24 8.089 71.102 -6.252 1.00 58.58 1CGP2265 ATOM 2111 CG PRO B 24 8.814 72.179 -5.492 1.00 58.18 1CGP2266 ATOM 2112 CD PRO B 24 8.386 71.823 -4.076 1.00 59.20 1CGP2267 ATOM 2113 N SER B 25 9.648 68.484 -7.065 1.00 60.52 1CGP2268 ATOM 2114 CA SER B 25 10.832 67.891 -7.678 1.00 60.16 1CGP2269 ATOM 2115 C SER B 25 11.807 69.017 -7.976 1.00 59.43 1CGP2270 ATOM 2116 O SER B 25 11.373 70.149 -8.212 1.00 60.25 1CGP2271 ATOM 2117 CB SER B 25 10.462 67.191 -8.976 1.00 60.64 1CGP2272 ATOM 2118 OG SER B 25 9.295 66.392 -8.798 1.00 63.25 1CGP2273 ATOM 2119 H SER B 25 8.802 68.335 -7.524 1.00 0.00 1CGP2274 ATOM 2120 HG SER B 25 8.989 66.129 -9.671 1.00 0.00 1CGP2275 ATOM 2121 N LYS B 26 13.100 68.700 -7.939 1.00 59.21 1CGP2276 ATOM 2122 CA LYS B 26 14.235 69.596 -8.114 1.00 59.50 1CGP2277 ATOM 2123 C LYS B 26 14.537 70.467 -6.891 1.00 57.05 1CGP2278 ATOM 2124 O LYS B 26 15.567 71.152 -6.873 1.00 56.24 1CGP2279 ATOM 2125 CB LYS B 26 14.039 70.510 -9.341 1.00 61.99 1CGP2280 ATOM 2126 CG LYS B 26 13.832 69.751 -10.654 1.00 65.41 1CGP2281 ATOM 2127 CD LYS B 26 12.484 70.136 -11.278 1.00 68.15 1CGP2282 ATOM 2128 CE LYS B 26 12.388 69.663 -12.725 1.00 70.06 1CGP2283 ATOM 2129 NZ LYS B 26 12.335 68.214 -12.840 1.00 72.65 1CGP2284 ATOM 2130 H LYS B 26 13.338 67.770 -7.759 1.00 0.00 1CGP2285 ATOM 2131 1HZ LYS B 26 11.530 67.847 -12.292 1.00 0.00 1CGP2286 ATOM 2132 2HZ LYS B 26 13.213 67.792 -12.477 1.00 0.00 1CGP2287 ATOM 2133 3HZ LYS B 26 12.216 67.955 -13.841 1.00 0.00 1CGP2288 ATOM 2134 N SER B 27 13.727 70.427 -5.823 1.00 54.14 1CGP2289 ATOM 2135 CA SER B 27 14.031 71.159 -4.602 1.00 53.16 1CGP2290 ATOM 2136 C SER B 27 15.333 70.737 -3.932 1.00 49.88 1CGP2291 ATOM 2137 O SER B 27 15.517 69.548 -3.683 1.00 47.51 1CGP2292 ATOM 2138 CB SER B 27 12.959 70.978 -3.538 1.00 55.53 1CGP2293 ATOM 2139 OG SER B 27 11.677 71.453 -3.882 1.00 57.70 1CGP2294 ATOM 2140 H SER B 27 12.872 69.954 -5.853 1.00 0.00 1CGP2295 ATOM 2141 HG SER B 27 11.348 70.807 -4.501 1.00 0.00 1CGP2296 ATOM 2142 N THR B 28 16.262 71.635 -3.645 1.00 47.24 1CGP2297 ATOM 2143 CA THR B 28 17.453 71.271 -2.919 1.00 45.69 1CGP2298 ATOM 2144 C THR B 28 17.094 71.378 -1.438 1.00 45.23 1CGP2299 ATOM 2145 O THR B 28 17.407 72.422 -0.863 1.00 47.43 1CGP2300 ATOM 2146 CB THR B 28 18.545 72.244 -3.359 1.00 44.16 1CGP2301 ATOM 2147 OG1 THR B 28 18.491 72.295 -4.787 1.00 44.10 1CGP2302 ATOM 2148 CG2 THR B 28 19.927 71.839 -2.868 1.00 44.69 1CGP2303 ATOM 2149 H THR B 28 16.212 72.535 -4.025 1.00 0.00 1CGP2304 ATOM 2150 HG1 THR B 28 18.402 71.416 -5.176 1.00 0.00 1CGP2305 ATOM 2151 N LEU B 29 16.503 70.344 -0.800 1.00 42.95 1CGP2306 ATOM 2152 CA LEU B 29 16.009 70.407 0.575 1.00 41.36 1CGP2307 ATOM 2153 C LEU B 29 17.087 70.626 1.622 1.00 42.23 1CGP2308 ATOM 2154 O LEU B 29 16.747 71.143 2.687 1.00 45.22 1CGP2309 ATOM 2155 CB LEU B 29 15.307 69.155 1.086 1.00 40.47 1CGP2310 ATOM 2156 CG LEU B 29 14.788 68.082 0.179 1.00 41.35 1CGP2311 ATOM 2157 CD1 LEU B 29 14.219 66.948 0.997 1.00 40.38 1CGP2312 ATOM 2158 CD2 LEU B 29 13.725 68.654 -0.702 1.00 41.79 1CGP2313 ATOM 2159 H LEU B 29 16.571 69.468 -1.230 1.00 0.00 1CGP2314 ATOM 2160 N ILE B 30 18.344 70.202 1.425 1.00 40.71 1CGP2315 ATOM 2161 CA ILE B 30 19.471 70.433 2.349 1.00 37.63 1CGP2316 ATOM 2162 C ILE B 30 20.562 71.060 1.498 1.00 39.13 1CGP2317 ATOM 2163 O ILE B 30 20.411 71.098 0.270 1.00 37.39 1CGP2318 ATOM 2164 CB ILE B 30 19.945 69.073 2.954 1.00 35.21 1CGP2319 ATOM 2165 CG1 ILE B 30 19.030 68.717 4.094 1.00 33.54 1CGP2320 ATOM 2166 CG2 ILE B 30 21.376 69.117 3.464 1.00 35.07 1CGP2321 ATOM 2167 CD1 ILE B 30 19.296 67.351 4.732 1.00 32.53 1CGP2322 ATOM 2168 H ILE B 30 18.504 69.734 0.581 1.00 0.00 1CGP2323 ATOM 2169 N HIS B 31 21.625 71.659 2.015 1.00 41.79 1CGP2324 ATOM 2170 CA HIS B 31 22.731 72.106 1.177 1.00 46.54 1CGP2325 ATOM 2171 C HIS B 31 23.997 71.853 1.967 1.00 49.77 1CGP2326 ATOM 2172 O HIS B 31 23.961 72.085 3.176 1.00 50.99 1CGP2327 ATOM 2173 CB HIS B 31 22.691 73.594 0.874 1.00 47.58 1CGP2328 ATOM 2174 CG HIS B 31 21.585 74.108 -0.051 1.00 49.48 1CGP2329 ATOM 2175 ND1 HIS B 31 20.260 73.903 -0.044 1.00 49.99 1CGP2330 ATOM 2176 CD2 HIS B 31 21.847 74.977 -1.084 1.00 49.34 1CGP2331 ATOM 2177 CE1 HIS B 31 19.724 74.619 -0.996 1.00 49.74 1CGP2332 ATOM 2178 NE2 HIS B 31 20.689 75.241 -1.628 1.00 50.44 1CGP2333 ATOM 2179 H HIS B 31 21.741 71.750 2.990 1.00 0.00 1CGP2334 ATOM 2180 HD1 HIS B 31 19.781 73.134 0.342 1.00 0.00 1CGP2335 ATOM 2181 HE2 HIS B 31 20.571 75.641 -2.515 1.00 0.00 1CGP2336 ATOM 2182 N GLN B 32 25.101 71.393 1.361 1.00 53.14 1CGP2337 ATOM 2183 CA GLN B 32 26.350 71.154 2.077 1.00 55.56 1CGP2338 ATOM 2184 C GLN B 32 26.896 72.478 2.555 1.00 58.06 1CGP2339 ATOM 2185 O GLN B 32 26.760 73.461 1.828 1.00 60.22 1CGP2340 ATOM 2186 CB GLN B 32 27.403 70.548 1.191 1.00 55.84 1CGP2341 ATOM 2187 CG GLN B 32 28.731 70.407 1.894 1.00 59.62 1CGP2342 ATOM 2188 CD GLN B 32 29.880 70.136 0.959 1.00 62.94 1CGP2343 ATOM 2189 OE1 GLN B 32 30.535 71.061 0.485 1.00 65.39 1CGP2344 ATOM 2190 NE2 GLN B 32 30.205 68.883 0.662 1.00 65.10 1CGP2345 ATOM 2191 H GLN B 32 25.103 71.276 0.388 1.00 0.00 1CGP2346 ATOM 2192 1HE2 GLN B 32 29.703 68.164 1.107 1.00 0.00 1CGP2347 ATOM 2193 2HE2 GLN B 32 30.944 68.741 0.038 1.00 0.00 1CGP2348 ATOM 2194 N GLY B 33 27.490 72.523 3.741 1.00 60.69 1CGP2349 ATOM 2195 CA GLY B 33 28.117 73.741 4.231 1.00 63.06 1CGP2350 ATOM 2196 C GLY B 33 27.324 74.545 5.262 1.00 64.29 1CGP2351 ATOM 2197 O GLY B 33 27.923 75.334 5.996 1.00 66.26 1CGP2352 ATOM 2198 H GLY B 33 27.523 71.692 4.258 1.00 0.00 1CGP2353 ATOM 2199 N GLU B 34 25.996 74.433 5.375 1.00 65.04 1CGP2354 ATOM 2200 CA GLU B 34 25.231 75.173 6.382 1.00 65.47 1CGP2355 ATOM 2201 C GLU B 34 25.330 74.370 7.674 1.00 64.81 1CGP2356 ATOM 2202 O GLU B 34 25.966 73.314 7.702 1.00 66.40 1CGP2357 ATOM 2203 CB GLU B 34 23.767 75.256 6.031 1.00 66.48 1CGP2358 ATOM 2204 CG GLU B 34 23.383 75.465 4.583 1.00 69.17 1CGP2359 ATOM 2205 CD GLU B 34 21.956 74.961 4.382 1.00 71.94 1CGP2360 ATOM 2206 OE1 GLU B 34 21.027 75.752 4.585 1.00 73.68 1CGP2361 ATOM 2207 OE2 GLU B 34 21.769 73.781 4.054 1.00 72.45 1CGP2362 ATOM 2208 H GLU B 34 25.529 73.791 4.801 1.00 0.00 1CGP2363 ATOM 2209 N LYS B 35 24.647 74.726 8.739 1.00 63.16 1CGP2364 ATOM 2210 CA LYS B 35 24.760 73.948 9.943 1.00 64.25 1CGP2365 ATOM 2211 C LYS B 35 23.501 73.110 10.051 1.00 61.78 1CGP2366 ATOM 2212 O LYS B 35 22.467 73.442 9.467 1.00 58.19 1CGP2367 ATOM 2213 CB LYS B 35 24.935 74.881 11.140 1.00 69.78 1CGP2368 ATOM 2214 CG LYS B 35 23.799 75.873 11.366 1.00 76.24 1CGP2369 ATOM 2215 CD LYS B 35 23.887 77.111 10.463 1.00 80.63 1CGP2370 ATOM 2216 CE LYS B 35 22.520 77.492 9.853 1.00 83.51 1CGP2371 ATOM 2217 NZ LYS B 35 22.199 76.727 8.650 1.00 84.52 1CGP2372 ATOM 2218 H LYS B 35 23.920 75.372 8.658 1.00 0.00 1CGP2373 ATOM 2219 1HZ LYS B 35 22.119 75.715 8.869 1.00 0.00 1CGP2374 ATOM 2220 2HZ LYS B 35 22.963 76.875 7.959 1.00 0.00 1CGP2375 ATOM 2221 3HZ LYS B 35 21.306 77.083 8.255 1.00 0.00 1CGP2376 ATOM 2222 N ALA B 36 23.621 71.998 10.757 1.00 61.77 1CGP2377 ATOM 2223 CA ALA B 36 22.549 71.047 10.942 1.00 63.70 1CGP2378 ATOM 2224 C ALA B 36 21.851 71.140 12.278 1.00 65.57 1CGP2379 ATOM 2225 O ALA B 36 22.419 71.058 13.364 1.00 65.65 1CGP2380 ATOM 2226 CB ALA B 36 23.084 69.641 10.790 1.00 64.02 1CGP2381 ATOM 2227 H ALA B 36 24.499 71.772 11.125 1.00 0.00 1CGP2382 ATOM 2228 N GLU B 37 20.547 71.234 12.168 1.00 68.19 1CGP2383 ATOM 2229 CA GLU B 37 19.685 71.489 13.298 1.00 70.20 1CGP2384 ATOM 2230 C GLU B 37 18.458 70.613 13.194 1.00 69.82 1CGP2385 ATOM 2231 O GLU B 37 17.817 70.307 14.196 1.00 71.16 1CGP2386 ATOM 2232 CB GLU B 37 19.219 72.934 13.303 1.00 73.65 1CGP2387 ATOM 2233 CG GLU B 37 19.912 73.951 12.353 1.00 79.71 1CGP2388 ATOM 2234 CD GLU B 37 19.656 73.898 10.823 1.00 82.79 1CGP2389 ATOM 2235 OE1 GLU B 37 19.364 72.841 10.241 1.00 82.91 1CGP2390 ATOM 2236 OE2 GLU B 37 19.780 74.959 10.194 1.00 85.06 1CGP2391 ATOM 2237 H GLU B 37 20.150 71.160 11.281 1.00 0.00 1CGP2392 ATOM 2238 N THR B 38 18.120 70.163 11.997 1.00 68.44 1CGP2393 ATOM 2239 CA THR B 38 16.886 69.442 11.730 1.00 66.39 1CGP2394 ATOM 2240 C THR B 38 17.138 68.020 11.255 1.00 64.29 1CGP2395 ATOM 2241 O THR B 38 18.036 67.827 10.434 1.00 65.35 1CGP2396 ATOM 2242 CB THR B 38 16.112 70.213 10.652 1.00 66.59 1CGP2397 ATOM 2243 OG1 THR B 38 16.803 71.450 10.418 1.00 67.84 1CGP2398 ATOM 2244 CG2 THR B 38 14.668 70.418 11.053 1.00 66.64 1CGP2399 ATOM 2245 H THR B 38 18.662 70.365 11.212 1.00 0.00 1CGP2400 ATOM 2246 HG1 THR B 38 16.210 72.178 10.630 1.00 0.00 1CGP2401 ATOM 2247 N LEU B 39 16.412 67.026 11.734 1.00 61.28 1CGP2402 ATOM 2248 CA LEU B 39 16.545 65.669 11.235 1.00 60.12 1CGP2403 ATOM 2249 C LEU B 39 15.358 65.577 10.310 1.00 59.42 1CGP2404 ATOM 2250 O LEU B 39 14.284 66.007 10.721 1.00 62.62 1CGP2405 ATOM 2251 CB LEU B 39 16.377 64.663 12.337 1.00 61.21 1CGP2406 ATOM 2252 CG LEU B 39 16.125 63.212 11.943 1.00 62.51 1CGP2407 ATOM 2253 CD1 LEU B 39 17.421 62.525 11.595 1.00 63.84 1CGP2408 ATOM 2254 CD2 LEU B 39 15.526 62.466 13.112 1.00 63.33 1CGP2409 ATOM 2255 H LEU B 39 15.632 67.243 12.285 1.00 0.00 1CGP2410 ATOM 2256 N TYR B 40 15.436 65.054 9.106 1.00 57.87 1CGP2411 ATOM 2257 CA TYR B 40 14.273 65.041 8.240 1.00 56.63 1CGP2412 ATOM 2258 C TYR B 40 13.842 63.590 8.095 1.00 55.61 1CGP2413 ATOM 2259 O TYR B 40 14.709 62.726 8.117 1.00 56.14 1CGP2414 ATOM 2260 CB TYR B 40 14.642 65.637 6.867 1.00 56.56 1CGP2415 ATOM 2261 CG TYR B 40 15.170 67.079 6.853 1.00 56.62 1CGP2416 ATOM 2262 CD1 TYR B 40 16.365 67.409 7.472 1.00 56.83 1CGP2417 ATOM 2263 CD2 TYR B 40 14.449 68.084 6.230 1.00 56.63 1CGP2418 ATOM 2264 CE1 TYR B 40 16.829 68.714 7.463 1.00 57.27 1CGP2419 ATOM 2265 CE2 TYR B 40 14.904 69.395 6.218 1.00 56.99 1CGP2420 ATOM 2266 CZ TYR B 40 16.100 69.709 6.837 1.00 57.27 1CGP2421 ATOM 2267 OH TYR B 40 16.547 71.021 6.863 1.00 56.80 1CGP2422 ATOM 2268 H TYR B 40 16.240 64.574 8.830 1.00 0.00 1CGP2423 ATOM 2269 HH TYR B 40 17.161 71.144 7.594 1.00 0.00 1CGP2424 ATOM 2270 N TYR B 41 12.574 63.225 8.028 1.00 54.57 1CGP2425 ATOM 2271 CA TYR B 41 12.148 61.869 7.716 1.00 54.55 1CGP2426 ATOM 2272 C TYR B 41 11.230 61.942 6.491 1.00 55.54 1CGP2427 ATOM 2273 O TYR B 41 10.280 62.729 6.441 1.00 56.55 1CGP2428 ATOM 2274 CB TYR B 41 11.421 61.283 8.913 1.00 53.13 1CGP2429 ATOM 2275 CG TYR B 41 10.820 59.907 8.687 1.00 54.01 1CGP2430 ATOM 2276 CD1 TYR B 41 9.583 59.781 8.081 1.00 54.86 1CGP2431 ATOM 2277 CD2 TYR B 41 11.497 58.784 9.103 1.00 54.71 1CGP2432 ATOM 2278 CE1 TYR B 41 9.016 58.541 7.891 1.00 56.28 1CGP2433 ATOM 2279 CE2 TYR B 41 10.938 57.532 8.921 1.00 56.08 1CGP2434 ATOM 2280 CZ TYR B 41 9.695 57.418 8.315 1.00 57.04 1CGP2435 ATOM 2281 OH TYR B 41 9.098 56.175 8.134 1.00 58.90 1CGP2436 ATOM 2282 H TYR B 41 11.893 63.872 8.304 1.00 0.00 1CGP2437 ATOM 2283 HH TYR B 41 8.246 56.299 7.708 1.00 0.00 1CGP2438 ATOM 2284 N ILE B 42 11.461 61.118 5.475 1.00 56.36 1CGP2439 ATOM 2285 CA ILE B 42 10.686 61.150 4.236 1.00 56.27 1CGP2440 ATOM 2286 C ILE B 42 9.371 60.422 4.428 1.00 55.55 1CGP2441 ATOM 2287 O ILE B 42 9.294 59.193 4.496 1.00 54.28 1CGP2442 ATOM 2288 CB ILE B 42 11.465 60.498 3.031 1.00 57.16 1CGP2443 ATOM 2289 CG1 ILE B 42 12.855 61.115 2.855 1.00 57.82 1CGP2444 ATOM 2290 CG2 ILE B 42 10.703 60.758 1.735 1.00 56.23 1CGP2445 ATOM 2291 CD1 ILE B 42 13.713 60.557 1.703 1.00 57.28 1CGP2446 ATOM 2292 H ILE B 42 12.189 60.467 5.594 1.00 0.00 1CGP2447 ATOM 2293 N VAL B 43 8.337 61.238 4.496 1.00 55.43 1CGP2448 ATOM 2294 CA VAL B 43 6.975 60.766 4.576 1.00 55.09 1CGP2449 ATOM 2295 C VAL B 43 6.715 60.248 3.169 1.00 55.67 1CGP2450 ATOM 2296 O VAL B 43 6.422 59.068 2.984 1.00 55.80 1CGP2451 ATOM 2297 CB VAL B 43 6.032 61.931 4.904 1.00 55.24 1CGP2452 ATOM 2298 CG1 VAL B 43 4.601 61.464 4.897 1.00 56.11 1CGP2453 ATOM 2299 CG2 VAL B 43 6.335 62.465 6.278 1.00 55.96 1CGP2454 ATOM 2300 H VAL B 43 8.472 62.194 4.337 1.00 0.00 1CGP2455 ATOM 2301 N LYS B 44 6.910 61.067 2.139 1.00 56.16 1CGP2456 ATOM 2302 CA LYS B 44 6.628 60.644 0.775 1.00 57.91 1CGP2457 ATOM 2303 C LYS B 44 7.642 61.220 -0.211 1.00 57.01 1CGP2458 ATOM 2304 O LYS B 44 8.105 62.329 0.057 1.00 57.38 1CGP2459 ATOM 2305 CB LYS B 44 5.244 61.120 0.449 1.00 61.39 1CGP2460 ATOM 2306 CG LYS B 44 4.648 60.738 -0.894 1.00 65.24 1CGP2461 ATOM 2307 CD LYS B 44 3.616 61.813 -1.209 1.00 68.30 1CGP2462 ATOM 2308 CE LYS B 44 2.424 61.842 -0.228 1.00 70.37 1CGP2463 ATOM 2309 NZ LYS B 44 1.749 63.134 -0.270 1.00 70.84 1CGP2464 ATOM 2310 H LYS B 44 7.310 61.946 2.312 1.00 0.00 1CGP2465 ATOM 2311 1HZ LYS B 44 1.418 63.335 -1.235 1.00 0.00 1CGP2466 ATOM 2312 2HZ LYS B 44 2.422 63.865 0.035 1.00 0.00 1CGP2467 ATOM 2313 3HZ LYS B 44 0.942 63.113 0.385 1.00 0.00 1CGP2468 ATOM 2314 N GLY B 45 7.998 60.516 -1.302 1.00 55.23 1CGP2469 ATOM 2315 CA GLY B 45 8.897 61.007 -2.352 1.00 52.04 1CGP2470 ATOM 2316 C GLY B 45 10.212 60.233 -2.470 1.00 48.73 1CGP2471 ATOM 2317 O GLY B 45 10.376 59.157 -1.883 1.00 49.05 1CGP2472 ATOM 2318 H GLY B 45 7.696 59.591 -1.383 1.00 0.00 1CGP2473 ATOM 2319 N SER B 46 11.143 60.698 -3.292 1.00 45.97 1CGP2474 ATOM 2320 CA SER B 46 12.476 60.134 -3.359 1.00 43.54 1CGP2475 ATOM 2321 C SER B 46 13.445 61.289 -3.506 1.00 42.33 1CGP2476 ATOM 2322 O SER B 46 13.178 62.263 -4.227 1.00 42.13 1CGP2477 ATOM 2323 CB SER B 46 12.671 59.205 -4.553 1.00 43.70 1CGP2478 ATOM 2324 OG SER B 46 11.642 59.082 -5.535 1.00 45.78 1CGP2479 ATOM 2325 H SER B 46 10.928 61.440 -3.899 1.00 0.00 1CGP2480 ATOM 2326 HG SER B 46 11.084 59.861 -5.502 1.00 0.00 1CGP2481 ATOM 2327 N VAL B 47 14.592 61.170 -2.865 1.00 39.69 1CGP2482 ATOM 2328 CA VAL B 47 15.582 62.218 -2.852 1.00 37.27 1CGP2483 ATOM 2329 C VAL B 47 16.966 61.696 -3.271 1.00 36.62 1CGP2484 ATOM 2330 O VAL B 47 17.206 60.486 -3.227 1.00 36.11 1CGP2485 ATOM 2331 CB VAL B 47 15.421 62.737 -1.426 1.00 36.84 1CGP2486 ATOM 2332 CG1 VAL B 47 16.380 62.075 -0.476 1.00 36.26 1CGP2487 ATOM 2333 CG2 VAL B 47 15.526 64.224 -1.489 1.00 37.67 1CGP2488 ATOM 2334 H VAL B 47 14.791 60.355 -2.369 1.00 0.00 1CGP2489 ATOM 2335 N ALA B 48 17.870 62.573 -3.714 1.00 35.37 1CGP2490 ATOM 2336 CA ALA B 48 19.214 62.236 -4.157 1.00 33.40 1CGP2491 ATOM 2337 C ALA B 48 20.268 63.002 -3.377 1.00 34.17 1CGP2492 ATOM 2338 O ALA B 48 20.222 64.231 -3.312 1.00 35.42 1CGP2493 ATOM 2339 CB ALA B 48 19.362 62.587 -5.608 1.00 31.03 1CGP2494 ATOM 2340 H ALA B 48 17.588 63.503 -3.824 1.00 0.00 1CGP2495 ATOM 2341 N VAL B 49 21.206 62.314 -2.751 1.00 34.01 1CGP2496 ATOM 2342 CA VAL B 49 22.260 62.949 -1.986 1.00 34.20 1CGP2497 ATOM 2343 C VAL B 49 23.385 63.212 -2.980 1.00 35.94 1CGP2498 ATOM 2344 O VAL B 49 23.743 62.321 -3.748 1.00 35.79 1CGP2499 ATOM 2345 CB VAL B 49 22.683 61.972 -0.850 1.00 33.78 1CGP2500 ATOM 2346 CG1 VAL B 49 23.941 62.408 -0.119 1.00 33.25 1CGP2501 ATOM 2347 CG2 VAL B 49 21.576 61.945 0.178 1.00 32.34 1CGP2502 ATOM 2348 H VAL B 49 21.226 61.348 -2.886 1.00 0.00 1CGP2503 ATOM 2349 N LEU B 50 24.011 64.376 -2.974 1.00 38.62 1CGP2504 ATOM 2350 CA LEU B 50 25.112 64.724 -3.871 1.00 40.80 1CGP2505 ATOM 2351 C LEU B 50 26.304 65.432 -3.227 1.00 40.86 1CGP2506 ATOM 2352 O LEU B 50 26.198 66.193 -2.263 1.00 38.51 1CGP2507 ATOM 2353 CB LEU B 50 24.699 65.674 -4.931 1.00 43.34 1CGP2508 ATOM 2354 CG LEU B 50 23.525 65.526 -5.802 1.00 44.45 1CGP2509 ATOM 2355 CD1 LEU B 50 23.024 66.921 -6.021 1.00 45.30 1CGP2510 ATOM 2356 CD2 LEU B 50 23.875 64.860 -7.118 1.00 45.66 1CGP2511 ATOM 2357 H LEU B 50 23.697 65.032 -2.324 1.00 0.00 1CGP2512 ATOM 2358 N ILE B 51 27.469 65.224 -3.792 1.00 42.17 1CGP2513 ATOM 2359 CA ILE B 51 28.614 66.019 -3.431 1.00 45.96 1CGP2514 ATOM 2360 C ILE B 51 29.120 66.597 -4.731 1.00 51.81 1CGP2515 ATOM 2361 O ILE B 51 28.917 65.986 -5.777 1.00 51.63 1CGP2516 ATOM 2362 CB ILE B 51 29.744 65.227 -2.794 1.00 43.19 1CGP2517 ATOM 2363 CG1 ILE B 51 29.845 63.788 -3.195 1.00 41.16 1CGP2518 ATOM 2364 CG2 ILE B 51 29.493 65.433 -1.334 1.00 44.48 1CGP2519 ATOM 2365 CD1 ILE B 51 31.167 63.192 -2.730 1.00 40.09 1CGP2520 ATOM 2366 H ILE B 51 27.538 64.529 -4.488 1.00 0.00 1CGP2521 ATOM 2367 N LYS B 52 29.764 67.765 -4.708 1.00 59.71 1CGP2522 ATOM 2368 CA LYS B 52 30.183 68.450 -5.919 1.00 65.45 1CGP2523 ATOM 2369 C LYS B 52 31.687 68.580 -5.898 1.00 67.41 1CGP2524 ATOM 2370 O LYS B 52 32.323 68.774 -4.859 1.00 67.35 1CGP2525 ATOM 2371 CB LYS B 52 29.597 69.871 -6.021 1.00 68.54 1CGP2526 ATOM 2372 CG LYS B 52 28.068 70.050 -6.074 1.00 71.93 1CGP2527 ATOM 2373 CD LYS B 52 27.612 71.384 -6.708 1.00 75.47 1CGP2528 ATOM 2374 CE LYS B 52 27.992 72.721 -5.994 1.00 77.93 1CGP2529 ATOM 2375 NZ LYS B 52 29.361 73.209 -6.189 1.00 78.76 1CGP2530 ATOM 2376 H LYS B 52 30.105 68.131 -3.866 1.00 0.00 1CGP2531 ATOM 2377 1HZ LYS B 52 29.542 73.349 -7.202 1.00 0.00 1CGP2532 ATOM 2378 2HZ LYS B 52 30.043 72.514 -5.820 1.00 0.00 1CGP2533 ATOM 2379 3HZ LYS B 52 29.489 74.110 -5.686 1.00 0.00 1CGP2534 ATOM 2380 N ASP B 53 32.244 68.414 -7.074 1.00 71.41 1CGP2535 ATOM 2381 CA ASP B 53 33.652 68.556 -7.299 1.00 75.86 1CGP2536 ATOM 2382 C ASP B 53 34.069 69.964 -6.951 1.00 78.07 1CGP2537 ATOM 2383 O ASP B 53 33.347 70.934 -7.202 1.00 77.08 1CGP2538 ATOM 2384 CB ASP B 53 33.878 68.230 -8.753 1.00 78.57 1CGP2539 ATOM 2385 CG ASP B 53 35.253 68.523 -9.301 1.00 80.86 1CGP2540 ATOM 2386 OD1 ASP B 53 36.165 67.719 -9.094 1.00 82.88 1CGP2541 ATOM 2387 OD2 ASP B 53 35.396 69.561 -9.942 1.00 81.92 1CGP2542 ATOM 2388 H ASP B 53 31.683 68.193 -7.842 1.00 0.00 1CGP2543 ATOM 2389 N GLU B 54 35.341 70.025 -6.542 1.00 81.96 1CGP2544 ATOM 2390 CA GLU B 54 36.012 71.243 -6.073 1.00 85.61 1CGP2545 ATOM 2391 C GLU B 54 35.966 72.496 -6.949 1.00 85.33 1CGP2546 ATOM 2392 O GLU B 54 36.551 73.515 -6.580 1.00 85.90 1CGP2547 ATOM 2393 CB GLU B 54 37.519 70.983 -5.767 1.00 88.05 1CGP2548 ATOM 2394 CG GLU B 54 37.903 70.117 -4.541 1.00 90.51 1CGP2549 ATOM 2395 CD GLU B 54 37.839 68.596 -4.749 1.00 92.06 1CGP2550 ATOM 2396 OE1 GLU B 54 38.337 68.107 -5.776 1.00 92.55 1CGP2551 ATOM 2397 OE2 GLU B 54 37.305 67.902 -3.875 1.00 91.97 1CGP2552 ATOM 2398 H GLU B 54 35.849 69.193 -6.533 1.00 0.00 1CGP2553 ATOM 2399 N GLU B 55 35.325 72.382 -8.114 1.00 84.41 1CGP2554 ATOM 2400 CA GLU B 55 35.017 73.445 -9.045 1.00 83.33 1CGP2555 ATOM 2401 C GLU B 55 34.429 72.610 -10.183 1.00 80.20 1CGP2556 ATOM 2402 O GLU B 55 35.095 72.415 -11.206 1.00 79.89 1CGP2557 ATOM 2403 CB GLU B 55 36.294 74.202 -9.512 1.00 86.39 1CGP2558 ATOM 2404 CG GLU B 55 36.239 75.746 -9.372 1.00 89.89 1CGP2559 ATOM 2405 CD GLU B 55 36.482 76.335 -7.964 1.00 91.89 1CGP2560 ATOM 2406 OE1 GLU B 55 35.539 76.434 -7.154 1.00 92.23 1CGP2561 ATOM 2407 OE2 GLU B 55 37.632 76.714 -7.694 1.00 92.35 1CGP2562 ATOM 2408 H GLU B 55 35.039 71.491 -8.380 1.00 0.00 1CGP2563 ATOM 2409 N GLY B 56 33.253 71.983 -10.037 1.00 75.86 1CGP2564 ATOM 2410 CA GLY B 56 32.761 71.192 -11.166 1.00 71.82 1CGP2565 ATOM 2411 C GLY B 56 31.591 70.233 -10.939 1.00 67.99 1CGP2566 ATOM 2412 O GLY B 56 30.755 70.497 -10.067 1.00 69.64 1CGP2567 ATOM 2413 H GLY B 56 32.746 72.012 -9.193 1.00 0.00 1CGP2568 ATOM 2414 N LYS B 57 31.546 69.091 -11.679 1.00 60.40 1CGP2569 ATOM 2415 CA LYS B 57 30.342 68.260 -11.699 1.00 52.83 1CGP2570 ATOM 2416 C LYS B 57 30.137 67.603 -10.340 1.00 47.46 1CGP2571 ATOM 2417 O LYS B 57 30.985 67.580 -9.455 1.00 43.99 1CGP2572 ATOM 2418 CB LYS B 57 30.403 67.157 -12.869 1.00 54.75 1CGP2573 ATOM 2419 CG LYS B 57 29.083 66.752 -13.752 1.00 52.77 1CGP2574 ATOM 2420 CD LYS B 57 29.073 65.544 -14.820 1.00 47.71 1CGP2575 ATOM 2421 CE LYS B 57 27.990 65.683 -15.951 1.00 44.45 1CGP2576 ATOM 2422 NZ LYS B 57 28.030 64.758 -17.085 1.00 36.08 1CGP2577 ATOM 2423 H LYS B 57 32.358 68.790 -12.125 1.00 0.00 1CGP2578 ATOM 2424 1HZ LYS B 57 27.873 63.786 -16.749 1.00 0.00 1CGP2579 ATOM 2425 2HZ LYS B 57 28.953 64.806 -17.563 1.00 0.00 1CGP2580 ATOM 2426 3HZ LYS B 57 27.283 65.005 -17.768 1.00 0.00 1CGP2581 ATOM 2427 N GLU B 58 28.950 67.098 -10.173 1.00 41.94 1CGP2582 ATOM 2428 CA GLU B 58 28.557 66.529 -8.927 1.00 39.63 1CGP2583 ATOM 2429 C GLU B 58 28.456 65.036 -9.089 1.00 37.75 1CGP2584 ATOM 2430 O GLU B 58 28.278 64.590 -10.207 1.00 37.89 1CGP2585 ATOM 2431 CB GLU B 58 27.253 67.134 -8.568 1.00 41.78 1CGP2586 ATOM 2432 CG GLU B 58 26.297 67.132 -9.736 1.00 44.78 1CGP2587 ATOM 2433 CD GLU B 58 25.084 68.009 -9.552 1.00 47.91 1CGP2588 ATOM 2434 OE1 GLU B 58 25.206 69.094 -8.969 1.00 50.38 1CGP2589 ATOM 2435 OE2 GLU B 58 24.020 67.594 -10.019 1.00 49.97 1CGP2590 ATOM 2436 H GLU B 58 28.387 66.939 -10.953 1.00 0.00 1CGP2591 ATOM 2437 N MET B 59 28.549 64.245 -8.036 1.00 37.88 1CGP2592 ATOM 2438 CA MET B 59 28.428 62.807 -8.044 1.00 37.10 1CGP2593 ATOM 2439 C MET B 59 27.302 62.434 -7.087 1.00 37.91 1CGP2594 ATOM 2440 O MET B 59 27.291 62.893 -5.945 1.00 39.17 1CGP2595 ATOM 2441 CB MET B 59 29.711 62.197 -7.576 1.00 36.99 1CGP2596 ATOM 2442 CG MET B 59 29.456 60.756 -7.274 1.00 39.14 1CGP2597 ATOM 2443 SD MET B 59 30.929 59.886 -6.783 1.00 43.70 1CGP2598 ATOM 2444 CE MET B 59 31.100 59.082 -8.344 1.00 44.89 1CGP2599 ATOM 2445 H MET B 59 28.682 64.699 -7.185 1.00 0.00 1CGP2600 ATOM 2446 N ILE B 60 26.389 61.553 -7.489 1.00 38.11 1CGP2601 ATOM 2447 CA ILE B 60 25.258 61.194 -6.659 1.00 36.75 1CGP2602 ATOM 2448 C ILE B 60 25.689 60.110 -5.674 1.00 36.25 1CGP2603 ATOM 2449 O ILE B 60 26.021 59.015 -6.095 1.00 35.52 1CGP2604 ATOM 2450 CB ILE B 60 24.099 60.665 -7.527 1.00 36.73 1CGP2605 ATOM 2451 CG1 ILE B 60 23.666 61.580 -8.666 1.00 36.99 1CGP2606 ATOM 2452 CG2 ILE B 60 22.925 60.577 -6.597 1.00 38.73 1CGP2607 ATOM 2453 CD1 ILE B 60 22.480 61.050 -9.506 1.00 34.68 1CGP2608 ATOM 2454 H ILE B 60 26.600 61.012 -8.282 1.00 0.00 1CGP2609 ATOM 2455 N LEU B 61 25.668 60.334 -4.368 1.00 37.23 1CGP2610 ATOM 2456 CA LEU B 61 26.056 59.325 -3.397 1.00 37.08 1CGP2611 ATOM 2457 C LEU B 61 24.965 58.330 -3.127 1.00 38.73 1CGP2612 ATOM 2458 O LEU B 61 25.355 57.243 -2.720 1.00 41.70 1CGP2613 ATOM 2459 CB LEU B 61 26.395 59.855 -2.034 1.00 36.78 1CGP2614 ATOM 2460 CG LEU B 61 27.687 60.545 -1.836 1.00 36.13 1CGP2615 ATOM 2461 CD1 LEU B 61 27.748 60.950 -0.377 1.00 34.98 1CGP2616 ATOM 2462 CD2 LEU B 61 28.821 59.658 -2.324 1.00 36.00 1CGP2617 ATOM 2463 H LEU B 61 25.250 61.169 -4.093 1.00 0.00 1CGP2618 ATOM 2464 N SER B 62 23.659 58.635 -3.144 1.00 38.77 1CGP2619 ATOM 2465 CA SER B 62 22.604 57.616 -3.109 1.00 39.44 1CGP2620 ATOM 2466 C SER B 62 21.258 58.264 -3.250 1.00 39.55 1CGP2621 ATOM 2467 O SER B 62 21.175 59.499 -3.250 1.00 38.94 1CGP2622 ATOM 2468 CB SER B 62 22.529 56.771 -1.812 1.00 40.22 1CGP2623 ATOM 2469 OG SER B 62 22.385 57.483 -0.606 1.00 43.04 1CGP2624 ATOM 2470 H SER B 62 23.380 59.573 -3.205 1.00 0.00 1CGP2625 ATOM 2471 HG SER B 62 23.234 57.497 -0.159 1.00 0.00 1CGP2626 ATOM 2472 N TYR B 63 20.252 57.421 -3.464 1.00 40.49 1CGP2627 ATOM 2473 CA TYR B 63 18.869 57.851 -3.494 1.00 42.15 1CGP2628 ATOM 2474 C TYR B 63 18.340 57.422 -2.138 1.00 43.70 1CGP2629 ATOM 2475 O TYR B 63 18.746 56.381 -1.616 1.00 45.45 1CGP2630 ATOM 2476 CB TYR B 63 18.081 57.137 -4.541 1.00 40.17 1CGP2631 ATOM 2477 CG TYR B 63 18.593 57.474 -5.902 1.00 39.91 1CGP2632 ATOM 2478 CD1 TYR B 63 18.279 58.697 -6.394 1.00 42.32 1CGP2633 ATOM 2479 CD2 TYR B 63 19.310 56.570 -6.637 1.00 40.11 1CGP2634 ATOM 2480 CE1 TYR B 63 18.682 59.029 -7.657 1.00 43.98 1CGP2635 ATOM 2481 CE2 TYR B 63 19.716 56.891 -7.902 1.00 40.67 1CGP2636 ATOM 2482 CZ TYR B 63 19.391 58.122 -8.394 1.00 43.03 1CGP2637 ATOM 2483 OH TYR B 63 19.750 58.474 -9.668 1.00 45.24 1CGP2638 ATOM 2484 H TYR B 63 20.394 56.452 -3.411 1.00 0.00 1CGP2639 ATOM 2485 HH TYR B 63 19.359 59.320 -9.881 1.00 0.00 1CGP2640 ATOM 2486 N LEU B 64 17.509 58.216 -1.507 1.00 44.99 1CGP2641 ATOM 2487 CA LEU B 64 16.916 57.863 -0.239 1.00 46.95 1CGP2642 ATOM 2488 C LEU B 64 15.455 57.950 -0.566 1.00 50.64 1CGP2643 ATOM 2489 O LEU B 64 15.063 58.896 -1.260 1.00 51.28 1CGP2644 ATOM 2490 CB LEU B 64 17.297 58.876 0.800 1.00 44.53 1CGP2645 ATOM 2491 CG LEU B 64 18.370 58.529 1.800 1.00 43.62 1CGP2646 ATOM 2492 CD1 LEU B 64 19.567 57.874 1.155 1.00 43.10 1CGP2647 ATOM 2493 CD2 LEU B 64 18.784 59.818 2.468 1.00 44.45 1CGP2648 ATOM 2494 H LEU B 64 17.247 59.044 -1.956 1.00 0.00 1CGP2649 ATOM 2495 N ASN B 65 14.633 56.987 -0.155 1.00 54.76 1CGP2650 ATOM 2496 CA ASN B 65 13.215 57.049 -0.487 1.00 58.21 1CGP2651 ATOM 2497 C ASN B 65 12.405 57.208 0.782 1.00 59.90 1CGP2652 ATOM 2498 O ASN B 65 12.963 57.434 1.868 1.00 58.80 1CGP2653 ATOM 2499 CB ASN B 65 12.730 55.790 -1.210 1.00 58.83 1CGP2654 ATOM 2500 CG ASN B 65 13.523 55.471 -2.469 1.00 59.69 1CGP2655 ATOM 2501 OD1 ASN B 65 14.486 54.721 -2.365 1.00 59.93 1CGP2656 ATOM 2502 ND2 ASN B 65 13.272 55.944 -3.687 1.00 59.86 1CGP2657 ATOM 2503 H ASN B 65 14.945 56.299 0.460 1.00 0.00 1CGP2658 ATOM 2504 1HD2 ASN B 65 12.540 56.573 -3.843 1.00 0.00 1CGP2659 ATOM 2505 2HD2 ASN B 65 13.824 55.601 -4.428 1.00 0.00 1CGP2660 ATOM 2506 N GLN B 66 11.071 57.177 0.651 1.00 63.47 1CGP2661 ATOM 2507 CA GLN B 66 10.206 57.278 1.815 1.00 66.53 1CGP2662 ATOM 2508 C GLN B 66 10.568 56.183 2.776 1.00 66.01 1CGP2663 ATOM 2509 O GLN B 66 10.787 55.036 2.364 1.00 66.51 1CGP2664 ATOM 2510 CB GLN B 66 8.728 57.140 1.461 1.00 69.23 1CGP2665 ATOM 2511 CG GLN B 66 8.127 55.784 1.163 1.00 73.22 1CGP2666 ATOM 2512 CD GLN B 66 6.657 55.891 0.788 1.00 76.66 1CGP2667 ATOM 2513 OE1 GLN B 66 6.201 55.229 -0.144 1.00 78.89 1CGP2668 ATOM 2514 NE2 GLN B 66 5.822 56.728 1.396 1.00 77.74 1CGP2669 ATOM 2515 H GLN B 66 10.682 57.244 -0.241 1.00 0.00 1CGP2670 ATOM 2516 1HE2 GLN B 66 6.143 57.367 2.071 1.00 0.00 1CGP2671 ATOM 2517 2HE2 GLN B 66 4.884 56.655 1.131 1.00 0.00 1CGP2672 ATOM 2518 N GLY B 67 10.681 56.640 4.019 1.00 65.25 1CGP2673 ATOM 2519 CA GLY B 67 11.086 55.787 5.122 1.00 63.48 1CGP2674 ATOM 2520 C GLY B 67 12.488 56.084 5.630 1.00 61.54 1CGP2675 ATOM 2521 O GLY B 67 12.874 55.610 6.701 1.00 61.92 1CGP2676 ATOM 2522 H GLY B 67 10.364 57.546 4.212 1.00 0.00 1CGP2677 ATOM 2523 N ASP B 68 13.309 56.813 4.873 1.00 59.13 1CGP2678 ATOM 2524 CA ASP B 68 14.643 57.143 5.317 1.00 55.30 1CGP2679 ATOM 2525 C ASP B 68 14.653 58.439 6.098 1.00 52.76 1CGP2680 ATOM 2526 O ASP B 68 13.742 59.258 5.979 1.00 52.25 1CGP2681 ATOM 2527 CB ASP B 68 15.552 57.259 4.101 1.00 55.39 1CGP2682 ATOM 2528 CG ASP B 68 15.915 55.923 3.460 1.00 54.97 1CGP2683 ATOM 2529 OD1 ASP B 68 16.710 55.197 4.056 1.00 55.87 1CGP2684 ATOM 2530 OD2 ASP B 68 15.441 55.621 2.363 1.00 53.66 1CGP2685 ATOM 2531 H ASP B 68 13.044 57.088 3.971 1.00 0.00 1CGP2686 ATOM 2532 N PHE B 69 15.616 58.617 6.959 1.00 51.01 1CGP2687 ATOM 2533 CA PHE B 69 15.820 59.884 7.600 1.00 51.15 1CGP2688 ATOM 2534 C PHE B 69 16.915 60.569 6.809 1.00 51.28 1CGP2689 ATOM 2535 O PHE B 69 17.729 59.897 6.175 1.00 53.86 1CGP2690 ATOM 2536 CB PHE B 69 16.315 59.729 8.986 1.00 52.49 1CGP2691 ATOM 2537 CG PHE B 69 15.273 59.309 9.996 1.00 53.26 1CGP2692 ATOM 2538 CD1 PHE B 69 14.540 60.275 10.644 1.00 52.61 1CGP2693 ATOM 2539 CD2 PHE B 69 15.110 57.978 10.292 1.00 53.61 1CGP2694 ATOM 2540 CE1 PHE B 69 13.642 59.911 11.604 1.00 53.03 1CGP2695 ATOM 2541 CE2 PHE B 69 14.201 57.623 11.253 1.00 54.24 1CGP2696 ATOM 2542 CZ PHE B 69 13.471 58.587 11.908 1.00 54.42 1CGP2697 ATOM 2543 H PHE B 69 16.242 57.888 7.127 1.00 0.00 1CGP2698 ATOM 2544 N ILE B 70 16.996 61.889 6.831 1.00 49.43 1CGP2699 ATOM 2545 CA ILE B 70 18.007 62.659 6.129 1.00 48.29 1CGP2700 ATOM 2546 C ILE B 70 18.560 63.605 7.191 1.00 49.11 1CGP2701 ATOM 2547 O ILE B 70 17.891 63.876 8.190 1.00 50.84 1CGP2702 ATOM 2548 CB ILE B 70 17.429 63.549 4.997 1.00 47.59 1CGP2703 ATOM 2549 CG1 ILE B 70 16.294 62.950 4.191 1.00 47.42 1CGP2704 ATOM 2550 CG2 ILE B 70 18.590 63.790 4.070 1.00 47.77 1CGP2705 ATOM 2551 CD1 ILE B 70 15.665 63.984 3.229 1.00 46.83 1CGP2706 ATOM 2552 H ILE B 70 16.345 62.353 7.386 1.00 0.00 1CGP2707 ATOM 2553 N GLY B 71 19.778 64.108 7.108 1.00 49.20 1CGP2708 ATOM 2554 CA GLY B 71 20.179 65.143 8.024 1.00 49.42 1CGP2709 ATOM 2555 C GLY B 71 20.974 64.551 9.150 1.00 52.06 1CGP2710 ATOM 2556 O GLY B 71 22.028 65.079 9.480 1.00 54.63 1CGP2711 ATOM 2557 H GLY B 71 20.446 63.638 6.554 1.00 0.00 1CGP2712 ATOM 2558 N GLU B 72 20.557 63.408 9.701 1.00 53.20 1CGP2713 ATOM 2559 CA GLU B 72 21.148 62.782 10.890 1.00 53.39 1CGP2714 ATOM 2560 C GLU B 72 22.620 62.884 11.201 1.00 53.67 1CGP2715 ATOM 2561 O GLU B 72 22.938 62.951 12.384 1.00 55.20 1CGP2716 ATOM 2562 CB GLU B 72 20.832 61.277 10.975 1.00 53.06 1CGP2717 ATOM 2563 CG GLU B 72 21.580 60.268 10.106 1.00 53.62 1CGP2718 ATOM 2564 CD GLU B 72 21.366 60.331 8.597 1.00 54.60 1CGP2719 ATOM 2565 OE1 GLU B 72 20.461 61.026 8.127 1.00 55.24 1CGP2720 ATOM 2566 OE2 GLU B 72 22.108 59.651 7.887 1.00 53.79 1CGP2721 ATOM 2567 H GLU B 72 19.731 63.025 9.345 1.00 0.00 1CGP2722 ATOM 2568 N LEU B 73 23.530 62.960 10.231 1.00 54.54 1CGP2723 ATOM 2569 CA LEU B 73 24.958 63.068 10.507 1.00 54.67 1CGP2724 ATOM 2570 C LEU B 73 25.365 64.194 11.444 1.00 55.68 1CGP2725 ATOM 2571 O LEU B 73 26.462 64.175 12.022 1.00 56.21 1CGP2726 ATOM 2572 CB LEU B 73 25.699 63.213 9.194 1.00 54.52 1CGP2727 ATOM 2573 CG LEU B 73 26.211 61.950 8.503 1.00 54.42 1CGP2728 ATOM 2574 CD1 LEU B 73 25.154 60.857 8.440 1.00 53.28 1CGP2729 ATOM 2575 CD2 LEU B 73 26.656 62.346 7.116 1.00 54.63 1CGP2730 ATOM 2576 H LEU B 73 23.219 63.025 9.307 1.00 0.00 1CGP2731 ATOM 2577 N GLY B 74 24.470 65.183 11.545 1.00 56.74 1CGP2732 ATOM 2578 CA GLY B 74 24.605 66.265 12.498 1.00 59.14 1CGP2733 ATOM 2579 C GLY B 74 24.229 65.809 13.909 1.00 60.74 1CGP2734 ATOM 2580 O GLY B 74 25.065 65.852 14.813 1.00 61.93 1CGP2735 ATOM 2581 H GLY B 74 23.706 65.210 10.929 1.00 0.00 1CGP2736 ATOM 2582 N LEU B 75 22.985 65.352 14.095 1.00 60.24 1CGP2737 ATOM 2583 CA LEU B 75 22.389 64.870 15.340 1.00 61.16 1CGP2738 ATOM 2584 C LEU B 75 23.216 64.530 16.570 1.00 62.61 1CGP2739 ATOM 2585 O LEU B 75 22.815 64.799 17.700 1.00 62.43 1CGP2740 ATOM 2586 CB LEU B 75 21.546 63.662 14.989 1.00 61.59 1CGP2741 ATOM 2587 CG LEU B 75 21.009 62.713 16.049 1.00 62.90 1CGP2742 ATOM 2588 CD1 LEU B 75 20.011 63.406 16.973 1.00 64.06 1CGP2743 ATOM 2589 CD2 LEU B 75 20.354 61.561 15.325 1.00 63.42 1CGP2744 ATOM 2590 H LEU B 75 22.423 65.439 13.299 1.00 0.00 1CGP2745 ATOM 2591 N PHE B 76 24.343 63.871 16.343 1.00 65.14 1CGP2746 ATOM 2592 CA PHE B 76 25.215 63.408 17.409 1.00 66.35 1CGP2747 ATOM 2593 C PHE B 76 26.254 64.417 17.922 1.00 69.81 1CGP2748 ATOM 2594 O PHE B 76 26.900 64.153 18.946 1.00 72.35 1CGP2749 ATOM 2595 CB PHE B 76 25.916 62.129 16.915 1.00 61.13 1CGP2750 ATOM 2596 CG PHE B 76 24.925 61.063 16.499 1.00 55.74 1CGP2751 ATOM 2597 CD1 PHE B 76 24.155 60.433 17.445 1.00 53.96 1CGP2752 ATOM 2598 CD2 PHE B 76 24.781 60.777 15.173 1.00 54.01 1CGP2753 ATOM 2599 CE1 PHE B 76 23.223 59.505 17.059 1.00 52.18 1CGP2754 ATOM 2600 CE2 PHE B 76 23.849 59.851 14.802 1.00 52.76 1CGP2755 ATOM 2601 CZ PHE B 76 23.072 59.215 15.733 1.00 51.69 1CGP2756 ATOM 2602 H PHE B 76 24.624 63.771 15.412 1.00 0.00 1CGP2757 ATOM 2603 N GLU B 77 26.504 65.560 17.284 1.00 72.46 1CGP2758 ATOM 2604 CA GLU B 77 27.500 66.461 17.810 1.00 75.46 1CGP2759 ATOM 2605 C GLU B 77 27.123 67.879 17.461 1.00 75.42 1CGP2760 ATOM 2606 O GLU B 77 26.695 68.178 16.343 1.00 75.91 1CGP2761 ATOM 2607 CB GLU B 77 28.837 66.065 17.213 1.00 78.70 1CGP2762 ATOM 2608 CG GLU B 77 30.036 66.413 18.091 1.00 83.19 1CGP2763 ATOM 2609 CD GLU B 77 30.420 67.893 18.112 1.00 85.09 1CGP2764 ATOM 2610 OE1 GLU B 77 31.013 68.356 17.128 1.00 86.39 1CGP2765 ATOM 2611 OE2 GLU B 77 30.124 68.572 19.107 1.00 85.50 1CGP2766 ATOM 2612 H GLU B 77 26.027 65.778 16.455 1.00 0.00 1CGP2767 ATOM 2613 N GLU B 78 27.301 68.778 18.423 1.00 75.42 1CGP2768 ATOM 2614 CA GLU B 78 26.931 70.163 18.226 1.00 76.48 1CGP2769 ATOM 2615 C GLU B 78 27.840 70.902 17.284 1.00 76.10 1CGP2770 ATOM 2616 O GLU B 78 29.049 70.698 17.288 1.00 76.00 1CGP2771 ATOM 2617 CB GLU B 78 26.947 70.930 19.514 1.00 78.73 1CGP2772 ATOM 2618 CG GLU B 78 25.541 71.379 19.832 1.00 81.73 1CGP2773 ATOM 2619 CD GLU B 78 24.759 70.322 20.594 1.00 83.54 1CGP2774 ATOM 2620 OE1 GLU B 78 24.866 70.322 21.825 1.00 84.51 1CGP2775 ATOM 2621 OE2 GLU B 78 24.051 69.523 19.970 1.00 84.52 1CGP2776 ATOM 2622 H GLU B 78 27.778 68.518 19.234 1.00 0.00 1CGP2777 ATOM 2623 N GLY B 79 27.225 71.771 16.489 1.00 76.34 1CGP2778 ATOM 2624 CA GLY B 79 27.963 72.643 15.578 1.00 75.91 1CGP2779 ATOM 2625 C GLY B 79 28.404 71.962 14.293 1.00 74.89 1CGP2780 ATOM 2626 O GLY B 79 29.356 72.371 13.625 1.00 75.30 1CGP2781 ATOM 2627 H GLY B 79 26.247 71.800 16.489 1.00 0.00 1CGP2782 ATOM 2628 N GLN B 80 27.649 70.938 13.927 1.00 73.51 1CGP2783 ATOM 2629 CA GLN B 80 27.957 70.150 12.761 1.00 71.74 1CGP2784 ATOM 2630 C GLN B 80 27.393 70.701 11.458 1.00 69.32 1CGP2785 ATOM 2631 O GLN B 80 26.247 71.160 11.412 1.00 69.66 1CGP2786 ATOM 2632 CB GLN B 80 27.461 68.782 13.103 1.00 72.92 1CGP2787 ATOM 2633 CG GLN B 80 28.642 68.041 13.697 1.00 74.06 1CGP2788 ATOM 2634 CD GLN B 80 29.224 67.161 12.614 1.00 74.91 1CGP2789 ATOM 2635 OE1 GLN B 80 30.248 67.426 11.968 1.00 74.75 1CGP2790 ATOM 2636 NE2 GLN B 80 28.473 66.088 12.404 1.00 75.51 1CGP2791 ATOM 2637 H GLN B 80 26.851 70.718 14.445 1.00 0.00 1CGP2792 ATOM 2638 1HE2 GLN B 80 27.678 65.942 12.960 1.00 0.00 1CGP2793 ATOM 2639 2HE2 GLN B 80 28.713 65.473 11.689 1.00 0.00 1CGP2794 ATOM 2640 N GLU B 81 28.202 70.698 10.400 1.00 65.52 1CGP2795 ATOM 2641 CA GLU B 81 27.781 71.208 9.103 1.00 61.80 1CGP2796 ATOM 2642 C GLU B 81 27.134 70.125 8.266 1.00 57.91 1CGP2797 ATOM 2643 O GLU B 81 27.370 68.935 8.477 1.00 58.04 1CGP2798 ATOM 2644 CB GLU B 81 28.956 71.742 8.318 1.00 63.41 1CGP2799 ATOM 2645 CG GLU B 81 29.372 73.182 8.533 1.00 65.51 1CGP2800 ATOM 2646 CD GLU B 81 30.589 73.517 7.671 1.00 68.34 1CGP2801 ATOM 2647 OE1 GLU B 81 31.713 73.273 8.121 1.00 70.12 1CGP2802 ATOM 2648 OE2 GLU B 81 30.429 74.006 6.547 1.00 69.16 1CGP2803 ATOM 2649 H GLU B 81 29.061 70.232 10.458 1.00 0.00 1CGP2804 ATOM 2650 N ARG B 82 26.319 70.496 7.295 1.00 53.46 1CGP2805 ATOM 2651 CA ARG B 82 25.683 69.493 6.462 1.00 52.30 1CGP2806 ATOM 2652 C ARG B 82 26.728 69.029 5.485 1.00 49.52 1CGP2807 ATOM 2653 O ARG B 82 27.401 69.872 4.884 1.00 47.31 1CGP2808 ATOM 2654 CB ARG B 82 24.502 70.052 5.689 1.00 54.33 1CGP2809 ATOM 2655 CG ARG B 82 23.634 70.864 6.621 1.00 56.89 1CGP2810 ATOM 2656 CD ARG B 82 22.158 70.800 6.333 1.00 59.52 1CGP2811 ATOM 2657 NE ARG B 82 21.550 69.686 7.033 1.00 60.45 1CGP2812 ATOM 2658 CZ ARG B 82 20.450 69.840 7.779 1.00 62.77 1CGP2813 ATOM 2659 NH1 ARG B 82 19.803 71.024 7.917 1.00 62.90 1CGP2814 ATOM 2660 NH2 ARG B 82 20.027 68.729 8.384 1.00 62.68 1CGP2815 ATOM 2661 H ARG B 82 26.152 71.455 7.196 1.00 0.00 1CGP2816 ATOM 2662 HE ARG B 82 21.951 68.795 6.981 1.00 0.00 1CGP2817 ATOM 2663 1HH1 ARG B 82 20.150 71.845 7.465 1.00 0.00 1CGP2818 ATOM 2664 2HH1 ARG B 82 19.002 71.091 8.512 1.00 0.00 1CGP2819 ATOM 2665 1HH2 ARG B 82 20.563 67.903 8.227 1.00 0.00 1CGP2820 ATOM 2666 2HH2 ARG B 82 19.233 68.711 8.988 1.00 0.00 1CGP2821 ATOM 2667 N SER B 83 26.834 67.707 5.351 1.00 47.00 1CGP2822 ATOM 2668 CA SER B 83 27.835 67.053 4.532 1.00 43.83 1CGP2823 ATOM 2669 C SER B 83 27.631 67.004 3.040 1.00 43.13 1CGP2824 ATOM 2670 O SER B 83 28.603 66.997 2.297 1.00 42.74 1CGP2825 ATOM 2671 CB SER B 83 27.996 65.660 5.021 1.00 43.05 1CGP2826 ATOM 2672 OG SER B 83 26.716 65.064 5.152 1.00 45.11 1CGP2827 ATOM 2673 H SER B 83 26.238 67.115 5.866 1.00 0.00 1CGP2828 ATOM 2674 HG SER B 83 26.608 64.395 4.470 1.00 0.00 1CGP2829 ATOM 2675 N ALA B 84 26.411 66.994 2.535 1.00 43.11 1CGP2830 ATOM 2676 CA ALA B 84 26.187 66.891 1.106 1.00 42.66 1CGP2831 ATOM 2677 C ALA B 84 24.892 67.606 0.770 1.00 42.93 1CGP2832 ATOM 2678 O ALA B 84 24.210 68.102 1.667 1.00 42.47 1CGP2833 ATOM 2679 CB ALA B 84 26.081 65.431 0.755 1.00 43.57 1CGP2834 ATOM 2680 H ALA B 84 25.626 67.145 3.109 1.00 0.00 1CGP2835 ATOM 2681 N TRP B 85 24.546 67.720 -0.497 1.00 44.35 1CGP2836 ATOM 2682 CA TRP B 85 23.291 68.326 -0.912 1.00 48.03 1CGP2837 ATOM 2683 C TRP B 85 22.214 67.244 -1.056 1.00 48.25 1CGP2838 ATOM 2684 O TRP B 85 22.522 66.086 -1.349 1.00 49.13 1CGP2839 ATOM 2685 CB TRP B 85 23.460 69.033 -2.252 1.00 51.72 1CGP2840 ATOM 2686 CG TRP B 85 24.474 70.169 -2.260 1.00 54.38 1CGP2841 ATOM 2687 CD1 TRP B 85 24.051 71.470 -2.249 1.00 55.17 1CGP2842 ATOM 2688 CD2 TRP B 85 25.844 70.045 -2.288 1.00 56.22 1CGP2843 ATOM 2689 NE1 TRP B 85 25.156 72.171 -2.270 1.00 56.59 1CGP2844 ATOM 2690 CE2 TRP B 85 26.229 71.371 -2.297 1.00 56.51 1CGP2845 ATOM 2691 CE3 TRP B 85 26.798 69.050 -2.310 1.00 57.76 1CGP2846 ATOM 2692 CZ2 TRP B 85 27.558 71.726 -2.329 1.00 57.34 1CGP2847 ATOM 2693 CZ3 TRP B 85 28.130 69.397 -2.338 1.00 58.16 1CGP2848 ATOM 2694 CH2 TRP B 85 28.507 70.724 -2.351 1.00 58.12 1CGP2849 ATOM 2695 H TRP B 85 25.100 67.269 -1.165 1.00 0.00 1CGP2850 ATOM 2696 HE1 TRP B 85 25.212 73.150 -2.263 1.00 0.00 1CGP2851 ATOM 2697 N VAL B 86 20.937 67.558 -0.888 1.00 47.01 1CGP2852 ATOM 2698 CA VAL B 86 19.875 66.571 -0.978 1.00 46.58 1CGP2853 ATOM 2699 C VAL B 86 18.858 67.279 -1.846 1.00 47.89 1CGP2854 ATOM 2700 O VAL B 86 18.269 68.270 -1.399 1.00 47.76 1CGP2855 ATOM 2701 CB VAL B 86 19.328 66.276 0.437 1.00 45.00 1CGP2856 ATOM 2702 CG1 VAL B 86 18.052 65.474 0.398 1.00 43.06 1CGP2857 ATOM 2703 CG2 VAL B 86 20.351 65.468 1.193 1.00 44.18 1CGP2858 ATOM 2704 H VAL B 86 20.683 68.497 -0.758 1.00 0.00 1CGP2859 ATOM 2705 N ARG B 87 18.723 66.846 -3.092 1.00 49.56 1CGP2860 ATOM 2706 CA ARG B 87 17.775 67.421 -4.031 1.00 52.09 1CGP2861 ATOM 2707 C ARG B 87 16.636 66.442 -4.269 1.00 52.08 1CGP2862 ATOM 2708 O ARG B 87 16.847 65.232 -4.257 1.00 53.49 1CGP2863 ATOM 2709 CB ARG B 87 18.503 67.742 -5.326 1.00 54.97 1CGP2864 ATOM 2710 CG ARG B 87 17.649 68.173 -6.511 1.00 59.76 1CGP2865 ATOM 2711 CD ARG B 87 18.378 69.202 -7.360 1.00 64.59 1CGP2866 ATOM 2712 NE ARG B 87 19.612 68.712 -7.968 1.00 69.34 1CGP2867 ATOM 2713 CZ ARG B 87 20.825 69.249 -7.692 1.00 71.70 1CGP2868 ATOM 2714 NH1 ARG B 87 21.040 70.204 -6.763 1.00 72.38 1CGP2869 ATOM 2715 NH2 ARG B 87 21.882 68.790 -8.360 1.00 72.31 1CGP2870 ATOM 2716 H ARG B 87 19.231 66.038 -3.336 1.00 0.00 1CGP2871 ATOM 2717 HE ARG B 87 19.564 67.961 -8.597 1.00 0.00 1CGP2872 ATOM 2718 1HH1 ARG B 87 20.284 70.607 -6.246 1.00 0.00 1CGP2873 ATOM 2719 2HH1 ARG B 87 21.966 70.561 -6.640 1.00 0.00 1CGP2874 ATOM 2720 1HH2 ARG B 87 21.763 68.079 -9.053 1.00 0.00 1CGP2875 ATOM 2721 2HH2 ARG B 87 22.788 69.180 -8.194 1.00 0.00 1CGP2876 ATOM 2722 N ALA B 88 15.417 66.915 -4.428 1.00 51.30 1CGP2877 ATOM 2723 CA ALA B 88 14.259 66.081 -4.645 1.00 53.01 1CGP2878 ATOM 2724 C ALA B 88 14.119 65.528 -6.064 1.00 54.79 1CGP2879 ATOM 2725 O ALA B 88 14.180 66.271 -7.051 1.00 54.51 1CGP2880 ATOM 2726 CB ALA B 88 13.048 66.894 -4.279 1.00 52.78 1CGP2881 ATOM 2727 H ALA B 88 15.296 67.877 -4.357 1.00 0.00 1CGP2882 ATOM 2728 N LYS B 89 13.936 64.210 -6.171 1.00 56.76 1CGP2883 ATOM 2729 CA LYS B 89 13.782 63.508 -7.440 1.00 58.74 1CGP2884 ATOM 2730 C LYS B 89 12.406 63.785 -8.006 1.00 58.86 1CGP2885 ATOM 2731 O LYS B 89 12.175 64.101 -9.172 1.00 57.67 1CGP2886 ATOM 2732 CB LYS B 89 13.876 61.994 -7.278 1.00 61.62 1CGP2887 ATOM 2733 CG LYS B 89 15.098 61.326 -7.880 1.00 66.25 1CGP2888 ATOM 2734 CD LYS B 89 14.918 59.818 -8.216 1.00 69.50 1CGP2889 ATOM 2735 CE LYS B 89 14.882 58.843 -7.020 1.00 71.65 1CGP2890 ATOM 2736 NZ LYS B 89 15.036 57.442 -7.389 1.00 72.03 1CGP2891 ATOM 2737 H LYS B 89 13.797 63.690 -5.355 1.00 0.00 1CGP2892 ATOM 2738 1HZ LYS B 89 15.941 57.328 -7.888 1.00 0.00 1CGP2893 ATOM 2739 2HZ LYS B 89 14.254 57.170 -8.019 1.00 0.00 1CGP2894 ATOM 2740 3HZ LYS B 89 15.029 56.827 -6.551 1.00 0.00 1CGP2895 ATOM 2741 N THR B 90 11.531 63.586 -7.031 1.00 60.04 1CGP2896 ATOM 2742 CA THR B 90 10.085 63.601 -7.122 1.00 61.08 1CGP2897 ATOM 2743 C THR B 90 9.553 64.596 -6.103 1.00 61.17 1CGP2898 ATOM 2744 O THR B 90 10.349 65.130 -5.327 1.00 62.19 1CGP2899 ATOM 2745 CB THR B 90 9.589 62.179 -6.825 1.00 61.71 1CGP2900 ATOM 2746 OG1 THR B 90 10.500 61.580 -5.899 1.00 61.84 1CGP2901 ATOM 2747 CG2 THR B 90 9.549 61.319 -8.075 1.00 63.28 1CGP2902 ATOM 2748 H THR B 90 11.867 63.499 -6.114 1.00 0.00 1CGP2903 ATOM 2749 HG1 THR B 90 11.296 61.435 -6.431 1.00 0.00 1CGP2904 ATOM 2750 N ALA B 91 8.256 64.884 -6.058 1.00 60.69 1CGP2905 ATOM 2751 CA ALA B 91 7.759 65.780 -5.043 1.00 60.92 1CGP2906 ATOM 2752 C ALA B 91 7.676 64.974 -3.758 1.00 61.47 1CGP2907 ATOM 2753 O ALA B 91 7.288 63.797 -3.749 1.00 61.71 1CGP2908 ATOM 2754 CB ALA B 91 6.401 66.276 -5.450 1.00 62.84 1CGP2909 ATOM 2755 H ALA B 91 7.625 64.430 -6.642 1.00 0.00 1CGP2910 ATOM 2756 N CYS B 92 8.049 65.628 -2.678 1.00 61.52 1CGP2911 ATOM 2757 CA CYS B 92 8.199 64.972 -1.410 1.00 63.25 1CGP2912 ATOM 2758 C CYS B 92 7.501 65.673 -0.270 1.00 65.59 1CGP2913 ATOM 2759 O CYS B 92 7.341 66.896 -0.302 1.00 68.17 1CGP2914 ATOM 2760 CB CYS B 92 9.667 64.869 -1.076 1.00 62.37 1CGP2915 ATOM 2761 SG CYS B 92 10.594 63.840 -2.234 1.00 63.65 1CGP2916 ATOM 2762 H CYS B 92 8.181 66.592 -2.733 1.00 0.00 1CGP2917 ATOM 2763 N GLU B 93 7.122 64.911 0.752 1.00 67.21 1CGP2918 ATOM 2764 CA GLU B 93 6.547 65.423 1.988 1.00 68.86 1CGP2919 ATOM 2765 C GLU B 93 7.624 65.093 3.007 1.00 69.04 1CGP2920 ATOM 2766 O GLU B 93 7.956 63.908 3.201 1.00 70.70 1CGP2921 ATOM 2767 CB GLU B 93 5.269 64.693 2.392 1.00 71.56 1CGP2922 ATOM 2768 CG GLU B 93 3.951 65.221 1.808 1.00 74.39 1CGP2923 ATOM 2769 CD GLU B 93 2.669 64.812 2.558 1.00 75.64 1CGP2924 ATOM 2770 OE1 GLU B 93 2.718 64.424 3.737 1.00 75.07 1CGP2925 ATOM 2771 OE2 GLU B 93 1.596 64.905 1.945 1.00 77.02 1CGP2926 ATOM 2772 H GLU B 93 7.385 63.971 0.707 1.00 0.00 1CGP2927 ATOM 2773 N VAL B 94 8.197 66.084 3.666 1.00 67.48 1CGP2928 ATOM 2774 CA VAL B 94 9.313 65.849 4.567 1.00 66.47 1CGP2929 ATOM 2775 C VAL B 94 8.883 66.131 5.990 1.00 67.19 1CGP2930 ATOM 2776 O VAL B 94 8.541 67.283 6.274 1.00 69.45 1CGP2931 ATOM 2777 CB VAL B 94 10.457 66.762 4.099 1.00 65.38 1CGP2932 ATOM 2778 CG1 VAL B 94 11.627 66.791 5.044 1.00 64.69 1CGP2933 ATOM 2779 CG2 VAL B 94 10.959 66.205 2.791 1.00 65.41 1CGP2934 ATOM 2780 H VAL B 94 7.826 66.987 3.577 1.00 0.00 1CGP2935 ATOM 2781 N ALA B 95 8.854 65.151 6.894 1.00 66.26 1CGP2936 ATOM 2782 CA ALA B 95 8.470 65.406 8.276 1.00 66.02 1CGP2937 ATOM 2783 C ALA B 95 9.706 65.817 9.038 1.00 65.42 1CGP2938 ATOM 2784 O ALA B 95 10.687 65.084 9.071 1.00 65.51 1CGP2939 ATOM 2785 CB ALA B 95 7.917 64.163 8.952 1.00 65.13 1CGP2940 ATOM 2786 H ALA B 95 9.221 64.272 6.672 1.00 0.00 1CGP2941 ATOM 2787 N GLU B 96 9.736 67.004 9.590 1.00 65.37 1CGP2942 ATOM 2788 CA GLU B 96 10.888 67.377 10.370 1.00 68.05 1CGP2943 ATOM 2789 C GLU B 96 10.631 67.480 11.851 1.00 68.90 1CGP2944 ATOM 2790 O GLU B 96 9.504 67.783 12.252 1.00 70.01 1CGP2945 ATOM 2791 CB GLU B 96 11.398 68.705 9.932 1.00 69.24 1CGP2946 ATOM 2792 CG GLU B 96 11.905 68.615 8.538 1.00 72.70 1CGP2947 ATOM 2793 CD GLU B 96 11.345 69.733 7.692 1.00 75.09 1CGP2948 ATOM 2794 OE1 GLU B 96 11.717 70.891 7.920 1.00 76.74 1CGP2949 ATOM 2795 OE2 GLU B 96 10.538 69.426 6.813 1.00 75.78 1CGP2950 ATOM 2796 H GLU B 96 9.042 67.657 9.373 1.00 0.00 1CGP2951 ATOM 2797 N ILE B 97 11.658 67.261 12.659 1.00 68.14 1CGP2952 ATOM 2798 CA ILE B 97 11.680 67.643 14.060 1.00 67.88 1CGP2953 ATOM 2799 C ILE B 97 13.033 68.304 14.188 1.00 68.23 1CGP2954 ATOM 2800 O ILE B 97 13.889 68.207 13.301 1.00 68.15 1CGP2955 ATOM 2801 CB ILE B 97 11.654 66.490 15.107 1.00 67.87 1CGP2956 ATOM 2802 CG1 ILE B 97 12.081 65.165 14.574 1.00 68.11 1CGP2957 ATOM 2803 CG2 ILE B 97 10.253 66.382 15.608 1.00 69.41 1CGP2958 ATOM 2804 CD1 ILE B 97 13.568 64.943 14.790 1.00 69.25 1CGP2959 ATOM 2805 H ILE B 97 12.480 66.869 12.275 1.00 0.00 1CGP2960 ATOM 2806 N SER B 98 13.289 69.034 15.247 1.00 70.07 1CGP2961 ATOM 2807 CA SER B 98 14.628 69.536 15.411 1.00 71.45 1CGP2962 ATOM 2808 C SER B 98 15.392 68.447 16.167 1.00 71.54 1CGP2963 ATOM 2809 O SER B 98 14.819 67.507 16.732 1.00 70.47 1CGP2964 ATOM 2810 CB SER B 98 14.545 70.843 16.187 1.00 72.87 1CGP2965 ATOM 2811 OG SER B 98 13.859 70.712 17.435 1.00 75.72 1CGP2966 ATOM 2812 H SER B 98 12.665 69.120 15.994 1.00 0.00 1CGP2967 ATOM 2813 HG SER B 98 13.673 71.605 17.758 1.00 0.00 1CGP2968 ATOM 2814 N TYR B 99 16.709 68.567 16.205 1.00 73.32 1CGP2969 ATOM 2815 CA TYR B 99 17.577 67.675 16.960 1.00 75.34 1CGP2970 ATOM 2816 C TYR B 99 17.301 67.663 18.464 1.00 76.75 1CGP2971 ATOM 2817 O TYR B 99 17.175 66.591 19.046 1.00 75.48 1CGP2972 ATOM 2818 CB TYR B 99 19.017 68.085 16.697 1.00 75.64 1CGP2973 ATOM 2819 CG TYR B 99 19.581 67.747 15.317 1.00 75.26 1CGP2974 ATOM 2820 CD1 TYR B 99 18.992 66.783 14.516 1.00 74.96 1CGP2975 ATOM 2821 CD2 TYR B 99 20.737 68.384 14.911 1.00 74.50 1CGP2976 ATOM 2822 CE1 TYR B 99 19.570 66.442 13.318 1.00 75.00 1CGP2977 ATOM 2823 CE2 TYR B 99 21.315 68.046 13.715 1.00 74.36 1CGP2978 ATOM 2824 CZ TYR B 99 20.729 67.074 12.935 1.00 75.33 1CGP2979 ATOM 2825 OH TYR B 99 21.365 66.666 11.781 1.00 75.61 1CGP2980 ATOM 2826 H TYR B 99 17.106 69.247 15.620 1.00 0.00 1CGP2981 ATOM 2827 HH TYR B 99 20.717 66.489 11.090 1.00 0.00 1CGP2982 ATOM 2828 N LYS B 100 17.178 68.838 19.111 1.00 78.55 1CGP2983 ATOM 2829 CA LYS B 100 16.819 68.986 20.535 1.00 79.94 1CGP2984 ATOM 2830 C LYS B 100 15.600 68.101 20.863 1.00 80.00 1CGP2985 ATOM 2831 O LYS B 100 15.599 67.235 21.756 1.00 79.51 1CGP2986 ATOM 2832 CB LYS B 100 16.424 70.442 20.871 1.00 81.20 1CGP2987 ATOM 2833 CG LYS B 100 17.344 71.609 20.511 1.00 83.48 1CGP2988 ATOM 2834 CD LYS B 100 16.508 72.700 19.796 1.00 85.22 1CGP2989 ATOM 2835 CE LYS B 100 16.615 74.149 20.341 1.00 85.94 1CGP2990 ATOM 2836 NZ LYS B 100 17.913 74.798 20.168 1.00 85.26 1CGP2991 ATOM 2837 H LYS B 100 17.357 69.643 18.580 1.00 0.00 1CGP2992 ATOM 2838 1HZ LYS B 100 18.154 74.828 19.158 1.00 0.00 1CGP2993 ATOM 2839 2HZ LYS B 100 18.643 74.259 20.675 1.00 0.00 1CGP2994 ATOM 2840 3HZ LYS B 100 17.867 75.765 20.546 1.00 0.00 1CGP2995 ATOM 2841 N LYS B 101 14.536 68.341 20.080 1.00 79.23 1CGP2996 ATOM 2842 CA LYS B 101 13.310 67.583 20.190 1.00 79.15 1CGP2997 ATOM 2843 C LYS B 101 13.598 66.103 19.972 1.00 77.94 1CGP2998 ATOM 2844 O LYS B 101 13.137 65.291 20.777 1.00 76.43 1CGP2999 ATOM 2845 CB LYS B 101 12.318 68.107 19.159 1.00 81.27 1CGP3000 ATOM 2846 CG LYS B 101 11.072 67.240 18.959 1.00 85.01 1CGP3001 ATOM 2847 CD LYS B 101 9.846 67.489 19.841 1.00 87.73 1CGP3002 ATOM 2848 CE LYS B 101 9.012 68.708 19.390 1.00 89.92 1CGP3003 ATOM 2849 NZ LYS B 101 8.622 68.647 17.986 1.00 90.67 1CGP3004 ATOM 2850 H LYS B 101 14.556 69.049 19.404 1.00 0.00 1CGP3005 ATOM 2851 1HZ LYS B 101 8.056 67.793 17.816 1.00 0.00 1CGP3006 ATOM 2852 2HZ LYS B 101 9.485 68.618 17.405 1.00 0.00 1CGP3007 ATOM 2853 3HZ LYS B 101 8.067 69.489 17.731 1.00 0.00 1CGP3008 ATOM 2854 N PHE B 102 14.363 65.732 18.927 1.00 76.87 1CGP3009 ATOM 2855 CA PHE B 102 14.694 64.344 18.662 1.00 75.67 1CGP3010 ATOM 2856 C PHE B 102 15.327 63.740 19.904 1.00 78.21 1CGP3011 ATOM 2857 O PHE B 102 14.899 62.659 20.310 1.00 79.17 1CGP3012 ATOM 2858 CB PHE B 102 15.674 64.175 17.482 1.00 70.89 1CGP3013 ATOM 2859 CG PHE B 102 15.723 62.711 17.036 1.00 67.63 1CGP3014 ATOM 2860 CD1 PHE B 102 14.587 62.086 16.554 1.00 66.34 1CGP3015 ATOM 2861 CD2 PHE B 102 16.885 61.969 17.149 1.00 66.49 1CGP3016 ATOM 2862 CE1 PHE B 102 14.613 60.751 16.192 1.00 65.28 1CGP3017 ATOM 2863 CE2 PHE B 102 16.905 60.633 16.774 1.00 65.58 1CGP3018 ATOM 2864 CZ PHE B 102 15.767 60.015 16.300 1.00 64.84 1CGP3019 ATOM 2865 H PHE B 102 14.604 66.392 18.254 1.00 0.00 1CGP3020 ATOM 2866 N ARG B 103 16.274 64.414 20.570 1.00 79.81 1CGP3021 ATOM 2867 CA ARG B 103 16.893 63.918 21.806 1.00 80.59 1CGP3022 ATOM 2868 C ARG B 103 15.903 63.578 22.946 1.00 81.23 1CGP3023 ATOM 2869 O ARG B 103 15.969 62.497 23.567 1.00 80.07 1CGP3024 ATOM 2870 CB ARG B 103 17.929 64.963 22.294 1.00 79.34 1CGP3025 ATOM 2871 CG ARG B 103 19.387 64.645 21.965 1.00 75.77 1CGP3026 ATOM 2872 CD ARG B 103 19.676 64.883 20.505 1.00 73.39 1CGP3027 ATOM 2873 NE ARG B 103 19.899 66.289 20.256 1.00 71.43 1CGP3028 ATOM 2874 CZ ARG B 103 21.124 66.806 20.290 1.00 70.33 1CGP3029 ATOM 2875 NH1 ARG B 103 22.196 66.086 20.610 1.00 70.50 1CGP3030 ATOM 2876 NH2 ARG B 103 21.282 68.087 20.004 1.00 70.32 1CGP3031 ATOM 2877 H ARG B 103 16.609 65.230 20.154 1.00 0.00 1CGP3032 ATOM 2878 HE ARG B 103 19.137 66.877 20.078 1.00 0.00 1CGP3033 ATOM 2879 1HH1 ARG B 103 22.111 65.113 20.828 1.00 0.00 1CGP3034 ATOM 2880 2HH1 ARG B 103 23.097 66.520 20.604 1.00 0.00 1CGP3035 ATOM 2881 1HH2 ARG B 103 20.487 68.644 19.763 1.00 0.00 1CGP3036 ATOM 2882 2HH2 ARG B 103 22.194 68.492 19.991 1.00 0.00 1CGP3037 ATOM 2883 N GLN B 104 14.946 64.485 23.214 1.00 80.69 1CGP3038 ATOM 2884 CA GLN B 104 13.892 64.237 24.198 1.00 79.39 1CGP3039 ATOM 2885 C GLN B 104 13.179 62.948 23.790 1.00 78.27 1CGP3040 ATOM 2886 O GLN B 104 13.088 61.965 24.523 1.00 78.23 1CGP3041 ATOM 2887 CB GLN B 104 12.874 65.353 24.196 1.00 79.89 1CGP3042 ATOM 2888 CG GLN B 104 13.429 66.759 24.327 1.00 80.56 1CGP3043 ATOM 2889 CD GLN B 104 12.373 67.839 24.076 1.00 82.09 1CGP3044 ATOM 2890 OE1 GLN B 104 11.175 67.594 23.864 1.00 81.43 1CGP3045 ATOM 2891 NE2 GLN B 104 12.819 69.096 24.085 1.00 81.97 1CGP3046 ATOM 2892 H GLN B 104 15.008 65.343 22.737 1.00 0.00 1CGP3047 ATOM 2893 1HE2 GLN B 104 13.774 69.258 24.231 1.00 0.00 1CGP3048 ATOM 2894 2HE2 GLN B 104 12.155 69.801 23.947 1.00 0.00 1CGP3049 ATOM 2895 N LEU B 105 12.754 62.893 22.540 1.00 78.05 1CGP3050 ATOM 2896 CA LEU B 105 12.060 61.754 21.994 1.00 78.62 1CGP3051 ATOM 2897 C LEU B 105 12.898 60.487 21.995 1.00 79.84 1CGP3052 ATOM 2898 O LEU B 105 12.324 59.404 22.030 1.00 79.27 1CGP3053 ATOM 2899 CB LEU B 105 11.624 62.147 20.606 1.00 79.17 1CGP3054 ATOM 2900 CG LEU B 105 10.436 63.112 20.400 1.00 80.51 1CGP3055 ATOM 2901 CD1 LEU B 105 10.306 64.231 21.431 1.00 80.63 1CGP3056 ATOM 2902 CD2 LEU B 105 10.665 63.735 19.047 1.00 81.35 1CGP3057 ATOM 2903 H LEU B 105 12.915 63.672 21.965 1.00 0.00 1CGP3058 ATOM 2904 N ILE B 106 14.235 60.592 21.998 1.00 82.02 1CGP3059 ATOM 2905 CA ILE B 106 15.151 59.460 22.132 1.00 84.83 1CGP3060 ATOM 2906 C ILE B 106 14.886 58.839 23.490 1.00 87.84 1CGP3061 ATOM 2907 O ILE B 106 14.541 57.658 23.584 1.00 88.98 1CGP3062 ATOM 2908 CB ILE B 106 16.658 59.928 22.018 1.00 83.98 1CGP3063 ATOM 2909 CG1 ILE B 106 17.022 60.013 20.544 1.00 83.67 1CGP3064 ATOM 2910 CG2 ILE B 106 17.628 58.972 22.719 1.00 84.13 1CGP3065 ATOM 2911 CD1 ILE B 106 18.440 60.554 20.278 1.00 82.79 1CGP3066 ATOM 2912 H ILE B 106 14.603 61.468 21.777 1.00 0.00 1CGP3067 ATOM 2913 N GLN B 107 15.010 59.658 24.533 1.00 91.51 1CGP3068 ATOM 2914 CA GLN B 107 14.810 59.196 25.900 1.00 94.73 1CGP3069 ATOM 2915 C GLN B 107 13.438 58.608 26.180 1.00 95.59 1CGP3070 ATOM 2916 O GLN B 107 13.313 57.674 26.978 1.00 96.80 1CGP3071 ATOM 2917 CB GLN B 107 15.070 60.352 26.867 1.00 96.10 1CGP3072 ATOM 2918 CG GLN B 107 16.561 60.639 26.979 1.00 98.71 1CGP3073 ATOM 2919 CD GLN B 107 17.331 59.442 27.533 1.00100.22 1CGP3074 ATOM 2920 OE1 GLN B 107 18.127 58.777 26.864 1.00101.27 1CGP3075 ATOM 2921 NE2 GLN B 107 17.114 59.122 28.802 1.00101.07 1CGP3076 ATOM 2922 H GLN B 107 15.281 60.586 24.348 1.00 0.00 1CGP3077 ATOM 2923 1HE2 GLN B 107 16.493 59.661 29.333 1.00 0.00 1CGP3078 ATOM 2924 2HE2 GLN B 107 17.616 58.359 29.144 1.00 0.00 1CGP3079 ATOM 2925 N VAL B 108 12.416 59.208 25.564 1.00 95.32 1CGP3080 ATOM 2926 CA VAL B 108 11.048 58.725 25.669 1.00 94.96 1CGP3081 ATOM 2927 C VAL B 108 10.920 57.395 24.936 1.00 94.97 1CGP3082 ATOM 2928 O VAL B 108 10.234 56.486 25.417 1.00 95.03 1CGP3083 ATOM 2929 CB VAL B 108 10.082 59.767 25.075 1.00 95.40 1CGP3084 ATOM 2930 CG1 VAL B 108 8.640 59.266 25.116 1.00 96.07 1CGP3085 ATOM 2931 CG2 VAL B 108 10.156 61.037 25.898 1.00 95.50 1CGP3086 ATOM 2932 H VAL B 108 12.616 60.050 25.102 1.00 0.00 1CGP3087 ATOM 2933 N ASN B 109 11.462 57.241 23.729 1.00 95.16 1CGP3088 ATOM 2934 CA ASN B 109 11.461 55.919 23.146 1.00 94.97 1CGP3089 ATOM 2935 C ASN B 109 12.618 55.583 22.218 1.00 94.58 1CGP3090 ATOM 2936 O ASN B 109 12.663 55.941 21.031 1.00 94.79 1CGP3091 ATOM 2937 CB ASN B 109 10.180 55.610 22.360 1.00 94.61 1CGP3092 ATOM 2938 CG ASN B 109 10.237 54.107 22.136 1.00 94.13 1CGP3093 ATOM 2939 OD1 ASN B 109 10.397 53.599 21.035 1.00 92.71 1CGP3094 ATOM 2940 ND2 ASN B 109 10.263 53.321 23.202 1.00 94.52 1CGP3095 ATOM 2941 H ASN B 109 11.846 57.984 23.218 1.00 0.00 1CGP3096 ATOM 2942 1HD2 ASN B 109 10.228 53.736 24.095 1.00 0.00 1CGP3097 ATOM 2943 2HD2 ASN B 109 10.281 52.355 23.053 1.00 0.00 1CGP3098 ATOM 2944 N PRO B 110 13.502 54.709 22.730 1.00 93.82 1CGP3099 ATOM 2945 CA PRO B 110 14.700 54.258 22.025 1.00 92.90 1CGP3100 ATOM 2946 C PRO B 110 14.489 53.711 20.613 1.00 91.00 1CGP3101 ATOM 2947 O PRO B 110 15.378 53.801 19.764 1.00 90.83 1CGP3102 ATOM 2948 CB PRO B 110 15.296 53.233 22.978 1.00 93.81 1CGP3103 ATOM 2949 CG PRO B 110 14.867 53.735 24.337 1.00 94.17 1CGP3104 ATOM 2950 CD PRO B 110 13.423 54.102 24.065 1.00 93.70 1CGP3105 ATOM 2951 N ASP B 111 13.301 53.201 20.287 1.00 88.36 1CGP3106 ATOM 2952 CA ASP B 111 13.093 52.573 19.013 1.00 86.14 1CGP3107 ATOM 2953 C ASP B 111 13.285 53.524 17.838 1.00 84.62 1CGP3108 ATOM 2954 O ASP B 111 13.704 53.023 16.788 1.00 83.96 1CGP3109 ATOM 2955 CB ASP B 111 11.711 51.959 19.081 1.00 87.19 1CGP3110 ATOM 2956 CG ASP B 111 11.193 51.233 17.852 1.00 88.87 1CGP3111 ATOM 2957 OD1 ASP B 111 11.967 50.733 17.035 1.00 89.25 1CGP3112 ATOM 2958 OD2 ASP B 111 9.974 51.174 17.716 1.00 90.31 1CGP3113 ATOM 2959 H ASP B 111 12.525 53.338 20.869 1.00 0.00 1CGP3114 ATOM 2960 N ILE B 112 13.117 54.857 17.924 1.00 83.24 1CGP3115 ATOM 2961 CA ILE B 112 13.464 55.664 16.749 1.00 82.15 1CGP3116 ATOM 2962 C ILE B 112 14.974 55.657 16.610 1.00 80.61 1CGP3117 ATOM 2963 O ILE B 112 15.464 55.429 15.504 1.00 81.67 1CGP3118 ATOM 2964 CB ILE B 112 13.081 57.188 16.747 1.00 82.72 1CGP3119 ATOM 2965 CG1 ILE B 112 12.687 57.793 18.088 1.00 83.51 1CGP3120 ATOM 2966 CG2 ILE B 112 11.982 57.271 15.703 1.00 82.22 1CGP3121 ATOM 2967 CD1 ILE B 112 13.871 58.220 18.971 1.00 84.27 1CGP3122 ATOM 2968 H ILE B 112 12.841 55.273 18.772 1.00 0.00 1CGP3123 ATOM 2969 N LEU B 113 15.730 55.781 17.713 1.00 77.68 1CGP3124 ATOM 2970 CA LEU B 113 17.188 55.770 17.666 1.00 74.94 1CGP3125 ATOM 2971 C LEU B 113 17.661 54.442 17.078 1.00 74.54 1CGP3126 ATOM 2972 O LEU B 113 18.630 54.404 16.320 1.00 75.78 1CGP3127 ATOM 2973 CB LEU B 113 17.780 55.945 19.069 1.00 71.86 1CGP3128 ATOM 2974 CG LEU B 113 19.287 56.115 19.188 1.00 69.48 1CGP3129 ATOM 2975 CD1 LEU B 113 19.708 57.463 18.666 1.00 68.86 1CGP3130 ATOM 2976 CD2 LEU B 113 19.682 56.036 20.630 1.00 68.50 1CGP3131 ATOM 2977 H LEU B 113 15.282 55.777 18.583 1.00 0.00 1CGP3132 ATOM 2978 N MET B 114 16.995 53.332 17.373 1.00 73.46 1CGP3133 ATOM 2979 CA MET B 114 17.366 52.071 16.766 1.00 73.06 1CGP3134 ATOM 2980 C MET B 114 17.100 52.091 15.280 1.00 72.19 1CGP3135 ATOM 2981 O MET B 114 18.071 51.968 14.528 1.00 73.43 1CGP3136 ATOM 2982 CB MET B 114 16.603 50.910 17.364 1.00 74.64 1CGP3137 ATOM 2983 CG MET B 114 17.160 50.488 18.718 1.00 75.75 1CGP3138 ATOM 2984 SD MET B 114 18.874 49.929 18.604 1.00 75.35 1CGP3139 ATOM 2985 CE MET B 114 18.592 48.207 18.297 1.00 75.98 1CGP3140 ATOM 2986 H MET B 114 16.327 53.390 18.086 1.00 0.00 1CGP3141 ATOM 2987 N ARG B 115 15.874 52.315 14.800 1.00 69.95 1CGP3142 ATOM 2988 CA ARG B 115 15.614 52.307 13.366 1.00 67.76 1CGP3143 ATOM 2989 C ARG B 115 16.504 53.319 12.653 1.00 64.60 1CGP3144 ATOM 2990 O ARG B 115 17.044 53.001 11.595 1.00 66.25 1CGP3145 ATOM 2991 CB ARG B 115 14.166 52.631 13.083 1.00 71.25 1CGP3146 ATOM 2992 CG ARG B 115 13.153 51.680 13.715 1.00 74.36 1CGP3147 ATOM 2993 CD ARG B 115 11.763 52.203 13.396 1.00 76.51 1CGP3148 ATOM 2994 NE ARG B 115 10.786 51.782 14.381 1.00 78.95 1CGP3149 ATOM 2995 CZ ARG B 115 9.505 51.562 14.049 1.00 81.54 1CGP3150 ATOM 2996 NH1 ARG B 115 9.071 51.741 12.801 1.00 81.84 1CGP3151 ATOM 2997 NH2 ARG B 115 8.617 51.166 14.974 1.00 82.83 1CGP3152 ATOM 2998 H ARG B 115 15.144 52.523 15.426 1.00 0.00 1CGP3153 ATOM 2999 HE ARG B 115 11.057 51.697 15.317 1.00 0.00 1CGP3154 ATOM 3000 1HH1 ARG B 115 9.700 52.045 12.084 1.00 0.00 1CGP3155 ATOM 3001 2HH1 ARG B 115 8.116 51.540 12.577 1.00 0.00 1CGP3156 ATOM 3002 1HH2 ARG B 115 8.912 51.044 15.922 1.00 0.00 1CGP3157 ATOM 3003 2HH2 ARG B 115 7.671 50.964 14.713 1.00 0.00 1CGP3158 ATOM 3004 N LEU B 116 16.787 54.504 13.192 1.00 59.38 1CGP3159 ATOM 3005 CA LEU B 116 17.721 55.425 12.567 1.00 54.92 1CGP3160 ATOM 3006 C LEU B 116 19.123 54.818 12.498 1.00 52.82 1CGP3161 ATOM 3007 O LEU B 116 19.751 54.911 11.441 1.00 53.36 1CGP3162 ATOM 3008 CB LEU B 116 17.733 56.722 13.361 1.00 53.65 1CGP3163 ATOM 3009 CG LEU B 116 18.725 57.826 13.025 1.00 53.82 1CGP3164 ATOM 3010 CD1 LEU B 116 18.667 58.200 11.561 1.00 54.30 1CGP3165 ATOM 3011 CD2 LEU B 116 18.382 59.033 13.849 1.00 53.48 1CGP3166 ATOM 3012 H LEU B 116 16.315 54.781 13.998 1.00 0.00 1CGP3167 ATOM 3013 N SER B 117 19.655 54.160 13.540 1.00 48.51 1CGP3168 ATOM 3014 CA SER B 117 20.983 53.566 13.500 1.00 43.66 1CGP3169 ATOM 3015 C SER B 117 21.083 52.456 12.504 1.00 41.58 1CGP3170 ATOM 3016 O SER B 117 22.135 52.204 11.916 1.00 41.37 1CGP3171 ATOM 3017 CB SER B 117 21.376 52.981 14.812 1.00 43.39 1CGP3172 ATOM 3018 OG SER B 117 21.415 54.015 15.763 1.00 44.07 1CGP3173 ATOM 3019 H SER B 117 19.168 54.129 14.388 1.00 0.00 1CGP3174 ATOM 3020 HG SER B 117 20.494 54.197 15.995 1.00 0.00 1CGP3175 ATOM 3021 N ALA B 118 19.970 51.786 12.328 1.00 38.93 1CGP3176 ATOM 3022 CA ALA B 118 19.916 50.761 11.326 1.00 40.16 1CGP3177 ATOM 3023 C ALA B 118 20.200 51.387 9.981 1.00 41.08 1CGP3178 ATOM 3024 O ALA B 118 21.069 50.912 9.250 1.00 41.74 1CGP3179 ATOM 3025 CB ALA B 118 18.554 50.136 11.300 1.00 40.50 1CGP3180 ATOM 3026 H ALA B 118 19.232 51.907 12.959 1.00 0.00 1CGP3181 ATOM 3027 N GLN B 119 19.519 52.509 9.709 1.00 43.22 1CGP3182 ATOM 3028 CA GLN B 119 19.737 53.262 8.487 1.00 45.41 1CGP3183 ATOM 3029 C GLN B 119 21.181 53.696 8.333 1.00 45.17 1CGP3184 ATOM 3030 O GLN B 119 21.795 53.433 7.297 1.00 46.97 1CGP3185 ATOM 3031 CB GLN B 119 18.812 54.473 8.460 1.00 46.46 1CGP3186 ATOM 3032 CG GLN B 119 17.570 53.912 7.826 1.00 49.79 1CGP3187 ATOM 3033 CD GLN B 119 16.422 54.877 7.610 1.00 52.22 1CGP3188 ATOM 3034 OE1 GLN B 119 16.583 56.086 7.465 1.00 53.68 1CGP3189 ATOM 3035 NE2 GLN B 119 15.214 54.333 7.561 1.00 53.26 1CGP3190 ATOM 3036 H GLN B 119 18.800 52.770 10.324 1.00 0.00 1CGP3191 ATOM 3037 1HE2 GLN B 119 15.143 53.370 7.690 1.00 0.00 1CGP3192 ATOM 3038 2HE2 GLN B 119 14.436 54.910 7.413 1.00 0.00 1CGP3193 ATOM 3039 N MET B 120 21.750 54.302 9.363 1.00 43.87 1CGP3194 ATOM 3040 CA MET B 120 23.156 54.665 9.382 1.00 42.96 1CGP3195 ATOM 3041 C MET B 120 24.021 53.452 8.962 1.00 44.11 1CGP3196 ATOM 3042 O MET B 120 24.759 53.520 7.968 1.00 43.42 1CGP3197 ATOM 3043 CB MET B 120 23.481 55.116 10.786 1.00 42.54 1CGP3198 ATOM 3044 CG MET B 120 22.653 56.253 11.334 1.00 41.68 1CGP3199 ATOM 3045 SD MET B 120 23.667 57.741 11.474 1.00 42.71 1CGP3200 ATOM 3046 CE MET B 120 24.674 57.129 12.787 1.00 40.64 1CGP3201 ATOM 3047 H MET B 120 21.145 54.539 10.099 1.00 0.00 1CGP3202 ATOM 3048 N ALA B 121 23.878 52.295 9.628 1.00 44.64 1CGP3203 ATOM 3049 CA ALA B 121 24.602 51.083 9.304 1.00 44.01 1CGP3204 ATOM 3050 C ALA B 121 24.510 50.714 7.831 1.00 45.84 1CGP3205 ATOM 3051 O ALA B 121 25.561 50.461 7.233 1.00 47.84 1CGP3206 ATOM 3052 CB ALA B 121 24.048 49.951 10.120 1.00 43.08 1CGP3207 ATOM 3053 H ALA B 121 23.249 52.263 10.373 1.00 0.00 1CGP3208 ATOM 3054 N ARG B 122 23.325 50.730 7.187 1.00 46.72 1CGP3209 ATOM 3055 CA ARG B 122 23.197 50.430 5.754 1.00 47.97 1CGP3210 ATOM 3056 C ARG B 122 23.925 51.388 4.866 1.00 46.43 1CGP3211 ATOM 3057 O ARG B 122 24.648 50.917 3.997 1.00 46.15 1CGP3212 ATOM 3058 CB ARG B 122 21.801 50.473 5.140 1.00 53.11 1CGP3213 ATOM 3059 CG ARG B 122 21.105 49.136 4.844 1.00 59.99 1CGP3214 ATOM 3060 CD ARG B 122 21.817 48.089 3.951 1.00 64.38 1CGP3215 ATOM 3061 NE ARG B 122 23.015 47.447 4.508 1.00 69.74 1CGP3216 ATOM 3062 CZ ARG B 122 23.098 46.848 5.728 1.00 72.31 1CGP3217 ATOM 3063 NH1 ARG B 122 22.073 46.728 6.597 1.00 74.74 1CGP3218 ATOM 3064 NH2 ARG B 122 24.258 46.309 6.110 1.00 70.85 1CGP3219 ATOM 3065 H ARG B 122 22.528 50.882 7.736 1.00 0.00 1CGP3220 ATOM 3066 HE ARG B 122 23.824 47.465 3.955 1.00 0.00 1CGP3221 ATOM 3067 1HH1 ARG B 122 21.164 47.092 6.403 1.00 0.00 1CGP3222 ATOM 3068 2HH1 ARG B 122 22.258 46.288 7.477 1.00 0.00 1CGP3223 ATOM 3069 1HH2 ARG B 122 24.991 46.281 5.445 1.00 0.00 1CGP3224 ATOM 3070 2HH2 ARG B 122 24.375 45.903 7.015 1.00 0.00 1CGP3225 ATOM 3071 N ARG B 123 23.738 52.696 5.029 1.00 45.33 1CGP3226 ATOM 3072 CA ARG B 123 24.434 53.681 4.214 1.00 43.97 1CGP3227 ATOM 3073 C ARG B 123 25.933 53.436 4.286 1.00 43.73 1CGP3228 ATOM 3074 O ARG B 123 26.557 53.304 3.239 1.00 43.03 1CGP3229 ATOM 3075 CB ARG B 123 24.088 55.078 4.705 1.00 42.72 1CGP3230 ATOM 3076 CG ARG B 123 22.626 55.310 4.419 1.00 41.56 1CGP3231 ATOM 3077 CD ARG B 123 22.003 56.431 5.221 1.00 42.31 1CGP3232 ATOM 3078 NE ARG B 123 20.554 56.274 5.178 1.00 42.13 1CGP3233 ATOM 3079 CZ ARG B 123 19.734 57.113 5.793 1.00 41.63 1CGP3234 ATOM 3080 NH1 ARG B 123 20.188 58.128 6.511 1.00 40.92 1CGP3235 ATOM 3081 NH2 ARG B 123 18.434 56.910 5.703 1.00 40.55 1CGP3236 ATOM 3082 H ARG B 123 23.123 52.978 5.741 1.00 0.00 1CGP3237 ATOM 3083 HE ARG B 123 20.161 55.515 4.700 1.00 0.00 1CGP3238 ATOM 3084 1HH1 ARG B 123 21.168 58.288 6.614 1.00 0.00 1CGP3239 ATOM 3085 2HH1 ARG B 123 19.535 58.754 6.928 1.00 0.00 1CGP3240 ATOM 3086 1HH2 ARG B 123 18.077 56.129 5.192 1.00 0.00 1CGP3241 ATOM 3087 2HH2 ARG B 123 17.806 57.552 6.138 1.00 0.00 1CGP3242 ATOM 3088 N LEU B 124 26.518 53.221 5.471 1.00 43.84 1CGP3243 ATOM 3089 CA LEU B 124 27.946 52.923 5.591 1.00 43.79 1CGP3244 ATOM 3090 C LEU B 124 28.264 51.691 4.803 1.00 43.70 1CGP3245 ATOM 3091 O LEU B 124 29.223 51.691 4.050 1.00 45.56 1CGP3246 ATOM 3092 CB LEU B 124 28.418 52.587 6.980 1.00 44.53 1CGP3247 ATOM 3093 CG LEU B 124 29.755 53.139 7.451 1.00 45.25 1CGP3248 ATOM 3094 CD1 LEU B 124 30.069 52.454 8.763 1.00 45.42 1CGP3249 ATOM 3095 CD2 LEU B 124 30.874 52.895 6.468 1.00 44.85 1CGP3250 ATOM 3096 H LEU B 124 25.952 53.275 6.275 1.00 0.00 1CGP3251 ATOM 3097 N GLN B 125 27.464 50.656 4.952 1.00 44.87 1CGP3252 ATOM 3098 CA GLN B 125 27.663 49.417 4.245 1.00 45.63 1CGP3253 ATOM 3099 C GLN B 125 27.709 49.625 2.723 1.00 42.93 1CGP3254 ATOM 3100 O GLN B 125 28.694 49.272 2.064 1.00 40.97 1CGP3255 ATOM 3101 CB GLN B 125 26.537 48.550 4.756 1.00 49.34 1CGP3256 ATOM 3102 CG GLN B 125 26.919 47.118 4.921 1.00 56.28 1CGP3257 ATOM 3103 CD GLN B 125 26.526 46.308 3.693 1.00 61.62 1CGP3258 ATOM 3104 OE1 GLN B 125 27.103 46.460 2.612 1.00 64.39 1CGP3259 ATOM 3105 NE2 GLN B 125 25.542 45.413 3.770 1.00 63.72 1CGP3260 ATOM 3106 H GLN B 125 26.757 50.695 5.629 1.00 0.00 1CGP3261 ATOM 3107 1HE2 GLN B 125 25.061 45.246 4.606 1.00 0.00 1CGP3262 ATOM 3108 2HE2 GLN B 125 25.344 44.939 2.937 1.00 0.00 1CGP3263 ATOM 3109 N VAL B 126 26.738 50.331 2.156 1.00 41.41 1CGP3264 ATOM 3110 CA VAL B 126 26.713 50.508 0.722 1.00 42.29 1CGP3265 ATOM 3111 C VAL B 126 27.774 51.475 0.267 1.00 41.44 1CGP3266 ATOM 3112 O VAL B 126 28.311 51.297 -0.831 1.00 43.58 1CGP3267 ATOM 3113 CB VAL B 126 25.353 51.039 0.150 1.00 43.31 1CGP3268 ATOM 3114 CG1 VAL B 126 24.262 50.128 0.683 1.00 45.98 1CGP3269 ATOM 3115 CG2 VAL B 126 25.038 52.480 0.527 1.00 45.55 1CGP3270 ATOM 3116 H VAL B 126 26.034 50.681 2.730 1.00 0.00 1CGP3271 ATOM 3117 N THR B 127 28.100 52.512 1.028 1.00 38.19 1CGP3272 ATOM 3118 CA THR B 127 29.093 53.444 0.602 1.00 35.27 1CGP3273 ATOM 3119 C THR B 127 30.439 52.770 0.654 1.00 35.85 1CGP3274 ATOM 3120 O THR B 127 31.233 53.047 -0.245 1.00 38.03 1CGP3275 ATOM 3121 CB THR B 127 28.996 54.613 1.493 1.00 35.33 1CGP3276 ATOM 3122 OG1 THR B 127 27.645 55.043 1.434 1.00 36.75 1CGP3277 ATOM 3123 CG2 THR B 127 29.901 55.736 1.050 1.00 38.41 1CGP3278 ATOM 3124 H THR B 127 27.597 52.714 1.841 1.00 0.00 1CGP3279 ATOM 3125 HG1 THR B 127 27.384 55.152 0.515 1.00 0.00 1CGP3280 ATOM 3126 N SER B 128 30.722 51.870 1.609 1.00 35.46 1CGP3281 ATOM 3127 CA SER B 128 31.941 51.083 1.587 1.00 35.62 1CGP3282 ATOM 3128 C SER B 128 32.013 50.296 0.288 1.00 36.69 1CGP3283 ATOM 3129 O SER B 128 33.052 50.260 -0.388 1.00 35.39 1CGP3284 ATOM 3130 CB SER B 128 31.958 50.151 2.775 1.00 35.58 1CGP3285 ATOM 3131 OG SER B 128 32.365 50.902 3.907 1.00 36.73 1CGP3286 ATOM 3132 H SER B 128 30.154 51.791 2.402 1.00 0.00 1CGP3287 ATOM 3133 HG SER B 128 32.248 50.349 4.686 1.00 0.00 1CGP3288 ATOM 3134 N GLU B 129 30.880 49.731 -0.130 1.00 38.01 1CGP3289 ATOM 3135 CA GLU B 129 30.816 49.078 -1.422 1.00 39.79 1CGP3290 ATOM 3136 C GLU B 129 31.222 50.087 -2.479 1.00 39.02 1CGP3291 ATOM 3137 O GLU B 129 32.134 49.768 -3.234 1.00 39.97 1CGP3292 ATOM 3138 CB GLU B 129 29.418 48.599 -1.723 1.00 42.21 1CGP3293 ATOM 3139 CG GLU B 129 29.295 47.733 -2.964 1.00 46.42 1CGP3294 ATOM 3140 CD GLU B 129 27.876 47.515 -3.481 1.00 49.42 1CGP3295 ATOM 3141 OE1 GLU B 129 26.944 48.204 -3.047 1.00 51.07 1CGP3296 ATOM 3142 OE2 GLU B 129 27.720 46.657 -4.353 1.00 50.26 1CGP3297 ATOM 3143 H GLU B 129 30.121 49.669 0.491 1.00 0.00 1CGP3298 ATOM 3144 N LYS B 130 30.666 51.308 -2.518 1.00 39.27 1CGP3299 ATOM 3145 CA LYS B 130 31.017 52.290 -3.545 1.00 37.89 1CGP3300 ATOM 3146 C LYS B 130 32.493 52.652 -3.599 1.00 37.06 1CGP3301 ATOM 3147 O LYS B 130 33.021 52.837 -4.704 1.00 36.21 1CGP3302 ATOM 3148 CB LYS B 130 30.229 53.582 -3.383 1.00 37.60 1CGP3303 ATOM 3149 CG LYS B 130 30.020 54.156 -4.763 1.00 38.30 1CGP3304 ATOM 3150 CD LYS B 130 29.263 55.462 -4.728 1.00 42.03 1CGP3305 ATOM 3151 CE LYS B 130 28.685 55.637 -6.120 1.00 43.73 1CGP3306 ATOM 3152 NZ LYS B 130 28.086 56.939 -6.298 1.00 44.33 1CGP3307 ATOM 3153 H LYS B 130 29.919 51.473 -1.910 1.00 0.00 1CGP3308 ATOM 3154 1HZ LYS B 130 28.813 57.681 -6.221 1.00 0.00 1CGP3309 ATOM 3155 2HZ LYS B 130 27.350 57.100 -5.581 1.00 0.00 1CGP3310 ATOM 3156 3HZ LYS B 130 27.661 56.989 -7.247 1.00 0.00 1CGP3311 ATOM 3157 N VAL B 131 33.179 52.756 -2.457 1.00 34.28 1CGP3312 ATOM 3158 CA VAL B 131 34.616 52.938 -2.480 1.00 34.23 1CGP3313 ATOM 3159 C VAL B 131 35.197 51.727 -3.192 1.00 34.93 1CGP3314 ATOM 3160 O VAL B 131 36.007 51.892 -4.100 1.00 36.62 1CGP3315 ATOM 3161 CB VAL B 131 35.186 53.020 -1.069 1.00 34.67 1CGP3316 ATOM 3162 CG1 VAL B 131 36.715 53.135 -1.081 1.00 35.44 1CGP3317 ATOM 3163 CG2 VAL B 131 34.638 54.257 -0.417 1.00 36.16 1CGP3318 ATOM 3164 H VAL B 131 32.663 52.788 -1.623 1.00 0.00 1CGP3319 ATOM 3165 N GLY B 132 34.766 50.513 -2.850 1.00 35.24 1CGP3320 ATOM 3166 CA GLY B 132 35.235 49.296 -3.498 1.00 36.62 1CGP3321 ATOM 3167 C GLY B 132 35.090 49.351 -5.013 1.00 37.64 1CGP3322 ATOM 3168 O GLY B 132 36.067 49.317 -5.765 1.00 37.42 1CGP3323 ATOM 3169 H GLY B 132 34.129 50.436 -2.104 1.00 0.00 1CGP3324 ATOM 3170 N ASN B 133 33.868 49.512 -5.476 1.00 37.54 1CGP3325 ATOM 3171 CA ASN B 133 33.582 49.633 -6.892 1.00 38.23 1CGP3326 ATOM 3172 C ASN B 133 34.352 50.757 -7.563 1.00 37.38 1CGP3327 ATOM 3173 O ASN B 133 34.842 50.573 -8.673 1.00 37.63 1CGP3328 ATOM 3174 CB ASN B 133 32.110 49.887 -7.138 1.00 39.77 1CGP3329 ATOM 3175 CG ASN B 133 31.216 48.724 -6.787 1.00 42.66 1CGP3330 ATOM 3176 OD1 ASN B 133 31.551 47.866 -5.976 1.00 45.74 1CGP3331 ATOM 3177 ND2 ASN B 133 30.029 48.638 -7.355 1.00 44.11 1CGP3332 ATOM 3178 H ASN B 133 33.164 49.538 -4.797 1.00 0.00 1CGP3333 ATOM 3179 1HD2 ASN B 133 29.765 49.339 -7.988 1.00 0.00 1CGP3334 ATOM 3180 2HD2 ASN B 133 29.490 47.862 -7.105 1.00 0.00 1CGP3335 ATOM 3181 N LEU B 134 34.527 51.922 -6.957 1.00 36.97 1CGP3336 ATOM 3182 CA LEU B 134 35.283 52.966 -7.609 1.00 37.89 1CGP3337 ATOM 3183 C LEU B 134 36.718 52.516 -7.774 1.00 37.86 1CGP3338 ATOM 3184 O LEU B 134 37.349 52.850 -8.775 1.00 39.56 1CGP3339 ATOM 3185 CB LEU B 134 35.202 54.269 -6.789 1.00 37.23 1CGP3340 ATOM 3186 CG LEU B 134 33.950 55.125 -7.030 1.00 37.77 1CGP3341 ATOM 3187 CD1 LEU B 134 33.989 56.351 -6.155 1.00 38.74 1CGP3342 ATOM 3188 CD2 LEU B 134 33.903 55.595 -8.484 1.00 36.78 1CGP3343 ATOM 3189 H LEU B 134 34.119 52.104 -6.090 1.00 0.00 1CGP3344 ATOM 3190 N ALA B 135 37.219 51.713 -6.836 1.00 36.91 1CGP3345 ATOM 3191 CA ALA B 135 38.593 51.252 -6.901 1.00 36.32 1CGP3346 ATOM 3192 C ALA B 135 38.897 49.977 -7.649 1.00 35.52 1CGP3347 ATOM 3193 O ALA B 135 40.022 49.832 -8.111 1.00 34.16 1CGP3348 ATOM 3194 CB ALA B 135 39.148 51.068 -5.502 1.00 37.31 1CGP3349 ATOM 3195 H ALA B 135 36.701 51.549 -6.019 1.00 0.00 1CGP3350 ATOM 3196 N PHE B 136 37.979 49.025 -7.747 1.00 33.57 1CGP3351 ATOM 3197 CA PHE B 136 38.269 47.754 -8.370 1.00 33.52 1CGP3352 ATOM 3198 C PHE B 136 37.597 47.453 -9.676 1.00 35.66 1CGP3353 ATOM 3199 O PHE B 136 37.923 46.452 -10.322 1.00 38.20 1CGP3354 ATOM 3200 CB PHE B 136 37.898 46.637 -7.459 1.00 33.94 1CGP3355 ATOM 3201 CG PHE B 136 38.547 46.636 -6.094 1.00 34.42 1CGP3356 ATOM 3202 CD1 PHE B 136 39.810 47.157 -5.882 1.00 33.37 1CGP3357 ATOM 3203 CD2 PHE B 136 37.823 46.117 -5.053 1.00 33.67 1CGP3358 ATOM 3204 CE1 PHE B 136 40.359 47.172 -4.621 1.00 32.40 1CGP3359 ATOM 3205 CE2 PHE B 136 38.374 46.136 -3.803 1.00 34.33 1CGP3360 ATOM 3206 CZ PHE B 136 39.633 46.661 -3.586 1.00 33.94 1CGP3361 ATOM 3207 H PHE B 136 37.126 49.165 -7.289 1.00 0.00 1CGP3362 ATOM 3208 N LEU B 137 36.614 48.244 -10.062 1.00 35.74 1CGP3363 ATOM 3209 CA LEU B 137 35.855 47.980 -11.263 1.00 36.51 1CGP3364 ATOM 3210 C LEU B 137 36.039 49.094 -12.265 1.00 40.08 1CGP3365 ATOM 3211 O LEU B 137 36.178 50.266 -11.899 1.00 41.16 1CGP3366 ATOM 3212 CB LEU B 137 34.403 47.867 -10.914 1.00 33.62 1CGP3367 ATOM 3213 CG LEU B 137 33.777 46.514 -10.868 1.00 31.90 1CGP3368 ATOM 3214 CD1 LEU B 137 34.626 45.530 -10.075 1.00 30.14 1CGP3369 ATOM 3215 CD2 LEU B 137 32.384 46.717 -10.314 1.00 30.39 1CGP3370 ATOM 3216 H LEU B 137 36.416 49.088 -9.597 1.00 0.00 1CGP3371 ATOM 3217 N ASP B 138 36.027 48.711 -13.544 1.00 43.22 1CGP3372 ATOM 3218 CA ASP B 138 36.164 49.681 -14.633 1.00 45.11 1CGP3373 ATOM 3219 C ASP B 138 34.791 50.255 -14.965 1.00 43.31 1CGP3374 ATOM 3220 O ASP B 138 33.781 49.611 -14.659 1.00 42.79 1CGP3375 ATOM 3221 CB ASP B 138 36.789 48.996 -15.874 1.00 48.54 1CGP3376 ATOM 3222 CG ASP B 138 35.962 47.918 -16.576 1.00 51.10 1CGP3377 ATOM 3223 OD1 ASP B 138 35.297 47.125 -15.904 1.00 52.92 1CGP3378 ATOM 3224 OD2 ASP B 138 35.991 47.879 -17.808 1.00 53.10 1CGP3379 ATOM 3225 H ASP B 138 35.927 47.758 -13.743 1.00 0.00 1CGP3380 ATOM 3226 N VAL B 139 34.705 51.395 -15.648 1.00 40.52 1CGP3381 ATOM 3227 CA VAL B 139 33.430 52.060 -15.851 1.00 39.06 1CGP3382 ATOM 3228 C VAL B 139 32.346 51.144 -16.374 1.00 37.47 1CGP3383 ATOM 3229 O VAL B 139 31.248 51.136 -15.818 1.00 37.48 1CGP3384 ATOM 3230 CB VAL B 139 33.645 53.267 -16.787 1.00 39.89 1CGP3385 ATOM 3231 CG1 VAL B 139 32.368 54.024 -17.108 1.00 39.35 1CGP3386 ATOM 3232 CG2 VAL B 139 34.452 54.292 -16.011 1.00 41.73 1CGP3387 ATOM 3233 H VAL B 139 35.534 51.786 -15.984 1.00 0.00 1CGP3388 ATOM 3234 N THR B 140 32.664 50.278 -17.321 1.00 35.34 1CGP3389 ATOM 3235 CA THR B 140 31.667 49.361 -17.843 1.00 35.30 1CGP3390 ATOM 3236 C THR B 140 31.057 48.532 -16.716 1.00 32.04 1CGP3391 ATOM 3237 O THR B 140 29.844 48.485 -16.541 1.00 30.54 1CGP3392 ATOM 3238 CB THR B 140 32.359 48.486 -18.941 1.00 37.98 1CGP3393 ATOM 3239 OG1 THR B 140 33.188 49.364 -19.733 1.00 40.18 1CGP3394 ATOM 3240 CG2 THR B 140 31.345 47.741 -19.819 1.00 36.86 1CGP3395 ATOM 3241 H THR B 140 33.508 50.354 -17.812 1.00 0.00 1CGP3396 ATOM 3242 HG1 THR B 140 33.550 48.887 -20.488 1.00 0.00 1CGP3397 ATOM 3243 N GLY B 141 31.892 48.034 -15.824 1.00 30.43 1CGP3398 ATOM 3244 CA GLY B 141 31.426 47.199 -14.738 1.00 31.18 1CGP3399 ATOM 3245 C GLY B 141 30.623 48.002 -13.742 1.00 31.72 1CGP3400 ATOM 3246 O GLY B 141 29.644 47.524 -13.166 1.00 31.56 1CGP3401 ATOM 3247 H GLY B 141 32.817 48.339 -15.809 1.00 0.00 1CGP3402 ATOM 3248 N ARG B 142 31.033 49.242 -13.529 1.00 32.33 1CGP3403 ATOM 3249 CA ARG B 142 30.269 50.128 -12.674 1.00 32.72 1CGP3404 ATOM 3250 C ARG B 142 28.888 50.355 -13.259 1.00 32.43 1CGP3405 ATOM 3251 O ARG B 142 27.906 50.186 -12.535 1.00 32.13 1CGP3406 ATOM 3252 CB ARG B 142 30.928 51.454 -12.532 1.00 34.67 1CGP3407 ATOM 3253 CG ARG B 142 32.117 51.377 -11.620 1.00 36.95 1CGP3408 ATOM 3254 CD ARG B 142 32.556 52.797 -11.383 1.00 38.18 1CGP3409 ATOM 3255 NE ARG B 142 33.954 52.867 -11.707 1.00 39.47 1CGP3410 ATOM 3256 CZ ARG B 142 34.507 53.974 -12.174 1.00 41.52 1CGP3411 ATOM 3257 NH1 ARG B 142 33.854 55.111 -12.360 1.00 40.33 1CGP3412 ATOM 3258 NH2 ARG B 142 35.792 53.916 -12.461 1.00 45.55 1CGP3413 ATOM 3259 H ARG B 142 31.885 49.511 -13.927 1.00 0.00 1CGP3414 ATOM 3260 HE ARG B 142 34.521 52.077 -11.593 1.00 0.00 1CGP3415 ATOM 3261 1HH1 ARG B 142 32.890 55.180 -12.137 1.00 0.00 1CGP3416 ATOM 3262 2HH1 ARG B 142 34.347 55.903 -12.721 1.00 0.00 1CGP3417 ATOM 3263 1HH2 ARG B 142 36.258 53.045 -12.320 1.00 0.00 1CGP3418 ATOM 3264 2HH2 ARG B 142 36.285 54.707 -12.821 1.00 0.00 1CGP3419 ATOM 3265 N ILE B 143 28.792 50.644 -14.567 1.00 30.56 1CGP3420 ATOM 3266 CA ILE B 143 27.510 50.852 -15.204 1.00 28.96 1CGP3421 ATOM 3267 C ILE B 143 26.684 49.569 -15.161 1.00 29.69 1CGP3422 ATOM 3268 O ILE B 143 25.464 49.606 -14.976 1.00 30.26 1CGP3423 ATOM 3269 CB ILE B 143 27.775 51.373 -16.644 1.00 26.79 1CGP3424 ATOM 3270 CG1 ILE B 143 28.430 52.757 -16.563 1.00 25.40 1CGP3425 ATOM 3271 CG2 ILE B 143 26.469 51.491 -17.424 1.00 27.29 1CGP3426 ATOM 3272 CD1 ILE B 143 28.563 53.559 -17.873 1.00 22.52 1CGP3427 ATOM 3273 H ILE B 143 29.616 50.752 -15.068 1.00 0.00 1CGP3428 ATOM 3274 N ALA B 144 27.289 48.400 -15.264 1.00 31.32 1CGP3429 ATOM 3275 CA ALA B 144 26.556 47.164 -15.087 1.00 33.46 1CGP3430 ATOM 3276 C ALA B 144 26.003 47.066 -13.680 1.00 35.08 1CGP3431 ATOM 3277 O ALA B 144 24.793 46.859 -13.539 1.00 34.97 1CGP3432 ATOM 3278 CB ALA B 144 27.438 45.966 -15.290 1.00 34.12 1CGP3433 ATOM 3279 H ALA B 144 28.204 48.387 -15.591 1.00 0.00 1CGP3434 ATOM 3280 N GLN B 145 26.828 47.245 -12.635 1.00 36.54 1CGP3435 ATOM 3281 CA GLN B 145 26.339 47.172 -11.269 1.00 38.46 1CGP3436 ATOM 3282 C GLN B 145 25.194 48.136 -11.110 1.00 37.78 1CGP3437 ATOM 3283 O GLN B 145 24.147 47.727 -10.619 1.00 38.81 1CGP3438 ATOM 3284 CB GLN B 145 27.361 47.572 -10.199 1.00 40.97 1CGP3439 ATOM 3285 CG GLN B 145 28.491 46.605 -9.905 1.00 44.50 1CGP3440 ATOM 3286 CD GLN B 145 28.031 45.164 -9.815 1.00 47.16 1CGP3441 ATOM 3287 OE1 GLN B 145 28.631 44.273 -10.414 1.00 48.82 1CGP3442 ATOM 3288 NE2 GLN B 145 26.942 44.851 -9.127 1.00 48.05 1CGP3443 ATOM 3289 H GLN B 145 27.776 47.411 -12.806 1.00 0.00 1CGP3444 ATOM 3290 1HE2 GLN B 145 26.410 45.536 -8.673 1.00 0.00 1CGP3445 ATOM 3291 2HE2 GLN B 145 26.705 43.901 -9.129 1.00 0.00 1CGP3446 ATOM 3292 N THR B 146 25.332 49.382 -11.568 1.00 36.74 1CGP3447 ATOM 3293 CA THR B 146 24.293 50.384 -11.448 1.00 34.43 1CGP3448 ATOM 3294 C THR B 146 22.970 50.041 -12.103 1.00 33.10 1CGP3449 ATOM 3295 O THR B 146 21.964 50.186 -11.426 1.00 30.34 1CGP3450 ATOM 3296 CB THR B 146 24.890 51.667 -11.979 1.00 33.28 1CGP3451 ATOM 3297 OG1 THR B 146 26.049 51.873 -11.174 1.00 32.27 1CGP3452 ATOM 3298 CG2 THR B 146 23.955 52.853 -11.911 1.00 33.31 1CGP3453 ATOM 3299 H THR B 146 26.196 49.677 -11.924 1.00 0.00 1CGP3454 ATOM 3300 HG1 THR B 146 26.016 52.747 -10.783 1.00 0.00 1CGP3455 ATOM 3301 N LEU B 147 22.878 49.575 -13.343 1.00 32.79 1CGP3456 ATOM 3302 CA LEU B 147 21.613 49.151 -13.914 1.00 33.56 1CGP3457 ATOM 3303 C LEU B 147 21.050 47.992 -13.108 1.00 36.24 1CGP3458 ATOM 3304 O LEU B 147 19.861 47.941 -12.844 1.00 37.39 1CGP3459 ATOM 3305 CB LEU B 147 21.851 48.759 -15.352 1.00 30.70 1CGP3460 ATOM 3306 CG LEU B 147 22.409 49.914 -16.153 1.00 30.65 1CGP3461 ATOM 3307 CD1 LEU B 147 22.768 49.440 -17.540 1.00 29.49 1CGP3462 ATOM 3308 CD2 LEU B 147 21.404 51.052 -16.151 1.00 29.49 1CGP3463 ATOM 3309 H LEU B 147 23.703 49.500 -13.879 1.00 0.00 1CGP3464 ATOM 3310 N LEU B 148 21.858 47.075 -12.607 1.00 40.08 1CGP3465 ATOM 3311 CA LEU B 148 21.391 45.994 -11.749 1.00 43.87 1CGP3466 ATOM 3312 C LEU B 148 20.682 46.490 -10.491 1.00 44.71 1CGP3467 ATOM 3313 O LEU B 148 19.601 46.047 -10.086 1.00 46.82 1CGP3468 ATOM 3314 CB LEU B 148 22.558 45.168 -11.310 1.00 47.02 1CGP3469 ATOM 3315 CG LEU B 148 22.492 43.710 -11.579 1.00 50.05 1CGP3470 ATOM 3316 CD1 LEU B 148 22.680 43.438 -13.074 1.00 51.23 1CGP3471 ATOM 3317 CD2 LEU B 148 23.553 43.050 -10.707 1.00 52.36 1CGP3472 ATOM 3318 H LEU B 148 22.813 47.076 -12.861 1.00 0.00 1CGP3473 ATOM 3319 N ASN B 149 21.368 47.431 -9.860 1.00 43.70 1CGP3474 ATOM 3320 CA ASN B 149 20.892 48.080 -8.664 1.00 42.70 1CGP3475 ATOM 3321 C ASN B 149 19.680 48.923 -8.965 1.00 40.98 1CGP3476 ATOM 3322 O ASN B 149 18.702 48.865 -8.237 1.00 39.73 1CGP3477 ATOM 3323 CB ASN B 149 21.972 48.971 -8.089 1.00 45.76 1CGP3478 ATOM 3324 CG ASN B 149 23.181 48.191 -7.601 1.00 47.97 1CGP3479 ATOM 3325 OD1 ASN B 149 23.142 46.968 -7.471 1.00 49.46 1CGP3480 ATOM 3326 ND2 ASN B 149 24.315 48.843 -7.336 1.00 50.01 1CGP3481 ATOM 3327 H ASN B 149 22.283 47.585 -10.158 1.00 0.00 1CGP3482 ATOM 3328 1HD2 ASN B 149 24.341 49.801 -7.525 1.00 0.00 1CGP3483 ATOM 3329 2HD2 ASN B 149 25.050 48.334 -6.944 1.00 0.00 1CGP3484 ATOM 3330 N LEU B 150 19.656 49.720 -10.022 1.00 38.63 1CGP3485 ATOM 3331 CA LEU B 150 18.524 50.542 -10.365 1.00 36.57 1CGP3486 ATOM 3332 C LEU B 150 17.353 49.668 -10.702 1.00 36.62 1CGP3487 ATOM 3333 O LEU B 150 16.239 50.049 -10.411 1.00 36.43 1CGP3488 ATOM 3334 CB LEU B 150 18.901 51.457 -11.528 1.00 34.82 1CGP3489 ATOM 3335 CG LEU B 150 19.897 52.569 -11.177 1.00 33.27 1CGP3490 ATOM 3336 CD1 LEU B 150 20.422 53.282 -12.411 1.00 33.31 1CGP3491 ATOM 3337 CD2 LEU B 150 19.186 53.554 -10.286 1.00 32.40 1CGP3492 ATOM 3338 H LEU B 150 20.448 49.769 -10.574 1.00 0.00 1CGP3493 ATOM 3339 N ALA B 151 17.501 48.472 -11.231 1.00 38.99 1CGP3494 ATOM 3340 CA ALA B 151 16.337 47.637 -11.404 1.00 44.60 1CGP3495 ATOM 3341 C ALA B 151 15.832 47.084 -10.087 1.00 49.54 1CGP3496 ATOM 3342 O ALA B 151 14.783 46.448 -9.996 1.00 51.91 1CGP3497 ATOM 3343 CB ALA B 151 16.683 46.499 -12.290 1.00 44.79 1CGP3498 ATOM 3344 H ALA B 151 18.347 48.209 -11.651 1.00 0.00 1CGP3499 ATOM 3345 N LYS B 152 16.605 47.296 -9.050 1.00 55.07 1CGP3500 ATOM 3346 CA LYS B 152 16.261 46.848 -7.722 1.00 60.85 1CGP3501 ATOM 3347 C LYS B 152 15.777 48.085 -6.910 1.00 61.19 1CGP3502 ATOM 3348 O LYS B 152 14.999 47.994 -5.958 1.00 61.63 1CGP3503 ATOM 3349 CB LYS B 152 17.576 46.149 -7.269 1.00 65.72 1CGP3504 ATOM 3350 CG LYS B 152 17.635 45.144 -6.113 1.00 71.37 1CGP3505 ATOM 3351 CD LYS B 152 17.605 43.617 -6.402 1.00 74.75 1CGP3506 ATOM 3352 CE LYS B 152 17.356 42.887 -5.025 1.00 77.00 1CGP3507 ATOM 3353 NZ LYS B 152 17.328 41.423 -5.013 1.00 76.89 1CGP3508 ATOM 3354 H LYS B 152 17.475 47.710 -9.199 1.00 0.00 1CGP3509 ATOM 3355 1HZ LYS B 152 18.261 41.060 -5.291 1.00 0.00 1CGP3510 ATOM 3356 2HZ LYS B 152 16.603 41.079 -5.672 1.00 0.00 1CGP3511 ATOM 3357 3HZ LYS B 152 17.100 41.099 -4.051 1.00 0.00 1CGP3512 ATOM 3358 N GLN B 153 16.181 49.308 -7.252 1.00 62.72 1CGP3513 ATOM 3359 CA GLN B 153 15.798 50.549 -6.586 1.00 62.80 1CGP3514 ATOM 3360 C GLN B 153 14.323 50.852 -6.795 1.00 63.04 1CGP3515 ATOM 3361 O GLN B 153 13.945 51.230 -7.901 1.00 62.02 1CGP3516 ATOM 3362 CB GLN B 153 16.598 51.691 -7.152 1.00 63.44 1CGP3517 ATOM 3363 CG GLN B 153 17.152 52.720 -6.203 1.00 65.14 1CGP3518 ATOM 3364 CD GLN B 153 16.138 53.505 -5.403 1.00 66.25 1CGP3519 ATOM 3365 OE1 GLN B 153 15.374 54.358 -5.853 1.00 67.04 1CGP3520 ATOM 3366 NE2 GLN B 153 16.165 53.190 -4.127 1.00 68.18 1CGP3521 ATOM 3367 H GLN B 153 16.822 49.354 -7.981 1.00 0.00 1CGP3522 ATOM 3368 1HE2 GLN B 153 16.784 52.503 -3.818 1.00 0.00 1CGP3523 ATOM 3369 2HE2 GLN B 153 15.588 53.701 -3.519 1.00 0.00 1CGP3524 ATOM 3370 N PRO B 154 13.475 50.771 -5.772 1.00 64.49 1CGP3525 ATOM 3371 CA PRO B 154 12.019 50.751 -5.873 1.00 64.50 1CGP3526 ATOM 3372 C PRO B 154 11.239 51.727 -6.752 1.00 63.89 1CGP3527 ATOM 3373 O PRO B 154 10.450 52.505 -6.228 1.00 64.66 1CGP3528 ATOM 3374 CB PRO B 154 11.595 50.811 -4.417 1.00 64.66 1CGP3529 ATOM 3375 CG PRO B 154 12.726 51.538 -3.725 1.00 64.59 1CGP3530 ATOM 3376 CD PRO B 154 13.881 50.801 -4.368 1.00 65.13 1CGP3531 ATOM 3377 N ASP B 155 11.404 51.745 -8.065 1.00 62.64 1CGP3532 ATOM 3378 CA ASP B 155 10.650 52.590 -8.967 1.00 63.21 1CGP3533 ATOM 3379 C ASP B 155 10.932 52.150 -10.390 1.00 64.57 1CGP3534 ATOM 3380 O ASP B 155 10.872 52.921 -11.352 1.00 65.54 1CGP3535 ATOM 3381 CB ASP B 155 11.037 54.055 -8.823 1.00 64.76 1CGP3536 ATOM 3382 CG ASP B 155 12.533 54.285 -8.665 1.00 67.83 1CGP3537 ATOM 3383 OD1 ASP B 155 13.306 53.992 -9.588 1.00 68.85 1CGP3538 ATOM 3384 OD2 ASP B 155 12.909 54.744 -7.583 1.00 70.15 1CGP3539 ATOM 3385 H ASP B 155 12.156 51.244 -8.443 1.00 0.00 1CGP3540 ATOM 3386 N ALA B 156 11.282 50.883 -10.548 1.00 65.11 1CGP3541 ATOM 3387 CA ALA B 156 11.457 50.348 -11.873 1.00 66.88 1CGP3542 ATOM 3388 C ALA B 156 10.122 49.695 -12.181 1.00 68.83 1CGP3543 ATOM 3389 O ALA B 156 9.542 49.002 -11.343 1.00 69.15 1CGP3544 ATOM 3390 CB ALA B 156 12.531 49.296 -11.883 1.00 66.96 1CGP3545 ATOM 3391 H ALA B 156 11.285 50.251 -9.803 1.00 0.00 1CGP3546 ATOM 3392 N MET B 157 9.557 49.924 -13.349 1.00 72.85 1CGP3547 ATOM 3393 CA MET B 157 8.306 49.282 -13.707 1.00 76.29 1CGP3548 ATOM 3394 C MET B 157 8.761 47.925 -14.191 1.00 76.22 1CGP3549 ATOM 3395 O MET B 157 9.826 47.747 -14.796 1.00 78.02 1CGP3550 ATOM 3396 CB MET B 157 7.567 49.954 -14.874 1.00 79.69 1CGP3551 ATOM 3397 CG MET B 157 7.131 51.400 -14.656 1.00 84.14 1CGP3552 ATOM 3398 SD MET B 157 8.486 52.524 -14.181 1.00 90.09 1CGP3553 ATOM 3399 CE MET B 157 9.395 52.832 -15.685 1.00 89.18 1CGP3554 ATOM 3400 H MET B 157 10.095 50.384 -14.021 1.00 0.00 1CGP3555 ATOM 3401 N THR B 158 7.969 46.953 -13.831 1.00 75.17 1CGP3556 ATOM 3402 CA THR B 158 8.102 45.600 -14.298 1.00 74.10 1CGP3557 ATOM 3403 C THR B 158 8.171 45.554 -15.820 1.00 73.87 1CGP3558 ATOM 3404 O THR B 158 7.469 46.355 -16.447 1.00 74.50 1CGP3559 ATOM 3405 CB THR B 158 6.886 44.967 -13.712 1.00 74.90 1CGP3560 ATOM 3406 OG1 THR B 158 7.085 45.075 -12.294 1.00 76.70 1CGP3561 ATOM 3407 CG2 THR B 158 6.602 43.590 -14.271 1.00 75.99 1CGP3562 ATOM 3408 H THR B 158 7.276 47.127 -13.162 1.00 0.00 1CGP3563 ATOM 3409 HG1 THR B 158 7.951 44.722 -12.064 1.00 0.00 1CGP3564 ATOM 3410 N HIS B 159 8.975 44.716 -16.470 1.00 73.91 1CGP3565 ATOM 3411 CA HIS B 159 8.887 44.611 -17.918 1.00 74.13 1CGP3566 ATOM 3412 C HIS B 159 8.845 43.114 -18.135 1.00 74.32 1CGP3567 ATOM 3413 O HIS B 159 9.627 42.408 -17.510 1.00 73.21 1CGP3568 ATOM 3414 CB HIS B 159 10.112 45.209 -18.593 1.00 75.16 1CGP3569 ATOM 3415 CG HIS B 159 9.980 45.477 -20.095 1.00 75.92 1CGP3570 ATOM 3416 ND1 HIS B 159 10.419 44.747 -21.122 1.00 76.59 1CGP3571 ATOM 3417 CD2 HIS B 159 9.395 46.605 -20.632 1.00 75.95 1CGP3572 ATOM 3418 CE1 HIS B 159 10.136 45.386 -22.239 1.00 76.73 1CGP3573 ATOM 3419 NE2 HIS B 159 9.522 46.506 -21.931 1.00 76.44 1CGP3574 ATOM 3420 H HIS B 159 9.627 44.127 -16.018 1.00 0.00 1CGP3575 ATOM 3421 HD1 HIS B 159 10.986 43.940 -21.060 1.00 0.00 1CGP3576 ATOM 3422 HE2 HIS B 159 9.260 47.213 -22.566 1.00 0.00 1CGP3577 ATOM 3423 N PRO B 160 7.988 42.557 -18.995 1.00 75.42 1CGP3578 ATOM 3424 CA PRO B 160 7.601 41.140 -18.991 1.00 77.03 1CGP3579 ATOM 3425 C PRO B 160 8.785 40.183 -19.043 1.00 78.24 1CGP3580 ATOM 3426 O PRO B 160 8.818 39.088 -18.470 1.00 78.16 1CGP3581 ATOM 3427 CB PRO B 160 6.672 41.035 -20.176 1.00 77.54 1CGP3582 ATOM 3428 CG PRO B 160 7.174 42.116 -21.104 1.00 77.09 1CGP3583 ATOM 3429 CD PRO B 160 7.373 43.244 -20.118 1.00 76.42 1CGP3584 ATOM 3430 N ASP B 161 9.741 40.689 -19.809 1.00 79.10 1CGP3585 ATOM 3431 CA ASP B 161 11.049 40.122 -19.889 1.00 79.66 1CGP3586 ATOM 3432 C ASP B 161 11.820 41.419 -19.642 1.00 76.84 1CGP3587 ATOM 3433 O ASP B 161 11.751 42.346 -20.467 1.00 75.97 1CGP3588 ATOM 3434 CB ASP B 161 11.264 39.525 -21.299 1.00 83.55 1CGP3589 ATOM 3435 CG ASP B 161 10.482 38.226 -21.610 1.00 85.94 1CGP3590 ATOM 3436 OD1 ASP B 161 10.548 37.264 -20.824 1.00 87.00 1CGP3591 ATOM 3437 OD2 ASP B 161 9.824 38.178 -22.661 1.00 86.17 1CGP3592 ATOM 3438 H ASP B 161 9.583 41.504 -20.314 1.00 0.00 1CGP3593 ATOM 3439 N GLY B 162 12.230 41.576 -18.373 1.00 74.40 1CGP3594 ATOM 3440 CA GLY B 162 13.127 42.629 -17.908 1.00 71.05 1CGP3595 ATOM 3441 C GLY B 162 12.599 43.509 -16.768 1.00 68.42 1CGP3596 ATOM 3442 O GLY B 162 11.540 43.286 -16.169 1.00 68.05 1CGP3597 ATOM 3443 H GLY B 162 11.775 41.062 -17.673 1.00 0.00 1CGP3598 ATOM 3444 N MET B 163 13.377 44.530 -16.425 1.00 65.66 1CGP3599 ATOM 3445 CA MET B 163 12.938 45.559 -15.497 1.00 62.94 1CGP3600 ATOM 3446 C MET B 163 13.273 46.862 -16.177 1.00 61.01 1CGP3601 ATOM 3447 O MET B 163 14.356 46.975 -16.767 1.00 60.75 1CGP3602 ATOM 3448 CB MET B 163 13.676 45.505 -14.190 1.00 64.25 1CGP3603 ATOM 3449 CG MET B 163 13.111 44.437 -13.272 1.00 66.55 1CGP3604 ATOM 3450 SD MET B 163 11.424 44.738 -12.680 1.00 69.75 1CGP3605 ATOM 3451 CE MET B 163 11.799 45.169 -10.998 1.00 68.43 1CGP3606 ATOM 3452 H MET B 163 14.306 44.540 -16.754 1.00 0.00 1CGP3607 ATOM 3453 N GLN B 164 12.344 47.818 -16.135 1.00 57.77 1CGP3608 ATOM 3454 CA GLN B 164 12.467 49.082 -16.835 1.00 55.11 1CGP3609 ATOM 3455 C GLN B 164 12.603 50.245 -15.890 1.00 51.02 1CGP3610 ATOM 3456 O GLN B 164 11.791 50.473 -15.006 1.00 49.85 1CGP3611 ATOM 3457 CB GLN B 164 11.253 49.280 -17.697 1.00 57.44 1CGP3612 ATOM 3458 CG GLN B 164 11.114 50.614 -18.417 1.00 61.54 1CGP3613 ATOM 3459 CD GLN B 164 9.813 50.611 -19.200 1.00 64.60 1CGP3614 ATOM 3460 OE1 GLN B 164 9.779 50.516 -20.433 1.00 65.94 1CGP3615 ATOM 3461 NE2 GLN B 164 8.679 50.622 -18.503 1.00 65.70 1CGP3616 ATOM 3462 H GLN B 164 11.549 47.712 -15.577 1.00 0.00 1CGP3617 ATOM 3463 1HE2 GLN B 164 8.718 50.587 -17.528 1.00 0.00 1CGP3618 ATOM 3464 2HE2 GLN B 164 7.849 50.648 -19.019 1.00 0.00 1CGP3619 ATOM 3465 N ILE B 165 13.641 51.007 -16.132 1.00 47.48 1CGP3620 ATOM 3466 CA ILE B 165 13.969 52.135 -15.308 1.00 44.52 1CGP3621 ATOM 3467 C ILE B 165 13.989 53.356 -16.232 1.00 45.15 1CGP3622 ATOM 3468 O ILE B 165 14.238 53.228 -17.434 1.00 44.29 1CGP3623 ATOM 3469 CB ILE B 165 15.349 51.827 -14.624 1.00 42.90 1CGP3624 ATOM 3470 CG1 ILE B 165 16.442 51.663 -15.651 1.00 42.33 1CGP3625 ATOM 3471 CG2 ILE B 165 15.270 50.523 -13.825 1.00 40.72 1CGP3626 ATOM 3472 CD1 ILE B 165 17.793 51.332 -15.012 1.00 43.42 1CGP3627 ATOM 3473 H ILE B 165 14.193 50.811 -16.919 1.00 0.00 1CGP3628 ATOM 3474 N LYS B 166 13.660 54.550 -15.743 1.00 46.18 1CGP3629 ATOM 3475 CA LYS B 166 13.753 55.780 -16.517 1.00 46.82 1CGP3630 ATOM 3476 C LYS B 166 15.022 56.359 -15.907 1.00 44.35 1CGP3631 ATOM 3477 O LYS B 166 15.141 56.495 -14.683 1.00 41.62 1CGP3632 ATOM 3478 CB LYS B 166 12.547 56.759 -16.261 1.00 51.42 1CGP3633 ATOM 3479 CG LYS B 166 12.539 58.129 -17.064 1.00 56.77 1CGP3634 ATOM 3480 CD LYS B 166 11.508 59.280 -16.753 1.00 57.99 1CGP3635 ATOM 3481 CE LYS B 166 9.971 59.025 -16.881 1.00 59.28 1CGP3636 ATOM 3482 NZ LYS B 166 9.454 58.656 -18.200 1.00 59.19 1CGP3637 ATOM 3483 H LYS B 166 13.438 54.631 -14.792 1.00 0.00 1CGP3638 ATOM 3484 1HZ LYS B 166 9.924 57.787 -18.526 1.00 0.00 1CGP3639 ATOM 3485 2HZ LYS B 166 9.623 59.423 -18.882 1.00 0.00 1CGP3640 ATOM 3486 3HZ LYS B 166 8.430 58.481 -18.130 1.00 0.00 1CGP3641 ATOM 3487 N ILE B 167 16.002 56.685 -16.726 1.00 42.64 1CGP3642 ATOM 3488 CA ILE B 167 17.254 57.194 -16.206 1.00 40.48 1CGP3643 ATOM 3489 C ILE B 167 17.902 57.904 -17.387 1.00 41.28 1CGP3644 ATOM 3490 O ILE B 167 17.634 57.614 -18.551 1.00 42.05 1CGP3645 ATOM 3491 CB ILE B 167 18.114 55.988 -15.649 1.00 39.40 1CGP3646 ATOM 3492 CG1 ILE B 167 19.330 56.523 -14.938 1.00 37.17 1CGP3647 ATOM 3493 CG2 ILE B 167 18.541 55.023 -16.754 1.00 39.11 1CGP3648 ATOM 3494 CD1 ILE B 167 19.066 56.972 -13.506 1.00 36.05 1CGP3649 ATOM 3495 H ILE B 167 15.840 56.717 -17.700 1.00 0.00 1CGP3650 ATOM 3496 N THR B 168 18.742 58.877 -17.106 1.00 41.84 1CGP3651 ATOM 3497 CA THR B 168 19.426 59.587 -18.151 1.00 42.93 1CGP3652 ATOM 3498 C THR B 168 20.893 59.196 -18.081 1.00 42.02 1CGP3653 ATOM 3499 O THR B 168 21.438 58.948 -16.998 1.00 41.36 1CGP3654 ATOM 3500 CB THR B 168 19.139 61.111 -17.919 1.00 44.01 1CGP3655 ATOM 3501 OG1 THR B 168 19.689 61.758 -19.039 1.00 47.77 1CGP3656 ATOM 3502 CG2 THR B 168 19.800 61.770 -16.734 1.00 43.35 1CGP3657 ATOM 3503 H THR B 168 18.923 59.096 -16.173 1.00 0.00 1CGP3658 ATOM 3504 HG1 THR B 168 19.104 61.637 -19.810 1.00 0.00 1CGP3659 ATOM 3505 N ARG B 169 21.544 59.138 -19.244 1.00 41.90 1CGP3660 ATOM 3506 CA ARG B 169 22.976 58.867 -19.334 1.00 41.20 1CGP3661 ATOM 3507 C ARG B 169 23.720 59.793 -18.401 1.00 41.71 1CGP3662 ATOM 3508 O ARG B 169 24.623 59.342 -17.716 1.00 42.20 1CGP3663 ATOM 3509 CB ARG B 169 23.560 59.100 -20.732 1.00 40.37 1CGP3664 ATOM 3510 CG ARG B 169 23.239 58.136 -21.886 1.00 39.37 1CGP3665 ATOM 3511 CD ARG B 169 21.815 58.215 -22.391 1.00 36.97 1CGP3666 ATOM 3512 NE ARG B 169 21.560 57.188 -23.367 1.00 34.96 1CGP3667 ATOM 3513 CZ ARG B 169 20.391 56.544 -23.414 1.00 36.40 1CGP3668 ATOM 3514 NH1 ARG B 169 19.357 56.782 -22.588 1.00 36.79 1CGP3669 ATOM 3515 NH2 ARG B 169 20.253 55.620 -24.352 1.00 38.53 1CGP3670 ATOM 3516 H ARG B 169 21.017 59.264 -20.063 1.00 0.00 1CGP3671 ATOM 3517 HE ARG B 169 22.252 56.959 -24.023 1.00 0.00 1CGP3672 ATOM 3518 1HH1 ARG B 169 19.430 57.485 -21.882 1.00 0.00 1CGP3673 ATOM 3519 2HH1 ARG B 169 18.518 56.240 -22.667 1.00 0.00 1CGP3674 ATOM 3520 1HH2 ARG B 169 21.003 55.454 -24.992 1.00 0.00 1CGP3675 ATOM 3521 2HH2 ARG B 169 19.400 55.103 -24.428 1.00 0.00 1CGP3676 ATOM 3522 N GLN B 170 23.321 61.062 -18.312 1.00 42.57 1CGP3677 ATOM 3523 CA GLN B 170 23.902 61.979 -17.348 1.00 45.93 1CGP3678 ATOM 3524 C GLN B 170 23.773 61.500 -15.910 1.00 45.86 1CGP3679 ATOM 3525 O GLN B 170 24.732 61.618 -15.147 1.00 46.36 1CGP3680 ATOM 3526 CB GLN B 170 23.256 63.339 -17.383 1.00 50.34 1CGP3681 ATOM 3527 CG GLN B 170 23.547 64.172 -18.608 1.00 54.40 1CGP3682 ATOM 3528 CD GLN B 170 22.845 65.523 -18.591 1.00 57.41 1CGP3683 ATOM 3529 OE1 GLN B 170 23.445 66.529 -18.949 1.00 58.90 1CGP3684 ATOM 3530 NE2 GLN B 170 21.564 65.632 -18.238 1.00 59.33 1CGP3685 ATOM 3531 H GLN B 170 22.731 61.401 -19.016 1.00 0.00 1CGP3686 ATOM 3532 1HE2 GLN B 170 21.050 64.824 -18.044 1.00 0.00 1CGP3687 ATOM 3533 2HE2 GLN B 170 21.203 66.545 -18.203 1.00 0.00 1CGP3688 ATOM 3534 N GLU B 171 22.638 60.924 -15.505 1.00 44.11 1CGP3689 ATOM 3535 CA GLU B 171 22.476 60.476 -14.131 1.00 42.44 1CGP3690 ATOM 3536 C GLU B 171 23.415 59.299 -13.912 1.00 38.95 1CGP3691 ATOM 3537 O GLU B 171 24.147 59.294 -12.915 1.00 38.12 1CGP3692 ATOM 3538 CB GLU B 171 21.031 60.019 -13.846 1.00 45.67 1CGP3693 ATOM 3539 CG GLU B 171 19.889 60.978 -13.456 1.00 47.03 1CGP3694 ATOM 3540 CD GLU B 171 19.869 61.378 -11.991 1.00 49.21 1CGP3695 ATOM 3541 OE1 GLU B 171 20.601 62.299 -11.630 1.00 53.26 1CGP3696 ATOM 3542 OE2 GLU B 171 19.130 60.778 -11.214 1.00 47.17 1CGP3697 ATOM 3543 H GLU B 171 21.964 60.708 -16.170 1.00 0.00 1CGP3698 ATOM 3544 N ILE B 172 23.443 58.344 -14.867 1.00 34.07 1CGP3699 ATOM 3545 CA ILE B 172 24.288 57.179 -14.688 1.00 31.24 1CGP3700 ATOM 3546 C ILE B 172 25.712 57.664 -14.604 1.00 31.24 1CGP3701 ATOM 3547 O ILE B 172 26.407 57.256 -13.682 1.00 32.27 1CGP3702 ATOM 3548 CB ILE B 172 24.167 56.140 -15.831 1.00 28.72 1CGP3703 ATOM 3549 CG1 ILE B 172 22.751 55.587 -15.870 1.00 27.72 1CGP3704 ATOM 3550 CG2 ILE B 172 25.130 54.963 -15.575 1.00 26.38 1CGP3705 ATOM 3551 CD1 ILE B 172 22.481 54.567 -16.989 1.00 27.13 1CGP3706 ATOM 3552 H ILE B 172 22.858 58.437 -15.647 1.00 0.00 1CGP3707 ATOM 3553 N GLY B 173 26.152 58.576 -15.451 1.00 30.84 1CGP3708 ATOM 3554 CA GLY B 173 27.479 59.147 -15.362 1.00 31.54 1CGP3709 ATOM 3555 C GLY B 173 27.749 59.657 -13.967 1.00 32.02 1CGP3710 ATOM 3556 O GLY B 173 28.706 59.237 -13.339 1.00 31.87 1CGP3711 ATOM 3557 H GLY B 173 25.590 58.831 -16.207 1.00 0.00 1CGP3712 ATOM 3558 N GLN B 174 26.874 60.478 -13.418 1.00 33.68 1CGP3713 ATOM 3559 CA GLN B 174 27.036 61.008 -12.073 1.00 34.45 1CGP3714 ATOM 3560 C GLN B 174 27.074 59.954 -10.974 1.00 33.83 1CGP3715 ATOM 3561 O GLN B 174 27.658 60.205 -9.921 1.00 35.71 1CGP3716 ATOM 3562 CB GLN B 174 25.906 61.963 -11.763 1.00 36.10 1CGP3717 ATOM 3563 CG GLN B 174 25.866 63.142 -12.702 1.00 40.47 1CGP3718 ATOM 3564 CD GLN B 174 24.685 64.081 -12.516 1.00 44.47 1CGP3719 ATOM 3565 OE1 GLN B 174 24.635 65.092 -13.215 1.00 47.12 1CGP3720 ATOM 3566 NE2 GLN B 174 23.667 63.882 -11.667 1.00 46.50 1CGP3721 ATOM 3567 H GLN B 174 26.129 60.796 -13.976 1.00 0.00 1CGP3722 ATOM 3568 1HE2 GLN B 174 23.623 63.062 -11.143 1.00 0.00 1CGP3723 ATOM 3569 2HE2 GLN B 174 23.014 64.611 -11.614 1.00 0.00 1CGP3724 ATOM 3570 N ILE B 175 26.368 58.840 -11.119 1.00 30.11 1CGP3725 ATOM 3571 CA ILE B 175 26.467 57.754 -10.170 1.00 28.29 1CGP3726 ATOM 3572 C ILE B 175 27.836 57.097 -10.329 1.00 30.96 1CGP3727 ATOM 3573 O ILE B 175 28.560 56.870 -9.369 1.00 32.88 1CGP3728 ATOM 3574 CB ILE B 175 25.365 56.730 -10.452 1.00 26.38 1CGP3729 ATOM 3575 CG1 ILE B 175 24.017 57.341 -10.216 1.00 24.39 1CGP3730 ATOM 3576 CG2 ILE B 175 25.534 55.519 -9.562 1.00 25.09 1CGP3731 ATOM 3577 CD1 ILE B 175 22.919 56.476 -10.834 1.00 21.15 1CGP3732 ATOM 3578 H ILE B 175 25.687 58.821 -11.821 1.00 0.00 1CGP3733 ATOM 3579 N VAL B 176 28.202 56.754 -11.554 1.00 32.94 1CGP3734 ATOM 3580 CA VAL B 176 29.393 55.990 -11.883 1.00 33.33 1CGP3735 ATOM 3581 C VAL B 176 30.729 56.649 -11.733 1.00 33.53 1CGP3736 ATOM 3582 O VAL B 176 31.637 56.027 -11.205 1.00 34.04 1CGP3737 ATOM 3583 CB VAL B 176 29.222 55.483 -13.313 1.00 34.28 1CGP3738 ATOM 3584 CG1 VAL B 176 30.483 55.057 -14.043 1.00 36.47 1CGP3739 ATOM 3585 CG2 VAL B 176 28.391 54.248 -13.137 1.00 35.35 1CGP3740 ATOM 3586 H VAL B 176 27.615 57.022 -12.282 1.00 0.00 1CGP3741 ATOM 3587 N GLY B 177 30.829 57.855 -12.269 1.00 34.30 1CGP3742 ATOM 3588 CA GLY B 177 32.033 58.658 -12.311 1.00 34.55 1CGP3743 ATOM 3589 C GLY B 177 32.611 58.702 -13.718 1.00 35.58 1CGP3744 ATOM 3590 O GLY B 177 33.763 58.319 -13.916 1.00 37.48 1CGP3745 ATOM 3591 H GLY B 177 30.024 58.240 -12.639 1.00 0.00 1CGP3746 ATOM 3592 N CYS B 178 31.849 59.122 -14.735 1.00 36.75 1CGP3747 ATOM 3593 CA CYS B 178 32.353 59.244 -16.106 1.00 38.48 1CGP3748 ATOM 3594 C CYS B 178 31.421 60.094 -16.974 1.00 39.92 1CGP3749 ATOM 3595 O CYS B 178 30.267 60.302 -16.592 1.00 41.34 1CGP3750 ATOM 3596 CB CYS B 178 32.497 57.863 -16.728 1.00 38.95 1CGP3751 ATOM 3597 SG CYS B 178 30.908 57.020 -16.822 1.00 39.77 1CGP3752 ATOM 3598 H CYS B 178 30.901 59.331 -14.585 1.00 0.00 1CGP3753 ATOM 3599 N SER B 179 31.844 60.614 -18.130 1.00 41.24 1CGP3754 ATOM 3600 CA SER B 179 31.050 61.475 -19.012 1.00 41.61 1CGP3755 ATOM 3601 C SER B 179 29.733 60.919 -19.474 1.00 40.18 1CGP3756 ATOM 3602 O SER B 179 29.671 59.731 -19.768 1.00 41.53 1CGP3757 ATOM 3603 CB SER B 179 31.798 61.779 -20.273 1.00 44.41 1CGP3758 ATOM 3604 OG SER B 179 33.144 62.103 -19.998 1.00 49.72 1CGP3759 ATOM 3605 H SER B 179 32.746 60.375 -18.446 1.00 0.00 1CGP3760 ATOM 3606 HG SER B 179 33.288 63.062 -20.009 1.00 0.00 1CGP3761 ATOM 3607 N ARG B 180 28.722 61.749 -19.695 1.00 39.26 1CGP3762 ATOM 3608 CA ARG B 180 27.481 61.238 -20.247 1.00 40.79 1CGP3763 ATOM 3609 C ARG B 180 27.686 60.493 -21.556 1.00 39.85 1CGP3764 ATOM 3610 O ARG B 180 27.094 59.444 -21.810 1.00 38.27 1CGP3765 ATOM 3611 CB ARG B 180 26.486 62.353 -20.494 1.00 43.67 1CGP3766 ATOM 3612 CG ARG B 180 27.042 63.643 -21.086 1.00 47.85 1CGP3767 ATOM 3613 CD ARG B 180 25.942 64.434 -21.788 1.00 48.61 1CGP3768 ATOM 3614 NE ARG B 180 25.578 63.742 -23.010 1.00 48.68 1CGP3769 ATOM 3615 CZ ARG B 180 26.043 64.150 -24.194 1.00 48.74 1CGP3770 ATOM 3616 NH1 ARG B 180 26.803 65.247 -24.381 1.00 47.85 1CGP3771 ATOM 3617 NH2 ARG B 180 25.682 63.418 -25.225 1.00 48.60 1CGP3772 ATOM 3618 H ARG B 180 28.796 62.677 -19.399 1.00 0.00 1CGP3773 ATOM 3619 HE ARG B 180 24.973 62.972 -22.967 1.00 0.00 1CGP3774 ATOM 3620 1HH1 ARG B 180 27.061 65.814 -23.600 1.00 0.00 1CGP3775 ATOM 3621 2HH1 ARG B 180 27.096 65.502 -25.302 1.00 0.00 1CGP3776 ATOM 3622 1HH2 ARG B 180 25.122 62.603 -25.077 1.00 0.00 1CGP3777 ATOM 3623 2HH2 ARG B 180 25.965 63.671 -26.145 1.00 0.00 1CGP3778 ATOM 3624 N GLU B 181 28.639 60.966 -22.352 1.00 39.10 1CGP3779 ATOM 3625 CA GLU B 181 28.902 60.263 -23.584 1.00 40.81 1CGP3780 ATOM 3626 C GLU B 181 29.670 58.978 -23.304 1.00 41.70 1CGP3781 ATOM 3627 O GLU B 181 29.487 58.016 -24.050 1.00 44.16 1CGP3782 ATOM 3628 CB GLU B 181 29.678 61.130 -24.556 1.00 39.82 1CGP3783 ATOM 3629 CG GLU B 181 30.915 61.767 -24.021 1.00 40.40 1CGP3784 ATOM 3630 CD GLU B 181 30.688 63.217 -23.653 1.00 41.12 1CGP3785 ATOM 3631 OE1 GLU B 181 30.199 63.484 -22.563 1.00 42.99 1CGP3786 ATOM 3632 OE2 GLU B 181 31.016 64.085 -24.449 1.00 39.82 1CGP3787 ATOM 3633 H GLU B 181 29.095 61.790 -22.116 1.00 0.00 1CGP3788 ATOM 3634 N THR B 182 30.500 58.853 -22.260 1.00 40.83 1CGP3789 ATOM 3635 CA THR B 182 31.136 57.578 -21.927 1.00 38.81 1CGP3790 ATOM 3636 C THR B 182 30.034 56.557 -21.638 1.00 39.75 1CGP3791 ATOM 3637 O THR B 182 30.017 55.439 -22.177 1.00 41.77 1CGP3792 ATOM 3638 CB THR B 182 32.024 57.790 -20.705 1.00 37.54 1CGP3793 ATOM 3639 OG1 THR B 182 32.967 58.799 -21.071 1.00 36.12 1CGP3794 ATOM 3640 CG2 THR B 182 32.648 56.508 -20.218 1.00 36.35 1CGP3795 ATOM 3641 H THR B 182 30.712 59.606 -21.681 1.00 0.00 1CGP3796 ATOM 3642 HG1 THR B 182 33.488 58.508 -21.829 1.00 0.00 1CGP3797 ATOM 3643 N VAL B 183 29.064 56.999 -20.830 1.00 39.23 1CGP3798 ATOM 3644 CA VAL B 183 27.906 56.181 -20.512 1.00 39.56 1CGP3799 ATOM 3645 C VAL B 183 27.276 55.739 -21.828 1.00 40.37 1CGP3800 ATOM 3646 O VAL B 183 27.089 54.544 -22.061 1.00 41.05 1CGP3801 ATOM 3647 CB VAL B 183 26.875 56.970 -19.707 1.00 38.99 1CGP3802 ATOM 3648 CG1 VAL B 183 25.726 56.057 -19.327 1.00 38.26 1CGP3803 ATOM 3649 CG2 VAL B 183 27.530 57.549 -18.475 1.00 39.17 1CGP3804 ATOM 3650 H VAL B 183 29.162 57.896 -20.438 1.00 0.00 1CGP3805 ATOM 3651 N GLY B 184 27.041 56.697 -22.720 1.00 40.72 1CGP3806 ATOM 3652 CA GLY B 184 26.470 56.438 -24.031 1.00 40.27 1CGP3807 ATOM 3653 C GLY B 184 27.171 55.294 -24.728 1.00 39.40 1CGP3808 ATOM 3654 O GLY B 184 26.574 54.244 -24.955 1.00 40.71 1CGP3809 ATOM 3655 H GLY B 184 27.172 57.623 -22.439 1.00 0.00 1CGP3810 ATOM 3656 N ARG B 185 28.460 55.476 -24.963 1.00 37.57 1CGP3811 ATOM 3657 CA ARG B 185 29.318 54.484 -25.577 1.00 36.43 1CGP3812 ATOM 3658 C ARG B 185 29.070 53.083 -25.021 1.00 34.03 1CGP3813 ATOM 3659 O ARG B 185 28.765 52.135 -25.763 1.00 32.11 1CGP3814 ATOM 3660 CB ARG B 185 30.751 54.908 -25.324 1.00 39.55 1CGP3815 ATOM 3661 CG ARG B 185 31.566 55.317 -26.546 1.00 42.41 1CGP3816 ATOM 3662 CD ARG B 185 31.329 56.720 -27.048 1.00 42.97 1CGP3817 ATOM 3663 NE ARG B 185 32.080 57.686 -26.273 1.00 43.39 1CGP3818 ATOM 3664 CZ ARG B 185 32.711 58.704 -26.867 1.00 44.30 1CGP3819 ATOM 3665 NH1 ARG B 185 32.716 58.873 -28.200 1.00 45.09 1CGP3820 ATOM 3666 NH2 ARG B 185 33.340 59.575 -26.087 1.00 43.46 1CGP3821 ATOM 3667 H ARG B 185 28.847 56.329 -24.675 1.00 0.00 1CGP3822 ATOM 3668 HE ARG B 185 32.094 57.624 -25.296 1.00 0.00 1CGP3823 ATOM 3669 1HH1 ARG B 185 32.230 58.234 -28.797 1.00 0.00 1CGP3824 ATOM 3670 2HH1 ARG B 185 33.212 59.644 -28.600 1.00 0.00 1CGP3825 ATOM 3671 1HH2 ARG B 185 33.304 59.446 -25.099 1.00 0.00 1CGP3826 ATOM 3672 2HH2 ARG B 185 33.845 60.355 -26.452 1.00 0.00 1CGP3827 ATOM 3673 N ILE B 186 29.097 52.954 -23.689 1.00 31.93 1CGP3828 ATOM 3674 CA ILE B 186 28.913 51.645 -23.076 1.00 30.99 1CGP3829 ATOM 3675 C ILE B 186 27.508 51.094 -23.178 1.00 29.99 1CGP3830 ATOM 3676 O ILE B 186 27.311 49.902 -23.393 1.00 27.82 1CGP3831 ATOM 3677 CB ILE B 186 29.370 51.724 -21.615 1.00 30.08 1CGP3832 ATOM 3678 CG1 ILE B 186 30.855 51.920 -21.662 1.00 28.94 1CGP3833 ATOM 3679 CG2 ILE B 186 29.059 50.457 -20.814 1.00 28.92 1CGP3834 ATOM 3680 CD1 ILE B 186 31.364 52.409 -20.326 1.00 30.38 1CGP3835 ATOM 3681 H ILE B 186 29.295 53.743 -23.135 1.00 0.00 1CGP3836 ATOM 3682 N LEU B 187 26.506 51.934 -23.036 1.00 31.94 1CGP3837 ATOM 3683 CA LEU B 187 25.124 51.519 -23.174 1.00 35.79 1CGP3838 ATOM 3684 C LEU B 187 24.891 50.990 -24.590 1.00 40.08 1CGP3839 ATOM 3685 O LEU B 187 24.104 50.068 -24.821 1.00 39.92 1CGP3840 ATOM 3686 CB LEU B 187 24.247 52.714 -22.890 1.00 33.37 1CGP3841 ATOM 3687 CG LEU B 187 23.421 52.779 -21.653 1.00 31.77 1CGP3842 ATOM 3688 CD1 LEU B 187 24.188 52.405 -20.414 1.00 31.56 1CGP3843 ATOM 3689 CD2 LEU B 187 22.927 54.198 -21.583 1.00 32.02 1CGP3844 ATOM 3690 H LEU B 187 26.716 52.861 -22.801 1.00 0.00 1CGP3845 ATOM 3691 N LYS B 188 25.602 51.550 -25.569 1.00 44.32 1CGP3846 ATOM 3692 CA LYS B 188 25.518 51.067 -26.925 1.00 48.55 1CGP3847 ATOM 3693 C LYS B 188 26.092 49.674 -26.880 1.00 49.21 1CGP3848 ATOM 3694 O LYS B 188 25.392 48.750 -27.298 1.00 49.55 1CGP3849 ATOM 3695 CB LYS B 188 26.334 51.947 -27.845 1.00 54.09 1CGP3850 ATOM 3696 CG LYS B 188 25.970 51.860 -29.335 1.00 60.15 1CGP3851 ATOM 3697 CD LYS B 188 26.584 53.040 -30.111 1.00 65.57 1CGP3852 ATOM 3698 CE LYS B 188 26.004 54.420 -29.684 1.00 68.88 1CGP3853 ATOM 3699 NZ LYS B 188 26.855 55.524 -30.116 1.00 70.23 1CGP3854 ATOM 3700 H LYS B 188 26.074 52.385 -25.365 1.00 0.00 1CGP3855 ATOM 3701 1HZ LYS B 188 26.936 55.487 -31.153 1.00 0.00 1CGP3856 ATOM 3702 2HZ LYS B 188 27.802 55.428 -29.700 1.00 0.00 1CGP3857 ATOM 3703 3HZ LYS B 188 26.438 56.433 -29.836 1.00 0.00 1CGP3858 ATOM 3704 N MET B 189 27.284 49.470 -26.303 1.00 49.89 1CGP3859 ATOM 3705 CA MET B 189 27.854 48.136 -26.235 1.00 51.44 1CGP3860 ATOM 3706 C MET B 189 26.954 47.104 -25.552 1.00 50.23 1CGP3861 ATOM 3707 O MET B 189 26.741 46.016 -26.098 1.00 49.90 1CGP3862 ATOM 3708 CB MET B 189 29.168 48.206 -25.524 1.00 55.94 1CGP3863 ATOM 3709 CG MET B 189 29.946 46.905 -25.680 1.00 62.45 1CGP3864 ATOM 3710 SD MET B 189 31.575 46.870 -24.865 1.00 70.36 1CGP3865 ATOM 3711 CE MET B 189 32.295 48.364 -25.530 1.00 67.18 1CGP3866 ATOM 3712 H MET B 189 27.781 50.261 -26.007 1.00 0.00 1CGP3867 ATOM 3713 N LEU B 190 26.335 47.428 -24.423 1.00 49.00 1CGP3868 ATOM 3714 CA LEU B 190 25.444 46.504 -23.732 1.00 49.56 1CGP3869 ATOM 3715 C LEU B 190 24.136 46.232 -24.495 1.00 50.78 1CGP3870 ATOM 3716 O LEU B 190 23.483 45.190 -24.297 1.00 49.30 1CGP3871 ATOM 3717 CB LEU B 190 25.122 47.049 -22.348 1.00 48.52 1CGP3872 ATOM 3718 CG LEU B 190 26.234 47.523 -21.428 1.00 47.67 1CGP3873 ATOM 3719 CD1 LEU B 190 25.608 47.933 -20.121 1.00 47.76 1CGP3874 ATOM 3720 CD2 LEU B 190 27.249 46.438 -21.176 1.00 47.80 1CGP3875 ATOM 3721 H LEU B 190 26.557 48.299 -24.036 1.00 0.00 1CGP3876 ATOM 3722 N GLU B 191 23.661 47.161 -25.329 1.00 53.39 1CGP3877 ATOM 3723 CA GLU B 191 22.544 46.896 -26.221 1.00 56.58 1CGP3878 ATOM 3724 C GLU B 191 22.981 45.888 -27.265 1.00 58.32 1CGP3879 ATOM 3725 O GLU B 191 22.291 44.890 -27.452 1.00 59.59 1CGP3880 ATOM 3726 CB GLU B 191 22.078 48.071 -27.032 1.00 58.85 1CGP3881 ATOM 3727 CG GLU B 191 21.351 49.149 -26.287 1.00 62.00 1CGP3882 ATOM 3728 CD GLU B 191 20.193 49.658 -27.123 1.00 63.69 1CGP3883 ATOM 3729 OE1 GLU B 191 19.145 49.006 -27.112 1.00 64.61 1CGP3884 ATOM 3730 OE2 GLU B 191 20.349 50.694 -27.772 1.00 65.38 1CGP3885 ATOM 3731 H GLU B 191 24.008 48.076 -25.287 1.00 0.00 1CGP3886 ATOM 3732 N ASP B 192 24.133 46.089 -27.932 1.00 58.74 1CGP3887 ATOM 3733 CA ASP B 192 24.605 45.179 -28.970 1.00 58.99 1CGP3888 ATOM 3734 C ASP B 192 24.791 43.776 -28.461 1.00 58.05 1CGP3889 ATOM 3735 O ASP B 192 24.795 42.808 -29.217 1.00 60.39 1CGP3890 ATOM 3736 CB ASP B 192 25.941 45.639 -29.564 1.00 62.32 1CGP3891 ATOM 3737 CG ASP B 192 25.861 46.920 -30.421 1.00 66.38 1CGP3892 ATOM 3738 OD1 ASP B 192 24.820 47.199 -31.043 1.00 67.17 1CGP3893 ATOM 3739 OD2 ASP B 192 26.864 47.646 -30.477 1.00 68.12 1CGP3894 ATOM 3740 H ASP B 192 24.627 46.910 -27.721 1.00 0.00 1CGP3895 ATOM 3741 N GLN B 193 25.050 43.650 -27.170 1.00 56.01 1CGP3896 ATOM 3742 CA GLN B 193 25.143 42.337 -26.561 1.00 53.94 1CGP3897 ATOM 3743 C GLN B 193 23.840 41.735 -26.101 1.00 52.06 1CGP3898 ATOM 3744 O GLN B 193 23.823 40.679 -25.473 1.00 51.69 1CGP3899 ATOM 3745 CB GLN B 193 26.055 42.386 -25.388 1.00 55.01 1CGP3900 ATOM 3746 CG GLN B 193 27.429 42.640 -25.898 1.00 56.93 1CGP3901 ATOM 3747 CD GLN B 193 28.406 42.644 -24.767 1.00 58.31 1CGP3902 ATOM 3748 OE1 GLN B 193 29.043 43.672 -24.555 1.00 60.13 1CGP3903 ATOM 3749 NE2 GLN B 193 28.555 41.532 -24.045 1.00 58.32 1CGP3904 ATOM 3750 H GLN B 193 25.338 44.450 -26.677 1.00 0.00 1CGP3905 ATOM 3751 1HE2 GLN B 193 28.024 40.732 -24.271 1.00 0.00 1CGP3906 ATOM 3752 2HE2 GLN B 193 29.187 41.572 -23.302 1.00 0.00 1CGP3907 ATOM 3753 N ASN B 194 22.735 42.387 -26.400 1.00 51.02 1CGP3908 ATOM 3754 CA ASN B 194 21.403 41.942 -26.050 1.00 51.50 1CGP3909 ATOM 3755 C ASN B 194 21.246 41.768 -24.553 1.00 48.25 1CGP3910 ATOM 3756 O ASN B 194 20.624 40.836 -24.052 1.00 46.25 1CGP3911 ATOM 3757 CB ASN B 194 21.056 40.606 -26.760 1.00 56.60 1CGP3912 ATOM 3758 CG ASN B 194 21.432 40.514 -28.244 1.00 61.30 1CGP3913 ATOM 3759 OD1 ASN B 194 21.078 41.357 -29.083 1.00 62.15 1CGP3914 ATOM 3760 ND2 ASN B 194 22.150 39.452 -28.633 1.00 63.06 1CGP3915 ATOM 3761 H ASN B 194 22.786 43.199 -26.934 1.00 0.00 1CGP3916 ATOM 3762 1HD2 ASN B 194 22.360 38.732 -27.992 1.00 0.00 1CGP3917 ATOM 3763 2HD2 ASN B 194 22.407 39.436 -29.574 1.00 0.00 1CGP3918 ATOM 3764 N LEU B 195 21.849 42.677 -23.807 1.00 47.02 1CGP3919 ATOM 3765 CA LEU B 195 21.707 42.649 -22.369 1.00 48.35 1CGP3920 ATOM 3766 C LEU B 195 20.802 43.798 -21.952 1.00 50.08 1CGP3921 ATOM 3767 O LEU B 195 20.076 43.718 -20.949 1.00 50.42 1CGP3922 ATOM 3768 CB LEU B 195 23.028 42.857 -21.664 1.00 47.82 1CGP3923 ATOM 3769 CG LEU B 195 24.196 41.936 -21.889 1.00 47.24 1CGP3924 ATOM 3770 CD1 LEU B 195 25.445 42.707 -21.534 1.00 46.63 1CGP3925 ATOM 3771 CD2 LEU B 195 24.058 40.669 -21.086 1.00 46.52 1CGP3926 ATOM 3772 H LEU B 195 22.355 43.421 -24.198 1.00 0.00 1CGP3927 ATOM 3773 N ILE B 196 20.866 44.904 -22.695 1.00 51.76 1CGP3928 ATOM 3774 CA ILE B 196 20.170 46.127 -22.343 1.00 51.95 1CGP3929 ATOM 3775 C ILE B 196 19.347 46.628 -23.528 1.00 51.93 1CGP3930 ATOM 3776 O ILE B 196 19.720 46.392 -24.685 1.00 52.42 1CGP3931 ATOM 3777 CB ILE B 196 21.347 47.067 -21.843 1.00 52.15 1CGP3932 ATOM 3778 CG1 ILE B 196 21.074 47.414 -20.404 1.00 53.42 1CGP3933 ATOM 3779 CG2 ILE B 196 21.489 48.369 -22.604 1.00 51.16 1CGP3934 ATOM 3780 CD1 ILE B 196 21.119 46.255 -19.389 1.00 54.64 1CGP3935 ATOM 3781 H ILE B 196 21.387 44.917 -23.524 1.00 0.00 1CGP3936 ATOM 3782 N SER B 197 18.225 47.285 -23.267 1.00 52.65 1CGP3937 ATOM 3783 CA SER B 197 17.458 47.926 -24.331 1.00 54.15 1CGP3938 ATOM 3784 C SER B 197 17.174 49.336 -23.864 1.00 53.35 1CGP3939 ATOM 3785 O SER B 197 16.847 49.481 -22.696 1.00 51.71 1CGP3940 ATOM 3786 CB SER B 197 16.169 47.191 -24.552 1.00 56.00 1CGP3941 ATOM 3787 OG SER B 197 16.439 45.794 -24.642 1.00 61.21 1CGP3942 ATOM 3788 H SER B 197 17.904 47.287 -22.340 1.00 0.00 1CGP3943 ATOM 3789 HG SER B 197 15.663 45.339 -24.970 1.00 0.00 1CGP3944 ATOM 3790 N ALA B 198 17.252 50.395 -24.652 1.00 54.58 1CGP3945 ATOM 3791 CA ALA B 198 17.099 51.733 -24.110 1.00 56.41 1CGP3946 ATOM 3792 C ALA B 198 16.472 52.712 -25.093 1.00 58.13 1CGP3947 ATOM 3793 O ALA B 198 16.403 52.404 -26.283 1.00 57.42 1CGP3948 ATOM 3794 CB ALA B 198 18.467 52.274 -23.710 1.00 54.85 1CGP3949 ATOM 3795 H ALA B 198 17.358 50.310 -25.622 1.00 0.00 1CGP3950 ATOM 3796 N HIS B 199 15.977 53.851 -24.581 1.00 60.84 1CGP3951 ATOM 3797 CA HIS B 199 15.486 55.013 -25.332 1.00 61.54 1CGP3952 ATOM 3798 C HIS B 199 15.077 56.024 -24.248 1.00 58.55 1CGP3953 ATOM 3799 O HIS B 199 13.872 56.222 -24.100 1.00 56.45 1CGP3954 ATOM 3800 CB HIS B 199 14.274 54.573 -26.193 1.00 66.88 1CGP3955 ATOM 3801 CG HIS B 199 13.802 55.570 -27.265 1.00 71.71 1CGP3956 ATOM 3802 ND1 HIS B 199 12.592 56.147 -27.350 1.00 73.05 1CGP3957 ATOM 3803 CD2 HIS B 199 14.556 56.018 -28.343 1.00 72.33 1CGP3958 ATOM 3804 CE1 HIS B 199 12.589 56.910 -28.424 1.00 73.25 1CGP3959 ATOM 3805 NE2 HIS B 199 13.772 56.831 -29.015 1.00 73.60 1CGP3960 ATOM 3806 H HIS B 199 15.811 53.803 -23.616 1.00 0.00 1CGP3961 ATOM 3807 HD1 HIS B 199 11.896 56.117 -26.654 1.00 0.00 1CGP3962 ATOM 3808 HE2 HIS B 199 14.075 57.446 -29.724 1.00 0.00 1CGP3963 ATOM 3809 N GLY B 200 15.943 56.644 -23.419 1.00 55.83 1CGP3964 ATOM 3810 CA GLY B 200 15.490 57.461 -22.264 1.00 55.94 1CGP3965 ATOM 3811 C GLY B 200 14.979 56.626 -21.038 1.00 56.68 1CGP3966 ATOM 3812 O GLY B 200 15.068 56.991 -19.843 1.00 53.92 1CGP3967 ATOM 3813 H GLY B 200 16.906 56.545 -23.560 1.00 0.00 1CGP3968 ATOM 3814 N LYS B 201 14.300 55.510 -21.401 1.00 57.10 1CGP3969 ATOM 3815 CA LYS B 201 13.894 54.378 -20.560 1.00 55.69 1CGP3970 ATOM 3816 C LYS B 201 14.791 53.173 -20.944 1.00 52.25 1CGP3971 ATOM 3817 O LYS B 201 14.949 52.856 -22.136 1.00 49.47 1CGP3972 ATOM 3818 CB LYS B 201 12.415 54.010 -20.810 1.00 58.52 1CGP3973 ATOM 3819 CG LYS B 201 12.079 53.681 -22.268 1.00 62.76 1CGP3974 ATOM 3820 CD LYS B 201 10.727 52.991 -22.375 1.00 66.34 1CGP3975 ATOM 3821 CE LYS B 201 10.589 52.263 -23.717 1.00 67.91 1CGP3976 ATOM 3822 NZ LYS B 201 9.377 51.461 -23.707 1.00 68.80 1CGP3977 ATOM 3823 H LYS B 201 13.923 55.514 -22.294 1.00 0.00 1CGP3978 ATOM 3824 1HZ LYS B 201 8.544 52.085 -23.738 1.00 0.00 1CGP3979 ATOM 3825 2HZ LYS B 201 9.366 50.911 -22.826 1.00 0.00 1CGP3980 ATOM 3826 3HZ LYS B 201 9.377 50.834 -24.535 1.00 0.00 1CGP3981 ATOM 3827 N THR B 202 15.446 52.529 -19.979 1.00 48.40 1CGP3982 ATOM 3828 CA THR B 202 16.340 51.431 -20.266 1.00 45.13 1CGP3983 ATOM 3829 C THR B 202 15.743 50.232 -19.569 1.00 44.93 1CGP3984 ATOM 3830 O THR B 202 15.153 50.355 -18.493 1.00 45.49 1CGP3985 ATOM 3831 CB THR B 202 17.757 51.636 -19.708 1.00 44.54 1CGP3986 ATOM 3832 OG1 THR B 202 18.299 52.843 -20.227 1.00 45.05 1CGP3987 ATOM 3833 CG2 THR B 202 18.668 50.511 -20.140 1.00 42.82 1CGP3988 ATOM 3834 H THR B 202 15.173 52.697 -19.057 1.00 0.00 1CGP3989 ATOM 3835 HG1 THR B 202 17.845 53.583 -19.822 1.00 0.00 1CGP3990 ATOM 3836 N ILE B 203 15.861 49.082 -20.210 1.00 44.29 1CGP3991 ATOM 3837 CA ILE B 203 15.417 47.812 -19.701 1.00 42.69 1CGP3992 ATOM 3838 C ILE B 203 16.681 46.973 -19.459 1.00 40.14 1CGP3993 ATOM 3839 O ILE B 203 17.532 46.737 -20.322 1.00 40.44 1CGP3994 ATOM 3840 CB ILE B 203 14.487 47.095 -20.718 1.00 43.62 1CGP3995 ATOM 3841 CG1 ILE B 203 13.369 47.948 -21.317 1.00 44.86 1CGP3996 ATOM 3842 CG2 ILE B 203 13.789 46.017 -19.925 1.00 43.32 1CGP3997 ATOM 3843 CD1 ILE B 203 13.688 48.726 -22.616 1.00 46.70 1CGP3998 ATOM 3844 H ILE B 203 16.291 49.104 -21.072 1.00 0.00 1CGP3999 ATOM 3845 N VAL B 204 16.802 46.529 -18.242 1.00 35.66 1CGP4000 ATOM 3846 CA VAL B 204 17.905 45.735 -17.811 1.00 33.52 1CGP4001 ATOM 3847 C VAL B 204 17.190 44.422 -18.016 1.00 34.76 1CGP4002 ATOM 3848 O VAL B 204 16.222 44.137 -17.289 1.00 33.54 1CGP4003 ATOM 3849 CB VAL B 204 18.152 46.039 -16.351 1.00 33.68 1CGP4004 ATOM 3850 CG1 VAL B 204 19.578 45.731 -16.026 1.00 34.95 1CGP4005 ATOM 3851 CG2 VAL B 204 17.920 47.494 -16.036 1.00 34.79 1CGP4006 ATOM 3852 H VAL B 204 16.037 46.658 -17.645 1.00 0.00 1CGP4007 ATOM 3853 N VAL B 205 17.534 43.675 -19.067 1.00 36.32 1CGP4008 ATOM 3854 CA VAL B 205 16.821 42.416 -19.319 1.00 37.04 1CGP4009 ATOM 3855 C VAL B 205 17.571 41.304 -18.609 1.00 36.28 1CGP4010 ATOM 3856 O VAL B 205 17.273 40.976 -17.464 1.00 36.91 1CGP4011 ATOM 3857 CB VAL B 205 16.664 41.989 -20.883 1.00 38.16 1CGP4012 ATOM 3858 CG1 VAL B 205 16.130 43.168 -21.691 1.00 37.93 1CGP4013 ATOM 3859 CG2 VAL B 205 17.966 41.582 -21.551 1.00 38.41 1CGP4014 ATOM 3860 H VAL B 205 18.310 43.901 -19.627 1.00 0.00 1CGP4015 TER 3861 VAL B 205 1CGP4016 HETATM 3862 P CMP B 2 23.678 65.720 6.729 1.00 41.99 1CGP4017 HETATM 3863 O1P CMP B 2 24.997 65.810 7.389 1.00 42.74 1CGP4018 HETATM 3864 O2P CMP B 2 22.572 66.557 7.224 1.00 43.89 1CGP4019 HETATM 3865 O5* CMP B 2 23.953 66.221 5.219 1.00 41.73 1CGP4020 HETATM 3866 C5* CMP B 2 23.624 65.422 4.078 1.00 41.20 1CGP4021 HETATM 3867 C4* CMP B 2 22.761 64.255 4.483 1.00 40.14 1CGP4022 HETATM 3868 O4* CMP B 2 22.618 63.290 3.431 1.00 39.89 1CGP4023 HETATM 3869 C3* CMP B 2 23.434 63.520 5.597 1.00 40.34 1CGP4024 HETATM 3870 O3* CMP B 2 23.163 64.193 6.798 1.00 39.81 1CGP4025 HETATM 3871 C2* CMP B 2 22.720 62.223 5.491 1.00 41.01 1CGP4026 HETATM 3872 O2* CMP B 2 21.373 62.395 5.925 1.00 42.52 1CGP4027 HETATM 3873 C1* CMP B 2 22.748 61.982 3.990 1.00 40.07 1CGP4028 HETATM 3874 N9 CMP B 2 24.022 61.342 3.578 1.00 39.22 1CGP4029 HETATM 3875 C8 CMP B 2 25.303 61.824 3.604 1.00 39.20 1CGP4030 HETATM 3876 N7 CMP B 2 26.193 61.006 3.137 1.00 40.62 1CGP4031 HETATM 3877 C5 CMP B 2 25.456 59.888 2.769 1.00 39.19 1CGP4032 HETATM 3878 C6 CMP B 2 25.821 58.656 2.196 1.00 38.91 1CGP4033 HETATM 3879 N6 CMP B 2 27.080 58.324 1.912 1.00 37.61 1CGP4034 HETATM 3880 N1 CMP B 2 24.831 57.774 1.957 1.00 39.29 1CGP4035 HETATM 3881 C2 CMP B 2 23.586 58.108 2.271 1.00 39.03 1CGP4036 HETATM 3882 N3 CMP B 2 23.123 59.224 2.814 1.00 39.10 1CGP4037 HETATM 3883 C4 CMP B 2 24.132 60.088 3.039 1.00 39.17 1CGP4038 HETATM 3884 H2* CMP B 2 20.916 61.590 5.656 1.00 0.00 1CGP4039 HETATM 3885 1H6 CMP B 2 27.855 58.962 2.083 1.00 0.00 1CGP4040 HETATM 3886 2H6 CMP B 2 27.267 57.405 1.546 1.00 0.00 1CGP4041 ATOM 3887 O5* G C 3 34.630 60.401 -18.674 1.00 33.80 1CGP4042 ATOM 3888 C5* G C 3 35.478 61.139 -17.778 1.00 37.16 1CGP4043 ATOM 3889 C4* G C 3 36.618 61.801 -18.510 1.00 37.74 1CGP4044 ATOM 3890 O4* G C 3 37.194 60.851 -19.387 1.00 39.81 1CGP4045 ATOM 3891 C3* G C 3 36.136 62.866 -19.458 1.00 38.35 1CGP4046 ATOM 3892 O3* G C 3 36.042 64.125 -18.832 1.00 39.54 1CGP4047 ATOM 3893 C2* G C 3 37.176 62.966 -20.503 1.00 39.01 1CGP4048 ATOM 3894 C1* G C 3 37.637 61.564 -20.547 1.00 40.45 1CGP4049 ATOM 3895 N9 G C 3 37.174 60.912 -21.772 1.00 42.04 1CGP4050 ATOM 3896 C8 G C 3 36.387 59.819 -21.932 1.00 43.54 1CGP4051 ATOM 3897 N7 G C 3 36.404 59.336 -23.133 1.00 45.44 1CGP4052 ATOM 3898 C5 G C 3 37.260 60.185 -23.813 1.00 46.05 1CGP4053 ATOM 3899 C6 G C 3 37.713 60.162 -25.144 1.00 47.22 1CGP4054 ATOM 3900 O6 G C 3 37.474 59.307 -25.983 1.00 50.17 1CGP4055 ATOM 3901 N1 G C 3 38.576 61.201 -25.439 1.00 47.79 1CGP4056 ATOM 3902 C2 G C 3 38.963 62.147 -24.537 1.00 48.48 1CGP4057 ATOM 3903 N2 G C 3 39.797 63.109 -24.913 1.00 49.04 1CGP4058 ATOM 3904 N3 G C 3 38.540 62.155 -23.285 1.00 48.21 1CGP4059 ATOM 3905 C4 G C 3 37.707 61.153 -22.989 1.00 44.97 1CGP4060 ATOM 3906 H1 G C 3 38.964 61.229 -26.375 1.00 0.00 1CGP4061 ATOM 3907 H5T G C 3 34.170 61.048 -19.238 1.00 0.00 1CGP4062 ATOM 3908 H21 G C 3 40.132 63.770 -24.225 1.00 0.00 1CGP4063 ATOM 3909 H22 G C 3 40.109 63.206 -25.875 1.00 0.00 1CGP4064 ATOM 3910 P T C 4 35.263 65.287 -19.592 1.00 45.45 1CGP4065 ATOM 3911 O1P T C 4 33.958 64.673 -19.951 1.00 46.46 1CGP4066 ATOM 3912 O2P T C 4 35.315 66.302 -18.516 1.00 48.12 1CGP4067 ATOM 3913 O5* T C 4 36.005 65.844 -20.912 1.00 47.73 1CGP4068 ATOM 3914 C5* T C 4 37.198 66.627 -20.791 1.00 48.71 1CGP4069 ATOM 3915 C4* T C 4 37.682 67.085 -22.125 1.00 50.18 1CGP4070 ATOM 3916 O4* T C 4 37.953 65.971 -22.935 1.00 50.17 1CGP4071 ATOM 3917 C3* T C 4 36.619 67.893 -22.785 1.00 52.67 1CGP4072 ATOM 3918 O3* T C 4 36.973 69.214 -22.429 1.00 57.63 1CGP4073 ATOM 3919 C2* T C 4 36.774 67.578 -24.234 1.00 50.48 1CGP4074 ATOM 3920 C1* T C 4 37.478 66.255 -24.237 1.00 50.32 1CGP4075 ATOM 3921 N1 T C 4 36.640 65.099 -24.632 1.00 50.83 1CGP4076 ATOM 3922 C2 T C 4 36.869 64.594 -25.888 1.00 52.26 1CGP4077 ATOM 3923 O2 T C 4 37.637 65.102 -26.701 1.00 54.13 1CGP4078 ATOM 3924 N3 T C 4 36.183 63.458 -26.239 1.00 52.73 1CGP4079 ATOM 3925 C4 T C 4 35.285 62.784 -25.458 1.00 51.49 1CGP4080 ATOM 3926 O4 T C 4 34.732 61.782 -25.878 1.00 51.56 1CGP4081 ATOM 3927 C5 T C 4 35.099 63.370 -24.173 1.00 50.63 1CGP4082 ATOM 3928 C5M T C 4 34.181 62.687 -23.213 1.00 50.92 1CGP4083 ATOM 3929 C6 T C 4 35.754 64.480 -23.800 1.00 50.75 1CGP4084 ATOM 3930 H3 T C 4 36.411 63.133 -27.168 1.00 0.00 1CGP4085 ATOM 3931 P C C 5 35.925 70.427 -22.262 1.00 68.55 1CGP4086 ATOM 3932 O1P C C 5 34.771 70.787 -21.404 1.00 71.40 1CGP4087 ATOM 3933 O2P C C 5 37.270 70.918 -21.870 1.00 71.51 1CGP4088 ATOM 3934 O5* C C 5 35.610 70.858 -23.807 1.00 71.47 1CGP4089 ATOM 3935 C5* C C 5 36.591 71.477 -24.665 1.00 71.58 1CGP4090 ATOM 3936 C4* C C 5 36.225 71.290 -26.111 1.00 72.59 1CGP4091 ATOM 3937 O4* C C 5 36.072 69.913 -26.356 1.00 71.78 1CGP4092 ATOM 3938 C3* C C 5 34.872 71.887 -26.411 1.00 74.97 1CGP4093 ATOM 3939 O3* C C 5 35.064 73.159 -27.023 1.00 78.21 1CGP4094 ATOM 3940 C2* C C 5 34.200 70.941 -27.350 1.00 72.83 1CGP4095 ATOM 3941 C1* C C 5 35.122 69.751 -27.404 1.00 71.29 1CGP4096 ATOM 3942 N1 C C 5 34.395 68.477 -27.189 1.00 69.63 1CGP4097 ATOM 3943 C2 C C 5 34.522 67.480 -28.157 1.00 69.33 1CGP4098 ATOM 3944 O2 C C 5 35.187 67.595 -29.188 1.00 69.54 1CGP4099 ATOM 3945 N3 C C 5 33.892 66.306 -27.952 1.00 68.97 1CGP4100 ATOM 3946 C4 C C 5 33.173 66.097 -26.866 1.00 68.54 1CGP4101 ATOM 3947 N4 C C 5 32.617 64.899 -26.737 1.00 69.95 1CGP4102 ATOM 3948 C5 C C 5 33.023 67.102 -25.862 1.00 68.25 1CGP4103 ATOM 3949 C6 C C 5 33.653 68.275 -26.067 1.00 68.30 1CGP4104 ATOM 3950 H41 C C 5 32.045 64.677 -25.934 1.00 0.00 1CGP4105 ATOM 3951 H42 C C 5 32.758 64.183 -27.445 1.00 0.00 1CGP4106 ATOM 3952 P A C 6 34.085 74.367 -26.630 1.00 86.13 1CGP4107 ATOM 3953 O1P A C 6 33.571 74.186 -25.256 1.00 89.16 1CGP4108 ATOM 3954 O2P A C 6 35.053 75.463 -26.891 1.00 87.83 1CGP4109 ATOM 3955 O5* A C 6 32.821 74.480 -27.618 1.00 87.69 1CGP4110 ATOM 3956 C5* A C 6 33.133 74.492 -29.006 1.00 88.49 1CGP4111 ATOM 3957 C4* A C 6 32.279 73.552 -29.845 1.00 89.34 1CGP4112 ATOM 3958 O4* A C 6 32.195 72.227 -29.326 1.00 88.66 1CGP4113 ATOM 3959 C3* A C 6 30.879 74.085 -29.875 1.00 90.92 1CGP4114 ATOM 3960 O3* A C 6 30.724 74.500 -31.238 1.00 93.37 1CGP4115 ATOM 3961 C2* A C 6 30.027 72.883 -29.443 1.00 89.27 1CGP4116 ATOM 3962 C1* A C 6 30.931 71.714 -29.785 1.00 87.61 1CGP4117 ATOM 3963 N9 A C 6 30.634 70.466 -29.029 1.00 85.45 1CGP4118 ATOM 3964 C8 A C 6 30.773 70.275 -27.686 1.00 84.58 1CGP4119 ATOM 3965 N7 A C 6 30.585 69.046 -27.304 1.00 84.27 1CGP4120 ATOM 3966 C5 A C 6 30.292 68.363 -28.469 1.00 83.26 1CGP4121 ATOM 3967 C6 A C 6 30.005 67.016 -28.708 1.00 82.26 1CGP4122 ATOM 3968 N6 A C 6 29.991 66.126 -27.729 1.00 81.97 1CGP4123 ATOM 3969 N1 A C 6 29.752 66.639 -29.959 1.00 81.14 1CGP4124 ATOM 3970 C2 A C 6 29.792 67.555 -30.912 1.00 81.34 1CGP4125 ATOM 3971 N3 A C 6 30.053 68.852 -30.819 1.00 82.54 1CGP4126 ATOM 3972 C4 A C 6 30.306 69.206 -29.538 1.00 83.83 1CGP4127 ATOM 3973 H61 A C 6 30.159 66.440 -26.785 1.00 0.00 1CGP4128 ATOM 3974 H62 A C 6 29.824 65.138 -27.876 1.00 0.00 1CGP4129 ATOM 3975 P C C 7 29.697 75.660 -31.658 1.00 94.81 1CGP4130 ATOM 3976 O1P C C 7 28.834 76.710 -31.063 1.00 94.88 1CGP4131 ATOM 3977 O2P C C 7 30.755 76.006 -32.646 1.00 94.63 1CGP4132 ATOM 3978 O5* C C 7 28.753 74.523 -32.258 1.00 92.37 1CGP4133 ATOM 3979 C5* C C 7 29.103 73.824 -33.454 1.00 90.71 1CGP4134 ATOM 3980 C4* C C 7 28.065 72.782 -33.734 1.00 90.12 1CGP4135 ATOM 3981 O4* C C 7 28.017 71.827 -32.672 1.00 90.83 1CGP4136 ATOM 3982 C3* C C 7 26.697 73.422 -33.749 1.00 89.08 1CGP4137 ATOM 3983 O3* C C 7 26.070 72.973 -34.944 1.00 88.10 1CGP4138 ATOM 3984 C2* C C 7 26.026 72.889 -32.477 1.00 89.46 1CGP4139 ATOM 3985 C1* C C 7 26.651 71.499 -32.403 1.00 89.80 1CGP4140 ATOM 3986 N1 C C 7 26.607 70.815 -31.066 1.00 88.73 1CGP4141 ATOM 3987 C2 C C 7 26.722 69.431 -31.037 1.00 88.23 1CGP4142 ATOM 3988 O2 C C 7 26.795 68.743 -32.048 1.00 88.65 1CGP4143 ATOM 3989 N3 C C 7 26.742 68.795 -29.845 1.00 87.94 1CGP4144 ATOM 3990 C4 C C 7 26.648 69.473 -28.705 1.00 88.11 1CGP4145 ATOM 3991 N4 C C 7 26.674 68.797 -27.560 1.00 88.54 1CGP4146 ATOM 3992 C5 C C 7 26.524 70.896 -28.702 1.00 88.32 1CGP4147 ATOM 3993 C6 C C 7 26.509 71.516 -29.900 1.00 88.55 1CGP4148 ATOM 3994 H41 C C 7 26.544 69.283 -26.684 1.00 0.00 1CGP4149 ATOM 3995 H42 C C 7 26.829 67.795 -27.534 1.00 0.00 1CGP4150 ATOM 3996 P A C 8 24.965 73.896 -35.635 1.00 82.52 1CGP4151 ATOM 3997 O1P A C 8 24.031 74.879 -35.027 1.00 79.78 1CGP4152 ATOM 3998 O2P A C 8 25.737 74.236 -36.854 1.00 80.90 1CGP4153 ATOM 3999 O5* A C 8 24.189 72.477 -35.868 1.00 80.27 1CGP4154 ATOM 4000 C5* A C 8 24.652 71.467 -36.794 1.00 78.49 1CGP4155 ATOM 4001 C4* A C 8 23.986 70.065 -36.668 1.00 76.75 1CGP4156 ATOM 4002 O4* A C 8 24.206 69.536 -35.349 1.00 75.14 1CGP4157 ATOM 4003 C3* A C 8 22.478 70.128 -36.922 1.00 76.25 1CGP4158 ATOM 4004 O3* A C 8 21.994 68.955 -37.618 1.00 77.12 1CGP4159 ATOM 4005 C2* A C 8 21.932 70.150 -35.520 1.00 74.42 1CGP4160 ATOM 4006 C1* A C 8 22.946 69.363 -34.691 1.00 73.78 1CGP4161 ATOM 4007 N9 A C 8 22.983 69.903 -33.297 1.00 72.12 1CGP4162 ATOM 4008 C8 A C 8 22.842 71.196 -32.858 1.00 71.36 1CGP4163 ATOM 4009 N7 A C 8 22.904 71.343 -31.564 1.00 70.65 1CGP4164 ATOM 4010 C5 A C 8 23.105 70.056 -31.111 1.00 69.70 1CGP4165 ATOM 4011 C6 A C 8 23.258 69.543 -29.828 1.00 69.39 1CGP4166 ATOM 4012 N6 A C 8 23.235 70.282 -28.723 1.00 68.82 1CGP4167 ATOM 4013 N1 A C 8 23.440 68.237 -29.729 1.00 70.09 1CGP4168 ATOM 4014 C2 A C 8 23.460 67.503 -30.828 1.00 70.10 1CGP4169 ATOM 4015 N3 A C 8 23.334 67.855 -32.083 1.00 70.14 1CGP4170 ATOM 4016 C4 A C 8 23.156 69.178 -32.152 1.00 70.53 1CGP4171 ATOM 4017 H61 A C 8 23.080 71.279 -28.793 1.00 0.00 1CGP4172 ATOM 4018 H62 A C 8 23.371 69.855 -27.815 1.00 0.00 1CGP4173 ATOM 4019 P C C 9 20.466 68.874 -38.187 1.00 77.91 1CGP4174 ATOM 4020 O1P C C 9 19.347 69.803 -38.473 1.00 76.96 1CGP4175 ATOM 4021 O2P C C 9 21.140 68.147 -39.292 1.00 77.65 1CGP4176 ATOM 4022 O5* C C 9 19.940 67.796 -37.114 1.00 78.91 1CGP4177 ATOM 4023 C5* C C 9 20.524 66.476 -37.018 1.00 78.66 1CGP4178 ATOM 4024 C4* C C 9 20.155 65.740 -35.719 1.00 77.31 1CGP4179 ATOM 4025 O4* C C 9 20.600 66.462 -34.561 1.00 77.44 1CGP4180 ATOM 4026 C3* C C 9 18.649 65.649 -35.617 1.00 76.23 1CGP4181 ATOM 4027 O3* C C 9 18.262 64.276 -35.597 1.00 75.14 1CGP4182 ATOM 4028 C2* C C 9 18.322 66.337 -34.322 1.00 76.65 1CGP4183 ATOM 4029 C1* C C 9 19.614 66.309 -33.540 1.00 78.19 1CGP4184 ATOM 4030 N1 C C 9 19.658 67.441 -32.567 1.00 79.09 1CGP4185 ATOM 4031 C2 C C 9 19.849 67.185 -31.217 1.00 79.56 1CGP4186 ATOM 4032 O2 C C 9 19.966 66.054 -30.762 1.00 79.64 1CGP4187 ATOM 4033 N3 C C 9 19.902 68.239 -30.361 1.00 79.93 1CGP4188 ATOM 4034 C4 C C 9 19.772 69.499 -30.786 1.00 80.15 1CGP4189 ATOM 4035 N4 C C 9 19.864 70.513 -29.921 1.00 80.95 1CGP4190 ATOM 4036 C5 C C 9 19.567 69.776 -32.164 1.00 80.13 1CGP4191 ATOM 4037 C6 C C 9 19.521 68.720 -33.005 1.00 79.80 1CGP4192 ATOM 4038 H41 C C 9 19.752 71.467 -30.238 1.00 0.00 1CGP4193 ATOM 4039 H42 C C 9 20.055 70.327 -28.942 1.00 0.00 1CGP4194 ATOM 4040 P T C 10 16.689 63.894 -35.545 1.00 74.05 1CGP4195 ATOM 4041 O1P T C 10 15.508 64.748 -35.818 1.00 73.86 1CGP4196 ATOM 4042 O2P T C 10 16.803 62.562 -36.193 1.00 73.23 1CGP4197 ATOM 4043 O5* T C 10 16.698 63.659 -33.962 1.00 73.17 1CGP4198 ATOM 4044 C5* T C 10 17.464 62.570 -33.411 1.00 69.52 1CGP4199 ATOM 4045 C4* T C 10 17.176 62.316 -31.944 1.00 65.32 1CGP4200 ATOM 4046 O4* T C 10 17.353 63.518 -31.186 1.00 63.97 1CGP4201 ATOM 4047 C3* T C 10 15.751 61.891 -31.751 1.00 63.77 1CGP4202 ATOM 4048 O3* T C 10 15.786 60.988 -30.660 1.00 63.44 1CGP4203 ATOM 4049 C2* T C 10 15.036 63.194 -31.438 1.00 63.21 1CGP4204 ATOM 4050 C1* T C 10 16.105 63.849 -30.590 1.00 62.88 1CGP4205 ATOM 4051 N1 T C 10 16.039 65.315 -30.548 1.00 61.75 1CGP4206 ATOM 4052 C2 T C 10 16.150 65.874 -29.305 1.00 61.61 1CGP4207 ATOM 4053 O2 T C 10 16.230 65.214 -28.279 1.00 60.74 1CGP4208 ATOM 4054 N3 T C 10 16.125 67.244 -29.243 1.00 63.02 1CGP4209 ATOM 4055 C4 T C 10 15.991 68.102 -30.303 1.00 62.83 1CGP4210 ATOM 4056 O4 T C 10 15.953 69.315 -30.110 1.00 62.91 1CGP4211 ATOM 4057 C5 T C 10 15.879 67.428 -31.565 1.00 62.51 1CGP4212 ATOM 4058 C5M T C 10 15.725 68.253 -32.810 1.00 64.91 1CGP4213 ATOM 4059 C6 T C 10 15.905 66.091 -31.657 1.00 62.14 1CGP4214 ATOM 4060 H3 T C 10 16.237 67.628 -28.314 1.00 0.00 1CGP4215 ATOM 4061 P T C 11 14.432 60.423 -30.079 1.00 65.95 1CGP4216 ATOM 4062 O1P T C 11 13.102 60.849 -30.594 1.00 67.80 1CGP4217 ATOM 4063 O2P T C 11 15.109 59.279 -30.751 1.00 66.17 1CGP4218 ATOM 4064 O5* T C 11 14.213 59.793 -28.628 1.00 63.61 1CGP4219 ATOM 4065 C5* T C 11 15.026 60.233 -27.545 1.00 58.49 1CGP4220 ATOM 4066 C4* T C 11 14.405 61.389 -26.836 1.00 54.66 1CGP4221 ATOM 4067 O4* T C 11 14.297 62.497 -27.665 1.00 54.39 1CGP4222 ATOM 4068 C3* T C 11 12.972 61.116 -26.524 1.00 52.93 1CGP4223 ATOM 4069 O3* T C 11 13.025 60.195 -25.443 1.00 50.63 1CGP4224 ATOM 4070 C2* T C 11 12.498 62.519 -26.200 1.00 55.15 1CGP4225 ATOM 4071 C1* T C 11 13.644 63.349 -26.728 1.00 57.02 1CGP4226 ATOM 4072 N1 T C 11 13.224 64.610 -27.408 1.00 60.27 1CGP4227 ATOM 4073 C2 T C 11 13.318 65.795 -26.678 1.00 61.12 1CGP4228 ATOM 4074 O2 T C 11 13.508 65.861 -25.465 1.00 60.81 1CGP4229 ATOM 4075 N3 T C 11 13.095 66.954 -27.379 1.00 62.30 1CGP4230 ATOM 4076 C4 T C 11 12.782 67.063 -28.715 1.00 63.61 1CGP4231 ATOM 4077 O4 T C 11 12.686 68.176 -29.235 1.00 65.79 1CGP4232 ATOM 4078 C5 T C 11 12.680 65.792 -29.391 1.00 62.90 1CGP4233 ATOM 4079 C5M T C 11 12.320 65.766 -30.866 1.00 64.01 1CGP4234 ATOM 4080 C6 T C 11 12.896 64.636 -28.740 1.00 61.83 1CGP4235 ATOM 4081 H3 T C 11 13.183 67.809 -26.844 1.00 0.00 1CGP4236 ATOM 4082 P T C 12 12.008 60.185 -24.216 1.00 45.44 1CGP4237 ATOM 4083 O1P T C 12 10.723 59.631 -24.646 1.00 45.01 1CGP4238 ATOM 4084 O2P T C 12 13.002 59.291 -23.615 1.00 45.25 1CGP4239 ATOM 4085 O5* T C 12 11.721 61.317 -23.201 1.00 45.44 1CGP4240 ATOM 4086 C5* T C 12 12.849 61.830 -22.499 1.00 46.38 1CGP4241 ATOM 4087 C4* T C 12 12.548 63.211 -22.003 1.00 46.75 1CGP4242 ATOM 4088 O4* T C 12 12.274 64.067 -23.107 1.00 46.30 1CGP4243 ATOM 4089 C3* T C 12 11.278 63.194 -21.147 1.00 47.34 1CGP4244 ATOM 4090 O3* T C 12 11.502 63.880 -19.933 1.00 47.26 1CGP4245 ATOM 4091 C2* T C 12 10.291 63.978 -21.968 1.00 46.83 1CGP4246 ATOM 4092 C1* T C 12 11.276 64.937 -22.583 1.00 46.64 1CGP4247 ATOM 4093 N1 T C 12 10.767 65.679 -23.709 1.00 46.44 1CGP4248 ATOM 4094 C2 T C 12 10.830 67.057 -23.678 1.00 46.40 1CGP4249 ATOM 4095 O2 T C 12 11.161 67.734 -22.719 1.00 47.74 1CGP4250 ATOM 4096 N3 T C 12 10.453 67.680 -24.804 1.00 46.45 1CGP4251 ATOM 4097 C4 T C 12 10.024 67.056 -25.924 1.00 48.40 1CGP4252 ATOM 4098 O4 T C 12 9.792 67.756 -26.898 1.00 52.18 1CGP4253 ATOM 4099 C5 T C 12 9.969 65.617 -25.866 1.00 47.28 1CGP4254 ATOM 4100 C5M T C 12 9.492 64.781 -27.033 1.00 48.14 1CGP4255 ATOM 4101 C6 T C 12 10.336 64.992 -24.778 1.00 46.15 1CGP4256 ATOM 4102 H3 T C 12 10.480 68.688 -24.844 1.00 0.00 1CGP4257 ATOM 4103 P T C 13 10.535 63.473 -18.747 1.00 49.28 1CGP4258 ATOM 4104 O1P T C 13 9.280 62.684 -18.837 1.00 51.01 1CGP4259 ATOM 4105 O2P T C 13 11.571 63.110 -17.752 1.00 51.72 1CGP4260 ATOM 4106 O5* T C 13 10.198 65.039 -18.630 1.00 51.05 1CGP4261 ATOM 4107 C5* T C 13 11.169 65.963 -18.116 1.00 53.58 1CGP4262 ATOM 4108 C4* T C 13 10.825 67.437 -18.349 1.00 55.36 1CGP4263 ATOM 4109 O4* T C 13 10.435 67.672 -19.724 1.00 56.01 1CGP4264 ATOM 4110 C3* T C 13 9.670 67.845 -17.484 1.00 56.41 1CGP4265 ATOM 4111 O3* T C 13 10.025 69.054 -16.798 1.00 56.98 1CGP4266 ATOM 4112 C2* T C 13 8.548 68.071 -18.503 1.00 56.01 1CGP4267 ATOM 4113 C1* T C 13 9.266 68.526 -19.757 1.00 54.90 1CGP4268 ATOM 4114 N1 T C 13 8.519 68.265 -21.039 1.00 52.74 1CGP4269 ATOM 4115 C2 T C 13 8.350 69.309 -21.942 1.00 51.73 1CGP4270 ATOM 4116 O2 T C 13 8.646 70.478 -21.727 1.00 51.52 1CGP4271 ATOM 4117 N3 T C 13 7.807 68.989 -23.161 1.00 51.62 1CGP4272 ATOM 4118 C4 T C 13 7.416 67.744 -23.557 1.00 52.17 1CGP4273 ATOM 4119 O4 T C 13 7.015 67.565 -24.703 1.00 52.69 1CGP4274 ATOM 4120 C5 T C 13 7.602 66.733 -22.562 1.00 51.40 1CGP4275 ATOM 4121 C5M T C 13 7.180 65.329 -22.878 1.00 51.42 1CGP4276 ATOM 4122 C6 T C 13 8.130 67.007 -21.370 1.00 51.47 1CGP4277 ATOM 4123 H3 T C 13 7.663 69.740 -23.826 1.00 0.00 1CGP4278 ATOM 4124 P C C 14 9.179 69.378 -15.488 1.00 63.05 1CGP4279 ATOM 4125 O1P C C 14 8.122 68.440 -15.020 1.00 64.03 1CGP4280 ATOM 4126 O2P C C 14 9.942 70.186 -14.511 1.00 65.30 1CGP4281 ATOM 4127 O5* C C 14 8.528 70.377 -16.562 1.00 65.56 1CGP4282 ATOM 4128 C5* C C 14 8.584 71.809 -16.509 1.00 66.35 1CGP4283 ATOM 4129 C4* C C 14 7.231 72.315 -16.958 1.00 67.26 1CGP4284 ATOM 4130 O4* C C 14 6.872 71.639 -18.170 1.00 66.69 1CGP4285 ATOM 4131 C3* C C 14 6.159 71.921 -15.960 1.00 68.83 1CGP4286 ATOM 4132 O3* C C 14 5.770 73.047 -15.101 1.00 71.52 1CGP4287 ATOM 4133 C2* C C 14 4.992 71.423 -16.796 1.00 67.74 1CGP4288 ATOM 4134 C1* C C 14 5.460 71.513 -18.244 1.00 66.30 1CGP4289 ATOM 4135 N1 C C 14 5.175 70.303 -19.045 1.00 65.02 1CGP4290 ATOM 4136 C2 C C 14 4.934 70.452 -20.405 1.00 64.77 1CGP4291 ATOM 4137 O2 C C 14 4.890 71.551 -20.953 1.00 64.39 1CGP4292 ATOM 4138 N3 C C 14 4.713 69.341 -21.155 1.00 64.08 1CGP4293 ATOM 4139 C4 C C 14 4.724 68.134 -20.600 1.00 63.96 1CGP4294 ATOM 4140 N4 C C 14 4.508 67.069 -21.363 1.00 63.80 1CGP4295 ATOM 4141 C5 C C 14 4.966 67.965 -19.205 1.00 65.15 1CGP4296 ATOM 4142 C6 C C 14 5.185 69.074 -18.472 1.00 64.84 1CGP4297 ATOM 4143 H41 C C 14 4.516 66.139 -20.965 1.00 0.00 1CGP4298 ATOM 4144 H42 C C 14 4.328 67.187 -22.354 1.00 0.00 1CGP4299 ATOM 4145 P G C 15 5.278 74.542 -15.519 1.00 72.72 1CGP4300 ATOM 4146 O1P G C 15 4.352 74.147 -14.433 1.00 73.63 1CGP4301 ATOM 4147 O2P G C 15 6.487 75.323 -15.169 1.00 74.64 1CGP4302 ATOM 4148 O5* G C 15 4.402 75.436 -16.492 1.00 71.53 1CGP4303 ATOM 4149 C5* G C 15 5.004 76.278 -17.468 1.00 70.32 1CGP4304 ATOM 4150 C4* G C 15 3.990 76.818 -18.479 1.00 70.02 1CGP4305 ATOM 4151 O4* G C 15 3.497 75.736 -19.281 1.00 68.63 1CGP4306 ATOM 4152 C3* G C 15 2.759 77.435 -17.791 1.00 70.66 1CGP4307 ATOM 4153 O3* G C 15 2.140 78.411 -18.657 1.00 72.91 1CGP4308 ATOM 4154 C2* G C 15 1.843 76.230 -17.646 1.00 69.48 1CGP4309 ATOM 4155 C1* G C 15 2.124 75.481 -18.953 1.00 67.70 1CGP4310 ATOM 4156 N9 G C 15 1.973 74.033 -18.823 1.00 65.15 1CGP4311 ATOM 4157 C8 G C 15 2.194 73.238 -17.751 1.00 64.47 1CGP4312 ATOM 4158 N7 G C 15 2.039 71.977 -17.996 1.00 64.26 1CGP4313 ATOM 4159 C5 G C 15 1.689 71.938 -19.327 1.00 64.37 1CGP4314 ATOM 4160 C6 G C 15 1.386 70.830 -20.159 1.00 65.26 1CGP4315 ATOM 4161 O6 G C 15 1.435 69.630 -19.898 1.00 64.72 1CGP4316 ATOM 4162 N1 G C 15 1.053 71.225 -21.435 1.00 65.38 1CGP4317 ATOM 4163 C2 G C 15 1.028 72.530 -21.865 1.00 65.25 1CGP4318 ATOM 4164 N2 G C 15 0.685 72.721 -23.134 1.00 65.61 1CGP4319 ATOM 4165 N3 G C 15 1.323 73.575 -21.087 1.00 64.71 1CGP4320 ATOM 4166 C4 G C 15 1.639 73.201 -19.836 1.00 64.02 1CGP4321 ATOM 4167 H1 G C 15 0.802 70.489 -22.083 1.00 0.00 1CGP4322 ATOM 4168 H3T G C 15 2.055 78.006 -19.523 1.00 0.00 1CGP4323 ATOM 4169 H21 G C 15 0.727 73.645 -23.544 1.00 0.00 1CGP4324 ATOM 4170 H22 G C 15 0.364 71.947 -23.703 1.00 0.00 1CGP4325 ATOM 4171 O5* G C 16 -5.319 62.940 -23.530 1.00 81.62 1CGP4326 ATOM 4172 C5* G C 16 -5.582 63.499 -24.818 1.00 82.69 1CGP4327 ATOM 4173 C4* G C 16 -4.486 64.469 -25.295 1.00 83.27 1CGP4328 ATOM 4174 O4* G C 16 -4.107 65.256 -24.151 1.00 83.82 1CGP4329 ATOM 4175 C3* G C 16 -3.197 63.806 -25.796 1.00 83.27 1CGP4330 ATOM 4176 O3* G C 16 -2.376 64.676 -26.588 1.00 83.68 1CGP4331 ATOM 4177 C2* G C 16 -2.426 63.658 -24.530 1.00 83.52 1CGP4332 ATOM 4178 C1* G C 16 -2.723 65.022 -23.919 1.00 84.17 1CGP4333 ATOM 4179 N9 G C 16 -2.478 65.023 -22.488 1.00 85.46 1CGP4334 ATOM 4180 C8 G C 16 -2.401 63.958 -21.638 1.00 86.95 1CGP4335 ATOM 4181 N7 G C 16 -2.129 64.275 -20.407 1.00 88.19 1CGP4336 ATOM 4182 C5 G C 16 -2.017 65.651 -20.441 1.00 87.53 1CGP4337 ATOM 4183 C6 G C 16 -1.734 66.537 -19.377 1.00 87.97 1CGP4338 ATOM 4184 O6 G C 16 -1.534 66.259 -18.187 1.00 87.24 1CGP4339 ATOM 4185 N1 G C 16 -1.717 67.850 -19.845 1.00 88.57 1CGP4340 ATOM 4186 C2 G C 16 -1.945 68.247 -21.159 1.00 88.37 1CGP4341 ATOM 4187 N2 G C 16 -1.896 69.547 -21.441 1.00 88.44 1CGP4342 ATOM 4188 N3 G C 16 -2.214 67.400 -22.154 1.00 87.42 1CGP4343 ATOM 4189 C4 G C 16 -2.235 66.122 -21.717 1.00 86.80 1CGP4344 ATOM 4190 H1 G C 16 -1.522 68.544 -19.130 1.00 0.00 1CGP4345 ATOM 4191 H5T G C 16 -5.052 63.690 -22.988 1.00 0.00 1CGP4346 ATOM 4192 H21 G C 16 -2.111 69.860 -22.380 1.00 0.00 1CGP4347 ATOM 4193 H22 G C 16 -1.650 70.224 -20.740 1.00 0.00 1CGP4348 ATOM 4194 P C C 17 -2.499 64.942 -28.172 1.00 85.87 1CGP4349 ATOM 4195 O1P C C 17 -1.390 63.989 -27.928 1.00 87.36 1CGP4350 ATOM 4196 O2P C C 17 -3.801 64.414 -28.659 1.00 86.72 1CGP4351 ATOM 4197 O5* C C 17 -1.932 66.031 -29.233 1.00 85.74 1CGP4352 ATOM 4198 C5* C C 17 -2.713 67.198 -29.490 1.00 83.82 1CGP4353 ATOM 4199 C4* C C 17 -2.372 68.380 -28.585 1.00 81.88 1CGP4354 ATOM 4200 O4* C C 17 -2.023 67.979 -27.273 1.00 80.19 1CGP4355 ATOM 4201 C3* C C 17 -1.153 69.076 -29.069 1.00 81.74 1CGP4356 ATOM 4202 O3* C C 17 -1.621 69.829 -30.200 1.00 82.83 1CGP4357 ATOM 4203 C2* C C 17 -0.759 69.892 -27.830 1.00 80.23 1CGP4358 ATOM 4204 C1* C C 17 -1.445 69.154 -26.693 1.00 78.72 1CGP4359 ATOM 4205 N1 C C 17 -0.549 68.720 -25.587 1.00 76.77 1CGP4360 ATOM 4206 C2 C C 17 -0.358 69.585 -24.525 1.00 76.98 1CGP4361 ATOM 4207 O2 C C 17 -0.777 70.735 -24.534 1.00 78.20 1CGP4362 ATOM 4208 N3 C C 17 0.331 69.170 -23.439 1.00 76.39 1CGP4363 ATOM 4209 C4 C C 17 0.829 67.942 -23.392 1.00 76.64 1CGP4364 ATOM 4210 N4 C C 17 1.487 67.567 -22.293 1.00 77.53 1CGP4365 ATOM 4211 C5 C C 17 0.660 67.032 -24.485 1.00 76.40 1CGP4366 ATOM 4212 C6 C C 17 -0.031 67.466 -25.553 1.00 75.66 1CGP4367 ATOM 4213 H41 C C 17 1.944 66.664 -22.270 1.00 0.00 1CGP4368 ATOM 4214 H42 C C 17 1.530 68.156 -21.473 1.00 0.00 1CGP4369 ATOM 4215 P G C 18 -0.613 70.431 -31.293 1.00 84.66 1CGP4370 ATOM 4216 O1P G C 18 0.508 69.780 -32.016 1.00 85.29 1CGP4371 ATOM 4217 O2P G C 18 -2.003 70.106 -31.713 1.00 85.10 1CGP4372 ATOM 4218 O5* G C 18 -0.422 72.048 -31.418 1.00 84.39 1CGP4373 ATOM 4219 C5* G C 18 0.070 73.028 -30.471 1.00 82.10 1CGP4374 ATOM 4220 C4* G C 18 1.519 72.904 -29.890 1.00 80.24 1CGP4375 ATOM 4221 O4* G C 18 1.623 71.886 -28.906 1.00 79.96 1CGP4376 ATOM 4222 C3* G C 18 2.546 72.506 -30.923 1.00 79.52 1CGP4377 ATOM 4223 O3* G C 18 3.052 73.763 -31.427 1.00 79.81 1CGP4378 ATOM 4224 C2* G C 18 3.540 71.629 -30.112 1.00 78.54 1CGP4379 ATOM 4225 C1* G C 18 3.037 71.760 -28.668 1.00 78.36 1CGP4380 ATOM 4226 N9 G C 18 3.263 70.557 -27.784 1.00 76.98 1CGP4381 ATOM 4227 C8 G C 18 3.170 69.219 -28.102 1.00 76.32 1CGP4382 ATOM 4228 N7 G C 18 3.341 68.397 -27.102 1.00 74.67 1CGP4383 ATOM 4229 C5 G C 18 3.569 69.241 -26.035 1.00 74.27 1CGP4384 ATOM 4230 C6 G C 18 3.825 68.912 -24.691 1.00 73.62 1CGP4385 ATOM 4231 O6 G C 18 3.873 67.809 -24.172 1.00 74.26 1CGP4386 ATOM 4232 N1 G C 18 4.012 70.015 -23.905 1.00 73.62 1CGP4387 ATOM 4233 C2 G C 18 3.960 71.305 -24.355 1.00 74.38 1CGP4388 ATOM 4234 N2 G C 18 4.184 72.251 -23.449 1.00 74.26 1CGP4389 ATOM 4235 N3 G C 18 3.717 71.642 -25.630 1.00 74.90 1CGP4390 ATOM 4236 C4 G C 18 3.529 70.557 -26.422 1.00 75.34 1CGP4391 ATOM 4237 H1 G C 18 4.212 69.817 -22.932 1.00 0.00 1CGP4392 ATOM 4238 H21 G C 18 4.132 73.226 -23.708 1.00 0.00 1CGP4393 ATOM 4239 H22 G C 18 4.418 72.012 -22.489 1.00 0.00 1CGP4394 ATOM 4240 P A C 19 4.599 74.225 -31.478 1.00 80.02 1CGP4395 ATOM 4241 O1P A C 19 5.982 73.901 -31.909 1.00 79.27 1CGP4396 ATOM 4242 O2P A C 19 3.746 75.098 -32.318 1.00 79.99 1CGP4397 ATOM 4243 O5* A C 19 4.698 74.857 -30.014 1.00 78.99 1CGP4398 ATOM 4244 C5* A C 19 4.236 76.151 -29.619 1.00 79.24 1CGP4399 ATOM 4245 C4* A C 19 5.090 76.758 -28.477 1.00 80.04 1CGP4400 ATOM 4246 O4* A C 19 5.358 75.713 -27.527 1.00 79.84 1CGP4401 ATOM 4247 C3* A C 19 6.480 77.263 -28.896 1.00 80.46 1CGP4402 ATOM 4248 O3* A C 19 6.860 78.255 -27.909 1.00 81.25 1CGP4403 ATOM 4249 C2* A C 19 7.333 75.996 -28.842 1.00 79.32 1CGP4404 ATOM 4250 C1* A C 19 6.743 75.290 -27.632 1.00 78.82 1CGP4405 ATOM 4251 N9 A C 19 6.788 73.814 -27.782 1.00 77.91 1CGP4406 ATOM 4252 C8 A C 19 6.702 73.010 -28.904 1.00 77.32 1CGP4407 ATOM 4253 N7 A C 19 6.720 71.724 -28.659 1.00 76.03 1CGP4408 ATOM 4254 C5 A C 19 6.833 71.678 -27.270 1.00 75.40 1CGP4409 ATOM 4255 C6 A C 19 6.912 70.617 -26.372 1.00 73.85 1CGP4410 ATOM 4256 N6 A C 19 6.845 69.366 -26.765 1.00 73.77 1CGP4411 ATOM 4257 N1 A C 19 7.031 70.889 -25.076 1.00 73.48 1CGP4412 ATOM 4258 C2 A C 19 7.065 72.158 -24.697 1.00 74.58 1CGP4413 ATOM 4259 N3 A C 19 6.995 73.255 -25.422 1.00 75.38 1CGP4414 ATOM 4260 C4 A C 19 6.880 72.936 -26.731 1.00 76.60 1CGP4415 ATOM 4261 H61 A C 19 6.882 68.610 -26.092 1.00 0.00 1CGP4416 ATOM 4262 H62 A C 19 6.755 69.164 -27.750 1.00 0.00 1CGP4417 ATOM 4263 P A C 20 8.295 79.001 -27.729 1.00 82.36 1CGP4418 ATOM 4264 O1P A C 20 9.038 78.831 -29.006 1.00 82.49 1CGP4419 ATOM 4265 O2P A C 20 8.043 80.372 -27.209 1.00 84.25 1CGP4420 ATOM 4266 O5* A C 20 9.099 78.205 -26.572 1.00 81.58 1CGP4421 ATOM 4267 C5* A C 20 8.772 78.319 -25.168 1.00 78.07 1CGP4422 ATOM 4268 C4* A C 20 9.664 77.451 -24.243 1.00 75.43 1CGP4423 ATOM 4269 O4* A C 20 9.491 76.040 -24.526 1.00 73.71 1CGP4424 ATOM 4270 C3* A C 20 11.151 77.766 -24.461 1.00 73.75 1CGP4425 ATOM 4271 O3* A C 20 11.750 77.799 -23.154 1.00 73.74 1CGP4426 ATOM 4272 C2* A C 20 11.638 76.591 -25.316 1.00 72.14 1CGP4427 ATOM 4273 C1* A C 20 10.778 75.441 -24.781 1.00 70.86 1CGP4428 ATOM 4274 N9 A C 20 10.655 74.345 -25.782 1.00 68.11 1CGP4429 ATOM 4275 C8 A C 20 10.681 74.403 -27.153 1.00 66.53 1CGP4430 ATOM 4276 N7 A C 20 10.571 73.253 -27.752 1.00 64.31 1CGP4431 ATOM 4277 C5 A C 20 10.466 72.362 -26.703 1.00 64.67 1CGP4432 ATOM 4278 C6 A C 20 10.324 70.978 -26.675 1.00 63.77 1CGP4433 ATOM 4279 N6 A C 20 10.304 70.252 -27.776 1.00 62.67 1CGP4434 ATOM 4280 N1 A C 20 10.234 70.384 -25.483 1.00 64.04 1CGP4435 ATOM 4281 C2 A C 20 10.291 71.142 -24.396 1.00 65.62 1CGP4436 ATOM 4282 N3 A C 20 10.430 72.450 -24.276 1.00 66.01 1CGP4437 ATOM 4283 C4 A C 20 10.512 73.012 -25.499 1.00 66.42 1CGP4438 ATOM 4284 H61 A C 20 10.435 70.679 -28.681 1.00 0.00 1CGP4439 ATOM 4285 H62 A C 20 10.143 69.256 -27.685 1.00 0.00 1CGP4440 ATOM 4286 P A C 21 13.337 77.707 -22.893 1.00 71.00 1CGP4441 ATOM 4287 O1P A C 21 14.444 77.410 -23.838 1.00 69.56 1CGP4442 ATOM 4288 O2P A C 21 12.966 79.121 -22.658 1.00 72.10 1CGP4443 ATOM 4289 O5* A C 21 13.634 77.103 -21.418 1.00 67.25 1CGP4444 ATOM 4290 C5* A C 21 12.779 76.119 -20.793 1.00 63.56 1CGP4445 ATOM 4291 C4* A C 21 13.092 74.629 -21.089 1.00 59.76 1CGP4446 ATOM 4292 O4* A C 21 12.914 74.267 -22.456 1.00 58.47 1CGP4447 ATOM 4293 C3* A C 21 14.560 74.368 -20.833 1.00 57.96 1CGP4448 ATOM 4294 O3* A C 21 14.716 73.870 -19.494 1.00 57.44 1CGP4449 ATOM 4295 C2* A C 21 14.924 73.334 -21.880 1.00 57.09 1CGP4450 ATOM 4296 C1* A C 21 13.618 73.028 -22.540 1.00 57.03 1CGP4451 ATOM 4297 N9 A C 21 13.823 72.643 -23.937 1.00 56.39 1CGP4452 ATOM 4298 C8 A C 21 14.043 73.468 -24.988 1.00 56.91 1CGP4453 ATOM 4299 N7 A C 21 14.087 72.849 -26.131 1.00 58.18 1CGP4454 ATOM 4300 C5 A C 21 13.889 71.510 -25.819 1.00 57.24 1CGP4455 ATOM 4301 C6 A C 21 13.818 70.341 -26.613 1.00 57.66 1CGP4456 ATOM 4302 N6 A C 21 13.972 70.343 -27.947 1.00 57.02 1CGP4457 ATOM 4303 N1 A C 21 13.606 69.186 -25.969 1.00 57.14 1CGP4458 ATOM 4304 C2 A C 21 13.473 69.194 -24.653 1.00 56.32 1CGP4459 ATOM 4305 N3 A C 21 13.521 70.211 -23.818 1.00 56.46 1CGP4460 ATOM 4306 C4 A C 21 13.730 71.370 -24.472 1.00 56.45 1CGP4461 ATOM 4307 H61 A C 21 14.238 71.210 -28.397 1.00 0.00 1CGP4462 ATOM 4308 H62 A C 21 13.817 69.520 -28.516 1.00 0.00 1CGP4463 ATOM 4309 P A C 22 16.173 73.648 -18.803 1.00 54.53 1CGP4464 ATOM 4310 O1P A C 22 17.396 74.305 -19.352 1.00 52.28 1CGP4465 ATOM 4311 O2P A C 22 15.937 73.651 -17.334 1.00 52.69 1CGP4466 ATOM 4312 O5* A C 22 16.211 72.085 -19.297 1.00 53.82 1CGP4467 ATOM 4313 C5* A C 22 15.436 70.945 -18.855 1.00 49.58 1CGP4468 ATOM 4314 C4* A C 22 15.888 69.669 -19.611 1.00 48.65 1CGP4469 ATOM 4315 O4* A C 22 15.765 69.835 -21.028 1.00 48.16 1CGP4470 ATOM 4316 C3* A C 22 17.380 69.357 -19.372 1.00 47.42 1CGP4471 ATOM 4317 O3* A C 22 17.354 68.176 -18.556 1.00 48.25 1CGP4472 ATOM 4318 C2* A C 22 17.983 69.173 -20.773 1.00 46.09 1CGP4473 ATOM 4319 C1* A C 22 16.764 69.029 -21.674 1.00 46.25 1CGP4474 ATOM 4320 N9 A C 22 16.933 69.594 -23.029 1.00 44.85 1CGP4475 ATOM 4321 C8 A C 22 17.151 70.888 -23.370 1.00 44.85 1CGP4476 ATOM 4322 N7 A C 22 17.201 71.112 -24.652 1.00 45.27 1CGP4477 ATOM 4323 C5 A C 22 17.003 69.866 -25.211 1.00 45.09 1CGP4478 ATOM 4324 C6 A C 22 16.927 69.434 -26.546 1.00 45.06 1CGP4479 ATOM 4325 N6 A C 22 17.053 70.261 -27.580 1.00 45.94 1CGP4480 ATOM 4326 N1 A C 22 16.697 68.143 -26.775 1.00 44.10 1CGP4481 ATOM 4327 C2 A C 22 16.560 67.342 -25.725 1.00 45.45 1CGP4482 ATOM 4328 N3 A C 22 16.609 67.620 -24.428 1.00 46.22 1CGP4483 ATOM 4329 C4 A C 22 16.837 68.931 -24.230 1.00 45.23 1CGP4484 ATOM 4330 H61 A C 22 17.286 71.228 -27.398 1.00 0.00 1CGP4485 ATOM 4331 H62 A C 22 16.910 69.950 -28.531 1.00 0.00 1CGP4486 ATOM 4332 P G C 23 18.526 67.137 -18.274 1.00 48.20 1CGP4487 ATOM 4333 O1P G C 23 19.735 67.871 -17.852 1.00 49.17 1CGP4488 ATOM 4334 O2P G C 23 17.787 66.318 -17.272 1.00 48.35 1CGP4489 ATOM 4335 O5* G C 23 18.978 66.216 -19.502 1.00 45.25 1CGP4490 ATOM 4336 C5* G C 23 18.159 65.150 -19.915 1.00 42.19 1CGP4491 ATOM 4337 C4* G C 23 18.579 64.585 -21.232 1.00 40.57 1CGP4492 ATOM 4338 O4* G C 23 18.581 65.570 -22.220 1.00 42.20 1CGP4493 ATOM 4339 C3* G C 23 19.949 64.077 -21.193 1.00 39.56 1CGP4494 ATOM 4340 O3* G C 23 19.738 62.767 -21.613 1.00 39.98 1CGP4495 ATOM 4341 C2* G C 23 20.745 64.929 -22.134 1.00 39.97 1CGP4496 ATOM 4342 C1* G C 23 19.658 65.281 -23.102 1.00 42.22 1CGP4497 ATOM 4343 N9 G C 23 19.934 66.509 -23.866 1.00 45.38 1CGP4498 ATOM 4344 C8 G C 23 20.269 67.750 -23.395 1.00 46.51 1CGP4499 ATOM 4345 N7 G C 23 20.441 68.646 -24.322 1.00 46.77 1CGP4500 ATOM 4346 C5 G C 23 20.199 67.950 -25.488 1.00 46.50 1CGP4501 ATOM 4347 C6 G C 23 20.243 68.409 -26.812 1.00 47.61 1CGP4502 ATOM 4348 O6 G C 23 20.455 69.561 -27.194 1.00 50.27 1CGP4503 ATOM 4349 N1 G C 23 19.956 67.384 -27.707 1.00 47.30 1CGP4504 ATOM 4350 C2 G C 23 19.658 66.087 -27.357 1.00 47.25 1CGP4505 ATOM 4351 N2 G C 23 19.456 65.178 -28.311 1.00 47.92 1CGP4506 ATOM 4352 N3 G C 23 19.611 65.676 -26.100 1.00 47.58 1CGP4507 ATOM 4353 C4 G C 23 19.891 66.652 -25.223 1.00 46.17 1CGP4508 ATOM 4354 H1 G C 23 19.978 67.643 -28.686 1.00 0.00 1CGP4509 ATOM 4355 H21 G C 23 19.185 64.238 -28.054 1.00 0.00 1CGP4510 ATOM 4356 H22 G C 23 19.583 65.401 -29.292 1.00 0.00 1CGP4511 ATOM 4357 P T C 24 21.034 61.922 -21.722 1.00 37.45 1CGP4512 ATOM 4358 O1P T C 24 22.214 61.942 -20.822 1.00 36.51 1CGP4513 ATOM 4359 O2P T C 24 19.954 60.904 -21.532 1.00 35.82 1CGP4514 ATOM 4360 O5* T C 24 21.472 62.019 -23.225 1.00 38.54 1CGP4515 ATOM 4361 C5* T C 24 20.687 61.317 -24.185 1.00 38.96 1CGP4516 ATOM 4362 C4* T C 24 21.244 61.589 -25.508 1.00 39.11 1CGP4517 ATOM 4363 O4* T C 24 21.366 62.977 -25.524 1.00 39.49 1CGP4518 ATOM 4364 C3* T C 24 22.646 61.095 -25.727 1.00 41.52 1CGP4519 ATOM 4365 O3* T C 24 22.551 59.815 -26.352 1.00 44.57 1CGP4520 ATOM 4366 C2* T C 24 23.250 62.137 -26.630 1.00 40.04 1CGP4521 ATOM 4367 C1* T C 24 22.231 63.233 -26.585 1.00 39.63 1CGP4522 ATOM 4368 N1 T C 24 22.733 64.587 -26.321 1.00 40.20 1CGP4523 ATOM 4369 C2 T C 24 22.918 65.347 -27.439 1.00 42.07 1CGP4524 ATOM 4370 O2 T C 24 22.762 64.889 -28.577 1.00 44.67 1CGP4525 ATOM 4371 N3 T C 24 23.290 66.669 -27.231 1.00 42.43 1CGP4526 ATOM 4372 C4 T C 24 23.495 67.287 -26.020 1.00 40.92 1CGP4527 ATOM 4373 O4 T C 24 23.801 68.483 -25.991 1.00 40.34 1CGP4528 ATOM 4374 C5 T C 24 23.283 66.397 -24.898 1.00 40.21 1CGP4529 ATOM 4375 C5M T C 24 23.449 66.914 -23.499 1.00 40.14 1CGP4530 ATOM 4376 C6 T C 24 22.921 65.112 -25.069 1.00 39.66 1CGP4531 ATOM 4377 H3 T C 24 23.412 67.221 -28.068 1.00 0.00 1CGP4532 ATOM 4378 P G C 25 23.881 58.956 -26.579 1.00 54.51 1CGP4533 ATOM 4379 O1P G C 25 25.091 59.418 -25.830 1.00 55.58 1CGP4534 ATOM 4380 O2P G C 25 23.424 57.550 -26.490 1.00 55.64 1CGP4535 ATOM 4381 O5* G C 25 24.128 59.289 -28.106 1.00 57.82 1CGP4536 ATOM 4382 C5* G C 25 23.274 58.971 -29.197 1.00 58.07 1CGP4537 ATOM 4383 C4* G C 25 24.005 59.418 -30.438 1.00 59.25 1CGP4538 ATOM 4384 O4* G C 25 24.305 60.816 -30.326 1.00 58.27 1CGP4539 ATOM 4385 C3* G C 25 25.330 58.678 -30.560 1.00 61.51 1CGP4540 ATOM 4386 O3* G C 25 25.379 58.103 -31.884 1.00 65.06 1CGP4541 ATOM 4387 C2* G C 25 26.380 59.748 -30.317 1.00 59.94 1CGP4542 ATOM 4388 C1* G C 25 25.687 61.076 -30.583 1.00 59.35 1CGP4543 ATOM 4389 N9 G C 25 26.144 62.122 -29.643 1.00 60.21 1CGP4544 ATOM 4390 C8 G C 25 26.450 61.951 -28.334 1.00 61.50 1CGP4545 ATOM 4391 N7 G C 25 26.767 63.044 -27.709 1.00 62.52 1CGP4546 ATOM 4392 C5 G C 25 26.669 64.034 -28.660 1.00 61.87 1CGP4547 ATOM 4393 C6 G C 25 26.901 65.434 -28.529 1.00 61.52 1CGP4548 ATOM 4394 O6 G C 25 27.204 66.074 -27.519 1.00 61.10 1CGP4549 ATOM 4395 N1 G C 25 26.704 66.080 -29.726 1.00 60.37 1CGP4550 ATOM 4396 C2 G C 25 26.332 65.459 -30.891 1.00 60.67 1CGP4551 ATOM 4397 N2 G C 25 26.194 66.221 -31.963 1.00 61.49 1CGP4552 ATOM 4398 N3 G C 25 26.109 64.147 -31.017 1.00 61.16 1CGP4553 ATOM 4399 C4 G C 25 26.293 63.485 -29.862 1.00 61.27 1CGP4554 ATOM 4400 H1 G C 25 26.835 67.082 -29.730 1.00 0.00 1CGP4555 ATOM 4401 H21 G C 25 25.850 65.807 -32.817 1.00 0.00 1CGP4556 ATOM 4402 H22 G C 25 26.427 67.207 -31.964 1.00 0.00 1CGP4557 ATOM 4403 P T C 26 26.711 57.479 -32.570 1.00 70.51 1CGP4558 ATOM 4404 O1P T C 26 28.057 57.493 -31.930 1.00 71.68 1CGP4559 ATOM 4405 O2P T C 26 26.227 56.267 -33.284 1.00 70.06 1CGP4560 ATOM 4406 O5* T C 26 26.580 58.727 -33.568 1.00 71.44 1CGP4561 ATOM 4407 C5* T C 26 27.589 58.925 -34.534 1.00 71.64 1CGP4562 ATOM 4408 C4* T C 26 28.272 60.258 -34.361 1.00 72.47 1CGP4563 ATOM 4409 O4* T C 26 28.155 60.842 -33.079 1.00 71.06 1CGP4564 ATOM 4410 C3* T C 26 29.731 59.992 -34.345 1.00 75.29 1CGP4565 ATOM 4411 O3* T C 26 30.116 59.709 -35.690 1.00 80.50 1CGP4566 ATOM 4412 C2* T C 26 30.298 61.296 -33.826 1.00 72.64 1CGP4567 ATOM 4413 C1* T C 26 29.123 61.895 -33.096 1.00 69.55 1CGP4568 ATOM 4414 N1 T C 26 29.442 62.274 -31.705 1.00 67.21 1CGP4569 ATOM 4415 C2 T C 26 29.533 63.615 -31.398 1.00 66.82 1CGP4570 ATOM 4416 O2 T C 26 29.452 64.532 -32.208 1.00 68.89 1CGP4571 ATOM 4417 N3 T C 26 29.730 63.928 -30.092 1.00 65.47 1CGP4572 ATOM 4418 C4 T C 26 29.842 63.051 -29.067 1.00 65.17 1CGP4573 ATOM 4419 O4 T C 26 29.927 63.489 -27.929 1.00 64.88 1CGP4574 ATOM 4420 C5 T C 26 29.754 61.676 -29.468 1.00 65.78 1CGP4575 ATOM 4421 C5M T C 26 29.879 60.578 -28.451 1.00 67.25 1CGP4576 ATOM 4422 C6 T C 26 29.563 61.334 -30.737 1.00 66.44 1CGP4577 ATOM 4423 H3 T C 26 29.788 64.924 -29.919 1.00 0.00 1CGP4578 ATOM 4424 P G C 27 31.065 58.447 -35.984 1.00 90.41 1CGP4579 ATOM 4425 O1P G C 27 31.589 57.098 -35.669 1.00 92.54 1CGP4580 ATOM 4426 O2P G C 27 30.354 58.704 -37.267 1.00 92.89 1CGP4581 ATOM 4427 O5* G C 27 32.252 59.512 -35.786 1.00 94.10 1CGP4582 ATOM 4428 C5* G C 27 32.563 60.566 -36.714 1.00 96.12 1CGP4583 ATOM 4429 C4* G C 27 33.875 61.231 -36.333 1.00 98.59 1CGP4584 ATOM 4430 O4* G C 27 33.781 61.898 -35.062 1.00 98.83 1CGP4585 ATOM 4431 C3* G C 27 34.952 60.159 -36.180 1.00 99.74 1CGP4586 ATOM 4432 O3* G C 27 36.146 60.697 -36.766 1.00100.40 1CGP4587 ATOM 4433 C2* G C 27 35.045 59.963 -34.664 1.00 99.39 1CGP4588 ATOM 4434 C1* G C 27 34.791 61.382 -34.173 1.00 99.54 1CGP4589 ATOM 4435 N9 G C 27 34.268 61.434 -32.779 1.00 99.72 1CGP4590 ATOM 4436 C8 G C 27 33.445 60.565 -32.103 1.00 99.96 1CGP4591 ATOM 4437 N7 G C 27 33.085 60.975 -30.915 1.00 99.95 1CGP4592 ATOM 4438 C5 G C 27 33.715 62.206 -30.793 1.00100.40 1CGP4593 ATOM 4439 C6 G C 27 33.698 63.136 -29.721 1.00100.89 1CGP4594 ATOM 4440 O6 G C 27 33.108 63.065 -28.646 1.00100.03 1CGP4595 ATOM 4441 N1 G C 27 34.472 64.255 -30.006 1.00101.83 1CGP4596 ATOM 4442 C2 G C 27 35.192 64.456 -31.171 1.00101.63 1CGP4597 ATOM 4443 N2 G C 27 35.945 65.556 -31.270 1.00101.94 1CGP4598 ATOM 4444 N3 G C 27 35.199 63.579 -32.175 1.00101.08 1CGP4599 ATOM 4445 C4 G C 27 34.447 62.484 -31.921 1.00100.20 1CGP4600 ATOM 4446 H1 G C 27 34.464 64.964 -29.283 1.00 0.00 1CGP4601 ATOM 4447 H21 G C 27 35.885 66.284 -30.568 1.00 0.00 1CGP4602 ATOM 4448 H22 G C 27 36.578 65.648 -32.055 1.00 0.00 1CGP4603 ATOM 4449 P A C 28 37.554 59.945 -36.668 1.00102.83 1CGP4604 ATOM 4450 O1P A C 28 38.485 58.952 -36.071 1.00102.38 1CGP4605 ATOM 4451 O2P A C 28 37.431 60.101 -38.142 1.00101.97 1CGP4606 ATOM 4452 O5* A C 28 37.832 61.385 -35.982 1.00105.29 1CGP4607 ATOM 4453 C5* A C 28 38.111 62.635 -36.642 1.00106.73 1CGP4608 ATOM 4454 C4* A C 28 39.041 63.522 -35.807 1.00108.38 1CGP4609 ATOM 4455 O4* A C 28 38.430 63.726 -34.519 1.00108.56 1CGP4610 ATOM 4456 C3* A C 28 40.422 62.856 -35.576 1.00110.59 1CGP4611 ATOM 4457 O3* A C 28 41.470 63.858 -35.488 1.00112.72 1CGP4612 ATOM 4458 C2* A C 28 40.232 62.159 -34.236 1.00109.81 1CGP4613 ATOM 4459 C1* A C 28 39.272 63.121 -33.508 1.00109.39 1CGP4614 ATOM 4460 N9 A C 28 38.496 62.340 -32.488 1.00108.20 1CGP4615 ATOM 4461 C8 A C 28 37.957 61.078 -32.588 1.00107.89 1CGP4616 ATOM 4462 N7 A C 28 37.366 60.655 -31.507 1.00107.08 1CGP4617 ATOM 4463 C5 A C 28 37.522 61.710 -30.622 1.00106.47 1CGP4618 ATOM 4464 C6 A C 28 37.108 61.880 -29.305 1.00105.41 1CGP4619 ATOM 4465 N6 A C 28 36.411 60.953 -28.663 1.00105.73 1CGP4620 ATOM 4466 N1 A C 28 37.411 63.024 -28.705 1.00104.56 1CGP4621 ATOM 4467 C2 A C 28 38.082 63.948 -29.380 1.00104.92 1CGP4622 ATOM 4468 N3 A C 28 38.529 63.921 -30.618 1.00106.07 1CGP4623 ATOM 4469 C4 A C 28 38.207 62.744 -31.200 1.00106.93 1CGP4624 ATOM 4470 H61 A C 28 36.191 60.092 -29.147 1.00 0.00 1CGP4625 ATOM 4471 H62 A C 28 36.089 61.067 -27.712 1.00 0.00 1CGP4626 ATOM 4472 P C C 29 43.039 63.525 -35.150 1.00118.66 1CGP4627 ATOM 4473 O1P C C 29 43.619 62.269 -35.686 1.00120.20 1CGP4628 ATOM 4474 O2P C C 29 43.382 64.813 -35.804 1.00119.82 1CGP4629 ATOM 4475 O5* C C 29 43.429 63.603 -33.562 1.00120.43 1CGP4630 ATOM 4476 C5* C C 29 43.474 64.857 -32.838 1.00119.81 1CGP4631 ATOM 4477 C4* C C 29 43.222 64.778 -31.309 1.00119.19 1CGP4632 ATOM 4478 O4* C C 29 41.985 64.090 -31.056 1.00119.13 1CGP4633 ATOM 4479 C3* C C 29 44.233 63.928 -30.550 1.00118.91 1CGP4634 ATOM 4480 O3* C C 29 45.478 64.613 -30.260 1.00118.81 1CGP4635 ATOM 4481 C2* C C 29 43.445 63.819 -29.271 1.00119.03 1CGP4636 ATOM 4482 C1* C C 29 41.984 63.781 -29.655 1.00118.96 1CGP4637 ATOM 4483 N1 C C 29 41.484 62.421 -29.274 1.00119.01 1CGP4638 ATOM 4484 C2 C C 29 40.813 62.294 -28.067 1.00118.96 1CGP4639 ATOM 4485 O2 C C 29 40.592 63.257 -27.349 1.00119.27 1CGP4640 ATOM 4486 N3 C C 29 40.374 61.080 -27.657 1.00119.01 1CGP4641 ATOM 4487 C4 C C 29 40.584 60.001 -28.407 1.00119.37 1CGP4642 ATOM 4488 N4 C C 29 40.153 58.817 -27.965 1.00119.48 1CGP4643 ATOM 4489 C5 C C 29 41.271 60.099 -29.661 1.00119.86 1CGP4644 ATOM 4490 C6 C C 29 41.697 61.321 -30.050 1.00119.40 1CGP4645 ATOM 4491 H41 C C 29 40.309 57.978 -28.508 1.00 0.00 1CGP4646 ATOM 4492 H42 C C 29 39.663 58.738 -27.084 1.00 0.00 1CGP4647 ATOM 4493 P A C 30 46.697 63.912 -29.407 1.00117.35 1CGP4648 ATOM 4494 O1P A C 30 47.132 62.758 -28.585 1.00117.19 1CGP4649 ATOM 4495 O2P A C 30 47.298 64.039 -30.754 1.00117.60 1CGP4650 ATOM 4496 O5* A C 30 47.108 65.252 -28.584 1.00115.32 1CGP4651 ATOM 4497 C5* A C 30 46.215 66.139 -27.865 1.00112.82 1CGP4652 ATOM 4498 C4* A C 30 45.612 65.657 -26.505 1.00110.71 1CGP4653 ATOM 4499 O4* A C 30 44.865 64.467 -26.730 1.00109.89 1CGP4654 ATOM 4500 C3* A C 30 46.643 65.329 -25.405 1.00109.36 1CGP4655 ATOM 4501 O3* A C 30 46.386 66.275 -24.326 1.00108.79 1CGP4656 ATOM 4502 C2* A C 30 46.290 63.870 -25.054 1.00109.01 1CGP4657 ATOM 4503 C1* A C 30 44.834 63.742 -25.502 1.00108.46 1CGP4658 ATOM 4504 N9 A C 30 44.379 62.360 -25.816 1.00107.06 1CGP4659 ATOM 4505 C8 A C 30 44.675 61.584 -26.904 1.00106.81 1CGP4660 ATOM 4506 N7 A C 30 44.068 60.438 -26.931 1.00106.76 1CGP4661 ATOM 4507 C5 A C 30 43.312 60.450 -25.774 1.00106.22 1CGP4662 ATOM 4508 C6 A C 30 42.447 59.510 -25.232 1.00105.80 1CGP4663 ATOM 4509 N6 A C 30 42.216 58.357 -25.837 1.00106.74 1CGP4664 ATOM 4510 N1 A C 30 41.853 59.800 -24.085 1.00105.29 1CGP4665 ATOM 4511 C2 A C 30 42.125 60.965 -23.521 1.00105.50 1CGP4666 ATOM 4512 N3 A C 30 42.912 61.945 -23.924 1.00105.58 1CGP4667 ATOM 4513 C4 A C 30 43.489 61.613 -25.087 1.00106.27 1CGP4668 ATOM 4514 H61 A C 30 42.713 58.153 -26.690 1.00 0.00 1CGP4669 ATOM 4515 H62 A C 30 41.556 57.673 -25.485 1.00 0.00 1CGP4670 ATOM 4516 P T C 31 47.080 66.436 -22.844 1.00105.10 1CGP4671 ATOM 4517 O1P T C 31 48.489 66.346 -23.324 1.00103.70 1CGP4672 ATOM 4518 O2P T C 31 46.447 67.777 -22.702 1.00103.78 1CGP4673 ATOM 4519 O5* T C 31 47.072 65.757 -21.374 1.00100.18 1CGP4674 ATOM 4520 C5* T C 31 45.926 65.262 -20.674 1.00 95.53 1CGP4675 ATOM 4521 C4* T C 31 46.026 63.750 -20.491 1.00 92.91 1CGP4676 ATOM 4522 O4* T C 31 45.734 63.034 -21.683 1.00 92.77 1CGP4677 ATOM 4523 C3* T C 31 47.482 63.350 -20.224 1.00 91.52 1CGP4678 ATOM 4524 O3* T C 31 47.772 63.000 -18.883 1.00 90.43 1CGP4679 ATOM 4525 C2* T C 31 47.689 62.088 -20.977 1.00 91.69 1CGP4680 ATOM 4526 C1* T C 31 46.285 61.762 -21.359 1.00 92.59 1CGP4681 ATOM 4527 N1 T C 31 46.300 60.804 -22.491 1.00 93.73 1CGP4682 ATOM 4528 C2 T C 31 45.367 59.795 -22.459 1.00 94.44 1CGP4683 ATOM 4529 O2 T C 31 44.515 59.685 -21.592 1.00 95.69 1CGP4684 ATOM 4530 N3 T C 31 45.393 58.879 -23.478 1.00 95.08 1CGP4685 ATOM 4531 C4 T C 31 46.264 58.866 -24.544 1.00 95.47 1CGP4686 ATOM 4532 O4 T C 31 46.156 57.977 -25.391 1.00 95.25 1CGP4687 ATOM 4533 C5 T C 31 47.214 59.969 -24.513 1.00 95.48 1CGP4688 ATOM 4534 C5M T C 31 48.258 60.139 -25.615 1.00 96.08 1CGP4689 ATOM 4535 C6 T C 31 47.203 60.875 -23.516 1.00 94.54 1CGP4690 ATOM 4536 H3 T C 31 44.708 58.140 -23.393 1.00 0.00 1CGP4691 ATOM 4537 P A C 32 47.528 64.007 -17.672 1.00 88.75 1CGP4692 ATOM 4538 O1P A C 32 48.739 63.152 -17.783 1.00 87.80 1CGP4693 ATOM 4539 O2P A C 32 47.634 65.441 -18.026 1.00 88.07 1CGP4694 ATOM 4540 O5* A C 32 47.030 63.919 -16.132 1.00 86.91 1CGP4695 ATOM 4541 C5* A C 32 45.797 63.296 -15.733 1.00 83.66 1CGP4696 ATOM 4542 C4* A C 32 45.844 61.743 -15.561 1.00 81.07 1CGP4697 ATOM 4543 O4* A C 32 46.317 61.109 -16.745 1.00 79.25 1CGP4698 ATOM 4544 C3* A C 32 46.792 61.283 -14.461 1.00 78.90 1CGP4699 ATOM 4545 O3* A C 32 46.045 60.444 -13.578 1.00 77.05 1CGP4700 ATOM 4546 C2* A C 32 47.861 60.488 -15.204 1.00 78.39 1CGP4701 ATOM 4547 C1* A C 32 47.037 59.953 -16.326 1.00 78.26 1CGP4702 ATOM 4548 N9 A C 32 47.775 59.549 -17.498 1.00 78.77 1CGP4703 ATOM 4549 C8 A C 32 48.733 60.230 -18.191 1.00 79.67 1CGP4704 ATOM 4550 N7 A C 32 49.081 59.671 -19.306 1.00 80.22 1CGP4705 ATOM 4551 C5 A C 32 48.296 58.539 -19.341 1.00 79.96 1CGP4706 ATOM 4552 C6 A C 32 48.181 57.531 -20.281 1.00 80.75 1CGP4707 ATOM 4553 N6 A C 32 48.886 57.569 -21.403 1.00 81.75 1CGP4708 ATOM 4554 N1 A C 32 47.318 56.543 -20.037 1.00 80.56 1CGP4709 ATOM 4555 C2 A C 32 46.618 56.591 -18.914 1.00 80.81 1CGP4710 ATOM 4556 N3 A C 32 46.628 57.489 -17.947 1.00 80.20 1CGP4711 ATOM 4557 C4 A C 32 47.506 58.453 -18.237 1.00 79.46 1CGP4712 ATOM 4558 H61 A C 32 49.586 58.287 -21.512 1.00 0.00 1CGP4713 ATOM 4559 H62 A C 32 48.714 56.904 -22.148 1.00 0.00 1CGP4714 ATOM 4560 P T C 33 46.705 59.966 -12.232 1.00 71.03 1CGP4715 ATOM 4561 O1P T C 33 47.740 60.456 -11.299 1.00 70.46 1CGP4716 ATOM 4562 O2P T C 33 45.298 60.018 -11.787 1.00 69.42 1CGP4717 ATOM 4563 O5* T C 33 47.029 58.481 -12.667 1.00 69.00 1CGP4718 ATOM 4564 C5* T C 33 45.959 57.554 -12.639 1.00 69.92 1CGP4719 ATOM 4565 C4* T C 33 46.472 56.170 -12.753 1.00 70.99 1CGP4720 ATOM 4566 O4* T C 33 47.084 56.078 -14.027 1.00 71.44 1CGP4721 ATOM 4567 C3* T C 33 47.560 55.854 -11.727 1.00 71.16 1CGP4722 ATOM 4568 O3* T C 33 47.423 54.495 -11.259 1.00 72.24 1CGP4723 ATOM 4569 C2* T C 33 48.826 56.003 -12.549 1.00 71.63 1CGP4724 ATOM 4570 C1* T C 33 48.340 55.441 -13.854 1.00 72.79 1CGP4725 ATOM 4571 N1 T C 33 49.116 55.777 -15.068 1.00 75.66 1CGP4726 ATOM 4572 C2 T C 33 49.089 54.846 -16.098 1.00 76.94 1CGP4727 ATOM 4573 O2 T C 33 48.582 53.736 -15.984 1.00 78.46 1CGP4728 ATOM 4574 N3 T C 33 49.721 55.190 -17.273 1.00 77.52 1CGP4729 ATOM 4575 C4 T C 33 50.382 56.371 -17.508 1.00 77.68 1CGP4730 ATOM 4576 O4 T C 33 50.869 56.565 -18.623 1.00 78.72 1CGP4731 ATOM 4577 C5 T C 33 50.378 57.280 -16.373 1.00 77.13 1CGP4732 ATOM 4578 C5M T C 33 51.113 58.611 -16.450 1.00 77.50 1CGP4733 ATOM 4579 C6 T C 33 49.759 56.965 -15.220 1.00 76.13 1CGP4734 ATOM 4580 H3* T C 33 46.908 54.014 -11.916 1.00 0.00 1CGP4735 ATOM 4581 H3 T C 33 49.673 54.529 -18.036 1.00 0.00 1CGP4736 TER 4582 T C 33 1CGP4737 ATOM 4583 O5* G D 3 48.587 51.928 -11.115 1.00 62.07 1CGP4738 ATOM 4584 C5* G D 3 47.476 51.045 -11.341 1.00 64.93 1CGP4739 ATOM 4585 C4* G D 3 47.655 50.150 -12.568 1.00 65.96 1CGP4740 ATOM 4586 O4* G D 3 47.835 50.930 -13.737 1.00 66.61 1CGP4741 ATOM 4587 C3* G D 3 48.887 49.300 -12.428 1.00 67.13 1CGP4742 ATOM 4588 O3* G D 3 48.464 48.098 -11.828 1.00 69.06 1CGP4743 ATOM 4589 C2* G D 3 49.284 49.080 -13.850 1.00 66.18 1CGP4744 ATOM 4590 C1* G D 3 48.897 50.350 -14.492 1.00 66.56 1CGP4745 ATOM 4591 N9 G D 3 49.977 51.339 -14.537 1.00 67.60 1CGP4746 ATOM 4592 C8 G D 3 50.326 52.320 -13.646 1.00 68.11 1CGP4747 ATOM 4593 N7 G D 3 51.213 53.158 -14.094 1.00 68.28 1CGP4748 ATOM 4594 C5 G D 3 51.472 52.689 -15.373 1.00 68.81 1CGP4749 ATOM 4595 C6 G D 3 52.336 53.195 -16.364 1.00 69.23 1CGP4750 ATOM 4596 O6 G D 3 52.994 54.227 -16.343 1.00 70.35 1CGP4751 ATOM 4597 N1 G D 3 52.309 52.431 -17.504 1.00 69.82 1CGP4752 ATOM 4598 C2 G D 3 51.528 51.320 -17.688 1.00 70.19 1CGP4753 ATOM 4599 N2 G D 3 51.604 50.711 -18.871 1.00 70.89 1CGP4754 ATOM 4600 N3 G D 3 50.703 50.839 -16.759 1.00 69.68 1CGP4755 ATOM 4601 C4 G D 3 50.731 51.572 -15.635 1.00 68.55 1CGP4756 ATOM 4602 H1 G D 3 52.946 52.705 -18.237 1.00 0.00 1CGP4757 ATOM 4603 H5T G D 3 48.571 52.534 -11.864 1.00 0.00 1CGP4758 ATOM 4604 H21 G D 3 50.975 49.950 -19.090 1.00 0.00 1CGP4759 ATOM 4605 H22 G D 3 52.292 50.984 -19.552 1.00 0.00 1CGP4760 ATOM 4606 P T D 4 49.488 46.918 -11.506 1.00 78.97 1CGP4761 ATOM 4607 O1P T D 4 49.985 46.487 -10.180 1.00 82.60 1CGP4762 ATOM 4608 O2P T D 4 48.049 46.735 -11.832 1.00 80.33 1CGP4763 ATOM 4609 O5* T D 4 50.375 46.126 -12.579 1.00 83.16 1CGP4764 ATOM 4610 C5* T D 4 49.811 45.400 -13.680 1.00 83.06 1CGP4765 ATOM 4611 C4* T D 4 50.749 45.500 -14.847 1.00 83.37 1CGP4766 ATOM 4612 O4* T D 4 51.035 46.874 -15.079 1.00 83.79 1CGP4767 ATOM 4613 C3* T D 4 52.073 44.859 -14.526 1.00 83.44 1CGP4768 ATOM 4614 O3* T D 4 51.978 43.496 -14.964 1.00 84.12 1CGP4769 ATOM 4615 C2* T D 4 53.048 45.681 -15.334 1.00 83.85 1CGP4770 ATOM 4616 C1* T D 4 52.284 46.939 -15.767 1.00 84.10 1CGP4771 ATOM 4617 N1 T D 4 53.017 48.201 -15.400 1.00 84.40 1CGP4772 ATOM 4618 C2 T D 4 53.923 48.731 -16.323 1.00 84.55 1CGP4773 ATOM 4619 O2 T D 4 54.148 48.249 -17.436 1.00 85.41 1CGP4774 ATOM 4620 N3 T D 4 54.585 49.873 -15.931 1.00 83.44 1CGP4775 ATOM 4621 C4 T D 4 54.449 50.539 -14.745 1.00 82.31 1CGP4776 ATOM 4622 O4 T D 4 55.125 51.529 -14.525 1.00 80.93 1CGP4777 ATOM 4623 C5 T D 4 53.497 49.943 -13.851 1.00 83.06 1CGP4778 ATOM 4624 C5M T D 4 53.231 50.588 -12.503 1.00 83.38 1CGP4779 ATOM 4625 C6 T D 4 52.828 48.824 -14.189 1.00 84.09 1CGP4780 ATOM 4626 H3 T D 4 55.254 50.233 -16.601 1.00 0.00 1CGP4781 ATOM 4627 P C D 5 51.864 42.233 -13.942 1.00 86.13 1CGP4782 ATOM 4628 O1P C D 5 51.496 41.309 -12.834 1.00 84.87 1CGP4783 ATOM 4629 O2P C D 5 51.135 42.142 -15.234 1.00 86.45 1CGP4784 ATOM 4630 O5* C D 5 53.461 42.083 -14.210 1.00 86.65 1CGP4785 ATOM 4631 C5* C D 5 53.935 41.356 -15.353 1.00 87.30 1CGP4786 ATOM 4632 C4* C D 5 55.309 41.802 -15.865 1.00 87.62 1CGP4787 ATOM 4633 O4* C D 5 55.332 43.206 -16.065 1.00 86.66 1CGP4788 ATOM 4634 C3* C D 5 56.404 41.508 -14.871 1.00 88.96 1CGP4789 ATOM 4635 O3* C D 5 56.752 40.131 -15.030 1.00 91.40 1CGP4790 ATOM 4636 C2* C D 5 57.483 42.445 -15.389 1.00 87.69 1CGP4791 ATOM 4637 C1* C D 5 56.677 43.648 -15.876 1.00 86.15 1CGP4792 ATOM 4638 N1 C D 5 56.678 44.806 -14.915 1.00 85.30 1CGP4793 ATOM 4639 C2 C D 5 56.978 46.051 -15.447 1.00 85.38 1CGP4794 ATOM 4640 O2 C D 5 57.233 46.209 -16.644 1.00 86.64 1CGP4795 ATOM 4641 N3 C D 5 56.998 47.132 -14.623 1.00 83.87 1CGP4796 ATOM 4642 C4 C D 5 56.737 47.028 -13.328 1.00 83.03 1CGP4797 ATOM 4643 N4 C D 5 56.783 48.142 -12.607 1.00 82.68 1CGP4798 ATOM 4644 C5 C D 5 56.419 45.760 -12.748 1.00 82.93 1CGP4799 ATOM 4645 C6 C D 5 56.403 44.689 -13.574 1.00 84.08 1CGP4800 ATOM 4646 H41 C D 5 56.602 48.118 -11.614 1.00 0.00 1CGP4801 ATOM 4647 H42 C D 5 56.999 49.034 -13.042 1.00 0.00 1CGP4802 ATOM 4648 P A D 6 57.159 39.189 -13.793 1.00 96.97 1CGP4803 ATOM 4649 O1P A D 6 57.185 38.830 -12.357 1.00 98.91 1CGP4804 ATOM 4650 O2P A D 6 56.694 38.188 -14.789 1.00 98.60 1CGP4805 ATOM 4651 O5* A D 6 58.622 39.659 -14.180 1.00 97.94 1CGP4806 ATOM 4652 C5* A D 6 59.345 39.196 -15.313 1.00 98.88 1CGP4807 ATOM 4653 C4* A D 6 60.750 39.601 -15.089 1.00100.63 1CGP4808 ATOM 4654 O4* A D 6 60.741 41.015 -14.822 1.00100.24 1CGP4809 ATOM 4655 C3* A D 6 61.359 38.852 -13.891 1.00101.80 1CGP4810 ATOM 4656 O3* A D 6 62.681 38.388 -14.262 1.00104.20 1CGP4811 ATOM 4657 C2* A D 6 61.398 39.910 -12.810 1.00101.16 1CGP4812 ATOM 4658 C1* A D 6 61.388 41.243 -13.568 1.00101.03 1CGP4813 ATOM 4659 N9 A D 6 60.645 42.268 -12.796 1.00101.38 1CGP4814 ATOM 4660 C8 A D 6 59.709 42.095 -11.805 1.00101.74 1CGP4815 ATOM 4661 N7 A D 6 59.270 43.198 -11.268 1.00101.57 1CGP4816 ATOM 4662 C5 A D 6 59.965 44.179 -11.955 1.00101.97 1CGP4817 ATOM 4663 C6 A D 6 59.947 45.571 -11.849 1.00102.17 1CGP4818 ATOM 4664 N6 A D 6 59.192 46.213 -10.961 1.00102.55 1CGP4819 ATOM 4665 N1 A D 6 60.741 46.255 -12.674 1.00102.36 1CGP4820 ATOM 4666 C2 A D 6 61.501 45.592 -13.538 1.00102.49 1CGP4821 ATOM 4667 N3 A D 6 61.614 44.290 -13.736 1.00102.28 1CGP4822 ATOM 4668 C4 A D 6 60.800 43.628 -12.891 1.00101.87 1CGP4823 ATOM 4669 H61 A D 6 58.666 45.676 -10.286 1.00 0.00 1CGP4824 ATOM 4670 H62 A D 6 59.134 47.224 -10.947 1.00 0.00 1CGP4825 ATOM 4671 P C D 7 63.664 37.451 -13.366 1.00106.45 1CGP4826 ATOM 4672 O1P C D 7 63.362 36.526 -12.242 1.00105.70 1CGP4827 ATOM 4673 O2P C D 7 64.369 36.957 -14.584 1.00106.07 1CGP4828 ATOM 4674 O5* C D 7 64.507 38.667 -12.758 1.00107.43 1CGP4829 ATOM 4675 C5* C D 7 65.424 39.445 -13.541 1.00108.52 1CGP4830 ATOM 4676 C4* C D 7 65.860 40.669 -12.758 1.00109.54 1CGP4831 ATOM 4677 O4* C D 7 64.778 41.559 -12.497 1.00109.69 1CGP4832 ATOM 4678 C3* C D 7 66.288 40.237 -11.370 1.00110.88 1CGP4833 ATOM 4679 O3* C D 7 67.643 39.765 -11.442 1.00112.87 1CGP4834 ATOM 4680 C2* C D 7 66.160 41.515 -10.592 1.00109.95 1CGP4835 ATOM 4681 C1* C D 7 65.172 42.358 -11.364 1.00109.20 1CGP4836 ATOM 4682 N1 C D 7 64.002 42.714 -10.501 1.00107.78 1CGP4837 ATOM 4683 C2 C D 7 63.681 44.059 -10.371 1.00106.68 1CGP4838 ATOM 4684 O2 C D 7 64.354 44.962 -10.864 1.00106.46 1CGP4839 ATOM 4685 N3 C D 7 62.602 44.400 -9.637 1.00105.50 1CGP4840 ATOM 4686 C4 C D 7 61.856 43.478 -9.037 1.00105.30 1CGP4841 ATOM 4687 N4 C D 7 60.809 43.893 -8.334 1.00104.79 1CGP4842 ATOM 4688 C5 C D 7 62.168 42.086 -9.147 1.00105.79 1CGP4843 ATOM 4689 C6 C D 7 63.244 41.756 -9.886 1.00106.59 1CGP4844 ATOM 4690 H41 C D 7 60.646 44.891 -8.246 1.00 0.00 1CGP4845 ATOM 4691 H42 C D 7 60.178 43.238 -7.891 1.00 0.00 1CGP4846 ATOM 4692 P A D 8 68.479 39.160 -10.192 1.00116.72 1CGP4847 ATOM 4693 O1P A D 8 67.514 38.842 -9.113 1.00118.55 1CGP4848 ATOM 4694 O2P A D 8 69.526 38.166 -10.520 1.00117.86 1CGP4849 ATOM 4695 O5* A D 8 69.215 40.522 -9.795 1.00116.41 1CGP4850 ATOM 4696 C5* A D 8 69.852 41.336 -10.776 1.00115.45 1CGP4851 ATOM 4697 C4* A D 8 69.919 42.786 -10.322 1.00116.06 1CGP4852 ATOM 4698 O4* A D 8 68.631 43.274 -9.902 1.00116.76 1CGP4853 ATOM 4699 C3* A D 8 70.809 42.909 -9.112 1.00115.51 1CGP4854 ATOM 4700 O3* A D 8 71.409 44.190 -9.221 1.00114.62 1CGP4855 ATOM 4701 C2* A D 8 69.849 42.811 -7.940 1.00116.36 1CGP4856 ATOM 4702 C1* A D 8 68.653 43.569 -8.489 1.00117.26 1CGP4857 ATOM 4703 N9 A D 8 67.405 43.115 -7.808 1.00118.00 1CGP4858 ATOM 4704 C8 A D 8 67.042 41.863 -7.350 1.00118.03 1CGP4859 ATOM 4705 N7 A D 8 65.860 41.815 -6.798 1.00118.27 1CGP4860 ATOM 4706 C5 A D 8 65.406 43.121 -6.895 1.00119.14 1CGP4861 ATOM 4707 C6 A D 8 64.213 43.728 -6.489 1.00120.00 1CGP4862 ATOM 4708 N6 A D 8 63.223 43.049 -5.899 1.00120.49 1CGP4863 ATOM 4709 N1 A D 8 64.090 45.046 -6.733 1.00120.70 1CGP4864 ATOM 4710 C2 A D 8 65.079 45.706 -7.336 1.00119.64 1CGP4865 ATOM 4711 N3 A D 8 66.239 45.249 -7.766 1.00119.01 1CGP4866 ATOM 4712 C4 A D 8 66.337 43.922 -7.509 1.00118.78 1CGP4867 ATOM 4713 H61 A D 8 63.354 42.072 -5.678 1.00 0.00 1CGP4868 ATOM 4714 H62 A D 8 62.338 43.488 -5.673 1.00 0.00 1CGP4869 ATOM 4715 P C D 9 72.403 44.734 -8.106 1.00111.24 1CGP4870 ATOM 4716 O1P C D 9 72.834 43.622 -7.217 1.00109.91 1CGP4871 ATOM 4717 O2P C D 9 73.296 45.234 -9.186 1.00109.81 1CGP4872 ATOM 4718 O5* C D 9 71.920 45.950 -7.188 1.00107.30 1CGP4873 ATOM 4719 C5* C D 9 71.659 47.271 -7.672 1.00103.15 1CGP4874 ATOM 4720 C4* C D 9 70.668 47.905 -6.725 1.00100.42 1CGP4875 ATOM 4721 O4* C D 9 69.443 47.149 -6.648 1.00 99.63 1CGP4876 ATOM 4722 C3* C D 9 71.225 47.815 -5.327 1.00 98.74 1CGP4877 ATOM 4723 O3* C D 9 72.154 48.911 -5.156 1.00 97.98 1CGP4878 ATOM 4724 C2* C D 9 69.979 47.894 -4.468 1.00 98.92 1CGP4879 ATOM 4725 C1* C D 9 68.840 47.414 -5.362 1.00 98.32 1CGP4880 ATOM 4726 N1 C D 9 68.222 46.193 -4.767 1.00 96.68 1CGP4881 ATOM 4727 C2 C D 9 67.042 46.306 -4.038 1.00 95.77 1CGP4882 ATOM 4728 O2 C D 9 66.509 47.384 -3.797 1.00 94.80 1CGP4883 ATOM 4729 N3 C D 9 66.475 45.173 -3.544 1.00 95.23 1CGP4884 ATOM 4730 C4 C D 9 67.029 43.972 -3.743 1.00 94.81 1CGP4885 ATOM 4731 N4 C D 9 66.432 42.872 -3.281 1.00 93.98 1CGP4886 ATOM 4732 C5 C D 9 68.244 43.845 -4.476 1.00 95.29 1CGP4887 ATOM 4733 C6 C D 9 68.796 44.974 -4.963 1.00 95.68 1CGP4888 ATOM 4734 H41 C D 9 66.874 41.970 -3.391 1.00 0.00 1CGP4889 ATOM 4735 H42 C D 9 65.530 42.934 -2.828 1.00 0.00 1CGP4890 ATOM 4736 P T D 10 71.957 50.160 -4.136 1.00 94.57 1CGP4891 ATOM 4737 O1P T D 10 73.304 49.696 -3.719 1.00 94.77 1CGP4892 ATOM 4738 O2P T D 10 71.810 50.978 -5.369 1.00 93.03 1CGP4893 ATOM 4739 O5* T D 10 71.384 50.975 -2.870 1.00 91.74 1CGP4894 ATOM 4740 C5* T D 10 70.149 51.692 -3.008 1.00 89.96 1CGP4895 ATOM 4741 C4* T D 10 68.991 51.237 -2.095 1.00 86.95 1CGP4896 ATOM 4742 O4* T D 10 68.766 49.826 -2.195 1.00 86.65 1CGP4897 ATOM 4743 C3* T D 10 69.301 51.508 -0.639 1.00 85.22 1CGP4898 ATOM 4744 O3* T D 10 68.680 52.738 -0.265 1.00 82.68 1CGP4899 ATOM 4745 C2* T D 10 68.672 50.331 0.059 1.00 85.22 1CGP4900 ATOM 4746 C1* T D 10 67.964 49.548 -1.038 1.00 85.62 1CGP4901 ATOM 4747 N1 T D 10 67.938 48.084 -0.734 1.00 84.22 1CGP4902 ATOM 4748 C2 T D 10 66.809 47.556 -0.135 1.00 83.35 1CGP4903 ATOM 4749 O2 T D 10 65.873 48.225 0.287 1.00 82.85 1CGP4904 ATOM 4750 N3 T D 10 66.809 46.208 0.074 1.00 83.57 1CGP4905 ATOM 4751 C4 T D 10 67.814 45.337 -0.238 1.00 84.20 1CGP4906 ATOM 4752 O4 T D 10 67.671 44.140 0.000 1.00 84.38 1CGP4907 ATOM 4753 C5 T D 10 68.956 45.965 -0.839 1.00 84.22 1CGP4908 ATOM 4754 C5M T D 10 70.175 45.135 -1.166 1.00 85.52 1CGP4909 ATOM 4755 C6 T D 10 68.983 47.279 -1.071 1.00 84.00 1CGP4910 ATOM 4756 H3 T D 10 65.981 45.809 0.498 1.00 0.00 1CGP4911 ATOM 4757 P T D 11 68.732 53.317 1.228 1.00 81.43 1CGP4912 ATOM 4758 O1P T D 11 70.055 52.913 1.739 1.00 81.97 1CGP4913 ATOM 4759 O2P T D 11 68.611 54.643 0.565 1.00 79.48 1CGP4914 ATOM 4760 O5* T D 11 67.840 53.401 2.534 1.00 81.02 1CGP4915 ATOM 4761 C5* T D 11 66.439 53.377 2.306 1.00 80.78 1CGP4916 ATOM 4762 C4* T D 11 65.860 52.073 2.777 1.00 80.54 1CGP4917 ATOM 4763 O4* T D 11 66.622 50.959 2.329 1.00 82.37 1CGP4918 ATOM 4764 C3* T D 11 65.927 52.000 4.273 1.00 79.35 1CGP4919 ATOM 4765 O3* T D 11 64.774 52.667 4.773 1.00 76.63 1CGP4920 ATOM 4766 C2* T D 11 65.906 50.519 4.532 1.00 81.69 1CGP4921 ATOM 4767 C1* T D 11 66.003 49.935 3.136 1.00 84.88 1CGP4922 ATOM 4768 N1 T D 11 66.779 48.657 3.188 1.00 88.34 1CGP4923 ATOM 4769 C2 T D 11 66.104 47.518 3.599 1.00 90.37 1CGP4924 ATOM 4770 O2 T D 11 64.949 47.512 4.013 1.00 91.92 1CGP4925 ATOM 4771 N3 T D 11 66.820 46.339 3.557 1.00 91.82 1CGP4926 ATOM 4772 C4 T D 11 68.128 46.175 3.168 1.00 92.35 1CGP4927 ATOM 4773 O4 T D 11 68.620 45.046 3.154 1.00 92.57 1CGP4928 ATOM 4774 C5 T D 11 68.772 47.407 2.771 1.00 92.02 1CGP4929 ATOM 4775 C5M T D 11 70.240 47.383 2.295 1.00 92.40 1CGP4930 ATOM 4776 C6 T D 11 68.091 48.578 2.798 1.00 90.43 1CGP4931 ATOM 4777 H3 T D 11 66.349 45.487 3.824 1.00 0.00 1CGP4932 ATOM 4778 P T D 12 64.557 52.894 6.334 1.00 75.11 1CGP4933 ATOM 4779 O1P T D 12 65.928 53.104 6.836 1.00 76.43 1CGP4934 ATOM 4780 O2P T D 12 63.504 53.853 6.730 1.00 74.10 1CGP4935 ATOM 4781 O5* T D 12 64.143 51.471 6.821 1.00 74.63 1CGP4936 ATOM 4782 C5* T D 12 62.807 51.021 6.720 1.00 74.71 1CGP4937 ATOM 4783 C4* T D 12 62.743 49.767 7.512 1.00 74.73 1CGP4938 ATOM 4784 O4* T D 12 63.663 48.841 6.967 1.00 74.46 1CGP4939 ATOM 4785 C3* T D 12 63.212 50.039 8.924 1.00 75.22 1CGP4940 ATOM 4786 O3* T D 12 62.068 50.135 9.795 1.00 76.20 1CGP4941 ATOM 4787 C2* T D 12 64.109 48.896 9.265 1.00 74.65 1CGP4942 ATOM 4788 C1* T D 12 64.073 48.022 8.034 1.00 73.77 1CGP4943 ATOM 4789 N1 T D 12 65.393 47.484 7.679 1.00 72.75 1CGP4944 ATOM 4790 C2 T D 12 65.513 46.129 7.610 1.00 72.71 1CGP4945 ATOM 4791 O2 T D 12 64.576 45.376 7.848 1.00 73.71 1CGP4946 ATOM 4792 N3 T D 12 66.744 45.633 7.259 1.00 72.53 1CGP4947 ATOM 4793 C4 T D 12 67.860 46.374 6.968 1.00 72.52 1CGP4948 ATOM 4794 O4 T D 12 68.909 45.820 6.644 1.00 72.17 1CGP4949 ATOM 4795 C5 T D 12 67.639 47.788 7.064 1.00 72.81 1CGP4950 ATOM 4796 C5M T D 12 68.778 48.737 6.768 1.00 74.44 1CGP4951 ATOM 4797 C6 T D 12 66.449 48.292 7.408 1.00 72.71 1CGP4952 ATOM 4798 H3 T D 12 66.840 44.627 7.216 1.00 0.00 1CGP4953 ATOM 4799 P T D 13 61.211 48.945 10.455 1.00 77.90 1CGP4954 ATOM 4800 O1P T D 13 61.182 50.141 11.333 1.00 77.94 1CGP4955 ATOM 4801 O2P T D 13 60.323 48.923 9.269 1.00 78.73 1CGP4956 ATOM 4802 O5* T D 13 60.777 47.727 11.380 1.00 80.07 1CGP4957 ATOM 4803 C5* T D 13 60.404 46.531 10.719 1.00 81.02 1CGP4958 ATOM 4804 C4* T D 13 61.525 45.536 10.745 1.00 81.44 1CGP4959 ATOM 4805 O4* T D 13 62.774 46.092 10.340 1.00 81.08 1CGP4960 ATOM 4806 C3* T D 13 61.751 45.113 12.171 1.00 81.98 1CGP4961 ATOM 4807 O3* T D 13 60.790 44.117 12.528 1.00 81.58 1CGP4962 ATOM 4808 C2* T D 13 63.138 44.539 12.104 1.00 82.02 1CGP4963 ATOM 4809 C1* T D 13 63.605 44.985 10.741 1.00 81.35 1CGP4964 ATOM 4810 N1 T D 13 65.049 45.338 10.801 1.00 80.51 1CGP4965 ATOM 4811 C2 T D 13 65.949 44.361 10.407 1.00 80.49 1CGP4966 ATOM 4812 O2 T D 13 65.617 43.224 10.088 1.00 81.29 1CGP4967 ATOM 4813 N3 T D 13 67.273 44.722 10.361 1.00 79.88 1CGP4968 ATOM 4814 C4 T D 13 67.777 45.952 10.666 1.00 78.97 1CGP4969 ATOM 4815 O4 T D 13 68.969 46.158 10.489 1.00 78.48 1CGP4970 ATOM 4816 C5 T D 13 66.778 46.904 11.081 1.00 78.84 1CGP4971 ATOM 4817 C5M T D 13 67.173 48.317 11.450 1.00 78.88 1CGP4972 ATOM 4818 C6 T D 13 65.483 46.576 11.137 1.00 79.40 1CGP4973 ATOM 4819 H3 T D 13 67.932 44.000 10.092 1.00 0.00 1CGP4974 ATOM 4820 P C D 14 60.401 43.974 14.064 1.00 86.15 1CGP4975 ATOM 4821 O1P C D 14 60.522 45.248 14.811 1.00 87.11 1CGP4976 ATOM 4822 O2P C D 14 59.187 43.151 14.238 1.00 88.02 1CGP4977 ATOM 4823 O5* C D 14 61.675 43.075 14.418 1.00 88.81 1CGP4978 ATOM 4824 C5* C D 14 61.758 41.660 14.221 1.00 90.35 1CGP4979 ATOM 4825 C4* C D 14 63.047 41.111 14.841 1.00 91.33 1CGP4980 ATOM 4826 O4* C D 14 64.183 41.638 14.172 1.00 90.36 1CGP4981 ATOM 4827 C3* C D 14 63.155 41.538 16.314 1.00 92.63 1CGP4982 ATOM 4828 O3* C D 14 62.775 40.493 17.244 1.00 95.74 1CGP4983 ATOM 4829 C2* C D 14 64.604 41.828 16.523 1.00 90.82 1CGP4984 ATOM 4830 C1* C D 14 65.212 41.877 15.134 1.00 89.68 1CGP4985 ATOM 4831 N1 C D 14 65.860 43.202 14.877 1.00 88.72 1CGP4986 ATOM 4832 C2 C D 14 67.127 43.187 14.339 1.00 88.34 1CGP4987 ATOM 4833 O2 C D 14 67.723 42.146 14.107 1.00 90.42 1CGP4988 ATOM 4834 N3 C D 14 67.757 44.344 14.060 1.00 86.55 1CGP4989 ATOM 4835 C4 C D 14 67.177 45.498 14.313 1.00 86.11 1CGP4990 ATOM 4836 N4 C D 14 67.873 46.588 14.051 1.00 85.68 1CGP4991 ATOM 4837 C5 C D 14 65.867 45.566 14.873 1.00 86.90 1CGP4992 ATOM 4838 C6 C D 14 65.252 44.394 15.142 1.00 88.10 1CGP4993 ATOM 4839 H41 C D 14 67.539 47.507 14.301 1.00 0.00 1CGP4994 ATOM 4840 H42 C D 14 68.769 46.470 13.587 1.00 0.00 1CGP4995 ATOM 4841 P G D 15 62.980 38.883 17.002 1.00100.02 1CGP4996 ATOM 4842 O1P G D 15 62.928 38.904 18.484 1.00101.64 1CGP4997 ATOM 4843 O2P G D 15 61.959 38.096 16.265 1.00101.62 1CGP4998 ATOM 4844 O5* G D 15 64.432 38.300 16.606 1.00 97.76 1CGP4999 ATOM 4845 C5* G D 15 64.690 37.406 15.527 1.00 94.55 1CGP5000 ATOM 4846 C4* G D 15 66.078 36.805 15.680 1.00 93.68 1CGP5001 ATOM 4847 O4* G D 15 67.041 37.876 15.746 1.00 92.75 1CGP5002 ATOM 4848 C3* G D 15 66.245 36.024 16.987 1.00 93.50 1CGP5003 ATOM 4849 O3* G D 15 67.148 34.921 16.785 1.00 94.23 1CGP5004 ATOM 4850 C2* G D 15 66.877 37.043 17.935 1.00 92.44 1CGP5005 ATOM 4851 C1* G D 15 67.766 37.855 16.998 1.00 91.68 1CGP5006 ATOM 4852 N9 G D 15 67.942 39.270 17.390 1.00 90.35 1CGP5007 ATOM 4853 C8 G D 15 67.062 40.081 18.045 1.00 89.63 1CGP5008 ATOM 4854 N7 G D 15 67.426 41.326 18.100 1.00 89.20 1CGP5009 ATOM 4855 C5 G D 15 68.643 41.347 17.437 1.00 89.78 1CGP5010 ATOM 4856 C6 G D 15 69.513 42.439 17.191 1.00 90.32 1CGP5011 ATOM 4857 O6 G D 15 69.331 43.617 17.493 1.00 90.75 1CGP5012 ATOM 4858 N1 G D 15 70.660 42.051 16.513 1.00 90.68 1CGP5013 ATOM 4859 C2 G D 15 70.938 40.756 16.121 1.00 90.83 1CGP5014 ATOM 4860 N2 G D 15 72.096 40.531 15.489 1.00 90.99 1CGP5015 ATOM 4861 N3 G D 15 70.107 39.728 16.347 1.00 90.70 1CGP5016 ATOM 4862 C4 G D 15 68.980 40.094 17.010 1.00 90.02 1CGP5017 ATOM 4863 H1 G D 15 71.312 42.794 16.289 1.00 0.00 1CGP5018 ATOM 4864 H3T G D 15 67.911 35.266 16.313 1.00 0.00 1CGP5019 ATOM 4865 H21 G D 15 72.324 39.607 15.153 1.00 0.00 1CGP5020 ATOM 4866 H22 G D 15 72.769 41.277 15.347 1.00 0.00 1CGP5021 ATOM 4867 O5* G D 16 76.184 50.417 20.584 1.00 96.80 1CGP5022 ATOM 4868 C5* G D 16 77.249 49.812 19.839 1.00 94.84 1CGP5023 ATOM 4869 C4* G D 16 76.744 49.015 18.622 1.00 93.45 1CGP5024 ATOM 4870 O4* G D 16 75.692 48.135 19.070 1.00 92.71 1CGP5025 ATOM 4871 C3* G D 16 76.155 49.893 17.509 1.00 93.01 1CGP5026 ATOM 4872 O3* G D 16 76.254 49.278 16.215 1.00 93.78 1CGP5027 ATOM 4873 C2* G D 16 74.679 49.884 17.877 1.00 92.48 1CGP5028 ATOM 4874 C1* G D 16 74.498 48.425 18.332 1.00 92.37 1CGP5029 ATOM 4875 N9 G D 16 73.272 48.251 19.185 1.00 91.82 1CGP5030 ATOM 4876 C8 G D 16 72.591 49.195 19.923 1.00 91.93 1CGP5031 ATOM 4877 N7 G D 16 71.507 48.748 20.502 1.00 91.17 1CGP5032 ATOM 4878 C5 G D 16 71.455 47.414 20.135 1.00 89.58 1CGP5033 ATOM 4879 C6 G D 16 70.490 46.444 20.460 1.00 88.44 1CGP5034 ATOM 4880 O6 G D 16 69.495 46.580 21.160 1.00 87.94 1CGP5035 ATOM 4881 N1 G D 16 70.785 45.225 19.901 1.00 88.48 1CGP5036 ATOM 4882 C2 G D 16 71.885 44.971 19.112 1.00 88.98 1CGP5037 ATOM 4883 N2 G D 16 72.059 43.733 18.658 1.00 89.83 1CGP5038 ATOM 4884 N3 G D 16 72.797 45.886 18.796 1.00 89.26 1CGP5039 ATOM 4885 C4 G D 16 72.520 47.092 19.334 1.00 90.17 1CGP5040 ATOM 4886 H1 G D 16 70.104 44.499 20.101 1.00 0.00 1CGP5041 ATOM 4887 H5T G D 16 75.535 49.717 20.710 1.00 0.00 1CGP5042 ATOM 4888 H21 G D 16 72.872 43.524 18.096 1.00 0.00 1CGP5043 ATOM 4889 H22 G D 16 71.400 42.998 18.868 1.00 0.00 1CGP5044 ATOM 4890 P C D 17 77.604 48.724 15.521 1.00 97.51 1CGP5045 ATOM 4891 O1P C D 17 76.880 48.359 14.283 1.00 98.67 1CGP5046 ATOM 4892 O2P C D 17 78.881 49.458 15.447 1.00 98.80 1CGP5047 ATOM 4893 O5* C D 17 77.800 47.408 16.390 1.00100.30 1CGP5048 ATOM 4894 C5* C D 17 78.795 46.414 16.154 1.00102.66 1CGP5049 ATOM 4895 C4* C D 17 78.195 45.162 15.510 1.00103.94 1CGP5050 ATOM 4896 O4* C D 17 76.900 44.870 16.055 1.00104.34 1CGP5051 ATOM 4897 C3* C D 17 78.041 45.361 14.040 1.00104.70 1CGP5052 ATOM 4898 O3* C D 17 79.252 44.822 13.495 1.00105.34 1CGP5053 ATOM 4899 C2* C D 17 76.783 44.577 13.722 1.00104.28 1CGP5054 ATOM 4900 C1* C D 17 76.121 44.208 15.051 1.00104.80 1CGP5055 ATOM 4901 N1 C D 17 74.702 44.692 15.149 1.00105.73 1CGP5056 ATOM 4902 C2 C D 17 73.657 43.775 15.351 1.00105.76 1CGP5057 ATOM 4903 O2 C D 17 73.824 42.555 15.388 1.00105.28 1CGP5058 ATOM 4904 N3 C D 17 72.385 44.256 15.485 1.00105.66 1CGP5059 ATOM 4905 C4 C D 17 72.127 45.574 15.418 1.00105.56 1CGP5060 ATOM 4906 N4 C D 17 70.871 45.996 15.549 1.00105.62 1CGP5061 ATOM 4907 C5 C D 17 73.175 46.526 15.208 1.00105.44 1CGP5062 ATOM 4908 C6 C D 17 74.431 46.043 15.080 1.00105.83 1CGP5063 ATOM 4909 H41 C D 17 70.103 45.349 15.648 1.00 0.00 1CGP5064 ATOM 4910 H42 C D 17 70.664 46.985 15.552 1.00 0.00 1CGP5065 ATOM 4911 P G D 18 79.440 44.319 11.980 1.00111.60 1CGP5066 ATOM 4912 O1P G D 18 79.091 45.665 11.469 1.00114.21 1CGP5067 ATOM 4913 O2P G D 18 80.852 43.876 11.921 1.00113.07 1CGP5068 ATOM 4914 O5* G D 18 78.551 43.246 11.185 1.00113.45 1CGP5069 ATOM 4915 C5* G D 18 78.394 41.923 11.705 1.00113.65 1CGP5070 ATOM 4916 C4* G D 18 76.986 41.328 11.492 1.00113.74 1CGP5071 ATOM 4917 O4* G D 18 75.952 42.114 12.086 1.00114.16 1CGP5072 ATOM 4918 C3* G D 18 76.675 41.242 10.016 1.00112.93 1CGP5073 ATOM 4919 O3* G D 18 76.761 39.821 9.785 1.00112.53 1CGP5074 ATOM 4920 C2* G D 18 75.293 41.884 9.891 1.00113.41 1CGP5075 ATOM 4921 C1* G D 18 74.760 41.896 11.315 1.00114.43 1CGP5076 ATOM 4922 N9 G D 18 73.798 43.016 11.534 1.00115.29 1CGP5077 ATOM 4923 C8 G D 18 73.963 44.357 11.275 1.00116.05 1CGP5078 ATOM 4924 N7 G D 18 72.944 45.108 11.612 1.00115.73 1CGP5079 ATOM 4925 C5 G D 18 72.027 44.207 12.126 1.00114.87 1CGP5080 ATOM 4926 C6 G D 18 70.736 44.449 12.651 1.00113.89 1CGP5081 ATOM 4927 O6 G D 18 70.136 45.505 12.814 1.00113.08 1CGP5082 ATOM 4928 N1 G D 18 70.152 43.288 13.052 1.00114.19 1CGP5083 ATOM 4929 C2 G D 18 70.724 42.039 12.971 1.00115.52 1CGP5084 ATOM 4930 N2 G D 18 69.982 41.013 13.367 1.00117.01 1CGP5085 ATOM 4931 N3 G D 18 71.937 41.795 12.491 1.00115.61 1CGP5086 ATOM 4932 C4 G D 18 72.535 42.929 12.082 1.00115.28 1CGP5087 ATOM 4933 H1 G D 18 69.229 43.433 13.432 1.00 0.00 1CGP5088 ATOM 4934 H21 G D 18 70.333 40.066 13.330 1.00 0.00 1CGP5089 ATOM 4935 H22 G D 18 69.043 41.196 13.708 1.00 0.00 1CGP5090 ATOM 4936 P A D 19 76.163 38.925 8.583 1.00110.94 1CGP5091 ATOM 4937 O1P A D 19 76.147 39.984 7.543 1.00111.85 1CGP5092 ATOM 4938 O2P A D 19 77.434 38.640 9.293 1.00111.31 1CGP5093 ATOM 4939 O5* A D 19 75.804 37.542 7.835 1.00108.80 1CGP5094 ATOM 4940 C5* A D 19 74.935 36.581 8.445 1.00105.88 1CGP5095 ATOM 4941 C4* A D 19 73.463 36.946 8.299 1.00102.96 1CGP5096 ATOM 4942 O4* A D 19 73.141 38.204 8.898 1.00100.86 1CGP5097 ATOM 4943 C3* A D 19 73.166 37.077 6.820 1.00102.19 1CGP5098 ATOM 4944 O3* A D 19 72.785 35.760 6.375 1.00103.28 1CGP5099 ATOM 4945 C2* A D 19 72.057 38.108 6.790 1.00100.29 1CGP5100 ATOM 4946 C1* A D 19 71.953 38.623 8.218 1.00 98.75 1CGP5101 ATOM 4947 N9 A D 19 71.840 40.086 8.167 1.00 95.72 1CGP5102 ATOM 4948 C8 A D 19 72.614 40.991 7.495 1.00 94.67 1CGP5103 ATOM 4949 N7 A D 19 72.252 42.228 7.656 1.00 93.82 1CGP5104 ATOM 4950 C5 A D 19 71.160 42.137 8.493 1.00 93.32 1CGP5105 ATOM 4951 C6 A D 19 70.329 43.116 9.034 1.00 92.97 1CGP5106 ATOM 4952 N6 A D 19 70.492 44.413 8.798 1.00 92.68 1CGP5107 ATOM 4953 N1 A D 19 69.336 42.692 9.817 1.00 93.11 1CGP5108 ATOM 4954 C2 A D 19 69.202 41.386 10.035 1.00 93.18 1CGP5109 ATOM 4955 N3 A D 19 69.915 40.369 9.594 1.00 93.13 1CGP5110 ATOM 4956 C4 A D 19 70.902 40.835 8.811 1.00 93.87 1CGP5111 ATOM 4957 H61 A D 19 71.177 44.709 8.115 1.00 0.00 1CGP5112 ATOM 4958 H62 A D 19 69.957 45.106 9.306 1.00 0.00 1CGP5113 ATOM 4959 P A D 20 71.279 35.320 5.961 1.00107.97 1CGP5114 ATOM 4960 O1P A D 20 71.748 35.705 4.606 1.00109.28 1CGP5115 ATOM 4961 O2P A D 20 71.715 34.037 6.561 1.00109.45 1CGP5116 ATOM 4962 O5* A D 20 69.658 35.300 5.954 1.00109.34 1CGP5117 ATOM 4963 C5* A D 20 68.867 34.894 7.095 1.00109.05 1CGP5118 ATOM 4964 C4* A D 20 67.488 35.622 7.282 1.00108.91 1CGP5119 ATOM 4965 O4* A D 20 67.663 37.031 7.546 1.00108.30 1CGP5120 ATOM 4966 C3* A D 20 66.625 35.528 6.017 1.00108.65 1CGP5121 ATOM 4967 O3* A D 20 65.238 35.439 6.380 1.00108.42 1CGP5122 ATOM 4968 C2* A D 20 66.895 36.846 5.323 1.00108.00 1CGP5123 ATOM 4969 C1* A D 20 66.997 37.779 6.520 1.00107.64 1CGP5124 ATOM 4970 N9 A D 20 67.778 38.965 6.143 1.00107.10 1CGP5125 ATOM 4971 C8 A D 20 68.852 39.088 5.293 1.00107.07 1CGP5126 ATOM 4972 N7 A D 20 69.300 40.302 5.158 1.00106.63 1CGP5127 ATOM 4973 C5 A D 20 68.455 41.033 5.980 1.00106.71 1CGP5128 ATOM 4974 C6 A D 20 68.398 42.396 6.276 1.00106.52 1CGP5129 ATOM 4975 N6 A D 20 69.245 43.281 5.759 1.00106.51 1CGP5130 ATOM 4976 N1 A D 20 67.440 42.788 7.124 1.00106.62 1CGP5131 ATOM 4977 C2 A D 20 66.611 41.878 7.631 1.00106.91 1CGP5132 ATOM 4978 N3 A D 20 66.554 40.576 7.442 1.00106.44 1CGP5133 ATOM 4979 C4 A D 20 67.530 40.223 6.585 1.00106.85 1CGP5134 ATOM 4980 H61 A D 20 69.939 42.974 5.091 1.00 0.00 1CGP5135 ATOM 4981 H62 A D 20 69.210 44.256 6.029 1.00 0.00 1CGP5136 ATOM 4982 P A D 21 64.118 35.359 5.230 1.00106.69 1CGP5137 ATOM 4983 O1P A D 21 64.105 35.369 3.745 1.00106.03 1CGP5138 ATOM 4984 O2P A D 21 63.421 34.296 6.003 1.00106.13 1CGP5139 ATOM 4985 O5* A D 21 63.596 36.790 5.715 1.00104.37 1CGP5140 ATOM 4986 C5* A D 21 62.905 36.994 6.958 1.00101.05 1CGP5141 ATOM 4987 C4* A D 21 62.256 38.380 7.009 1.00 97.77 1CGP5142 ATOM 4988 O4* A D 21 63.268 39.386 6.754 1.00 96.43 1CGP5143 ATOM 4989 C3* A D 21 61.172 38.530 5.936 1.00 95.32 1CGP5144 ATOM 4990 O3* A D 21 60.089 39.321 6.465 1.00 93.56 1CGP5145 ATOM 4991 C2* A D 21 61.910 39.273 4.825 1.00 94.67 1CGP5146 ATOM 4992 C1* A D 21 62.893 40.154 5.603 1.00 93.69 1CGP5147 ATOM 4993 N9 A D 21 64.083 40.451 4.775 1.00 90.83 1CGP5148 ATOM 4994 C8 A D 21 64.845 39.604 4.013 1.00 90.29 1CGP5149 ATOM 4995 N7 A D 21 65.815 40.191 3.367 1.00 88.99 1CGP5150 ATOM 4996 C5 A D 21 65.685 41.514 3.731 1.00 87.53 1CGP5151 ATOM 4997 C6 A D 21 66.410 42.642 3.384 1.00 86.19 1CGP5152 ATOM 4998 N6 A D 21 67.435 42.598 2.552 1.00 85.59 1CGP5153 ATOM 4999 N1 A D 21 66.021 43.797 3.917 1.00 85.48 1CGP5154 ATOM 5000 C2 A D 21 64.985 43.817 4.737 1.00 86.20 1CGP5155 ATOM 5001 N3 A D 21 64.221 42.835 5.143 1.00 87.18 1CGP5156 ATOM 5002 C4 A D 21 64.636 41.686 4.590 1.00 88.55 1CGP5157 ATOM 5003 H61 A D 21 67.669 41.736 2.083 1.00 0.00 1CGP5158 ATOM 5004 H62 A D 21 67.991 43.429 2.403 1.00 0.00 1CGP5159 ATOM 5005 P A D 22 58.843 39.703 5.529 1.00 87.05 1CGP5160 ATOM 5006 O1P A D 22 58.785 39.612 4.044 1.00 84.74 1CGP5161 ATOM 5007 O2P A D 22 58.229 38.637 6.357 1.00 85.13 1CGP5162 ATOM 5008 O5* A D 22 58.120 41.046 6.024 1.00 83.20 1CGP5163 ATOM 5009 C5* A D 22 58.774 42.192 6.602 1.00 79.97 1CGP5164 ATOM 5010 C4* A D 22 59.329 43.248 5.605 1.00 76.91 1CGP5165 ATOM 5011 O4* A D 22 60.490 42.788 4.926 1.00 75.59 1CGP5166 ATOM 5012 C3* A D 22 58.325 43.536 4.481 1.00 74.90 1CGP5167 ATOM 5013 O3* A D 22 57.592 44.747 4.718 1.00 72.40 1CGP5168 ATOM 5014 C2* A D 22 59.191 43.699 3.244 1.00 75.00 1CGP5169 ATOM 5015 C1* A D 22 60.565 43.710 3.827 1.00 74.64 1CGP5170 ATOM 5016 N9 A D 22 61.510 43.244 2.826 1.00 74.10 1CGP5171 ATOM 5017 C8 A D 22 61.648 41.996 2.289 1.00 74.37 1CGP5172 ATOM 5018 N7 A D 22 62.679 41.870 1.510 1.00 74.54 1CGP5173 ATOM 5019 C5 A D 22 63.251 43.127 1.536 1.00 74.19 1CGP5174 ATOM 5020 C6 A D 22 64.387 43.635 0.926 1.00 74.44 1CGP5175 ATOM 5021 N6 A D 22 65.186 42.864 0.193 1.00 75.10 1CGP5176 ATOM 5022 N1 A D 22 64.679 44.918 1.159 1.00 74.10 1CGP5177 ATOM 5023 C2 A D 22 63.883 45.625 1.946 1.00 73.38 1CGP5178 ATOM 5024 N3 A D 22 62.799 45.261 2.591 1.00 73.19 1CGP5179 ATOM 5025 C4 A D 22 62.541 43.971 2.335 1.00 73.84 1CGP5180 ATOM 5026 H61 A D 22 64.893 41.917 -0.008 1.00 0.00 1CGP5181 ATOM 5027 H62 A D 22 66.077 43.207 -0.141 1.00 0.00 1CGP5182 ATOM 5028 P G D 23 56.613 45.248 3.558 1.00 67.91 1CGP5183 ATOM 5029 O1P G D 23 55.637 44.703 2.581 1.00 67.16 1CGP5184 ATOM 5030 O2P G D 23 56.169 45.810 4.861 1.00 66.44 1CGP5185 ATOM 5031 O5* G D 23 57.426 46.322 2.757 1.00 64.59 1CGP5186 ATOM 5032 C5* G D 23 57.913 47.463 3.448 1.00 64.36 1CGP5187 ATOM 5033 C4* G D 23 58.875 48.095 2.547 1.00 63.32 1CGP5188 ATOM 5034 O4* G D 23 59.786 47.092 2.166 1.00 65.30 1CGP5189 ATOM 5035 C3* G D 23 58.230 48.518 1.274 1.00 62.68 1CGP5190 ATOM 5036 O3* G D 23 58.097 49.923 1.385 1.00 61.78 1CGP5191 ATOM 5037 C2* G D 23 59.173 48.053 0.186 1.00 64.02 1CGP5192 ATOM 5038 C1* G D 23 60.347 47.491 0.935 1.00 66.13 1CGP5193 ATOM 5039 N9 G D 23 60.857 46.343 0.188 1.00 68.30 1CGP5194 ATOM 5040 C8 G D 23 60.330 45.089 0.064 1.00 69.19 1CGP5195 ATOM 5041 N7 G D 23 60.960 44.332 -0.784 1.00 69.57 1CGP5196 ATOM 5042 C5 G D 23 61.971 45.146 -1.242 1.00 70.06 1CGP5197 ATOM 5043 C6 G D 23 62.966 44.871 -2.191 1.00 71.75 1CGP5198 ATOM 5044 O6 G D 23 63.095 43.847 -2.853 1.00 73.94 1CGP5199 ATOM 5045 N1 G D 23 63.810 45.952 -2.372 1.00 72.95 1CGP5200 ATOM 5046 C2 G D 23 63.683 47.164 -1.725 1.00 73.27 1CGP5201 ATOM 5047 N2 G D 23 64.553 48.127 -2.033 1.00 75.68 1CGP5202 ATOM 5048 N3 G D 23 62.735 47.423 -0.827 1.00 71.55 1CGP5203 ATOM 5049 C4 G D 23 61.922 46.373 -0.647 1.00 69.47 1CGP5204 ATOM 5050 H1 G D 23 64.574 45.806 -3.022 1.00 0.00 1CGP5205 ATOM 5051 H21 G D 23 64.483 49.021 -1.564 1.00 0.00 1CGP5206 ATOM 5052 H22 G D 23 65.278 47.985 -2.725 1.00 0.00 1CGP5207 ATOM 5053 P T D 24 57.949 50.746 0.049 1.00 61.38 1CGP5208 ATOM 5054 O1P T D 24 56.645 50.300 -0.479 1.00 61.45 1CGP5209 ATOM 5055 O2P T D 24 57.943 51.976 0.874 1.00 60.64 1CGP5210 ATOM 5056 O5* T D 24 58.990 50.888 -1.160 1.00 61.96 1CGP5211 ATOM 5057 C5* T D 24 60.282 51.486 -0.992 1.00 62.98 1CGP5212 ATOM 5058 C4* T D 24 61.217 51.142 -2.135 1.00 64.37 1CGP5213 ATOM 5059 O4* T D 24 61.223 49.735 -2.265 1.00 63.76 1CGP5214 ATOM 5060 C3* T D 24 60.723 51.639 -3.500 1.00 67.13 1CGP5215 ATOM 5061 O3* T D 24 61.237 52.986 -3.768 1.00 70.56 1CGP5216 ATOM 5062 C2* T D 24 61.291 50.611 -4.455 1.00 64.97 1CGP5217 ATOM 5063 C1* T D 24 61.765 49.506 -3.564 1.00 64.69 1CGP5218 ATOM 5064 N1 T D 24 61.341 48.171 -4.086 1.00 65.68 1CGP5219 ATOM 5065 C2 T D 24 62.143 47.584 -5.056 1.00 66.16 1CGP5220 ATOM 5066 O2 T D 24 63.092 48.151 -5.601 1.00 68.19 1CGP5221 ATOM 5067 N3 T D 24 61.807 46.304 -5.442 1.00 65.77 1CGP5222 ATOM 5068 C4 T D 24 60.758 45.554 -4.975 1.00 65.98 1CGP5223 ATOM 5069 O4 T D 24 60.610 44.397 -5.369 1.00 66.05 1CGP5224 ATOM 5070 C5 T D 24 59.958 46.235 -3.989 1.00 66.56 1CGP5225 ATOM 5071 C5M T D 24 58.734 45.522 -3.419 1.00 67.91 1CGP5226 ATOM 5072 C6 T D 24 60.261 47.487 -3.580 1.00 66.13 1CGP5227 ATOM 5073 H3 T D 24 62.425 45.880 -6.119 1.00 0.00 1CGP5228 ATOM 5074 P G D 25 60.774 54.011 -4.969 1.00 76.56 1CGP5229 ATOM 5075 O1P G D 25 60.185 54.814 -6.067 1.00 78.36 1CGP5230 ATOM 5076 O2P G D 25 61.159 54.703 -3.710 1.00 76.87 1CGP5231 ATOM 5077 O5* G D 25 62.007 53.207 -5.601 1.00 79.37 1CGP5232 ATOM 5078 C5* G D 25 63.361 53.662 -5.539 1.00 82.72 1CGP5233 ATOM 5079 C4* G D 25 64.050 53.630 -6.903 1.00 85.13 1CGP5234 ATOM 5080 O4* G D 25 64.051 52.302 -7.461 1.00 85.67 1CGP5235 ATOM 5081 C3* G D 25 63.308 54.501 -7.877 1.00 86.43 1CGP5236 ATOM 5082 O3* G D 25 64.340 55.081 -8.703 1.00 87.74 1CGP5237 ATOM 5083 C2* G D 25 62.367 53.506 -8.573 1.00 85.55 1CGP5238 ATOM 5084 C1* G D 25 63.163 52.203 -8.587 1.00 84.98 1CGP5239 ATOM 5085 N9 G D 25 62.305 50.996 -8.400 1.00 83.97 1CGP5240 ATOM 5086 C8 G D 25 61.095 50.873 -7.776 1.00 83.48 1CGP5241 ATOM 5087 N7 G D 25 60.639 49.659 -7.722 1.00 82.46 1CGP5242 ATOM 5088 C5 G D 25 61.614 48.918 -8.355 1.00 82.40 1CGP5243 ATOM 5089 C6 G D 25 61.672 47.538 -8.602 1.00 82.60 1CGP5244 ATOM 5090 O6 G D 25 60.889 46.659 -8.260 1.00 82.33 1CGP5245 ATOM 5091 N1 G D 25 62.808 47.192 -9.289 1.00 83.64 1CGP5246 ATOM 5092 C2 G D 25 63.793 48.065 -9.691 1.00 84.06 1CGP5247 ATOM 5093 N2 G D 25 64.802 47.575 -10.413 1.00 85.10 1CGP5248 ATOM 5094 N3 G D 25 63.745 49.369 -9.446 1.00 83.52 1CGP5249 ATOM 5095 C4 G D 25 62.628 49.722 -8.781 1.00 82.71 1CGP5250 ATOM 5096 H1 G D 25 62.870 46.203 -9.492 1.00 0.00 1CGP5251 ATOM 5097 H21 G D 25 65.534 48.186 -10.744 1.00 0.00 1CGP5252 ATOM 5098 H22 G D 25 64.821 46.589 -10.645 1.00 0.00 1CGP5253 ATOM 5099 P T D 26 64.207 55.276 -10.290 1.00 94.87 1CGP5254 ATOM 5100 O1P T D 26 62.827 55.653 -10.680 1.00 97.07 1CGP5255 ATOM 5101 O2P T D 26 64.958 56.131 -9.327 1.00 94.86 1CGP5256 ATOM 5102 O5* T D 26 65.023 55.325 -11.652 1.00 97.05 1CGP5257 ATOM 5103 C5* T D 26 65.876 54.221 -11.881 1.00 99.08 1CGP5258 ATOM 5104 C4* T D 26 65.193 52.984 -12.467 1.00100.21 1CGP5259 ATOM 5105 O4* T D 26 64.083 52.534 -11.712 1.00 99.95 1CGP5260 ATOM 5106 C3* T D 26 64.583 53.281 -13.821 1.00101.43 1CGP5261 ATOM 5107 O3* T D 26 65.631 53.317 -14.801 1.00102.80 1CGP5262 ATOM 5108 C2* T D 26 63.698 52.055 -14.000 1.00101.21 1CGP5263 ATOM 5109 C1* T D 26 63.702 51.457 -12.606 1.00100.24 1CGP5264 ATOM 5110 N1 T D 26 62.357 50.859 -12.320 1.00 99.15 1CGP5265 ATOM 5111 C2 T D 26 62.244 49.487 -12.470 1.00 98.18 1CGP5266 ATOM 5112 O2 T D 26 63.143 48.764 -12.903 1.00 97.65 1CGP5267 ATOM 5113 N3 T D 26 61.032 48.939 -12.112 1.00 97.59 1CGP5268 ATOM 5114 C4 T D 26 59.935 49.607 -11.629 1.00 97.10 1CGP5269 ATOM 5115 O4 T D 26 58.945 48.967 -11.293 1.00 96.32 1CGP5270 ATOM 5116 C5 T D 26 60.125 51.027 -11.524 1.00 97.55 1CGP5271 ATOM 5117 C5M T D 26 58.993 51.912 -11.044 1.00 97.55 1CGP5272 ATOM 5118 C6 T D 26 61.296 51.597 -11.860 1.00 98.65 1CGP5273 ATOM 5119 H3 T D 26 60.961 47.938 -12.230 1.00 0.00 1CGP5274 ATOM 5120 P G D 27 65.842 54.602 -15.747 1.00104.05 1CGP5275 ATOM 5121 O1P G D 27 65.238 55.948 -15.658 1.00104.11 1CGP5276 ATOM 5122 O2P G D 27 67.292 54.447 -16.029 1.00105.05 1CGP5277 ATOM 5123 O5* G D 27 65.008 53.723 -16.760 1.00103.69 1CGP5278 ATOM 5124 C5* G D 27 65.504 52.546 -17.401 1.00104.11 1CGP5279 ATOM 5125 C4* G D 27 64.342 51.960 -18.121 1.00104.90 1CGP5280 ATOM 5126 O4* G D 27 63.364 51.503 -17.180 1.00104.56 1CGP5281 ATOM 5127 C3* G D 27 63.676 53.068 -18.957 1.00106.62 1CGP5282 ATOM 5128 O3* G D 27 63.505 52.595 -20.301 1.00108.65 1CGP5283 ATOM 5129 C2* G D 27 62.347 53.300 -18.267 1.00105.47 1CGP5284 ATOM 5130 C1* G D 27 62.090 51.921 -17.692 1.00104.83 1CGP5285 ATOM 5131 N9 G D 27 61.054 51.954 -16.614 1.00104.06 1CGP5286 ATOM 5132 C8 G D 27 60.596 52.980 -15.820 1.00104.21 1CGP5287 ATOM 5133 N7 G D 27 59.638 52.629 -14.992 1.00103.88 1CGP5288 ATOM 5134 C5 G D 27 59.432 51.285 -15.262 1.00102.62 1CGP5289 ATOM 5135 C6 G D 27 58.505 50.363 -14.695 1.00101.60 1CGP5290 ATOM 5136 O6 G D 27 57.658 50.524 -13.819 1.00 98.99 1CGP5291 ATOM 5137 N1 G D 27 58.648 49.121 -15.282 1.00102.25 1CGP5292 ATOM 5138 C2 G D 27 59.558 48.796 -16.268 1.00103.21 1CGP5293 ATOM 5139 N2 G D 27 59.597 47.551 -16.729 1.00103.33 1CGP5294 ATOM 5140 N3 G D 27 60.410 49.656 -16.790 1.00103.49 1CGP5295 ATOM 5141 C4 G D 27 60.291 50.877 -16.248 1.00103.25 1CGP5296 ATOM 5142 H1 G D 27 58.009 48.402 -14.965 1.00 0.00 1CGP5297 ATOM 5143 H21 G D 27 60.314 47.292 -17.395 1.00 0.00 1CGP5298 ATOM 5144 H22 G D 27 58.916 46.868 -16.435 1.00 0.00 1CGP5299 ATOM 5145 P A D 28 63.006 53.516 -21.540 1.00115.30 1CGP5300 ATOM 5146 O1P A D 28 61.726 54.069 -22.044 1.00116.30 1CGP5301 ATOM 5147 O2P A D 28 64.117 54.479 -21.360 1.00117.24 1CGP5302 ATOM 5148 O5* A D 28 63.508 52.364 -22.603 1.00118.01 1CGP5303 ATOM 5149 C5* A D 28 63.232 50.934 -22.663 1.00118.91 1CGP5304 ATOM 5150 C4* A D 28 61.761 50.451 -22.544 1.00120.06 1CGP5305 ATOM 5151 O4* A D 28 61.244 50.734 -21.236 1.00120.45 1CGP5306 ATOM 5152 C3* A D 28 60.845 51.166 -23.541 1.00120.67 1CGP5307 ATOM 5153 O3* A D 28 60.323 50.259 -24.533 1.00121.11 1CGP5308 ATOM 5154 C2* A D 28 59.708 51.664 -22.664 1.00120.52 1CGP5309 ATOM 5155 C1* A D 28 59.827 50.855 -21.393 1.00120.58 1CGP5310 ATOM 5156 N9 A D 28 59.174 51.618 -20.301 1.00120.84 1CGP5311 ATOM 5157 C8 A D 28 59.231 52.961 -20.015 1.00121.22 1CGP5312 ATOM 5158 N7 A D 28 58.488 53.337 -19.011 1.00120.88 1CGP5313 ATOM 5159 C5 A D 28 57.895 52.154 -18.601 1.00120.60 1CGP5314 ATOM 5160 C6 A D 28 56.993 51.871 -17.581 1.00120.26 1CGP5315 ATOM 5161 N6 A D 28 56.503 52.791 -16.764 1.00120.26 1CGP5316 ATOM 5162 N1 A D 28 56.614 50.605 -17.442 1.00120.23 1CGP5317 ATOM 5163 C2 A D 28 57.087 49.681 -18.263 1.00120.76 1CGP5318 ATOM 5164 N3 A D 28 57.940 49.815 -19.257 1.00121.13 1CGP5319 ATOM 5165 C4 A D 28 58.311 51.104 -19.372 1.00120.83 1CGP5320 ATOM 5166 H61 A D 28 56.715 53.766 -16.919 1.00 0.00 1CGP5321 ATOM 5167 H62 A D 28 55.930 52.520 -15.973 1.00 0.00 1CGP5322 ATOM 5168 P C D 29 59.273 50.808 -25.649 1.00122.60 1CGP5323 ATOM 5169 O1P C D 29 59.167 52.262 -25.952 1.00123.32 1CGP5324 ATOM 5170 O2P C D 29 59.444 49.859 -26.772 1.00122.75 1CGP5325 ATOM 5171 O5* C D 29 57.949 50.390 -24.795 1.00122.21 1CGP5326 ATOM 5172 C5* C D 29 57.604 49.026 -24.473 1.00120.50 1CGP5327 ATOM 5173 C4* C D 29 56.419 48.900 -23.489 1.00119.07 1CGP5328 ATOM 5174 O4* C D 29 56.708 49.693 -22.336 1.00118.12 1CGP5329 ATOM 5175 C3* C D 29 55.086 49.482 -23.992 1.00118.17 1CGP5330 ATOM 5176 O3* C D 29 54.423 48.578 -24.920 1.00117.99 1CGP5331 ATOM 5177 C2* C D 29 54.360 49.504 -22.659 1.00117.81 1CGP5332 ATOM 5178 C1* C D 29 55.453 49.851 -21.658 1.00117.64 1CGP5333 ATOM 5179 N1 C D 29 55.266 51.243 -21.160 1.00116.93 1CGP5334 ATOM 5180 C2 C D 29 54.636 51.411 -19.945 1.00116.75 1CGP5335 ATOM 5181 O2 C D 29 54.253 50.463 -19.273 1.00116.45 1CGP5336 ATOM 5182 N3 C D 29 54.447 52.665 -19.465 1.00117.22 1CGP5337 ATOM 5183 C4 C D 29 54.857 53.738 -20.140 1.00117.24 1CGP5338 ATOM 5184 N4 C D 29 54.656 54.949 -19.608 1.00117.14 1CGP5339 ATOM 5185 C5 C D 29 55.513 53.586 -21.405 1.00117.49 1CGP5340 ATOM 5186 C6 C D 29 55.694 52.328 -21.868 1.00117.34 1CGP5341 ATOM 5187 H41 C D 29 54.944 55.784 -20.100 1.00 0.00 1CGP5342 ATOM 5188 H42 C D 29 54.217 55.032 -18.699 1.00 0.00 1CGP5343 ATOM 5189 P A D 30 53.189 48.983 -25.925 1.00114.68 1CGP5344 ATOM 5190 O1P A D 30 52.697 50.258 -26.516 1.00112.96 1CGP5345 ATOM 5191 O2P A D 30 53.306 47.792 -26.803 1.00114.18 1CGP5346 ATOM 5192 O5* A D 30 52.186 48.600 -24.730 1.00112.22 1CGP5347 ATOM 5193 C5* A D 30 51.959 47.265 -24.241 1.00108.27 1CGP5348 ATOM 5194 C4* A D 30 50.688 47.242 -23.424 1.00104.98 1CGP5349 ATOM 5195 O4* A D 30 50.766 48.260 -22.400 1.00103.14 1CGP5350 ATOM 5196 C3* A D 30 49.493 47.572 -24.321 1.00103.61 1CGP5351 ATOM 5197 O3* A D 30 48.380 46.721 -23.956 1.00103.25 1CGP5352 ATOM 5198 C2* A D 30 49.229 49.053 -24.021 1.00102.99 1CGP5353 ATOM 5199 C1* A D 30 49.705 49.223 -22.581 1.00102.03 1CGP5354 ATOM 5200 N9 A D 30 50.234 50.584 -22.366 1.00100.03 1CGP5355 ATOM 5201 C8 A D 30 51.270 51.173 -23.017 1.00 99.82 1CGP5356 ATOM 5202 N7 A D 30 51.561 52.369 -22.594 1.00 99.76 1CGP5357 ATOM 5203 C5 A D 30 50.649 52.594 -21.588 1.00 98.59 1CGP5358 ATOM 5204 C6 A D 30 50.451 53.691 -20.754 1.00 97.58 1CGP5359 ATOM 5205 N6 A D 30 51.189 54.787 -20.829 1.00 96.80 1CGP5360 ATOM 5206 N1 A D 30 49.472 53.604 -19.858 1.00 97.74 1CGP5361 ATOM 5207 C2 A D 30 48.741 52.497 -19.817 1.00 98.27 1CGP5362 ATOM 5208 N3 A D 30 48.825 51.395 -20.543 1.00 98.58 1CGP5363 ATOM 5209 C4 A D 30 49.830 51.513 -21.433 1.00 99.28 1CGP5364 ATOM 5210 H61 A D 30 51.903 54.858 -21.539 1.00 0.00 1CGP5365 ATOM 5211 H62 A D 30 51.041 55.554 -20.182 1.00 0.00 1CGP5366 ATOM 5212 P T D 31 46.984 46.692 -24.812 1.00 99.12 1CGP5367 ATOM 5213 O1P T D 31 46.344 46.363 -26.114 1.00 97.14 1CGP5368 ATOM 5214 O2P T D 31 47.201 45.613 -23.803 1.00 98.42 1CGP5369 ATOM 5215 O5* T D 31 46.160 47.927 -24.144 1.00 94.32 1CGP5370 ATOM 5216 C5* T D 31 45.514 47.827 -22.859 1.00 88.66 1CGP5371 ATOM 5217 C4* T D 31 45.032 49.160 -22.303 1.00 83.52 1CGP5372 ATOM 5218 O4* T D 31 46.079 50.079 -22.007 1.00 81.40 1CGP5373 ATOM 5219 C3* T D 31 44.259 49.887 -23.376 1.00 81.43 1CGP5374 ATOM 5220 O3* T D 31 42.933 49.331 -23.573 1.00 80.93 1CGP5375 ATOM 5221 C2* T D 31 44.185 51.258 -22.795 1.00 80.96 1CGP5376 ATOM 5222 C1* T D 31 45.354 51.306 -21.814 1.00 81.47 1CGP5377 ATOM 5223 N1 T D 31 46.099 52.542 -22.149 1.00 81.93 1CGP5378 ATOM 5224 C2 T D 31 45.753 53.744 -21.517 1.00 81.75 1CGP5379 ATOM 5225 O2 T D 31 44.911 53.867 -20.632 1.00 81.66 1CGP5380 ATOM 5226 N3 T D 31 46.427 54.863 -21.932 1.00 81.36 1CGP5381 ATOM 5227 C4 T D 31 47.395 54.903 -22.900 1.00 82.11 1CGP5382 ATOM 5228 O4 T D 31 47.873 55.981 -23.216 1.00 81.83 1CGP5383 ATOM 5229 C5 T D 31 47.712 53.629 -23.495 1.00 82.82 1CGP5384 ATOM 5230 C5M T D 31 48.810 53.532 -24.549 1.00 83.21 1CGP5385 ATOM 5231 C6 T D 31 47.068 52.514 -23.112 1.00 82.81 1CGP5386 ATOM 5232 H3 T D 31 46.211 55.727 -21.455 1.00 0.00 1CGP5387 ATOM 5233 P A D 32 41.844 48.892 -22.438 1.00 77.30 1CGP5388 ATOM 5234 O1P A D 32 40.970 48.809 -23.629 1.00 77.21 1CGP5389 ATOM 5235 O2P A D 32 42.123 47.664 -21.643 1.00 76.05 1CGP5390 ATOM 5236 O5* A D 32 41.153 49.975 -21.469 1.00 74.25 1CGP5391 ATOM 5237 C5* A D 32 41.500 50.069 -20.071 1.00 71.26 1CGP5392 ATOM 5238 C4* A D 32 41.023 51.361 -19.355 1.00 68.17 1CGP5393 ATOM 5239 O4* A D 32 41.674 52.520 -19.900 1.00 67.53 1CGP5394 ATOM 5240 C3* A D 32 39.531 51.572 -19.553 1.00 65.99 1CGP5395 ATOM 5241 O3* A D 32 38.985 52.197 -18.370 1.00 63.15 1CGP5396 ATOM 5242 C2* A D 32 39.492 52.482 -20.779 1.00 67.09 1CGP5397 ATOM 5243 C1* A D 32 40.734 53.332 -20.599 1.00 67.35 1CGP5398 ATOM 5244 N9 A D 32 41.333 53.733 -21.887 1.00 68.07 1CGP5399 ATOM 5245 C8 A D 32 41.252 53.166 -23.132 1.00 67.94 1CGP5400 ATOM 5246 N7 A D 32 41.924 53.795 -24.048 1.00 68.95 1CGP5401 ATOM 5247 C5 A D 32 42.486 54.846 -23.358 1.00 70.14 1CGP5402 ATOM 5248 C6 A D 32 43.321 55.878 -23.761 1.00 71.86 1CGP5403 ATOM 5249 N6 A D 32 43.743 56.008 -25.014 1.00 74.81 1CGP5404 ATOM 5250 N1 A D 32 43.705 56.757 -22.835 1.00 72.23 1CGP5405 ATOM 5251 C2 A D 32 43.282 56.604 -21.587 1.00 71.53 1CGP5406 ATOM 5252 N3 A D 32 42.495 55.682 -21.079 1.00 70.48 1CGP5407 ATOM 5253 C4 A D 32 42.129 54.820 -22.041 1.00 69.44 1CGP5408 ATOM 5254 H61 A D 32 43.387 55.384 -25.722 1.00 0.00 1CGP5409 ATOM 5255 H62 A D 32 44.425 56.712 -25.263 1.00 0.00 1CGP5410 ATOM 5256 P T D 33 37.416 52.380 -18.299 1.00 55.19 1CGP5411 ATOM 5257 O1P T D 33 36.214 51.639 -18.753 1.00 53.36 1CGP5412 ATOM 5258 O2P T D 33 37.879 52.240 -16.894 1.00 52.58 1CGP5413 ATOM 5259 O5* T D 33 37.165 53.918 -18.607 1.00 54.06 1CGP5414 ATOM 5260 C5* T D 33 37.659 54.888 -17.688 1.00 56.00 1CGP5415 ATOM 5261 C4* T D 33 37.619 56.332 -18.195 1.00 58.07 1CGP5416 ATOM 5262 O4* T D 33 38.514 56.467 -19.300 1.00 59.11 1CGP5417 ATOM 5263 C3* T D 33 36.209 56.752 -18.653 1.00 58.36 1CGP5418 ATOM 5264 O3* T D 33 35.844 58.031 -18.138 1.00 58.01 1CGP5419 ATOM 5265 C2* T D 33 36.381 56.893 -20.136 1.00 59.92 1CGP5420 ATOM 5266 C1* T D 33 37.849 57.335 -20.219 1.00 60.99 1CGP5421 ATOM 5267 N1 T D 33 38.455 57.174 -21.584 1.00 62.17 1CGP5422 ATOM 5268 C2 T D 33 39.420 58.101 -21.988 1.00 62.66 1CGP5423 ATOM 5269 O2 T D 33 39.734 59.090 -21.325 1.00 62.22 1CGP5424 ATOM 5270 N3 T D 33 39.991 57.879 -23.230 1.00 62.97 1CGP5425 ATOM 5271 C4 T D 33 39.692 56.837 -24.087 1.00 62.94 1CGP5426 ATOM 5272 O4 T D 33 40.313 56.705 -25.139 1.00 61.95 1CGP5427 ATOM 5273 C5 T D 33 38.678 55.939 -23.594 1.00 63.38 1CGP5428 ATOM 5274 C5M T D 33 38.203 54.770 -24.449 1.00 65.29 1CGP5429 ATOM 5275 C6 T D 33 38.109 56.125 -22.395 1.00 62.75 1CGP5430 ATOM 5276 H3* T D 33 36.427 58.700 -18.513 1.00 0.00 1CGP5431 ATOM 5277 H3 T D 33 40.687 58.557 -23.515 1.00 0.00 1CGP5432 TER 5278 T D 33 1CGP5433 CONECT 1919 1920 1921 1922 1927 1CGP5434 CONECT 1920 1919 1CGP5435 CONECT 1921 1919 1CGP5436 CONECT 1922 1919 1923 1CGP5437 CONECT 1923 1922 1924 1CGP5438 CONECT 1924 1923 1925 1926 1CGP5439 CONECT 1925 1924 1930 1CGP5440 CONECT 1926 1924 1927 1928 1CGP5441 CONECT 1927 1919 1926 1CGP5442 CONECT 1928 1926 1929 1930 1CGP5443 CONECT 1929 1928 1CGP5444 CONECT 1930 1925 1928 1931 1CGP5445 CONECT 1931 1930 1932 1940 1CGP5446 CONECT 1932 1931 1933 1CGP5447 CONECT 1933 1932 1934 1CGP5448 CONECT 1934 1933 1935 1940 1CGP5449 CONECT 1935 1934 1936 1937 1CGP5450 CONECT 1936 1935 1CGP5451 CONECT 1937 1935 1938 1CGP5452 CONECT 1938 1937 1939 1CGP5453 CONECT 1939 1938 1940 1CGP5454 CONECT 1940 1931 1934 1939 1CGP5455 CONECT 1941 1929 1CGP5456 CONECT 1942 1936 1CGP5457 CONECT 1943 1936 1CGP5458 CONECT 3862 3863 3864 3865 3870 1CGP5459 CONECT 3863 3862 1CGP5460 CONECT 3864 3862 1CGP5461 CONECT 3865 3862 3866 1CGP5462 CONECT 3866 3865 3867 1CGP5463 CONECT 3867 3866 3868 3869 1CGP5464 CONECT 3868 3867 3873 1CGP5465 CONECT 3869 3867 3870 3871 1CGP5466 CONECT 3870 3862 3869 1CGP5467 CONECT 3871 3869 3872 3873 1CGP5468 CONECT 3872 3871 1CGP5469 CONECT 3873 3868 3871 3874 1CGP5470 CONECT 3874 3873 3875 3883 1CGP5471 CONECT 3875 3874 3876 1CGP5472 CONECT 3876 3875 3877 1CGP5473 CONECT 3877 3876 3878 3883 1CGP5474 CONECT 3878 3877 3879 3880 1CGP5475 CONECT 3879 3878 1CGP5476 CONECT 3880 3878 3881 1CGP5477 CONECT 3881 3880 3882 1CGP5478 CONECT 3882 3881 3883 1CGP5479 CONECT 3883 3874 3877 3882 1CGP5480 CONECT 3884 3872 1CGP5481 CONECT 3885 3879 1CGP5482 CONECT 3886 3879 1CGP5483 MASTER 49 3 2 12 24 0 10 6 5274 4 50 38 1CGPA 6 END 1CGP5485 weblogo-3.8.0/tests/data/1beo.msf000066400000000000000000000041611467613320200165760ustar00rootroot00000000000000MSF 1beo Name: elib_phycr Len: 98 Name: elib_phydr Len: 98 Name: elia_phyme Len: 98 Name: elib_phyci Len: 98 Name: elia_phydr Len: 98 Name: elia_phycp Len: 98 Name: elib_phyme Len: 98 Name: eli_phypr Len: 98 Name: eli1_phycr Len: 98 Name: eli2_phycr Len: 98 Name: eli3_phycr Len: 98 Name: lh2_rat Len: 98 // 1 50 elib_phycr TACTATQQTA AYKTLVSILS DASFNQCSTD SGYSMLTAKA LPTTAQYKLM elib_phydr TTCTSTQQTA AYTTLVSILS DSSFNKCASD SGYSMLTAKA LPTTAQYKLM elia_phyme TTCTSTQQTA AYVTLVSILS DSSFNQCATD SGYSMLTATA LPTTAQYKLM elib_phyci TACTATQQTA AYKTLVSILS ESSFSQCSKD SGYSMLTATA LPTNAQYKLM elia_phydr TTCTSTQQTA AYVTLVSILS DSSFNQCATD SGYSMLTATA LPTDAQYKLM elia_phycp ~~CTTTQQTA AYVALVSILS DSSFNQCATD SGYSMLTATA LPTTAQYKLM elib_phyme TACTTTQQTA AYKTLVSILS ESSFNQCSKD SGYSMLTATA LPTNAQYKLM eli_phypr TTCTTTQQTA AYVALVSILS DTSFNQCSTD SGYSMLTATS LPTTEQYKLM eli1_phycr TTCTTTQQTA AYVALVSILS DSSFNQCATD SGYSMLTATS LPTTDQYKLM eli2_phycr TACTTTQQTA AYVALVSILS ESFFSTCASD SGYSMLTATA LPTTAQYELM eli3_phycr TACTTTQQTS AYVTLVTLLS KSYFTTCASD SGYSMLTATA LPTTAQYELM lh2_rat ~~~~ATLQTG TPSGPASELS NASLSPSSTP TTLTDLTSPT LPT....... 51 98 elib_phycr CASTACNTMI KKIVTLNPPN CDLTVPTSGL VLNVYSYANG FSNKCSSL elib_phydr CASTACNTMI KKIVSLNPPN CDLTVPTSGL VLNVYEYANG FSTKCASL elia_phyme CASTACNTMI NKIVTLNPPD CELTVPTSGL VLNVYSYANG FSATCASL elib_phyci CASTACNTMI KKIVALNPPD CDLTVPTSGL VLDVYTYANG FSSKCASL elia_phydr CSSTACNTMI KKIVSLNAPN CDLTVPTSGL VLNVYEYANG FSTKCASL elia_phycp CASTACNTMI TKIVSLNPPD CELTVPTSGL VLNVYSYANG FSATCASL elib_phyme CASTACKSMI NKIVVLNPPD CDLTVPTSGL VLDVYTYANG FSTKCASL eli_phypr CASTACKTMI NKIVTLNPPD CELTVPTSGL VLNVFTYANG FSSTCASL eli1_phycr CASTACNSMI AKIISLNAPD CELTVPTSGL VLNVYSYANG FSATCASL eli2_phycr CASTACQEMI EEIIALNPPD CDLTVPTSGL VINVYEYAND FASTCASL eli3_phycr CASTACQEMI AEIITLSPPD CDLTVPTSGL VIDVYTYANG FASTCASL lh2_rat .........V TSVLTSVPGN LEATSPTALH KRLLPTFSN~ ~~~~~~~~weblogo-3.8.0/tests/data/1crn.dssp000066400000000000000000000233031467613320200167760ustar00rootroot00000000000000==== Secondary Structure Definition by the program DSSP, updated CMBI version by ElmK / April 1,2000 ==== DATE=9-MAY-2003 . REFERENCE W. KABSCH AND C.SANDER, BIOPOLYMERS 22 (1983) 2577-2637 . HEADER PLANT SEED PROTEIN 30-APR-81 1CRN . COMPND CRAMBIN . SOURCE ABYSSINIAN CABBAGE (CRAMBE ABYSSINICA) SEED . AUTHOR W.A.HENDRICKSON,M.M.TEETER . 46 1 3 3 0 TOTAL NUMBER OF RESIDUES, NUMBER OF CHAINS, NUMBER OF SS-BRIDGES(TOTAL,INTRACHAIN,INTERCHAIN) . 3010.0 ACCESSIBLE SURFACE OF PROTEIN (ANGSTROM**2) . 27 58.7 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(J) , SAME NUMBER PER 100 RESIDUES . 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS IN PARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES . 3 6.5 TOTAL NUMBER OF HYDROGEN BONDS IN ANTIPARALLEL BRIDGES, SAME NUMBER PER 100 RESIDUES . 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-5), SAME NUMBER PER 100 RESIDUES . 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-4), SAME NUMBER PER 100 RESIDUES . 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-3), SAME NUMBER PER 100 RESIDUES . 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-2), SAME NUMBER PER 100 RESIDUES . 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I-1), SAME NUMBER PER 100 RESIDUES . 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+0), SAME NUMBER PER 100 RESIDUES . 0 0.0 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+1), SAME NUMBER PER 100 RESIDUES . 1 2.2 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+2), SAME NUMBER PER 100 RESIDUES . 5 10.9 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+3), SAME NUMBER PER 100 RESIDUES . 15 32.6 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+4), SAME NUMBER PER 100 RESIDUES . 1 2.2 TOTAL NUMBER OF HYDROGEN BONDS OF TYPE O(I)-->H-N(I+5), SAME NUMBER PER 100 RESIDUES . 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 *** HISTOGRAMS OF *** . 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 RESIDUES PER ALPHA HELIX . 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 PARALLEL BRIDGES PER LADDER . 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 ANTIPARALLEL BRIDGES PER LADDER . 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 LADDERS PER SHEET . # RESIDUE AA STRUCTURE BP1 BP2 ACC N-H-->O O-->H-N N-H-->O O-->H-N TCO KAPPA ALPHA PHI PSI X-CA Y-CA Z-CA 1 1 T 0 0 77 0, 0.0 34,-2.8 0, 0.0 2,-0.4 0.000 360.0 360.0 360.0 147.7 17.0 12.8 4.3 2 2 T E -A 34 0A 21 32,-0.2 2,-0.4 36,-0.1 32,-0.2 -0.848 360.0-172.4-107.8 144.3 13.9 11.5 6.1 3 3 a E -A 33 0A 0 30,-2.4 30,-2.8 -2,-0.4 42,-0.2 -0.997 8.4-157.3-131.2 133.3 13.7 10.7 9.8 4 4 b - 0 0 0 42,-2.5 42,-2.6 -2,-0.4 28,-0.2 -0.889 18.9-136.5-118.9 151.2 10.6 9.0 11.4 5 5 P S S+ 0 0 52 0, 0.0 2,-0.3 0, 0.0 40,-0.3 0.623 84.6 3.5 -76.2 -19.0 9.4 9.0 15.0 6 6 S S > S- 0 0 48 38,-0.1 4,-1.9 1,-0.1 5,-0.1 -0.954 76.2-102.4-157.9 166.0 8.7 5.3 15.3 7 7 I H > S+ 0 0 123 -2,-0.3 4,-2.6 2,-0.2 5,-0.2 0.901 121.0 54.0 -63.6 -42.1 8.9 2.1 13.3 8 8 V H > S+ 0 0 98 1,-0.2 4,-2.5 2,-0.2 5,-0.2 0.898 107.5 51.3 -55.9 -44.6 5.1 2.2 12.5 9 9 A H > S+ 0 0 6 1,-0.2 4,-2.3 2,-0.2 -1,-0.2 0.910 111.0 47.6 -61.4 -43.8 5.6 5.8 11.1 10 10 R H X S+ 0 0 55 -4,-1.9 4,-2.5 2,-0.2 -1,-0.2 0.906 111.1 50.4 -63.2 -43.3 8.5 4.6 8.8 11 11 S H X S+ 0 0 63 -4,-2.6 4,-1.7 2,-0.2 -2,-0.2 0.911 112.8 47.1 -61.2 -42.4 6.5 1.6 7.6 12 12 N H X S+ 0 0 82 -4,-2.5 4,-2.5 1,-0.2 -1,-0.2 0.877 110.2 53.6 -64.9 -39.5 3.5 3.9 6.8 13 13 F H X S+ 0 0 5 -4,-2.3 4,-2.0 1,-0.2 -1,-0.2 0.908 106.5 51.2 -59.1 -47.2 5.9 6.4 5.1 14 14 N H X S+ 0 0 87 -4,-2.5 4,-0.6 1,-0.2 -1,-0.2 0.870 111.8 47.2 -62.8 -35.2 7.3 3.6 2.8 15 15 V H >< S+ 0 0 99 -4,-1.7 3,-1.3 2,-0.2 -2,-0.2 0.927 108.8 54.9 -69.2 -41.2 3.8 2.6 1.7 16 16 c H 3<>S+ 0 0 18 -4,-2.5 5,-0.8 1,-0.3 -2,-0.2 0.862 107.5 51.8 -56.7 -36.0 2.9 6.3 1.1 17 17 R H ><5S+ 0 0 94 -4,-2.0 3,-1.6 1,-0.2 -1,-0.3 0.673 84.9 88.5 -77.1 -16.1 5.9 6.5 -1.2 18 18 L T <<5S+ 0 0 144 -3,-1.3 -1,-0.2 -4,-0.6 -2,-0.2 0.881 91.3 43.1 -53.2 -46.2 4.9 3.4 -3.3 19 19 P T 3 5S- 0 0 107 0, 0.0 -1,-0.3 0, 0.0 -2,-0.1 0.550 126.2 -97.4 -77.2 -7.6 2.8 5.4 -5.8 20 20 G T < 5 + 0 0 53 -3,-1.6 -3,-0.2 1,-0.2 -2,-0.1 0.547 61.2 169.9 106.3 7.3 5.4 8.2 -6.0 21 21 T < - 0 0 37 -5,-0.8 -1,-0.2 1,-0.1 5,-0.1 -0.260 44.7 -97.9 -52.7 136.3 3.8 10.6 -3.5 22 22 P >> - 0 0 81 0, 0.0 4,-2.2 0, 0.0 3,-0.7 -0.194 26.6-120.9 -57.0 146.6 6.1 13.5 -2.7 23 23 E H 3> S+ 0 0 70 1,-0.2 4,-2.5 2,-0.2 5,-0.1 0.872 110.6 61.4 -56.4 -36.2 8.1 13.1 0.5 24 24 A H 3> S+ 0 0 63 1,-0.2 4,-1.7 2,-0.2 -1,-0.2 0.876 106.9 44.1 -63.4 -34.9 6.6 16.3 1.9 25 25 I H <> S+ 0 0 99 -3,-0.7 4,-1.8 2,-0.2 -1,-0.2 0.907 112.8 51.0 -74.8 -37.9 3.1 14.9 1.8 26 26 c H X S+ 0 0 0 -4,-2.2 4,-1.9 2,-0.2 6,-0.4 0.848 106.4 58.4 -64.9 -31.7 4.2 11.5 3.2 27 27 A H X S+ 0 0 12 -4,-2.5 4,-2.7 -5,-0.2 5,-0.5 0.957 110.0 39.9 -62.0 -54.0 5.9 13.5 6.0 28 28 T H < S+ 0 0 120 -4,-1.7 -1,-0.2 1,-0.2 -2,-0.2 0.830 113.9 56.1 -68.8 -25.5 2.7 15.2 7.2 29 29 Y H < S+ 0 0 176 -4,-1.8 -1,-0.2 -5,-0.2 -2,-0.2 0.894 123.2 22.6 -67.6 -36.3 0.7 12.0 6.7 30 30 T H < S- 0 0 24 -4,-1.9 -2,-0.2 -3,-0.2 -3,-0.2 0.628 101.8-110.7-109.0 -18.5 3.0 10.0 8.9 31 31 G S < S+ 0 0 35 -4,-2.7 -3,-0.2 1,-0.4 -4,-0.1 0.338 74.1 133.2 91.8 -3.1 4.8 12.3 11.4 32 32 b - 0 0 5 -5,-0.5 -1,-0.4 -6,-0.4 2,-0.3 -0.337 44.9-142.4 -69.5 164.4 8.1 11.7 9.6 33 33 I E -A 3 0A 51 -30,-2.8 -30,-2.4 -3,-0.1 2,-0.5 -0.885 6.3-134.8-129.8 157.0 10.3 14.8 8.8 34 34 I E -A 2 0A 78 -2,-0.3 -32,-0.2 -32,-0.2 3,-0.0 -0.975 25.5-178.3-111.6 129.6 12.6 15.9 6.0 35 35 I - 0 0 34 -34,-2.8 5,-0.0 -2,-0.5 -2,-0.0 -0.898 32.4-131.9-124.1 158.1 15.9 17.5 6.9 36 36 P S S+ 0 0 143 0, 0.0 -1,-0.1 0, 0.0 -34,-0.1 0.804 89.0 59.3 -78.2 -24.4 18.6 18.9 4.7 37 37 G S S- 0 0 41 2,-0.1 -2,-0.2 -36,-0.1 3,-0.0 0.011 85.1-118.1 -89.7-161.7 21.5 17.0 6.5 38 38 A S S+ 0 0 80 1,-0.1 2,-0.7 2,-0.0 -36,-0.1 0.404 83.1 88.8-120.8 1.2 22.0 13.2 7.0 39 39 T - 0 0 127 -38,-0.1 -2,-0.1 -36,-0.0 -1,-0.1 -0.889 62.5-154.0-114.6 104.5 21.9 12.9 10.8 40 40 a - 0 0 46 -2,-0.7 -38,-0.0 -38,-0.1 -2,-0.0 -0.513 23.2-112.6 -75.5 145.4 18.5 12.3 12.3 41 41 P > - 0 0 53 0, 0.0 3,-2.1 0, 0.0 -1,-0.1 -0.214 29.4-103.2 -71.2 162.7 17.9 13.4 15.9 42 42 G G > S+ 0 0 75 1,-0.3 3,-0.5 2,-0.1 -2,-0.1 0.710 119.9 55.0 -61.9 -23.1 17.3 11.0 18.7 43 43 D G 3 S+ 0 0 116 1,-0.2 -1,-0.3 2,-0.1 3,-0.1 0.477 111.7 45.3 -89.7 -2.0 13.6 11.6 18.8 44 44 Y G < S+ 0 0 66 -3,-2.1 -40,-0.3 1,-0.1 -1,-0.2 -0.513 75.2 140.6-130.3 60.0 13.3 10.7 15.1 45 45 A < 0 0 70 -3,-0.5 -3,-0.1 -40,-0.3 -1,-0.1 0.452 360.0 360.0 -88.8 -2.5 15.4 7.7 15.2 46 46 N 0 0 76 -42,-2.6 -42,-2.5 -3,-0.1 -39,-0.1 -0.256 360.0 360.0-112.9 360.0 13.5 5.4 12.9 weblogo-3.8.0/tests/data/AST1.fa000077500000000000000000000005221467613320200162610ustar00rootroot00000000000000>AST1 MNRFFLRGALVARLLSESAWKQYPQYADVAIQRPIFVTGLVRTGTTALHRLLGADPAHQG LHMWLAEFPQPRPPRETWESNPLYRQLDAQFTQHHRDNPGYTGLHFMAAYELEECWQLLR QSLHSVSYETLAHVPSYAQWLSEQDWTPSYQRHRRNLQLIGLNDADKRWVLKNPSHLFAL DALMATYPDALVIQTHRPVETIMASMCSLAQHTAEGWSTTFVGAQIGADAMDTWSRGLER FNTARAKYNPAQFYDVDYKELIADPLGTVADIYRHFGLTLTEEAKAAMAKTHADSQSGER APKHSYSLADYGLSVETVKERFAGLZ weblogo-3.8.0/tests/data/AST2.fa000077500000000000000000000006211467613320200162620ustar00rootroot00000000000000>AST2 MMAAMAPQCPLDADALHAQASADTGLHDFGPDDYRERLEVYLTALREIDGLHAAGTVNFY GQLLQILKNRLLLTDLLKRHPEIHDIELRSPVVIAGLPRTGTTHLHNLLAAPPTFRTMPY WESVEPFPMPNEVGVQPDPRRTRMDVAVAVINTVMPHFALMHEMTTDHVHEEIQLLANDV STMLLETLAEVPRWRAYYQAHDQTPHYEYLATQLRAMQFLRGGRRWLLKSPQHLEQVPVL DRVFPDSIVVFTHRDPVPVALSMIAMITYSARMHRSPVPVRQIAESWIDRLGQMLAALVR DRDVIGPDRSIDIRFDDFMADELGVAERVYALADEPFTDDARAAVADYLAGHRRGRLGNV ETSYEMFGLDEDSLRERFAPYVERFLAZ weblogo-3.8.0/tests/data/Rv3829c.fasta000066400000000000000000000010551467613320200173400ustar00rootroot00000000000000>Rv3829c MTGYDAIVIGAGHNGLTAAVLLQRAGLRTACLDAKRYAGGMASTVELFDG YRFEIAGSVQFPTSSAVSSELGLDSLPTVDLEVMSVALRGVGDDPVVQFT DPTKMLTHLHRVHGADAVTGMAGLLAWSQAPTRALGRFEAGTLPKSFDEM YACATNEFERSAIDDMLFGSVTDVLDRHFPDREKHGALRGSMTVLAVNTL YRGPATPGSAAALAFGLGVPEGDFVRWKKLRGGIGALTTHLSQLLERTGG EVRLRSKVTEIVVDNSRSSARVRGVRTAAGDTLTSPIVVSAIAPDVTINE LIDPAVLPSEIRDRYLRIDHRGSYLQMHFALAQPPAFAAPYQALNDPSMQ ASMGIFCTPEQVQQQWEDCRRGIVPADPTVVLQIPSLHDPSLAPAGKQAA SAFAMWFPIEGGSKYGGYGRAKVEMGQNVIDKITRLAPNFKGSILRYTTF TPKHMGVMFGAPGGDYCHALLHSDQIGPNRPGPKGFIGQPIPIAGLYLGS AGCHGGPGITFIPGYNAARQALADRRAANCCVLSGR *weblogo-3.8.0/tests/data/TAT_mase_nuc.txt000066400000000000000000000264141467613320200203110ustar00rootroot00000000000000;; Modified by adf on Sat Nov 9 17:38:25 1996 ;; Modified by adf on Sat Nov 9 16:27:39 1996 ;; Modified by kam on Mon Nov 20 12:58:58 1995 ;; Modified by kxm on Sat Nov 5 01:21:01 1994 ;; Modified by kxm on Sat Nov 5 01:12:11 1994 ;; Modified by kxm on Sat Nov 5 00:44:35 1994 ;; Modified by kxm on Sat Nov 5 00:03:23 1994 ;; Modified by kxm on Fri Nov 4 23:58:34 1994 ;; Modified by kxm on Fri Nov 4 23:17:50 1994 ;; Modified by kxm on Fri Nov 4 23:12:24 1994 ;; Modified by kxm on Fri Nov 4 22:57:56 1994 ;; Modified by kxm on Fri Nov 4 12:15:17 1994 ;; Modified by kxm on Thu Nov 3 21:30:26 1994 ;; Modified by kxm on Thu Nov 3 19:40:25 1994 ;; Modified by kam on Thu Mar 18 09:56:44 1993 ;; Modified by kam on Fri Mar 12 11:51:25 1993 ; LOCUS HIVU455 ; ; Modified by kam on Mon Jul 20 12:24:18 1992 ; Modified by kxm on Fri Nov 4 12:15:17 1994 ; Written from MASE, from file "HIV1TAT.mase-nuc" ; Modified by adf on Sat Nov 9 16:27:39 1996 A_U455 ATGGAGCCAGTAGATCCTAACCTAGAGCCCTGGAAACACCCGGGAAGTCAGCCTACAACTGCTTGTAGCA ACTGTTATTGTAAAGTGTGTTGCTGGCATTGCCAACTTTGCTTTCTGAAAAAAGGCTTAGGCATTTCCTA TGGCAAGAAGAAGCGGAAACCCCGACGAGGACCTCCTCAAGGCAGTAAGGATCATCAAACTCTTATACCA AAGCAACCCTTGCCCCAATCCCAGAGGGTCTCGGCAGGCCAGGAAGAATCGAAGAAGAAGGTGGAGAGCA AGGCAAAGACAGATCGATTCGCT ; LOCUS HIVHXB2R ; ; Modified by kam on Mon Jul 20 12:24:18 1992 ; Modified by kxm on Fri Nov 4 12:15:17 1994 ; Written from MASE, from file "HIV1TAT.mase-nuc" ; Modified by adf on Sat Nov 9 16:27:39 1996 B_HXB2R ATGGAGCCAGTAGATCCTAGACTAGAGCCCTGGAAGCATCCAGGAAGTCAGCCTAAAACTGCTTGTACCA ATTGCTATTGTAAAAAGTGTTGCTTTCATTGCCAAGTTTGTTTCATAACAAAAGCCTTAGGCATCTCCTA TGGCAGGAAGAAGCGGAGACAGCGACGAAGAGCTCATCAGAACAGTCAGACTCATCAAGCTTCTCTATCA AAGCAACCCACCTCCCAACCCCGAGGGGACCCGACAGGCCCGAAGGAATAGAAGAAGAAGGTGGAGAGAG AGACAGAGACAGATCCATTCGATTAG ; HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (UG268) PROVIRAL DNA ; ENCODING ENV, TAT, VPU, REV, AND NEF GENES. ; Modified by kxm on Thu Nov 3 16:33:55 1994 ; Modified by kxm on Thu Nov 3 17:45:53 1994 ; Modified by kxm on Thu Nov 3 17:56:16 1994 ; Modified by kxm on Thu Nov 3 18:05:51 1994 ; Modified by kxm on Thu Nov 3 18:56:08 1994 ; Modified by kxm on Fri Nov 4 12:15:17 1994 ; Modified by cxc on Mon Nov 7 11:17:23 1994 ; Modified by kam on Mon Nov 20 12:19:08 1995 ; Written from MASE, from file "HIV1TAT.mase-nuc" ; Modified by adf on Sat Nov 9 16:27:39 1996 ; Modified by adf on Sat Nov 9 17:38:25 1996 C_UG268A %CAGGAAGTCAGCCTAAAACTCCTTGTACTAAGTGTTTTGGTAAAAAATGTAGTTATCATTGTCAAGTTT GCTTTCTGAACAAAGGCTTAGGCATCTCCTATGGCAGGAAGAAGCGGAGACAGCGACGAAACGCTCCTCC AAGCAGTGAGGATCATCAAAATCTTATATCAAAGCAACCCTTACCCCAACCCCGAGGGGACCCGACAGGC CCGGAGAAATCGAAGAAGAAGGTGGAGAGCAAGACAGAGACAGATCCGTGAGATTAA ; LOCUS HIVELI ; ; Modified by kam on Mon Jul 20 12:24:18 1992 ; Modified by kxm on Fri Nov 4 12:15:17 1994 ; Modified by kxm on Fri Nov 4 23:17:50 1994 ; Modified by kam on Mon Nov 20 12:19:08 1995 ; Written from MASE, from file "HIV1TAT.mase-nuc" ; Modified by adf on Sat Nov 9 16:27:39 1996 D_ELI ATGGATCCAGTAGATCCTAACCTAGAGCCCTGGAACCATCCAGGAAGTCAGCCTAGGACTCCTTGTAACA AGTGTCATTGTAAAAAGTGTTGCTATCATTGCCCAGTTTGCTTCTTAAACAAAGGCTTAGGCATCTCCTA TGGCAGGAAGAAGCGGAGACAGCGACGAGGACCTCCTCAAGGCGGTCAGGCTCATCAAGTTCCTATACCA AAGCAACCCTCCTCCCAGCCCCGAGGGGACCCGACAGGCCCGAAGGAACAGAAGAAGAAGGTGGAGAGCG AGGCAGAGACAGATCCGTGAGATTGCTGA ; Region 70 to 290 stored ; ; Region 70 to 290, from file bz163a.mase-nuc ; Written from MASE, from file "HIV1TAT.mase-nuc" ; Modified by adf on Sat Nov 9 16:27:39 1996 F_BZ163A ATGGAGCTAGTAGATCCTAACTTAGATCCCTGGAACCATCCAGGAAGCCAGCCTACAACTCCTTGTACAA AATGCTATTGTAAACGATGTTGCTTTCATTGTCAATGGTGCTTTACAACGAAGGGCTTAGGCATCTCCTA TGGCAGGAAGAAGCGGAAACAGCGGCACCGAACTCCTCAGAGCAGCCAGATACATCAAGATCTTGTACCA AAGCAACCCATATCCCAAGCCCGAGGGAACCCGACAGGCCCGAAGAAATCGAAGAAGGAGGTGGAGAGCA AGGCAGAGACAGATCCGTGAGATTAGTAG ; Modified by kam on Mon Jul 20 12:10:15 1992 ; Modified by kxm on Fri Nov 4 12:15:17 1994 ; Modified by kxm on Sat Nov 5 00:44:35 1994 ; Modified by kam on Mon Nov 20 12:19:08 1995 ; Written from MASE, from file "HIV1TAT.mase-nuc" ; Modified by adf on Sat Nov 9 16:27:39 1996 O_ANT70 ATGGATCCAGTAGATCCTGAGGTGCCCCCTTGGCACCACCCTGGAAGTCAGCCCCAGATCCCTTGTAATA ATTGCTATTGCAAAAGATGCTGCTATCATTGCTATGTTTGTTTCGTAAGAAAGGGTTTGGGAATCTCCTA TGGCAGGAAGAAGCGAGGACGACCAGCTGCTGCAAGCCATCCAGATCATAAAGATCCTGTACCAAAGCAA TCCCCAACCATCACCAAGAGGAAGCAGGAACGCCAGGAAGAACAGGAGGAGGAGGTGGAGAAGAAGGCAG GCCCAGGTGGATACCCTCGCCGCAAGGGTTCTTGCCACTGTTGTACACGGACCTCAGAACAA ; ; Modified by rkl on Wed Jun 30 09:36:11 1993 ; Modified by kxm on Fri Nov 4 12:15:17 1994 ; Modified by kxm on Sat Nov 5 00:44:35 1994 ; Modified by kam on Mon Nov 20 12:19:08 1995 ; Written from MASE, from file "HIV1TAT.mase-nuc" ; Modified by adf on Sat Nov 9 16:27:39 1996 O_MVP5180 ATGGATCCAGTAGATCCTGAGATGCCCCCTTGGCATCACCCTGGGAGCAAGCCCCAAACCCCTTGTAATA ATTGCTATTGCAAAAGATGCTGCTATCATTGCTATGTTTGTTTCACAAAGAAGGGTTTGGGAATCTCCCA TGGCAGGAAGAAGCGAAGAAGACCAGCAGCTGCTGCAAGCTATCCAGATAATAAAGATCCTGTACCAGAG CAATCCCTGTCCCACACCGGCAGGAAGCAGAAACGCCAGGAAGAACAGGAGAAGAAGGTGGAGAAGGAGA CAGGCCCAAGTGGACAGCCTTGCCACCAGGATTCTTGCAACAGTTGTACACGGATCTCAGGACAATAA ; LOCUS SIVCPZ ; ; Modified by kam on Fri Jul 17 11:13:21 1992 ; Modified by kxm on Fri Nov 4 12:15:17 1994 ; Modified by kxm on Fri Nov 4 23:12:24 1994 ; Written from MASE, from file "HIV1TAT.mase-nuc" ; Modified by adf on Sat Nov 9 16:27:39 1996 CPZGAB ATGGATCCAATAGATCCTGACCTGGAGCCCTGGAAACACCCAGGCAGTCAGCCAAGAACAGTTTGTAATA ATTGCTATTGCAAAGCTTGTTGTTATCACTGTATATATTGCTTCACAAAAAAAGGCTTAGGAATCTCCTA TGGCAGGAAGAAGCGAACCACAAGACGACGCACGGCTCCTGCAGGCAGTAAAAATAATCAAGATTCTATA CCAAAGCAACCCTTATCCCAGTCCAGAGGGAACAAGGAAGGCTCGGAGAAATCGACGAAGGAGGTGGCGA GCAAGACAGAAGCAGATCAGTGAGATTAG ; ; Modified by kxm on Fri Nov 4 12:15:17 1994 ; Modified by kxm on Fri Nov 4 23:12:24 1994 ; Modified by kxm on Fri Nov 4 23:58:34 1994 ; Modified by acs on Mon Nov 27 10:24:48 1995 ; Modified by kam on Thu Nov 30 09:43:33 1995 ; Modified by bwb on Fri Dec 1 09:03:00 1995 ; Written from MASE, from file "HIV1TAT.mase-nuc" ; Modified by adf on Sat Nov 9 16:27:39 1996 CPZANT ATGGACCCCGTAGACGCTGAAACACCTCCATGGTTACACCCTCCTGCTACACCAGCAACGCCATGCAATA ACTGTTACTGTAAATGCTGTTGTTACCATTGCCCTCTCTGCTTCACAAAAAAAGGCTTGGGGATTTCCTA TGGCAGGAAGAGAAGAGCTCGAAGGAACAGACGAACAACTGCTGAAAGCAGTGAAAATAATCAAGATCCT GTATCAAAATCCCTACCCAAAACCAGCAGGATCCAGAGCAGCCAGAAGAAATAAGAGAAGAAGGTGGAAG AAAAGACAGGATCAGGTGGAGGGCCTTGC ;; Modified by cxc on Thu Oct 20 14:56:54 1994 ; LOCUS HIV2ROD.nuc ; ; Modified by kam on Thu Jul 29 11:47:29 1993 ; Modified by cxc on Fri Oct 28 14:37:09 1994 ; Written from MASE, from file "HIV2SIVTAT.mase-nuc" ; Modified by adf on Sat Nov 9 16:27:39 1996 A_ROD ATGGAGACACCCTTGAAGGCGCCAGAGAGCTCATTAAAGTCCTGCAACGAGCCCTTTTCACGCACTTCAG AGCAGGATGTGGCCACTCAAGAATTGGCCAGACAAGGGGAGGAAATCCTCTCTCAGCTATACCGACCCCT AGAAACATGCAATAACTCATGCTATTGTAAGCGATGCTGCTACCATTGTCAGATGTGTTTTCTAAACAAG GGGCTCGGGATATGTTATGAACGAAAGGGCAGACGAAGAAGGACTCCAAAGAAAACTAAGACTCATCCGT CTCCTACACCAGACAAATCCATATCCACAAGGACCGGGGACAGCCAGCCAACGAAGAAACAGAAGAAGAC GGTGGAAGCAACGGTGGAGACAGATACTGGCCCTGGCCGA ;; Modified by bwb on Wed Sep 14 11:35:17 1994 ; HIV2 (ISOLATE EHO) PROVIRUS NUCLEOCAPSID CORE PROTEIN (GAG) ; GENE, 3' END THROUGH THE 3' LTR. ; Modified by bwb on Wed Sep 14 11:35:17 1994 ; Modified by bwb on Thu Sep 15 15:12:52 1994 ; Written from MASE, from file "HIV2SIVTAT.mase-nuc" ; Modified by adf on Sat Nov 9 16:27:39 1996 B_EHOA ATGGAAATACCCTTGAAGGAGCAGGAGAGCTCATTAAACTCCTCCAGCGGGCACTCTTCCTCCACTTCAG AGGGGGTTGCCAACACTCAAGGATTGGACAACCGGGGGGAGGAAATCCTCTCTCAGCTATACCGCCCTCT TAAGGCATGCAGTAATACATGCTACTGTAAAAAATGTTCCTACCATTGCCAGCTTTGCTTTCTTAAAAAG GGCCTGGGGATATGTTATGAACGCTCGAGAAAGAGATCTTCAAAAAGGGCTAAGACTACTACATCTTCTG CACCAAACAACAGATCCCTATCCGCAAGGACCGGGGACAGCCAGCCAACGAAGAAACAGAAGAAGGAGGT GGAAACAACGAGGGCTACAGATCTTGGCCCTGGCAGATCGAATACATCCACTTCCCGATTCGCCAACTGA ; LOCUS SIVMM251.nuc ; ; Modified by kam on Wed Sep 2 10:04:14 1992 ; Modified by cxc on Fri Oct 28 14:37:09 1994 ; Written from MASE, from file "HIV2SIVTAT.mase-nuc" ; Modified by adf on Sat Nov 9 16:27:39 1996 D_MM251 ATGGAGACACCCTTGAGGGAGCAGGAGAACTCATTAGAATCCTCCAACGAGCGCTCTTCATGCATTTTAG AGGCGGATGCAACCACTCCAGAATCGGCCAACCTGGGGGAGGAAATCCTCTCTCAACTATACCGCCCTCT TGAGGCGTGCTATAACACATGCTATTGTAAAAAGTGTTGCTACCATTGCCAGTTTTGTTTTCTTAAAAAG GGATTGGGGATATGTTATGAGCAGTCACGAAAGAGAAGAAGAACTCCGAAAAAGGCTAAGGCTAATACAT CTTCTGCATCAAACAAACTCATACCCAACAGGACCCGGCACTGCCAACCAGAGAAGGCAAAGAAGGAGAC GGTGGAGAAGGCGGTGGCAACAGCTCCTGGCCTTGGCAGA ; LOCUS SIVSTM.nuc ; ; Modified by kam on Wed Sep 2 10:04:14 1992 ; Modified by cxc on Fri Oct 28 14:37:09 1994 ; Written from MASE, from file "HIV2SIVTAT.mase-nuc" ; Modified by adf on Sat Nov 9 16:27:39 1996 STM_STM ATGGAGACACCCTTGAAGGAGCAGGAGAGCTCATTAAGATCCTCCAGCGAGCCCTCTTCATGCACTTCAG AGGCGGTTGCCGCCACTCCAGGATTGGCCAACCAGGAGGAGGAAATCCTTTGGCAACTATACCGCCCACT AGAGGAGTGTTGTAACAAGTGCTTTTGCAAAAAATGTTGCTATCACTGCCAGCTGTGTTTTGTTACAAAA GGTCTTGGAATAACCTATGAGCGATCAAGAAGAAGAGTTAAGAAAAAGGCTAAGACTTATCCAATTTCTG CATCAAACAACAGATCCCTATCCACAAGGGCCAGGAACAGCCAACCAAAGAAGGAACAGAAGAAGGAGGT GGAGACAGAGGTGGAATCAACTCCTGGCCTTGGCAAA ;; Modified by rkl on Mon Apr 19 10:38:05 1993 ;; Modified by rkl on Mon Apr 19 10:30:34 1993 ; LOCUS SIVAGM3 ; ; Modified by rkl on Mon Apr 19 10:30:34 1993 ; Modified by adf on Wed Oct 19 13:36:17 1994 ; Modified by adf on Wed Oct 19 13:40:23 1994 ; Written from MASE, from file "AGMTAT.mase-nuc" ; Modified by adf on Sat Nov 9 16:27:39 1996 VER_AGM3 ATGGACAAGGGGGAGGACGAGCAGGGCGCGTACCACCAGGACTTGATTGAACAACTCAAAGCACCCCTGA AGCGGTGTACAAACAAGTGCTATTGTAAATGTTGCTGTTATCACTGTCAGCTTTGCTTTTTACAAAAGGG ATTAGGTGTTACCTATCATGCCCCTAGGATCAGAAGAAAGAAGATTGCTCCGCTTGATCGCTTTCCTGAA CAAAAACAATCCATATCCACCCGTGGAAGGGACAGCCAGACAACGCAGAAGGGCCAGGAGAAGGTGGAGA CAAGCGCAAGAACAGCTCCGAGCCTTGGCAGAAAGAATCTGGCACAGCAGAGTGGAAGAGCAACTGGTGC AAGC ; ; LOCUS SIVAGM677 ; ; Modified by rkl on Mon Apr 19 10:30:34 1993 ; Modified by rkl on Mon Apr 19 10:38:05 1993 ; Modified by adf on Wed Oct 19 13:36:17 1994 ; Modified by adf on Wed Oct 19 13:40:23 1994 ; Written from MASE, from file "AGMTAT.mase-nuc" ; Modified by adf on Sat Nov 9 16:27:39 1996 GRI_AGM677 ATGGACAAGGAGGAGGAGCCCCACCCCCTCCTCCAGGACTTGCATAGGCCATTACAACCATGTACTAATA AATGCTATTGCAAAAAATGCTGTTATCACTGTGAGCTTTGCTTCCTGCAGAAGGGCTTAGGAGTGCGTTA TCATGTCTCTAGGAAAAGAAGAAAAACAAGCACTCAAGATAATCAAGACCCTATACGGCAGCAATCCATA TCCACAGTTCAGCGGAACGGCCAGACAACGGAGGAGGGCAAGACAGAGGTGGAG ; ; LOCUS SIVAGMSAB ; ; Modified by rkl on Mon Apr 19 10:30:34 1993 ; Modified by rkl on Mon Apr 19 10:38:05 1993 ; Modified by adf on Wed Oct 19 13:36:17 1994 ; Modified by adf on Wed Oct 19 13:40:23 1994 ; Written from MASE, from file "AGMTAT.mase-nuc" ; Modified by adf on Sat Nov 9 16:27:39 1996 SAB_SAB1C ATGGACCAGGAGCAGGAGGCCCGCCCCCAGGTCTGGGAGGAGCTTCAGGAGGAGCTGCATCGGCCGCTCC AGGCCTGTGATAATACTTGCTTCTGCAAAGTTTGCTGCTTTCATTGTATTCTCTGCTTCCATAAAAAGGC CCTAGGCATTCGCTATTATGTCCCTAGGCCAAGAAGAGCTTCTAAGAAGATTTCGCATAATCAAGTTTCT CTACACAAC ; ; LOCUS SIVSYK ; ; Modified by rkl on Mon Apr 19 10:30:34 1993 ; Modified by rkl on Mon Apr 19 10:38:05 1993 ; Modified by adf on Wed Oct 19 13:36:17 1994 ; Modified by adf on Wed Oct 19 13:40:23 1994 ; Modified by kam on Mon Feb 5 11:31:14 1996 ; Written from MASE, from file "AGMTAT.mase-nuc" ; Modified by adf on Sat Nov 9 16:27:39 1996 SYK_SYK ATGTCCTCAACGGACCAGATATGCCAGACACAGAGGGTACCCCCATCCTTCTTAGAAGGAACATTCCTAG AGAAAGGACCACCAACACCATGTAATAAATGCTTTTGCAAAAACTGTTGCTATCATTGCCAGCTTTGTTT CCTTCAAAAGGGATTGGGAATCACTTATGCCAGACCAAGGAAGCGAGCAGCTCGCAGTATTTCTGAGGAT GATAGCGCACCTACAGGAACCCTACCCAGGGCCGGAAGGACCCAGGCAAACCCGCAGACGAAGAAGAAGG CAGTGGAGACAGAGAAGGACTCAACGTCTCTACCTTCAGCAGAGAATCTT weblogo-3.8.0/tests/data/blosum35.blast000066400000000000000000000040301467613320200177340ustar00rootroot00000000000000# Matrix made by matblas from blosum35.iij # * column uses minimum score # BLOSUM Clustered Scoring Matrix in 1/4 Bit Units # Blocks Database = /data/blocks_5.0/blocks.dat # Cluster Percentage: >= 35 # Entropy = 0.2111, Expected = -0.1550 A R N D C Q E G H I L K M F P S T W Y V B Z X * 5 -1 -1 -1 -2 0 -1 0 -2 -1 -2 0 0 -2 -2 1 0 -2 -1 0 -1 -1 0 -5 -1 8 -1 -1 -3 2 -1 -2 -1 -3 -2 2 0 -1 -2 -1 -2 0 0 -1 -1 0 -1 -5 -1 -1 7 1 -1 1 -1 1 1 -1 -2 0 -1 -1 -2 0 0 -2 -2 -2 4 0 0 -5 -1 -1 1 8 -3 -1 2 -2 0 -3 -2 -1 -3 -3 -1 -1 -1 -3 -2 -2 5 1 -1 -5 -2 -3 -1 -3 15 -3 -1 -3 -4 -4 -2 -2 -4 -4 -4 -3 -1 -5 -5 -2 -2 -2 -2 -5 0 2 1 -1 -3 7 2 -2 -1 -2 -2 0 -1 -4 0 0 0 -1 0 -3 0 4 -1 -5 -1 -1 -1 2 -1 2 6 -2 -1 -3 -1 1 -2 -3 0 0 -1 -1 -1 -2 0 5 -1 -5 0 -2 1 -2 -3 -2 -2 7 -2 -3 -3 -1 -1 -3 -2 1 -2 -1 -2 -3 0 -2 -1 -5 -2 -1 1 0 -4 -1 -1 -2 12 -3 -2 -2 1 -3 -1 -1 -2 -4 0 -4 0 -1 -1 -5 -1 -3 -1 -3 -4 -2 -3 -3 -3 5 2 -2 1 1 -1 -2 -1 -1 0 4 -2 -3 0 -5 -2 -2 -2 -2 -2 -2 -1 -3 -2 2 5 -2 3 2 -3 -2 0 0 0 2 -2 -2 0 -5 0 2 0 -1 -2 0 1 -1 -2 -2 -2 5 0 -1 0 0 0 0 -1 -2 0 1 0 -5 0 0 -1 -3 -4 -1 -2 -1 1 1 3 0 6 0 -3 -1 0 1 0 1 -2 -2 0 -5 -2 -1 -1 -3 -4 -4 -3 -3 -3 1 2 -1 0 8 -4 -1 -1 1 3 1 -2 -3 -1 -5 -2 -2 -2 -1 -4 0 0 -2 -1 -1 -3 0 -3 -4 10 -2 0 -4 -3 -3 -1 0 -1 -5 1 -1 0 -1 -3 0 0 1 -1 -2 -2 0 -1 -1 -2 4 2 -2 -1 -1 0 0 0 -5 0 -2 0 -1 -1 0 -1 -2 -2 -1 0 0 0 -1 0 2 5 -2 -2 1 -1 -1 0 -5 -2 0 -2 -3 -5 -1 -1 -1 -4 -1 0 0 1 1 -4 -2 -2 16 3 -2 -3 -1 -1 -5 -1 0 -2 -2 -5 0 -1 -2 0 0 0 -1 0 3 -3 -1 -2 3 8 0 -2 -1 -1 -5 0 -1 -2 -2 -2 -3 -2 -3 -4 4 2 -2 1 1 -3 -1 1 -2 0 5 -2 -2 0 -5 -1 -1 4 5 -2 0 0 0 0 -2 -2 0 -2 -2 -1 0 -1 -3 -2 -2 5 0 -1 -5 -1 0 0 1 -2 4 5 -2 -1 -3 -2 1 -2 -3 0 0 -1 -1 -1 -2 0 4 0 -5 0 -1 0 -1 -2 -1 -1 -1 -1 0 0 0 0 -1 -1 0 0 -1 -1 0 -1 0 -1 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1 weblogo-3.8.0/tests/data/blosum35.blast.new000066400000000000000000000041141467613320200205270ustar00rootroot00000000000000# Matrix made by matblas from blosum35.iij # * column uses minimum score # BLOSUM Clustered Scoring Matrix in 1/4 Bit Units # Blocks Database = /data/blocks_5.0/blocks.dat # Cluster Percentage: >= 35 # Entropy = 0.2111, Expected = -0.1550 A R N D C Q E G H I L K M F P S T W Y V B Z X * A 5 -1 -1 -1 -2 0 -1 0 -2 -1 -2 0 0 -2 -2 1 0 -2 -1 0 -1 -1 0 -5 R -1 8 -1 -1 -3 2 -1 -2 -1 -3 -2 2 0 -1 -2 -1 -2 0 0 -1 -1 0 -1 -5 N -1 -1 7 1 -1 1 -1 1 1 -1 -2 0 -1 -1 -2 0 0 -2 -2 -2 4 0 0 -5 D -1 -1 1 8 -3 -1 2 -2 0 -3 -2 -1 -3 -3 -1 -1 -1 -3 -2 -2 5 1 -1 -5 C -2 -3 -1 -3 15 -3 -1 -3 -4 -4 -2 -2 -4 -4 -4 -3 -1 -5 -5 -2 -2 -2 -2 -5 Q 0 2 1 -1 -3 7 2 -2 -1 -2 -2 0 -1 -4 0 0 0 -1 0 -3 0 4 -1 -5 E -1 -1 -1 2 -1 2 6 -2 -1 -3 -1 1 -2 -3 0 0 -1 -1 -1 -2 0 5 -1 -5 G 0 -2 1 -2 -3 -2 -2 7 -2 -3 -3 -1 -1 -3 -2 1 -2 -1 -2 -3 0 -2 -1 -5 H -2 -1 1 0 -4 -1 -1 -2 12 -3 -2 -2 1 -3 -1 -1 -2 -4 0 -4 0 -1 -1 -5 I -1 -3 -1 -3 -4 -2 -3 -3 -3 5 2 -2 1 1 -1 -2 -1 -1 0 4 -2 -3 0 -5 L -2 -2 -2 -2 -2 -2 -1 -3 -2 2 5 -2 3 2 -3 -2 0 0 0 2 -2 -2 0 -5 K 0 2 0 -1 -2 0 1 -1 -2 -2 -2 5 0 -1 0 0 0 0 -1 -2 0 1 0 -5 M 0 0 -1 -3 -4 -1 -2 -1 1 1 3 0 6 0 -3 -1 0 1 0 1 -2 -2 0 -5 F -2 -1 -1 -3 -4 -4 -3 -3 -3 1 2 -1 0 8 -4 -1 -1 1 3 1 -2 -3 -1 -5 P -2 -2 -2 -1 -4 0 0 -2 -1 -1 -3 0 -3 -4 10 -2 0 -4 -3 -3 -1 0 -1 -5 S 1 -1 0 -1 -3 0 0 1 -1 -2 -2 0 -1 -1 -2 4 2 -2 -1 -1 0 0 0 -5 T 0 -2 0 -1 -1 0 -1 -2 -2 -1 0 0 0 -1 0 2 5 -2 -2 1 -1 -1 0 -5 W -2 0 -2 -3 -5 -1 -1 -1 -4 -1 0 0 1 1 -4 -2 -2 16 3 -2 -3 -1 -1 -5 Y -1 0 -2 -2 -5 0 -1 -2 0 0 0 -1 0 3 -3 -1 -2 3 8 0 -2 -1 -1 -5 V 0 -1 -2 -2 -2 -3 -2 -3 -4 4 2 -2 1 1 -3 -1 1 -2 0 5 -2 -2 0 -5 B -1 -1 4 5 -2 0 0 0 0 -2 -2 0 -2 -2 -1 0 -1 -3 -2 -2 5 0 -1 -5 Z -1 0 0 1 -2 4 5 -2 -1 -3 -2 1 -2 -3 0 0 -1 -1 -1 -2 0 4 0 -5 X 0 -1 0 -1 -2 -1 -1 -1 -1 0 0 0 0 -1 -1 0 0 -1 -1 0 -1 0 -1 -5 * -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1 weblogo-3.8.0/tests/data/cap.fa000066400000000000000000000036561467613320200163240ustar00rootroot00000000000000>aldB -18->4 attcgtgatagctgtcgtaaag >ansB 103->125 ttttgttacctgcctctaactt >araB1 109->131 aagtgtgacgccgtgcaaataa >araB2 147->169 tgccgtgattatagacactttt >cdd 1 107->129 atttgcgatgcgtcgcgcattt >cdd 2 57->79 taatgagattcagatcacatat >crp 1 115->137 taatgtgacgtcctttgcatac >crp 2 gaaggcgacctgggtcatgctg >cya 151->173 aggtgttaaattgatcacgttt >cytR 1 125->147 cgatgcgaggcggatcgaaaaa >cytR 2 106->128 aaattcaatattcatcacactt >dadAX 1 95->117 agatgtgagccagctcaccata >dadAX 2 32->54 agatgtgattagattattattc >deoP2 1 75->97 aattgtgatgtgtatcgaagtg >deoP2 2 128->150 ttatttgaaccagatcgcatta >fur 136->158 aaatgtaagctgtgccacgttt >gal 56->78 aagtgtgacatggaataaatta >glpACB (glpTQ) 1 54->76 ttgtttgatttcgcgcatattc >glpACB (glpTQ) 2 94->116 aaacgtgatttcatgcgtcatt >glpACB (glpTQ) 144->166 atgtgtgcggcaattcacattt >glpD (glpE) 95->117 taatgttatacatatcactcta >glpFK 1 120->142 ttttatgacgaggcacacacat >glpFK 2 95->117 aagttcgatatttctcgttttt >gut (srlA) 72->94 ttttgcgatcaaaataacactt >ilvB 87->109 aaacgtgatcaacccctcaatt >lac 1 (lacZ) 88->110 taatgtgagttagctcactcat >lac 2 (lacZ) 16->38 aattgtgagcggataacaattt >malEpKp1 110->132 ttgtgtgatctctgttacagaa >malEpKp2 139->161 TAAtgtggagatgcgcacaTAA >malEpKp3 173->195 TTTtgcaagcaacatcacgAAA >malEpKp4 205->227 GACctcggtttagttcacaGAA >malT 121->143 aattgtgacacagtgcaaattc >melR 52->74 aaccgtgctcccactcgcagtc >mtl 302->324 TCTTGTGATTCAGATCACAAAG >nag 156->178 ttttgtgagttttgtcaccaaa >nupG2 97->119 aaatgttatccacatcacaatt >nupG1 47->69 ttatttgccacaggtaacaaaa >ompA 166->188 atgcctgacggagttcacactt >ompR 161->183 taacgtgatcatatcaacagaa >ptsH A 316->338 Ttttgtggcctgcttcaaactt >ptsH B 188->210 ttttatgatttggttcaattct >rhaS (rhaB) 161->183 aattgtgaacatcatcacgttc >rot 1 (ppiA) 182->204 ttttgtgatctgtttaaatgtt >rot 2 (ppiA) 129->151 agaggtgattttgatcacggaa >tdcA 60->82 atttgtgagtggtcgcacatat >tnaL 73->95 gattgtgattcgattcacattt >tsx 2 146->168 gtgtgtaaacgtgaacgcaatc >tsx 1 107->129 aactgtgaaacgaaacatattt >uxuAB 165->187 TCTTGTGATGTGGTTAACCAAT weblogo-3.8.0/tests/data/chain_B.fasta000066400000000000000000000027241467613320200176070ustar00rootroot00000000000000>1 AAMLLGRD >2 GAMLLGRD >3 AAALIGRD >4 AAALYARD >5 AAALIGRD >6 AAMLLGRD >7 AAMLIGRD >8 AAALLGRD >9 AAALLGRD >10 AAALLGRD >11 AAMLLGRD >12 AAALLGRD >13 AAALLGRD >14 AAALIGRD >15 AAALIGRD >16 AAALIGRD >17 AAALLGRD >18 AAALIGRD >19 AAALLGRD >20 AAALLGRD >21 AAALIGRD >22 AAMLLGRD >23 IAALLGRW >24 AAALLARD >25 AAALLGRD >26 IAALLGRD >27 AAMLLGRD >28 AAALLGRD >29 AAALLGRD >30 AAMLLGRD >31 AAMLLGRD >32 IAALLGRD >33 IAALLGRD >34 VAALLGRD >35 GAALIGRE >36 AAALLGRD >37 AAALLARD >38 AAALLGRD >39 AAALLGRD >40 AAMLLGRD >41 AAALLARD >42 AAALLGRD >43 AAMLLGRD >44 VAMLLGRD >45 AAMLLARD >46 AAALLARD >47 AAALIGRD >48 AAMLIGRD >49 AAALIGRD >50 AAALIGRD >51 AAMLLGRD >52 AAALLGRD >53 AAALLARD >54 AAALLARE >55 AAMLLGRD >56 AAALLARD >57 AAALLGRD >58 AAALLGRD >59 AAALIGRD >60 AAALLARD >61 AAALIGRD >62 AAALIARD >63 AAALLGRD >64 IAALLGRD >65 AAMLIGRD >66 AAALLGRD >67 AAALIGRD >68 ALALLARD >69 AAALLARD >70 IAMLLGRD >71 IAMLLGRD >72 AAALIGRD >73 AAALLGRE >74 AAALIGRD >75 IAALLGRD >76 AAMLLGRD >77 AAALLARD >78 AAALLARD >79 ALALLARD >80 AAMLLGRD >81 AAMLLGRD >82 AAALLGRD >83 AAALLGRE >84 AAALLARD >85 AAALLGRD >86 AAALLGRD >87 AAALIARD >88 AAALLGRD >89 AAALLGRD >90 AAALLGRD >91 AAALLGRD >92 AAALIGRD >93 AAMLLGRD >94 AAALLARD >95 AAALYARD >96 AAALLARD >97 AAALISRD >98 AAALLGRE >99 AAMLLGRD >100 AAALIGRD weblogo-3.8.0/tests/data/clustal.aln000066400000000000000000000106631467613320200174100ustar00rootroot00000000000000CLUSTAL W (1.82) ALEU_HORVU MAHAR----VLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLES CATH_HUMAN M----------WATLPLL--------CAGAWLLGVPVCGAAELSVNSLEK CATH_RAT M----------WTALPLL--------CAGAWLLSAG--ATAELTVNAIEK CATL_HUMAN MNPTL----IL-----------------------AAFCLGIASATLTFDH CATL_RAT MTPLL----LL-----------------------AVLCLGTALATPKFDQ CYS1_DICDI MK--V----ILLFVLAVFTV------------------FVSSRGIPPEEQ PAPA_CARPA MAMIPSISKLLFVAICLFVYMGLSFG---------------DFSIVGYSQ * ALEU_HORVU AVLGALGRTRHALRFARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTN CATH_HUMAN ------------FHFKSWMSKHRKTY-STEEYHHRLQTFASNWRKINAHN CATH_RAT ------------FHFTSWMKQHQKTY-SSREYSHRLQVFANNWRKIQAHN CATL_HUMAN SLEA---------QWTKWKAMHNRLYGMNEEGWRR-AVWEKNMKMIELHN CATL_RAT TFNA---------QWHQWKSTHRRLYGTNEEEWRR-AVWEKNMRMIQLHN CYS1_DICDI S------------QFLEFQDKFNKKYS-HEEYLERFEIFKSNLGKIEELN PAPA_CARPA NDLTSTERLIQLFE--SWMLKHNKIYKNIDEKIYRFEIFKDNLKYIDETN . * * * . . * ALEU_HORVU RK----GLPYRLGINRFSDMSWEEFQATRL--GAAQTCSATLAGNHLMRD CATH_HUMAN NG----NHTFKMALNQFSDMSFAEIKHKYL-WSEPQNCSAT--KSNYLRG CATH_RAT QR----NHTFKMGLNQFSDMSFAEIKHKYL-WSEPQNCSAT--KSNYLRG CATL_HUMAN QEYREGKHSFTMAMNAFGDMTSEEFRQVMNGFQNRKPRKGKVFQEPLFYE CATL_RAT GEYSNGKHGFTMEMNAFGDMTNEEFRQIVNGYRHQKHKKGRLFQEPLMLQ CYS1_DICDI LIAINHKADTKFGVNKFADLSSDEFKNYYLN-NKEAIFTDDLPVADYLDD PAPA_CARPA KK----NNSYWLGLNVFADMSNDEFKEKYTGSIAGNYTTTELSYEEVLND .* *.*.. *.. ALEU_HORVU --AAALPETKDWREDG-IVSPVKNQAHCGSCWTFSTTGALEAAYTQATGK CATH_HUMAN --TGPYPPSVDWRKKGNFVSPVKNQGACGSCWTFSTTGALESAIAIATGK CATH_RAT --TGPYPSSMDWRKKGNVVSPVKNQGACGSCWTFSTTGALESAVAIASGK CATL_HUMAN --A---PRSVDWREKG-YVTPVKNQGQCGSCWAFSATGALEGQMFRKTGR CATL_RAT --I---PKTVDWREKG-CVTPVKNQGQCGSCWAFSASGCLEGQMFLKTGK CYS1_DICDI EFINSIPTAFDWRTRGA-VTPVKNQGQCGSCWSFSTTGNVEGQHFISQNK PAPA_CARPA G-DVNIPEYVDWRQKGA-VTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGN * *** * *.*****. *****.**. .*. ALEU_HORVU NISLSEQQLVDCAGGFNNF--------GCNGGLPSQAFEYIKYNGGIDTE CATH_HUMAN MLSLAEQQLVDCAQDFNNY--------GCQGGLPSQAFEYILYNKGIMGE CATH_RAT MMTLAEQQLVDCAQNFNNH--------GCQGGLPSQAFEYILYNKGIMGE CATL_HUMAN LISLSEQNLVDCSGPQGNE--------GCNGGLMDYAFQYVQDNGGLDSE CATL_RAT LISLSEQNLVDCSHDQGNQ--------GCNGGLMDFAFQYIKENGGLDSE CYS1_DICDI LVSLSEQNLVDCDHECMEYEGEEACDEGCNGGLQPNAYNYIIKNGGIQTE PAPA_CARPA LNEYSEQELLDCDRRSY----------GCNGGYPWSALQLVA-QYGIHYR .**.*.** **.** * . . . *. ALEU_HORVU ESYPYKGVNGV-CHYKAENA-AVQVLDSVNITLNAEDELKNAVGLVRPVS CATH_HUMAN DTYPYQGKDGY-CKFQPGKA-IGFVKDVANITIYDEEAMVEAVALYNPVS CATH_RAT DSYPYIGKNGQ-CKFNPEKA-VAFVKNVVNITLNDEAAMVEAVALYNPVS CATL_HUMAN ESYPYEATEES-CKYNPKYS-VANDTGFVDIP-KQEKALMKAVATVGPIS CATL_RAT ESYPYEAKDGS-CKYRAEYA-VANDTGFVDIP-QQEKALMKAVATVGPIS CYS1_DICDI SSYPYTAETGTQCNFNSANI-GAKISNFTMIP-KNETVMAGYIVSTGPLA PAPA_CARPA NTYPYEGVQRY-CRSREKGPYAAKTDGVRQVQPYNEGALLYSIAN-QPVS .*** . * . * . . *.. ALEU_HORVU VAFQVIDG-FRQYKSGVYTSDHCGTTPDDVNHAVLAVGYG----V-ENGV CATH_HUMAN FAFEVTQD-FMMYRTGIYSSTSCHKTPDKVNHAVLAVGYG----E-KNGI CATH_RAT FAFEVTED-FMMYKSGVYSSNSCHKTPDKVNHAVLAVGYG----E-QNGL CATL_HUMAN VAIDAGHESFLFYKEGIYFEPDC--SSEDMDHGVLVVGYGFESTE-SDNN CATL_RAT VAMDASHPSLQFYSSGIYYEPNC--SSKDLDHGVLVVGYGYEGTD-SNKD CYS1_DICDI IAADAVE--WQFYIGGVF-DIPCN--PNSLDHGILIVGYSAKNTIFRKNM PAPA_CARPA VVLEAAGKDFQLYRGGIFVGP-CG---NKVDHAVAAVGYG---------P . * *.. * ..*.. ***. ALEU_HORVU PYWLIKNSWGADWGDNGYFKMEMGK-N---MCAIATCASYPVVAA CATH_HUMAN PYWIVKNSWGPQWGMNGYFLIERGK-N---MCGLAACASYPIPLV CATH_RAT LYWIVKNSWGSNWGNNGYFLIERGK-N---MCGLAACASYPIPQV CATL_HUMAN KYWLVKNSWGEEWGMGGYVKMAKDRRN---HCGIASAASYPTV-- CATL_RAT KYWLVKNSWGKEWGMDGYIKIAKDRNN---HCGLATAASYPIVN- CYS1_DICDI PYWIVKNSWGADWGEQGYIYLRRGKNT----CGVSNFVSTSI--I PAPA_CARPA NYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPV-KN * ..***** ** ** . . *.. . weblogo-3.8.0/tests/data/clustal181.aln000066400000000000000000000225421467613320200176410ustar00rootroot00000000000000CLUSTAL X (1.81) multiple sequence alignment Chaetosphaeridium_globosum ----MIQPQSYLNVADNSGARKIMCIRILGGS-NKKYGHIGDTIIGVVKE Physcomitrella_patens_subsp_pa ----MIQPQTYLNVADNSGARKLMCIQILGAS-NRKYAHIGDIIIAVVKE Adiantum_capillus_veneris ----MIQIQSYLDVADNSGARKLMCIRVLGTG-NRKYADIGDIIIAVVKE Marchantia_polymorpha ----MIQPQTYLNVADNSGARKLMCIRVIGTS-NRKYANIGDIIIAVVKE Psilotum_nudum ----MIQPQSYLKVTDNSGARKLMCIRILGTN-NCKYANTGDTIIAVVKE Lotus_corniculatus_var_japonic ----MIQPQTHLNVADNSGARKLMCIRIIGAS-NRRYAYIGDIVVAVIKE Spinacia_oleracea ----MIQPQTHLNVADNSGARELMCIRIIGAS-NRRYARIGDVIVAVIKE Arabidopsis_thaliana ----MIQPQTYLNVADNSGARELMCIRIIGAS-NRRYAHIGDVIVAVIKE Oenothera_elata_subsp_hookeri ----MIQPQTRLNVADNSGARELMCIRIIGAS-NRRYAHIGDIIVAVIKE Atropa_belladonna ----MIQPQTHLNVADNSGARELMCIRIIGAS-NRRYAHIGDVIVAVIKE Nicotiana_tabacum ----MIQPQTHLNVADNSGARELMCIRIIGAS-NRRYAHIGDVIVAVIKE Calycanthus_floridus_var_glauc ----MIQPQTHLNVADNSGARELMCIRIIGAS-NRRYAHIGDVIVAVIKE Panax_ginseng ----MIQPQTLLNVADNSGARELMCIRIIGAS-NRRYAHIGDVIVAVIKE Amborella_trichopoda ----MIQAQTYLNVADNSGARELMCIRIVGAS-NPRYAHIGDVIVAVIKE Oryza_nivara ----MIQPQTLLNVADNSGARKLMCIRVIGAASNQRYARIGDVIVAVIKD Oryza_sativa_japonica ----MIQPQTLLNVADNSGARKLMCIRVIGAASNQRYARIGDVIVAVIKD Triticum_aestivum ----MIQPQTLLNVADNSGARKLMCIRVIGAAGNQRYARIGDVIVAVIKD Saccharum_officinarum ----MIQPQTLLNVADNSGARKLMCIRVIGAAGNQRYARIGDVIIAVIKD Zea_mays ----MIQPQTLLNVADNSGARKLMCIRVIGAAGNQRYARIGDVIIAVIKD Pinus_thunbergii ----MIQSQTYLNIADNSGARKIMCIRVLGAS-NRKCAHIGDVIIAIIKE Anthoceros_formosae ----MIQPQTYLNVADNSGARKLMCIRILGAS-NRKYGNIGDIIIAVTKE Huperzia_lucidula ----MIQPQTYLNVADNSGAKKPMCIRILKAS-NRKYANTGNVIVAVVKE Mesostigma_viride ----MIQAQSYLNVADNSGAKKIMCIRVLGGS-QRKYAAIGDVIIGVVKD Chlamydomonas_reinhardtii_TPA ----MIKPLSYLNVADNSGARELMCIRALGGS-YRESANIGDVIIAVVKD Chlorella_vulgaris ----MIQPQTYLRVADNTGARELMCIRVLGGG-KQRAATVGDIIIAVVKD Odontella_sinensis ----MIYPQTMLTVADNTGARKIMCIRVLG-G-NRKYAKIGDTIIGVVKE Porphyra_purpurea ----MIQTQSYLNVADNSGARKIMCIRVLGTS-NPSYASIGDVIIGVVKD Nephroselmis_olivacea ----MIQPQTILQVADNSGARQLMCIRVLG-G-RKRYASIGDVIIAVVKD Cyanophora_paradoxa ----MIQPQSYLTAADNSGARKLMCIRVLGGG-NRRYARIGDVIVAVVKD Cyanidioschyzon_merolae ----MIQVQTRLKVADNTGAKEVMCIRVLKAS----TATLGDVIIVVVKE Euglena_gracilis ----MIKPQTYLKIADNTGAQKIMCIRILGPN--CQYANIGDIIIAVVKE Euglena_longa ----MIQTQTYLNVSDNSGAKKIMCISIISTK--RKYAKIGDTIIAVVKK Eimeria_tenella ----MTQINTYFNIADNSGVKKILCIQNLTKK--TKKIEIGDLIVGVIKK Pinus_koraiensis -----------------------MTTAALSSD---------RIIIPLSRS Gracilaria_tenuistipitata_var_ ----MKMKKTNIKMHVKRGE----TVQIISGR---EKGKIGKIIKVLPKS Cyanidium_caldarium ----------MINVRVINKKRRIQKYKVSVKS--------GDTIKVISGK Guillardia_theta MRRHNIEIGRFVKIRYGHQINSIGVIIDIIDN--NRCLIDGYSGRQVINS Synechococcus_sp_WH_8102 -----------------------MAVKERVGT---VVSDKMEKTVVVAVE : . Chaetosphaeridium_globosum AIPNMTLKKSEVVRAVIVRTCKELKRK-NGTILRFDENAAVIINQEG-NP Physcomitrella_patens_subsp_pa AIPNMPLKKSEVVRAVVVRTCKELKRK-NGTIIQFDDNAAVIINQEG-NP Adiantum_capillus_veneris AVPNMFLKRSEVVRAVVVRTRRGLKRR-NGMVLEFDDNAAVIINQEG-NP Marchantia_polymorpha AVPNMPIKKSEIVRAVIVRTCKEFKRN-NGSIIKFDDNAAVVINQEG-NP Psilotum_nudum SVPNMPVKKSEIVRAVIVRTRKEMKRD-NGIIIRFDDNAAVVINREG-NL Lotus_corniculatus_var_japonic AVPNTPLERSEVIRAVIVRTCKELKRS-NGIIIQYDDNAAVVIDQEG-NP Spinacia_oleracea AIPNTPLERSEVIRAVVVRTCKELKRD-NGMIIRYDDNAAVIIDQEG-NP Arabidopsis_thaliana AIPNTPLERSEVIRAVIVRTCKELKRN-NGTIIRYDDNAAVVIDQEG-NP Oenothera_elata_subsp_hookeri ALPSTSLERSEVVRAVIVRTCKELKCD-DGIIIRYDDNAAVVIDQEG-NP Atropa_belladonna AVPNMPLERSEIVRAVIVRTCKELKRD-NGMIIRYDDNAAVVIDQEG-NP Nicotiana_tabacum AVPNMPLERSEVVRAVIVRTCKELKRD-NGMIIRYDDNAAVVIDQEGRKS Calycanthus_floridus_var_glauc AVPNMPLERSEVIRAVIVRTCKELKRD-NGMIIRYDDNAAVVIDQEG-NP Panax_ginseng AVPNMPLARSEVVRAVIVRTCKELKRD-NGMIIRYDDNAAVVIDQEG-NP Amborella_trichopoda AVPNMPLERSEVIRAVIVRTCKELKRD-NGIIIRYDDNAAVVIDPEG-NP Oryza_nivara AVPQMPLERSEVIRAVIVRTCKEFKCE-DGIIIRYDDNAAVIIDQKG-NP Oryza_sativa_japonica AVPQMPLERSEVIRAVIVRTCKEFKCE-DGIIIRYDDNAAVIIDQKG-NP Triticum_aestivum ALPQMPLERSEVIRAVIVRTCKEFKCE-DGIIIRYDDNAAVIIDQKG-NP Saccharum_officinarum AVPQMPLERSEVIRAVIVRTRKEFKGD-DGIIIRYDDNAAVIIDQKG-NP Zea_mays AVPQMPLERSEVIRAVIVRTRKEFKGD-DGIIIRYDDNAAVIIDQKG-NP Pinus_thunbergii AVPNMPLEKSEVVRAVVIRTCKEFERD-NGMMIRSDDNAAVVIDQEG-NP Anthoceros_formosae AVPNMPLKKSEVVRAVIVRTCKEVRRD-NGMTIRFDDNVAATTNQEG-NP Huperzia_lucidula AVPNMPLRKSEIVRAVVVRTCKELKRN-NGMIIQFDDNAAVIINQEG-NP Mesostigma_viride SVPNMSLKKSEVVRAVVVRTCKGIRRE-NGMTIRFDDNAAVVINKDG-NP Chlamydomonas_reinhardtii_TPA ALPNMPVKRSDIVRAVIVRTRKGIRRE-NGMAIRFDDNAAVIINKEG-NP Chlorella_vulgaris ATPNMPVKRSDIVRAVIVRTRKNVRRV-NGTSIRFDENAAVIINKEN-NP Odontella_sinensis AIPNMPIKRSDIVRAIVVRTSKTIRRP-DGMYIRFDDNAAVIVNLDN-NP Porphyra_purpurea ASPNMPVKRSDVVRAVVVRTRKALRRN-DGMSIRFDDNAAVIINQDN-NP Nephroselmis_olivacea AIPNMPVKKSDVVRAVVVRTSKPVRRD-TGMLIRFDDNAAVIVNQEG-NP Cyanophora_paradoxa GIPNIPIKKSDTVKAVIVRTRKELKRD-NGMNICFDDNAAVIINADG-NP Cyanidioschyzon_merolae ALPNMMVKKSQIFRAVVVRTKQAVRRA-NGMHIRFDENAVVLIDQEN-NP Euglena_gracilis AIPNMVVKKSDIVKAVIVRTVKGVRRE-SGMAIRFDENAAVIINNDR-SP Euglena_longa ASPNKIIKKSMIVKALIIRTTKPLYRKHNNMYISFNENAAIIINTDN-TL Eimeria_tenella INNTSKLIYSNIVYGIVIRLKKNINLY-KKYNISFNDNSAVLVDKNL-NP Pinus_koraiensis N-------------SLQVRITTALTTS------DFS-------------- Gracilaria_tenuistipitata_var_ S-------------QVIIDNLNIATKH---LKAQKEGDSGQIIRIEK--- Cyanidium_caldarium Y------------KNIVAKVLRVLKYS---NEIIVKGVNIKIKHIKP--- Guillardia_theta NRIIPTYLKIQINRNIKSKKLNQILLN-DSILLKVSKLKFMIINKIN--- Synechococcus_sp_WH_8102 SRFPHPIYQKTVSRTTRYKAHDEDNSCRVGDRVRITETRPMSRHKRW-AI Chaetosphaeridium_globosum RGTRIFGPVARELREANFTKIVSLAPEVL- Physcomitrella_patens_subsp_pa KGTRVFGPVARELRESNFTKIVSLAPEVL- Adiantum_capillus_veneris RGTRIFGPVARELRECNFARVVSLAPEVL- Marchantia_polymorpha KGTRVFGPIARELRESNFTKIVSLAPEVL- Psilotum_nudum KGTRVHGPVDRELWKKNFTKIVSLAPEAF- Lotus_corniculatus_var_japonic KGTRIFCAIARELRQFNFTKIVSLAPEIL- Spinacia_oleracea KGTRIFGAIARELRQK-FAKIVSLAPEVL- Arabidopsis_thaliana KGTRVFGAIPRELRQLNFTKIVSLAPEVL- Oenothera_elata_subsp_hookeri KGTRVFGAIAHELRELSFTKIVSLAPEVL- Atropa_belladonna KGTRIFGAIARELRELNFTKIVSLAPEVL- Nicotiana_tabacum KGTRIFGAIARELRELNFTKIVSLAPEVL- Calycanthus_floridus_var_glauc KGTRVFGAIARELRKLNFTKIVSLAPEVL- Panax_ginseng KGTRVFGAIARELRQLNFTKIVSLAPEVL- Amborella_trichopoda KGTRVFGSIAGELRHLNFTKIVSLAPEVF- Oryza_nivara KGTRVFGAIAEELRELNFTKIVSLAPEVL- Oryza_sativa_japonica KGTRVFGAIAEELRELNFTKIVSLAPEVL- Triticum_aestivum KGTRVFGAIAEELRGLNFTKIVSLAPEVL- Saccharum_officinarum KGTRVFGAVAEELRELNYTKIVSLAPEVL- Zea_mays KGTRVFGAVAEELRELNLTKIVSLAPEVL- Pinus_thunbergii KGTRVFGPVAQELRQLNFTKIVSLAPEVL- Anthoceros_formosae KGTRVFGPVARESRGYNFTKIIPLAPEVL- Huperzia_lucidula RGTRVFGPVARESREFNFTKIVSLAPEVL- Mesostigma_viride KGTRVFGPVARELRDRNFTKIVSLAPEVL- Chlamydomonas_reinhardtii_TPA RGTRVFGPIARELRDKNFTKIVSLAPEVL- Chlorella_vulgaris RGTRVFGPVARELRDGNFTKIISLAPEVL- Odontella_sinensis RGTRVFGPVAREIRDKNFSKIVSLAPEVL- Porphyra_purpurea RGTRVFGPIARELRDKNFSKIISLAPEVV- Nephroselmis_olivacea RGTRVFGPVARELRDRQFMKIISLAPEVL- Cyanophora_paradoxa RGTRVFGPVARELRDKNFTKIISLAPEVL- Cyanidioschyzon_merolae KGTRVFGPIARELREANFMKIVSLAPEVI- Euglena_gracilis KGTRIFGPIARELREKEFVKIMSLAPEVV- Euglena_longa KGTNIFGPVPRELMNIGFTNLNSTAKLII- Eimeria_tenella IGSRIFGTIPKFLKKKNYLKLYSLTVDFI- Pinus_koraiensis RG--MLGTAS---------LIIAIITSPI- Gracilaria_tenuistipitata_var_ ------PIHSSNVIQYKLDSNTSIKDRV-- Cyanidium_caldarium VRDNEMGSLKSLEFPINISKVVLLESRKKE Guillardia_theta ----QEKDKFNDFEAFKFLIGKKFKSCK-- Synechococcus_sp_WH_8102 AEVLSHSPKADKSAGSTAPAPEAAAKEVSE weblogo-3.8.0/tests/data/clustal_glualign.aln000066400000000000000000000716471467613320200213030ustar00rootroot00000000000000CLUSTAL W (1.82) multiple sequence alignment GE0000012 GCTCTAGTAGCACAG-----C-GGATAGTGCAGCAGTTTCCTAAACTGCA--G------- 45 GE0000169 GTCCTCGTAGCTCAG-----CAGGATAGAGCGGTTGCCTCCTAAGCAGCA--G------- 46 GE0004091 GTCCCAGTAGCTCAG-----CTGGATAGAGCAACGGCCTTCTAAGCCGTC--G------- 46 GE0003789 GGGTGTGTAGCTTAG-----ATGG-TAGAGCAGTGGCCTCCAAAGCCGCC--G------- 45 GE0003790 GGGTGTGTAGCTTAG-----ATGG-TAGAGCAGTGGCCTCCAAAGCCGCC--G------- 45 GE0001564 GGGTGTGTAGCTTAG-----CTGG-TAGAGCAGTGGCCTCCAAAGCCGCC--G------- 45 GE0004931 GGCGGTGTAGCTCAG-----CTGGCTAGAGC-GTACGGTTCATACCCGTGA-G------- 46 GE0004954 GGCGGTGTAGCTCAG-----CTGGCTAGAGC-GTACGGTTCATACCCGTGA-G------- 46 GE0000297 TCCGGAGTAGC-TCA-----GCGGT-AGAGCAGTGGACTGTTAATCCATT--G------- 44 GE0000298 TCCGGAGTAGC-TCA-----GCGGT-AGAGCAGTGGACTGTTAATCCATT--G------- 44 GE0000318 TCCGGAGTAGC-TCA-----GCGGT-AGAGCAGTGGACTGTTAATCCATT--G------- 44 GE0004107 TCCGCAGTAGC-TCA-----GTGGT-AGAGCTATCGGCTGTTAACCGATC--G------- 44 GE0004108 TCCGCAGTAGC-TCA-----GTGGT-AGAGCTATCGGCTGTTAACCGATC--G------- 44 GE0004215 TCCGCAGTAGC-TCA-----GTGGT-AGAGCTATCGGCTGTTAACCGATC--G------- 44 GE0004221 TCCGCAGTAGC-TCA-----GTGGT-AGAGCTATCGGCTGTTAACCGATC--G------- 44 GE0004161 TCCACAGTAGC-TCA-----GTGGT-AGAGCTATCGGCTGTTAACCGATC--G------- 44 GE0004182 TCCACAGTAGC-TCA-----GTGGT-AGAGCTATCGGCTGTTAACCGATC--G------- 44 GE0004186 TCCACAGTAGC-TCA-----GTGGT-AGAGCTATCGGCTGTTAACCGATC--G------- 44 GE0000386 GGTGGCATAGC-CAA-----GCGGT-AAGGCCGAGGCCTGCAAAGCC-TC--T------- 43 GE0002012 GGTGGCATCGC-CAA-----GCGGT-AAGGCCGAGGCCTGCAAAGCC-TC--T------- 43 GE0004312 GGCGGCATAGC-CAA-----GTGGT-AAGGCAGAGGTCTGCAAAACC-TT--T------- 43 GE0004328 GGCGGCATAGC-CAA-----GTGGT-AAGGCAGAGGTCTGCAAAACC-TT--T------- 43 GE0005592 AGGGGCATAGT-GTA-----ACGGT-AGAACAGAGGTCTCCAAAACC-TC--C------- 43 GE0005602 AGGGGCATAGT-GTA-----ACGGT-AGAACAGAGGTCTCCAAAACC-TC--C------- 43 GE0000435 TGGGGTGTGGC-CAA-----GCGGT-AAGGCAGCGGTTTTTGGTACCGTG--C------- 44 GE0000436 TGGGGTGTGGC-CAA-----GCGGT-AAGGCAGCGGTTTTTGGTACCGTG--C------- 44 GE0002070 TGGGGTGTGGC-CAA-----GCGGT-AAGGCAGCGGTTTTTGGTACCGCG--C------- 44 GE0004429 TGGGCTATAGC-CAA-----GCGGT-AAGGCAACGGACTTTGACTCCGTC--A------- 44 GE0004457 TGGGCTATAGC-CAA-----GCGGT-AAGGCAACGGACTTTGACTCCGTC--A------- 44 GE0004494 TGGGCTATAGC-CAA-----GCGGT-AAGGCAACGGACTTTGACTCCGTC--A------- 44 GE0004330 TGGGCTATAGC-CAA-----GCGGT-AAGGCAATGGACTTTGACTCCGTG--A------- 44 GE0001033 GGCGGTATAGCTCAG-----GTGGTTAGAGCAGCAGAATCATAATCTGCG--T------- 46 GE0002394 GGCGGTATAGCTCAG-----GTGGTTAGAGCAGCGGAATCATAATCCGCG--T------- 46 GE0004968 CGCGGGGTGGAGCAG-----TTCGGTAGCTCGTCGGGCTCATAACCCGAA--G------- 46 GE0004982 CGCGGGGTGGAGCAG-----TTCGGTAGCTCGTCGGGCTCATAACCCGAA--G------- 46 GE0000991 CGCGGGATAGAGTAG-----TG-GTCATCTCGTTGGGCTCATAACCCAAA--G------- 45 GE0001069 GGGGCGGTAGC-TCA-----GTGGTTAGAGCTGCGGACTCATAACCCGTA--G------- 45 GE0002428 GGGGCAATAGC-TCA-----GCGGTTAGAGCTGCGGACTCATAACCCGTA--G------- 45 GE0003643 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0003644 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0003561 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0003560 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0003559 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0003476 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0003475 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0003474 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0003330 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0003329 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0003328 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0003327 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0003326 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0003325 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0003324 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0003323 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0002900 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0002899 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0002898 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0002897 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0002896 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0002895 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0002894 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0002893 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0002892 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0002891 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0002890 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0002889 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0002888 GCACCGATAGCTCAA-----TTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0001839 GCACCGATAGCTCAA-----CTGGATAGAGTACCTGGCTTCGGACCAGGTG--------- 46 GE0001800 GCACCAGTAGCTCAG-----T-GGATAGAGTACCTGGCTACGAACCAGGTG--------- 45 GE0001817 GCACCAGTAGCTCAG-----T-GGATAGAGTACCTGGCTACGAACCAGGTG--------- 45 GE0000125 GCACCAGTAGCTCAG-----TCGGATAGAGTACCTGGCTACGAACCAGGTG--------- 46 GE0004001 GCGCCCGTAGCTCAA-----TTGGATAGAGCGTTTGACTACGGATCAAAAG--------- 46 GE0000251 GGACCGATAGCTCAG-----T-GGATAGAGCATTCGCCTTCTAAGCGAATG--------- 45 GE0000252 GGACCGATAGCTCAG-----T-GGATAGAGCATTCGCCTTCTAAGCGAATG--------- 45 GE0001911 GGACCGATAGCTCAG-----T-GGATAGAGCATCCGCCTTCTAAGCGGATG--------- 45 GE0001920 GGACCGATAGCTCAG-----T-GGATAGAGCATCCGCCTTCTAAGCGGATG--------- 45 GE0001923 GGACCGATAGCTCAG-----T-GGATAGAGCATCCGCCTTCTAAGCGGATG--------- 45 GE0001486 GCCCAGATAGCTCAG-----T--GGTAGAGCACTTGCATGGTAAGCAAGCG--------- 44 GE0003745 GCCCAGGTAGCTCAG-----T--GGTAGAGCACTTGCATGGTAAGCAAGTG--------- 44 GE0000050 GGGGTATTAGCTCAG-----TTGGT-AGAGCGCAACAATGGCATTGTTGAG--------- 45 GE0001713 GGGGTATTAGCTCAG-----TTGGT-AGAGCGCAACAATGGCATTGTTGAG--------- 45 GE0001633 GGGGTATTAGCTCAG-----TTGGTTAGAGCGTCACGTTGACATCGTGAAG--------- 46 GE0003866 -----ATTAGCTCAG-----TTGGTTAGAGCGTCACGTTGACATCGTGAAG--------- 41 GE0000520 GCGGGTGTAGCTCAG-----TGG--TAGAGCGTCACGTTGCCAACGTGAAG--------- 44 GE0002095 GCGGGTGTAGCTCAG-----TGG--TAGAGCGCCACGTTGCCAACGTGAAG--------- 44 GE0000649 GCGGTTATAGCTCAG-----TTGGTTAGAGCGCGACACTGATAATGTCGAG--------- 46 GE0000087 GGGGACTTAGCTTAG-----TTGGT-AGAGCGTCTGATTTGCATTCAGAAG--------- 45 GE0001752 GGGGACTTAGCTTAG-----TTGGT-AGAGCATCTGATTTGCATTCAGAAG--------- 45 GE0001759 GGGGACTTAGCTTAG-----TTGGT-AGAGCATCTGATTTGCATTCAGAAG--------- 45 GE0000839 GGGGCCTTAGCTCAG-----CTGGG-AGAGCGCCTGCTTTGCACGCAGGAG--------- 45 GE0003939 GGGGCCTTAGCTCAG-----CTGGG-AGAGCGCCTGCTTTGCACGCAGGAG--------- 45 GE0003956 GGGGCCTTAGCTCAG-----CTGGG-AGAGCGCCTGCTTTGCACGCAGGAG--------- 45 GE0005900 GGGGCTATAGCTCAT-----TTGGT-AGAGCGCTTGCATGGCATGCAAGAT--------- 45 GE0005903 GGGGCTATAGCTCAT-----TTGGT-AGAGCGCTTGCATGGCATGCAAGAT--------- 45 GE0005911 GGGGCTATAGCTCAT-----TTGGT-AGAGCGCTTGCATGGCATGCAAGAT--------- 45 GE0003911 GGGGCCATAGCTCAG-----CTGGG-AGAGCGCTACGCTGGCAGCGTAGAG--------- 45 GE0003912 GGGGCCATAGCTCAG-----CTGGG-AGAGCGCTACGCTGGCAGCGTAGAG--------- 45 GE0003935 GGGGCCATAGCTCAG-----CTGGG-AGAGCGCTACGCTGGCAGCGTAGAG--------- 45 GE0005407 GCTTCCATAGCTCAG-----CAGGT-AGAGCACTTCCATGGTAAGGAAGAG--------- 45 GE0005417 GCTTCCATAGCTCAG-----CAGGT-AGAGCACTTCCATGGTAAGGAAGAG--------- 45 GE0005799 GATTCCGTAGCTCAG-----CTGGG-AGAGCGCTACCTTGACAGGGTAGAG--------- 45 GE0000946 GGGTCTTTAGCTCAG-----C-GGTTAGAGCACCTCACTTTTAATGAGGGG--------- 45 GE0002360 GGGTCTTTAGCTCAG-----C-GGTTAGAGCATCTCACTTTTAATGAGAGG--------- 45 GE0004798 GGGCCTGTAGCTCAG-----CTGGTTAGAGCGCACGCCTGATAAGCGTGAG--------- 46 GE0004857 GGGCCTGTAGCTCAG-----CTGGTTAGAGCGCACGCCTGATAAGCGTGAG--------- 46 GE0004862 GGGCCTGTAGCTCAG-----CTGGTTAGAGCGCACGCCTGATAAGCGTGAG--------- 46 GE0005014 GGACCTTTAGCTCAG-----TTGGTTAGAGCAGACGGCTCATAACCGTCCG--------- 46 GE0001683 GGATGCGTAGCTCAG-----C-GGTTAGAGCACCTGTCTTACACACAGGGG--------- 45 GE0001710 GGATGCGTAGCTCAG-----C-GGTTAGAGCACCTGTCTTACACACAGGGG--------- 45 GE0004261 GGTCCGGTAGTTCAG-----TTGGTTAGAATGCCTGCCTGTCACGCAGGAG--------- 46 GE0004264 GGTCCGGTAGTTCAG-----TTGGTTAGAATGCCTGCCTGTCACGCAGGAG--------- 46 GE0001145 CTGGGTGTAGCGCAGC----CTGGT-AGCGCACTTGCATGGGGTGCAAGGG--------- 46 GE0001146 CTGGGTGTAGCGCAGC----CTGGT-AGCGCACTTGCATGGGGTGCAAGGG--------- 46 GE0002504 CTGGATGTAGCGCAGC----CTGGT-AGCGCACTTGCATGGGGTGCAAGGG--------- 46 GE0002505 CTGGATGTAGCGCAGC----CTGGT-AGCGCACTTGCATGGGGTGCAAGGG--------- 46 GE0002596 CGGAGTATAGCGCAGC----CTGGTTAGCGCGGTTGCTTTGGGAGCAATAG--------- 47 GE0002597 CGGAGTATAGCGCAGC----CTGGTTAGCGCGGTTGCTTTGGGAGCAATAG--------- 47 GE0001189 CGGAGTATAGCGCAGC----TTGGTTAGCGCGGTTGCTTTGGGAGCAATAG--------- 47 GE0005822 GGAGGATTAGCTCAGC----TGGG--AGAGCATTTGCCTTACAAGCAGAGG--------- 45 GE0005845 GGAGGATTAGCTCAGC----TGGG--AGAGCATTTGCCTTACAAGCAGAGG--------- 45 GE0005871 GGAGGATTAGCTCAGC----TGGG--AGAGCATCTGCCTTACAAGCAGAGG--------- 45 GE0005200 CGGGAAGTAGCTCAGC----TTGGT-AGAGCACATGGTTTGGGACCATGGG--------- 46 GE0005201 CGGGAAGTAGCTCAGC----TTGGT-AGAGCACATGGTTTGGGACCATGGG--------- 46 GE0005223 CGGGAAGTAGCTCAGC----TTGGT-AGAGCACATGGTTTGGGACCATGGG--------- 46 GE0005453 GCCGGTGTAGCTCAA-----TTGGT-AAAGCAACTGACTTGTAATCAGTAG--------- 45 GE0005464 GCCGGTGTAGCTCAA-----TTGGT-AAAGCAACTGACTTGTAATCAGTAG--------- 45 GE0005525 GCCGGTGTAGCTCAA-----TTGGT-AGAGCAACTGACTTGTAATCAGTAG--------- 45 GE0005534 GCCGGTGTAGCTCAA-----TTGGT-AGAGCAACTGACTTGTAATCAGTAG--------- 45 GE0001532 GCTGGAGTAGCTCAA-----TTGGC-AGAGCATTCGATTTGTAATCGAACG--------- 45 GE0000591 GCGAACGTAGCTCAG-----CTGGTTAGAGCGTCGGATTGTGGTTCCGAAG--------- 46 GE0002118 GCGAACGTAGCTCAG-----TTGGTTAGAGCGTCGGATTGTGGTTCCGAAG--------- 46 GE0004030 GCGCTCGTAGCTCAG-----TTGGATAGAGCGGTGGTTTCCGGTACCACGTCT------- 48 GE0001107 GGCTAGATAGCTCAG-----ATGGT-AGAGCAGAGGATTGAAGATCCTTGT--------- 45 GE0002463 GGCTAGATAGCTCAG-----CTGGT-AGAGCAGAGGACTGAAGATCCTTGT--------- 45 GE0005068 GGCTCGGTAGCTCAG-----TTGGT-AGAGCAACGGACTGAAAATCCGTGT--------- 45 GE0005094 GGCTCGGTAGCTCAG-----TTGGT-AGAGCAACGGACTGAAAATCCGTGT--------- 45 GE0005154 GGCTCGGTAGCTCAG-----TTGGT-AGAGCAACGGACTGAAAATCCGTGT--------- 45 GE0005174 GGCTCGGTAGCTCAG-----TTGGT-AGAGCAACGGACTGAAAATCCGTGT--------- 45 GE0005177 GGCTCGGTAGCTCAG-----TTGGT-AGAGCAACGGACTGAAAATCCGTGT--------- 45 GE0005098 GGCTCGGTAGCTCAG-----TTGGT-AAAGCAACGGACTGAAAATCCGTGT--------- 45 GE0005105 GGCTCGGTAGCTCAG-----TTGGT-AAAGCAACGGACTGAAAATCCGTGT--------- 45 GE0005142 GGCTCGGTAGCTCAG-----TTGGT-AAAGCAACGGACTGAAAATCCGTGT--------- 45 GE0001435 GCCTAAATAGCTCAG-----TTGGT-AGAGCAACACATTCGTAACGTGTAG--------- 45 GE0001439 GCCTAAATAGCTCAG-----TTGGT-AGAGCAACACATTCGTAACGTGTAG--------- 45 GE0001465 GCCTAAATAGCTCAG-----TTGGT-AGAGCAACACATTCGTAACGTGTAG--------- 45 GE0003714 GCCTAAATAGCTCAG-----TTGGT-AGAGCAACGCATTCGTAACGCGTAG--------- 45 GE0003720 GCCTAAATAGCTCAG-----TTGGT-AGAGCAACGCATTCGTAACGCGTAG--------- 45 GE0000340 GCGGGAGTAGTTCAA-----TTGGTTAGAGCACCGCCCTGTCAAGGCGGAA--------- 46 GE0001951 GCGGGAGTAGTTCAA-----CTGGTTAGAGCACCGCCCTGTCAAGGCGGAA--------- 46 GE0004611 GCGGGTGTAGTTTAG-----TGG--TAAAACCTCAGCCTTCCAAGCTGATG--------- 44 GE0004617 GCGGGTGTAGTTTAG-----TGG--TAAAACCTCAGCCTTCCAAGCTGATG--------- 44 GE0004647 GCGGGTGTAGTTTAG-----TGG--TAAAACCTCAGCCTTCCAAGCTGATG--------- 44 GE0004679 GCGGGTGTAGTTTAG-----TGG--TAAAACCTCAGCCTTCCAAGCTGATG--------- 44 GE0004680 GCGGGTGTAGTTTAG-----TGG--TAAAACCTCAGCCTTCCAAGCTGATG--------- 44 GE0000552 GCGCCCGTAGCTCAA-----TGG--TAGAGCTGTAGCCTTCCAAGCTACCG--------- 44 GE0004569 GCGGAAGTAGTTCAG-----TGG--TAGAACACCACCTTGCCAAGGTGGGG--------- 44 GE0000479 GGCCCCATCGTCTAGCC---TGGCCCAGGACATCGGATTTTCATTCCGGTA--------- 48 GE0000480 GGCCCCATCGTCTAGCC---TGGCCCAGGACATCGGATTTTCATTCCGGTA--------- 48 GE0004523 GGCCCGTTGGTCAAGC------GGTTAAGACACCGCCCTTTCACGGCGGTA--------- 45 GE0004524 GGCCCGTTGGTCAAGC------GGTTAAGACACCGCCCTTTCACGGCGGTA--------- 45 GE0004544 GGCCCGTTGGTCAAGC------GGTTAAGACACCGCCCTTTCACGGCGGTA--------- 45 GE0004711 GCGGTTGTGGCGAAGT------GGTTAACGCACCAGATTGTGGCTCTGGCA--------- 45 GE0004739 GCGGTTGTGGCGAAGT------GGTTAACGCACCAGATTGTGGCTCTGGCA--------- 45 GE0000801 GCGGAAGTGGCGGAATT-GGTATACG----CGCTATCTTGAGGTGGTAGTGGAGCTTTC- 54 GE0000802 GCGGAAGTGGCGGAATT-GGTATACG----CGCTATCTTGAGGTGGTAGTGGAGCTTTC- 54 GE0000215 GCGGATGTGGCGGAATT-GGCAGACG----CGCTAGAATCAGGCTCTAGTGTCTTTACAG 55 GE0002550 GCGGTCGTGGCGGAAT--GGCAGACG----CGCTAGGTTGAGGGCCTAGTGGGTGAATAA 54 GE0002551 GCGGTCGTGGCGGAAT--GGCAGACG----CGCTAGGTTGAGGGCCTAGTGGGTGAATAA 54 GE0000765 GCAGCTATGGCGAAATC-GGTAGACG----CGCTAGATTCAGGTTCTAGTGAGCTTATG- 54 GE0000766 GCAGCTATGGCGAAATC-GGTAGACG----CGCTAGATTCAGGTTCTAGTGAGCTTATG- 54 GE0002224 GCAGCTATGGCGGAACC-GGTAGACG----CGCTAGATTCAGGTTCTAGTGAGCTTTTG- 54 GE0002225 GCAGCTATGGCGGAACC-GGTAGACG----CGCTAGATTCAGGTTCTAGTGAGCTTTTG- 54 GE0002269 GCTCAGATGGTGGAAT--GGTAGACA----CTAGGGACTTAAAATCCCTTGGGCTTTGG- 53 GE0002270 GCTCAGATGGTGGAAT--GGTAGACA----CTAGGGACTTAAAATCCCTTGGGCTTTGG- 53 GE0000891 GCTCAGATGGTGGAAT--GGTAGACA----CTAGGGACTTAAAATCCCTTGGGCGTAGG- 53 GE0002315 GCCCAGGTGGTGAAATT-GGTAGACA----CGCTGGATTTAGGATCC--AGTGCTTCGC- 52 GE0002316 GCCCAGGTGGTGAAATT-GGTAGACA----CGCTGGATTTAGGATCC--AGTGCTTCGC- 52 GE0000910 GCCCAGGTGGTGAAATT-GGTAGACA----CGCTGGATTTAGGATCC--AGTGCTTTCG- 52 GE0000713 GCCGGTGTGGCGGAAT--GGTAGACG----CGGTAGACTCAAAATCTACTCTTAGCAAT- 53 GE0000714 GCCGGTGTGGCGGAAT--GGTAGACG----CGGTAGACTCAAAATCTACTCTTAGCAAT- 53 GE0002201 GCCGGCGTGGCGGAAT--GGTAGACG----CGGTAGACTCAAAATCTACTCTTAGCAGT- 53 GE0002202 GCCGGCGTGGCGGAAT--GGTAGACG----CGGTAGACTCAAAATCTACTCTTAGCAGT- 53 GE0004877 GCCGGTGTGGCGGAATT-GGCAGGCG----CGCACGACTCAAAATCG--TGTTCCTTCT- 52 GE0004878 GCCGGTGTGGCGGAATT-GGCAGGCG----CGCACGACTCAAAATCG--TGTTCCTTCT- 52 GE0001609 GGGGGTGTCGCATAGTG-GTCAATTG----CATCGGACTGTAAATCC--GGCTCCTTACG 53 GE0003848 GGGGGTGTCGCATAGCG-GTCAATTG----CATCGGACTGTAAATCC--GACTCCTTACG 53 GE0005698 GGAGGGGTAGCGAAGTG-GCTAAACG----CGGCGGACTGTAAATCC--GCTCCCTCA-G 52 GE0005729 GGAGGGGTAGCGAAGTG-GCTAAACG----CGGCGGACTGTAAATCC--GCTCCCTCA-G 52 GE0005751 GGAGGGGTAGCGAAGTG-GCTAAACG----CGGCGGACTGTAAATCC--GCTCCCTCA-G 52 GE0005643 GGAGGGGTAGCGAAGTG--CTAAACG----CGGCGGACTGTAAATCC--GCTCCCTCA-G 51 GE0002686 GGAAGAGTGGCAGAGT--GGTCGAA--TG-CATCTGATTCGAAATCAGAAGTCCCTCAAC 55 GE0002687 GGAAGAGTGGCAGAGT--GGTCGAA--TG-CATCTGATTCGAAATCAGAAGTCCCTCAAC 55 GE0001233 GGAAGAGTGGCAGAGT--GGTCGAA--TG-CGTCTGATTCGAAATCAGAAGTTCTCTTAC 55 GE0002641 ----GAATGGCAGAGC--GGTTTAA--TG-CACCTGTCTTGAAAACAGGAGACCT--GAA 49 GE0002642 ----GAATGGCAGAGC--GGTTTAA--TG-CACCTGTCTTGAAAACAGGAGACCT--GAA 49 GE0001391 GGAAGAATGGCAGAGC--GGTTTAA--TG-CACCTGTCTTGAAAACAGGAGACCT--GAA 53 GE0002730 GGAAAGATGACTGAGT--GGTCGAAAGTA-CGTCCCTGCTAAGGACGCGTACCCCTTAAA 57 GE0002731 GGAAAGATGACTGAGT--GGTCGAAAGTA-CGTCCCTGCTAAGGACGCGTACCCCTTAAA 57 GE0001275 GGAAAGATGACTGAGT--GGTCGAAAGTA-CGTCCCTGCTAAGGACGCGTACCCCT-AAA 56 GE0001276 GGAAAGATGACTGAGT--GGTCGAAAGTA-CGTCCCTGCTAAGGACGCGTACCCCT-AAA 56 GE0001320 GGAGAGATGTCCGAGT--GGCTTAAGGAG-CACGCTTGGAAAGCGTGTGTGCG-TTAACG 56 GE0001321 GGAGAGATGTCCGAGT--GGCTTAAGGAG-CACGCTTGGAAAGCGTGTGTGCG-TTAACG 56 GE0003146 GGAGAGATGTCCGAGT--GGCTTAAGGAG-CACGCTTGGAAAGCGTGTGTGCG-TTAACG 56 GE0003147 GGAGAGATGTCCGAGT--GGCTTAAGGAG-CACGCTTGGAAAGCGTGTGTGCG-TTAACG 56 GE0003148 GGAGAGATGTCCGAGT--GGCTTAAGGAG-CACGCTTGGAAAGCGTGTGTGCG-TTAACG 56 GE0003149 GGAGAGATGTCCGAGT--GGCTTAAGGAG-CACGCTTGGAAAGCGTGTGTGCG-TTAACG 56 GE0003150 GGAGAGATGTCCGAGT--GGCTTAAGGAG-CACGCTTGGAAAGCGTGTGTGCG-TTAACG 56 GE0003151 GGAGAGATGTCCGAGT--GGCTTAAGGAG-CACGCTTGGAAAGCGTGTGTGCG-TTAACG 56 GE0003152 GGAGAGATGTCCGAGT--GGCTTAAGGAG-CACGCTTGGAAAGCGTGTGTGCG-TTAACG 56 GE0003153 GGAGAGATGTCCGAGT--GGCTTAAGGAG-CACGCTTGGAAAGCGTGTGTGCG-TTAACG 56 GE0003154 GGAGAGATGTCCGAGT--GGCTTAAGGAG-CACGCTTGGAAAGCGTGTGTGCG-TTAACG 56 GE0005323 GGAGAGCTGTCCGAGT--GGTCGAAGGAG-CACGATTGGAAATCGTGTAGGCGGTCAACT 57 GE0005242 GGAGAAGTACTCAAGT--GGCTGAAGAGG-CGCCCCTGCTAAGGGTGTAGGTCGCGTAAG 57 GE0005247 GGAGAAGTACTCAAGT--GGCTGAAGAGG-CGCCCCTGCTAAGGGTGTAGGTCGCGTAAG 57 GE0005282 GGAGAAGTACTCAAGT--GGCTGAAGAGG-CGCCCCTGCTAAGGGTGTAGGTCGTGTAAG 57 GE0005335 GGAGGAATACCCAAGTCCGGCTGAAGGGATCGGTCTTGAAAACCGACAGGGGTGTCAAAG 60 GE0005359 GGAGGAATACCCAAGTCCGGCTGAAGGGATCGGTCTTGAAAACCGACAGGGGTGTCAAAG 60 GE0005388 GGAGGAATACCCAAGTCTGGCTGAAGGGATCGGTCTTGAAAACCGACAGGG-TGTCAAAG 59 * GE0000012 ----GTCGGGAGTTCGAATCTCTCCTAGAGC---- 72 GE0000169 ----GCCATGCGTTCGAATCGCATCGAGGAC---- 73 GE0004091 ----GTCGGGAGTTCGAATCTCTCCTGGGAC---- 73 GE0003789 ----GTCGGGGGTTCGAATCCCTCCGCACTC---- 72 GE0003790 ----GTCGGGGGTTCGAATCCCTCCGCACTC---- 72 GE0001564 ----GTCGGGGGTTCGATTCCCTTCGCACCC---- 72 GE0004931 ----GTCGGGGGTTCGATCCCCTCCGCCGCTACCA 77 GE0004954 ----GTCGGGGGTTCGATCCCCTCCGCCGCTACCA 77 GE0000297 ----GTCGTTGGTTCGAACCCATCCTCCGGA---- 71 GE0000298 ----GTCGTTGGTTCGAACCCATCCTCCGGA---- 71 GE0000318 ----GTCGTTGGTTCGAACCCATCCTCCGGA---- 71 GE0004107 ----GTCGTAGGTTCGAATCCTACCTGCGGAG--- 72 GE0004108 ----GTCGTAGGTTCGAATCCTACCTGCGGAG--- 72 GE0004215 ----GTCGTAGGTTCGAATCCTACCTGCGGAGCC- 74 GE0004221 ----GTCGTAGGTTCGAATCCTACCTGCGGAGCC- 74 GE0004161 ----GTCGCAGGTTCGAATCCTGCCTGTGGAGCCA 75 GE0004182 ----GTCGCAGGTTCGAATCCTGCCTGTGGAGCCA 75 GE0004186 ----GTCGCAGGTTCGAATCCTGCCTGTGGAGCCA 75 GE0000386 ----ATCCCCGGTTCGATTCCGGGTGCCACC---- 70 GE0002012 ----ATCCCCGGTTCGATTCCGGGTGCCACC---- 70 GE0004312 ----ATCCCCGGTTCGAATCCGGGTGTCGCC---- 70 GE0004328 ----ATCCCCGGTTCGAATCCGGGTGTCGCC---- 70 GE0005592 ----GGTGTGGGTTCGATTCCTACTGCCCCTGCCA 74 GE0005602 ----GGTGTGGGTTCGATTCCTACTGCCCCTGCCA 74 GE0000435 ----ATCGGAGGTTCGAATCCTTCCACCCCA---- 71 GE0000436 ----ATCGGAGGTTCGAATCCTTCCACCCCA---- 71 GE0002070 ----ATCGGAGGTTCGAATCCTTCCACCCCA---- 71 GE0004429 ----TGCGTTGGTTCGAATCCAGCTAGCCCAGTC- 74 GE0004457 ----TGCGTTGGTTCGAATCCAGCTAGCCCAGTC- 74 GE0004494 ----TGCGTTGGTTCGAATCCAGCTAGCCCAGCC- 74 GE0004330 ----T-CGTTGGTTCGAATCCAGCTAGCCCA---- 70 GE0001033 ----GTCGTTGGTTCAAATCCGACTACCGCT---- 73 GE0002394 ----GTCGTTGGTTCAAGTCCGACTACCGCT---- 73 GE0004968 ----GTCGCAGGTTCAAATCCTGCCCCCGCAACCA 77 GE0004982 ----GTCGCAGGTTCAAATCCTGCCCCCGCAACCA 77 GE0000991 ----GTCGGAGGTTCGAATCCTTCTCCCGCT---- 72 GE0001069 ----GTCACAGGTTCAAATCCTGTCCGCCCC---- 72 GE0002428 ----GTCCCTGGTTCAAATCCAGGTTGCCCC---- 72 GE0003643 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0003644 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0003561 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0003560 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0003559 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0003476 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0003475 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0003474 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0003330 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0003329 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0003328 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0003327 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0003326 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0003325 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0003324 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0003323 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0002900 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0002899 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0002898 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0002897 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0002896 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0002895 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0002894 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0002893 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0002892 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0002891 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0002890 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0002889 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0002888 ----GTTGGAGGTTCGAGCCCTCTTCGGTGC---- 73 GE0001839 ----GTTGGAGGTTCGAACCCTCTTCGGTGC---- 73 GE0001800 ----GTCAGAGGTTCAAATCCTCTTTGGTGC---- 72 GE0001817 ----GTCAGAGGTTCAAATCCTCTTTGGTGC---- 72 GE0000125 ----GTCAGAGGTTCGAGTCCTCTCTGGTGC---- 73 GE0004001 ----GTTAGGGGTTCGACTCCTCTCGGGCGCGCCA 77 GE0000251 ----GTCGCAGGTTCGAGTCCTGCTCGGTCC---- 72 GE0000252 ----GTCGCAGGTTCGAGTCCTGCTCGGTCC---- 72 GE0001911 ----GTCGCAGGTTCGAATCCTGCTCGGTCC---- 72 GE0001920 ----GTCGCAGGTTCGAATCCTGCTCGGTCC---- 72 GE0001923 ----GTCGCAGGTTCGAATCCTGCTCGGTCC---- 72 GE0001486 ----GTCGTAGGTTCAATTCCTATTCTGGGC---- 71 GE0003745 ----GCCGTAGGTTCAATTCCTATTCTGGGC---- 71 GE0000050 ----GTCAGCGGTTCGACCCCGCTATGCTCC---- 72 GE0001713 ----GTCAGCGGTTCGATCCCGCTATGCTCC---- 72 GE0001633 ----GTCAGCTGTTCAAGTCAGCTATATCCC---- 73 GE0003866 ----GTCAGCTGTTCAAGTCAGCTATATCCC---- 68 GE0000520 ----GTCGTGAGTTCAAGCCTCATCACCCGC---- 71 GE0002095 ----GTCGTGAGTTCAAGCCTCATCACCCGC---- 71 GE0000649 ----GTCCCAAGTTCAAGTCTTGGTAACCGC---- 73 GE0000087 ----GTCAGGAGTTCGAATCTCCTAGTCTCC---- 72 GE0001752 ----GTCAGGAGTTCGAATCTCCTAGTCTCC---- 72 GE0001759 ----GTCAGGAGTTCGAATCTCCTAGTCTCC---- 72 GE0000839 ----GTCAGCGGTTCGATCCCGCTAGGCTCCA--- 73 GE0003939 ----GTCAGCGGTTCGATCCCGCTAGGCTCCACCA 76 GE0003956 ----GTCAGCGGTTCGATCCCGCTAGGCTCCACCA 76 GE0005900 ----GTCAGCGGTTCGATTCCGCTTAGCTCCACG- 75 GE0005903 ----GTCAGCGGTTCGATTCCGCTTAGCTCCACG- 75 GE0005911 ----GTCAGCGGTTCGATTCCGCTTAGCTCCACG- 75 GE0003911 ----GTCAGGGGTTCGAGCCCCCTTGGCTCC---- 72 GE0003912 ----GTCAGGGGTTCGAGCCCCCTTGGCTCC---- 72 GE0003935 ----GTCAGGGGTTCGAGCCCCCTTGGCTCC---- 72 GE0005407 ----GTCAGCGGTTCGAGCCCGCTTGGAAGCT--- 73 GE0005417 ----GTCAGCGGTTCGAGCCCGCTTGGAAGCT--- 73 GE0005799 ----GTCGCTGGTTCGAGCCCAGTCGGAATC---- 72 GE0000946 ----GTCGAAGGTTCAAATCCTTCAAGACCC---- 72 GE0002360 ----GTCGAAGGTTCGAATCCTTCAAGACCC---- 72 GE0004798 ----GTCGATGGTTCGAGTCCATTCAGGCCCACCA 77 GE0004857 ----GTCGGTGGTTCGAGTCCACTCAGGCCCACCA 77 GE0004862 ----GTCGGTGGTTCGAGTCCACTCAGGCCCACCA 77 GE0005014 ----GTCGTAGGTTCGAGTCCTACAAGGTCCACCA 77 GE0001683 ----GTCATAGGTTCAAATCCTGTCGTGTCC---- 72 GE0001710 ----GTCATAGGTTCAAATCCTGTCGTGTCC---- 72 GE0004261 ----GTCGCGGGTTCGAGTCCCGTCCGGACCGCC- 76 GE0004264 ----GTCGCGGGTTCGAGTCCCGTCCGGACCGCC- 76 GE0001145 ----GGCGGAGGTTCAAATCCTCTCATCCAG---- 73 GE0001146 ----GGCGGAGGTTCAAATCCTCTCATCCAG---- 73 GE0002504 ----GGCGGAGGTTCAAATCCTCTCATCCAG---- 73 GE0002505 ----GGCGGAGGTTCAAATCCTCTCATCCAG---- 73 GE0002596 ----GTCGGGGGTTCGAATCCCTCTACTCCG---- 74 GE0002597 ----GTCGGGGGTTCGAATCCCTCTACTCCG---- 74 GE0001189 ----GTCGGGGGTTCGAATCCCTCTACTCCG---- 74 GE0005822 ----GTCGGCGGTTCGAGCCCGTCATCCTCCACCA 76 GE0005845 ----GTCGGCGGTTCGAGCCCGTCATCCTCCACCA 76 GE0005871 ----GTCGGCGGTTCGAGCCCGTCATCCTCCACCA 76 GE0005200 ----GTCGCAGGTTCGAATCCTGTCTTCCCGACCA 77 GE0005201 ----GTCGCAGGTTCGAATCCTGTCTTCCCGACCA 77 GE0005223 ----GTCGCAGGTTCGAATCCTGTCTTCCCGACCA 77 GE0005453 ----GTTGGGGGTTCAAGTCCTCTTGCCGGC---- 72 GE0005464 ----GTTGGGGGTTCAAGTCCTCTTGCCGGC---- 72 GE0005525 ----GTTGGGGGTTCAAGTCCTCTTGCCGGC---- 72 GE0005534 ----GTTGGGGGTTCAAGTCCTCTTGCCGGCACCA 76 GE0001532 ----GTTGAGGGTTCAATTCCTTTCTCCAGC---- 72 GE0000591 ----GTCGCGGGTTCAAGCCCCGTCGTTCGC---- 73 GE0002118 ----GTCGCGGGTTCGAACCCCGTCGTTCGC---- 73 GE0004030 ----GTCGGGGGTTCGAATCCCTCCGAGCGC---- 75 GE0001107 ----GTCGTCGGTTCGATCCCGGCTCTGGCC---- 72 GE0002463 ----GTCGTCGGTTCGATCCCGGCTCTGGCC---- 72 GE0005068 ----GTCGGCGGTTCGATTCCGTCCCGAGCCA--- 73 GE0005094 ----GTCGGCGGTTCGATTCCGTCCCGAGCCA--- 73 GE0005154 ----GTCGGCGGTTCGATTCCGTCCCGAGCCACCA 76 GE0005174 ----GTCGGCGGTTCGATTCCGTCCCGAGCCACCA 76 GE0005177 ----GTCGGCGGTTCGATTCCGTCCCGAGCCACCA 76 GE0005098 ----GTCGGCGGTTCGATTCCGTCCCGAGCCACCA 76 GE0005105 ----GTCGGCGGTTCGATTCCGTCCCGAGCCACCA 76 GE0005142 ----GTCGGCGGTTCGATTCCGTCCCGAGCCACCA 76 GE0001435 ----GTCGTCGGTTCGATCCCGGCTTTGGGC---- 72 GE0001439 ----GTCGTCGGTTCGATCCCGGCTTTGGGC---- 72 GE0001465 ----GTCGTCGGTTCGATCCCGGCTTTGGGC---- 72 GE0003714 ----GTCGTCGGTTCGATCCCGGCTTTGGGC---- 72 GE0003720 ----GTCGTCGGTTCGATCCCGGCTTTGGGC---- 72 GE0000340 ----GTTGCGGGTTCGACCCCCGTCTCTCGC---- 73 GE0001951 ----GTTGCGGGTTCGAGCCCCGTCTCTCGC---- 73 GE0004611 -----TCGTGAGTTCGATTCTCATCACCCGCTCCA 74 GE0004617 -----TCGTGAGTTCGATTCTCATCACCCGCTCCA 74 GE0004647 -----TCGTGGGTTCGATTCCCATCACCCGCTCCA 74 GE0004679 -----TCGTGGGTTCGATTCCCATCACCCGCTCCA 74 GE0004680 -----TCGTGGGTTCGATTCCCATCACCCGCTCCA 74 GE0000552 -----GTGTCAGTTCGATTCTGATCGGGCGC---- 70 GE0004569 ----GTCGCGGGTTCGAATCCCGTCTTCCGCTCCA 75 GE0000479 ----A-CAGGGGTTCGAATCCCCTTGGGGTC---- 74 GE0000480 ----A-CAGGGGTTCGAATCCCCTTGGGGTC---- 74 GE0004523 ----A-CACGGGTTCGAATCCCGTACGGGTCA--- 72 GE0004524 ----A-CACGGGTTCGAATCCCGTACGGGTCA--- 72 GE0004544 ----A-CACGGGTTCGAATCCCGTACGGGTCA--- 72 GE0004711 ----CTCGTGGGTTCGATTCCCATCAATCGCCCC- 75 GE0004739 ----TTCGTGGGTTCGATTCCCATCAATCGCCCC- 75 GE0000801 ----CTTAGGGGTTCGAGTCCCCTCTTTCGC---- 81 GE0000802 ----CTTAGGGGTTCGAGTCCCCTCTTTCGC---- 81 GE0000215 --A-CGTGGGGGTTCAAGTCCCTTCATCCGCACCA 87 GE0002550 --CCCGTGGAGGTTCAAGTCCTCTCGGCCGCATC- 86 GE0002551 --CCCGTGGAGGTTCAAGTCCTCTCGGCCGCATC- 86 GE0000765 --CTCATGGAAGTTCAAGTCTTCTTAGCTGC---- 83 GE0000766 --CTCATGGAAGTTCAAGTCTTCTTAGCTGC---- 83 GE0002224 --CTCATGGAAGTTCAAGTCTTCTTAGCTGC---- 83 GE0002225 --CTCATGGAAGTTCAAGTCTTCTTAGCTGC---- 83 GE0002269 --CCCGTGCAAGTTCGAGTCTTGTTCTGAGC---- 82 GE0002270 --CCCGTGCAAGTTCGAGTCTTGTTCTGAGC---- 82 GE0000891 --CCCGTGCAAGTTCGAGTCTTGTTCTGAGC---- 82 GE0002315 --GGCATGTAGGTTCAAGTCCTATCCTGGGC---- 81 GE0002316 --GGCATGTAGGTTCAAGTCCTATCCTGGGC---- 81 GE0000910 --GGCATGTAGGTTCAAGTCCTATCCTGGGC---- 81 GE0000713 --AAGGTGTTGGTTCGAGTCCGATCACCGGC---- 82 GE0000714 --AAGGTGTTGGTTCGAGTCCGATCACCGGC---- 82 GE0002201 --AAGGTGTTGGTTCGAGTCCAATCGCCGGC---- 82 GE0002202 --AAGGTGTTGGTTCGAGTCCAATCGCCGGC---- 82 GE0004877 --GGAGTGTCGGTTCGACCCCGACCACCGGTA--- 82 GE0004878 --GGAGTGTCGGTTCGACCCCGACCACCGGTA--- 82 GE0001609 --GATACGTTGGTTCAAATCCAGCCACCCCC---- 82 GE0003848 --GATACGTTGGTTCAAATCCAGCCACCCCC---- 82 GE0005698 --GGTTCGGCAGTTCGAATCTGCCCCCCTCCACCA 85 GE0005729 --GGTTCGGCAGTTCGAATCTGCCCCCCTCCACCA 85 GE0005751 --GGTTCGGCAGTTCGAATCTGCCCCCCTCCACCA 85 GE0005643 --GGTTCGGCAGTTCGAATCTGCCCCCCTCCACC- 83 GE0002686 GGGGACCGGGGGTTCAAATCCCTTCTCTTCC---- 86 GE0002687 GGGGACCGGGGGTTCAAATCCCTTCTCTTCC---- 86 GE0001233 AGGAACCAGGGGTTCGAATCCCTTCTCTT------ 84 GE0002641 AGGGTCCGGGGGTTCGAATCCCTCTT--------- 75 GE0002642 AGGGTCCGGGGGTTCGAATCCCTCTT--------- 75 GE0001391 AGGGTCCGGGGGTTCGAATCCCTCTTCTTCC---- 84 GE0002730 GGGTACCGAGGGTTCGAATCCCTCTCTTTCC---- 88 GE0002731 GGGTACCGAGGGTTCGAATCCCTCTCTTTCC---- 88 GE0001275 GGGTACCGAGGGTTCGAATCCCTCTCTTTCC---- 87 GE0001276 GGGTACCGAGGGTTCGAATCCCTCTCTTTCC---- 87 GE0001320 C-GTACCGTGGGTTCGAATCCCACTCTCTCC---- 86 GE0001321 C-GTACCGTGGGTTCGAATCCCACTCTCTCC---- 86 GE0003146 C-GTACCGAGGGTTCGAATCCCTCTCTCTCC---- 86 GE0003147 C-GTACCGAGGGTTCGAATCCCTCTCTCTCC---- 86 GE0003148 C-GTACCGAGGGTTCGAATCCCTCTCTCTCC---- 86 GE0003149 C-GTACCGAGGGTTCGAATCCCTCTCTCTCC---- 86 GE0003150 C-GTACCGAGGGTTCGAATCCCTCTCTCTCC---- 86 GE0003151 C-GTACCGAGGGTTCGAATCCCTCTCTCTCC---- 86 GE0003152 C-GTACCGAGGGTTCGAATCCCTCTCTCTCC---- 86 GE0003153 C-GTACCGAGGGTTCGAATCCCTCTCTCTCC---- 86 GE0003154 C-GTACCGAGGGTTCGAATCCCTCTCTCTCC---- 86 GE0005323 CCGTCTCAAGGGTTCGAATCCCTTGCTCTCCGCC- 91 GE0005242 C-GGCGCGAGGGTTCAAATCCCTCCTTCTCCGCCA 91 GE0005247 C-GGCGCGAGGGTTCAAATCCCTCCTTCTCCGCCA 91 GE0005282 C-GGCGCGAGGGTTCAAATCCCTCCTTCTCCGCCA 91 GE0005335 C-C-CGCGGGGGTTCGAATCCCTCTTCCTCCGCC- 92 GE0005359 C-C-CGCGGGGGTTCGAATCCCTCTTCCTCCGCC- 92 GE0005388 C-C-CGCGGGGGTTCGAATCCCTCTTCCTCCGCC- 91 **** * * weblogo-3.8.0/tests/data/clustal_headerless.aln000066400000000000000000000076601467613320200216120ustar00rootroot00000000000000AGO1___SCHPO ----IPKSNPLGN----------VPTLILGGDVYHPGVGATG-----------V---S-I O02095_CAEEL -----IGSEAFNK----------PNRLIVGFVTSQRVGGNPD-----------Y--PI-S O16386_CAEEL -----LRSGVFSN----------SKRLIIGFETSQR-GGLGD-----------A--PI-A O16720_CAEEL --LPNVRPR-IFN----------EPVIFLGCDITHPAAGDTR-----------K--PS-I O48771_ARATH GIEYSYNIPLINK----------IPTLILGMDVSHGPPGRAD-----------V--PS-V O62275_CAEEL --------------FVDAKKQL-DSHLIIGVGISAPPAGTKYAMEN---KGVLN--PN-V O67434_AQUAE -------LKEIEG----------KVDAFVGIDISRITRDGKT-----------------V O76922_DROME -------QVVIPL----------HGLMTVGFDVCHSPKNKNK-----------S-----Y PINH___ARATH VDAISCRIPLVSD----------IPTIIFGADVTHPENGEES-----------S--PS-I PIWI___ARCFU --------------ILNVDPEK-GSDIIIGTGATRIDNVNLF-----------------C PIWI___DROME -------MIELPL----------SGLMTIGFDIAKSTRDRKR-----------A-----Y PIWL1__HUMAN -------RVDIPL----------KLVMIVGIDCYHDMTAGRR-----------S-----I Q17567_CAEEL -------KVNIPL----------KSTMIVGYDLYHDSTLKGK-----------T-----V Q19645_CAEEL -ADIPRDLACWNE----------VSTFVIGMDVAHPDRNAAR-------EG--N--PS-T Q21495_CAEEL -----VNSETWND----------SGLLLIGLSTAPYLNSYSS-----------E--NVTT Q21691_CAEEL -VPESVGHRVVCNNSAEMRAKLYAKTQFIGFEMSHTGARTRFDIQKVMFDG--D--PT-V Q23415_CAEEL --------------VSDAKKSMTDEQLIIGVGVSAPPAGTKYMMDN---KGHLN--PQ-I Q9ZVD5_ARATH SVERTPAFTVISK----------VPTIILGMDVSHGSPGQSD-----------V--PS-I TAG76__CAEEL IVADKITNKYLVD----------QPTMVVGIDVTHPTQAEMR-----------MNMPS-V Y1321__METJA --------------ILDSKT---PYDYIMGLDTGLGIFGNHR-----------------V YQ53___CAEEL -IPNAVRGKAVCSNNETLRKKLLEHVQFIGFEISHGASRTLFDRSRSQMDG--E--PS-V AGO1___SCHPO ----VSVPVHYTVLHDE----IQMPPDQ-FQTLCYNLCYVYARATSAVS--------LVP O02095_CAEEL ----TAKATKFTLIFTTKAGPQAEPLWH-LEQLTNDLCYDHQIVFHPVG--------LPV O16386_CAEEL ----TSKLVKYSLIFNTK---KNEKLSV-YERLTNELCYEMQIVFHPTS--------LPI O16720_CAEEL ----TSRPSHYHVLWDD----NDLTADE-LQQLTYQMCHTYVRCTRSVS--------IPA O48771_ARATH ----TSRPAHYHVLLDE----IGFSPDD-LQNLIHSLSYKLLNSIFNVSSLLCVFVLSVA O62275_CAEEL ----TAKTPLYTVLADD----AKVSMTA-LEDITYKLCHLHQIVGLPTS--------LPT O67434_AQUAE ----THQPIKVRKVYGE------LPVEV-LCSQILSLTLMNYSSFQPIK--------LPA O76922_DROME ----TVSPTSYNVISDN----MGLNADK-LQMLSYKMTHMYYNYSGTIR--------VPA PINH___ARATH ----TSRPAHYHVLWDE----NNFTADG-IQSLTNNLCYTYARCTRSVS--------IVP PIWI___ARCFU EMVTPIKPLSVEIVSDN-WT-SEEYYHN-VHEILDEIYYLSKMNWRGFR---SRN--LPV PIWI___DROME ----TVSPTSYNVLYSS----MGLSPEK-MQKLTYKMCHLYYNWSGTTR--------VPA PIWL1__HUMAN ----SVSPTHYNVIYDN----SGLKPDH-IQRLTYKLCHIYYNWPGVIR--------VPA Q17567_CAEEL ----TVTPVSYNIIHDD----TGLGPDK-HQQLAFKLCHLYYNWQGTVR--------VPA Q19645_CAEEL ----TAKVPSFLVIRDD----EEVSDEH-VAKMVCAVCSLHQLVNSPTS--------IPT Q21495_CAEEL ----TCKATKYTVLY-----PESPKMEW-IQRMTNDLCYMHEIVFHPVS--------LPA Q21691_CAEEL ----TVKPTKYTIIVND----CRWSKNE-IMNVTYHLAFAHQVSYAPPA--------IPN Q23415_CAEEL ----TAKTPLYTILADD----CNAPMDR-LEELTYTLCHHHQIVALSTS--------IPT Q9ZVD5_ARATH ----TTRPTHYHVLYDE----IGFSADE-LQELVHSLSYVYQRSTSAIS--------VVA TAG76__CAEEL ----TSRPARYHVLLDE----CKFTADE-IQSITYGMCHTYGRCTRSVS--------IPT Y1321__METJA SN--PVKLSTWLRFNCG-NE-EGLKINESIMQLLYDLTKMNYSALYGEG--RYLR--IPA YQ53___CAEEL ----TVRPCKYTILVND----AKWSKNE-LMHLTYFRAFGHQVSYQPPS--------VPD AGO1___SCHPO PVYYAHLVSNLARYQDV O02095_CAEEL PLYIADRYSQRGAMVLA O16386_CAEEL PLHIAGTYSERGSQMLA O16720_CAEEL PAYYAHLVAFRARYHLV O48771_ARATH PVRYAHLAAAQVAQFTK O62275_CAEEL PLYVANEYAKRGRNLWN O67434_AQUAE TVHYSDKITKLMLRGIE O76922_DROME VCHYAHKLAFLVAESIN PINH___ARATH PAYYAHLAAFRARFYLE PIWI___ARCFU TVNYPKLVAGIIANVNR PIWI___DROME VCQYAKKLATLVGTNLH PIWL1__HUMAN PCQYAHKLAFLVGQSIH Q17567_CAEEL PCQYAHKLAFLTAQSLH Q19645_CAEEL PVYVAHELAKRGTGLYK Q21495_CAEEL PLYLTAEMAERGTKNLA Q21691_CAEEL VSYAAQNLAKRGHNNYK Q23415_CAEEL PLYVANEYAKRGRDLWS Q9ZVD5_ARATH PICYAHLAAAQLGTFMK TAG76__CAEEL PVYYADLVATRARCHVK Y1321__METJA PIHYADKFVKALGKNWK YQ53___CAEEL VLYAAENLAKRGRNNYK weblogo-3.8.0/tests/data/clustalw.pir000066400000000000000000000121601467613320200176110ustar00rootroot00000000000000>DL;804Angiostrongylus_cantonensis -------------------------------------------------- ----------------------------------ATT-AAGCCATG-CA- T-GAG-GA--GTTC-A--GC------TT--TA-A----G-T-GA--AA-C -TGCGAACGGCTCATTAG-AGCAGATG-T-GATT---TATT-CG--G--A A-A--A-T--CC-T----ATT-GGA--TAACTGCG--GTAAT-TCTGGAG CTAATACATGCGTAT-A-A-AC-CCTG-AC---T--T-T--C---GAAA- -GGGTGCAAT-TA-TTAGAG---C---AA-A-TCAAT-CAT--------- ----T-T---TC----------G-GA------TG----TAGTT------- ---T---GCT---G-A-C-TC-TGAATA-A---CG--CAG--CATA-TCG G-CGGC-T-T-GT---TCGCCGATAAT-CCGAAAA----AG---TGT-C- TGCCC-TATCA--AC---CT---GA-TGGTAGTCTATTAGTCTA-CCATG GTTATTACGGGTAACGGAGAATAAGGGTT-CGACTCCGGAGAGGGAGCCT TAGAAACGGCTACCACATCCAAGGAAGGCAGCAG-GCGCGAAACTTATCC AA-T-CTTG-----A-ATAGATGA-GATAGTGACT--------------- --------AAAAATAAAAA--GACCA---TTCC-T-AT-G--GAACG-GT TATTTCAATGAGT--TGATCATAAACCTTTTTT--C-G-AGTA--TCCAG TGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTC--CACTA GTGTA-AATCGTCATTGCTGCGGTTAAAAAGC-TCGTAGTTGGAT-C-TG AGTTGC---AT--GCA-AT-G-ATTCG--C-CT----T--TG--G--CGT ----TAAT------C---AT-TG-TTGTG---ACTA---T------T-T- --G--CTG--G-T-T--TTCT-AT--TG-A--AA-----TTTC-----G- A-TT-----TCTTTA-GTG-GC-TA--GCGA-GTT-TA-CTTTGA-AT-A AATTAAAGTGCT-CAGAACAAG---CGTT-----T--GC-TT-G--AAT- G-GTCGAT-CATGGAATAA-----TAAAAGAGGAC--TTCG---GT-T-- ----CTATT-T----ATTGGTTC-AG---G-AA------CTG------AA GT-AATGATTAAGAGGGACA--ATTC-GGGGGCATTCGTATCCCTGCGCG AGAGGTGAAATTCGTG-GACCG-CAGGGGGACGCCCTAAAGCGAAAG-CA TTTGCC-AAGAAT--GTCTTCATTAATCA-AGAACGAAAGTCAGAGGTTC GAAGGCGATTAGATA--CCGCCC-TAGTTCTGACCGTAAACTATGCCATC TAGC-GA--TCC-GAT--GG-GG--TA--T--TG--T-T----GCCTT-- GTCGAGG-AGCTT-CCCGGAAACGA--AA-GTCTTTCGGT-TCCTGGGGT AGTATGGTTGC-AAAGCT-G-AAACTTAAAGA-AATTGACGGAATGGCAC CACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGA--AAACT -CACCC-GGCCCGGACACCGTAA-GGATTGAC-----AGATTGA--A--- AGCTCTTTCTC-GATTTGGTGGTTGGTGGTGCATGGCCGTTCTTAGTTG- GTGGAG-CGATTTGTCTGGTTTATTCC-GAT-AACGAGCGAGACTCT-AG -C-C--TG-CTAAA-TA-G--TGA--CTA---------------GA---- TT-----------AT------T----GAGTC-------TA-G----T--C -------TA-------------C-TT-----CTT-AG---AGGGATAAG- CGG---TGTT-T-----A-G-C--CGCA--CG-AGATTGAGCGATAACAG GTCTGTGATGCCCTTAGATGTCCGGGG-CTG-CACGCGCGCTACAATGGA AG-AAT-CAGC--TGGC---CTA--T----CCAT-TGC-CG-A-AAGGT- AT----T----GGTAAACCG-TTGAAACT--CTTCC-GTG-ACCGGGATA GGGAATTGT--A-ATT---------ATT---TCCC-TTGAACG-AGGAAT TCCTAGTAAGTGTG-AGTCATCAGCTCACGCTGATTACGTCCC-TGCCAT TTGTACACACCGCCCGTCGCTGTC-CGGG-ACTG--AGC-TGTC--TCGA GAGGACT-GCGG-A-CTA----CT--GTA----TTGA-GG---CCT---- ---T---CGGG------TCG-----CGATA----TGGCG---GG-AAA-C AG-TTC-AATC-G-CAATG-G--CTTGAACCGGGTAAAAGTCGT-AACAA GGTATCTG------------------------------------------ --------------------------- * >DL;815Parelaphostrongylus_odocoil -------------------------------------------------- ----------------------------------ATT-AAGCCATG-CA- T-GTG-GA--GTTC-A--AC------TT--CA-A---AG-T-GA--AA-C -TGCGAACGGCTCATTAG-AGCAGATG-T-CATT---TATT-CG--G--A A-A--A-T--CC-T--T-AAT-GGA--TAACTGCG--GTAAT-TCTGGAG CTAATACATATGCAT-A-A-AC-CCTG-AC---T--C-TG-T---GAAA- -GGGTGCAAT-TA-TTAGAG---C---AA-A-TCAAT-CAT--------- ----T-T---TC----------G-GA------TG----TAGTT------- ---T---GCT---G-A-C-TC-TGAATA-A---CG--CAG--CATA-TCG G-CGGC-T-T-GT---TCGCCGATATT-CCGAAAA----AG---TGT-C- TGCCC-TATCA--AC---CT---GA-TGGTAGTCTATTAGTCTA-CCATG GTTATTACGGGTAACGGAGAATAAGGGTT-CGACTCCGGAGAGGGAGCCT TAGAAACGGCTACCACATCCAAGGAAGGCAGCAG-GCGCGAAACTTATCC AA-T-CTTG-----A-ATAGATGA-GATAGTGACT--------------- --------AAAAATAAAAA--GACCA---TTCC-T-AT-G--GAACG-GT CATTTCAATGAGT--TGATCATAAACCTTTTTT--C-G-AGTA--TCAAG TGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTC--CACTA GTGTA-AATCGTCATTGCTGCGGTTAAAAAGC-TCGTAGTTGGAT-C-TG AGTCGC---AT--GCA-AT-G-ATTCG--C-CT----T--TG--G--CGT ----TAAT------C---AT-TG-TTGTG---ACTA---T------T-T- --G--CTG--G-T-T--TTCT-AT--TG-A--AA-----TTTC-----G- A-TT-----TCTATA-GTG-GC-TA--GCGA-GTT-TA-CTTTGA-AT-A AATTAAAGTGCT-CAGAACAAG---CGTT-----T--GC-TT-G--AAT- G-GTCGAT-CATGGAATAA-----TAAAAGAGGAC--TTCG---GT-T-- ----CTATT-T----ATTGGTTC-AG---G-AA------CTG------AA AT-AATGGTTAAGAGGGACA--ATTC-GGGGGCATTCGTATCCCTGCGCG AGAGGTGAAATTCGTG-GACCG-CAGGGGGACGCCCTAAAGCGAAAG-CA TTTGCC-AAGAAT--GTCTTCATTAATCA-AGAACGAAAGTCAGAGGTTC GAAGGCGATTAGATA--CCGCCC-TAGTTCTGACCGTAAACTATGCCATC TAGC-GA--TCC-GAT--GG-GG--TA--T--TG--T-T----GCCTT-- GTCGAGG-AGCTT-CCCGGAAACGA--AA-GTCTTTCGGT-TCCTGGGGT AGTATGGTTGC-AAAGCT-G-AAACTTAAAGA-AATTGACGGAATGGCAC CACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGA--AAACT -CACCC-GGCCCGGACACCGTAA-GGATTGAC-----AGATTGA--A--- AGCTCTTTCTC-GATTTGGTGGTTGGTGGTGCATGGCCGTTCTTAGTTG- GTGGAG-CGATTTGTCTGGTTTATTCC-GAT-AACGAGCGAGACTCT-AG -C-C--TG-CTAAA-TA-G--TGA--CTA---------------GA---- T------------ACG-----T----ATGTC-------TA-G----T--C -------TA-------------C-TT-----CTT-AG---AGGGATAAG- CGG---TGTT-T-----A-G-C--CGCA--CG-AGATTGAGCGATAACAG GTCTGTGATGCCCTTAGATGTTCGGGG-CTG-CACGCGCGCTACAATGGA AG-AAT-CAGC--TGGC---CTA--T----CCAT-TAC-CG-A-AAGGT- AT----T----GGTAAACCG-TTGAAACT--CTTCC-GTG-ACCGGGATA GGGAATTGT--A-ATT---------ATT---TCCC-TTGAACG-AGGAAT TCCTAGTAAGTGTG-AGTCATCAGCTCACGCTGATTACGTCCC-TGCCAT TTGTACACACCGCCCGTCGCTGTC-CGGG-ACTG--AGC-TGTC--TCGA GAGGACT-GCGG-A-CTA----CT--GTA----TTGA-GG---CCT---- ---T---CGGG------TCG-----CGATA----TGGCG---GG-AAA-C AG-TTC-AATC-G-CAATG-G--CTTGAACCGGGTAAAAGTCGT-A---- -------------------------------------------------- --------------------------- * weblogo-3.8.0/tests/data/clustalw182.aln000066400000000000000000000642201467613320200200300ustar00rootroot00000000000000CLUSTAL W (1.82) multiple sequence alignment Bks ----TPSCFLKVS-----RLEAQLLLER-YPECGN-----LLLRPS--GDGADGVSVTTR 43 Brdg1 ----MPACFYTVS-----RKEATEMLQK-NPSLGN-----MILRP---GSDSRNYSITIR 42 BC007586 ----QVWYHGAIS-----RTDAENLLRL-CKE-AS-----YLVRNS--ETSKNDFSLSLK 42 Shb ----QIWYHGAIS-----RGDAENLLRL-CKE-CS-----YLVRNS--QTSKHDYPLSLR 42 Shd ----QPWFHGPLN-----RADAESLLSL-CKE-GS-----YLVRLS--ETNPQDCSLSLR 42 Hsh2 ----PEWFHGAIS-----REDAENLLES-QPL-GS-----FLIRVS--HS-HVGYTLSYK 41 Vrap ----PAWFHGFIT-----RREAERLLEP-KPQ-GC-----YLVRFS--ES-AVTFVLTYR 41 Sh2a ----APWFHGILT-----LKKANELLLS-TGMPGS-----FLIRVS--ER-IKGYALSYL 42 Abl ----HSWYHGPVS-----RNAAEYLLSSGIN--GS-----FLVRES-ESS-PSQRSISLR 42 Arg ----HSWYHGPVS-----RSAAEYLLSSLIN--GS-----FLVRES-ESS-PGQLSISLR 42 Hck ----EEWFFKGIS-----RKDAERQLLAPGNMLGS-----FMIRDS-ETT-KGSYSLSVR 44 Lck ----EPWFFKNLS-----RKDAERQLLAPGNTHGS-----FLIRES-EST-AGSFSLSVR 44 Lyn ----EEWFFKDIT-----RKDAERQLLAPGNSAGA-----FLIRES-ETL-KGSFSLSVR 44 Blk ----ERWFFRSQG-----RKEAERQLLAPINKAGS-----FLIRES-ETN-KGAFSLSVK 44 Fgr ----EEWYFGKIG-----RKDAERQLLSPGNPQGA-----FLIRES-ETT-KGAYSLSIR 44 Fyn ----EEWYFGKLG-----RKDAERQLLSFGNPRGT-----FLIRES-ETT-KGAYSLSIR 44 Yes ----EEWYFGKMG-----RKDAERLLLNPGNQRGI-----FLVRES-ETT-KGAYSLSIR 44 Src ----EEWYFGKIT-----RRESERLLLNAENPRGT-----FLVRES-ETT-KGAYCLSVS 44 Frk ----EPWFFGAIG-----RSDAEKQLLYSENKTGS-----FLIRES-ESQ-KGEFSLSV- 43 Slap ----HGWLFEGLG-----RDKAEELLQLPDTKVGS-----FMIRES-ETK-KGFYSLSVR 44 Slap2 ----HGWLYEGLS-----REKAEELLLLPGNPGGA-----FLIRES-QTR-RGSYSLSVR 44 Brk ----EPWFFGCIS-----RSEAVRRLQAEGNATGA-----FLIRVS-EKP-SADYVLSVR 44 Srms ----QPWYFSGVS-----RTQAQQLLLSPPNEPGA-----FLIRPS-ESS-LGGYSLSVR 44 SykC ----MPWFHGKIS-----REESEQIVLIGSKTNGK-----FLIRA--RDN-NGSYALCLL 43 Zap70C ----MPWYHSSLT-----REEAERKLYSGAQTDGK-----FLLRP--RKE-QGTYALSLI 43 SykN ----LPFFFGNIT-----REEAEDYLVQGGMSDGL-----YLLRQS-RNY-LGGFALSVA 44 Zap70N ----LPFFYGSIS-----RAEAEEHLKLAGMADGL-----FLLRQC-LRS-LGGYVLSLV 44 Csk ----MPWFHGKIT-----REQAERLLYPPET--GL-----FLVRES-TNY-PGDYTLCVS 42 Lsk ----MPWFHGKIS-----GQEAVQQLQPPED--GL-----FLVRES-ARH-PGDYVLCVS 42 Cis1 ----SGWYWGSIT-----ASEARQHLQ--KMPEGT-----FLVRDS-THP-SYLFTLSVK 42 Socs2 ----TGWYWGSMT-----VNEAKEKLK--EAPEGT-----FLIRDS-SHS-DYLLTISVK 42 Socs3 ----SGFYWSAVT-----GGEANLLLS--AEPAGT-----FLIRDS-SDQ-RHFFTLSVK 42 Socs1 ----CGFYWGPLS-----VHGAHERLR--AEPVGT-----FLVRDS-RQR-NCFFALSVK 42 Nap4 ----CGWYWGPMN-----WEDAEMKLK--GKPDGS-----FLVRDS-SDP-RYILSLSFR 42 Socs4 ----QGWYWGPIT-----RWEAEGKLA--NVPDGS-----FLVRDS-SDD-RYLLSLSFR 42 Socs5 ----NPCYWGVMD-----RYEAEALLE--GKPEGT-----FLLRDS-AQE-DYLFSVSFR 42 Socs7 ----NPCYWGVMD-----KYAAEALLE--GKPEGT-----FLLRDS-AQE-DYLFSVSFR 42 Crk ----SSWYWGRLS-----RQEAVALLQ--GQRHGV-----FLVRDS-STS-PGDYVLSVS 42 CrkL ----SAWYMGPVS-----RQEAQTRLQ--GQRHGM-----FLVRDS-STC-PGDYVLSVS 42 Pi3kCaplha ----KTWNVGSSN-----RNKAENLLR--GKRDGT-----FLVRES-SK--QGCYACSVV 41 Pi3kCgamma ----KTWFVEDIN-----RVQAEDLLY--GKPDGA-----FLIRES-SK--KGCYACSVV 41 Pi3kCbeta ----RTWYVGKIN-----RTQAEEMLS--GKRDGT-----FLIRES-SQ--RGCYACSVV 41 Pi3kNalpha ----AEWYWGDIS-----REEVNEKLR--DTADGT-----FLVRDA-STKMHGDYTLTLR 43 Pi3kNgamma ----AEWYWGDIS-----REEVNDKLR--DMPDGT-----FLVRDA-STKMQGDYTLTLR 43 Pi3kNbeta ----AEWYWGDIS-----REEVNEKLR--DTPDGT-----FLVRDA-SSKIQGEYTLTLR 43 Vav1 ----HLWYAGPME-----RAGAESILA--NRSDGT-----FLVRQR-VKD-AAEFAISIK 42 Vav3 ----QPWYAGAME-----RLQAETELI--NRVNST-----YLVRHR-TKE-SGEYAISIK 42 Vav2 ----YPWFAGNME-----RQQTDNLLK--SHASGT-----YLIRER-PAE-AERFAISIK 42 Mist ----NEWYIGEYS-----RQAVE-EAFMKENKDGS-----FLVRDCSTKSKEEPYVLAVF 45 Slp76 ----EEWYVSYIT-----RPEAE-AALRKINQDGT-----FLVRDSSKKTTTNPYVLMVL 45 Blnk ----KPWYAGACD-----RKSAE-EALHRSNKDGS-----FLIRKSSGHDSKQPYTLVVF 45 Plcg1C ----KEWYHASLT-----RAQAE-HMLMRVPRDGA-----FLVRK---RNEPNSYAISFR 42 Plcg2C ----KPWYYDSLS-----RGEAE-DMLMRIPRDGA-----FLIRK---REGSDSYAITFR 42 Btk ----YEWYSKHMT-----RSQAE-QLLKQEGKEGG-----FIVRD---SSKAGKYTVSVF 42 Txk ----YEWYHRNIT-----RNQAE-HLLRQESKEGA-----FIVRD---SRHLGSYTISVF 42 Itk ----YEWYNKSIS-----RDKAE-KLLLDTGKEGA-----FMVRD---SRTAGTYTVSVF 42 Tec ----YEWYCRNMN-----RSKAE-QLLRSEDKEGG-----FMVRD---SSQPGLYTVSLY 42 Bmx ----YDWFAGNIS-----RSQSE-QLLRQKGKEGA-----FMVRN---SSQVGMYTVSLF 42 Eat2 ----LPYYHGRLT-----KQDCE-TLLLKEGVDGN-----FLLRDS--ESIPGVLCLCVS 43 Sap ----VAVYHGKIS-----RETGE-KLLLATGLDGS-----YLLRDS--ESVPGVYCLCVL 43 Ship ----PCWNHGNIT-----RSKAE-ELLSRTGKDGS-----FLVRAS--ESISRAYALCVL 43 Ship2 ----PSWYHRDLS-----RAAAE-ELLARAGRDGS-----FLVRDS--ESVAGAFALCVL 43 Nck ----NPWYYGKVT-----RHQAE-MALNERGHEGD-----FLIRDS--ESSPNDFSVSLK 43 Nck2 ----REWYYGNVT-----RHQAQ-CALNERGVEGD-----FLIRDS--ESSPSDFSVSLK 43 Dapp1 ----LGWYHGNLT-----RHAAE-ALLLSNGCDGS-----YLLRDS--NETTGLYSLSVR 43 Grap ----HPWYSGRIS-----RQLAE-EILMKRNHLGA-----FLIRES--ESSPGEFSVSVN 43 Grb2 ----HPWFFGKIP-----RAKAE-EMLSKQRHDGA-----FLIRES--ESAPGDFSLSVK 43 Grap2 ----PKWFHEGLS-----RHQAE-NLLMG-KEVGF-----FIIRAS--QSSPGDFSISVR 42 Shp1C ----ERWYHGHMS-----GGQAE-TLLQAKGEPWT-----FLVRES--LSQPGDFVLSVL 43 Shp2C ----ERWFHGHLS-----GKEAE-KLLTEKGKHGS-----FLVRES--QSHPGDFVLSVR 43 Shp1N ----VRWFHRDLS-----GLDAE-TLLKGRGVHGS-----FLARPS--RKNQGDFSLSVR 43 Shp2N ----RRWFHPNIT-----GVEAE-NLLLTRGVDGS-----FLARPS--KSNPGDFTLSVR 43 Aps ----YPWFHGTLS-----RVKAAQLVLA----GGPRNHGLFVIRQS--ETRPGEYVLTFN 45 Sh2b ----YPWFHGMLS-----RLKAAQLVLT----GGTGSHGVFLVRQS--ETRRGEYVLTFN 45 Lnk ----YPWFHGPIS-----RVKAAQLVQL----QGPDAHGVFLVRQS--ETRRGEYVLTFN 45 Fer ----QDWYHGAIP-----RIEAQELLKK----QGD-----FLVRES--HGKPGEYVLSVY 40 Fes ----QLWYHGAIP-----RAEVAELLVH----SGD-----FLVRES--QGKQ-EYVLSVL 39 Nsp2 ----HAWYHGRIP-----RQVSENLVQR----DGD-----FLVRDS--LSSPGNFVLTCQ 40 Nsp3 ----HAWYHGRIP-----REVSETLVQR----NGD-----FLIRDS--LTSLGDYVLTCR 40 Nsp1 ----QPWYHGLLS-----RQKAEALLQQ----DGD-----FLVRAS--GSRGGNPVISCR 40 Shca ----EPWFHGKLS-----RREAEALLQL----NGD-----FLVRES--TTTPGQYVLTGL 40 Shcd QLWSEECYHGKLS-----RKAAESLLVK----DGD-----FLVRES--ATSPGQYVLSGL 44 Shcc ----ETWYQGEMS-----RKEAEGLLEK----DGD-----FLVRKS--TTNPGSFVLTGM 40 Shcb ----EPWYHGRMS-----RRAAERMLRA----DGD-----FLVRDS--VTNPGQYVLTGM 40 Grb10 ----QHWFHGRIS-----REESHRIIKQ----QGLVD-GLFLLRDS--QSNPKAFVLTLC 44 Grb14 ----QPWFHHKIS-----RDEAQRLIIQ----QGLVD-GVFLVRDS--QSNPKTFVLSMS 44 Grb7 ----QLWFHGRIS-----REESQRLIGQ----QGLVD-GLFLVRES--QRNPQGFVLSLC 44 Plcg1N ----EKWFHGKLGAGRDGRHIAERLLTEYCIETGAPD-GSFLVRES--ETFVGDYTLSFW 53 Plcg2N ----EKWFHKKV----EKRTSAEKLLQEYCMETGGKD-GTFLVRES--ETFPNDYTLSFW 49 Chimerin1 ----GREFHGMIS-----REAADQLLIV---AEGS-----YLIRES--QRQPGTYTLALR 41 Chimerin2 ----GREFHGIIS-----REQADELLGG---VEGA-----YILRES--QRQPGCYTLALR 41 Tens1 ----KFWYKADIS-----REQAIAMLKD--KEPGS-----FIVRDS--HSFRGAYGLAMK 42 Tensin ----KYWYKPEIS-----REQAIALLKD--QEPGA-----FIIRDS--HSFRGAYGLAMK 42 Tenc1 ----KFWYKPHLS-----RDQAIALLKD--KDPGA-----FLIRDS--HSFQGAYGLALK 42 Cten ----KYWFKPNIT-----REQAIELLRK--EEPGA-----FVIRDS--SSYRGSFGLALK 42 Rin2 ----PIWLQLSLS-----EEEAAEVLQA--QPPGI-----FLVHKS--TKMQ-KKVLSLR 41 Rin3 ----PVWLQLSLG-----QAEVARILHR--VVAGM-----FLVRRD--SSSK-QLVLCVH 41 Rin1 ----PVWLQLQAN-----AAAALHMLRT--EPPGT-----FLVRKS--NTRQ-CQALCMR 41 Stat1 ----PLWNDGCIMG--FISKERERALLK-DQQPGT-----FLLRFS-ESSREGAITFTWV 47 Stat4 ----PLWIDGYVMG--FVSKEKERLLLK-DKMPGT-----FLLRFS-ES-HLGGITFTWV 46 Stat3 ----ALWNEGYIMG--FISKERERAILS-TKPPGT-----FLLRFS-ESSKEGGVTFTWV 47 Stat2 ----DLWNDGRIMG--FVSRSQERRLLK-KTMSGT-----FLLRFS-ES-SEGGITCSWV 46 Stat5a ----PHWNDGAILG--FVNKQQAHDLLI-NKPDGT-----FLLRFS-DS-EIGGITIAWK 46 Stat5b ----PHWNDGAILG--FVNKQQAHDLLI-NKPDGT-----FLLRFS-DS-EIGGITIAWK 46 Stat6 ----SYWSDRLIIG--FISKQYVTSLLL-NEPDGT-----FLLRFS-DS-EIGGITIAHV 46 Jak2 ----QSNCHGPIS-----MDFAISKLKKAGNQTGL-----YVLRCS--PKDFNKYFLTF- 43 Jak3 ----AEQCHGPIT-----LDFAINKLKTGGSRPGS-----YVLRRS--PQDFDSFLLTV- 43 Jak1 ----QNGCHGPIC-----TEYAINKLRQEGSEEGM-----YVLRWS--CTDFDNILMTVT 44 Cbl ----HPGYMAFLT-----YDEVKARLQKFIHKPGS-----YIFRLS--CTRLGQWAIGYV 44 Cblb ----HPGYMAFLT-----YDEVKARLQKYSTKPGS-----YIFRLS--CTRLGQWAIGYV 44 Cblc ----HPGYMAFLT-----YDEVQERLQACRDKPGS-----YIFRPS--CTRLGQWAIGYV 44 RasGapN ----NQWYHGKLD-----RTIAEERLRQ-AGKSGS-----YLIRES--DRRPGSFVLSFL 43 RasGapC ----KIWFHGKIS-----KQEAYNLLMT-VGQVCS-----FLVRPS--DNTPGDYSLYFR 43 Tyk2 -----DGIHGPLL-----EPFVQAKLRP---EDGL-----YLIHWS--TSHPYRLILTVA 40 Sh3bp2 ----NSVFVNTTE------SCEVERLFKATSPRGEPQDGLYCIRNS--STKSGKVLVVWD 48 Supt6h ----HPSFHNINF------KQAEKMMET--MDQGD-----VIIRPS--SKGENHLTVTWK 41 : Bks QMHNG--------------THVVRHYKVKREGPKY-------VIDVEQPFS------CTS 76 Brdg1 QEID---------------IPRIKHYKVMSVGQNY-------TIELEKPVT------LPN 74 BC007586 S------------------SQGFMHMKLSRTKEH-------KYVLGQNSPP------FSS 71 Shb S------------------NQGFMHMKLAKTKE--------KYVLGQNSPP------FDS 70 Shd S------------------SQGFLHLKFARTREN-------QVVLGQHSGP------FPS 71 Hsh2 A------------------QSSCCHFMVKLLDDG-------TFMIPGEKVA------HTS 70 Vrap S------------------RTCCRHFLLAQLRDG-------RHVVLGEDSA------HAR 70 Sh2a S------------------EDGCKHFLIDASADA-------YSFLGVDQLQ------HAT 71 Abl ------------------YEGRVYHYRINTASDGK------LYVSSESR--------FNT 70 Arg ------------------YEGRVYHYRINTTADGK------VYVTAESR--------FST 70 Hck DYDP-----R--------QGDTVKHYKIRTLDNGG------FYISPRST--------FST 77 Lck DFDQ-----N--------QGEVVKHYKIRNLDNGG------FYISPRIT--------FPG 77 Lyn DFDP-----V--------HGDVIKHYKIRSLDNGG------YYISPRIT--------FPC 77 Blk DVT------T--------QGELIKHYKIRCLDEGG------YYISPRIT--------FPS 76 Fgr DWDQ-----T--------RGDHVKHYKIRKLDMGG------YYITTRVQ--------FNS 77 Fyn DWDD-----M--------KGDHVKHYKIRKLDNGG------YYITTRAQ--------FET 77 Yes DWDE-----I--------RGDNVKHYKIRKLDNGG------YYITTRAQ--------FDT 77 Src DFDN-----A--------KGLNVKHYKIRKLDSGG------FYITSRTQ--------FNS 77 Frk ---------L--------DGAVVKHYRIKRLDEGG------FFLTRRRI--------FST 72 Slap HR-------------------QVKHYRIFRLPNNW------YYISPRLT--------FQC 71 Slap2 LSRP-----A--------SWDRIRHYRIHCLDNGW------LYISPRLT--------FPS 77 Brk ------------------DTQAVRHYKIWRRAGGR------LHLNEAVS--------FLS 72 Srms ------------------AQAKVCHYRVSMAADGS------LYLQKGRL--------FPG 72 SykC ------------------HEGKVLHYRIDKDKTGK------LSIPEGKK--------FDT 71 Zap70C ------------------YGKTVYHYLISQDKAGK------YCIPEGTK--------FDT 71 SykN ------------------HGRKAHHYTIERELNGT------YAIAGGRT--------HAS 72 Zap70N ------------------HDVRFHHFPIERQLNGT------YAIAGGKA--------HCG 72 Csk ------------------CDGKVEHYRIMYH-ASK------LSIDEEVY--------FEN 69 Lsk ------------------FGRDVIHYRVLHR-DGH------LTIDEAVF--------FCN 69 Cis1 ------------------TTRGPTNVRIEYA-DSS------FRLDSNCLSRPR-ILAFPD 76 Socs2 ------------------TSAGPTNLRIEYQ-DGK------FRLDSIICVKSK-LKQFDS 76 Socs3 ------------------TQSGTKNLRIQCE-GGS------FSLQSDPRSTQP-VPRFDC 76 Socs1 ------------------MASGPTSIRVHFQ-AGR------FHLDG---SRE----SFDC 70 Nap4 ------------------SQGITHHTRMEHY-RGT------FSLWCHPKFEDR-CQSVVE 76 Socs4 ------------------SHGKTLHTRIEHS-NGR------FSFYEQPDVEG--HTSIVD 75 Socs5 ------------------RYNRSLHARIEQW-NHN------FSFDAHDPCVFH-SSTVTG 76 Socs7 ------------------RYSRSLHARIEQW-NHN------FSFDAHDPCVFH-SPDITG 76 Crk ------------------ENSRVSHYIINSS-GPR------PPVPPSPAQPPP-GVSPSR 76 CrkL ------------------ENSRVSHYIINSL-PNR------------------------R 59 Pi3kCaplha ------------------VDGEVKHCVINKT-ATG------YGFAEPYNL-------YSS 69 Pi3kCgamma ------------------ADGEVKHCVIYST-ARG------YGFAEPYNL-------YSS 69 Pi3kCbeta ------------------VDGDTKHCVIYRT-ATG------FGFAEPYNL-------YGS 69 Pi3kNalpha ------------------KGGNNKLIKIFHR-DGK------YGFSDPLT--------FSS 70 Pi3kNgamma ------------------KGGNNKLIKIYHR-DGK------YGFSDPLT--------FNS 70 Pi3kNbeta ------------------KGGNNKLIKVFHR-DGH------YGFSEPLT--------FCS 70 Vav1 ------------------YNVEVKHIKIMTA-EGL------YRITEKKA--------FRG 69 Vav3 ------------------YNNEAKHIKILTR-DGF------FHIAENRK--------FKS 69 Vav2 ------------------FNDEVKHIKVVEK-DNW------IHITEAKK--------FDS 69 Mist YE-------N--------KVYNVKIRFLERNQQFA------LGTGLRGDEK------FDS 78 Slp76 YK-------D--------KVYNIQIRYQKESQVYL------LGTGLRGKED------FLS 78 Blnk FN-------K--------RVYNIPVRFIEATKQYA------LGRKKNGEEY------FGS 78 Plcg1C AE-------G--------KIKHCRVQ--QEGQTVM------LG----NSE-------FDS 68 Plcg2C AR-------G--------KVKHCRIN--RDGRHFV------LG----TSAY------FES 69 Btk AK----STGD--------PQGVIRHYVVCSTPQS--------QYYLAEKHL------FST 76 Txk MG----ARRS--------TEAAIKHYQIKKNDSG--------QWYVAERHA------FQS 76 Itk TKA---VVSE--------NNPCIKHYHIKETNDNP------KRYYVAEKYV------FDS 79 Tec TK----FGGE--------GSSGFRHYHIKETTTSP------KKYYLAEKHA------FGS 78 Bmx SK----AVND--------KKGTVKHYHVHTNAEN--------KLYLAENYC------FDS 76 Eat2 FK-------N--------IVYTYRIFREKHGYYRI------QTAEGSPKQV------FPS 76 Sap YH-------G--------YIYTYRVSQTETGSWSA------ETAPGVHKRY------FRK 76 Ship YR-------N--------CVYTYRILPNEDDKFTV------QASEGVSMRF------FTK 76 Ship2 YQ-------K--------HVHTYRILPDGEDFLAV------QTSQGVPVRR------FQT 76 Nck AQG------------------KNKHFKVQLKETV---------YCIG-QRK------FST 69 Nck2 ASG------------------KNKHFKVQLVDNV---------YCIG-QRR------FHT 69 Dapp1 AKD------------------SVKHFHVEYTGYS---------FKFG-FNE------FSS 69 Grap YGD------------------QVQHFKVLREASG---------KYFLWEEK------FNS 70 Grb2 FGN------------------DVQHFKVLRDGAG---------KYFLWVVK------FNS 70 Grap2 HED------------------DVQHFKVMRDNKG---------NYFLWTEK------FPS 69 Shp1C SDQPKAGPGS---------PLRVTHIKVMCEGGR---------YTVGGLET------FDS 79 Shp2C TGDDKGESND--------GKSKVTHVMIRCQELK---------YDVGGGER------FDS 80 Shp1N VGD------------------QVTHIRIQNSGDF---------YDLYGGEK------FAT 70 Shp2N RNG------------------AVTHIKIQNTGDY---------YDLYGGEK------FAT 70 Aps F------------------QGKAKHLRLSLNGHG--------QCHVQHL-------WFQS 72 Sh2b F------------------QGKAKHLRLSLNEEG--------QCRVQHL-------WFQS 72 Lnk F------------------QGIAKHLRLSLTERG--------QCRVQHL-------HFPS 72 Fer S------------------DGQRRHFIIQYVDN---------MYRFEGT-------GFSN 66 Fes W------------------DGLPRHFIIQSLDN---------LYRLEGE-------GFPS 65 Nsp2 W------------------KNLAQHFKINRTVLRLSEAYSRVQYQFEME-------SFDS 75 Nsp3 W------------------RNQALHFKINKVVVKAGESYTHIQYLFEQE-------SFDH 75 Nsp1 W------------------RGSALHFEVFRVALRPRPGRPTALFQLEDE-------QFPS 75 Shca Q------------------SGQPKHLLLVDPEG---------VVRTKDH-------RFES 66 Shcd Q------------------GGQAKHLLLVDPEG---------KVRTKDH-------VFDN 70 Shcc H------------------NGQAKHLLLVDPEG---------TIQTKDR-------VFDS 66 Shcb H------------------AGQPKHLLLVDPEG---------VVRTKDV-------LFES 66 Grb10 H------------------HQKIKNFQILPCEDD-----GQTFFSLDDGNT-----KFSD 76 Grb14 H------------------GQKIKHFQIIPVEDD-----GEMFHTLDDGHT-----RFTD 76 Grb7 H------------------LQKVKHYLILPSEEE-----GRLYFSMDDGQT-----RFTD 76 Plcg1N R------------------NGKVQHCRIHSRQDA-----GTPKFFLTDN-L-----VFDS 84 Plcg2N R------------------SGRVQHCRIRSTMEG-----GTLKYYLTDN-L-----RFRR 80 Chimerin1 ------------------FGSQTRNFRLYYDGKH---------FVGEKR--------FES 66 Chimerin2 ------------------FGNQTLNYRLFHDGKH---------FVGEKR--------FES 66 Tens1 VATPPPSVLQLNKKAGDLANELVRHFLIECTPKG---------VRLKGCSN---EPYFGS 90 Tensin VSSPPPTIMQQNKK-GDMTHELVRHFLIETGPRG---------VKLKGCPN---EPNFGS 89 Tenc1 VATPPPSAQP--WK-GDPVEQLVRHFLIETGPKG---------VKIKGCPS---EPYFGS 87 Cten VQEVPASAQN---RPGEDSNDLIRHFLIESSAKG---------VHLKGADE---EPYFGS 87 Rin2 LP--CEFGAP------------LKEFAIKESTYT---------FSLEGS-----GISFAD 73 Rin3 FPSLNESSAE------------VLEYTIKEEKSI---------LYLEGS-----ALVFED 75 Rin1 LP---EASGPS----------FVSSHYILESPGG---------VSLEGS-----ELMFPD 74 Stat1 ERS--------------QNGGEPDFHAVEPYTKKE---LSAVTFPDIIRNYKVMAAENIP 90 Stat4 DHS--------------ESG-EVRFHSVEPYNKGR---LSALPFADILRDYKVIMAENIP 88 Stat3 EKD--------------ISG-KTQIQSVEPYTKQQ---LNNMSFAEIIMGYKIMDATNIL 89 Stat2 EHQ--------------DDD-KVLIYSVQPYTKEV---LQSLPLTEIIRHYQLLTEENIP 88 Stat5a FD---------------SPER--NLWNLKPFTTRD---FSIRSLADRLG----------D 76 Stat5b FD---------------SQER--MFWNLMPFTTRD---FSIRSLADRLG----------D 76 Stat6 IR---------------GQDGSPQIENIQPFSAKD---LSIRSLGDRIR----------D 78 Jak2 AVERE-------------NVIEYKHCLITKNENEE------YNLSGTKKN-------FSS 77 Jak3 CVQNP-------------LGPDYKGCLIRRSPTGT------FLLVGLSRP-------HSS 77 Jak1 CFEKSEQVQG--------AQKQFKNFQIEVQ-KGR------YSLHGSDRS-------FPS 82 Cbl TA----------------DGNILQTIPHNKPLFQALIDGFREGFYLFPDGR-------NQ 81 Cblb TG----------------DGNILQTIPHNKPLFQALIDGSREGFYLYPDGR-------SY 81 Cblc SS----------------DGSILQTIPANKPLSQVLLEGQKDGFYLYPDGK-------TH 81 RasGapN S-----------------QMNVVNHFRIIAMCGDY--------YIGGRR--------FSS 70 RasGapC T------------------NENIQRFKICPTPNNQ--------FMMGGR-------YYNS 70 Tyk2 QRSQ--------------APDGMQSLRLRKFPIEQ----QDGAFVLEGWGR-----SFPS 77 Sh3bp2 ET-----------------SNKVRNYRIFEKDSK---------FYLEGEVL------FVS 76 Supt6h VS-----------------DGIYQHVDVREEGKEN-------AFSLGATLWIN-SEEFED 76 Bks LDAVVNYFVSHTK------KALVP--------FLLDEDYEKVLGYVE- 109 Brdg1 LFSVIDYFVKETR------GNLRP--------FICSTD---------- 98 BC007586 VPEIVHHYASRK----LPIKGA----------EHMSLLYP-------- 97 Shb VPEVIHYYTTRK----LPIKGA----------EHLSLLYPVAVRTL-- 102 Shd VPELVLHYSSRP----LPVQGA----------EHLALLY--------- 96 Hsh2 LDALVTFHQQKP----IEPRR-----------ELLTQPC--------- 94 Vrap LQDLLLHYTAHP----LSPYG-----------ETLTEPLARQ------ 97 Sh2a LADLVEYHKEEP----ITSLGK----------ELLLYPC--------- 96 Abl LAELVHHHSTVAD-------GLI---------TTLHYPA--------- 93 Arg LAELVHHHSTVAD-------GLV---------TTLHYPAP-------- 94 Hck LQELVDHYKKGND-------GLC---------QKLSVPC--------- 100 Lck LHELVRHYTNASD-------GLC---------TRLSRPC--------- 100 Lyn ISDMIKHYQKQAD-------GLC---------RRLEKAC--------- 100 Blk LQALVQHYSKKGD-------GLC---------QRLTLPC--------- 99 Fgr VQELVQHYMEVND-------GLC---------NLLIAPC--------- 100 Fyn LQQLVQHYSERAA-------GLC---------CRLVVPC--------- 100 Yes LQKLVKHYTEHAD-------GLC---------HKLTTVC--------- 100 Src LQQLVAYYSKHAD-------GLC---------HRLTTVC--------- 100 Frk LNEFVSHYTKTSD-------GLC---------VKLGKPC--------- 95 Slap LEDLVNHYSEVAD-------GLC---------CVLTTPC--------- 94 Slap2 LQALVDHYSELAD-------DIC---------CLLKEPC--------- 100 Brk LPELVNYHRAQSL-------SHG---------LRLAAPC--------- 95 Srms LEELLTYYKANWK-------LIQ---------NPLLQPC--------- 95 SykC LWQLVEHYSYKAD-------GLL---------RVLTVPCQKIGTQ--- 100 Zap70C LWQLVEYLKLKAD-------GLI---------YCLKEACPNSSASNAS 103 SykN PADLCHYHSQESD-------GLV---------CLLKKPFNRPQ----- 99 Zap70N PAELCEFYSRDPD-------GLP---------CNLRKPC--------- 95 Csk LMQLVEHYTSDAD-------GLC---------TRLIKPK--------- 92 Lsk LMDMVEHYSKDKG-------AIC---------TKLVRPK--------- 92 Cis1 VVSLVQHYVASCTADTRSDSPDP---------AP-TPALPMPK----- 109 Socs2 VVHLIDYYVQMCK-DKRTGPEAP---------RNGTVHLYLTKPL--- 111 Socs3 VLKLVYHYMPPPG-----APSFP---------SPPTEPSS-------- 102 Socs1 LFELLEHYVAAPR--RMLGAPLR---------QRRVRPL--------- 98 Nap4 FIKRAIMHSKNGKFLYFLRSRVP---------GLPPTPVQLLYPV--- 112 Socs4 LIEHSIRDSENGAFCYS-RSRLP---------GSATYPVRLTNPV--- 110 Socs5 LLEH---YKDPSSCMFF----------------EPLLTISL------- 98 Socs7 LLEH---YKDPSACMFF----------------EPLLSTPL------- 98 Crk LRIGDQEFDSLPALLEFYKIHYL---------DTTTLIEPV------- 108 CrkL FKIGDQEFDHLPALLEFYKIHYL---------DTTTLIEPA------- 91 Pi3kCaplha LKELVLHYQHTSLVQHN--DSLN---------VTLAYP---------- 96 Pi3kCgamma LKELVLHYQQTSLVQHN--DSLN---------VRLAYPV--------- 97 Pi3kCbeta LKELVLHYQHASLVQHN--DALT---------VTLAHPVR-------- 98 Pi3kNalpha VVELINHYRNESLAQYN--PKLD---------VKLLYPV--------- 98 Pi3kNgamma VVELINHYHHESLAQYN--PKLD---------VKLMYPV--------- 98 Pi3kNbeta VVDLINHYRHESLAQYN--AKLD---------TRLLYPV--------- 98 Vav1 LTELVEFYQQNSLKDCF--KSLD---------TTLQFPF--------- 97 Vav3 LMELVEYYKHHSLKEGF--RTLD---------TTLQFPY--------- 97 Vav2 LLELVEYYQCHSLKESF--KQLD---------TTLKYPY--------- 97 Mist VEDIIEHYKNFP-------IILIDGKDKTGV-HRKQCHLTQPL----- 113 Slp76 VSDIIDYFRKMP-------LLLIDGKNRG---SRYQCTLTHA------ 110 Blnk VAEIIRNHQHSP-------LVLIDSQNNTKDSTRLKYAVKVS------ 113 Plcg1C LVDLISYYEKHP-------LYRK---------MKLRYPI--------- 91 Plcg2C LVELVSYYEKHS-------LYRK---------MRLRYPV--------- 92 Btk IPELINYHQHNS-------AGLI---------SRLKYPV--------- 99 Txk IPELIWYHQHNA-------AGLM---------TRLRYPV--------- 99 Itk IPLLINYHQHNG-------GGLV---------TRLRYPV--------- 102 Tec IPEIIEYHKHNA-------AGLV---------TRLRYPV--------- 101 Bmx IPKLIHYHQHNS-------AGMI---------TRLRHPV--------- 99 Eat2 LKELISKFEKPN-------QGMV---------VHLLKPI--------- 99 Sap IKNLISAFQKPD-------QGIV---------IPLQYPVEKKSSARST 108 Ship LDQLIEFYKKEN-------MGLV---------THLQYPVPLE------ 102 Ship2 LGELIGLYAQPN-------QGLV---------CALLLPV--------- 99 Nck MEELVEHYKKAP--IFTSEQGEK---------LYLVKHL--------- 97 Nck2 MDELVEHYKKAP--IFTSEHGEK---------LYLVRA---------- 96 Dapp1 LKDFVKHFANQP--LIGSETGTL---------MVLKHPYPRKV----- 101 Grap LNELVDFYRTTT---I-------------------------------- 83 Grb2 LNELVDYHRSTS---VSRNQQIF---------LRDIE----------- 95 Grap2 LNKLVDYYRTNS---ISRQKQIF---------LRDRTREDQ------- 98 Shp1C LTDLVEHFKKTG---IEEASGAF---------VYLRQPY--------- 106 Shp2C LTDLVEHYKKNP---MVETLGTV---------LQLKQPL--------- 107 Shp1N LTELVEYYTQQQG-VLQDRDGTI---------IHLKYPL--------- 99 Shp2N LAELVQYYMEHHG-QLKEKNGDV---------IELKYP---------- 98 Aps VLDMLRHFHTH---PIPLESGGSA-------DITLRSYV--------- 101 Sh2b IFDMLEHFRVH---PIPLESGGSS-------DVVLVSYV--------- 101 Lnk VVDMLHHFQRS---PIPLECGAAC-------DVRLSSYV--------- 101 Fer IPQLIDHHYTT---KQVITKKSG--------VVLLNPI---------- 93 Fes IPLLIDHLLST---QQPLTKKSG--------VVLHRAV---------- 92 Nsp2 IPGLVRCYVGN---RRPISQQSG--------AIIF------------- 99 Nsp3 VPALVRYHVGS---RKAVSEQSG--------AIIYCPVNRTFP----- 107 Nsp1 IPALVHSYMTG---RRPLSQATG--------AVVSRPVT--------- 103 Shca VSHLISYHMDN---HLPIISAGS--------ELCLQQPV--------- 94 Shcd VGHLIRYHMDN---SLPIISSGS--------EVSLKQP---------- 97 Shcc ISHLINHHLES---SLPIVSAGS--------ELCLQQPV--------- 94 Shcb ISHLIDHHLQNG--QPPIVAAES--------ELHLRGVVSREP----- 99 Grb10 LIQLVDFY--------QLNKGV-------------------------- 90 Grb14 LIQLVEFY--------QLNKGVL--------PCKLKHYC--------- 99 Grb7 LLQLVEFH--------QLNRGIL--------PCLLRHCC--------- 99 Plcg1N LYDLITHYQQV-----PLRCNEF--------EMRLSEPV--------- 110 Plcg2N MYALIQHYRET-----HLPCAEF--------ELRLTDPVP-------- 107 Chimerin1 IHDLVTDGLITLY------IETK----------AAEYIAK-------- 90 Chimerin2 IHDLVTDGLITLY------IETK----------AAEYISK-------- 90 Tens1 LTALVCQHSITP-------LALP---------C-LLIPERDPL----- 116 Tensin LSALVYQHSIIP-------LALP---------CKLVIPNR-------- 113 Tenc1 LSALVSQHSISP-------ISLP---------CCLRIPSK-------- 111 Cten LSAFVCQHSIMA-------LALP---------CKLTIPQ--------- 110 Rin2 LFRLIAFYCISR-------DVLP---------FTLKLPY--------- 96 Rin3 IFRLIAFYCVSR-------DLLP---------FTLRLPQ--------- 98 Rin1 LVQLICAYCHTR-------DILL---------LPLQLPR--------- 97 Stat1 ENPLKYLYPNIDK-----DHAFG---------KYYSRPK--------- 115 Stat4 ENPLKYLYPDIPK-----DKAFG---------KHYSS----------- 111 Stat3 VSPLVYLYPDIPK-----EEAFG---------KYCRP----------- 112 Stat2 ENPLRFLYPRIPR-----DEAFG---------CYYQEK---------- 112 Stat5a LSYLIYVFPDRPK-----DEVFS---------KYYTPVL--------- 101 Stat5b LNYLIYVFPDRPK-----DEVYS---------KYYTPVCESAT----- 105 Stat6 LAQLKNLYPKKPK-----DEAFR---------SHYKPEQ--------- 103 Jak2 LKDLLN-CYQ--------METVR------------------------- 91 Jak3 LRELLATCWDGGL----HVDGVA---------VTLTSCC--------- 103 Jak1 LGDLMSHLKKQIL----RTDNIS---------FMLKRCC--------- 108 Cbl NPDLTGLCEPTPQ-------------------DHIK------------ 98 Cblb NPDLTGLCEPTPH-------------------DHIK------------ 98 Cblc NPDLTELGQAEPQ-------------------QRIHVSEEQLQLYW-- 108 RasGapN LSDLIGYYSHVS-------CLLKG--------EKLLYPV--------- 94 RasGapC IGDIIDHYRKEQ-------IVEG---------YYLKEPV--------- 93 Tyk2 VRELGAALQGCLLRAGDDCFSLRR--------CCLPQPGETS------ 111 Sh3bp2 VGSMVEHYHTHVLP-----SHQS---------LLLRHPY--------- 101 Supt6h LDEIVARYVQPMAS---FARDLLN--------HKYYQDCSG------- 106 weblogo-3.8.0/tests/data/clustalw2.aln000066400000000000000000002041221467613320200176540ustar00rootroot00000000000000CLUSTAL 2.0.10 multiple sequence alignment sp|P12180|PETL_ORYSJ -------------------------------------------------- tr|Q7U572|Q7U572_SYNPX -------------------------------------------------- sp|P0C428|PSBT_ORYSI -------------------------------------------------- sp|P74787|PSBT_SYNY3 -------------------------------------------------- sp|P12186|PSAI_ORYSJ -------------------------------------------------- tr|Q7UZX5|Q7UZX5_PROMP -------------------------------------------------- sp|Q6ENI6|PSBM_ORYNI -------------------------------------------------- tr|Q7NCI2|Q7NCI2_GLOVI -------------------------------------------------- tr|Q7V6E4|Q7V6E4_PROMM -------------------------------------------------- tr|Q7V512|Q7V512_PROMM -------------------------------------------------- tr|Q8YRD7|Q8YRD7_ANASP -------------------------------------------------- tr|Q93P10|Q93P10_PROMP -------------------------------------------------- tr|Q949Q5|Q949Q5_ARATH -------------------------------------------------- sp|P0C405|PSBI_ORYSA -------------------------------------------------- sp|P0C515|YCF4_ORYSJ -------------------------------------------------- sp|Q6ENI5|PETN_ORYNI -------------------------------------------------- tr|P73952|P73952_SYNY3 -------------------------------------------------- tr|Q7TU23|Q7TU23_PROMP -------------------------------------------------- sp|P73528|PSBZ_SYNY3 -------------------------------------------------- sp|Q57038|CYB6_SYNY3 -------------------------------------------------- sp|P73676|PSBY_SYNY3 -------------------------------------------------- sp|P27589|PETD_SYNY3 -------------------------------------------------- sp|P0C390|PETG_ORYSA -------------------------------------------------- tr|Q7U8X4|Q7U8X4_SYNPX -------------------------------------------------- sp|P0C415|PSBJ_ORYSI -------------------------------------------------- sp|P74367|PS11_SYNY3 -------------------------------------------------- sp|P0C357|PSAB_ORYSI MELRFPRFSQGLAQDPTTRRIWFGIATAHDFESHDDITEERLYQNIFASH 50 sp|P0C374|PSAJ_ORYSI -------------------------------------------------- tr|Q7V658|Q7V658_PROMM -------------------------------------------------- sp|P0C410|PSBK_ORYSJ -------------------------------------------------- tr|Q7V2Y4|Q7V2Y4_PROMP -------------------------------------------------- tr|Q7NCH9|Q7NCH9_GLOVI -------------------------------------------------- sp|Q9LU86|PRXQ_ARATH -------------------------------------------------- sp|P0C400|PSBF_ORYSI -------------------------------------------------- tr|Q7VDW1|Q7VDW1_PROMA -------------------------------------------------- sp|P0C370|PSBE_ORYSJ -------------------------------------------------- tr|Q36688|Q36688_ORYSA -------------------------------------------------- tr|Q2LIK6|Q2LIK6_9ORYZ -------------------------------------------------- sp|Q9S7W1|CB4C_ARATH -------------------------------------------------- tr|Q7U9C4|Q7U9C4_SYNPX -------------------------------------------------- sp|P80471|LIPC_SOLTU -------------------------------------------------- sp|Q55356|PSB28_SYNY3 -------------------------------------------------- sp|P0C511|RBL_ORYSI -------------------------------------------------- sp|P0C421|PSBH_ORYSI -------------------------------------------------- sp|P0C516|YCF3_ORYSA -------------------------------------------------- sp|P0C389|CYF_ORYSJ -------------------------------------------------- tr|Q7VC13|Q7VC13_PROMA -------------------------------------------------- tr|Q7NL78|Q7NL78_GLOVI -------------------------------------------------- tr|Q7U4P2|Q7U4P2_SYNPX -------------------------------------------------- tr|Q9SF54|Q9SF54_ARATH -------------------------------------------------- sp|O98679|NDHK_PEA -------------------------------------------------- tr|Q7UZS7|Q7UZS7_PROMP -------------------------------------------------- sp|P0C359|PSAC_ORYSA -------------------------------------------------- tr|Q7V2Z3|Q7V2Z3_PROMP -------------------------------------------------- tr|Q9SGH4|Q9SGH4_ARATH -------------------------------------------------- sp|Q55013|CY550_SYNY3 -------------------------------------------------- sp|P12180|PETL_ORYSJ -------------------------------------------------- tr|Q7U572|Q7U572_SYNPX -------------------------------------------------- sp|P0C428|PSBT_ORYSI -------------------------------------------------- sp|P74787|PSBT_SYNY3 -------------------------------------------------- sp|P12186|PSAI_ORYSJ -------------------------------------------------- tr|Q7UZX5|Q7UZX5_PROMP -------------------------------------------------- sp|Q6ENI6|PSBM_ORYNI -------------------------------------------------- tr|Q7NCI2|Q7NCI2_GLOVI -------------------------------------------------- tr|Q7V6E4|Q7V6E4_PROMM -------------------------------------------------- tr|Q7V512|Q7V512_PROMM -------------------------------------------------- tr|Q8YRD7|Q8YRD7_ANASP -------------------------MVSLVMSGLTFWAVNTIQQDAQVND 25 tr|Q93P10|Q93P10_PROMP -------------------------------------------------- tr|Q949Q5|Q949Q5_ARATH -------------------------------------------------- sp|P0C405|PSBI_ORYSA -------------------------------------------------- sp|P0C515|YCF4_ORYSJ -------------------------------------------------- sp|Q6ENI5|PETN_ORYNI -------------------------------------------------- tr|P73952|P73952_SYNY3 -------------------------------------------------- tr|Q7TU23|Q7TU23_PROMP -------------------------------------------------- sp|P73528|PSBZ_SYNY3 -------------------------------------------------- sp|Q57038|CYB6_SYNY3 -------------------------------------------------- sp|P73676|PSBY_SYNY3 -------------------------------------------------- sp|P27589|PETD_SYNY3 -------------------------------------------------- sp|P0C390|PETG_ORYSA -------------------------------------------------- tr|Q7U8X4|Q7U8X4_SYNPX -------------------------------------------------- sp|P0C415|PSBJ_ORYSI -------------------------------------------------- sp|P74367|PS11_SYNY3 -------------------------------------------------- sp|P0C357|PSAB_ORYSI FGQLAIIFLWTSGNLFHVAWQGNFESWIQDPLHVRPIAHAIWDPHFGQPA 100 sp|P0C374|PSAJ_ORYSI -------------------------------------------------- tr|Q7V658|Q7V658_PROMM -------------------------------------------------- sp|P0C410|PSBK_ORYSJ -------------------------------------------------- tr|Q7V2Y4|Q7V2Y4_PROMP -----------------------------MGLPWYRVHTVVINDPGRLLA 21 tr|Q7NCH9|Q7NCH9_GLOVI -------------------------------------------------- sp|Q9LU86|PRXQ_ARATH -------------------------------------------------- sp|P0C400|PSBF_ORYSI -------------------------------------------------- tr|Q7VDW1|Q7VDW1_PROMA -------------------------------------------------- sp|P0C370|PSBE_ORYSJ -------------------------------------------------- tr|Q36688|Q36688_ORYSA -------------------------------------------------- tr|Q2LIK6|Q2LIK6_9ORYZ -------------------------------------------------- sp|Q9S7W1|CB4C_ARATH -------------------------------------------------- tr|Q7U9C4|Q7U9C4_SYNPX -------------------------------------------------- sp|P80471|LIPC_SOLTU -------------------------------------------------- sp|Q55356|PSB28_SYNY3 -------------------------------------------------- sp|P0C511|RBL_ORYSI -------------------------------------MSPQTETKASVGF 13 sp|P0C421|PSBH_ORYSI -------------------------------------------------- sp|P0C516|YCF3_ORYSA -------------------------------------------------- sp|P0C389|CYF_ORYSJ -------------------------------------------------- tr|Q7VC13|Q7VC13_PROMA -------------------------------------------------- tr|Q7NL78|Q7NL78_GLOVI -------------------------------------------------- tr|Q7U4P2|Q7U4P2_SYNPX -------------------------------------------------- tr|Q9SF54|Q9SF54_ARATH -------------------------------------------------- sp|O98679|NDHK_PEA -------------------------------------------------- tr|Q7UZS7|Q7UZS7_PROMP -------------------------------------------------- sp|P0C359|PSAC_ORYSA -------------------------------------------------- tr|Q7V2Z3|Q7V2Z3_PROMP -------------------------------------------------- tr|Q9SGH4|Q9SGH4_ARATH -------------------------------------------------- sp|Q55013|CY550_SYNY3 -------------------------------------------------- sp|P12180|PETL_ORYSJ -------------------------------------------------- tr|Q7U572|Q7U572_SYNPX -------------------------------------------------- sp|P0C428|PSBT_ORYSI -------------------------------------------------- sp|P74787|PSBT_SYNY3 -------------------------------------------------- sp|P12186|PSAI_ORYSJ -------------------------------------------------- tr|Q7UZX5|Q7UZX5_PROMP -------------------------------------------------- sp|Q6ENI6|PSBM_ORYNI -------------------------------------------------- tr|Q7NCI2|Q7NCI2_GLOVI -------------------------------------------------- tr|Q7V6E4|Q7V6E4_PROMM -------------------------------------------------- tr|Q7V512|Q7V512_PROMM -------------------------------------------------- tr|Q8YRD7|Q8YRD7_ANASP TRFGRDLGLLLAANVAPLVADHNLTEVAQFSQRFYSSTSSVRYMLYADET 75 tr|Q93P10|Q93P10_PROMP -------------------------------------------------- tr|Q949Q5|Q949Q5_ARATH -------------------------------------------------- sp|P0C405|PSBI_ORYSA -------------------------------------------------- sp|P0C515|YCF4_ORYSJ -------------------------------------------------- sp|Q6ENI5|PETN_ORYNI -------------------------------------------------- tr|P73952|P73952_SYNY3 -------------------------------------------------- tr|Q7TU23|Q7TU23_PROMP -------------------------------------------------- sp|P73528|PSBZ_SYNY3 -------------------------------------------------- sp|Q57038|CYB6_SYNY3 -------------------------------------------------- sp|P73676|PSBY_SYNY3 -------------------------------------------------- sp|P27589|PETD_SYNY3 -------------------------------------------------- sp|P0C390|PETG_ORYSA -------------------------------------------------- tr|Q7U8X4|Q7U8X4_SYNPX -------------------------------------------------- sp|P0C415|PSBJ_ORYSI -------------------------------------------------- sp|P74367|PS11_SYNY3 -------------------------------------------------- sp|P0C357|PSAB_ORYSI VEAFTRGGAAGPVNIAYSGVYQWWYTIGLRTNEDLYTGALFLLFLSTLSL 150 sp|P0C374|PSAJ_ORYSI -------------------------------------------------- tr|Q7V658|Q7V658_PROMM -------------------------------------------------- sp|P0C410|PSBK_ORYSJ -------------------------------------------------- tr|Q7V2Y4|Q7V2Y4_PROMP VHLMHTALLAGWAGSMALYELAIFDPSDAVLNPMWRQGMYVMPFMARLGI 71 tr|Q7NCH9|Q7NCH9_GLOVI -------------------------------------------------- sp|Q9LU86|PRXQ_ARATH -------------------------------------------------- sp|P0C400|PSBF_ORYSI -------------------------------------------------- tr|Q7VDW1|Q7VDW1_PROMA -------------------------------------------------- sp|P0C370|PSBE_ORYSJ -------------------------------------------------- tr|Q36688|Q36688_ORYSA -------------------------------------------------- tr|Q2LIK6|Q2LIK6_9ORYZ -------------------------------------------------- sp|Q9S7W1|CB4C_ARATH ----------------------------------MATTTAAAASGIFGIR 16 tr|Q7U9C4|Q7U9C4_SYNPX -------------------------------------------------- sp|P80471|LIPC_SOLTU -------------------------------------MASISSLNQIPCK 13 sp|Q55356|PSB28_SYNY3 -------------------------------------------------- sp|P0C511|RBL_ORYSI KAGVKDYKLTYYTPEYETKDTDILAAFRVTPQPGVPPEEAGAAVAAESST 63 sp|P0C421|PSBH_ORYSI -------------------------------------------------- sp|P0C516|YCF3_ORYSA -------------------------------------------------- sp|P0C389|CYF_ORYSJ -------------------------------------------------- tr|Q7VC13|Q7VC13_PROMA -------------------------------------------------- tr|Q7NL78|Q7NL78_GLOVI -------------------------------------------------- tr|Q7U4P2|Q7U4P2_SYNPX ----------------MPIDSVTAALEALDHQDAGVRYHGAWWLGKNRSA 34 tr|Q9SF54|Q9SF54_ARATH -------------------------------------------------- sp|O98679|NDHK_PEA -------------------------------------------------- tr|Q7UZS7|Q7UZS7_PROMP -------------------------------------------------- sp|P0C359|PSAC_ORYSA -------------------------------------------------- tr|Q7V2Z3|Q7V2Z3_PROMP -------------------------------------------------- tr|Q9SGH4|Q9SGH4_ARATH -------------------------------------------------- sp|Q55013|CY550_SYNY3 -------------------------------------------------- sp|P12180|PETL_ORYSJ -------------------------------------------------- tr|Q7U572|Q7U572_SYNPX ------------------------------------------------MR 2 sp|P0C428|PSBT_ORYSI -------------------------------------------------- sp|P74787|PSBT_SYNY3 -------------------------------------------------- sp|P12186|PSAI_ORYSJ -------------------------------------------------- tr|Q7UZX5|Q7UZX5_PROMP -------------------------------------------------- sp|Q6ENI6|PSBM_ORYNI -------------------------------------------------- tr|Q7NCI2|Q7NCI2_GLOVI -------------------------------------------------- tr|Q7V6E4|Q7V6E4_PROMM -------------------------------------------------- tr|Q7V512|Q7V512_PROMM -------------------------------------------------- tr|Q8YRD7|Q8YRD7_ANASP GKIFFGIPFWEPEVENSLSIERRIQLPEEYPGDGEKPMVRQHMSPDGIVT 125 tr|Q93P10|Q93P10_PROMP ---------------------MTIAVGSAPQRGWFDVLDDWLKRDRFVFI 29 tr|Q949Q5|Q949Q5_ARATH ----------------------------------------------MAAT 4 sp|P0C405|PSBI_ORYSA -------------------------------------------------- sp|P0C515|YCF4_ORYSJ ---------------------------------------MNWRSEHIWIE 11 sp|Q6ENI5|PETN_ORYNI -------------------------------------------------- tr|P73952|P73952_SYNY3 ---------------------------------------------MLKKS 5 tr|Q7TU23|Q7TU23_PROMP -------------------------------------------------- sp|P73528|PSBZ_SYNY3 -------------------------------------------------- sp|Q57038|CYB6_SYNY3 ----------------------------------MFSKEVTESKVFQWFN 16 sp|P73676|PSBY_SYNY3 -------------------------------------------------- sp|P27589|PETD_SYNY3 ------------------------------------------------MS 2 sp|P0C390|PETG_ORYSA -------------------------------------------------- tr|Q7U8X4|Q7U8X4_SYNPX -------------------------------------------------M 1 sp|P0C415|PSBJ_ORYSI -------------------------------------------------- sp|P74367|PS11_SYNY3 ------------------------------------------------MS 2 sp|P0C357|PSAB_ORYSI IGGWLHLQPKWKPSLSWFKNAESRLNHHLSGLFGVSSLAWTGHLVHVAIP 200 sp|P0C374|PSAJ_ORYSI -------------------------------------------------- tr|Q7V658|Q7V658_PROMM -------------------------------------------------- sp|P0C410|PSBK_ORYSJ -------------------------------------------------- tr|Q7V2Y4|Q7V2Y4_PROMP TSSWNGWDITGATGVDPGFWSFEGVAAAHIVFSGLLMLASIWHWTYWDLD 121 tr|Q7NCH9|Q7NCH9_GLOVI -------------------------------------------------- sp|Q9LU86|PRXQ_ARATH -------------------------------------------MAASSSS 7 sp|P0C400|PSBF_ORYSI -------------------------------------------------- tr|Q7VDW1|Q7VDW1_PROMA -------------------------------MRFRPLLALVLAFCLTFIA 19 sp|P0C370|PSBE_ORYSJ -------------------------------------------------- tr|Q36688|Q36688_ORYSA --------------------------------------------MASSAT 6 tr|Q2LIK6|Q2LIK6_9ORYZ -------------------------------------------------- sp|Q9S7W1|CB4C_ARATH IQDPRPGTGRVQARFGFSFGKKKPAPPPKKSRQVQDDGDRLVWFPGANPP 66 tr|Q7U9C4|Q7U9C4_SYNPX -------------------------------------------------- sp|P80471|LIPC_SOLTU TLQITSQYSKPTSKISTLPISSTNFPSKTELHRSISVKEFTNPKPKFTAQ 63 sp|Q55356|PSB28_SYNY3 -------------------------------------------------- sp|P0C511|RBL_ORYSI GTWTTVWTDGLTSLDRYKGRCYHIEPVVGEDNQYIAYVAYPLDLFEEGSV 113 sp|P0C421|PSBH_ORYSI -------------------------------------------------- sp|P0C516|YCF3_ORYSA -----------------------------------------MPRSRINGN 9 sp|P0C389|CYF_ORYSJ --------MENRNTFSWVKEQMTRSISVSIMIYVITRTSISNAYPIFAQQ 42 tr|Q7VC13|Q7VC13_PROMA -------------------------------------------------- tr|Q7NL78|Q7NL78_GLOVI -------------------------------------------------- tr|Q7U4P2|Q7U4P2_SYNPX EGVPRLVECLLDERDKTCTGGYPLRRQAARSLGMIKDSRCLPELLKTLET 84 tr|Q9SF54|Q9SF54_ARATH MASPATFQFSRTKLNLQINLVERKSPSKLSFPLLFRDQAKSTPIRFPVIR 50 sp|O98679|NDHK_PEA --------------MNSIEFPLLDQKTKNSVISTTLNDLSNWSRLSSLWP 36 tr|Q7UZS7|Q7UZS7_PROMP -------------------------------------------------- sp|P0C359|PSAC_ORYSA -------------------------------------------------- tr|Q7V2Z3|Q7V2Z3_PROMP -----------------------------------------------MTV 3 tr|Q9SGH4|Q9SGH4_ARATH -------------------------------MAHFIDLNSLTNTLPSLPK 19 sp|Q55013|CY550_SYNY3 -------------------------------------------------- sp|P12180|PETL_ORYSJ -------------------------------------------------- tr|Q7U572|Q7U572_SYNPX RLFAALLSALLVFGFAPVAKADVAGLTPCSESARFQQRAAAATTPQAKAR 52 sp|P0C428|PSBT_ORYSI -------------------------------------------------- sp|P74787|PSBT_SYNY3 -------------------------------------------------- sp|P12186|PSAI_ORYSJ -------------------------------------------------- tr|Q7UZX5|Q7UZX5_PROMP -------------------------------------------------- sp|Q6ENI6|PSBM_ORYNI -------------------------------------------------- tr|Q7NCI2|Q7NCI2_GLOVI -------------------------------------------------- tr|Q7V6E4|Q7V6E4_PROMM -------------------------------------------------- tr|Q7V512|Q7V512_PROMM --------------MTDENLPLGPKTLNEKYRDRGHVEEWAVQPAADPCV 36 tr|Q8YRD7|Q8YRD7_ANASP DVFIPLIVDKKYLGVLAIGINPNQTAVISTNFTRDVTIAVFITIWVMVIL 175 tr|Q93P10|Q93P10_PROMP GWSGLLLLPCAYLAIGGWFVGTTFVTSWYTHGIASSYLEGANFLTAAVST 79 tr|Q949Q5|Q949Q5_ARATH FATPSTVIGLGGSSITTKPFSSSFLKPTLSAKNPLRLAGASGGRVTCFER 54 sp|P0C405|PSBI_ORYSA -------------------------------------------------- sp|P0C515|YCF4_ORYSJ LLKGSRKRGNFFWACILFLGSLGFLAVGASSYLGKNIISVLPSQQILFFP 61 sp|Q6ENI5|PETN_ORYNI -------------------------------------------------- tr|P73952|P73952_SYNY3 LSTAVVLVTLLLSFTLTACGGVGIASLQRYSDTKDGYEFLYPNGWIGVDV 55 tr|Q7TU23|Q7TU23_PROMP -------------------------------------------------- sp|P73528|PSBZ_SYNY3 -------------------------------------------------- sp|Q57038|CYB6_SYNY3 DRLEVQAISDDIASKYVPPHVNIFYCLGGLTLTCFLIQFATGFAMTFYYK 66 sp|P73676|PSBY_SYNY3 -------------------------------------------------- sp|P27589|PETD_SYNY3 IIKKPDLSDPDLRAKLAKGMGHNYYGEPAWPNDILYMFPICILGALGLIA 52 sp|P0C390|PETG_ORYSA -------------------------------------------------- tr|Q7U8X4|Q7U8X4_SYNPX SIVSNSIINADAEARYLSPGELDQIKAFVTGGQRRLRVAQVLCESRERIV 51 sp|P0C415|PSBJ_ORYSI -------------------------------------------------- sp|P74367|PS11_SYNY3 FLKNQLSRLLALILVVAIGLTACDSGTGLTGNYSQDTLTVIATLREAIDL 52 sp|P0C357|PSAB_ORYSI ASRGEYVRWNNFLDVLPYPQGLGPLLTGQWNLYAQNPDSSNHLFGTTQGA 250 sp|P0C374|PSAJ_ORYSI -------------------------------------------------- tr|Q7V658|Q7V658_PROMM -------------------------------------------------- sp|P0C410|PSBK_ORYSJ -------------------------------------------------- tr|Q7V2Y4|Q7V2Y4_PROMP LWEDERTGEPALDLPRIFGIHLLLSGITCFGFGAFHCANVGIWISDPYGL 171 tr|Q7NCH9|Q7NCH9_GLOVI -------------------------------------------------- sp|Q9LU86|PRXQ_ARATH FTLCNHTTLRTLPLRKTLVTKTQFSVPTKSSESNFFGSTLTHSSYISPVS 57 sp|P0C400|PSBF_ORYSI -------------------------------------------------- tr|Q7VDW1|Q7VDW1_PROMA APSSVSASGERGNSRFADVVNTGKANDCPTVSAGSQGSLSIDGGLTDICM 69 sp|P0C370|PSBE_ORYSJ -------------------------------------------------- tr|Q36688|Q36688_ORYSA TVAPFQGLKSTAGMPVARRSNSSFGNVSNGGRIRCMQVWPIEGIKKFETL 56 tr|Q2LIK6|Q2LIK6_9ORYZ -------------------------------------------------- sp|Q9S7W1|CB4C_ARATH EWLDGSMIGDRGFDPFGLGKPAEYLQYDFDGLDQNLAKNVAGDIIGIIQE 116 tr|Q7U9C4|Q7U9C4_SYNPX -------------------------------------------------- sp|P80471|LIPC_SOLTU ATNYDKEDEWGPEVEQIRPGGVAVVEEEPPKEPSEIELLKKQLADSLYGT 113 sp|Q55356|PSB28_SYNY3 --------------------------------MAEIQFSKGVAETVVPEV 18 sp|P0C511|RBL_ORYSI TNMFTSIVGNVFGFKALRALRLEDLRIPPTYSKTFQGPPHGIQVERDKLN 163 sp|P0C421|PSBH_ORYSI -------------------------------------------------- sp|P0C516|YCF3_ORYSA FIDKTFSIVANILLRIIPTTSGEKRAFTYYRDGMLAQSEGNYAEALQNYY 59 sp|P0C389|CYF_ORYSJ GYENPREATGRIVCANCHLANKPVDIEVPQAVLPDTVFEAVLRIPYDMQL 92 tr|Q7VC13|Q7VC13_PROMA ------------------------------------------------MI 2 tr|Q7NL78|Q7NL78_GLOVI -------------------------------------------------- tr|Q7U4P2|Q7U4P2_SYNPX DDVQLHEATLRALIQIKSDQCSSSLINYLDRDIPNKPIEALIEALTEQRM 134 tr|Q9SF54|Q9SF54_ARATH ASSSSSASNHKPSLLKTTFISLTAAAALFSASFYFVNKRAAMTPVAVVET 100 sp|O98679|NDHK_PEA LLYGTSCCFIEFASLIGSRFDFDRYGLVPRSSPRQADLILTAGTVTMKMA 86 tr|Q7UZS7|Q7UZS7_PROMP --------------------------MTETLVGQFPKHIGSTGGLLNSAE 24 sp|P0C359|PSAC_ORYSA -------------------------------------------------- tr|Q7V2Z3|Q7V2Z3_PROMP SKSNQILSNDRDLENISNKNIEDIKEFINTANSRLDAIDSITNNSHAIAA 53 tr|Q9SGH4|Q9SGH4_ARATH LPESRKTGKSSGFACRRTEEFQEPDSVQITRRMTLGFAVSIGLTGILGEN 69 sp|Q55013|CY550_SYNY3 ---------MKRFFLVAIASVLFFFNTMVGSANAVELTESTRTIPLDEAG 41 sp|P12180|PETL_ORYSJ -----------------------------------MLTITSYFGF----- 10 tr|Q7U572|Q7U572_SYNPX FEMYSQASCGDDGLPHLIVDGRWSHAGDFVYPGIMFLYVAGCIGWAGREY 102 sp|P0C428|PSBT_ORYSI ---------------------------------------MEALVY----- 6 sp|P74787|PSBT_SYNY3 ---------------------------------------MESVAY----- 6 sp|P12186|PSAI_ORYSJ -------------------------------M-MDFN--LPSIFV----- 11 tr|Q7UZX5|Q7UZX5_PROMP -------------------------------MPSDFSTFLPSIFV----- 14 sp|Q6ENI6|PSBM_ORYNI ---------------------------------MEVNI-LAFIAT----- 11 tr|Q7NCI2|Q7NCI2_GLOVI -----------------------------------MN--IALLAI----- 8 tr|Q7V6E4|Q7V6E4_PROMM ---------------------------------MGITD-IANVDLAG--- 13 tr|Q7V512|Q7V512_PROMM GNLATPVNSGYFVKALVNNLPLYREGISANFRGLETGAAIGYFIYGPFLV 86 tr|Q8YRD7|Q8YRD7_ANASP AGVVNALTITKPIKELLVGVKQIAAGNFKQRIDLPLGGELGELILNFNEM 225 tr|Q93P10|Q93P10_PROMP PGDAMGHSLLFLWGPEAQGSFVRWLQLGGLWNFVALHGVFGLIGFMLRQF 129 tr|Q949Q5|Q949Q5_ARATH NWLRRDLNVVGFGLIGWLAPSSIPAINGKSLTGLFFDSIGTELAHFPTPP 104 sp|P0C405|PSBI_ORYSA ----------------------------------MLT--LKLFVY----- 9 sp|P0C515|YCF4_ORYSJ QGVVMSFYGIAGLFISAYLWCTILWNVGSGYDRFDRKEGVVCIFRWG--- 108 sp|Q6ENI5|PETN_ORYNI ---------------------------------------MDIVSL----- 6 tr|P73952|P73952_SYNY3 KGASPGVDVVFRDLIERDENLSVIISEIPSDKTLTDLGTATDVGYR---- 101 tr|Q7TU23|Q7TU23_PROMP -------------------------------MQAVNFFFVNALLFAS--- 16 sp|P73528|PSBZ_SYNY3 ---------------------------------MSIVFQIALAAL----- 12 sp|Q57038|CYB6_SYNY3 PTVTEAFASVQYIMNEVNFGWLIRSIHRWSASMMVLMMILHVFRVYLTGG 116 sp|P73676|PSBY_SYNY3 -------------------------------MDWRVIVVVSPLLIAA--- 16 sp|P27589|PETD_SYNY3 G-LAILDPAMIGEPADPFATPLEILPEWYLYPTFQILRILPNKLLG---- 97 sp|P0C390|PETG_ORYSA ----------------------------------MIEVFLFGIVLG---- 12 tr|Q7U8X4|Q7U8X4_SYNPX KQAGGQLFQKRPDVISPGGNAYGEEMTATCLRDMDYYLRLVTYGIVAG-- 99 sp|P0C415|PSBJ_ORYSI --------------------------------MADTTGRIPLWLIG---- 14 sp|P74367|PS11_SYNY3 PQDAPNRQEVQDTARGQINDYISRYRRKGDAGGLKSFTTMQTALN----- 97 sp|P0C357|PSAB_ORYSI GTAILTLLGGFHPQTQSLWLTDIAHHHLAIAFIFLIAGHMYRTNFGIGHS 300 sp|P0C374|PSAJ_ORYSI ------------------------------MRDIKTYLSVAPVLS----- 15 tr|Q7V658|Q7V658_PROMM -----------------------------------MRKFFESWPMA---- 11 sp|P0C410|PSBK_ORYSJ -------------MPNILSLTCICFNSVIYPTSFFFAKLPEAYAIFN--- 34 tr|Q7V2Y4|Q7V2Y4_PROMP TGHVEQVAPSWGADGFNPFNPGGIVANHIAAGLLGIIGGIFHITNRPGER 221 tr|Q7NCH9|Q7NCH9_GLOVI ---------------------------------MGSSG-ITTITYV---- 12 sp|Q9LU86|PRXQ_ARATH SSSLKGLIFAKVNKGQAAPDFTLKDQNGKPVSLKKYKGKPVVLYFYP--- 104 sp|P0C400|PSBF_ORYSI ---------------------------------MTIDRTYPIFTVR---- 13 tr|Q7VDW1|Q7VDW1_PROMA HPTEVYVKVAKSRRSKAEFVPAKIISPRNNTTVEQVYGDVSGSTFKEQGG 119 sp|P0C370|PSBE_ORYSJ --------------------------MSGSTGERSFADIITSIRYW---- 20 tr|Q36688|Q36688_ORYSA SYLPPLTVEDLLKQIEYLLRSKWVPCLEFSKVGFVYRENHKSPGYYDG-- 104 tr|Q2LIK6|Q2LIK6_9ORYZ --------------------------------MTQSNPNEQNVELN---- 14 sp|Q9S7W1|CB4C_ARATH SSEIKPTPFQPYTEVFGIQRFRECELIHGRWAMLGTLGAIAVEALTGIAW 166 tr|Q7U9C4|Q7U9C4_SYNPX -------------------------------MTPSLSNFLSSLVWG---- 15 sp|P80471|LIPC_SOLTU NRGLSASSETRAEIVELITQLESKNPNPAPTEALTLLNGKWILAYTSFSG 163 sp|Q55356|PSB28_SYNY3 RLSKSKNGQSGMAKFYFLEPTILAKESTDDITGMYLIDDEGEIITR---- 64 sp|P0C511|RBL_ORYSI KYGRPLLGCTIKPKLGLSAKNYGRACYECLRGGLDFTKDDENVNSQPFMR 213 sp|P0C421|PSBH_ORYSI --------MATQTVEDSSRPGPRQTRVGNLLKPLNSEYGKVAPGWG---- 38 sp|P0C516|YCF3_ORYSA EAMRLEIDPYDRSYILYNIGLIHTSNGEHTKALEYYFRALERNPFLP--- 106 sp|P0C389|CYF_ORYSJ KQVLANGKKGGLNVGAVLILPEGFELAPPDRISPELKEKIGNLSFQSYRP 142 tr|Q7VC13|Q7VC13_PROMA TTLLATAAPEFHWSPKCAAIMILCNVLAYAIARANIAQPNEGFEIPNS-- 50 tr|Q7NL78|Q7NL78_GLOVI --------MSRYFKVTACIPSLKRVRTGRELQNTFFTKLVPYENWFTEQ- 41 tr|Q7U4P2|Q7U4P2_SYNPX WDVSEKIQPFLNDKSERIAGSAAAFFYSYTGEMTYLNKVISLLDHQNRFI 184 tr|Q9SF54|Q9SF54_ARATH TLEKHLETQSNDVNALSLLTEIKFKSDKHEQAIVFLDRLIEIEPYERKWP 150 sp|O98679|NDHK_PEA PSLVRLYEQMPEPKYVIAMGACTITGGMFSTDSYSTVRGVDKLIPVDVYL 136 tr|Q7UZS7|Q7UZS7_PROMP TEEKYAISWNSSKEQAFELPTGGAAIMHEGDNLMYFARKEQCLALG---- 70 sp|P0C359|PSAC_ORYSA --------------MSHSVKIYDTCIGCTQCVRACPTDVLEMIPWDG--- 33 tr|Q7V2Z3|Q7V2Z3_PROMP DAVTAMICENQDSVNTKISLDTTNKMSVCLRDGEIILRIVSYLLISDD-- 101 tr|Q9SGH4|Q9SGH4_ARATH NVSLAQDNGFWIDGPLPIPPIYNNIVNEKTGTRTFIKKGVYVADIGTKG- 118 sp|Q55013|CY550_SYNY3 GTTTLTARQFTNGQKIFVDTCTQCHLQGKTKTNNNVSLGLADLAGAE--- 88 sp|P12180|PETL_ORYSJ -----------------------------LLAALTLTLALFIGLNKIRLI 31 tr|Q7U572|Q7U572_SYNPX LKATRGKNAAMNEIQID-----LGIAFKSLLAAATWPLAAFGEFTSGKLL 147 sp|P0C428|PSBT_ORYSI ----------------------------TFLLVSTLGIIFFAIFFREPPK 28 sp|P74787|PSBT_SYNY3 ----------------------------ILVLTMALAVLFFAIAFREPPR 28 sp|P12186|PSAI_ORYSJ -----------------------------PLVGLVFPAIAMASLFLYVQK 32 tr|Q7UZX5|Q7UZX5_PROMP -----------------------------PLIGLVTPAVFLVLIGRLITA 35 sp|Q6ENI6|PSBM_ORYNI -----------------------------ALFILVPTAFLLIIYVKTVSQ 32 tr|Q7NCI2|Q7NCI2_GLOVI -----------------------------ALLVLVCCGFLVIVWVQ--SE 27 tr|Q7V6E4|Q7V6E4_PROMM -----------------------------LCLVVVFHCGVLALRLGVTLH 34 tr|Q7V512|Q7V512_PROMM MG-----------PLRT-----TDFATTAALLATVGAVHILTALLVLYNV 120 tr|Q8YRD7|Q8YRD7_ANASP AERLERYEEQNIEELTA-----EKAKLETLVSTIADGAVLIDNNMQVILV 270 tr|Q93P10|Q93P10_PROMP EIAG------------------LVGIRPYNALAFSAVIAVFTSIFLIYPL 161 tr|Q949Q5|Q949Q5_ARATH ALTS---------------------QFWLWLVTWHLGLFLCLTFGQIGFK 133 sp|P0C405|PSBI_ORYSA -----------------------------TVVIFFVSLFIFGFLSNDPGR 30 sp|P0C515|YCF4_ORYSJ ---------------------------FPGIKRRVFLRFLMRDIQSIRIQ 131 sp|Q6ENI5|PETN_ORYNI ------------------------------AWAALMVVFTFSLSLVVWGR 26 tr|P73952|P73952_SYNY3 ---------------------------FMKTVNDASQGDRQAELINAEAR 124 tr|Q7TU23|Q7TU23_PROMP -----------------------------LIAVVGVPVLYVTQPSTEDGQ 37 sp|P73528|PSBZ_SYNY3 -----------------------------VLFSFVMVVGVPVAYASPQNW 33 sp|Q57038|CYB6_SYNY3 FKKP---------------------RELTWVVGVMLAVTTVTFGVTGYSL 145 sp|P73676|PSBY_SYNY3 -----------------------------TWAAINIGAAAIRQLQDVLGR 37 sp|P27589|PETD_SYNY3 ---------------------------IAGMAAIPLGLMLVPFIESVNKF 120 sp|P0C390|PETG_ORYSA ------------------------------LIPITLAGLFVTAYLQYRRG 32 tr|Q7U8X4|Q7U8X4_SYNPX -----------------------------DVTPIEEIGVIGAKELYRSLG 120 sp|P0C415|PSBJ_ORYSI -----------------------------TVTGIAVIGLIGVFFYGSYSG 35 sp|P74367|PS11_SYNY3 -----------------------------SLAGYYTSYGARPIPEKLKKR 118 sp|P0C357|PSAB_ORYSI IKDLLEAHTPPGGRLGRGHKGLYDTINNSIHFQLGLALASLGVITSLVAQ 350 sp|P0C374|PSAJ_ORYSI -----------------------------TLWFGALAGLLIEINRLFPDA 36 tr|Q7V658|Q7V658_PROMM -----------------------------AVLWVWLTAGIIVEFNRFYPD 32 sp|P0C410|PSBK_ORYSJ -----------------------------PIVDFMPVIPVLFFLLAFVWQ 55 tr|Q7V2Y4|Q7V2Y4_PROMP LYRALKLG---------------------SLEGVLASALAAVLFVSFVVA 250 tr|Q7NCH9|Q7NCH9_GLOVI -----------------------------LILALIILAIFFAVFFPEKKS 33 sp|Q9LU86|PRXQ_ARATH ---------------------------ADETPGCTKQACAFRDSYEKFKK 127 sp|P0C400|PSBF_ORYSI ---------------------------WLAVHGLAVPTVFFLGSISAMQF 36 tr|Q7VDW1|Q7VDW1_PROMA -------------------------IDFQLITVLAPNGEEFPFVFSAKQM 144 sp|P0C370|PSBE_ORYSJ -----------------------------VIHSITIPSLFIAGWLFVSTG 41 tr|Q36688|Q36688_ORYSA ----------------------------RYWTMWKLPMFGCTDATQVLKE 126 tr|Q2LIK6|Q2LIK6_9ORYZ ------------------------------RTSLYWGLLLIFVLAVLFSN 34 sp|Q9S7W1|CB4C_ARATH QDAGKVELVEGSSYLG--------QPLPFSLTTLIWIEVLVVGYIEFQRN 208 tr|Q7U9C4|Q7U9C4_SYNPX -----------------------------GLIVVVPATIGLILISQTDRL 36 sp|P80471|LIPC_SOLTU -----------------------------LFPLLSRGNLPLVRVEEISQT 184 sp|Q55356|PSB28_SYNY3 -----------------------------EVKGKFINGRPTAIEATVILN 85 sp|P0C511|RBL_ORYSI WRDRFVFCAEAIYKSQAETG---------EIKGHYLNATAGTCEEMIKRA 254 sp|P0C421|PSBH_ORYSI -----------------------------TTPFMGVAMALFAVFLSIILE 59 sp|P0C516|YCF3_ORYSA ----------------------------QAFNNMAVICHYRGEQAILQGD 128 sp|P0C389|CYF_ORYSJ NKKNILVIG--------------------PVPGKKYSEIVFPILSPDPAM 172 tr|Q7VC13|Q7VC13_PROMA ----------------------------KFFGGMSHASVVAANCLGHILG 72 tr|Q7NL78|Q7NL78_GLOVI ----------------------------QRIQKAGGKVLSVKLFTGVQGA 63 tr|Q7U4P2|Q7U4P2_SYNPX RQS--------------------AAFDLARIGTIKATDPILTAKIPNNVK 214 tr|Q9SF54|Q9SF54_ARATH AMKAR------------------------ILSYHGKSESAIEAFEEILEK 176 sp|O98679|NDHK_PEA PG--------------------------CPPKPEAVIDAITKLRKKISRE 160 tr|Q7UZS7|Q7UZS7_PROMP ----------------------------TQLRGFKPRIENFKIYRIFPGG 92 sp|P0C359|PSAC_ORYSA -----------------------------CKAKQIASAPRTEDCVGCKRC 54 tr|Q7V2Z3|Q7V2Z3_PROMP ----------------------------ESVLSKNCLKDLKNTYLALGVP 123 tr|Q9SGH4|Q9SGH4_ARATH -----------------------------RMYRVKKNAFDLLAMEDLIGP 139 sp|Q55013|CY550_SYNY3 -----------------------------PRRDNVLALVEFLKNPKSYDG 109 sp|P12180|PETL_ORYSJ -------------------------------------------------- tr|Q7U572|Q7U572_SYNPX EDDNKVTVSPR--------------------------------------- 158 sp|P0C428|PSBT_ORYSI VPTKKVK------------------------------------------- 35 sp|P74787|PSBT_SYNY3 IEK----------------------------------------------- 31 sp|P12186|PSAI_ORYSJ NKIV---------------------------------------------- 36 tr|Q7UZX5|Q7UZX5_PROMP TD------------------------------------------------ 37 sp|Q6ENI6|PSBM_ORYNI ND------------------------------------------------ 34 tr|Q7NCI2|Q7NCI2_GLOVI NK------------------------------------------------ 29 tr|Q7V6E4|Q7V6E4_PROMM EA------------------------------------------------ 36 tr|Q7V512|Q7V512_PROMM PGKAPTVPPPDVTVANPPADLFTRKGWADFTSGFWLGGCAGAAFAWFLCN 170 tr|Q8YRD7|Q8YRD7_ANASP NPTARHIFGWEGADDVVGSNVLHHLPPAVQMEITRPLYEMAAGECDSAEF 320 tr|Q93P10|Q93P10_PROMP GQHSWFFAPSFGVAAIFRYILFIQGFHNITLNPFHMMGVAGILGGALLCA 211 tr|Q949Q5|Q949Q5_ARATH GRTEDYF------------------------------------------- 140 sp|P0C405|PSBI_ORYSA NPGRDE-------------------------------------------- 36 sp|P0C515|YCF4_ORYSJ VKEGLFPRRILYMEIRGQGAIPLTRTDEKFFTPREIEQKAAELAYFLRIP 181 sp|Q6ENI5|PETN_ORYNI SGL----------------------------------------------- 29 tr|P73952|P73952_SYNY3 DEDGQVYYTLEYRVLVGDNVERHDLASVTTNRGKLITFDLSTAEDRWDTV 174 tr|Q7TU23|Q7TU23_PROMP KESRRKIYSIAAVWLVLVFATGIVSALV---------------------- 65 sp|P73528|PSBZ_SYNY3 DRSKPLLYLGSGIWAILVIVVALLNFLVV--------------------- 62 sp|Q57038|CYB6_SYNY3 PWDQVGYWAVKIVSGVPAAIPVVGDQLVTLMRGSESVGQATLTRFYSLHT 195 sp|P73676|PSBY_SYNY3 EA------------------------------------------------ 39 sp|P27589|PETD_SYNY3 QNPFRRPIAMTVFLFGTAAALWLGAGATFPIDKSLTLGLF---------- 160 sp|P0C390|PETG_ORYSA DQLDL--------------------------------------------- 37 tr|Q7U8X4|Q7U8X4_SYNPX TPLEAMAEAVREMKTVAMGLLTGDDAAEAGTYFDYVVGALA--------- 161 sp|P0C415|PSBJ_ORYSI LGSSL--------------------------------------------- 40 sp|P74367|PS11_SYNY3 LQLEFTQAERSIERGV---------------------------------- 134 sp|P0C357|PSAB_ORYSI HMYSLPSYAFIAQDFTTQAALYTHHQYIAGFIMTGAFAHGAIFFIRDYNP 400 sp|P0C374|PSAJ_ORYSI LSFPFFSF------------------------------------------ 44 tr|Q7V658|Q7V658_PROMM LLFHPMGL------------------------------------------ 40 sp|P0C410|PSBK_ORYSJ AAVSFR-------------------------------------------- 61 tr|Q7V2Y4|Q7V2Y4_PROMP GTMWYGSATTPIELFGPTRYQWDSGYFKTEINRRVQTAIDNGATKEEAYA 300 tr|Q7NCH9|Q7NCH9_GLOVI K------------------------------------------------- 34 sp|Q9LU86|PRXQ_ARATH AGAEVIGISGDDSASHKAFASKYKLPYTLLSDEGNKVRKDWGVPGDLFGA 177 sp|P0C400|PSBF_ORYSI IQR----------------------------------------------- 39 tr|Q7VDW1|Q7VDW1_PROMA AVDFKGKSIAPGAEASGTTYTPSYRTGDFLDPKSRAKDTGVEYAQGLVAL 194 sp|P0C370|PSBE_ORYSJ LAYDVFGSPRPNEYFTESRQGIPLITDRFDSLEQLDEFSRSF-------- 83 tr|Q36688|Q36688_ORYSA LEEAKKAYPDAFVRIIGFDNVRQVQLISFIAYKPPGCEESGGN------- 169 tr|Q2LIK6|Q2LIK6_9ORYZ YFFN---------------------------------------------- 38 sp|Q9S7W1|CB4C_ARATH SELDPEKRIYPGGYFDPLGLAADPEKLDTLKLAEIKHSRLAMVAFLIFAL 258 tr|Q7U9C4|Q7U9C4_SYNPX DRKL---------------------------------------------- 40 sp|P80471|LIPC_SOLTU IDSESFTVQNSVVFAGPLATTSISTNAKFEVRSPKRVQIKFEEGIIGTPQ 234 sp|Q55356|PSB28_SYNY3 SQPEWDRFMRFMERYGAENGLGFSKSE----------------------- 112 sp|P0C511|RBL_ORYSI VFARELGVPIVMHDYLTGGFTANTSLAHYCRDNGLLLHIHRAMHAVIDRQ 304 sp|P0C421|PSBH_ORYSI IYNSSVLLDGILMN------------------------------------ 73 sp|P0C516|YCF3_ORYSA SEIAEAWFDQAAEYWKQAIALTPGNYIEAQNWLKITKRFEFE-------- 170 sp|P0C389|CYF_ORYSJ KKDVHFLKYPIYVGGNRGRGQIYPDGSKSNNTVYNATSTGVVRKILRKEK 222 tr|Q7VC13|Q7VC13_PROMA IGSILGLAARGVL------------------------------------- 85 tr|Q7NL78|Q7NL78_GLOVI NTGVGA-------------------------------------------- 69 tr|Q7U4P2|Q7U4P2_SYNPX MFAIKAILNKSLSRSNQADSIPDTDLASIHSSLFKALDSLARDNFSGNLL 264 tr|Q9SF54|Q9SF54_ARATH DPIRVDAYHYLVMEYYNSKPKLTEIEKRINKVIRRCKKEKKTKEILGFRM 226 sp|O98679|NDHK_PEA IDEDPISYQRENRSFTTNHKFDVGRSTHTGNSNQGLFYQPSSISEMTSDT 210 tr|Q7UZS7|Q7UZS7_PROMP DIEFLHPKDGVFSEKVNEGREKVGHNPRRIGENPNPAGLKFTTKETFE-- 140 sp|P0C359|PSAC_ORYSA ESACPTDFLSVRVYLGPETTRSMALSY----------------------- 81 tr|Q7V2Z3|Q7V2Z3_PROMP LKNAIRVFELMRDATISDLKSTVNSMKGEKEFLSDLISNTEFQFERIINL 173 tr|Q9SGH4|Q9SGH4_ARATH DTLNYVKKYLRLKSTFLFYDFDNLISAAASEDKQPLTDLANRLFDNFEKL 189 sp|Q55013|CY550_SYNY3 EDDYSELHPNISRPDIYPEMRNYTEDDIFDVAGYTLIAPKLDERWGGTIY 159 sp|P12180|PETL_ORYSJ -------------------------------------------------- tr|Q7U572|Q7U572_SYNPX -------------------------------------------------- sp|P0C428|PSBT_ORYSI -------------------------------------------------- sp|P74787|PSBT_SYNY3 -------------------------------------------------- sp|P12186|PSAI_ORYSJ -------------------------------------------------- tr|Q7UZX5|Q7UZX5_PROMP -------------------------------------------------- sp|Q6ENI6|PSBM_ORYNI -------------------------------------------------- tr|Q7NCI2|Q7NCI2_GLOVI -------------------------------------------------- tr|Q7V6E4|Q7V6E4_PROMM -------------------------------------------------- tr|Q7V512|Q7V512_PROMM TLHMQPLLNVPMNVWAS--------------------------------- 187 tr|Q8YRD7|Q8YRD7_ANASP RLTLNQPSNRTIRILLTTVLNLQRESIKGIAITVQDITREVELNEAKSQF 370 tr|Q93P10|Q93P10_PROMP IHGATVQNTLYEDTSVYTDGKVQSSTFRAFDPTQEEETYSMITANRFWSQ 261 tr|Q949Q5|Q949Q5_ARATH -------------------------------------------------- sp|P0C405|PSBI_ORYSA -------------------------------------------------- sp|P0C515|YCF4_ORYSJ MEVF---------------------------------------------- 185 sp|Q6ENI5|PETN_ORYNI -------------------------------------------------- tr|P73952|P73952_SYNY3 KSLFDTVASSFHVY------------------------------------ 188 tr|Q7TU23|Q7TU23_PROMP -------------------------------------------------- sp|P73528|PSBZ_SYNY3 -------------------------------------------------- sp|Q57038|CYB6_SYNY3 FVLPWAIAVLLLLHFLMIRKQGISGPL----------------------- 222 sp|P73676|PSBY_SYNY3 -------------------------------------------------- sp|P27589|PETD_SYNY3 -------------------------------------------------- sp|P0C390|PETG_ORYSA -------------------------------------------------- tr|Q7U8X4|Q7U8X4_SYNPX -------------------------------------------------- sp|P0C415|PSBJ_ORYSI -------------------------------------------------- sp|P74367|PS11_SYNY3 -------------------------------------------------- sp|P0C357|PSAB_ORYSI EQNEDNVLARMLDHKEAIISHLSWASLFLGFHTLGLYVHNDVMLAFGTPE 450 sp|P0C374|PSAJ_ORYSI -------------------------------------------------- tr|Q7V658|Q7V658_PROMM -------------------------------------------------- sp|P0C410|PSBK_ORYSJ -------------------------------------------------- tr|Q7V2Y4|Q7V2Y4_PROMP SIPEKLAFYDYVGNSPAKGGLFRVGALVNGDGLPTGWQGHIAFTDKEGND 350 tr|Q7NCH9|Q7NCH9_GLOVI -------------------------------------------------- sp|Q9LU86|PRXQ_ARATH LPGRQTYVLDKNGVVQLIYNNQFQPEKHIDETLKFLKAA----------- 216 sp|P0C400|PSBF_ORYSI -------------------------------------------------- tr|Q7VDW1|Q7VDW1_PROMA GGDDEELAKENIKRDLDGKGVITLAIDSVDSDTAEFAGSFVAIQPSDNDL 244 sp|P0C370|PSBE_ORYSJ -------------------------------------------------- tr|Q36688|Q36688_ORYSA -------------------------------------------------- tr|Q2LIK6|Q2LIK6_9ORYZ -------------------------------------------------- sp|Q9S7W1|CB4C_ARATH QAAFTGKGPVSFLATFNN-------------------------------- 276 tr|Q7U9C4|Q7U9C4_SYNPX -------------------------------------------------- sp|P80471|LIPC_SOLTU LTDSIVLPENVEFLGQKIDLSPFKGLITSVQDTASSVAKSISSQPPIKFP 284 sp|Q55356|PSB28_SYNY3 -------------------------------------------------- sp|P0C511|RBL_ORYSI KNHGMHFRVLAKALRMSGGDHIHAGTVVGKLEGEREMTLGFVDLLRDDFI 354 sp|P0C421|PSBH_ORYSI -------------------------------------------------- sp|P0C516|YCF3_ORYSA -------------------------------------------------- sp|P0C389|CYF_ORYSJ GGYEISIVDASDGRQVIDLIPPGPELLVSEGESIKLDQPLTSNPNVGGFG 272 tr|Q7VC13|Q7VC13_PROMA -------------------------------------------------- tr|Q7NL78|Q7NL78_GLOVI -------------------------------------------------- tr|Q7U4P2|Q7U4P2_SYNPX IEQDNQIPETYPGDGSTESDLLSNAFDNLRSPSLTSRKSGIKQLVRGANR 314 tr|Q9SF54|Q9SF54_ARATH LIAQIRFIEGKSVEAIRICEELVKEDPNDFTIYLFQGVVYTLMNKGEEAA 276 sp|O98679|NDHK_PEA FLKYKKVQYPATNEKVN--------------------------------- 227 tr|Q7UZS7|Q7UZS7_PROMP -------------------------------------------------- sp|P0C359|PSAC_ORYSA -------------------------------------------------- tr|Q7V2Z3|Q7V2Z3_PROMP LR------------------------------------------------ 175 tr|Q9SGH4|Q9SGH4_ARATH EDAAKTKNLAETESCYKDTKFLLQEVMTRMA------------------- 220 sp|Q55013|CY550_SYNY3 F------------------------------------------------- 160 sp|P12180|PETL_ORYSJ -------------------------------------------------- tr|Q7U572|Q7U572_SYNPX -------------------------------------------------- sp|P0C428|PSBT_ORYSI -------------------------------------------------- sp|P74787|PSBT_SYNY3 -------------------------------------------------- sp|P12186|PSAI_ORYSJ -------------------------------------------------- tr|Q7UZX5|Q7UZX5_PROMP -------------------------------------------------- sp|Q6ENI6|PSBM_ORYNI -------------------------------------------------- tr|Q7NCI2|Q7NCI2_GLOVI -------------------------------------------------- tr|Q7V6E4|Q7V6E4_PROMM -------------------------------------------------- tr|Q7V512|Q7V512_PROMM -------------------------------------------------- tr|Q8YRD7|Q8YRD7_ANASP ISNVSHELRTPLFNIKSFIETLHDYGEDLSLEERQEFLQTVNHETDRLTR 420 tr|Q93P10|Q93P10_PROMP IFGIAFSNKRFLHFLMLFVPVMGMWTSSIGIVGLALNLRAYDFVSQEIRA 311 tr|Q949Q5|Q949Q5_ARATH -------------------------------------------------- sp|P0C405|PSBI_ORYSA -------------------------------------------------- sp|P0C515|YCF4_ORYSJ -------------------------------------------------- sp|Q6ENI5|PETN_ORYNI -------------------------------------------------- tr|P73952|P73952_SYNY3 -------------------------------------------------- tr|Q7TU23|Q7TU23_PROMP -------------------------------------------------- sp|P73528|PSBZ_SYNY3 -------------------------------------------------- sp|Q57038|CYB6_SYNY3 -------------------------------------------------- sp|P73676|PSBY_SYNY3 -------------------------------------------------- sp|P27589|PETD_SYNY3 -------------------------------------------------- sp|P0C390|PETG_ORYSA -------------------------------------------------- tr|Q7U8X4|Q7U8X4_SYNPX -------------------------------------------------- sp|P0C415|PSBJ_ORYSI -------------------------------------------------- sp|P74367|PS11_SYNY3 -------------------------------------------------- sp|P0C357|PSAB_ORYSI KQILIEPIFAQWIQSAHGKTTYGFDILLSSTSGPAFNAGRTLWLPGWLNA 500 sp|P0C374|PSAJ_ORYSI -------------------------------------------------- tr|Q7V658|Q7V658_PROMM -------------------------------------------------- sp|P0C410|PSBK_ORYSJ -------------------------------------------------- tr|Q7V2Y4|Q7V2Y4_PROMP LEVRRIPNFFENFPVILEDKEGNVRADIPFRRAEAKYSFEQTGITATIYG 400 tr|Q7NCH9|Q7NCH9_GLOVI -------------------------------------------------- sp|Q9LU86|PRXQ_ARATH -------------------------------------------------- sp|P0C400|PSBF_ORYSI -------------------------------------------------- tr|Q7VDW1|Q7VDW1_PROMA GSKEPVDVKIIGELYGRKA------------------------------- 263 sp|P0C370|PSBE_ORYSJ -------------------------------------------------- tr|Q36688|Q36688_ORYSA -------------------------------------------------- tr|Q2LIK6|Q2LIK6_9ORYZ -------------------------------------------------- sp|Q9S7W1|CB4C_ARATH -------------------------------------------------- tr|Q7U9C4|Q7U9C4_SYNPX -------------------------------------------------- sp|P80471|LIPC_SOLTU ITNNNAQSWLLTTYLDDELRISRGDAGSVFVLIKEGSPLLKP-------- 326 sp|Q55356|PSB28_SYNY3 -------------------------------------------------- sp|P0C511|RBL_ORYSI EKDRARGIFFTQDWVSMPGVIPVASGGIHVWHMPALTEIFGDDSVLQFGG 404 sp|P0C421|PSBH_ORYSI -------------------------------------------------- sp|P0C516|YCF3_ORYSA -------------------------------------------------- sp|P0C389|CYF_ORYSJ QGDAEIVLQDPLRVQGLLFFFASVILAQVFLVLKKKQFEKVQLYEMNF-- 320 tr|Q7VC13|Q7VC13_PROMA -------------------------------------------------- tr|Q7NL78|Q7NL78_GLOVI -------------------------------------------------- tr|Q7U4P2|Q7U4P2_SYNPX FKIDLLDLYFSESDQDITMGLIKAMAELKNPHYANALIDAIGVEIGNHCQ 364 tr|Q9SF54|Q9SF54_ARATH KQFEHVARVIPRNHPSRETAARTTNSNEWRVIVAYDNVYCYLSTFARLSM 326 sp|O98679|NDHK_PEA -------------------------------------------------- tr|Q7UZS7|Q7UZS7_PROMP -------------------------------------------------- sp|P0C359|PSAC_ORYSA -------------------------------------------------- tr|Q7V2Z3|Q7V2Z3_PROMP -------------------------------------------------- tr|Q9SGH4|Q9SGH4_ARATH -------------------------------------------------- sp|Q55013|CY550_SYNY3 -------------------------------------------------- sp|P12180|PETL_ORYSJ -------------------------------------------------- tr|Q7U572|Q7U572_SYNPX -------------------------------------------------- sp|P0C428|PSBT_ORYSI -------------------------------------------------- sp|P74787|PSBT_SYNY3 -------------------------------------------------- sp|P12186|PSAI_ORYSJ -------------------------------------------------- tr|Q7UZX5|Q7UZX5_PROMP -------------------------------------------------- sp|Q6ENI6|PSBM_ORYNI -------------------------------------------------- tr|Q7NCI2|Q7NCI2_GLOVI -------------------------------------------------- tr|Q7V6E4|Q7V6E4_PROMM -------------------------------------------------- tr|Q7V512|Q7V512_PROMM -------------------------------------------------- tr|Q8YRD7|Q8YRD7_ANASP LVNDVLDLSKLESGRSYSFDGVDLAQAIEQTLRTYQLNARDKGIELIQDV 470 tr|Q93P10|Q93P10_PROMP AEDPEFETFYTKNILLNEGMRAWMSSVDQPHENFVFPEEVLPRGNAL--- 358 tr|Q949Q5|Q949Q5_ARATH -------------------------------------------------- sp|P0C405|PSBI_ORYSA -------------------------------------------------- sp|P0C515|YCF4_ORYSJ -------------------------------------------------- sp|Q6ENI5|PETN_ORYNI -------------------------------------------------- tr|P73952|P73952_SYNY3 -------------------------------------------------- tr|Q7TU23|Q7TU23_PROMP -------------------------------------------------- sp|P73528|PSBZ_SYNY3 -------------------------------------------------- sp|Q57038|CYB6_SYNY3 -------------------------------------------------- sp|P73676|PSBY_SYNY3 -------------------------------------------------- sp|P27589|PETD_SYNY3 -------------------------------------------------- sp|P0C390|PETG_ORYSA -------------------------------------------------- tr|Q7U8X4|Q7U8X4_SYNPX -------------------------------------------------- sp|P0C415|PSBJ_ORYSI -------------------------------------------------- sp|P74367|PS11_SYNY3 -------------------------------------------------- sp|P0C357|PSAB_ORYSI VNENSNSLFLTIGPGDFLVHHAIALGLHTTTLILVKGALDARGSKLMPDK 550 sp|P0C374|PSAJ_ORYSI -------------------------------------------------- tr|Q7V658|Q7V658_PROMM -------------------------------------------------- sp|P0C410|PSBK_ORYSJ -------------------------------------------------- tr|Q7V2Y4|Q7V2Y4_PROMP GDLNGQTFTDPAVVKRLARKAQLGEAFKFDRETYKSDGVFRSSPRAWFTY 450 tr|Q7NCH9|Q7NCH9_GLOVI -------------------------------------------------- sp|Q9LU86|PRXQ_ARATH -------------------------------------------------- sp|P0C400|PSBF_ORYSI -------------------------------------------------- tr|Q7VDW1|Q7VDW1_PROMA -------------------------------------------------- sp|P0C370|PSBE_ORYSJ -------------------------------------------------- tr|Q36688|Q36688_ORYSA -------------------------------------------------- tr|Q2LIK6|Q2LIK6_9ORYZ -------------------------------------------------- sp|Q9S7W1|CB4C_ARATH -------------------------------------------------- tr|Q7U9C4|Q7U9C4_SYNPX -------------------------------------------------- sp|P80471|LIPC_SOLTU -------------------------------------------------- sp|Q55356|PSB28_SYNY3 -------------------------------------------------- sp|P0C511|RBL_ORYSI GTLGHPWGNAPGAAANRVALEACVQARNEGRDLAREGNEIIRSACKWSPE 454 sp|P0C421|PSBH_ORYSI -------------------------------------------------- sp|P0C516|YCF3_ORYSA -------------------------------------------------- sp|P0C389|CYF_ORYSJ -------------------------------------------------- tr|Q7VC13|Q7VC13_PROMA -------------------------------------------------- tr|Q7NL78|Q7NL78_GLOVI -------------------------------------------------- tr|Q7U4P2|Q7U4P2_SYNPX GNIRRVAACALGDINWNAKISSQSLHAVFNKLKWTLHSPEDWGLRYSACL 414 tr|Q9SF54|Q9SF54_ARATH ASLFNKFG------------------------------------------ 334 sp|O98679|NDHK_PEA -------------------------------------------------- tr|Q7UZS7|Q7UZS7_PROMP -------------------------------------------------- sp|P0C359|PSAC_ORYSA -------------------------------------------------- tr|Q7V2Z3|Q7V2Z3_PROMP -------------------------------------------------- tr|Q9SGH4|Q9SGH4_ARATH -------------------------------------------------- sp|Q55013|CY550_SYNY3 -------------------------------------------------- sp|P12180|PETL_ORYSJ -------------------------------------------------- tr|Q7U572|Q7U572_SYNPX -------------------------------------------------- sp|P0C428|PSBT_ORYSI -------------------------------------------------- sp|P74787|PSBT_SYNY3 -------------------------------------------------- sp|P12186|PSAI_ORYSJ -------------------------------------------------- tr|Q7UZX5|Q7UZX5_PROMP -------------------------------------------------- sp|Q6ENI6|PSBM_ORYNI -------------------------------------------------- tr|Q7NCI2|Q7NCI2_GLOVI -------------------------------------------------- tr|Q7V6E4|Q7V6E4_PROMM -------------------------------------------------- tr|Q7V512|Q7V512_PROMM -------------------------------------------------- tr|Q8YRD7|Q8YRD7_ANASP APGLPLVLGNYDLLLQVLANLVGNALKFTSSGGKIAIRTYVLNTKSNSPN 520 tr|Q93P10|Q93P10_PROMP -------------------------------------------------- tr|Q949Q5|Q949Q5_ARATH -------------------------------------------------- sp|P0C405|PSBI_ORYSA -------------------------------------------------- sp|P0C515|YCF4_ORYSJ -------------------------------------------------- sp|Q6ENI5|PETN_ORYNI -------------------------------------------------- tr|P73952|P73952_SYNY3 -------------------------------------------------- tr|Q7TU23|Q7TU23_PROMP -------------------------------------------------- sp|P73528|PSBZ_SYNY3 -------------------------------------------------- sp|Q57038|CYB6_SYNY3 -------------------------------------------------- sp|P73676|PSBY_SYNY3 -------------------------------------------------- sp|P27589|PETD_SYNY3 -------------------------------------------------- sp|P0C390|PETG_ORYSA -------------------------------------------------- tr|Q7U8X4|Q7U8X4_SYNPX -------------------------------------------------- sp|P0C415|PSBJ_ORYSI -------------------------------------------------- sp|P74367|PS11_SYNY3 -------------------------------------------------- sp|P0C357|PSAB_ORYSI KDFGYSFPCDGPGRGGTCDISAWDAFYLAVFWMLNTIGWVTFYWHWKHIT 600 sp|P0C374|PSAJ_ORYSI -------------------------------------------------- tr|Q7V658|Q7V658_PROMM -------------------------------------------------- sp|P0C410|PSBK_ORYSJ -------------------------------------------------- tr|Q7V2Y4|Q7V2Y4_PROMP AHLCFGLLFLFGHWWHASRTLYKDSFAGIDSEIGDQVEFGLFKKLGDETT 500 tr|Q7NCH9|Q7NCH9_GLOVI -------------------------------------------------- sp|Q9LU86|PRXQ_ARATH -------------------------------------------------- sp|P0C400|PSBF_ORYSI -------------------------------------------------- tr|Q7VDW1|Q7VDW1_PROMA -------------------------------------------------- sp|P0C370|PSBE_ORYSJ -------------------------------------------------- tr|Q36688|Q36688_ORYSA -------------------------------------------------- tr|Q2LIK6|Q2LIK6_9ORYZ -------------------------------------------------- sp|Q9S7W1|CB4C_ARATH -------------------------------------------------- tr|Q7U9C4|Q7U9C4_SYNPX -------------------------------------------------- sp|P80471|LIPC_SOLTU -------------------------------------------------- sp|Q55356|PSB28_SYNY3 -------------------------------------------------- sp|P0C511|RBL_ORYSI LAAACEIWKAIKFEFEPVDKLDS--------------------------- 477 sp|P0C421|PSBH_ORYSI -------------------------------------------------- sp|P0C516|YCF3_ORYSA -------------------------------------------------- sp|P0C389|CYF_ORYSJ -------------------------------------------------- tr|Q7VC13|Q7VC13_PROMA -------------------------------------------------- tr|Q7NL78|Q7NL78_GLOVI -------------------------------------------------- tr|Q7U4P2|Q7U4P2_SYNPX ALEGIGNADSIKLLNEAKAKETDPVLSARLDKAILKSKNKTSIHHIENKK 464 tr|Q9SF54|Q9SF54_ARATH -------------------------------------------------- sp|O98679|NDHK_PEA -------------------------------------------------- tr|Q7UZS7|Q7UZS7_PROMP -------------------------------------------------- sp|P0C359|PSAC_ORYSA -------------------------------------------------- tr|Q7V2Z3|Q7V2Z3_PROMP -------------------------------------------------- tr|Q9SGH4|Q9SGH4_ARATH -------------------------------------------------- sp|Q55013|CY550_SYNY3 -------------------------------------------------- sp|P12180|PETL_ORYSJ -------------------------------------------------- tr|Q7U572|Q7U572_SYNPX -------------------------------------------------- sp|P0C428|PSBT_ORYSI -------------------------------------------------- sp|P74787|PSBT_SYNY3 -------------------------------------------------- sp|P12186|PSAI_ORYSJ -------------------------------------------------- tr|Q7UZX5|Q7UZX5_PROMP -------------------------------------------------- sp|Q6ENI6|PSBM_ORYNI -------------------------------------------------- tr|Q7NCI2|Q7NCI2_GLOVI -------------------------------------------------- tr|Q7V6E4|Q7V6E4_PROMM -------------------------------------------------- tr|Q7V512|Q7V512_PROMM -------------------------------------------------- tr|Q8YRD7|Q8YRD7_ANASP QPAQVRIEVSDTGIGIAQEDQQAIFDRFFRVENRVHTLEGTGLGLSIVRN 570 tr|Q93P10|Q93P10_PROMP -------------------------------------------------- tr|Q949Q5|Q949Q5_ARATH -------------------------------------------------- sp|P0C405|PSBI_ORYSA -------------------------------------------------- sp|P0C515|YCF4_ORYSJ -------------------------------------------------- sp|Q6ENI5|PETN_ORYNI -------------------------------------------------- tr|P73952|P73952_SYNY3 -------------------------------------------------- tr|Q7TU23|Q7TU23_PROMP -------------------------------------------------- sp|P73528|PSBZ_SYNY3 -------------------------------------------------- sp|Q57038|CYB6_SYNY3 -------------------------------------------------- sp|P73676|PSBY_SYNY3 -------------------------------------------------- sp|P27589|PETD_SYNY3 -------------------------------------------------- sp|P0C390|PETG_ORYSA -------------------------------------------------- tr|Q7U8X4|Q7U8X4_SYNPX -------------------------------------------------- sp|P0C415|PSBJ_ORYSI -------------------------------------------------- sp|P74367|PS11_SYNY3 -------------------------------------------------- sp|P0C357|PSAB_ORYSI LWQGNVSQFNESSTYLMGWLRDYLWLNSSQLINGYNPFGMNSLSVWAWMF 650 sp|P0C374|PSAJ_ORYSI -------------------------------------------------- tr|Q7V658|Q7V658_PROMM -------------------------------------------------- sp|P0C410|PSBK_ORYSJ -------------------------------------------------- tr|Q7V2Y4|Q7V2Y4_PROMP RRIPGRV------------------------------------------- 507 tr|Q7NCH9|Q7NCH9_GLOVI -------------------------------------------------- sp|Q9LU86|PRXQ_ARATH -------------------------------------------------- sp|P0C400|PSBF_ORYSI -------------------------------------------------- tr|Q7VDW1|Q7VDW1_PROMA -------------------------------------------------- sp|P0C370|PSBE_ORYSJ -------------------------------------------------- tr|Q36688|Q36688_ORYSA -------------------------------------------------- tr|Q2LIK6|Q2LIK6_9ORYZ -------------------------------------------------- sp|Q9S7W1|CB4C_ARATH -------------------------------------------------- tr|Q7U9C4|Q7U9C4_SYNPX -------------------------------------------------- sp|P80471|LIPC_SOLTU -------------------------------------------------- sp|Q55356|PSB28_SYNY3 -------------------------------------------------- sp|P0C511|RBL_ORYSI -------------------------------------------------- sp|P0C421|PSBH_ORYSI -------------------------------------------------- sp|P0C516|YCF3_ORYSA -------------------------------------------------- sp|P0C389|CYF_ORYSJ -------------------------------------------------- tr|Q7VC13|Q7VC13_PROMA -------------------------------------------------- tr|Q7NL78|Q7NL78_GLOVI -------------------------------------------------- tr|Q7U4P2|Q7U4P2_SYNPX VL------------------------------------------------ 466 tr|Q9SF54|Q9SF54_ARATH -------------------------------------------------- sp|O98679|NDHK_PEA -------------------------------------------------- tr|Q7UZS7|Q7UZS7_PROMP -------------------------------------------------- sp|P0C359|PSAC_ORYSA -------------------------------------------------- tr|Q7V2Z3|Q7V2Z3_PROMP -------------------------------------------------- tr|Q9SGH4|Q9SGH4_ARATH -------------------------------------------------- sp|Q55013|CY550_SYNY3 -------------------------------------------------- sp|P12180|PETL_ORYSJ -------------------------------------------------- tr|Q7U572|Q7U572_SYNPX -------------------------------------------------- sp|P0C428|PSBT_ORYSI -------------------------------------------------- sp|P74787|PSBT_SYNY3 -------------------------------------------------- sp|P12186|PSAI_ORYSJ -------------------------------------------------- tr|Q7UZX5|Q7UZX5_PROMP -------------------------------------------------- sp|Q6ENI6|PSBM_ORYNI -------------------------------------------------- tr|Q7NCI2|Q7NCI2_GLOVI -------------------------------------------------- tr|Q7V6E4|Q7V6E4_PROMM -------------------------------------------------- tr|Q7V512|Q7V512_PROMM -------------------------------------------------- tr|Q8YRD7|Q8YRD7_ANASP IVERHRSRVNLVSEVGVGTTFWFDLILFEDEAPKKMVESGEEKAAMPTS- 619 tr|Q93P10|Q93P10_PROMP -------------------------------------------------- tr|Q949Q5|Q949Q5_ARATH -------------------------------------------------- sp|P0C405|PSBI_ORYSA -------------------------------------------------- sp|P0C515|YCF4_ORYSJ -------------------------------------------------- sp|Q6ENI5|PETN_ORYNI -------------------------------------------------- tr|P73952|P73952_SYNY3 -------------------------------------------------- tr|Q7TU23|Q7TU23_PROMP -------------------------------------------------- sp|P73528|PSBZ_SYNY3 -------------------------------------------------- sp|Q57038|CYB6_SYNY3 -------------------------------------------------- sp|P73676|PSBY_SYNY3 -------------------------------------------------- sp|P27589|PETD_SYNY3 -------------------------------------------------- sp|P0C390|PETG_ORYSA -------------------------------------------------- tr|Q7U8X4|Q7U8X4_SYNPX -------------------------------------------------- sp|P0C415|PSBJ_ORYSI -------------------------------------------------- sp|P74367|PS11_SYNY3 -------------------------------------------------- sp|P0C357|PSAB_ORYSI LFGHLVWATGFMFLISWRGYWQELIETLAWAHERTPLANLIRWRDKPVAL 700 sp|P0C374|PSAJ_ORYSI -------------------------------------------------- tr|Q7V658|Q7V658_PROMM -------------------------------------------------- sp|P0C410|PSBK_ORYSJ -------------------------------------------------- tr|Q7V2Y4|Q7V2Y4_PROMP -------------------------------------------------- tr|Q7NCH9|Q7NCH9_GLOVI -------------------------------------------------- sp|Q9LU86|PRXQ_ARATH -------------------------------------------------- sp|P0C400|PSBF_ORYSI -------------------------------------------------- tr|Q7VDW1|Q7VDW1_PROMA -------------------------------------------------- sp|P0C370|PSBE_ORYSJ -------------------------------------------------- tr|Q36688|Q36688_ORYSA -------------------------------------------------- tr|Q2LIK6|Q2LIK6_9ORYZ -------------------------------------------------- sp|Q9S7W1|CB4C_ARATH -------------------------------------------------- tr|Q7U9C4|Q7U9C4_SYNPX -------------------------------------------------- sp|P80471|LIPC_SOLTU -------------------------------------------------- sp|Q55356|PSB28_SYNY3 -------------------------------------------------- sp|P0C511|RBL_ORYSI -------------------------------------------------- sp|P0C421|PSBH_ORYSI -------------------------------------------------- sp|P0C516|YCF3_ORYSA -------------------------------------------------- sp|P0C389|CYF_ORYSJ -------------------------------------------------- tr|Q7VC13|Q7VC13_PROMA -------------------------------------------------- tr|Q7NL78|Q7NL78_GLOVI -------------------------------------------------- tr|Q7U4P2|Q7U4P2_SYNPX -------------------------------------------------- tr|Q9SF54|Q9SF54_ARATH -------------------------------------------------- sp|O98679|NDHK_PEA -------------------------------------------------- tr|Q7UZS7|Q7UZS7_PROMP -------------------------------------------------- sp|P0C359|PSAC_ORYSA -------------------------------------------------- tr|Q7V2Z3|Q7V2Z3_PROMP -------------------------------------------------- tr|Q9SGH4|Q9SGH4_ARATH -------------------------------------------------- sp|Q55013|CY550_SYNY3 -------------------------------------------------- sp|P12180|PETL_ORYSJ ---------------------------------- tr|Q7U572|Q7U572_SYNPX ---------------------------------- sp|P0C428|PSBT_ORYSI ---------------------------------- sp|P74787|PSBT_SYNY3 ---------------------------------- sp|P12186|PSAI_ORYSJ ---------------------------------- tr|Q7UZX5|Q7UZX5_PROMP ---------------------------------- sp|Q6ENI6|PSBM_ORYNI ---------------------------------- tr|Q7NCI2|Q7NCI2_GLOVI ---------------------------------- tr|Q7V6E4|Q7V6E4_PROMM ---------------------------------- tr|Q7V512|Q7V512_PROMM ---------------------------------- tr|Q8YRD7|Q8YRD7_ANASP ---------------------------------- tr|Q93P10|Q93P10_PROMP ---------------------------------- tr|Q949Q5|Q949Q5_ARATH ---------------------------------- sp|P0C405|PSBI_ORYSA ---------------------------------- sp|P0C515|YCF4_ORYSJ ---------------------------------- sp|Q6ENI5|PETN_ORYNI ---------------------------------- tr|P73952|P73952_SYNY3 ---------------------------------- tr|Q7TU23|Q7TU23_PROMP ---------------------------------- sp|P73528|PSBZ_SYNY3 ---------------------------------- sp|Q57038|CYB6_SYNY3 ---------------------------------- sp|P73676|PSBY_SYNY3 ---------------------------------- sp|P27589|PETD_SYNY3 ---------------------------------- sp|P0C390|PETG_ORYSA ---------------------------------- tr|Q7U8X4|Q7U8X4_SYNPX ---------------------------------- sp|P0C415|PSBJ_ORYSI ---------------------------------- sp|P74367|PS11_SYNY3 ---------------------------------- sp|P0C357|PSAB_ORYSI SIVQARLVGLAHFSVGYIFTYAAFLIASTSGKFG 734 sp|P0C374|PSAJ_ORYSI ---------------------------------- tr|Q7V658|Q7V658_PROMM ---------------------------------- sp|P0C410|PSBK_ORYSJ ---------------------------------- tr|Q7V2Y4|Q7V2Y4_PROMP ---------------------------------- tr|Q7NCH9|Q7NCH9_GLOVI ---------------------------------- sp|Q9LU86|PRXQ_ARATH ---------------------------------- sp|P0C400|PSBF_ORYSI ---------------------------------- tr|Q7VDW1|Q7VDW1_PROMA ---------------------------------- sp|P0C370|PSBE_ORYSJ ---------------------------------- tr|Q36688|Q36688_ORYSA ---------------------------------- tr|Q2LIK6|Q2LIK6_9ORYZ ---------------------------------- sp|Q9S7W1|CB4C_ARATH ---------------------------------- tr|Q7U9C4|Q7U9C4_SYNPX ---------------------------------- sp|P80471|LIPC_SOLTU ---------------------------------- sp|Q55356|PSB28_SYNY3 ---------------------------------- sp|P0C511|RBL_ORYSI ---------------------------------- sp|P0C421|PSBH_ORYSI ---------------------------------- sp|P0C516|YCF3_ORYSA ---------------------------------- sp|P0C389|CYF_ORYSJ ---------------------------------- tr|Q7VC13|Q7VC13_PROMA ---------------------------------- tr|Q7NL78|Q7NL78_GLOVI ---------------------------------- tr|Q7U4P2|Q7U4P2_SYNPX ---------------------------------- tr|Q9SF54|Q9SF54_ARATH ---------------------------------- sp|O98679|NDHK_PEA ---------------------------------- tr|Q7UZS7|Q7UZS7_PROMP ---------------------------------- sp|P0C359|PSAC_ORYSA ---------------------------------- tr|Q7V2Z3|Q7V2Z3_PROMP ---------------------------------- tr|Q9SGH4|Q9SGH4_ARATH ---------------------------------- sp|Q55013|CY550_SYNY3 ---------------------------------- weblogo-3.8.0/tests/data/cox2.gcg000066400000000000000000000031751467613320200166020ustar00rootroot00000000000000cox2_leita 421 bp cox2_leita Length: 176 (today) Check: 4015 .. 1 MAFILSFWMI FLLDSVIVLL SFVCFVCVWI CALLFSTVLL VSKLNNIYCT 51 WDFTASKFID VYWFTIGGMF SLGLLLRLCL LLYFGHLNFV SFDLCKVVGF 101 QWYWVYFIFG ETTIFSNLIL ESDYMIGDLR LLQCNHVLTL LSLVIYKLWL 151 SAVDVIHSFA ISSLGVKVEN LVAVMK cox2_crifa 421 bp cox2_crifa Length: 210 (today) Check: 195 .. 1 MAFILSFWMI FLIDAVIVLL SFVCFVCIWI CSLFFSSFLL VSKINNVYCT 51 WDFTASKFID AYWFTIGGMF VLCLLLRLCL LLYFGCLNFV SFDLCKVVGF 101 QWYWVYFIFG ETTIFSNLIL ESDYLIGDLR LLQCNHVLTL LSLVIYKLWL 151 SAVDVIHSFA VSSLGIKVDC IPGRCNEIVL FSSNNSTVYG QCSELCGVLH 201 GFMPIVICFI cox2_bsalt.pep 421 bp cox2_bsalt.pep Length: 210 (today) Check: 3916 .. 1 MSFIISFWML FLIDSLIVLL SGAIFVCIWI CSLFFLCILF ICKLDYIFCS 51 WDFISAKFID LYWFTLGCLF IVCLLIRLCL LLYFSCLNFV CFDLCKCIGF 101 QWYWVYFIFG ETTIFSNLIL ESDYLIGDLR LLQCNHVLTL LSLVIYKVWL 151 SAIDVIHSFT LANLGIKVD? ?PGRCNEIII FSNSSSTIYG QCSELCGVLH 201 GFMPIVVSFV cox2_trybb 421 bp cox2_trybb Length: 209 (today) Check: 8937 .. 1 MSFILTFWMI FLMDSIIVLI SFSIFLSVWI CALIIATVLT VTKINNIYCT 51 WDFISSKFID TYWFVLGMMF ILCLLLRLCL LLYFSCINFV SFDLCKVIGF 101 QWYWVYFLFG ETTIFSNLIL ESDYLIGDLR ILQCNHVLTL LSLVIYKLWV 151 SAVDVIHSFT ISSLGIKVEN PGRCNEIILF ATNNATLYGQ CSELCGVLHG 201 FMPIVINFI cox2_tborr 421 bp cox2_tborr Length: 210 (today) Check: 8444 .. 1 MLFFINQLLL LLVDTFVILE IFSLFVCVFI IVMYILFINY NIFLKNINVY 51 LDFIGSKYLD LYWFLIGIFF VIVLLIRLCL LLYYSWISLL IFDLCKIMGF 101 QWYWIFFVFK ENVIFSNLLI ESDYWIGDLR LLQCNNTFNL ICLVVYKIWV 151 TSIDVIHSFT ISTLGIKIDC IPGRCNELTI FSNIGGTFYG QCSELCGVLH 201 GFMPVVIEFIweblogo-3.8.0/tests/data/cox2.msf000066400000000000000000000031661467613320200166270ustar00rootroot00000000000000 mini.msf MSF: 166 Type: N January 01, 1776 12:00 Check: 8077 .. Name: cox2_leita Len: 166 Check: 2103 Weight: 1.00 Name: cox2_crifa Len: 166 Check: 1179 Weight: 1.00 Name: cox2_trybb Len: 166 Check: 999 Weight: 1.00 Name: Cox2_bsalt Len: 166 Check: 2740 Weight: 1.00 Name: cox2_tborr Len: 166 Check: 1056 Weight: 1.00 // cox2_leita MAFILSFWMI FLLDSVIVL? ???LSFVCFV CVWICALLFS TVLLVSKLN? cox2_crifa MAFILSFWMI FLIDAVIVL? ???LSFVCFV CIWICSLFFS SFLLVSKIN? cox2_trybb MSFILTFWMI FLMDSIIVL? ???ISFSIFL SVWICALIIA TVLTVTKIN? Cox2_bsalt MSFIISF?ML FLIDSLIVL? ???LSGAIFV CIWICSLFFL CILFICKLD? cox2_tborr MLFFINQLLL LLVDTFVIL? ???EIFSLFV CVFIIVMYIL FINYNIFLK? cox2_leita ?NIYCTWDFT ASKFIDVYWF TIGGMFSLGL ?LLRLCLLLY FGHLN????? cox2_crifa ?NVYCTWDFT ASKFIDAYWF TIGGMFVLCL ?LLRLCLLLY FGCLN????? cox2_trybb ?NIYCTWDFI SSKFIDTYWF VLGMMFILCL ?LLRLCLLLY FSCIN????? Cox2_bsalt ?YIFCS?DFI SAKFIDLY?F TLGCLFIVCL ?LIRLCLLLY FSCLN????? cox2_tborr ?NINVYLDFI GSKYLDLYWF LIGIFFVIVL ?LIRLCLLLY YSWIS????? cox2_leita ???FVSFDLC KVVGFQWYWV YFIFG????? ??ETTIFSNL ILESDYMIGD cox2_crifa ???FVSFDLC KVVGFQWYWV YFIFG????? ??ETTIFSNL ILESDYLIGD cox2_trybb ???FVSFDLC KVIGFQWYWV YFLFG????? ??ETTIFSNL ILESDYLIGD Cox2_bsalt ???FVCFDLC KCIGFQ?Y?V YFIFG????? ??ETTIFSNL ILESDYLIGD cox2_tborr ???LLIFDLC KIMGFQWYWI FFVFK????? ??ENVIFSNL LIESDYWIGD cox2_leita LR???????? ?????? cox2_crifa LR???????? ?????? cox2_trybb LR???????? ?????? Cox2_bsalt LR???????? ?????? cox2_tborr LR???????? ?????? weblogo-3.8.0/tests/data/cox2.nbrf000066400000000000000000000027431467613320200167710ustar00rootroot00000000000000>P1;cox2_leita cox2_leita 176 bp, 176 bases, DE32618C checksum. MAFILSFWMI FLLDSVIVLL SFVCFVCVWI CALLFSTVLL VSKLNNIYCT WDFTASKFID VYWFTIGGMF SLGLLLRLCL LLYFGHLNFV SFDLCKVVGF QWYWVYFIFG ETTIFSNLIL ESDYMIGDLR LLQCNHVLTL LSLVIYKLWL SAVDVIHSFA ISSLGVKVEN LVAVMK* >P1;cox2_crifa cox2_crifa 210 bp, 210 bases, 95726DC8 checksum. MAFILSFWMI FLIDAVIVLL SFVCFVCIWI CSLFFSSFLL VSKINNVYCT WDFTASKFID AYWFTIGGMF VLCLLLRLCL LLYFGCLNFV SFDLCKVVGF QWYWVYFIFG ETTIFSNLIL ESDYLIGDLR LLQCNHVLTL LSLVIYKLWL SAVDVIHSFA VSSLGIKVDC IPGRCNEIVL FSSNNSTVYG QCSELCGVLH GFMPIVICFI* >P1;cox2_bsalt.pep cox2_bsalt.pep 210 bp, 210 bases, 2CFBBFE6 checksum. MSFIISFWML FLIDSLIVLL SGAIFVCIWI CSLFFLCILF ICKLDYIFCS WDFISAKFID LYWFTLGCLF IVCLLIRLCL LLYFSCLNFV CFDLCKCIGF QWYWVYFIFG ETTIFSNLIL ESDYLIGDLR LLQCNHVLTL LSLVIYKVWL SAIDVIHSFT LANLGIKVD? ?PGRCNEIII FSNSSSTIYG QCSELCGVLH GFMPIVVSFV* >P1;cox2_trybb cox2_trybb 209 bp, 209 bases, 7A522BE5 checksum. MSFILTFWMI FLMDSIIVLI SFSIFLSVWI CALIIATVLT VTKINNIYCT WDFISSKFID TYWFVLGMMF ILCLLLRLCL LLYFSCINFV SFDLCKVIGF QWYWVYFLFG ETTIFSNLIL ESDYLIGDLR ILQCNHVLTL LSLVIYKLWV SAVDVIHSFT ISSLGIKVEN PGRCNEIILF ATNNATLYGQ CSELCGVLHG FMPIVINFI* >P1;cox2_tborr cox2_tborr 210 bp, 210 bases, 4F4581DF checksum. MLFFINQLLL LLVDTFVILE IFSLFVCVFI IVMYILFINY NIFLKNINVY LDFIGSKYLD LYWFLIGIFF VIVLLIRLCL LLYYSWISLL IFDLCKIMGF QWYWIFFVFK ENVIFSNLLI ESDYWIGDLR LLQCNNTFNL ICLVVYKIWV TSIDVIHSFT ISTLGIKIDC IPGRCNELTI FSNIGGTFYG QCSELCGVLH GFMPVVIEFI*weblogo-3.8.0/tests/data/cox2.phylip000066400000000000000000000023271467613320200173450ustar00rootroot00000000000000 5 176 cox2_leita MAFILSFWMI FLLDSVIVLL SFVCFVCVWI CALLFSTVLL VSKLNNIYCT cox2_crifa MAFILSFWMI FLIDAVIVLL SFVCFVCIWI CSLFFSSFLL VSKINNVYCT cox2_bsalt MSFIISFWML FLIDSLIVLL SGAIFVCIWI CSLFFLCILF ICKLDYIFCS cox2_trybb MSFILTFWMI FLMDSIIVLI SFSIFLSVWI CALIIATVLT VTKINNIYCT cox2_tborr MLFFINQLLL LLVDTFVILE IFSLFVCVFI IVMYILFINY NIFLKNINVY WDFTASKFID VYWFTIGGMF SLGLLLRLCL LLYFGHLNFV SFDLCKVVGF WDFTASKFID AYWFTIGGMF VLCLLLRLCL LLYFGCLNFV SFDLCKVVGF WDFISAKFID LYWFTLGCLF IVCLLIRLCL LLYFSCLNFV CFDLCKCIGF WDFISSKFID TYWFVLGMMF ILCLLLRLCL LLYFSCINFV SFDLCKVIGF LDFIGSKYLD LYWFLIGIFF VIVLLIRLCL LLYYSWISLL IFDLCKIMGF QWYWVYFIFG ETTIFSNLIL ESDYMIGDLR LLQCNHVLTL LSLVIYKLWL QWYWVYFIFG ETTIFSNLIL ESDYLIGDLR LLQCNHVLTL LSLVIYKLWL QWYWVYFIFG ETTIFSNLIL ESDYLIGDLR LLQCNHVLTL LSLVIYKVWL QWYWVYFLFG ETTIFSNLIL ESDYLIGDLR ILQCNHVLTL LSLVIYKLWV QWYWIFFVFK ENVIFSNLLI ESDYWIGDLR LLQCNNTFNL ICLVVYKIWV SAVDVIHSFA ISSLGVKVEN LVAVMK SAVDVIHSFA VSSLGIKVDC IPGRCN SAIDVIHSFT LANLGIKVD? ?PGRCN SAVDVIHSFT ISSLGIKVEN PGRCNE TSIDVIHSFT ISTLGIKIDC IPGRCNweblogo-3.8.0/tests/data/cox2b.phylip000066400000000000000000000022401467613320200175010ustar00rootroot00000000000000 5 166 cox2_leita MAFILSFWMI FLLDSVIVL? ???LSFVCFV CVWICALLFS TVLLVSKLN? cox2_crifa MAFILSFWMI FLIDAVIVL? ???LSFVCFV CIWICSLFFS SFLLVSKIN? cox2_trybb MSFILTFWMI FLMDSIIVL? ???ISFSIFL SVWICALIIA TVLTVTKIN? Cox2_bsalt MSFIISFWML FLIDSLIVL? ???LSGAIFV CIWICSLFFL CILFICKLD? cox2_tborr MLFFINQLLL LLVDTFVIL? ???EIFSLFV CVFIIVMYIL FINYNIFLK? ?NIYCTWDFT ASKFIDVYWF TIGGMFSLGL ?LLRLCLLLY FGHLN????? ?NVYCTWDFT ASKFIDAYWF TIGGMFVLCL ?LLRLCLLLY FGCLN????? ?NIYCTWDFI SSKFIDTYWF VLGMMFILCL ?LLRLCLLLY FSCIN????? ?YIFCSWDFI SAKFIDLYWF TLGCLFIVCL ?LIRLCLLLY FSCLN????? ?NINVYLDFI GSKYLDLYWF LIGIFFVIVL ?LIRLCLLLY YSWIS????? ???FVSFDLC KVVGFQWYWV YFIFG????? ??ETTIFSNL ILESDYMIGD ???FVSFDLC KVVGFQWYWV YFIFG????? ??ETTIFSNL ILESDYLIGD ???FVSFDLC KVIGFQWYWV YFLFG????? ??ETTIFSNL ILESDYLIGD ???FVCFDLC KCIGFQWYWV YFIFG????? ??ETTIFSNL ILESDYLIGD ???LLIFDLC KIMGFQWYWI FFVFK????? ??ENVIFSNL LIESDYWIGD LR???????? ?????? LR???????? ?????? LR???????? ?????? LR???????? ?????? LR???????? ??????weblogo-3.8.0/tests/data/crab.nbrf000066400000000000000000000046111467613320200170210ustar00rootroot00000000000000>P1;CRAB_ANAPL ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN). MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ SDVPERSIPI TREEKPAIAG AQRK* >P1;CRAB_BOVIN ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN). MDIAIHHPWI RRPFFPFHSP SRLFDQFFGE HLLESDLFPA STSLSPFYLR PPSFLRAPSW IDTGLSEMRL EKDRFSVNLD VKHFSPEELK VKVLGDVIEV HGKHEERQDE HGFISREFHR KYRIPADVDP LAITSSLSSD GVLTVNGPRK QASGPERTIP ITREEKPAVT AAPKK* >P1;CRAB_CHICK ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN). MDITIHNPLV RRPLFSWLTP SRIFDQIFGE HLQESELLPT SPSLSPFLMR SPFFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMIEIH GKHEERQDEH GFIAREFSRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ SDVPERSIPI TREEKPAIAG SQRK* >P1;CRAB_HUMAN ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN) (ROSENTHAL FIBER). MDIAIHHPWI RRPFFPFHSP SRLFDQFFGE HLLESDLFPT STSLSPFYLR PPSFLRAPSW FDTGLSEMRL EKDRFSVNLD VKHFSPEELK VKVLGDVIEV HGKHEERQDE HGFISREFHR KYRIPADVDP LTITSSLSSD GVLTVNGPRK QVSGPERTIP ITREEKPAVT AAPKK* >P1;CRAB_MESAU ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN). MDIAIHHPWI RRPFFPFHSP SRLFDQFFGE HLLESDLFST ATSLSPFYLR PPSFLRAPSW IDTGLSEMRM EKDRFSVNLD VKHFSPEELK VKVLGDVVEV HGKHEERQDE HGFISREFHR KYRIPADVDP LTITSSLSSD GVLTVNGPRK QASGPERTIP ITREEKPAVT AAPKK* >P1;CRAB_MOUSE ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN) (P23). MDIAIHHPWI RRPFFPFHSP SRLFDQFFGE HLLESDLFST ATSLSPFYLR PPSFLRAPSW IDTGLSEMRL EKDRFSVNLD VKHFSPEELK VKVLGDVIEV HGKHEERQDE HGFISREFHR KYRIPADVDP LAITSSLSSD GVLTVNGPRK QVSGPERTIP ITREEKPAVA AAPKK* >P1;CRAB_RABIT ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN). MDIAIHHPWI RRPFFPFHSP SRLFDQFFGE HLLESDLFPT STSLSPFYLR PPSFLRAPSW IDTGLSEMRL EKDRFSVNLD VKHFSPEELK VKVLGDVIEV HGKHEERQDE HGFISREFHR KYRIPADVDP LTITSSLSSD GVLTVNGPRK QAPGPERTIP ITREEKPAVT AAPKK* >P1;CRAB_RAT ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN). MDIAIHHPWI RRPFFPFHSP SRLFDQFFGE HLLESDLFST ATSLSPFYLR PPSFLRAPSW IDTGLSEMRM EKDRFSVNLD VKHFSPEELK VKVLGDVIEV HGKHEERQDE HGFISREFHR KYRIPADVDP LTITSSLSSD GVLTVNGPRK QASGPERTIP ITREEKPAVT AAPKK* >P1;CRAB_SQUAC ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN). MDIAIQHPWL RRPLFPSSIF PSRIFDQNFG EHFDPDLFPS FSSMLSPFYW RMGAPMARMP SWAQTGLSEL RLDKDKFAIH LDVKHFTPEE LRVKILGDFI EVQAQHEERQ DEHGYVSREF HRKYKVPAGV DPLVITCSLS ADGVLTITGP RKVADVPERS VPISRDEKPA VAGPQQK*weblogo-3.8.0/tests/data/dist.20comp000066400000000000000000000151421467613320200172270ustar00rootroot00000000000000ClassName = DirichletReg Name = dist.20comp Alphabet = ExtAA Order = A C D E F G H I K L M N P Q R S T V W Y AlphaChar= 20 NumDistr= 20 comment= The 1216 ids in this set were chosen from one of Dunbrack's culled PDB comment= sets (20% 3.0 Ang) with fragments removed (no piece >=20 residues) and comment= further restricting the set to those that had >=10 chains in comment= t2k-thin62 (t2k alignments thinned to 62% residue identity). comment= comment= The t2k-thin62 alignments were used to get the column counts, with no comment= weighting. comment= comment= Encoding cost in bits using optimum regularizer from small sample: comment= For test with 314585 columns comment= 0 1 2 3 4 comment= optimum regularizer 4.166909 3.761509 3.559019 3.440795 3.362272 comment= Savings over background 0 0.4054 0.6079 0.7261 0.8046 comment= comment= Log-prob(data | regularizer) 3.10736 bits/char (1.0595 bits saved) Number= 0 Mixture= 0.118635 Alpha= 38.9068 2.5669 0.370774 1.44056 2.9283 1.21428 0.97375 1.03532 3.09741 2.54321 4.45023 1.16301 1.2358 1.08008 1.97643 2.78802 2.01298 2.67868 3.74557 0.410179 1.19537 Comment= Q M R T V I K E L H >< Y W S A F N D P C , G Number= 1 Mixture= 0.116771 Alpha= 34.0172 2.50787 0.228286 3.74106 3.03401 0.4579 3.5709 0.972283 0.34445 2.57772 0.837683 0.264509 2.80803 1.84689 1.65971 2.08515 3.79011 1.92961 0.604308 0.200458 0.55629 Comment= N D S Q E K G P H R T >< A W , Y C M F L , V I Number= 2 Mixture= 0.0839451 Alpha= 20.5573 1.53868 0.122294 0.801739 1.74177 0.231959 0.582686 0.583441 0.370793 3.94398 0.813473 0.260941 0.911761 0.373579 1.49984 3.71333 1.17303 0.953111 0.546242 0.0792836 0.31536 Comment= K R Q , E H N >< S A T D M , Y P L C G V W I F Number= 3 Mixture= 0.0706342 Alpha= 10.6105 0.382593 0.10393 0.0302879 0.0624518 0.80017 0.0505664 0.0410875 1.66573 0.074861 4.90828 0.719483 0.0410838 0.0682095 0.079238 0.0881338 0.0858233 0.154562 1.00948 0.0797825 0.164767 Comment= L , M I , F V >< W C , Y A T , Q H R P S K , E N , G D Number= 4 Mixture= 0.0687598 Alpha= 23.6749 2.23394 0.570614 0.289279 0.30002 2.12034 0.998395 0.322163 2.55709 0.313104 4.12883 1.10293 0.390912 0.658897 0.313286 0.424506 0.992988 1.30493 3.09516 0.431337 1.12613 Comment= F M , L V I W C Y A T >< S P H G , N Q R , K D E Number= 5 Mixture= 0.0625805 Alpha= 31.8975 2.70283 0.0625563 4.14249 10.0799 0.211644 0.813422 0.42774 0.36793 2.59637 0.699532 0.228439 1.063 0.734675 2.43315 1.50938 1.63213 1.19589 0.65561 0.0899207 0.250834 Comment= E , D Q , K A >< R S N T H P , M G V , W Y L I F C Number= 6 Mixture= 0.0580265 Alpha= 0.121746 0.00537672 0.00757924 0.0118262 0.00704899 0.00208465 0.0285007 0.00521748 0.00172387 0.00508969 0.00632526 0.00088775 0.00522821 0.0104857 0.00172908 0.00608784 0.00410175 0.00466313 0.00160838 0.00251289 0.00366817 Comment= C , G , P H W D N >< R E Y K T S L A , F Q M , I V Number= 7 Mixture= 0.0551574 Alpha= 16.0251 0.626135 0.163768 0.0365417 0.0600313 0.574623 0.0715377 0.0591798 5.07885 0.0763446 2.49034 0.358724 0.0455369 0.0957408 0.0534047 0.0810176 0.117994 0.326469 5.43037 0.0494101 0.229061 Comment= I V ,, L M >< F C , A Y T W , H P , S Q R K N , E G D Number= 8 Mixture= 0.0468342 Alpha= 17.0288 0.973071 0.22054 0.566033 0.6393 1.95722 0.681537 1.02681 0.602807 0.58915 1.39446 0.375235 0.682389 0.386498 0.515409 0.889406 0.832358 0.657265 0.718106 0.698962 2.62227 Comment= Y , W F H , M >< R N Q C L S T A K E D I V G P Number= 9 Mixture= 0.0451463 Alpha= 19.377 7.61537 0.706652 0.146257 0.30079 0.350714 1.4097 0.169752 0.901333 0.213755 1.31586 0.420008 0.207333 0.202484 0.239804 0.25426 1.60805 0.981565 2.00443 0.0655797 0.263306 Comment= A , C , V S M >< T G I L , F Y H Q W N , R E P K D Number= 10 Mixture= 0.0405728 Alpha= 25.896 1.8832 0.129465 0.94377 1.19092 0.386733 0.929517 0.331773 0.62983 1.03159 1.0316 0.218096 0.569141 11.5287 0.541324 0.798838 1.43455 0.927807 0.949527 0.119681 0.319962 Comment= P ,,,>< S A K E T D Q R H N , V G L W M I Y F C Number= 11 Mixture= 0.0396313 Alpha= 36.7748 1.74247 0.169971 1.52036 0.992363 0.310239 22.4882 0.465764 0.262031 1.10621 0.495215 0.191912 1.80494 0.655939 0.619611 0.848604 1.622 0.655503 0.414462 0.101954 0.307101 Comment= G ,,, N >< S D A K H , Q R E P T C Y , W M F V L , I Number= 12 Mixture= 0.0349161 Alpha= 2.83144 0.0670238 0.0338125 0.00791097 0.0168524 0.877469 0.0154565 0.0780456 0.152439 0.0200816 0.327316 0.0737535 0.0138475 0.0264786 0.0163551 0.0244423 0.0322599 0.0432955 0.148994 0.215284 0.640326 Comment= F Y W ,, M L H >< I C V , T A , P S Q R K , N E G , D Number= 13 Mixture= 0.0321127 Alpha= 14.0263 0.815096 0.205353 0.477846 0.375615 0.152601 0.425373 0.164154 0.316463 0.338321 0.331542 0.14924 0.655764 0.284447 0.258584 0.308435 3.49932 4.48875 0.589395 0.0351409 0.154839 Comment= T S ,, N >< C A D V Q , H M P K E R G I Y F , L W Number= 14 Mixture= 0.0273166 Alpha= 3.44479 0.474214 0.152165 0.0105189 0.034434 0.0257615 0.0476519 0.00611497 0.48937 0.0354143 0.360611 0.0982885 0.0299312 0.0834673 0.0259538 0.0234012 0.0891168 0.339496 1.10909 0.00646119 0.00332728 Comment= V , C I , T A M L >< P , S , Q N K F G W E R , H , D , Y Number= 15 Mixture= 0.0254724 Alpha= 20.5453 0.551619 0.0608604 10.3798 1.93102 0.105669 0.738914 0.385215 0.133247 0.563812 0.205654 0.0677289 1.94283 0.37973 0.440017 0.39716 1.19039 0.660318 0.211909 0.0386401 0.160771 Comment= D ,, N , E >< S H Q T K , G P R A , Y C W M V F , I L Number= 16 Mixture= 0.024399 Alpha= 2.35081 0.127624 0.0319621 0.118859 0.178977 0.0273779 0.0591804 0.299987 0.0332517 0.10796 0.124812 0.0664956 0.210617 0.0400719 0.274157 0.190973 0.162483 0.108077 0.0526538 0.033998 0.101289 Comment= H , Q N , R M Y W E S >< C D T K A L , P G V F , I Number= 17 Mixture= 0.0225499 Alpha= 2.65285 0.89738 0.089521 0.0427292 0.0334136 0.0233354 0.610527 0.00869405 0.00269214 0.0201024 0.0231746 0.0145827 0.0436343 0.0793107 0.0198705 0.0292587 0.510413 0.137974 0.0371611 0.0110513 0.0180191 Comment= A , S G C ,>< T P , N W D M , Q F R Y E V K H , L ,, I Number= 18 Mixture= 0.0138156 Alpha= 11.7158 0.311036 0.197499 1.12597 0.194769 0.152485 0.636091 0.469855 0.14881 0.369246 0.215269 0.06982 4.99574 0.099792 0.227196 0.270685 1.18863 0.635224 0.186391 0.0193464 0.201948 Comment= N ,,, H D S C T >< G K Q Y , R F A M E , V I P L W Number= 19 Mixture= 0.0127238 Alpha= 3.13702 0.0857215 0.0113884 0.0034858 0.0656184 0.02952 0.0692149 0.0034858 0.0993031 0.751119 0.186025 0.055619 0.0552037 0.0730833 0.148809 1.16193 0.0642702 0.0962008 0.108956 0.0254982 0.0425675 Comment= R K ,, Q >< M W L T P I , V N Y S E A G , C F ,, H , D EndClassName = DirichletReg weblogo-3.8.0/tests/data/dna.msf000066400000000000000000000264531467613320200165220ustar00rootroot00000000000000PileUp MSF: 705 Type: N Check: 2677 .. Name: Cow oo Len: 705 Check: 4675 Weight: 0.0 Name: Carp oo Len: 705 Check: 6669 Weight: 100.0 Name: Chicken oo Len: 705 Check: 5185 Weight: 100.0 Name: Human oo Len: 705 Check: 3974 Weight: 100.0 Name: Loach oo Len: 705 Check: 3713 Weight: 100.0 Name: Mouse oo Len: 705 Check: 4218 Weight: 100.0 Name: Rat oo Len: 705 Check: 3143 Weight: 100.0 Name: Seal oo Len: 705 Check: 4879 Weight: 100.0 Name: Whale oo Len: 705 Check: 1453 Weight: 100.0 Name: Frog oo Len: 705 Check: 4768 Weight: 100.0 // Cow ATGGCATATC CCATACAACT AGGATTCCAA GATGCAACAT CACCAATCAT Carp ATGGCACACC CAACGCAACT AGGTTTCAAG GACGCGGCCA TACCCGTTAT Chicken ATGGCCAACC ACTCCCAACT AGGCTTTCAA GACGCCTCAT CCCCCATCAT Human ATGGCACATG CAGCGCAAGT AGGTCTACAA GACGCTACTT CCCCTATCAT Loach ATGGCACATC CCACACAATT AGGATTCCAA GACGCGGCCT CACCCGTAAT Mouse ATGGCCTACC CATTCCAACT TGGTCTACAA GACGCCACAT CCCCTATTAT Rat ATGGCTTACC CATTTCAACT TGGCTTACAA GACGCTACAT CACCTATCAT Seal ATGGCATACC CCCTACAAAT AGGCCTACAA GATGCAACCT CTCCCATTAT Whale ATGGCATATC CATTCCAACT AGGTTTCCAA GATGCAGCAT CACCCATCAT Frog ATGGCACACC CATCACAATT AGGTTTTCAA GACGCAGCCT CTCCAATTAT Cow AGAAGAACTA CTTCACTTTC ATGACCACAC GCTAATAATT GTCTTCTTAA Carp AGAGGAACTT CTTCACTTCC ACGACCACGC ATTAATAATT GTGCTCCTAA Chicken AGAAGAGCTC GTTGAATTCC ACGACCACGC CCTGATAGTC GCACTAGCAA Human AGAAGAGCTT ATCACCTTTC ATGATCACGC CCTCATAATC ATTTTCCTTA Loach AGAAGAACTT CTTCACTTCC ATGACCATGC CCTAATAATT GTATTTTTGA Mouse AGAAGAGCTA ATAAATTTCC ATGATCACAC ACTAATAATT GTTTTCCTAA Rat AGAAGAACTT ACAAACTTTC ATGACCACAC CCTAATAATT GTATTCCTCA Seal AGAGGAGTTA CTACACTTCC ATGACCACAC ATTAATAATT GTGTTCCTAA Whale AGAAGAGCTC CTACACTTTC ACGATCATAC ACTAATAATC GTTTTTCTAA Frog AGAAGAATTA CTTCACTTCC ACGACCATAC CCTCATAGCC GTTTTTCTTA Cow TTAGCTCATT AGTACTTTAC ATTATTTCAC TAATACTAAC GACAAAGCTG Carp TTAGCACTTT AGTTTTATAT ATTATTACTG CAATGGTATC AACTAAACTT Chicken TTTGCAGCTT AGTACTCTAC CTTCTAACTC TTATACTTAT AGAAAAACTA Human TCTGCTTCCT AGTCCTGTAT GCCCTTTTCC TAACACTCAC AACAAAACTA Loach TTAGCGCCCT AGTACTTTAT GTTATTATTA CAACCGTCTC AACAAAACTC Mouse TTAGCTCCTT AGTCCTCTAT ATCATCTCGC TAATATTAAC AACAAAACTA Rat TCAGCTCCCT AGTACTTTAT ATTATTTCAC TAATACTAAC AACAAAACTA Seal TTAGCTCATT AGTACTCTAC ATTATCTCAC TTATACTAAC CACGAAACTC Whale TTAGCTCTTT AGTTCTCTAC ATTATTACCC TAATGCTTAC AACCAAATTA Frog TTAGTACGCT AGTTCTTTAC ATTATTACTA TTATAATAAC TACTAAACTA Cow ACCCATACAA GCACGATAGA TGCACAAGAA GTAGAGACAA TCTGAACCAT Carp ACTAATAAAT ATATTCTAGA CTCCCAAGAA ATCGAAATCG TATGAACCAT Chicken TCA...TCAA ACACCGTAGA TGCCCAAGAA GTTGAACTAA TCTGAACCAT Human ACTAATACTA ACATCTCAGA CGCTCAGGAA ATAGAAACCG TCTGAACTAT Loach ACTAACATAT ATATTTTGGA CTCACAAGAA ATTGAAATCG TATGAACTGT Mouse ACACATACAA GCACAATAGA TGCACAAGAA GTTGAAACCA TTTGAACTAT Rat ACACACACAA GCACAATAGA CGCCCAAGAA GTAGAAACAA TTTGAACAAT Seal ACCCACACAA GTACAATAGA CGCACAAGAA GTGGAAACGG TGTGAACGAT Whale ACACATACTA GTACAATAGA CGCCCAAGAA GTAGAAACTG TCTGAACTAT Frog ACTAATACAA ACCTAATGGA CGCACAAGAG ATCGAAATAG TGTGAACTAT Cow TCTGCCCGCC ATCATCTTAA TTCTAATTGC TCTTCCTTCT TTACGAATTC Carp TCTACCAGCC GTCATTTTAG TACTAATCGC CCTGCCCTCC CTACGCATCC Chicken CCTACCCGCT ATTGTCCTAG TCCTGCTTGC CCTCCCCTCC CTCCAAATCC Human CCTGCCCGCC ATCATCCTAG TCCTCATCGC CCTCCCATCC CTACGCATCC Loach GCTCCCTGCC CTAATCCTCA TTTTAATCGC CCTCCCCTCA CTACGAATTC Mouse TCTACCAGCT GTAATCCTTA TCATAATTGC TCTCCCCTCT CTACGCATTC Rat TCTCCCAGCT GTCATTCTTA TTCTAATTGC CCTTCCCTCC CTACGAATTC Seal CCTACCCGCT ATCATTTTAA TTCTCATTGC CCTACCATCA TTACGAATCC Whale CCTCCCAGCC ATTATCTTAA TTTTAATTGC CTTGCCTTCA TTACGGATCC Frog TATACCAGCT ATTAGCCTCA TCATAATTGC CCTTCCATCC CTTCGTATCC Cow TATACATAAT AGATGAAATC AATAACCCAT CTCTTACAGT AAAAACCATA Carp TGTACCTTAT AGACGAAATT AACGACCCTC ACCTGACAAT TAAAGCAATA Chicken TCTACATAAT AGACGAAATC GACGAACCTG ATCTCACCCT AAAAGCCATC Human TTTACATAAC AGACGAGGTC AACGATCCCT CCCTTACCAT CAAATCAATT Loach TATATCTTAT AGACGAGATT AATGACCCCC ACCTAACAAT TAAGGCCATG Mouse TATATATAAT AGACGAAATC AACAACCCCG TATTAACCGT TAAAACCATA Rat TATACATAAT AGACGAGATT AATAACCCAG TTCTAACAGT AAAAACTATA Seal TCTACATAAT GGACGAGATC AATAACCCTT CCTTGACCGT AAAAACTATA Whale TTTACATAAT AGACGAAGTC AATAACCCCT CCCTCACTGT AAAAACAATA Frog TATATTTAAT AGATGAAGTT AATGATCCAC ACTTAACAAT TAAAGCAATC Cow GGACATCAGT GATACTGAAG CTATGAGTAT ACAGATTATG AGGACTTAAG Carp GGACACCAAT GATACTGAAG TTACGAGTAT ACAGACTATG AAAATCTAGG Chicken GGACACCAAT GATACTGAAC CTATGAATAC ACAGACTTCA AGGACCTCTC Human GGCCACCAAT GGTACTGAAC CTACGAGTAC ACCGACTACG GCGGACTAAT Loach GGGCACCAAT GATACTGAAG CTACGAGTAT ACTGATTATG AAAACTTAAG Mouse GGGCACCAAT GATACTGAAG CTACGAATAT ACTGACTATG AAGACCTATG Rat GGACACCAAT GATACTGAAG CTATGAATAT ACTGACTATG AAGACCTATG Seal GGACATCAGT GATACTGAAG CTATGAGTAC ACAGACTACG AAGACCTGAA Whale GGTCACCAAT GATATTGAAG CTATGAGTAT ACCGACTACG AAGACCTAAG Frog GGCCACCAAT GATACTGAAG CTACGAATAT ACTAACTATG AGGATCTCTC Cow CTTCGACTCC TACATAATTC CAACATCAGA ATTAAAGCCA GGGGAGCTAC Carp ATTCGACTCC TATATAGTAC CAACCCAAGA CCTTGCCCCC GGACAATTCC Chicken ATTTGACTCC TACATAACCC CAACAACAGA CCTCCCCCTA GGCCACTTCC Human CTTCAACTCC TACATACTTC CCCCATTATT CCTAGAACCA GGCGACCTGC Loach TTTTGACTCC TACATAATCC CCACCCAGGA CCTAACCCCT GGACAATTCC Mouse CTTTGATTCA TATATAATCC CAACAAACGA CCTAAAACCT GGTGAACTAC Rat CTTTGACTCC TACATAATCC CAACCAATGA CCTAAAACCA GGTGAACTTC Seal CTTTGACTCA TATATGATCC CCACACAAGA ACTAAAGCCC GGAGAACTAC Whale CTTCGACTCC TATATAATCC CAACATCAGA CCTAAAGCCA GGAGAACTAC Frog ATTTGACTCT TATATAATTC CAACTAATGA CCTTACCCCT GGACAATTCC Cow GACTATTAGA AGTCGATAAT CGAGTTGTAC TACCAATAGA AATAACAATC Carp GACTTCTGGA AACAGACCAC CGAATAGTTG TTCCAATAGA ATCCCCAGTC Chicken GCCTACTAGA AGTCGACCAT CGCATTGTAA TCCCCATAGA ATCCCCCATT Human GACTCCTTGA CGTTGACAAT CGAGTAGTAC TCCCGATTGA AGCCCCCATT Loach GGCTACTAGA GACAGACCAC CGAATGGTTG TTCCCATAGA ATCCCCTATT Mouse GACTGCTAGA AGTTGATAAC CGAGTCGTTC TGCCAATAGA ACTTCCAATC Rat GTCTATTAGA AGTTGATAAT CGGGTAGTCT TACCAATAGA ACTTCCAATT Seal GACTGCTAGA AGTAGACAAT CGAGTAGTCC TCCCAATAGA AATAACAATC Whale GATTATTAGA AGTAGATAAC CGAGTTGTCT TACCTATAGA AATAACAATC Frog GGCTGCTAGA AGTTGATAAT CGAATAGTAG TCCCAATAGA ATCTCCAACC Cow CGAATGTTAG TCTCCTCTGA AGACGTATTA CACTCATGAG CTGTGCCCTC Carp CGTGTCCTAG TATCTGCTGA AGACGTGCTA CATTCTTGAG CTGTTCCATC Chicken CGAGTAATCA TCACCGCTGA TGACGTCCTC CACTCATGAG CCGTACCCGC Human CGTATAATAA TTACATCACA AGACGTCTTG CACTCATGAG CTGTCCCCAC Loach CGCATTCTTG TTTCCGCCGA AGATGTACTA CACTCCTGGG CCCTTCCAGC Mouse CGTATATTAA TTTCATCTGA AGACGTCCTC CACTCATGAG CAGTCCCCTC Rat CGTATACTAA TCTCATCCGA AGACGTCCTG CACTCATGAG CCATCCCTTC Seal CGCATACTAA TCTCATCAGA AGATGTACTC CACTCATGAG CCGTACCGTC Whale CGAATATTAG TCTCATCAGA AGACGTACTC CACTCATGGG CCGTACCCTC Frog CGACTTTTAG TTACAGCCGA AGACGTCCTC CACTCGTGAG CTGTACCCTC Cow TCTAGGACTA AAAACAGACG CAATCCCAGG CCGTCTAAAC CAAACAACCC Carp CCTTGGCGTA AAAATGGACG CAGTCCCAGG ACGACTAAAT CAAGCCGCCT Chicken CCTCGGGGTA AAAACAGACG CAATCCCTGG ACGACTAAAT CAAACCTCCT Human ATTAGGCTTA AAAACAGATG CAATTCCCGG ACGTCTAAAC CAAACCACTT Loach CATGGGGGTA AAGATAGACG CGGTCCCAGG ACGCCTTAAC CAAACCGCCT Mouse CCTAGGACTT AAAACTGATG CCATCCCAGG CCGACTAAAT CAAGCAACAG Rat ACTAGGGTTA AAAACCGACG CAATCCCCGG CCGCCTAAAC CAAGCTACAG Seal CCTAGGACTA AAAACTGATG CTATCCCAGG ACGACTAAAC CAAACAACCC Whale CTTGGGCCTA AAAACAGATG CAATCCCAGG ACGCCTAAAC CAAACAACCT Frog CTTGGGTGTC AAAACAGATG CAATCCCAGG ACGACTTCAT CAAACATCAT Cow TTATATCGTC CCGTCCAGGC TTATATTACG GTCAATGCTC AGAAATTTGC Carp TTATTGCCTC ACGCCCAGGG GTCTTTTACG GACAATGCTC TGAAATTTGT Chicken TCATCACCAC TCGACCAGGA GTGTTTTACG GACAATGCTC AGAAATCTGC Human TCACCGCTAC ACGACCGGGG GTATACTACG GTCAATGCTC TGAAATCTGT Loach TTATTGCCTC CCGCCCCGGG GTATTCTATG GGCAATGCTC AGAAATCTGT Mouse TAACATCAAA CCGACCAGGG TTATTCTATG GCCAATGCTC TGAAATTTGT Rat TCACATCAAA CCGACCAGGT CTATTCTATG GCCAATGCTC TGAAATTTGC Seal TAATAACCAT ACGACCAGGA CTGTACTACG GTCAATGCTC AGAAATCTGT Whale TAATATCAAC ACGACCAGGC CTATTTTATG GACAATGCTC AGAGATCTGC Frog TTATTGCTAC TCGTCCGGGA GTATTTTACG GACAATGTTC AGAAATTTGC Cow GGGTCAAACC ACAGTTTCAT ACCCATTGTC CTTGAGTTAG TCCCACTAAA Carp GGAGCTAATC ACAGCTTTAT ACCAATTGTA GTTGAAGCAG TACCTCTCGA Chicken GGAGCTAACC ACAGCTACAT ACCCATTGTA GTAGAGTCTA CCCCCCTAAA Human GGAGCAAACC ACAGTTTCAT GCCCATCGTC CTAGAATTAA TTCCCCTAAA Loach GGAGCAAACC ACAGCTTTAT ACCCATCGTA GTAGAAGCGG TCCCACTATC Mouse GGATCTAACC ATAGCTTTAT GCCCATTGTC CTAGAAATGG TTCCACTAAA Rat GGCTCAAATC ACAGCTTCAT ACCCATTGTA CTAGAAATAG TGCCTCTAAA Seal GGTTCAAACC ACAGCTTCAT ACCTATTGTC CTCGAATTGG TCCCACTATC Whale GGCTCAAACC ACAGTTTCAT ACCAATTGTC CTAGAACTAG TACCCCTAGA Frog GGAGCAAACC ACAGCTTTAT ACCAATTGTA GTTGAAGCAG TACCGCTAAC Cow GTACTTTGAA AAATGATCTG CGTCAATATT A......... .......... Carp ACACTTCGAA AACTGATCCT CATTAATACT AGAAGACGCC TCGCTAGGAA Chicken ACACTTTGAA GCCTGATCCT CACTA..... .......... ...CTGTCAT Human AATCTTTGAA ATA....... .......... ....GGGCCC GTATTTACCC Loach TCACTTCGAA AACTGGTCCA CCCTTATACT AAAAGACGCC TCACTAGGAA Mouse ATATTTCGAA AACTGATCTG CTTCAATAAT T......... .......... Rat ATATTTCGAA AACTGATCAG CTTCTATAAT T......... .......... Seal CCACTTCGAG AAATGATCTA CCTCAATGCT T......... .......... Whale AGTCTTTGAA AAATGATCTG TATCAATACT A......... .......... Frog CGACTTTGAA AACTGATCTT CATCAATACT A...GAAGCA TCACTA.... Cow ..TAA Carp GCTAA Chicken CTTAA Human TATAG Loach GCTAA Mouse ..TAA Rat ..TAA Seal ..TAA Whale ..TAA Frog ..AGA weblogo-3.8.0/tests/data/dna.phy000066400000000000000000000161711467613320200165310ustar00rootroot0000000000000010 705 Cow ATGGCATATCCCATACAACTAGGATTCCAAGATGCAACATCACCAATCATAGAAGAACTA Carp ATGGCACACCCAACGCAACTAGGTTTCAAGGACGCGGCCATACCCGTTATAGAGGAACTT Chicken ATGGCCAACCACTCCCAACTAGGCTTTCAAGACGCCTCATCCCCCATCATAGAAGAGCTC Human ATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTT Loach ATGGCACATCCCACACAATTAGGATTCCAAGACGCGGCCTCACCCGTAATAGAAGAACTT Mouse ATGGCCTACCCATTCCAACTTGGTCTACAAGACGCCACATCCCCTATTATAGAAGAGCTA Rat ATGGCTTACCCATTTCAACTTGGCTTACAAGACGCTACATCACCTATCATAGAAGAACTT Seal ATGGCATACCCCCTACAAATAGGCCTACAAGATGCAACCTCTCCCATTATAGAGGAGTTA Whale ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTC Frog ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTA CTTCACTTTCATGACCACACGCTAATAATTGTCTTCTTAATTAGCTCATTAGTACTTTAC CTTCACTTCCACGACCACGCATTAATAATTGTGCTCCTAATTAGCACTTTAGTTTTATAT GTTGAATTCCACGACCACGCCCTGATAGTCGCACTAGCAATTTGCAGCTTAGTACTCTAC ATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCCTGTAT CTTCACTTCCATGACCATGCCCTAATAATTGTATTTTTGATTAGCGCCCTAGTACTTTAT ATAAATTTCCATGATCACACACTAATAATTGTTTTCCTAATTAGCTCCTTAGTCCTCTAT ACAAACTTTCATGACCACACCCTAATAATTGTATTCCTCATCAGCTCCCTAGTACTTTAT CTACACTTCCATGACCACACATTAATAATTGTGTTCCTAATTAGCTCATTAGTACTCTAC CTACACTTTCACGATCATACACTAATAATCGTTTTTCTAATTAGCTCTTTAGTTCTCTAC CTTCACTTCCACGACCATACCCTCATAGCCGTTTTTCTTATTAGTACGCTAGTTCTTTAC ATTATTTCACTAATACTAACGACAAAGCTGACCCATACAAGCACGATAGATGCACAAGAA ATTATTACTGCAATGGTATCAACTAAACTTACTAATAAATATATTCTAGACTCCCAAGAA CTTCTAACTCTTATACTTATAGAAAAACTATCA---TCAAACACCGTAGATGCCCAAGAA GCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAA GTTATTATTACAACCGTCTCAACAAAACTCACTAACATATATATTTTGGACTCACAAGAA ATCATCTCGCTAATATTAACAACAAAACTAACACATACAAGCACAATAGATGCACAAGAA ATTATTTCACTAATACTAACAACAAAACTAACACACACAAGCACAATAGACGCCCAAGAA ATTATCTCACTTATACTAACCACGAAACTCACCCACACAAGTACAATAGACGCACAAGAA ATTATTACCCTAATGCTTACAACCAAATTAACACATACTAGTACAATAGACGCCCAAGAA ATTATTACTATTATAATAACTACTAAACTAACTAATACAAACCTAATGGACGCACAAGAG GTAGAGACAATCTGAACCATTCTGCCCGCCATCATCTTAATTCTAATTGCTCTTCCTTCT ATCGAAATCGTATGAACCATTCTACCAGCCGTCATTTTAGTACTAATCGCCCTGCCCTCC GTTGAACTAATCTGAACCATCCTACCCGCTATTGTCCTAGTCCTGCTTGCCCTCCCCTCC ATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCATCGCCCTCCCATCC ATTGAAATCGTATGAACTGTGCTCCCTGCCCTAATCCTCATTTTAATCGCCCTCCCCTCA GTTGAAACCATTTGAACTATTCTACCAGCTGTAATCCTTATCATAATTGCTCTCCCCTCT GTAGAAACAATTTGAACAATTCTCCCAGCTGTCATTCTTATTCTAATTGCCCTTCCCTCC GTGGAAACGGTGTGAACGATCCTACCCGCTATCATTTTAATTCTCATTGCCCTACCATCA GTAGAAACTGTCTGAACTATCCTCCCAGCCATTATCTTAATTTTAATTGCCTTGCCTTCA ATCGAAATAGTGTGAACTATTATACCAGCTATTAGCCTCATCATAATTGCCCTTCCATCC TTACGAATTCTATACATAATAGATGAAATCAATAACCCATCTCTTACAGTAAAAACCATA CTACGCATCCTGTACCTTATAGACGAAATTAACGACCCTCACCTGACAATTAAAGCAATA CTCCAAATCCTCTACATAATAGACGAAATCGACGAACCTGATCTCACCCTAAAAGCCATC CTACGCATCCTTTACATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATT CTACGAATTCTATATCTTATAGACGAGATTAATGACCCCCACCTAACAATTAAGGCCATG CTACGCATTCTATATATAATAGACGAAATCAACAACCCCGTATTAACCGTTAAAACCATA CTACGAATTCTATACATAATAGACGAGATTAATAACCCAGTTCTAACAGTAAAAACTATA TTACGAATCCTCTACATAATGGACGAGATCAATAACCCTTCCTTGACCGTAAAAACTATA TTACGGATCCTTTACATAATAGACGAAGTCAATAACCCCTCCCTCACTGTAAAAACAATA CTTCGTATCCTATATTTAATAGATGAAGTTAATGATCCACACTTAACAATTAAAGCAATC GGACATCAGTGATACTGAAGCTATGAGTATACAGATTATGAGGACTTAAGCTTCGACTCC GGACACCAATGATACTGAAGTTACGAGTATACAGACTATGAAAATCTAGGATTCGACTCC GGACACCAATGATACTGAACCTATGAATACACAGACTTCAAGGACCTCTCATTTGACTCC GGCCACCAATGGTACTGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCC GGGCACCAATGATACTGAAGCTACGAGTATACTGATTATGAAAACTTAAGTTTTGACTCC GGGCACCAATGATACTGAAGCTACGAATATACTGACTATGAAGACCTATGCTTTGATTCA GGACACCAATGATACTGAAGCTATGAATATACTGACTATGAAGACCTATGCTTTGACTCC GGACATCAGTGATACTGAAGCTATGAGTACACAGACTACGAAGACCTGAACTTTGACTCA GGTCACCAATGATATTGAAGCTATGAGTATACCGACTACGAAGACCTAAGCTTCGACTCC GGCCACCAATGATACTGAAGCTACGAATATACTAACTATGAGGATCTCTCATTTGACTCT TACATAATTCCAACATCAGAATTAAAGCCAGGGGAGCTACGACTATTAGAAGTCGATAAT TATATAGTACCAACCCAAGACCTTGCCCCCGGACAATTCCGACTTCTGGAAACAGACCAC TACATAACCCCAACAACAGACCTCCCCCTAGGCCACTTCCGCCTACTAGAAGTCGACCAT TACATACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTTGACAAT TACATAATCCCCACCCAGGACCTAACCCCTGGACAATTCCGGCTACTAGAGACAGACCAC TATATAATCCCAACAAACGACCTAAAACCTGGTGAACTACGACTGCTAGAAGTTGATAAC TACATAATCCCAACCAATGACCTAAAACCAGGTGAACTTCGTCTATTAGAAGTTGATAAT TATATGATCCCCACACAAGAACTAAAGCCCGGAGAACTACGACTGCTAGAAGTAGACAAT TATATAATCCCAACATCAGACCTAAAGCCAGGAGAACTACGATTATTAGAAGTAGATAAC TATATAATTCCAACTAATGACCTTACCCCTGGACAATTCCGGCTGCTAGAAGTTGATAAT CGAGTTGTACTACCAATAGAAATAACAATCCGAATGTTAGTCTCCTCTGAAGACGTATTA CGAATAGTTGTTCCAATAGAATCCCCAGTCCGTGTCCTAGTATCTGCTGAAGACGTGCTA CGCATTGTAATCCCCATAGAATCCCCCATTCGAGTAATCATCACCGCTGATGACGTCCTC CGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACATCACAAGACGTCTTG CGAATGGTTGTTCCCATAGAATCCCCTATTCGCATTCTTGTTTCCGCCGAAGATGTACTA CGAGTCGTTCTGCCAATAGAACTTCCAATCCGTATATTAATTTCATCTGAAGACGTCCTC CGGGTAGTCTTACCAATAGAACTTCCAATTCGTATACTAATCTCATCCGAAGACGTCCTG CGAGTAGTCCTCCCAATAGAAATAACAATCCGCATACTAATCTCATCAGAAGATGTACTC CGAGTTGTCTTACCTATAGAAATAACAATCCGAATATTAGTCTCATCAGAAGACGTACTC CGAATAGTAGTCCCAATAGAATCTCCAACCCGACTTTTAGTTACAGCCGAAGACGTCCTC CACTCATGAGCTGTGCCCTCTCTAGGACTAAAAACAGACGCAATCCCAGGCCGTCTAAAC CATTCTTGAGCTGTTCCATCCCTTGGCGTAAAAATGGACGCAGTCCCAGGACGACTAAAT CACTCATGAGCCGTACCCGCCCTCGGGGTAAAAACAGACGCAATCCCTGGACGACTAAAT CACTCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATTCCCGGACGTCTAAAC CACTCCTGGGCCCTTCCAGCCATGGGGGTAAAGATAGACGCGGTCCCAGGACGCCTTAAC CACTCATGAGCAGTCCCCTCCCTAGGACTTAAAACTGATGCCATCCCAGGCCGACTAAAT CACTCATGAGCCATCCCTTCACTAGGGTTAAAAACCGACGCAATCCCCGGCCGCCTAAAC CACTCATGAGCCGTACCGTCCCTAGGACTAAAAACTGATGCTATCCCAGGACGACTAAAC CACTCATGGGCCGTACCCTCCTTGGGCCTAAAAACAGATGCAATCCCAGGACGCCTAAAC CACTCGTGAGCTGTACCCTCCTTGGGTGTCAAAACAGATGCAATCCCAGGACGACTTCAT CAAACAACCCTTATATCGTCCCGTCCAGGCTTATATTACGGTCAATGCTCAGAAATTTGC CAAGCCGCCTTTATTGCCTCACGCCCAGGGGTCTTTTACGGACAATGCTCTGAAATTTGT CAAACCTCCTTCATCACCACTCGACCAGGAGTGTTTTACGGACAATGCTCAGAAATCTGC CAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGT CAAACCGCCTTTATTGCCTCCCGCCCCGGGGTATTCTATGGGCAATGCTCAGAAATCTGT CAAGCAACAGTAACATCAAACCGACCAGGGTTATTCTATGGCCAATGCTCTGAAATTTGT CAAGCTACAGTCACATCAAACCGACCAGGTCTATTCTATGGCCAATGCTCTGAAATTTGC CAAACAACCCTAATAACCATACGACCAGGACTGTACTACGGTCAATGCTCAGAAATCTGT CAAACAACCTTAATATCAACACGACCAGGCCTATTTTATGGACAATGCTCAGAGATCTGC CAAACATCATTTATTGCTACTCGTCCGGGAGTATTTTACGGACAATGTTCAGAAATTTGC GGGTCAAACCACAGTTTCATACCCATTGTCCTTGAGTTAGTCCCACTAAAGTACTTTGAA GGAGCTAATCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCTCTCGAACACTTCGAA GGAGCTAACCACAGCTACATACCCATTGTAGTAGAGTCTACCCCCCTAAAACACTTTGAA GGAGCAAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAA GGAGCAAACCACAGCTTTATACCCATCGTAGTAGAAGCGGTCCCACTATCTCACTTCGAA GGATCTAACCATAGCTTTATGCCCATTGTCCTAGAAATGGTTCCACTAAAATATTTCGAA GGCTCAAATCACAGCTTCATACCCATTGTACTAGAAATAGTGCCTCTAAAATATTTCGAA GGTTCAAACCACAGCTTCATACCTATTGTCCTCGAATTGGTCCCACTATCCCACTTCGAG GGCTCAAACCACAGTTTCATACCAATTGTCCTAGAACTAGTACCCCTAGAAGTCTTTGAA GGAGCAAACCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCGCTAACCGACTTTGAA AAATGATCTGCGTCAATATTA---------------------TAA AACTGATCCTCATTAATACTAGAAGACGCCTCGCTAGGAAGCTAA GCCTGATCCTCACTA------------------CTGTCATCTTAA ATA---------------------GGGCCCGTATTTACCCTATAG AACTGGTCCACCCTTATACTAAAAGACGCCTCACTAGGAAGCTAA AACTGATCTGCTTCAATAATT---------------------TAA AACTGATCAGCTTCTATAATT---------------------TAA AAATGATCTACCTCAATGCTT---------------------TAA AAATGATCTGTATCAATACTA---------------------TAA AACTGATCTTCATCAATACTA---GAAGCATCACTA------AGA weblogo-3.8.0/tests/data/dna.pir000066400000000000000000000162301467613320200165170ustar00rootroot00000000000000>DL; Cow Cow ATGGCATATCCCATACAACTAGGATTCCAAGATGCAACATCACCAATCATAGAAGAACTACTTCACTTTCATGAC CACACGCTAATAATTGTCTTCTTAATTAGCTCATTAGTACTTTACATTATTTCACTAATACTAACGACAAAGCTG ACCCATACAAGCACGATAGATGCACAAGAAGTAGAGACAATCTGAACCATTCTGCCCGCCATCATCTTAATTCTA ATTGCTCTTCCTTCTTTACGAATTCTATACATAATAGATGAAATCAATAACCCATCTCTTACAGTAAAAACCATA GGACATCAGTGATACTGAAGCTATGAGTATACAGATTATGAGGACTTAAGCTTCGACTCCTACATAATTCCAACA TCAGAATTAAAGCCAGGGGAGCTACGACTATTAGAAGTCGATAATCGAGTTGTACTACCAATAGAAATAACAATC CGAATGTTAGTCTCCTCTGAAGACGTATTACACTCATGAGCTGTGCCCTCTCTAGGACTAAAAACAGACGCAATC CCAGGCCGTCTAAACCAAACAACCCTTATATCGTCCCGTCCAGGCTTATATTACGGTCAATGCTCAGAAATTTGC GGGTCAAACCACAGTTTCATACCCATTGTCCTTGAGTTAGTCCCACTAAAGTACTTTGAAAAATGATCTGCGTCA ATATTA---------------------TAA* >DL; Carp Carp ATGGCACACCCAACGCAACTAGGTTTCAAGGACGCGGCCATACCCGTTATAGAGGAACTTCTTCACTTCCACGAC CACGCATTAATAATTGTGCTCCTAATTAGCACTTTAGTTTTATATATTATTACTGCAATGGTATCAACTAAACTT ACTAATAAATATATTCTAGACTCCCAAGAAATCGAAATCGTATGAACCATTCTACCAGCCGTCATTTTAGTACTA ATCGCCCTGCCCTCCCTACGCATCCTGTACCTTATAGACGAAATTAACGACCCTCACCTGACAATTAAAGCAATA GGACACCAATGATACTGAAGTTACGAGTATACAGACTATGAAAATCTAGGATTCGACTCCTATATAGTACCAACC CAAGACCTTGCCCCCGGACAATTCCGACTTCTGGAAACAGACCACCGAATAGTTGTTCCAATAGAATCCCCAGTC CGTGTCCTAGTATCTGCTGAAGACGTGCTACATTCTTGAGCTGTTCCATCCCTTGGCGTAAAAATGGACGCAGTC CCAGGACGACTAAATCAAGCCGCCTTTATTGCCTCACGCCCAGGGGTCTTTTACGGACAATGCTCTGAAATTTGT GGAGCTAATCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCTCTCGAACACTTCGAAAACTGATCCTCATTA ATACTAGAAGACGCCTCGCTAGGAAGCTAA* >DL; Chicken Chicken ATGGCCAACCACTCCCAACTAGGCTTTCAAGACGCCTCATCCCCCATCATAGAAGAGCTCGTTGAATTCCACGAC CACGCCCTGATAGTCGCACTAGCAATTTGCAGCTTAGTACTCTACCTTCTAACTCTTATACTTATAGAAAAACTA TCA---TCAAACACCGTAGATGCCCAAGAAGTTGAACTAATCTGAACCATCCTACCCGCTATTGTCCTAGTCCTG CTTGCCCTCCCCTCCCTCCAAATCCTCTACATAATAGACGAAATCGACGAACCTGATCTCACCCTAAAAGCCATC GGACACCAATGATACTGAACCTATGAATACACAGACTTCAAGGACCTCTCATTTGACTCCTACATAACCCCAACA ACAGACCTCCCCCTAGGCCACTTCCGCCTACTAGAAGTCGACCATCGCATTGTAATCCCCATAGAATCCCCCATT CGAGTAATCATCACCGCTGATGACGTCCTCCACTCATGAGCCGTACCCGCCCTCGGGGTAAAAACAGACGCAATC CCTGGACGACTAAATCAAACCTCCTTCATCACCACTCGACCAGGAGTGTTTTACGGACAATGCTCAGAAATCTGC GGAGCTAACCACAGCTACATACCCATTGTAGTAGAGTCTACCCCCCTAAAACACTTTGAAGCCTGATCCTCACTA ------------------CTGTCATCTTAA* >DL; Human Human ATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTTATCACCTTTCATGAT CACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCCTGTATGCCCTTTTCCTAACACTCACAACAAAACTA ACTAATACTAACATCTCAGACGCTCAGGAAATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTC ATCGCCCTCCCATCCCTACGCATCCTTTACATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATT GGCCACCAATGGTACTGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCCTACATACTTCCCCCA TTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTTGACAATCGAGTAGTACTCCCGATTGAAGCCCCCATT CGTATAATAATTACATCACAAGACGTCTTGCACTCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATT CCCGGACGTCTAAACCAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGT GGAGCAAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATA------------ ---------GGGCCCGTATTTACCCTATAG* >DL; Loach Loach ATGGCACATCCCACACAATTAGGATTCCAAGACGCGGCCTCACCCGTAATAGAAGAACTTCTTCACTTCCATGAC CATGCCCTAATAATTGTATTTTTGATTAGCGCCCTAGTACTTTATGTTATTATTACAACCGTCTCAACAAAACTC ACTAACATATATATTTTGGACTCACAAGAAATTGAAATCGTATGAACTGTGCTCCCTGCCCTAATCCTCATTTTA ATCGCCCTCCCCTCACTACGAATTCTATATCTTATAGACGAGATTAATGACCCCCACCTAACAATTAAGGCCATG GGGCACCAATGATACTGAAGCTACGAGTATACTGATTATGAAAACTTAAGTTTTGACTCCTACATAATCCCCACC CAGGACCTAACCCCTGGACAATTCCGGCTACTAGAGACAGACCACCGAATGGTTGTTCCCATAGAATCCCCTATT CGCATTCTTGTTTCCGCCGAAGATGTACTACACTCCTGGGCCCTTCCAGCCATGGGGGTAAAGATAGACGCGGTC CCAGGACGCCTTAACCAAACCGCCTTTATTGCCTCCCGCCCCGGGGTATTCTATGGGCAATGCTCAGAAATCTGT GGAGCAAACCACAGCTTTATACCCATCGTAGTAGAAGCGGTCCCACTATCTCACTTCGAAAACTGGTCCACCCTT ATACTAAAAGACGCCTCACTAGGAAGCTAA* >DL; Mouse Mouse ATGGCCTACCCATTCCAACTTGGTCTACAAGACGCCACATCCCCTATTATAGAAGAGCTAATAAATTTCCATGAT CACACACTAATAATTGTTTTCCTAATTAGCTCCTTAGTCCTCTATATCATCTCGCTAATATTAACAACAAAACTA ACACATACAAGCACAATAGATGCACAAGAAGTTGAAACCATTTGAACTATTCTACCAGCTGTAATCCTTATCATA ATTGCTCTCCCCTCTCTACGCATTCTATATATAATAGACGAAATCAACAACCCCGTATTAACCGTTAAAACCATA GGGCACCAATGATACTGAAGCTACGAATATACTGACTATGAAGACCTATGCTTTGATTCATATATAATCCCAACA AACGACCTAAAACCTGGTGAACTACGACTGCTAGAAGTTGATAACCGAGTCGTTCTGCCAATAGAACTTCCAATC CGTATATTAATTTCATCTGAAGACGTCCTCCACTCATGAGCAGTCCCCTCCCTAGGACTTAAAACTGATGCCATC CCAGGCCGACTAAATCAAGCAACAGTAACATCAAACCGACCAGGGTTATTCTATGGCCAATGCTCTGAAATTTGT GGATCTAACCATAGCTTTATGCCCATTGTCCTAGAAATGGTTCCACTAAAATATTTCGAAAACTGATCTGCTTCA ATAATT---------------------TAA* >DL; Rat Rat ATGGCTTACCCATTTCAACTTGGCTTACAAGACGCTACATCACCTATCATAGAAGAACTTACAAACTTTCATGAC CACACCCTAATAATTGTATTCCTCATCAGCTCCCTAGTACTTTATATTATTTCACTAATACTAACAACAAAACTA ACACACACAAGCACAATAGACGCCCAAGAAGTAGAAACAATTTGAACAATTCTCCCAGCTGTCATTCTTATTCTA ATTGCCCTTCCCTCCCTACGAATTCTATACATAATAGACGAGATTAATAACCCAGTTCTAACAGTAAAAACTATA GGACACCAATGATACTGAAGCTATGAATATACTGACTATGAAGACCTATGCTTTGACTCCTACATAATCCCAACC AATGACCTAAAACCAGGTGAACTTCGTCTATTAGAAGTTGATAATCGGGTAGTCTTACCAATAGAACTTCCAATT CGTATACTAATCTCATCCGAAGACGTCCTGCACTCATGAGCCATCCCTTCACTAGGGTTAAAAACCGACGCAATC CCCGGCCGCCTAAACCAAGCTACAGTCACATCAAACCGACCAGGTCTATTCTATGGCCAATGCTCTGAAATTTGC GGCTCAAATCACAGCTTCATACCCATTGTACTAGAAATAGTGCCTCTAAAATATTTCGAAAACTGATCAGCTTCT ATAATT---------------------TAA* >DL; Seal Seal ATGGCATACCCCCTACAAATAGGCCTACAAGATGCAACCTCTCCCATTATAGAGGAGTTACTACACTTCCATGAC CACACATTAATAATTGTGTTCCTAATTAGCTCATTAGTACTCTACATTATCTCACTTATACTAACCACGAAACTC ACCCACACAAGTACAATAGACGCACAAGAAGTGGAAACGGTGTGAACGATCCTACCCGCTATCATTTTAATTCTC ATTGCCCTACCATCATTACGAATCCTCTACATAATGGACGAGATCAATAACCCTTCCTTGACCGTAAAAACTATA GGACATCAGTGATACTGAAGCTATGAGTACACAGACTACGAAGACCTGAACTTTGACTCATATATGATCCCCACA CAAGAACTAAAGCCCGGAGAACTACGACTGCTAGAAGTAGACAATCGAGTAGTCCTCCCAATAGAAATAACAATC CGCATACTAATCTCATCAGAAGATGTACTCCACTCATGAGCCGTACCGTCCCTAGGACTAAAAACTGATGCTATC CCAGGACGACTAAACCAAACAACCCTAATAACCATACGACCAGGACTGTACTACGGTCAATGCTCAGAAATCTGT GGTTCAAACCACAGCTTCATACCTATTGTCCTCGAATTGGTCCCACTATCCCACTTCGAGAAATGATCTACCTCA ATGCTT---------------------TAA* >DL; Whale Whale ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTCCTACACTTTCACGAT CATACACTAATAATCGTTTTTCTAATTAGCTCTTTAGTTCTCTACATTATTACCCTAATGCTTACAACCAAATTA ACACATACTAGTACAATAGACGCCCAAGAAGTAGAAACTGTCTGAACTATCCTCCCAGCCATTATCTTAATTTTA ATTGCCTTGCCTTCATTACGGATCCTTTACATAATAGACGAAGTCAATAACCCCTCCCTCACTGTAAAAACAATA GGTCACCAATGATATTGAAGCTATGAGTATACCGACTACGAAGACCTAAGCTTCGACTCCTATATAATCCCAACA TCAGACCTAAAGCCAGGAGAACTACGATTATTAGAAGTAGATAACCGAGTTGTCTTACCTATAGAAATAACAATC CGAATATTAGTCTCATCAGAAGACGTACTCCACTCATGGGCCGTACCCTCCTTGGGCCTAAAAACAGATGCAATC CCAGGACGCCTAAACCAAACAACCTTAATATCAACACGACCAGGCCTATTTTATGGACAATGCTCAGAGATCTGC GGCTCAAACCACAGTTTCATACCAATTGTCCTAGAACTAGTACCCCTAGAAGTCTTTGAAAAATGATCTGTATCA ATACTA---------------------TAA* >DL; Frog Frog ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTACTTCACTTCCACGAC CATACCCTCATAGCCGTTTTTCTTATTAGTACGCTAGTTCTTTACATTATTACTATTATAATAACTACTAAACTA ACTAATACAAACCTAATGGACGCACAAGAGATCGAAATAGTGTGAACTATTATACCAGCTATTAGCCTCATCATA ATTGCCCTTCCATCCCTTCGTATCCTATATTTAATAGATGAAGTTAATGATCCACACTTAACAATTAAAGCAATC GGCCACCAATGATACTGAAGCTACGAATATACTAACTATGAGGATCTCTCATTTGACTCTTATATAATTCCAACT AATGACCTTACCCCTGGACAATTCCGGCTGCTAGAAGTTGATAATCGAATAGTAGTCCCAATAGAATCTCCAACC CGACTTTTAGTTACAGCCGAAGACGTCCTCCACTCGTGAGCTGTACCCTCCTTGGGTGTCAAAACAGATGCAATC CCAGGACGACTTCATCAAACATCATTTATTGCTACTCGTCCGGGAGTATTTTACGGACAATGTTCAGAAATTTGC GGAGCAAACCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCGCTAACCGACTTTGAAAACTGATCTTCATCA ATACTA---GAAGCATCACTA------AGA* weblogo-3.8.0/tests/data/example1.saf000066400000000000000000000005471467613320200174540ustar00rootroot00000000000000t2_11751 EFQEDQENVN PEKAAPAQQP RTRAGLAVLR AGNSRGAGGA PTLPETLNVA name_1 EFQEDQENVN PEKAAPAQQP RTRAGLAVLR AGNSRGAGGA PTLPETLNVA name_2 ...EDQENvk PEKAAPAQQP RTRAGLAVLR AGNSRG.... ...PETLNV. name_22 ...EDQENvk PEKAAPAQQP RTRAGLAVLR AGNSRG.... ...PETLNV. t2_11751 GGAPTLPETL NVAGGAPTLP ETLNVAGGAP TLPETLNV name_1 GGAPTLPETL NVAGGAPTLP ETLNVAGGAP TLPETLNV weblogo-3.8.0/tests/data/example2.saf000066400000000000000000000010621467613320200174460ustar00rootroot00000000000000 10 20 30 40 t2_11751 EFQEDQENVN PEKAAPAQQP RTRAGLAVLR AGNSRGAGGA PTLPETLNVA name_1 EFQEDQENVN PEKAAPAQQP RTRAGLAVLR AGNSRGAGGA PTLPETLNVA name_2 ...EDQENvk PEKAAPAQQP RTRAGLAVLR AGNSRG.... ...PETLNV. name_22 ...EDQENvk PEKAAPAQQP RTRAGLAVLR AGNSRG.... ...PETLNV. 50 60 70 80 90 t2_11751 GGAPTLPETL NVAGGAPTLP ETLNVAGGAP TLPETLNV name_22 .......... .......... .......... ........ name_1 GGAPTLPETL NVAGGAPTLP ETLNVAGGAP TLPETLNV name_2 .......... NVAGGAPTLP weblogo-3.8.0/tests/data/genbank/000077500000000000000000000000001467613320200166445ustar00rootroot00000000000000weblogo-3.8.0/tests/data/genbank/NT_019265.gb000066400000000000000000000065021467613320200203300ustar00rootroot00000000000000LOCUS NT_019265 1250660 bp DNA CON 16-OCT-2001 DEFINITION Homo sapiens chromosome 1 working draft sequence segment. ACCESSION NT_019265 VERSION NT_019265.6 GI:16156830 KEYWORDS . SOURCE human. ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 1250660) AUTHORS NCBI Annotation Project. TITLE Direct Submission JOURNAL Submitted (11-OCT-2001) National Center for Biotechnology Information, NIH, Bethesda, MD 20894, USA COMMENT GENOME ANNOTATION REFSEQ: NCBI contigs are derived from assembled genomic sequence data. They may include both draft and finished sequence. On Oct 16, 2001 this sequence version replaced gi:15294341. COMPLETENESS: not full length. FEATURES Location/Qualifiers source 1..1250660 /organism="Homo sapiens" /db_xref="taxon:9606" /chromosome="1" source 1..3290 /note="Accession AL391218 sequenced by The Sanger Centre" /organism="Homo sapiens" /db_xref="taxon:9606" /clone="RP11-13G5" misc_feature 215902..365470 /standard_name="RP11-242F24" /note="FISH-mapped clone" variation 217508 /allele="T" /allele="C" /db_xref="dbSNP:811400" mRNA join(342430..342515,363171..363300,365741..365814, 376398..376499,390169..390297,391257..391379, 392606..392679,398230..398419,399082..399167, 399534..399650,405844..405913,406704..406761, 406868..407010,407962..408091,408508..409092) /gene="FLJ10737" /product="hypothetical protein FLJ10737" /transcript_id="XM_057697.1" /db_xref="LocusID:55735" CONTIG join(AL391218.9:105173..108462,gap(100), complement(AL512330.12:1..182490), complement(AL590128.4:9034..81287),gap(100), AL591163.7:85799..94832,gap(100),AL591163.7:94933..113245,gap(100), AL591163.7:42173..44897,complement(AL590128.4:1..6208), AL591163.7:51307..52779,gap(100),AL591163.7:52880..85698,gap(100), AL591163.7:113346..126143,complement(AL159177.12:184729..186047), AL031447.4:1..112158,complement(AL159177.12:1..72671), complement(AL591866.12:23507..86371),AL031848.11:1..142965, AL031847.17:1..166418,AL035406.25:1..161651, complement(AL356261.20:94599..98345), complement(AC026968.3:54432..54579),gap(100), complement(AC062024.2:98529..107911),gap(100), AC062024.2:7713..11594,gap(100),complement(AL356261.20:1..94498), complement(AL356693.18:19988..70853),gap(100), AL356693.18:17351..19887,gap(100), complement(AL356693.18:3037..17250),gap(100), complement(AL356693.18:1..2936),gap(100),AC026968.3:675..2393, gap(100),AC026968.3:1..574,gap(100),AL356261.20:179029..182233) // weblogo-3.8.0/tests/data/genbank/cor6_6.gb000066400000000000000000000351671467613320200202700ustar00rootroot00000000000000LOCUS ATCOR66M 513 bp mRNA PLN 02-MAR-1992 DEFINITION A.thaliana cor6.6 mRNA. ACCESSION X55053 VERSION X55053.1 GI:16229 KEYWORDS antifreeze protein homology; cold-regulated gene; cor6.6 gene; KIN1 homology. SOURCE thale cress. ORGANISM Arabidopsis thaliana Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; euphyllophytes; Spermatophyta; Magnoliophyta; eudicotyledons; Rosidae; Capparales; Brassicaceae; Arabidopsis. REFERENCE 1 (bases 1 to 513) AUTHORS Thomashow,M.F. TITLE Direct Submission JOURNAL Submitted (01-FEB-1991) M.F. Thomashow, Dept. Crop and Soil Sciences, Dept. Microbiology, Michigan State University, East Lansing, Michigan 48824, USA REFERENCE 2 (bases 1 to 513) AUTHORS Gilmour,S.J., Artus,N.N. and Thomashow,M.F. TITLE cDNA sequence analysis and expression of two cold-regulated genes of Arabidopsis thaliana JOURNAL Plant Mol. Biol. 18 (1), 13-21 (1992) MEDLINE 92119220 COMMENT Cor6.6 homologous to KIN1. KIN1 is a cold-regulated Arabidopsis gene with suggested similarity to type I fish antifreeze proteins. FEATURES Location/Qualifiers source 1..513 /organism="Arabidopsis thaliana" /strain="Columbia" /db_xref="taxon:3702" gene 50..250 /gene="cor6.6" CDS 50..250 /gene="cor6.6" /note="cold regulated" /codon_start=1 /protein_id="CAA38894.1" /db_xref="GI:16230" /db_xref="SWISS-PROT:P31169" /translation="MSETNKNAFQAGQAAGKAEEKSNVLLDKAKDAAAAAGASAQQAG KSISDAAVGGVNFVKDKTGLNK" BASE COUNT 194 a 82 c 104 g 133 t ORIGIN 1 aacaaaacac acatcaaaaa cgattttaca agaaaaaaat atctgaaaaa tgtcagagac 61 caacaagaat gccttccaag ccggtcaggc cgctggcaaa gctgaggaga agagcaatgt 121 tctgctggac aaggccaagg atgctgctgc tgcagctgga gcttccgcgc aacaggcggg 181 aaagagtata tcggatgcgg cagtgggagg tgttaacttc gtgaaggaca agaccggcct 241 gaacaagtag cgatccgagt caactttggg agttataatt tcccttttct aattaattgt 301 tgggattttc aaataaaatt tgggagtcat aattgattct cgtactcatc gtacttgttg 361 ttgtttttag tgttgtaatg ttttaatgtt tcttctccct ttagatgtac tacgtttgga 421 actttaagtt taatcaacaa aatctagttt aagttctaaa aaaaaaaaaa aaaaaaaaaa 481 aaaaaaaaaa aaaaaaaaaa aaaaaaaaaa aaa // LOCUS ATKIN2 880 bp DNA PLN 23-JUL-1992 DEFINITION A.thaliana kin2 gene. ACCESSION X62281 VERSION X62281.1 GI:16353 KEYWORDS kin2 gene. SOURCE thale cress. ORGANISM Arabidopsis thaliana Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; euphyllophytes; Spermatophyta; Magnoliophyta; eudicotyledons; Rosidae; Capparales; Brassicaceae; Arabidopsis. REFERENCE 1 (bases 1 to 880) AUTHORS Borg-Franck,M.E. TITLE Direct Submission JOURNAL Submitted (27-SEP-1991) M.E. Borg-Franck, Inst of Biotechnology, University of Helsinki, Karvaamokuja 3, SF-00380 Helsinki, FINLAND REFERENCE 2 (bases 1 to 880) AUTHORS Kurkela,S. and Borg-Franck,M. TITLE Structure and expression of kin2, one of two cold- and ABA-induced genes of Arabidopsis thaliana JOURNAL Plant Mol. Biol. 19 (4), 689-692 (1992) MEDLINE 92329728 FEATURES Location/Qualifiers source 1..880 /organism="Arabidopsis thaliana" /strain="ssp. L. Heynh, Colombia" /db_xref="taxon:3702" TATA_signal 9..20 exon 44..160 /gene="kin2" /number=1 prim_transcript 44..>579 /gene="kin2" mRNA join(44..160,320..390,504..>579) /gene="kin2" gene 44..579 /gene="kin2" CDS join(104..160,320..390,504..579) /gene="kin2" /codon_start=1 /protein_id="CAA44171.1" /db_xref="GI:16354" /db_xref="SWISS-PROT:P31169" /translation="MSETNKNAFQAGQAAGKAERRRAMFCWTRPRMLLLQLELPRNRA GKSISDAAVGGVNFVKDKTGLNK" intron 161..319 /gene="kin2" /number=1 exon 320..390 /gene="kin2" /number=2 intron 391..503 /gene="kin2" /number=2 exon 504..>579 /gene="kin2" /number=3 polyA_signal 620..625 polyA_signal 641..646 polyA_site 785 polyA_site 800 BASE COUNT 263 a 155 c 160 g 302 t ORIGIN 1 atttggccta taaatataaa cccttaagcc cacatatctt ctcaatccat cacaaacaaa 61 acacacatca aaaacgattt tacaagaaaa aaatatctga aaaatgtcag agaccaacaa 121 gaatgccttc caagccggtc aggccgctgg caaagctgag gtactctttc tctcttagaa 181 cagagtactg atagattgtt caagttataa ctctttgaaa acagttgaaa cttgatcact 241 cctagaactt ccattttctt gtttaattta gtttgtcgta attatgtaat tgattttgtg 301 ttgaccatgg ttgttatata ggagaagagc aatgttctgc tggacaaggc caaggatgct 361 gctgctgcag ctggagcttc cgcgcaacag gtaaacgatc tatacacaca ttatgacatt 421 tatgtaaaga atgaaaagtc ttcttagagc atacatttac gcagatttct gatattttca 481 tatggtttga tgtaaatgtt ataggcggga aagagtatat cggatgcggc agtgggaggt 541 gttaacttcg tgaaggacaa gaccggcctg aacaagtagc gatccgagtc aactttggga 601 gttataattt cccttttcta attaattgtt gggattttca aataaaattt gggagtcata 661 attgattctc gtactcatcg tacttgttgt tgtttttagt gttgtaatgt tttaatgttt 721 cttctccctt tagatgtact acgtttggaa ctttaagttt aatcaacaaa atctagttta 781 agttctaaga actttgtttt accatcctct tttttattgc acttaatgct tatagacttt 841 tatctccatc catttctcaa ttcggctacg ttgaattata // LOCUS BNAKINI 441 bp mRNA PLN 27-APR-1993 DEFINITION Rapeseed Kin1 protein (kin1) mRNA, complete cds. ACCESSION M81224 VERSION M81224.1 GI:167145 KEYWORDS . SOURCE Brassica napus (cultivar Jet neuf) cold induced leaf cDNA to mRNA. ORGANISM Brassica napus Eukaryota; Viridiplantae; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids II; Brassicales; Brassicaceae; Brassica. REFERENCE 1 (bases 1 to 441) AUTHORS Orr,W., Iu,B., White,T., Robert,L.S. and Singh,J. TITLE Nucleotide sequence of a winter B. napus Kin 1 cDNA JOURNAL Plant Physiol. 98, 1532-1534 (1992) FEATURES Location/Qualifiers source 1..441 /organism="Brassica napus" /cultivar="Jet neuf" /db_xref="taxon:3708" /dev_stage="cold induced" /tissue_type="leaf" gene 34..300 /gene="kin1" CDS 34..231 /gene="kin1" /codon_start=1 /evidence=experimental /protein_id="AAA32993.1" /db_xref="GI:167146" /translation="MADNKQSFQAGQASGRAEEKGNVLMDKVKDAATAAGASAQTAGQ KITEAAGGAVNLVKEKTGMNK" polyA_signal 241..247 /gene="kin1" /note="putative" polyA_signal 294..300 /gene="kin1" /note="putative" polyA_site 441 /gene="kin1" BASE COUNT 129 a 76 c 110 g 126 t ORIGIN 1 aaaaaaacac aacaaaactc aataaataaa caaatggcag acaacaagca gagcttccaa 61 gccggtcaag cctctggtcg tgctgaggag aagggtaatg tgctgatgga caaggtcaag 121 gatgctgcta ccgcagctgg agcgtctgcg caaaccgcgg gacagaagat aacggaggcg 181 gcagggggag ccgttaatct cgtgaaggag aagaccggca tgaacaagta gccccattgg 241 aaataaaatt gggagttata gtttcccttt ttaatgttaa tcgttgtggt tttaaataaa 301 aattgggtgt tctaattgat cttcaccgta gttgttgttg ttgttgtttt tagtgtttga 361 agtaatgttt tcaaccttta ggtgtatgtc ttgatgttta tgtacttagt tcccccttaa 421 tgaacatctg atttaagctt c // LOCUS ARU237582 206 bp DNA PLN 24-MAR-1999 DEFINITION Armoracia rusticana csp14 gene (partial), exons 2-3. ACCESSION AJ237582 VERSION AJ237582.1 GI:4538892 KEYWORDS cold shock protein; csp14 gene. SOURCE horseradish. ORGANISM Armoracia rusticana Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta; euphyllophytes; Spermatophyta; Magnoliophyta; eudicotyledons; Rosidae; Capparales; Brassicaceae; Armoracia. REFERENCE 1 (bases 1 to 206) AUTHORS Baymiev,A.K., Gimalov,F.R. and Vakhitov,V.A. JOURNAL Unpublished REFERENCE 2 (bases 1 to 206) AUTHORS Baymiev,A.K. TITLE Direct Submission JOURNAL Submitted (20-MAR-1999) Baymiev A.K., Departament of Biochemistry and Cytochemistry, Ufa Scientific Centre, pr. Oktyabrya 69, Ufa, Bashkortostan, Russia, 450054, RUSSIA FEATURES Location/Qualifiers source 1..206 /organism="Armoracia rusticana" /db_xref="taxon:3704" /country="Russia:Bashkortostan" mRNA join(<1..48,143..>206) /gene="csp14" exon 1..48 /gene="csp14" /number=2 gene 1..206 /gene="csp14" CDS join(<1..48,143..>206) /gene="csp14" /codon_start=2 /product="cold shock protein" /protein_id="CAB39890.1" /db_xref="GI:4538893" /translation="DKAKDAAAAAGASAQQAGKNISDAAAGGVNFVKEKTG" intron 49..142 /gene="csp14" /number=2 exon 143..206 /gene="csp14" /number=3 BASE COUNT 65 a 38 c 53 g 48 t 2 others ORIGIN 1 ggacaaggcc aaggatgctg ctgctgcagc tggagcttcc gcgcaacaag taaacagata 61 cacacacatg acacatatat aantacatat cacaagtagg tcgtagattt ctgatatntt 121 tgtattgtgt attacgtata taggcgggaa agaacatatc ggatgcagca gctggaggtg 181 ttaacttcgt gaaggagaag accggc // LOCUS BRRBIF72 282 bp mRNA PLN 01-MAR-1996 DEFINITION Brassica rapa (clone bif72) kin mRNA, complete cds. ACCESSION L31939 VERSION L31939.1 GI:1209261 KEYWORDS . SOURCE Brassica rapa flower cDNA to mRNA. ORGANISM Brassica rapa Eukaryota; Viridiplantae; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids II; Brassicales; Brassicaceae; Brassica. REFERENCE 1 (bases 1 to 282) AUTHORS Kim,J.-B., Kim,H.-U., Park,B.-S., Yun,C.-H., Cho,W.-S., Ryu,J.-C. and Chung,T.-Y. TITLE Nucleotide sequences of kin gene in chinese cabbage JOURNAL Unpublished (1994) FEATURES Location/Qualifiers source 1..282 /organism="Brassica rapa" /db_xref="taxon:3711" /dev_stage="flower" gene 24..221 /gene="kin" CDS 24..221 /gene="kin" /codon_start=1 /protein_id="AAA91051.1" /db_xref="GI:1209262" /translation="MADNKQSFQAGQAAGRAEEKGNVLLMDKVKDAATAAGALQTAGQ KITEAAGGAVNLVKEKTGMNK" BASE COUNT 88 a 56 c 80 g 58 t ORIGIN 1 aacaaaactc aataaataaa caaatggcag acaacaagca gagcttccaa gccggtcaag 61 ccgctggtcg tgctgaggag aagggtaatg tgctgctgat ggacaaggtc aaggatgctg 121 ctaccgcagc tggagctctc caaaccgcgg gacagaagat aacggaggcg gcagggggag 181 ccgttaatct cgtgaaggag aagaccggca tgaacaagta gccccattgg aaacaaaatt 241 gggagttata gtttcctttt taatattaat cgttgtggtt tt // LOCUS AF297471 497 bp DNA PLN 14-SEP-2000 DEFINITION Brassica napus BN28a (BN28a) gene, complete cds. ACCESSION AF297471 VERSION AF297471.1 GI:10121868 KEYWORDS . SOURCE rape. ORGANISM Brassica napus Eukaryota; Viridiplantae; Embryophyta; Tracheophyta; Spermatophyta; Magnoliophyta; eudicotyledons; core eudicots; Rosidae; eurosids II; Brassicales; Brassicaceae; Brassica. REFERENCE 1 (bases 1 to 497) AUTHORS Byass,L.J. and Flanagan,A.M. TITLE BN28a, a low temperature-induced gene of Brassica napus JOURNAL Unpublished REFERENCE 2 (bases 1 to 497) AUTHORS Byass,L.J. and Flanagan,A.M. TITLE Direct Submission JOURNAL Submitted (18-AUG-2000) AFNS, University of Alberta, 4-10 Agriculture/Forestry Centre, Edmonton, Alberta T6G 2P5, Canada FEATURES Location/Qualifiers source 1..497 /organism="Brassica napus" /cultivar="Cascade" /db_xref="taxon:3708" mRNA join(<1..54,241..309,423..>497) /gene="BN28a" /product="BN28a" gene <1..>497 /gene="BN28a" CDS join(1..54,241..309,423..497) /gene="BN28a" /note="low temperature-induced; similar to Brassica napus Kin1 in Accession Number M81224" /codon_start=1 /product="BN28a" /protein_id="AAG13407.1" /db_xref="GI:10121869" /translation="MADNKQSFQAGQAAGRAEEKGNVLMDKVKDAATAAGASAQTAGQ KITEAAGGAVNLVKEKTGMNK" BASE COUNT 155 a 89 c 116 g 137 t ORIGIN 1 atggcagaca acaagcagag cttccaagcc ggtcaagccg ctggtcgtgc tgaggtctct 61 ttctctcttt aactctctga tcaaatgcag ttgctgcggt taaacaatca cactttataa 121 aataaagaga agttatttat attttcttga accaagtaaa tgaatgtatt ttgaccaaaa 181 aaagaagaag taaatgaatg tattaattga tttcgtgtgg acaatggtgt gtaaatatag 241 gagaagggta atgtgctgat ggacaaggtc aaggatgctg ctaccgcagc tggagcgtct 301 gcgcaaaccg taagcgatct accccatgat atataaataa acatacgtct ctactctcta 361 ctgtacatgt tcgtagatct catatctttt tatgctgttc taacatgtat ttacgtttat 421 aggcgggaca gaagataacg gaggcggcag ggggagccgt taatctcgtg aaggagaaga 481 ccggcatgaa caagtag // weblogo-3.8.0/tests/data/genbank/cox2.gb000066400000000000000000000035111467613320200200310ustar00rootroot00000000000000LOCUS cox2_leita 176 bp DEFINITION cox2_leita 421 bp, 176 bases, F21F24E0 checksum. ORIGIN 1 MAFILSFWMI FLLDSVIVLL SFVCFVCVWI CALLFSTVLL VSKLNNIYCT 51 WDFTASKFID VYWFTIGGMF SLGLLLRLCL LLYFGHLNFV SFDLCKVVGF 101 QWYWVYFIFG ETTIFSNLIL ESDYMIGDLR LLQCNHVLTL LSLVIYKLWL 151 SAVDVIHSFA ISSLGVKVEN LVAVMK // LOCUS cox2_crifa 210 bp DEFINITION cox2_crifa 421 bp, 210 bases, 58772705 checksum. ORIGIN 1 MAFILSFWMI FLIDAVIVLL SFVCFVCIWI CSLFFSSFLL VSKINNVYCT 51 WDFTASKFID AYWFTIGGMF VLCLLLRLCL LLYFGCLNFV SFDLCKVVGF 101 QWYWVYFIFG ETTIFSNLIL ESDYLIGDLR LLQCNHVLTL LSLVIYKLWL 151 SAVDVIHSFA VSSLGIKVDC IPGRCNEIVL FSSNNSTVYG QCSELCGVLH 201 GFMPIVICFI // LOCUS cox2_bsalt.pep 210 bp DEFINITION cox2_bsalt.pep 421 bp, 210 bases, E1FEF52B checksum. ORIGIN 1 MSFIISFWML FLIDSLIVLL SGAIFVCIWI CSLFFLCILF ICKLDYIFCS 51 WDFISAKFID LYWFTLGCLF IVCLLIRLCL LLYFSCLNFV CFDLCKCIGF 101 QWYWVYFIFG ETTIFSNLIL ESDYLIGDLR LLQCNHVLTL LSLVIYKVWL 151 SAIDVIHSFT LANLGIKVD? ?PGRCNEIII FSNSSSTIYG QCSELCGVLH 201 GFMPIVVSFV // LOCUS cox2_trybb 209 bp DEFINITION cox2_trybb 421 bp, 209 bases, A81E7510 checksum. ORIGIN 1 MSFILTFWMI FLMDSIIVLI SFSIFLSVWI CALIIATVLT VTKINNIYCT 51 WDFISSKFID TYWFVLGMMF ILCLLLRLCL LLYFSCINFV SFDLCKVIGF 101 QWYWVYFLFG ETTIFSNLIL ESDYLIGDLR ILQCNHVLTL LSLVIYKLWV 151 SAVDVIHSFT ISSLGIKVEN PGRCNEIILF ATNNATLYGQ CSELCGVLHG 201 FMPIVINFI // LOCUS cox2_tborr 210 bp DEFINITION cox2_tborr 421 bp, 210 bases, 8240CB12 checksum. ORIGIN 1 MLFFINQLLL LLVDTFVILE IFSLFVCVFI IVMYILFINY NIFLKNINVY 51 LDFIGSKYLD LYWFLIGIFF VIVLLIRLCL LLYYSWISLL IFDLCKIMGF 101 QWYWIFFVFK ENVIFSNLLI ESDYWIGDLR LLQCNNTFNL ICLVVYKIWV 151 TSIDVIHSFT ISTLGIKIDC IPGRCNELTI FSNIGGTFYG QCSELCGVLH 201 GFMPVVIEFI // weblogo-3.8.0/tests/data/genbank/dbsource_wrap.gb000066400000000000000000000045231467613320200220210ustar00rootroot00000000000000LOCUS SCX3_BUTOC 64 aa linear INV 16-OCT-2001 DEFINITION Neurotoxin III. ACCESSION P01485 PID g134354 VERSION P01485 GI:134354 DBSOURCE swissprot: locus SCX3_BUTOC, accession P01485; class: standard. created: Jul 21, 1986. sequence updated: Jul 21, 1986. annotation updated: Oct 16, 2001. xrefs: gi: gi: 69530 xrefs (non-sequence databases): HSSP P01484, InterPro IPR003614, InterPro IPR002061, InterPro IPR001219, Pfam PF00537, PRINTS PR00284, ProDom PD000908, SMART SM00505 KEYWORDS Neurotoxin; Sodium channel inhibitor; Amidation. SOURCE Tunisian scorpion. ORGANISM Buthus occitanus tunetanus Eukaryota; Metazoa; Arthropoda; Chelicerata; Arachnida; Scorpiones; Buthoidea; Buthidae; Buthus. REFERENCE 1 (residues 1 to 64) AUTHORS Vargas,O., Gregoire,J., Martin,M.-F., Bechis,G. and Rochat,H. TITLE Neurotoxins from the venoms of two scorpions: Buthus occitanus tunetanus and Buthus occitanus mardochei JOURNAL Toxicon 20, 79-79 (1982) REMARK SEQUENCE. COMMENT [FUNCTION] BINDS TO SODIUM CHANNELS AND INHIBITS THE INACTIVATION OF THE ACTIVATED CHANNELS, THEREBY BLOCKING NEURONAL TRANSMISSION. [SUBCELLULAR LOCATION] SECRETED. [SIMILARITY] BELONGS TO THE ALPHA/BETA-SCORPION TOXIN FAMILY. ALPHA-TOXIN SUBFAMILY. FEATURES Location/Qualifiers source 1..64 /organism="Buthus occitanus tunetanus" /db_xref="taxon:6871" Protein 1..64 /product="Neurotoxin III" Bond bond(12,63) /bond_type="disulfide" /note="BY SIMILARITY." Bond bond(16,36) /bond_type="disulfide" /note="BY SIMILARITY." Bond bond(22,46) /bond_type="disulfide" /note="BY SIMILARITY." Bond bond(26,48) /bond_type="disulfide" /note="BY SIMILARITY." Site 64 /site_type="amidation" ORIGIN 1 vkdgyivddr nctyfcgrna ycneectklk gesgycqwas pygnacycyk vpdhvrtkgp 61 grcn // weblogo-3.8.0/tests/data/genbank/iro.gb000066400000000000000000000111731467613320200177520ustar00rootroot00000000000000LOCUS IRO125195 1326 bp mRNA PRI 11-AUG-1999 DEFINITION Homo sapiens mRNA full length insert cDNA clone EUROIMAGE 125195. ACCESSION AL109817 VERSION AL109817.1 GI:5731880 KEYWORDS FLI_CDNA. SOURCE human. ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 1326) AUTHORS Auffray,C., Ansorge,W., Ballabio,A., Estivill,X., Gibson,K., Lehrach,H., Poustka,A. and Lundeberg,J. TITLE The European IMAGE consortium for integrated Molecular analysis of human gene transcripts JOURNAL Unpublished REFERENCE 2 (bases 1 to 1326) AUTHORS Carim,L., Estivill,X., Sumoy,L. and Escarceller,M. TITLE Direct Submission JOURNAL Submitted (11-AUG-1999) Dept. Genetica Molecular, Institut de Recerca Oncologica (IRO), Hospital Duran i Reynals, Autovia de Castelldefels Km 2,7 L'Hospitalet de Llobregat, 08907 Barcelona, Catalunya, SPAIN. Tel: ++34-93-260-7775 Fax: ++34-93-260-7776 WWW site: http://www.iro.es e-mail enquiries: lsumoy@iro.es, mescarceller@iro.es COMMENT EURO-IMAGE Consortium Contact: Auffray C CNRS UPR 420 - Genetique Moleculaire et Biologie du Developement IFR 1221 - Rue Guy Moquet 19, Batiment G - BP 8 94801 Villejuif Cedex, FRANCE Tel: ++33-1-49 58 34 98 Fax: ++33-1-49 58 35 09 e-mail: auffray@infobiogen.fr This clone is available royalty-free through IMAGE Consortium Distributors. IMPORTANT: This sequence represents the full insert of this IMAGE cDNA clone. No attempt has been made to verify whether this corresponds to the full-length of the original mRNA from which it was derived. FEATURES Location/Qualifiers source 1..1326 /organism="Homo sapiens" /db_xref="taxon:9606" /chromosome="21" /clone="IMAGE cDNA clone 125195" /clone_lib="Soares fetal liver spleen 1NFLS" /note="contains Alu repeat; likely to be be derived from unprocessed nuclear RNA or genomic DNA; encodes putative exons identical to FTCD; formimino transferase cyclodeaminase; formimino transferase (EC 2.1.2.5) /formimino tetrahydro folate cyclodeaminase (EC 4.3.1.4)" gene 341..756 /gene="FTCD" exon 341..384 /gene="FTCD" /number=1 intron 385..617 /gene="FTCD" /number=1 exon 618..756 /gene="FTCD" /number=2 BASE COUNT 258 a 404 c 400 g 264 t ORIGIN 1 cacaggccca gagccactcc tgcctacagg ttctgagggc tcaggggacc tcctgggccc 61 tcaggctctt tagctgagaa taagggccct gagggaacta cctgcttctc acatccccgg 121 gtctctgacc atctgctgtg tgccccgacc ccccctaccc tgctcctcca ccaagcctga 181 tgccaagggc tataaaccac tggcccaaca gaagcttggt tcccagagaa ctggtccctg 241 cctgggacat gctccttgct acagcccctt gtgggagctc agagggcatg gctgctcccc 301 ctacggtccc tcgcccagtg gttctgtctc tttatggcag gaagcaatga ggctccccaa 361 gaacacacct gaggaaaagg acaggtgagc ctggagggcc ggccgcaccg tgggcctctg 421 tgtctgggga gttggtggcc aggatcccga gtacctgggt gctgtgacgg ggcgtggttg 481 gcctgggcgt gctgggtgtt tgggaatgac ttcccatcgc ccgcttctgc agcctgctca 541 gccctgttgg ggtgcagtgt gtccactgcc tgcctgtgtg tgccgctgtg ctcaggctct 601 cctcttgctc ctttcaggcg cacggcggcc ctacaggagg gtctgaggcg ggcagtctct 661 gtgccgctga cgctggcgga gacggtggcc tcgctgtggc cggccctgca ggaactggcc 721 cggtgtggga acctggcctg ccggtcagac ctccaggtag gggggcccgg gggaccccag 781 gcctcctgcc gcaaagcagg aagcagctgt tggggctgag ttgctggaga gcacggtggt 841 tggctgggct gagccaggta gggagacctc acttcacggg cagttcccgg ggctttggcc 901 tcctccaaca gggccggggt gtccgctgcc ttctaagatc tcgctcacgg cggcaccaca 961 gacggagacc caaatgtgtc tgcagagccc accctgacca ctgtataagt gtatactccc 1021 ccaagacccc ttgtatcacc cccactgtcg tgttctagaa aacacctatg tcagcccagg 1081 cacaatggtt ctcgcctgtg gtcccagcac tttgggaggc tgaggcggga ggatcacttg 1141 aatagaggag gtcgagacca gcctgggcaa catagtggga ccctggctgt acaatagata 1201 catatgagcc aggcacggtg gtgcctgtgg tcccagctcc ctgcccagcc agcctcctgt 1261 ctccagagaa gttctccatt aaaaaataat ttagcaaaaa aaaaaaaaaa aaaaaaaaaa 1321 aaaaaa // weblogo-3.8.0/tests/data/genbank/noref.gb000066400000000000000000000103371467613320200202730ustar00rootroot00000000000000LOCUS NM_006141 1622 bp mRNA PRI 01-NOV-2000 DEFINITION Homo sapiens dynein, cytoplasmic, light intermediate polypeptide 2 (DNCLI2), mRNA. ACCESSION NM_006141 VERSION NM_006141.1 GI:5453633 KEYWORDS . SOURCE human. ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. The reference sequence was derived from AF035812.1. FEATURES Location/Qualifiers source 1..1622 /organism="Homo sapiens" /db_xref="taxon:9606" /map="16" gene 1..1622 /gene="DNCLI2" /note="LIC2" /db_xref="LocusID:1783" CDS 7..1485 /gene="DNCLI2" /note="similar to R. norvegicus and G. gallus dynein light intermediate chain 2, Swiss-Prot Accession Numbers Q62698 and Q90828, respectively" /codon_start=1 /db_xref="LocusID:1783" /product="dynein, cytoplasmic, light intermediate polypeptide 2" /protein_id="NP_006132.1" /db_xref="GI:5453634" /translation="MAPVGVEKKLLLGPNGPAVAAAGDLTSEEEEGQSLWSSILSEVS TRARSKLPSGKNILVFGEDGSGKTTLMTKLQGAEHGKKGRGLEYLYLSVHDEDRDDHT RCNVWILDGDLYHKGLLKFAVSAESLPETLVIFVADMSRPWTVMESLQKWASVLREHI DKMKIPPEKMRELERKFVKDFQDYMEPEEGCQGSPQRRGPLTSGSDEENVALPLGDNV LTHNLGIPVLVVCTKCDAVSVLEKEHDYRDEHLDFIQSHLRRFCLQYGAALIYTSVKE EKNLDLLYKYIVHKTYGFHFTTPALVVEKDAVFIPAGWDNEKKIAILHENFTTVKPED AYEDFIVKPPVRKLVHDKELAAEDEQVFLMKQQSLLAKQPATPTRASESPARGPSGSP RTQGRGGPASVPSSSPGTSVKKPDPNIKNNAASEGVLASFFNSLLSKKTGSPGSPGAG GVQSTAKKSGQKTVLSNVQEELDRMTRKPDSMVTNSSTENEA" BASE COUNT 474 a 356 c 428 g 364 t ORIGIN 1 ggcaagatgg cgccggtggg ggtggagaag aagctgctgc taggtcccaa cgggcccgcg 61 gtggcggccg ccggcgacct gaccagtgag gaggaggaag gccagagcct atggtcctcc 121 attctgagcg aagtgtccac ccgcgccagg tccaagctgc cgtccggcaa gaacatcctg 181 gtcttcggtg aagatggttc tggtaaaaca accctcatga ctaaactaca aggagctgag 241 catggcaaaa aaggaagagg cctagaatat ctctacctca gtgtccatga tgaggaccga 301 gatgatcaca cgcgctgcaa cgtgtggatt ctggatggag acttgtacca caaaggcctg 361 ctgaaatttg cagtttctgc tgaatccttg ccagagaccc tcgtcatttt tgttgcagac 421 atgtctagac cttggactgt gatggaatct ctgcagaaat gggctagtgt tttacgtgag 481 cacattgata aaatgaaaat tccaccagaa aaaatgaggg agctggaacg gaagtttgtg 541 aaagattttc aagactatat ggaacctgaa gaaggttgtc aaggttcccc acagagaaga 601 ggccctctga cctcaggctc cgatgaagaa aatgttgccc tgcctctggg tgacaatgtg 661 ctgactcata acctggggat cccggtgttg gtggtgtgca caaagtgtga tgcggtgagt 721 gtcctggaga aggagcacga ttacagggat gagcatttgg actttatcca gtcacacctg 781 cggaggttct gccttcagta tggagctgcc ttgatttaca catcagtgaa agaagagaaa 841 aacctcgact tgttgtataa gtatattgtt cataaaacat acggtttcca cttcaccaca 901 cctgccttag ttgtggaaaa ggatgccgtt tttatacctg caggctggga caatgaaaag 961 aaaatagcta ttttacatga aaattttaca accgtgaagc cggaagatgc atatgaagac 1021 tttattgtga aacctcccgt gagaaagctg gtccacgaca aagagttggc agcagaagat 1081 gagcaggtgt tcctaatgaa gcaacagtca ctccttgcca agcaaccagc cactcccacg 1141 agagcttctg aatctcctgc aagaggaccc tctggctctc caaggaccca gggtcgggga 1201 gggccagcca gtgtgcctag ctcctcccca ggcacgtcag taaaaaagcc ggacccaaac 1261 atcaaaaata atgcagcaag tgaaggggtg ttggccagct tcttcaacag tctgttgagt 1321 aaaaagacag gctctcctgg aagtcctggt gctggtgggg tgcagagcac agccaagaag 1381 tcaggacaaa agactgtgtt gtcaaatgtt caggaagaac tggatagaat gactcgaaag 1441 ccagactcta tggtaacaaa ctcttcaaca gaaaatgaag cctgaacctc cttaaaaagt 1501 gcatatgtcg aatgaccaaa taactatgta tattgatctg ctaagaccag gatttttctg 1561 atatggcaca tgctatcagt tttttggggc aggggagatg aactttaaaa aaaaaaaaaa 1621 aa // weblogo-3.8.0/tests/data/genbank/origin_line.gb000066400000000000000000000035701467613320200214610ustar00rootroot00000000000000LOCUS NC_002678 7036074 bp DNA circular BCT 28-MAR-2001 DEFINITION Mesorhizobium loti, complete genome. ACCESSION NC_002678 VERSION NC_002678.1 GI:13470324 KEYWORDS . SOURCE Mesorhizobium loti. ORGANISM Mesorhizobium loti Bacteria; Proteobacteria; alpha subdivision; Rhizobiaceae group; Phyllobacteriaceae; Mesorhizobium. REFERENCE 1 (sites) AUTHORS Kaneko,T., Nakamura,Y., Sato,S., Asamizu,E., Kato,T., Sasamoto,S., Watanabe,A., Idesawa,K., Ishikawa,A., Kawashima,K., Kimura,T., Kishida,Y., Kiyokawa,C., Kohara,M., Matsumoto,M., Matsuno,A., Mochizuki,Y., Nakayama,S., Nakazaki,N., Shimpo,S., Sugimoto,M., Takeuchi,C., Yamada,M. and Tabata,S. TITLE Complete genome structure of the nitrogen-fixing symbiotic bacterium Mesorhizobium loti JOURNAL DNA Res. 7, 331-338 (2000) REFERENCE 2 (bases 1 to 7036074) AUTHORS Kaneko,T. TITLE Direct Submission JOURNAL Submitted (05-DEC-2000) Takakazu Kaneko, Kazusa DNA Research Institute, The First Laboratory for Plant Gene Research; Yana 1532-3, Kisarazu, Chiba 292-0812, Japan (E-mail:kaneko@kazusa.or.jp, URL:http://www.kazusa.or.jp/rhizobase/, Tel:81-438-52-3935, Fax:81-438-52-3934) FEATURES Location/Qualifiers source 1..7036074 /organism="Mesorhizobium loti" /strain="MAFF303099" /db_xref="taxon:381" gene 287..1084 /gene="mlr0002" BASE COUNT 1311257 a2224835 c2190093 g1309889 t ORIGIN 1 ttaattaact gtcttcgatt gcgtttaatt gacggttttc gattaaaagc ggtaccgggg 61 tttgggaggt actatggcgg caggaatgct gggcgatctg gttggcaaga tcctcgacaa 121 gatatcgggc accagtttgc tggcgaccgg gcttttgctg ctgactgcct ttgtcagcgc // weblogo-3.8.0/tests/data/genbank/pri1.gb000066400000000000000000000053571467613320200200430ustar00rootroot00000000000000LOCUS HUGLUT1 741 bp DNA PRI 16-NOV-1994 DEFINITION Human fructose transporter (GLUT5) gene, promoter and exon 1. ACCESSION U05344 VERSION U05344.1 GI:452475 KEYWORDS . SOURCE human. ORGANISM Homo sapiens Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Primates; Catarrhini; Hominidae; Homo. REFERENCE 1 (bases 1 to 741) AUTHORS Mahraoui,L., Takeda,J., Mesonero,J., Chantret,I., Dussaulx,E., Bell,G.I. and Brot-Laroche,E. TITLE Regulation of expression of the human fructose transporter (GLUT5) by cyclic AMP JOURNAL Biochem. J. 301 (Pt 1), 169-175 (1994) MEDLINE 94311827 REFERENCE 2 (bases 1 to 741) AUTHORS Takeda,J. TITLE Direct Submission JOURNAL Submitted (24-JAN-1994) Jun Takeda, Howard Hughes Medical Institute, The University of Chicago, 5841 S. Maryland Ave., Chicago, IL 60637, USA FEATURES Location/Qualifiers source 1..741 /organism="Homo sapiens" /db_xref="taxon:9606" /chromosome="1" /map="1p31" /clone="lambda hGT5-157" /tissue_type="liver" /clone_lib="partial Hae III/Alu I fetal human liver library in lambda Ch4A of Maniatis" /dev_stage="fetal" repeat_region 1..73 /rpt_family="Alu" promoter 1..513 5'UTR 514..609 /gene="GLUT5" exon 514..642 /gene="GLUT5" /number=1 /product="fructose transporter" BASE COUNT 206 a 172 c 195 g 168 t ORIGIN 1 gatcatgcat gcactccagc ctgggacaag agcgaaactc cgtctcaaaa aaaaaaaaaa 61 aaaaaaaaaa aaacagaaaa tgagaaactt tccccaaaca gtattacacg gtgacttggg 121 caaaactgac tctccaccaa gagacacttg actgtagttt tcctggcagg gagagcatct 181 ttgaggtctc tagtggccca atctgttgcc ctcagattac ctggtgtcat gtagggtgga 241 ggacagctgt tgtttgccat gcgttcctga cagaaataac ccttccagtc attcaccatg 301 agcctgactg gtagagactt tagcaatggg gaaataccgt agactgttcc atcaggacaa 361 tgctgggcct gcagtcccca gggggcaccc acttacttag ccaaacccca gacgtttcat 421 ttaaaagcag aagtgaaagg aagaccaggt tcctgaaagg gttattctga cttaatctgg 481 ctataaaaat gctattggct gttatttggc atggccaaag tgcacccaga atgtcttctc 541 tctccattca gtgcacgcgt tactttggct aaaaggaggt gagcggcact ctgcccttcc 601 agagcaagca tggagcaaca ggatcagagc atgaaggaag gggtgagtgt gttgctcagg 661 gagaggggcc aagagcaggc ttggctgcca gggcctgtgc agccttcctg gagagtcgct 721 ggggggctcc tggtgtttgc a // weblogo-3.8.0/tests/data/genbank/protein_refseq.gb000066400000000000000000000041551467613320200222100ustar00rootroot00000000000000LOCUS NP_034640 182 aa ROD 01-NOV-2000 DEFINITION interferon beta, fibroblast [Mus musculus]. ACCESSION NP_034640 PID g6754304 VERSION NP_034640.1 GI:6754304 DBSOURCE REFSEQ: accession NM_010510.1 KEYWORDS . SOURCE house mouse. ORGANISM Mus musculus Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Rodentia; Sciurognathi; Muridae; Murinae; Mus. REFERENCE 1 (residues 1 to 182) AUTHORS Higashi,Y., Sokawa,Y., Watanabe,Y., Kawade,Y., Ohno,S., Takaoka,C. and Taniguchi,T. TITLE structure and expression of a cloned cdna for mouse interferon-beta JOURNAL J. Biol. Chem. 258, 9522-9529 (1983) MEDLINE 83265757 COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final NCBI review. The reference sequence was derived from K00020.1. FEATURES Location/Qualifiers source 1..182 /organism="Mus musculus" /db_xref="taxon:10090" /chromosome="4" /map="4 42.6 cM" Protein 1..182 /product="interferon beta, fibroblast" sig_peptide 1..21 Region 1..182 /region_name="Interferon alpha/beta domain" /db_xref="CDD:pfam00143" /note="interferon" mat_peptide 22..182 /product="ifn-beta" Region 56..170 /region_name="Interferon alpha, beta and delta." /db_xref="CDD:IFabd" /note="IFabd" CDS 1..182 /gene="Ifnb" /db_xref="LocusID:15977" /db_xref="MGD:MGI:107657" /coded_by="NM_010510.1:21..569" ORIGIN 1 mnnrwilhaa fllcfsttal sinykqlqlq ertnirkcqe lleqlngkin ltyradfkip 61 memtekmqks ytafaiqeml qnvflvfrnn fsstgwneti vvrlldelhq qtvflktvle 121 ekqeerltwe msstalhlks yywrvqrylk lmkynsyawm vvraeifrnf liirrltrnf 181 qn // weblogo-3.8.0/tests/data/globin.fa000066400000000000000000000365351467613320200170350ustar00rootroot00000000000000; globin.fasta: aligned globin sequences >Lamprey GLOBIN V - SEA LAMPREY PIVDTGSVA-P------------------LSAAEKTKIRSAWAPVYSTY---ETSGVDILVKFFTSTPAAQEFFPKFKGL TT-----ADQLKKSA---DVRWHA-ERIINAVNDAVASMDDTEKMS--MKL-RDLSGKH----AKSFQV-----DPQYFK VLAAVI-AD-TVAAGD--AGFEKLMSM------I---CILLR----S-----A-----Y------------ >Hagfish GLOBIN III - ATLANTIC HAGFISH PITDHGQPP-T------------------LSEGDKKAIRESWPQIYKNF---EQNSLAVLLEFLKKFPKAQDSFPKFSAK KS-------HLEQDP---AVKLQA-EVIINAVNHTIGLMDKEAAMK--KYL-KDLSTKH----STEFQV-----NPDMFK ELSAVF-VS-TMG-GK--AAYEKLFSI------I---ATLLR----S-----T-----YDA---------- >Frog HEMOGLOBIN BETA CHAIN - EDIBLE FROG ----------GS-----------------------DLVSGFWGKV--DA---HKIGGEALARLLVVYPWTQRYFTTFGNL GSADAIC-----HNA---KVLAHG-EKVLAAIGEGLKHPENLKAHY--AKL-SEYHSNK----LHVDPANFRLLGNVFIT VLARHF-QH-EFTPELQ-HALEAHFCA------V---GDALA----K-----A-----YH----------- >African Elephant HEMOGLOBIN BETA CHAIN - AFRICAN ELEPHANT ----------VN-----------------LTAAEKTQVTNLWGKV--NV---KELGGEALSRLLVVYPWTRRFFEHFGDL STAEAVL-----HNA---KVLAHG-EKVLTSFGEGLKHLDNLKGTF--ADL-SELHCDK----LHVDPENFRLLGNVLVI VLARHF-GK-EFTPDVQ-AAYEKVVAG------V---ANALA----H-----K-----YH----------- >Goat HEMOGLOBIN BETA-A CHAIN - GOAT ----------M------------------LTAEEKAAVTGFWGKV--KV---DEVGAEALGRLLVVYPWTQRFFEHFGDL SSADAVM-----NNA---KVKAHG-KKVLDSFSNGMKHLDDLKGTF--AQL-SELHCDK----LHVDPENFKLLGNVLVV VLARHH-GS-EFTPLLQ-AEFQKVVAG------V---ANALA----H-----R-----YH----------- >Primate HEMOGLOBIN BETA CHAIN - HUMAN, CHIMPANZEES, AND GORILLA ----------VH-----------------LTPEEKSAVTALWGKV--NV---DEVGGEALGRLLVVYPWTQRFFESFGDL STPDAVM-----GNP---KVKAHG-KKVLGAFSDGLAHLDNLKGTF--ATL-SELHCDK----LHVDPENFRLLGNVLVC VLAHHF-GK-EFTPPVQ-AAYQKVVAG------V---ANALA----H-----K-----YH----------- >Gibbon HEMOGLOBIN BETA CHAIN - COMMON GIBBON (TENTATIVE SEQUENCE) ----------VH-----------------LTPEEKSAVTALWGKV--NV---DEVGGEALGRLLVVYPWTQRFFESFGDL STPDAVM-----GNP---KVKAHG-KKVLGAFSDGLAHLDNLKGTF--AQL-SELHCDK----LHVDPENFRLLGNVLVC VLAHHF-GK-EFTPQVQ-AAYQKVVAG------V---ANALA----H-----K-----YH----------- >Dog HEMOGLOBIN BETA CHAIN - DOG AND COYOTE ----------VH-----------------LTAEEKSLVSGLWGKV--NV---DEVGGEALGRLLIVYPWTQRFFDSFGDL STPDAVM-----SNA---KVKAHG-KKVLNSFSDGLKNLDNLKGTF--AKL-SELHCDK----LHVDPENFKLLGNVLVC VLAHHF-GK-EFTPQVQ-AAYQKVVAG------V---ANALA----H-----K-----YH----------- >Horse HEMOGLOBIN BETA CHAIN - HORSE ----------VQ-----------------LSGEEKAAVLALWDKV--NE---EEVGGEALGRLLVVYPWTQRFFDSFGDL SNPGAVM-----GNP---KVKAHG-KKVLHSFGEGVHHLDNLKGTF--AAL-SELHCDK----LHVDPENFRLLGNVLVV VLARHF-GK-DFTPELQ-ASYQKVVAG------V---ANALA----H-----K-----YH----------- >Human, Chimp HEMOGLOBIN GAMMA CHAINS - HUMAN AND CHIMPANZEE ----------GH-----------------FTEEDKATITSLWGKV--NV---EDAGGETLGRLLVVYPWTQRFFDSFGNL SSASAIM-----GNP---KVKAHG-KKVLTSLGDAIKHLDDLKGTF--AQL-SELHCDK----LHVDPENFKLLGNVLVT VLAIHF-GK-EFTPEVQ-ASWQKMVTA------V---ASALS----S-----R-----YH----------- >Nile Crocodile HEMOGLOBIN BETA CHAIN - NILE CROCODILE ----------AS-----------------FDPHEKQLIGDLWHKV--DV---AHCGGEALSRMLIVYPWKRRYFENFGDI SNAQAIM-----HNE---KVQAHG-KKVLASFGEAVCHLDGIRAHF--ANL-SKLHCEK----LHVDPENFKLLGDIIII VLAAHY-PK-DFGLECH-AAYQKLVRQ------V---AAALA----A-----E-----YH----------- >Chicken HEMOGLOBIN BETA CHAIN - CHICKEN ----------VH-----------------WTAEEKQLITGLWGKV--NV---AECGAEALARLLIVYPWTQRFFASFGNL SSPTAIL-----GNP---MVRAHG-KKVLTSFGDAVKNLDNIKNTF--SQL-SELHCDK----LHVDPENFRLLGDILII VLAAHF-SK-DFTPECQ-AAWQKLVRV------V---AHALA----R-----K-----YH----------- >NA Opossum HEMOGLOBIN BETA CHAIN - NORTH AMERICAN OPOSSUM ----------VH-----------------LTSEEKNCITTIWSKV--QV---DQTGGEALGRMLVVYPWTTRFFGSFGDL SSPGAVM-----SNS---KVQAHG-AKVLTSFGEAVKHLDDLKGTY--AKL-SELHCDK----LHVDPENFKMLG-IIVI CLAEHF-GK-DFTPECV-A--WKLVAG------V---AHALA----H-----K-----YH----------- >Carp HEMOGLOBIN BETA CHAINS - CARP ----------VE-----------------WTDAERSAIIALWGKL--NP---DELGPEALARCLIVYPWTQRFFASYGNL SSPAAIM-----GNP---KVAAHG-RTVEGGLMRAIKDMDNIKATY--APL-SVMHSEK----LHVDPDNFRLLADCITV CAAMKFGPS-GFSPNVQ-EAWQKFLSV------V---VNALK----R-----Q-----YH----------- >Shark HEMOGLOBIN BETA CHAIN - PORT JACKSON SHARK ----------VH-----------------WSEVELHEITTTWKSI--DK---HSLGAKALARMFIVYPWTTRYFGNLKEF TA----------CSY---GVKEHA-KKVTGALGVAVTHLGDVKSQF--TDL-SKKHAEE----LHVDVESFKLLAKCFVV ELGILL-KD-KFAPQTQ-AIWEKYFGV------V---VDAIS----K-----E-----YH----------- >Shark HEMOGLOBIN ALPHA CHAIN - PORT JACKSON SHARK ----------S-TSTSTSD----------YSAADRAELAALSKVLAQNA---EAFGAEALARMFTVYAATKSYFKDYKDF TA----------AAP---SIKAHG-AKVVTALAKACDHLDDLKTHL--HKL-ATFHGSE----LKVDPANFQYLSYCLEV ALAVHL--T-EFSPETH-CALDKFLTN------V---CHELS----S-----R-----YR----------- >Carp HEMOGLOBIN ALPHA CHAIN - CARP ----------S------------------LSDKDKAAVKIAWAKISPKA---DDIGAEALGRMLTVYPQTKTYFAHWADL SP----------GSG---PVKHGK-KVIMGAVGDAVSKIDDLVGGL--ASL-SELHASK----LRVDPANFKILANHIVV GIMFYL-PG-DFPPEVH-MSVDKFFQN------L---ALALS----E-----K-----YR----------- >Bullfrog HEMOGLOBIN ALPHA CHAIN - BULLFROG TADPOLE ----------S------------------LSASEKAAVLSIVGKIGSQG---SALGSEALTRLFLSFPQTKTYFPHF-DL TP----------GSA---DLNTHG-GKIINALAGAANHLDDLAGNL--SSL-SDLHAYN----LRVDPGNFPLLAHIIQV VLATHF-PG-DFTAEVQ-AAWDKFLAL------V---SAVLT----S-----K-----YR----------- >Nile Crocodile HEMOGLOBIN ALPHA CHAIN - NILE CROCODILE ----------V------------------LSSDDKCNVKAVWSKVAGHL---EEYGAEALERMFCAYPQTKIYFPHF-DL SH----------GSA---QIRAHG-KKVFAALHEAVNHIDDLPGAL--CRL-SELHAHS----LRVDPVNFKFLAQCVLV VVAIHH-PG-SLTPEVH-ASLDKFLCA------V---SSVLT----S-----K-----YR----------- >Ostrich HEMOGLOBIN ALPHA CHAIN - OSTRICH ----------V------------------LSGTDKTNVKGIFSKISSHA---EEYGAETLERMFITYPQTKTYFPHF-DL HH----------GSA---QIKAHG-KKVANALIEAVNHIDDISGAL--SKL-SDLHAQK----LRVDPVNFKLLGQCFLV VVAIHH-PS-ALTPEVH-ASLDKFLCA------V---GAVLT----A-----K-----YR----------- >Kangaroo HEMOGLOBIN ALPHA CHAIN - EASTERN GRAY KANGAROO ----------V------------------LSAADKGHVKAIWGKVGGHA---GEYAAEGLERTFHSFPTTKTYFPHF-DL SH----------GSA---QIQAHG-KKIADALGQAVEHIDDLPGTL--SKL-SDLHAHK----LRVDPVNFKLLSHCLLV TFAAHL-GD-AFTPEVH-ASLDKFLAA------V---STVLT----S-----K-----YR----------- >Armadillo HEMOGLOBIN ALPHA CHAIN - NINE-BANDED ARMADILLO ----------V------------------LSAADKTHVKAFWGKVGGHA---AEFGAEALERMFASFPPTKTYFSHM-DL SH----------GSA---QVKAHG-KKVADALTLAVGHLDDLPGAL--STL-SDLHAHK----LRVDPVNFKFLSHCLLV TLACHL-PD-DFTPAVH-ASMDKFMAG------V---STVLV----S-----K-----YR----------- >Horse HEMOGLOBIN ALPHA CHAINS - HORSE ----------V------------------LSAADKTNVKAAWSKVGGHA---GEYGAEALERMFLGFPTTKTYFPHF-DL SH----------GSA---QVKAHG-KKVGDALTLAVGHLDDLPGAL--SNL-SDLHAHK----LRVDPVNFKLLSHCLLS TLAVHL-PN-DFTPAVH-ASLDKFLSS------V---STVLT----S-----K-----YR----------- >Primate HEMOGLOBIN ALPHA CHAIN - HUMAN AND CHIMPANZEES ----------V------------------LSPADKTNVKAAWGKVGAHA---GEYGAEALERMFLSFPTTKTYFPHF-DL SH----------GSA---QVKGHG-KKVADALTNAVAHVDDMPNAL--SAL-SDLHAHK----LRVDPVNFKLLSHCLLV TLAAHL-PA-EFTPAVH-ASLDKFLAS------V---STVLT----S-----K-----YR----------- >Macaque HEMOGLOBIN ALPHA CHAIN - RHESUS MACAQUE AND JAPANESE MACAQUE ----------V------------------LSPADKSNVKAAWGKVGGHA---GEYGAEALERMFLSFPTTKTYFPHF-DL SH----------GSA---QVKGHG-KKVADALTLAVGHVDDMPNAL--SAL-SDLHAHK----LRVDPVNFKLLSHCLLV TLAAHL-PA-EFTPAVH-ASLDKFLAS------V---STVLT----S-----K-----YR----------- >Badger HEMOGLOBIN ALPHA CHAIN - EURASIAN BADGER ----------V------------------LSPADKANIKATWDKIGGHA---GEYGGEALERTFASFPTTKTYFPHF-DL SH----------GSA---QVKGHG-KKVADALTNAVAHLDDLPGAL--SAL-SDLHAYK----LRVDPVNFKLLSHCLLV TLACHH-PA-EFTPAVH-ASLDKFLSS------V---STVLT----S-----K-----YR----------- >Ind Elephant HEMOGLOBIN ALPHA CHAIN - INDIAN ELEPHANT ----------V------------------LSDKDKTNVKATWSKVGDHA---SDYVAEALERMFFSFPTTKTYFPHF-DL SH----------GSG---QVKGHG-KKVGEALTQAVGHLDDLPSAL--SAL-SDLHAHK----LRVDPVNFKLLSHCLLV TLSSHQ-PT-EFTPEVH-ASLDKFLSN------V---STVLT----S-----K-----YR----------- >Hyrax HEMOGLOBIN ALPHA CHAIN - ABYSSINIAN HYRAX ----------V------------------LSAADKNNVKGAWEKVGTHA---GEYGAEALERMFLSFPTTKTYFPHF-DL TH----------GSA---QVKAHG-QKVGAALTKAVGHLDDLPNAL--SDL-SDLHAHK----LRVDPVNFKLLSHCLLV TLSRHL-PEQEFTPAVH-ASLDKFFSN------V---STVLT----S-----K-----YR----------- >Tuna MYOGLOBIN - YELLOWFIN TUNA ----------A----------------------DFDAVLKCWGPVEADY---TTMGGLVLTRLFKEHPETQKLFPKFAGI -A-----QADIAGNA---AISAHG-ATVLKKLGELLKAKGSHAAIL--KPL-ANSHATK----HKIPINNFKLISEVLVK VMHEK---A-GLDAGGQ-TALRNVMGI------I---IADLE----ANYKELG-----FSG---------- >Shark MYOGLOBIN - PORT JACKSON SHARK ----------T----------------------EWEHVNKVWAVVEPDI---PAVGLAILLRLFKEHKETKDLFPKFKEI -P-----VQQLGNNE---DLRKHG-VTVLRALGNILKQKGKHSTNV--KEL-ADTHINK----HKIPPKNFVLITNIAVK VLTEMY-PS-DMTGPMQ-ESFSKVFTV------I---CSDLE----TLYKEAN-----FQG---------- >Turtle MYOGLOBIN - MAP TURTLE ----------G------------------LSDDEWHHVLGIWAKVEPDL---SAHGQEVIIRLFQVHPETQERFAKFKNL KT-----IDELRSSE---EVKKHG-TTVLTALGRILKLKNNHEPEL--KPL-AESHATK----HKIPVKYLEFICEIIVK VIAEKH-PS-DFGADSQ-AAMRKALEL------F---RNDMA----SKYKEFG-----FQG---------- >Chicken MYOGLOBIN - CHICKEN ----------G------------------LSDQEWQQVLTIWGKVEADI---AGHGHEVLMRLFHDHPETLDRFDKFKGL KT-----EPDMKGSE---DLKKHG-QTVLTALGAQLKKKGHHEADL--KPL-AQTHATK----HKIPVKYLEFISEVIIK VIAEKH-AA-DFGADSQ-AAMKKALEL------F---RDDMA----SKYKEFG-----FQG---------- >Dog MYOGLOBIN - DOG, BAT-EARED FOX, AFRICAN HUNTING DOG, AND CAPE FOX ----------G------------------LSDGEWQIVLNIWGKVETDL---AGHGQEVLIRLFKNHPETLDKFDKFKHL KT-----EDEMKGSE---DLKKHG-NTVLTALGGILKKKGHHEAEL--KPL-AQSHATK----HKIPVKYLEFISDAIIQ VLQSKH-SG-DFHADTE-AAMKKALEL------F---RNDIA----AKYKELG-----FQG---------- >Badger MYOGLOBIN - EURASIAN BADGER ----------G------------------LSDGEWQLVLNVWGKVEADL---AGHGQEVLIRLFKGHPETLEKFDKFKHL KS-----EDEMKGSE---DLKKHG-NTVLTALGGILKKKGHQEAEL--KPL-AQSHATK----HKIPVKYLEFISDAIAQ VLQSKH-PG-NFAAEAQ-GAMKKALEL------F---RNDIA----AKYKELG-----FQG---------- >Dolphin MYOGLOBIN - SADDLEBACK DOLPHIN ----------G------------------LSDGEWQLVLNVWGKVEADV---AGHGQDILIRLFKGHPETLEKFDKFKHL KT-----EADMKASE---DLKKHG-DTVLTALGAILKKKGHHDAEL--KPL-AQSHATK----HKIPIKYLEFISEAIIH VLHSRH-PA-QFGADAQ-GAMNKALEL------F---RKDIA----AKYKELG-----FHG---------- >Horse, Zebra MYOGLOBIN - HORSE AND PLAINS ZEBRA ----------G------------------LSDGEWQQVLNVWGKVEADI---AGHGQEVLIRLFTGHPETLEKFDKFKHL KT-----EAEMKASE---DLKKHG-TVVLTALGGILKKKGHHEAEL--KPL-AQSHATK----HKIPIKYLEFISDAIIH VLHSKH-PG-NFGADAQ-GAMTKALEL------F---RNDIA----AKYKELG-----FQG---------- >African Elephant MYOGLOBIN - AFRICAN ELEPHANT ----------G------------------LSDGEWELVLKTWGKVEADI---PGHGEFVLVRLFTGHPETLEKFDKFKHL KT-----EGEMKASE---DLKKQG-VTVLTALGGILKKKGHHEAEI--QPL-AQSHATK----HKIPIKYLEFISDAIIH VLQSKH-PA-EFGADAQ-AAMKKALEL------F---RNDIA----AKYKELG-----FQG---------- >Aardvark MYOGLOBIN - AARDVARK ----------G------------------LSDAEWQLVLNVWGKVEADI---PGHGQDVLIRLFKGHPETLEKFDRFKHL KT-----EDEMKASE---DLKKHG-TTVLTALGGILKKKGQHEAEI--QPL-AQSHATK----HKIPVKYLEFISEAIIQ VIQSKH-SG-DFGADAQ-GAMSKALEL------F---RNDIA----AKYKELG-----FQG---------- >Human MYOGLOBIN - HUMAN ----------G------------------LSDGEWQLVLNVWGKVEADI---PGHGQEVLIRLFKGHPETLEKFDKFKHL KS-----EDEMKASE---DLKKHG-ATVLTALGGILKKKGHHEAEI--KPL-AQSHATK----HKIPVKYLEFISECIIQ VLQSKH-PG-DFGADAQ-GAMNKALEL------F---RKDMA----SNYKELG-----FQG---------- >Macaque MYOGLOBIN - CRAB-EATING MACAQUE (TENTATIVE SEQUENCE) ----------G------------------LSDGEWQLVLNVWGKVEADI---PSHGQEVLIRLFKGHPETLEKFDKFKHL KS-----EDEMKASE---DLKKHG-VTVLTALGGILKKKGHHEAEI--KPL-AQSHATK----HKIPVKYLELISESIIQ VLQSKH-PG-DFGADAQ-GAMNKALEL------F---RNDMA----AKYKELG-----FQG---------- >NA Opossum MYOGLOBIN - NORTH AMERICAN OPOSSUM ----------G------------------LSDGEWQLVLNAWGKVEADI---PGHGQEVLIRLFKGHPETLEKFDKFKHL KS-----EDEMKASE---DLKKHG-ATVLTALGNILKKKGNHEAEL--KPL-AQSHATK----HKISVQFLEFISEAIIQ VIQSKH-PG-DFGGDAQ-AAMGKALEL------F---RNDMA----AKYKELG-----FQG---------- >Earthworm GLOBIN AIII - COMMON EARTHWORM ---------KK------------------QCGVLEGLKVKSEWGRAYGS---GHDREAFSQAIWRATFAQVPESRSLFKR VH-----GDH-TSDP---AFIAHA-ERVLGGLDIAISTLDQPATLK--EEL-DHLQVQHEG--RKIPDNYFDAFKTAILH VVAAQL-GE-RCYSNN--EEIHDAIACDGFARVL---PQVLE----R-----G-----IKGHH-------- >SMALL CHAIN - TYLORRHYNCHUS HETEROCHAETUS ----------T------------------DCGILQRIKVKQQWAQVYSV---GESRTDFAIDVFNNFFRTNPD-RSLFNR VN-----GDN-VYSP---EFKAHM-VRVFAGFDILISVLDDKPVLD--QAL-AHYAAFH----KQFGTIPFKAFGQTMFQ TIAEHI--------HG--ADIGAWRAC------Y---AEQIV----T-----G-----ITA---------- >BloodwormGLOBIN, MAJOR MONOMERIC COMPONENT - BLOODWORM ----------G------------------LSAAQRQVIAATWKDIAGND---NGAGVGKDCLI--KHLSAHPQMAAVFGF SG-----ASD-PAVA---DLGAKV-LAIGVAVSHLGDGKMVAQMKA--VGV-RHKGYGN----KHIKGQYFEPLGASLLS AMEHRI-GG-KMNAAA-KDAWAAAYAD------I---SGALI----S-----G-----LQS---------- >Whelk GLOBIN - WHELK ----------G------------------LDGAQKTALKESWKVLGADGPTMMKNGSLLFGLLFKTYPDTKKHFKHFDDA TF-----AAM-DTTG---VGKAHG-VAVFSGLGSMICSIDDDDCV---GLA-KKLSRNH--LARGVSAADF-KLLEAVFK FLDEAT-QR-KATDAQ-KDADGALLTM------L---IKA------------H-----V------------ >Snail GLOBIN - WATER SNAIL ----------S------------------LQPASKSALASSWKTLAKDAATIQNNGATLFSLLFKQFPDTRNYFTHFGNM SD-----AEM-KTTG---VGKAHS-MAVFAGIGSMIDSMDDADCMN--GLA-LKLSRNH--IQRKIGASRFGEMRQVFPN FLDEAL-GG-GASGDV-KGAWDALLAY------LQDNKQA------------Q-----A----L------- >Clam GLOBIN I - BLOOD CLAM ----------P--------SVQGAAAQ--LTADVKKDLRDSWKVIGSDK---KGNGVALMTTLFADNQETIGYFKRLGNV SQ-----GM---AND---KLRGHS-ITLMYALQNFIDQLDNTDDLV--CVV-EKFAVNH--ITRKISAAEFGKINGP--- -IKKVL-AS-KNFGDK-YANAWAKLVA------V---VQA------------A-----L------------ >Midge larvaGLOBIN CTT-II BETA - MIDGE LARVA ----------A------------------PLSADEASLV---RGSWAQV---KHSEVDILYYIFKANPDIMAKFPQFAGK DL-----ETL-KGTGQFATHAGRI-VGFVSEIVALMGNSANMPAME--TLI-KDMAANH--KARGIPKAQFNEFRASLVS YLQSKV----SWNDSL-GAAWTQGLDN------V---FNMMF----S-----Y-----L------------ >Midge larva GLOBINS CTT-I AND CTT-IA - MIDGE LARVA ----------G------------------P-SGDQIAAA---KASWNTV---KNNQVDILYAVFKANPDIQTAFSQFAGK DL-----DSI-KGTPDFSKHAGRV-VGLFSEVMDLLGNDANTPTIL--AKA-KDFGKSH--KSRASP-AQLDNFRKSLVV YLKGAT----KWDSAV-ESSWAPVLDF------V---FSTLK----N-----E-----L------------ >Bacteria BACTERIAL HEMOGLOBIN - VITREOSCILLA SP -----------------------------MLDQQTINII---KATVPVL---KEHGVTITTTFYKNLFAKHPEVRPLFDM GR-----Q---ESLEQ-------P-KALAMTVLAAAQNIENLPAIL--PAV-KKIAVKH--CQAGVAAAHYPIVGQELLG AIKEVL-GD-AATDDI-LDAWGKAYGV------I---ADVFI----Q-----VEADLYA-----Q-AVE-- >P andersonii ONLEGUME HEMOGLOBIN I - PARASPONIA ANDERSONII ----------V----------------NKVFTEEQEALV---VKAWAVM---KKNSAELGLQFLK-IFEIAPSAKNLFSY LK-----DSP-VPLEQNPKLKPHA-TTFVMTTESAVQLRKAGKVTVK-ESDLKRIGAIH--FKTGVVNEHFEVTRFALLE TIKEAV-PE-MWSPEM-KNAWGVAYDQ------L---VAAIK----F-----E-----M-----KPSST-- >Yellow Lupin LEGHEMOGLOBIN I - YELLOW LUPIN ----------G------------------VLTDVQVALV---KSSFEEF---NANIPKNTHRFFTLVLEIAPGAKDLFSF LK-----GSS-EVPQNNPDLQAHAGKVFKLTYEAAIQLEVNGAVAS--DATLKSLGSVH--VSKGVVDAHFPVVKEAILK TIKEVV-GD-KWSEEL-NTAWTIAYDE------L---AIIIK----K-----E-----M-----K-DAA-- >Garden Pea LEGHEMOGLOBIN I - GARDEN PEA ----------G-------------------FTDKQEALV---NSSSE-F---KQNLPGYSILFYTIVLEKAPAAKGLFSF LK-----DTA-GVE-DSPKLQAHAEQVFGLVRDSAAQLRTKGEVVL-GNATL---GAIH--VQKGVTNPHFVVVKEALLQ TIKKAS-GN-NWSEEL-NTAWEVAYDG------L---ATAIKKAMKT---------------------A-- >Broad Bean LEGHEMOGLOBIN I - BROAD BEAN ----------G-------------------FTEKQEALV---NSSSQLF---KQNPSNYSVLFYTIILQKAPTAKAMFSF LK-----DSA-GVV-DSPKLGAHAEKVFGMVRDSAVQLRATGEVVL--DGKD---GSIH--IQKGVLDPHFVVVKEALLK TIKEAS-GD-KWSEEL-SAAWEVAYDG------L---ATAIK----A---------------------A-- >Kidney Bean LEGHEMOGLOBIN A - KIDNEY BEAN ----------G------------------AFTEKQEALV---NSSWEAF---KGNIPQYSVVFYTSILEKAPAAKNLFSF LA-----NGV-DPT--NPKLTAHAESLFGLVRDSAAQLRANGAVVA--DAAL---GSIH--SQKGVSNDQFLVVKEALLK TLKQAV-GD-KWTDQL-STALELAYDE------L---AAAIK----K---------------------AYA >Soybean LEGHEMOGLOBIN C1 - SOYBEAN ----------G------------------AFTEKQEALV---SSSFEAF---KANIPQYSVVFYNSILEKAPAAKDLFSF LA-----NGV-DPT--NPKLTGHAEKLFALVRDSAGQLKTNGTVVA--DAAL---VSIH--AQKAVTDPQFVVVKEALLK TIKEAV-GG-NWSDEL-SSAWEVAYDE------L---AAAIK----K---------------------A-- weblogo-3.8.0/tests/data/intelligenetics.txt000066400000000000000000000051521467613320200211650ustar00rootroot00000000000000;H.sapiens fau mRNA, 518 bases HSFAU ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtc gccaatatgcagctctttgtccgcgcccaggagctacacaccttcgaggt gaccggccaggaaacggtcgcccagatcaaggctcatgtagcctcactgg agggcattgccccggaagatcaagtcgtgctcctggcaggcgcgcccctg gaggatgaggccactctgggccagtgcggggtggaggccctgactaccct ggaagtagcaggccgcatgcttggaggtaaagttcatggttccctggccc gtgctggaaaagtgagaggtcagactcctaaggtggccaaacaggagaag aagaagaagaagacaggtcgggctaagcggcggatgcagtacaaccggcg ctttgtcaacgttgtgcccacctttggcaagaagaagggccccaatgcca actcttaagtcttttgtaattctggctttctctaataaaaaagccactta gttcagtcaaaaaaaaaa1 ;H.sapiens fau 1 gene, 2016 bases HSFAU1 ctaccattttccctctcgattctatatgtacactcgggacaagttctcct gatcgaaaacggcaaaactaaggccccaagtaggaatgccttagttttcg gggttaacaatgattaacactgagcctcacacccacgcgatgccctcagc tcctcgctcagcgctctcaccaacagccgtagcccgcagccccgctggac accggttctccatccccgcagcgtagcccggaacatggtagctgccatct ttacctgctacgccagccttctgtgcgcgcaactgtctggtcccgccccg tcctgcgcgagctgctgcccaggcaggttcgccggtgcgagcgtaaaggg gcggagctaggactgccttgggcggtacaaatagcagggaaccgcgcggt cgctcagcagtgacgtgacacgcagcccacggtctgtactgacgcgccct cgcttcttcctctttctcgactccatcttcgcggtagctgggaccgccgt tcaggtaagaatggggccttggctggatccgaagggcttgtagcaggttg gctgcggggtcagaaggcgcggggggaaccgaagaacggggcctgctccg tggccctgctccagtccctatccgaactccttgggaggcactggccttcc gcacgtgagccgccgcgaccaccatcccgtcgcgatcgtttctggaccgc tttccactcccaaatctcctttatcccagagcatttcttggcttctctta caagccgtcttttctttactcagtcgccaatatgcagctctttgtccgcg cccaggagctacacaccttcgaggtgaccggccaggaaacggtcgcccag atcaaggtaaggctgcttggtgcgccctgggttccattttcttgtgctct tcactctcgcggcccgagggaacgcttacgagccttatctttccctgtag gctcatgtagcctcactggagggcattgccccggaagatcaagtcgtgct cctggcaggcgcgcccctggaggatgaggccactctgggccagtgcgggg tggaggccctgactaccctggaagtagcaggccgcatgcttggaggtgag tgagagaggaatgttctttgaagtaccggtaagcgtctagtgagtgtggg gtgcatagtcctgacagctgagtgtcacacctatggtaatagagtacttc tcactgtcttcagttcagagtgattcttcctgtttacatccctcatgttg aacacagacgtccatgggagactgagccagagtgtagttgtatttcagtc acatcacgagatcctagtctggttatcagcttccacactaaaaattaggt cagaccaggccccaaagtgctctataaattagaagctggaagatcctgaa atgaaacttaagatttcaaggtcaaatatctgcaactttgttctcattac ctattgggcgcagcttctctttaaaggcttgaattgagaaaagaggggtt ctgctgggtggcaccttcttgctcttacctgctggtgccttcctttccca ctacaggtaaagtccatggttccctggcccgtgctggaaaagtgagaggt cagactcctaaggtgagtgagagtattagtggtcatggtgttaggacttt ttttcctttcacagctaaaccaagtccctgggctcttactcggtttgcct tctccctccctggagatgagcctgagggaagggatgctaggtgtggaaga caggaaccagggcctgattaaccttcccttctccaggtggccaaacagga gaagaagaagaagaagacaggtcgggctaagcggcggatgcagtacaacc ggcgctttgtcaacgttgtgcccacctttggcaagaagaagggccccaat gccaactcttaagtcttttgtaattctggctttctctaataaaaaagcca cttagttcagtcatcgcattgtttcatctttacttgcaaggcctcaggga gaggtgtgcttctcgg1 weblogo-3.8.0/tests/data/nexus/000077500000000000000000000000001467613320200164015ustar00rootroot00000000000000weblogo-3.8.0/tests/data/nexus/dna.nex000066400000000000000000000201061467613320200176560ustar00rootroot00000000000000#NEXUS Begin data; Dimensions ntax=10 nchar=705; Format datatype=dna interleave=yes gap=- missing=?; Matrix Cow ATGGCATATCCCATACAACTAGGATTCCAAGATGCAACATCACCAATCATAGAAGAACTA Carp ATGGCACACCCAACGCAACTAGGTTTCAAGGACGCGGCCATACCCGTTATAGAGGAACTT Chicken ATGGCCAACCACTCCCAACTAGGCTTTCAAGACGCCTCATCCCCCATCATAGAAGAGCTC Human ATGGCACATGCAGCGCAAGTAGGTCTACAAGACGCTACTTCCCCTATCATAGAAGAGCTT Loach ATGGCACATCCCACACAATTAGGATTCCAAGACGCGGCCTCACCCGTAATAGAAGAACTT Mouse ATGGCCTACCCATTCCAACTTGGTCTACAAGACGCCACATCCCCTATTATAGAAGAGCTA Rat ATGGCTTACCCATTTCAACTTGGCTTACAAGACGCTACATCACCTATCATAGAAGAACTT Seal ATGGCATACCCCCTACAAATAGGCCTACAAGATGCAACCTCTCCCATTATAGAGGAGTTA Whale ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTC Frog ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTA Cow CTTCACTTTCATGACCACACGCTAATAATTGTCTTCTTAATTAGCTCATTAGTACTTTAC Carp CTTCACTTCCACGACCACGCATTAATAATTGTGCTCCTAATTAGCACTTTAGTTTTATAT Chicken GTTGAATTCCACGACCACGCCCTGATAGTCGCACTAGCAATTTGCAGCTTAGTACTCTAC Human ATCACCTTTCATGATCACGCCCTCATAATCATTTTCCTTATCTGCTTCCTAGTCCTGTAT Loach CTTCACTTCCATGACCATGCCCTAATAATTGTATTTTTGATTAGCGCCCTAGTACTTTAT Mouse ATAAATTTCCATGATCACACACTAATAATTGTTTTCCTAATTAGCTCCTTAGTCCTCTAT Rat ACAAACTTTCATGACCACACCCTAATAATTGTATTCCTCATCAGCTCCCTAGTACTTTAT Seal CTACACTTCCATGACCACACATTAATAATTGTGTTCCTAATTAGCTCATTAGTACTCTAC Whale CTACACTTTCACGATCATACACTAATAATCGTTTTTCTAATTAGCTCTTTAGTTCTCTAC Frog CTTCACTTCCACGACCATACCCTCATAGCCGTTTTTCTTATTAGTACGCTAGTTCTTTAC Cow ATTATTTCACTAATACTAACGACAAAGCTGACCCATACAAGCACGATAGATGCACAAGAA Carp ATTATTACTGCAATGGTATCAACTAAACTTACTAATAAATATATTCTAGACTCCCAAGAA Chicken CTTCTAACTCTTATACTTATAGAAAAACTATCA---TCAAACACCGTAGATGCCCAAGAA Human GCCCTTTTCCTAACACTCACAACAAAACTAACTAATACTAACATCTCAGACGCTCAGGAA Loach GTTATTATTACAACCGTCTCAACAAAACTCACTAACATATATATTTTGGACTCACAAGAA Mouse ATCATCTCGCTAATATTAACAACAAAACTAACACATACAAGCACAATAGATGCACAAGAA Rat ATTATTTCACTAATACTAACAACAAAACTAACACACACAAGCACAATAGACGCCCAAGAA Seal ATTATCTCACTTATACTAACCACGAAACTCACCCACACAAGTACAATAGACGCACAAGAA Whale ATTATTACCCTAATGCTTACAACCAAATTAACACATACTAGTACAATAGACGCCCAAGAA Frog ATTATTACTATTATAATAACTACTAAACTAACTAATACAAACCTAATGGACGCACAAGAG Cow GTAGAGACAATCTGAACCATTCTGCCCGCCATCATCTTAATTCTAATTGCTCTTCCTTCT Carp ATCGAAATCGTATGAACCATTCTACCAGCCGTCATTTTAGTACTAATCGCCCTGCCCTCC Chicken GTTGAACTAATCTGAACCATCCTACCCGCTATTGTCCTAGTCCTGCTTGCCCTCCCCTCC Human ATAGAAACCGTCTGAACTATCCTGCCCGCCATCATCCTAGTCCTCATCGCCCTCCCATCC Loach ATTGAAATCGTATGAACTGTGCTCCCTGCCCTAATCCTCATTTTAATCGCCCTCCCCTCA Mouse GTTGAAACCATTTGAACTATTCTACCAGCTGTAATCCTTATCATAATTGCTCTCCCCTCT Rat GTAGAAACAATTTGAACAATTCTCCCAGCTGTCATTCTTATTCTAATTGCCCTTCCCTCC Seal GTGGAAACGGTGTGAACGATCCTACCCGCTATCATTTTAATTCTCATTGCCCTACCATCA Whale GTAGAAACTGTCTGAACTATCCTCCCAGCCATTATCTTAATTTTAATTGCCTTGCCTTCA Frog ATCGAAATAGTGTGAACTATTATACCAGCTATTAGCCTCATCATAATTGCCCTTCCATCC Cow TTACGAATTCTATACATAATAGATGAAATCAATAACCCATCTCTTACAGTAAAAACCATA Carp CTACGCATCCTGTACCTTATAGACGAAATTAACGACCCTCACCTGACAATTAAAGCAATA Chicken CTCCAAATCCTCTACATAATAGACGAAATCGACGAACCTGATCTCACCCTAAAAGCCATC Human CTACGCATCCTTTACATAACAGACGAGGTCAACGATCCCTCCCTTACCATCAAATCAATT Loach CTACGAATTCTATATCTTATAGACGAGATTAATGACCCCCACCTAACAATTAAGGCCATG Mouse CTACGCATTCTATATATAATAGACGAAATCAACAACCCCGTATTAACCGTTAAAACCATA Rat CTACGAATTCTATACATAATAGACGAGATTAATAACCCAGTTCTAACAGTAAAAACTATA Seal TTACGAATCCTCTACATAATGGACGAGATCAATAACCCTTCCTTGACCGTAAAAACTATA Whale TTACGGATCCTTTACATAATAGACGAAGTCAATAACCCCTCCCTCACTGTAAAAACAATA Frog CTTCGTATCCTATATTTAATAGATGAAGTTAATGATCCACACTTAACAATTAAAGCAATC Cow GGACATCAGTGATACTGAAGCTATGAGTATACAGATTATGAGGACTTAAGCTTCGACTCC Carp GGACACCAATGATACTGAAGTTACGAGTATACAGACTATGAAAATCTAGGATTCGACTCC Chicken GGACACCAATGATACTGAACCTATGAATACACAGACTTCAAGGACCTCTCATTTGACTCC Human GGCCACCAATGGTACTGAACCTACGAGTACACCGACTACGGCGGACTAATCTTCAACTCC Loach GGGCACCAATGATACTGAAGCTACGAGTATACTGATTATGAAAACTTAAGTTTTGACTCC Mouse GGGCACCAATGATACTGAAGCTACGAATATACTGACTATGAAGACCTATGCTTTGATTCA Rat GGACACCAATGATACTGAAGCTATGAATATACTGACTATGAAGACCTATGCTTTGACTCC Seal GGACATCAGTGATACTGAAGCTATGAGTACACAGACTACGAAGACCTGAACTTTGACTCA Whale GGTCACCAATGATATTGAAGCTATGAGTATACCGACTACGAAGACCTAAGCTTCGACTCC Frog GGCCACCAATGATACTGAAGCTACGAATATACTAACTATGAGGATCTCTCATTTGACTCT Cow TACATAATTCCAACATCAGAATTAAAGCCAGGGGAGCTACGACTATTAGAAGTCGATAAT Carp TATATAGTACCAACCCAAGACCTTGCCCCCGGACAATTCCGACTTCTGGAAACAGACCAC Chicken TACATAACCCCAACAACAGACCTCCCCCTAGGCCACTTCCGCCTACTAGAAGTCGACCAT Human TACATACTTCCCCCATTATTCCTAGAACCAGGCGACCTGCGACTCCTTGACGTTGACAAT Loach TACATAATCCCCACCCAGGACCTAACCCCTGGACAATTCCGGCTACTAGAGACAGACCAC Mouse TATATAATCCCAACAAACGACCTAAAACCTGGTGAACTACGACTGCTAGAAGTTGATAAC Rat TACATAATCCCAACCAATGACCTAAAACCAGGTGAACTTCGTCTATTAGAAGTTGATAAT Seal TATATGATCCCCACACAAGAACTAAAGCCCGGAGAACTACGACTGCTAGAAGTAGACAAT Whale TATATAATCCCAACATCAGACCTAAAGCCAGGAGAACTACGATTATTAGAAGTAGATAAC Frog TATATAATTCCAACTAATGACCTTACCCCTGGACAATTCCGGCTGCTAGAAGTTGATAAT Cow CGAGTTGTACTACCAATAGAAATAACAATCCGAATGTTAGTCTCCTCTGAAGACGTATTA Carp CGAATAGTTGTTCCAATAGAATCCCCAGTCCGTGTCCTAGTATCTGCTGAAGACGTGCTA Chicken CGCATTGTAATCCCCATAGAATCCCCCATTCGAGTAATCATCACCGCTGATGACGTCCTC Human CGAGTAGTACTCCCGATTGAAGCCCCCATTCGTATAATAATTACATCACAAGACGTCTTG Loach CGAATGGTTGTTCCCATAGAATCCCCTATTCGCATTCTTGTTTCCGCCGAAGATGTACTA Mouse CGAGTCGTTCTGCCAATAGAACTTCCAATCCGTATATTAATTTCATCTGAAGACGTCCTC Rat CGGGTAGTCTTACCAATAGAACTTCCAATTCGTATACTAATCTCATCCGAAGACGTCCTG Seal CGAGTAGTCCTCCCAATAGAAATAACAATCCGCATACTAATCTCATCAGAAGATGTACTC Whale CGAGTTGTCTTACCTATAGAAATAACAATCCGAATATTAGTCTCATCAGAAGACGTACTC Frog CGAATAGTAGTCCCAATAGAATCTCCAACCCGACTTTTAGTTACAGCCGAAGACGTCCTC Cow CACTCATGAGCTGTGCCCTCTCTAGGACTAAAAACAGACGCAATCCCAGGCCGTCTAAAC Carp CATTCTTGAGCTGTTCCATCCCTTGGCGTAAAAATGGACGCAGTCCCAGGACGACTAAAT Chicken CACTCATGAGCCGTACCCGCCCTCGGGGTAAAAACAGACGCAATCCCTGGACGACTAAAT Human CACTCATGAGCTGTCCCCACATTAGGCTTAAAAACAGATGCAATTCCCGGACGTCTAAAC Loach CACTCCTGGGCCCTTCCAGCCATGGGGGTAAAGATAGACGCGGTCCCAGGACGCCTTAAC Mouse CACTCATGAGCAGTCCCCTCCCTAGGACTTAAAACTGATGCCATCCCAGGCCGACTAAAT Rat CACTCATGAGCCATCCCTTCACTAGGGTTAAAAACCGACGCAATCCCCGGCCGCCTAAAC Seal CACTCATGAGCCGTACCGTCCCTAGGACTAAAAACTGATGCTATCCCAGGACGACTAAAC Whale CACTCATGGGCCGTACCCTCCTTGGGCCTAAAAACAGATGCAATCCCAGGACGCCTAAAC Frog CACTCGTGAGCTGTACCCTCCTTGGGTGTCAAAACAGATGCAATCCCAGGACGACTTCAT Cow CAAACAACCCTTATATCGTCCCGTCCAGGCTTATATTACGGTCAATGCTCAGAAATTTGC Carp CAAGCCGCCTTTATTGCCTCACGCCCAGGGGTCTTTTACGGACAATGCTCTGAAATTTGT Chicken CAAACCTCCTTCATCACCACTCGACCAGGAGTGTTTTACGGACAATGCTCAGAAATCTGC Human CAAACCACTTTCACCGCTACACGACCGGGGGTATACTACGGTCAATGCTCTGAAATCTGT Loach CAAACCGCCTTTATTGCCTCCCGCCCCGGGGTATTCTATGGGCAATGCTCAGAAATCTGT Mouse CAAGCAACAGTAACATCAAACCGACCAGGGTTATTCTATGGCCAATGCTCTGAAATTTGT Rat CAAGCTACAGTCACATCAAACCGACCAGGTCTATTCTATGGCCAATGCTCTGAAATTTGC Seal CAAACAACCCTAATAACCATACGACCAGGACTGTACTACGGTCAATGCTCAGAAATCTGT Whale CAAACAACCTTAATATCAACACGACCAGGCCTATTTTATGGACAATGCTCAGAGATCTGC Frog CAAACATCATTTATTGCTACTCGTCCGGGAGTATTTTACGGACAATGTTCAGAAATTTGC Cow GGGTCAAACCACAGTTTCATACCCATTGTCCTTGAGTTAGTCCCACTAAAGTACTTTGAA Carp GGAGCTAATCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCTCTCGAACACTTCGAA Chicken GGAGCTAACCACAGCTACATACCCATTGTAGTAGAGTCTACCCCCCTAAAACACTTTGAA Human GGAGCAAACCACAGTTTCATGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAA Loach GGAGCAAACCACAGCTTTATACCCATCGTAGTAGAAGCGGTCCCACTATCTCACTTCGAA Mouse GGATCTAACCATAGCTTTATGCCCATTGTCCTAGAAATGGTTCCACTAAAATATTTCGAA Rat GGCTCAAATCACAGCTTCATACCCATTGTACTAGAAATAGTGCCTCTAAAATATTTCGAA Seal GGTTCAAACCACAGCTTCATACCTATTGTCCTCGAATTGGTCCCACTATCCCACTTCGAG Whale GGCTCAAACCACAGTTTCATACCAATTGTCCTAGAACTAGTACCCCTAGAAGTCTTTGAA Frog GGAGCAAACCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCGCTAACCGACTTTGAA Cow AAATGATCTGCGTCAATATTA---------------------TAA Carp AACTGATCCTCATTAATACTAGAAGACGCCTCGCTAGGAAGCTAA Chicken GCCTGATCCTCACTA------------------CTGTCATCTTAA Human ATA---------------------GGGCCCGTATTTACCCTATAG Loach AACTGGTCCACCCTTATACTAAAAGACGCCTCACTAGGAAGCTAA Mouse AACTGATCTGCTTCAATAATT---------------------TAA Rat AACTGATCAGCTTCTATAATT---------------------TAA Seal AAATGATCTACCTCAATGCTT---------------------TAA Whale AAATGATCTGTATCAATACTA---------------------TAA Frog AACTGATCTTCATCAATACTA---GAAGCATCACTA------AGA ; End; weblogo-3.8.0/tests/data/nexus/protein.nex000066400000000000000000000053761467613320200206100ustar00rootroot00000000000000#NEXUS Begin data; Dimensions ntax=10 nchar=234; Format datatype=protein gap=- interleave; Matrix Cow MAYPMQLGFQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQE Carp MAHPTQLGFKDAAMPVMEELLHFHDHALMIVLLISTLVLYIITAMVSTKLTNKYILDSQE Chicken MANHSQLGFQDASSPIMEELVEFHDHALMVALAICSLVLYLLTLMLMEKLS-SNTVDAQE Human MAHAAQVGLQDATSPIMEELITFHDHALMIIFLICFLVLYALFLTLTTKLTNTNISDAQE Loach MAHPTQLGFQDAASPVMEELLHFHDHALMIVFLISALVLYVIITTVSTKLTNMYILDSQE Mouse MAYPFQLGLQDATSPIMEELMNFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQE Rat MAYPFQLGLQDATSPIMEELTNFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQE Seal MAYPLQMGLQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQE Whale MAYPFQLGFQDAASPIMEELLHFHDHTLMIVFLISSLVLYIITLMLTTKLTHTSTMDAQE Frog MAHPSQLGFQDAASPIMEELLHFHDHTLMAVFLISTLVLYIITIMMTTKLTNTNLMDAQE Cow VETIWTILPAIILILIALPSLRILYMMDEINNPSLTVKTMGHQWYWSYEYTDYEDLSFDS Carp IEIVWTILPAVILVLIALPSLRILYLMDEINDPHLTIKAMGHQWYWSYEYTDYENLGFDS Chicken VELIWTILPAIVLVLLALPSLQILYMMDEIDEPDLTLKAIGHQWYWTYEYTDFKDLSFDS Human METVWTILPAIILVLIALPSLRILYMTDEVNDPSLTIKSIGHQWYWTYEYTDYGGLIFNS Loach IEIVWTVLPALILILIALPSLRILYLMDEINDPHLTIKAMGHQWYWSYEYTDYENLSFDS Mouse VETIWTILPAVILIMIALPSLRILYMMDEINNPVLTVKTMGHQWYWSYEYTDYEDLCFDS Rat VETIWTILPAVILILIALPSLRILYMMDEINNPVLTVKTMGHQWYWSYEYTDYEDLCFDS Seal VETVWTILPAIILILIALPSLRILYMMDEINNPSLTVKTMGHQWYWSYEYTDYEDLNFDS Whale VETVWTILPAIILILIALPSLRILYMMDEVNNPSLTVKTMGHQWYWSYEYTDYEDLSFDS Frog IEMVWTIMPAISLIMIALPSLRILYLMDEVNDPHLTIKAIGHQWYWSYEYTNYEDLSFDS Cow YMIPTSELKPGELRLLEVDNRVVLPMEMTIRMLVSSEDVLHSWAVPSLGLKTDAIPGRLN Carp YMVPTQDLAPGQFRLLETDHRMVVPMESPVRVLVSAEDVLHSWAVPSLGVKMDAVPGRLN Chicken YMTPTTDLPLGHFRLLEVDHRIVIPMESPIRVIITADDVLHSWAVPALGVKTDAIPGRLN Human YMLPPLFLEPGDLRLLDVDNRVVLPIEAPIRMMITSQDVLHSWAVPTLGLKTDAIPGRLN Loach YMIPTQDLTPGQFRLLETDHRMVVPMESPIRILVSAEDVLHSWALPAMGVKMDAVPGRLN Mouse YMIPTNDLKPGELRLLEVDNRVVLPMELPIRMLISSEDVLHSWAVPSLGLKTDAIPGRLN Rat YMIPTNDLKPGELRLLEVDNRVVLPMELPIRMLISSEDVLHSWAIPSLGLKTDAIPGRLN Seal YMIPTQELKPGELRLLEVDNRVVLPMEMTIRMLISSEDVLHSWAVPSLGLKTDAIPGRLN Whale YMIPTSDLKPGELRLLEVDNRVVLPMEMTIRMLVSSEDVLHSWAVPSLGLKTDAIPGRLN Frog YMIPTNDLTPGQFRLLEVDNRMVVPMESPTRLLVTAEDVLHSWAVPSLGVKTDAIPGRLH Cow QTTLMSSRPGLYYGQCSEICGSNHSFMPIVLELVPLKYFEKWSASML------- Carp QAAFIASRPGVFYGQCSEICGANHSFMPIVVEAVPLEHFENWSSLMLEDASLGS Chicken QTSFITTRPGVFYGQCSEICGANHSYMPIVVESTPLKHFEAWSSL------LSS Human QTTFTATRPGVYYGQCSEICGANHSFMPIVLELIPLKIFEM-------GPVFTL Loach QTAFIASRPGVFYGQCSEICGANHSFMPIVVEAVPLSHFENWSTLMLKDASLGS Mouse QATVTSNRPGLFYGQCSEICGSNHSFMPIVLEMVPLKYFENWSASMI------- Rat QATVTSNRPGLFYGQCSEICGSNHSFMPIVLEMVPLKYFENWSASMI------- Seal QTTLMTMRPGLYYGQCSEICGSNHSFMPIVLELVPLSHFEKWSTSML------- Whale QTTLMSTRPGLFYGQCSEICGSNHSFMPIVLELVPLEVFEKWSVSML------- Frog QTSFIATRPGVFYGQCSEICGANHSFMPIVVEAVPLTDFENWSSSML-EASL-- ; End; weblogo-3.8.0/tests/data/nexus/test_Nexus_input.nex000066400000000000000000000067561467613320200225130ustar00rootroot00000000000000#NEXUS [ NEXUS test file. Weird, but NEXUS standard compatible.] begin data; dimensions ntax=9 nchar=48; format datatype=dna gap=- missing=? interleave=yes; taxlabels t1 't2 the name' 'isn''that [a] strange name?' 'one should be punished, for (that)!' t5 t6 t7 t8 t9; charlabels 1 'a', 2 'b', 3 'c', 5 'f', 10 'A', 11 'B', 23 'x', 24 'y', 30 '1,2,3 can''t decide for a name?!', 48 final; matrix [interleaved matrix: secont taxon name is spelled either with quotes or with underscores, but must be treated as the same name] t1 A-C-G-Tc-gtgtgtgctct-t-t 't2 the name' A-C-GcTc-gtg-----tct-t-t 'isn''that [a] strange name?' A-CcGcTc-gtgtgtgct------ 'one should be punished, for (that)!' A-C-G-T----------------- t5 A-C?G-T?--acgt??-???-??? t6 AcCaGtTc-?--aaaaaaaa-a-a t7 A?C-GgTg-ggggggggggg-g-g t8 AtCtGtTt-ttttttttttt-?-? [last taxon of the matrix] t9 cccccccc-cccccccccccNc-c t1 ------ac-gtgtgtgctct-t-t t2_the_name ----acac-gtg-----tct-t-t 'isn''that [a] strange name?' --acacac-gtgtgtgct------ 'one should be punished, for (that)!' ------------------------ t5 --??---?--acgt??-???-??? t6 acgactac-?--aaaaaaaa-a-a t7 ??--?ggg-ggggggggggg-g-g t8 tttttttt-ttttttttttt-?-? [last taxon of the matrix] t9 cccccccc-cccccccccccNc-c ; end; [t5 --??---?--a[last quarter of sequence starts here]cgt??-???-???] [ this is a [nested ] comment] [ a special commend was [& not cut out] here] begin sets; [simple blocks dividing the data into three parts] charset c1=1-8; charset c2= 9-16; charset c3 = 17-24 ; [characters can be specified by their character labels] charset byname= 1 f-'1,2,3 can''t decide for a name?!'; charset pos1=1-48\3; charset pos2=b-final\3; charset pos3=3-11\3 12-48\3; charset mix=pos2 1; charset mux=mix 9 c3 ; [big chinks are nice for testing] charset bigchunk=2-47; charset firsthalf=1-24; charset secondhalf=25-48; charset big=1 3 5 7; [classical subdivision into codon positions] charpartition codons = a : pos1, b: pos2 , c:pos3 ; [some taxon sets] taxset normal=1 3 4-6 8; taxset tbyname1=3 t1-t6; taxset tbyname2 = 't2 the_name' - t7; taxset tbyname3 = t1 - t2_the_name; taxset reference=1 2 tbyname1; [another character partition] charpartition part=one:c1, two:c2, three:c3; [and a taxpartition] taxpartition taxpart=goodnames:1 5-9, badnames: 2 3 4; end; [unknown blocks should be read and ignored] begin spam; this is a unknown block; and should be completely ignored; end; [Some trees] begin trees; translate 3 t1, 4 't2 the name' ,1 'isn''that [a] strange name?', 2 'one should be punished, for (that)!' , 9 t5, 7 t6 , 8 t7, 5 t8, 6 t9; tree tree1 = [&R] [&W3.5] (1,(2,3),(4,(5,6,(7,(8,9))))); tree tree1 = (1,(2,(4,(5,6,(7,(8,(9,3))))))); tree tree1 = (1,(2:0.5,(4:0.3,(5:1.2,6:3.4,(7:1,(8:99.9,(9:99,3:0.98)12:13)33:0.44)1:2.0)3:4.0)0.3:0.4)10:100); end; weblogo-3.8.0/tests/data/pam250.mat000077500000000000000000000036031467613320200167530ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 250 substitution matrix, scale = ln(2)/3 = 0.231049 # # Expected score = -0.844, Entropy = 0.354 bits # # Lowest score = -8, Highest score = 17 # A R N D C Q E G H I L K M F P S T W Y V B Z X A 2 -2 0 0 -2 0 0 1 -1 -1 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 R -2 6 0 -1 -4 1 -1 -3 2 -2 -3 3 0 -4 0 0 -1 2 -4 -2 -1 0 -1 N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -3 0 1 0 -4 -2 -2 2 1 0 D 0 -1 2 4 -5 2 3 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -4 -2 3 3 -1 C -2 -4 -4 -5 12 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -8 0 -2 -4 -5 -3 Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 3 -1 E 0 -1 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 -1 0 0 -7 -4 -2 3 3 -1 G 1 -3 0 1 -3 -1 0 5 -2 -3 -4 -2 -3 -5 0 1 0 -7 -5 -1 0 0 -1 H -1 2 2 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 I -1 -2 -2 -2 -2 -2 -2 -3 -2 5 2 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 -1 L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -3 -3 -1 K -1 3 1 0 -5 1 0 -2 0 -2 -3 5 0 -5 -1 0 0 -3 -4 -2 1 0 -1 M -1 0 -2 -3 -5 -1 -2 -3 -2 2 4 0 6 0 -2 -2 -1 -4 -2 2 -2 -2 -1 F -3 -4 -3 -6 -4 -5 -5 -5 -2 1 2 -5 0 9 -5 -3 -3 0 7 -1 -4 -5 -2 P 1 0 0 -1 -3 0 -1 0 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 0 -1 S 1 0 1 0 0 -1 0 1 -1 -1 -3 0 -2 -3 1 2 1 -2 -3 -1 0 0 0 T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 0 W -6 2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17 0 -6 -5 -6 -4 Y -3 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -4 -2 7 -5 -3 -3 0 10 -2 -3 -4 -2 V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 -1 B 0 -1 2 3 -4 1 3 0 1 -2 -3 1 -2 -4 -1 0 0 -5 -3 -2 3 2 -1 Z 0 0 1 3 -5 3 3 0 2 -2 -3 0 -2 -5 0 0 -1 -6 -4 -2 2 3 -1 X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1 0 0 -4 -2 -1 -1 -1 -1 weblogo-3.8.0/tests/data/pfam.txt000066400000000000000000001465421467613320200167370ustar00rootroot00000000000000# STOCKHOLM 1.0 #=GF ID 14-3-3 #=GF AC PF00244 #=GF DE 14-3-3 protein #=GF AU Finn RD #=GF AL Clustalw #=GF SE Prosite #=GF GA 25 25 #=GF TC 35.40 35.40 #=GF NC 19.10 19.10 #=GF TP Domain #=GF BM hmmbuild -f HMM SEED #=GF BM hmmcalibrate --seed 0 HMM #=GF RN [1] #=GF RM 95327195 #=GF RT Structure of a 14-3-3 protein and implications for #=GF RT coordination of multiple signalling pathways. #=GF RA Xiao B, Smerdon SJ, Jones DH, Dodson GG, Soneji Y, Aitken #=GF RA A, Gamblin SJ; #=GF RL Nature 1995;376:188-191. #=GF RN [2] #=GF RM 95327196 #=GF RT Crystal structure of the zeta isoform of the 14-3-3 #=GF RT protein. #=GF RA Liu D, Bienkowska J, Petosa C, Collier RJ, Fu H, Liddington #=GF RA R; #=GF RL Nature 1995;376:191-194. #=GF RN [3] #=GF RM 96182649 #=GF RT Interaction of 14-3-3 with signaling proteins is mediated #=GF RT by the recognition of phosphoserine. #=GF RA Muslin AJ, Tanner JW, Allen PM, Shaw AS; #=GF RL Cell 1996;84:889-897. #=GF RN [4] #=GF RM 97424374 #=GF RT The 14-3-3 protein binds its target proteins with a common #=GF RT site located towards the C-terminus. #=GF RA Ichimura T, Ito M, Itagaki C, Takahashi M, Horigome T, #=GF RA Omata S, Ohno S, Isobe T #=GF RL FEBS Lett 1997;413:273-276. #=GF RN [5] #=GF RM 96394689 #=GF RT Molecular evolution of the 14-3-3 protein family. #=GF RA Wang W, Shakes DC #=GF RL J Mol Evol 1996;43:384-398. #=GF RN [6] #=GF RM 96300316 #=GF RT Function of 14-3-3 proteins. #=GF RA Jin DY, Lyu MS, Kozak CA, Jeang KT #=GF RL Nature 1996;382:308-308. #=GF DR PROSITE; PDOC00633; #=GF DR SMART; 14_3_3; #=GF DR PRINTS; PR00305; #=GF DR SCOP; 1a4o; fa; #=GF DR INTERPRO; IPR000308; #=GF DR PDB; 1a37 A; 3; 228; #=GF DR PDB; 1a37 B; 3; 228; #=GF DR PDB; 1a38 A; 3; 228; #=GF DR PDB; 1a38 B; 3; 228; #=GF DR PDB; 1a4o A; 3; 228; #=GF DR PDB; 1a4o B; 3; 228; #=GF DR PDB; 1a4o C; 3; 228; #=GF DR PDB; 1a4o D; 3; 228; #=GF DR PDB; 1qja B; 3; 229; #=GF DR PDB; 1qja A; 3; 230; #=GF DR PDB; 1qjb A; 3; 232; #=GF DR PDB; 1qjb B; 3; 232; #=GF SQ 148 #=GS O61131/11-251 AC O61131 #=GS 143L_ARATH/7-245 AC P48349 #=GS O49082/8-245 AC O49082 #=GS 143R_ARATH/7-245 AC P42647 #=GS 1433_XENLA/1-227 AC P29309 #=GS 1433_ENTHI/1-236 AC P42650 #=GS Q24902/13-244 AC Q24902 #=GS 1432_ENTHI/4-238 AC P42649 #=GS O24222/3-240 AC O24222 #=GS 143Z_SHEEP/3-236 AC P29361 #=GS 1433_CANAL/5-240 AC O42766 #=GS 143X_MAIZE/1-56 AC P29306 #=GS 143B_BOVIN/4-237 AC P29358 #=GS Q42106/1-38 AC Q42106 #=GS Q9VEA8/4-239 AC Q9VEA8 #=GS O96436/9-256 AC O96436 #=GS P93787/9-246 AC P93787 #=GS 1435_LYCES/5-242 AC P93210 #=GS 1434_LYCES/6-243 AC P42652 #=GS 1431_LYCES/9-246 AC P93206 #=GS Q9XEW6/1-118 AC Q9XEW6 #=GS 1433_LYCES/9-246 AC P93209 #=GS 143E_DROME/4-239 AC P92177 #=GS 143G_BOVIN/3-240 AC P29359 #=GS 1433_TOBAC/5-239 AC Q41246 #=GS Q9UR29/5-240 AC Q9UR29 #=GS Q9UP48/1-164 AC Q9UP48 #=GS Q9SP07/8-245 AC Q9SP07 #=GS Q42260/1-75 AC Q42260 #=GS 143G_RAT/3-240 AC P35214 #=GS Q9XEW7/1-93 AC Q9XEW7 #=GS 1432_MAIZE/8-245 AC Q01526 #=GS 1433_TRIHA/3-238 AC Q99002 #=GS Q9XYW8/1-233 AC Q9XYW8 #=GS Q9S9Z8/5-240 AC Q9S9Z8 #=GS 1431_SCHMA/14-246 AC Q26540 #=GS Q21539/1-97 AC Q21539 #=GS 1438_LYCES/7-131 AC P93213 #=GS Q9T0N0/8-245 AC Q9T0N0 #=GS O24221/9-246 AC O24221 #=GS 143B_HUMAN/4-237 AC P31946 #=GS O24223/8-249 AC O24223 #=GS O70456/3-238 AC O70456 #=GS O80367/7-242 AC O80367 #=GS Q9SEC9/1-127 AC Q9SEC9 #=GS O77642/3-238 AC O77642 #=GS Q28541/1-40 AC Q28541 #=GS 1433_ORYSA/8-245 AC Q06967 #=GS Q9XG89/8-245 AC Q9XG89 #=GS 143A_TOBAC/5-241 AC P93342 #=GS 1433_SOLTU/5-242 AC Q41418 #=GS 143B_RAT/4-237 AC P35213 #=GS 1435_SOLTU/5-243 AC P93784 #=GS Q39558/8-246 AC Q39558 #=GS 143S_HUMAN/3-238 AC P31947 #=GS O61132/1-232 AC O61132 #=GS 143B_SOYBN/6-244 AC Q96451 #=GS 143C_SOYBN/7-242 AC Q96452 #=GS 1433_MESCR/7-244 AC P93259 #=GS 1433_CAEEL/5-237 AC P41932 #=GS O76466/1-54 AC O76466 #=GS BMH1_YEAST/4-240 AC P29311 #=GS 143E_ARATH/5-240 AC P48347 #=GS Q9SCA7/1-230 AC Q9SCA7 #=GS Q06854/1-144 AC Q06854 #=GS 143T_MOUSE/3-236 AC P35216 #=GS 143P_ARATH/4-241 AC P42644 #=GS 143O_ARATH/5-242 AC Q01525 #=GS 143M_ARATH/7-242 AC Q96299 #=GS 143K_ARATH/7-245 AC P48348 #=GS 143Z_MOUSE/3-236 AC P35215 #=GS 143U_ARATH/7-244 AC P42645 #=GS 143F_MOUSE/3-240 AC P11576 #=GS 143H_ARATH/11-248 AC P46077 #=GS 143B_VICFA/7-242 AC P42654 #=GS 1431_ENTHI/4-239 AC P42648 #=GS 143A_VICFA/8-245 AC P42653 #=GS 1433_OENHO/8-245 AC P29307 #=GS 143A_LYCES/11-138 AC P93207 #=GS 1433_DICDI/3-238 AC P54632 #=GS O24001/9-246 AC O24001 #=GS 1432_SCHMA/1-205 AC Q26537 #=GS Q42058/7-112 AC Q42058 #=GS Q9SHV6/16-54 AC Q9SHV6 #=GS 1433_CHLRE/5-242 AC P52908 #=GS O70455/5-238 AC O70455 #=GS Q9XEW4/21-220 AC Q9XEW4 #=GS O60955/9-251 AC O60955 #=GS P93785/3-240 AC P93785 #=GS O65165/1-21 AC O65165 #=GS Q9UAH0/5-239 AC Q9UAH0 #=GS O57468/4-239 AC O57468 #=GS O96945/8-241 AC O96945 #=GS Q9U491/4-239 AC Q9U491 #=GS 1432_LYCES/3-240 AC P93208 #=GS Q42053/5-100 AC Q42053 #=GS O81976/1-54 AC O81976 #=GS Q9U408/13-244 AC Q9U408 #=GS 1436_LYCES/5-243 AC P93211 #=GS 1437_LYCES/5-129 AC P93212 #=GS Q9XEW5/1-219 AC Q9XEW5 #=GS Q9V5G6/6-144 AC Q9V5G6 #=GS O61173/2-194 AC O61173 #=GS O70457/4-241 AC O70457 #=GS Q42020/1-90 AC Q42020 #=GS 1433_SPIOL/1-198 AC P29308 #=GS Q42083/11-79 AC Q42083 #=GS Q9SFK4/1-214 AC Q9SFK4 #=GS 1431_MAIZE/8-245 AC P49106 #=GS Q9XEW3/1-100 AC Q9XEW3 #=GS Q9XEW8/1-86 AC Q9XEW8 #=GS 143Z_XENLA/3-238 AC Q91896 #=GS Q9U8K4/15-247 AC Q9U8K4 #=GS 1439_LYCES/7-131 AC P93214 #=GS 143Z_DROME/6-239 AC P29310 #=GS O49152/7-242 AC O49152 #=GS 1433_HELAN/8-246 AC O65352 #=GS 143E_HUMAN/4-239 AC P42655 #=GS 143G_HUMAN/4-238 AC Q9UN99 #=GS 143C_ARATH/10-247 AC P42643 #=GS Q9UDP2/1-212 AC Q9UDP2 #=GS 143B_TOBAC/3-241 AC O49995 #=GS O57469/3-236 AC O57469 #=GS Q9SWP7/7-245 AC Q9SWP7 #=GS Q9XZV0/2-235 AC Q9XZV0 #=GS 1434_SOLTU/5-241 AC Q43643 #=GS 143A_SOYBN/6-243 AC Q96450 #=GS 143T_HUMAN/3-236 AC P27348 #=GS 1433_FUCVE/4-237 AC Q39757 #=GS 1433_PEA/8-245 AC P46266 #=GS 143F_TOBAC/5-243 AC O49998 #=GS 143E_TOBAC/6-243 AC O49997 #=GS P93786/8-245 AC P93786 #=GS 143D_SOYBN/7-242 AC Q96453 #=GS 143C_TOBAC/8-245 AC P93343 #=GS 1434_CAEEL/5-238 AC Q20655 #=GS 143Z_HUMAN/3-236 AC P29312 #=GS BMH2_YEAST/4-240 AC P34730 #=GS 143D_TOBAC/9-246 AC O49996 #=GS Q9XYW7/4-229 AC Q9XYW7 #=GS O24533/1-181 AC O24533 #=GS 143F_HUMAN/3-240 AC Q04917 #=GS 143A_HORVU/8-245 AC P29305 #=GS RA25_SCHPO/5-240 AC P42657 #=GS 1433_NEOCA/9-251 AC Q25538 #=GS RA24_SCHPO/6-241 AC P42656 #=GS 143B_HORVU/9-246 AC Q43470 #=GS 143N_ARATH/5-242 AC Q96300 #=GS 143Z_HUMAN/3-236 DR PDB; 1a37 A; 3; 228; #=GS 143Z_HUMAN/3-236 DR PDB; 1a37 B; 3; 228; #=GS 143Z_HUMAN/3-236 DR PDB; 1a38 A; 3; 228; #=GS 143Z_HUMAN/3-236 DR PDB; 1a38 B; 3; 228; #=GS 143Z_HUMAN/3-236 DR PDB; 1a4o A; 3; 228; #=GS 143Z_HUMAN/3-236 DR PDB; 1a4o B; 3; 228; #=GS 143Z_HUMAN/3-236 DR PDB; 1a4o C; 3; 228; #=GS 143Z_HUMAN/3-236 DR PDB; 1a4o D; 3; 228; #=GS 143Z_HUMAN/3-236 DR PDB; 1qja B; 3; 229; #=GS 143Z_HUMAN/3-236 DR PDB; 1qja A; 3; 230; #=GS 143Z_HUMAN/3-236 DR PDB; 1qjb A; 3; 232; #=GS 143Z_HUMAN/3-236 DR PDB; 1qjb B; 3; 232; O61131/11-251 RSDCTYRSKLAEQAERYDEMADAMRTLVEQCVnn.......dkdELTVEERNLLSVAYKNAVGARRASWRIISSVEQKEMSKA.NVHNKNIAATYRKKVEEELNNIC.QDILN.LLTKKLIPNT..SESESKVFYYKMKGDYYRYISEFS.CDE.GKKEASNFAQEAYQKATDIAENELPSTHPIRLGLALNYSVFFY..EILNQPHQACEMAKRAF...DDAITEFDNV..SEDS..YKDSTLI.MQLLRDNLTLWTSDLQGDQ O61132/1-232 ---------LAEQAERYDEMADAMRTLVEQCVnn.......dkdELTVEERNLLSVAYKNAVGARRASWRIISSVEQKEMSKA.NVHNKNVAATYRKKVEEELNNIC.QDILN.LLTKKLIPNT..SESESKVFYYKMKGDYYRYISEFS.CDE.GKKEASNFAQEAYQKDTDIAENELPSTHPIRLGLALNYSVFFY..EILNQLHQACEMAKRAF...DDAITEFDNV..SEDS..YKDSTLI.MQLLRDNLTLWTSDLQGDQ O96436/9-256 REEHVYRAKLAEQAERYDEMAEAMKNLVENCLdqnnsppgakgdELTVEERNLLSVAYKNAVGARRASWRIISSVEQKEANRN.HMANKALAASYRQKVENELNKIC.QEILT.LLTDKLLPRT..TDSESRVFYFKMKGDYYRYISEFS.NEE.GKKASAEQAEESYKRATDTAEAELPSTHPIRLGLALNYSVFYY..EILNQPQKACEMAKLAF...DDAITEFDSV..SEDS..YKDSTLI.MQLLRDNLTLWTSDLQTQE O60955/9-251 RDEYVYKAKLAEQAERYDEMAEAMKNLVENCLdeq.....qpkdELSVEERNLLSVAYKNAVGARRASWRIISSVEQKELSKQ.HMQNKALAAEYRQKVEEELNKIC.HDILQ.LLTDKLIPKT..SDSESKVFYYKMKGDYYRYISEFS.GEE.GKKQAADQAQESYQKATETAEAELPSTHPIRLGLALNYSVFFY..EILNLPQQACEMAKRAF...DDAITEFDNV..SEDS..YKDSTLI.MQLLRDNLTLWTSDLQADQ 1433_NEOCA/9-251 RDEYVYKAKLAEQAERYDEMAEAMKNLVENCLdeq.....qpkdELSVEERNLLSVAYKNAVGARRASWRIISSVEQKELSKQ.HMQNKALAAEYRQKVEEELNKIC.HDILQ.LLTDKLIPKT..SDSESKVFYYKMKGDYYRYISEFS.GEE.GKKQAADQAQESYQKATETAEGHSPATHPIRLGLALNYSVFFY..EILNLPQQACEMAKRAF...DDAITEFDNV..SEDS..YKDSTLI.MQLLRDNLTLWTSDLQADQ Q21539/1-97 --------------------------------............---------------------------------------.-----------------------.-----.----------..-----------MVADHFRYLVQYD.-DI.NREEHAHKSRIAYQEALGIAKDKMQPTHPIRLGLALNASALNF..DVLNLPKEANEIAQSAL...DSAHRELEKMksSLDS..YDISNL-.------------------- O65165/1-21 --------------------------------............---------------------------------------.-----------------------.-----.----------..------------------------.---.-------------------------------------------..-----------------...----------..----..-----LI.MQLLRDNLTLWTSDMQEDG Q9U491/4-239 REALVYRAKLAEQLERYDEMVDAMKEVVEMAE............ELTVEERNLLSVAYKNVIGSRRSSWRVFSAVEQTEGNRG.NAEKQACAKKFREVLESELDRVS.KDILE.LIDKYLIKSA..TKSDSKVFYLKMKGDYFRYMAEFS.VDP.QRKKAAEESNKAYQEASEIAATQLFPTHPIRLGLALNYSVYFY..EIMNDPDEACRLAQAAF...DDAIAKLDQL..SEES..YKDSTLI.MQLLRDNLTLWTSDPERDD 1433_XENLA/1-227 -------AKLSEQAERYDDMAASMKAVTELGA............ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEG--.NDKRQQMAREYREKVETELQDIC.KDVLD.LLDRFLVPNA..TPPESKVFYLKMKGDYYRYLSEVA.SGD.SKQETVASSQQAYQEAFEISKSEMQPTHPIRLGLALNFSVFYY..EILNSPEKACSLAKSAF...DEAIRELDTL..NEES..YKDSTLI.MQLLRDNLTLWTSENQGEE 143B_BOVIN/4-237 KSELVQKAKLAEQAERYDDMAAAMKAVTEQGH............ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTER--.NEKKQQMGKEYREKIEAELQDIC.NDVLQ.LLDKYLIPNA..TQPESKVFYLKMKGDYFRYLSEVA.SGD.NKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYY..EILNSPEKACSLAKTAF...DEAIAELDTL..NEES..YKDSTLI.MQLLRDNLTLWTSENQGDE 143B_HUMAN/4-237 KSELVQKAKLAEQAERYDDMAAAMKAVTEQGH............ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTER--.NEKKQQMGKEYREKIEAELQDIC.NDVLE.LLDKYLIPNA..TQPESKVFYLKMKGDYFRYLSEVA.SGD.NKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYY..EILNSPEKACSLAKTAF...DEAIAELDTL..NEES..YKDSTLI.MQLLRDNLTLWTSENQGDE 143B_RAT/4-237 KSELVQKAKLAEQAERYDDMAAAMKAVTEQGH............ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTER--.NEKKQQMGKEYREKIEAELQDIC.SDVLE.LLDKYLILNA..THAESKVFYLKMKGDYFRYLSEVA.SGD.NKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYY..EILNSPEKACSLAKTAF...DEAIAELDTL..NEES..YKDSTLI.MQLLRDNLTLWTSENQGDE O70455/5-238 KSELVHKAKLAEQAERYDDMAAAMKAVTEQGH............ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTER--.DEKKQQMGKEYREKIEAELQDIC.NDVLE.LLDKYLILNA..TQAESKVFYLKMKGDYFRYLSEVA.SGE.NKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYY..EILNSPEKACSLAKTAF...DEAIAELDTL..NEES..YKDSTLI.MQLLRDNLTLWTSENQGDE 143Z_SHEEP/3-236 KNELVQKAKLAEQAERYDDMAACMKSVTEQGA............ELSNEERNLLSVAYKNVVGARRSSWRVVSSIEQKTEG--.AEKKQQMAREYREKIETELRDIC.NDVLS.LLEKFLIPNR..SQPESKVFYLKMKGDYYRYLAEVA.AGD.DKKGIVDQSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYY..EILNSPEKACSLAKTAF...DEAIAELDTL..SEES..YKDSTLI.MQLLRDNLTLWTSDTQGDE 143Z_MOUSE/3-236 KNELVQKAKLAEQAERYDDMAACMKSVTEQGA............ELSNEERNLLSVAYKNVVGARRSSWRVVSSIEQKTEG--.AEKKQQMAREYREKIETELRDIC.NDVLS.LLEKFLIPNA..SQPESKVFYLKMKGDYYRYLAEVA.AGD.DKKGIVDQSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYY..EILNSPEKACSLAKTAF...DEAIAELDTL..SEES..YKDSTLI.MQLLRDNLTLWTSDTQGDE 143Z_HUMAN/3-236 KNELVQKAKLAEQAERYDDMAACMKSVTEQGA............ELSNEERNLLSVAYKNVVGARRSSWRVVSSIEQKTEG--.AEKKQQMAREYREKIETELRDIC.NDVLS.LLEKFLIPNA..SQAESKVFYLKMKGDYYRYLAEVA.AGD.DKKGIVDQSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYY..EILNSPEKACSLAKTAF...DEAIAELDTL..SEES..YKDSTLI.MQLLRDNLTLWTSDTQGDE #=GR 143Z_HUMAN/3-236 SS HHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSC............CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTT--.CCHHHHHHHHHHHHHHHHHHHHH.HHHHH.HHHHTTTTCC..CSCHHHHHHHHHHHHHHHHHHHHC.CSC.HHHHHHHHHHHHHHHHHHHHHCHCCTTCHCHHHHHHHHHHHHC..HTSCCHHHCHHHHHHHH...HHHHTTCGGC..CTTT..HHHHHHH.HHHHHHHHHHCTCCCXXXX #=GR 143Z_HUMAN/3-236 SA 26310320300350512510050022003352............4045500400120033002310402420152179179--.38752510440144014203510.43002.0035201642..754403000010100011100201.867.7465125302500340252067635113122100001001127..31372485135106412...5415867932..3994..6651462.142043126627759XXXX 143Z_XENLA/3-238 KNELVQKAKLAEQAERYDDMAACMKRVTEEGG............ELSNEERNLLSVAYKNVVGARRSSWRVVSSIEQKTEG--.AEKKQEMSREYREKIEAELREIC.NDVLN.LLDKFLIANA..TQPESKVFYLKMKGDYYRYLAEVA.AGN.AKTEIVGQSQKAYQDAFDISKTEMQPTHPIRLGLALKLLCVLTneESSTVQDKACALAKAAF...DEAIAELDTL..SEES..YKDSTLI.MQLLRDNLTLWTSDTQGDE O57469/3-236 KNELVQKAKLAEQAERYDDMAACMKRVTEEGG............ELSNEERNLLSVAYKNVVGARRSSWRVVSSIEQKTEG--.AEKKQEMSREYREKIEAELREIC.NDVLN.LLDKFLIANA..TQPESKVFYLKMKGDYYRYLAEVA.AGN.AKTEIVGQSQKAYQDAFDISKTEMQPTHPIRLGLALNFSVFYY..EILNCPDKACALAKAAF...DEAIAELDTL..SEES..YKDSTLI.MQLLRDNLTLWTSDTQGDE Q9UP48/1-164 --------------------------------............---------------------------------------.-DKKLQLIKDYREKVESELRSIC.TTVLE.LLDKYLIANA..TNPESKVFYLKMKGDYFRYLAEVA.CGD.DRKQTIDNSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYY..EILNNPELACTLAKTAF...DEAIAELDTL..NEDS..YKDSTLI.MQLLRDNLTLWTSDSAGEE 143T_HUMAN/3-236 KTELIQKAKLAEQAERYDDMATCMKAVTEQGA............ELSNEERNLLSVAYKNVVGGRRSAWRVISSIEQKTDT--.SDKKLQLIKDYREKVESELRSIC.TTVLE.LLDKYLIANA..TNPESKVFYLKMKGDYFRYLAEVA.CGD.DRKQTIDNSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYY..EILNNPELACTLAKTAF...DEAIAELDTL..NEDS..YKDSTLI.MQLLRDNLTLWTSDSAGEE 143T_MOUSE/3-236 KTELIQKAKLAEQAERYDDMATCMKAVTEQGA............ELSNEERNLLSVAYKNVVGGRRSAWRVISSIEQKTDT--.SDKKLQLIKDYREKVESELRSIC.TTVLE.LLDKYLIANA..TNPESKVFYLKMKGDYFRYLAEVA.CGD.DRKQTIENSQGAYQEAFDISKKEMQPTHPIRLGLALNFSVFYY..EILNNPELACTLAKTAF...DEAIAELDTL..NEDS..YKDSTLI.MQLLRDNLTLWTSDSAGEE Q9V5G6/6-144 KEELVQKAKLAEQSERYDDMAQAMKSVTETGV............ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEA--.SARKQQLAREYRERVEKELREIC.YEVLEgLLDKYLIPKA..SNPESKVFYLKMKGDYYRYLAEVA.TGD.ARNS---------------------------------------..-----------------...----------..----..-------.------------------- 143Z_DROME/6-239 KEELVQKAKLAEQSERYDDMAQAMKSVTETGV............ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEA--.SARKQQLAREYRERVEKELREIC.YEVLG.LLDKYLIPKA..SNPESKVFYLKMKGDYYRYLAEVA.TGD.ARNTVVDDSQTAYQDAFDISKGKMQPTHPIRLGLALNFSVFYY..EILNSPDKACQLAKQAF...DDAIAELDTL..NEDS..YKDSTLI.MQLLRDNLTLWTSDTQGDE 143G_BOVIN/3-240 REQLVQKARLAEQAERYDDMAAAMKNVTELNE............PLSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTSADG.NEKKIEMVRAYREKIEKELEAVC.QDVLS.LLDNYLIKNCseTQIESKVFYLKMKGDYYRYLAEVA.TGE.KRATVVESSEKAYSEAHEISKEHMQPTHPIRLGLALNYSVFYY..EIQNAPEQACHLAKTAF...DDAIAELDTL..NEDS..YKDSTLI.MQLLRDNLTLWTSDQQDDD 143G_RAT/3-240 REQLVQKARLAEQAERYDDMAAAMKNVTELNE............PLSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTSADG.NEKKIEMVRAYREKIEKELEAVC.QDVLS.LLDNYLIKNCseTQYESKVFYLKMKGDYYRYLAEVA.TGE.KRATVVESSEKAYSEAHEISKEHMQPTHPIRLGLALNYSVFYY..EIQNAPEQACHLAKTAF...DDAIAELDTL..NEDS..YKDSTLI.MQLLRDNLTLWTSDQQDDD Q9UDP2/1-212 --------------------------VTELNE............PLSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTSADG.NEKKIEMVRAYREKIEKELEAVC.QDVLS.LLDNYLIKNCseTQYESKVFYLKMKGDYYRYLAEVA.TGE.KRATVVESSEKAYSEAHEISKEHMQPTHPIRLGLALNYSVFYY..EIQNAPEQACHLAKTAF...DDAIAELDTL..NEDS..YKDSTLI.MQLLRDNLTLWTSDQQDDD O70457/4-241 REQLVQKARLAEQAERYDDMAAAMKNVTELNE............PLSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTSADG.NEKKIEMVRAYREKIEKELEAVC.QDVLS.LLDNYLIKNCseTQYESKVFYLKMKGDYYRYLAEVA.TGE.KRATVVESFEKAYSEAHEISKEHMQPTHPIRLGLALNYSVFYY..EIQNAPEQACHLAKTAF...DDAIAELDTL..NEDS..YKDSTLI.MQLLRDNLTLWTSDQQDDD 143G_HUMAN/4-238 -EQLVQKARLAEQAEGYDDMAAAMKNVTELNE............PLSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTSADG.NE-KIEMVRAYREKVEKELEAVC.QDVLS.LVDNYLYKNCseTQYERKDLYLKMKGDYYRYLAEVA.TGE.KRGDVVESSEKAYSE-REISKEHMQPTHPIRLGLALNYSVFYY..EIQNAPEQACHLAKTEF...EDAIAELDTL..NEES..YKDSTLI.MQLLRDNLTLWTSDQQDDH Q28541/1-40 --------------------------------............---------------------------------------.-----------------------.-----.----------..------------------------.---.-------------------------------------------..-----------------...DDAIAELDTL..NEDS..YKDSTLI.MQLLRDNLTLWTSDQQDEE 143F_MOUSE/3-240 REQLLQRARLAEQAERYDDMASAMKAVTELNE............PLSNEDRNLLSVAYKNVVGARRSSWRVISSIEQKTMADG.NEKKLEKVKAYREKIEKELETVC.NDVLA.LLDKFLIKNCndFQYESKVFYLKMKGDYYRYLAEVA.SGE.KKNSVVEASEAAYKEAFEISKEHMQPTHPIRLGLALNFSVFYY..EIQNAPEQACLLAKQAF...DDAIAELDTL..NEDS..YKDSTLI.MQLLRDNLTLWTSDQQDEE 143F_HUMAN/3-240 REQLLQRARLAEQAERYDDMASAMKAVTELNE............PLSNEDRNLLSVAYKNVVGARRSSWRVISSIEQKTMADG.NEKKLEKVKAYREKIEKELETVC.NDVLS.LLDKFLIKNCndFQYESKVFYLKMKGDYYRYLAEVA.SGE.KKNSVVEASEAAYKEAFEISKEQMQPTHPIRLGLALNFSVFYY..EIQNAPEQACLLAKQAF...DDAIAELDTL..NEDS..YKDSTLI.MQLLRDNLTLWTSDQQDEE 1433_CAEEL/5-237 VEELVQRAKLAEQAERYDDMAAAMKKVTEQGQ............ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEG--.SEKKQQLAKEYRVKVEQELNDIC.QDVLK.LLDEFLIVKA..GAAESKAFYLKMKGDYYRYLAEVA.S-E.DRAAVVEKSQKAYQEALDIAKDKMQPTHPIRLGLALNFSVFYY..EILNTPEHACQLAKQAF...DDAIAELDTL..NEDS..YKDSTLI.MQLLRDNLTLWTSDVGAED O76466/1-54 --------------------------------............---------------------------------------.-----------------------.-----.----------..------------------------.---.-------------------------------------------..---NSPDKACQLAKQAF...DDAIAELDTL..NEDS..YKDSTLI.MQLLRDNLTLWTSDTAGDE 1434_CAEEL/5-238 KEELVNRAKLAEQAERYDDMAASMKKVTELGA............ELSNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEG--.SEKKQQMAKEYREKVEKELRDIC.QDVLN.LLDKFLIPKA..GAAESKVFYLKMKGDYYRYLAEVA.SGD.DRNSVVEKSQQSYQEAFDIAKDKMQPTHPIRLGLALNFSVFFY..EILNAPDKACQLAKQAF...DDAIAELDTL..NEDS..YKDSTLI.MQLLRDNLTLWTSDAATDD 1432_SCHMA/1-205 -----------------------------SNN............ELTNEERNLLSVAYKNVVGARRSSWRVISSIEQKTEG--.SERKQQMAKDYREKIEKELKDIC.HEVLT.LLDKFLIPKA..TTAESKVFYLKMKGDYYRYLAEVA.TGD.ERQKVIEESQRAYNDAFDIAKNQMQPTHPIRLGLALNFSVFYY..EILNAPDRACHLAKQAF...DDAIAELDTL..NEDS..YKDSTLI.MQLLRDNLTLWTSDTGGDD O96945/8-241 -SPLTTKARIAEQAERYEDMAKFMKEVTEKAT...........eELSPDDRNLLSVAYKNVVGTRRSSWRVISSIEQKSSD--.-ENKKEMAKAYREKIEKELDEIC.NEVLT.LLDDHLLKKA..TSDESKVFYQKMKGDYYRYLAEVTpSGD.KREDVVVKAKDSYNKALEVATEKMPPTHPIRLGLALNFSVFHY..EIQNAPEKACEMAKKAF...DEAIAELDNL..KEDS..YKDSTLI.MQLLRDNLTLWTSEGQTEE O70456/3-238 RASLIQKAKLAEQAERYEDMAAFMKSAVEKGE............ELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKSNEEG.SEEKGPEVKEYREKVETELRGVC.DTVLG.LLDSHLIKGA..GDAESRVFYLKMKGDYYRYLAEVA.TGD.DKKRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHY..EIANSPEEAISLAKTTF...DEAMADLHTL..SEDS..YKDSTLI.MQLLRDNLTLWTADSAGEE O77642/3-238 RASLIQKAKLAEQAERYEDMAAFMKSAVEKGE............ELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKSNEES.SEEKGPEVQEYREKVETELRGVC.DTVLG.LLDTHLIKEA..GDAESRVFYLKMKGDYYRYLAEVA.TGD.DKKRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHY..EIANSPEEAISLAKTTF...DEAMADLHTL..SEDS..YKDSTLI.MQLLRDNLTLWTADNAGEE 143S_HUMAN/3-238 RASLIQKAKLAEQAERYEDMAAFMKGAVEKGE............ELSCEERNLLSVAYKNVVGGQRAAWRVLSSIEQKSNEEG.SEEKGPEVREYREKVETELQGVC.DTVLG.LLDSHLIKEA..GDAESRVFYLKMKGDYYRYLAEVA.TGD.DKKRIIDSARSAYQEAMDISKKEMPPTNPIRLGLALNFSVFHY..EIANSPEEAISLAKTTF...DEAMADLHTL..SEDS..YKDSTLI.MQLLRDNLTLWTADNAGEE 1431_SCHMA/14-246 NTDLVHIAKLAEQAERYDDMAAAMKRYTEASG............NLGNEERNLLSVAYKNVVGARRSAWRVIHGSEMKAVN--.DRTKKQIAEEYRIKMEKELNTIC.NQVLA.LLEDYLLPNA..SPDDSKVFFLKMQGDYYRYLAEVA.TDD.ARTEVVQKSLDAYTKATTAA-ENLPTTHPIRLGLALNFSVFFY..EIQNDAAKACELAKSAF...DSAIAELDQL..QDDS..YKDSTLI.MQLLRDNLTLWASDQTAEG Q9U8K4/15-247 -SDLVQIAKLAEQAERYDDMAAAMKAYAELPA............ELGSEERNLFSVAYKNVVGARRSAWRVISAVEHKHDE--.NSKKRQLTKEYRVKMEEELNEIC.REVLT.LLSKYLTPKS..NGFESQVFYRKMEGDYYRFLAEVA.TGD.ARKEVVEKSQAAYEKATEIAEEMLPSTHPIRLGLALNFSMFYY..EIKCDPTQACNLAKRAF...DTSIGELDSL..QDDS..YKDSTLI.MQLLRDNLTLWASDQPEAE Q9SHV6/16-54 --------------------------------............---------------------------------------.-----------------------.-----.----------..------------------------.---.-------------------------------------------..-----------------...-EALMMLDAL..GDEL..YKDSTLI.MKILRDNLTFWTSDMTDEA Q24902/13-244 VDELVQRAKLAEQAERYDDMAGACKTMAEMGN............ELNNEERNLLSVAYKNVLGARRSSWRIMSSIAKKQAG--.-TPLADQTDIYLKKVEEELIPIC.NDVLA.-LPVLPITEK..IGAEAKIFYYKMMGDYYRYLAEVQ.EGE.QNDKSTEAAEEANQKATSLAEAELSVTHPIRLGLALNFSVFYY..EIKNMPEKACSLAKAAF...DAAITEVDSI..KDET..YKDSTLI.MQLLRDNLTLWNSECETDS Q9U408/13-244 VDELVQRAKLAEQAERYDDMAGACKTMAKMRN............ELNNEEANLLSVAYKNVVGARRSSWRIMSSIAKKQAG--.-TPLAHQHDIYLKKVEEELIQIC.NDVLA.-LPVLPITEK..IGAEAKIFYYKMMGDYYRYSAEVQ.EGE.QNDKSTEAAEEANQKATSLAEAELSVTHPIRLGLALNFSVFYY..EIKNMPEKACSLAKAAF...DAAITEVDSI..KDET..YKDSTLI.MQLLRDNLTLWNSECETDS 143L_ARATH/7-245 RDQYVYMAKLAEQAERYEEMVQFMEQLVTGATp.........aeELTVEERNLLSVAYKNVIGSLRAAWRIVSSIEQKEESRK.NDEHVSLVKDYRSKVESELSSVC.SGILK.LLDSHLIPSA..GASESKVFYLKMKGDYHRYMAEFK.SGD.ERKTAAEDTMLAYKAAQDIAAADMAPTHPIRLGLALNFSVFYY..EILNSSDKACNMAKQAF...EEAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDMQEQM 143R_ARATH/7-245 RDQYVYMAKLAEQAERYEEMVQFMEQLVTGATp.........aeELTVEERNLLSVAYKNVIGSLRAAWRIVSSIEQKEESRK.NDEHVSLVKDYRSKVESELSSVC.SGILK.LLDSHLIPSA..GASESKVFYLKMKGDYHRYMAEFK.SGD.ERKTAAEDTMLAYKAAQDIAAADMAPTHPIRLGLALNFSVFYY..EILNSSDKACNMAKQAF...EEAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDYAGAD 143K_ARATH/7-245 RDQYVYMAKLAEQAERYEEMVQFMEQLVSGATp.........agELTVEERNLLSGAYKNVIGSLRAAWRIVSSLEQKEESRK.NEEHVSLVKDYRSKVETELSSIF.SGILR.LLDSHLIPSA..TARESKVFYLKMKGDYHRYLAEFK.SGD.ERKTAAEDAMIAYKAAQDVAVADLAPTHPIRLGLALNFSVFYY..EILNSSEKACSMAKQAF...EEAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDMQEQM Q9SWP7/7-245 RDQYVYMAKLAEQAERYEEMVQFMEQLVSGATp.........agELTVEERNLLSVAYKNVIGSLRAAWRIVSSIEQKEESRK.NEEHVSLVKDYRSKVETELSSIC.SGILR.LLDSHLIPSA..TASESKVFYLKMKGDYHRYLAEFK.SGD.ERKTAAEDTMIAYKAAQDVAVADLAPTHPIRLGLALNFSVFYY..EILNSSEKACSMAKQAF...EEAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDMQEQM Q9SEC9/1-127 --------------------------------............---------------------------------------.-----------------------.-----.----------..GTRESKVFYLKMKGDYHRYMAEFK.VGD.ERKNAAEDTMNSYKAAQDIALADLAPTHPIRLGLALNFSVFYY..EILNSSDKACSMAKQAF...EEAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDSQDQL 143B_SOYBN/6-244 REQYVYLANVSEQAERYEEMVEFMQKVVVGSTp.........asELTVEERNLLSVAYKNVIGSLRAAWRIVSSIEQKEEGRK.NDDHVSLVKHYRSKVENELTQVC.ATILS.LLDSNLVPSA..SASESKVFYLKMKGDYHRYLAEFK.VGD.ERKTATEDTMLSYKAAQDIASADLPPTHPIRLGLALNFSVFYY..EILNQSDKACAMAKQAF...EEAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDVQDQL O24533/1-181 --------------------------------............-----------VAYKNVIGSLRAAWRIVSSIEQKEEGRK.NDDHVVLVKDYRSKVEAELSNVC.ASILE.LLDKNLIPSG..SSSESKVFYYKMKGDYHRYLAEFK.IGE.ERKSAAEDTMLSYKAAQDIAAADLPSTHPIRLGLALNFSVFYY..EILNQSDKACAMAKQAF...EEAIAELDTL..GEES..YKDSTLI.MQLFRDN------------ P93787/9-246 REQCLYLAKLAEQAERYEEMVKFMDKLVIGSGs..........sELTVEERNLLSVAYKNVIGSLRAAWRIVSSIEQKEEGRK.NDEHVVLVKDYRSKVESELSDVC.AGILK.ILDQYLIPSA..SAGESKVFYLKMKGDYYRYLAEFK.VGN.ERKEAAEDTMLAYKAAQDIAVAELAPTHPIRLGLALNFSVFYY..EILNASEKACSMAKQAF...EEAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDMQEQM 1431_LYCES/9-246 REQCLYLANVAEQAERYEEMVKFMDKLVIGSGs..........sELTVEERNLLSVAYKNVIGSLRAAWRIVSSIEQKEEGRK.NDEHVVLVKDYRSKVESELSDVC.AGILK.ILDQYLIPSA..SAGESKVFYLKMKGDYYRYLAEFK.VGN.ERKEAAEDTMLAYKAAQDIAVADVAPTHPIRLGLALNFSVFYY..EILNASEKACSMAKQAF...EEAIAELDTM..GEES..YKDSTLI.MQLLRDNLTLWTSDMQEQM 143D_TOBAC/9-246 REQCLYLAKLAEQAERYEEMVKFMDRLVAVSAs..........sELTVEERNLLSVAYKNVIGSLRAAWRIVSSIEQKEEGRK.NEEHVVLVKDYRSKVESELSDVC.AGILK.ILDQYLIPSA..AAGESKVFYLKMKGDYYRYLAEFK.VGN.ERKEAAEDTMLAYKAAQDIALAELAPTHPIRLGLALNYSVFYY..EILNASEKACSMAKQAF...EEAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDMQEQM Q9XEW6/1-118 ----------AEQAERYEEMVQFMQKLVIGNTp.........ggELNVEERNLLSVAYKNVIGSLRAAWRIVSSIEQKEEGRK.NEDHVVLVKEYRSKVESELSDIC.ASILR.LLDSNLIPSA..TASESKVFYLKMKGDY--------.---.-------------------------------------------..-----------------...----------..----..-------.------------------- Q9XEW3/1-100 ----------AEQAERYEEMVLFMQKLVLGNTp.........ggELNVEERNLLSVAYKNVIGSLRAAWRIVSSIEQKEEGRK.NEDHVVLVKEYRSKVESELSDVC.ASILR.LLDSNLVP--..------------------------.---.-------------------------------------------..-----------------...----------..----..-------.------------------- 143A_LYCES/11-138 REQCLYLAKLAEQAERYEEMVQFMDKLVLNSTp.........adDLTVEERNLLSVAYKNVIGSLRAAWRIVSSIEQKEESRK.NEEHVHLVKEYRGKVENELSQVC.AGILK.LLESNLVPSA..TTSESKVFHLKMKGDY--------.---.-------------------------------------------..-----------------...----------..----..-------.------------------- Q42020/1-90 --------------------------------............--------------------------------------G.NDDHVSLIRDYRSKIETELSDIC.DGILK.LLDTILVPAA..ASGDSKVFYLKMKGDYHRYLAEFK.SGQ.ERKDAAEHTLXAYKAAQDIANSEL-------------------..-----------------...----------..----..-------.------------------- 143C_ARATH/10-247 RDEFVYMAKLAEQAERYEEMVEFMEKVAKAVDk..........dELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NDDHVSLIRDYRSKIETELSDIC.DGILK.LLDTILVPAA..ASGDSKVFYLKMKGDYHRYLAEFK.SGQ.ERKDAAEHTLTAYKAAQDIANSELAPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DEAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWASDMQDDV Q9XEW7/1-93 ---DICRIXLAEQAERYEEMVEFMEKVTKGVEv..........eELTVEERNLLSVAYKNVIGARRASWRIIWSIEQKEESRG.NDEHVVTIREYRSKVESYLSACS.-----.----------..------------------------.---.-------------------------------------------..-----------------...----------..----..-------.------------------- Q9XEW8/1-86 ----------AEQAERYEEMVEFMEKVTKGVEv..........eELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NDEHVVTIREYRSKVESYLSACS.-----.----------..------------------------.---.-------------------------------------------..-----------------...----------..----..-------.------------------- O49082/8-245 REENVYMAKLAEQAERYEEMVEFMEKVARTVDt..........eELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDHVALIKDYRGKIEAELSKIC.DGILK.LLDSHLVPSS..TAAESKVFYLKMKGDYHRYLAEFK.SGA.ERKEAAESTLLAYKSAQDIALAELAPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DEAISELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDINEEA Q9SP07/8-245 REENVYMAKLAEQAERYEEMVEFMEKVARTVDt..........eELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDHVALIKDYRGKIEAELSKIC.DGILK.LLDSHLVPSS..TAPESKVFYLKMKGDYHRYLAEFK.SGA.ERKEAAESTLLAYKSAQDIALAELAPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DEAISELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDINEEA O24222/3-240 REENVYMAKLAEQAERYEEMVEYMEKVAKTVDv..........eELTVEERNLLSVAYKNVIGARRASWRIVSSIEQKEEGRG.NEEHVTLIKEYRGKIEAELSKIC.DGILK.LLDSHLVPSS..TAAESKVFYLKMKGDYHRYLAEFK.TGA.ERKEAAESTMVAYKAAQDIALADLAPTHPIRLGLALNFSVFYY..EILNSPDKACNLAKQAF...DEAISELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDLTEDG 1432_MAIZE/8-245 REENVYMAKLAEQAERYEEMVEFMEKVAKTVDs..........eELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEEGRG.NEDRVTLIKDYRGKIETELTKIC.DGILK.LLESHLVPSS..TAPESKVFYLKMKGDYYRYLAEFK.TGA.ERKDAAENTMVAYKAAQDIALAELAPTHPIRLGLALNFSVFYY..EILNSPDRACSLAKQAF...DEAISELDTL..SEES..YKDSTLI.MQLLHDNLTLWTSDISEDP 1431_MAIZE/8-245 REENVYMAKLAEQAERYEEMVEFMEKVAKTVDs..........eELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEEGRG.NEDRVTLIKDYRGKIETELTKIC.DGILK.LLETHLVPSS..TAPESKVFYLKMKGDYYRYLAEFK.TGA.ERKDAAENTMVAYKAAQDIALAELAPTHPIRLGLALNFSVFYY..EILNSPDRACSLAKQAF...DEAISELDTL..SEES..YKDSTLI.MQLLRDNLTLWTSDISEDP O24221/9-246 REENVYMAKLAEQAERYEEMVEFMEKVAKTVDs..........eELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDRVTLIKDYRGKIETELTKIC.DGILK.LLESHLVPSS..TAPESKVFYLKMKGDYYRYLAEFK.TGA.ERKDAAENTMVAYKAAQDIALAELPPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DEAISELDTL..SEES..YKDSTLI.MQLLRDNLTLWTSDISEDT O24001/9-246 REENVYMAKLAEQAERYEEMVEFMEKVAKTVDs..........eELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDRVTLIKEYRGKIETELSKIC.DGILK.LLETHLVPSS..TAPESKVFYLKMKGDYYRYLAEFK.SGP.ERKDAAENTMVAYKAAQDIALAELAPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DEAISELDTL..SEES..YKDSTLI.MQLLRDNLTLWTSDITEDT 143B_HORVU/9-246 REENVYMAKLAEQAERYEEMVEFMEKVAKTVDs..........eELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDRVTLIKDYRGKIEVELTKIC.DGILK.LLDSHLVPSS..TAPESKVFYLKMKGDYYRYLAEFK.SGT.ERKDAAENTMVAYKAAQEIALAELPPTHPIRLGLALNFSVFYY..EILNSPDRACDLAKQAF...DEAISELDSL..SEES..YKDSTLI.MQLLRDNLTLWTSDISEDA 143P_ARATH/4-241 REENVYMAKLAEQAERYEEMVEFMEKVAKTVDv..........eELSVEERNLLSVAYKNVIGARRASWRIISSIEQKEESKG.NEDHVAIIKDYRGEIESELSKIC.DGILN.VLEAHLIPSA..SPAESKVFYLKMKGDYHRYLAEFK.AGA.ERKEAAESTLVAYKSASDIATAELAPTHPIRLGLALNFSVFYY..EILNSPDRACSLAKQAF...DDAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDMTDEA Q42053/5-100 REENVYMAKLAEQAERYEEMVEFMEKVAKTVDv..........eELSVEERNLLSVAYKNVIGARRASWRIISSIEQKEESKG.NEDHVAIIKDYRGKIESELSKIC.-----.----------..------------------------.---.-------------------------------------------..-----------------...----------..----..-------.------------------- 1433_ORYSA/8-245 REENVYMAKLAEQAERYEEMVEFMEKVAKTTDv..........gELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEAYVASIKEYRSRIETELSKIC.DGILK.LLDSHLVPSA..TAAESNVFYLKMKGDYHRYLAEFK.SGA.ERKEAAENTLVAYKSAQDIALADLPTTHPIRLGLALNLSVFYY..EILNSPDRACNLAKQAF...DDAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDNAEDG 143A_HORVU/8-245 REENVYMAKLAEQAERYEEMVEFMEKVAKTADv..........gELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEAYVASIKEYRTRIETELSKIC.DGILK.LLDSHLVPSA..TAAESKVFYLKMKGDYHRYLAEFK.AGA.ERKEAAENTLVAYKSAQDIALADLPTTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DEAIAELDSL..GEES..YKDSTLI.MQLLRDNLTLWTSDNAEEG 1434_LYCES/6-243 REENVYLAKLAEQAERYEEMIEFMEKVAKTADv..........eELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDHVNTIKEYRSKIEADLSKIC.DGILS.LLESNLIPSA..STAESKVFHLKMKGDYHRYLAEFK.TGT.ERKEAAENTLLAYKSAQDIALAELAPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DEAISELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDNADDV 1433_SOLTU/5-242 REENVYMAKLAEQAERYEEMVEFMEKVAKVDV...........eELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDHVSSIKEYRVKIEAELSKIC.DGILS.LLESHLVPSA..STAESKVFYLKMKGDYHRYLAEFK.TGArERKEAAENTLLAYKSAQDIALAELTPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DDAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDTTDDA 143E_TOBAC/6-243 REENVYMAKLAEQAERYEEMVEFMEKVAKTVDv..........eELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDHVSSIKEYRGKIEAELSKIC.DGILN.LLESHLIPVA..STAESKVFYLKMKGDYHRYLAEFK.TGA.ERKEAAENTLLAYKSAQDIALAELAPTHPIRLGLALNFSVFYY..EILNSSDRACNLAKQAF...DDAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDTTVSL 1433_MESCR/7-244 REENVYMAKLAEQAERYEEMVEFMEKVAKMTDt..........eELSVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDHVSTIKEYRGKIETELSKIC.DGILN.LLESHLIPSA..STAESKVFYLKMKGDYHRYLAEFK.TGA.ERKEAAENTLLAYKSAQDIALAELAPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DEAISELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDNAEEG 143U_ARATH/7-244 REENVYLAKLAEQAERYEEMVEFMEKVAKTVEt..........eELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEDSRG.NSDHVSIIKDYRGKIETELSKIC.DGILN.LLEAHLIPAA..SLAESKVFYLKMKGDYHRYLAEFK.TGA.ERKEAAESTLVAYKSAQDIALADLAPTHPIRLGLALNFSVFYY..EILNSSDRACSLAKQAF...DEAISELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDLNDEA 143N_ARATH/5-242 REENVYLAKLAEQAERYEEMVEFMEKVAKTVDt..........dELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NDDHVSIIKDYRGKIETELSKIC.DGILN.LLDSHLVPTA..SLAESKVFYLKMKGDYHRYLAEFK.TGA.ERKEAAESTLVAYKSAQDIALADLAPTHPIRLGLALNFSVFYY..EILNSPDRACSLAKQAF...DEAISELDTL..GEES..YKDSTLI.MQLLRDNLTLWNSDINDEA O81976/1-54 --------------------------------............---------------------------------------.-----------------------.-----.----------..------------------------.---.-------------------------------------------..---NSSDRACNLAKQAF...DEAISELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDITDDA 143A_SOYBN/6-243 REENVYMAKLADEAERYEEMVEFMEKVAKTVEv..........eELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDHVAIIKEYRGKIEAELSKIC.DGILN.LLESNLIPSA..ASPESKVFYLKMKGDYHRYLAEFK.TGA.ERKEAAESTLLAYKSAQDIALADLAPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DEAISELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDITDIA 1435_LYCES/5-242 REENVYMANVADEAERYEEMVEFMEKVVAALNg..........eELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDHVASIKKYRSQIENELTSIC.NGILK.LLDSKLIGSA..ATGDSKVFYLKMKGDYYRYLAEFK.TGT.ERKEAAENTLSAYKSAQDIANGELAPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DEAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDMQDDG 1434_SOLTU/5-241 REENVYMANVAARAERYEEMVEFMEKVVAALD...........tELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDHVASIKKYRSQIENELTSIC.NGILK.LLDSKLIGSA..ATGDSKVFYLKMKGDYYRYLAEFK.TGT.ERKEAAENTLSAYKSAQDIANGELAPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DEAIADVDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDMQDDG 1435_SOLTU/5-243 REENVYMAKLAEQAERYEEMVEFMEKVVAAADg.........aeELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDHVASIKEYRSKIESELTSIC.NGILK.LLDSKLIGSA..ATGDSKVFYLKMKGDYHRYLAEFK.TGA.ERKEAAENTLSAYKAAQDIANAELAPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DEAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDMQDDG 1436_LYCES/5-243 REENVYMANVAEQRRSYEEMVEFMEKVVAAADg.........aeELTVEERILLSVAYKNVMGARRASWRIISSIEQKEESRG.NEDHVASIKEYRSKIESELTSIC.NGILK.LLDSKLIGSA..ATGDSKVFYLKMKGDYHRYLAEFK.TGA.ERKEAAENTLSAYKAAQDIANAELAPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DEAIAELDTL..GEES..YKDSTLI.MQLLRDNLTSWTSDMQDDG 143A_TOBAC/5-241 REENVYLAKLAEQAERYEEMVEFMEKVVGAGD...........dELTIEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDHVASIKTYRSKIESELTSIC.NGILK.LLDSKLIGTA..ATGDSKVFYLKMKGDYYRYLAEFK.TGA.ERKEAAENTLSAYKSAQDIANGELAPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DEAIAELGTL..GEES..YKDSTLI.MQLFCDNLTLWTSDMQDDG 143F_TOBAC/5-243 RDEFVYMAKLAEQAERYEEMVDFMEKVVTAADg.........geELTIEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDHVTSIKTYRSKIESELTSIC.NGILK.LLDSNLIRAA..STGDSKVFYLKMKGDYHRYLAEFK.TGA.ERKEAAENTLSSYKSAQDIANAELAPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DEAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDMQDEG 1433_HELAN/8-246 REENVYLAKLAEQAERYEEMVEFMEKVVAAADg.........geELTIEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEGHVSTIRDYRSKIESELSSIC.DGILK.VLDSKLIGSA..SGGDSKVFYLKMKGDYYRYLAEFK.TGD.ERKLAAENTLSAYKAAQDIANAELAPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DEAIAELDTL..GEDS..YKDSTLI.MQLLRDNLTLWTSDMQDDT 1433_LYCES/9-246 REENVYMAKLADRAESDEEMVEFMEKVSNSLGs..........eELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEEHVNSIREYRSKIENELSKIC.DGILK.LLDSKLIPSA..TSGDSKVFYLKMKGDYHRYLAEFK.TGA.ERKEAAESTLTAYKAAQDIASAELAPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DEAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDMQDDG Q9SCA7/1-230 --ENVYMAKLADRAESDEEMVEFMEKVSNSLGs..........eELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEEHVNSIREYRSKIENELSKIC.DGILK.LLDSKLIPSA..TSGDSKVFYLKMKGDYHRYLAEFK.TGA.ERKEAAESTLTAYKAAQDIASAELAPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DEAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTS------ P93786/8-245 REENVYMAKLAEQAERYEEMVEFMEKVSNSLGs..........eELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEEHVNSIREYRSKIENELSKIC.DGILK.LLDSKLIPSA..TSGDSKVFYLKMKGDYHRYLAEFK.TGA.ERKEAAESTLTAYKAAQDIASAELAPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DEAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDMQDDG 143C_TOBAC/8-245 REENVYMAKLAEQAERYEEMVEFMEKVSNSLGs..........eELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEEHVNSIREYRSKIENELSKIC.DGILK.LLDAKLIPSA..ASGDSKVFYLKMKGDYHRYLAEFK.TGA.ERKEAAESTLTAYKAAQDIATTELAPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DEAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDMQDDG Q42260/1-75 --------------------------------............---------------------------------------.-----------------------.-----.----------..------------------------.---.-------------------------PTHPIRLGLALNSSVFYY..EILNSPDRGCNLAKQGF...DEAIAELDTL..GEES..NKDSTLI.MQLLRDNLTLWTSDMQDDV P93785/3-240 REENVYMAKLAEQAERYEEMVQFMEKVSTSLGs..........eELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEEHVKCIKEYRSKIESELSNIC.DGILK.LLDSNLIPSA..SNGDSKVFYLKMKGDYHRYLAEFK.TGA.ERKEAAESTLSAYKAAQDIANTELAPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DEAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDMQDDG 1432_LYCES/3-240 REENVYMANVAEQAERYEEMVQFMEKVSTSLGs..........eELTVEERNLLSVAYKNVIGARTLAWRIISSIEQKEESRG.NEEHVKCIKEYRSKIESELSDIC.DGILK.LLDSNLIPSA..SNGDSKVFYLKMKGDYHRYLAEFK.TGA.ERKEAAESTLSAYKAAQDIANTELAPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DEAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDMQDDG 143B_TOBAC/3-241 REENVYMAKLAEQAERYEEMVSFMEKVSTSLGt.........seELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDHVKCIQEYRSKIESELSNIC.DGILK.LLDSCLIPSA..SAGDSKVFYLKMKGDYHRYLAEFK.TGA.ERKEAAESTLSAYKAAQDIANAELAPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DEAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDMQDDG Q9T0N0/8-245 REENVYMAKLAEQAERYEEMVEFMEKVSANADs..........eELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDHVDVIRDYRSKIESELSNIC.DGILK.LLDTRLIPSA..SSGDSKVFYLKMKGDYHRYLAEFK.TGA.ERKEAAESTLAAYKSAQDIANAELPPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DEAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDMQDDG 1433_PEA/8-245 REENVYMAKLAEQAERYEEMVEFMEKVSANADs..........eELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDHVAVIRDYRSKIESELSNIC.DGILK.LLDTRLIPSA..SSGDSKVFYLKMKGDYHRYLAEFK.TGA.ERKEAAESTLTGYKSAQDIANAELPPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DEAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDMQDDG 1433_OENHO/8-245 REENVYLAKLAEQAERYEEMVEFMEKVCAAADs..........eELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NDDHVSTIRDYRSKIETELSNIC.GGILK.LLDSRLIPSA..ASGDSKVFYLKMKGDYHRYLAEFK.TGA.ERKEAAESTLSAYKAAQDIANAELAPTHPIRLGLALNFSVFYY..EILNSPDRACNLANEAF...DEAIAELDTL..EEES..YKDSTLI.MQLLRDNLTLWTSDMQDDG Q9XG89/8-245 REEFVYMAKLAEQAERYEEMVEFMEKVTAAVEs..........eELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NDEHVTVIRDYRSKIETELSNIC.NGILK.LLDSRLIPSA..ALGDSKVFYLKMKGDYHRYLAEFK.SGA.ERKDAAESTLTAYKSAQDIANTELPPTHPIRLGLALNFSVFYY..EILNSPDRACGLAKQAF...DEAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDMQDDG 143A_VICFA/8-245 REEFVYMAKLAEQAERYEEMVEFMEKVTAAVEs..........eELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NDEHVSVIRDYRSKIETELSNIC.NGILK.LLDSRLIPSA..ALGDSKVFYLKMKGDYHRYLAEFK.SGA.ERKDAAESTLTAYKSAQDIANTELPPTHPIRLGLALNFSVFYY..EILNSPDRACGLAKQAF...DEAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDMQDDG Q39558/8-246 REEFVYLAKLAEQAERYEEMVEFMEKVSAAVDn..........eELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NDDHVSIIRDYRSKIETELSNICgFRILN.LLDSRLIPSA..ASGDSKVFYLKMKGDYHRYLAEFK.TGA.ERKEAAESTLTAYKSAQDIANAELPPTHPIRLGLALNFSVFYY..EILNSPDRACSLAKQAF...DEAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDIRGSR 143O_ARATH/5-242 REELVYMAKLAEQAERYEEMVEFMEKVSAAVDg..........dELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NDDHVTAIREYRSKIETELSGIC.DGILK.LLDSRLIPAA..ASGDSKVFYLKMKGDYHRYLAEFK.TGQ.ERKDAAEHTLAAYKSAQDIANAELAPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DEAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDMQDDA 143H_ARATH/11-248 REEFVYLAKLAEQAERYEEMVEFMEKVAEAVDk..........dELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESRG.NDDHVTTIRDYRSKIESELSKIC.DGILK.LLDTRLVPAS..ANGDSKVFYLKMKGDYHRYLAEFK.TGQ.ERKDAAEHTLTAYKAAQDIANAELAPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DEAIAELDTL..GEES..YKDSTLI.MQLLRDNLTLWTSDMQDES Q42083/11-79 REEFVYLAKLAAEAERYEEMVEFMEKVAEAVDk..........dELTVEERNLLSVAYKNVIGARRASWRIISSIEQKK----.-----------------------.-----.----------..------------------------.---.-------------------------------------------..-----------------...----------..----..-------.------------------- 1433_SPIOL/1-198 --------------------------------............------RNLLSVAYKNVVGARRASWRIISSIEQKEESRG.NEDHVSVIRDYRSRIEKELSDNC.DGILK.LLDTKLVPAA..SSGDSKVFYLKMKGDYHRYLAEFK.TGA.QRKEAAESTLTAYKAAQDIANAELAPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...VEAIAELDTL..GEDS..YKDSTLI.MQLLRDNLTLWTSDMQDEA 143X_MAIZE/1-56 --------------------------------............---------------------------------------.-----------------------.-----.----------..------------------------.---.-------------------------------------------..-ILNSPDRACNLAKQAF...DEAISELDSL..GEES..YKDSTLI.MQLLXDNLTLWTSDTNEDG O24223/8-249 REESVYKAKLAEQAERYEEMVEYMERVARAAGgas......ggeELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEEGRG.NDAHAATIRSYRGKIEAELARIC.DGILA.LLDSHLVPSA..GAAESKVFYLKMKGDYHRYLAEFK.SGD.ERKQAAESTMNAYKAAQDIALADLAPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKQAF...DEAISELDSL..GEES..YKDSTLI.MQLLRDNLTLWTSDANDDG Q42106/1-38 --------------------------------............---------------------------------------.-----------------------.-----.----------..------------------------.---.-------------------------------------------..-----------------...--AIXELDTL..NEES..YKDSTLI.MQLLRDNLTLWTSDISEEG Q9XEW4/21-220 -----------------------------ENE............ELTVEERNFLSVAYKNVIGARRASWRIISSIEQKEESRG.NEDHVSVIRDYRAKIETELSSIC.DGILK.LLDSRLIPTA..SAGDPKVFYLKMKGDYHRYLAEFK.TGA.ERKEAAESTLTAYKAAQDIANAELAPTHPIRXGLALNFSVFYY..EILNSPDRACSLAKQAF...DEAISELDTL..GEES..YKDSTLI.MQLLRDNLTLWT------- 1433_CHLRE/5-242 REECVYMAKLAEQAERYDEMVEEMKKVAKLVHd..........qELSVEERNLLSVAYKNVIGARRASWRIISSIEQKEEAKG.NEEHVQRIRKYRTVVEEELSKIC.ASILQ.LLDDHLIPTA..STGESKVFYLKMKGDYHRYLAEFK.TGA.DRKEAAEHTLLAYKAAQDIALVDLPPTHPIRLGLALNFSVFYY..EILNSPERACHLAKQAF...DEAIAELDSL..GEES..YKDSTLI.MQLLRDNLTLWTSDMQDPA Q9VEA8/4-239 RENNVYKAKLAEQAERYDEMVEAMKKVASMDV............ELTVEERNLLSVAYKNVIGARRASWRIITSIEQKEENKG.AEEKLEMIKTYRGQVEKELRDIC.SDILN.VLEKHLIPCA..TSGESKVFYYKMKGDYHRYLAEFA.TGS.DRKDAAENSLIAYKAASDIAMNDLPPTHPIRLGLALNFSVFYY..EILNSPDRACRLAKAAF...DDAIAELDTL..SEES..YKDSTLI.MQLLRDNLTLWTSDMQAED 143E_DROME/4-239 RENNVYKAKLAEQAERYDEMVEAMKKVASMDV............ELTVEERNLLSVAYKNVIGARRASWRIITSIEQKEENKG.AEEKLEMIKTYRGQVEKELRDIC.SDILN.VLEKHLIPCA..TSGESKVFYYKMKGDYHRYLAEFA.TGS.DRKDAAENSLIAYKAASDIAMNDLPPTHPIRLGLALNFSVFYY..EILNSPDRACRLAKAAF...DDAIAELDTL..SEES..YKDSTLI.MQLLRDNLTLWTSDMQAED O57468/4-239 REDLVYRAKLAEQAERYDEMVESMKKVAGMDV............ELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKG.GEDKLKMIREYRQMVETELKSIC.NDILD.VLDKHLIPAA..SSGESKVFYYKMKGDYHRYLAEFA.QGN.DRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYY..EILNSPDRACRLAKAAF...DDAIAELDTL..SEES..YKDSTLI.MQLLRDNLTLWTSDMQGDG 143E_HUMAN/4-239 REDLVYQAKLAEQAERYDEMVESMKKVAGMDV............ELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEENKG.GEDKLKMIREYRQMVETELKLIC.CDILD.VLDKHLIPAA..NTGESKVFYYKMKGDYHRYLAEFA.TGN.DRKEAAENSLVAYKAASDIAMTELPPTHPIRLGLALNFSVFYY..EILNSPDRACRLAKAAF...DDAIAELDTL..SEES..YKDSTLI.MQLLRDNLTLWTSDMQGDG 1433_DICDI/3-238 REENVYMAKLAEQAERYEEMVETMKKVAELDV............ELTVEERNLLSVAYKNVIGARRASWRIISSIEQKEESKG.NENHVKKIKEYKCKVEKELTDIC.NDILE.VLESHLIVSS..ASGESKVFYYKMKGDYFRYLAEFA.TGN.PRKTSAESSLIAYKAASDIAVTELPPTHPIRLGLALNFSVFYY..EILNSPDRACNLAKTAF...DDAIAELDTL..SEDS..YKDSTLI.MQLLRDNLTLWTSDVHNME 1433_CANAL/5-240 REDSVYLAKLAEQAERYEEMVENMKAVASSGQ............ELSVEERNLLSVAYKNVIGARRASWRIVSSIEQKEEAKG.NESQVALIRDYRAKIEAELSKIC.EDILS.VLSDHLITSA..QTGESKVFYYKMKGDYHRYLAEFA.IAV.FRKEAADLSLEAYKAASDVAVTELPPTHPIRLGLALNFSVFYY..EILNSPDRACHLAKQAF...DDAVADLETL..SEDS..YKDSTLI.MQLLRDNLTLWTDLSEAPA Q9UR29/5-240 REDSVYLAKLAEQAERYEEMVENMKRVASSDQ............ELTVEERNLLSVAYKNVIGARRASWRIVSSIEQKEESKG.NEAQVSMIKGYREKIETELAEIC.EDILD.VLDKHLIPSA..ASGESKVFYHKMMGDYHRYLAEFA.TGD.KRKESADKSLEAYKAASDVAVTELPPTHPIRLGLALNFSVFYY..EILNSPDRACHLAKQAF...DDAIAELDTL..SEES..YKDSTLI.MQLLRDNLTLWTSDMQDSA 1433_TRIHA/3-238 HEDAVYLAKLAEQAERYEEMVENMKIVASEDR............DLTVEERNLLSVAYKNVIGARRASWRIVTSIEQKEESKG.NSSQVTLIKEYRQKIENELAKIC.DDILE.VLDQHLIPSA..KSGESKVFYHKIKGDYHRYLAEFA.IGD.RRKDSADKSLEAYKAATEVAQTELPPTHPIRLGLALNFSVFYY..EILNAPDQACHLAKQAF...DDAIAELDTL..SEES..YKDSTLI.MQLLRDNLTLWTSSEAETP BMH1_YEAST/4-240 REDSVYLAKLAEQAERYEEMVENMKTVASSGQ............ELSVEERNLLSVAYKNVIGARRASWRIVSSIEQKEESKEkSEHQVELICSYRSKIETELTKIS.DDILS.VLDSHLIPSA..TTGESKVFYYKMKGDYHRYLAEFS.SGD.AREKATNASLEAYKTASEIATTELPPTHPIRLGLALNFSVFYY..EIQNSPDKACHLAKQAF...DDAIAELDTL..SEES..YKDSTLI.MQLLRDNLTLWTSDMSESG Q06854/1-144 --------------------------------............---------------------------------------.---------------------IS.DDILS.VLDSHLIPSA..TTGESKVFYYKMKGDYHRYLAEFS.SGD.AREKATNASLEAYKTASEIATTELPPTHPIRLGLALNFSVFYY..EIQNSPDKACHLRKQAF...DDAIAELDTL..SEES..YKDSTLI.MQLLRDNLTLWTSDMSESG BMH2_YEAST/4-240 REDSVYLAKLAEQAERYEEMVENMKAVASSGQ............ELSVEERNLLSVAYKNVIGARRASWRIVSSIEQKEESKEkSEHQVELIRSYRSKIETELTKIS.DDILS.VLDSHLIPSA..TTGESKVFYYKMKGDYHRYLAEFS.SGD.AREKATNSSLEAYKTASEIATTELPPTHPIRLGLALNFSVFYY..EIQNSPDKACHLAKQAF...DDAIAELDTL..SEES..YKDSTLI.MQLLRDNLTLWTSDISESG RA25_SCHPO/5-240 RENSVYLAKLAEQAERYEEMVENMKKVACSND............KLSVEERNLLSVAYKNIIGARRASWRIISSIEQKEESRG.NTRQAALIKEYRKKIEDELSDIC.HDVLS.VLEKHLIPAA..TTGESKVFYYKMKGDYYRYLAEFT.VGE.VCKEAADSSLEAYKAASDIAVAELPPTDPMRLGLALNFSVFYY..EILDSPESACHLAKQVF...DEAISELDSL..SEES..YKDSTLI.MQLLRDNLTLWTSDAEYNQ RA24_SCHPO/6-241 REDAVYLAKLAEQAERYEGMVENMKSVASTDQ............ELTVEERNLLSVAYKNVIGARRASWRIVSSIEQKEESKG.NTAQVELIKEYRQKIEQELDTIC.QDILT.VLEKHLIPNA..ASAESKVFYYKMKGDYYRYLAEFA.VGE.KRQHSADQSLEGYKAASEIATAELAPTHPIRLGLALNFSVFYY..EILNSPDRACYLAKQAF...DEAISELDSL..SEES..YKDSTLI.MQLLRDNLTLWTSDAEYSA 1433_FUCVE/4-237 RDDLVYMAKLAEQAERFDEMVDHMKAVAQQPK............ELSVEERNLLSVAYKNVIGSRRASWRVISSIEGKDTV--.-SDQLPLIRDYKSKIETELTDIC.ADILK.IIEAELIPNS..TSEEGKVFYYKMKGDYHRYLAEFQ.SAD.ERKTSASDALDAYQLASDHANQDLPPTHPIRLGLALNFSVFYY..EILNSPDRACGLAKAAF...DDAIAELDTL..SEES..YKDSTLIiMQLLRDNLTLWTSDQGEAE 1433_TOBAC/5-239 REKQVYLARLAEQAERYDEMVEAMKTVAKMDV............ELTVEERNLVSVGYKNVIGARRASWRILSSIEQKEESKG.HDQNVKRIKTYQQRVEDELTKYA.LT-LS.VIDEHVVPSS..TSGESTVFYYKMKGDYYRYLAEFK.SGD.DRKEAADQSLKAYEAATATASADLAPTHPIRLGLALNFSVFYY..EILNSPERACHLAKQAF...DEAIAELDSL..SEES..YKDSTLI.MQLLRDNFTLWTSDLEEGG 1437_LYCES/5-129 REKQVYLARLAEQAHTYDEMVEAMKAIAKMDV............ELTVEERNLVSVGYNNVIGATRASWRILSSIEQKEESKG.HEQNVKRIKTYRQRVEDELTKYA.AYILS.VIDELLVPSS..TTGESIVFYYKMKGDY--------.---.-------------------------------------------..-----------------...----------..----..-------.------------------- Q9S9Z8/5-240 RAKQVYLAKLNEQAERYDEMVEAMKKVAALDV............ELTIEERNLLSVGYKNVIGARRASWRILSSIEQKEESKG.NEQNAKRIKDYRTKVEEELSKIC.YDILA.VIDKHLVPFA..TSGESTVFYYKMKGDYFRYLAEFK.SGA.DREEAADLSLKAYEAATSSASTELSTTHPIRLGLALNFSVFYY..EILNSPERACHLAKRAF...DEAIAELDSL..NEDS..YKDSTLI.MQLLRDNLTLWTSDLEEGG 143E_ARATH/5-240 REKQVYLAKLSEQTERYDEMVEAMKKVAQLDV............ELTVEERNLVSVGYKNVIGARRASWRILSSIEQKEESKG.NDENVKRLKNYRKRVEDELAKVC.NDILS.VIDKHLIPSS..NAVESTVFFYKMKGDYYRYLAEFS.SGA.ERKEAADQSLEAYKAAVAAAENGLAPTHPVRLGLALNFSVFYY..EILNSPESACQLAKQAF...DDAIAELDSL..NEES..YKDSTLI.MQLLRDNLTLWTSDLNEEG 1438_LYCES/7-131 RESLVYIARLAEQRERYDEMVDAMKNVANLDV............ELTVEERNLLSVGYKNVVGSRRASWRILSSIEQKEDASG.NEQNVKRIQGYRQKVESELTDIC.NNIMT.VIDEHLIPSC..TAGESTVFYYKMKGDY--------.---.-------------------------------------------..-----------------...----------..----..-------.------------------- 1439_LYCES/7-131 RENFVYVAKLAEQAERYDEMVEAMKNVANMDV............ELTVEERNLLSVGYKNVVGSRRASWRILSSIEQKEESRG.NEQNVKRIKEYLQKVESELTNIC.NDIMV.VIDQHLIPSC..SAGESTVFYHKMKGDY--------.---.-------------------------------------------..-----------------...----------..----..-------.------------------- 143C_SOYBN/7-242 RENFVYVAKLAEQAERYEEMVEAMKNVANLNV............ELTVEERNLLSVGYKNVVGARRASWRILSSIEQKEEAKG.NDVSVKRIKEYRLKVESELSNIC.SDIMT.VIDEYLIPSS..SSGEPSVFFYKMKGDYYRYLAEFK.SGD.ERKEAADHSMKAYQLASTTAEAELASTHPIRLGLALNFSVFYY..EILNSPERACHLAKQAF...DEAISELDTL..SEES..YKDSTLI.MQLLRDNLTLWTSDIPEDG 143B_VICFA/7-242 RENFVYIAKLAEQAERYEEMVDSMKNVANLDV............ELTIEERNLLSVGYKNVIGARRASWRILSSIEQKEESKG.NDVNAKRIKEYRHKVETELSNIC.IDVMR.VIDEHLIPSA..AAGESTVFYYKMKGDYYRYLAEFK.TGN.EKKEAGDQSMKAYESATTAAEAELPPTHPIRLGLALNFSVFYY..EILNSPERACHLAKQAF...DEAISELDTL..NEES..YKDSTLI.MQLLRDNLTLWTSDIPEDG O49152/7-242 RETFVYVAKLAEQAERYEEMVDSMKNVATLDV............ELTVEERNLLSVGYKNVIGARRASWRILSSIEQKEEAKG.NEVNAKRIKEYRQKVESELTNIC.NDVMR.VIDEHLIPSA..SAGESTVFYYKMKGDYYRYLAEFK.TGN.EKKEAGDQSMKAYESATAAAEAELPPTHPIRLGLALNFSVFYY..EILNSPERACHLAKQAF...DEAISELDTL..NEES..YKDSTLI.MQLLRDNLTLWTSDIPEDG 143D_SOYBN/7-242 RENFVYIAKLAEQAERYEEMVESMKNVANLDV............ELTVEERNLLSVGYKNVIGARRASWRILSSIEQKEETKG.NELNAKRIKEYRQKVELELSNIC.NDVMR.VIDEHLIPSA..AAGESTVFYYKMKGDYYRYLAEFK.SGN.EKKEAADQSMKAYESATAAAEADLPPTHPIRLGLALNFSVFYY..EILNSPERACHLAKQAF...DEAISELDTL..NEES..YKDSTLI.MQLLRDNLTLWTSDIPEDG Q9XEW5/1-219 ----------AEQAERYDEMVDAMKKVAKLDV............ELTVEERNLLSVGYKNVIGARRASWRILSSIEQKEESKG.NETNVKRIKEYRKKVEAELTGVC.NDIMT.VIDEHLIPSS..IPGESAVFYYKMKGDYYRYLAEFK.SGN.ERKEAADQSLKAYETATSTAARDLSPTHPIRLGLALNFSVFYY..EIMNSPERACHLAKQSF...DEAISELDTL..SEES..YKDSTLI.MPLLKDNLTLWT------- O80367/7-242 RDTFVYLAKLSEQAERYEEMVESMKSVAKLNV............DLTVEERNLLSVGYKNVIGSRRASWRIFSSIEQKEAVKG.NDVNVKRIKEYMEKVELELSNIC.IDIMS.VLDEHLIPSA..SEGESTVFFNKMKGDYYRYLAEFK.SGN.ERKEAADQSLKAYEIATTAAEAKLPPTHPIRLGLALNFSVFYY..EIMNAPERACHLAKQAF...DEAISELDTL..NEES..YKDSTLI.MQLLRDNLTLWTSDISEEG 143M_ARATH/7-242 RDTFVYLAKLSEQAERYEEMVESMKSVAKLNV............DLTVEERNLLSVGYKNVIGSRRASWRIFSSIEQKEAVKG.NDVNVKRIKEYMEKVELELSNIC.IDIMS.VLDEHLIPSA..SEGESTVFFNKMKGDYYRYLAEFK.SGN.ERKEAADQSLKAYEIATTAAEAKLPPTHPIRLGLALNFSVFYY..EIMNAPERACHLAKQAF...DEAISELDTL..SEES..YKDSTLI.MQLLRDNLTLWTSDISEEG Q42058/7-112 RDTFVYLAKLSEXAERYEEMVESMKSVAKLNV............DLTVEERNLLSVGYKNVIGSRRASWRIFSSIEQKEAVKG.NDXNVKRIKEYMEKVELELSNIC.IDIMS.VLDEHLI---..------------------------.---.-------------------------------------------..-----------------...----------..----..-------.------------------- 1433_ENTHI/1-236 SEDCVFLSKLAEQSERYDEMVQYMKQVAALNT............ELSVEERNLLSVAYKNVIGSRRASWRIITSLEQKEQAKG.NDKHVEIIKGYRAKIEDELAKYC.DDVLK.VIKENLLPNA..STSESKVFYKKMEGDYYRYYAEFT.VDE.KRQEVADKSLAAYTEATEISNADLAPTHPIRLGLALNFSVFYY..EIMNDADKACQLAKQAF...DDSIAKLDEV..PESS..YKDSTLI.MQLLRDNLTLWTSDTADEE 1431_ENTHI/4-239 REDCVYTAKLAEQSERYDEMVQCMKQVAEMEA............ELSIEERNLLSVAYKNVIGAKRASWRIISSLEQKEQAKG.NDKHVEIIKGYRAKIEKELSTCC.DDVLK.VIQENLLPKA..STSESKVFFKKMEGDYYRYFAEFT.VDE.KRKEVADKSLAAYTEATEISNAELAPTHPIRLGLALNFSVFYF..EIMNDADKACQLAKQAF...DDAIAKLDEV..PENM..YKDSTLI.MQLLRDNLTLWTSDACDEE 1432_ENTHI/4-238 REDLVYLSKLAEQSERYEEMVQYMKQVAEMGT............ELSVEERNLISVAYKNVVGSRRASWRIISSLEQKEQAKG.NTQRVELIKTYRAKIEQELSQKC.DDVLK.IITEFLLKNS..TSIESKVFFKKMEGDYYRYYAEFT.VDE.KRKEVADKSLAAYQEATDTA-ASLVPTHPIRLGLALNFSVFYY..QIMNDADKACQLAKEAF...DEAIQKLDEV..PEES..YKESTLI.MQLLRDNLTLWTSDMGDDE Q9UAH0/5-239 REELIYMAKIAEQTERFEDMLEYMKKVVQTGQ............ELSVEERNLLSVAYKNTVGSRRSAWRSISAIQQKEESKG.S-KHLDLLTNQKKKIETELNLYC.DDILK.LLNDFLIKNA..TNAEAQVFFLKMKGDYYRYIAEYA.QGD.EHKKAADGALDSYNKACEIANSELRPTHPIRLGLALNFSVFHY..EVLNDPSKACTLAKTAF...DEAIGDIERI..QEDQ..YKDATTI.MQLIRDNLTLWTSEFQDDA Q9XYW8/1-233 -----YLAMLAEQCSRYKEMVQFLEDMVKQRD...........kDLNSDERNLLSIAYKNSISGGRSAVRTIMAYEAKEKKKE.NSTFLPYITEYKKQVEDELTKLC.QGVLK.TTDEQLLKKA..EDDEAKVFYIKMKGDYNRYIAEYA.EGD.LKKQVSDDALKAYDEATEIA-KTLPVLNPIALGLALNFSVFYY..EVINDHKKAIEIAKAAV...EKADKELPNI..DEDAdeNRDTVSI.YNLLKENLDMWVSEEEGDQ O61173/2-194 -EKNVYLAMLAEQCSRYKEMVQFLEDMVKQRD...........kDLNSDERNLLSIAYKNSISGGRSAVRTIMAYEAKEKKKE.NSTFLPYITEYKKQVEDELTKLC.QGVLK.TTDEQLLKKA..EDDEAKVFYIKMKGDYNRYIAEYA.EGD.LKKQVSDDALKAYDEATEIA-KTLPVLNPIALGLALNFSVFYY..EVINDHKKAIEIAKA--...----------..----..-------.------------------- Q9XYW7/4-229 -EKQVYLAMLAEQCSRYEDMMTFLEDMVKAKA...........eDLSSDERNLLSIAYKNTISLDRQAIRTLLAYESKEAKKA.ESPYLDYIKEYKAKVQKELEDLC.NKINR.TIDDNLLPKA..TTDEAKVFYHKMKGDYCRYIAENV.DGD.TKKKYSDEGLAAYNAALEAA-KNIDYKNPVKLGLALNLSVFYY..EVVGNKDEACKLAEDTLsksKEALNGADE-..EEDE..VKDAMSI.VNLLEENL----------- Q9SFK4/1-214 -----------------------MRKVCELDI............ELSEEERDLLTTGYKNVMEAKRVSLRVISSIEKMEDSKG.NDQNVKLIKGQQEMVKYEFFNVC.NDILS.LIDSHLIPST.tTNVESIVLFNRVKGDYFRYMAEFG.SDA.ERKENADNSLDAYKVAMEMAENSLAPTNMVRLGLALNFSIFNY..EIHKSIESACKLVKKAY...DEAITELDGL..DKNI..CEESMYI.IEMLKYNLSTWTSGDGNGN Q9XZV0/2-235 KEELLNRCKLNDLIENYGEMFEYLKELSHIKI............DLQPDELDLITRCTKCYIGHKRGQYRKILTLIDKDKIVD.NQKNSALLEILRKKLSEEILLLC.NSTIE.LSQNFLNNNV..FPKKTQLFFTKIIADHYRYIYEIN.GKE.DIKLKAKEYYE--KGLQTIKTCKYNSTETAYLTFYLNYSVFLH..DTMRNTEESIKVSKACL...YEALKDTEDI..VDNS..QKDIVLL.CQMLKDNISLWKTETNEDN #=GC SS_cons HHHHHHHHHHHHHTTCHHHHHHHHHHHHTTSC............CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCTTT--.CCHHHHHHHHHHHHHHHHHHHHH.HHHHH.HHHHTTTTCC..CSCHHHHHHHHHHHHHHHHHHHHC.CSC.HHHHHHHHHHHHHHHHHHHHHCHCCTTCHCHHHHHHHHHHHHC..HTSCCHHHCHHHHHHHH...HHHHTTCGGC..CTTT..HHHHHHH.HHHHHHHHHHCTCCCXXXX #=GC SA_cons 26310320300350512510050022003352............4045500400120033002310402420152179179--.38752510440144014203510.43002.0035201642..754403000010100011100201.867.7465125302500340252067635113122100001001127..31372485135106412...5415867932..3994..6651462.142043126627759XXXX // weblogo-3.8.0/tests/data/pfam_example.txt000066400000000000000000000502561467613320200204460ustar00rootroot00000000000000# STOCKHOLM 1.0 #=GF ID GP120 #=GF AC PF00516 #=GF DE Envelope glycoprotein GP120 #=GF GA -267.6 -267.6 #=GF NC -267.7 -267.7 #=GF TC -267.6 -267.6 ENV_SIVM1/24-528 QYVTVFYGVPAWRNATIPLFCATKNR.......DTWGTTQCLPDNDDYSE ENV_HV2NZ/24-502 QFVTVFYGIPAWRNASIPLFCATKNR.......DTWGTIQCLPDNDDYQE ENV_HV2G1/23-502 QYVTVFYGVPVWRNASIPLFCATKNR.......DTWGTIQCKPDNDDYQE ENV_HV2D1/24-501 QYVTVFYGIPAWRNASIPLFCATKNR.......DTWGTIQCLPDNDDYQE ENV_HV2CA/25-512 QYVTVFYGVPAWKNASIPLFCATKNR.......DTWGTIQCLPDNDDYQE ENV_HV2BE/24-510 QYVTVFYGIPAWKNASIPLFCATKNR.......DTWGTIQCLPDNDDYQE ENV_HV2D2/24-513 QYVTVFYGIPAWRNATVPLICATTNR.......DTWGTVQCLPDNGDYTE ENV_SIVAI/22-522 LYVTVFYGIPVWKNSTVQAFCMTPNT.......NMWATTNCIPDDHDNTE ENV_SIVA1/24-538 QWITVFYGVPVWKNSSVQAFCMTPTT.......RLWATTNCIPDDHDYTE ENV_SIVCZ/33-496 LWVTVYYGVPVWHDADPVLFCASDAKAHSTEAHNIWATQACVPTDPSPQE ENV_HV1ZH/33-511 LWVTVYYGVPVWKDAETTLFCASDAKAYDTEKHNVWATHACVPTDPNPQE ENV_HV1W1/33-510 LWVTVYYGVPVWKEATTTLFCASDAKAYSTEAHKVWATHACVPTNPNPQE ENV_HV1J3/33-523 LWVTVYYGVPVWKEAATTLFCASDAKAYDTEVHNVWATHACVPTDPNPQE ENV_HV1B1/34-511 LWVTVYYGVPVWKEATTTLFCASDAKAYDTEVHNVWATHACVPTDPNPQE ENV_HV1A2/33-509 LWVTVYYGVPVWKEATTTLFCASDARAYDTEVHNVWATHACVPTDPNPQE ENV_HV1RH/33-519 LWVTVYYGVPVWKEATTTLFCASEAKAYKTEVHNVWAKHACVPTDPNPQE ENV_HV1BN/34-507 LWVTVYYGVPVWKEANTTLFCASDAKAYDTEIHNVWATHACVPTDPNPQE ENV_HV1OY/33-509 LWVTVYYGVPVWKEATTTLFCASDARAYATEVHNVWATHACVPTDPNPQE ENV_HV1C4/35-522 LWVTVYYGVPVWKEATTTLFCASDAKAYDTEAHNVWATHACVPTNPNPQE ENV_HV1Z8/33-518 LWVTVYYGVPVWKEATTTLFCASDAKSYEPEAHNIWATHACVPTDPNPRE ENV_HV1EL/33-508 LWVTVYYGVPVWKEATTTLFCASDAKSYETEAHNIWATHACVPTDPNPQE ENV_HV1ND/33-501 LWVTVYYGVPIWKEATTTLFCASDAKAYKKEAHNIWATHACVPTDPNPQE ENV_HV1MA/33-513 LWVTVYYGVPVWKEATTTLFCASDAKSYETEVHNIWATHACVPTDPNPQE ENV_SIVGB/47-569 QYVTVFYGVPVWKEAKTHLICATDNS.......SLWVTTNCIPSLPDYDE ENV_SIVM1/24-528 LALN.VTESFDAWE..NTVTEQAIEDVWQLFETSIKPCVKLSPLCITMRC ENV_HV2NZ/24-502 ITLN.VTEAFDAWN..NTVTEQAVEDVWNLFETSIKPCVKLTPLCVAMNC ENV_HV2G1/23-502 ITLN.VTEAFDAWD..NTVTEQAVEDVWSLFETSIKPCVKLTPLCVAMSC ENV_HV2D1/24-501 ITLN.VTEAFDAWD..NTVTEQAIEDVWRLFETSIKPCVKLTPLCVAMNC ENV_HV2CA/25-512 IPLN.VTEAFDAWD..NTITEQAIEDVWNLFETSIKPCVKLTPLCVAMKC ENV_HV2BE/24-510 IILN.VTEAFDAWN..NTVTEQAVEDVWHLFETSIKPCVKLTPLCVAMNC ENV_HV2D2/24-513 IRLN.ITEAFDAWD..NTVTQQAVDDVWRLFETSIKPCVKLTPLCVAMNC ENV_SIVAI/22-522 VPLN.ITEAFEAWD..NPLVKQAESNIHLLFEQTMRPCVKLSPICIKMSC ENV_SIVA1/24-538 VPLN.ITEPFEAWADRNPLVAQAGSNIHLLFEQTLKPCVKLSPLCIKMNC ENV_SIVCZ/33-496 VFLPNVIESFNMWK..NNMVDQMHEDIISLWDQSLKPCVKLTPLCVTLQC ENV_HV1ZH/33-511 LSLGNVTEKFDMWK..NNMVEQMHEDVISLWDQSLKPCVKLTPLCVTLSC ENV_HV1W1/33-510 VVLENVTENFNMWK..NNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNC ENV_HV1J3/33-523 VVLENVTEKFNMWK..NNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNC ENV_HV1B1/34-511 VVLVNVTENFNMWK..NDMVEQMHEDIISLWDQSLKPCVKLTPLCVSLKC ENV_HV1A2/33-509 VVLGNVTENFNMWK..NNMVEQMQEDIISLWDQSLKPCVKLTPLCVTLNC ENV_HV1RH/33-519 VLLENVTENFNMWK..NNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNC ENV_HV1BN/34-507 LVMGNVTENFNMWK..NDMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNC ENV_HV1OY/33-509 VVLGNVTENFDMWK..NNMVEQMQEDIISLWDQSLKPCVKLTPLCVTLDC ENV_HV1C4/35-522 VVLENVTENFNMWK..NNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNC ENV_HV1Z8/33-518 IEMENVTENFNMWK..NNMVEQMHEDIISLWDQNLKPCVKLTPLCVTLNC ENV_HV1EL/33-508 IALENVTENFNMWK..NNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNC ENV_HV1ND/33-501 IELENVTENFNMWK..NNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNC ENV_HV1MA/33-513 IELENVTEGFNMWK..NNMVEQMHEDIISLWDQSLKPCVKLTPLCVTLNC ENV_SIVGB/47-569 VEIPDIKENFTGLIRENQIVYQAWHAMGSMLDTILKPCVKINPYCVKMQC ENV_SIVM1/24-528 NKSETDKWGLTKSSTTTASTTTTTTAKSV.......ETRDIVNETSPCVV ENV_HV2NZ/24-502 TR...........N.....MTTWTGRTDT.......QNITIINDTS.HAR ENV_HV2G1/23-502 N........STTNN.....TTT...TGST.......TGMSEINETS.PSY ENV_HV2D1/24-501 NITSGTTATPSP........................PNITIIDENSTCIG ENV_HV2CA/25-512 N.......ISTSDT.....TMIRTTTPST.......AKEAPISDNSPCIR ENV_HV2BE/24-510 SRVQGNTTTPNPRT.....SSSTTSRPPT.......SAASIINETSNCIE ENV_HV2D2/24-513 SKTETN..PGNASS.....TTTTKPTTTS.......RGLKTINETDPCIK ENV_SIVAI/22-522 VELNGT.............ATTKATTTAT.........TTMTTPCQNCST ENV_SIVA1/24-538 VELKGS......AT.....STPATSTTAG..TKLPCVRNKTDSNLQSCND ENV_SIVCZ/33-496 SKANFS..............QAKNLTNQTS.................... ENV_HV1ZH/33-511 HNITIK................DNNTNVD..................... ENV_HV1W1/33-510 IDKNIT...............DWENKTIIG.................... ENV_HV1J3/33-523 IDWGND............TSPNATNTTSS..................... ENV_HV1B1/34-511 TDLKN.................DTNTNSS..................... ENV_HV1A2/33-509 TD.................LGKATNTNSS..................... ENV_HV1RH/33-519 TDA...............NLNGTNVTSSS..................... ENV_HV1BN/34-507 HDFNA.................TNATSNSGK................... ENV_HV1OY/33-509 TDVNTTS..........SSLRNATNTTSS..................... ENV_HV1C4/35-522 TDLNTN...............NTTNTTELSI................I.. ENV_HV1Z8/33-518 TNAGG.................NKTTNGNN..................TT ENV_HV1EL/33-508 SDELR.................NNGTMGN...................NV ENV_HV1ND/33-501 TDELR.................NSKGNGK..................... ENV_HV1MA/33-513 TNVNG.................TAVNGTNAG................SNR ENV_SIVGB/47-569 QETENVS...........ATTAKPITTPTT......TSTVASSTEIYLDV ENV_SIVM1/24-528 HDNCTGLEQEPMISCKFNMTGLKRDKKKEYNETWYSADLVCEQG.NSTG. ENV_HV2NZ/24-502 ADNCTGLKEEEMIDCQFSMTGLERDKRKQYTEAWYSKDVVCDNNTSS... ENV_HV2G1/23-502 SDNCTGLGKEEIVNCQFYMTGLERDKKKQYNETWYSKDVVCE.SNNTKD. ENV_HV2D1/24-501 DNNCTGLGKEEVVECEFNMTGLEQDKKRKYNDAWYSRDVVCDKTNG.... ENV_HV2CA/25-512 TNNCSGLEEEKIVKCHFNMTGLERDKKKQYNETWYSSDVVCDNSTDQTT. ENV_HV2BE/24-510 NNTCAGLGYEEMMQCEFNMKGLEQDKKRRYKDTWYLEDVVCDNTT..... ENV_HV2D2/24-513 NDSCTGLGEEEIMQCNFSMTGLRRDELKQYKDTWYSEDLECN...NTRK. ENV_SIVAI/22-522 EQIEGEMAEEPASNCTFAIAGYQRDVKKNYSMTWYDQELVCNNKTGSEK. ENV_SIVA1/24-538 TIIEKEMNDEAASNCTFAMAGYIRDQKKNYSVVWNDAEIFCKRSTSHNG. ENV_SIVCZ/33-496 ......SPPLEMKNCSFNVTTELRDKKKQVYSLFYVEDVVNLGNEN.... ENV_HV1ZH/33-511 .....TEMKEEIKNCSYNMTTELRDKQRKIYSLFYRLDIVPIGGNSS... ENV_HV1W1/33-510 .......G.GEVKNCSFNITTSIRDKVHKEYALFYKLDVVPIKSNNDSS. ENV_HV1J3/33-523 ..GGEKMEKGEMKNCSFNITTSIRDKVQKEHALFYKHDVVPINNSTK... ENV_HV1B1/34-511 .SGRMIMEKGEIKNCSFNISTSIRGKVQKEYAFFYKLDIIPIDNDT.... ENV_HV1A2/33-509 ..NWKEEIKGEIKNCSFNITTSIRDKIQKENALFRNLDVVPIDN...... ENV_HV1RH/33-519 ..GGTMMENGEIKNCSFQVTTSRRDKTQKKYALFYKLDVVPIEKGNISPK ENV_HV1BN/34-507 .....MMEGGEMKNCSFNITTSIRDKMQKEYALFYKLDIVPIDNDK.... ENV_HV1OY/33-509 ..SWETMEKGELKNCSFNTTTSIRDKMQEQYALFYKLDVLPIDK...... ENV_HV1C4/35-522 .VVWEQRGKGEMRNCSFNITTSIRDKVQREYALFYKLDVEPIDDNKNTT. ENV_HV1Z8/33-518 NQEEQMMEKGEMKNCSFNITTVISDKKKQVHALFYRLDVVPIDDDNSAN. ENV_HV1EL/33-508 .....TTEEKGMKNCSFNVTTVLKDKKQQVYALFYRLDIVPIDNDS.... ENV_HV1ND/33-501 .....VEEEEKRKNCSFNVR..D..KREQVYALFYKLDIVPIDNNN.... ENV_HV1MA/33-513 TNAELKMEIGEVKNCSFNITPVGS.DKRQEYATFYNLDLVQIDDSD.... ENV_SIVGB/47-569 DKNNTEEKVERNHVCRYNITGLCRDSKEEIVTNFRGDDVKCENN...... ENV_SIVM1/24-528 .......NESRCYMNHCNTSVIQECCDKDYWDAIRCRYCAPPGYALLRCN ENV_HV2NZ/24-502 ........QSKCYMNHCNTSVITESCDKHYWDAMRFRYCAPPGFALLRCN ENV_HV2G1/23-502 .......GKNRCYMNHCNTSVITESCDKHYWDAIKFRYCAPPGYALLRCN ENV_HV2D1/24-501 ........TGTCYMRHCNTSVIKESCDKHYWDAMKFRYCAPPGFALLRCN ENV_HV2CA/25-512 .......NETTCYMNHCNTSVITESCDKHYWDAMRFRYCAPPGFAILRCN ENV_HV2BE/24-510 ........AGTCYMRHCNTSIIKESCDKHYWDAMRFRYCAPPGFALLRCN ENV_HV2D2/24-513 .......YTSRCYIRTCNTTIIQESCDKHYWDSLRFRYCAPPGFFLLRCN ENV_SIVAI/22-522 .......GSKDCYMIHCNDSVIKEACDKTYWDTLRVRYCAPAGYALLKCN ENV_SIVA1/24-538 .......T.KECYMIHCNDSVIKEACDKTYWDELRLRYCAPAGYALLKCN ENV_SIVCZ/33-496 .........NTYRIINCNTTAITQACPKTSFEPIPIHYCAPAGFAILKCN ENV_HV1ZH/33-511 .....NGDSSKYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCR ENV_HV1W1/33-510 .......TYTRYRLIHCNTSVITQACSKVSFEPIPIHYCAPAGFAILKCN ENV_HV1J3/33-523 .DNIKNDNSTRYRLISCNTSVITQACPKISFEPIPIHYCAPAGFAIIKCN ENV_HV1B1/34-511 .........TSYTLTSCNTSVITQACPKVSFEPIPIHYCAPAGFAILKCN ENV_HV1A2/33-509 ASTTTN..YTNYRLIHCNRSVITQACPKVSFEPIPIHYCTPAGFAILKCN ENV_HV1RH/33-519 NNTSNNTSYGNYTLIHCNSSVITQACPKVSFEPIPIHYCTPAGFAILKCN ENV_HV1BN/34-507 .......TNTRYRLISCNTSVITQACPKVTFEPIPIHYCAPAGFAILKCN ENV_HV1OY/33-509 NDTK.......FRLIHCNTSTITQACPKISFEPIPMHYCTPAGFAILKCN ENV_HV1C4/35-522 .......NNTKYRLINCNTSVITQACPKVSFEPIPIHYCTPTGFALLKCN ENV_HV1Z8/33-518 ...TSNTNYTNYRLINCNTSAITQACPKVTFEPIPIHYCAPAGFAILKCK ENV_HV1EL/33-508 .....STNSTNYRLINCNTSAITQACPKVSFEPIPIHYCAPAGFAILKCR ENV_HV1ND/33-501 .....RTNSTNYRLINCDTSTITQACPKISFEPIPIHFCAPAGFAILKCR ENV_HV1MA/33-513 ........NSSYRLINCNTSVITQACPKVTFDPIPIHYCAPAGFAILKCN ENV_SIVGB/47-569 ..........TCYMNHCNESVNTEDCQKGLLIRC.ILGCVPPGYVMLRY. ENV_SIVM1/24-528 DTNYSGFMPNCSKVVVSSCTRMMETQTSTWFRFNGTRAENRTYIY.WHGR ENV_HV2NZ/24-502 DTNYSGFAPNCSKVVAATCTRMMETQTSTWFGFNGTRAENRTYIY.WHGK ENV_HV2G1/23-502 DTNYSGFEPKCSKVVASTCTRMMETQTSTWFGFNGTRAENRTYIY.WHGR ENV_HV2D1/24-501 DTNYSGFEPKCSKVVAASCTRMMETQTSTWFGFNGTRAENRTYIY.WHGK ENV_HV2CA/25-512 DTKYSGFAPNCSKVVASTCTRMMETQTSTWFGFNGTRAENRTYIY.WHGK ENV_HV2BE/24-510 DTNYSGFEPKCTKVVAASCTRMMETQTSTWFGFNGTRAENRTYIY.WHGR ENV_HV2D2/24-513 DTNYSGFMPNCSKVVASSCTRMMETQSSTWFGFNGTRAENRTYIY.WHEK ENV_SIVAI/22-522 DKDYRGFAPKCKNVSVVHCTRLINTTITTGIGLNGSRSENRTEIW.QKGG ENV_SIVA1/24-538 DWDYAGFKPECSNVSVVHCTTLMNTTVTTGLLLNGSYSENRTQIW.QKHG ENV_SIVCZ/33-496 DKDFSGKGK.CTNVSTVHCTHGIKPVVTTQLLINGSLAEGNITVR.VENK ENV_HV1ZH/33-511 DEEFEGKGP.CRNVSTVQCTHGIRPVVSTQLLLNGSLAEGEVRIR.SENF ENV_HV1W1/33-510 DKKFNGTGP.CTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIVIR.SENF ENV_HV1J3/33-523 DKKFNGTGP.CTNVSTVQCTHGIKPVVSTQLLLNGSLAEEEVVIR.SENF ENV_HV1B1/34-511 NKTFNGTGP.CTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIR.SANF ENV_HV1A2/33-509 NKTFNGKGP.CTNVSTVQCTHGIRPIVSTQLLLNGSLAEEEVVIR.SDNF ENV_HV1RH/33-519 DKKFNGTGP.CKNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIR.SENF ENV_HV1BN/34-507 NKKFNGTGP.CTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIR.SENF ENV_HV1OY/33-509 DKKFNGTGP.CTNVSTVQCTHGIKPVVSTQLLLNGSLAEEEVIIR.SSNF ENV_HV1C4/35-522 DKKFNGTGP.CTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVVIR.SENF ENV_HV1Z8/33-518 DKKFNGTGP.CKKVSTVQCTHGIRPVVSTQLLLNGSLAEEEIIIR.SENL ENV_HV1EL/33-508 DKKFNGTGP.CTNVSTVQCTHGIRPVVSTQLLLNGSLAEEEVIIR.SENL ENV_HV1ND/33-501 DKKFNGTGP.CSNVSTVQCTHGIRPVVSTQLLLNGSLAEEEIIIR.SENL ENV_HV1MA/33-513 DKKFNGTEI.CKNVSTVQCTHGIKPVVSTQLLLNGSLAEEEIMIR.SENL ENV_SIVGB/47-569 NEKLN.NNKLCSNISAVQCTQHLVATVSSFFGFNGTMHKEGELIPIDDKY ENV_SIVM1/24-528 .......DNRTIISLNKHYNLTMKCRRPGNKTVLPVTIMS...ALVFHS. ENV_HV2NZ/24-502 .......DNRTIISLNNFYNLTMHCKRPGNKTVLPITFMS...GFKFHS. ENV_HV2G1/23-502 .......DNRTIISLNKYYNLSIHCKRPGNKTVVPITLMS...GLVFHS. ENV_HV2D1/24-501 .......DNRTIISLNKYYNLTMHCKRPGNKTVVPITLMS...GRRFHS. ENV_HV2CA/25-512 .......DNRTIISLNKHYNLSMYCRRPGNKTVVPITLMS...GQRFHS. ENV_HV2BE/24-510 .......DNRTIISLNKYYNLTMRCKRPGNKTVLPITLMS...GLVFHS. ENV_HV2D2/24-513 .......DNRTIISLNTYYNLSIHCKRPGNKTVVPIRTVS...GLLFHS. ENV_SIVAI/22-522 ND.....NDTVIIKLNKFYNLTVRCRRPGNKTVLPVTIMA...GLVFHS. ENV_SIVA1/24-538 VS.....NDSVLILLNKHYNLTVTCKRPGNKTVLPVTIMA...GLVFHS. ENV_SIVCZ/33-496 S......KNTDVWIVQLVEAVSLNCHRPGNNTRG.EVQIG..PGMTFYNI ENV_HV1ZH/33-511 T......DNAKIIIVQLVKPVNITCMRPNNNTRK.SISIG..PGRAFFAT ENV_HV1W1/33-510 T......DNAKTIIVHLNESVEINCTRPNNNVRRRHIHIG..PGRAFYTG ENV_HV1J3/33-523 T......DNAKTIIVQLKEPVVINCTRPSKTTRR.RIHIG..PGRAFYTT ENV_HV1B1/34-511 T......DNAKTIIVQLNQSVEINCTRPNNNTRK.SIRIQRGPGRAFVTI ENV_HV1A2/33-509 T......NNAKTIIVQLNESVAINCTRPNNNTRK.SIYIG..PGRAFHTT ENV_HV1RH/33-519 T......DNVKTIIVQLNASVQINCTRPNNNTRK.SITKG..PGRVIYAT ENV_HV1BN/34-507 T......NNVKTIIVQLNESVEINCTRPNNNTRK.RITMG..PGRVYYTT ENV_HV1OY/33-509 T......NNAKIIIVQLNKSVEINCTRPNNNTRN.RISIG..PGRAFHTT ENV_HV1C4/35-522 T......NNAKTIIVQLNVSVEINCTRPNNHTRK.RVTLG..PGRVWYTT ENV_HV1Z8/33-518 T......NNVKTIIVHLNESVEINCTRPDNKITRQSTPIG..LGQALYTT ENV_HV1EL/33-508 T......NNAKNIIAHLNESVKITCARP.YQNTRQRTPIG..LGQSLYTT ENV_HV1ND/33-501 T......NNVKTIIVQLNASIVINCTRP.YKYTRQRTSIG..LRQSLYTI ENV_HV1MA/33-513 T......DNTKNIIVQLNETVTINCTRP.GNNTRRGIHFG..PGQALYTT ENV_SIVGB/47-569 RGPEEFHQRKFVYKVPGKYGLKIECHRKGNRSVVSTPSAT...GLLFYHG ENV_SIVM1/24-528 .QPVNER..PKQAWCRFGG.NWKEAIKEVKQTIVKHPRYTG.TNNTDKIN ENV_HV2NZ/24-502 QPVINKK..PRQAWCWFEG.QWKEAMQEVKETLAKHPRYKGNRSRTENIK ENV_HV2G1/23-502 .QPINTR..PRQAWCWFKG.KWREAMQEVKQTLIKHPRYKG.TNDTKNIN ENV_HV2D1/24-501 RPVYNKK..PGQAWCWFQG.NWIEAMREVKQTLAKHPRYGG.TNDTGKIN ENV_HV2CA/25-512 RPIINKR..PRQAWCWFKG.NWTEAMQEVKQTLAEHPRYKG.TKNITDIT ENV_HV2BE/24-510 QPINTR...PRQAWCRFGG.RWREAMQEVKQTLVQHPRYKG.INDTGKIN ENV_HV2D2/24-513 .QPINKR..PRQAWCWFKG.NWTEAIKEVKRTIIKHPRYKGGAKNITSVK ENV_SIVAI/22-522 .QKYNTR..LKQAWCHFQG.DWKGAWKEVREEVKKVKN.....LTEVSIE ENV_SIVA1/24-538 .QKYNTR..LRQAWCHFQG.NWKGAWKEVQEEIVKLPKERY..QGTNDTN ENV_SIVCZ/33-496 ENVVG...DTRSAYCKINGTTWNRTVEEVKKALATSSNRTA.....ANIT ENV_HV1ZH/33-511 GDIIG...DIRQAHCNVSRTEWNDTLSKVAAQLRKHFVNTS.....TDII ENV_HV1W1/33-510 .EIRG...NIRQAHCNISRAKWNNTLKQIVEKLREQFKN.......KTIV ENV_HV1J3/33-523 KQIAG...DLRQAHCNINRARWNATLKQIVGKLRKQFVN.......KTIV ENV_HV1B1/34-511 GKIG....NMRQAHCNISRAKWNNTLKQIDSKLREQFGNN......KTII ENV_HV1A2/33-509 GRIIG...DIRKAHCNISRAQWNNTLEQIVKKLREQFGNN......KTIV ENV_HV1RH/33-519 GQIIG...DIRKAHCNLSRAQWNNTLKQVVTKLREQFD.N......KTIV ENV_HV1BN/34-507 GQIIG...DIRRAHCNLSRSKWENTLKQIVTKLRVQFKN.......KTIV ENV_HV1OY/33-509 KQIIG...DIRQAHCNLSRATWEKTLEQIATKLRKQFR.N......KTIA ENV_HV1C4/35-522 GEILG...NIRQAHCNISRAQWNNTLQQIATTLREQFGN.......KTIA ENV_HV1Z8/33-518 RIKG....DIRQAYCNISAAAWNKTLQQVAKKLGDLLN.Q......TTII ENV_HV1EL/33-508 RSR....SIIGQAHCNISRAQWSKTLQQVARKLGTLLN.K......TIIK ENV_HV1ND/33-501 TGKKKKTGYIGQAHCKISRAEWNKALQQVATKLGNLLN.K......TTIT ENV_HV1MA/33-513 GIVG....DIRRAYCTINETEWDKTLQQVAVKLGSLLN.K......TKII ENV_SIVGB/47-569 LEPGK...NLKKGMCTFKG.RWGLALWSLAKELNKLNDSIKVNQTCKNFT ENV_SIVM1/24-528 LT.APR........................GGDPEVTFMWTNCRGEFLYC ENV_HV2NZ/24-502 FK.APG.......................RGSDPEVTYMWTNCRGESLYC ENV_HV2G1/23-502 FT.KPG.......................RGSDPEVAYMWTNCRGEFLYC ENV_HV2D1/24-501 FT.KPG.......................IGSDPEVTYMWTNCRGEFLYC ENV_HV2CA/25-512 FK.APE.......................RGSDPEVTYMWSNCRGEFFYC ENV_HV2BE/24-510 FT.KPG.......................AGSDPEVAFMWTNCRGEFLYC ENV_HV2D2/24-513 LV.SEHG......................KGSDPETTYMWTNCRGEFLYC ENV_SIVAI/22-522 NI.HLRR......................IWGDPESANFWFNCQGEFFYC ENV_SIVA1/24-538 KI.FLQR......................QFGDPEAANLWFNCQGEFFYC ENV_SIVCZ/33-496 LN.RAS........................GGDPEVTHHMFNCGGEFFYC ENV_HV1ZH/33-511 FA.NSS........................GGDVEITTHSFNCGGEFFYC ENV_HV1W1/33-510 FN.HSS........................GGDPEIVTHSFNCGGEFFYC ENV_HV1J3/33-523 FN.RSS........................GGDPEIVMHSFNCGGEFFYC ENV_HV1B1/34-511 FK.QSS........................GGDPEIVTHSFNCGGEFFYC ENV_HV1A2/33-509 FN.QSS........................GGDPEIVMHSFNCRGEFFYC ENV_HV1RH/33-519 FT.SSS........................GGDPEIVLHSFNCGGEFFYC ENV_HV1BN/34-507 FN.RSS........................GGDPEIVMHSFNCGGEFFFC ENV_HV1OY/33-509 FD.RSS........................GGDPEIVMHSFNCGGEFFYC ENV_HV1C4/35-522 FN.QSS........................GGDPEIVMHSFNCGGEFFYC ENV_HV1Z8/33-518 FK.PPA........................GGDPEITTHSFNCGGEFFYC ENV_HV1EL/33-508 FK.PSS........................GGDPEITTHSFNCGGEFFYC ENV_HV1ND/33-501 FK.PSS........................GGDPEITSHMLNCGGDFFYC ENV_HV1MA/33-513 FN.SSS........................GGDPEITTHSFNCRGEFFYC ENV_SIVGB/47-569 STGEENKQNTDKQKEFAKCIKTLKIDNYTTSGDRAAEMMMMTCQGEMFFC ENV_SIVM1/24-528 KMNWFLN........WVED.....RSLTTQKPKERH.......KRNYVPC ENV_HV2NZ/24-502 NMTWFLN........WVENR............TGQK.......QRNYAPC ENV_HV2G1/23-502 NMTWFLN........WVENR............PNQT.......QHNYAPC ENV_HV2D1/24-501 NMTWFLN........WVENK............TNQT.......HGNYAPC ENV_HV2CA/25-512 NMTWFLN........WVENK............PNTT.......KRNYAPC ENV_HV2BE/24-510 NMTWFLN........WVEDK............N..........QTRRNYC ENV_HV2D2/24-513 NMTWFLN........WVENK............TNTT.......RRNYAPC ENV_SIVAI/22-522 KMDWFIN........YLNNRTEDAEGTNRTCDKGKP.GPGPCVQRTYVAC ENV_SIVA1/24-538 KMDWFLN........YLNNLTVDADHNHCKNNAGKGRSPGPCVQRTYVAC ENV_SIVCZ/33-496 NTSQIFT.........................DNITNG......IIILPC ENV_HV1ZH/33-511 NTSGLFN......GTWLNGTSNN.........TWKIDTVN...DTIILPC ENV_HV1W1/33-510 DSTQLFN......STWNVTGIST.........EGNNNTE.ENGDTITLPC ENV_HV1J3/33-523 NSTQLFNSTWLSNSTW.NDTEGS.........NNTGGN.....DTITLPC ENV_HV1B1/34-511 NSTQLFNSTWF..NST.WSTKGS.........NNTEGS.....DTITLPC ENV_HV1A2/33-509 NTTQLFN......NTW.RLNHTE.........GTKGN......DTIILPC ENV_HV1RH/33-519 NTTQLFN......STW.NSTEGS.........NNTGGN.....DTITLPC ENV_HV1BN/34-507 NTTQLFN......STWYRNTTGN.........ITEG.N.....SPITLPC ENV_HV1OY/33-509 NTSQLFN......STW.NDTTRA.........NSTEV.......TITLPC ENV_HV1C4/35-522 NSTQLFN......SAWNVTSNGT.........WSVTRKQKDTGDIITLPC ENV_HV1Z8/33-518 NTSRLFN......STWNSS..TW.........NNDTLNSE...GTIKLPC ENV_HV1EL/33-508 NTSGLFN......STWNIS..AW.........NNITESNNSTNTNITLQC ENV_HV1ND/33-501 NTSRLFN......STWNQT..............NSTGFNN...GTVTLPC ENV_HV1MA/33-513 NTSKLFN......STWQNNGARL.........SNSTESTG....SITLPC ENV_SIVGB/47-569 NVTRIMR.......AWNDP.............NEKK.......WYPYASC ENV_SIVM1/24-528 HIRQIINTWHKVGKNVYLPPREG...DLTCNSTVTSLIANI..NWTDGN. ENV_HV2NZ/24-502 RIRQIINTWHRVGKNLYLPPREG...ELTCNSTVTSIIANI..DAGDQ.. ENV_HV2G1/23-502 HIRQIINTWHKVGKNVYLPPREG...QLTCNSTVTSIIANI..DV.NSN. ENV_HV2D1/24-501 HIRQIINTWHKVGTNVYLPPREG...ELTCNSTVTSIIANI..DSDGN.. ENV_HV2CA/25-512 HIRQIINTWHKVGKNVYLPPREG...ELTCNSTVTSIIANI..DERDNQ. ENV_HV2BE/24-510 HIKQIINTWHKVGKNVYLPPREG...ELACESTVTSIIANI..DIDKNRT ENV_HV2D2/24-513 HIRQIINTWHKVGKNIYLPPREG...ELSCNSTVTSLIANI..NSDNS.. ENV_SIVAI/22-522 HIRQVVNDWYTVSKKVYAPPREG...HLECNSSVTALYVAI..DYNNKSG ENV_SIVA1/24-538 HIRSVINDWYTISKKTYAPPREG...HLQCTSTVTGMTVEL..NYNNQNR ENV_SIVCZ/33-496 RIRQIVSSWMRVGRGIYAPPIRG...NITCNSNITGLLLTS..DTPVTNN ENV_HV1ZH/33-511 RIKQIVNMWQRVGQAMYAPPIKG...VIKCVSNITGILLTR..DGVGNNT ENV_HV1W1/33-510 RIKQIINMWQGVGKAMYAPPIGG...QIRCSSNITGLLLTR..DGGNSSS ENV_HV1J3/33-523 RIKQIINMWQEVGKAMYAPPIEG...QIRCSSNITGLLLTR..DGGDNQN ENV_HV1B1/34-511 RIKQIINMWQEVGKAMYAPPISG...QIRCSSNITGLLLTR..DGGNSNN ENV_HV1A2/33-509 RIKQIINMWQEVGKAMYAPPIGG...QISCSSNITGLLLTR..DGGTNVT ENV_HV1RH/33-519 RIKQIVNMWQEVGKAMYAPPISG...QIKCISNITGLLLTR..DGGEDTT ENV_HV1BN/34-507 RIKQIINMWQEVGKAMYAPPIRG...QIKCSSNITGLLLTR..DGG...N ENV_HV1OY/33-509 RIKQIVNMWQEVGKAMYAPPISG...QIRCSSKITGLLLTR..DGGKNTT ENV_HV1C4/35-522 RIKQIINRWQVVGKAMYALPIKG...LIRCSSNITGLLLTR..DGGGENQ ENV_HV1Z8/33-518 RIKQIINMWQGVGKAMYAPPIEG...LIKCTSNITGLLLTR..DGG..VN ENV_HV1EL/33-508 RIKQIIKMVAGR.KAIYAPPIER...NILCSSNITGLLLTR..DGG..IN ENV_HV1ND/33-501 RIKQIVNLWQRVGKAMYAPPIEG...LIKCSSNITGLLLTR..DGG..AN ENV_HV1MA/33-513 RIKQIINMWQKTGKAMYAPPIAG...VINCLSNITGLILTR..DGGNSSD ENV_SIVGB/47-569 QIRQIVDDWMQVGRKIYLPPTSGFNNHIRCTHRVTEMYFEMQKIDSNETK ENV_SIVM1/24-528 .......QTSITMSAEVAELYRLELGDYKLVEITPIGLAPTNVKRYTTGG ENV_HV2NZ/24-502 ........TNITFSAEAAELYRLELGDYKLVEITPIGFAPTSVKRYSSAH ENV_HV2G1/23-502 .......QTNITFSAEVAELYRLELGDYKLIEVTPIGFAPTREKRYSSAP ENV_HV2D1/24-501 .......QTNITFSAEVAELYRLELGDYKLIEVTPIPFAPTKEKRYSSAP ENV_HV2CA/25-512 .......TTNITFSADVAELYRLELGDYKLVEITPIGFAPTSQKRYSPAH ENV_HV2BE/24-510 .......HTNITFSAEVAELYRLELGDYKLIEITPIGFAPTDQRRYSSTP ENV_HV2D2/24-513 .......TTNISVSAEVSELYRLELGDYKLVEITPIGFAPTDVRRYSSVK ENV_SIVAI/22-522 .......PINVTLSPQVRSIWAYELGDYKLVEITPIGFAPTDVRRYTG.P ENV_SIVA1/24-538 ........TNVTLSPQIETIWAAELGRYKLVEITPIGFAPTEVRRYTGGQ ENV_SIVCZ/33-496 S....GNLTFRPTGGNMKDIWRSELYKYKVVRIEPLSVAPTKARRHTVA. ENV_HV1ZH/33-511 .....SNETFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKAKRRVVA. ENV_HV1W1/33-510 .....REEIFRPGGGNMRDNWRSELYKYKVVKIEPLGVAPTKAKRRVVQ. ENV_HV1J3/33-523 .....ETETFRPGGGNMRDNWRSELYKYKVVKIELLGVAPTKAKRRVVQ. ENV_HV1B1/34-511 .....ESEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKAKRRVVQ. ENV_HV1A2/33-509 N....DTEVFRPGGGDMRDNWRSELYKYKVIKIEPLGIAPTKAKRRVVQ. ENV_HV1RH/33-519 N....TTEIFRLGGGNMRDNWRSELYKYKVVRIEPLGVAPTRAKRRVVQ. ENV_HV1BN/34-507 NNETTDTEIFRPGGGNMRDNWRSELYKYKVVKIEPLGVAPTKAKRRVVQ. ENV_HV1OY/33-509 N....GIEIFRPAGGDMRDNWRSELYKYKVVKIEPLGVAPTKARRRVVQ. ENV_HV1C4/35-522 .....TTEIFRPGGGDMRDNWRSELYKYKVVKIEPLGVAPTKAKRRVVQ. ENV_HV1Z8/33-518 NS...TNETFRPGGGDMKDNWRNELYKYKVVRIEPLGIAPTRAKRRVVE. ENV_HV1EL/33-508 NS...TNETFRPGGGDMRDNWRSELYKYKVVQIEPLGVAPTRAKRRVVE. ENV_HV1ND/33-501 NS...SHETIRPGGGDMRDNWRSELYKYKVVKIEPIGVAPTKARRRVVE. ENV_HV1MA/33-513 NS...DNETLRPGGGDMRDNWISELYKYKVVRIEPLGVAPTKAKRRVVE. ENV_SIVGB/47-569 ......MQIKFLPPSETSNQFVAYGAHYKLVKIMPIGIAPTDVKRHTLPE ENV_SIVM1/24-528 TSRNKR ENV_HV2NZ/24-502 Q.RHTR ENV_HV2G1/23-502 V.RNKR ENV_HV2D1/24-501 V.RNKR ENV_HV2CA/25-512 G.RPKR ENV_HV2BE/24-510 V.RNKR ENV_HV2D2/24-513 P.RNKR ENV_SIVAI/22-522 T.REKR ENV_SIVA1/24-538 E.RQKR ENV_SIVCZ/33-496 ..RQKD ENV_HV1ZH/33-511 ..REKR ENV_HV1W1/33-510 ..REKR ENV_HV1J3/33-523 ..REKR ENV_HV1B1/34-511 ..REKR ENV_HV1A2/33-509 ..REKR ENV_HV1RH/33-519 ..REKR ENV_HV1BN/34-507 ..REKR ENV_HV1OY/33-509 ..REKR ENV_HV1C4/35-522 ..REKR ENV_HV1Z8/33-518 ..REKR ENV_HV1EL/33-508 ..REKR ENV_HV1ND/33-501 ..REKR ENV_HV1MA/33-513 ..REKR ENV_SIVGB/47-569 HHKEKR // weblogo-3.8.0/tests/data/phylip_test_1.phy000077500000000000000000000063431467613320200205560ustar00rootroot00000000000000 10 234 Cow MAYPMQLGFQ DATSPIMEEL LHFHDHTLMI VFLISSLVLY IISLMLTTKL Carp MAHPTQLGFK DAAMPVMEEL LHFHDHALMI VLLISTLVLY IITAMVSTKL Chicken MANHSQLGFQ DASSPIMEEL VEFHDHALMV ALAICSLVLY LLTLMLMEKL Human MAHAAQVGLQ DATSPIMEEL ITFHDHALMI IFLICFLVLY ALFLTLTTKL Loach MAHPTQLGFQ DAASPVMEEL LHFHDHALMI VFLISALVLY VIITTVSTKL Mouse MAYPFQLGLQ DATSPIMEEL MNFHDHTLMI VFLISSLVLY IISLMLTTKL Rat MAYPFQLGLQ DATSPIMEEL TNFHDHTLMI VFLISSLVLY IISLMLTTKL Seal MAYPLQMGLQ DATSPIMEEL LHFHDHTLMI VFLISSLVLY IISLMLTTKL Whale MAYPFQLGFQ DAASPIMEEL LHFHDHTLMI VFLISSLVLY IITLMLTTKL Frog MAHPSQLGFQ DAASPIMEEL LHFHDHTLMA VFLISTLVLY IITIMMTTKL THTSTMDAQE VETIWTILPA IILILIALPS LRILYMMDEI NNPSLTVKTM TNKYILDSQE IEIVWTILPA VILVLIALPS LRILYLMDEI NDPHLTIKAM S-SNTVDAQE VELIWTILPA IVLVLLALPS LQILYMMDEI DEPDLTLKAI TNTNISDAQE METVWTILPA IILVLIALPS LRILYMTDEV NDPSLTIKSI TNMYILDSQE IEIVWTVLPA LILILIALPS LRILYLMDEI NDPHLTIKAM THTSTMDAQE VETIWTILPA VILIMIALPS LRILYMMDEI NNPVLTVKTM THTSTMDAQE VETIWTILPA VILILIALPS LRILYMMDEI NNPVLTVKTM THTSTMDAQE VETVWTILPA IILILIALPS LRILYMMDEI NNPSLTVKTM THTSTMDAQE VETVWTILPA IILILIALPS LRILYMMDEV NNPSLTVKTM TNTNLMDAQE IEMVWTIMPA ISLIMIALPS LRILYLMDEV NDPHLTIKAI GHQWYWSYEY TDYEDLSFDS YMIPTSELKP GELRLLEVDN RVVLPMEMTI GHQWYWSYEY TDYENLGFDS YMVPTQDLAP GQFRLLETDH RMVVPMESPV GHQWYWTYEY TDFKDLSFDS YMTPTTDLPL GHFRLLEVDH RIVIPMESPI GHQWYWTYEY TDYGGLIFNS YMLPPLFLEP GDLRLLDVDN RVVLPIEAPI GHQWYWSYEY TDYENLSFDS YMIPTQDLTP GQFRLLETDH RMVVPMESPI GHQWYWSYEY TDYEDLCFDS YMIPTNDLKP GELRLLEVDN RVVLPMELPI GHQWYWSYEY TDYEDLCFDS YMIPTNDLKP GELRLLEVDN RVVLPMELPI GHQWYWSYEY TDYEDLNFDS YMIPTQELKP GELRLLEVDN RVVLPMEMTI GHQWYWSYEY TDYEDLSFDS YMIPTSDLKP GELRLLEVDN RVVLPMEMTI GHQWYWSYEY TNYEDLSFDS YMIPTNDLTP GQFRLLEVDN RMVVPMESPT RMLVSSEDVL HSWAVPSLGL KTDAIPGRLN QTTLMSSRPG LYYGQCSEIC RVLVSAEDVL HSWAVPSLGV KMDAVPGRLN QAAFIASRPG VFYGQCSEIC RVIITADDVL HSWAVPALGV KTDAIPGRLN QTSFITTRPG VFYGQCSEIC RMMITSQDVL HSWAVPTLGL KTDAIPGRLN QTTFTATRPG VYYGQCSEIC RILVSAEDVL HSWALPAMGV KMDAVPGRLN QTAFIASRPG VFYGQCSEIC RMLISSEDVL HSWAVPSLGL KTDAIPGRLN QATVTSNRPG LFYGQCSEIC RMLISSEDVL HSWAIPSLGL KTDAIPGRLN QATVTSNRPG LFYGQCSEIC RMLISSEDVL HSWAVPSLGL KTDAIPGRLN QTTLMTMRPG LYYGQCSEIC RMLVSSEDVL HSWAVPSLGL KTDAIPGRLN QTTLMSTRPG LFYGQCSEIC RLLVTAEDVL HSWAVPSLGV KTDAIPGRLH QTSFIATRPG VFYGQCSEIC GSNHSFMPIV LELVPLKYFE KWSASML--- ---- GANHSFMPIV VEAVPLEHFE NWSSLMLEDA SLGS GANHSYMPIV VESTPLKHFE AWSSL----- -LSS GANHSFMPIV LELIPLKIFE M-------GP VFTL GANHSFMPIV VEAVPLSHFE NWSTLMLKDA SLGS GSNHSFMPIV LEMVPLKYFE NWSASMI--- ---- GSNHSFMPIV LEMVPLKYFE NWSASMI--- ---- GSNHSFMPIV LELVPLSHFE KWSTSML--- ---- GSNHSFMPIV LELVPLEVFE KWSVSML--- ---- GANHSFMPIV VEAVPLTDFE NWSSSML-EA SL-- weblogo-3.8.0/tests/data/phylip_test_2.phy000077500000000000000000000005411467613320200205510ustar00rootroot00000000000000 6 20 A W U A 0001111000 0011112300 Weights 00112221A0 1110201200 Archaeopt CGATGCTTAC CGCCGATGCT HesperorniCGTTACTCGT TGTCGTTACT BaluchitheTAATGTTAAT TGTTAATGTT B. virginiTAATGTTCGT TGTTAATGTT BrontosaurCAAAACCCAT CATCAAAACC B.subtilisGGCAGCCAAT CACGGCAGCC 1 ((dmras1,ddrasa),((hschras,spras),(scras1,scras2))); weblogo-3.8.0/tests/data/phylip_test_3.phy000077500000000000000000000004401467613320200205500ustar00rootroot00000000000000 6 20 AW A 0001111000 0011112300 Weights 00112221A0 1110201200 Archaeopt CGATGCTTAC CGCCGATGCT HesperorniCGTTACTCGT TGTCGTTACT BaluchitheTAATGTTAAT TGTTAATGTT B. virginiTAATGTTCGT TGTTAATGTT BrontosaurCAAAACCCAT CATCAAAACC B.subtilisGGCAGCCAAT CACGGCAGCC weblogo-3.8.0/tests/data/phylip_test_4.phy000077500000000000000000000005441467613320200205560ustar00rootroot00000000000000 6 25 W W 0101001111 0101110101 01011 dmras1 GTCGTCGTTG GACCTGGAGG CGTGG hschras GTGGTGGTGG GCGCCGGCCG TGTGG ddrasa GTTATTGTTG GTGGTGGTGG TGTCG spras GTAGTTGTAG GAGATGGTGG TGTTG scras1 GTAGTTGTCG GTGGAGGTGG CGTTG scras2 GTCGTCGTTG GTGGTGGTGG TGTTG 1 ((dmras1,ddrasa),((hschras,spras),(scras1,scras2))); weblogo-3.8.0/tests/data/phylip_test_5.phy000077500000000000000000000010711467613320200205530ustar00rootroot00000000000000 6 50 W W 0101001111 0101110101 01011 dmras1 GTCGTCGTTG GACCTGGAGG CGTGG hschras GTGGTGGTGG GCGCCGGCCG TGTGG ddrasa GTTATTGTTG GTGGTGGTGG TGTCG spras GTAGTTGTAG GAGATGGTGG TGTTG scras1 GTAGTTGTCG GTGGAGGTGG CGTTG scras2 GTCGTCGTTG GTGGTGGTGG TGTTG 0101001111 0101110101 01011 GTCGTCGTTG GACCTGGAGG CGTGG GTGGTGGTGG GCGCCGGCCG TGTGG GTTATTGTTG GTGGTGGTGG TGTCG GTAGTTGTAG GAGATGGTGG TGTTG GTAGTTGTCG GTGGAGGTGG CGTTG GTCGTCGTTG GTGGTGGTGG TGTTG 1 ((dmras1,ddrasa),((hschras,spras),(scras1,scras2))); weblogo-3.8.0/tests/data/phylip_test_6.corrupt.phy000066400000000000000000000010711467613320200222460ustar00rootroot00000000000000 7 50 W W 0101001111 0101110101 01011 dmras1 GTCGTCGTTG GACCTGGAGG CGTGG hschras GTGGTGGTGG GCGCCGGCCG TGTGG ddrasa GTTATTGTTG GTGGTGGTGG TGTCG spras GTAGTTGTAG GAGATGGTGG TGTTG scras1 GTAGTTGTCG GTGGAGGTGG CGTTG scras2 GTCGTCGTTG GTGGTGGTGG TGTTG 0101001111 0101110101 01011 GTCGTCGTTG GACCTGGAGG CGTGG GTGGTGGTGG GCGCCGGCCG TGTGG GTTATTGTTG GTGGTGGTGG TGTCG GTAGTTGTAG GAGATGGTGG TGTTG GTAGTTGTCG GTGGAGGTGG CGTTG GTCGTCGTTG GTGGTGGTGG TGTTG 1 ((dmras1,ddrasa),((hschras,spras),(scras1,scras2))); weblogo-3.8.0/tests/data/phylip_test_7.corrupt.phy000066400000000000000000000010011467613320200222400ustar00rootroot00000000000000 6 50 W W 0101001111 0101110101 01011 dmras1 GTCGTCGTTG GACCTGGAGG CGTGG hschras GTGGTGGTGG GCGCCGGCCG TGTGG ddrasa GTTATTGTTG GTGGTGGTGG TGTCG spras GTAGTTGTAG GAGATGGTGG TGTTG scras1 GTAGTTGTCG GTGGAGGTGG CGTTG scras2 GTCGTCGTTG GTGGTGGTGG TGTTG 0101001111 0101110101 01011 GTCGTCGTTG GACCTGGAGG CGTGG GTGGTGGTGG GCGCCGGCCG TGTGG GTTATTGTTG GTGGTGGTGG TGTCG GTAGTTGTAG GAGATGGTGG TGTTG 1 ((dmras1,ddrasa),((hschras,spras),(scras1,scras2))); weblogo-3.8.0/tests/data/protein.pir000066400000000000000000000047761467613320200174510ustar00rootroot00000000000000>P1; Cow Cow MAYPMQLGFQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEVETIWTILPAIILILI ALPSLRILYMMDEINNPSLTVKTMGHQWYWSYEYTDYEDLSFDSYMIPTSELKPGELRLLEVDNRVVLPMEMTIRM LVSSEDVLHSWAVPSLGLKTDAIPGRLNQTTLMSSRPGLYYGQCSEICGSNHSFMPIVLELVPLKYFEKWSASML- ------* >P1; Carp Carp MAHPTQLGFKDAAMPVMEELLHFHDHALMIVLLISTLVLYIITAMVSTKLTNKYILDSQEIEIVWTILPAVILVLI ALPSLRILYLMDEINDPHLTIKAMGHQWYWSYEYTDYENLGFDSYMVPTQDLAPGQFRLLETDHRMVVPMESPVRV LVSAEDVLHSWAVPSLGVKMDAVPGRLNQAAFIASRPGVFYGQCSEICGANHSFMPIVVEAVPLEHFENWSSLMLE DASLGS* >P1; Chicken Chicken MANHSQLGFQDASSPIMEELVEFHDHALMVALAICSLVLYLLTLMLMEKLS-SNTVDAQEVELIWTILPAIVLVLL ALPSLQILYMMDEIDEPDLTLKAIGHQWYWTYEYTDFKDLSFDSYMTPTTDLPLGHFRLLEVDHRIVIPMESPIRV IITADDVLHSWAVPALGVKTDAIPGRLNQTSFITTRPGVFYGQCSEICGANHSYMPIVVESTPLKHFEAWSSL--- ---LSS* >P1; Human Human MAHAAQVGLQDATSPIMEELITFHDHALMIIFLICFLVLYALFLTLTTKLTNTNISDAQEMETVWTILPAIILVLI ALPSLRILYMTDEVNDPSLTIKSIGHQWYWTYEYTDYGGLIFNSYMLPPLFLEPGDLRLLDVDNRVVLPIEAPIRM MITSQDVLHSWAVPTLGLKTDAIPGRLNQTTFTATRPGVYYGQCSEICGANHSFMPIVLELIPLKIFEM------- GPVFTL* >P1; Loach Loach MAHPTQLGFQDAASPVMEELLHFHDHALMIVFLISALVLYVIITTVSTKLTNMYILDSQEIEIVWTVLPALILILI ALPSLRILYLMDEINDPHLTIKAMGHQWYWSYEYTDYENLSFDSYMIPTQDLTPGQFRLLETDHRMVVPMESPIRI LVSAEDVLHSWALPAMGVKMDAVPGRLNQTAFIASRPGVFYGQCSEICGANHSFMPIVVEAVPLSHFENWSTLMLK DASLGS* >P1; Mouse Mouse MAYPFQLGLQDATSPIMEELMNFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEVETIWTILPAVILIMI ALPSLRILYMMDEINNPVLTVKTMGHQWYWSYEYTDYEDLCFDSYMIPTNDLKPGELRLLEVDNRVVLPMELPIRM LISSEDVLHSWAVPSLGLKTDAIPGRLNQATVTSNRPGLFYGQCSEICGSNHSFMPIVLEMVPLKYFENWSASMI- ------* >P1; Rat Rat MAYPFQLGLQDATSPIMEELTNFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEVETIWTILPAVILILI ALPSLRILYMMDEINNPVLTVKTMGHQWYWSYEYTDYEDLCFDSYMIPTNDLKPGELRLLEVDNRVVLPMELPIRM LISSEDVLHSWAIPSLGLKTDAIPGRLNQATVTSNRPGLFYGQCSEICGSNHSFMPIVLEMVPLKYFENWSASMI- ------* >P1; Seal Seal MAYPLQMGLQDATSPIMEELLHFHDHTLMIVFLISSLVLYIISLMLTTKLTHTSTMDAQEVETVWTILPAIILILI ALPSLRILYMMDEINNPSLTVKTMGHQWYWSYEYTDYEDLNFDSYMIPTQELKPGELRLLEVDNRVVLPMEMTIRM LISSEDVLHSWAVPSLGLKTDAIPGRLNQTTLMTMRPGLYYGQCSEICGSNHSFMPIVLELVPLSHFEKWSTSML- ------* >P1; Whale Whale MAYPFQLGFQDAASPIMEELLHFHDHTLMIVFLISSLVLYIITLMLTTKLTHTSTMDAQEVETVWTILPAIILILI ALPSLRILYMMDEVNNPSLTVKTMGHQWYWSYEYTDYEDLSFDSYMIPTSDLKPGELRLLEVDNRVVLPMEMTIRM LVSSEDVLHSWAVPSLGLKTDAIPGRLNQTTLMSTRPGLFYGQCSEICGSNHSFMPIVLELVPLEVFEKWSVSML- ------* >P1; Frog Frog MAHPSQLGFQDAASPIMEELLHFHDHTLMAVFLISTLVLYIITIMMTTKLTNTNLMDAQEIEMVWTIMPAISLIMI ALPSLRILYLMDEVNDPHLTIKAIGHQWYWSYEYTNYEDLSFDSYMIPTNDLTPGQFRLLEVDNRMVVPMESPTRL LVTAEDVLHSWAVPSLGVKTDAIPGRLHQTSFIATRPGVFYGQCSEICGANHSFMPIVVEAVPLTDFENWSSSML- EASL--*weblogo-3.8.0/tests/data/readme.txt000066400000000000000000000014621467613320200172400ustar00rootroot00000000000000 # Name Description AST1.fa fasta fle with one sequence AST2.fa Another fasta file Rv3829c.fasta a single fasta sequence (from BLAST2 parser ) Rv3829c.blast example BLAST version 2.10.0 output Rv3829c.psiblast example PSI-BLAST version 2.10.0 output TAT_mase_nuc.txt An IG (intelligenetics) sequence file blosum35.blast blosum35.blast.new clustal.aln clustal181.aln clustal_glualign.aln clustalw182.aln clustalw.pir PIR file from clustalw cox2.gb cox2.gcg cox2.msf cox2.nbrf cox2.phylip phylip format cox2b.phylip phylip format crab.nbrf dist.20comp dna.phy phylip format dna.pir globin.fa A multiple sequence alignment fasta file intelligenetics.txt An IG (intelligenetics) sequence file pam250.mat protein.pir weblogo-3.8.0/tests/data/rhod.pir000066400000000000000000000024271467613320200167140ustar00rootroot00000000000000>P1;S27231 rhodopsin - northern leopard frog MNGTEGPNFY IPMSNKTGVV RSPFDYPQYY LAEPWKYSVL AAYMFLLILL GLPINFMTLY VTIQHKKLRT PLNYILLNLG VCNHFMVLCG FTITMYTSLH GYFVFGQTGC YFEGFFATLG GEIALWSLVV LAIERYIVVC KPMSNFRFGE NHAMMGVAFT WIMALACAVP PLFGWSRYIP EGMQCSCGVD YYTLKPEVNN ESFVIYMFVV HFLIPLIIIS FCYGRLVCTV KEAAAQQQES ATTQKAEKEV TRMVIIMVIF FLICWVPYAY VAFYIFTHQG SEFGPIFMTV PAFFAKSSAI YNPVIYIMLN KQFRNCMITT LCCGKNPFGD DDASSAATSK TEATSVSTSQ VSPA* >P1;I51200 rhodopsin - African clawed frog MNGTEGPNFY VPMSNKTGVV RSPFDYPQYY LAEPWQYSAL AAYMFLLILL GLPINFMTLF VTIQHKKLRT PLNYILLNLV FANHFMVLCG FTVTMYTSMH GYFIFGPTGC YIEGFFATLG GEVALWSLVV LAVERYIVVC KPMANFRFGE NHAIMGVAFT WIMALSCAAP PLFGWSRYIP EGMQCSCGVD YYTLKPEVNN ESFVIYMFIV HFTIPLIVIF FCYGRLLCTV KEAAAQQQES LTTQKAEKEV TRMVVIMVVF FLICWVPYAY VAFYIFTHQG SNFGPVFMTV PAFFAKSSAI YNPVIYIVLN KQFRNCLITT LCCGKNPFGD EDGSSAATSK TEASSVSSSQ VSPA* >P1;JN0120 rhodopsin - Japanese lamprey MNGTEGDNFY VPFSNKTGLA RSPYEYPQYY LAEPWKYSAL AAYMFFLILV GFPVNFLTLF VTVQHKKLRT PLNYILLNLA MANLFMVLFG FTVTMYTSMN GYFVFGPTMC SIEGFFATLG GEVALWSLVV LAIERYIVIC KPMGNFRFGN THAIMGVAFT WIMALACAAP PLVGWSRYIP EGMQCSCGPD YYTLNPNFNN ESYVVYMFVV HFLVPFVIIF FCYGRLLCTV KEAAAAQQES ASTQKAEKEV TRMVVLMVIG FLVCWVPYAS VAFYIFTHQG SDFGATFMTL PAFFAKSSAL YNPVIYILMN KQFRNCMITT LCCGKNPLGD DE-SGASTSKT EVSSVSTSPV SPA* weblogo-3.8.0/tests/data/scop/000077500000000000000000000000001467613320200162035ustar00rootroot00000000000000weblogo-3.8.0/tests/data/scop/dir.cla.scop.txt_test000066400000000000000000000024261467613320200222660ustar00rootroot00000000000000d3sdha_ 3sdh A: a.1.1.2 14984 cl=46456,cf=46457,sf=46458,fa=46463,dm=46464,sp=46465,px=14984 d3sdhb_ 3sdh B: a.1.1.2 14985 cl=46456,cf=46457,sf=46458,fa=46463,dm=46464,sp=46465,px=14985 d3hbia_ 3hbi A: a.1.1.2 14986 cl=46456,cf=46457,sf=46458,fa=46463,dm=46464,sp=46465,px=14986 d3hbib_ 3hbi B: a.1.1.2 14987 cl=46456,cf=46457,sf=46458,fa=46463,dm=46464,sp=46465,px=14987 d4sdha_ 4sdh A: a.1.1.2 14988 cl=46456,cf=46457,sf=46458,fa=46463,dm=46464,sp=46465,px=14988 d4sdhb_ 4sdh B: a.1.1.2 14989 cl=46456,cf=46457,sf=46458,fa=46463,dm=46464,sp=46465,px=14989 d4hbia_ 4hbi A: a.1.1.2 14990 cl=46456,cf=46457,sf=46458,fa=46463,dm=46464,sp=46465,px=14990 d4hbib_ 4hbi B: a.1.1.2 14991 cl=46456,cf=46457,sf=46458,fa=46463,dm=46464,sp=46465,px=14991 d5hbia_ 5hbi A: a.1.1.2 14992 cl=46456,cf=46457,sf=46458,fa=46463,dm=46464,sp=46465,px=14992 d5hbib_ 5hbi B: a.1.1.2 14993 cl=46456,cf=46457,sf=46458,fa=46463,dm=46464,sp=46465,px=14993 d7hbia_ 7hbi A: a.1.1.2 14994 cl=46456,cf=46457,sf=46458,fa=46463,dm=46464,sp=46465,px=14994 d7hbib_ 7hbi B: a.1.1.2 14995 cl=46456,cf=46457,sf=46458,fa=46463,dm=46464,sp=46465,px=14995 d1hbia_ 1hbi A: a.1.1.2 14996 cl=46456,cf=46457,sf=46458,fa=46463,dm=46464,sp=46465,px=14996 d1hbib_ 1hbi B: a.1.1.2 14997 cl=46456,cf=46457,sf=46458,fa=46463,dm=46464,sp=46465,px=14997 weblogo-3.8.0/tests/data/scop/dir.des.scop.txt_test000066400000000000000000000012271467613320200223000ustar00rootroot0000000000000014984 px a.1.1.2 d3sdha_ 3sdh A: 14985 px a.1.1.2 d3sdhb_ 3sdh B: 14986 px a.1.1.2 d3hbia_ 3hbi A: 14987 px a.1.1.2 d3hbib_ 3hbi B: 14988 px a.1.1.2 d4sdha_ 4sdh A: 14989 px a.1.1.2 d4sdhb_ 4sdh B: 14990 px a.1.1.2 d4hbia_ 4hbi A: 14991 px a.1.1.2 d4hbib_ 4hbi B: 14992 px a.1.1.2 d5hbia_ 5hbi A: 14993 px a.1.1.2 d5hbib_ 5hbi B: 14994 px a.1.1.2 d7hbia_ 7hbi A: 14995 px a.1.1.2 d7hbib_ 7hbi B: 14996 px a.1.1.2 d1hbia_ 1hbi A: 14997 px a.1.1.2 d1hbib_ 1hbi B: 46456 cl a - All alpha proteins 46457 cf a.1 - Globin-like 46458 sf a.1.1 - Globin-like 46463 fa a.1.1.2 - Globins 46464 dm a.1.1.2 - Hemoglobin I 46465 sp a.1.1.2 - Ark clam (Scapharca inaequivalvis) weblogo-3.8.0/tests/data/scop/dir.hie.scop.txt_test000066400000000000000000000006041467613320200222700ustar00rootroot000000000000000 - 46456 14984 46465 - 14985 46465 - 14986 46465 - 14987 46465 - 14988 46465 - 14989 46465 - 14990 46465 - 14991 46465 - 14992 46465 - 14993 46465 - 14994 46465 - 14995 46465 - 14996 46465 - 14997 46465 - 46456 0 46457 46457 46456 46458 46458 46457 46463 46463 46458 46464 46464 46463 46465 46465 46464 14984,14985,14986,14987,14988,14989,14990,14991,14992,14993,14994,14995,14996,14997 weblogo-3.8.0/tests/data/scop/dirtest.txt000066400000000000000000000032471467613320200204300ustar00rootroot00000000000000# dir.cla.scop.txt # SCOP release 1.55 (July 2001) [File format version 1.00] # http://scop.mrc-lmb.cam.ac.uk/scop/ # Copyright (c) 1994-2001 the scop authors; see http://scop.mrc-lmb.cam.ac.uk/scop/lic/copy.html d1dlwa_ 1dlw A: a.1.1.1 14982 cl=46456,cf=46457,sf=46458,fa=46459,dm=46460,sp=46461,px=14982 d1dlya_ 1dly A: a.1.1.1 14983 cl=46456,cf=46457,sf=46458,fa=46459,dm=46460,sp=46462,px=14983 d3sdha_ 3sdh A: a.1.1.2 14984 cl=46456,cf=46457,sf=46458,fa=46463,dm=46464,sp=46465,px=14984 d3sdhb_ 3sdh B: a.1.1.2 14985 cl=46456,cf=46457,sf=46458,fa=46463,dm=46464,sp=46465,px=14985 d3hbia_ 3hbi A: a.1.1.2 14986 cl=46456,cf=46457,sf=46458,fa=46463,dm=46464,sp=46465,px=14986 d3hbib_ 3hbi B: a.1.1.2 14987 cl=46456,cf=46457,sf=46458,fa=46463,dm=46464,sp=46465,px=14987 d4sdha_ 4sdh A: a.1.1.2 14988 cl=46456,cf=46457,sf=46458,fa=46463,dm=46464,sp=46465,px=14988 d4sdhb_ 4sdh B: a.1.1.2 14989 cl=46456,cf=46457,sf=46458,fa=46463,dm=46464,sp=46465,px=14989 d4hbia_ 4hbi A: a.1.1.2 14990 cl=46456,cf=46457,sf=46458,fa=46463,dm=46464,sp=46465,px=14990 d4hbib_ 4hbi B: a.1.1.2 14991 cl=46456,cf=46457,sf=46458,fa=46463,dm=46464,sp=46465,px=14991 d5hbia_ 5hbi A: a.1.1.2 14992 cl=46456,cf=46457,sf=46458,fa=46463,dm=46464,sp=46465,px=14992 d5hbib_ 5hbi B: a.1.1.2 14993 cl=46456,cf=46457,sf=46458,fa=46463,dm=46464,sp=46465,px=14993 d7hbia_ 7hbi A: a.1.1.2 14994 cl=46456,cf=46457,sf=46458,fa=46463,dm=46464,sp=46465,px=14994 d7hbib_ 7hbi B: a.1.1.2 14995 cl=46456,cf=46457,sf=46458,fa=46463,dm=46464,sp=46465,px=14995 d1hbia_ 1hbi A: a.1.1.2 14996 cl=46456,cf=46457,sf=46458,fa=46463,dm=46464,sp=46465,px=14996 d1hbib_ 1hbi B: a.1.1.2 14997 cl=46456,cf=46457,sf=46458,fa=46463,dm=46464,sp=46465,px=14997 weblogo-3.8.0/tests/data/scop/domtest.txt000066400000000000000000000005741467613320200204310ustar00rootroot00000000000000d3sdha_ 3sdh a: 1.001.001.001.001.001 d3sdhb_ 3sdh b: 1.001.001.001.001.001 d3hbia_ 3hbi a: 1.001.001.001.001.001 d3hbib_ 3hbi b: 1.001.001.001.001.001 d4sdha_ 4sdh a: 1.001.001.001.001.001 d4sdhb_ 4sdh b: 1.001.001.001.001.001 d4hbia_ 4hbi a: 1.001.001.001.001.001 d4hbib_ 4hbi b: 1.001.001.001.001.001 d5hbia_ 5hbi a: 1.001.001.001.001.001 d5hbib_ 5hbi b: 1.001.001.001.001.001 weblogo-3.8.0/tests/data/scop/raftest.txt000066400000000000000000000440551467613320200204240ustar00rootroot00000000000000# A very short Astral Atom-Seqres Rapid Access Format file for testing # 101m_ 0.01 38 010301 111011 0 153 0 mm 1 vv 2 ll 3 ss 4 ee 5 gg 6 ee 7 ww 8 qq 9 ll 10 vv 11 ll 12 hh 13 vv 14 ww 15 aa 16 kk 17 vv 18 ee 19 aa 20 dd 21 vv 22 aa 23 gg 24 hh 25 gg 26 qq 27 dd 28 ii 29 ll 30 ii 31 rr 32 ll 33 ff 34 kk 35 ss 36 hh 37 pp 38 ee 39 tt 40 ll 41 ee 42 kk 43 ff 44 dd 45 rr 46 vv 47 kk 48 hh 49 ll 50 kk 51 tt 52 ee 53 aa 54 ee 55 mm 56 kk 57 aa 58 ss 59 ee 60 dd 61 ll 62 kk 63 kk 64 hh 65 gg 66 vv 67 tt 68 vv 69 ll 70 tt 71 aa 72 ll 73 gg 74 aa 75 ii 76 ll 77 kk 78 kk 79 kk 80 gg 81 hh 82 hh 83 ee 84 aa 85 ee 86 ll 87 kk 88 pp 89 ll 90 aa 91 qq 92 ss 93 hh 94 aa 95 tt 96 kk 97 hh 98 kk 99 ii 100 pp 101 ii 102 kk 103 yy 104 ll 105 ee 106 ff 107 ii 108 ss 109 ee 110 aa 111 ii 112 ii 113 hh 114 vv 115 ll 116 hh 117 ss 118 rr 119 hh 120 pp 121 gg 122 nn 123 ff 124 gg 125 aa 126 dd 127 aa 128 qq 129 gg 130 aa 131 mm 132 nn 133 kk 134 aa 135 ll 136 ee 137 ll 138 ff 139 rr 140 kk 141 dd 142 ii 143 aa 144 aa 145 kk 146 yy 147 kk 148 ee 149 ll 150 gg 151 yy 152 qq 153 gg 102l_ 0.01 38 010301 111010 1 162 1 mm 2 nn 3 ii 4 ff 5 ee 6 mm 7 ll 8 rr 9 ii 10 dd 11 ee 12 gg 13 ll 14 rr 15 ll 16 kk 17 ii 18 yy 19 kk 20 dd 21 tt 22 ee 23 gg 24 yy 25 yy 26 tt 27 ii 28 gg 29 ii 30 gg 31 hh 32 ll 33 ll 34 tt 35 kk 36 ss 37 pp 38 ss 39 ll 40 nn 40Aaa 41 aa 42 aa 43 kk 44 ss 45 ee 46 ll 47 dd 48 kk 49 aa 50 ii 51 gg 52 rr 53 nn 54 tt 55 nn 56 gg 57 vv 58 ii 59 tt 60 kk 61 dd 62 ee 63 aa 64 ee 65 kk 66 ll 67 ff 68 nn 69 qq 70 dd 71 vv 72 dd 73 aa 74 aa 75 vv 76 rr 77 gg 78 ii 79 ll 80 rr 81 nn 82 aa 83 kk 84 ll 85 kk 86 pp 87 vv 88 yy 89 dd 90 ss 91 ll 92 dd 93 aa 94 vv 95 rr 96 rr 97 aa 98 aa 99 ll 100 ii 101 nn 102 mm 103 vv 104 ff 105 qq 106 mm 107 gg 108 ee 109 tt 110 gg 111 vv 112 aa 113 gg 114 ff 115 tt 116 nn 117 ss 118 ll 119 rr 120 mm 121 ll 122 qq 123 qq 124 kk 125 rr 126 ww 127 dd 128 ee 129 aa 130 aa 131 vv 132 nn 133 ll 134 aa 135 kk 136 ss 137 rr 138 ww 139 yy 140 nn 141 qq 142 tt 143 pp 144 nn 145 rr 146 aa 147 kk 148 rr 149 vv 150 ii 151 tt 152 tt 153 ff 154 rr 155 tt 156 gg 157 tt 158 ww 159 dd 160 aa 161 yy 162 kk E .n E .l 102m_ 0.01 38 010301 111011 0 153 0 mm 1 vv 2 ll 3 ss 4 ee 5 gg 6 ee 7 ww 8 qq 9 ll 10 vv 11 ll 12 hh 13 vv 14 ww 15 aa 16 kk 17 vv 18 ee 19 aa 20 dd 21 vv 22 aa 23 gg 24 hh 25 gg 26 qq 27 dd 28 ii 29 ll 30 ii 31 rr 32 ll 33 ff 34 kk 35 ss 36 hh 37 pp 38 ee 39 tt 40 ll 41 ee 42 kk 43 ff 44 dd 45 rr 46 ff 47 kk 48 hh 49 ll 50 kk 51 tt 52 ee 53 aa 54 ee 55 mm 56 kk 57 aa 58 ss 59 ee 60 dd 61 ll 62 kk 63 kk 64 aa 65 gg 66 vv 67 tt 68 vv 69 ll 70 tt 71 aa 72 ll 73 gg 74 aa 75 ii 76 ll 77 kk 78 kk 79 kk 80 gg 81 hh 82 hh 83 ee 84 aa 85 ee 86 ll 87 kk 88 pp 89 ll 90 aa 91 qq 92 ss 93 hh 94 aa 95 tt 96 kk 97 hh 98 kk 99 ii 100 pp 101 ii 102 kk 103 yy 104 ll 105 ee 106 ff 107 ii 108 ss 109 ee 110 aa 111 ii 112 ii 113 hh 114 vv 115 ll 116 hh 117 ss 118 rr 119 hh 120 pp 121 gg 122 nn 123 ff 124 gg 125 aa 126 dd 127 aa 128 qq 129 gg 130 aa 131 mm 132 nn 133 kk 134 aa 135 ll 136 ee 137 ll 138 ff 139 rr 140 kk 141 dd 142 ii 143 aa 144 aa 145 kk 146 yy 147 kk 148 ee 149 ll 150 gg 151 yy 152 qq 153 gg 103l_ 0.01 38 010301 111010 1 162 1 mm 2 nn 3 ii 4 ff 5 ee 6 mm 7 ll 8 rr 9 ii 10 dd 11 ee 12 gg 13 ll 14 rr 15 ll 16 kk 17 ii 18 yy 19 kk 20 dd 21 tt 22 ee 23 gg 24 yy 25 yy 26 tt 27 ii 28 gg 29 ii 30 gg 31 hh 32 ll 33 ll 34 tt M .k M .s M .p M .s M .l M .n 40Ass 40Bll 40Cdd 41 aa 42 aa 43 kk 44 ss 45 ee 46 ll 47 dd 48 kk 49 aa 50 ii 51 gg 52 rr 53 nn 54 tt 55 nn 56 gg 57 vv 58 ii 59 tt 60 kk 61 dd 62 ee 63 aa 64 ee 65 kk 66 ll 67 ff 68 nn 69 qq 70 dd 71 vv 72 dd 73 aa 74 aa 75 vv 76 rr 77 gg 78 ii 79 ll 80 rr 81 nn 82 aa 83 kk 84 ll 85 kk 86 pp 87 vv 88 yy 89 dd 90 ss 91 ll 92 dd 93 aa 94 vv 95 rr 96 rr 97 aa 98 aa 99 ll 100 ii 101 nn 102 mm 103 vv 104 ff 105 qq 106 mm 107 gg 108 ee 109 tt 110 gg 111 vv 112 aa 113 gg 114 ff 115 tt 116 nn 117 ss 118 ll 119 rr 120 mm 121 ll 122 qq 123 qq 124 kk 125 rr 126 ww 127 dd 128 ee 129 aa 130 aa 131 vv 132 nn 133 ll 134 aa 135 kk 136 ss 137 rr 138 ww 139 yy 140 nn 141 qq 142 tt 143 pp 144 nn 145 rr 146 aa 147 kk 148 rr 149 vv 150 ii 151 tt 152 tt 153 ff 154 rr 155 tt 156 gg 157 tt 158 ww 159 dd 160 aa 161 yy 162 kk E .n E .l 103m_ 0.01 38 010301 111011 0 153 0 mm 1 vv 2 ll 3 ss 4 ee 5 gg 6 ee 7 ww 8 qq 9 ll 10 vv 11 ll 12 hh 13 vv 14 ww 15 aa 16 kk 17 vv 18 ee 19 aa 20 dd 21 vv 22 aa 23 gg 24 hh 25 gg 26 qq 27 dd 28 ii 29 ll 30 ii 31 rr 32 ll 33 ff 34 kk 35 ss 36 hh 37 pp 38 ee 39 tt 40 ll 41 ee 42 kk 43 ff 44 dd 45 rr 46 ff 47 kk 48 hh 49 ll 50 kk 51 tt 52 ee 53 aa 54 ee 55 mm 56 kk 57 aa 58 ss 59 ee 60 dd 61 ll 62 kk 63 kk 64 aa 65 gg 66 vv 67 tt 68 vv 69 ll 70 tt 71 aa 72 ll 73 gg 74 aa 75 ii 76 ll 77 kk 78 kk 79 kk 80 gg 81 hh 82 hh 83 ee 84 aa 85 ee 86 ll 87 kk 88 pp 89 ll 90 aa 91 qq 92 ss 93 hh 94 aa 95 tt 96 kk 97 hh 98 kk 99 ii 100 pp 101 ii 102 kk 103 yy 104 ll 105 ee 106 ff 107 ii 108 ss 109 ee 110 aa 111 ii 112 ii 113 hh 114 vv 115 ll 116 hh 117 ss 118 rr 119 hh 120 pp 121 gg 122 nn 123 ff 124 gg 125 aa 126 dd 127 aa 128 qq 129 gg 130 aa 131 mm 132 nn 133 kk 134 aa 135 ll 136 ee 137 ll 138 ff 139 rr 140 kk 141 dd 142 ii 143 aa 144 aa 145 kk 146 yy 147 kk 148 ee 149 ll 150 gg 151 yy 152 qq 153 gg 104lA 0.01 38 010301 111010 1 162 1 mm 2 nn 3 ii 4 ff 5 ee 6 mm 7 ll 8 rr 9 ii 10 dd 11 ee 12 gg 13 ll 14 rr 15 ll 16 kk 17 ii 18 yy 19 kk 20 dd 21 tt 22 ee 23 gg 24 yy 25 yy 26 tt 27 ii 28 gg 29 ii 30 gg 31 hh 32 ll 33 ll 34 tt 35 kk 36 ss 37 pp 38 ss 39 ll 40 nn 41 aa 42 aa 43 kk 44 ss 44Aaa 44Baa 45 ee 46 ll 47 dd 48 kk 49 aa 50 ii 51 gg 52 rr 53 nn 54 tt 55 nn 56 gg 57 vv 58 ii 59 tt 60 kk 61 dd 62 ee 63 aa 64 ee 65 kk 66 ll 67 ff 68 nn 69 qq 70 dd 71 vv 72 dd 73 aa 74 aa 75 vv 76 rr 77 gg 78 ii 79 ll 80 rr 81 nn 82 aa 83 kk 84 ll 85 kk 86 pp 87 vv 88 yy 89 dd 90 ss 91 ll 92 dd 93 aa 94 vv 95 rr 96 rr 97 aa 98 aa 99 ll 100 ii 101 nn 102 mm 103 vv 104 ff 105 qq 106 mm 107 gg 108 ee 109 tt 110 gg 111 vv 112 aa 113 gg 114 ff 115 tt 116 nn 117 ss 118 ll 119 rr 120 mm 121 ll 122 qq 123 qq 124 kk 125 rr 126 ww 127 dd 128 ee 129 aa 130 aa 131 vv 132 nn 133 ll 134 aa 135 kk 136 ss 137 rr 138 ww 139 yy 140 nn 141 qq 142 tt 143 pp 144 nn 145 rr 146 aa 147 kk 148 rr 149 vv 150 ii 151 tt 152 tt 153 ff 154 rr 155 tt 156 gg 157 tt 158 ww 159 dd 160 aa 161 yy 162 kk E .n E .l 104lB 0.01 38 010301 111010 1 162 1 mm 2 nn 3 ii 4 ff 5 ee 6 mm 7 ll 8 rr 9 ii 10 dd 11 ee 12 gg 13 ll 14 rr 15 ll 16 kk 17 ii 18 yy 19 kk 20 dd 21 tt 22 ee 23 gg 24 yy 25 yy 26 tt 27 ii 28 gg 29 ii 30 gg 31 hh 32 ll 33 ll 34 tt 35 kk 36 ss 37 pp 38 ss 39 ll 40 nn 41 aa 42 aa 43 kk 44 ss 44Aaa 44Baa 45 ee 46 ll 47 dd 48 kk 49 aa 50 ii 51 gg 52 rr 53 nn 54 tt 55 nn 56 gg 57 vv 58 ii 59 tt 60 kk 61 dd 62 ee 63 aa 64 ee 65 kk 66 ll 67 ff 68 nn 69 qq 70 dd 71 vv 72 dd 73 aa 74 aa 75 vv 76 rr 77 gg 78 ii 79 ll 80 rr 81 nn 82 aa 83 kk 84 ll 85 kk 86 pp 87 vv 88 yy 89 dd 90 ss 91 ll 92 dd 93 aa 94 vv 95 rr 96 rr 97 aa 98 aa 99 ll 100 ii 101 nn 102 mm 103 vv 104 ff 105 qq 106 mm 107 gg 108 ee 109 tt 110 gg 111 vv 112 aa 113 gg 114 ff 115 tt 116 nn 117 ss 118 ll 119 rr 120 mm 121 ll 122 qq 123 qq 124 kk 125 rr 126 ww 127 dd 128 ee 129 aa 130 aa 131 vv 132 nn 133 ll 134 aa 135 kk 136 ss 137 rr 138 ww 139 yy 140 nn 141 qq 142 tt 143 pp 144 nn 145 rr 146 aa 147 kk 148 rr 149 vv 150 ii 151 tt 152 tt 153 ff 154 rr 155 tt 156 gg 157 tt 158 ww 159 dd 160 aa 161 yy 162 kk E .n E .l 104m_ 0.01 38 010301 111011 1 153 1 vv 2 ll 3 ss 4 ee 5 gg 6 ee 7 ww 8 qq 9 ll 10 vv 11 ll 12 hh 13 vv 14 ww 15 aa 16 kk 17 vv 18 ee 19 aa 20 dd 21 vv 22 aa 23 gg 24 hh 25 gg 26 qq 27 dd 28 ii 29 ll 30 ii 31 rr 32 ll 33 ff 34 kk 35 ss 36 hh 37 pp 38 ee 39 tt 40 ll 41 ee 42 kk 43 ff 44 dd 45 rr 46 ff 47 kk 48 hh 49 ll 50 kk 51 tt 52 ee 53 aa 54 ee 55 mm 56 kk 57 aa 58 ss 59 ee 60 dd 61 ll 62 kk 63 kk 64 hh 65 gg 66 vv 67 tt 68 vv 69 ll 70 tt 71 aa 72 ll 73 gg 74 aa 75 ii 76 ll 77 kk 78 kk 79 kk 80 gg 81 hh 82 hh 83 ee 84 aa 85 ee 86 ll 87 kk 88 pp 89 ll 90 aa 91 qq 92 ss 93 hh 94 aa 95 tt 96 kk 97 hh 98 kk 99 ii 100 pp 101 ii 102 kk 103 yy 104 ll 105 ee 106 ff 107 ii 108 ss 109 ee 110 aa 111 ii 112 ii 113 hh 114 vv 115 ll 116 hh 117 ss 118 rr 119 hh 120 pp 121 gg 122 dd 123 ff 124 gg 125 aa 126 dd 127 aa 128 qq 129 gg 130 aa 131 mm 132 nn 133 kk 134 aa 135 ll 136 ee 137 ll 138 ff 139 rr 140 kk 141 dd 142 ii 143 aa 144 aa 145 kk 146 yy 147 kk 148 ee 149 ll 150 gg 151 yy 152 qq 153 gg 105m_ 0.01 38 010301 111011 1 153 1 vv 2 ll 3 ss 4 ee 5 gg 6 ee 7 ww 8 qq 9 ll 10 vv 11 ll 12 hh 13 vv 14 ww 15 aa 16 kk 17 vv 18 ee 19 aa 20 dd 21 vv 22 aa 23 gg 24 hh 25 gg 26 qq 27 dd 28 ii 29 ll 30 ii 31 rr 32 ll 33 ff 34 kk 35 ss 36 hh 37 pp 38 ee 39 tt 40 ll 41 ee 42 kk 43 ff 44 dd 45 rr 46 ff 47 kk 48 hh 49 ll 50 kk 51 tt 52 ee 53 aa 54 ee 55 mm 56 kk 57 aa 58 ss 59 ee 60 dd 61 ll 62 kk 63 kk 64 hh 65 gg 66 vv 67 tt 68 vv 69 ll 70 tt 71 aa 72 ll 73 gg 74 aa 75 ii 76 ll 77 kk 78 kk 79 kk 80 gg 81 hh 82 hh 83 ee 84 aa 85 ee 86 ll 87 kk 88 pp 89 ll 90 aa 91 qq 92 ss 93 hh 94 aa 95 tt 96 kk 97 hh 98 kk 99 ii 100 pp 101 ii 102 kk 103 yy 104 ll 105 ee 106 ff 107 ii 108 ss 109 ee 110 aa 111 ii 112 ii 113 hh 114 vv 115 ll 116 hh 117 ss 118 rr 119 hh 120 pp 121 gg 122 dd 123 ff 124 gg 125 aa 126 dd 127 aa 128 qq 129 gg 130 aa 131 mm 132 nn 133 kk 134 aa 135 ll 136 ee 137 ll 138 ff 139 rr 140 kk 141 dd 142 ii 143 aa 144 aa 145 kk 146 yy 147 kk 148 ee 149 ll 150 gg 151 yy 152 qq 153 gg 106m_ 0.01 38 010301 111011 0 153 0 mm 1 vv 2 ll 3 ss 4 ee 5 gg 6 ee 7 ww 8 qq 9 ll 10 vv 11 ll 12 hh 13 vv 14 ww 15 aa 16 kk 17 vv 18 ee 19 aa 20 dd 21 vv 22 aa 23 gg 24 hh 25 gg 26 qq 27 dd 28 ii 29 ll 30 ii 31 rr 32 ll 33 ff 34 kk 35 ss 36 hh 37 pp 38 ee 39 tt 40 ll 41 ee 42 kk 43 ff 44 dd 45 rr 46 ff 47 kk 48 hh 49 ll 50 kk 51 tt 52 ee 53 aa 54 ee 55 mm 56 kk 57 aa 58 ss 59 ee 60 dd 61 ll 62 kk 63 kk 64 hh 65 gg 66 vv 67 tt 68 ff 69 ll 70 tt 71 aa 72 ll 73 gg 74 aa 75 ii 76 ll 77 kk 78 kk 79 kk 80 gg 81 hh 82 hh 83 ee 84 aa 85 ee 86 ll 87 kk 88 pp 89 ll 90 aa 91 qq 92 ss 93 hh 94 aa 95 tt 96 kk 97 hh 98 kk 99 ii 100 pp 101 ii 102 kk 103 yy 104 ll 105 ee 106 ff 107 ii 108 ss 109 ee 110 aa 111 ii 112 ii 113 hh 114 vv 115 ll 116 hh 117 ss 118 rr 119 hh 120 pp 121 gg 122 nn 123 ff 124 gg 125 aa 126 dd 127 aa 128 qq 129 gg 130 aa 131 mm 132 nn 133 kk 134 aa 135 ll 136 ee 137 ll 138 ff 139 rr 140 kk 141 dd 142 ii 143 aa 144 aa 145 kk 146 yy 147 kk 148 ee 149 ll 150 gg 151 yy 152 qq 153 gg 107l_ 0.01 38 010301 111010 1 162 1 mm 2 nn 3 ii 4 ff 5 ee 6 mm 7 ll 8 rr 9 ii 10 dd 11 ee 12 gg 13 ll 14 rr 15 ll 16 kk 17 ii 18 yy 19 kk 20 dd 21 tt 22 ee 23 gg 24 yy 25 yy 26 tt 27 ii 28 gg 29 ii 30 gg 31 hh 32 ll 33 ll 34 tt 35 kk 36 ss 37 pp 38 ss 39 ll 40 nn 41 aa 42 aa 43 kk 44 gg 45 ee 46 ll 47 dd 48 kk 49 aa 50 ii 51 gg 52 rr 53 nn 54 tt 55 nn 56 gg 57 vv 58 ii 59 tt 60 kk 61 dd 62 ee 63 aa 64 ee 65 kk 66 ll 67 ff 68 nn 69 qq 70 dd 71 vv 72 dd 73 aa 74 aa 75 vv 76 rr 77 gg 78 ii 79 ll 80 rr 81 nn 82 aa 83 kk 84 ll 85 kk 86 pp 87 vv 88 yy 89 dd 90 ss 91 ll 92 dd 93 aa 94 vv 95 rr 96 rr 97 aa 98 aa 99 ll 100 ii 101 nn 102 mm 103 vv 104 ff 105 qq 106 mm 107 gg 108 ee 109 tt 110 gg 111 vv 112 aa 113 gg 114 ff 115 tt 116 nn 117 ss 118 ll 119 rr 120 mm 121 ll 122 qq 123 qq 124 kk 125 rr 126 ww 127 dd 128 ee 129 aa 130 aa 131 vv 132 nn 133 ll 134 aa 135 kk 136 ss 137 rr 138 ww 139 yy 140 nn 141 qq 142 tt 143 pp 144 nn 145 rr 146 aa 147 kk 148 rr 149 vv 150 ii 151 tt 152 tt 153 ff 154 rr 155 tt 156 gg 157 tt 158 ww 159 dd 160 aa 161 yy 162 kk E .n E .l 107m_ 0.01 38 010301 111011 0 153 0 mm 1 vv 2 ll 3 ss 4 ee 5 gg 6 ee 7 ww 8 qq 9 ll 10 vv 11 ll 12 hh 13 vv 14 ww 15 aa 16 kk 17 vv 18 ee 19 aa 20 dd 21 vv 22 aa 23 gg 24 hh 25 gg 26 qq 27 dd 28 ii 29 ll 30 ii 31 rr 32 ll 33 ff 34 kk 35 ss 36 hh 37 pp 38 ee 39 tt 40 ll 41 ee 42 kk 43 ff 44 dd 45 rr 46 ff 47 kk 48 hh 49 ll 50 kk 51 tt 52 ee 53 aa 54 ee 55 mm 56 kk 57 aa 58 ss 59 ee 60 dd 61 ll 62 kk 63 kk 64 hh 65 gg 66 vv 67 tt 68 ff 69 ll 70 tt 71 aa 72 ll 73 gg 74 aa 75 ii 76 ll 77 kk 78 kk 79 kk 80 gg 81 hh 82 hh 83 ee 84 aa 85 ee 86 ll 87 kk 88 pp 89 ll 90 aa 91 qq 92 ss 93 hh 94 aa 95 tt 96 kk 97 hh 98 kk 99 ii 100 pp 101 ii 102 kk 103 yy 104 ll 105 ee 106 ff 107 ii 108 ss 109 ee 110 aa 111 ii 112 ii 113 hh 114 vv 115 ll 116 hh 117 ss 118 rr 119 hh 120 pp 121 gg 122 nn 123 ff 124 gg 125 aa 126 dd 127 aa 128 qq 129 gg 130 aa 131 mm 132 nn 133 kk 134 aa 135 ll 136 ee 137 ll 138 ff 139 rr 140 kk 141 dd 142 ii 143 aa 144 aa 145 kk 146 yy 147 kk 148 ee 149 ll 150 gg 151 yy 152 qq 153 gg 108l_ 0.01 38 010301 111010 1 162 1 mm 2 nn 3 ii 4 ff 5 ee 6 mm 7 ll 8 rr 9 ii 10 dd 11 ee 12 gg 13 ll 14 rr 15 ll 16 kk 17 ii 18 yy 19 kk 20 dd 21 tt 22 ee 23 gg 24 yy 25 yy 26 tt 27 ii 28 gg 29 ii 30 gg 31 hh 32 ll 33 ll 34 tt 35 kk 36 ss 37 pp 38 ss 39 ll 40 nn 41 aa 42 aa 43 kk 44 ii 45 ee 46 ll 47 dd 48 kk 49 aa 50 ii 51 gg 52 rr 53 nn 54 tt 55 nn 56 gg 57 vv 58 ii 59 tt 60 kk 61 dd 62 ee 63 aa 64 ee 65 kk 66 ll 67 ff 68 nn 69 qq 70 dd 71 vv 72 dd 73 aa 74 aa 75 vv 76 rr 77 gg 78 ii 79 ll 80 rr 81 nn 82 aa 83 kk 84 ll 85 kk 86 pp 87 vv 88 yy 89 dd 90 ss 91 ll 92 dd 93 aa 94 vv 95 rr 96 rr 97 aa 98 aa 99 ll 100 ii 101 nn 102 mm 103 vv 104 ff 105 qq 106 mm 107 gg 108 ee 109 tt 110 gg 111 vv 112 aa 113 gg 114 ff 115 tt 116 nn 117 ss 118 ll 119 rr 120 mm 121 ll 122 qq 123 qq 124 kk 125 rr 126 ww 127 dd 128 ee 129 aa 130 aa 131 vv 132 nn 133 ll 134 aa 135 kk 136 ss 137 rr 138 ww 139 yy 140 nn 141 qq 142 tt 143 pp 144 nn 145 rr 146 aa 147 kk 148 rr 149 vv 150 ii 151 tt 152 tt 153 ff 154 rr 155 tt 156 gg 157 tt 158 ww 159 dd 160 aa 161 yy 162 kk E .n E .l 108m_ 0.01 38 010301 111011 0 153 0 mm 1 vv 2 ll 3 ss 4 ee 5 gg 6 ee 7 ww 8 qq 9 ll 10 vv 11 ll 12 hh 13 vv 14 ww 15 aa 16 kk 17 vv 18 ee 19 aa 20 dd 21 vv 22 aa 23 gg 24 hh 25 gg 26 qq 27 dd 28 ii 29 ll 30 ii 31 rr 32 ll 33 ff 34 kk 35 ss 36 hh 37 pp 38 ee 39 tt 40 ll 41 ee 42 kk 43 ff 44 dd 45 rr 46 ff 47 kk 48 hh 49 ll 50 kk 51 tt 52 ee 53 aa 54 ee 55 mm 56 kk 57 aa 58 ss 59 ee 60 dd 61 ll 62 kk 63 kk 64 hh 65 gg 66 vv 67 tt 68 ff 69 ll 70 tt 71 aa 72 ll 73 gg 74 aa 75 ii 76 ll 77 kk 78 kk 79 kk 80 gg 81 hh 82 hh 83 ee 84 aa 85 ee 86 ll 87 kk 88 pp 89 ll 90 aa 91 qq 92 ss 93 hh 94 aa 95 tt 96 kk 97 hh 98 kk 99 ii 100 pp 101 ii 102 kk 103 yy 104 ll 105 ee 106 ff 107 ii 108 ss 109 ee 110 aa 111 ii 112 ii 113 hh 114 vv 115 ll 116 hh 117 ss 118 rr 119 hh 120 pp 121 gg 122 nn 123 ff 124 gg 125 aa 126 dd 127 aa 128 qq 129 gg 130 aa 131 mm 132 nn 133 kk 134 aa 135 ll 136 ee 137 ll 138 ff 139 rr 140 kk 141 dd 142 ii 143 aa 144 aa 145 kk 146 yy 147 kk 148 ee 149 ll 150 gg 151 yy 152 qq 153 gg 109l_ 0.01 38 010301 111010 1 162 1 mm 2 nn 3 ii 4 ff 5 ee 6 mm 7 ll 8 rr 9 ii 10 dd 11 ee 12 gg 13 ll 14 rr 15 ll 16 kk 17 ii 18 yy 19 kk 20 dd 21 tt 22 ee 23 gg 24 yy 25 yy 26 tt 27 ii 28 gg 29 ii 30 gg 31 hh 32 ll 33 ll 34 tt 35 kk 36 ss 37 pp 38 ss 39 ll 40 nn 41 aa 42 aa 43 kk 44 kk 45 ee 46 ll 47 dd 48 kk 49 aa 50 ii 51 gg 52 rr 53 nn 54 tt 55 nn 56 gg 57 vv 58 ii 59 tt 60 kk 61 dd 62 ee 63 aa 64 ee 65 kk 66 ll 67 ff 68 nn 69 qq 70 dd 71 vv 72 dd 73 aa 74 aa 75 vv 76 rr 77 gg 78 ii 79 ll 80 rr 81 nn 82 aa 83 kk 84 ll 85 kk 86 pp 87 vv 88 yy 89 dd 90 ss 91 ll 92 dd 93 aa 94 vv 95 rr 96 rr 97 aa 98 aa 99 ll 100 ii 101 nn 102 mm 103 vv 104 ff 105 qq 106 mm 107 gg 108 ee 109 tt 110 gg 111 vv 112 aa 113 gg 114 ff 115 tt 116 nn 117 ss 118 ll 119 rr 120 mm 121 ll 122 qq 123 qq 124 kk 125 rr 126 ww 127 dd 128 ee 129 aa 130 aa 131 vv 132 nn 133 ll 134 aa 135 kk 136 ss 137 rr 138 ww 139 yy 140 nn 141 qq 142 tt 143 pp 144 nn 145 rr 146 aa 147 kk 148 rr 149 vv 150 ii 151 tt 152 tt 153 ff 154 rr 155 tt 156 gg 157 tt 158 ww 159 dd 160 aa 161 yy 162 kk E .n E .l 109m_ 0.01 38 010301 111011 0 153 0 mm 1 vv 2 ll 3 ss 4 ee 5 gg 6 ee 7 ww 8 qq 9 ll 10 vv 11 ll 12 hh 13 vv 14 ww 15 aa 16 kk 17 vv 18 ee 19 aa 20 dd 21 vv 22 aa 23 gg 24 hh 25 gg 26 qq 27 dd 28 ii 29 ll 30 ii 31 rr 32 ll 33 ff 34 kk 35 ss 36 hh 37 pp 38 ee 39 tt 40 ll 41 ee 42 kk 43 ff 44 dd 45 rr 46 ff 47 kk 48 hh 49 ll 50 kk 51 tt 52 ee 53 aa 54 ee 55 mm 56 kk 57 aa 58 ss 59 ee 60 dd 61 ll 62 kk 63 kk 64 hh 65 gg 66 vv 67 tt 68 vv 69 ll 70 tt 71 aa 72 ll 73 gg 74 aa 75 ii 76 ll 77 kk 78 kk 79 kk 80 gg 81 hh 82 hh 83 ee 84 aa 85 ee 86 ll 87 kk 88 pp 89 ll 90 aa 91 qq 92 ss 93 hh 94 aa 95 tt 96 kk 97 hh 98 kk 99 ii 100 pp 101 ii 102 kk 103 yy 104 ll 105 ee 106 ff 107 ii 108 ss 109 ee 110 aa 111 ii 112 ii 113 hh 114 vv 115 ll 116 hh 117 ss 118 rr 119 hh 120 pp 121 gg 122 nn 123 ff 124 gg 125 aa 126 dd 127 aa 128 qq 129 gg 130 aa 131 mm 132 nn 133 kk 134 aa 135 ll 136 ee 137 ll 138 ff 139 rr 140 kk 141 dd 142 ii 143 aa 144 aa 145 kk 146 yy 147 kk 148 ee 149 ll 150 gg 151 yy 152 qq 153 gg weblogo-3.8.0/tests/data/ssearch/000077500000000000000000000000001467613320200166675ustar00rootroot00000000000000weblogo-3.8.0/tests/data/ssearch/fasta_out_compact.txt000066400000000000000000000112221467613320200231210ustar00rootroot00000000000000# /Users/gec/Work/StringKernal/Junk/fasta/fasta34 -m 9 -d 0 -Q single.fa testset.fa FASTA searches a protein or DNA sequence data bank version 3.4t24 June 23, 2004 Please cite: W.R. Pearson & D.J. Lipman PNAS (1988) 85:2444-2448 Query library single.fa vs testset.fa library searching testset.fa library 1>>>d1pfsa_ 2.24.6.1.2 Gene V protein [Pseudomonas phage pf3] - 78 aa vs testset.fa library opt E() < 20 0 0: 22 0 0: one = represents 1 library sequences 24 0 0: 26 0 0: 28 0 0: 30 0 0: 32 0 0: 34 0 1:* 36 5 3:==*== 38 0 5: * 40 7 6:=====*= 42 7 8:=======* 44 10 8:=======*== 46 7 9:======= * 48 7 8:=======* 50 7 8:=======* 52 9 7:======*== 54 4 6:==== * 56 4 5:====* 58 5 4:===*= 60 5 3:==*== 62 1 3:= * 64 3 2:=*= 66 1 2:=* 68 2 1:*= 70 2 1:*= 72 2 1:*= 74 1 1:* 76 0 0: 78 3 0:=== 80 0 0: 82 0 0: 84 0 0: 86 0 0: 88 0 0: 90 0 0: 92 0 0: 94 0 0: 96 0 0: 98 0 0: 100 0 0: 102 0 0: 104 0 0: 106 0 0: 108 0 0: 110 0 0: 112 0 0: 114 0 0: 116 0 0: 118 0 0: >120 1 0:= 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 5.0980+/-0.0217; mu= 2.2844+/- 0.849 mean_var=62.2146+/-17.240, 0's: 0 Z-trim: 1 B-trim: 0 in 0/19 Lambda= 0.162603 Kolmogorov-Smirnov statistic: 0.0665 (N=20) at 56 FASTA (3.47 Mar 2004) function [optimized, BL50 matrix (15:-5)] ktup: 2 join: 36, opt: 24, gap-pen: -12/-2, width: 16 Scan time: 0.000 The best scores are: opt bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1pfsa_ 2.24.6.1.2 Gene V protein [Pseudomonas ph ( 78) 534 132.9 5.5e-35 1.000 1.000 534 78 1 78 1 78 1 78 1 78 0 0 0 d4ptp__ 2.29.1.2.1 Trypsin(ogen) [bovine (Bos tau ( 223) 52 20.1 1.4 0.429 0.857 52 14 51 64 1 78 8 21 1 223 0 0 0 d1fus__ 4.1.1.1.2 RNase F1 [Fusarium moniliforme] ( 106) 48 19.0 1.5 0.333 0.515 48 33 40 72 1 78 24 50 1 106 0 6 0 d1jbc__ 2.18.1.1.1 Concanavalin A [jack bean (Can ( 237) 52 20.1 1.5 0.361 0.556 52 36 23 52 1 78 190 225 1 237 6 0 0 d1cyo__ 4.62.1.1.1 Cytochrome b5 [bovine (Bos tau ( 88) 44 18.0 2.4 0.393 0.607 44 28 7 34 1 78 58 84 1 88 0 1 0 d2sga__ 2.29.1.1.2 Protease A [Streptomyces grise ( 181) 46 18.7 3.1 0.381 0.714 46 21 2 22 1 78 36 56 1 181 0 0 0 d1ckaa_ 2.20.2.1.1 C-Crk, N-terminal SH3 domain [ ( 57) 40 17.0 3.2 0.343 0.571 40 35 24 57 1 78 20 53 1 57 1 1 0 d1rgea_ 4.1.1.1.1 RNase Sa [Streptomyces aureofac ( 96) 42 17.6 3.5 0.400 0.560 42 25 33 53 1 78 25 49 1 96 4 0 0 d2olba_ 3.68.1.1.1 Oligo-peptide binding protein ( 517) 50 19.9 3.9 0.367 0.633 50 30 48 77 1 78 312 340 1 517 0 1 0 d1pls__ 2.35.1.1.5 Pleckstrin, N-terminal domain ( 113) 42 17.6 4 0.368 0.737 42 19 15 33 1 78 72 90 1 113 0 0 0 d1burs_ 4.35.1.1.2 Ribulose 1,5-bisphosphate carb ( 123) 41 17.4 5.1 0.357 0.536 41 28 49 73 1 78 20 47 1 123 3 0 0 d1ifc__ 2.39.1.2.2 Intestinal fatty acid binding ( 131) 40 17.2 6.2 0.278 0.667 40 18 9 26 1 78 34 51 1 131 0 0 0 d1lkka_ 4.47.1.1.1 p56-lck tyrosine kinase [human ( 105) 38 16.6 7.1 0.312 0.625 38 32 35 64 1 78 23 54 1 105 2 0 0 d8rxna_ 7.34.3.1.1 Rubredoxin [Desulfovibrio vulg ( 52) 34 15.5 7.6 0.353 0.647 34 17 56 71 1 78 15 31 1 52 1 0 0 d1lcpa2 3.50.1.3.1 (160-484) Leucine aminopeptida ( 325) 43 18.1 8 0.290 0.613 43 31 36 66 1 78 283 312 1 325 0 1 0 d1ra9__ 3.51.1.1.1 Dihydrofolate reductase, proka ( 159) 38 16.7 9.9 0.267 0.550 38 60 19 76 1 78 51 109 1 159 2 1 0 >>>d1pfsa_, 78 aa vs testset.fa library 78 residues in 1 query sequences 13355 residues in 93 library sequences Scomplib [34t24] start: Tue Aug 15 22:58:37 2006 done: Tue Aug 15 22:58:37 2006 Total Scan time: 0.000 Total Display time: 0.010 Function used was FASTA [version 3.4t24 June 23, 2004] weblogo-3.8.0/tests/data/ssearch/megablast.xml000066400000000000000000001767551467613320200213750ustar00rootroot00000000000000 blastn BLASTN 2.2.14 [May-07-2006] Zheng Zhang, Scott Schwartz, Lukas Wagner, and Webb Miller (2000), "A greedy algorithm for aligning DNA sequences", J Comput Biol 2000; 7(1-2):203-14. nr 1_7499 Query1 675 10 1 -2 0 0 L; 1 1_7499 Query1 675 1 gi|343717|gb|M10217.1|XELMTCG Xenopus laevis mitochondrial DNA, complete genome M10217 17553 1 1247.61 675 0 1 675 9109 9783 1 1 675 675 0 675 ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTACTTCACTTCCACGACCATACCCTCATAGCCGTTTTTCTTATTAGTACGCTAGTTCTTTACATTATTACTATTATAATAACTACTAAACTAACTAATACAAACCTAATGGACGCACAAGAGATCGAAATAGTGTGAACTATTATACCAGCTATTAGCCTCATCATAATTGCCCTTCCATCCCTTCGTATCCTATATTTAATAGATGAAGTTAATGATCCACACTTAACAATTAAAGCAATCGGCCACCAATGATACTGAAGCTACGAATATACTAACTATGAGGATCTCTCATTTGACTCTTATATAATTCCAACTAATGACCTTACCCCTGGACAATTCCGGCTGCTAGAAGTTGATAATCGAATAGTAGTCCCAATAGAATCTCCAACCCGACTTTTAGTTACAGCCGAAGACGTCCTCCACTCGTGAGCTGTACCCTCCTTGGGTGTCAAAACAGATGCAATCCCAGGACGACTTCATCAAACATCATTTATTGCTACTCGTCCGGGAGTATTTTACGGACAATGTTCAGAAATTTGCGGAGCAAACCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCGCTAACCGACTTTGAAAACTGATCTTCATCA ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTACTTCACTTCCACGACCATACCCTCATAGCCGTTTTTCTTATTAGTACGCTAGTTCTTTACATTATTACTATTATAATAACTACTAAACTAACTAATACAAACCTAATGGACGCACAAGAGATCGAAATAGTGTGAACTATTATACCAGCTATTAGCCTCATCATAATTGCCCTTCCATCCCTTCGTATCCTATATTTAATAGATGAAGTTAATGATCCACACTTAACAATTAAAGCAATCGGCCACCAATGATACTGAAGCTACGAATATACTAACTATGAGGATCTCTCATTTGACTCTTATATAATTCCAACTAATGACCTTACCCCTGGACAATTCCGGCTGCTAGAAGTTGATAATCGAATAGTAGTCCCAATAGAATCTCCAACCCGACTTTTAGTTACAGCCGAAGACGTCCTCCACTCGTGAGCTGTACCCTCCTTGGGTGTCAAAACAGATGCAATCCCAGGACGACTTCATCAAACATCATTTATTGCTACTCGTCCGGGAGTATTTTACGGACAATGTTCAGAAATTTGCGGAGCAAACCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCGCTAACCGACTTTGAAAACTGATCTTCATCA ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 2 gi|4096592|gb|U33552.1|XLU33552 Xenopus laevis cytochrome c oxidase II mRNA, mitochondrial gene encoding mitochondrial protein, partial cds U33552 651 1 1044.48 565 0 24 672 9 651 1 1 622 622 6 649 TTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTACTTCACTTCCACGACCATACCCTCATAGCCGTTTTTCTTATTAGTACGCTAGTTCTTTACATTATTACTATTATAATAACTACTAAACTAACTAATACAAACCTAATGGACGCACAAGAGATCGAAATAGTGTGAACTATTATACCAGCTATTAGCCTCATCATAATTGCCCTTCCATCCCTTCGTATCCTATATTTAATAGATGAAGTTAATGATCCACACTTAACAATTAAAGCAATCGGCCACCAATGATACTGAAGCTACGAATATACTAACTATGAGGATCTCTCATTTGACTCTTATATAATTCCAACTAATGACCTTACCCCTGGACAATTCCGGCTGCTAGAAGTTGATAATCGAATAGTAGTCCCAATAGAATCTCCAACCCGACTTTTAGTTACAGCCGAAGACGTCCTCCACTCGTGAGCTGTACCCTCCTTGGGTGTCAAAACAGATGCAATCCCAGGACGACTTCATCAAACATCATTTATTGCTACTCGTCCGGGAGTATTTTACGGACAATGTTCAGAAATTTGCGGAGCAAACCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCGCTAACCGACTTTGAAAACTGATCTTCA TTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTACTTCACTTCCACGACCATACGCTCATAGCCGTTTTTCTTATTAGTACGCTAGTTCTTTATATCATCACCATTATAATAACTACTAAACTAACTAATTC-----TA-TGGACGCCCAAGAGATCGAAATAGTATGAACTATTATACCAGCCATTATCCTTATTATAATTGCCCTTCCATCCCTTCGTATTCTTTATTTAATGGATGAAGTTAATGATCCACACTTAACAATTAAAGCAATCGGCCACCAATGATACTGAAGCTACGAATATACTAACTATGAGGATCTCTCATTTGACTCTTATATAATTCCAACTAATGACCTTACCCCTGGACAATTCCGGCTGCTAGAAGTTGATAATCGAATAGTAGTCCCAATAGAATCTCCAACCCGACTTTTAGTTACAGCCGAAGACGTCCTCCACTCATGAGCTGTACCCTCCTTGGGCGTTAAAACAGATGCAATCCCAGGACGACTTCATCAAACATCATTTATTGCTACTCGTCCGGGAGTATTTTACGGACAATGTTCAGAAATTTGCGGAGCCAACCACAGCTTTATACCTATTGTAGTTGAAGCAGTACCGCTAGCCGACTTTGAAAACTGATCTTCA ||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||| || || || ||||||||||||||||||||||||||| | || ||||||| ||||||||||||||||| ||||||||||||||||| |||| ||| || |||||||||||||||||||||||||| || |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||| || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| |||||||||||||||||||||||| ||||||||||||||||||||||| 3 gi|55274401|gb|AY789013.1| Xenopus tropicalis mitochondrion, complete genome AY789013 17610 1 638.214 345 8.72929e-180 1 675 7111 7785 1 1 572 572 14 682 ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAA-TTACTT-CACTTCCACGACCATACCCTCATAGCCGTTTTTCTTATTAGTACGCTAGTTCTTTACATTATTACTATTATAATAACTACTAAACTAACTAATACAAAC-CTAATGGACGCACAAGAGATCGAAATAGTGTGAACTATTATACCAGCTATTAGCCTCATCATAATTGCCCTTCCATCCCTTCGTATCCTATAT-TTAATAGATGAAGTTAATGATCCACA-CTTAACAATTAAAGCAATCGGCCACCAATGATACTGAAGCTACGAATATACTAACTATGAGGATCTCTCATTTGACTCTTATATAATTCCAACTAATGACCTTACCCCTGGACAATTCCGGCTGCTAGAAGTTGATAATCGAATAGTAGT-CCCAATAGAATCTCCAACCCGACTTTTAGTTACAGCCGAAGACGTCCTCCACTCGTGAGCTGTACCC-TCCTTGGGTGTCAAAACAGATGCAATCCCAGGACGACTTCATCAAACATCATTTATTGCTACTCGTCCGGGAGTATTTTACGGACAATGTTCAGAAATTTGCGGAGCAAACCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCGCTAACCGACTTTGAAAACTGATCTTCATCA ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATGGAAGAACTT--TTGCACTTCCACGACCACACCCTCATAGCCGTATTCCTTATTAGTACGCTCGTTCTTTACATCATTACAATCATGATAACCACTAAACTAACCAACACCAACTCCA-TAGACGCCCAAGAAATCGAAATAGTTTGAACCATTATACCAGCAATTATCCTAATCATAATTGCCCTGCCGTCCCTACGAATTCTTTATCTTA-TAGACGAAGTAAATGACCCCCATCTTA-CAGTAAAAACAATCGGCCATCAATGATACTGAAGCTATGAATACACTAACTACGAAGACCTATCATTCGACTCGTACATAATCCCAACCAGCGATCTGACCCCAGGTCAATTCCGATTGTTAGAAGTCGACAACCGAATAGTAGTTCCCA-TGGAGTCTCCTATTCGGCTCTTAGTGACCGCTGAAGACGTTCTTCACTCCTGAGCTCT-CCCATCCTTCGGAGTAAAAACAGATGCTATCCCAGGACGACTTAATCAAACATCATTCATCGCCACTCGACCAGGAGTATTCTACGGACAATGCTCAGAAATTTGCGGAGCTAATCACAGCTTCATACCGATCGTAGTCGAAGCAGTCCCACTAAACGACTTCGAGAACTGATCTTCATCA |||||||||||||||||||||||||||||||||||||||||||||||||| |||||| || || |||||||||||||| |||||||||||||| || |||||||||||||| ||||||||||| ||||| || || ||||| ||||||||||| || || ||| | | | ||||| ||||| ||||||||||| ||||| ||||||||||| |||| ||| |||||||||||||| || ||||| || || || ||| ||| |||| ||||| ||||| || || |||| || | ||| |||||||||| ||||||||||||||||| ||||| |||||||| || || || ||||| ||||| || ||||| ||||| | || || ||||| || |||||||| || ||||||| || || ||||||||||| |||| | || ||||| | || || ||||| || || |||||||| || ||||| |||||| | ||| ||||| || || ||||||||||| ||||||||||||||| ||||||||||||| || || ||||| || |||||||| ||||||||||| ||||||||||||||||| || |||||||| ||||| || ||||| |||||||| || |||| |||||| || ||||||||||||||| 4 gi|56972345|gb|BC088071.1| Xenopus tropicalis cDNA clone IMAGE:7024642 BC088071 725 1 599.435 324 4.11922e-168 22 675 1 654 1 1 551 551 14 661 GGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAA-TTACTT-CACTTCCACGACCATACCCTCATAGCCGTTTTTCTTATTAGTACGCTAGTTCTTTACATTATTACTATTATAATAACTACTAAACTAACTAATACAAAC-CTAATGGACGCACAAGAGATCGAAATAGTGTGAACTATTATACCAGCTATTAGCCTCATCATAATTGCCCTTCCATCCCTTCGTATCCTATAT-TTAATAGATGAAGTTAATGATCCACA-CTTAACAATTAAAGCAATCGGCCACCAATGATACTGAAGCTACGAATATACTAACTATGAGGATCTCTCATTTGACTCTTATATAATTCCAACTAATGACCTTACCCCTGGACAATTCCGGCTGCTAGAAGTTGATAATCGAATAGTAGT-CCCAATAGAATCTCCAACCCGACTTTTAGTTACAGCCGAAGACGTCCTCCACTCGTGAGCTGTACCC-TCCTTGGGTGTCAAAACAGATGCAATCCCAGGACGACTTCATCAAACATCATTTATTGCTACTCGTCCGGGAGTATTTTACGGACAATGTTCAGAAATTTGCGGAGCAAACCACAGCTTTATACCAATTGTAGTTGAAGCAGTACCGCTAACCGACTTTGAAAACTGATCTTCATCA GGTTTTCAAGACGCAGCCTCTCCAATTATGGAAGAACTT--TTGCACTTCCACGACCACACCCTCATAGCCGTATTCCTTATTAGTACGCTCGTTCTTTACATCATTACAATCATGATAACCACTAAACTAACCAACACCAACTCCA-TAGACGCCCAAGAAATCGAAATAGTTTGAACCATTATACCAGCAATTATCCTAATCATAATTGCCCTGCCGTCCCTACGAATTCTTTATCTTA-TAGACGAAGTAAATGACCCCCATCTTA-CAGTAAAAACAATCGGCCATCAATGATACTGAAGCTATGAATACACTAACTACGAAGACCTATCATTCGACTCGTACATAATCCCAACCAGCGATCTGACCCCAGGTCAATTCCGATTGTTAGAAGTCGACAACCGAATAGTAGTTCCCA-TGGAGTCTCCTATTCGGCTCTTAGTGACCGCTGAAGACGTTCTTCACTCCTGAGCTCT-CCCATCCTTCGGAGTAAAAACAGATGCTATCCCAGGACGACTTAATCAAACATCATTCATCGCCACTCGACCAGGAGTATTCTACGGACAATGCTCAGAAATTTGCGGAGCTAATCACAGCTTCATACCGATCGTAGTCGAAGCAGTCCCACTAAACGACTTCGAGAACTGATCTTCATCA ||||||||||||||||||||||||||||| |||||| || || |||||||||||||| |||||||||||||| || |||||||||||||| ||||||||||| ||||| || || ||||| ||||||||||| || || ||| | | | ||||| ||||| ||||||||||| ||||| ||||||||||| |||| ||| |||||||||||||| || ||||| || || || ||| ||| |||| ||||| ||||| || || |||| || | ||| |||||||||| ||||||||||||||||| ||||| |||||||| || || || ||||| ||||| || ||||| ||||| | || || ||||| || |||||||| || ||||||| || || ||||||||||| |||| | || ||||| | || || ||||| || || |||||||| || ||||| |||||| | ||| ||||| || || ||||||||||| ||||||||||||||| ||||||||||||| || || ||||| || |||||||| ||||||||||| ||||||||||||||||| || |||||||| ||||| || ||||| |||||||| || |||| |||||| || ||||||||||||||| 5 gi|49066306|gb|AY659995.1| Ambystoma calforniense mitochondrion, complete genome AY659995 16374 1 516.336 279 4.26753e-143 1 636 7002 7637 1 1 526 526 18 645 ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTACTTCACTTCCACGACCATACCCTCATAGCCGTTTTTCTT-ATTAGTACGCT-AGTTCTTTACATTATTACTATTA-TAATAACTACTAAACTAACTAATACAAAC-CTAATGGACGCACAAGAGATCGAAATAGTGTGAACTATTATACCAGCTATTAGCCTCATCATAATTGCCCTTCCATCCCTTCGTATCCTATATTTAATAGATGAAGTTAATGATCCACACTTAACAATTAAAGCAATCGGCCACCAATGATACTGAAGCTACGAATATACTAACTATGAGGATCTC-TCATTTGACTCTTATATAATTCCAACT-AATGACCTTACC-CCTGGACAATTCCGGCTGCTAGAAGTTGATAATCGAATAGTAGTCCCAATAGAATCTCCAACCCGACTTTTAGTTACAGCCGAAGACGTCCTCCACTCGTGAGCTGTACCCTCCTTGGGTGTCAAAACAGATGCAATCCCAGGACGACTTCATCAAACATCATTTATTGC-TACTCGTCC-GGGAGTATTTTACGGACAATGTTCAGAAATTTGCGGAGCAAACCACAGCTTTATACCAATTGTAGTTGAA ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCACCAATCATGGAAGAACTACTTCATTTTCACGATCATGCCTTAATGGCCGTGTTT-TTGATTAGCAC-CTTAGTCCTTTACATTATTAC-AGTAATAATAACTACAAAATTAACTAACACTAATGCTA-TAGATGCACAAGAAATTGAAATAGTATGAACTATTATACCAGCCATTATTTTAATTGTAATTGCCCTACCTTCACTACGAATCTTATATTTAATAGATGAAATTAATGACCCGCACTTAACTGTTAAAGCAATTGGACATCAATGATACTGAAGTTACGAATATACGAATTATGATGATTTAGT-ATTTGACTCATACATGCTTCCAACACAAA-AC-TTAAATCCTGGTGAATTTCGACTACTGGAAGTGGATAATCGAATAGTTGTACCTATAGAATCCCCAATTCGAATATTAATTTCAGCGGAAGATGTTCTTCACTCATGAGCTATACCATCAATAGGAATTAAAACAGATGCCATCCCAGGGCGACTAAATCAAACAACCTTTATTGCCT-CTCGACCCGGG-GTTTTTTATGGTCAATGCTCAGAAATTTGCGGAGCAAACCACAGCTTTATACCAATTGTAGTTGAA ||||||||||||||||||||||||||||||||||||||||| ||||| || |||||| ||||||| || ||||| ||| || | || ||||| ||| || ||||| || || ||| |||||||||||||| | || |||||||||| ||| ||||||| || || ||| | || |||||||| || |||||||| ||||||||||||||||| |||| | || |||||||||| || || || || ||| ||||||||||||||||| ||||||| || |||||||| |||||||||| || || |||||||||||||| ||||||||||| || ||||| ||| | | ||||||||| || || ||||||| || || ||| ||||| |||| || || || ||||| |||||||||||||| || || |||||||| |||| ||| | ||| || |||| ||||| || || ||||| |||||| |||| || | || | ||||||||||| |||||||| ||||| |||||||| | |||||||| | |||| || ||| || ||||| || ||||| |||||||||||||||||||||||||||||||||||||||||||||||| 6 gi|49066264|gb|AY659992.1| Ambystoma tigrinum tigrinum mitochondrion, complete genome AY659992 16375 1 516.336 279 4.26753e-143 1 636 7003 7638 1 1 524 524 14 643 ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTACTTCACTTCCACGACCATACCCTCATAGCCGTTTTTCTTA-TTAGTACGCT-AGTTCTTTACATTATTACTATTA-TAATAACTACTAAACTAACTAATACAAAC-CTAATGGACGCACAAGAGATCGAAATAGTGTGAACTATTATACCAGCTATTAGCCTCATCATAATTGCCCTTCCATCCCTTCGTATCCTATATTTAATAGATGAAGTTAATGATCCACACTTAACAATTAAAGCAATCGGCCACCAATGATACTGAAGCTACGAATATACTAACTATGAGGATCTC-TCATTTGACTCTTATATAATTCCAACT-AATGACCTTACCCCTGGACAATTCCGGCTGCTAGAAGTTGATAATCGAATAGTAGTCCCAATAGAATCTCCAACCCGACTTTTAGTTACAGCCGAAGACGTCCTCCACTCGTGAGCTGTACCCTCCTTGGGTGTCAAAACAGATGCAATCCCAGGACGACTTCATCAAACATCATTTATTGCTACTCGTCC-GGGAGTATTTTACGGACAATGTTCAGAAATTTGCGGAGCAAACCACAGCTTTATACCAATTGTAGTTGAA ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCACCAATTATGGAGGAGCTACTTCATTTTCACGATCATGCCTTAATGGCCGTGTT-CTTAATTAGCAC-CTTAGTCCTTTACATTATTAC-AGTAATAATAACTACAAAACTAACTAACACTAATGCTA-TAGATGCACAAGAAATTGAAATAGTATGAACTATTATACCAGCCATTATTTTAATTGTAATCGCCCTACCTTCACTACGAATTTTATACTTAATAGATGAAATTAATGACCCGCACTTAACTGTTAAAGCAATTGGACATCAATGATACTGAAGTTATGAATATACAAATTATGATGATCTAGTG-TTTGACTCATATATACTTCCAACACAAA-ACCTAAATCCGGGGGAATTTCGGCTTCTTGAAGTAGATAACCGAATAGTTGTGCCAATAGAGTCCCCAATTCGAATATTAATTTCAGCAGAAGATGTCCTTCACTCATGAGCTATACCATCAATAGGAATTAAAACAGATGCCATCCCAGGGCGACTAAATCAAACAACTTTTATTGCTTCTCGACCAGGG-GTTTTTTATGGTCAATGCTCAGAAATTTGCGGAGCAAACCACAGCTTTATACCAATTGTAGTTGAA ||||||||||||||||||||||||||||||||||||||||| |||||||| || || ||||||| || ||||| ||| || | || ||||| || |||| |||| || || ||| |||||||||||||| | || |||||||||| ||||||||||| || || ||| | || |||||||| || |||||||| ||||||||||||||||| |||| | || |||| ||||| || || || || || |||| |||||||||||| ||||||| || |||||||| |||||||||| || || |||||||||||||| || |||||||| || ||||| ||||| | |||||||| |||||| ||||||| || |||| | || || |||| ||||| || ||||| ||||| |||||||| || |||||||| || |||| ||| | ||| || |||| ||||| ||||| ||||| |||||| |||| || | || | ||||||||||| |||||||| ||||| |||||||| | ||||||||| |||| || ||| || ||||| || ||||| |||||||||||||||||||||||||||||||||||||||||||||||| 7 gi|49066292|gb|AY659994.1| Ambystoma dumerilii mitochondrion, complete genome AY659994 16370 1 466.476 252 4.35907e-128 1 636 6999 7634 1 1 520 520 24 648 ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTACTTCACTTCCACGACCATACCCTCATAGCCGTTTTTCTTA-TTAGTACGCT-AGTTCTTTACATTATTACTATTA-TAATAACTACTAAACTAACTAATACAAAC-CTAATGGACGCACAAGAGATCGAAATAGTGTGAACTATTATACCAGCTATTAGCCTCATCATAATTGCCCTT-CCATCCCTTCGTATCCTATATTTAATAGATGAAGTTAATGATCCACACTTAACAATTAAAGCAATCGGCCACCAATGATACTGAAGCTACGAATATACTAACTATGAGGATCTC-TCATTTGACTCTTATATAATTCC-A-ACTAATGACCTTACC-CCTGGACAATTCCGGCTGCTAGAAGTTGATAATCGAATAGTAGTCCCAATAGAATCTCCAACCCGACTTTTAGT-TACAGCCGAAGACGTCCTCCACTCGTGAGCTGTACCCTCCTTGGGTGTCAAAACAGATGCAATCCCAGGACGACTTCATCAAACATCATTTATTGC-TACTCGTCCGGGAGTATTT-TACGGACAATGTTCAGAAATTTGCGGAGCAAACCACAGCTTTATACCAATTGTAGTTGAA ATGGCACATCCATCACAATTAGGTTTTCAAGACGCAGCCTCACCAATTATGGAAGAGCTACTTCATTTTCACGATCATGCATTAATGGCCGTGTT-CTTAATTAGCAC-CTTAGTCCTTTACATTATTAC-AGTAATAATAACCACAAAACTAACTAACACTAATGCTA-TAGATGCACAAGAAATTGAAATAGTATGAACTATTATACCAGCCATTATTTTAATTGTAATTGCC-TTACCTTCACTACGAATTTTATATTTAATAGATGAAATTAATGACCCGCACTTAACTGTTAAAGCAATTGGACATCAATGATATTGAAGTTATGAATACACAAACTATGATGATTTAGTG-TTTGACTCATATATACTTCCTACACAAA--AC-TTAAATCCGGGGGAATTTCGGCTTCTGGAAGTAGATAACCGAATAGTTGTACCTATAGAATCTCCAATTCGAATATTAATCT-CAGCGGAAGATGTCCTTCACTCATGAGCTATGCCGTCGATAGGAATTAAAACAGATGCTATTCCAGGGCGACTAAATCAAACAACTTTTATTGCCTCC-CGACCAGGTGT-TTTCTACGGTCAATGCTCAGAAATTTGCGGAGCAAACCACAGCTTTATACCAATTGTAGTTGAA |||||||| |||||||||||||||||||||||||||||||| |||||||| ||||| ||||||| || ||||| ||| | | || ||||| || |||| |||| || || ||| |||||||||||||| | || ||||||| || ||||||||||| || || ||| | || |||||||| || |||||||| ||||||||||||||||| |||| | || |||||||| || || || || || || ||||||||||||||||| ||||||| || |||||||| |||||||||| || || |||||||| ||||| || ||||| || |||||||| ||| | | |||||||| |||||| |||| | || || || ||| || || |||| ||||| || ||||| ||||| |||||||| || || ||||||||||||| ||| | ||| | | |||| ||||| ||||| ||||| |||||| | || || | || | ||||||||||| || ||||| ||||| |||||||| | |||||||| | | || || || || ||| ||||| ||||| |||||||||||||||||||||||||||||||||||||||||||||||| 8 gi|49066250|gb|AY659991.1| Ambystoma mexicanum mitochondrion, complete genome AY659991 16370 1 466.476 252 4.35907e-128 1 636 6999 7634 1 1 519 519 22 647 ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTACTTCACTTCCACGACCATACCCTCATAGCCGTTTTTCTTA-TTAGTACGCT-AGTTCTTTACATTATTACTATTA-TAATAACTACTAAACTAACTAATACAAAC-CTAATGGACGCACAAGAGATCGAAATAGTGTGAACTATTATACCAGCTATTAGCCTCATCATAATTGCCCTT-CCATCCCTTCGTATCCTATATTTAATAGATGAAGTTAATGATCCACACTTAACAATTAAAGCAATCGGCCACCAATGATACTGAAGCTACGAATATACTAACTATGAGGATCTCTCA-T-TT-GACTCTTATATAATTCCAACT-AATGACCTTACC-CCTGGACAATTCCGGCTGCTAGAAGTTGATAATCGAATAGTAGTCCCAATAGAATCTCCAACCCGACTTTTAGTTACAGCCGAAGACGTCCTCCACTCGTGAGCTGTACCCTCCTTGGGTGTCAAAACAGATGCAATCCCAGGACGACTTCATCAAACATCATTTATTGCTACTCGTCCGGGAGTATTT-TACGGACAATGTTCAGAAATTTGCGGAGCAAACCACAGCTTTATACCAATTGTAGTTGAA ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCACCAATTATGGAGGAGCTACTTCATTTTCACGATCATGCCTTAATGGCCGTGTT-CTTAATTAGCAC-CTTAGTCCTTTACATTATTAC-AGTAATAATAACTACAAAACTAACTAACACTAATGCTA-TAGATGCACAAGAAATTGAAATAGTATGAACTATTATACCAGCCATTATTTTAATTGTAATTGCC-TTACCTTCACTACGAATTTTATACTTAATAGATGAAATTAATGACCCTCACTTAACTGTTAAAGCAATTGGACATCAATGATATTGAAGTTATGAATACACAAATTACGATGA-CT-T-AGTGTTTGACTCATATATACTTCCAACACAAA-AC-TTAAATCCGGGGGAATTTCGGCTTCTGGAAGTAGATAACCGAATAGTTGTACCTATAGAGTCCCCAATTCGAATATTAATTTCAGCGGAAGATGTCCTTCACTCATGAGCTATACCATCAATAGGAATTAAAACAGATGCAATTCCAGGTCGACTAAATCAAACAACTTTTATTGCTTCCCGACCAGGTGT-TTTCTATGGTCAATGTTCAGAAATTTGCGGAGCAAACCATAGCTTTATACCAATTGTAGTTGAA ||||||||||||||||||||||||||||||||||||||||| |||||||| || || ||||||| || ||||| ||| || | || ||||| || |||| |||| || || ||| |||||||||||||| | || |||||||||| ||||||||||| || || ||| | || |||||||| || |||||||| ||||||||||||||||| |||| | || |||||||| || || || || || || |||| |||||||||||| ||||||| || |||||||| |||||||||| || || |||||||| ||||| || ||||| || || || || || || | | | || ||||| |||||| ||||||| || || ||| || || |||| ||||| || ||||| ||||| |||||||| || || ||||| || |||| ||| | ||| || |||| ||||| ||||| ||||| |||||| |||| || | || | |||||||||||||| ||||| ||||| |||||||| | ||||||||| | || || || || ||| || || ||||||||||||||||||||||||||||| |||||||||||||||||||||||| 9 gi|49066278|gb|AY659993.1| Ambystoma andersoni mitochondrion, complete genome AY659993 16370 1 455.396 246 9.43574e-125 1 636 6999 7634 1 1 518 518 24 648 ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTACTTCACTTCCACGACCATACCCTCATAGCCGTTTTTCTTA-TTAGTACGCT-AGTTCTTTACATTATTACTATTA-TAATAACTACTAAACTAACTAATACAAAC-CTAATGGACGCACAAGAGATCGAAATAGTGTGAACTATTATACCA-GCTATTAGCCTCATCATAATTGCCCTT-CCATCCCTTCGTATCCTATATTTAATAGATGAAGTTAATGATCCACACTTAACAATTAAAGCAATCGGCCACCAATGATACTGAAGCTACGAATATACTAACTATGAGGATCTCTCA-T-TT-GACTCTTATATAATTCCAACT-AATGACCTTACC-CCTGGACAATTCCGGCTGCTAGAAGTTGATAATCGAATAGTAGTCCCAATAGAATCTCCAACCCGACTTTTAGTTACAGCCGAAGACGTCCTCCACTCGTGAGCTGTACCCTCCTTGGGTGTCAAAACAGATGCAATCCCAGGACGACTTCATCAAACATCATTTATTGCTACTCGTCCGGGAGTATTT-TACGGACAATGTTCAGAAATTTGCGGAGCAAACCACAGCTTTATACCAATTGTAGTTGAA ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCACCAATTATGGAGGAGCTACTTCATTTTCACGATCATGCCTTAATGGCCGTGTT-CTTAATTAGCAC-CTTAGTCCTTTACATTATTAC-AGTAATAATAACTACAAAACTAACTAACACTAATGCTA-TAGATGCACAAGAAATTGGGATAGTATGAACTATTATACCACGCC-TTATTTTAATTGTAATTGCC-TTACCTTCACTACGAATTTTATACTTAATAGATGAAATTAATGACCCTCACTTAACTGTTAAAGCAATTGGACATCAATGATATTGAAGTTATGAATACACAAATTACGATGA-CT-T-AGTGTTTGACTCATATATACTTCCAACACAAA-AC-TTAAATCCGGGGGAATTTCGGCTTCTGGAAGTAGATAACCGAATAGTTGTACCTATAGAGTCCCCAATTCGAATATTAATTTCAGCGGAAGATGTCCTTCACTCATGAGCTATACCATCAATAGGAATTAAAACAGATGCAATCCCAGGTCGACTAAATCAAACAACTTTTATTGCTTCTCGACCAGGTGT-TTTCTATGGTCAATGTTCAGAAATTTGCGGAGCAAACCATAGCTTTATACCAATTGTAGTTGAA ||||||||||||||||||||||||||||||||||||||||| |||||||| || || ||||||| || ||||| ||| || | || ||||| || |||| |||| || || ||| |||||||||||||| | || |||||||||| ||||||||||| || || ||| | || |||||||| || | ||||| ||||||||||||||| || ||| | || |||||||| || || || || || || |||| |||||||||||| ||||||| || |||||||| |||||||||| || || |||||||| ||||| || ||||| || || || || || || | | | || ||||| |||||| ||||||| || || ||| || || |||| ||||| || ||||| ||||| |||||||| || || ||||| || |||| ||| | ||| || |||| ||||| ||||| ||||| |||||| |||| || | || | |||||||||||||||||||| ||||| |||||||| | ||||||||| |||| || || || ||| || || ||||||||||||||||||||||||||||| |||||||||||||||||||||||| 10 gi|44843533|emb|AJ584639.1| Ambystoma mexicanum complete mitochondrial genome AJ584639 16369 1 449.856 243 4.39002e-123 1 636 6998 7633 1 1 518 518 26 649 ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCTCCAATTATAGAAGAATTACTTCACTTCCACGACCATACCCTCATAGCCGTTTTTCTTA-TTAGTACGCT-AGTTCTTTACATTATTACTATTA-TAATAACTACTAAACTAACTAATACAAAC-CTAATGGACGCACAAGAGATCGAAATAGTGTGAACTATTATACCAGCT-ATTAGCCTCA-TCATAATTGCCCTT-CCATCCCTTCGTATCCTATATTTAATAGATGAAGTTAATGATCCACACTTAACAATTAAAGCAATCGGCCACCAATGATACTGAAGCTACGAATATACTAACTATGAGGATCTCTCA-T-TT-GACTCTTATATAATTCCAACT-AATGACCTTACC-CCTGGACAATTCCGGCTGCTAGAAGTTGATAATCGAATAGTAGTCCCAATAGAATCTCCAACCCGACTTTTAGTTACAGCCGAAGACGTCCTCCACTCGTGAGCTGTACCCTCCTTGGGTGTCAAAACAGATGCAATCCCAGGACGACTTCATCAAACATCATTTATTGCTACTCGTCCGGGAGTATTT-TACGGACAATGTTCAGAAATTTGCGGAGCAAACCACAGCTTTATACCAATTGTAGTTGAA ATGGCACACCCATCACAATTAGGTTTTCAAGACGCAGCCTCACCAATTATGGAGGAGCTACTTCATTTTCACGATCATGCCTTAATGGCCGTGTT-CTTAATTAGCAC-CTTAGTCCTTTACATTATTAC-AGTAATAATAACTACAAAACTAACTAACACTAATGCTA-TAGATGCACAAGAAATTGAAATAGTATGAACTATTATACCAGCCGA--AGTTTTAATTGTAATTGCC-TTACCTTCACTACGAATTTTATACTTAATAGATGAAATTAATGACCCTCACTTAACTGTTAAAGCAATTGGACATCAATGATATTGAAGTTATGAATACACAAATTACGATGA-CT-T-AGTGTTTGACTCATATATACTTCCAACACAAA-AC-TTAAATCCGGGGGAATTTCGGCTTCTGGAAGTAGATAACCGAATAGTTGTACCTATAGAGTCCCCAATTCGAATATTAATTTCAGCGGAAGATGTCCTTCACTCATGAGCTATACCATCAATAGGAATTAAAACAGATGCAATTCCAGGTCGACTAAATCAAACAACTTTTATTGCTTCCCGACCAGGTGT-TTTCTATGGTCAATGTTCAGAAATTTGCGGAGCAAACCATAGCTTTATACCAATTGTAGTTGAA ||||||||||||||||||||||||||||||||||||||||| |||||||| || || ||||||| || ||||| ||| || | || ||||| || |||| |||| || || ||| |||||||||||||| | || |||||||||| ||||||||||| || || ||| | || |||||||| || |||||||| ||||||||||||||||| | || | | | |||||||| || || || || || || |||| |||||||||||| ||||||| || |||||||| |||||||||| || || |||||||| ||||| || ||||| || || || || || || | | | || ||||| |||||| ||||||| || || ||| || || |||| ||||| || ||||| ||||| |||||||| || || ||||| || |||| ||| | ||| || |||| ||||| ||||| ||||| |||||| |||| || | || | |||||||||||||| ||||| ||||| |||||||| | ||||||||| | || || || || ||| || || ||||||||||||||||||||||||||||| |||||||||||||||||||||||| 4432516 928057554 0 0 0.620991 1.33271 1.12409 2 2_7499 Query2 675 1 gi|12772|emb|X61145.1|MIBPCG Balaenoptera physalus mitochondrial complete genome X61145 16398 1 1247.61 675 0 1 675 7472 8146 1 1 675 675 0 675 ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTCCTACACTTTCACGATCATACACTAATAATCGTTTTTCTAATTAGCTCTTTAGTTCTCTACATTATTACCCTAATGCTTACAACCAAATTAACACATACTAGTACAATAGACGCCCAAGAAGTAGAAACTGTCTGAACTATCCTCCCAGCCATTATCTTAATTTTAATTGCCTTGCCTTCATTACGGATCCTTTACATAATAGACGAAGTCAATAACCCCTCCCTCACTGTAAAAACAATAGGTCACCAATGATATTGAAGCTATGAGTATACCGACTACGAAGACCTAAGCTTCGACTCCTATATAATCCCAACATCAGACCTAAAGCCAGGAGAACTACGATTATTAGAAGTAGATAACCGAGTTGTCTTACCTATAGAAATAACAATCCGAATATTAGTCTCATCAGAAGACGTACTCCACTCATGGGCCGTACCCTCCTTGGGCCTAAAAACAGATGCAATCCCAGGACGCCTAAACCAAACAACCTTAATATCAACACGACCAGGCCTATTTTATGGACAATGCTCAGAGATCTGCGGCTCAAACCACAGTTTCATACCAATTGTCCTAGAACTAGTACCCCTAGAAGTCTTTGAAAAATGATCTGTATCA ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTCCTACACTTTCACGATCATACACTAATAATCGTTTTTCTAATTAGCTCTTTAGTTCTCTACATTATTACCCTAATGCTTACAACCAAATTAACACATACTAGTACAATAGACGCCCAAGAAGTAGAAACTGTCTGAACTATCCTCCCAGCCATTATCTTAATTTTAATTGCCTTGCCTTCATTACGGATCCTTTACATAATAGACGAAGTCAATAACCCCTCCCTCACTGTAAAAACAATAGGTCACCAATGATATTGAAGCTATGAGTATACCGACTACGAAGACCTAAGCTTCGACTCCTATATAATCCCAACATCAGACCTAAAGCCAGGAGAACTACGATTATTAGAAGTAGATAACCGAGTTGTCTTACCTATAGAAATAACAATCCGAATATTAGTCTCATCAGAAGACGTACTCCACTCATGGGCCGTACCCTCCTTGGGCCTAAAAACAGATGCAATCCCAGGACGCCTAAACCAAACAACCTTAATATCAACACGACCAGGCCTATTTTATGGACAATGCTCAGAGATCTGCGGCTCAAACCACAGTTTCATACCAATTGTCCTAGAACTAGTACCCCTAGAAGTCTTTGAAAAATGATCTGTATCA ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| 2 gi|62086580|dbj|AP006467.1| Megaptera novaeangliae mitochondrial DNA, complete genome AP006467 16398 1 1020.47 552 0 1 675 7065 7739 1 1 635 635 2 676 ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTCCTACACTTTC-ACGATCATACACTAATAATCGTTTTTCTAATTAGCTCTTTAGTTCTCTACATTATTACCCTAATGCTTACAACCAAATTAACACATACTAGTACAATAGACGCCCAAGAAGTAGAAACTGTCTGAACTATCCTCCCAGCCATTATCTTAATTTTAATTGCCTTGCCTTCATTACGGATCCTTTACATAATAGACGAAGTCAATAACCCCTCCCTCACTGTAAAAACAATAGGTCACCAATGATATTGAAGCTATGAGTATACCGACTACGAAGACCTAAGCTTCGACTCCTATATAATCCCAACATCAGACCTAAAGCCAGGAGAACTACGATTATTAGAAGTAGATAACCGAGTTGTCTTACCTATAGAAATAACAATCCGAATATTAGTCTCATCAGAAGACGTACTCCACTCATGGGCCGTACCCTCCTTGGGCCTAAAAACAGATGCAATCCCAGGACGCCTAAACCAAACAACCTTAATATCAACACGACCAGGCCTATTTTATGGACAATGCTCAGAGATCTGCGGCTCAAACCACAGTTTCATACCAATTGTCCTAGAACTAGTACCCCTAGAAGTCTTTGAAAAATGATCTGTATCA ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATTATAGAAGAACTCCTACA-TTTCCATGATCATACACTAATAATCGTTTTTCTAATTAGCTCCTTAGTCCTCTACATTATTACCCTGATACTTACAACCAAACTAACACATACTAGTACAATAGATGCCCAAGAAGTAGAAACTGTCTGAACCATCCTTCCAGCCATCATCTTAATTTTAATTGCCTTACCTTCCTTACGAATCCTTTACATGATAGACGAAGTCAATAACCCCTCCCTCACTGTAAAAACAATAGGCCACCAATGATACTGAAGCTATGAATATACTGACTACGAAGACCTAAGTTTCGACTCCTACATAATCCCAACACCAGACCTAAAACCAGGAGAGCTGCGATTATTAGAAGTAGATAACCGAGTTGTTTTACCCATAGAAATAACAATCCGAATATTAGTCTCATCAGAAGACGTACTCCACTCATGAGCCGTACCCTCCTTAGGCCTAAAAACGGATGCAATCCCAGGACGCCTAAACCAAACAACCTTAATATCAACACGACCAGGCCTATTCTACGGACAATGCTCAGAAATCTGCGGCTCAAACCATAGTTTTATACCAATTGTCCTAGAATTAGTACCCCTAGAAACCTTTGAAAAATGATCTGTATCA ||||||||||||||||||||||||||||||||||||||||||||||| |||||||| |||||||| |||| | ||||||||||||||||||||||||||||||||||| ||||| ||||||||||||||||| || |||||||||||| |||||||||||||||||||||| |||||||||||||||||||||||||| ||||| |||||||| |||||||||||||||||||| ||||| ||||| ||||||||||| |||||||||||||||||||||||||||||||||||||||||||| ||||||||||| ||||||||||| ||||| ||||||||||||||||| ||||||||||| |||||||||||| |||||||||| |||||||| || ||||||||||||||||||||||||||||| ||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| || |||||||||||||| ||||||||||||||||| ||||| |||||||||||||||||| |||||||||||||| |||||||||||||||||||||| 3 gi|414126|emb|X72204.1|MIBMCG Balaenoptera musculus mitochondrial DNA complete genome X72204 16402 1 931.832 504 0 1 675 7469 8143 1 1 619 619 2 676 ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTCCTACACTTTCACGATCATACACTAATAATCGTTTTTCTAATTAGCTCTTTAGTTCTCTACATTATTACCCTAATGCTTACAACCAAATTAACACATACTAGTACAATAGACGCCCAAGAAGTAGAAACTGTCTGAACTATCCTCCCAGCCATTATCTTAATTTTAATTGCCTTGCCTTCATTACGGATCCTTTACATAATAGACGAAGTCAATAACCCCTCCCTCACTGTAAAAACAATAGGTCACCAATGATATTGAAGCTATGAGTATACCGACTACGAAGACCTAAGCTTCGACTCCTATATAATCCCAACATCAGACCTAAAGCCAGGAGAACTACGATTATTAGAAGTAGATAACCGAGTTGTCTTACCTATAGAAATAACAATCCGAATATTAGTCTCATCAGAAGACGTACTCCACTCATGGGCCGTACCCTC-CTTGGGCCTAAAAACAGATGCAATCCCAGGACGCCTAAACCAAACAACCTTAATATCAACACGACCAGGCCTATTTTATGGACAATGCTCAGAGATCTGCGGCTCAAACCACAGTTTCATACCAATTGTCCTAGAACTAGTACCCCTAGAAGTCTTTGAAAAATGATCTGTATCA ATGGCATATCCATTCCAACTAGGCTTCCAAGATGCAACATCACCTATCATAGAAGAACTCCTACACTTTCACGACCACACATTAATAATTGTATTCCTAATTAGCTCCTTAGTTCTCTACATTATCACCCTAATACTTACAACCAAACTAACACATACTAGTACAATAGACGCCCAAGAAGTAGAAACTGTCTGAACTATCCTCCCAGCCATCATCTTAATTTTAATCGCCCTACCTTCCCTACGAATCCTCTATATAATAGACGAAGTCAACAACCCCTCCCTCACTGTAAAAACAATAGGCCACCAATGATATTGAAGCTATGAGTATACTGATTACGAAGACCTAAGCTTTGACTCTTACATAATCCCAACGTCAGACCTAAAGCCAGGAGAATTACGACTACTAGAAGTAGACAACCGAGTTGTCCTACCCATAGAAATAACAATCCGAATGCTAGTCTCATCAGAAGACGTACTCCACTCATGAGCCGTACCCTCTCTAGG-CCTAAAAACGGACGCAATCCCAGGACGTCTAAACCAAACAACCTTAATATCAACACGACCAGGCCTATTCTACGGACAATGCTCAGAAATCTGTGGCTCAAACCATAGTTTTATACCAATCGTCCTAGAACTAGTGCCCTTAGAATTCTTTGAAAAATGATCTGCATCA ||||||||||||||||||||||| |||||||||||| ||||||| ||||||||||| ||||||||||||||||| || ||| ||||||| || || ||||||||||| ||||||||||||||||| |||||||| |||||||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||| ||| | ||||| |||| ||||| || ||||||||||||||||| ||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| || ||||||||||||||||| ||||| || ||||||||||| ||||||||||||||||||||| ||||| || |||||||||| |||||||||||| |||| |||||||||||||||||||| ||||||||||||||||||||||||||||||| ||||||||||| || || ||||||||| || |||||||||||||| ||||||||||||||||||||||||||||||||||||||||| || |||||||||||||| ||||| ||||||||||| ||||| |||||||| |||||||||||||| ||| ||||| |||||||||||||||||| |||| 4 gi|62086636|dbj|AP006471.1| Eschrichtius robustus mitochondrial DNA, complete genome AP006471 16413 1 926.292 501 0 1 675 7062 7736 1 1 618 618 2 676 ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTCCTACACTTTCACGATCATACACTAATAATCGTTTTTCTAATTAGCTCTTTAGTTCTCTACATTATTACCCTAATGCTTACAACCAAATTAACACATACTAGTACAATAGACGCCCAAGAAGTAGAAACTGTCTGAACTATCCTCCCAGCCATTATCTTAATTTTAATTGCCTTGCCTTCATTACGGATCCTTTACATAATAGACGAAGTCAATAACCCCTCCCTCACTGTAAAAACAATAGGTCACCAATGATATTGAAGCTATGAGTATACCGACTACGAAGACCTAAGCTTCGACTCCTATATAATCCCAACATCAGACCTAAAGCCAGGAGAACTACGATTATTAGAAGTAGATAACCGAGTTGTCTTACCTATAGAAATAACAATCCGAATATTAGTCTCATCAGAAGACGTACTCCACTCATGGGCCGTACCCTCCTTGGGCCTAAAAACAGATGCAATCCCAGGACGCCTAAACCAAACAACCTTAATATCAACACGACCAGGCCTATTTTATGGACAATGCTCAGAGATCTGCGGCTCAAACCACAGTTTCATACCAATTGTCCTAGAACTAGTACCCCTAGA-AGTCTTTGAAAAATGATCTGTATCA ATGGCATACCCATTCCAACTAGGCTTCCAAGATGCAACATCACCCATTATAGAAGAACTCCTACACTTTCACGACCACACACTAATAATTGTTTTCCTAATTAGCTCTTTAGTTCTCTACATCATCACTCTAATACTTACAACCAAACTAACACACACCAGCACAATAGATGCCCAAGAAGTAGAGACCATCTGAACCATCCTCCCAGCTATCATCCTAATTTTAATTGCCCTGCCTTCCCTACGGATCCTTTATATAATAGACGAAGTCAACAACCCCTCCCTCACTGTAAAAACAATAGGCCACCAATGATACTGAAGTTATGAATATACCGACTACGAAGACCTAAGCTTCGACTCCTACATAATTCCAACATCAGATCTAAAGCCAGGAGAACTACGACTATTGGAAGTAGACAACCGAGTTGTTTTACCCATAGAAATAACAATCCGAATACTAGTCTCATCAGAAGACGTACTCCATTCATGAGCCGTACCCTCCTTAGGCCTAAAAACAGATGCAATCCCAGGGCGCCTAAACCAAACAACCTTAATATCAACGCGACCAGGCCTATTCTATGGACAATGTTCAGAAATCTGCGGCTCAAACCATAGTTTTATACCAATTGTCCTAGAACTAGTACCCCTAGAGATT-TTTGAAAAGTGATCTGCATCA |||||||| |||||||||||||| |||||||||||| |||||||||| |||||||| ||||||||||||||||| || ||||||||||| ||||| |||||||||||||||||||||||||| || || ||||| |||||||||||| ||||||| || || |||||||| |||||||||||||| || ||||||| ||||||||||| || ||| |||||||||||||| ||||||| ||||||||||||| ||||||||||||||||| ||||||||||||||||||||||||||||| ||||||||||| ||||| ||||| ||||||||||||||||||||||||||||||||||| ||||| ||||||||||| ||||||||||||||||||||| |||| |||||||| ||||||||||| ||||| ||||||||||||||||||||| ||||||||||||||||||||||||| ||||| |||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||||||||||||||| |||||||||||||| ||||||||||| ||||| ||||||||||||||||| ||||| |||||||||||||||||||||||||||||||| | | |||||||| ||||||| |||| 5 gi|38602445|emb|AJ554053.1|ERO554053 Eschrichtius robustus complete mitochondrial genome AJ554053 16412 1 926.292 501 0 1 675 7061 7735 1 1 618 618 2 676 ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTCCTACACTTTCACGATCATACACTAATAATCGTTTTTCTAATTAGCTCTTTAGTTCTCTACATTATTACCCTAATGCTTACAACCAAATTAACACATACTAGTACAATAGACGCCCAAGAAGTAGAAACTGTCTGAACTATCCTCCCAGCCATTATCTTAATTTTAATTGCCTTGCCTTCATTACGGATCCTTTACATAATAGACGAAGTCAATAACCCCTCCCTCACTGTAAAAACAATAGGTCACCAATGATATTGAAGCTATGAGTATACCGACTACGAAGACCTAAGCTTCGACTCCTATATAATCCCAACATCAGACCTAAAGCCAGGAGAACTACGATTATTAGAAGTAGATAACCGAGTTGTCTTACCTATAGAAATAACAATCCGAATATTAGTCTCATCAGAAGACGTACTCCACTCATGGGCCGTACCCTCCTTGGGCCTAAAAACAGATGCAATCCCAGGACGCCTAAACCAAACAACCTTAATATCAACACGACCAGGCCTATTTTATGGACAATGCTCAGAGATCTGCGGCTCAAACCACAGTTTCATACCAATTGTCCTAGAACTAGTACCCCTAGA-AGTCTTTGAAAAATGATCTGTATCA ATGGCATACCCATTCCAACTAGGCTTCCAAGATGCAACATCACCCATTATAGAAGAACTCCTACACTTTCACGACCACACACTAATAATTGTTTTCCTAATTAGCTCTTTAGTTCTCTACATCATCACTCTAATACTTACAACCAAACTAACACACACCAGCACAATAGATGCCCAAGAAGTAGAGACCATCTGAACCATCCTCCCAGCTATCATCCTAATTTTAATTGCCCTGCCTTCCCTACGGATCCTTTATATAATAGACGAAGTCAACAACCCCTCCCTCACTGTAAAAACAATAGGCCACCAATGATACTGAAGTTATGAATATACCGACTACGAAGACCTAAGCTTCGACTCCTACATAATTCCAACATCAGATCTAAAGCCAGGAGAACTACGACTATTGGAAGTAGACAACCGAGTTGTTTTACCCATAGAAATAACAATCCGAATACTAGTCTCATCAGAAGACGTACTCCATTCATGAGCCGTACCCTCCTTAGGCCTAAAAACAGATGCAATCCCAGGGCGCCTAAACCAAACAACCTTAATATCAACGCGACCAGGCCTATTCTATGGACAATGTTCAGAAATCTGCGGCTCAAACCATAGTTTTATACCAATTGTCCTAGAACTAGTACCCCTAGAGATT-TTTGAAAAGTGATCTGCATCA |||||||| |||||||||||||| |||||||||||| |||||||||| |||||||| ||||||||||||||||| || ||||||||||| ||||| |||||||||||||||||||||||||| || || ||||| |||||||||||| ||||||| || || |||||||| |||||||||||||| || ||||||| ||||||||||| || ||| |||||||||||||| ||||||| ||||||||||||| ||||||||||||||||| ||||||||||||||||||||||||||||| ||||||||||| ||||| ||||| ||||||||||||||||||||||||||||||||||| ||||| ||||||||||| ||||||||||||||||||||| |||| |||||||| ||||||||||| ||||| ||||||||||||||||||||| ||||||||||||||||||||||||| ||||| |||||||||||||| |||||||||||||||||||||||||| ||||||||||||||||||||||||||||| |||||||||||||| ||||||||||| ||||| ||||||||||||||||| ||||| |||||||||||||||||||||||||||||||| | | |||||||| ||||||| |||| 6 gi|62086622|dbj|AP006470.1| Balaenoptera borealis mitochondrial DNA, complete genome AP006470 16410 1 909.672 492 0 1 675 7058 7732 1 1 614 614 0 675 ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTCCTACACTTTCACGATCATACACTAATAATCGTTTTTCTAATTAGCTCTTTAGTTCTCTACATTATTACCCTAATGCTTACAACCAAATTAACACATACTAGTACAATAGACGCCCAAGAAGTAGAAACTGTCTGAACTATCCTCCCAGCCATTATCTTAATTTTAATTGCCTTGCCTTCATTACGGATCCTTTACATAATAGACGAAGTCAATAACCCCTCCCTCACTGTAAAAACAATAGGTCACCAATGATATTGAAGCTATGAGTATACCGACTACGAAGACCTAAGCTTCGACTCCTATATAATCCCAACATCAGACCTAAAGCCAGGAGAACTACGATTATTAGAAGTAGATAACCGAGTTGTCTTACCTATAGAAATAACAATCCGAATATTAGTCTCATCAGAAGACGTACTCCACTCATGGGCCGTACCCTCCTTGGGCCTAAAAACAGATGCAATCCCAGGACGCCTAAACCAAACAACCTTAATATCAACACGACCAGGCCTATTTTATGGACAATGCTCAGAGATCTGCGGCTCAAACCACAGTTTCATACCAATTGTCCTAGAACTAGTACCCCTAGAAGTCTTTGAAAAATGATCTGTATCA ATGGCATATCCATTTCAACTAGGCTTCCAAGACGCAACATCACCCATTATAGAAGAACTCCTACACTTTCACGACCATACATTAATAATCGTATTTCTAATTAGCTCTTTAGTTCTCTACATTATTACCCTAATACTTACAACCAAACTAACACATACCAGCACAATAGATGCCCAAGAAGTAGAAACCGTCTGAACCATCCTCCCAGCCATCATCTTAATCCTAATCGCCTTACCCTCCCTACGGATCCTTTACATAATAGACGAAGTCAACAACCCCTCCCTCACTGTAAAAACAATAGGCCACCAATGATATTGAAGCTACGAATATACTGACTATGAAGACCTAAGTTTTGACTCTTACATAATCCCAACGTCAGATCTAAAACCAGGAGAACTACGACTATTAGAGGTAGACAACCGAGTTATTTTACCCATAGAAATAACGATCCGAATACTAGTCTCATCAGAAGACGTACTCCACTCATGAGCCGTACCCTCCCTAGGCCTAAAAACGGATGCAATCCCAGGACGCCTAAATCAAACAACCCTAATATCAACACGACCAGGCCTATTCTATGGACAATGCTCAGAAATCTGTGGCTCAAACCATAGTTTTATACCAATTGTACTAGAATTAGTACCCCTAGAAATCTTCGAAAAATGATCTGCATCA |||||||||||||| |||||||| |||||||| ||| |||||||||| |||||||| ||||||||||||||||| |||||| |||||||||| ||||||||||||||||||||||||||||||||||||||||| |||||||||||| |||||||||| || |||||||| ||||||||||||||||| |||||||| |||||||||||||| |||||||| |||| ||||| || || ||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||| |||||||||||||||||||| || ||||| ||||| ||||||||||| || ||||| || ||||||||||| ||||| ||||| ||||||||||||||| ||||||| ||||| ||||||||| | ||||| ||||||||||| ||||||||| ||||||||||||||||||||||||||||||| |||||||||||| | ||||||||||| ||||||||||||||||||||||| ||||||||| ||||||||||||||||||||||||| ||||||||||||||||| ||||| ||||||||||| ||||| ||||||||||| |||||| |||||||||||||| |||| ||||||||||||| |||| 7 gi|38602459|emb|AJ554054.1|BAC554054 Balaenoptera acutorostrata complete mitochondrial genome AJ554054 16417 1 904.132 489 0 1 675 7062 7736 1 1 613 613 0 675 ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTCCTACACTTTCACGATCATACACTAATAATCGTTTTTCTAATTAGCTCTTTAGTTCTCTACATTATTACCCTAATGCTTACAACCAAATTAACACATACTAGTACAATAGACGCCCAAGAAGTAGAAACTGTCTGAACTATCCTCCCAGCCATTATCTTAATTTTAATTGCCTTGCCTTCATTACGGATCCTTTACATAATAGACGAAGTCAATAACCCCTCCCTCACTGTAAAAACAATAGGTCACCAATGATATTGAAGCTATGAGTATACCGACTACGAAGACCTAAGCTTCGACTCCTATATAATCCCAACATCAGACCTAAAGCCAGGAGAACTACGATTATTAGAAGTAGATAACCGAGTTGTCTTACCTATAGAAATAACAATCCGAATATTAGTCTCATCAGAAGACGTACTCCACTCATGGGCCGTACCCTCCTTGGGCCTAAAAACAGATGCAATCCCAGGACGCCTAAACCAAACAACCTTAATATCAACACGACCAGGCCTATTTTATGGACAATGCTCAGAGATCTGCGGCTCAAACCACAGTTTCATACCAATTGTCCTAGAACTAGTACCCCTAGAAGTCTTTGAAAAATGATCTGTATCA ATGGCATATCCATTTCAATTAGGCTTCCAAGATGCAACATCACCTATTATAGAAGAACTCCTACACTTTCATGACCACACACTAATAATCGTCTTCCTAATTAGCTCCCTAGTCCTATACATTATTACCCTGATACTCACGACCAAACTAACACACACCAGTACTATAGACGCCCAGGAAGTAGAGACCGTTTGAACTATCCTTCCAGCCATCATCCTAATTTTAATCGCCCTACCTTCCTTACGAATCCTTTACATAATAGACGAAGTTAATAACCCCTCCCTCACTGTAAAAACAATGGGCCACCAATGATACTGAAGCTACGAATATACTGACTACGAAGACCTAAGCTTCGACTCTTACATAATCCCAACATCAGATCTAAAACCAGGAGAACTACGATTATTAGAAGTAGATAATCGAGTTGTCTTACCCATAGAAATAACAATCCGAATACTAGTCTCATCAGAAGACGTACTACACTCATGAGCCGTACCCTCCCTAGGCCTAAAAACAGATGCAATCCCAGGACGCCTAAACCAAACAACCTTAATATCAACACGACCAGGCCTATTCTATGGACAGTGCTCAGAAATCTGCGGCTCAAACCACAGTTTTATACCAATTGTCCTAGAAATGGTACCCCTAGAAATCTTTGAAAAATGATCTGCATCA |||||||||||||| ||| |||| |||||||||||| ||||||| || |||||||| |||||||||||||| || || |||||||||||||| || ||||||||||| |||| || |||||||||||||| || || || |||||| ||||||| || ||||| ||||||||||| |||||||| || || ||||||||||| |||||||| ||| |||||||||| ||| | ||||| ||||| ||||||||||||||||||||||| ||||||||||||||||||||||||||||| || ||||||||||| |||||||| || ||||| |||||||||||||||||||||||||| || ||||||||||||||||| ||||| |||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||| |||||||||||||||||||||| |||||||| |||||||||||| | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||| |||||||| ||||||||||||||||||||||| |||||||||||||||||| | |||||||||||| |||||||||||||||||| |||| 8 gi|62086594|dbj|AP006468.1| Balaenoptera bonaerensis mitochondrial DNA, complete genome AP006468 16416 1 898.592 486 0 1 675 7061 7735 1 1 612 612 0 675 ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTCCTACACTTTCACGATCATACACTAATAATCGTTTTTCTAATTAGCTCTTTAGTTCTCTACATTATTACCCTAATGCTTACAACCAAATTAACACATACTAGTACAATAGACGCCCAAGAAGTAGAAACTGTCTGAACTATCCTCCCAGCCATTATCTTAATTTTAATTGCCTTGCCTTCATTACGGATCCTTTACATAATAGACGAAGTCAATAACCCCTCCCTCACTGTAAAAACAATAGGTCACCAATGATATTGAAGCTATGAGTATACCGACTACGAAGACCTAAGCTTCGACTCCTATATAATCCCAACATCAGACCTAAAGCCAGGAGAACTACGATTATTAGAAGTAGATAACCGAGTTGTCTTACCTATAGAAATAACAATCCGAATATTAGTCTCATCAGAAGACGTACTCCACTCATGGGCCGTACCCTCCTTGGGCCTAAAAACAGATGCAATCCCAGGACGCCTAAACCAAACAACCTTAATATCAACACGACCAGGCCTATTTTATGGACAATGCTCAGAGATCTGCGGCTCAAACCACAGTTTCATACCAATTGTCCTAGAACTAGTACCCCTAGAAGTCTTTGAAAAATGATCTGTATCA ATGGCATATCCATTTCAATTAGGCTTCCAAGATGCAACATCACCTATTATAGAAGAACTCCTACACTTTCATGACCACACACTAATAATCGTCTTCCTAATTAGCTCCCTAGTCCTATATATTATTACCCTGATACTCACGACCAAACTAACACACACCAGTACTATAGACGCCCAGGAAGTAGAGACCGTTTGAACTATCCTTCCAGCCATCATCCTAATTTTAATCGCCCTACCTTCCTTACGAATCCTTTACATAATAGACGAAGTTAATAACCCCTCCCTCACTGTAAAAACAATGGGCCACCAATGATACTGAAGCTACGAATATACTGACTACGAAGACCTAAGCTTCGACTCTTACATAATCCCAACATCAGATCTAAAACCAGGAGAACTACGATTATTAGAAGTAGATAATCGAGTTGTCTTACCCATAGAAATAACAATCCGAATACTAGTCTCATCAGAAGACGTACTACACTCATGAGCCGTACCCTCCCTAGGCCTAAAAACAGATGCAATCCCAGGACGCCTAAACCAAACAACCTTAATATCAACACGACCAGGCCTATTCTATGGACAGTGCTCAGAAATCTGCGGCTCAAACCACAGTTTTATACCAATTGTCCTAGAAATGGTACCCCTAGAAATCTTTGAAAAATGATCTGCATCA |||||||||||||| ||| |||| |||||||||||| ||||||| || |||||||| |||||||||||||| || || |||||||||||||| || ||||||||||| |||| || || ||||||||||| || || || |||||| ||||||| || ||||| ||||||||||| |||||||| || || ||||||||||| |||||||| ||| |||||||||| ||| | ||||| ||||| ||||||||||||||||||||||| ||||||||||||||||||||||||||||| || ||||||||||| |||||||| || ||||| |||||||||||||||||||||||||| || ||||||||||||||||| ||||| |||||||||||||||||||||||||||||||| |||||||||||||| ||||||||||||||||||||| |||||||||||||||||||||| |||||||| |||||||||||| | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||| |||||||| ||||||||||||||||||||||| |||||||||||||||||| | |||||||||||| |||||||||||||||||| |||| 9 gi|62086566|dbj|AP006466.1| Balaenoptera bonaerensis mitochondrial DNA, complete genome AP006466 16421 1 889.359 481 0 1 670 7060 7729 1 1 608 608 2 671 ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTCCTACACTTTCACGATCATACACTAATAATCGTTTTTCTAATTAGCTCTTTAGTTCTCTACATTATTACCCTAATGCTTACAACCAAATTAACACATACTAGTACAATAGACGCCCAAGAAGTAGAAACTGTCTGAACTATCCTCCCAGCCATTATCTTAATTTTAATTGCCTTGCCTTCATTACGGATCCTTTACATAATAGACGAAGTCAATAACCCCTCCCTCACTGTAAAAACAATAGGTCACCAATGATATTGAAGCTATGAGTATACCGACTACGAAGACCTAAGCTTCGACTCCTATATAATCCCAACATCAGACCTAAAGCCAGGAGAACTACGATTATTAGAAGTAGATAACCGAGTTGTCTTACCTATAGAAATAACAATCCGAATATTAGTCTCATCAGAAGACGTACTCCACTCATGGGCCGTACCCTC-CTTGGGCCTAAAAACAGATGCAATCCCAGGACGCCTAAACCAAACAACCTTAATATCAACACGACCAGGCCTATTTTATGGACAATGCTCAGAGATCTGCGGCTCAAACCACAGTTTCATACCAATTGTCCTAGAACTAGTACCCCTAGAAGTCTTTGAAAAATGATCTG ATGGCATATCCATTTCAATTAGGCTTCCAAGATGCAACATCACCTATTATAGAAGAACTCCTACACTTTCATGACCACACACTAATAATCGTCTTCCTAATTAGCTCCCTAGTCCTATATATCATTACCCTAATACTCACGACCAAACTAACACATACCAGTACTATAGACGCCCAGGAAGTAGAAACCATTTGAACCATCCTTCCAGCCATCATCCTAATCTTAATCGCCCTACCTTCCTTACGAATCCTTTACATGATAGACGAAGTTAATAATCCCTCCCTCACTGTAAAAACAATGGGCCACCAATGATACTGAAGCTACGAATATACTGACTACGAAGACCTAAGCTTCGACTCTTACATAATCCCAACATCAGACCTAAAGCCAGGAGAACTACGATTATTAGAAGTAGATAATCGAGTTGTCTTACCTATAGAAATAACAATCCGAATACTAGTCTCATCAGAAGACGTACTACACTCATGAGCCGTACCCTCTCTAGG-CCTAAAAACAGATGCAATCCCAGGACGCCTAAACCAAACAACCTTAATGTCAACACGACCAGGCCTATTCTATGGACAGTGCTCAGAGATCTGCGGCTCAAACCACAGTTTTATACCGATTGTCCTAGAATTAGTACCCCTAGAAATCTTTGAAAAATGATCTG |||||||||||||| ||| |||| |||||||||||| ||||||| || |||||||| |||||||||||||| || || |||||||||||||| || ||||||||||| |||| || || || ||||||||||| || || |||||| |||||||||| ||||| ||||||||||| ||||||||||| | ||||| ||||| |||||||| ||| |||| ||||| ||| | ||||| ||||| ||||||||||| ||||||||||| ||||| ||||||||||||||||||||||| || ||||||||||| |||||||| || ||||| |||||||||||||||||||||||||| || |||||||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||| |||||||||||||||||||||| |||||||| ||||||||||| || || |||||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||| |||||||| |||||||||||||||||||||||||||||||| ||||| |||||||||||| |||||||||||||| |||||||||||||||||| 10 gi|90265620|dbj|AB201257.1| Balaenoptera omurai mitochondrial DNA, complete genome, isolate:NSMT-32992 AB201257 16404 1 887.512 480 0 1 675 7052 7726 1 1 611 611 2 676 ATGGCATATCCATTCCAACTAGGTTTCCAAGATGCAGCATCACCCATCATAGAAGAGCTCCTACACTTTCACGATCATACACTAATAATCGTTTTTCTAATTAGCTCTTTAGTTCTCTACATTATTACCCTAATGCTTACAACCAAATTAACACATACTAGTACAATAGACGCCCAAGAAGTAGAAACTGTCTGAACTATCCTCCCAGCCATTATCTTAATTTTAATTGCCTTGCCTTCATTACGGATCCTTTACATAATAGACGAAGTCAATAACCCCTCCCTCACTGTAAAAACAATAGGTCACCAATGATATTGAAGCTATGAGTATACCGACTACGAAGACCTAAGCTTCGACTCCTATATAATCCCAACATCAGACCTAAAGCCAGGAGAACTACGATTATTAGAAGTAGATAACCGAGTTGTCTTACCTATAGAAATAACAATCCGAATATTAGTCTCATCAGAAGACGTACTCCACTCATGGGCCGTACCCTCCTTGGGCCTAAAAACAGATGCAATCCCAGGACGCCTAAACCAAACAACCTTAATATCAACACGACCAGGCCTATTTTATGGACAATGCTCAGAGATCTGCGGCTCAAACCACAGTTTCATACCAATTGTCCTAGAACTAGTACCCCTAGAAGTCTTT-GAAAAATGATCTGTATCA ATGGCATATCCATTTCAACTAGGCTTCCAAGATGCAACATCACCCATCATAGAAGAACTCCTACATTTTCACGACCATACATTAATAATTGTCTTCCTAATTAGCTCTTTGGTTCTCTATATTATTACCCTAATACTTACAACCAAACTAACACACACTAGCACAATAGATGCTCAAGAAGTAGAGACCGTCTGAACCATCCTTCCAGCCATTATCCTAATTTTAATCGCCTTACCTTCCCTACGAATCCTCTACATGATAGACGAAGTCAACAATCCTTCCCTCACTGTAAAAACAATGGGTCACCAATGATATTGAAGCTATGAATATACTGACTATGAAGACCTAAATTTCGACTCTTACATAATCCCAACATCAGATTTAAAACCAGGAGAACTACGATTACTAGAAGTAGATAACCGAGTTGTTTTACCCATAGAAATAACAATCCGAATACTAGTCTCATCAGAAGACGTACTCCACTCATGGGCCGTACCCTCCCTGGGTCTAAAAACGGATGCAATCCCAGGACGCCTGAACCAAACAACCCTAATATCAACACGACCTGGCCTATTCTATGGCCAATGCTCAGAAATCTGTGGCTCAAACCACAGTTTTATACCAATTGTCCTAGAATTAGTACCCCTAGAAAT-TTTCGAAAAGTGATCTGCATCA |||||||||||||| |||||||| |||||||||||| ||||||||||||||||||| |||||||| |||||||| |||||| ||||||| || || |||||||||||||| |||||||| |||||||||||||| |||||||||||| ||||||| ||||| |||||||| || ||||||||||| || |||||||| ||||| |||||||||||| |||||||||| ||||| ||||| |||| ||||| ||||| |||||||||||||| || || |||||||||||||||||||| |||||||||||||||||||||||||| ||||| ||||| |||||||||| |||||||| || ||||||||||||||||| |||| |||||||||||||||||| |||||||||||||||||||||| ||||| ||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||||| |||| |||||||| |||||||||||||||||||| |||||||||||| |||||||||||||||| |||||||| ||||| ||||||||||| ||||| ||||||||||||||||| |||||||||||||||||| |||||||||||||| | ||| ||||| ||||||| |||| 4432516 928057554 0 0 0.620991 1.33271 1.12409 weblogo-3.8.0/tests/data/ssearch/ssearch_out.txt000066400000000000000000000376641467613320200217670ustar00rootroot00000000000000# ssearch34 -Q single.fa testset.fa SSEARCH searches a sequence data bank version 3.4t24 June 23, 2004 Please cite: T. F. Smith and M. S. Waterman, (1981) J. Mol. Biol. 147:195-197; W.R. Pearson (1991) Genomics 11:635-650 Query library single.fa vs testset.fa library searching testset.fa library 1>>>d1pfsa_ 2.24.6.1.2 Gene V protein [Pseudomonas phage pf3] - 78 aa vs testset.fa library opt E() < 20 0 0: 22 0 0: one = represents 1 library sequences 24 0 0: 26 0 0: 28 0 0: 30 0 0: 32 2 0:== 34 0 1:* 36 2 3:==* 38 3 5:=== * 40 4 6:==== * 42 2 8:== * 44 9 8:=======*= 46 10 9:========*= 48 8 8:=======* 50 8 8:=======* 52 5 7:===== * 54 8 6:=====*== 56 5 5:====* 58 7 4:===*=== 60 2 3:==* 62 4 3:==*= 64 3 2:=*= 66 2 2:=* 68 1 1:* 70 1 1:* 72 1 1:* 74 1 1:* 76 1 0:= 78 2 0:== 80 1 0:= 82 0 0: 84 0 0: 86 0 0: 88 0 0: 90 0 0: 92 0 0: 94 0 0: 96 0 0: 98 0 0: 100 0 0: 102 0 0: 104 0 0: 106 0 0: 108 0 0: 110 0 0: 112 0 0: 114 0 0: 116 0 0: 118 0 0: >120 1 0:= 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 7.2437+/-0.0204; mu= -3.4950+/- 0.925 mean_var=32.6334+/- 9.107, 0's: 0 Z-trim: 1 B-trim: 0 in 0/19 Lambda= 0.224514 Kolmogorov-Smirnov statistic: 0.1096 (N=24) at 42 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.020 The best scores are: s-w bits E(93) d1pfsa_ 2.24.6.1.2 Gene V protein [Pseudomonas ph ( 78) 534 177.3 2.4e-48 d1fus__ 4.1.1.1.2 RNase F1 [Fusarium moniliforme] ( 106) 48 19.6 0.97 d4ptp__ 2.29.1.2.1 Trypsin(ogen) [bovine (Bos tau ( 223) 52 20.2 1.3 d1jbc__ 2.18.1.1.1 Concanavalin A [jack bean (Can ( 237) 52 20.2 1.5 d1cyo__ 4.62.1.1.1 Cytochrome b5 [bovine (Bos tau ( 88) 44 18.5 1.8 d1ckaa_ 2.20.2.1.1 C-Crk, N-terminal SH3 domain [ ( 57) 40 17.6 2.1 d1rgea_ 4.1.1.1.1 RNase Sa [Streptomyces aureofac ( 96) 42 17.7 3.1 d2sga__ 2.29.1.1.2 Protease A [Streptomyces grise ( 181) 46 18.5 3.6 d1pls__ 2.35.1.1.5 Pleckstrin, N-terminal domain ( 113) 42 17.6 4.1 d1burs_ 4.35.1.1.2 Ribulose 1,5-bisphosphate carb ( 123) 41 17.2 5.8 d8rxna_ 7.34.3.1.1 Rubredoxin [Desulfovibrio vulg ( 52) 34 15.7 6.9 d2olba_ 3.68.1.1.1 Oligo-peptide binding protein ( 517) 50 18.8 7.9 d1xsoa_ 2.1.7.1.3 Cu,Zn superoxide dismutase, SOD ( 150) 41 17.0 7.9 d1ifc__ 2.39.1.2.2 Intestinal fatty acid binding ( 131) 40 16.8 8 d1lkka_ 4.47.1.1.1 p56-lck tyrosine kinase [human ( 105) 38 16.4 8.7 d3sdhb_ 1.1.1.1.1 Hemoglobin I [ark clam (Scaphar ( 145) 40 16.7 9.3 >>d1pfsa_ 2.24.6.1.2 Gene V protein [Pseudomonas phage p (78 aa) s-w opt: 534 Z-score: 935.7 bits: 177.3 E(): 2.4e-48 Smith-Waterman score: 534; 100.000% identity (100.000% similar) in 78 aa overlap (1-78:1-78) 10 20 30 40 50 60 d1pfsa MNIQITFTDSVRQGTSAKGNPYTFQEGFLHLEDKPHPLQCQFFVESVIPAGSYQVPYRIN :::::::::::::::::::::::::::::::::::::::::::::::::::::::::::: d1pfsa MNIQITFTDSVRQGTSAKGNPYTFQEGFLHLEDKPHPLQCQFFVESVIPAGSYQVPYRIN 10 20 30 40 50 60 70 d1pfsa VNNGRPELAFDFKAMKRA :::::::::::::::::: d1pfsa VNNGRPELAFDFKAMKRA 70 >>d1fus__ 4.1.1.1.2 RNase F1 [Fusarium moniliforme] (106 aa) s-w opt: 48 Z-score: 81.0 bits: 19.6 E(): 0.97 Smith-Waterman score: 48; 33.333% identity (51.515% similar) in 33 aa overlap (40-72:24-50) 10 20 30 40 50 60 d1pfsa SVRQGTSAKGNPYTFQEGFLHLEDKPHPLQCQFFVESVIPAGSYQVPYRINVNNGRPELA ::.. .. ::: :. : .: d1fus_ XSATTCGSTNYSASQVRAAANAACQYY-QNDDTAGSSTYPHTYNNYEG----- 10 20 30 40 70 d1pfsa FDFKAMKRA ::: d1fus_ FDFPVDGPYQEFPIKSGGVYTGGSPGADRVVINTNCEYAGAITHTGASGNNFVGCSGTN 50 60 70 80 90 100 >>d4ptp__ 2.29.1.2.1 Trypsin(ogen) [bovine (Bos taurus)] (223 aa) s-w opt: 52 Z-score: 78.6 bits: 20.2 E(): 1.3 Smith-Waterman score: 52; 42.857% identity (85.714% similar) in 14 aa overlap (51-64:8-21) 30 40 50 60 70 d1pfsa PYTFQEGFLHLEDKPHPLQCQFFVESVIPAGSYQVPYRINVNNGRPELAFDFKAMKRA :. :::....:.: d4ptp_ IVGGYTCGANTVPYQVSLNSGYHFCGGSLINSQWVVS 10 20 30 d4ptp_ AAHCYKSGIQVRLGEDNINVVEGNEQFISASKSIVHPSYNSNTLNNDIMLIKLKSAASLN 40 50 60 70 80 90 >>d1jbc__ 2.18.1.1.1 Concanavalin A [jack bean (Canavali (237 aa) s-w opt: 52 Z-score: 77.8 bits: 20.2 E(): 1.5 Smith-Waterman score: 52; 36.111% identity (55.556% similar) in 36 aa overlap (23-52:190-225) 10 20 30 40 d1pfsa MNIQITFTDSVRQGTSAKGNPYTFQEGFLHLEDKP--HPLQ-CQFFV---ES .:. : : .: :: . ::. .: d1jbc_ SSNGSPQGSSVGRALFYAPVHIWESSAVVASFEATFTFLIKSPDSHPADGIAFFISNIDS 160 170 180 190 200 210 50 60 70 d1pfsa VIPAGSYQVPYRINVNNGRPELAFDFKAMKRA ::.:: d1jbc_ SIPSGSTGRLLGLFPDAN 220 230 >>d1cyo__ 4.62.1.1.1 Cytochrome b5 [bovine (Bos taurus)] (88 aa) s-w opt: 44 Z-score: 76.4 bits: 18.5 E(): 1.8 Smith-Waterman score: 44; 39.286% identity (60.714% similar) in 28 aa overlap (7-34:58-84) 10 20 30 d1pfsa MNIQITFTDSVRQGTSAKGNPYTFQEGFLHLEDKPH : : : ..:.:. :: : :: .:. d1cyo_ KVYDLTKFLEEHPGGEEVLREQAGGDATENFED-VGHSTDARELSKTFIIGELHPDDRSK 30 40 50 60 70 80 40 50 60 70 d1pfsa PLQCQFFVESVIPAGSYQVPYRINVNNGRPELAFDFKAMKRA d1cyo_ IT >>d1ckaa_ 2.20.2.1.1 C-Crk, N-terminal SH3 domain [mouse (57 aa) s-w opt: 40 Z-score: 74.9 bits: 17.6 E(): 2.1 Smith-Waterman score: 40; 34.286% identity (57.143% similar) in 35 aa overlap (24-57:20-53) 10 20 30 40 50 d1pfsa MNIQITFTDSVRQGTSAKGNPYTFQEG-FLHLEDKPHPLQCQFFVESVIPAGSYQVPYRI :..: .:...:::. : .: : ::: d1ckaa AEYVRALFDFNGNDEEDLPFKKGDILRIRDKPEE-QWWNAEDSEGKRGMIPVPYVE 10 20 30 40 50 60 70 d1pfsa NVNNGRPELAFDFKAMKRA d1ckaa KY >>d1rgea_ 4.1.1.1.1 RNase Sa [Streptomyces aureofaciens] (96 aa) s-w opt: 42 Z-score: 71.8 bits: 17.7 E(): 3.1 Smith-Waterman score: 42; 40.000% identity (56.000% similar) in 25 aa overlap (33-53:25-49) 10 20 30 40 50 d1pfsa IQITFTDSVRQGTSAKGNPYTFQEGFLHLEDKPHPLQCQFFV----ESVIPAGSYQVPYR : : : . . : :::.:. :: d1rgea DVSGTVCLSALPPEATDTLNLIASDGPFPYSQDGVVFQNRESVLPTQSYGYYHE 10 20 30 40 50 60 70 d1pfsa INVNNGRPELAFDFKAMKRA d1rgea YTVITPGARTRGTRRIITGEATQEDYYTGDHYATFSLIDQTC 60 70 80 90 >>d2sga__ 2.29.1.1.2 Protease A [Streptomyces griseus, s (181 aa) s-w opt: 46 Z-score: 70.7 bits: 18.5 E(): 3.6 Smith-Waterman score: 46; 38.095% identity (71.429% similar) in 21 aa overlap (2-22:36-56) 10 20 30 d1pfsa MNIQITFTDSVRQGTSAKGNPYTFQEGFLHL ::. ... ..: ::: .: : d2sga_ AITTGGSRCSLGFNVSVNGVAHALTAGHCTNISASWSIGTRTGTSFPNNDYGIIRHSNPA 10 20 30 40 50 60 40 50 60 70 d1pfsa EDKPHPLQCQFFVESVIPAGSYQVPYRINVNNGRPELAFDFKAMKRA d2sga_ AADGRVYLYNGSYQDITTAGNAFVGQAVQRSGSTTGLRSGSVTGLNATVNYGSSGIVYGM 70 80 90 100 110 120 >>d1pls__ 2.35.1.1.5 Pleckstrin, N-terminal domain [Huma (113 aa) s-w opt: 42 Z-score: 69.7 bits: 17.6 E(): 4.1 Smith-Waterman score: 42; 36.842% identity (73.684% similar) in 19 aa overlap (15-33:72-90) 10 20 30 40 d1pfsa MNIQITFTDSVRQGTSAKGNPYTFQEGFLHLEDKPHPLQCQFFV :..: . . :: .::. .: d1pls_ NSPKGMIPLKGSTLTSPCQDFGKRMFVFKITTTKQQDHFFQAAFLEERDAWVRDINKAIK 50 60 70 80 90 100 50 60 70 d1pfsa ESVIPAGSYQVPYRINVNNGRPELAFDFKAMKRA d1pls_ CIEGLEHHHHHH 110 >>d1burs_ 4.35.1.1.2 Ribulose 1,5-bisphosphate carboxyla (123 aa) s-w opt: 41 Z-score: 66.9 bits: 17.2 E(): 5.8 Smith-Waterman score: 41; 35.714% identity (53.571% similar) in 28 aa overlap (49-73:20-47) 20 30 40 50 60 70 d1pfsa GNPYTFQEGFLHLEDKPHPLQCQFFVESVIPAGSYQVPYRIN---VNNGRPELAFDFKAM : . :. ..: ::: : : :. : d1burs MQVWPILGMKKYETLSYLPPLTTEQLLAEVNYLLVNNWIPCLEFEVKDG 10 20 30 40 d1pfsa KRA d1burs FVYREHLKSPGYYDGRYWTMWKLPMFGCTDPAQVLNELEECKKAYPDAFIRIIGFDNKRQ 50 60 70 80 90 100 >>d8rxna_ 7.34.3.1.1 Rubredoxin [Desulfovibrio vulgaris] (52 aa) s-w opt: 34 Z-score: 65.5 bits: 15.7 E(): 6.9 Smith-Waterman score: 34; 35.294% identity (64.706% similar) in 17 aa overlap (56-71:15-31) 30 40 50 60 70 d1pfsa EGFLHLEDKPHPLQCQFFVESVIPAGSYQVPYRINVNNG-RPELAFDFKAMKRA : . . .:: .: .:: d8rxna MKKYVCTVCGYEYDPAEGDPDNGVKPGTSFDDLPADWVCPVCGA 10 20 30 40 d8rxna PKSEFEAA 50 >>d2olba_ 3.68.1.1.1 Oligo-peptide binding protein (OPPA (517 aa) s-w opt: 50 Z-score: 64.4 bits: 18.8 E(): 7.9 Smith-Waterman score: 50; 36.667% identity (63.333% similar) in 30 aa overlap (48-77:312-340) 20 30 40 50 60 70 d1pfsa KGNPYTFQEGFLHLEDKPHPLQCQFFVESVIPAGSYQVPYRINVNNGRPELAFDFKAMKR .:: :: :: ... .:: : .. .:: d2olba APFNDVRVRTALKLALDRDIIVNKVKNQGDLPAYSYTPPYTDGAKLVEPEW-FKWSQQKR 290 300 310 320 330 340 d1pfsa A d2olba NEEAKKLLAEAGFTADKPLTFDLLYNTSDLHKKLAIAVASIWKKNLGVNVNLENQEWKTF 350 360 370 380 390 400 >>d1xsoa_ 2.1.7.1.3 Cu,Zn superoxide dismutase, SOD [Afr (150 aa) s-w opt: 41 Z-score: 64.4 bits: 17.0 E(): 7.9 Smith-Waterman score: 41; 30.769% identity (53.846% similar) in 39 aa overlap (31-66:36-72) 10 20 30 40 50 d1pfsa MNIQITFTDSVRQGTSAKGNPYTFQEGFLHLEDKPHPLQCQFFVESV---IPAGSYQVPY : : : .. . : ... . :::. : d1xsoa VLAGSGDVKGVVHFEQQDEGAVSVEGKIEGLTDGLHGFHIHVFGDNTNGCMSAGSHFNPE 10 20 30 40 50 60 60 70 d1pfsa RINVNNGRPELAFDFKAMKRA : :.: : d1xsoa --NKNHGAPGDTDRHVGDLGNVTAEGGVAQFKITDSLISLKGPNSIIGRTAVVHEKADDL 70 80 90 100 110 120 >>d1ifc__ 2.39.1.2.2 Intestinal fatty acid binding prote (131 aa) s-w opt: 40 Z-score: 64.3 bits: 16.8 E(): 8 Smith-Waterman score: 40; 27.778% identity (66.667% similar) in 18 aa overlap (9-26:34-51) 10 20 30 d1pfsa MNIQITFTDSVRQGTSAKGNPYTFQEGFLHLEDKPHPL :... . .:: .: .: d1ifc_ GTWKVDRNENYEKFMEKMGINVVKRKLGAHDNLKLTITQEGNKFTVKESSNFRNIDVVFE 10 20 30 40 50 60 40 50 60 70 d1pfsa QCQFFVESVIPAGSYQVPYRINVNNGRPELAFDFKAMKRA d1ifc_ LGVDFAYSLADGTELTGTWTMEGNKLVGKFKRVDNGKELIAVREISGNELIQTYTYEGVE 70 80 90 100 110 120 >>d1lkka_ 4.47.1.1.1 p56-lck tyrosine kinase [human (Hom (105 aa) s-w opt: 38 Z-score: 63.6 bits: 16.4 E(): 8.7 Smith-Waterman score: 38; 31.250% identity (62.500% similar) in 32 aa overlap (35-64:23-54) 10 20 30 40 50 60 d1pfsa ITFTDSVRQGTSAKGNPYTFQEGFLHLEDKPHPLQCQFFV-ESVIPAGSYQVPYR-INVN : . .:.. :: :::... : .. : d1lkka LEPEPWFFKNLSRKDAERQLLAPGNTHGSFLIRESESTAGSFSLSVRDFDQN 10 20 30 40 50 70 d1pfsa NGRPELAFDFKAMKRA .: d1lkka QGEVVKHYKIRNLDNGGFYISPRITFPGLHELVRHYTNASDGLCTRLSRPCQT 60 70 80 90 100 >>d3sdhb_ 1.1.1.1.1 Hemoglobin I [ark clam (Scapharca in (145 aa) s-w opt: 40 Z-score: 63.0 bits: 16.7 E(): 9.3 Smith-Waterman score: 40; 27.027% identity (54.054% similar) in 37 aa overlap (10-40:55-91) 10 20 30 d1pfsa MNIQITFTDSVRQGTSA---KGNPYTFQ---EGFLHLED .: :: . .:. :.. ..:. : d3sdhb GSDKKGNGVALMTTLFADNQETIGYFKRLGNVSQGMANDKLRGHSITLMYALQNFIDQLD 30 40 50 60 70 80 40 50 60 70 d1pfsa KPHPLQCQFFVESVIPAGSYQVPYRINVNNGRPELAFDFKAMKRA .: : : d3sdhb NPDDLVCVVEKFAVNHITRKISAAEFGKINGPIKKVLASKNFGDKYANAWAKLVAVVQAA 90 100 110 120 130 140 78 residues in 1 query sequences 13355 residues in 93 library sequences Scomplib [34t24] start: Tue Aug 15 22:46:28 2006 done: Tue Aug 15 22:46:28 2006 Total Scan time: 0.020 Total Display time: 0.010 Function used was SSEARCH [version 3.4t24 June 23, 2004] weblogo-3.8.0/tests/data/ssearch/ssearch_out_compact.txt000066400000000000000000000111731467613320200234600ustar00rootroot00000000000000# ssearch34 -m 9 -d 0 -Q single.fa testset.fa SSEARCH searches a sequence data bank version 3.4t24 June 23, 2004 Please cite: T. F. Smith and M. S. Waterman, (1981) J. Mol. Biol. 147:195-197; W.R. Pearson (1991) Genomics 11:635-650 Query library single.fa vs testset.fa library searching testset.fa library 1>>>d1pfsa_ 2.24.6.1.2 Gene V protein [Pseudomonas phage pf3] - 78 aa vs testset.fa library opt E() < 20 0 0: 22 0 0: one = represents 1 library sequences 24 0 0: 26 0 0: 28 0 0: 30 0 0: 32 2 0:== 34 0 1:* 36 2 3:==* 38 3 5:=== * 40 4 6:==== * 42 2 8:== * 44 9 8:=======*= 46 10 9:========*= 48 8 8:=======* 50 8 8:=======* 52 5 7:===== * 54 8 6:=====*== 56 5 5:====* 58 7 4:===*=== 60 2 3:==* 62 4 3:==*= 64 3 2:=*= 66 2 2:=* 68 1 1:* 70 1 1:* 72 1 1:* 74 1 1:* 76 1 0:= 78 2 0:== 80 1 0:= 82 0 0: 84 0 0: 86 0 0: 88 0 0: 90 0 0: 92 0 0: 94 0 0: 96 0 0: 98 0 0: 100 0 0: 102 0 0: 104 0 0: 106 0 0: 108 0 0: 110 0 0: 112 0 0: 114 0 0: 116 0 0: 118 0 0: >120 1 0:= 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 7.2437+/-0.0204; mu= -3.4950+/- 0.925 mean_var=32.6334+/- 9.107, 0's: 0 Z-trim: 1 B-trim: 0 in 0/19 Lambda= 0.224514 Kolmogorov-Smirnov statistic: 0.1096 (N=24) at 42 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.020 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1pfsa_ 2.24.6.1.2 Gene V protein [Pseudomonas ph ( 78) 534 177.3 2.4e-48 1.000 1.000 534 78 1 78 1 78 1 78 1 78 0 0 0 d1fus__ 4.1.1.1.2 RNase F1 [Fusarium moniliforme] ( 106) 48 19.6 0.97 0.333 0.515 48 33 40 72 1 78 24 50 1 106 0 6 0 d4ptp__ 2.29.1.2.1 Trypsin(ogen) [bovine (Bos tau ( 223) 52 20.2 1.3 0.429 0.857 52 14 51 64 1 78 8 21 1 223 0 0 0 d1jbc__ 2.18.1.1.1 Concanavalin A [jack bean (Can ( 237) 52 20.2 1.5 0.361 0.556 52 36 23 52 1 78 190 225 1 237 6 0 0 d1cyo__ 4.62.1.1.1 Cytochrome b5 [bovine (Bos tau ( 88) 44 18.5 1.8 0.393 0.607 44 28 7 34 1 78 58 84 1 88 0 1 0 d1ckaa_ 2.20.2.1.1 C-Crk, N-terminal SH3 domain [ ( 57) 40 17.6 2.1 0.343 0.571 40 35 24 57 1 78 20 53 1 57 1 1 0 d1rgea_ 4.1.1.1.1 RNase Sa [Streptomyces aureofac ( 96) 42 17.7 3.1 0.400 0.560 42 25 33 53 1 78 25 49 1 96 4 0 0 d2sga__ 2.29.1.1.2 Protease A [Streptomyces grise ( 181) 46 18.5 3.6 0.381 0.714 46 21 2 22 1 78 36 56 1 181 0 0 0 d1pls__ 2.35.1.1.5 Pleckstrin, N-terminal domain ( 113) 42 17.6 4.1 0.368 0.737 42 19 15 33 1 78 72 90 1 113 0 0 0 d1burs_ 4.35.1.1.2 Ribulose 1,5-bisphosphate carb ( 123) 41 17.2 5.8 0.357 0.536 41 28 49 73 1 78 20 47 1 123 3 0 0 d8rxna_ 7.34.3.1.1 Rubredoxin [Desulfovibrio vulg ( 52) 34 15.7 6.9 0.353 0.647 34 17 56 71 1 78 15 31 1 52 1 0 0 d2olba_ 3.68.1.1.1 Oligo-peptide binding protein ( 517) 50 18.8 7.9 0.367 0.633 50 30 48 77 1 78 312 340 1 517 0 1 0 d1xsoa_ 2.1.7.1.3 Cu,Zn superoxide dismutase, SOD ( 150) 41 17.0 7.9 0.308 0.538 41 39 31 66 1 78 36 72 1 150 3 2 0 d1ifc__ 2.39.1.2.2 Intestinal fatty acid binding ( 131) 40 16.8 8 0.278 0.667 40 18 9 26 1 78 34 51 1 131 0 0 0 d1lkka_ 4.47.1.1.1 p56-lck tyrosine kinase [human ( 105) 38 16.4 8.7 0.312 0.625 38 32 35 64 1 78 23 54 1 105 2 0 0 d3sdhb_ 1.1.1.1.1 Hemoglobin I [ark clam (Scaphar ( 145) 40 16.7 9.3 0.270 0.541 40 37 10 40 1 78 55 91 1 145 6 0 0 >>>d1pfsa_, 78 aa vs testset.fa library 78 residues in 1 query sequences 13355 residues in 93 library sequences Scomplib [34t24] start: Tue Aug 15 22:53:20 2006 done: Tue Aug 15 22:53:20 2006 Total Scan time: 0.020 Total Display time: 0.010 Function used was SSEARCH [version 3.4t24 June 23, 2004] weblogo-3.8.0/tests/data/ssearch/ssearch_out_compact2_dbvdb.txt000066400000000000000000001765321467613320200247160ustar00rootroot00000000000000# ssearch34 -H -m 9 -d 0 -Q shortset.fa testset.fa SSEARCH searches a sequence data bank version 3.4t24 June 23, 2004 Please cite: T. F. Smith and M. S. Waterman, (1981) J. Mol. Biol. 147:195-197; W.R. Pearson (1991) Genomics 11:635-650 Query library shortset.fa vs testset.fa library searching testset.fa library 1>>>d1cbn__ 7.11.1.1.1 Crambin [abyssinian cabbage (Crambe abyssinica)] - 46 aa vs testset.fa library 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 2.3138+/-0.0438; mu= 18.9049+/- 2.176 mean_var=37.1184+/-10.107, 0's: 0 Z-trim: 3 B-trim: 0 in 0/18 Lambda= 0.210513 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.010 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1cbn__ 7.11.1.1.1 Crambin [abyssinian cabbage (C ( 46) 338 106.1 2.3e-27 1.000 1.000 338 46 1 46 1 46 1 46 1 46 0 0 0 d1isua_ 7.29.1.1.1 HIPIP (high potential iron pro ( 62) 55 20.4 0.2 0.370 0.556 55 27 22 46 1 46 30 56 1 62 2 0 0 d2erl__ 1.10.1.1.1 ER-1 [Euplotes raikovi] ( 40) 51 18.8 0.37 0.364 0.591 51 22 23 41 1 46 16 37 1 40 3 0 0 d1arb__ 2.29.1.1.1 Achromobacter protease [Achrom ( 263) 53 20.8 0.6 0.364 0.568 53 44 6 45 1 46 68 110 1 263 4 1 0 d2eng__ 2.33.1.1.1 Endoglucanase V [Humicola inso ( 205) 47 18.8 1.9 0.333 0.519 47 27 18 44 1 46 137 163 1 205 0 0 0 d1fus__ 4.1.1.1.2 RNase F1 [Fusarium moniliforme] ( 106) 45 17.7 2.1 0.244 0.511 45 45 2 46 1 46 4 44 1 106 0 4 0 d1rie__ 7.35.1.2.1 The rieske iron-sulfur protein ( 127) 44 17.6 2.8 0.400 0.600 44 20 25 44 1 46 69 87 1 127 0 1 0 d3ebx__ 7.5.1.1.1 Erabutoxin B (also neurotoxin B ( 62) 42 16.4 3 0.357 0.464 42 28 19 41 1 46 19 44 1 62 5 2 0 e1ben.2c1 7.1.1.1.2 Insulin [human (Homo sapiens) ( 21) 38 14.4 4 0.400 0.600 38 15 3 16 1 46 6 20 1 21 1 0 0 d3pte__ 5.3.1.1.1 D-ala carboxypeptidase/transpep ( 347) 43 18.0 5.5 0.346 0.538 43 26 21 46 1 46 189 211 1 347 0 3 0 d5p21__ 3.24.1.3.1 cH-p21 Ras protein [human (Hom ( 166) 41 16.8 5.8 0.385 0.615 41 13 28 40 1 46 39 51 1 166 0 0 0 d1tpg_1 7.10.1.1.13 (51-91) Plasminogen activator ( 41) 37 14.6 6.8 0.375 0.625 37 16 4 19 1 46 12 26 1 41 0 1 0 d2sn3__ 7.3.6.1.1 scorpion toxin [Centruroides sc ( 65) 37 14.9 8.4 0.320 0.480 37 25 16 40 1 46 46 65 1 65 0 5 0 d2sga__ 2.29.1.1.2 Protease A [Streptomyces grise ( 181) 39 16.3 9.1 0.714 0.714 39 7 14 20 1 46 129 135 1 181 0 0 0 d1lcpa2 3.50.1.3.1 (160-484) Leucine aminopeptida ( 325) 40 17.0 9.7 0.409 0.636 40 22 23 42 1 46 182 203 1 325 2 0 0 d1tgxc_ 7.5.1.1.2 gamma-Cardiotoxin [snake (Naja ( 60) 36 14.6 9.9 0.241 0.448 36 29 14 41 1 46 19 43 1 60 1 4 0 >>>d1cbn__, 46 aa vs testset.fa library 2>>>d2erl__ 1.10.1.1.1 ER-1 [Euplotes raikovi] - 40 aa vs testset.fa library 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 3.3544+/-0.0208; mu= 9.6709+/- 0.998 mean_var=41.9829+/-15.940, 0's: 0 Z-trim: 1 B-trim: 5 in 1/17 Lambda= 0.197942 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.010 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d2erl__ 1.10.1.1.1 ER-1 [Euplotes raikovi] ( 40) 297 90.0 1.2e-22 1.000 1.000 297 40 1 40 1 40 1 40 1 40 0 0 0 d2sn3__ 7.3.6.1.1 scorpion toxin [Centruroides sc ( 65) 58 22.0 0.058 0.257 0.686 58 35 1 34 1 40 10 43 1 65 1 1 0 d1cbn__ 7.11.1.1.1 Crambin [abyssinian cabbage (C ( 46) 51 19.8 0.19 0.364 0.591 51 22 16 37 1 40 23 41 1 46 0 3 0 e1ben.2c1 7.1.1.1.2 Insulin [human (Homo sapiens) ( 21) 46 18.0 0.3 0.333 0.667 46 18 11 28 1 40 3 20 1 21 0 0 0 d7rsa__ 4.4.1.1.1 Ribonuclease A (also ribonuclea ( 124) 46 18.9 0.96 0.375 0.583 46 24 6 29 1 40 52 73 1 124 0 2 0 d1tpg_1 7.10.1.1.13 (51-91) Plasminogen activator ( 41) 42 17.2 1 0.308 0.538 42 26 3 28 1 40 12 34 1 41 0 3 0 d1lit__ 4.88.1.1.1 Lithostathine, inhibitor of st ( 131) 44 18.3 1.5 0.400 0.667 44 15 19 31 1 40 1 15 1 131 2 0 0 d3ebx__ 7.5.1.1.1 Erabutoxin B (also neurotoxin B ( 62) 41 17.1 1.6 0.259 0.519 41 27 9 35 1 40 7 31 1 62 0 2 0 d1bpi__ 7.6.1.1.1 Pancreatic trypsin inhibitor [b ( 58) 40 16.8 1.9 0.333 0.778 40 9 28 36 1 40 30 38 1 58 0 0 0 d1ptx__ 7.3.6.1.4 scorpion toxin [Androctonus aus ( 64) 39 16.5 2.5 0.324 0.588 39 34 10 39 1 40 16 49 1 64 4 0 0 d1isua_ 7.29.1.1.1 HIPIP (high potential iron pro ( 62) 38 16.2 2.9 0.250 0.625 38 16 22 37 1 40 19 34 1 62 0 0 0 d1poa__ 1.80.1.2.1 Snake phospholipase A2 [taiwan ( 118) 40 17.1 3 0.323 0.516 40 31 1 31 1 40 41 63 1 118 0 8 0 d1amm_1 2.9.1.1.1 (1-85) gamma-Crystallin [bovine ( 85) 38 16.4 3.6 0.300 0.500 38 30 9 30 1 40 14 43 1 85 8 0 0 d1amm_2 2.9.1.1.1 (86-174) gamma-Crystallin [bovi ( 89) 38 16.4 3.7 0.353 0.588 38 17 21 37 1 40 9 25 1 89 0 0 0 d1mla_2 4.31.18.1.1 (126-195) Probable ACP-bindin ( 70) 36 15.7 4.7 0.833 1.000 36 6 2 7 1 40 19 24 1 70 0 0 0 d4ptp__ 2.29.1.2.1 Trypsin(ogen) [bovine (Bos tau ( 223) 39 17.2 5.5 0.417 0.750 39 12 2 13 1 40 108 119 1 223 0 0 0 d1rcf__ 3.13.4.1.3 Flavodoxin [Anabaena 7120] ( 169) 38 16.7 5.6 0.364 0.727 38 11 29 39 1 40 47 57 1 169 0 0 0 d1arb__ 2.29.1.1.1 Achromobacter protease [Achrom ( 263) 39 17.2 6.1 0.353 0.647 39 17 11 25 1 40 2 18 1 263 2 0 0 d1pls__ 2.35.1.1.5 Pleckstrin, N-terminal domain ( 113) 35 15.7 7.7 0.667 1.000 35 6 7 12 1 40 99 104 1 113 0 0 0 d1tgxc_ 7.5.1.1.2 gamma-Cardiotoxin [snake (Naja ( 60) 32 14.5 9.1 0.263 0.526 32 19 19 37 1 40 14 30 1 60 0 2 0 d2eng__ 2.33.1.1.1 Endoglucanase V [Humicola inso ( 205) 36 16.3 9.3 0.462 0.538 36 13 25 37 1 40 191 203 1 205 0 0 0 >>>d2erl__, 40 aa vs testset.fa library 3>>>d8rxna_ 7.34.3.1.1 Rubredoxin [Desulfovibrio vulgaris] - 52 aa vs testset.fa library 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 2.0499+/-0.0385; mu= 21.9713+/- 1.974 mean_var=38.1093+/-11.756, 0's: 0 Z-trim: 1 B-trim: 2 in 1/17 Lambda= 0.207758 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.010 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d8rxna_ 7.34.3.1.1 Rubredoxin [Desulfovibrio vulg ( 52) 392 120.7 1.2e-31 1.000 1.000 392 52 1 52 1 52 1 52 1 52 0 0 0 d1bbo_1 7.30.1.1.8 (1-27) Enhancer binding protei ( 27) 55 19.2 0.22 0.429 0.643 55 14 3 16 1 52 1 14 1 27 0 0 0 d8tlne1 1.47.1.1.2 (156-316) Thermolysin [Bacillu ( 161) 53 20.0 0.72 0.500 0.700 53 20 14 32 1 52 52 71 1 161 1 0 0 d1utg__ 1.60.1.1.1 Uteroglobin [Rabbit (Oryctolag ( 70) 49 18.2 1.2 0.304 0.609 49 23 12 34 1 52 27 49 1 70 0 0 0 d1rie__ 7.35.1.2.1 The rieske iron-sulfur protein ( 127) 44 17.1 4.1 0.391 0.478 44 23 4 26 1 52 87 108 1 127 0 1 0 d1ra9__ 3.51.1.1.1 Dihydrofolate reductase, proka ( 159) 44 17.3 4.5 0.444 0.500 44 18 21 37 1 52 116 133 1 159 1 0 0 d2ctb__ 3.50.1.1.1 Carboxypeptidase A [bovine (Bo ( 307) 45 18.2 4.9 0.364 0.636 45 22 17 38 1 52 43 64 1 307 0 0 0 d1igd__ 4.11.1.1.1 Immunoglobulin-binding protein ( 61) 40 15.3 6.8 0.500 0.667 40 12 21 32 1 52 41 52 1 61 0 0 0 d2eng__ 2.33.1.1.1 Endoglucanase V [Humicola inso ( 205) 42 16.9 7.5 0.235 0.500 42 34 9 42 1 52 130 162 1 205 0 1 0 d1hms__ 2.39.1.2.1 Muscle fatty acid binding prot ( 131) 41 16.3 7.7 0.364 0.636 41 22 10 31 1 52 67 87 1 131 0 1 0 d1ptx__ 7.3.6.1.4 scorpion toxin [Androctonus aus ( 64) 39 15.1 8.5 0.375 0.500 39 16 24 39 1 52 1 16 1 64 0 0 0 d1ctj__ 1.3.1.1.1 Cytochrome c6 (synonym: cytochr ( 89) 39 15.4 9.7 0.400 0.600 39 15 5 19 1 52 73 87 1 89 0 0 0 >>>d8rxna_, 52 aa vs testset.fa library 4>>>d1lkka_ 4.47.1.1.1 p56-lck tyrosine kinase [human (Homo sapiens)] - 105 aa vs testset.fa library 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 5.7678+/-0.0487; mu= 6.0174+/- 2.315 mean_var=43.5373+/-14.195, 0's: 0 Z-trim: 2 B-trim: 3 in 1/18 Lambda= 0.194376 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.020 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1lkka_ 4.47.1.1.1 p56-lck tyrosine kinase [human ( 105) 719 206.7 6.3e-57 1.000 1.000 719 105 1 105 1 105 1 105 1 105 0 0 0 d1bpi__ 7.6.1.1.1 Pancreatic trypsin inhibitor [b ( 58) 68 24.2 0.029 0.370 0.630 68 27 70 96 1 105 4 30 1 58 0 0 0 d1cus__ 3.13.7.1.1 Cutinase [fungus (Fusarium sol ( 197) 64 22.9 0.25 0.250 0.587 64 92 7 97 1 105 85 163 1 197 1 13 0 d1hms__ 2.39.1.2.1 Muscle fatty acid binding prot ( 131) 55 20.4 0.9 0.349 0.674 55 43 26 68 1 105 53 89 1 131 0 6 0 d2ctb__ 3.50.1.1.1 Carboxypeptidase A [bovine (Bo ( 307) 59 21.4 1.1 0.222 0.556 59 72 15 83 1 105 228 292 1 307 3 7 0 d1plc__ 2.5.1.1.2 Plastocyanin [poplar (Populus n ( 99) 51 19.4 1.4 0.306 0.667 51 36 39 74 1 105 52 86 1 99 0 1 0 d1xsoa_ 2.1.7.1.3 Cu,Zn superoxide dismutase, SOD ( 150) 51 19.3 2.3 0.395 0.684 51 38 39 72 1 105 8 45 1 150 4 0 0 d3pte__ 5.3.1.1.1 D-ala carboxypeptidase/transpep ( 347) 53 19.7 3.9 0.462 0.692 53 13 70 82 1 105 197 209 1 347 0 0 0 d1burd1 3.1.9.1.2 (137-460) Ribulose 1,5-bisphosp ( 324) 52 19.4 4.4 0.368 0.579 52 19 83 101 1 105 86 104 1 324 0 0 0 d3sdhb_ 1.1.1.1.1 Hemoglobin I [ark clam (Scaphar ( 145) 47 18.2 4.7 0.247 0.584 47 89 15 96 1 105 4 91 1 145 7 1 0 d1ycc__ 1.3.1.1.4 Mitochondrial cytochrome c [bak ( 108) 45 17.7 5 0.253 0.506 45 83 25 104 1 105 36 108 1 108 3 10 0 d1ifc__ 2.39.1.2.2 Intestinal fatty acid binding ( 131) 46 17.9 5.1 0.379 0.655 46 29 61 89 1 105 92 118 1 131 0 2 0 d1lam_1 3.33.1.1.1 (1-159) Leucine aminopeptidase ( 159) 47 18.2 5.2 0.275 0.549 47 51 33 83 1 105 11 59 1 159 0 2 0 d8tlne1 1.47.1.1.2 (156-316) Thermolysin [Bacillu ( 161) 46 17.9 6.3 0.304 0.536 46 56 25 76 1 105 26 81 1 161 4 0 0 d2prk__ 3.26.1.1.6 Proteinase K [fungus (Tritirac ( 279) 49 18.6 6.5 0.277 0.523 49 65 31 94 1 105 10 66 1 279 1 8 0 d1aab__ 1.17.1.1.1 HMG1, fragments A and B [rat/h ( 83) 41 16.6 7.9 0.304 0.696 41 23 8 30 1 105 37 59 1 83 0 0 0 d2eng__ 2.33.1.1.1 Endoglucanase V [Humicola inso ( 205) 46 17.8 8.2 0.304 0.739 46 23 24 46 1 105 97 119 1 205 0 0 0 d1hfc__ 4.46.1.5.1 Fibroblast collagenase [human ( 157) 44 17.3 8.9 0.288 0.525 44 59 2 53 1 105 93 151 1 157 7 0 0 d1eco__ 1.1.1.1.13 Erythrocruorin [Midge (Chirono ( 136) 43 17.1 9.2 0.237 0.537 43 80 8 80 1 105 38 116 1 136 7 1 0 >>>d1lkka_, 105 aa vs testset.fa library 5>>>d1ctj__ 1.3.1.1.1 Cytochrome c6 (synonym: cytochrome c553) [(Monoraphidium braunii)] - 89 aa vs testset.fa library 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 7.3875+/-0.0341; mu= -0.5633+/- 1.525 mean_var=44.4193+/-13.668, 0's: 0 Z-trim: 1 B-trim: 9 in 1/18 Lambda= 0.192437 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.010 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1ctj__ 1.3.1.1.1 Cytochrome c6 (synonym: cytochr ( 89) 613 174.9 1.6e-47 1.000 1.000 613 89 1 89 1 89 1 89 1 89 0 0 0 d1ezm_1 1.47.1.1.1 (154-298) Elastase [Pseudomona ( 145) 68 23.3 0.11 0.333 0.593 68 54 19 67 1 89 5 55 1 145 5 3 0 d1ycc__ 1.3.1.1.4 Mitochondrial cytochrome c [bak ( 108) 57 20.4 0.63 0.346 0.577 57 26 7 29 1 89 11 36 1 108 3 0 0 d1cpq__ 1.20.3.2.5 Cytochrome c' [(Rhodobacter ca ( 129) 53 19.2 1.7 0.471 0.706 53 17 5 19 1 89 106 122 1 129 2 0 0 d1mla_2 4.31.18.1.1 (126-195) Probable ACP-bindin ( 70) 47 17.9 2.3 0.462 0.923 47 13 16 28 1 89 54 66 1 70 0 0 0 d1tca__ 3.48.1.7.1 Triacylglycerol lipase [yeast ( 317) 58 20.1 2.4 0.267 0.533 58 75 17 87 1 89 89 161 1 317 4 2 0 d1rcf__ 3.13.4.1.3 Flavodoxin [Anabaena 7120] ( 169) 48 17.7 6.5 0.262 0.541 48 61 23 79 1 89 27 85 1 169 4 2 0 d8rxna_ 7.34.3.1.1 Rubredoxin [Desulfovibrio vulg ( 52) 39 15.9 6.8 0.400 0.600 39 15 73 87 1 89 5 19 1 52 0 0 0 d1fus__ 4.1.1.1.2 RNase F1 [Fusarium moniliforme] ( 106) 44 16.8 7.2 0.360 0.640 44 25 8 27 1 89 76 100 1 106 5 0 0 e1ben.2d1 7.1.1.1.2 Insulin [human (Homo sapiens) ( 28) 34 14.9 7.4 0.304 0.652 34 23 37 59 1 89 2 23 1 28 0 1 0 d1isua_ 7.29.1.1.1 HIPIP (high potential iron pro ( 62) 39 15.8 8.7 0.667 0.889 39 9 20 28 1 89 36 44 1 62 0 0 0 e1ben.2c1 7.1.1.1.2 Insulin [human (Homo sapiens) ( 21) 31 14.2 8.7 0.667 1.000 31 6 51 56 1 89 13 18 1 21 0 0 0 d1amm_1 2.9.1.1.1 (1-85) gamma-Crystallin [bovine ( 85) 41 16.1 9.2 0.357 0.571 41 14 11 24 1 89 11 24 1 85 0 0 0 d1xsoa_ 2.1.7.1.3 Cu,Zn superoxide dismutase, SOD ( 150) 45 16.9 9.6 0.224 0.653 45 49 41 86 1 89 7 54 1 150 3 1 0 d1cus__ 3.13.7.1.1 Cutinase [fungus (Fusarium sol ( 197) 47 17.3 9.6 0.278 0.557 47 97 5 88 1 89 46 140 1 197 13 2 0 >>>d1ctj__, 89 aa vs testset.fa library 6>>>d1bpi__ 7.6.1.1.1 Pancreatic trypsin inhibitor [bovine (Bos taurus)] - 58 aa vs testset.fa library 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= -0.4844+/-0.0241; mu= 31.2372+/- 1.074 mean_var=51.5607+/-17.615, 0's: 0 Z-trim: 2 B-trim: 0 in 0/19 Lambda= 0.178614 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.000 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1bpi__ 7.6.1.1.1 Pancreatic trypsin inhibitor [b ( 58) 434 116.8 2.1e-30 1.000 1.000 434 58 1 58 1 58 1 58 1 58 0 0 0 d1lkka_ 4.47.1.1.1 p56-lck tyrosine kinase [human ( 105) 68 23.5 0.049 0.370 0.630 68 27 4 30 1 58 70 96 1 105 0 0 0 d1burd1 3.1.9.1.2 (137-460) Ribulose 1,5-bisphosp ( 324) 58 22.6 0.27 0.345 0.586 58 29 4 31 1 58 72 100 1 324 1 0 0 d1ifc__ 2.39.1.2.2 Intestinal fatty acid binding ( 131) 49 18.9 1.4 0.571 0.786 49 14 29 42 1 58 113 126 1 131 0 0 0 d2prk__ 3.26.1.1.6 Proteinase K [fungus (Tritirac ( 279) 46 19.3 2.3 0.250 0.611 46 36 21 54 1 58 23 58 1 279 2 0 0 d2olba_ 3.68.1.1.1 Oligo-peptide binding protein ( 517) 44 19.8 3.1 0.429 0.500 44 14 2 15 1 58 313 326 1 517 0 0 0 d1isua_ 7.29.1.1.1 HIPIP (high potential iron pro ( 62) 44 16.4 3.7 0.333 0.556 44 27 8 34 1 58 34 59 1 62 0 1 0 d2eng__ 2.33.1.1.1 Endoglucanase V [Humicola inso ( 205) 43 18.1 3.9 0.269 0.500 43 52 3 50 1 58 128 174 1 205 4 5 0 d1ezm_1 1.47.1.1.1 (154-298) Elastase [Pseudomona ( 145) 42 17.3 4.8 0.297 0.541 42 37 20 53 1 58 103 135 1 145 3 4 0 d2mhr__ 1.20.4.1.4 Myohemerythin [sipunculan worm ( 118) 40 16.4 7 0.556 0.778 40 9 45 53 1 58 29 37 1 118 0 0 0 d2erl__ 1.10.1.1.1 ER-1 [Euplotes raikovi] ( 40) 40 14.7 7.6 0.333 0.778 40 9 30 38 1 58 28 36 1 40 0 0 0 d4ptp__ 2.29.1.2.1 Trypsin(ogen) [bovine (Bos tau ( 223) 39 17.2 7.8 0.211 0.447 39 38 2 37 1 58 132 169 1 223 2 0 0 d1ezm_2 4.46.1.1.1 (1-153) Elastase [Pseudomonas ( 153) 39 16.6 8.1 0.207 0.483 39 29 9 37 1 58 53 81 1 153 0 0 0 d1flp__ 1.1.1.1.2 Hemoglobin I [clam (Lucina pect ( 142) 39 16.5 8.1 0.308 0.462 39 39 25 57 1 58 84 122 1 142 6 0 0 d1tca__ 3.48.1.7.1 Triacylglycerol lipase [yeast ( 317) 38 17.5 9 0.538 0.615 38 13 46 58 1 58 13 25 1 317 0 0 0 >>>d1bpi__, 58 aa vs testset.fa library 7>>>d1rgea_ 4.1.1.1.1 RNase Sa [Streptomyces aureofaciens] - 96 aa vs testset.fa library 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 8.4282+/-0.0346; mu= -7.1760+/- 1.706 mean_var=26.6967+/- 8.972, 0's: 0 Z-trim: 1 B-trim: 2 in 1/17 Lambda= 0.248225 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.010 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1rgea_ 4.1.1.1.1 RNase Sa [Streptomyces aureofac ( 96) 643 233.1 5.9e-65 1.000 1.000 643 96 1 96 1 96 1 96 1 96 0 0 0 d1burs_ 4.35.1.1.2 Ribulose 1,5-bisphosphate carb ( 123) 50 20.3 0.84 0.340 0.528 50 53 8 52 1 96 15 62 1 123 8 5 0 d1jbc__ 2.18.1.1.1 Concanavalin A [jack bean (Can ( 237) 55 21.1 0.96 0.410 0.590 55 39 14 50 1 96 192 227 1 237 2 3 0 d1aac__ 2.5.1.1.1 Amicyanin [Paracoccus denitrifi ( 105) 48 19.8 0.99 0.250 0.482 48 56 33 85 1 96 41 95 1 105 3 1 0 d1fus__ 4.1.1.1.2 RNase F1 [Fusarium moniliforme] ( 106) 45 18.8 2.1 0.239 0.630 45 46 23 67 1 96 33 71 1 106 1 7 0 d1pfsa_ 2.24.6.1.2 Gene V protein [Pseudomonas ph ( 78) 42 18.2 2.3 0.400 0.560 42 25 25 49 1 96 33 53 1 78 0 4 0 d1whi__ 2.23.1.1.1 Ribosomal protein L14 [Bacillu ( 122) 44 18.2 3.6 0.319 0.553 44 47 35 78 1 96 61 105 1 122 3 2 0 d1cbn__ 7.11.1.1.1 Crambin [abyssinian cabbage (C ( 46) 35 16.5 4.4 0.360 0.440 35 25 44 66 1 96 18 42 1 46 2 0 0 e1ben.2c1 7.1.1.1.2 Insulin [human (Homo sapiens) ( 21) 27 14.9 6.1 0.333 0.833 27 6 91 96 1 96 2 7 1 21 0 0 0 d8tlne1 1.47.1.1.2 (156-316) Thermolysin [Bacillu ( 161) 44 17.7 6.3 0.232 0.482 44 56 34 86 1 96 41 96 1 161 3 0 0 d1mla_1 3.12.1.1.1 (1-125,196-305) Catalytic doma ( 236) 47 18.2 6.7 0.371 0.486 47 35 38 71 1 96 185 218 1 236 1 1 0 d1ezm_1 1.47.1.1.1 (154-298) Elastase [Pseudomona ( 145) 42 17.2 8.3 0.318 0.636 42 22 75 96 1 96 123 144 1 145 0 0 0 d1arb__ 2.29.1.1.1 Achromobacter protease [Achrom ( 263) 47 18.0 8.3 0.286 0.657 47 35 2 36 1 96 2 34 1 263 0 2 0 d1xyzb_ 3.1.1.3.1 Xylanase XynZ (family F) [Clost ( 320) 48 18.1 9.7 0.357 0.571 48 28 11 38 1 96 179 206 1 320 0 0 0 d1igd__ 4.11.1.1.1 Immunoglobulin-binding protein ( 61) 34 15.7 9.8 0.200 0.600 34 35 55 85 1 96 8 42 1 61 4 0 0 >>>d1rgea_, 96 aa vs testset.fa library 8>>>d1cus__ 3.13.7.1.1 Cutinase [fungus (Fusarium solani, subsp. pisi)] - 197 aa vs testset.fa library 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 12.6187+/-0.0302; mu= -19.9093+/- 1.294 mean_var=61.1400+/-18.142, 0's: 0 Z-trim: 1 B-trim: 0 in 0/19 Lambda= 0.164026 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.030 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1cus__ 3.13.7.1.1 Cutinase [fungus (Fusarium sol ( 197) 1291 310.5 1.2e-87 1.000 1.000 1291 197 1 197 1 197 1 197 1 197 0 0 0 d1lkka_ 4.47.1.1.1 p56-lck tyrosine kinase [human ( 105) 64 21.1 0.84 0.272 0.543 64 92 85 163 1 197 7 97 1 105 13 1 0 d8tlne1 1.47.1.1.2 (156-316) Thermolysin [Bacillu ( 161) 61 19.8 3.3 0.235 0.523 61 153 32 181 1 197 17 159 1 161 3 10 0 d1aab__ 1.17.1.1.1 HMG1, fragments A and B [rat/h ( 83) 52 18.7 3.6 0.275 0.525 52 40 66 105 1 197 3 42 1 83 0 0 0 d1rcf__ 3.13.4.1.3 Flavodoxin [Anabaena 7120] ( 169) 60 19.4 4.2 0.250 0.558 60 104 38 133 1 197 17 119 1 169 8 1 0 d1cpq__ 1.20.3.2.5 Cytochrome c' [(Rhodobacter ca ( 129) 55 18.7 5.5 0.298 0.544 55 57 17 69 1 197 50 105 1 129 4 1 0 d1ptf__ 4.48.1.1.2 Histidine-containing phosphoca ( 87) 50 18.1 5.5 0.216 0.608 50 51 67 117 1 197 32 81 1 87 0 1 0 d2mcm__ 2.1.6.1.1 Macromycin [Streptomyces macrom ( 112) 52 18.2 6.6 0.231 0.596 52 52 28 79 1 197 40 90 1 112 0 1 0 d2alp__ 2.29.1.1.3 alpha-Lytic protease [Lysobact ( 198) 59 19.0 6.8 0.233 0.586 59 116 11 107 1 197 12 127 1 198 19 0 0 d1mla_1 3.12.1.1.1 (1-125,196-305) Catalytic doma ( 236) 61 19.2 7.1 0.272 0.570 61 114 20 122 1 197 4 110 1 236 11 7 0 d1tgxc_ 7.5.1.1.2 gamma-Cardiotoxin [snake (Naja ( 60) 43 17.0 7.9 0.333 0.444 43 27 155 181 1 197 14 37 1 60 0 3 0 d1ctj__ 1.3.1.1.1 Cytochrome c6 (synonym: cytochr ( 89) 47 17.4 9.2 0.278 0.557 47 97 46 140 1 197 5 88 1 89 2 13 0 >>>d1cus__, 197 aa vs testset.fa library 9>>>d1arb__ 2.29.1.1.1 Achromobacter protease [Achromobacter lyticus, strain m497-1] - 263 aa vs testset.fa library 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 8.5459+/-0.0158; mu= 0.2421+/- 0.678 mean_var=65.7440+/-19.828, 0's: 0 Z-trim: 3 B-trim: 0 in 0/18 Lambda= 0.158178 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.030 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1arb__ 2.29.1.1.1 Achromobacter protease [Achrom ( 263) 1803 417.4 1.4e-119 1.000 1.000 1803 263 1 263 1 263 1 263 1 263 0 0 0 d4ptp__ 2.29.1.2.1 Trypsin(ogen) [bovine (Bos tau ( 223) 93 27.3 0.033 0.207 0.502 93 217 31 234 1 263 20 215 1 223 13 21 0 d2sga__ 2.29.1.1.2 Protease A [Streptomyces grise ( 181) 89 26.5 0.047 0.189 0.576 89 132 95 221 1 263 36 163 1 181 5 4 0 d2prk__ 3.26.1.1.6 Proteinase K [fungus (Tritirac ( 279) 73 22.6 1.1 0.228 0.495 73 206 4 178 1 263 32 230 1 279 31 7 0 d2sn3__ 7.3.6.1.1 scorpion toxin [Centruroides sc ( 65) 59 20.2 1.3 0.312 0.562 59 32 206 237 1 263 19 50 1 65 0 0 0 d1xnb__ 2.18.1.8.1 Xylanase II [Bacillus circulan ( 185) 66 21.2 1.8 0.193 0.500 66 166 90 247 1 263 1 164 1 185 8 2 0 d1epne_ 2.32.1.2.1 Endothiapepsin [chestnut bligh ( 330) 70 21.8 2.1 0.275 0.541 70 109 162 261 1 263 25 125 1 330 9 8 0 d1cbn__ 7.11.1.1.1 Crambin [abyssinian cabbage (C ( 46) 53 19.0 2.2 0.364 0.568 53 44 68 110 1 263 6 45 1 46 1 4 0 d1lit__ 4.88.1.1.1 Lithostathine, inhibitor of st ( 131) 61 20.3 2.5 0.229 0.505 61 105 74 176 1 263 6 96 1 131 2 14 0 d8tlne1 1.47.1.1.2 (156-316) Thermolysin [Bacillu ( 161) 59 19.7 4.5 0.177 0.522 59 113 119 231 1 263 9 112 1 161 0 9 0 d2alp__ 2.29.1.1.3 alpha-Lytic protease [Lysobact ( 198) 60 19.8 5.1 0.209 0.516 60 182 52 230 1 263 31 184 1 198 3 28 0 d1fus__ 4.1.1.1.2 RNase F1 [Fusarium moniliforme] ( 106) 54 18.8 5.6 0.194 0.548 54 93 108 196 1 263 5 97 1 106 4 0 0 d1cus__ 3.13.7.1.1 Cutinase [fungus (Fusarium sol ( 197) 57 19.1 8 0.500 0.857 57 14 28 41 1 263 154 167 1 197 0 0 0 d1csee_ 3.26.1.1.1 Subtilisin Carlsberg [Bacillus ( 274) 59 19.4 9 0.254 0.522 59 67 102 165 1 263 201 253 1 274 3 14 0 d3pte__ 5.3.1.1.1 D-ala carboxypeptidase/transpep ( 347) 61 19.8 9 0.229 0.534 61 118 70 181 1 263 140 245 1 347 6 12 0 >>>d1arb__, 263 aa vs testset.fa library 10>>>d1igd__ 4.11.1.1.1 Immunoglobulin-binding protein G, separate domains [group G streptococcus (Streptomyces griseus)] - 61 aa vs testset.fa library 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 8.6855+/-0.0218; mu= -12.1134+/- 1.039 mean_var=48.1471+/-14.933, 0's: 0 Z-trim: 1 B-trim: 0 in 0/19 Lambda= 0.184837 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.010 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1igd__ 4.11.1.1.1 Immunoglobulin-binding protein ( 61) 383 108.5 7.4e-28 1.000 1.000 383 61 1 61 1 61 1 61 1 61 0 0 0 d1mnta_ 1.32.1.1.2 Mnt repressor [Salmonella bact ( 66) 47 18.9 0.78 0.235 0.529 47 34 8 41 1 61 21 54 1 66 0 0 0 d4lzm__ 4.2.1.3.1 Phage T4 lysozyme [Escherichia ( 162) 51 19.1 1.6 0.308 0.615 51 39 19 57 1 61 30 67 1 162 0 1 0 d1flp__ 1.1.1.1.2 Hemoglobin I [clam (Lucina pect ( 142) 49 18.7 1.8 0.308 0.615 49 39 15 49 1 61 90 128 1 142 4 0 0 d8rxna_ 7.34.3.1.1 Rubredoxin [Desulfovibrio vulg ( 52) 40 17.2 1.9 0.500 0.667 40 12 41 52 1 61 21 32 1 52 0 0 0 d1fus__ 4.1.1.1.2 RNase F1 [Fusarium moniliforme] ( 106) 46 18.2 2 0.314 0.629 46 35 16 50 1 61 4 38 1 106 0 0 0 d8tlne2 4.46.1.1.2 (1-155) Thermolysin [Bacillus ( 155) 49 18.7 2.1 0.450 0.650 49 20 38 56 1 61 29 48 1 155 1 0 0 d1epne_ 2.32.1.2.1 Endothiapepsin [chestnut bligh ( 330) 54 19.3 2.8 0.302 0.674 54 43 5 47 1 61 89 125 1 330 0 6 0 d1lam_1 3.33.1.1.1 (1-159) Leucine aminopeptidase ( 159) 46 17.8 3.8 0.438 0.750 46 16 37 52 1 61 117 132 1 159 0 0 0 d1cpq__ 1.20.3.2.5 Cytochrome c' [(Rhodobacter ca ( 129) 43 17.2 4.7 0.450 0.800 43 20 14 32 1 61 18 37 1 129 1 0 0 d2alp__ 2.29.1.1.3 alpha-Lytic protease [Lysobact ( 198) 45 17.4 6.4 0.357 0.571 45 28 19 46 1 61 112 139 1 198 0 0 0 d193l__ 4.2.1.2.1 Lysozyme [chicken (Gallus gallu ( 129) 41 16.7 6.7 0.273 0.545 41 33 18 50 1 61 21 53 1 129 0 0 0 d1isua_ 7.29.1.1.1 HIPIP (high potential iron pro ( 62) 34 15.5 7.5 0.250 0.432 34 44 1 44 1 61 6 49 1 62 0 0 0 d1aab__ 1.17.1.1.1 HMG1, fragments A and B [rat/h ( 83) 36 15.7 8.2 0.226 0.613 36 31 15 45 1 61 6 36 1 83 0 0 0 d1cbn__ 7.11.1.1.1 Crambin [abyssinian cabbage (C ( 46) 30 14.6 9.6 0.353 0.588 30 17 4 20 1 61 27 43 1 46 0 0 0 d1hms__ 2.39.1.2.1 Muscle fatty acid binding prot ( 131) 39 16.1 9.8 0.357 0.571 39 28 6 33 1 61 103 130 1 131 0 0 0 >>>d1igd__, 61 aa vs testset.fa library 11>>>d1csee_ 3.26.1.1.1 Subtilisin Carlsberg [Bacillus subtilis] - 274 aa vs testset.fa library 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 15.0570+/- 0.049; mu= -31.6935+/- 2.248 mean_var=78.9700+/-28.401, 0's: 0 Z-trim: 2 B-trim: 3 in 1/18 Lambda= 0.144326 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.040 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1csee_ 3.26.1.1.1 Subtilisin Carlsberg [Bacillus ( 274) 1717 363.5 2.6e-103 1.000 1.000 1717 274 1 274 1 274 1 274 1 274 0 0 0 d2prk__ 3.26.1.1.6 Proteinase K [fungus (Tritirac ( 279) 481 106.2 7.9e-26 0.373 0.688 481 260 1 246 1 274 2 250 1 279 14 11 0 d3chy__ 3.13.2.1.1 CheY protein [Escherichia coli ( 128) 79 23.8 0.23 0.227 0.667 79 66 92 156 1 274 39 104 1 128 1 0 0 d2alp__ 2.29.1.1.3 alpha-Lytic protease [Lysobact ( 198) 81 23.4 0.44 0.266 0.597 81 154 42 184 1 274 21 168 1 198 11 6 0 d2sga__ 2.29.1.1.2 Protease A [Streptomyces grise ( 181) 71 21.5 1.5 0.277 0.605 71 119 38 149 1 274 77 181 1 181 7 14 0 d1epne_ 2.32.1.2.1 Endothiapepsin [chestnut bligh ( 330) 76 21.5 2.7 0.223 0.518 76 220 48 265 1 274 67 267 1 330 2 19 0 d1xsoa_ 2.1.7.1.3 Cu,Zn superoxide dismutase, SOD ( 150) 64 20.4 2.8 0.281 0.562 64 89 17 97 1 274 22 108 1 150 8 2 0 d2mcm__ 2.1.6.1.1 Macromycin [Streptomyces macrom ( 112) 59 19.8 3 0.250 0.598 59 112 40 138 1 274 2 109 1 112 13 4 0 d2eng__ 2.33.1.1.1 Endoglucanase V [Humicola inso ( 205) 68 20.7 3.1 0.256 0.610 68 82 126 204 1 274 50 124 1 205 3 7 0 d1cpq__ 1.20.3.2.5 Cytochrome c' [(Rhodobacter ca ( 129) 61 20.0 3.1 0.275 0.550 61 109 52 160 1 274 9 106 1 129 0 11 0 d1whi__ 2.23.1.1.1 Ribosomal protein L14 [Bacillu ( 122) 57 19.3 4.8 0.429 0.810 57 21 136 156 1 274 9 29 1 122 0 0 0 d1fus__ 4.1.1.1.2 RNase F1 [Fusarium moniliforme] ( 106) 54 18.9 5.4 0.297 0.649 54 37 126 160 1 274 69 105 1 106 2 0 0 d1ptf__ 4.48.1.1.2 Histidine-containing phosphoca ( 87) 50 18.4 6.3 0.286 0.714 50 28 60 87 1 274 54 81 1 87 0 0 0 d1bbo_1 7.30.1.1.8 (1-27) Enhancer binding protei ( 27) 29 16.0 10 0.231 0.769 29 13 234 246 1 274 9 21 1 27 0 0 0 >>>d1csee_, 274 aa vs testset.fa library 12>>>d1csei_ 4.21.1.1.1 Eglin C [leech (Hirudo medicinalis)] - 63 aa vs testset.fa library 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 7.8456+/-0.0273; mu= -7.1289+/- 1.319 mean_var=23.3126+/- 5.964, 0's: 0 Z-trim: 1 B-trim: 9 in 1/18 Lambda= 0.265631 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.010 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1csei_ 4.21.1.1.1 Eglin C [leech (Hirudo medicin ( 63) 435 169.8 2.9e-46 1.000 1.000 435 63 1 63 1 63 1 63 1 63 0 0 0 d1ezm_1 1.47.1.1.1 (154-298) Elastase [Pseudomona ( 145) 53 22.1 0.19 0.289 0.658 53 38 4 35 1 63 50 87 1 145 6 0 0 d1cbn__ 7.11.1.1.1 Crambin [abyssinian cabbage (C ( 46) 36 17.4 1.6 0.444 0.611 36 18 25 42 1 63 13 29 1 46 0 1 0 d1cyo__ 4.62.1.1.1 Cytochrome b5 [bovine (Bos tau ( 88) 41 18.3 1.6 0.310 0.552 41 29 5 32 1 63 10 38 1 88 1 0 0 d8tlne2 4.46.1.1.2 (1-155) Thermolysin [Bacillus ( 155) 44 18.5 2.4 0.293 0.561 44 41 19 58 1 63 103 142 1 155 1 1 0 d1bpi__ 7.6.1.1.1 Pancreatic trypsin inhibitor [b ( 58) 36 17.0 2.6 0.375 0.500 36 16 35 50 1 63 9 24 1 58 0 0 0 d1xnb__ 2.18.1.8.1 Xylanase II [Bacillus circulan ( 185) 44 18.2 3.4 0.283 0.543 44 46 10 55 1 63 117 160 1 185 0 2 0 e6rlx.2c1 7.1.1.1.4 Relaxin [human (Homo sapiens) ( 24) 27 14.9 4.4 0.364 0.727 27 11 53 63 1 63 4 14 1 24 0 0 0 d1aab__ 1.17.1.1.1 HMG1, fragments A and B [rat/h ( 83) 36 16.4 5.4 0.269 0.654 36 26 8 33 1 63 57 82 1 83 0 0 0 d2sn3__ 7.3.6.1.1 scorpion toxin [Centruroides sc ( 65) 33 15.7 7.1 0.667 1.000 33 6 30 35 1 63 51 56 1 65 0 0 0 e1ben.2d1 7.1.1.1.2 Insulin [human (Homo sapiens) ( 28) 26 14.3 7.8 0.750 1.000 26 4 48 51 1 63 25 28 1 28 0 0 0 d1burd2 4.31.9.1.2 (1-136) Ribulose 1,5-bisphosph ( 136) 38 16.4 8.6 0.320 0.480 38 25 28 52 1 63 13 36 1 136 0 1 0 d1rie__ 7.35.1.2.1 The rieske iron-sulfur protein ( 127) 37 16.1 9.7 0.381 0.619 37 21 9 27 1 63 35 55 1 127 2 0 0 >>>d1csei_, 63 aa vs testset.fa library 13>>>d1jbc__ 2.18.1.1.1 Concanavalin A [jack bean (Canavalia ensiformis)] - 237 aa vs testset.fa library 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 9.7867+/-0.0517; mu= -7.7514+/- 2.455 mean_var=61.9080+/-15.905, 0's: 0 Z-trim: 1 B-trim: 0 in 0/18 Lambda= 0.163005 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.030 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1jbc__ 2.18.1.1.1 Concanavalin A [jack bean (Can ( 237) 1539 367.8 1e-104 1.000 1.000 1539 237 1 237 1 237 1 237 1 237 0 0 0 d3pte__ 5.3.1.1.1 D-ala carboxypeptidase/transpep ( 347) 74 22.9 0.96 0.306 0.565 74 62 56 110 1 237 62 123 1 347 7 0 0 d1ezm_1 1.47.1.1.1 (154-298) Elastase [Pseudomona ( 145) 62 20.9 1.7 0.254 0.563 62 71 133 202 1 237 24 87 1 145 1 7 0 d1rgea_ 4.1.1.1.1 RNase Sa [Streptomyces aureofac ( 96) 55 19.6 2.7 0.410 0.590 55 39 192 227 1 237 14 50 1 96 3 2 0 d2cba__ 2.47.1.1.2 Carbonic anhydrase [human (Hom ( 258) 64 20.8 3 0.232 0.512 64 125 91 210 1 237 29 143 1 258 5 10 0 d1pfsa_ 2.24.6.1.2 Gene V protein [Pseudomonas ph ( 78) 52 19.0 3.2 0.361 0.556 52 36 190 225 1 237 23 52 1 78 0 6 0 d2sga__ 2.29.1.1.2 Protease A [Streptomyces grise ( 181) 60 20.2 3.3 0.215 0.508 60 130 103 227 1 237 35 156 1 181 5 8 0 d1ckaa_ 2.20.2.1.1 C-Crk, N-terminal SH3 domain [ ( 57) 48 18.4 3.7 0.333 0.533 48 30 28 54 1 237 24 53 1 57 3 0 0 d1cus__ 3.13.7.1.1 Cutinase [fungus (Fusarium sol ( 197) 58 19.6 5.1 0.333 0.667 58 33 209 237 1 237 58 90 1 197 4 0 0 d2eng__ 2.33.1.1.1 Endoglucanase V [Humicola inso ( 205) 57 19.4 6.4 0.270 0.510 57 100 145 234 1 237 42 132 1 205 10 9 0 d1amm_2 2.9.1.1.1 (86-174) gamma-Crystallin [bovi ( 89) 48 18.0 7.3 0.267 0.567 48 30 20 49 1 237 52 81 1 89 0 0 0 d1rcf__ 3.13.4.1.3 Flavodoxin [Anabaena 7120] ( 169) 54 18.8 7.6 0.292 0.584 54 89 34 115 1 237 1 82 1 169 7 7 0 >>>d1jbc__, 237 aa vs testset.fa library 14>>>d1hms__ 2.39.1.2.1 Muscle fatty acid binding protein (m-fabp) [human (Homo sapiens)] - 131 aa vs testset.fa library 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 7.2177+/-0.0472; mu= 0.4442+/- 2.290 mean_var=40.8305+/-12.223, 0's: 0 Z-trim: 2 B-trim: 0 in 0/19 Lambda= 0.200716 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.020 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1hms__ 2.39.1.2.1 Muscle fatty acid binding prot ( 131) 836 246.7 8.9e-69 1.000 1.000 836 131 1 131 1 131 1 131 1 131 0 0 0 d1ifc__ 2.39.1.2.2 Intestinal fatty acid binding ( 131) 253 77.8 5.9e-18 0.321 0.679 253 131 3 131 1 131 1 131 1 131 2 0 0 d1lkka_ 4.47.1.1.1 p56-lck tyrosine kinase [human ( 105) 55 20.7 0.78 0.349 0.674 55 43 53 89 1 131 26 68 1 105 6 0 0 d5p21__ 3.24.1.3.1 cH-p21 Ras protein [human (Hom ( 166) 56 20.6 1.2 0.205 0.551 56 78 2 79 1 131 76 150 1 166 0 3 0 d1rcf__ 3.13.4.1.3 Flavodoxin [Anabaena 7120] ( 169) 54 20.1 1.9 0.290 0.581 54 31 84 114 1 131 109 139 1 169 0 0 0 d2cba__ 2.47.1.1.2 Carbonic anhydrase [human (Hom ( 258) 53 19.5 4.2 0.350 0.675 53 40 66 100 1 131 64 101 1 258 5 2 0 d8rxna_ 7.34.3.1.1 Rubredoxin [Desulfovibrio vulg ( 52) 41 17.1 4.5 0.364 0.636 41 22 67 87 1 131 10 31 1 52 1 0 0 d1pls__ 2.35.1.1.5 Pleckstrin, N-terminal domain ( 113) 46 18.0 5.1 0.320 0.640 46 25 67 91 1 131 32 55 1 113 0 1 0 d8tlne2 4.46.1.1.2 (1-155) Thermolysin [Bacillus ( 155) 46 17.8 8 0.333 0.593 46 27 97 123 1 131 115 139 1 155 0 2 0 d1igd__ 4.11.1.1.1 Immunoglobulin-binding protein ( 61) 39 16.4 8.4 0.357 0.571 39 28 103 130 1 131 6 33 1 61 0 0 0 d1tpg_1 7.10.1.1.13 (51-91) Plasminogen activator ( 41) 36 15.8 8.6 0.292 0.583 36 24 16 39 1 131 18 41 1 41 0 0 0 >>>d1hms__, 131 aa vs testset.fa library 15>>>d7rsa__ 4.4.1.1.1 Ribonuclease A (also ribonuclease B, S) [bovine (Bos taurus)] - 124 aa vs testset.fa library 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 4.3765+/-0.0433; mu= 15.1441+/- 2.201 mean_var=54.1475+/-14.359, 0's: 0 Z-trim: 2 B-trim: 0 in 0/19 Lambda= 0.174295 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.020 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d7rsa__ 4.4.1.1.1 Ribonuclease A (also ribonuclea ( 124) 840 216.9 7.5e-60 1.000 1.000 840 124 1 124 1 124 1 124 1 124 0 0 0 d1poa__ 1.80.1.2.1 Snake phospholipase A2 [taiwan ( 118) 80 25.7 0.024 0.226 0.604 80 53 58 110 1 124 71 118 1 118 0 5 0 d1xyzb_ 3.1.1.3.1 Xylanase XynZ (family F) [Clost ( 320) 61 21.3 1.4 0.242 0.560 61 91 30 114 1 124 193 272 1 320 6 11 0 d3ebx__ 7.5.1.1.1 Erabutoxin B (also neurotoxin B ( 62) 53 18.7 1.6 0.218 0.582 53 55 26 75 1 124 3 57 1 62 5 0 0 d1tpg_1 7.10.1.1.13 (51-91) Plasminogen activator ( 41) 49 17.6 2.4 0.326 0.512 49 43 58 99 1 124 1 38 1 41 1 5 0 d1aab__ 1.17.1.1.1 HMG1, fragments A and B [rat/h ( 83) 52 18.6 2.4 0.225 0.675 52 40 2 41 1 124 20 58 1 83 0 1 0 d2erl__ 1.10.1.1.1 ER-1 [Euplotes raikovi] ( 40) 46 16.8 3.9 0.375 0.583 46 24 52 73 1 124 6 29 1 40 2 0 0 d1krn__ 7.12.1.1.1 Plasminogen kringle 4 [human ( ( 79) 46 17.0 6.5 0.263 0.579 46 38 65 101 1 124 2 39 1 79 1 0 0 d193l__ 4.2.1.2.1 Lysozyme [chicken (Gallus gallu ( 129) 47 17.5 7.9 0.295 0.526 47 78 5 68 1 124 31 104 1 129 14 4 0 d2eng__ 2.33.1.1.1 Endoglucanase V [Humicola inso ( 205) 49 18.1 7.9 0.233 0.567 49 30 93 122 1 124 14 43 1 205 0 0 0 d1lit__ 4.88.1.1.1 Lithostathine, inhibitor of st ( 131) 47 17.5 8 0.292 0.479 47 48 65 112 1 124 1 46 1 131 0 2 0 >>>d7rsa__, 124 aa vs testset.fa library 16>>>d2sn3__ 7.3.6.1.1 scorpion toxin [Centruroides sculpturatus ewing, variant 3] - 65 aa vs testset.fa library 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 2.5987+/-0.0426; mu= 19.6281+/- 2.089 mean_var=53.8270+/-16.497, 0's: 0 Z-trim: 2 B-trim: 2 in 1/18 Lambda= 0.174813 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.010 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d2sn3__ 7.3.6.1.1 scorpion toxin [Centruroides sc ( 65) 495 130.0 2.8e-34 1.000 1.000 495 65 1 65 1 65 1 65 1 65 0 0 0 d1ptx__ 7.3.6.1.4 scorpion toxin [Androctonus aus ( 64) 124 36.5 4.1e-06 0.403 0.581 124 62 1 57 1 65 2 57 1 64 5 6 0 d2erl__ 1.10.1.1.1 ER-1 [Euplotes raikovi] ( 40) 58 19.4 0.34 0.257 0.686 58 35 10 43 1 65 1 34 1 40 1 1 0 d1isua_ 7.29.1.1.1 HIPIP (high potential iron pro ( 62) 56 19.3 0.59 0.326 0.512 56 43 7 44 1 65 17 58 1 62 5 1 0 d1arb__ 2.29.1.1.1 Achromobacter protease [Achrom ( 263) 59 21.2 0.67 0.312 0.562 59 32 19 50 1 65 206 237 1 263 0 0 0 d4ptp__ 2.29.1.2.1 Trypsin(ogen) [bovine (Bos tau ( 223) 51 19.0 2.5 0.250 0.442 51 52 3 47 1 65 164 215 1 223 7 0 0 d1pls__ 2.35.1.1.5 Pleckstrin, N-terminal domain ( 113) 47 17.5 3.7 0.875 1.000 47 8 1 8 1 65 7 14 1 113 0 0 0 d1amm_1 2.9.1.1.1 (1-85) gamma-Crystallin [bovine ( 85) 44 16.5 5.4 0.375 0.562 44 16 36 51 1 65 10 25 1 85 0 0 0 e6rlx.2c1 7.1.1.1.4 Relaxin [human (Homo sapiens) ( 24) 40 14.5 6.1 0.357 0.571 40 14 12 25 1 65 11 24 1 24 0 0 0 d1poa__ 1.80.1.2.1 Snake phospholipase A2 [taiwan ( 118) 43 16.5 7.4 0.389 0.667 43 18 34 51 1 65 79 95 1 118 0 1 0 d2sga__ 2.29.1.1.2 Protease A [Streptomyces grise ( 181) 44 17.1 7.5 0.271 0.500 44 48 3 50 1 65 90 135 1 181 0 2 0 d1rie__ 7.35.1.2.1 The rieske iron-sulfur protein ( 127) 43 16.6 7.6 0.368 0.526 43 19 24 42 1 65 74 92 1 127 0 0 0 d1utg__ 1.60.1.1.1 Uteroglobin [Rabbit (Oryctolag ( 70) 41 15.6 8.2 0.421 0.579 41 19 39 57 1 65 1 19 1 70 0 0 0 d1fus__ 4.1.1.1.2 RNase F1 [Fusarium moniliforme] ( 106) 42 16.2 8.3 0.240 0.540 42 50 17 64 1 65 16 63 1 106 2 2 0 d1tpg_1 7.10.1.1.13 (51-91) Plasminogen activator ( 41) 39 14.7 9.1 0.346 0.500 39 26 40 65 1 65 17 34 1 41 0 8 0 d1lit__ 4.88.1.1.1 Lithostathine, inhibitor of st ( 131) 42 16.3 9.1 0.300 0.433 42 30 30 58 1 65 72 101 1 131 1 0 0 d2eng__ 2.33.1.1.1 Endoglucanase V [Humicola inso ( 205) 43 16.9 9.3 0.241 0.517 43 29 31 58 1 65 1 29 1 205 1 0 0 >>>d2sn3__, 65 aa vs testset.fa library 17>>>d1ifc__ 2.39.1.2.2 Intestinal fatty acid binding protein [rat (Rattus rattus)] - 131 aa vs testset.fa library 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 14.8304+/-0.0272; mu= -33.6391+/- 1.257 mean_var=76.1984+/-23.253, 0's: 0 Z-trim: 2 B-trim: 0 in 0/19 Lambda= 0.146927 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.010 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1ifc__ 2.39.1.2.2 Intestinal fatty acid binding ( 131) 844 185.6 2.1e-50 1.000 1.000 844 131 1 131 1 131 1 131 1 131 0 0 0 d1hms__ 2.39.1.2.1 Muscle fatty acid binding prot ( 131) 253 60.3 1.1e-12 0.321 0.679 253 131 1 131 1 131 3 131 1 131 0 2 0 d3sdhb_ 1.1.1.1.1 Hemoglobin I [ark clam (Scaphar ( 145) 64 20.1 1.6 0.234 0.596 64 47 74 120 1 131 31 77 1 145 0 0 0 d1bpi__ 7.6.1.1.1 Pancreatic trypsin inhibitor [b ( 58) 49 18.5 1.9 0.571 0.786 49 14 113 126 1 131 29 42 1 58 0 0 0 e6rlx.2d1 7.1.1.1.4 Relaxin [human (Homo sapiens) ( 25) 34 16.7 2.8 0.417 0.583 34 12 81 92 1 131 1 12 1 25 0 0 0 d1ptf__ 4.48.1.1.2 Histidine-containing phosphoca ( 87) 50 18.0 4 0.227 0.636 50 66 18 81 1 131 1 64 1 87 2 2 0 d1pls__ 2.35.1.1.5 Pleckstrin, N-terminal domain ( 113) 52 18.0 5.2 0.246 0.594 52 69 42 106 1 131 7 70 1 113 4 5 0 >>>d1ifc__, 131 aa vs testset.fa library 18>>>d1ptx__ 7.3.6.1.4 scorpion toxin [Androctonus australius hector, toxin II] - 64 aa vs testset.fa library 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 1.9648+/-0.0186; mu= 22.4573+/- 0.787 mean_var=41.7970+/-11.623, 0's: 0 Z-trim: 2 B-trim: 0 in 0/19 Lambda= 0.198382 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.010 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1ptx__ 7.3.6.1.4 scorpion toxin [Androctonus aus ( 64) 500 147.2 1.9e-39 1.000 1.000 500 64 1 64 1 64 1 64 1 64 0 0 0 d2sn3__ 7.3.6.1.1 scorpion toxin [Centruroides sc ( 65) 124 39.6 4.7e-07 0.403 0.581 124 62 2 57 1 64 1 57 1 65 6 5 0 d1amm_1 2.9.1.1.1 (1-85) gamma-Crystallin [bovine ( 85) 54 19.8 0.57 0.234 0.489 54 47 9 54 1 64 38 84 1 85 1 0 0 d1poa__ 1.80.1.2.1 Snake phospholipase A2 [taiwan ( 118) 50 18.9 1.4 0.350 0.500 50 40 4 42 1 64 34 63 1 118 1 10 0 d1tpg_1 7.10.1.1.13 (51-91) Plasminogen activator ( 41) 45 16.6 2.5 0.345 0.621 45 29 22 48 1 64 1 25 1 41 2 4 0 d4ptp__ 2.29.1.2.1 Trypsin(ogen) [bovine (Bos tau ( 223) 47 18.6 3.2 0.268 0.500 47 56 4 58 1 64 154 208 1 223 1 1 0 d2cba__ 2.47.1.1.2 Carbonic anhydrase [human (Hom ( 258) 47 18.7 3.4 0.250 0.469 47 32 28 59 1 64 111 142 1 258 0 0 0 d193l__ 4.2.1.2.1 Lysozyme [chicken (Gallus gallu ( 129) 45 17.6 3.9 0.258 0.452 45 31 5 29 1 64 53 83 1 129 6 0 0 d2eng__ 2.33.1.1.1 Endoglucanase V [Humicola inso ( 205) 45 18.0 4.6 0.444 0.611 45 18 43 60 1 64 84 98 1 205 0 3 0 d1lit__ 4.88.1.1.1 Lithostathine, inhibitor of st ( 131) 44 17.3 4.7 0.308 0.769 44 13 26 38 1 64 102 114 1 131 0 0 0 d1isua_ 7.29.1.1.1 HIPIP (high potential iron pro ( 62) 42 16.1 5.3 0.278 0.444 42 36 28 63 1 64 21 55 1 62 0 1 0 e6rlx.2c1 7.1.1.1.4 Relaxin [human (Homo sapiens) ( 24) 38 14.1 7.9 0.333 0.611 38 18 19 36 1 64 8 24 1 24 0 1 0 d2erl__ 1.10.1.1.1 ER-1 [Euplotes raikovi] ( 40) 39 14.8 7.9 0.324 0.588 39 34 16 49 1 64 10 39 1 40 0 4 0 d2olba_ 3.68.1.1.1 Oligo-peptide binding protein ( 517) 44 18.5 7.9 0.538 0.769 44 13 23 35 1 64 341 353 1 517 0 0 0 d8rxna_ 7.34.3.1.1 Rubredoxin [Desulfovibrio vulg ( 52) 39 15.0 8.7 0.375 0.500 39 16 1 16 1 64 24 39 1 52 0 0 0 e1ben.2c1 7.1.1.1.2 Insulin [human (Homo sapiens) ( 21) 37 13.7 9.1 0.400 0.600 37 15 12 23 1 64 7 21 1 21 3 0 0 d1epne_ 2.32.1.2.1 Endothiapepsin [chestnut bligh ( 330) 42 17.5 9.8 0.321 0.500 42 28 17 44 1 64 55 81 1 330 0 1 0 >>>d1ptx__, 64 aa vs testset.fa library 19>>>d3sdhb_ 1.1.1.1.1 Hemoglobin I [ark clam (Scapharca inaequivalvis)] - 145 aa vs testset.fa library 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 9.5459+/-0.0148; mu= -9.4798+/- 0.616 mean_var=45.9478+/-18.806, 0's: 0 Z-trim: 3 B-trim: 0 in 0/19 Lambda= 0.189209 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.010 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d3sdhb_ 1.1.1.1.1 Hemoglobin I [ark clam (Scaphar ( 145) 933 259.5 1.5e-72 1.000 1.000 933 145 1 145 1 145 1 145 1 145 0 0 0 d1bvc__ 1.1.1.1.4 Myoglobin [sperm whale (Physete ( 153) 121 37.8 8.7e-06 0.256 0.562 121 121 21 137 1 145 14 131 1 153 4 3 0 d1flp__ 1.1.1.1.2 Hemoglobin I [clam (Lucina pect ( 142) 116 36.5 2e-05 0.232 0.641 116 142 9 145 1 145 2 138 1 142 5 5 0 d1ifc__ 2.39.1.2.2 Intestinal fatty acid binding ( 131) 64 22.4 0.32 0.234 0.596 64 47 31 77 1 145 74 120 1 131 0 0 0 d1eco__ 1.1.1.1.13 Erythrocruorin [Midge (Chirono ( 136) 58 20.7 1.1 0.188 0.580 58 112 27 134 1 145 14 121 1 136 4 4 0 e1ben.2c1 7.1.1.1.2 Insulin [human (Homo sapiens) ( 21) 34 16.3 3.4 0.455 0.727 34 11 69 79 1 145 9 19 1 21 0 0 0 d1aab__ 1.17.1.1.1 HMG1, fragments A and B [rat/h ( 83) 47 18.3 3.4 0.259 0.741 47 27 4 30 1 145 32 57 1 83 0 1 0 d2mcm__ 2.1.6.1.1 Macromycin [Streptomyces macrom ( 112) 48 18.2 4.8 0.400 0.880 48 25 4 27 1 145 57 79 1 112 1 2 0 d1lkka_ 4.47.1.1.1 p56-lck tyrosine kinase [human ( 105) 47 18.0 5.2 0.247 0.584 47 89 4 91 1 145 15 96 1 105 1 7 0 d2mhr__ 1.20.4.1.4 Myohemerythin [sipunculan worm ( 118) 48 18.2 5.3 0.286 0.653 48 49 84 129 1 145 38 83 1 118 3 3 0 d2hbg__ 1.1.1.1.3 Glycera globin [marine bloodwor ( 147) 50 18.4 5.4 0.218 0.545 50 55 9 61 1 145 2 56 1 147 2 0 0 d3pte__ 5.3.1.1.1 D-ala carboxypeptidase/transpep ( 347) 58 19.6 5.6 0.480 0.600 58 25 56 80 1 145 165 187 1 347 0 2 0 d8rxna_ 7.34.3.1.1 Rubredoxin [Desulfovibrio vulg ( 52) 38 16.4 7.9 0.600 0.600 38 10 84 93 1 145 32 41 1 52 0 0 0 d1whi__ 2.23.1.1.1 Ribosomal protein L14 [Bacillu ( 122) 45 17.3 9.7 0.353 0.618 45 34 114 144 1 145 13 46 1 122 3 0 0 >>>d3sdhb_, 145 aa vs testset.fa library 20>>>d1aac__ 2.5.1.1.1 Amicyanin [Paracoccus denitrificans] - 105 aa vs testset.fa library 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 6.1827+/-0.0359; mu= 2.5332+/- 1.711 mean_var=32.8707+/-10.781, 0's: 0 Z-trim: 2 B-trim: 0 in 0/18 Lambda= 0.223702 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.020 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1aac__ 2.5.1.1.1 Amicyanin [Paracoccus denitrifi ( 105) 700 230.1 5.7e-64 1.000 1.000 700 105 1 105 1 105 1 105 1 105 0 0 0 d1plc__ 2.5.1.1.2 Plastocyanin [poplar (Populus n ( 99) 109 39.4 1.4e-06 0.242 0.582 109 91 24 104 1 105 8 98 1 99 10 0 0 d1whi__ 2.23.1.1.1 Ribosomal protein L14 [Bacillu ( 122) 53 21.2 0.5 0.275 0.627 53 51 5 55 1 105 2 51 1 122 0 1 0 d1rgea_ 4.1.1.1.1 RNase Sa [Streptomyces aureofac ( 96) 48 19.7 1.1 0.250 0.482 48 56 41 95 1 105 33 85 1 96 1 3 0 d1ezm_2 4.46.1.1.1 (1-153) Elastase [Pseudomonas ( 153) 50 20.1 1.3 0.283 0.509 50 53 15 62 1 105 31 83 1 153 5 0 0 d8tlne2 4.46.1.1.2 (1-155) Thermolysin [Bacillus ( 155) 48 19.4 2.1 0.273 0.545 48 44 18 61 1 105 37 79 1 155 0 1 0 d2prk__ 3.26.1.1.6 Proteinase K [fungus (Tritirac ( 279) 50 19.8 3 0.226 0.538 50 93 3 90 1 105 15 104 1 279 5 3 0 d1eco__ 1.1.1.1.13 Erythrocruorin [Midge (Chirono ( 136) 45 18.5 3.4 0.226 0.548 45 84 1 82 1 105 45 125 1 136 2 3 0 d4ptp__ 2.29.1.2.1 Trypsin(ogen) [bovine (Bos tau ( 223) 47 18.9 4.3 0.208 0.542 47 48 1 48 1 105 171 218 1 223 0 0 0 d1mla_1 3.12.1.1.1 (1-125,196-305) Catalytic doma ( 236) 47 18.9 4.7 0.237 0.605 47 38 2 37 1 105 120 157 1 236 2 0 0 d4lzm__ 4.2.1.3.1 Phage T4 lysozyme [Escherichia ( 162) 43 17.8 6.7 0.250 0.544 43 68 39 104 1 105 87 150 1 162 2 4 0 d2olba_ 3.68.1.1.1 Oligo-peptide binding protein ( 517) 50 19.4 7 0.289 0.644 50 45 13 57 1 105 351 392 1 517 0 3 0 d1epne_ 2.32.1.2.1 Endothiapepsin [chestnut bligh ( 330) 47 18.7 7.3 0.222 0.519 47 81 9 89 1 105 46 123 1 330 0 3 0 d1isua_ 7.29.1.1.1 HIPIP (high potential iron pro ( 62) 36 16.1 8.4 0.556 0.778 36 9 5 13 1 105 29 37 1 62 0 0 0 d1ptx__ 7.3.6.1.4 scorpion toxin [Androctonus aus ( 64) 36 16.0 8.8 0.600 0.700 36 10 16 25 1 105 1 10 1 64 0 0 0 d1lit__ 4.88.1.1.1 Lithostathine, inhibitor of st ( 131) 40 16.9 9.6 0.212 0.538 40 52 41 91 1 105 18 62 1 131 1 7 0 >>>d1aac__, 105 aa vs testset.fa library 21>>>d256bb_ 1.20.3.1.1 Cytochrome b562 [Escherichia coli] - 106 aa vs testset.fa library 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 5.5511+/-0.0312; mu= 5.1418+/- 1.499 mean_var=31.5876+/-10.079, 0's: 0 Z-trim: 1 B-trim: 0 in 0/19 Lambda= 0.228200 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.020 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d256bb_ 1.20.3.1.1 Cytochrome b562 [Escherichia c ( 106) 676 226.6 6.3e-63 1.000 1.000 676 106 1 106 1 106 1 106 1 106 0 0 0 d2olba_ 3.68.1.1.1 Oligo-peptide binding protein ( 517) 65 24.9 0.17 0.348 0.674 65 46 48 93 1 106 431 471 1 517 0 5 0 d1cpq__ 1.20.3.2.5 Cytochrome c' [(Rhodobacter ca ( 129) 53 21.4 0.45 0.274 0.435 53 62 45 106 1 106 65 126 1 129 0 0 0 d4xis__ 3.1.11.1.4 D-xylose isomerase [streptomyc ( 386) 51 20.4 2.8 0.288 0.576 51 59 19 76 1 106 143 199 1 386 1 2 0 d1hfc__ 4.46.1.5.1 Fibroblast collagenase [human ( 157) 46 19.1 2.8 0.279 0.605 46 43 47 89 1 106 11 51 1 157 0 2 0 d1flp__ 1.1.1.1.2 Hemoglobin I [clam (Lucina pect ( 142) 44 18.4 3.8 0.353 0.588 44 34 54 85 1 106 57 90 1 142 2 0 0 d1jbc__ 2.18.1.1.1 Concanavalin A [jack bean (Can ( 237) 46 18.9 4.6 0.265 0.647 46 34 51 84 1 106 200 229 1 237 0 4 0 d2phy__ 4.57.2.1.1 Photoactive yellow protein [Ec ( 125) 42 17.8 5.1 0.243 0.527 42 74 2 64 1 106 10 82 1 125 11 1 0 d1lam_1 3.33.1.1.1 (1-159) Leucine aminopeptidase ( 159) 43 18.1 5.5 0.250 0.688 43 32 49 79 1 106 11 42 1 159 1 0 0 d2mhr__ 1.20.4.1.4 Myohemerythin [sipunculan worm ( 118) 41 17.5 5.9 0.236 0.491 41 55 21 73 1 106 38 92 1 118 2 0 0 d1rro__ 1.31.1.4.1 Oncomodulin [rat (Rattus norve ( 108) 40 17.2 6.7 0.204 0.612 40 49 38 83 1 106 6 54 1 108 3 0 0 d1mnta_ 1.32.1.1.2 Mnt repressor [Salmonella bact ( 66) 37 16.4 7.1 0.429 0.786 37 14 68 81 1 106 48 61 1 66 0 0 0 d1eco__ 1.1.1.1.13 Erythrocruorin [Midge (Chirono ( 136) 41 17.5 7.1 0.303 0.667 41 33 14 46 1 106 24 54 1 136 0 2 0 d1utg__ 1.60.1.1.1 Uteroglobin [Rabbit (Oryctolag ( 70) 37 16.4 7.6 0.333 0.521 37 48 13 56 1 106 24 67 1 70 4 4 0 d1xsoa_ 2.1.7.1.3 Cu,Zn superoxide dismutase, SOD ( 150) 41 17.4 8 0.412 0.647 41 17 66 82 1 106 122 138 1 150 0 0 0 d1amm_2 2.9.1.1.1 (86-174) gamma-Crystallin [bovi ( 89) 38 16.7 8.1 0.241 0.621 38 29 47 70 1 106 16 44 1 89 5 0 0 >>>d256bb_, 106 aa vs testset.fa library 22>>>d1plc__ 2.5.1.1.2 Plastocyanin [poplar (Populus nigra variant italica)] - 99 aa vs testset.fa library 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 7.0280+/-0.0276; mu= 0.7782+/- 1.266 mean_var=33.2037+/- 9.619, 0's: 0 Z-trim: 2 B-trim: 3 in 1/17 Lambda= 0.222578 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.020 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1plc__ 2.5.1.1.2 Plastocyanin [poplar (Populus n ( 99) 648 211.6 1.9e-58 1.000 1.000 648 99 1 99 1 99 1 99 1 99 0 0 0 d1aac__ 2.5.1.1.1 Amicyanin [Paracoccus denitrifi ( 105) 109 38.4 2.6e-06 0.242 0.582 109 91 8 98 1 99 24 104 1 105 0 10 0 d2eng__ 2.33.1.1.1 Endoglucanase V [Humicola inso ( 205) 57 21.2 0.79 0.273 0.489 57 88 22 97 1 99 22 109 1 205 12 0 0 d1lkka_ 4.47.1.1.1 p56-lck tyrosine kinase [human ( 105) 51 19.8 1.1 0.306 0.667 51 36 52 86 1 99 39 74 1 105 1 0 0 d4xis__ 3.1.11.1.4 D-xylose isomerase [streptomyc ( 386) 58 21.0 1.7 0.311 0.600 58 45 2 39 1 99 189 231 1 386 7 2 0 d193l__ 4.2.1.2.1 Lysozyme [chicken (Gallus gallu ( 129) 47 18.3 3.5 0.217 0.600 47 60 6 65 1 99 49 107 1 129 0 1 0 d3ebx__ 7.5.1.1.1 Erabutoxin B (also neurotoxin B ( 62) 41 17.0 4.2 0.273 0.545 41 44 22 64 1 99 18 61 1 62 1 0 0 d1isua_ 7.29.1.1.1 HIPIP (high potential iron pro ( 62) 40 16.7 5.2 0.333 0.733 40 15 10 24 1 99 38 52 1 62 0 0 0 d1rie__ 7.35.1.2.1 The rieske iron-sulfur protein ( 127) 45 17.7 5.3 0.353 0.706 45 17 72 87 1 99 76 92 1 127 1 0 0 e1ben.2d1 7.1.1.1.2 Insulin [human (Homo sapiens) ( 28) 34 15.4 5.7 0.444 0.778 34 9 78 86 1 99 20 28 1 28 0 0 0 d2mhr__ 1.20.4.1.4 Myohemerythin [sipunculan worm ( 118) 44 17.5 5.8 0.391 0.739 44 23 50 71 1 99 91 113 1 118 1 0 0 d1ycc__ 1.3.1.1.4 Mitochondrial cytochrome c [bak ( 108) 43 17.2 6.3 0.239 0.609 43 46 21 66 1 99 33 77 1 108 0 1 0 d1cpq__ 1.20.3.2.5 Cytochrome c' [(Rhodobacter ca ( 129) 44 17.4 6.7 0.230 0.554 44 74 25 91 1 99 44 115 1 129 7 2 0 d1lit__ 4.88.1.1.1 Lithostathine, inhibitor of st ( 131) 44 17.4 6.8 0.350 0.700 44 20 16 35 1 99 94 111 1 131 0 2 0 d1ckaa_ 2.20.2.1.1 C-Crk, N-terminal SH3 domain [ ( 57) 38 16.1 7.1 0.275 0.600 38 40 59 98 1 99 15 51 1 57 0 3 0 d1mnta_ 1.32.1.1.2 Mnt repressor [Salmonella bact ( 66) 39 16.3 7.1 0.309 0.471 39 68 8 63 1 99 3 66 1 66 12 4 0 d1mla_2 4.31.18.1.1 (126-195) Probable ACP-bindin ( 70) 38 16.0 9.6 0.500 0.900 38 10 4 13 1 99 8 17 1 70 0 0 0 >>>d1plc__, 99 aa vs testset.fa library 23>>>d1amm_1 2.9.1.1.1 (1-85) gamma-Crystallin [bovine (Bos taurus) isoform II (B)] - 85 aa vs testset.fa library 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= -2.4987+/-0.0228; mu= 46.6892+/- 0.998 mean_var=58.5007+/-15.993, 0's: 0 Z-trim: 2 B-trim: 0 in 0/19 Lambda= 0.167685 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.010 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1amm_1 2.9.1.1.1 (1-85) gamma-Crystallin [bovine ( 85) 657 164.0 2.9e-44 1.000 1.000 657 85 1 85 1 85 1 85 1 85 0 0 0 d1amm_2 2.9.1.1.1 (86-174) gamma-Crystallin [bovi ( 89) 218 57.9 2.7e-12 0.390 0.683 218 82 2 81 1 85 4 85 1 89 2 0 0 d1poa__ 1.80.1.2.1 Snake phospholipase A2 [taiwan ( 118) 54 18.8 2.1 0.260 0.500 54 50 6 54 1 85 27 73 1 118 1 3 0 d1ptx__ 7.3.6.1.4 scorpion toxin [Androctonus aus ( 64) 54 17.5 2.6 0.234 0.489 54 47 38 84 1 85 9 54 1 64 0 1 0 d3ebx__ 7.5.1.1.1 Erabutoxin B (also neurotoxin B ( 62) 52 17.0 3.7 0.346 0.615 52 26 11 34 1 85 32 57 1 62 2 0 0 d1lit__ 4.88.1.1.1 Lithostathine, inhibitor of st ( 131) 50 18.0 3.8 0.200 0.453 50 75 22 79 1 85 1 75 1 131 17 0 0 d2olba_ 3.68.1.1.1 Oligo-peptide binding protein ( 517) 46 19.9 4.2 0.205 0.500 46 44 34 77 1 85 389 432 1 517 0 0 0 d1xnb__ 2.18.1.8.1 Xylanase II [Bacillus circulan ( 185) 47 18.0 5.4 0.196 0.510 47 51 26 76 1 85 89 136 1 185 0 3 0 d1ckaa_ 2.20.2.1.1 C-Crk, N-terminal SH3 domain [ ( 57) 48 15.8 7.4 0.385 0.615 48 26 57 82 1 85 26 50 1 57 0 1 0 d1krn__ 7.12.1.1.1 Plasminogen kringle 4 [human ( ( 79) 47 16.3 7.6 0.259 0.519 47 27 23 49 1 85 42 68 1 79 0 0 0 d2eng__ 2.33.1.1.1 Endoglucanase V [Humicola inso ( 205) 44 17.5 8.4 0.391 0.522 44 23 18 34 1 85 12 33 1 205 6 1 0 d2prk__ 3.26.1.1.6 Proteinase K [fungus (Tritirac ( 279) 43 17.9 8.7 0.333 0.611 43 18 2 19 1 85 57 74 1 279 0 0 0 d1ycc__ 1.3.1.1.4 Mitochondrial cytochrome c [bak ( 108) 45 16.4 9.3 0.323 0.581 45 31 4 31 1 85 13 43 1 108 3 0 0 >>>d1amm_1, 85 aa vs testset.fa library 2636 residues in 23 query sequences 13355 residues in 93 library sequences Scomplib [34t24] start: Tue Aug 15 22:56:22 2006 done: Tue Aug 15 22:56:23 2006 Total Scan time: 0.370 Total Display time: 0.170 Function used was SSEARCH [version 3.4t24 June 23, 2004] weblogo-3.8.0/tests/data/ssearch/ssearch_out_compact_dbvdb.txt000066400000000000000000002622501467613320200246250ustar00rootroot00000000000000# ssearch34 -m 9 -d 0 -Q shortset.fa testset.fa SSEARCH searches a sequence data bank version 3.4t24 June 23, 2004 Please cite: T. F. Smith and M. S. Waterman, (1981) J. Mol. Biol. 147:195-197; W.R. Pearson (1991) Genomics 11:635-650 Query library shortset.fa vs testset.fa library searching testset.fa library 1>>>d1cbn__ 7.11.1.1.1 Crambin [abyssinian cabbage (Crambe abyssinica)] - 46 aa vs testset.fa library opt E() < 20 0 0: 22 0 0: one = represents 1 library sequences 24 0 0: 26 0 0: 28 0 0: 30 0 0: 32 0 0: 34 2 1:*= 36 0 3: * 38 3 5:=== * 40 11 6:=====*===== 42 4 8:==== * 44 7 8:=======* 46 7 9:======= * 48 9 8:=======*= 50 3 8:=== * 52 8 7:======*= 54 7 6:=====*= 56 8 5:====*=== 58 0 4: * 60 6 3:==*=== 62 5 3:==*== 64 2 2:=* 66 1 2:=* 68 1 1:* 70 1 1:* 72 2 1:*= 74 1 1:* 76 1 0:= 78 0 0: 80 0 0: 82 0 0: 84 1 0:= 86 0 0: 88 1 0:= 90 0 0: 92 0 0: 94 1 0:= 96 0 0: 98 0 0: 100 0 0: 102 0 0: 104 0 0: 106 0 0: 108 0 0: 110 0 0: 112 0 0: 114 0 0: 116 0 0: 118 0 0: >120 1 0:= 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 2.3138+/-0.0438; mu= 18.9049+/- 2.176 mean_var=37.1184+/-10.107, 0's: 0 Z-trim: 3 B-trim: 0 in 0/18 Lambda= 0.210513 Kolmogorov-Smirnov statistic: 0.1091 (N=22) at 50 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.010 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1cbn__ 7.11.1.1.1 Crambin [abyssinian cabbage (C ( 46) 338 106.1 2.3e-27 1.000 1.000 338 46 1 46 1 46 1 46 1 46 0 0 0 d1isua_ 7.29.1.1.1 HIPIP (high potential iron pro ( 62) 55 20.4 0.2 0.370 0.556 55 27 22 46 1 46 30 56 1 62 2 0 0 d2erl__ 1.10.1.1.1 ER-1 [Euplotes raikovi] ( 40) 51 18.8 0.37 0.364 0.591 51 22 23 41 1 46 16 37 1 40 3 0 0 d1arb__ 2.29.1.1.1 Achromobacter protease [Achrom ( 263) 53 20.8 0.6 0.364 0.568 53 44 6 45 1 46 68 110 1 263 4 1 0 d2eng__ 2.33.1.1.1 Endoglucanase V [Humicola inso ( 205) 47 18.8 1.9 0.333 0.519 47 27 18 44 1 46 137 163 1 205 0 0 0 d1fus__ 4.1.1.1.2 RNase F1 [Fusarium moniliforme] ( 106) 45 17.7 2.1 0.244 0.511 45 45 2 46 1 46 4 44 1 106 0 4 0 d1rie__ 7.35.1.2.1 The rieske iron-sulfur protein ( 127) 44 17.6 2.8 0.400 0.600 44 20 25 44 1 46 69 87 1 127 0 1 0 d3ebx__ 7.5.1.1.1 Erabutoxin B (also neurotoxin B ( 62) 42 16.4 3 0.357 0.464 42 28 19 41 1 46 19 44 1 62 5 2 0 e1ben.2c1 7.1.1.1.2 Insulin [human (Homo sapiens) ( 21) 38 14.4 4 0.400 0.600 38 15 3 16 1 46 6 20 1 21 1 0 0 d3pte__ 5.3.1.1.1 D-ala carboxypeptidase/transpep ( 347) 43 18.0 5.5 0.346 0.538 43 26 21 46 1 46 189 211 1 347 0 3 0 d5p21__ 3.24.1.3.1 cH-p21 Ras protein [human (Hom ( 166) 41 16.8 5.8 0.385 0.615 41 13 28 40 1 46 39 51 1 166 0 0 0 d1tpg_1 7.10.1.1.13 (51-91) Plasminogen activator ( 41) 37 14.6 6.8 0.375 0.625 37 16 4 19 1 46 12 26 1 41 0 1 0 d2sn3__ 7.3.6.1.1 scorpion toxin [Centruroides sc ( 65) 37 14.9 8.4 0.320 0.480 37 25 16 40 1 46 46 65 1 65 0 5 0 d2sga__ 2.29.1.1.2 Protease A [Streptomyces grise ( 181) 39 16.3 9.1 0.714 0.714 39 7 14 20 1 46 129 135 1 181 0 0 0 d1lcpa2 3.50.1.3.1 (160-484) Leucine aminopeptida ( 325) 40 17.0 9.7 0.409 0.636 40 22 23 42 1 46 182 203 1 325 2 0 0 d1tgxc_ 7.5.1.1.2 gamma-Cardiotoxin [snake (Naja ( 60) 36 14.6 9.9 0.241 0.448 36 29 14 41 1 46 19 43 1 60 1 4 0 >>>d1cbn__, 46 aa vs testset.fa library 2>>>d2erl__ 1.10.1.1.1 ER-1 [Euplotes raikovi] - 40 aa vs testset.fa library opt E() < 20 0 0: 22 0 0: one = represents 1 library sequences 24 0 0: 26 0 0: 28 0 0: 30 0 0: 32 0 0: 34 0 1:* 36 0 3: * 38 1 5:= * 40 2 6:== * 42 9 8:=======*= 44 3 8:=== * 46 12 9:========*=== 48 9 8:=======*= 50 7 8:=======* 52 6 7:======* 54 10 6:=====*==== 56 4 5:====* 58 4 4:===* 60 4 3:==*= 62 2 3:==* 64 2 2:=* 66 2 2:=* 68 2 1:*= 70 2 1:*= 72 3 1:*== 74 0 1:* 76 2 0:== 78 1 0:= 80 2 0:== 82 0 0: 84 0 0: 86 0 0: 88 0 0: 90 1 0:= 92 0 0: 94 1 0:= 96 0 0: 98 0 0: 100 0 0: 102 1 0:= 104 0 0: 106 0 0: 108 0 0: 110 0 0: 112 0 0: 114 0 0: 116 0 0: 118 0 0: >120 1 0:= 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 3.3544+/-0.0208; mu= 9.6709+/- 0.998 mean_var=41.9829+/-15.940, 0's: 0 Z-trim: 1 B-trim: 5 in 1/17 Lambda= 0.197942 Kolmogorov-Smirnov statistic: 0.1793 (N=21) at 44 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.010 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d2erl__ 1.10.1.1.1 ER-1 [Euplotes raikovi] ( 40) 297 90.0 1.2e-22 1.000 1.000 297 40 1 40 1 40 1 40 1 40 0 0 0 d2sn3__ 7.3.6.1.1 scorpion toxin [Centruroides sc ( 65) 58 22.0 0.058 0.257 0.686 58 35 1 34 1 40 10 43 1 65 1 1 0 d1cbn__ 7.11.1.1.1 Crambin [abyssinian cabbage (C ( 46) 51 19.8 0.19 0.364 0.591 51 22 16 37 1 40 23 41 1 46 0 3 0 e1ben.2c1 7.1.1.1.2 Insulin [human (Homo sapiens) ( 21) 46 18.0 0.3 0.333 0.667 46 18 11 28 1 40 3 20 1 21 0 0 0 d7rsa__ 4.4.1.1.1 Ribonuclease A (also ribonuclea ( 124) 46 18.9 0.96 0.375 0.583 46 24 6 29 1 40 52 73 1 124 0 2 0 d1tpg_1 7.10.1.1.13 (51-91) Plasminogen activator ( 41) 42 17.2 1 0.308 0.538 42 26 3 28 1 40 12 34 1 41 0 3 0 d1lit__ 4.88.1.1.1 Lithostathine, inhibitor of st ( 131) 44 18.3 1.5 0.400 0.667 44 15 19 31 1 40 1 15 1 131 2 0 0 d3ebx__ 7.5.1.1.1 Erabutoxin B (also neurotoxin B ( 62) 41 17.1 1.6 0.259 0.519 41 27 9 35 1 40 7 31 1 62 0 2 0 d1bpi__ 7.6.1.1.1 Pancreatic trypsin inhibitor [b ( 58) 40 16.8 1.9 0.333 0.778 40 9 28 36 1 40 30 38 1 58 0 0 0 d1ptx__ 7.3.6.1.4 scorpion toxin [Androctonus aus ( 64) 39 16.5 2.5 0.324 0.588 39 34 10 39 1 40 16 49 1 64 4 0 0 d1isua_ 7.29.1.1.1 HIPIP (high potential iron pro ( 62) 38 16.2 2.9 0.250 0.625 38 16 22 37 1 40 19 34 1 62 0 0 0 d1poa__ 1.80.1.2.1 Snake phospholipase A2 [taiwan ( 118) 40 17.1 3 0.323 0.516 40 31 1 31 1 40 41 63 1 118 0 8 0 d1amm_1 2.9.1.1.1 (1-85) gamma-Crystallin [bovine ( 85) 38 16.4 3.6 0.300 0.500 38 30 9 30 1 40 14 43 1 85 8 0 0 d1amm_2 2.9.1.1.1 (86-174) gamma-Crystallin [bovi ( 89) 38 16.4 3.7 0.353 0.588 38 17 21 37 1 40 9 25 1 89 0 0 0 d1mla_2 4.31.18.1.1 (126-195) Probable ACP-bindin ( 70) 36 15.7 4.7 0.833 1.000 36 6 2 7 1 40 19 24 1 70 0 0 0 d4ptp__ 2.29.1.2.1 Trypsin(ogen) [bovine (Bos tau ( 223) 39 17.2 5.5 0.417 0.750 39 12 2 13 1 40 108 119 1 223 0 0 0 d1rcf__ 3.13.4.1.3 Flavodoxin [Anabaena 7120] ( 169) 38 16.7 5.6 0.364 0.727 38 11 29 39 1 40 47 57 1 169 0 0 0 d1arb__ 2.29.1.1.1 Achromobacter protease [Achrom ( 263) 39 17.2 6.1 0.353 0.647 39 17 11 25 1 40 2 18 1 263 2 0 0 d1pls__ 2.35.1.1.5 Pleckstrin, N-terminal domain ( 113) 35 15.7 7.7 0.667 1.000 35 6 7 12 1 40 99 104 1 113 0 0 0 d1tgxc_ 7.5.1.1.2 gamma-Cardiotoxin [snake (Naja ( 60) 32 14.5 9.1 0.263 0.526 32 19 19 37 1 40 14 30 1 60 0 2 0 d2eng__ 2.33.1.1.1 Endoglucanase V [Humicola inso ( 205) 36 16.3 9.3 0.462 0.538 36 13 25 37 1 40 191 203 1 205 0 0 0 >>>d2erl__, 40 aa vs testset.fa library 3>>>d8rxna_ 7.34.3.1.1 Rubredoxin [Desulfovibrio vulgaris] - 52 aa vs testset.fa library opt E() < 20 0 0: 22 0 0: one = represents 1 library sequences 24 0 0: 26 0 0: 28 0 0: 30 0 0: 32 0 0: 34 3 1:*== 36 6 3:==*=== 38 3 5:=== * 40 4 6:==== * 42 4 8:==== * 44 9 8:=======*= 46 9 9:========* 48 3 8:=== * 50 5 8:===== * 52 8 7:======*= 54 9 6:=====*=== 56 5 5:====* 58 6 4:===*== 60 5 3:==*== 62 4 3:==*= 64 2 2:=* 66 1 2:=* 68 2 1:*= 70 1 1:* 72 0 1:* 74 0 1:* 76 0 0: 78 0 0: 80 1 0:= 82 1 0:= 84 0 0: 86 0 0: 88 0 0: 90 0 0: 92 1 0:= 94 0 0: 96 0 0: 98 0 0: 100 0 0: 102 0 0: 104 0 0: 106 0 0: 108 0 0: 110 0 0: 112 0 0: 114 0 0: 116 0 0: 118 0 0: >120 1 0:= 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 2.0499+/-0.0385; mu= 21.9713+/- 1.974 mean_var=38.1093+/-11.756, 0's: 0 Z-trim: 1 B-trim: 2 in 1/17 Lambda= 0.207758 Kolmogorov-Smirnov statistic: 0.1091 (N=21) at 50 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.010 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d8rxna_ 7.34.3.1.1 Rubredoxin [Desulfovibrio vulg ( 52) 392 120.7 1.2e-31 1.000 1.000 392 52 1 52 1 52 1 52 1 52 0 0 0 d1bbo_1 7.30.1.1.8 (1-27) Enhancer binding protei ( 27) 55 19.2 0.22 0.429 0.643 55 14 3 16 1 52 1 14 1 27 0 0 0 d8tlne1 1.47.1.1.2 (156-316) Thermolysin [Bacillu ( 161) 53 20.0 0.72 0.500 0.700 53 20 14 32 1 52 52 71 1 161 1 0 0 d1utg__ 1.60.1.1.1 Uteroglobin [Rabbit (Oryctolag ( 70) 49 18.2 1.2 0.304 0.609 49 23 12 34 1 52 27 49 1 70 0 0 0 d1rie__ 7.35.1.2.1 The rieske iron-sulfur protein ( 127) 44 17.1 4.1 0.391 0.478 44 23 4 26 1 52 87 108 1 127 0 1 0 d1ra9__ 3.51.1.1.1 Dihydrofolate reductase, proka ( 159) 44 17.3 4.5 0.444 0.500 44 18 21 37 1 52 116 133 1 159 1 0 0 d2ctb__ 3.50.1.1.1 Carboxypeptidase A [bovine (Bo ( 307) 45 18.2 4.9 0.364 0.636 45 22 17 38 1 52 43 64 1 307 0 0 0 d1igd__ 4.11.1.1.1 Immunoglobulin-binding protein ( 61) 40 15.3 6.8 0.500 0.667 40 12 21 32 1 52 41 52 1 61 0 0 0 d2eng__ 2.33.1.1.1 Endoglucanase V [Humicola inso ( 205) 42 16.9 7.5 0.235 0.500 42 34 9 42 1 52 130 162 1 205 0 1 0 d1hms__ 2.39.1.2.1 Muscle fatty acid binding prot ( 131) 41 16.3 7.7 0.364 0.636 41 22 10 31 1 52 67 87 1 131 0 1 0 d1ptx__ 7.3.6.1.4 scorpion toxin [Androctonus aus ( 64) 39 15.1 8.5 0.375 0.500 39 16 24 39 1 52 1 16 1 64 0 0 0 d1ctj__ 1.3.1.1.1 Cytochrome c6 (synonym: cytochr ( 89) 39 15.4 9.7 0.400 0.600 39 15 5 19 1 52 73 87 1 89 0 0 0 >>>d8rxna_, 52 aa vs testset.fa library 4>>>d1lkka_ 4.47.1.1.1 p56-lck tyrosine kinase [human (Homo sapiens)] - 105 aa vs testset.fa library opt E() < 20 0 0: 22 0 0: one = represents 1 library sequences 24 0 0: 26 0 0: 28 0 0: 30 0 0: 32 0 0: 34 0 1:* 36 1 3:= * 38 4 5:====* 40 4 6:==== * 42 6 8:====== * 44 11 8:=======*=== 46 7 9:======= * 48 10 8:=======*== 50 2 8:== * 52 6 7:======* 54 5 6:=====* 56 5 5:====* 58 8 4:===*==== 60 3 3:==* 62 4 3:==*= 64 2 2:=* 66 2 2:=* 68 5 1:*==== 70 1 1:* 72 0 1:* 74 1 1:* 76 0 0: 78 1 0:= 80 2 0:== 82 0 0: 84 0 0: 86 0 0: 88 0 0: 90 1 0:= 92 0 0: 94 0 0: 96 0 0: 98 0 0: 100 0 0: 102 0 0: 104 0 0: 106 0 0: 108 1 0:= 110 0 0: 112 0 0: 114 0 0: 116 0 0: 118 0 0: >120 1 0:= 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 5.7678+/-0.0487; mu= 6.0174+/- 2.315 mean_var=43.5373+/-14.195, 0's: 0 Z-trim: 2 B-trim: 3 in 1/18 Lambda= 0.194376 Kolmogorov-Smirnov statistic: 0.1339 (N=21) at 54 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.020 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1lkka_ 4.47.1.1.1 p56-lck tyrosine kinase [human ( 105) 719 206.7 6.3e-57 1.000 1.000 719 105 1 105 1 105 1 105 1 105 0 0 0 d1bpi__ 7.6.1.1.1 Pancreatic trypsin inhibitor [b ( 58) 68 24.2 0.029 0.370 0.630 68 27 70 96 1 105 4 30 1 58 0 0 0 d1cus__ 3.13.7.1.1 Cutinase [fungus (Fusarium sol ( 197) 64 22.9 0.25 0.250 0.587 64 92 7 97 1 105 85 163 1 197 1 13 0 d1hms__ 2.39.1.2.1 Muscle fatty acid binding prot ( 131) 55 20.4 0.9 0.349 0.674 55 43 26 68 1 105 53 89 1 131 0 6 0 d2ctb__ 3.50.1.1.1 Carboxypeptidase A [bovine (Bo ( 307) 59 21.4 1.1 0.222 0.556 59 72 15 83 1 105 228 292 1 307 3 7 0 d1plc__ 2.5.1.1.2 Plastocyanin [poplar (Populus n ( 99) 51 19.4 1.4 0.306 0.667 51 36 39 74 1 105 52 86 1 99 0 1 0 d1xsoa_ 2.1.7.1.3 Cu,Zn superoxide dismutase, SOD ( 150) 51 19.3 2.3 0.395 0.684 51 38 39 72 1 105 8 45 1 150 4 0 0 d3pte__ 5.3.1.1.1 D-ala carboxypeptidase/transpep ( 347) 53 19.7 3.9 0.462 0.692 53 13 70 82 1 105 197 209 1 347 0 0 0 d1burd1 3.1.9.1.2 (137-460) Ribulose 1,5-bisphosp ( 324) 52 19.4 4.4 0.368 0.579 52 19 83 101 1 105 86 104 1 324 0 0 0 d3sdhb_ 1.1.1.1.1 Hemoglobin I [ark clam (Scaphar ( 145) 47 18.2 4.7 0.247 0.584 47 89 15 96 1 105 4 91 1 145 7 1 0 d1ycc__ 1.3.1.1.4 Mitochondrial cytochrome c [bak ( 108) 45 17.7 5 0.253 0.506 45 83 25 104 1 105 36 108 1 108 3 10 0 d1ifc__ 2.39.1.2.2 Intestinal fatty acid binding ( 131) 46 17.9 5.1 0.379 0.655 46 29 61 89 1 105 92 118 1 131 0 2 0 d1lam_1 3.33.1.1.1 (1-159) Leucine aminopeptidase ( 159) 47 18.2 5.2 0.275 0.549 47 51 33 83 1 105 11 59 1 159 0 2 0 d8tlne1 1.47.1.1.2 (156-316) Thermolysin [Bacillu ( 161) 46 17.9 6.3 0.304 0.536 46 56 25 76 1 105 26 81 1 161 4 0 0 d2prk__ 3.26.1.1.6 Proteinase K [fungus (Tritirac ( 279) 49 18.6 6.5 0.277 0.523 49 65 31 94 1 105 10 66 1 279 1 8 0 d1aab__ 1.17.1.1.1 HMG1, fragments A and B [rat/h ( 83) 41 16.6 7.9 0.304 0.696 41 23 8 30 1 105 37 59 1 83 0 0 0 d2eng__ 2.33.1.1.1 Endoglucanase V [Humicola inso ( 205) 46 17.8 8.2 0.304 0.739 46 23 24 46 1 105 97 119 1 205 0 0 0 d1hfc__ 4.46.1.5.1 Fibroblast collagenase [human ( 157) 44 17.3 8.9 0.288 0.525 44 59 2 53 1 105 93 151 1 157 7 0 0 d1eco__ 1.1.1.1.13 Erythrocruorin [Midge (Chirono ( 136) 43 17.1 9.2 0.237 0.537 43 80 8 80 1 105 38 116 1 136 7 1 0 >>>d1lkka_, 105 aa vs testset.fa library 5>>>d1ctj__ 1.3.1.1.1 Cytochrome c6 (synonym: cytochrome c553) [(Monoraphidium braunii)] - 89 aa vs testset.fa library opt E() < 20 0 0: 22 0 0: one = represents 1 library sequences 24 0 0: 26 0 0: 28 0 0: 30 0 0: 32 0 0: 34 1 1:* 36 5 3:==*== 38 3 5:=== * 40 4 6:==== * 42 5 8:===== * 44 6 8:====== * 46 8 9:========* 48 12 8:=======*==== 50 8 8:=======* 52 4 7:==== * 54 6 6:=====* 56 5 5:====* 58 8 4:===*==== 60 2 3:==* 62 4 3:==*= 64 4 2:=*== 66 2 2:=* 68 0 1:* 70 0 1:* 72 0 1:* 74 2 1:*= 76 1 0:= 78 0 0: 80 0 0: 82 0 0: 84 1 0:= 86 0 0: 88 0 0: 90 0 0: 92 0 0: 94 0 0: 96 0 0: 98 1 0:= 100 0 0: 102 0 0: 104 0 0: 106 0 0: 108 0 0: 110 0 0: 112 0 0: 114 0 0: 116 0 0: 118 0 0: >120 1 0:= 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 7.3875+/-0.0341; mu= -0.5633+/- 1.525 mean_var=44.4193+/-13.668, 0's: 0 Z-trim: 1 B-trim: 9 in 1/18 Lambda= 0.192437 Kolmogorov-Smirnov statistic: 0.0895 (N=20) at 46 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.030 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1ctj__ 1.3.1.1.1 Cytochrome c6 (synonym: cytochr ( 89) 613 174.9 1.6e-47 1.000 1.000 613 89 1 89 1 89 1 89 1 89 0 0 0 d1ezm_1 1.47.1.1.1 (154-298) Elastase [Pseudomona ( 145) 68 23.3 0.11 0.333 0.593 68 54 19 67 1 89 5 55 1 145 5 3 0 d1ycc__ 1.3.1.1.4 Mitochondrial cytochrome c [bak ( 108) 57 20.4 0.63 0.346 0.577 57 26 7 29 1 89 11 36 1 108 3 0 0 d1cpq__ 1.20.3.2.5 Cytochrome c' [(Rhodobacter ca ( 129) 53 19.2 1.7 0.471 0.706 53 17 5 19 1 89 106 122 1 129 2 0 0 d1mla_2 4.31.18.1.1 (126-195) Probable ACP-bindin ( 70) 47 17.9 2.3 0.462 0.923 47 13 16 28 1 89 54 66 1 70 0 0 0 d1tca__ 3.48.1.7.1 Triacylglycerol lipase [yeast ( 317) 58 20.1 2.4 0.267 0.533 58 75 17 87 1 89 89 161 1 317 4 2 0 d1rcf__ 3.13.4.1.3 Flavodoxin [Anabaena 7120] ( 169) 48 17.7 6.5 0.262 0.541 48 61 23 79 1 89 27 85 1 169 4 2 0 d8rxna_ 7.34.3.1.1 Rubredoxin [Desulfovibrio vulg ( 52) 39 15.9 6.8 0.400 0.600 39 15 73 87 1 89 5 19 1 52 0 0 0 d1fus__ 4.1.1.1.2 RNase F1 [Fusarium moniliforme] ( 106) 44 16.8 7.2 0.360 0.640 44 25 8 27 1 89 76 100 1 106 5 0 0 e1ben.2d1 7.1.1.1.2 Insulin [human (Homo sapiens) ( 28) 34 14.9 7.4 0.304 0.652 34 23 37 59 1 89 2 23 1 28 0 1 0 d1isua_ 7.29.1.1.1 HIPIP (high potential iron pro ( 62) 39 15.8 8.7 0.667 0.889 39 9 20 28 1 89 36 44 1 62 0 0 0 e1ben.2c1 7.1.1.1.2 Insulin [human (Homo sapiens) ( 21) 31 14.2 8.7 0.667 1.000 31 6 51 56 1 89 13 18 1 21 0 0 0 d1amm_1 2.9.1.1.1 (1-85) gamma-Crystallin [bovine ( 85) 41 16.1 9.2 0.357 0.571 41 14 11 24 1 89 11 24 1 85 0 0 0 d1xsoa_ 2.1.7.1.3 Cu,Zn superoxide dismutase, SOD ( 150) 45 16.9 9.6 0.224 0.653 45 49 41 86 1 89 7 54 1 150 3 1 0 d1cus__ 3.13.7.1.1 Cutinase [fungus (Fusarium sol ( 197) 47 17.3 9.6 0.278 0.557 47 97 5 88 1 89 46 140 1 197 13 2 0 >>>d1ctj__, 89 aa vs testset.fa library 6>>>d1bpi__ 7.6.1.1.1 Pancreatic trypsin inhibitor [bovine (Bos taurus)] - 58 aa vs testset.fa library opt E() < 20 0 0: 22 0 0: one = represents 1 library sequences 24 0 0: 26 0 0: 28 0 0: 30 0 0: 32 0 0: 34 1 1:* 36 0 3: * 38 1 5:= * 40 4 6:==== * 42 8 8:=======* 44 7 8:=======* 46 4 9:==== * 48 3 8:=== * 50 12 8:=======*==== 52 13 7:======*====== 54 6 6:=====* 56 4 5:====* 58 4 4:===* 60 7 3:==*==== 62 5 3:==*== 64 5 2:=*=== 66 0 2: * 68 1 1:* 70 2 1:*= 72 1 1:* 74 1 1:* 76 0 0: 78 1 0:= 80 0 0: 82 0 0: 84 0 0: 86 0 0: 88 0 0: 90 1 0:= 92 0 0: 94 0 0: 96 0 0: 98 0 0: 100 0 0: 102 0 0: 104 1 0:= 106 0 0: 108 0 0: 110 0 0: 112 0 0: 114 0 0: 116 0 0: 118 0 0: >120 1 0:= 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= -0.4844+/-0.0241; mu= 31.2372+/- 1.074 mean_var=51.5607+/-17.615, 0's: 0 Z-trim: 2 B-trim: 0 in 0/19 Lambda= 0.178614 Kolmogorov-Smirnov statistic: 0.2214 (N=20) at 48 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.020 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1bpi__ 7.6.1.1.1 Pancreatic trypsin inhibitor [b ( 58) 434 116.8 2.1e-30 1.000 1.000 434 58 1 58 1 58 1 58 1 58 0 0 0 d1lkka_ 4.47.1.1.1 p56-lck tyrosine kinase [human ( 105) 68 23.5 0.049 0.370 0.630 68 27 4 30 1 58 70 96 1 105 0 0 0 d1burd1 3.1.9.1.2 (137-460) Ribulose 1,5-bisphosp ( 324) 58 22.6 0.27 0.345 0.586 58 29 4 31 1 58 72 100 1 324 1 0 0 d1ifc__ 2.39.1.2.2 Intestinal fatty acid binding ( 131) 49 18.9 1.4 0.571 0.786 49 14 29 42 1 58 113 126 1 131 0 0 0 d2prk__ 3.26.1.1.6 Proteinase K [fungus (Tritirac ( 279) 46 19.3 2.3 0.250 0.611 46 36 21 54 1 58 23 58 1 279 2 0 0 d2olba_ 3.68.1.1.1 Oligo-peptide binding protein ( 517) 44 19.8 3.1 0.429 0.500 44 14 2 15 1 58 313 326 1 517 0 0 0 d1isua_ 7.29.1.1.1 HIPIP (high potential iron pro ( 62) 44 16.4 3.7 0.333 0.556 44 27 8 34 1 58 34 59 1 62 0 1 0 d2eng__ 2.33.1.1.1 Endoglucanase V [Humicola inso ( 205) 43 18.1 3.9 0.269 0.500 43 52 3 50 1 58 128 174 1 205 4 5 0 d1ezm_1 1.47.1.1.1 (154-298) Elastase [Pseudomona ( 145) 42 17.3 4.8 0.297 0.541 42 37 20 53 1 58 103 135 1 145 3 4 0 d2mhr__ 1.20.4.1.4 Myohemerythin [sipunculan worm ( 118) 40 16.4 7 0.556 0.778 40 9 45 53 1 58 29 37 1 118 0 0 0 d2erl__ 1.10.1.1.1 ER-1 [Euplotes raikovi] ( 40) 40 14.7 7.6 0.333 0.778 40 9 30 38 1 58 28 36 1 40 0 0 0 d4ptp__ 2.29.1.2.1 Trypsin(ogen) [bovine (Bos tau ( 223) 39 17.2 7.8 0.211 0.447 39 38 2 37 1 58 132 169 1 223 2 0 0 d1ezm_2 4.46.1.1.1 (1-153) Elastase [Pseudomonas ( 153) 39 16.6 8.1 0.207 0.483 39 29 9 37 1 58 53 81 1 153 0 0 0 d1flp__ 1.1.1.1.2 Hemoglobin I [clam (Lucina pect ( 142) 39 16.5 8.1 0.308 0.462 39 39 25 57 1 58 84 122 1 142 6 0 0 d1tca__ 3.48.1.7.1 Triacylglycerol lipase [yeast ( 317) 38 17.5 9 0.538 0.615 38 13 46 58 1 58 13 25 1 317 0 0 0 >>>d1bpi__, 58 aa vs testset.fa library 7>>>d1rgea_ 4.1.1.1.1 RNase Sa [Streptomyces aureofaciens] - 96 aa vs testset.fa library opt E() < 20 0 0: 22 0 0: one = represents 1 library sequences 24 0 0: 26 0 0: 28 0 0: 30 2 0:== 32 0 0: 34 1 1:* 36 4 3:==*= 38 1 5:= * 40 6 6:=====* 42 8 8:=======* 44 5 8:===== * 46 5 9:===== * 48 5 8:===== * 50 4 8:==== * 52 10 7:======*=== 54 6 6:=====* 56 12 5:====*======= 58 4 4:===* 60 4 3:==*= 62 3 3:==* 64 2 2:=* 66 3 2:=*= 68 1 1:* 70 1 1:* 72 0 1:* 74 2 1:*= 76 0 0: 78 0 0: 80 2 0:== 82 1 0:= 84 0 0: 86 0 0: 88 0 0: 90 0 0: 92 0 0: 94 0 0: 96 0 0: 98 0 0: 100 0 0: 102 0 0: 104 0 0: 106 0 0: 108 0 0: 110 0 0: 112 0 0: 114 0 0: 116 0 0: 118 0 0: >120 1 0:= 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 8.4282+/-0.0346; mu= -7.1760+/- 1.706 mean_var=26.6967+/- 8.972, 0's: 0 Z-trim: 1 B-trim: 2 in 1/17 Lambda= 0.248225 Kolmogorov-Smirnov statistic: 0.1628 (N=22) at 50 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.010 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1rgea_ 4.1.1.1.1 RNase Sa [Streptomyces aureofac ( 96) 643 233.1 5.9e-65 1.000 1.000 643 96 1 96 1 96 1 96 1 96 0 0 0 d1burs_ 4.35.1.1.2 Ribulose 1,5-bisphosphate carb ( 123) 50 20.3 0.84 0.340 0.528 50 53 8 52 1 96 15 62 1 123 8 5 0 d1jbc__ 2.18.1.1.1 Concanavalin A [jack bean (Can ( 237) 55 21.1 0.96 0.410 0.590 55 39 14 50 1 96 192 227 1 237 2 3 0 d1aac__ 2.5.1.1.1 Amicyanin [Paracoccus denitrifi ( 105) 48 19.8 0.99 0.250 0.482 48 56 33 85 1 96 41 95 1 105 3 1 0 d1fus__ 4.1.1.1.2 RNase F1 [Fusarium moniliforme] ( 106) 45 18.8 2.1 0.239 0.630 45 46 23 67 1 96 33 71 1 106 1 7 0 d1pfsa_ 2.24.6.1.2 Gene V protein [Pseudomonas ph ( 78) 42 18.2 2.3 0.400 0.560 42 25 25 49 1 96 33 53 1 78 0 4 0 d1whi__ 2.23.1.1.1 Ribosomal protein L14 [Bacillu ( 122) 44 18.2 3.6 0.319 0.553 44 47 35 78 1 96 61 105 1 122 3 2 0 d1cbn__ 7.11.1.1.1 Crambin [abyssinian cabbage (C ( 46) 35 16.5 4.4 0.360 0.440 35 25 44 66 1 96 18 42 1 46 2 0 0 e1ben.2c1 7.1.1.1.2 Insulin [human (Homo sapiens) ( 21) 27 14.9 6.1 0.333 0.833 27 6 91 96 1 96 2 7 1 21 0 0 0 d8tlne1 1.47.1.1.2 (156-316) Thermolysin [Bacillu ( 161) 44 17.7 6.3 0.232 0.482 44 56 34 86 1 96 41 96 1 161 3 0 0 d1mla_1 3.12.1.1.1 (1-125,196-305) Catalytic doma ( 236) 47 18.2 6.7 0.371 0.486 47 35 38 71 1 96 185 218 1 236 1 1 0 d1ezm_1 1.47.1.1.1 (154-298) Elastase [Pseudomona ( 145) 42 17.2 8.3 0.318 0.636 42 22 75 96 1 96 123 144 1 145 0 0 0 d1arb__ 2.29.1.1.1 Achromobacter protease [Achrom ( 263) 47 18.0 8.3 0.286 0.657 47 35 2 36 1 96 2 34 1 263 0 2 0 d1xyzb_ 3.1.1.3.1 Xylanase XynZ (family F) [Clost ( 320) 48 18.1 9.7 0.357 0.571 48 28 11 38 1 96 179 206 1 320 0 0 0 d1igd__ 4.11.1.1.1 Immunoglobulin-binding protein ( 61) 34 15.7 9.8 0.200 0.600 34 35 55 85 1 96 8 42 1 61 4 0 0 >>>d1rgea_, 96 aa vs testset.fa library 8>>>d1cus__ 3.13.7.1.1 Cutinase [fungus (Fusarium solani, subsp. pisi)] - 197 aa vs testset.fa library opt E() < 20 0 0: 22 1 0:= one = represents 1 library sequences 24 0 0: 26 0 0: 28 0 0: 30 0 0: 32 2 0:== 34 3 1:*== 36 4 3:==*= 38 1 5:= * 40 7 6:=====*= 42 3 8:=== * 44 4 8:==== * 46 6 9:====== * 48 7 8:=======* 50 6 8:====== * 52 8 7:======*= 54 6 6:=====* 56 6 5:====*= 58 9 4:===*===== 60 5 3:==*== 62 4 3:==*= 64 3 2:=*= 66 3 2:=*= 68 0 1:* 70 3 1:*== 72 0 1:* 74 0 1:* 76 0 0: 78 0 0: 80 0 0: 82 1 0:= 84 0 0: 86 0 0: 88 0 0: 90 0 0: 92 0 0: 94 0 0: 96 0 0: 98 0 0: 100 0 0: 102 0 0: 104 0 0: 106 0 0: 108 0 0: 110 0 0: 112 0 0: 114 0 0: 116 0 0: 118 0 0: >120 1 0:= 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 12.6187+/-0.0302; mu= -19.9093+/- 1.294 mean_var=61.1400+/-18.142, 0's: 0 Z-trim: 1 B-trim: 0 in 0/19 Lambda= 0.164026 Kolmogorov-Smirnov statistic: 0.1306 (N=20) at 50 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.030 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1cus__ 3.13.7.1.1 Cutinase [fungus (Fusarium sol ( 197) 1291 310.5 1.2e-87 1.000 1.000 1291 197 1 197 1 197 1 197 1 197 0 0 0 d1lkka_ 4.47.1.1.1 p56-lck tyrosine kinase [human ( 105) 64 21.1 0.84 0.272 0.543 64 92 85 163 1 197 7 97 1 105 13 1 0 d8tlne1 1.47.1.1.2 (156-316) Thermolysin [Bacillu ( 161) 61 19.8 3.3 0.235 0.523 61 153 32 181 1 197 17 159 1 161 3 10 0 d1aab__ 1.17.1.1.1 HMG1, fragments A and B [rat/h ( 83) 52 18.7 3.6 0.275 0.525 52 40 66 105 1 197 3 42 1 83 0 0 0 d1rcf__ 3.13.4.1.3 Flavodoxin [Anabaena 7120] ( 169) 60 19.4 4.2 0.250 0.558 60 104 38 133 1 197 17 119 1 169 8 1 0 d1cpq__ 1.20.3.2.5 Cytochrome c' [(Rhodobacter ca ( 129) 55 18.7 5.5 0.298 0.544 55 57 17 69 1 197 50 105 1 129 4 1 0 d1ptf__ 4.48.1.1.2 Histidine-containing phosphoca ( 87) 50 18.1 5.5 0.216 0.608 50 51 67 117 1 197 32 81 1 87 0 1 0 d2mcm__ 2.1.6.1.1 Macromycin [Streptomyces macrom ( 112) 52 18.2 6.6 0.231 0.596 52 52 28 79 1 197 40 90 1 112 0 1 0 d2alp__ 2.29.1.1.3 alpha-Lytic protease [Lysobact ( 198) 59 19.0 6.8 0.233 0.586 59 116 11 107 1 197 12 127 1 198 19 0 0 d1mla_1 3.12.1.1.1 (1-125,196-305) Catalytic doma ( 236) 61 19.2 7.1 0.272 0.570 61 114 20 122 1 197 4 110 1 236 11 7 0 d1tgxc_ 7.5.1.1.2 gamma-Cardiotoxin [snake (Naja ( 60) 43 17.0 7.9 0.333 0.444 43 27 155 181 1 197 14 37 1 60 0 3 0 d1ctj__ 1.3.1.1.1 Cytochrome c6 (synonym: cytochr ( 89) 47 17.4 9.2 0.278 0.557 47 97 46 140 1 197 5 88 1 89 2 13 0 >>>d1cus__, 197 aa vs testset.fa library 9>>>d1arb__ 2.29.1.1.1 Achromobacter protease [Achromobacter lyticus, strain m497-1] - 263 aa vs testset.fa library opt E() < 20 0 0: 22 0 0: one = represents 1 library sequences 24 0 0: 26 0 0: 28 0 0: 30 0 0: 32 1 0:= 34 1 1:* 36 2 3:==* 38 7 5:====*== 40 5 6:=====* 42 8 8:=======* 44 10 8:=======*== 46 7 9:======= * 48 9 8:=======*= 50 5 8:===== * 52 6 7:======* 54 5 6:=====* 56 3 5:=== * 58 6 4:===*== 60 2 3:==* 62 2 3:==* 64 2 2:=* 66 1 2:=* 68 2 1:*= 70 0 1:* 72 1 1:* 74 2 1:*= 76 1 0:= 78 1 0:= 80 1 0:= 82 0 0: 84 0 0: 86 0 0: 88 0 0: 90 0 0: 92 0 0: 94 0 0: 96 0 0: 98 0 0: 100 0 0: 102 0 0: 104 1 0:= 106 1 0:= 108 0 0: 110 0 0: 112 0 0: 114 0 0: 116 0 0: 118 0 0: >120 1 0:= 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 8.5459+/-0.0158; mu= 0.2421+/- 0.678 mean_var=65.7440+/-19.828, 0's: 0 Z-trim: 3 B-trim: 0 in 0/18 Lambda= 0.158178 Kolmogorov-Smirnov statistic: 0.0467 (N=24) at 66 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.030 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1arb__ 2.29.1.1.1 Achromobacter protease [Achrom ( 263) 1803 417.4 1.4e-119 1.000 1.000 1803 263 1 263 1 263 1 263 1 263 0 0 0 d4ptp__ 2.29.1.2.1 Trypsin(ogen) [bovine (Bos tau ( 223) 93 27.3 0.033 0.207 0.502 93 217 31 234 1 263 20 215 1 223 13 21 0 d2sga__ 2.29.1.1.2 Protease A [Streptomyces grise ( 181) 89 26.5 0.047 0.189 0.576 89 132 95 221 1 263 36 163 1 181 5 4 0 d2prk__ 3.26.1.1.6 Proteinase K [fungus (Tritirac ( 279) 73 22.6 1.1 0.228 0.495 73 206 4 178 1 263 32 230 1 279 31 7 0 d2sn3__ 7.3.6.1.1 scorpion toxin [Centruroides sc ( 65) 59 20.2 1.3 0.312 0.562 59 32 206 237 1 263 19 50 1 65 0 0 0 d1xnb__ 2.18.1.8.1 Xylanase II [Bacillus circulan ( 185) 66 21.2 1.8 0.193 0.500 66 166 90 247 1 263 1 164 1 185 8 2 0 d1epne_ 2.32.1.2.1 Endothiapepsin [chestnut bligh ( 330) 70 21.8 2.1 0.275 0.541 70 109 162 261 1 263 25 125 1 330 9 8 0 d1cbn__ 7.11.1.1.1 Crambin [abyssinian cabbage (C ( 46) 53 19.0 2.2 0.364 0.568 53 44 68 110 1 263 6 45 1 46 1 4 0 d1lit__ 4.88.1.1.1 Lithostathine, inhibitor of st ( 131) 61 20.3 2.5 0.229 0.505 61 105 74 176 1 263 6 96 1 131 2 14 0 d8tlne1 1.47.1.1.2 (156-316) Thermolysin [Bacillu ( 161) 59 19.7 4.5 0.177 0.522 59 113 119 231 1 263 9 112 1 161 0 9 0 d2alp__ 2.29.1.1.3 alpha-Lytic protease [Lysobact ( 198) 60 19.8 5.1 0.209 0.516 60 182 52 230 1 263 31 184 1 198 3 28 0 d1fus__ 4.1.1.1.2 RNase F1 [Fusarium moniliforme] ( 106) 54 18.8 5.6 0.194 0.548 54 93 108 196 1 263 5 97 1 106 4 0 0 d1cus__ 3.13.7.1.1 Cutinase [fungus (Fusarium sol ( 197) 57 19.1 8 0.500 0.857 57 14 28 41 1 263 154 167 1 197 0 0 0 d1csee_ 3.26.1.1.1 Subtilisin Carlsberg [Bacillus ( 274) 59 19.4 9 0.254 0.522 59 67 102 165 1 263 201 253 1 274 3 14 0 d3pte__ 5.3.1.1.1 D-ala carboxypeptidase/transpep ( 347) 61 19.8 9 0.229 0.534 61 118 70 181 1 263 140 245 1 347 6 12 0 >>>d1arb__, 263 aa vs testset.fa library 10>>>d1igd__ 4.11.1.1.1 Immunoglobulin-binding protein G, separate domains [group G streptococcus (Streptomyces griseus)] - 61 aa vs testset.fa library opt E() < 20 0 0: 22 0 0: one = represents 1 library sequences 24 0 0: 26 0 0: 28 0 0: 30 0 0: 32 0 0: 34 0 1:* 36 0 3: * 38 0 5: * 40 3 6:=== * 42 6 8:====== * 44 4 8:==== * 46 7 9:======= * 48 8 8:=======* 50 14 8:=======*====== 52 8 7:======*= 54 7 6:=====*= 56 7 5:====*== 58 7 4:===*=== 60 4 3:==*= 62 4 3:==*= 64 3 2:=*= 66 1 2:=* 68 1 1:* 70 1 1:* 72 1 1:* 74 1 1:* 76 4 0:==== 78 0 0: 80 0 0: 82 1 0:= 84 0 0: 86 0 0: 88 0 0: 90 0 0: 92 0 0: 94 0 0: 96 0 0: 98 0 0: 100 0 0: 102 0 0: 104 0 0: 106 0 0: 108 0 0: 110 0 0: 112 0 0: 114 0 0: 116 0 0: 118 0 0: >120 1 0:= 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 8.6855+/-0.0218; mu= -12.1134+/- 1.039 mean_var=48.1471+/-14.933, 0's: 0 Z-trim: 1 B-trim: 0 in 0/19 Lambda= 0.184837 Kolmogorov-Smirnov statistic: 0.2214 (N=20) at 48 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.010 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1igd__ 4.11.1.1.1 Immunoglobulin-binding protein ( 61) 383 108.5 7.4e-28 1.000 1.000 383 61 1 61 1 61 1 61 1 61 0 0 0 d1mnta_ 1.32.1.1.2 Mnt repressor [Salmonella bact ( 66) 47 18.9 0.78 0.235 0.529 47 34 8 41 1 61 21 54 1 66 0 0 0 d4lzm__ 4.2.1.3.1 Phage T4 lysozyme [Escherichia ( 162) 51 19.1 1.6 0.308 0.615 51 39 19 57 1 61 30 67 1 162 0 1 0 d1flp__ 1.1.1.1.2 Hemoglobin I [clam (Lucina pect ( 142) 49 18.7 1.8 0.308 0.615 49 39 15 49 1 61 90 128 1 142 4 0 0 d8rxna_ 7.34.3.1.1 Rubredoxin [Desulfovibrio vulg ( 52) 40 17.2 1.9 0.500 0.667 40 12 41 52 1 61 21 32 1 52 0 0 0 d1fus__ 4.1.1.1.2 RNase F1 [Fusarium moniliforme] ( 106) 46 18.2 2 0.314 0.629 46 35 16 50 1 61 4 38 1 106 0 0 0 d8tlne2 4.46.1.1.2 (1-155) Thermolysin [Bacillus ( 155) 49 18.7 2.1 0.450 0.650 49 20 38 56 1 61 29 48 1 155 1 0 0 d1epne_ 2.32.1.2.1 Endothiapepsin [chestnut bligh ( 330) 54 19.3 2.8 0.302 0.674 54 43 5 47 1 61 89 125 1 330 0 6 0 d1lam_1 3.33.1.1.1 (1-159) Leucine aminopeptidase ( 159) 46 17.8 3.8 0.438 0.750 46 16 37 52 1 61 117 132 1 159 0 0 0 d1cpq__ 1.20.3.2.5 Cytochrome c' [(Rhodobacter ca ( 129) 43 17.2 4.7 0.450 0.800 43 20 14 32 1 61 18 37 1 129 1 0 0 d2alp__ 2.29.1.1.3 alpha-Lytic protease [Lysobact ( 198) 45 17.4 6.4 0.357 0.571 45 28 19 46 1 61 112 139 1 198 0 0 0 d193l__ 4.2.1.2.1 Lysozyme [chicken (Gallus gallu ( 129) 41 16.7 6.7 0.273 0.545 41 33 18 50 1 61 21 53 1 129 0 0 0 d1isua_ 7.29.1.1.1 HIPIP (high potential iron pro ( 62) 34 15.5 7.5 0.250 0.432 34 44 1 44 1 61 6 49 1 62 0 0 0 d1aab__ 1.17.1.1.1 HMG1, fragments A and B [rat/h ( 83) 36 15.7 8.2 0.226 0.613 36 31 15 45 1 61 6 36 1 83 0 0 0 d1cbn__ 7.11.1.1.1 Crambin [abyssinian cabbage (C ( 46) 30 14.6 9.6 0.353 0.588 30 17 4 20 1 61 27 43 1 46 0 0 0 d1hms__ 2.39.1.2.1 Muscle fatty acid binding prot ( 131) 39 16.1 9.8 0.357 0.571 39 28 6 33 1 61 103 130 1 131 0 0 0 >>>d1igd__, 61 aa vs testset.fa library 11>>>d1csee_ 3.26.1.1.1 Subtilisin Carlsberg [Bacillus subtilis] - 274 aa vs testset.fa library opt E() < 20 0 0: 22 0 0: one = represents 1 library sequences 24 0 0: 26 0 0: 28 0 0: 30 1 0:= 32 1 0:= 34 2 1:*= 36 1 3:= * 38 0 4: * 40 5 6:=====* 42 5 8:===== * 44 8 8:=======* 46 5 9:===== * 48 11 8:=======*=== 50 11 7:======*==== 52 6 7:======* 54 9 6:=====*=== 56 5 5:====* 58 3 4:===* 60 5 3:==*== 62 2 2:=* 64 0 2: * 66 1 2:=* 68 2 1:*= 70 0 1:* 72 5 1:*==== 74 0 1:* 76 0 0: 78 1 0:= 80 0 0: 82 0 0: 84 0 0: 86 1 0:= 88 0 0: 90 0 0: 92 1 0:= 94 0 0: 96 0 0: 98 0 0: 100 0 0: 102 0 0: 104 0 0: 106 0 0: 108 0 0: 110 0 0: 112 0 0: 114 0 0: 116 0 0: 118 0 0: >120 2 0:== 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 15.0570+/- 0.049; mu= -31.6935+/- 2.248 mean_var=78.9700+/-28.401, 0's: 0 Z-trim: 2 B-trim: 3 in 1/18 Lambda= 0.144326 Kolmogorov-Smirnov statistic: 0.1278 (N=20) at 46 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.040 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1csee_ 3.26.1.1.1 Subtilisin Carlsberg [Bacillus ( 274) 1717 363.5 2.6e-103 1.000 1.000 1717 274 1 274 1 274 1 274 1 274 0 0 0 d2prk__ 3.26.1.1.6 Proteinase K [fungus (Tritirac ( 279) 481 106.2 7.9e-26 0.373 0.688 481 260 1 246 1 274 2 250 1 279 14 11 0 d3chy__ 3.13.2.1.1 CheY protein [Escherichia coli ( 128) 79 23.8 0.23 0.227 0.667 79 66 92 156 1 274 39 104 1 128 1 0 0 d2alp__ 2.29.1.1.3 alpha-Lytic protease [Lysobact ( 198) 81 23.4 0.44 0.266 0.597 81 154 42 184 1 274 21 168 1 198 11 6 0 d2sga__ 2.29.1.1.2 Protease A [Streptomyces grise ( 181) 71 21.5 1.5 0.277 0.605 71 119 38 149 1 274 77 181 1 181 7 14 0 d1epne_ 2.32.1.2.1 Endothiapepsin [chestnut bligh ( 330) 76 21.5 2.7 0.223 0.518 76 220 48 265 1 274 67 267 1 330 2 19 0 d1xsoa_ 2.1.7.1.3 Cu,Zn superoxide dismutase, SOD ( 150) 64 20.4 2.8 0.281 0.562 64 89 17 97 1 274 22 108 1 150 8 2 0 d2mcm__ 2.1.6.1.1 Macromycin [Streptomyces macrom ( 112) 59 19.8 3 0.250 0.598 59 112 40 138 1 274 2 109 1 112 13 4 0 d2eng__ 2.33.1.1.1 Endoglucanase V [Humicola inso ( 205) 68 20.7 3.1 0.256 0.610 68 82 126 204 1 274 50 124 1 205 3 7 0 d1cpq__ 1.20.3.2.5 Cytochrome c' [(Rhodobacter ca ( 129) 61 20.0 3.1 0.275 0.550 61 109 52 160 1 274 9 106 1 129 0 11 0 d1whi__ 2.23.1.1.1 Ribosomal protein L14 [Bacillu ( 122) 57 19.3 4.8 0.429 0.810 57 21 136 156 1 274 9 29 1 122 0 0 0 d1fus__ 4.1.1.1.2 RNase F1 [Fusarium moniliforme] ( 106) 54 18.9 5.4 0.297 0.649 54 37 126 160 1 274 69 105 1 106 2 0 0 d1ptf__ 4.48.1.1.2 Histidine-containing phosphoca ( 87) 50 18.4 6.3 0.286 0.714 50 28 60 87 1 274 54 81 1 87 0 0 0 d1bbo_1 7.30.1.1.8 (1-27) Enhancer binding protei ( 27) 29 16.0 10 0.231 0.769 29 13 234 246 1 274 9 21 1 27 0 0 0 >>>d1csee_, 274 aa vs testset.fa library 12>>>d1csei_ 4.21.1.1.1 Eglin C [leech (Hirudo medicinalis)] - 63 aa vs testset.fa library opt E() < 20 0 0: 22 0 0: one = represents 1 library sequences 24 0 0: 26 0 0: 28 0 0: 30 0 0: 32 2 0:== 34 6 1:*===== 36 5 3:==*== 38 4 5:====* 40 3 6:=== * 42 8 8:=======* 44 9 8:=======*= 46 6 9:====== * 48 10 8:=======*== 50 3 8:=== * 52 3 7:=== * 54 8 6:=====*== 56 3 5:=== * 58 4 4:===* 60 4 3:==*= 62 4 3:==*= 64 2 2:=* 66 0 2: * 68 2 1:*= 70 0 1:* 72 1 1:* 74 2 1:*= 76 2 0:== 78 0 0: 80 0 0: 82 0 0: 84 0 0: 86 0 0: 88 0 0: 90 0 0: 92 0 0: 94 1 0:= 96 0 0: 98 0 0: 100 0 0: 102 0 0: 104 0 0: 106 0 0: 108 0 0: 110 0 0: 112 0 0: 114 0 0: 116 0 0: 118 0 0: >120 1 0:= 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 7.8456+/-0.0273; mu= -7.1289+/- 1.319 mean_var=23.3126+/- 5.964, 0's: 0 Z-trim: 1 B-trim: 9 in 1/18 Lambda= 0.265631 Kolmogorov-Smirnov statistic: 0.0893 (N=21) at 36 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.010 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1csei_ 4.21.1.1.1 Eglin C [leech (Hirudo medicin ( 63) 435 169.8 2.9e-46 1.000 1.000 435 63 1 63 1 63 1 63 1 63 0 0 0 d1ezm_1 1.47.1.1.1 (154-298) Elastase [Pseudomona ( 145) 53 22.1 0.19 0.289 0.658 53 38 4 35 1 63 50 87 1 145 6 0 0 d1cbn__ 7.11.1.1.1 Crambin [abyssinian cabbage (C ( 46) 36 17.4 1.6 0.444 0.611 36 18 25 42 1 63 13 29 1 46 0 1 0 d1cyo__ 4.62.1.1.1 Cytochrome b5 [bovine (Bos tau ( 88) 41 18.3 1.6 0.310 0.552 41 29 5 32 1 63 10 38 1 88 1 0 0 d8tlne2 4.46.1.1.2 (1-155) Thermolysin [Bacillus ( 155) 44 18.5 2.4 0.293 0.561 44 41 19 58 1 63 103 142 1 155 1 1 0 d1bpi__ 7.6.1.1.1 Pancreatic trypsin inhibitor [b ( 58) 36 17.0 2.6 0.375 0.500 36 16 35 50 1 63 9 24 1 58 0 0 0 d1xnb__ 2.18.1.8.1 Xylanase II [Bacillus circulan ( 185) 44 18.2 3.4 0.283 0.543 44 46 10 55 1 63 117 160 1 185 0 2 0 e6rlx.2c1 7.1.1.1.4 Relaxin [human (Homo sapiens) ( 24) 27 14.9 4.4 0.364 0.727 27 11 53 63 1 63 4 14 1 24 0 0 0 d1aab__ 1.17.1.1.1 HMG1, fragments A and B [rat/h ( 83) 36 16.4 5.4 0.269 0.654 36 26 8 33 1 63 57 82 1 83 0 0 0 d2sn3__ 7.3.6.1.1 scorpion toxin [Centruroides sc ( 65) 33 15.7 7.1 0.667 1.000 33 6 30 35 1 63 51 56 1 65 0 0 0 e1ben.2d1 7.1.1.1.2 Insulin [human (Homo sapiens) ( 28) 26 14.3 7.8 0.750 1.000 26 4 48 51 1 63 25 28 1 28 0 0 0 d1burd2 4.31.9.1.2 (1-136) Ribulose 1,5-bisphosph ( 136) 38 16.4 8.6 0.320 0.480 38 25 28 52 1 63 13 36 1 136 0 1 0 d1rie__ 7.35.1.2.1 The rieske iron-sulfur protein ( 127) 37 16.1 9.7 0.381 0.619 37 21 9 27 1 63 35 55 1 127 2 0 0 >>>d1csei_, 63 aa vs testset.fa library 13>>>d1jbc__ 2.18.1.1.1 Concanavalin A [jack bean (Canavalia ensiformis)] - 237 aa vs testset.fa library opt E() < 20 0 0: 22 0 0: one = represents 1 library sequences 24 0 0: 26 0 0: 28 0 0: 30 0 0: 32 0 0: 34 0 1:* 36 2 3:==* 38 4 5:====* 40 9 6:=====*=== 42 7 8:=======* 44 6 8:====== * 46 7 9:======= * 48 6 8:====== * 50 5 8:===== * 52 10 7:======*=== 54 5 6:=====* 56 7 5:====*== 58 7 4:===*=== 60 4 3:==*= 62 2 3:==* 64 2 2:=* 66 2 2:=* 68 0 1:* 70 1 1:* 72 4 1:*=== 74 0 1:* 76 1 0:= 78 0 0: 80 1 0:= 82 0 0: 84 0 0: 86 0 0: 88 0 0: 90 0 0: 92 0 0: 94 0 0: 96 0 0: 98 0 0: 100 0 0: 102 0 0: 104 0 0: 106 0 0: 108 0 0: 110 0 0: 112 0 0: 114 0 0: 116 0 0: 118 0 0: >120 1 0:= 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 9.7867+/-0.0517; mu= -7.7514+/- 2.455 mean_var=61.9080+/-15.905, 0's: 0 Z-trim: 1 B-trim: 0 in 0/18 Lambda= 0.163005 Kolmogorov-Smirnov statistic: 0.1091 (N=20) at 50 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.030 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1jbc__ 2.18.1.1.1 Concanavalin A [jack bean (Can ( 237) 1539 367.8 1e-104 1.000 1.000 1539 237 1 237 1 237 1 237 1 237 0 0 0 d3pte__ 5.3.1.1.1 D-ala carboxypeptidase/transpep ( 347) 74 22.9 0.96 0.306 0.565 74 62 56 110 1 237 62 123 1 347 7 0 0 d1ezm_1 1.47.1.1.1 (154-298) Elastase [Pseudomona ( 145) 62 20.9 1.7 0.254 0.563 62 71 133 202 1 237 24 87 1 145 1 7 0 d1rgea_ 4.1.1.1.1 RNase Sa [Streptomyces aureofac ( 96) 55 19.6 2.7 0.410 0.590 55 39 192 227 1 237 14 50 1 96 3 2 0 d2cba__ 2.47.1.1.2 Carbonic anhydrase [human (Hom ( 258) 64 20.8 3 0.232 0.512 64 125 91 210 1 237 29 143 1 258 5 10 0 d1pfsa_ 2.24.6.1.2 Gene V protein [Pseudomonas ph ( 78) 52 19.0 3.2 0.361 0.556 52 36 190 225 1 237 23 52 1 78 0 6 0 d2sga__ 2.29.1.1.2 Protease A [Streptomyces grise ( 181) 60 20.2 3.3 0.215 0.508 60 130 103 227 1 237 35 156 1 181 5 8 0 d1ckaa_ 2.20.2.1.1 C-Crk, N-terminal SH3 domain [ ( 57) 48 18.4 3.7 0.333 0.533 48 30 28 54 1 237 24 53 1 57 3 0 0 d1cus__ 3.13.7.1.1 Cutinase [fungus (Fusarium sol ( 197) 58 19.6 5.1 0.333 0.667 58 33 209 237 1 237 58 90 1 197 4 0 0 d2eng__ 2.33.1.1.1 Endoglucanase V [Humicola inso ( 205) 57 19.4 6.4 0.270 0.510 57 100 145 234 1 237 42 132 1 205 10 9 0 d1amm_2 2.9.1.1.1 (86-174) gamma-Crystallin [bovi ( 89) 48 18.0 7.3 0.267 0.567 48 30 20 49 1 237 52 81 1 89 0 0 0 d1rcf__ 3.13.4.1.3 Flavodoxin [Anabaena 7120] ( 169) 54 18.8 7.6 0.292 0.584 54 89 34 115 1 237 1 82 1 169 7 7 0 >>>d1jbc__, 237 aa vs testset.fa library 14>>>d1hms__ 2.39.1.2.1 Muscle fatty acid binding protein (m-fabp) [human (Homo sapiens)] - 131 aa vs testset.fa library opt E() < 20 0 0: 22 0 0: one = represents 1 library sequences 24 0 0: 26 0 0: 28 0 0: 30 0 0: 32 1 0:= 34 0 1:* 36 1 3:= * 38 5 4:===*= 40 11 6:=====*===== 42 8 8:=======* 44 5 8:===== * 46 7 9:======= * 48 10 8:=======*== 50 4 7:==== * 52 5 7:===== * 54 9 6:=====*=== 56 2 5:== * 58 7 4:===*=== 60 4 3:==*= 62 3 2:=*= 64 3 2:=*= 66 1 2:=* 68 1 1:* 70 1 1:* 72 0 1:* 74 0 1:* 76 1 0:= 78 1 0:= 80 0 0: 82 1 0:= 84 0 0: 86 0 0: 88 0 0: 90 0 0: 92 0 0: 94 0 0: 96 0 0: 98 0 0: 100 0 0: 102 0 0: 104 0 0: 106 0 0: 108 0 0: 110 0 0: 112 0 0: 114 0 0: 116 0 0: 118 0 0: >120 2 0:== 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 7.2177+/-0.0472; mu= 0.4442+/- 2.290 mean_var=40.8305+/-12.223, 0's: 0 Z-trim: 2 B-trim: 0 in 0/19 Lambda= 0.200716 Kolmogorov-Smirnov statistic: 0.0548 (N=22) at 52 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.020 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1hms__ 2.39.1.2.1 Muscle fatty acid binding prot ( 131) 836 246.7 8.9e-69 1.000 1.000 836 131 1 131 1 131 1 131 1 131 0 0 0 d1ifc__ 2.39.1.2.2 Intestinal fatty acid binding ( 131) 253 77.8 5.9e-18 0.321 0.679 253 131 3 131 1 131 1 131 1 131 2 0 0 d1lkka_ 4.47.1.1.1 p56-lck tyrosine kinase [human ( 105) 55 20.7 0.78 0.349 0.674 55 43 53 89 1 131 26 68 1 105 6 0 0 d5p21__ 3.24.1.3.1 cH-p21 Ras protein [human (Hom ( 166) 56 20.6 1.2 0.205 0.551 56 78 2 79 1 131 76 150 1 166 0 3 0 d1rcf__ 3.13.4.1.3 Flavodoxin [Anabaena 7120] ( 169) 54 20.1 1.9 0.290 0.581 54 31 84 114 1 131 109 139 1 169 0 0 0 d2cba__ 2.47.1.1.2 Carbonic anhydrase [human (Hom ( 258) 53 19.5 4.2 0.350 0.675 53 40 66 100 1 131 64 101 1 258 5 2 0 d8rxna_ 7.34.3.1.1 Rubredoxin [Desulfovibrio vulg ( 52) 41 17.1 4.5 0.364 0.636 41 22 67 87 1 131 10 31 1 52 1 0 0 d1pls__ 2.35.1.1.5 Pleckstrin, N-terminal domain ( 113) 46 18.0 5.1 0.320 0.640 46 25 67 91 1 131 32 55 1 113 0 1 0 d8tlne2 4.46.1.1.2 (1-155) Thermolysin [Bacillus ( 155) 46 17.8 8 0.333 0.593 46 27 97 123 1 131 115 139 1 155 0 2 0 d1igd__ 4.11.1.1.1 Immunoglobulin-binding protein ( 61) 39 16.4 8.4 0.357 0.571 39 28 103 130 1 131 6 33 1 61 0 0 0 d1tpg_1 7.10.1.1.13 (51-91) Plasminogen activator ( 41) 36 15.8 8.6 0.292 0.583 36 24 16 39 1 131 18 41 1 41 0 0 0 >>>d1hms__, 131 aa vs testset.fa library 15>>>d7rsa__ 4.4.1.1.1 Ribonuclease A (also ribonuclease B, S) [bovine (Bos taurus)] - 124 aa vs testset.fa library opt E() < 20 0 0: 22 0 0: one = represents 1 library sequences 24 0 0: 26 0 0: 28 0 0: 30 0 0: 32 1 0:= 34 2 1:*= 36 5 3:==*== 38 6 5:====*= 40 10 6:=====*==== 42 7 8:=======* 44 7 8:=======* 46 8 9:========* 48 4 8:==== * 50 10 8:=======*== 52 10 7:======*=== 54 5 6:=====* 56 0 5: * 58 5 4:===*= 60 1 3:= * 62 1 3:= * 64 3 2:=*= 66 1 2:=* 68 0 1:* 70 1 1:* 72 0 1:* 74 2 1:*= 76 1 0:= 78 1 0:= 80 0 0: 82 0 0: 84 0 0: 86 0 0: 88 0 0: 90 0 0: 92 0 0: 94 0 0: 96 0 0: 98 0 0: 100 0 0: 102 0 0: 104 0 0: 106 0 0: 108 0 0: 110 1 0:= 112 0 0: 114 0 0: 116 0 0: 118 0 0: >120 1 0:= 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 4.3765+/-0.0433; mu= 15.1441+/- 2.201 mean_var=54.1475+/-14.359, 0's: 0 Z-trim: 2 B-trim: 0 in 0/19 Lambda= 0.174295 Kolmogorov-Smirnov statistic: 0.0914 (N=21) at 40 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.020 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d7rsa__ 4.4.1.1.1 Ribonuclease A (also ribonuclea ( 124) 840 216.9 7.5e-60 1.000 1.000 840 124 1 124 1 124 1 124 1 124 0 0 0 d1poa__ 1.80.1.2.1 Snake phospholipase A2 [taiwan ( 118) 80 25.7 0.024 0.226 0.604 80 53 58 110 1 124 71 118 1 118 0 5 0 d1xyzb_ 3.1.1.3.1 Xylanase XynZ (family F) [Clost ( 320) 61 21.3 1.4 0.242 0.560 61 91 30 114 1 124 193 272 1 320 6 11 0 d3ebx__ 7.5.1.1.1 Erabutoxin B (also neurotoxin B ( 62) 53 18.7 1.6 0.218 0.582 53 55 26 75 1 124 3 57 1 62 5 0 0 d1tpg_1 7.10.1.1.13 (51-91) Plasminogen activator ( 41) 49 17.6 2.4 0.326 0.512 49 43 58 99 1 124 1 38 1 41 1 5 0 d1aab__ 1.17.1.1.1 HMG1, fragments A and B [rat/h ( 83) 52 18.6 2.4 0.225 0.675 52 40 2 41 1 124 20 58 1 83 0 1 0 d2erl__ 1.10.1.1.1 ER-1 [Euplotes raikovi] ( 40) 46 16.8 3.9 0.375 0.583 46 24 52 73 1 124 6 29 1 40 2 0 0 d1krn__ 7.12.1.1.1 Plasminogen kringle 4 [human ( ( 79) 46 17.0 6.5 0.263 0.579 46 38 65 101 1 124 2 39 1 79 1 0 0 d193l__ 4.2.1.2.1 Lysozyme [chicken (Gallus gallu ( 129) 47 17.5 7.9 0.295 0.526 47 78 5 68 1 124 31 104 1 129 14 4 0 d2eng__ 2.33.1.1.1 Endoglucanase V [Humicola inso ( 205) 49 18.1 7.9 0.233 0.567 49 30 93 122 1 124 14 43 1 205 0 0 0 d1lit__ 4.88.1.1.1 Lithostathine, inhibitor of st ( 131) 47 17.5 8 0.292 0.479 47 48 65 112 1 124 1 46 1 131 0 2 0 >>>d7rsa__, 124 aa vs testset.fa library 16>>>d2sn3__ 7.3.6.1.1 scorpion toxin [Centruroides sculpturatus ewing, variant 3] - 65 aa vs testset.fa library opt E() < 20 0 0: 22 0 0: one = represents 1 library sequences 24 0 0: 26 0 0: 28 0 0: 30 0 0: 32 2 0:== 34 2 1:*= 36 0 3: * 38 3 4:===* 40 4 6:==== * 42 4 8:==== * 44 11 8:=======*=== 46 11 9:========*== 48 4 8:==== * 50 8 7:======*= 52 8 7:======*= 54 4 6:==== * 56 6 5:====*= 58 5 4:===*= 60 2 3:==* 62 5 2:=*=== 64 5 2:=*=== 66 1 2:=* 68 1 1:* 70 1 1:* 72 0 1:* 74 1 1:* 76 0 0: 78 0 0: 80 0 0: 82 0 0: 84 2 0:== 86 0 0: 88 1 0:= 90 0 0: 92 0 0: 94 0 0: 96 0 0: 98 0 0: 100 0 0: 102 0 0: 104 0 0: 106 0 0: 108 0 0: 110 0 0: 112 0 0: 114 0 0: 116 0 0: 118 0 0: >120 2 0:== 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 2.5987+/-0.0426; mu= 19.6281+/- 2.089 mean_var=53.8270+/-16.497, 0's: 0 Z-trim: 2 B-trim: 2 in 1/18 Lambda= 0.174813 Kolmogorov-Smirnov statistic: 0.0854 (N=22) at 42 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.010 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d2sn3__ 7.3.6.1.1 scorpion toxin [Centruroides sc ( 65) 495 130.0 2.8e-34 1.000 1.000 495 65 1 65 1 65 1 65 1 65 0 0 0 d1ptx__ 7.3.6.1.4 scorpion toxin [Androctonus aus ( 64) 124 36.5 4.1e-06 0.403 0.581 124 62 1 57 1 65 2 57 1 64 5 6 0 d2erl__ 1.10.1.1.1 ER-1 [Euplotes raikovi] ( 40) 58 19.4 0.34 0.257 0.686 58 35 10 43 1 65 1 34 1 40 1 1 0 d1isua_ 7.29.1.1.1 HIPIP (high potential iron pro ( 62) 56 19.3 0.59 0.326 0.512 56 43 7 44 1 65 17 58 1 62 5 1 0 d1arb__ 2.29.1.1.1 Achromobacter protease [Achrom ( 263) 59 21.2 0.67 0.312 0.562 59 32 19 50 1 65 206 237 1 263 0 0 0 d4ptp__ 2.29.1.2.1 Trypsin(ogen) [bovine (Bos tau ( 223) 51 19.0 2.5 0.250 0.442 51 52 3 47 1 65 164 215 1 223 7 0 0 d1pls__ 2.35.1.1.5 Pleckstrin, N-terminal domain ( 113) 47 17.5 3.7 0.875 1.000 47 8 1 8 1 65 7 14 1 113 0 0 0 d1amm_1 2.9.1.1.1 (1-85) gamma-Crystallin [bovine ( 85) 44 16.5 5.4 0.375 0.562 44 16 36 51 1 65 10 25 1 85 0 0 0 e6rlx.2c1 7.1.1.1.4 Relaxin [human (Homo sapiens) ( 24) 40 14.5 6.1 0.357 0.571 40 14 12 25 1 65 11 24 1 24 0 0 0 d1poa__ 1.80.1.2.1 Snake phospholipase A2 [taiwan ( 118) 43 16.5 7.4 0.389 0.667 43 18 34 51 1 65 79 95 1 118 0 1 0 d2sga__ 2.29.1.1.2 Protease A [Streptomyces grise ( 181) 44 17.1 7.5 0.271 0.500 44 48 3 50 1 65 90 135 1 181 0 2 0 d1rie__ 7.35.1.2.1 The rieske iron-sulfur protein ( 127) 43 16.6 7.6 0.368 0.526 43 19 24 42 1 65 74 92 1 127 0 0 0 d1utg__ 1.60.1.1.1 Uteroglobin [Rabbit (Oryctolag ( 70) 41 15.6 8.2 0.421 0.579 41 19 39 57 1 65 1 19 1 70 0 0 0 d1fus__ 4.1.1.1.2 RNase F1 [Fusarium moniliforme] ( 106) 42 16.2 8.3 0.240 0.540 42 50 17 64 1 65 16 63 1 106 2 2 0 d1tpg_1 7.10.1.1.13 (51-91) Plasminogen activator ( 41) 39 14.7 9.1 0.346 0.500 39 26 40 65 1 65 17 34 1 41 0 8 0 d1lit__ 4.88.1.1.1 Lithostathine, inhibitor of st ( 131) 42 16.3 9.1 0.300 0.433 42 30 30 58 1 65 72 101 1 131 1 0 0 d2eng__ 2.33.1.1.1 Endoglucanase V [Humicola inso ( 205) 43 16.9 9.3 0.241 0.517 43 29 31 58 1 65 1 29 1 205 1 0 0 >>>d2sn3__, 65 aa vs testset.fa library 17>>>d1ifc__ 2.39.1.2.2 Intestinal fatty acid binding protein [rat (Rattus rattus)] - 131 aa vs testset.fa library opt E() < 20 0 0: 22 0 0: one = represents 1 library sequences 24 0 0: 26 0 0: 28 1 0:= 30 2 0:== 32 0 0: 34 2 1:*= 36 4 3:==*= 38 6 4:===*== 40 5 6:=====* 42 9 8:=======*= 44 8 8:=======* 46 4 9:==== * 48 7 8:=======* 50 11 7:======*==== 52 4 7:==== * 54 4 6:==== * 56 6 5:====*= 58 5 4:===*= 60 6 3:==*=== 62 2 2:=* 64 0 2: * 66 1 2:=* 68 1 1:* 70 0 1:* 72 1 1:* 74 0 1:* 76 2 0:== 78 0 0: 80 0 0: 82 0 0: 84 0 0: 86 0 0: 88 0 0: 90 0 0: 92 0 0: 94 0 0: 96 0 0: 98 0 0: 100 0 0: 102 0 0: 104 0 0: 106 0 0: 108 0 0: 110 0 0: 112 0 0: 114 0 0: 116 0 0: 118 0 0: >120 2 0:== 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 14.8304+/-0.0272; mu= -33.6391+/- 1.257 mean_var=76.1984+/-23.253, 0's: 0 Z-trim: 2 B-trim: 0 in 0/19 Lambda= 0.146927 Kolmogorov-Smirnov statistic: 0.0651 (N=19) at 42 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.010 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1ifc__ 2.39.1.2.2 Intestinal fatty acid binding ( 131) 844 185.6 2.1e-50 1.000 1.000 844 131 1 131 1 131 1 131 1 131 0 0 0 d1hms__ 2.39.1.2.1 Muscle fatty acid binding prot ( 131) 253 60.3 1.1e-12 0.321 0.679 253 131 1 131 1 131 3 131 1 131 0 2 0 d3sdhb_ 1.1.1.1.1 Hemoglobin I [ark clam (Scaphar ( 145) 64 20.1 1.6 0.234 0.596 64 47 74 120 1 131 31 77 1 145 0 0 0 d1bpi__ 7.6.1.1.1 Pancreatic trypsin inhibitor [b ( 58) 49 18.5 1.9 0.571 0.786 49 14 113 126 1 131 29 42 1 58 0 0 0 e6rlx.2d1 7.1.1.1.4 Relaxin [human (Homo sapiens) ( 25) 34 16.7 2.8 0.417 0.583 34 12 81 92 1 131 1 12 1 25 0 0 0 d1ptf__ 4.48.1.1.2 Histidine-containing phosphoca ( 87) 50 18.0 4 0.227 0.636 50 66 18 81 1 131 1 64 1 87 2 2 0 d1pls__ 2.35.1.1.5 Pleckstrin, N-terminal domain ( 113) 52 18.0 5.2 0.246 0.594 52 69 42 106 1 131 7 70 1 113 4 5 0 >>>d1ifc__, 131 aa vs testset.fa library 18>>>d1ptx__ 7.3.6.1.4 scorpion toxin [Androctonus australius hector, toxin II] - 64 aa vs testset.fa library opt E() < 20 0 0: 22 0 0: one = represents 1 library sequences 24 0 0: 26 0 0: 28 0 0: 30 0 0: 32 0 0: 34 1 1:* 36 5 3:==*== 38 3 4:===* 40 3 6:=== * 42 6 8:====== * 44 6 8:====== * 46 7 9:======= * 48 8 8:=======* 50 9 7:======*== 52 5 7:===== * 54 7 6:=====*= 56 10 5:====*===== 58 2 4:== * 60 3 3:==* 62 3 2:=*= 64 4 2:=*== 66 0 2: * 68 3 1:*== 70 2 1:*= 72 2 1:*= 74 0 1:* 76 0 0: 78 1 0:= 80 0 0: 82 0 0: 84 0 0: 86 1 0:= 88 0 0: 90 0 0: 92 0 0: 94 0 0: 96 0 0: 98 0 0: 100 0 0: 102 0 0: 104 0 0: 106 0 0: 108 0 0: 110 0 0: 112 0 0: 114 0 0: 116 0 0: 118 0 0: >120 2 0:== 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 1.9648+/-0.0186; mu= 22.4573+/- 0.787 mean_var=41.7970+/-11.623, 0's: 0 Z-trim: 2 B-trim: 0 in 0/19 Lambda= 0.198382 Kolmogorov-Smirnov statistic: 0.0978 (N=21) at 52 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.000 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1ptx__ 7.3.6.1.4 scorpion toxin [Androctonus aus ( 64) 500 147.2 1.9e-39 1.000 1.000 500 64 1 64 1 64 1 64 1 64 0 0 0 d2sn3__ 7.3.6.1.1 scorpion toxin [Centruroides sc ( 65) 124 39.6 4.7e-07 0.403 0.581 124 62 2 57 1 64 1 57 1 65 6 5 0 d1amm_1 2.9.1.1.1 (1-85) gamma-Crystallin [bovine ( 85) 54 19.8 0.57 0.234 0.489 54 47 9 54 1 64 38 84 1 85 1 0 0 d1poa__ 1.80.1.2.1 Snake phospholipase A2 [taiwan ( 118) 50 18.9 1.4 0.350 0.500 50 40 4 42 1 64 34 63 1 118 1 10 0 d1tpg_1 7.10.1.1.13 (51-91) Plasminogen activator ( 41) 45 16.6 2.5 0.345 0.621 45 29 22 48 1 64 1 25 1 41 2 4 0 d4ptp__ 2.29.1.2.1 Trypsin(ogen) [bovine (Bos tau ( 223) 47 18.6 3.2 0.268 0.500 47 56 4 58 1 64 154 208 1 223 1 1 0 d2cba__ 2.47.1.1.2 Carbonic anhydrase [human (Hom ( 258) 47 18.7 3.4 0.250 0.469 47 32 28 59 1 64 111 142 1 258 0 0 0 d193l__ 4.2.1.2.1 Lysozyme [chicken (Gallus gallu ( 129) 45 17.6 3.9 0.258 0.452 45 31 5 29 1 64 53 83 1 129 6 0 0 d2eng__ 2.33.1.1.1 Endoglucanase V [Humicola inso ( 205) 45 18.0 4.6 0.444 0.611 45 18 43 60 1 64 84 98 1 205 0 3 0 d1lit__ 4.88.1.1.1 Lithostathine, inhibitor of st ( 131) 44 17.3 4.7 0.308 0.769 44 13 26 38 1 64 102 114 1 131 0 0 0 d1isua_ 7.29.1.1.1 HIPIP (high potential iron pro ( 62) 42 16.1 5.3 0.278 0.444 42 36 28 63 1 64 21 55 1 62 0 1 0 e6rlx.2c1 7.1.1.1.4 Relaxin [human (Homo sapiens) ( 24) 38 14.1 7.9 0.333 0.611 38 18 19 36 1 64 8 24 1 24 0 1 0 d2erl__ 1.10.1.1.1 ER-1 [Euplotes raikovi] ( 40) 39 14.8 7.9 0.324 0.588 39 34 16 49 1 64 10 39 1 40 0 4 0 d2olba_ 3.68.1.1.1 Oligo-peptide binding protein ( 517) 44 18.5 7.9 0.538 0.769 44 13 23 35 1 64 341 353 1 517 0 0 0 d8rxna_ 7.34.3.1.1 Rubredoxin [Desulfovibrio vulg ( 52) 39 15.0 8.7 0.375 0.500 39 16 1 16 1 64 24 39 1 52 0 0 0 e1ben.2c1 7.1.1.1.2 Insulin [human (Homo sapiens) ( 21) 37 13.7 9.1 0.400 0.600 37 15 12 23 1 64 7 21 1 21 3 0 0 d1epne_ 2.32.1.2.1 Endothiapepsin [chestnut bligh ( 330) 42 17.5 9.8 0.321 0.500 42 28 17 44 1 64 55 81 1 330 0 1 0 >>>d1ptx__, 64 aa vs testset.fa library 19>>>d3sdhb_ 1.1.1.1.1 Hemoglobin I [ark clam (Scapharca inaequivalvis)] - 145 aa vs testset.fa library opt E() < 20 0 0: 22 0 0: one = represents 1 library sequences 24 0 0: 26 0 0: 28 2 0:== 30 1 0:= 32 1 0:= 34 2 1:*= 36 1 3:= * 38 2 4:== * 40 4 6:==== * 42 5 8:===== * 44 7 8:=======* 46 5 8:===== * 48 11 8:=======*=== 50 15 7:======*======== 52 5 6:=====* 54 7 6:=====*= 56 5 5:====* 58 4 4:===* 60 1 3:= * 62 2 2:=* 64 1 2:=* 66 2 2:=* 68 3 1:*== 70 2 1:*= 72 0 1:* 74 0 1:* 76 0 0: 78 0 0: 80 1 0:= 82 0 0: 84 0 0: 86 0 0: 88 1 0:= 90 0 0: 92 0 0: 94 0 0: 96 0 0: 98 0 0: 100 0 0: 102 0 0: 104 0 0: 106 0 0: 108 0 0: 110 0 0: 112 0 0: 114 0 0: 116 0 0: 118 0 0: >120 3 0:=== 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 9.5459+/-0.0148; mu= -9.4798+/- 0.616 mean_var=45.9478+/-18.806, 0's: 0 Z-trim: 3 B-trim: 0 in 0/19 Lambda= 0.189209 Kolmogorov-Smirnov statistic: 0.1015 (N=22) at 46 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.020 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d3sdhb_ 1.1.1.1.1 Hemoglobin I [ark clam (Scaphar ( 145) 933 259.5 1.5e-72 1.000 1.000 933 145 1 145 1 145 1 145 1 145 0 0 0 d1bvc__ 1.1.1.1.4 Myoglobin [sperm whale (Physete ( 153) 121 37.8 8.7e-06 0.256 0.562 121 121 21 137 1 145 14 131 1 153 4 3 0 d1flp__ 1.1.1.1.2 Hemoglobin I [clam (Lucina pect ( 142) 116 36.5 2e-05 0.232 0.641 116 142 9 145 1 145 2 138 1 142 5 5 0 d1ifc__ 2.39.1.2.2 Intestinal fatty acid binding ( 131) 64 22.4 0.32 0.234 0.596 64 47 31 77 1 145 74 120 1 131 0 0 0 d1eco__ 1.1.1.1.13 Erythrocruorin [Midge (Chirono ( 136) 58 20.7 1.1 0.188 0.580 58 112 27 134 1 145 14 121 1 136 4 4 0 e1ben.2c1 7.1.1.1.2 Insulin [human (Homo sapiens) ( 21) 34 16.3 3.4 0.455 0.727 34 11 69 79 1 145 9 19 1 21 0 0 0 d1aab__ 1.17.1.1.1 HMG1, fragments A and B [rat/h ( 83) 47 18.3 3.4 0.259 0.741 47 27 4 30 1 145 32 57 1 83 0 1 0 d2mcm__ 2.1.6.1.1 Macromycin [Streptomyces macrom ( 112) 48 18.2 4.8 0.400 0.880 48 25 4 27 1 145 57 79 1 112 1 2 0 d1lkka_ 4.47.1.1.1 p56-lck tyrosine kinase [human ( 105) 47 18.0 5.2 0.247 0.584 47 89 4 91 1 145 15 96 1 105 1 7 0 d2mhr__ 1.20.4.1.4 Myohemerythin [sipunculan worm ( 118) 48 18.2 5.3 0.286 0.653 48 49 84 129 1 145 38 83 1 118 3 3 0 d2hbg__ 1.1.1.1.3 Glycera globin [marine bloodwor ( 147) 50 18.4 5.4 0.218 0.545 50 55 9 61 1 145 2 56 1 147 2 0 0 d3pte__ 5.3.1.1.1 D-ala carboxypeptidase/transpep ( 347) 58 19.6 5.6 0.480 0.600 58 25 56 80 1 145 165 187 1 347 0 2 0 d8rxna_ 7.34.3.1.1 Rubredoxin [Desulfovibrio vulg ( 52) 38 16.4 7.9 0.600 0.600 38 10 84 93 1 145 32 41 1 52 0 0 0 d1whi__ 2.23.1.1.1 Ribosomal protein L14 [Bacillu ( 122) 45 17.3 9.7 0.353 0.618 45 34 114 144 1 145 13 46 1 122 3 0 0 >>>d3sdhb_, 145 aa vs testset.fa library 20>>>d1aac__ 2.5.1.1.1 Amicyanin [Paracoccus denitrificans] - 105 aa vs testset.fa library opt E() < 20 0 0: 22 0 0: one = represents 1 library sequences 24 0 0: 26 0 0: 28 0 0: 30 0 0: 32 0 0: 34 0 1:* 36 3 3:==* 38 3 4:===* 40 2 6:== * 42 5 8:===== * 44 13 8:=======*===== 46 8 9:========* 48 10 8:=======*== 50 7 7:======* 52 6 7:======* 54 2 6:== * 56 7 5:====*== 58 3 4:===* 60 7 3:==*==== 62 3 2:=*= 64 4 2:=*== 66 0 2: * 68 2 1:*= 70 1 1:* 72 1 1:* 74 1 1:* 76 0 0: 78 1 0:= 80 1 0:= 82 0 0: 84 0 0: 86 1 0:= 88 0 0: 90 0 0: 92 0 0: 94 0 0: 96 0 0: 98 0 0: 100 0 0: 102 0 0: 104 0 0: 106 0 0: 108 0 0: 110 0 0: 112 0 0: 114 0 0: 116 0 0: 118 0 0: >120 2 0:== 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 6.1827+/-0.0359; mu= 2.5332+/- 1.711 mean_var=32.8707+/-10.781, 0's: 0 Z-trim: 2 B-trim: 0 in 0/18 Lambda= 0.223702 Kolmogorov-Smirnov statistic: 0.1069 (N=22) at 42 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.020 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1aac__ 2.5.1.1.1 Amicyanin [Paracoccus denitrifi ( 105) 700 230.1 5.7e-64 1.000 1.000 700 105 1 105 1 105 1 105 1 105 0 0 0 d1plc__ 2.5.1.1.2 Plastocyanin [poplar (Populus n ( 99) 109 39.4 1.4e-06 0.242 0.582 109 91 24 104 1 105 8 98 1 99 10 0 0 d1whi__ 2.23.1.1.1 Ribosomal protein L14 [Bacillu ( 122) 53 21.2 0.5 0.275 0.627 53 51 5 55 1 105 2 51 1 122 0 1 0 d1rgea_ 4.1.1.1.1 RNase Sa [Streptomyces aureofac ( 96) 48 19.7 1.1 0.250 0.482 48 56 41 95 1 105 33 85 1 96 1 3 0 d1ezm_2 4.46.1.1.1 (1-153) Elastase [Pseudomonas ( 153) 50 20.1 1.3 0.283 0.509 50 53 15 62 1 105 31 83 1 153 5 0 0 d8tlne2 4.46.1.1.2 (1-155) Thermolysin [Bacillus ( 155) 48 19.4 2.1 0.273 0.545 48 44 18 61 1 105 37 79 1 155 0 1 0 d2prk__ 3.26.1.1.6 Proteinase K [fungus (Tritirac ( 279) 50 19.8 3 0.226 0.538 50 93 3 90 1 105 15 104 1 279 5 3 0 d1eco__ 1.1.1.1.13 Erythrocruorin [Midge (Chirono ( 136) 45 18.5 3.4 0.226 0.548 45 84 1 82 1 105 45 125 1 136 2 3 0 d4ptp__ 2.29.1.2.1 Trypsin(ogen) [bovine (Bos tau ( 223) 47 18.9 4.3 0.208 0.542 47 48 1 48 1 105 171 218 1 223 0 0 0 d1mla_1 3.12.1.1.1 (1-125,196-305) Catalytic doma ( 236) 47 18.9 4.7 0.237 0.605 47 38 2 37 1 105 120 157 1 236 2 0 0 d4lzm__ 4.2.1.3.1 Phage T4 lysozyme [Escherichia ( 162) 43 17.8 6.7 0.250 0.544 43 68 39 104 1 105 87 150 1 162 2 4 0 d2olba_ 3.68.1.1.1 Oligo-peptide binding protein ( 517) 50 19.4 7 0.289 0.644 50 45 13 57 1 105 351 392 1 517 0 3 0 d1epne_ 2.32.1.2.1 Endothiapepsin [chestnut bligh ( 330) 47 18.7 7.3 0.222 0.519 47 81 9 89 1 105 46 123 1 330 0 3 0 d1isua_ 7.29.1.1.1 HIPIP (high potential iron pro ( 62) 36 16.1 8.4 0.556 0.778 36 9 5 13 1 105 29 37 1 62 0 0 0 d1ptx__ 7.3.6.1.4 scorpion toxin [Androctonus aus ( 64) 36 16.0 8.8 0.600 0.700 36 10 16 25 1 105 1 10 1 64 0 0 0 d1lit__ 4.88.1.1.1 Lithostathine, inhibitor of st ( 131) 40 16.9 9.6 0.212 0.538 40 52 41 91 1 105 18 62 1 131 1 7 0 >>>d1aac__, 105 aa vs testset.fa library 21>>>d256bb_ 1.20.3.1.1 Cytochrome b562 [Escherichia coli] - 106 aa vs testset.fa library opt E() < 20 0 0: 22 0 0: one = represents 1 library sequences 24 0 0: 26 0 0: 28 0 0: 30 0 0: 32 1 0:= 34 1 1:* 36 1 3:= * 38 4 5:====* 40 7 6:=====*= 42 7 8:=======* 44 6 8:====== * 46 5 9:===== * 48 7 8:=======* 50 7 8:=======* 52 8 7:======*= 54 6 6:=====* 56 7 5:====*== 58 4 4:===* 60 3 3:==* 62 3 3:==* 64 5 2:=*=== 66 3 2:=*= 68 2 1:*= 70 1 1:* 72 2 1:*= 74 0 1:* 76 0 0: 78 0 0: 80 0 0: 82 0 0: 84 0 0: 86 1 0:= 88 0 0: 90 0 0: 92 0 0: 94 1 0:= 96 0 0: 98 0 0: 100 0 0: 102 0 0: 104 0 0: 106 0 0: 108 0 0: 110 0 0: 112 0 0: 114 0 0: 116 0 0: 118 0 0: >120 1 0:= 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 5.5511+/-0.0312; mu= 5.1418+/- 1.499 mean_var=31.5876+/-10.079, 0's: 0 Z-trim: 1 B-trim: 0 in 0/19 Lambda= 0.228200 Kolmogorov-Smirnov statistic: 0.1091 (N=22) at 50 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.010 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d256bb_ 1.20.3.1.1 Cytochrome b562 [Escherichia c ( 106) 676 226.6 6.3e-63 1.000 1.000 676 106 1 106 1 106 1 106 1 106 0 0 0 d2olba_ 3.68.1.1.1 Oligo-peptide binding protein ( 517) 65 24.9 0.17 0.348 0.674 65 46 48 93 1 106 431 471 1 517 0 5 0 d1cpq__ 1.20.3.2.5 Cytochrome c' [(Rhodobacter ca ( 129) 53 21.4 0.45 0.274 0.435 53 62 45 106 1 106 65 126 1 129 0 0 0 d4xis__ 3.1.11.1.4 D-xylose isomerase [streptomyc ( 386) 51 20.4 2.8 0.288 0.576 51 59 19 76 1 106 143 199 1 386 1 2 0 d1hfc__ 4.46.1.5.1 Fibroblast collagenase [human ( 157) 46 19.1 2.8 0.279 0.605 46 43 47 89 1 106 11 51 1 157 0 2 0 d1flp__ 1.1.1.1.2 Hemoglobin I [clam (Lucina pect ( 142) 44 18.4 3.8 0.353 0.588 44 34 54 85 1 106 57 90 1 142 2 0 0 d1jbc__ 2.18.1.1.1 Concanavalin A [jack bean (Can ( 237) 46 18.9 4.6 0.265 0.647 46 34 51 84 1 106 200 229 1 237 0 4 0 d2phy__ 4.57.2.1.1 Photoactive yellow protein [Ec ( 125) 42 17.8 5.1 0.243 0.527 42 74 2 64 1 106 10 82 1 125 11 1 0 d1lam_1 3.33.1.1.1 (1-159) Leucine aminopeptidase ( 159) 43 18.1 5.5 0.250 0.688 43 32 49 79 1 106 11 42 1 159 1 0 0 d2mhr__ 1.20.4.1.4 Myohemerythin [sipunculan worm ( 118) 41 17.5 5.9 0.236 0.491 41 55 21 73 1 106 38 92 1 118 2 0 0 d1rro__ 1.31.1.4.1 Oncomodulin [rat (Rattus norve ( 108) 40 17.2 6.7 0.204 0.612 40 49 38 83 1 106 6 54 1 108 3 0 0 d1mnta_ 1.32.1.1.2 Mnt repressor [Salmonella bact ( 66) 37 16.4 7.1 0.429 0.786 37 14 68 81 1 106 48 61 1 66 0 0 0 d1eco__ 1.1.1.1.13 Erythrocruorin [Midge (Chirono ( 136) 41 17.5 7.1 0.303 0.667 41 33 14 46 1 106 24 54 1 136 0 2 0 d1utg__ 1.60.1.1.1 Uteroglobin [Rabbit (Oryctolag ( 70) 37 16.4 7.6 0.333 0.521 37 48 13 56 1 106 24 67 1 70 4 4 0 d1xsoa_ 2.1.7.1.3 Cu,Zn superoxide dismutase, SOD ( 150) 41 17.4 8 0.412 0.647 41 17 66 82 1 106 122 138 1 150 0 0 0 d1amm_2 2.9.1.1.1 (86-174) gamma-Crystallin [bovi ( 89) 38 16.7 8.1 0.241 0.621 38 29 47 70 1 106 16 44 1 89 5 0 0 >>>d256bb_, 106 aa vs testset.fa library 22>>>d1plc__ 2.5.1.1.2 Plastocyanin [poplar (Populus nigra variant italica)] - 99 aa vs testset.fa library opt E() < 20 0 0: 22 0 0: one = represents 1 library sequences 24 0 0: 26 0 0: 28 1 0:= 30 0 0: 32 0 0: 34 2 1:*= 36 3 3:==* 38 2 4:== * 40 7 6:=====*= 42 7 8:=======* 44 9 8:=======*= 46 4 9:==== * 48 2 8:== * 50 11 7:======*==== 52 10 7:======*=== 54 3 6:=== * 56 6 5:====*= 58 5 4:===*= 60 1 3:= * 62 4 2:=*== 64 2 2:=* 66 5 2:=*=== 68 3 1:*== 70 1 1:* 72 0 1:* 74 0 1:* 76 1 0:= 78 0 0: 80 1 0:= 82 1 0:= 84 0 0: 86 0 0: 88 0 0: 90 0 0: 92 0 0: 94 0 0: 96 0 0: 98 0 0: 100 0 0: 102 0 0: 104 0 0: 106 0 0: 108 0 0: 110 0 0: 112 0 0: 114 0 0: 116 0 0: 118 0 0: >120 2 0:== 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= 7.0280+/-0.0276; mu= 0.7782+/- 1.266 mean_var=33.2037+/- 9.619, 0's: 0 Z-trim: 2 B-trim: 3 in 1/17 Lambda= 0.222578 Kolmogorov-Smirnov statistic: 0.1190 (N=22) at 48 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.010 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1plc__ 2.5.1.1.2 Plastocyanin [poplar (Populus n ( 99) 648 211.6 1.9e-58 1.000 1.000 648 99 1 99 1 99 1 99 1 99 0 0 0 d1aac__ 2.5.1.1.1 Amicyanin [Paracoccus denitrifi ( 105) 109 38.4 2.6e-06 0.242 0.582 109 91 8 98 1 99 24 104 1 105 0 10 0 d2eng__ 2.33.1.1.1 Endoglucanase V [Humicola inso ( 205) 57 21.2 0.79 0.273 0.489 57 88 22 97 1 99 22 109 1 205 12 0 0 d1lkka_ 4.47.1.1.1 p56-lck tyrosine kinase [human ( 105) 51 19.8 1.1 0.306 0.667 51 36 52 86 1 99 39 74 1 105 1 0 0 d4xis__ 3.1.11.1.4 D-xylose isomerase [streptomyc ( 386) 58 21.0 1.7 0.311 0.600 58 45 2 39 1 99 189 231 1 386 7 2 0 d193l__ 4.2.1.2.1 Lysozyme [chicken (Gallus gallu ( 129) 47 18.3 3.5 0.217 0.600 47 60 6 65 1 99 49 107 1 129 0 1 0 d3ebx__ 7.5.1.1.1 Erabutoxin B (also neurotoxin B ( 62) 41 17.0 4.2 0.273 0.545 41 44 22 64 1 99 18 61 1 62 1 0 0 d1isua_ 7.29.1.1.1 HIPIP (high potential iron pro ( 62) 40 16.7 5.2 0.333 0.733 40 15 10 24 1 99 38 52 1 62 0 0 0 d1rie__ 7.35.1.2.1 The rieske iron-sulfur protein ( 127) 45 17.7 5.3 0.353 0.706 45 17 72 87 1 99 76 92 1 127 1 0 0 e1ben.2d1 7.1.1.1.2 Insulin [human (Homo sapiens) ( 28) 34 15.4 5.7 0.444 0.778 34 9 78 86 1 99 20 28 1 28 0 0 0 d2mhr__ 1.20.4.1.4 Myohemerythin [sipunculan worm ( 118) 44 17.5 5.8 0.391 0.739 44 23 50 71 1 99 91 113 1 118 1 0 0 d1ycc__ 1.3.1.1.4 Mitochondrial cytochrome c [bak ( 108) 43 17.2 6.3 0.239 0.609 43 46 21 66 1 99 33 77 1 108 0 1 0 d1cpq__ 1.20.3.2.5 Cytochrome c' [(Rhodobacter ca ( 129) 44 17.4 6.7 0.230 0.554 44 74 25 91 1 99 44 115 1 129 7 2 0 d1lit__ 4.88.1.1.1 Lithostathine, inhibitor of st ( 131) 44 17.4 6.8 0.350 0.700 44 20 16 35 1 99 94 111 1 131 0 2 0 d1ckaa_ 2.20.2.1.1 C-Crk, N-terminal SH3 domain [ ( 57) 38 16.1 7.1 0.275 0.600 38 40 59 98 1 99 15 51 1 57 0 3 0 d1mnta_ 1.32.1.1.2 Mnt repressor [Salmonella bact ( 66) 39 16.3 7.1 0.309 0.471 39 68 8 63 1 99 3 66 1 66 12 4 0 d1mla_2 4.31.18.1.1 (126-195) Probable ACP-bindin ( 70) 38 16.0 9.6 0.500 0.900 38 10 4 13 1 99 8 17 1 70 0 0 0 >>>d1plc__, 99 aa vs testset.fa library 23>>>d1amm_1 2.9.1.1.1 (1-85) gamma-Crystallin [bovine (Bos taurus) isoform II (B)] - 85 aa vs testset.fa library opt E() < 20 0 0: 22 0 0: one = represents 1 library sequences 24 0 0: 26 0 0: 28 1 0:= 30 2 0:== 32 3 0:=== 34 1 1:* 36 2 3:==* 38 5 4:===*= 40 5 6:=====* 42 4 8:==== * 44 7 8:=======* 46 6 9:====== * 48 10 8:=======*== 50 11 7:======*==== 52 6 7:======* 54 5 6:=====* 56 4 5:====* 58 5 4:===*= 60 3 3:==* 62 1 2:=* 64 4 2:=*== 66 0 2: * 68 1 1:* 70 3 1:*== 72 1 1:* 74 1 1:* 76 0 0: 78 0 0: 80 0 0: 82 0 0: 84 0 0: 86 0 0: 88 0 0: 90 0 0: 92 0 0: 94 0 0: 96 0 0: 98 0 0: 100 0 0: 102 0 0: 104 0 0: 106 0 0: 108 0 0: 110 0 0: 112 0 0: 114 0 0: 116 0 0: 118 0 0: >120 2 0:== 13355 residues in 93 sequences Expectation_n fit: rho(ln(x))= -2.4987+/-0.0228; mu= 46.6892+/- 0.998 mean_var=58.5007+/-15.993, 0's: 0 Z-trim: 2 B-trim: 0 in 0/19 Lambda= 0.167685 Kolmogorov-Smirnov statistic: 0.0577 (N=21) at 32 Smith-Waterman (PGopt) (4.2 Mar 2004) function [BL50 matrix (15:-5)], gap-penalty: -12/-2 Scan time: 0.010 The best scores are: s-w bits E(93) %_id %_sim sw alen an0 ax0 pn0 px0 an1 ax1 pn1 px1 gapq gapl fs d1amm_1 2.9.1.1.1 (1-85) gamma-Crystallin [bovine ( 85) 657 164.0 2.9e-44 1.000 1.000 657 85 1 85 1 85 1 85 1 85 0 0 0 d1amm_2 2.9.1.1.1 (86-174) gamma-Crystallin [bovi ( 89) 218 57.9 2.7e-12 0.390 0.683 218 82 2 81 1 85 4 85 1 89 2 0 0 d1poa__ 1.80.1.2.1 Snake phospholipase A2 [taiwan ( 118) 54 18.8 2.1 0.260 0.500 54 50 6 54 1 85 27 73 1 118 1 3 0 d1ptx__ 7.3.6.1.4 scorpion toxin [Androctonus aus ( 64) 54 17.5 2.6 0.234 0.489 54 47 38 84 1 85 9 54 1 64 0 1 0 d3ebx__ 7.5.1.1.1 Erabutoxin B (also neurotoxin B ( 62) 52 17.0 3.7 0.346 0.615 52 26 11 34 1 85 32 57 1 62 2 0 0 d1lit__ 4.88.1.1.1 Lithostathine, inhibitor of st ( 131) 50 18.0 3.8 0.200 0.453 50 75 22 79 1 85 1 75 1 131 17 0 0 d2olba_ 3.68.1.1.1 Oligo-peptide binding protein ( 517) 46 19.9 4.2 0.205 0.500 46 44 34 77 1 85 389 432 1 517 0 0 0 d1xnb__ 2.18.1.8.1 Xylanase II [Bacillus circulan ( 185) 47 18.0 5.4 0.196 0.510 47 51 26 76 1 85 89 136 1 185 0 3 0 d1ckaa_ 2.20.2.1.1 C-Crk, N-terminal SH3 domain [ ( 57) 48 15.8 7.4 0.385 0.615 48 26 57 82 1 85 26 50 1 57 0 1 0 d1krn__ 7.12.1.1.1 Plasminogen kringle 4 [human ( ( 79) 47 16.3 7.6 0.259 0.519 47 27 23 49 1 85 42 68 1 79 0 0 0 d2eng__ 2.33.1.1.1 Endoglucanase V [Humicola inso ( 205) 44 17.5 8.4 0.391 0.522 44 23 18 34 1 85 12 33 1 205 6 1 0 d2prk__ 3.26.1.1.6 Proteinase K [fungus (Tritirac ( 279) 43 17.9 8.7 0.333 0.611 43 18 2 19 1 85 57 74 1 279 0 0 0 d1ycc__ 1.3.1.1.4 Mitochondrial cytochrome c [bak ( 108) 45 16.4 9.3 0.323 0.581 45 31 4 31 1 85 13 43 1 108 3 0 0 >>>d1amm_1, 85 aa vs testset.fa library 2636 residues in 23 query sequences 13355 residues in 93 library sequences Scomplib [34t24] start: Tue Aug 15 22:54:43 2006 done: Tue Aug 15 22:54:44 2006 Total Scan time: 0.390 Total Display time: 0.180 Function used was SSEARCH [version 3.4t24 June 23, 2004] weblogo-3.8.0/tests/data/ssearch/xbt001.xml000066400000000000000000011703461467613320200204430ustar00rootroot00000000000000 blastp BLASTP 2.2.12 [Aug-07-2005] Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. nr gi|49176427|ref|NP_418280.3| component of Sec-independent translocase [Escherichia coli K12] 103 BLOSUM62 10 11 1 L; 1 gi|49176427|ref|NP_418280.3| component of Sec-independent translocase [Escherichia coli K12] 103 1 gi|49176427|ref|NP_418280.3| component of Sec-independent translocase [Escherichia coli K12] >gi|26250604|ref|NP_756644.1| Sec-independent protein translocase protein tatA [Escherichia coli CFT073] >gi|30064867|ref|NP_839038.1| hypothetical protein S3840 [Shigella flexneri 2a str. 2457T] >gi|24115132|ref|NP_709642.1| hypothetical protein SF3914 [Shigella flexneri 2a str. 301] >gi|24054404|gb|AAN45349.1| orf, conserved hypothetical protein [Shigella flexneri 2a str. 301] >gi|2367310|gb|AAC76839.1| component of Sec-independent translocase [Escherichia coli K12] >gi|30043127|gb|AAP18849.1| hypothetical protein S3840 [Shigella flexneri 2a str. 2457T] >gi|26111035|gb|AAN83218.1| Sec-independent protein translocase protein tatA [Escherichia coli CFT073] >gi|3193217|gb|AAC19240.1| MttA1 [Escherichia coli] >gi|7444818|pir||E65188 hypothetical 11.3 kD protein in udp-rfaH intergenic region - Escherichia coli (strain K-12) NP_418280 103 1 185.267 469 4.20576e-46 1 103 1 103 0 0 103 103 0 103 MRLCLIIIYHRGTCMGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV MRLCLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV MRLCLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV 2 gi|15804428|ref|NP_290468.1| twin arginine translocation protein; sec-independent protein export [Escherichia coli O157:H7 EDL933] >gi|12518713|gb|AAG59032.1| twin arginine translocation protein; sec-independent protein export [Escherichia coli O157:H7 EDL933] >gi|25302684|pir||D86071 hypothetical protein tatA [imported] - Escherichia coli (strain O157:H7, substrain EDL933) NP_290468 103 1 182.57 462 2.72609e-45 1 103 1 103 0 0 102 102 0 103 MRLCLIIIYHRGTCMGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV MRLCLIIIYHRXTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV MRLCLIIIYHR TCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV 3 gi|74314349|ref|YP_312768.1| hypothetical protein SSO_4011 [Shigella sonnei Ss046] >gi|73857826|gb|AAZ90533.1| conserved hypothetical protein [Shigella sonnei Ss046] YP_312768 103 1 182.57 462 2.72609e-45 1 103 1 103 0 0 102 102 0 103 MRLCLIIIYHRGTCMGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV MRPCLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV MR CLIIIYHRGTCMGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV 4 gi|75256240|ref|ZP_00727918.1| COG1826: Sec-independent protein secretion pathway components [Escherichia coli E22] >gi|75238286|ref|ZP_00722285.1| COG1826: Sec-independent protein secretion pathway components [Escherichia coli E110019] >gi|75237629|ref|ZP_00721649.1| COG1826: Sec-independent protein secretion pathway components [Escherichia coli F11] >gi|75230797|ref|ZP_00717260.1| COG1826: Sec-independent protein secretion pathway components [Escherichia coli B7A] >gi|75209537|ref|ZP_00709758.1| COG1826: Sec-independent protein secretion pathway components [Escherichia coli B171] >gi|75197719|ref|ZP_00707789.1| COG1826: Sec-independent protein secretion pathway components [Escherichia coli HS] >gi|75188578|ref|ZP_00701845.1| COG1826: Sec-independent protein secretion pathway components [Escherichia coli E24377A] >gi|75177802|ref|ZP_00697867.1| COG1826: Sec-independent protein secretion pathway components [Shigella boydii BS512] >gi|3123496|emb|CAA06724.1| TatA protein [Escherichia coli] >gi|13364242|dbj|BAB38189.1| Sec-independent protein translocase [Escherichia coli O157:H7] >gi|60415956|sp|P69428|TATA_ECOLI Sec-independent protein translocase protein tatA >gi|60415959|sp|P69431|TATA_SHIFL Sec-independent protein translocase protein tatA >gi|60415958|sp|P69430|TATA_ECO57 Sec-independent protein translocase protein tatA >gi|60415957|sp|P69429|TATA_ECOL6 Sec-independent protein translocase protein tatA >gi|15834020|ref|NP_312793.1| Sec-independent protein translocase [Escherichia coli O157:H7] ZP_00727918 89 1 154.836 390 6.0872e-37 15 103 1 89 0 0 89 89 0 89 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV MGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV MGGISIWQLLIIAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV 5 gi|148236|gb|AAA67633.1| o261 [Escherichia coli] AAA67633 261 1 124.79 312 6.74582e-28 34 95 19 80 0 0 62 62 0 62 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDA FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDA FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDA 6 gi|29143650|ref|NP_806992.1| sec-independent protein translocase protein [Salmonella enterica subsp. enterica serovar Typhi Ty2] >gi|16504464|emb|CAD07919.1| sec-independent protein translocase protein [Salmonella enterica subsp. enterica serovar Typhi] >gi|16422538|gb|AAL22817.1| component of Sec-independent protein secretion pathway [Salmonella typhimurium LT2] >gi|62182441|ref|YP_218858.1| component of Sec-independent protein secretion pathway [Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67] >gi|16762161|ref|NP_457778.1| sec-independent protein translocase protein [Salmonella enterica subsp. enterica serovar Typhi str. CT18] >gi|56415827|ref|YP_152902.1| sec-independent protein translocase protein [Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150] >gi|29139285|gb|AAO70852.1| sec-independent protein translocase protein [Salmonella enterica subsp. enterica serovar Typhi Ty2] >gi|56130084|gb|AAV79590.1| sec-independent protein translocase protein [Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150] >gi|62130074|gb|AAX67777.1| component of Sec-independent protein secretion pathway [Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67] >gi|6960229|gb|AAF33419.1| 83% identity with amino acids 10-79 of E. coli hypothetical protein (YIGT) (SP:P27856) [Salmonella typhimurium LT2] >gi|68064449|sp|P0A2H3|TATA_SALTY Sec-independent protein translocase protein tatA >gi|68064450|sp|P0A2H4|TATA_SALTI Sec-independent protein translocase protein tatA >gi|25302682|pir||AI0915 sec-independent protein translocase protein [imported] - Salmonella enterica subsp. enterica serovar Typhi (strain CT18) >gi|16767243|ref|NP_462858.1| Sec-independent protein secretion pathway component [Salmonella typhimurium LT2] NP_806992 84 1 122.094 305 4.37251e-27 15 103 1 84 0 0 75 79 5 89 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV MGGISIWQLLIVAVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDDDAKQDKTSQDADFTAKSIADKQG-----EAKKEDAKSQDKEQV MGGISIWQLLI+AVIVVLLFGTKKLGSIGSDLGASIKGFKKAMSDD+ KQDKTSQDADFTAK+IADKQ +AK EDAK DKEQV 7 gi|49609685|emb|CAG73118.1| sec-independent protein translocase [Erwinia carotovora subsp. atroseptica SCRI1043] >gi|50119159|ref|YP_048326.1| sec-independent protein translocase [Erwinia carotovora subsp. atroseptica SCRI1043] CAG73118 86 1 88.9669 219 4.10205e-17 15 103 1 86 0 0 59 67 7 91 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEP--KQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV MGGISLWNLLIIAVIVILLFGTNKLRTLGSDLGASIKGFKKAMGDDQPSTNADKAQPDADFSTKSIADNQSD-----AKQGDTKSQHKEQV MGGIS+W LLIIAVIV+LLFGT KL ++GSDLGASIKGFKKAM DD+P DK DADF+ K+IAD Q+D AK D K KEQV 8 gi|37528238|ref|NP_931583.1| Sec-independent protein translocase protein [Photorhabdus luminescens subsp. laumondii TTO1] >gi|36787675|emb|CAE16782.1| Sec-independent protein translocase protein [Photorhabdus luminescens subsp. laumondii TTO1] NP_931583 86 1 83.1889 204 2.25087e-15 15 103 1 86 0 0 59 71 7 91 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDD-EPKQ-DKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV MGGISIWQLLIIAVIVVLLFGTNKLRTLGSDLGASIKGFKKAIGDDNQPQQAQKTSSDADFETKNITEKQS-----VAQSETSESKNKEQV MGGISIWQLLIIAVIVVLLFGT KL ++GSDLGASIKGFKKA+ DD +P+Q KTS DADF K I +KQ+ A++E ++ +KEQV 9 gi|59710656|ref|YP_203432.1| Sec-independent protein translocase protein TatA [Vibrio fischeri ES114] >gi|71657992|sp|Q5E8V2|TATA_VIBF1 Sec-independent protein translocase protein tatA/E homolog >gi|59478757|gb|AAW84544.1| Sec-independent protein translocase protein TatA [Vibrio fischeri ES114] YP_203432 82 1 82.0333 201 5.01441e-15 15 102 1 81 0 0 52 70 7 88 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ MGGISIWQLLIIAVIIVLLFGTKKLRGVGSDLGSAVKGFKKAISEDEPAKE-AKKDADFVPQNLEKKEAETVEKQ------KQNDKEQ MGGISIWQLLIIAVI+VLLFGTKKL +GSDLG+++KGFKKA+S+DEP ++ +DADF + + K+A+T ++Q K++DKEQ 10 gi|54307340|ref|YP_128360.1| putative TatA protein [Photobacterium profundum SS9] >gi|46911760|emb|CAG18558.1| putative TatA protein [Photobacterium profundum SS9] YP_128360 87 1 78.1814 191 7.2408e-14 15 103 1 87 0 0 51 67 6 91 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDE--PKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV MGGISIWQLLIIALIIVLLFGTKKLRSLGGDLGSAVKGFKKAIGDEELTVKKDNTEADADFEQKTLSKEEQQSEDPVQKSQ----KDKEQV MGGISIWQLLIIA+I+VLLFGTKKL S+G DLG+++KGFKKA+ D+E K+D T DADF KT++ ++ + K++ DKEQV 11 gi|45437890|gb|AAS63439.1| Sec-independent protein translocase protein TatA [Yersinia pestis biovar Medievalis str. 91001] >gi|51594613|ref|YP_068804.1| Sec-independent protein translocase protein TatA [Yersinia pseudotuberculosis IP 32953] >gi|22124367|ref|NP_667790.1| hypothetical protein y0452 [Yersinia pestis KIM] >gi|77633885|ref|ZP_00795999.1| COG1826: Sec-independent protein secretion pathway components [Yersinia pestis Angola] >gi|77630676|ref|ZP_00793262.1| COG1826: Sec-independent protein secretion pathway components [Yersinia pseudotuberculosis IP 31758] >gi|51587895|emb|CAH19498.1| Sec-independent protein translocase protein TatA [Yersinia pseudotuberculosis IP 32953] >gi|15981691|emb|CAC93245.1| Sec-independent protein translocase protein TatA [Yersinia pestis CO92] >gi|21957146|gb|AAM84041.1| hypothetical protein [Yersinia pestis KIM] >gi|45443023|ref|NP_994562.1| Sec-independent protein translocase protein TatA [Yersinia pestis biovar Medievalis str. 91001] >gi|16123912|ref|NP_407225.1| Sec-independent protein translocase protein TatA [Yersinia pestis CO92] >gi|25302681|pir||AI0459 Sec-independent protein translocase protein TatA [imported] - Yersinia pestis (strain CO92) >gi|24212497|sp|Q8ZAM2|TATA_YERPE Sec-independent protein translocase protein tatA/E homolog AAS63439 88 1 77.0258 188 1.61308e-13 15 102 1 87 0 0 59 66 9 92 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDE----PKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ MGSIGWAQLLIIAVIVVLLFGTNKLRTLGSDLGASIKGFKKAMGDDSQTPPTNVDKTSNDADF-AKSITEKQ----QPVAKAEESKSHEKEQ MG I QLLIIAVIVVLLFGT KL ++GSDLGASIKGFKKAM DD DKTS DADF AK+I +KQ Q AK E++K H+KEQ 12 gi|75856473|ref|ZP_00764101.1| COG1826: Sec-independent protein secretion pathway components [Vibrio sp. Ex25] ZP_00764101 81 1 76.6406 187 2.10675e-13 15 102 1 80 0 0 54 66 8 88 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ MGGISVWQLLIIAVIVVLLFGTKKLRGIGGDLGGAVKGFKKAMSEDEPA--KNDKDADFEPKSLEEQQ----KKEAAPETKK--DKEQ MGGIS+WQLLIIAVIVVLLFGTKKL IG DLG ++KGFKKAMS+DEP K +DADF K++ ++Q +++A E K DKEQ 13 gi|75829371|ref|ZP_00758676.1| COG1826: Sec-independent protein secretion pathway components [Vibrio cholerae MO10] >gi|75828068|ref|ZP_00757503.1| COG1826: Sec-independent protein secretion pathway components [Vibrio cholerae O395] >gi|75823218|ref|ZP_00752737.1| COG1826: Sec-independent protein secretion pathway components [Vibrio cholerae RC385] >gi|75816411|ref|ZP_00746882.1| COG1826: Sec-independent protein secretion pathway components [Vibrio cholerae V52] >gi|9654483|gb|AAF93264.1| tatA protein [Vibrio cholerae O1 biovar eltor str. N16961] >gi|15640118|ref|NP_229745.1| tatA protein [Vibrio cholerae O1 biovar eltor str. N16961] >gi|11356194|pir||G82366 tatA protein VC0086 [imported] - Vibrio cholerae (strain N16961 serogroup O1) >gi|9979012|sp|P57051|TATA_VIBCH Sec-independent protein translocase protein tatA/E homolog ZP_00758676 82 1 76.2554 186 2.7515e-13 15 102 1 81 0 0 55 63 11 90 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAK--RHDKEQ MGGISIWQLLIIAVIVVLLFGTKKLRGIGSDLGSAVKGFKKAMSEEESNSAANQKDADFETK---------NLEQAKTNASAEVKKDKEQ MGGISIWQLLIIAVIVVLLFGTKKL IGSDLG+++KGFKKAMS++E +DADF K N EQAKT + + DKEQ 14 gi|75820019|ref|ZP_00750077.1| COG1826: Sec-independent protein secretion pathway components [Vibrio cholerae V51] ZP_00750077 82 1 75.8702 185 3.59357e-13 15 102 1 81 0 0 55 63 11 90 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDA--KRHDKEQ MGGISIWQLLIIAVIVVLLFGTKKLRGIGSDLGSAVKGFKKAMSEEESNSAANQKDADFETK---------NLEQAKTNASVEVKKDKEQ MGGISIWQLLIIAVIVVLLFGTKKL IGSDLG+++KGFKKAMS++E +DADF K N EQAKT + + DKEQ 15 gi|28896872|ref|NP_796477.1| TatA protein [Vibrio parahaemolyticus RIMD 2210633] >gi|28805080|dbj|BAC58361.1| TatA protein [Vibrio parahaemolyticus RIMD 2210633] >gi|32130181|sp|Q87TH1|TATA_VIBPA Sec-independent protein translocase protein tatA/E homolog NP_796477 81 1 73.1738 178 2.32928e-12 15 102 1 80 0 0 53 65 8 88 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ MGGISVWQLLIIAVIVVLLFGTKKLRGIGGDLGSAVKGFKKAMSDED--SAKNEKDADFEPKSLEKQQ----QKEAAPETKK--DKEQ MGGIS+WQLLIIAVIVVLLFGTKKL IG DLG+++KGFKKAMSD++ K +DADF K++ +Q Q++A E K DKEQ 16 gi|27364353|ref|NP_759881.1| Sec-independent protein secretion pathway component TatA [Vibrio vulnificus CMCP6] >gi|27360472|gb|AAO09408.1| Sec-independent protein secretion pathway component TatA [Vibrio vulnificus CMCP6] >gi|32130186|sp|Q8DDQ2|TATA_VIBVU Sec-independent protein translocase protein tatA/E homolog NP_759881 78 1 72.4034 176 3.97316e-12 15 102 1 77 0 0 54 65 11 88 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ MGGISIWQLLIIAVIVVLLFGTKKLRGIGSDLGGAIKGFKKAMNEEESEK----KDADFEPKSL-----EQQSKQAATESKK--DKEQ MGGISIWQLLIIAVIVVLLFGTKKL IGSDLG +IKGFKKAM+++E ++ +DADF K++ + +QA TE K DKEQ 17 gi|37678364|ref|NP_932973.1| Sec-independent protein secretion pathway component [Vibrio vulnificus YJ016] >gi|37197103|dbj|BAC92944.1| Sec-independent protein secretion pathway component [Vibrio vulnificus YJ016] >gi|71153586|sp|Q7MQ30|TATA_VIBVY Sec-independent protein translocase protein tatA/E homolog NP_932973 78 1 72.4034 176 3.97316e-12 15 102 1 77 0 0 54 65 11 88 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ MGGISIWQLLIIAVIVVLLFGTKKLRGIGSDLGGAIKGFKKAMNEEESEK----KDADFEPKSL-----EQQNKQAATESKK--DKEQ MGGISIWQLLIIAVIVVLLFGTKKL IGSDLG +IKGFKKAM+++E ++ +DADF K++ + +QA TE K DKEQ 18 gi|71277787|ref|YP_266931.1| Sec-independent protein translocase protein TatA [Colwellia psychrerythraea 34H] >gi|71143527|gb|AAZ24000.1| Sec-independent protein translocase protein TatA [Colwellia psychrerythraea 34H] YP_266931 85 1 72.4034 176 3.97316e-12 15 102 1 84 0 0 48 64 4 88 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ MGGIGIWQLVIVAVIVVLLFGTKKLRNIGGDLGSAIKGFKSAIGED--KEQKNS--AEKTSDTLADSSKSTTEEVVKTTESKTKESDQ MGGI IWQL+I+AVIVVLLFGTKKL +IG DLG++IKGFK A+ +D K+ K S A+ T+ T+AD T +E KT ++K + +Q 19 gi|68541995|ref|ZP_00581733.1| Twin-arginine translocation protein TatA/E [Shewanella baltica OS155] >gi|68520382|gb|EAN43890.1| Twin-arginine translocation protein TatA/E [Shewanella baltica OS155] ZP_00581733 79 1 69.707 169 2.57533e-11 15 90 1 79 0 0 46 60 3 79 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKT---IADKQADTNQEQA MGGISIWQLLIVALIVVLLFGTKKLRSLGGDLGGAVKGFKNAMSSEEDKKALEDTEAAKTAQTTQQATEKKPESNKEQA MGGISIWQLLI+A+IVVLLFGTKKL S+G DLG ++KGFK AMS +E K+ +A TA+T +K+ ++N+EQA 20 gi|77813363|ref|ZP_00812641.1| Twin-arginine translocation protein TatA/E [Shewanella putrefaciens CN-32] >gi|77811811|gb|EAO96181.1| Twin-arginine translocation protein TatA/E [Shewanella putrefaciens CN-32] ZP_00812641 79 1 69.707 169 2.57533e-11 15 90 1 79 0 0 47 60 3 79 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKT---IADKQADTNQEQA MGGISIWQLLIIALIVVLLFGTKKLRSLGGDLGGAVKGFKNAMSSEEDKKALEDTEAAKTAQTTQQATEKKPESNKEQA MGGISIWQLLIIA+IVVLLFGTKKL S+G DLG ++KGFK AMS +E K+ +A TA+T +K+ ++N+EQA 21 gi|52306607|gb|AAU37107.1| TatA protein [Mannheimia succiniciproducens MBEL55E] >gi|52424555|ref|YP_087692.1| TatA protein [Mannheimia succiniciproducens MBEL55E] AAU37107 75 1 69.3218 168 3.36348e-11 15 102 1 74 0 0 49 60 14 88 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ MGGISIWQLLIIVAIIVLLFGTKKLRTLGTDLGESVKGFKKAMNEDEPK------DAEFKSLN-KDESATAGSEKVK-------DKEQ MGGISIWQLLII I+VLLFGTKKL ++G+DLG S+KGFKKAM++DEPK DA+F + D+ A E+ K DKEQ 22 gi|75429751|ref|ZP_00732413.1| sec-independent protein secretion pathway components [Actinobacillus succinogenes 130Z] >gi|74276959|gb|EAO50546.1| sec-independent protein secretion pathway components [Actinobacillus succinogenes 130Z] ZP_00732413 74 1 69.3218 168 3.36348e-11 15 95 1 74 0 0 48 59 7 81 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDA MGGISIWQLLIIVAIVVLLFGTKKLRTLGSDLGESVKGFKKAMA-EEPK------DAEFKSLDKAENTAQTKKEEKEKEQA MGGISIWQLLII IVVLLFGTKKL ++GSDLG S+KGFKKAM+ +EPK DA+F + A+ A T +E+ + E A 23 gi|32033565|ref|ZP_00133892.1| COG1826: Sec-independent protein secretion pathway components [Actinobacillus pleuropneumoniae serovar 1 str. 4074] ZP_00133892 76 1 68.1662 165 7.49305e-11 15 94 1 74 0 0 43 60 6 80 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTED MGGISIWQLLIIVAIIVLLFGTKKLRTLGTDLGESVKGFKKAMADDK------SQPQDASFEKVEAKEAASTEQKAKEKE MGGISIWQLLII I+VLLFGTKKL ++G+DLG S+KGFKKAM+DD+ SQ D + + + K+A + +++AK ++ 24 gi|12722097|gb|AAK03773.1| unknown [Pasteurella multocida subsp. multocida str. Pm70] >gi|15603554|ref|NP_246628.1| hypothetical protein PM1689 [Pasteurella multocida subsp. multocida str. Pm70] >gi|24212511|sp|Q9CKD3|TATA_PASMU Sec-independent protein translocase protein tatA/E homolog AAK03773 76 1 67.0106 162 1.66928e-10 15 102 1 75 0 0 53 63 13 88 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ MGGISITQLLIIVAIVVLLFGTKKLRTLGSDLGESVKGFKKAMADDNKE-----KDAEF--KSLSDDSETT----AKTEKAK--DKEQ MGGISI QLLII IVVLLFGTKKL ++GSDLG S+KGFKKAM+DD + +DA+F K+++D T AKTE AK DKEQ 25 gi|68546478|ref|ZP_00586025.1| Twin-arginine translocation protein TatA/E [Shewanella amazonensis SB2B] >gi|68515892|gb|EAN39606.1| Twin-arginine translocation protein TatA/E [Shewanella amazonensis SB2B] ZP_00586025 77 1 66.6254 161 2.18014e-10 15 102 1 75 0 0 48 56 13 88 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ MGGISIWQLLIIALIVVLLFGTKKLRSLGGDLGGAIKGFKNAMSDEEKK-------------ALEDKEAAAQTTQQATEKKPEADKKE MGGISIWQLLIIA+IVVLLFGTKKL S+G DLG +IKGFK AMSD+E K + DK+A Q TE DK++ 26 gi|33151888|ref|NP_873241.1| sec-independent protein secretion pathway component TatA [Haemophilus ducreyi 35000HP] >gi|33148109|gb|AAP95630.1| sec-independent protein secretion pathway component TatA [Haemophilus ducreyi 35000HP] >gi|71153585|sp|Q7VN63|TATA_HAEDU Sec-independent protein translocase protein tatA/E homolog NP_873241 74 1 65.855 159 3.71876e-10 15 95 1 74 0 0 45 58 7 81 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDA MGGISIWQLLIIVAIIVLLFGTKKLRTLGTDLGESVKGFKKAMAEDK------SQDANFD-KVEAKESTSTTEKTKEKEQA MGGISIWQLLII I+VLLFGTKKL ++G+DLG S+KGFKKAM++D+ SQDA+F K A + T ++ + E A 27 gi|24375687|ref|NP_719730.1| Sec-independent protein translocase protein TatA [Shewanella oneidensis MR-1] >gi|24350613|gb|AAN57174.1| Sec-independent protein translocase protein TatA [Shewanella oneidensis MR-1] NP_719730 88 1 65.855 159 3.71876e-10 15 102 1 87 0 0 48 59 1 88 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ MGGISIWQLLIIALIVVLLFGTKKLRSLGGDLGGAVKGFKNAMSSEEDKKALEDAEAAKPVQTAQTVQSAQPTQQA-TEKKPESNKEQ MGGISIWQLLIIA+IVVLLFGTKKL S+G DLG ++KGFK AMS +E K+ +A +T Q+ +QA TE +KEQ 28 gi|71278553|ref|YP_269744.1| Sec-independent protein translocase protein TatA [Colwellia psychrerythraea 34H] >gi|71144293|gb|AAZ24766.1| Sec-independent protein translocase protein TatA [Colwellia psychrerythraea 34H] YP_269744 79 1 65.4698 158 4.85685e-10 15 100 1 78 0 0 47 62 10 87 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTE-DAKRHDK MGGISIWQLVMIAVIVVLLFGTKKLKNLGADLGSSIKGFKKAITDVDDEDRTESKN---------DVLADTSNTEARVEVDVKEKDK MGGISIWQL++IAVIVVLLFGTKKL ++G+DLG+SIKGFKKA++D + + S++ D ADT+ +A+ E D K DK 29 gi|69159855|gb|EAN71956.1| Twin-arginine translocation protein TatA/E [Shewanella denitrificans OS217] >gi|69941450|ref|ZP_00633384.1| Twin-arginine translocation protein TatA/E [Shewanella denitrificans OS-217] EAN71956 79 1 65.0846 157 6.34325e-10 15 102 1 78 0 0 47 62 12 89 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQ-ADTNQEQAKTEDAKRHDKEQ MGGISIWQLLIIALIVILLFGTKKLRSLGGDLGGAVKGFKNAMTSETSEEEK---------KALEDSQTAQTSQQAEKKPESK--DKEQ MGGISIWQLLIIA+IV+LLFGTKKL S+G DLG ++KGFK AM+ + +++K K + D Q A T+Q+ K ++K DKEQ 30 gi|69949858|ref|ZP_00637822.1| Twin-arginine translocation protein TatA/E [Shewanella frigidimarina NCIMB 400] >gi|69166482|gb|EAN75453.1| Twin-arginine translocation protein TatA/E [Shewanella frigidimarina NCIMB 400] ZP_00637822 81 1 64.3142 155 1.08199e-09 15 94 1 78 0 0 41 58 2 80 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTED MGGISIWQLLIVALIVILLFGTKKLRSLGGDLGGAVKGFKNAMTPEDENKSLDDKEKDQTAAT--SQQAAEKQPETESKD MGGISIWQLLI+A+IV+LLFGTKKL S+G DLG ++KGFK AM+ ++ + ++ D TA T +QA Q + +++D 31 gi|48863844|ref|ZP_00317737.1| hypothetical protein Mdeg02000203 [Microbulbifer degradans 2-40] ZP_00317737 83 1 63.929 154 1.41313e-09 15 93 3 81 0 0 41 53 0 79 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTE LGGISIWQLLIVLVIVLLLFGTKRLKGLGGDLGGAIKGFKKAMSDDEAAKQEAEEAEQKKVAAEEAAAAKTAEQKEKTE +GGISIWQLLI+ VIV+LLFGTK+L +G DLG +IKGFKKAMSDDE + + + A T +++ KTE 32 gi|77361831|ref|YP_341406.1| twin-arginine translocase subunit, sec-independent protein export [Pseudoalteromonas haloplanktis TAC125] >gi|76876742|emb|CAI87964.1| twin-arginine translocase subunit, sec-independent protein export [Pseudoalteromonas haloplanktis TAC125] YP_341406 82 1 60.4622 145 1.5624e-08 16 87 4 81 0 0 39 53 6 78 GGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSD------DEPKQDKTSQDADFTAKTIADKQADTNQ GGISLWQLLIVLAIIVLLFGTKKLRGIGGDLGGAVKGFKKAMSDEKNTDKEKPEQIQKSEESAPLDSAHTEKNKDNNK GGIS+WQLLI+ I+VLLFGTKKL IG DLG ++KGFKKAMSD ++P+Q + S+++ +K D N+ 33 gi|67676224|ref|ZP_00472975.1| Twin-arginine translocation protein TatA/E [Chromohalobacter salexigens DSM 3043] >gi|67519761|gb|EAM23710.1| Twin-arginine translocation protein TatA/E [Chromohalobacter salexigens DSM 3043] ZP_00472975 90 1 60.077 144 2.04055e-08 15 92 2 73 0 0 40 55 6 78 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKT LGGISIWQLLIVLGIVILIFGTKKLRNLGSDLGGAVKGFKSAVGEEEQKK----QDGEETAQHRV--AHDTNEEPLDT +GGISIWQLLI+ IV+L+FGTKKL ++GSDLG ++KGFK A+ ++E K+ QD + TA+ DTN+E T 34 gi|74317722|ref|YP_315462.1| twin-arginine translocation protein TatA/E [Thiobacillus denitrificans ATCC 25259] >gi|74057217|gb|AAZ97657.1| twin-arginine translocation protein TatA/E [Thiobacillus denitrificans ATCC 25259] >gi|52007795|ref|ZP_00335172.1| COG1826: Sec-independent protein secretion pathway components [Thiobacillus denitrificans ATCC 25259] YP_315462 70 1 59.3066 142 3.48066e-08 15 82 1 68 0 0 34 46 0 68 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQ MGSFSIWHWLIVLVVVLLIFGTKKLRNIGSDLGGAVKGFKEGMKDDAPKISESDKGGHTIDAEVKDKQ MG SIW LI+ V+V+L+FGTKKL +IGSDLG ++KGFK+ M DD PK ++ + + DKQ 35 gi|77166504|ref|YP_345029.1| Twin-arginine translocation protein TatA/E [Nitrosococcus oceani ATCC 19707] >gi|76884818|gb|ABA59499.1| Twin-arginine translocation protein TatA/E [Nitrosococcus oceani ATCC 19707] YP_345029 90 1 58.5362 140 5.9371e-08 15 95 3 76 0 0 41 58 7 81 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDA VGGISIWQLLIVLVIILLLFGTKKLRSIGTDLGSAIKGFRNSLRDEE------RRDAE-EAATIEHKQAHKAENPSQRQQA +GGISIWQLLI+ VI++LLFGTKKL SIG+DLG++IKGF+ ++ D+E +DA+ A TI KQA + ++ + A 36 gi|16128610|ref|NP_415160.1| component of Sec-independent translocase [Escherichia coli K12] >gi|26246607|ref|NP_752647.1| Sec-independent protein translocase protein tatE [Escherichia coli CFT073] >gi|30062184|ref|NP_836355.1| hypothetical protein S0676 [Shigella flexneri 2a str. 2457T] >gi|24112073|ref|NP_706583.1| hypothetical protein SF0654 [Shigella flexneri 2a str. 301] >gi|15800341|ref|NP_286353.1| hypothetical protein Z0772 [Escherichia coli O157:H7 EDL933] >gi|24050900|gb|AAN42290.1| orf, conserved hypothetical protein [Shigella flexneri 2a str. 301] >gi|74311162|ref|YP_309581.1| hypothetical protein SSO_0580 [Shigella sonnei Ss046] >gi|1786845|gb|AAC73728.1| component of Sec-independent translocase [Escherichia coli K12] >gi|75514720|ref|ZP_00736975.1| COG1826: Sec-independent protein secretion pathway components [Escherichia coli 53638] >gi|75258637|ref|ZP_00730044.1| COG1826: Sec-independent protein secretion pathway components [Escherichia coli E22] >gi|75240782|ref|ZP_00724689.1| COG1826: Sec-independent protein secretion pathway components [Escherichia coli F11] >gi|75236608|ref|ZP_00720696.1| COG1826: Sec-independent protein secretion pathway components [Escherichia coli E110019] >gi|75229489|ref|ZP_00716036.1| COG1826: Sec-independent protein secretion pathway components [Escherichia coli B7A] >gi|75210746|ref|ZP_00710878.1| COG1826: Sec-independent protein secretion pathway components [Escherichia coli B171] >gi|75194810|ref|ZP_00704880.1| COG1826: Sec-independent protein secretion pathway components [Escherichia coli HS] >gi|75189665|ref|ZP_00702932.1| COG1826: Sec-independent protein secretion pathway components [Escherichia coli E24377A] >gi|75177456|ref|ZP_00697537.1| COG1826: Sec-independent protein secretion pathway components [Shigella boydii BS512] >gi|73854639|gb|AAZ87346.1| conserved hypothetical protein [Shigella sonnei Ss046] >gi|30040429|gb|AAP16161.1| hypothetical protein S0676 [Shigella flexneri 2a str. 2457T] >gi|13360123|dbj|BAB34088.1| Sec-independent protein translocase [Escherichia coli O157:H7] >gi|1778544|gb|AAB40827.1| HI0187 homolog [Escherichia coli] >gi|26107006|gb|AAN79190.1| Sec-independent protein translocase protein tatE [Escherichia coli CFT073] >gi|4062250|dbj|BAA35270.1| Hypothetical protein (lip 3' region) [Escherichia coli K12] >gi|67473128|sp|P0A843|TATE_ECOLI Sec-independent protein translocase protein tatE >gi|67473131|sp|P0A846|TATE_SHIFL Sec-independent protein translocase protein tatE >gi|67473130|sp|P0A845|TATE_ECO57 Sec-independent protein translocase protein tatE >gi|67473129|sp|P0A844|TATE_ECOL6 Sec-independent protein translocase protein tatE >gi|12513528|gb|AAG54961.1| orf, hypothetical protein [Escherichia coli O157:H7 EDL933] >gi|15829919|ref|NP_308692.1| Sec-independent protein translocase [Escherichia coli O157:H7] NP_415160 67 1 57.3806 137 1.32265e-07 15 82 1 67 0 0 38 51 1 68 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQ MGEISITKLLVVAALVVLLFGTKKLRTLGGDLGAAIKGFKKAMNDDDAAA-KKGADVDLQAEKLSHKE MG ISI +LL++A +VVLLFGTKKL ++G DLGA+IKGFKKAM+DD+ K D D A+ ++ K+ 37 gi|12831974|emb|CAC29147.1| TatA protein [Pseudomonas stutzeri] CAC29147 76 1 56.9954 136 1.72743e-07 16 80 4 71 0 0 36 50 3 68 GGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPK---QDKTSQDADFTAKTIAD GGISIWQLLIILLIVIMLFGTKRLKGVGSDLGDAIKGFRKSMGTDEEKPSVEEKQNHTIDAQARKVEE GGISIWQLLII +IV++LFGTK+L +GSDLG +IKGF+K+M DE K ++K + D A+ + + 38 gi|32029972|ref|ZP_00132908.1| COG1826: Sec-independent protein secretion pathway components [Haemophilus somnus 2336] >gi|23467861|ref|ZP_00123438.1| COG1826: Sec-independent protein secretion pathway components [Haemophilus somnus 129PT] ZP_00132908 73 1 56.6102 135 2.2561e-07 17 94 2 71 0 0 38 57 8 78 GISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTED GLSWQQLLILLLVVVVIFGTKKLRNIGSDLGGAVKDFKKAMNDDQPK------DAEF--KKISEEVEQTSVENSKQKE G+S QLLI+ ++VV++FGTKKL +IGSDLG ++K FKKAM+DD+PK DA+F K I+++ T+ E +K ++ 39 gi|455172|gb|AAA24073.1| ORF; putative AAA24073 67 1 56.225 134 2.94655e-07 15 82 1 67 0 0 38 50 1 68 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQ MGEISITKLLVVAALVVLLFGTKKLRTLGGDLGAAIKGFKKAMIDDDAAA-KKGADVDLQAEKLSHKE MG ISI +LL++A +VVLLFGTKKL ++G DLGA+IKGFKKAM DD+ K D D A+ ++ K+ 40 gi|1224007|gb|AAA92108.1| ORF4 AAA92108 192 1 55.8398 133 3.84832e-07 16 70 4 62 0 0 36 48 4 59 GGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDE----PKQDKTSQD GGISIWQLLIILLIVVMLFGTKRLKSLGSDLGDAIKGFRKSMDNEENKAPPVEEQKGQD GGISIWQLLII +IVV+LFGTK+L S+GSDLG +IKGF+K+M ++E P +++ QD 41 gi|68056990|gb|AAX87243.1| Sec-independent protein translocase protein TatA/E [Haemophilus influenzae 86-028NP] >gi|68248791|ref|YP_247903.1| Sec-independent protein translocase protein TatA/E [Haemophilus influenzae 86-028NP] AAX87243 95 1 55.0694 131 6.56423e-07 2 94 8 93 0 0 39 60 7 93 RLCLIIIYHRGTCMGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTED RAKFFLFYRTEFIMFGLSPAQLIILLVVILLIFGTKKLRNAGSDLGAAVKGFKKAM-----KEDEKVKDAEF--KSIDNETASAKKENIKEKE R + Y M G+S QL+I+ V+++L+FGTKKL + GSDLGA++KGFKKAM K+D+ +DA+F K+I ++ A +E K ++ 42 gi|56461470|ref|YP_156751.1| Sec-independent protein secretion pathway component, TatA family [Idiomarina loihiensis L2TR] >gi|56180480|gb|AAV83202.1| Sec-independent protein secretion pathway component, TatA family [Idiomarina loihiensis L2TR] YP_156751 73 1 54.299 129 1.11969e-06 17 66 2 51 0 0 33 43 0 50 GISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDK GVSPWQLLILLVIVVLLFGTKRLRSLGSDLGNAVKGFKKSMGDEDDSKDK G+S WQLLI+ VIVVLLFGTK+L S+GSDLG ++KGFKK+M D++ +DK 43 gi|76793313|ref|ZP_00775802.1| Twin-arginine translocation protein TatA/E [Pseudoalteromonas atlantica T6c] >gi|76591415|gb|EAO67616.1| Twin-arginine translocation protein TatA/E [Pseudoalteromonas atlantica T6c] ZP_00775802 84 1 53.9138 128 1.46236e-06 15 101 1 84 0 0 43 57 11 91 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTN----QEQAKTEDAKRHDKE MFGISPMQLIIILVIVVLLFGTKKLRNMGGDLGSAVKGFKKAVSDDD-------KDADFKADEKVEDNSKANDQTVQQNVKSESDTKAKSE M GIS QL+II VIVVLLFGTKKL ++G DLG+++KGFKKA+SDD+ +DADF A + + N Q+ K+E + E 44 gi|42630489|ref|ZP_00156028.1| COG1826: Sec-independent protein secretion pathway components [Haemophilus influenzae R2866] >gi|42629145|ref|ZP_00154694.1| COG1826: Sec-independent protein secretion pathway components [Haemophilus influenzae R2846] ZP_00156028 75 1 53.5286 127 1.9099e-06 15 94 1 73 0 0 37 57 7 80 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTED MFGLSPAQLIILLVVILLIFGTKKLRNAGSDLGAAVKGFKKAM-----KEDEKVKDAEF--KSIDNETASAKKENIKEKE M G+S QL+I+ V+++L+FGTKKL + GSDLGA++KGFKKAM K+D+ +DA+F K+I ++ A +E K ++ 45 gi|1074302|pir||B64145 hypothetical protein HI0187 - Haemophilus influenzae (strain Rd KW20) B64145 109 1 53.1434 126 2.49441e-06 2 93 8 92 0 0 39 59 7 92 RLCLIIIYHRGTCMGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTE RAKFFLFYRTEFIMFGLSPAQLIILLVVILLIFGTKKLRNAGSDLGAAVKGFKKAM-----KEDEKVKDAEF--KSIDNETASAKKGKYKRE R + Y M G+S QL+I+ V+++L+FGTKKL + GSDLGA++KGFKKAM K+D+ +DA+F K+I ++ A + + K E 46 gi|67641583|ref|ZP_00440359.1| COG1826: Sec-independent protein secretion pathway components [Burkholderia mallei GB8 horse 4] >gi|67635791|ref|ZP_00434743.1| COG1826: Sec-independent protein secretion pathway components [Burkholderia mallei 10399] >gi|67760276|ref|ZP_00498999.1| COG1826: Sec-independent protein secretion pathway components [Burkholderia pseudomallei S13] >gi|67756151|ref|ZP_00495038.1| COG1826: Sec-independent protein secretion pathway components [Burkholderia pseudomallei Pasteur] >gi|67737955|ref|ZP_00488671.1| COG1826: Sec-independent protein secretion pathway components [Burkholderia pseudomallei 668] >gi|67716050|ref|ZP_00485411.1| COG1826: Sec-independent protein secretion pathway components [Burkholderia pseudomallei 1710b] >gi|67684327|ref|ZP_00478308.1| COG1826: Sec-independent protein secretion pathway components [Burkholderia pseudomallei 1710a] >gi|67671615|ref|ZP_00468402.1| COG1826: Sec-independent protein secretion pathway components [Burkholderia pseudomallei 1655] >gi|67651364|ref|ZP_00448787.1| COG1826: Sec-independent protein secretion pathway components [Burkholderia mallei SAVP1] >gi|67646939|ref|ZP_00445189.1| COG1826: Sec-independent protein secretion pathway components [Burkholderia mallei NCTC 10247] >gi|67629330|ref|ZP_00429188.1| COG1826: Sec-independent protein secretion pathway components [Burkholderia mallei 10229] >gi|76809713|ref|YP_335046.1| TatA [Burkholderia pseudomallei 1710b] >gi|76579166|gb|ABA48641.1| TatA [Burkholderia pseudomallei 1710b] >gi|52427678|gb|AAU48271.1| twin-arginine translocation protein, TatA/E family [Burkholderia mallei ATCC 23344] >gi|52211149|emb|CAH37138.1| Sec-independent protein translocase protein TatA [Burkholderia pseudomallei K96243] >gi|53720735|ref|YP_109721.1| Sec-independent protein translocase protein TatA [Burkholderia pseudomallei K96243] >gi|69991749|ref|ZP_00643311.1| COG1826: Sec-independent protein secretion pathway components [Burkholderia mallei FMH] ZP_00440359 77 1 52.7582 125 3.25779e-06 15 65 1 51 0 0 29 39 0 51 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQD MGGLSIWHWLIVLLIVALVFGTKKLRNIGNDLGSAVKGFKDGMKESEAPAD MGG+SIW LI+ +IV L+FGTKKL +IG+DLG+++KGFK M + E D 47 gi|67545726|ref|ZP_00423646.1| Twin-arginine translocation protein TatA/E [Burkholderia vietnamiensis G4] >gi|67533055|gb|EAM29828.1| Twin-arginine translocation protein TatA/E [Burkholderia vietnamiensis G4] >gi|74019444|ref|ZP_00690060.1| Twin-arginine translocation protein TatA/E [Burkholderia ambifaria AMMD] >gi|72607861|gb|EAO43817.1| Twin-arginine translocation protein TatA/E [Burkholderia ambifaria AMMD] ZP_00423646 76 1 52.7582 125 3.25779e-06 15 97 1 75 0 0 35 51 8 83 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKR MGGLSIWHWLIVLLIVALVFGTKKLRNIGNDLGSAVKGFKDGM-----KEGETPADAQQLPRT---GTVDVNAKETTRSDSNK MGG+SIW LI+ +IV L+FGTKKL +IG+DLG+++KGFK M K+ +T DA +T D N ++ D+ + 48 gi|45435806|gb|AAS61363.1| sec-independent protein translocase protein [Yersinia pestis biovar Medievalis str. 91001] >gi|51595437|ref|YP_069628.1| sec-independent protein translocase protein [Yersinia pseudotuberculosis IP 32953] >gi|22125073|ref|NP_668496.1| hypothetical protein y1170 [Yersinia pestis KIM] >gi|77636535|ref|ZP_00798608.1| COG1826: Sec-independent protein secretion pathway components [Yersinia pestis Angola] >gi|77632039|ref|ZP_00794625.1| COG1826: Sec-independent protein secretion pathway components [Yersinia pseudotuberculosis IP 31758] >gi|51588719|emb|CAH20330.1| sec-independent protein translocase protein [Yersinia pseudotuberculosis IP 32953] >gi|15980584|emb|CAC92840.1| sec-independent protein translocase protein [Yersinia pestis CO92] >gi|21957926|gb|AAM84747.1| hypothetical protein [Yersinia pestis KIM] >gi|45440947|ref|NP_992486.1| sec-independent protein translocase protein [Yersinia pestis biovar Medievalis str. 91001] >gi|16122810|ref|NP_406123.1| sec-independent protein translocase protein [Yersinia pestis CO92] >gi|25302680|pir||AI0316 sec-independent protein translocase protein [imported] - Yersinia pestis (strain CO92) >gi|24212499|sp|Q8ZDH1|TATE_YERPE Sec-independent protein translocase protein tatE AAS61363 85 1 52.7582 125 3.25779e-06 15 96 1 84 0 0 34 58 2 84 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTA--KTIADKQADTNQEQAKTEDAK MEGLSITKLLVVGILIVLLFGTSKLRTLGADLGAALKGFKKAMRNDDEVSTSVLGETKMSAETKTVAETKAASDSQAAASVERK M G+SI +LL++ +++VLLFGT KL ++G+DLGA++KGFKKAM +D+ + +A KT+A+ +A ++ + A + + K 49 gi|49610761|emb|CAG74206.1| Sec-independent protein translocase protein [Erwinia carotovora subsp. atroseptica SCRI1043] >gi|50120235|ref|YP_049402.1| Sec-independent protein translocase protein [Erwinia carotovora subsp. atroseptica SCRI1043] CAG74206 65 1 52.7582 125 3.25779e-06 15 76 1 63 0 0 37 47 1 63 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEP-KQDKTSQDADFTAK MEGISIAKLLVIGALIVLLFGTNKLRSLGGDLGAAIKGFKKAMNDDQSVKTDDTAALNDSSRK M GISI +LL+I ++VLLFGT KL S+G DLGA+IKGFKKAM+DD+ K D T+ D + K 50 gi|67663266|ref|ZP_00460549.1| Twin-arginine translocation protein TatA/E [Burkholderia cenocepacia HI2424] >gi|67659452|ref|ZP_00456814.1| Twin-arginine translocation protein TatA/E [Burkholderia cenocepacia AU 1054] >gi|67103109|gb|EAM20236.1| Twin-arginine translocation protein TatA/E [Burkholderia cenocepacia HI2424] >gi|67093009|gb|EAM10556.1| Twin-arginine translocation protein TatA/E [Burkholderia cenocepacia AU 1054] ZP_00460549 76 1 52.373 124 4.25481e-06 15 65 1 51 0 0 29 39 0 51 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQD MGGLSIWHWLIVLLIVALVFGTKKLRNIGNDLGSAVKGFKDGMKEGETPAD MGG+SIW LI+ +IV L+FGTKKL +IG+DLG+++KGFK M + E D 51 gi|33594634|ref|NP_882278.1| Sec-independent protein translocase protein [Bordetella pertussis Tohama I] >gi|33598762|ref|NP_886405.1| Sec-independent protein translocase protein [Bordetella parapertussis 12822] >gi|33603836|ref|NP_891396.1| Sec-independent protein translocase protein [Bordetella bronchiseptica RB50] >gi|33577961|emb|CAE35226.1| Sec-independent protein translocase protein [Bordetella bronchiseptica RB50] >gi|33574892|emb|CAE39555.1| Sec-independent protein translocase protein [Bordetella parapertussis] >gi|33564710|emb|CAE44033.1| Sec-independent protein translocase protein [Bordetella pertussis Tohama I] NP_882278 75 1 52.373 124 4.25481e-06 15 69 1 58 0 0 31 41 3 58 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSD---DEPKQDKTSQ MGSFSIWHWLIVLVIIALVFGTKKLRNVGSDLGSAVKGFKEGMKDASADKPADQVTQQ MG SIW LI+ VI+ L+FGTKKL ++GSDLG+++KGFK+ M D D+P T Q 52 gi|46310681|ref|ZP_00211309.1| COG1826: Sec-independent protein secretion pathway components [Burkholderia cepacia R18194] ZP_00211309 76 1 52.373 124 4.25481e-06 15 65 1 51 0 0 29 39 0 51 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQD MGGLSIWHWLIVLLIVALVFGTKKLRNIGNDLGSAVKGFKDGMKEGEAPAD MGG+SIW LI+ +IV L+FGTKKL +IG+DLG+++KGFK M + E D 53 gi|58584031|ref|YP_203047.1| sec-independent protein translocase [Xanthomonas oryzae pv. oryzae KACC10331] >gi|21244935|ref|NP_644517.1| sec-independent protein translocase [Xanthomonas axonopodis pv. citri str. 306] >gi|21110652|gb|AAM39053.1| sec-independent protein translocase [Xanthomonas axonopodis pv. citri str. 306] >gi|58428625|gb|AAW77662.1| sec-independent protein translocase [Xanthomonas oryzae pv. oryzae KACC10331] >gi|24212477|sp|Q8PEX2|TATA_XANAC Sec-independent protein translocase protein tatA/E homolog YP_203047 75 1 51.9878 123 5.55696e-06 15 88 1 73 0 0 34 49 1 74 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQE MGGFSIWHWLIVLVIVLLVFGTKRLTSGAKDLGSAVKEFKKGMHDDDKPAGKLGDDSR-TAEQAREAQAERDRD MGG SIW LI+ VIV+L+FGTK+L S DLG+++K FKK M DD+ K D+ TA+ + QA+ +++ 54 gi|17429965|emb|CAD16649.1| PROBABLE SIGNAL PEPTIDE PROTEIN [Ralstonia solanacearum] >gi|17547661|ref|NP_521063.1| PROBABLE SIGNAL PEPTIDE PROTEIN [Ralstonia solanacearum GMI1000] >gi|24212492|sp|Q8XV89|TATA_RALSO Sec-independent protein translocase protein tatA/E homolog CAD16649 85 1 51.9878 123 5.55696e-06 15 71 1 60 0 0 30 44 3 60 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAM---SDDEPKQDKTSQDA MGSFSIWHWLIVLLIIMMVFGTKKLRNIGSDLGSAVKGFKEGMREGSEDKPAGSQQGQQA MG SIW LI+ +I++++FGTKKL +IGSDLG+++KGFK+ M S+D+P + Q A 55 gi|47573371|ref|ZP_00243410.1| COG1826: Sec-independent protein secretion pathway components [Rubrivivax gelatinosus PM1] ZP_00243410 76 1 51.9878 123 5.55696e-06 15 86 1 66 0 0 35 47 6 72 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTN MGSFSIWHWLIVLLIVVLVFGTKKLKNIGSDLGGAVKGFKDGV------RDGSTAPADPAQQVTANKSADAN MG SIW LI+ +IVVL+FGTKKL +IGSDLG ++KGFK + +D ++ AD + A+K AD N 56 gi|16273687|ref|NP_438355.1| Sec-independent protein secretion pathway component TatA [Haemophilus influenzae Rd KW20] >gi|9988065|sp|P57046|TATA_HAEIN Sec-independent protein translocase protein tatA/E homolog NP_438355 89 1 51.6026 122 7.25761e-06 15 93 1 72 0 0 37 56 7 79 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTE MFGLSPAQLIILLVVILLIFGTKKLRNAGSDLGAAVKGFKKAM-----KEDEKVKDAEF--KSIDNETASAKKGKYKRE M G+S QL+I+ V+++L+FGTKKL + GSDLGA++KGFKKAM K+D+ +DA+F K+I ++ A + + K E 57 gi|73542784|ref|YP_297304.1| Twin-arginine translocation protein TatA/E [Ralstonia eutropha JMP134] >gi|72120197|gb|AAZ62460.1| Twin-arginine translocation protein TatA/E [Ralstonia eutropha JMP134] >gi|53760639|ref|ZP_00165809.2| COG1826: Sec-independent protein secretion pathway components [Ralstonia eutropha JMP134] YP_297304 73 1 51.2174 121 9.47873e-06 15 77 1 70 0 0 34 44 7 70 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPK-------QDKTSQDADFTAKT MGSFSIWHWLIVLVIVMLVFGTKKLRNIGQDLGGAVKGFKDGMKEGDDKAAPAKELRDSTTIDVDAKEKT MG SIW LI+ VIV+L+FGTKKL +IG DLG ++KGFK M + + K +D T+ D D KT 58 gi|26987777|ref|NP_743202.1| Sec-independent protein translocase TatA [Pseudomonas putida KT2440] >gi|24982471|gb|AAN66666.1| Sec-independent protein translocase TatA [Pseudomonas putida KT2440] NP_743202 77 1 51.2174 121 9.47873e-06 15 97 1 75 0 0 35 49 8 83 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKR MGGIGIWQLVIVLLIVFLLFGTKRLKGLGSDVGEAIQGFRKSMGGD--------NDASAADQAHVQQQCPLNGQVAQQSQADR MGGI IWQL+I+ +IV LLFGTK+L +GSD+G +I+GF+K+M D DA + +Q N + A+ A R 59 gi|29142636|ref|NP_805978.1| sec-independent protein translocase protein TatE [Salmonella enterica subsp. enterica serovar Typhi Ty2] >gi|16501883|emb|CAD05109.1| sec-independent protein translocase protein TatE [Salmonella enterica subsp. enterica serovar Typhi] >gi|16419144|gb|AAL19583.1| putative Sec-independent protein secretion pathway component [Salmonella typhimurium LT2] >gi|62179231|ref|YP_215648.1| putative Sec-independent protein secretion pathway component [Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67] >gi|16759591|ref|NP_455208.1| sec-independent protein translocase protein TatE [Salmonella enterica subsp. enterica serovar Typhi str. CT18] >gi|56414233|ref|YP_151308.1| sec-independent protein translocase protein TatE [Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150] >gi|29138267|gb|AAO69838.1| sec-independent protein translocase protein TatE [Salmonella enterica subsp. enterica serovar Typhi Ty2] >gi|56128490|gb|AAV77996.1| sec-independent protein translocase protein TatE [Salmonella enterica subsp. enterica serovar Paratyphi A str. ATCC 9150] >gi|62126864|gb|AAX64567.1| putative Sec-independent protein secretion pathway component [Salmonella enterica subsp. enterica serovar Choleraesuis str. SC-B67] >gi|61248019|sp|P0A2H5|TATE_SALTY Sec-independent protein translocase protein tatE >gi|61248020|sp|P0A2H6|TATE_SALTI Sec-independent protein translocase protein tatE >gi|25302676|pir||AC0580 sec-independent protein translocase protein TatE [imported] - Salmonella enterica subsp. enterica serovar Typhi (strain CT18) >gi|16764009|ref|NP_459624.1| Sec-independent protein secretion pathway component [Salmonella typhimurium LT2] NP_805978 67 1 50.447 119 1.61683e-05 15 82 1 67 0 0 35 49 1 68 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQ MGEISITKLLVVAALVVLLFGTKKLRTLGGDLGTAIKGFKKAMNDEDAGV-KKDVDGSVQAEKLSHKE MG ISI +LL++A +VVLLFGTKKL ++G DLG +IKGFKKAM+D++ K D A+ ++ K+ 60 gi|18389921|gb|AAL68797.1| TatA [Ralstonia eutropha] AAL68797 77 1 50.447 119 1.61683e-05 15 77 1 74 0 0 35 44 11 74 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPK-----------QDKTSQDADFTAKT MGSFSIWHWLIVLVIVMLVFGTKKLRNIGQDLGGAVKGFKDGMKDGEGKAAADPAQSKELRDSTTIDVEAKEKT MG SIW LI+ VIV+L+FGTKKL +IG DLG ++KGFK M D E K +D T+ D + KT 61 gi|48781637|ref|ZP_00278228.1| COG1826: Sec-independent protein secretion pathway components [Burkholderia fungorum LB400] ZP_00278228 79 1 49.6766 117 2.75789e-05 15 69 1 55 0 0 28 39 0 55 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQ MGSLSIWHWLIVLLIVALVFGTKKLRNIGTDLGGAVKGFKEGMKEAETPAGEAQQ MG +SIW LI+ +IV L+FGTKKL +IG+DLG ++KGFK+ M + E + Q 62 gi|77456610|ref|YP_346115.1| Twin-arginine translocation protein TatA/E [Pseudomonas fluorescens PfO-1] >gi|77380613|gb|ABA72126.1| Twin-arginine translocation protein TatA/E [Pseudomonas fluorescens PfO-1] YP_346115 92 1 49.6766 117 2.75789e-05 34 67 20 53 0 0 22 28 0 34 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKT FGTKKLKNLGTDVGESIKGFRKAMNDDEKPADPT FGTKKL ++G+D+G SIKGF+KAM+DDE D T 63 gi|1684735|emb|CAA98158.1| ORF57 protein [Pseudomonas stutzeri] >gi|9979022|sp|P95557|TATA_PSEST Sec-independent protein translocase protein tatA/E homolog CAA98158 57 1 49.6766 117 2.75789e-05 17 61 2 46 0 0 30 40 0 45 GISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDE GISVWQLLIILLIVVMLFGTKRLRGLGSDLGSAINGFRKSVSDGE GIS+WQLLII +IVV+LFGTK+L +GSDLG++I GF+K++SD E 64 gi|56476124|ref|YP_157713.1| Sec-independent protein translocase subunit A [Azoarcus sp. EbN1] >gi|56312167|emb|CAI06812.1| Sec-independent protein translocase subunit A [Azoarcus sp. EbN1] YP_157713 75 1 49.2914 116 3.60191e-05 15 69 1 55 0 0 30 37 0 55 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQ MGSFSIWHWLIVLVIVVLVFGTKKLRNVGQDLGGAVKGFKDGMRDSEKSGEDVQQ MG SIW LI+ VIVVL+FGTKKL ++G DLG ++KGFK M D E + Q 65 gi|34496078|ref|NP_900293.1| Sec-independent protein translocase protein TatA [Chromobacterium violaceum ATCC 12472] >gi|34101932|gb|AAQ58299.1| Sec-independent protein translocase protein TatA [Chromobacterium violaceum ATCC 12472] NP_900293 68 1 49.2914 116 3.60191e-05 15 82 1 68 0 0 32 44 0 68 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQ MGSLSIWHWLIVLLIVVLVFGTKKLPGIGKDLGNAVKGFKEGMNEGAKDGQPPAKDAGRIIDGEADKK MG +SIW LI+ +IVVL+FGTKKL IG DLG ++KGFK+ M++ ++DA ADK+ 66 gi|67848115|ref|ZP_00503233.1| Twin-arginine translocation protein TatA/E [Polaromonas sp. JS666] >gi|67781162|gb|EAM40776.1| Twin-arginine translocation protein TatA/E [Polaromonas sp. JS666] ZP_00503233 83 1 48.9062 115 4.70425e-05 15 83 1 69 0 0 31 42 0 69 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQA MGSFSIWHWLIVLLIVVMVFGTKKLKNMGSDLGSAVKGFKDGMKDGGQSAAATDDKPAAPAGQVTNAQA MG SIW LI+ +IVV++FGTKKL ++GSDLG+++KGFK M D T A + + QA 67 gi|26991692|ref|NP_747117.1| Sec-independent protein translocase TatA [Pseudomonas putida KT2440] >gi|24986793|gb|AAN70581.1| Sec-independent protein translocase TatA [Pseudomonas putida KT2440] NP_747117 90 1 48.9062 115 4.70425e-05 34 102 20 85 0 0 26 40 3 69 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ FGTKKLKNFGSDLGESIKGFRKAMNEEE---TKPAEQTPPPAQPVPPVQNTAQPQQGHTIEGQAHPVQE FGTKKL + GSDLG SIKGF+KAM+++E K ++ A+ + Q +Q T + + H ++ 68 gi|15601293|ref|NP_232924.1| tatA protein [Vibrio cholerae O1 biovar eltor str. N16961] >gi|9657940|gb|AAF96436.1| tatA protein [Vibrio cholerae O1 biovar eltor str. N16961] >gi|11356195|pir||A82448 tatA protein VCA0533 [imported] - Vibrio cholerae (strain N16961 serogroup O1) NP_232924 78 1 48.521 114 6.14393e-05 15 98 1 77 0 0 38 54 7 84 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRH MGGISVGKLLILGCIVALVFGTKKLRTIGEDAGYAIRSFQKALRGDE----VTTQSS--TAEESVDSFA-IEQESSHSSDSQRH MGGIS+ +LLI+ IV L+FGTKKL +IG D G +I+ F+KA+ DE T+Q + TA+ D A QE + + D++RH 69 gi|66770480|ref|YP_245242.1| sec-independent protein translocase [Xanthomonas campestris pv. campestris str. 8004] >gi|21233515|ref|NP_639432.1| sec-independent protein translocase [Xanthomonas campestris pv. campestris str. ATCC 33913] >gi|21115368|gb|AAM43314.1| sec-independent protein translocase [Xanthomonas campestris pv. campestris str. ATCC 33913] >gi|66575812|gb|AAY51222.1| sec-independent protein translocase [Xanthomonas campestris pv. campestris str. 8004] >gi|24212476|sp|Q8P3H8|TATA_XANCP Sec-independent protein translocase protein tatA/E homolog YP_245242 75 1 48.1358 113 8.02423e-05 15 88 1 73 0 0 32 48 1 74 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQE MGSFSIWHWLIVLVIVLLVFGTKRLTSGAKDLGSAVKEFKKGMHDDDKPAGKLGDDSR-SAEQAREAQAERDRD MG SIW LI+ VIV+L+FGTK+L S DLG+++K FKK M DD+ K D+ +A+ + QA+ +++ 70 gi|53804435|ref|YP_113945.1| Sec-independent protein translocase protein TatA [Methylococcus capsulatus str. Bath] >gi|53758196|gb|AAU92487.1| Sec-independent protein translocase protein TatA [Methylococcus capsulatus str. Bath] YP_113945 70 1 48.1358 113 8.02423e-05 17 88 2 67 0 0 30 51 6 72 GISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQE GIGVWELLLLFLIVLVVFGTKRLRNIGGDLGGAIKSFRQAMSENE---DKPSEGG---ARTLEGEVVDKKEK GI +W+LL++ +IV+++FGTK+L +IG DLG +IK F++AMS++E DK S+ A+T+ + D ++ 71 gi|75825357|ref|ZP_00754793.1| COG1826: Sec-independent protein secretion pathway components [Vibrio cholerae O395] ZP_00754793 80 1 48.1358 113 8.02423e-05 15 98 1 79 0 0 33 51 5 84 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRH MGGISVGKLLILGCIVALIFGTKKLRTIGEDAGYAIRSFQKALRSDE-----VTTQSSTTEESVDSFSFAIEQEPSHSSDSQRH MGGIS+ +LLI+ IV L+FGTKKL +IG D G +I+ F+KA+ DE + + T +++ QE + + D++RH 72 gi|71908987|ref|YP_286574.1| Twin-arginine translocation protein TatA/E [Dechloromonas aromatica RCB] >gi|71848608|gb|AAZ48104.1| Twin-arginine translocation protein TatA/E [Dechloromonas aromatica RCB] >gi|41723355|ref|ZP_00150282.1| COG1826: Sec-independent protein secretion pathway components [Dechloromonas aromatica RCB] YP_286574 76 1 48.1358 113 8.02423e-05 15 74 1 58 0 0 31 41 2 60 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFT MGSFSIWHWLIVLVIVMLIFGTKKLRNVGQDLGGAVKGFKDGMK--EANADKPAEEAQPT MG SIW LI+ VIV+L+FGTKKL ++G DLG ++KGFK M E DK +++A T 73 gi|68526571|gb|EAN49542.1| Twin-arginine translocation protein TatA/E [Ralstonia metallidurans CH34] >gi|68559139|ref|ZP_00598474.1| Twin-arginine translocation protein TatA/E [Ralstonia metallidurans CH34] EAN49542 77 1 47.7506 112 0.0001048 15 82 1 77 0 0 36 47 9 77 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSD---DEP------KQDKTSQDADFTAKTIADKQ MGSFSIWHWLIVLVIVMLVFGTKKLRNIGQDLGGAVKGFKDGMKEGNTDEPATPTPAKELRDSTTIDVEAKEKSRQQ MG SIW LI+ VIV+L+FGTKKL +IG DLG ++KGFK M + DEP K+ + S D AK + +Q 74 gi|71736448|ref|YP_272670.1| sec-independent protein translocase TatA [Pseudomonas syringae pv. phaseolicola 1448A] >gi|71557001|gb|AAZ36212.1| sec-independent protein translocase TatA [Pseudomonas syringae pv. phaseolicola 1448A] YP_272670 91 1 47.7506 112 0.0001048 34 102 20 84 0 0 30 41 6 70 FGTKKLGSIGSDLGASIKGFKKAMSDDE-PKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ FGTKKLKGLGSDVGESIKGFRKAMNDDDKPAEQPAPQPQQAQA---APQGSPLNQPH--TIDAQAHKVDE FGTKKL +GSD+G SIKGF+KAM+DD+ P + Q A A + + NQ T DA+ H ++ 75 gi|56460344|ref|YP_155625.1| Sec-independent protein secretion pathway component, TatA family [Idiomarina loihiensis L2TR] >gi|56179354|gb|AAV82076.1| Sec-independent protein secretion pathway component, TatA family [Idiomarina loihiensis L2TR] YP_155625 72 1 47.7506 112 0.0001048 16 101 4 72 0 0 32 54 17 86 GGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKE GGMSMVQLGVLLVIVILLFGSKKLRTLGSDLGSAIKGFKSSITDEP-----------------SDREKDIQRHQNLTSEEERHHEQ GG+S+ QL ++ VIV+LLFG+KKL ++GSDLG++IKGFK +++D+ +D++ D + Q T + +RH ++ 76 gi|68214708|ref|ZP_00566522.1| Twin-arginine translocation protein TatA/E [Methylobacillus flagellatus KT] >gi|68186844|gb|EAN01544.1| Twin-arginine translocation protein TatA/E [Methylobacillus flagellatus KT] ZP_00566522 72 1 47.3654 111 0.000136873 15 78 1 62 0 0 29 44 2 64 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTI MGSFSIWHWLIVLAIVILIFGTKRLRNLGSDVGGAVKGFKEAV--NEGKSAAAALDDDAKGQTV MG SIW LI+ IV+L+FGTK+L ++GSD+G ++KGFK+A+ +E K + D D +T+ 77 gi|30248650|ref|NP_840720.1| mttA/Hcf106 family [Nitrosomonas europaea ATCC 19718] >gi|30180245|emb|CAD84550.1| mttA/Hcf106 family [Nitrosomonas europaea ATCC 19718] NP_840720 76 1 47.3654 111 0.000136873 15 87 1 73 0 0 29 43 0 73 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQ MGSFSIWHWLVVLAIVVLVFGTKKLRNLGSDLGGAVRGFKEGMKGAEEESTPPPPAQQVTGHSIKSEIEEKDQ MG SIW L++ IVVL+FGTKKL ++GSDLG +++GFK+ M E + T +I + + +Q 78 gi|75822907|ref|ZP_00752458.1| COG1826: Sec-independent protein secretion pathway components [Vibrio cholerae RC385] ZP_00752458 78 1 47.3654 111 0.000136873 15 98 1 77 0 0 33 50 7 84 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRH MGGISVGKLLILGCIVALVFGTKKLRTIGEDAGYAIRSFQKALRGDEVTTQSSTTEESVDSFAI-------EQESSHSSDSQRH MGGIS+ +LLI+ IV L+FGTKKL +IG D G +I+ F+KA+ DE ++ + + I QE + + D++RH 79 gi|70733926|ref|YP_257566.1| sec-independent protein translocase TatA [Pseudomonas fluorescens Pf-5] >gi|68348225|gb|AAY95831.1| sec-independent protein translocase TatA [Pseudomonas fluorescens Pf-5] YP_257566 93 1 47.3654 111 0.000136873 34 99 20 92 0 0 29 40 7 73 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQ-ADTNQ------EQAKTEDAKRHD FGTKKLKNLGTDVGESIKGFRKAMNDDEKPAEPVVPPAAQPVPPVQPQQSAPLNQPHTIDVQAQKVEEPTRKD FGTKKL ++G+D+G SIKGF+KAM+DDE + A + +Q A NQ + K E+ R D 80 gi|63254358|gb|AAY35454.1| Twin-arginine translocation protein TatA/E [Pseudomonas syringae pv. syringae B728a] >gi|66043651|ref|YP_233492.1| Twin-arginine translocation protein TatA/E [Pseudomonas syringae pv. syringae B728a] AAY35454 91 1 46.9802 110 0.000178761 34 102 20 84 0 0 27 38 4 69 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ FGTKKLKGLGSDVGESIKGFRKAMNDD----DKPAEQPAPQPQQAQPAPQGSPLNQPHTIDAQAHKVDE FGTKKL +GSD+G SIKGF+KAM+DD DK ++ + + Q T DA+ H ++ 81 gi|73354814|gb|AAZ75668.1| TatA [Pseudomonas syringae pv. maculicola] AAZ75668 91 1 46.9802 110 0.000178761 34 66 20 52 0 0 20 27 0 33 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDK FGTKKLKGLGSDVGESIKGFRKAMHDDDKPEEQ FGTKKL +GSD+G SIKGF+KAM DD+ +++ 82 gi|50083761|ref|YP_045271.1| Sec-independent protein translocase protein [Acinetobacter sp. ADP1] >gi|49529737|emb|CAG67449.1| Sec-independent protein translocase protein [Acinetobacter sp. ADP1] YP_045271 78 1 46.595 109 0.000233469 15 77 6 70 0 0 30 43 2 65 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSD--DEPKQDKTSQDADFTAKT MAGLSIWHVVIFLIVVVLLFGTSKLKNLGKDVGGAVKDFKKSMRDETEENAQLHTPRTIDAEVKT M G+SIW ++I ++VVLLFGT KL ++G D+G ++K FKK+M D +E Q T + D KT 83 gi|71548504|ref|ZP_00668728.1| Twin-arginine translocation protein TatA/E [Nitrosomonas eutropha C71] >gi|71485685|gb|EAO18234.1| Twin-arginine translocation protein TatA/E [Nitrosomonas eutropha C71] ZP_00668728 77 1 46.2098 108 0.00030492 15 61 1 47 0 0 26 35 0 47 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDE MGSFSIWHWLVVLAIVVLVFGTKKLRNLGSDLGGAVRGFKEGMKGAE MG SIW L++ IVVL+FGTKKL ++GSDLG +++GFK+ M E 84 gi|55247002|gb|EAL42253.1| ENSANGP00000028218 [Anopheles gambiae str. PEST] >gi|57965302|ref|XP_561091.1| ENSANGP00000028218 [Anopheles gambiae str. PEST] EAL42253 53 1 45.8246 107 0.000398238 15 61 3 49 0 0 26 37 0 47 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDE LGGIHIWHLLILLVVVVVVFGSKRLAGAGEDLGTAIRDFRKALRDDE +GGI IW LLI+ V+VV++FG+K+L G DLG +I+ F+KA+ DDE 85 gi|50084688|ref|YP_046198.1| Sec-independent protein secretion pathway, translocase protein [Acinetobacter sp. ADP1] >gi|49530664|emb|CAG68376.1| Sec-independent protein secretion pathway, translocase protein [Acinetobacter sp. ADP1] YP_046198 71 1 45.4394 106 0.000520115 17 74 2 59 0 0 29 41 0 58 GISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFT GLSIWHILLFAVIVILLFGTSKLKSLGKDLGGAIKDFKDSVNSDDQKLLQNQQYKDIS G+SIW +L+ AVIV+LLFGT KL S+G DLG +IK FK +++ D+ K + Q D + 86 gi|28872267|ref|NP_794886.1| sec-independent protein translocase TatA [Pseudomonas syringae pv. tomato str. DC3000] >gi|28855521|gb|AAO58581.1| sec-independent protein translocase TatA [Pseudomonas syringae pv. tomato str. DC3000] NP_794886 91 1 45.0542 105 0.000679292 34 102 20 84 0 0 26 37 4 69 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ FGTKKLKGLGTDVGESIKGFRKAMHDD----DKPAEQPAPQPQQAQPAPQGSPLNQPHTIDAQAHKVDE FGTKKL +G+D+G SIKGF+KAM DD DK ++ + + Q T DA+ H ++ 87 gi|49082486|gb|AAT50643.1| PA5068 [synthetic construct] AAT50643 83 1 45.0542 105 0.000679292 34 97 20 81 0 0 25 38 2 64 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKR FGTKRLKNLGSDVGEAIKGFRKAVNTEE--DDKKDQPAAQPAQPLNQPHTIDAQAQKVEEPARK FGTK+L ++GSD+G +IKGF+KA++ +E DK Q A A+ + Q Q E A++ 88 gi|53726598|ref|ZP_00141543.2| COG1826: Sec-independent protein secretion pathway components [Pseudomonas aeruginosa UCBPP-PA14] >gi|9951361|gb|AAG08453.1| translocation protein TatA [Pseudomonas aeruginosa PAO1] >gi|15600261|ref|NP_253755.1| translocation protein TatA [Pseudomonas aeruginosa PAO1] >gi|11352708|pir||G83011 translocation protein TatA PA5068 [imported] - Pseudomonas aeruginosa (strain PAO1) >gi|24212512|sp|Q9HUB5|TATA_PSEAE Sec-independent protein translocase protein tatA/E homolog ZP_00141543 82 1 45.0542 105 0.000679292 34 97 20 81 0 0 25 38 2 64 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKR FGTKRLKNLGSDVGEAIKGFRKAVNTEE--DDKKDQPAAQPAQPLNQPHTIDAQAQKVEEPARK FGTK+L ++GSD+G +IKGF+KA++ +E DK Q A A+ + Q Q E A++ 89 gi|68213616|ref|ZP_00565447.1| Twin-arginine translocation protein TatA/E [Methylobacillus flagellatus KT] >gi|68187989|gb|EAN02672.1| Twin-arginine translocation protein TatA/E [Methylobacillus flagellatus KT] ZP_00565447 54 1 44.669 104 0.000887182 15 61 1 47 0 0 23 34 0 47 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDE MGSFSIWHWLIVLAVVTMVFGTKRLRNMGSDLGGALKNFKEASKDPD MG SIW LI+ +V ++FGTK+L ++GSDLG ++K FK+A D + 90 gi|74023810|ref|ZP_00694377.1| Twin-arginine translocation protein TatA/E [Rhodoferax ferrireducens DSM 15236] >gi|72603427|gb|EAO39432.1| Twin-arginine translocation protein TatA/E [Rhodoferax ferrireducens DSM 15236] ZP_00694377 79 1 44.2838 103 0.0011587 34 93 19 78 0 0 24 32 0 60 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTE FGTKKLRNIGSDLGGAVKGFKDGMKEGSDKAADAPAAAPQQVASSATAAKETIDVEAKTK FGTKKL +IGSDLG ++KGFK M + K A + A +T +AKT+ 91 gi|71066554|ref|YP_265281.1| twin-arginine translocation protein TatA/E [Psychrobacter arcticus 273-4] >gi|71039539|gb|AAZ19847.1| twin-arginine translocation protein TatA/E [Psychrobacter arcticus 273-4] YP_265281 87 1 43.8986 102 0.0015133 15 85 1 75 0 0 31 43 4 75 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDK----TSQDADFTAKTIADKQADT MGSFSITHWLILLVVVVVVFGTSKLRNAGKDLGGAVKGFKEAVKDENTEHAKKHVVLDHDAGTNPPNITGTQSDT MG SI LI+ V+VV++FGT KL + G DLG ++KGFK+A+ D+ + K DA I Q+DT 92 gi|15611372|ref|NP_223023.1| hypothetical protein jhp0303 [Helicobacter pylori J99] >gi|4154834|gb|AAD05888.1| putative [Helicobacter pylori J99] >gi|7444815|pir||A71948 hypothetical protein jhp0303 - Helicobacter pylori (strain J99) >gi|9979057|sp|Q9ZMB8|TATA_HELPJ Sec-independent protein translocase protein tatA/E homolog NP_223023 79 1 43.5134 101 0.00197644 15 93 1 78 0 0 31 48 3 80 MGGI-SIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTE MGGFTSIWHWVIVLLVIVLLFGAKKIPELAKGLGSGIKNFKKAVKDDEEEAKNELKTLD--AQATQTKVHETSEIKSKQE MGG SIW +I+ +++VLLFG KK+ + LG+ IK FKKA+ DDE + + D A+ K +T++ ++K E 93 gi|13471183|ref|NP_102752.1| sec-independent protein translocase protein tatA/E [Mesorhizobium loti MAFF303099] >gi|14021927|dbj|BAB48538.1| sec-independent protein translocase protein TatA/E [Mesorhizobium loti MAFF303099] >gi|24212508|sp|Q98LC5|TATA_RHILO Sec-independent protein translocase protein tatA/E homolog NP_102752 73 1 42.743 99 0.00337129 15 81 1 69 0 0 28 41 2 69 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQD--ADFTAKTIADK MGSFSIWHWMIVLVIVLLVFGRGKIPELMGDMAKGIKSFKKGMADDDVADDKRTVEHRADETVSAVKEK MG SIW +I+ VIV+L+FG K+ + D+ IK FKK M+DD+ DK + + AD T + +K 94 gi|42523995|ref|NP_969375.1| twin-arginine-dependent translocase protein [Bdellovibrio bacteriovorus HD100] >gi|39576203|emb|CAE80368.1| twin-arginine-dependent translocase protein [Bdellovibrio bacteriovorus HD100] NP_969375 81 1 42.743 99 0.00337129 34 96 19 76 0 0 21 36 5 63 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAK FGPSKLPNLGRSLGESIRGFKKGLNEDPAADEKEAKQ-----QITQNPQRPVNEQQPQTEEKK FG KL ++G LG SI+GFKK +++D +K ++ + + Q N++Q +TE+ K 95 gi|67158086|ref|ZP_00419176.1| Twin-arginine translocation protein TatA/E [Azotobacter vinelandii AvOP] >gi|67085069|gb|EAM04546.1| Twin-arginine translocation protein TatA/E [Azotobacter vinelandii AvOP] ZP_00419176 85 1 42.3578 98 0.00440304 34 99 20 85 0 0 21 35 0 66 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHD FGTKRLKTLGSDIGEAIKGFRKAVNTEEGENRPAEPQTGTSAGDTLNKTQTIEGQAQKVDTPVRKD FGTK+L ++GSD+G +IKGF+KA++ +E + +A +K + K + R D 96 gi|15644948|ref|NP_207118.1| conserved hypothetical secreted protein [Helicobacter pylori 26695] >gi|2313428|gb|AAD07397.1| conserved hypothetical secreted protein [Helicobacter pylori 26695] >gi|7429236|pir||H64559 conserved hypothetical secreted protein HP0320 - Helicobacter pylori (strain 26695) >gi|9978986|sp|O25088|TATA_HELPY Sec-independent protein translocase protein tatA/E homolog NP_207118 79 1 42.3578 98 0.00440304 15 90 1 79 0 0 29 47 3 79 MGGI-SIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDD--EPKQDKTSQDADFTAKTIADKQADTNQEQA MGGFTSIWHWVIVLLVIVLLFGAKKIPELAKGLGSGIKNFKKAVKDDEEEAKNEPKTLDAQATQTKVHESSEIKSKQES MGG SIW +I+ +++VLLFG KK+ + LG+ IK FKKA+ DD E K + + DA T + + +++++ 97 gi|13277311|emb|CAC34414.1| putative TatA protein [Legionella pneumophila] CAC34414 61 1 41.5874 96 0.00751045 15 61 3 49 0 0 26 35 0 47 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDE LSGISPLSLLLILAIIIALFGTSKLKTIGSDLGEAIKNFRKAMNSEE + GIS LL+I I++ LFGT KL +IGSDLG +IK F+KAM+ +E 98 gi|54298906|ref|YP_125275.1| Putative TatA protein(twin arginine translocation) [Legionella pneumophila str. Paris] >gi|54295733|ref|YP_128148.1| Putative TatA protein(twin arginine translocation) [Legionella pneumophila str. Lens] >gi|53755565|emb|CAH17064.1| Putative TatA protein(twin arginine translocation) [Legionella pneumophila str. Lens] >gi|53752691|emb|CAH14126.1| Putative TatA protein(twin arginine translocation) [Legionella pneumophila str. Paris] >gi|47132321|gb|AAT11788.1| TatA protein [Legionella pneumophila] YP_125275 61 1 41.5874 96 0.00751045 15 61 3 49 0 0 27 35 0 47 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDE LSGISPLSLLLILAIIVALFGTSKLKTIGSDLGEAIKNFRKAMNSEE + GIS LL+I I+V LFGT KL +IGSDLG +IK F+KAM+ +E 99 gi|71363513|ref|ZP_00654157.1| Twin-arginine translocation protein TatA/E [Psychrobacter cryohalolentis K5] >gi|71161313|gb|EAO11109.1| Twin-arginine translocation protein TatA/E [Psychrobacter cryohalolentis K5] ZP_00654157 94 1 41.5874 96 0.00751045 15 69 1 55 0 0 25 39 0 55 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQ MGSFSITHWLILLVVVVVVFGTAKLKNAGKDLGGAVKGFKEAVKDEEAEHARKNR MG SI LI+ V+VV++FGT KL + G DLG ++KGFK+A+ D+E + + ++ 100 gi|71362217|ref|ZP_00653377.1| Twin-arginine translocation protein TatA/E [Psychrobacter cryohalolentis K5] >gi|71162335|gb|EAO12126.1| Twin-arginine translocation protein TatA/E [Psychrobacter cryohalolentis K5] ZP_00653377 80 1 41.5874 96 0.00751045 15 87 1 73 0 0 27 42 0 73 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQ MGSFSITHWLILLVVVVVVFGTSKLRNAGKDLGGAVKGFKEAVKDENTEHAKKQVVLDHDGNAHTEERPTTTK MG SI LI+ V+VV++FGT KL + G DLG ++KGFK+A+ D+ + K D +++ T + 101 gi|27379862|ref|NP_771391.1| hypothetical protein bsl4751 [Bradyrhizobium japonicum USDA 110] >gi|27353015|dbj|BAC50016.1| bsl4751 [Bradyrhizobium japonicum USDA 110] NP_771391 77 1 41.2022 95 0.00980895 15 85 1 66 0 0 27 38 5 71 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADT MGSLSIWHWILVIAVVLLLFGRGKISDLMGDVAQGIKAFKKGMQDDDKPADKPE-----PAKSIEHNAAPT MG +SIW +++ +V+LLFG K+ + D+ IK FKK M DD+ DK AK+I A T 102 gi|39935914|ref|NP_948190.1| putative sec-independent protein translocase protein tatA/E [Rhodopseudomonas palustris CGA009] >gi|39649768|emb|CAE28290.1| putative sec-independent protein translocase protein tatA/E [Rhodopseudomonas palustris CGA009] NP_948190 78 1 40.817 94 0.0128109 15 88 1 76 0 0 25 41 2 76 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTS--QDADFTAKTIADKQADTNQE MGSLSIWHWIVVIAVVLLLFGRGKISDLMGDVAQGIKSFKKGLQDDEKTAEKSEPVKSIDHTSTPGATNRTDVGSK MG +SIW +++ +V+LLFG K+ + D+ IK FKK + DDE +K+ + D T+ A + D + 103 gi|17935600|ref|NP_532390.1| SEC-independent protein translocase protein [Agrobacterium tumefaciens str. C58] >gi|17740143|gb|AAL42706.1| SEC-independent protein translocase protein [Agrobacterium tumefaciens str. C58] >gi|15156802|gb|AAK87479.1| AGR_C_3135p [Agrobacterium tumefaciens str. C58] >gi|15889013|ref|NP_354694.1| hypothetical protein AGR_C_3135 [Agrobacterium tumefaciens str. C58] >gi|25520668|pir||F97565 hypothetical protein AGR_C_3135 [imported] - Agrobacterium tumefaciens (strain C58, Cereon) >gi|25522636|pir||AD2786 SEC-independent protein translocase protein [imported] - Agrobacterium tumefaciens (strain C58, Dupont) >gi|24212489|sp|Q8UEP9|TATA_AGRT5 Sec-independent protein translocase protein tatA/E homolog NP_532390 70 1 40.817 94 0.0128109 15 84 1 67 0 0 30 43 3 70 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQAD MGSFSVWHWLIVLVIVLVLFGRGKIPELMGDVAKGIKSFKKGMADED--QTPPPADANANAKTV-DHKAD MG S+W LI+ VIV++LFG K+ + D+ IK FKK M+D++ Q DA+ AKT+ D +AD 104 gi|62289827|ref|YP_221620.1| Sec-independent protein translocase protein TatA, hypothetical [Brucella abortus biovar 1 str. 9-941] >gi|17983053|gb|AAL52265.1| SEC-INDEPENDENT PROTEIN TRANSLOCASE PROTEIN TATA [Brucella melitensis 16M] >gi|62195959|gb|AAX74259.1| Sec-independent protein translocase protein TatA, hypothetical [Brucella abortus biovar 1 str. 9-941] >gi|17987367|ref|NP_540001.1| SEC-INDEPENDENT PROTEIN TRANSLOCASE PROTEIN TATA [Brucella melitensis 16M] >gi|25302679|pir||AF3387 sec-independent protein translocase protein tatA [imported] - Brucella melitensis (strain 16M) >gi|54039707|sp|P66888|TATA_BRUSU Sec-independent protein translocase protein tatA/E homolog >gi|54042236|sp|P66887|TATA_BRUME Sec-independent protein translocase protein tatA/E homolog YP_221620 72 1 40.4318 93 0.0167315 15 71 1 57 0 0 24 36 0 57 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDA MGSFSIWHWLIVLAVVLLLFGRGKIPELMGDVAKGIKNFKQGMADEDAKEDPRTIDA MG SIW LI+ +V+LLFG K+ + D+ IK FK+ M+D++ K+D + DA 105 gi|23347697|gb|AAN29810.1| Sec-independent protein translocase protein TatA, putative [Brucella suis 1330] >gi|23501768|ref|NP_697895.1| Sec-independent protein translocase protein TatA, putative [Brucella suis 1330] AAN29810 80 1 40.4318 93 0.0167315 15 71 9 65 0 0 24 36 0 57 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDA MGSFSIWHWLIVLAVVLLLFGRGKIPELMGDVAKGIKNFKQGMADEDAKEDPRTIDA MG SIW LI+ +V+LLFG K+ + D+ IK FK+ M+D++ K+D + DA 106 gi|75675971|ref|YP_318392.1| twin-arginine translocation protein TatA/E [Nitrobacter winogradskyi Nb-255] >gi|74420841|gb|ABA05040.1| twin-arginine translocation protein TatA/E [Nitrobacter winogradskyi Nb-255] YP_318392 78 1 40.4318 93 0.0167315 15 66 1 52 0 0 21 32 0 52 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDK MGSLSIWHWIVVVAVILLLFGRGKISDLMGDVAQGIKAFKKGMKDDEKTAEK MG +SIW +++ +++LLFG K+ + D+ IK FKK M DDE +K 107 gi|69928230|ref|ZP_00625391.1| Twin-arginine translocation protein TatA/E [Nitrobacter hamburgensis X14] >gi|69143234|gb|EAN61762.1| Twin-arginine translocation protein TatA/E [Nitrobacter hamburgensis X14] ZP_00625391 79 1 40.4318 93 0.0167315 15 66 1 52 0 0 21 32 0 52 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDK MGSLSIWHWIVVIAVILLLFGRGKISDLMGDVAQGIKAFKKGMQDDEKTAEK MG +SIW +++ +++LLFG K+ + D+ IK FKK M DDE +K 108 gi|77689454|ref|ZP_00804635.1| Twin-arginine translocation protein TatA/E [Rhodopseudomonas palustris BisB5] >gi|77653821|gb|EAO85595.1| Twin-arginine translocation protein TatA/E [Rhodopseudomonas palustris BisB5] ZP_00804635 79 1 40.0466 92 0.0218521 15 79 1 67 0 0 25 37 2 67 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTS--QDADFTAKTIA MGSLSIWHWIVVIAVVLLLFGRGKISDLMGDVAQGIKSFKKGLQDDEKTAEKPDPVKSIDHNAPTAA MG +SIW +++ +V+LLFG K+ + D+ IK FKK + DDE +K + D A T A 109 gi|77743614|ref|ZP_00812071.1| Twin-arginine translocation protein TatA/E [Rhodopseudomonas palustris BisA53] >gi|77696516|gb|EAO87698.1| Twin-arginine translocation protein TatA/E [Rhodopseudomonas palustris BisA53] ZP_00812071 78 1 39.6614 91 0.0285397 15 67 1 53 0 0 23 34 0 53 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKT MGSLSIWHWLVVIVVVLLLFGRGKISDLMGDVAQGIKSFKKGLQDDDKTAEKT MG +SIW L++ V+V+LLFG K+ + D+ IK FKK + DD+ +KT 110 gi|71066141|ref|YP_264868.1| twin-arginine translocation protein TatE [Psychrobacter arcticus 273-4] >gi|71039126|gb|AAZ19434.1| twin-arginine translocation protein TatE [Psychrobacter arcticus 273-4] YP_264868 89 1 39.2762 90 0.037274 34 61 19 46 0 0 16 22 0 28 FGTKKLGSIGSDLGASIKGFKKAMSDDE FGTAKLKNAGKDLGGAVKGFKEAVKDEE FGT KL + G DLG ++KGFK+A+ D+E 111 gi|28199457|ref|NP_779771.1| SEC-independent protein translocase [Xylella fastidiosa Temecula1] >gi|71900614|ref|ZP_00682740.1| Twin-arginine translocation protein TatA/E [Xylella fastidiosa Ann-1] >gi|71898114|ref|ZP_00680300.1| Twin-arginine translocation protein TatA/E [Xylella fastidiosa Ann-1] >gi|71732088|gb|EAO34144.1| Twin-arginine translocation protein TatA/E [Xylella fastidiosa Ann-1] >gi|71729608|gb|EAO31713.1| Twin-arginine translocation protein TatA/E [Xylella fastidiosa Ann-1] >gi|71274575|ref|ZP_00650863.1| Twin-arginine translocation protein TatA/E [Xylella fastidiosa Dixon] >gi|71164307|gb|EAO14021.1| Twin-arginine translocation protein TatA/E [Xylella fastidiosa Dixon] >gi|28057572|gb|AAO29420.1| SEC-independent protein translocase [Xylella fastidiosa Temecula1] >gi|32130179|sp|Q87B80|TATA_XYLFT Sec-independent protein translocase protein tatA/E homolog NP_779771 71 1 38.891 89 0.0486813 15 75 1 61 0 0 24 40 0 61 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTA MGSFSLLHWLVVLVIVLLVFGTKRLANGAKDIGSAIKEFKKSLHEDDKPTDQLGSTSQSTA MG S+ L++ VIV+L+FGTK+L + D+G++IK FKK++ +D+ D+ + TA 112 gi|15837166|ref|NP_297854.1| hypothetical protein XF0564 [Xylella fastidiosa 9a5c] >gi|9105426|gb|AAF83374.1| conserved hypothetical protein [Xylella fastidiosa 9a5c] >gi|11360714|pir||B82791 conserved hypothetical protein XF0564 [imported] - Xylella fastidiosa (strain 9a5c) >gi|9979030|sp|Q9PFU3|TATA_XYLFA Sec-independent protein translocase protein tatA/E homolog NP_297854 71 1 38.891 89 0.0486813 15 75 1 61 0 0 24 40 0 61 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTA MGSFSLLHWLVVLVIVLLVFGTKRLANGAKDIGSAIKEFKKSLREDDKPTDQLGSTSQSTA MG S+ L++ VIV+L+FGTK+L + D+G++IK FKK++ +D+ D+ + TA 113 gi|15074462|emb|CAC46108.1| HYPOTHETICAL TRANSMEMBRANE PROTEIN [Sinorhizobium meliloti] >gi|15965282|ref|NP_385635.1| HYPOTHETICAL TRANSMEMBRANE PROTEIN [Sinorhizobium meliloti 1021] >gi|24212503|sp|Q92Q25|TATA_RHIME Sec-independent protein translocase protein tatA/E homolog CAC46108 68 1 38.891 89 0.0486813 15 81 1 63 0 0 28 35 4 67 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADK MGSFSIWHWLIVLAVVLLLFGRGKIPELMGDVAKGIKNFKKGMGDDE----VASADKSVDGKTVDHK MG SIW LI+ +V+LLFG K+ + D+ IK FKK M DDE S D KT+ K 114 gi|27462871|gb|AAO15625.1| Sec-independent protein translocase TatA [Rhizobium leguminosarum bv. viciae] AAO15625 63 1 38.1206 87 0.0830377 15 85 1 62 0 0 30 40 9 71 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADT MGSFSMWHWLIVLVIVLLLFGRGKIPELMGDVAKGIKSFKKGMTD---------EDAPDTAKTVDHKADET MG S+W LI+ VIV+LLFG K+ + D+ IK FKK M+D +DA TAKT+ K +T 115 gi|35211273|dbj|BAC88652.1| gsl0711 [Gloeobacter violaceus PCC 7421] >gi|37520280|ref|NP_923657.1| hypothetical protein gsl0711 [Gloeobacter violaceus PCC 7421] BAC88652 72 1 38.1206 87 0.0830377 34 70 21 57 0 0 17 24 0 37 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQD FGPKKLPEMGSALGKAIRGFKSGVSDEPAPQQSASKE FG KKL +GS LG +I+GFK +SD+ Q S++ 116 gi|34482347|emb|CAE09348.1| hypothetical protein [Wolinella succinogenes] >gi|34556633|ref|NP_906448.1| hypothetical protein WS0187 [Wolinella succinogenes DSM 1740] CAE09348 80 1 37.7354 86 0.108451 34 85 20 71 0 0 18 26 0 52 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADT FGAKKIPDLAKGLGSGIKNFKKAMKEDEESEVSVTKSEKIEEAPKNEKSAST FG KK+ + LG+ IK FKKAM +DE + ++ +K A T 117 gi|32262257|gb|AAP77305.1| component of Sec-independent protein secretion pathway TatA [Helicobacter hepaticus ATCC 51449] >gi|32266207|ref|NP_860239.1| component of Sec-independent protein secretion pathway TatA [Helicobacter hepaticus ATCC 51449] AAP77305 82 1 37.7354 86 0.108451 34 99 20 81 0 0 22 37 6 67 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTE-DAKRHD FGAKKIPELAKGLGSGIKNFKKAVKEDE--EDNQSEE---NTKSQIKQSESKNENVSKTHTDSQKQD FG KK+ + LG+ IK FKKA+ +DE +D S++ K+ + N+ +KT D+++ D 118 gi|76261408|ref|ZP_00769019.1| Twin-arginine translocation protein TatA/E [Chloroflexus aurantiacus J-10-fl] >gi|76163681|gb|EAO57850.1| Twin-arginine translocation protein TatA/E [Chloroflexus aurantiacus J-10-fl] ZP_00769019 62 1 37.3502 85 0.141641 15 69 2 57 0 0 25 39 1 56 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAM-SDDEPKQDKTSQ IGGLGWGELLIILIIVIAIFGAGKLAGLGGALGSSIREFRKAVKGDDEPRSDAKTE +GG+ +LLII +IV+ +FG KL +G LG+SI+ F+KA+ DDEP+ D ++ 119 gi|69933726|ref|ZP_00628928.1| sec-independent translocation protein mttA/Hcf106 [Paracoccus denitrificans PD1222] >gi|69155362|gb|EAN68465.1| sec-independent translocation protein mttA/Hcf106 [Paracoccus denitrificans PD1222] ZP_00628928 159 1 37.3502 85 0.141641 34 97 88 149 0 0 22 34 4 65 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQA-DTNQEQAKTEDAKR FGRGKVSSLMGEVGKGITAFKKGVKDGAEEYDRAAEDA---KKPIGQSPAEDATRAQAQTNEAMR FG K+ S+ ++G I FKK + D + D+ ++DA K I A D + QA+T +A R 120 gi|15605662|ref|NP_213037.1| hypothetical protein aq_064b [Aquifex aeolicus VF5] >gi|2982827|gb|AAC06450.1| hypothetical protein [Aquifex aeolicus VF5] >gi|7444819|pir||B70306 conserved hypothetical protein aq_064b - Aquifex aeolicus >gi|9978994|sp|O66477|TAT2_AQUAE Sec-independent protein translocase tatA/E-like protein 2 NP_213037 59 1 36.965 84 0.184989 21 66 7 52 0 0 19 33 0 46 WQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDK WQLILILLVILVIFGASKLPEVGKGLGEGIRNFKKALSGEEEEKGK WQL++I ++++++FG KL +G LG I+ FKKA+S +E ++ K 121 gi|68538777|ref|ZP_00578553.1| Twin-arginine translocation protein TatA/E [Sphingopyxis alaskensis RB2256] >gi|68523891|gb|EAN47017.1| Twin-arginine translocation protein TatA/E [Sphingopyxis alaskensis RB2256] ZP_00578553 77 1 36.5798 83 0.241603 15 75 1 66 0 0 25 37 5 66 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDE-----PKQDKTSQDADFTA MGSFSIWHWLVVGILVLLLFGKGRFSDMMGDVAKGIKSFKKGMSEDDAPTPAPKQIDAQRAPDLSA MG SIW L++ ++V+LLFG + + D+ IK FKK MS+D+ PKQ + D +A 122 gi|68136098|ref|ZP_00544086.1| Twin-arginine translocation protein TatA/E [Methanosarcina barkeri str. fusaro] >gi|72397188|gb|AAZ71461.1| sec-independent protein translocase, protein [Methanosarcina barkeri str. fusaro] >gi|73670026|ref|YP_306041.1| sec-independent protein translocase, protein [Methanosarcina barkeri str. fusaro] ZP_00544086 130 1 36.1946 82 0.315543 34 100 18 84 0 0 19 34 0 67 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDK FGPKKLPELARSLGSAMGEFKKAQRASELELNQFDAYTRKAANTVASEEKEKGKEQKETPSSSKEAK FG KKL + LG+++ FKKA E + ++ A T+A ++ + +EQ +T + + K 123 gi|20259265|gb|AAM14368.1| putative Tha4 protein [Arabidopsis thaliana] >gi|15810475|gb|AAL07125.1| putative Tha4 protein [Arabidopsis thaliana] >gi|11762160|gb|AAG40358.1| AT5g28750 [Arabidopsis thaliana] >gi|7682781|gb|AAF67362.1| Hypothetical protein T32B20.e [Arabidopsis thaliana] >gi|15241912|ref|NP_198227.1| thylakoid assembly protein, putative [Arabidopsis thaliana] AAM14368 147 1 35.8094 81 0.412112 17 103 65 147 0 0 25 46 4 87 GISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV GLGVPELAVIAGVAALLFGPKKLPEIGKSIGKTVKSFQQAAKEFESELKTEPEESVAESSQV----ATSNKEEEKKTEVSSSSKENV G+ + +L +IA + LLFG KKL IG +G ++K F++A + E + +++ + + A +N+E+ K + KE V 124 gi|75910646|ref|YP_324942.1| Twin-arginine translocation protein TatA/E [Anabaena variabilis ATCC 29413] >gi|75704371|gb|ABA24047.1| Twin-arginine translocation protein TatA/E [Anabaena variabilis ATCC 29413] >gi|46135166|ref|ZP_00162467.2| COG1826: Sec-independent protein secretion pathway components [Anabaena variabilis ATCC 29413] YP_324942 90 1 35.8094 81 0.412112 34 95 22 83 0 0 17 34 0 62 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDA FGPKKLPEIGRSLGKAIRGFQEASNEFQSEFKREAEQLEQAVKTTAELEPKQIESVKSEQDS FG KKL IG LG +I+GF++A ++ + + + ++ + KT A+ + + +D+ 125 gi|39982657|gb|AAR34117.1| twin-arginine translocation protein, TatA/E family [Geobacter sulfurreducens PCA] >gi|39995893|ref|NP_951844.1| twin-arginine translocation protein, TatA/E family [Geobacter sulfurreducens PCA] AAR34117 57 1 35.8094 81 0.412112 35 71 21 57 0 0 17 23 0 37 GTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDA GPSKLPQLGQALGSSIKSFKKGMNEDEVKVINKTNEA G KL +G LG+SIK FKK M++DE K + +A 126 gi|33635687|emb|CAE22011.1| mttA/Hcf106 family [Prochlorococcus marinus str. MIT 9313] >gi|33864103|ref|NP_895663.1| mttA/Hcf106 family [Prochlorococcus marinus str. MIT 9313] CAE22011 91 1 35.4242 80 0.538235 17 96 5 86 0 0 27 43 2 82 GISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADF--TAKTIADKQADTNQEQAKTEDAK GIGLPEMAVIGAIALLVFGPKRLPEFGRTLGKTLKGFQAASKEFEREIHKTMAEPESIEQAATEESMQQDTNAIGETPQEAK GI + ++ +I I +L+FG K+L G LG ++KGF+ A + E + KT + + A T Q DTN ++AK 127 gi|76791934|ref|ZP_00774438.1| Twin-arginine translocation protein TatA/E [Pseudoalteromonas atlantica T6c] >gi|76592906|gb|EAO69092.1| Twin-arginine translocation protein TatA/E [Pseudoalteromonas atlantica T6c] ZP_00774438 68 1 35.4242 80 0.538235 18 85 3 67 0 0 22 44 3 68 ISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADT LSVWQLVLVALLFILLFGRGRIPALMGDLAQGIKSFKRGISEDESQDE---QGVEKTSGETLEKKSPT +S+WQL+++A++ +LLFG ++ ++ DL IK FK+ +S+DE + + Q + T+ +K++ T 128 gi|23129516|ref|ZP_00111343.1| COG1826: Sec-independent protein secretion pathway components [Nostoc punctiforme PCC 73102] ZP_00111343 91 1 35.4242 80 0.538235 17 80 5 68 0 0 21 40 0 64 GISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIAD GIGLPEMAVIMVVALLIFGPKKLPEIGRSVGKTIRSFQEASKEFQSEFQKEAEQLEETVKTTAE GI + ++ +I V+ +L+FG KKL IG +G +I+ F++A + + + K ++ + T KT A+ 129 gi|48764199|ref|ZP_00268751.1| COG1826: Sec-independent protein secretion pathway components [Rhodospirillum rubrum] ZP_00268751 96 1 35.039 79 0.702957 15 61 1 47 0 0 22 31 0 47 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDE MGFSSIWHWIIVLVVVLLLFGAGKIPRLMGDVAKGVKAFKKGMADDE MG SIW +I+ V+V+LLFG K+ + D+ +K FKK M+DDE 130 gi|15677995|ref|NP_273645.1| hypothetical protein NMB0601 [Neisseria meningitidis MC58] >gi|7379525|emb|CAB84088.1| putative sec-independent protein translocase component [Neisseria meningitidis Z2491] >gi|66731901|gb|AAY52136.1| conserved hypothetical protein [Neisseria meningitidis MC58] >gi|15793779|ref|NP_283601.1| sec-independent protein translocase component [Neisseria meningitidis Z2491] >gi|59800638|ref|YP_207350.1| TatA [Neisseria gonorrhoeae FA 1090] >gi|59717533|gb|AAW88938.1| sec-independent protein translocase [Neisseria gonorrhoeae FA 1090] >gi|11354072|pir||E81925 probable sec-independent protein translocase component NMA0805 [imported] - Neisseria meningitidis (strain Z2491 serogroup A) >gi|54039709|sp|P66892|TATA_NEIMB Sec-independent protein translocase protein tatA/E homolog >gi|54042238|sp|P66891|TATA_NEIMA Sec-independent protein translocase protein tatA/E homolog NP_273645 67 1 35.039 79 0.702957 15 70 1 56 0 0 21 36 0 56 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQD MGSFSLTHWIIVLIIVVLIFGTKKLRNVGKDLGGAVHDFKQGLNEGTDGKEAQKDD MG S+ +I+ +IVVL+FGTKKL ++G DLG ++ FK+ +++ ++ D 131 gi|50917153|ref|XP_468973.1| putative sec-independent protein transporter [Oryza sativa (japonica cultivar-group)] >gi|41469490|gb|AAS07275.1| putative sec-independent protein transporter [Oryza sativa (japonica cultivar-group)] XP_468973 170 1 35.039 79 0.702957 14 70 83 139 0 0 20 36 0 57 CMGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQD CLFGLGVPELVVIAGVAALVFGPKQLPEIGRSIGKTVKSFQQAAKEFETELKKESDD C+ G+ + +L++IA + L+FG K+L IG +G ++K F++A + E + K S D 132 gi|16329622|ref|NP_440350.1| hypothetical protein slr1046 [Synechocystis sp. PCC 6803] >gi|1652105|dbj|BAA17030.1| slr1046 [Synechocystis sp. PCC 6803] >gi|7470329|pir||S74990 hypothetical protein slr1046 - Synechocystis sp. (strain PCC 6803) NP_440350 126 1 35.039 79 0.702957 34 94 63 123 0 0 15 34 0 61 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTED FGPKKLPEVGRSLGKALRGFQEASKEFETELKREAQNLEKSVQIKAELEESKTPESSSSSE FG KKL +G LG +++GF++A + E + + +Q+ + + + A+ + E + + + 133 gi|71083667|ref|YP_266387.1| Twin-arginine translocation protein TatA/E [Candidatus Pelagibacter ubique HTCC1062] >gi|71062780|gb|AAZ21783.1| Twin-arginine translocation protein TatA/E [Candidatus Pelagibacter ubique HTCC1062] YP_266387 66 1 35.039 79 0.702957 18 70 3 58 0 0 24 35 3 56 ISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMS---DDEPKQDKTSQD IGIWQIAIVVILVVLLFGRGKISSLMGDVAKGIKSFKKGMATDITDEPEPKNVSEN I IWQ+ I+ ++VVLLFG K+ S+ D+ IK FKK M+ DEP+ S++ 134 gi|17130190|dbj|BAB72802.1| asl0845 [Nostoc sp. PCC 7120] >gi|25530529|pir||AC1912 hypothetical protein asl0845 [imported] - Nostoc sp. (strain PCC 7120) >gi|17228340|ref|NP_484888.1| hypothetical protein asl0845 [Nostoc sp. PCC 7120] BAB72802 90 1 35.039 79 0.702957 34 95 22 83 0 0 16 34 0 62 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDA FGPKKLPEIGRSMGKAIRGFQEASNEFQSEFKREAEQLEQAVKTTAELEPKQIESVKSEQDS FG KKL IG +G +I+GF++A ++ + + + ++ + KT A+ + + +D+ 135 gi|68246031|gb|EAN28138.1| Twin-arginine translocation protein TatA/E [Magnetococcus sp. MC-1] >gi|69259242|ref|ZP_00607441.1| Twin-arginine translocation protein TatA/E [Magnetococcus sp. MC-1] EAN28138 69 1 34.6538 78 0.91809 34 71 20 59 0 0 17 24 2 40 FGTKKLGSIGSDLGASIKGFKKAMS--DDEPKQDKTSQDA FGAGKLPKVMGDMGRGVKSFKKAMNAEDDAPAEPEVSKPA FG KL + D+G +K FKKAM+ DD P + + S+ A 136 gi|15604583|ref|NP_221101.1| hypothetical protein RP749 [Rickettsia prowazekii str. Madrid E] >gi|3861278|emb|CAA15177.1| unknown [Rickettsia prowazekii] >gi|7467844|pir||A71635 hypothetical protein RP749 - Rickettsia prowazekii >gi|9979048|sp|Q9ZCJ1|TATA_RICPR Sec-independent protein translocase protein tatA/E homolog NP_221101 54 1 34.6538 78 0.91809 34 68 19 53 0 0 16 20 0 35 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTS FGAGKLPQVMSDLAKGLKAFKEGMKDDGNDNDKTN FG KL + SDL +K FK+ M DD DKT+ 137 gi|77685166|ref|ZP_00800574.1| Twin-arginine translocation protein TatA/E [Alkaliphilus metalliredigenes QYMF] >gi|77639020|gb|EAO81400.1| Twin-arginine translocation protein TatA/E [Alkaliphilus metalliredigenes QYMF] ZP_00800574 69 1 34.6538 78 0.91809 34 72 21 62 0 0 19 24 3 42 FGTKKLGSIGSDLGASIKGFK---KAMSDDEPKQDKTSQDAD FGPSKLPEIGKSLGKSIKEFKKFSKEMKDDLSLEERETKDKD FG KL IG LG SIK FK K M DD +++ ++D D 138 gi|39985226|gb|AAR36581.1| twin-arginine translocation protein, TatA/E family [Geobacter sulfurreducens PCA] >gi|39998280|ref|NP_954231.1| twin-arginine translocation protein, TatA/E family [Geobacter sulfurreducens PCA] AAR36581 78 1 34.2686 77 1.19906 12 65 13 77 0 0 26 37 11 65 GTCMGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKA-----------MSDDEPKQD GYCMFGFGMPELIVILIIVLVVFGAGRLPEIGGALGKSIRNFKKASEGKEEIEIKPQKKDEPKKD G CM G + +L++I +IV+++FG +L IG LG SI+ FKKA DEPK+D 139 gi|1825636|gb|AAB42258.1| Hypothetical protein ZK354.3 [Caenorhabditis elegans] >gi|17544554|ref|NP_500777.1| ZK354.3 [Caenorhabditis elegans] AAB42258 312 1 33.8834 76 1.56602 54 102 261 309 0 0 15 26 0 49 KKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ KKEEKKEEKKDDKKEDDKEKSATKSEDKKSDEKKTEEKKSDEKKNEKSE KK +E K DK D + +A DK++D + + K D K+++K + 140 gi|65321915|ref|ZP_00394874.1| COG5386: Cell surface protein [Bacillus anthracis str. A2012] >gi|47530087|ref|YP_021436.1| lpxtg-motif cell wall anchor domain protein, putative [Bacillus anthracis str. 'Ames Ancestor'] >gi|49187439|ref|YP_030691.1| LPXTG-motif cell wall anchor domain protein, putative [Bacillus anthracis str. Sterne] >gi|47505235|gb|AAT33911.1| LPXTG-motif cell wall anchor domain protein, putative [Bacillus anthracis str. 'Ames Ancestor'] >gi|49181366|gb|AAT56742.1| LPXTG-motif cell wall anchor domain protein, putative [Bacillus anthracis str. Sterne] >gi|30259275|gb|AAP28480.1| LPXTG-motif cell wall anchor domain protein, putative [Bacillus anthracis str. Ames] >gi|30264617|ref|NP_846994.1| LPXTG-motif cell wall anchor domain protein, putative [Bacillus anthracis str. Ames] ZP_00394874 237 1 33.8834 76 1.56602 41 103 151 215 0 0 18 37 2 65 SIGSDLG--ASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV AVGGDNGVAATTKNNDQAKTDTQVKEEKTKVESKETAKEVNKETKNENGKAEKTDNPKTGDEARI ++G D G A+ K +A +D + K++KT ++ TAK + + + N + KT++ K D+ ++ 141 gi|30022625|ref|NP_834256.1| Cell surface protein [Bacillus cereus ATCC 14579] >gi|29898183|gb|AAP11457.1| Cell surface protein [Bacillus cereus ATCC 14579] NP_834256 237 1 33.8834 76 1.56602 41 103 151 215 0 0 18 37 2 65 SIGSDLG--ASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV AVGGDNGVAATTKNNDQAKTDTQVKEEKTKVESKETAKEVNKETKNENGKAEKTDNPKTGDEARI ++G D G A+ K +A +D + K++KT ++ TAK + + + N + KT++ K D+ ++ 142 gi|55623442|ref|XP_517520.1| PREDICTED: similar to Acidic leucine-rich nuclear phosphoprotein 32 family member C (Tumorigenic protein pp32r1) [Pan troglodytes] XP_517520 234 1 33.8834 76 1.56602 48 101 154 205 0 0 14 31 2 54 ASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKE SDIKGYVEGLDDEEEGEDEEEYDED--AQVVEDEEGEDEEEEGEEEDVSGGEEE + IKG+ + + D+E +D+ D D A+ + D++ + +E+ + ED ++E 143 gi|75762866|ref|ZP_00742681.1| Cell surface protein [Bacillus thuringiensis serovar israelensis ATCC 35646] >gi|74489647|gb|EAO53048.1| Cell surface protein [Bacillus thuringiensis serovar israelensis ATCC 35646] ZP_00742681 237 1 33.8834 76 1.56602 41 103 151 215 0 0 18 37 2 65 SIGSDLG--ASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV AVGGDNGVAATTKNNDQAKTDTQVKEEKTKVESKETAKEVNKETKNENGKAEKTDNPKTGDEARI ++G D G A+ K +A +D + K++KT ++ TAK + + + N + KT++ K D+ ++ 144 gi|22945598|gb|AAN10511.1| CG18497-PC, isoform C [Drosophila melanogaster] >gi|24580583|ref|NP_722616.1| CG18497-PC, isoform C [Drosophila melanogaster] >gi|6715140|gb|AAF26299.1| split ends [Drosophila melanogaster] AAN10511 5476 1 33.8834 76 1.56602 51 102 1819 1870 0 0 17 25 0 52 KGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ KSDKNASSSDKRKNSSTSQSSKSATPRIEDDSSEADDTADKAEKNQRHEKEK K K A S D+ K TSQ + I D ++ + K E +RH+KE+ 145 gi|10727420|gb|AAF51534.2| CG18497-PB, isoform B [Drosophila melanogaster] >gi|24580581|ref|NP_524718.2| CG18497-PB, isoform B [Drosophila melanogaster] AAF51534 5533 1 33.8834 76 1.56602 51 102 1876 1927 0 0 17 25 0 52 KGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ KSDKNASSSDKRKNSSTSQSSKSATPRIEDDSSEADDTADKAEKNQRHEKEK K K A S D+ K TSQ + I D ++ + K E +RH+KE+ 146 gi|10727421|gb|AAF51535.2| CG18497-PA, isoform A [Drosophila melanogaster] >gi|24580579|ref|NP_722615.1| CG18497-PA, isoform A [Drosophila melanogaster] >gi|46397733|sp|Q8SX83|SPEN_DROME Split ends protein AAF51535 5560 1 33.8834 76 1.56602 51 102 1876 1927 0 0 17 25 0 52 KGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ KSDKNASSSDKRKNSSTSQSSKSATPRIEDDSSEADDTADKAEKNQRHEKEK K K A S D+ K TSQ + I D ++ + K E +RH+KE+ 147 gi|71481981|ref|ZP_00661682.1| Twin-arginine translocation protein TatA/E [Prosthecochloris vibrioformis DSM 265] >gi|71283129|gb|EAO14957.1| Twin-arginine translocation protein TatA/E [Prosthecochloris vibrioformis DSM 265] ZP_00661682 69 1 33.8834 76 1.56602 34 82 20 69 0 0 19 27 1 50 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAK-TIADKQ FGAKKLPELAKGLGRGMKEFKKAQTEIEEEFNNAIEDTPAQKKETIKDKE FG KKL + LG +K FKKA ++ E + + +D K TI DK+ 148 gi|71150623|ref|ZP_00649545.1| Twin-arginine translocation protein TatA/E [Thiomicrospira denitrificans ATCC 33889] >gi|71087818|gb|EAO03597.1| Twin-arginine translocation protein TatA/E [Thiomicrospira denitrificans ATCC 33889] ZP_00649545 81 1 33.8834 76 1.56602 34 96 20 76 0 0 19 31 6 63 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAK FGAKKIPELAKGIGKGIKNFKAEMKNEDDDTEVKS------ASTEAPKKVESAEEVASKESSK FG KK+ + +G IK FK M +++ + S A T A K+ ++ +E A E +K 149 gi|20151563|gb|AAM11141.1| LD15253p [Drosophila melanogaster] AAM11141 1521 1 33.8834 76 1.56602 51 102 1392 1443 0 0 17 25 0 52 KGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ KSDKNASSSDKRKNSSTSQSSKSATPRIEDDSSEADDTADKAEKNQRHEKEK K K A S D+ K TSQ + I D ++ + K E +RH+KE+ 150 gi|6979936|gb|AAF34661.1| split ends long isoform [Drosophila melanogaster] AAF34661 5554 1 33.8834 76 1.56602 51 102 1870 1921 0 0 17 25 0 52 KGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ KSDKNASSSDKRKNSSTSQSSKSATPRIEDDSSEADDTADKAEKNQRHEKEK K K A S D+ K TSQ + I D ++ + K E +RH+KE+ 151 gi|6467825|gb|AAF13218.1| Spen RNP motif protein long isoform [Drosophila melanogaster] AAF13218 5533 1 33.8834 76 1.56602 51 102 1876 1927 0 0 17 25 0 52 KGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ KSDKNASSSDKRKNSSTSQSSKSATPRIEDDSSEADDTADKAEKNQRHEKEK K K A S D+ K TSQ + I D ++ + K E +RH+KE+ 152 gi|61102013|ref|ZP_00377467.1| hypothetical protein ELI2708 [Erythrobacter litoralis HTCC2594] >gi|60736120|gb|EAL74381.1| hypothetical protein ELI2708 [Erythrobacter litoralis HTCC2594] ZP_00377467 80 1 33.8834 76 1.56602 15 61 1 47 0 0 19 33 0 47 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDE MGQIGIWQILIIALVILVLFGRGKISDMMGDFGKGVSSFKKGLNEED MG I IWQ+LIIA+++++LFG K+ + D G + FKK +++++ 153 gi|68056232|ref|ZP_00540361.1| Twin-arginine translocation protein TatA/E [Exiguobacterium sp. 255-15] >gi|68007169|gb|EAM86442.1| Twin-arginine translocation protein TatA/E [Exiguobacterium sp. 255-15] ZP_00540361 68 1 33.4982 75 2.04529 34 69 28 67 0 0 17 24 4 40 FGTKKLGSIGSDLGASIKGFKKA----MSDDEPKQDKTSQ FGPKKLPELGRAAGQTLKEFKSATHGIMDDDKDKKDETKE FG KKL +G G ++K FK A M DD+ K+D+T + 154 gi|68190120|gb|EAN04781.1| Twin-arginine translocation protein TatA/E [Mesorhizobium sp. BNC1] >gi|69279521|ref|ZP_00614376.1| Twin-arginine translocation protein TatA/E [Mesorhizobium sp. BNC1] EAN04781 71 1 33.4982 75 2.04529 15 67 1 52 0 0 24 34 1 53 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKT MGSFSIWHWLIVLVVVLLLFGRGKIPELMGDMAKGIKNFRKGMT-DEAEEAKT MG SIW LI+ V+V+LLFG K+ + D+ IK F+K M+ DE ++ KT 155 gi|15605663|ref|NP_213038.1| hypothetical protein aq_064c [Aquifex aeolicus VF5] >gi|2982828|gb|AAC06451.1| hypothetical protein [Aquifex aeolicus VF5] >gi|7444822|pir||C70306 conserved hypothetical protein aq_064c - Aquifex aeolicus >gi|9978997|sp|O66478|TAT1_AQUAE Sec-independent protein translocase tatA/E-like protein 1 NP_213038 77 1 33.4982 75 2.04529 16 93 4 76 0 0 26 47 5 78 GGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTE GGISMTELIIILAVILLLFGAGRLPEAGRALGEGIRNFRKALSGETEVKEVKAED----VKT-EERKEEKKEEKEKVE GGIS+ +L+II +++LLFG +L G LG I+ F+KA+S + ++ ++D KT +++ + +E+ K E 156 gi|60493413|emb|CAH08199.1| aerotolerance-related exported protein [Bacteroides fragilis NCTC 9343] >gi|60681979|ref|YP_212123.1| aerotolerance-related exported protein [Bacteroides fragilis NCTC 9343] >gi|4838140|gb|AAD30860.1| BatC [Bacteroides fragilis] CAH08199 238 1 33.4982 75 2.04529 43 101 111 173 0 0 18 34 6 64 GSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQ-----ADTNQEQAKTEDAKRHDKE GKDYQKAVEAYKMSLRNN-PKDDETRYNLALAQKLLKDQQQNQQNQDQNQDQNKDDQQKQQDKK G D +++ +K ++ ++ PK D+T + K + D+Q D NQ+Q K + K+ DK+ 157 gi|50877510|emb|CAG37350.1| related to Sec-independent protein translocase protein TatA [Desulfotalea psychrophila LSv54] >gi|51246473|ref|YP_066357.1| similar to Sec-independent protein translocase protein TatA [Desulfotalea psychrophila LSv54] CAG37350 84 1 33.4982 75 2.04529 34 61 20 47 0 0 15 20 0 28 FGTKKLGSIGSDLGASIKGFKKAMSDDE FGGKKLPKLGSSLGQAMKSFKQGVSDVE FG KKL +GS LG ++K FK+ +SD E 158 gi|42739647|gb|AAS43573.1| conserved domain protein [Bacillus cereus ATCC 10987] >gi|42783718|ref|NP_980965.1| hypothetical protein BCE4672 [Bacillus cereus ATCC 10987] AAS43573 236 1 33.4982 75 2.04529 41 103 151 215 0 0 18 37 2 65 SIGSDLG--ASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQV AVGGDNGVTAATKNNDQAKTDTQVKEEKTKVESKETAKEASKETKNENGKAEKTDNPKTGDEARI ++G D G A+ K +A +D + K++KT ++ TAK + + + N + KT++ K D+ ++ 159 gi|53713708|ref|YP_099700.1| conserved hypothetical protein BatC [Bacteroides fragilis YCH46] >gi|52216573|dbj|BAD49166.1| conserved hypothetical protein BatC [Bacteroides fragilis YCH46] YP_099700 238 1 33.4982 75 2.04529 43 101 111 173 0 0 18 34 6 64 GSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQ-----ADTNQEQAKTEDAKRHDKE GKDYQKAVEAYKMSLRNN-PKDDETRYNLALAQKLLKDQQQNQQNQDQNQDQNKDDQQKQQDKK G D +++ +K ++ ++ PK D+T + K + D+Q D NQ+Q K + K+ DK+ 160 gi|33860901|ref|NP_892462.1| mttA/Hcf106 family [Prochlorococcus marinus subsp. pastoris str. CCMP1986] >gi|33633843|emb|CAE18802.1| mttA/Hcf106 family [Prochlorococcus marinus subsp. pastoris str. CCMP1986] NP_892462 96 1 33.113 74 2.67123 34 99 22 87 0 0 17 34 0 66 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHD FGPKKLPELGKQLGKTLKSLKKASNEFQNEIDQVINEPESENLPKSPQKKFTNDLDQVTKESEEKD FG KKL +G LG ++K KKA ++ + + D+ + + + ++ TN T++++ D 161 gi|48851224|ref|ZP_00305466.1| COG1826: Sec-independent protein secretion pathway components [Novosphingobium aromaticivorans DSM 12444] ZP_00305466 83 1 33.113 74 2.67123 15 63 1 49 0 0 19 35 0 49 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPK MGGLSLPHLIVLALVVLILFGRGRISEMMGDFGKGIKSFKQGMNDEDSK MGG+S+ L+++A++V++LFG ++ + D G IK FK+ M+D++ K 162 gi|67938449|ref|ZP_00530974.1| Twin-arginine translocation protein TatA/E [Chlorobium phaeobacteroides BS1] >gi|67915292|gb|EAM64615.1| Twin-arginine translocation protein TatA/E [Chlorobium phaeobacteroides BS1] ZP_00530974 69 1 33.113 74 2.67123 34 70 20 56 0 0 16 21 0 37 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQD FGAKKLPELAKGLGKGMKEFKKAQSEIEEELNKAVDD FG KKL + LG +K FKKA S+ E + +K D 163 gi|45657833|ref|YP_001919.1| sec-independent protein secretion pathway component [Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130] >gi|24214626|ref|NP_712107.1| mttA/Hcf106 family protein [Leptospira interrogans serovar Lai str. 56601] >gi|45601073|gb|AAS70556.1| sec-independent protein secretion pathway component [Leptospira interrogans serovar Copenhageni str. Fiocruz L1-130] >gi|24195601|gb|AAN49125.1| mttA/Hcf106 family protein [Leptospira interrogans serovar lai str. 56601] >gi|59798911|sp|Q8F4W2|TATA_LEPIN Sec-independent protein translocase protein tatA/E homolog >gi|59798776|sp|Q72QX8|TATA_LEPIC Sec-independent protein translocase protein tatA/E homolog YP_001919 90 1 33.113 74 2.67123 34 97 32 86 0 0 17 33 9 64 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKR FGGKRLPSLAKDLGDGIRSFRKSL---------TGESDDSSQQISQEQERSVPKEETKTSKSKK FG K+L S+ DLG I+ F+K++ T + D + + +++ +E+ KT +K+ 164 gi|57238048|ref|YP_179297.1| twin-arginine translocation protein, TatA/E family [Campylobacter jejuni RM1221] >gi|57166852|gb|AAW35631.1| twin-arginine translocation protein, TatA/E family [Campylobacter jejuni RM1221] >gi|6968609|emb|CAB73430.1| hypothetical protein Cj1176c [Campylobacter jejuni subsp. jejuni NCTC 11168] >gi|11346722|pir||B81323 hypothetical protein Cj1176c [imported] - Campylobacter jejuni (strain NCTC 11168) >gi|9979042|sp|Q9PNB9|TATA_CAMJE Sec-independent protein translocase protein tatA/E homolog >gi|15792500|ref|NP_282323.1| hypothetical protein Cj1176c [Campylobacter jejuni subsp. jejuni NCTC 11168] YP_179297 79 1 33.113 74 2.67123 34 91 21 77 0 0 18 30 1 58 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAK FGAKKIPELAKGLGKGIKTFKDEMNNDD-EVAKNTQKIEENKNTTNNTNADASIDETK FG KK+ + LG IK FK M++D+ + K +Q + T + AD + ++ K 165 gi|56962648|ref|YP_174374.1| sec-independent protein translocase protein TatA [Bacillus clausii KSM-K16] >gi|56908886|dbj|BAD63413.1| sec-independent protein translocase protein TatA [Bacillus clausii KSM-K16] YP_174374 63 1 33.113 74 2.67123 15 68 1 57 0 0 20 38 3 57 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFK---KAMSDDEPKQDKTS MGGLSVGSVVLIALVALLIFGPKKLPELGKAAGSTLREFKNATKGLADDDDDTKSTN MGG+S+ +++IA++ +L+FG KKL +G G++++ FK K ++DD+ T+ 166 gi|33239734|ref|NP_874676.1| Sec-independent protein secretion pathway component TatA [Prochlorococcus marinus subsp. marinus str. CCMP1375] >gi|33237259|gb|AAP99328.1| Sec-independent protein secretion pathway component TatA [Prochlorococcus marinus subsp. marinus str. CCMP1375] NP_874676 84 1 33.113 74 2.67123 17 94 5 74 0 0 24 43 8 78 GISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTED GIGLPEIAVIAAIALFIFGPKKLPALGRGLGKTLRSLQKASSEFENELQK--------AVSASDKTDQGNQHELKHKE GI + ++ +IA I + +FG KKL ++G LG +++ +KA S+ E + K A + +DK NQ + K ++ 167 gi|21674434|ref|NP_662499.1| Sec-independent protein translocase protein TatE, putative [Chlorobium tepidum TLS] >gi|21647618|gb|AAM72841.1| Sec-independent protein translocase protein TatE, putative [Chlorobium tepidum TLS] NP_662499 67 1 33.113 74 2.67123 34 76 20 62 0 0 16 24 0 43 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAK FGAQKLPELAKGLGKGIKEFKKAQNEIEEEFNKATDDSSSKEK FG +KL + LG IK FKKA ++ E + +K + D+ K 168 gi|39968009|ref|XP_365395.1| hypothetical protein MG02097.4 [Magnaporthe grisea 70-15] XP_365395 823 1 32.7278 73 3.48874 35 102 68 139 0 0 20 32 4 72 GTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAK----TEDAKRHDKEQ GAPLIGKAVDKIVDKVSGGDKKKKEEEEAKKKAEADAAAAAEAEAKKKADAEAAEAKKKKEAEDKKKKDEEE G +G + + G K ++E + K DA A+ A K+AD +AK ED K+ D+E+ 169 gi|4877986|gb|AAD31523.1| THA9 [Zea mays] AAD31523 169 1 32.7278 73 3.48874 14 66 74 126 0 0 19 33 0 53 CMGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDK CLFGLGVPELAVIAGVAALVFGPKQLPEIGRSLGKTVKSFQEAAKEFESELKK C+ G+ + +L +IA + L+FG K+L IG LG ++K F++A + E + K 170 gi|67934419|ref|ZP_00527476.1| Twin-arginine translocation protein TatA/E [Solibacter usitatus Ellin6076] >gi|67858348|gb|EAM53485.1| Twin-arginine translocation protein TatA/E [Solibacter usitatus Ellin6076] ZP_00527476 56 1 32.7278 73 3.48874 34 69 20 55 0 0 14 20 0 36 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQ FGGKKIPEVAKGLGEGIRNFKSALKGDEEKVEEKKQ FG KK+ + LG I+ FK A+ DE K ++ Q 171 gi|42523658|ref|NP_969038.1| twin-argine protein translocase component [Bdellovibrio bacteriovorus HD100] >gi|39575865|emb|CAE80031.1| twin-argine protein translocase component [Bdellovibrio bacteriovorus HD100] NP_969038 79 1 32.7278 73 3.48874 15 102 1 77 0 0 24 45 11 88 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ MGEFSLTHILLLAVIFLIFFGPSRLPQLGQSMGKAIRGFKQGLN-----------EIDVDAKDIHDNQQVSHQNKQSMGQTQKQGENQ MG S+ +L++AVI ++ FG +L +G +G +I+GFK+ ++ + D AK I D Q ++Q + ++ + Q 172 gi|71546080|ref|ZP_00666945.1| Twin-arginine translocation protein TatA/E [Syntrophobacter fumaroxidans MPOB] >gi|71488143|gb|EAO20575.1| Twin-arginine translocation protein TatA/E [Syntrophobacter fumaroxidans MPOB] ZP_00666945 73 1 32.7278 73 3.48874 34 71 18 55 0 0 16 20 0 38 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDA FGPGKLPDIGKSLGKGIRNFKKATDEESPVPQVPSKTA FG KL IG LG I+ FKKA ++ P S+ A 173 gi|68002197|ref|ZP_00534828.1| Twin-arginine translocation protein TatA/E [Geobacter metallireducens GS-15] >gi|67993414|gb|EAM80570.1| Twin-arginine translocation protein TatA/E [Geobacter metallireducens GS-15] ZP_00534828 60 1 32.3426 72 4.55643 34 75 20 60 0 0 18 24 1 42 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTA FGPAKLPQLGQSLGAGIRNFKKA-TLEEPEQIATKDKEEGAA FG KL +G LGA I+ FKKA + +EP+Q T + A 174 gi|67481641|ref|XP_656170.1| hypothetical protein 16.t00066 [Entamoeba histolytica HM-1:IMSS] >gi|56473354|gb|EAL50784.1| hypothetical protein 16.t00066 [Entamoeba histolytica HM-1:IMSS] XP_656170 434 1 32.3426 72 4.55643 36 101 165 233 0 0 21 32 3 69 TKKLGSIGSDLGASIKGFKKAMSDDEPK---QDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKE TKGSESSKTDLTKSCKGQKAHTKEDEKKLHSSDSESSDSESSYSDSDSESSDSEDEESSTESDSPSDRE TK S +DL S KG K +DE K D S D++ + + +D+ E++ TE D+E 175 gi|50935447|ref|XP_477251.1| putative Calreticulin precursor [Oryza sativa (japonica cultivar-group)] >gi|51978962|ref|XP_507358.1| PREDICTED OJ1058_C08.28-2 gene product [Oryza sativa (japonica cultivar-group)] >gi|51963340|ref|XP_506239.1| PREDICTED OJ1058_C08.28-2 gene product [Oryza sativa (japonica cultivar-group)] >gi|50509013|dbj|BAD31961.1| putative Calreticulin precursor [Oryza sativa (japonica cultivar-group)] >gi|34393218|dbj|BAC82932.1| putative Calreticulin precursor [Oryza sativa (japonica cultivar-group)] XP_477251 424 1 32.3426 72 4.55643 55 100 383 423 0 0 16 27 5 46 KAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDK KAGEDDDDLDDEDAEDEDK-----ADEKADSDAEDGKDSDDEKHDE KA DD+ D+ ++D D AD++AD++ E K D ++HD+ 176 gi|50978634|ref|NP_001003013.1| acidic (leucine-rich) nuclear phosphoprotein 32 family, member A [Canis familiaris] >gi|26984047|gb|AAN85118.1| inhibitor-1 of protein phosphatase type 2A [Canis familiaris] NP_001003013 249 1 32.3426 72 4.55643 51 101 161 209 0 0 13 29 2 51 KGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKE EGYVEGLDDDEEDEDEEEYDED--AQVVEDEEDEEEEEEGEEEDVSGEEEE +G+ + + DDE +D+ D D A+ + D++ + +E+ + ED ++E 177 gi|70936814|ref|XP_739300.1| 40S ribosomal subunit protein S6, putative [Plasmodium chabaudi] >gi|56516193|emb|CAH81548.1| 40S ribosomal subunit protein S6, putative [Plasmodium chabaudi] XP_739300 184 1 32.3426 72 4.55643 45 101 97 154 0 0 19 33 3 59 DLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTI--ADKQADTNQEQAKTEDAKRHDKE DVGKKLK-VKKNISKDAKKNDKEKNSKDDKSKTKKNVDKKSEKSEKSKKVENKKVNEKQ D+G +K KK +S D K DK D +KT DK+++ +++ K E+ K ++K+ 178 gi|68075857|ref|XP_679848.1| hypothetical protein PB104900.00.0 [Plasmodium berghei] >gi|56500688|emb|CAH97504.1| hypothetical protein PB104900.00.0 [Plasmodium berghei] XP_679848 340 1 32.3426 72 4.55643 38 100 94 159 0 0 23 30 3 66 KLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTI---ADKQADTNQEQAKTEDAKRHDK KLVSLGKAHVPKNDKTKEAMKSNNNKEDKKIDDNKEDKKTDDNKEDKKTDDNKEDKKTDDNKEDKK KL S+G K+AM + K+DK D KT DK+ D N+E KT+D K K 179 gi|39594005|emb|CAE70115.1| Hypothetical protein CBG16567 [Caenorhabditis briggsae] CAE70115 192 1 32.3426 72 4.55643 58 102 141 185 0 0 14 24 0 45 SDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ SDDSSSSDDSDDDSDSEAEEDTEKKASTEEDSGKRDDAEERTFER SDD D + D+D A+ +K+A T ++ K +DA+ E+ 180 gi|66809957|ref|XP_638702.1| hypothetical protein DDB0185950 [Dictyostelium discoideum] >gi|60467300|gb|EAL65333.1| hypothetical protein DDB0185950 [Dictyostelium discoideum] XP_638702 721 1 32.3426 72 4.55643 54 102 24 70 0 0 15 27 2 49 KKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ EQKMEVDEPKKDATASDS--TTADLENKKESSGSDDTATTDVKKDDSKQ ++ M DEPK+D T+ D+ T + +K+ + + T D K+ D +Q 181 gi|68550463|ref|ZP_00589911.1| Twin-arginine translocation protein TatA/E [Pelodictyon phaeoclathratiforme BU-1] >gi|68242628|gb|EAN24841.1| Twin-arginine translocation protein TatA/E [Pelodictyon phaeoclathratiforme BU-1] ZP_00589911 69 1 32.3426 72 4.55643 34 68 20 64 0 0 17 25 10 45 FGTKKLGSIGSDLGASIKGFKKAMS----------DDEPKQDKTS FGAKKLPELARGLGKGMKEFKKAQTEIEEEFNSVVDEKPKKEKTA FG KKL + LG +K FKKA + D++PK++KT+ 182 gi|51473916|ref|YP_067673.1| TatA/E-like Sec-independent protein translocase protein [Rickettsia typhi str. Wilmington] >gi|51460228|gb|AAU04191.1| TatA/E-like Sec-independent protein translocase protein [Rickettsia typhi str. Wilmington] YP_067673 53 1 32.3426 72 4.55643 34 66 19 51 0 0 15 18 0 33 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDK FGAGKLPQVMSDLAKGLKAFKEGMKDDGNDNDK FG KL + SDL +K FK+ M DD DK 183 gi|61857708|ref|XP_612559.1| PREDICTED: similar to acidic (leucine-rich) nuclear phosphoprotein 32 family, member A [Bos taurus] XP_612559 236 1 32.3426 72 4.55643 51 101 148 196 0 0 13 29 2 51 KGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKE EGYVEGLDDDEEDEDEEEYDED--AQVVEDEEDEEEEEEGEEEDVSGEEEE +G+ + + DDE +D+ D D A+ + D++ + +E+ + ED ++E 184 gi|39982651|gb|AAR34111.1| twin-arginine translocation protein, TatA/E family [Geobacter sulfurreducens PCA] >gi|39995887|ref|NP_951838.1| twin-arginine translocation protein, TatA/E family [Geobacter sulfurreducens PCA] AAR34111 59 1 32.3426 72 4.55643 34 63 20 49 0 0 15 19 0 30 FGTKKLGSIGSDLGASIKGFKKAMSDDEPK FGPGKLPQLGQSLGASIRNFKKASLEEPEK FG KL +G LGASI+ FKKA ++ K 185 gi|50877509|emb|CAG37349.1| related to Sec-independent protein translocase protein TatE [Desulfotalea psychrophila LSv54] >gi|51246472|ref|YP_066356.1| similar to Sec-independent protein translocase protein TatE [Desulfotalea psychrophila LSv54] CAG37349 66 1 32.3426 72 4.55643 34 72 20 60 0 0 17 24 2 41 FGTKKLGSIGSDLGASIKGFKKAMSDDE--PKQDKTSQDAD FGAGKLPEIGSGIGKGIKNFKEATKSEEAAKKIDKSEEKSE FG KL IGS +G IK FK+A +E K DK+ + ++ 186 gi|52699323|ref|ZP_00340731.1| COG1826: Sec-independent protein secretion pathway components [Rickettsia akari str. Hartford] ZP_00340731 53 1 32.3426 72 4.55643 34 66 19 51 0 0 15 17 0 33 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDK FGAGKLPQVMSDLAKGLKAFKNGMQDDGSDNDK FG KL + SDL +K FK M DD DK 187 gi|62426215|ref|ZP_00381343.1| COG1826: Sec-independent protein secretion pathway components [Brevibacterium linens BL2] ZP_00381343 93 1 32.3426 72 4.55643 34 100 19 93 0 0 21 34 8 75 FGTKKLGSIGSDLGASIKGFKKAM----SDDEPKQ----DKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDK FGAPKLPALARSLGQSMKIFKSEVKDLRDDDEPKKTEPGELNREATENDTSTTAEAARKPEQPAKEKQDPQSHEK FG KL ++ LG S+K FK + DDEPK+ + + + T A+ Q + +D + H+K 188 gi|11131838|sp|Q9SLY8|CRTC_ORYSA Calreticulin precursor >gi|6682833|dbj|BAA88900.1| calcium-binding protein [Oryza sativa] Q9SLY8 424 1 32.3426 72 4.55643 55 100 383 423 0 0 16 27 5 46 KAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDK KAGEDDDDLDDEDAEDEDK-----ADEKADSDAEDGKDSDDEKHDE KA DD+ D+ ++D D AD++AD++ E K D ++HD+ 189 gi|56543690|gb|AAV89844.1| Sec-independent protein secretion pathway component [Zymomonas mobilis subsp. mobilis ZM4] >gi|56552116|ref|YP_162955.1| Sec-independent protein secretion pathway component [Zymomonas mobilis subsp. mobilis ZM4] AAV89844 87 1 32.3426 72 4.55643 15 61 1 47 0 0 19 31 0 47 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDE MGGMSITHWIVVAVVVMIFFGKGRFSDMMGDVAKGIKSFKKGMSEDD MGG+SI +++AV+V++ FG + + D+ IK FKK MS+D+ 190 gi|67923730|ref|ZP_00517196.1| Twin-arginine translocation protein TatA/E [Crocosphaera watsonii WH 8501] >gi|67854438|gb|EAM49731.1| Twin-arginine translocation protein TatA/E [Crocosphaera watsonii WH 8501] ZP_00517196 95 1 31.9574 71 5.95088 34 96 22 93 0 0 19 35 9 72 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQ---------ADTNQEQAKTEDAK FGPKKLPEIGRSLGKAVRGFQDASKEFENEFKREAQQLEESVTMKAELEENKMANPTPMDNNQTKMNTQTSE FG KKL IG LG +++GF+ A + E + + +Q + + A+ + D NQ + T+ ++ 191 gi|67462585|ref|XP_647954.1| hypothetical protein 707.t00002 [Entamoeba histolytica HM-1:IMSS] >gi|56463733|gb|EAL42569.1| hypothetical protein 707.t00002 [Entamoeba histolytica HM-1:IMSS] XP_647954 140 1 31.9574 71 5.95088 51 102 41 95 0 0 16 30 3 55 KGFKKAMSDDEPKQDKTSQDADFTAKT---IADKQADTNQEQAKTEDAKRHDKEQ KNYKKIKTQEENKEETKNEDENYKEKEEIKVLQKQIKRLEEEIKEYQAKRKEEEQ K +KK + +E K++ ++D ++ K + KQ +E+ K AKR ++EQ 192 gi|51970620|dbj|BAD44002.1| unknown protein [Arabidopsis thaliana] BAD44002 784 1 31.9574 71 5.95088 39 102 167 232 0 0 21 35 6 68 LGSIGSDLGASIKGFKKAMS----DDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ LDSMGSELGDSRKKRKKKRSEEKQDHEDVDELANEDLEHEESEFSDEESE--EEPVGKRDRKRHKKKK L S+GS+LG S K KK S D E + ++D + +D++++ +E D KRH K++ 193 gi|34581241|ref|ZP_00142721.1| hypothetical protein [Rickettsia sibirica 246] >gi|53732344|ref|ZP_00154116.2| COG1826: Sec-independent protein secretion pathway components [Rickettsia rickettsii] >gi|28262626|gb|EAA26130.1| unknown [Rickettsia sibirica 246] ZP_00142721 53 1 31.9574 71 5.95088 34 66 19 51 0 0 15 17 0 33 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDK FGAGKLPQVMSDLAKGLKAFKDGMKDDGSDNDK FG KL + SDL +K FK M DD DK 194 gi|4877984|gb|AAD31522.1| THA4 [Zea mays] AAD31522 170 1 31.9574 71 5.95088 14 66 84 136 0 0 18 33 0 53 CMGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDK CLFGLGVPELAVIAGVAALVFGPKQLPEIGRSIGKTVKSFQQAAKEFETELKK C+ G+ + +L +IA + L+FG K+L IG +G ++K F++A + E + K 195 gi|9757886|dbj|BAB08393.1| unnamed protein product [Arabidopsis thaliana] >gi|15238687|ref|NP_197295.1| MA3 domain-containing protein [Arabidopsis thaliana] BAB08393 707 1 31.9574 71 5.95088 39 102 147 212 0 0 21 35 6 68 LGSIGSDLGASIKGFKKAMS----DDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ LDSMGSELGDSRKKRKKKRSEEKQDHEDVDELANEDLEHEESEFSDEESE--EEPVGKRDRKRHKKKK L S+GS+LG S K KK S D E + ++D + +D++++ +E D KRH K++ 196 gi|32422107|ref|XP_331497.1| predicted protein [Neurospora crassa] >gi|28919664|gb|EAA29078.1| predicted protein [Neurospora crassa] XP_331497 216 1 31.9574 71 5.95088 59 102 42 85 0 0 13 26 0 44 DDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ EDKEEEDKEEENKEEEDKEEEDKEEEDKEEEDKEEENKEEDKEE +D+ ++DK ++ + K DK+ + +E+ K E+ K DKE+ 197 gi|68552035|ref|ZP_00591428.1| Twin-arginine translocation protein TatA/E [Prosthecochloris aestuarii DSM 271] >gi|68241158|gb|EAN23426.1| Twin-arginine translocation protein TatA/E [Prosthecochloris aestuarii DSM 271] ZP_00591428 70 1 31.9574 71 5.95088 34 70 20 56 0 0 15 21 0 37 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQD FGAKKLPELAKGLGKGMKEFKKAQTEIEDEFNKAMSD FG KKL + LG +K FKKA ++ E + +K D 198 gi|68177649|ref|ZP_00550794.1| Twin-arginine translocation protein TatA/E [Desulfuromonas acetoxidans DSM 684] >gi|67982303|gb|EAM71712.1| Twin-arginine translocation protein TatA/E [Desulfuromonas acetoxidans DSM 684] ZP_00550794 58 1 31.9574 71 5.95088 34 66 20 54 0 0 16 22 2 35 FGTKKLGSIGSDLGASIKGFKKAM--SDDEPKQDK FGAKRLPQLGSGLGKGIKNFKQGIKENDTESLEDK FG K+L +GS LG IK FK+ + +D E +DK 199 gi|67934756|ref|ZP_00527782.1| Twin-arginine translocation protein TatA/E [Chlorobium phaeobacteroides DSM 266] >gi|67776249|gb|EAM35909.1| Twin-arginine translocation protein TatA/E [Chlorobium phaeobacteroides DSM 266] ZP_00527782 65 1 31.9574 71 5.95088 34 77 20 63 0 0 16 24 0 44 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKT FGAKKLPELARGLGRGMKEFKKAQTEIEEEFNKVVEEPPAKEKT FG KKL + LG +K FKKA ++ E + +K ++ KT 200 gi|42550455|gb|EAA73298.1| hypothetical protein FG04514.1 [Gibberella zeae PH-1] >gi|46117344|ref|XP_384690.1| hypothetical protein FG04514.1 [Gibberella zeae PH-1] EAA73298 297 1 31.9574 71 5.95088 38 101 188 251 0 0 22 29 0 64 KLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKE KLKSHGPDLPASQSFAKKHPRDSEDEDDVSSEEESDTDDDDDDDDDDDKTDEAKSEGDTAIDNE KL S G DL AS KK D E + D +S++ T D D ++AK+E D E 201 gi|15893083|ref|NP_360797.1| hypothetical protein RC1160 [Rickettsia conorii str. Malish 7] >gi|15620287|gb|AAL03698.1| unknown [Rickettsia conorii str. Malish 7] >gi|25504411|pir||H97844 hypothetical protein RC1160 [imported] - Rickettsia conorii (strain Malish 7) >gi|24212502|sp|Q92GG3|TATA_RICCN Sec-independent protein translocase protein tatA/E homolog NP_360797 53 1 31.9574 71 5.95088 34 66 19 51 0 0 15 17 0 33 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDK FGAGKLPQVMSDLAKGLKAFKDGMKDDGSDNDK FG KL + SDL +K FK M DD DK 202 gi|57233621|ref|YP_182297.1| twin-arginine translocation protein, TatA/E family [Dehalococcoides ethenogenes 195] >gi|57224069|gb|AAW39126.1| twin-arginine translocation protein, TatA/E family [Dehalococcoides ethenogenes 195] YP_182297 65 1 31.9574 71 5.95088 34 70 20 56 0 0 13 23 0 37 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQD FGIGKLPQVGDAIGKGIRNFRKASSGEEEKEEVETKE FG KL +G +G I+ F+KA S +E K++ +++ 203 gi|75908036|ref|YP_322332.1| Twin-arginine translocation protein TatA/E [Anabaena variabilis ATCC 29413] >gi|75701761|gb|ABA21437.1| Twin-arginine translocation protein TatA/E [Anabaena variabilis ATCC 29413] >gi|53764126|ref|ZP_00159794.2| COG1826: Sec-independent protein secretion pathway components [Anabaena variabilis ATCC 29413] YP_322332 56 1 31.9574 71 5.95088 34 66 20 56 0 0 14 24 4 37 FGTKKLGSIGSDLGASIKGFKKAM----SDDEPKQDK FGPKKIPELGSALGKTLRGFKEELKTPSEDTNPEEEK FG KK+ +GS LG +++GFK+ + D P+++K 204 gi|72383453|ref|YP_292808.1| Twin-arginine translocation protein TatA/E [Prochlorococcus marinus str. NATL2A] >gi|72003303|gb|AAZ59105.1| Twin-arginine translocation protein TatA/E [Prochlorococcus marinus str. NATL2A] YP_292808 71 1 31.9574 71 5.95088 17 82 5 70 0 0 17 39 0 66 GISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQ GVGLPEIAVIAGLALVIFGPKRLPELGRTIGKTLKGLQSASTEFEREIKNAMTEEESANENIADKE G+ + ++ +IA + +++FG K+L +G +G ++KG + A ++ E + + + + IADK+ 205 gi|1666185|emb|CAB04766.1| ORF13(1) [Rhodococcus erythropolis] >gi|9979018|sp|P72267|TATA_RHOER Sec-independent protein translocase protein tatA/E homolog CAB04766 98 1 31.9574 71 5.95088 15 71 1 60 0 0 25 35 3 60 MGGISIWQXXXXXXXXXXXFGTKKLGSIGSDLGASIKGFK---KAMSDDEPKQDKTSQDA MGAMSPWHWAIVALVVVILFGSKKLPDAARGLGRSLRIFKSEVKEMQNDNSTPAPTAQSA MG +S W I+A++VV+LFG+KKL LG S++ FK K M +D T+Q A 206 gi|72138252|ref|XP_800288.1| PREDICTED: hypothetical protein XP_795195 [Strongylocentrotus purpuratus] XP_800288 946 1 31.9574 71 5.95088 59 102 855 898 0 0 13 25 0 44 DDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ EDQDKEDKDEEDKDEEDKDKEDKDAEEEEEEDNADEEEDADKDE +D+ K+DK +D D K DK A+ +E+ ++ + DK++ 207 gi|67923190|ref|ZP_00516678.1| Twin-arginine translocation protein TatA/E [Crocosphaera watsonii WH 8501] >gi|67854976|gb|EAM50247.1| Twin-arginine translocation protein TatA/E [Crocosphaera watsonii WH 8501] ZP_00516678 50 1 31.5722 70 7.7721 34 64 20 50 0 0 11 23 0 31 FGTKKLGSIGSDLGASIKGFKKAMSDDEPKQ FGPKKIPELGSSLGKTLRGFKEGVNNPKDEE FG KK+ +GS LG +++GFK+ +++ + ++ 208 gi|3329623|gb|AAC26930.1| Hypothetical protein F36H12.3 [Caenorhabditis elegans] >gi|17540204|ref|NP_500767.1| F36H12.3 [Caenorhabditis elegans] AAC26930 335 1 31.5722 70 7.7721 36 102 75 141 0 0 19 31 0 67 TKKLGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ SKKSEGKKSDKKEEKKEEKKEEKEDKKEEKKEEKKEDDKKDEKKDEKKDEKEEDKKSEDKKEDEKEK +KK SD K KK +D+ ++ K + D D++ D +E K+ED K +KE+ 209 gi|39597929|emb|CAE68621.1| Hypothetical protein CBG14505 [Caenorhabditis briggsae] CAE68621 2691 1 31.5722 70 7.7721 55 102 1679 1730 0 0 16 27 4 52 KAMSDDEPKQDKTSQDADFTAKTIADK----QADTNQEQAKTEDAKRHDKEQ KDESEEKNKEDNMEESKDFTEMTVDNTISLGECSTTQYEEKTIDIDEHEEEQ K S+++ K+D + DFT T+ + + T Q + KT D H++EQ 210 gi|68182025|ref|ZP_00555006.1| hypothetical protein JannDRAFT_2282 [Jannaschia sp. CCS1] >gi|67977679|gb|EAM67298.1| hypothetical protein JannDRAFT_2282 [Jannaschia sp. CCS1] ZP_00555006 438 1 31.5722 70 7.7721 39 92 235 288 0 0 14 28 0 54 LGSIGSDLGASIKGFKKAMSDDEPKQDKTSQDADFTAKTIADKQADTNQEQAKT VGAVDQDMDPEARDTDASAADDETISDETTYDDDAEAEAAHDETVEDDTEQTET +G++ D+ + + +DDE D+T+ D D A+ D+ + + EQ +T 211 gi|21204492|dbj|BAB95189.1| ebh [Staphylococcus aureus subsp. aureus MW2] >gi|21283053|ref|NP_646141.1| hypothetical protein MW1324 [Staphylococcus aureus subsp. aureus MW2] BAB95189 9904 1 31.5722 70 7.7721 35 95 5270 5342 0 0 19 36 12 73 GTKKLGSIGSDLGASIKGFKKAMSDD----------EPKQDKTS--QDADFTAKTIADKQADTNQEQAKTEDA GVNQVSTTASELNTAMSNLQRGINDEAATKAAQKYTDADRDKQTAYNDAVTAAKTLLDKTAGTNENKAAVEQA G ++ + S+L ++ ++ ++D+ + +DK + DA AKT+ DK A TN+ +A E A 212 gi|39593039|emb|CAE64508.1| Hypothetical protein CBG09238 [Caenorhabditis briggsae] CAE64508 960 1 31.5722 70 7.7721 55 102 410 459 0 0 19 33 4 51 KAMSDDEPKQD---KTSQDADFTAKTIADKQADTNQEQAKTEDAKRHDKEQ KKEADDKAKKDLEAKTKKEADEKAKKEADEKA-KKEAEAKTKEAEAKTKKE K +DD+ K+D KT ++AD AK AD++A + +AKT++A+ K++ 2934173 1011751523 0 0 0.041 0.267 0.14 weblogo-3.8.0/tests/data/ssearch/xbt002.xml000066400000000000000000000105471467613320200204370ustar00rootroot00000000000000 blastn BLASTN 2.2.12 [Aug-07-2005] Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. nr gi|1348916|gb|G26684.1|G26684 human STS STS_D11570, sequence tagged site 285 10 1 -3 5 2 1 gi|1348916|gb|G26684.1|G26684 human STS STS_D11570, sequence tagged site 285 1 gi|9950606|gb|AE004854.1| Pseudomonas aeruginosa PAO1, section 415 of 529 of the complete genome AE004854 11884 1 38.1576 19 1.0598 68 86 6012 6030 1 1 19 19 0 19 CAGGCCAGCGACTTCTGGG CAGGCCAGCGACTTCTGGG ||||||||||||||||||| 2 gi|15073988|emb|AL591786.1|SME591786 Sinorhizobium meliloti 1021 complete chromosome; segment 5/12 AL591786 299350 1 36.1753 18 4.18768 204 224 83648 83628 1 -1 20 20 0 21 TGAAAGGAAATNAAAATGGAA TGAAAGGAAATCAAAATGGAA ||||||||||| ||||||||| 371021 1233631384 0 0 0.710603 1.37406 1.30725 weblogo-3.8.0/tests/data/ssearch/xbt003.xml000066400000000000000000003671641467613320200204520ustar00rootroot00000000000000 blastx BLASTX 2.2.12 [Aug-07-2005] Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. nr gi|1347369|gb|G25137.1|G25137 human STS EST48004, sequence tagged site 556 BLOSUM62 10 11 1 L; 1 gi|1347369|gb|G25137.1|G25137 human STS EST48004, sequence tagged site 556 1 gi|12654095|gb|AAH00859.1| Unknown (protein for IMAGE:3459481) [Homo sapiens] AAH00859 319 1 247.284 630 1.69599e-64 1 399 156 288 1 0 122 123 0 133 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFEGPYTDFTPWTTEEQKLLEQALKTYPVNTPERWEKIAEAVPGRTKK DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERF GPYTDFTP TTE QKL EQAL TYPVNT ERW IA AVPGR K+ 2 gi|51493021|ref|XP_168590.4| PREDICTED: zuotin related factor 1 [Homo sapiens] XP_168590 520 1 247.284 630 1.69599e-64 1 399 357 489 1 0 122 123 0 133 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFEGPYTDFTPWTTEEQKLLEQALKTYPVNTPERWEKIAEAVPGRTKK DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERF GPYTDFTP TTE QKL EQAL TYPVNT ERW IA AVPGR K+ 3 gi|51492817|ref|XP_379909.2| PREDICTED: similar to Zuotin related factor-1 (M-phase phosphoprotein 11) [Homo sapiens] XP_379909 584 1 247.284 630 1.69599e-64 1 399 416 548 1 0 122 123 0 133 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFEGPYTDFTPWTTEEQKLLEQALKTYPVNTPERWEKIAEAVPGRTKK DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERF GPYTDFTP TTE QKL EQAL TYPVNT ERW IA AVPGR K+ 4 gi|67968477|dbj|BAE00600.1| unnamed protein product [Macaca fascicularis] BAE00600 621 1 245.358 625 6.44477e-64 1 399 458 590 1 0 121 122 0 133 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNAAPSERFEGPYTDFTPWTTEEQKLLEQALKTYPVNTPERWEKIAEAVPGRTKK DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNA PSERF GPYTDFTP TTE QKL EQAL TYPVNT ERW IA AVPGR K+ 5 gi|1770454|emb|CAA66913.1| M-phase phosphoprotein 11 [Homo sapiens] CAA66913 582 1 244.202 622 1.43575e-63 1 399 419 551 1 0 121 122 0 133 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE DLQLLIKAVNLFPARTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFEGPYTDFTPWTTEEQKLLEQALKTYPVNTPERWEKIAEAVPGRTKK DLQLLIKAVNLFPA TNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERF GPYTDFTP TTE QKL EQAL TYPVNT ERW IA AVPGR K+ 6 gi|12230855|sp|Q99543|ZRF1_HUMAN Zuotin-related factor 1 (M-phase phosphoprotein 11) Q99543 568 1 244.202 622 1.43575e-63 1 399 405 537 1 0 121 122 0 133 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE DLQLLIKAVNLFPARTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFEGPYTDFTPWTTEEQKLLEQALKTYPVNTPERWEKIAEAVPGRTKK DLQLLIKAVNLFPA TNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERF GPYTDFTP TTE QKL EQAL TYPVNT ERW IA AVPGR K+ 7 gi|76615186|ref|XP_584591.2| PREDICTED: similar to DnaJ (Hsp40) homolog, subfamily C, member 2 isoform 2 isoform 1 [Bos taurus] >gi|76615184|ref|XP_871283.1| PREDICTED: similar to DnaJ (Hsp40) homolog, subfamily C, member 2 isoform 2 isoform 2 [Bos taurus] XP_584591 475 1 243.817 621 1.87514e-63 1 399 312 444 1 0 121 122 0 133 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFEGPCTDFTPWTTEEQKLLEQALKTYPVNTPERWEKIAEAVPGRTKK DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERF GP TDFTP TTE QKL EQAL TYPVNT ERW IA AVPGR K+ 8 gi|73981816|ref|XP_540394.2| PREDICTED: similar to DnaJ (Hsp40) homolog, subfamily C, member 2 isoform 2 isoform 2 [Canis familiaris] XP_540394 508 1 243.817 621 1.87514e-63 1 399 345 477 1 0 121 122 0 133 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFEGPCTDFTPWTTEEQKLLEQALKTYPVNTPERWEKIAEAVPGRTKK DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERF GP TDFTP TTE QKL EQAL TYPVNT ERW IA AVPGR K+ 9 gi|73981814|ref|XP_849517.1| PREDICTED: similar to DnaJ (Hsp40) homolog, subfamily C, member 2 isoform 2 isoform 3 [Canis familiaris] XP_849517 521 1 243.817 621 1.87514e-63 1 399 358 490 1 0 121 122 0 133 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFEGPCTDFTPWTTEEQKLLEQALKTYPVNTPERWEKIAEAVPGRTKK DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERF GP TDFTP TTE QKL EQAL TYPVNT ERW IA AVPGR K+ 10 gi|57032822|gb|AAH88838.1| Dnajc2 protein [Rattus norvegicus] AAH88838 621 1 230.72 587 1.6427e-59 1 399 458 590 1 0 115 117 0 133 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVAPQADSAAPSERFEGPCIDSIPWTTEEQKLLEQALKTYPVNTPERWEKIAEAVPGRTKK DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGV PQAD+A PSERF GP D P TTE QKL EQAL TYPVNT ERW IA AVPGR K+ 11 gi|32481976|gb|AAP84341.1| zuotin related factor 2 [Rattus norvegicus] AAP84341 200 1 230.72 587 1.6427e-59 1 399 37 169 1 0 115 117 0 133 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVAPQADSAAPSERFEGPCIDSIPWTTEEQKLLEQALKTYPVNTPERWEKIAEAVPGRTKK DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGV PQAD+A PSERF GP D P TTE QKL EQAL TYPVNT ERW IA AVPGR K+ 12 gi|32481974|gb|AAP84340.1| zuotin related factor 3 [Rattus norvegicus] AAP84340 547 1 230.72 587 1.6427e-59 1 399 384 516 1 0 115 117 0 133 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVAPQADSAAPSERFEGPCIDSIPWTTEEQKLLEQALKTYPVNTPERWEKIAEAVPGRTKK DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGV PQAD+A PSERF GP D P TTE QKL EQAL TYPVNT ERW IA AVPGR K+ 13 gi|32481970|gb|AAP84338.1| zuotin related factor 1 [Rattus norvegicus] AAP84338 621 1 230.72 587 1.6427e-59 1 399 458 590 1 0 115 117 0 133 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVAPQADSAAPSERFEGPCIDSIPWTTEEQKLLEQALKTYPVNTPERWEKIAEAVPGRTKK DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGV PQAD+A PSERF GP D P TTE QKL EQAL TYPVNT ERW IA AVPGR K+ 14 gi|6677659|ref|NP_033610.1| DnaJ (Hsp40) homolog, subfamily C, member 2 isoform 2 [Mus musculus] >gi|74203507|dbj|BAE20907.1| unnamed protein product [Mus musculus] >gi|30354366|gb|AAH52027.1| DnaJ (Hsp40) homolog, subfamily C, member 2, isoform 2 [Mus musculus] >gi|1060925|dbj|BAA09854.1| MIDA1 [Mus musculus] >gi|2137417|pir||A57591 Id-associated protein 1 - mouse NP_033610 621 1 227.639 579 1.39063e-58 1 399 458 590 1 0 114 116 0 133 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVISKAKSLQKLDPHQKDDINKKAFDKFKKEHGVASQADSAAPSERFEGPCIDSTPWTTEEQKLLEQALKTYPVNTPERWEKIAEAVPGRTKK DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVI KAKSLQKLDPHQKDDINKKAFDKFKKEHGV QAD+A PSERF GP D TP TTE QKL EQAL TYPVNT ERW IA AVPGR K+ 15 gi|39794437|gb|AAH64251.1| Dnajc2-prov protein [Xenopus tropicalis] AAH64251 635 1 216.083 549 4.18708e-55 1 399 471 604 1 0 108 115 1 134 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQA-DNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE DLQLLIKAVNLFPAGTNARWEVIANYMNLHSISGIKRTSKDVINKAKSLQKLDPQQKDDINKKAFDKFKKEHRVVPQSVDNAVPSERFEGPAADMSPWTTEEQKLLEQALKTYPVNTPERWEKIAEAVPGRSKK DLQLLIKAVNLFPAGTN+RWEVIANYMN+HS SG+KRT+KDVI KAKSLQKLDP QKDDINKKAFDKFKKEH VVPQ+ DNA PSERF GP D +P TTE QKL EQAL TYPVNT ERW IA AVPGR K+ 16 gi|47086411|ref|NP_997976.1| zuotin related factor 1 [Danio rerio] >gi|45709493|gb|AAH67568.1| Zgc:85671 [Danio rerio] NP_997976 618 1 194.126 492 1.70388e-48 1 399 454 589 1 0 100 111 3 136 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVV-PQADNATPSERF--XGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE DLQLLIKAVNLFPAGTNARWEVIANYMNQHSSSGVRRTAKDVINKAKTLQKLDPHQKDEINRKAFEKFKKEHSAVPPTVDNAMPSERFDAVGADSNAAAWTTEEQKLLEQALKTYPVSTAERWERISEAVPGRSKK DLQLLIKAVNLFPAGTN+RWEVIANYMN HSSSGV+RTAKDVI KAK+LQKLDPHQKD+IN+KAF+KFKKEH V P DNA PSERF G ++ TTE QKL EQAL TYPV+T ERW I+ AVPGR K+ 17 gi|32766539|gb|AAH55125.1| Zgc:85671 protein [Danio rerio] AAH55125 620 1 194.126 492 1.70388e-48 1 399 454 589 1 0 100 111 3 136 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVV-PQADNATPSERF--XGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE DLQLLIKAVNLFPAGTNARWEVIANYMNQHSSSGVRRTAKDVINKAKTLQKLDPHQKDEINRKAFEKFKKEHSAVPPTVDNAMPSERFDAVGADSNAAAWTTEEQKLLEQALKTYPVSTAERWERISEAVPGRSKK DLQLLIKAVNLFPAGTN+RWEVIANYMN HSSSGV+RTAKDVI KAK+LQKLDPHQKD+IN+KAF+KFKKEH V P DNA PSERF G ++ TTE QKL EQAL TYPV+T ERW I+ AVPGR K+ 18 gi|5577977|gb|AAD45407.1| gliosarcoma-related antigen MIDA1 [Rattus norvegicus] AAD45407 562 1 189.889 481 3.21338e-47 1 312 458 561 1 0 94 95 0 104 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKL DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVAPQADSAAPSERFEGPCIDSIPWTTEEQKL DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGV PQAD+A PSERF GP D P TTE QKL 19 gi|50728035|ref|XP_415961.1| PREDICTED: similar to zuotin related factor 1 [Gallus gallus] XP_415961 420 1 188.348 477 9.3495e-47 55 399 291 405 1 0 91 97 0 115 RWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE RWEVIANYMNLHSTTGIKRTAKDVINKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQMDTAAPSERFEGSPLDSSPWTTEEQKLLEQALKTYPVNTPERWEKIAAAVPGRSKK RWEVIANYMN+HS++G+KRTAKDVI KAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQ D A PSERF G D +P TTE QKL EQAL TYPVNT ERW IA AVPGR K+ 20 gi|47208143|emb|CAF93399.1| unnamed protein product [Tetraodon nigroviridis] CAF93399 549 1 145.206 365 9.07675e-34 1 267 455 544 1 0 72 80 1 90 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVP-QADNATPSERFXG DLQLLIKAVNLFPAGTNARWEVIANYMNQHSTSGMKRTAKDVINKAKNLQRLDPVQKDEINKKAFEKFRKEHTSVPLSVDNAVPSERFDG DLQLLIKAVNLFPAGTN+RWEVIANYMN HS+SG+KRTAKDVI KAK+LQ+LDP QKD+INKKAF+KF+KEH VP DNA PSERF G 21 gi|76615182|ref|XP_882962.1| PREDICTED: similar to Zuotin-related factor 1 (M-phase phosphoprotein 11) isoform 3 [Bos taurus] XP_882962 124 1 144.05 362 2.02209e-33 157 399 13 93 1 0 69 70 0 81 DPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE DPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFEGPCTDFTPWTTEEQKLLEQALKTYPVNTPERWEKIAEAVPGRTKK DPHQKDDINKKAFDKFKKEHGVVPQADNATPSERF GP TDFTP TTE QKL EQAL TYPVNT ERW IA AVPGR K+ 22 gi|72061332|ref|XP_788523.1| PREDICTED: similar to zuotin related factor 1 [Strongylocentrotus purpuratus] XP_788523 623 1 124.405 311 1.65801e-27 1 399 453 595 1 0 68 89 10 143 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGV-VPQADNATPSERFXGPYTDFTPXT---------TEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE DTQLLIKAANIFPPGTSSRYEVIANYINNHSTSGSNRNAKDIINKTKNLPRLDGGMKAAANEKAFEKFQQATGAKLKKSDEAPPSENFEGGEGAAAPAAAVEGPKAWQTDEQKRLEQALKTFPASATDRWDKISEAVPTRTKK D QLLIKA N+FP GT+SR+EVIANY+N HS+SG R AKD+I K K+L +LD K N+KAF+KF++ G + ++D A PSE F G P T+ QK EQAL T+P + +RW I+ AVP R K+ 23 gi|66503903|ref|XP_396658.2| PREDICTED: similar to CG10565-PA [Apis mellifera] XP_396658 617 1 115.546 288 7.70178e-25 1 399 446 594 1 0 68 85 16 149 DLQLLIKAVNLFPAGTNSRWEVIANYMNIH--SSSGVKRTAKDVIGKAKSLQKLD---PHQKDDINKKAFDKFKKEHGVVPQADNATP--SERFXGPY---------TDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE DLQLLIKAVNLFPAGTNQRWEVVANFINQHSTSSTGITRDAKEVLAKAKDLQSTDFSRSSLKEQANKKAYDNFIAEKKTKESIEDRMPAVTERLDHPILNGINSEQKKESQPWTPAEQKLLEQALKTYPTSVPDRWDQIAACIPTRTNK DLQLLIKAVNLFPAGTN RWEV+AN++N H SS+G+ R AK+V+ KAK LQ D K+ NKKA+D F E ++ P +ER P + P T QKL EQAL TYP + +RW IA +P R + 24 gi|72008661|ref|XP_786271.1| PREDICTED: similar to zuotin related factor 1 [Strongylocentrotus purpuratus] XP_786271 193 1 98.9821 245 7.45978e-20 58 399 42 165 1 0 55 74 10 124 WEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGV-VPQADNATPSERFXGPYTDFTPXT---------TEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE YEVIANYINNHSTSGSNRAAKDIINKTKNLQRLDGGMKAAANEKAFEKFQQATGAKLKKSDEAPPSENFEGGEGAAAPAAAAEGPKAWQTDEQKRLEQALKTFPASATDRWDKISEAVPTRTKK +EVIANY+N HS+SG R AKD+I K K+LQ+LD K N+KAF+KF++ G + ++D A PSE F G P T+ QK EQAL T+P + +RW I+ AVP R K+ 25 gi|54641476|gb|EAL30226.1| GA10399-PA [Drosophila pseudoobscura] EAL30226 637 1 88.9669 219 7.71966e-17 1 399 436 613 1 0 66 86 47 179 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHS-SSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKA-------FDKFKKE-------------------------HGVVP-QADNATPSER---FXGPYTDFT---------PXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE NVQLLIKAVNLFPAGTAQRWDVIATFINQHSGSGGAQVLARDVLNKAKALQNSD-HSKSSLKTQANDAAFASFEKSKKEVQVSNDITIGEEAPSQESKENVKQNGGAHPNQVNNQKPKQNGISTPSPMTNGTGGAGAGASKTWTKEEQALLEQAIKSYPTTTPDRWDRIAACIPNRSKK ++QLLIKAVNLFPAGT RW+VIA ++N HS S G + A+DV+ KAK+LQ D H K + +A F+K KKE G P Q +N P + P T+ T T E Q L EQA+ +YP T +RW IA +P R K+ 26 gi|55245384|gb|EAL41766.1| ENSANGP00000029085 [Anopheles gambiae str. PEST] >gi|57971654|ref|XP_564715.1| ENSANGP00000029085 [Anopheles gambiae str. PEST] EAL41766 300 1 88.5817 218 1.00822e-16 1 399 144 277 1 0 59 76 5 136 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSS--SGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTX-ERWXXIAVAVPGRXKE NVQLLIKAVNLFPAGTISRWEVIANYLNQHGTELGDMKFYAKDALNKAKELQAGD-FSKSDL-KTVVNQQAYESPMARQRNRPAVPERRQPRRRRKRTWSKEEQALLEQAIKTYPVSCGPDRWDRIAECIPNRTKK ++QLLIKAVNLFPAGT SRWEVIANY+N H + +K AKD + KAK LQ D K D+ K ++ E + Q + ER + E Q L EQA+ TYPV+ +RW IA +P R K+ 27 gi|6677657|ref|NP_033609.1| DnaJ (Hsp40) homolog, subfamily C, member 2 isoform 1 [Mus musculus] >gi|1731448|sp|P54103|ZRF1_MOUSE Zuotin-related factor 1 >gi|1256832|gb|AAC52486.1| zuotin related factor NP_033609 514 1 85.8853 211 6.53508e-16 1 141 458 504 1 0 41 44 0 47 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAK DLQLLIKAVNLFPAGRNSRWDVIANYMNIHSSSGVKRTAKDVISEVR DLQLLIKAVNLFPAG NSRW+VIANYMNIHSSSGVKRTAKDVI + + 28 gi|7296390|gb|AAF51678.1| CG10565-PA [Drosophila melanogaster] >gi|17862382|gb|AAL39668.1| LD23875p [Drosophila melanogaster] >gi|21356311|ref|NP_649284.1| CG10565-PA [Drosophila melanogaster] AAF51678 646 1 84.3445 207 1.90142e-15 1 399 439 622 1 0 63 85 55 186 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHS-SSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKA-------FDKFK-----------------------KEHGVVPQADNATPSERFXGPYTDFTPX----------------------TTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE NVQLLIKAVNLFPAGTAQRWDVIATFINQHSPDNTVLVNARDVLNKAKALQNTD-HSKSSLKTQANDAAFASFEKSKKDVQTCKDITLGEETAQASKENLKQNGVDHKANNQSTKQNGTAP-APANPTAAPAPVPATNGSTGGGAASKTWTKEEQALLEQAIKTYPTTTPDRWDCIAACIPNRSKK ++QLLIKAVNLFPAGT RW+VIA ++N HS + V A+DV+ KAK+LQ D H K + +A F+K K K++GV +A+N + + P P T E Q L EQA+ TYP T +RW IA +P R K+ 29 gi|55245385|gb|EAA03986.2| ENSANGP00000009397 [Anopheles gambiae str. PEST] >gi|58378250|ref|XP_308338.2| ENSANGP00000009397 [Anopheles gambiae str. PEST] EAA03986 589 1 80.4925 197 2.74564e-14 1 399 376 565 1 0 62 84 57 190 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSS--SGVKRTAKDVIGKAKSLQKLDPHQKD---DINKKAFDKFK------------------------KEHGVVPQADNATPSERFXGPYTDFTPXT---------------------------TEXQKLXEQALNTYPVNTX-ERWXXIAVAVPGRXKE NVQLLIKAVNLFPAGTISRWEVIANYLNQHGTELGDMKFYAKDALNKAKELQAGDFSKSDLKTVVNQQAYESFERSKKDLKIIDNSEISTKEAAELASKEKGQSDSKPKSAAAEKKASPMVNGVQQTDGKAAKPASSAGTAPAKKEKEANKVWSKEEQALLEQAIKTYPVSCGPDRWDRIAECIPNRTKK ++QLLIKAVNLFPAGT SRWEVIANY+N H + +K AKD + KAK LQ D + D +N++A++ F+ KE G + +E+ P + T E Q L EQA+ TYPV+ +RW IA +P R K+ 30 gi|56755797|gb|AAW26077.1| SJCHGC05986 protein [Schistosoma japonicum] AAW26077 161 1 68.9366 167 8.2669e-11 4 396 2 134 1 0 49 67 14 139 LQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFK---KEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYP-----VNTXERWXXIAVAVPGRXK IHVLVKAVNILPAGTPKRWEAIAAYVNQHVNS-ASVSGKDALKQAKLLKQEDSNLRKTANTNAFDSFTNSVKETDAVKNVAITTHLEA-----EGSRPWTVVEQRALEQALKSYPSTAGYSGSDDRWQLIANVVGTRTR + +L+KAVN+ PAGT RWE IA Y+N H +S + KD + +AK L++ D + + N AFD F KE V T E P T Q+ EQAL +YP + +RW IA V R + 31 gi|39584134|emb|CAE61509.1| Hypothetical protein CBG05408 [Caenorhabditis briggsae] CAE61509 589 1 55.0694 131 1.23532e-06 1 399 460 572 1 0 44 62 26 136 DLQLLIKAVNLFPAGTNSRWEVIANYMNIH--SSSGV-KRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE EIQLLVKASNTFPPGTVERWVQIADYINEHRKDSQGLPPKTEKQVIKQCKAVQTMN--------------VKLPSTTQNQLGTALPDE-------DVWSAT--EQKTLEEALKKHPASDPERWEKISTEVGTKTKK ++QLL+KA N FP GT RW IA+Y+N H S G+ +T K VI + K++Q ++ K Q A P E D T QK E+AL +P + ERW I+ V + K+ 32 gi|23508859|ref|NP_701527.1| DNA-binding chaperone, putative [Plasmodium falciparum 3D7] >gi|23496695|gb|AAN36251.1| DNA-binding chaperone, putative [Plasmodium falciparum 3D7] NP_701527 939 1 53.1434 126 4.69423e-06 1 345 774 899 1 0 38 60 25 133 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLD-----------------PHQKDDINKKAFDKF-KKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVN EVSLLAKALKLYPGGTRNRWVLISNSIK-------TKTVKEVIKKTKEMFENDTLKNLGRNFDETPFDHFKNQNKGVMKKIDDNLDKREYKLTKENNNQVETDNLNGDVEKKKPWTHEEQHLLEQALIKYPTS ++ LL KA+ L+P GT +RW +I+N + +T K+VI K K + + D +Q + KK D K+E+ + + +N ++ G P T E Q L EQAL YP + 33 gi|12322899|gb|AAG51437.1| putative cell division related protein; 50012-47994 [Arabidopsis thaliana] >gi|15229761|ref|NP_187752.1| DNAJ heat shock N-terminal domain-containing protein / cell division protein-related [Arabidopsis thaliana] AAG51437 663 1 52.373 124 8.00714e-06 1 390 486 640 1 0 45 72 51 168 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKS--LQKLDPHQKDDINKKAFDKF----------------KKEHG----VVPQADNATPSERFX----------------GPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGR EIDMLRKGMIKYPKGTSRRWEVISEYI------GTGRSVEEILKATKTVLLQKPD-------SAKAFDSFLEKRKPSASITSPLSTREELGESLPTMTTTTNAKPSKETVVGKSSSSQSSDNNGEVGGSSDADSWSTVQERALVQALKTFPKETSQRWERVAAAVPGK ++ +L K + +P GT+ RWEVI+ Y+ G R+ ++++ K+ LQK D + KAFD F ++E G + NA PS+ G +D +T ++ QAL T+P T +RW +A AVPG+ 34 gi|68075771|ref|XP_679805.1| DNA-binding chaperone, putative [Plasmodium berghei] >gi|56500634|emb|CAH98046.1| DNA-binding chaperone, putative [Plasmodium berghei] XP_679805 859 1 51.9878 123 1.04577e-05 1 399 694 839 1 0 44 68 27 153 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLD--PHQKDDINKKAFDKFKKEH-GVVPQADNATPSERF---------------XGPYTDFTPXTTEXQKLXEQALNTYP--VNTXERWXXIAVAVPGRXKE EVSLLSKALKLYPGGTKNRWNVIANSIK-------TKNVKEVIKKAKEMFENETLKNLSKNFEESAFDNFKNQNKGVMKKIDNKLDKREYKHINDQNNISSAHSSDNNSEQKKPWTHEEQMLLEKALMKHPATIPTKERLKLVANELKTRSVE ++ LL KA+ L+P GT +RW VIAN + + K+VI KAK + + + + + + AFD FK ++ GV+ + DN + P T E Q L E+AL +P + T ER +A + R E 35 gi|66358504|ref|XP_626430.1| zuotin related factor-1 like protein with a DNAJ domain at the N-terminus and 2 SANT domains, orthologs in plasmodium [Cryptosporidium parvum] >gi|46227848|gb|EAK88768.1| zuotin related factor-1 like protein with a DNAJ domain at the N-terminus and 2 SANT domains, orthologs in plasmodium [Cryptosporidium parvum] XP_626430 677 1 51.6026 122 1.36581e-05 1 390 513 656 1 0 40 66 20 147 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKF-KKEHGVVPQADNATPSERFXG-------PYTDFTPX-------TTEXQKLXEQALNTYP--VNTXERWXXIAVAVPGR EMSLLAKALQKYPGGYKNRWDMISEYLKNTKTKEQILTKVKELSESEKLAKLSNEVKED---SAFDTFIQSNKGVLKKFDNIPDVRDYSGTSIINNSAKNDATQQKKEIDLWTRDQQCSLERALKQYPSSLPSNERWELISSCIPGK ++ LL KA+ +P G +RW++I+ Y+ + T + +++ L KL K+D AFD F + GV+ + DN + G D T T + Q E+AL YP + + ERW I+ +PG+ 36 gi|50923697|ref|XP_472209.1| OSJNBa0083D01.10 [Oryza sativa (japonica cultivar-group)] >gi|39546277|emb|CAE05696.3| OSJNBa0083D01.10 [Oryza sativa (japonica cultivar-group)] XP_472209 256 1 51.2174 121 1.78381e-05 1 390 72 233 1 0 45 74 58 175 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKS--LQKLDPHQKDDINKKAFDKFKKEHGVVPQADN---------ATPSERFXG--------------------------PYTDFTPXTT-------EXQKLX-EQALNTYPVNTXERWXXIAVAVPGR EIELLRKAIQKYPKGTSRRWEVVSEFI------GTGRSVEEILKATKTVLLQKPD-------STKAFDSFLEKRKPAPSIASPLSVRTETVGLPTEKAAGNASSKAPAQHASSKTSDEKAAAPAPAPVSNGTPSGTADPEAWSEAQVLALVQALKAFPKDASQRWERVAAAVPGK +++LL KA+ +P GT+ RWEV++ ++ G R+ ++++ K+ LQK D + KAFD F ++ P + P+E+ G P ++ TP T E Q L QAL +P + +RW +A AVPG+ 37 gi|1572812|gb|AAB09157.1| Dnaj domain (prokaryotic heat shock protein) protein 11 [Caenorhabditis elegans] >gi|17540268|ref|NP_501006.1| DNaJ domain (prokaryotic heat shock protein) family member (dnj-11) [Caenorhabditis elegans] AAB09157 589 1 50.0618 118 3.9739e-05 1 399 460 572 1 0 42 61 26 136 DLQLLIKAVNLFPAGTNSRWEVIANYMNIH--SSSGV-KRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE EIQLLVKASNTFPPGTVERWVQIADYINEHRKDSTGLPPKTEKQVIKQCKAVQTMN--------------VKLPSTTQNQLGTALPDE-------DVWSAT--EQKTLEDAIKKHKSSDPERWEKISTEVGTKSKK ++QLL+KA N FP GT RW IA+Y+N H S+G+ +T K VI + K++Q ++ K Q A P E D T QK E A+ + + ERW I+ V + K+ 38 gi|23486826|gb|EAA20902.1| zuotin related factor-1 [Plasmodium yoelii yoelii] EAA20902 848 1 49.6766 117 5.19008e-05 1 399 683 828 1 0 41 68 15 147 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLD-----------PHQKDDINKKAFDKF-KKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYP--VNTXERWXXIAVAVPGRXKE EISLLSKALKLYPGGTKDRWTVIANSIKTKNVKEVIKKAKEMF-ENETLKNLSKNFEESAFDNFKNQNKGVMKKIDDKLDKREYKDINDQNNLSSAHSSDNNSEQKKPWTHEEQMLLEKALMKHPATIPTKERLKLVSNELKTRSVE ++ LL KA+ L+P GT RW VIAN + + V + AK++ + ++L+ L +Q + KK DK K+E+ + +N + + P T E Q L E+AL +P + T ER ++ + R E 39 gi|67615225|ref|XP_667421.1| zuotin related factor-1 [Cryptosporidium hominis] >gi|54658551|gb|EAL37186.1| zuotin related factor-1 [Cryptosporidium hominis] XP_667421 673 1 49.2914 116 6.77845e-05 1 390 509 652 1 0 39 65 20 147 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKF-KKEHGVVPQADNATPSERFXG-------PYTDFTPX-------TTEXQKLXEQALNTYP--VNTXERWXXIAVAVPGR EMSLLAKALQKYPGGYKNRWDMISEYLKNTKTKEQILTKVKELSESEKLAKLSNEVKEE---SAFDTFIQSNKGVLKKFDNIPDVRDYSGTSIINNSAKNDVTHQKKEIDLWTRDQQCSLERALKQYPSSLPLNERWELISSCIPGK ++ LL KA+ +P G +RW++I+ Y+ + T + +++ L KL K++ AFD F + GV+ + DN + G D T T + Q E+AL YP + ERW I+ +PG+ 40 gi|70951177|ref|XP_744850.1| DNA-binding chaperone, putative [Plasmodium chabaudi] >gi|56524970|emb|CAH80605.1| DNA-binding chaperone, putative [Plasmodium chabaudi] XP_744850 621 1 49.2914 116 6.77845e-05 1 399 456 601 1 0 43 69 27 153 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLD--PHQKDDINKKAFDKFKKEH-GVVPQADNATPSERF---------XGPYTDFT------PXTTEXQKLXEQALNTYP--VNTXERWXXIAVAVPGRXKE EISLLSKALKLYPGGTKNRWTVIANSIK-------TKNVKEVIKKTKEMFENETLKNLSKNFEESAFDNFKNQNKGVMKKIDDKLDKREYKHINDQNHVSNPNSSDNNSEQKKPWTHEEQMLLEKALMKHPATIPTKERLKLVANELKTRTVE ++ LL KA+ L+P GT +RW VIAN + + K+VI K K + + + + + + AFD FK ++ GV+ + D+ + P + P T E Q L E+AL +P + T ER +A + R E 41 gi|8978347|dbj|BAA98200.1| cell division related protein-like [Arabidopsis thaliana] >gi|15239928|ref|NP_196229.1| DNAJ heat shock N-terminal domain-containing protein / cell division protein-related [Arabidopsis thaliana] BAA98200 663 1 48.1358 113 0.000151008 1 390 481 640 1 0 45 73 56 173 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKS--LQKLDPHQKDDINKKAFDKF----------------KKEHG--VVP----QADNATP-------------------SERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGR EIDMLRKGTTKFPKGTSQRWEVISEYI------GTGRSVEEILKATKTVLLQKPD-------SAKAFDSFLENRKPAASINSPLSTREELGEPIIPTKAHEDNNSTKTETAEQNGKTKENNNSNGNSEPAAASGSDPDGWSAVQERALVQALKTFPKETNQRWERVATAVPGK ++ +L K FP GT+ RWEVI+ Y+ G R+ ++++ K+ LQK D + KAFD F ++E G ++P + +N+T SE +D + ++ QAL T+P T +RW +A AVPG+ 42 gi|31442292|dbj|BAC77346.1| gonidia forming protein GlsA [Lilium longiflorum] BAC77346 655 1 47.3654 111 0.000257581 1 390 476 633 1 0 44 72 54 171 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKS--LQKLDPHQKDDINKKAFDKFKKEH-----------------GVVPQADNA------TPSERFXGPYT-DFTPXT---------------TEXQKLXEQALNTYPVNTXERWXXIAVAVPGR EIELLRKGIQKYQKGTSRRWEVISEYI------GTGRSVEEILKATKTVLLQKPD-------SSKAFDSFLEKRKPAKAIVSPLTTRLESEGSTVEAGDASSKSIPTPSLSSSSPEKPDGTPVSLPNGVPSVPEQDTWSATQERALIQALKTFPKDVNQRWERVAAAIPGK +++LL K + + GT+ RWEVI+ Y+ G R+ ++++ K+ LQK D + KAFD F ++ G +A +A TPS P D TP + ++ QAL T+P + +RW +A A+PG+ 43 gi|55243553|gb|EAA06445.2| ENSANGP00000012466 [Anopheles gambiae str. PEST] >gi|58380898|ref|XP_310857.2| ENSANGP00000012466 [Anopheles gambiae str. PEST] EAA06445 480 1 46.2098 108 0.000573831 1 399 311 439 1 0 38 63 18 140 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLD---PHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGP---YTDFTPXTTEXQKLXEQALNTYPVN-TXERWXXIAVAVPGRXKE DLVELVRLVKKYPGGTSNRWELIAELM--------QRSVEEITYMAAKMKECGYRLPHQSEGARG---DESGGSSGAPVAAKVKTKTRDTAGGGELAASGSTWTQQQQQALEVAIQKYPKSANYDRWQKIANSVPGKSKE DL L++ V +P GT++RWE+IA M +R+ +++ A +++ PHQ + D+ G A T + G + T + Q+ E A+ YP + +RW IA +VPG+ KE 44 gi|66816347|ref|XP_642183.1| DNAJ heat shock N-terminal domain-containing protein [Dictyostelium discoideum] >gi|60470282|gb|EAL68262.1| myb domain-containing protein [Dictyostelium discoideum] XP_642183 634 1 45.8246 107 0.000749446 1 399 451 614 1 0 46 65 51 174 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINK-------KAFDKFKKEHG---------------------------------VVPQADNATP-SERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE ELHLLAKAIQKFPPGVTKRWESVASCI-------PTRSLKDVIAKAKTSQ---PTQQQSFSKPEAAPSGSDYDKLKAKVGHMEIKSELSSKVDLGQYPVGTTSNGTESTTTATAPSTVDTAKPAAKKETTTTTASVEWTPEEQKLLEEALQKVDKNAEDRWDQIAARLGTKSKK +L LL KA+ FP G RWE +A+ + R+ KDVI KAK+ Q P Q+ +K +DK K + G D A P +++ T T E QKL E+AL N +RW IA + + K+ 45 gi|56789643|gb|AAH88511.1| DnaJ (Hsp40) homolog, subfamily C, member 1 [Xenopus tropicalis] >gi|58332554|ref|NP_001011351.1| DnaJ (Hsp40) homolog, subfamily C, member 1 [Xenopus tropicalis] AAH88511 535 1 44.669 104 0.00166959 88 399 411 514 1 0 30 44 0 104 HSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE HSTAARVRKRKSTKGATDAVPPLRGEAEEKVRSRRQRDFDVEQEAEELADSDSDTRKKEQGRSLEELWTQNQQKLLELALQQYPKGTGERWDKIAKCVPGKSKE HS++ R K G ++ L ++ + + F E AD+ + + + + T QKL E AL YP T ERW IA VPG+ KE 46 gi|72108961|ref|XP_794997.1| PREDICTED: similar to DnaJ homolog subfamily C member 1 (DnaJ protein homolog MTJ1) [Strongylocentrotus purpuratus] XP_794997 327 1 44.2838 103 0.00218055 1 399 202 302 1 0 35 53 32 133 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE EVSSLVKIMSKYPGGTTDRWTRIAEE--------IKKPVDVVTKKAKQLKS--------------QKFATNVDAAAQDDLVNESCAW----------SQRQQKVLEKAMQVYPRSVDDRWDKIADSVPGKTKE ++ L+K ++ +P GT RW IA +K+ V KAK L+ KF Q D S + + QK+ E+A+ YP + +RW IA +VPG+ KE 47 gi|73948752|ref|XP_858895.1| PREDICTED: similar to DnaJ (Hsp40) homolog, subfamily C, member 1 isoform 2 [Canis familiaris] XP_858895 412 1 43.8986 102 0.00284789 1 399 188 391 1 0 48 76 75 206 DLQLLIKAVNLFPAGTNSRWEVIANYM----------------NIHSSSGVKRTAK-------------------DVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQ--------------ADNATPSERFXGP-YTDFT-----------------------PXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE DLSQLTRSMVKFPGGTPGRWEKIAHELGRSVTDVTTKAKQLKDSVTCSSGMVRLSELKSTAQNSRPTKAPTALPDDIITQREDAKQAREEEEED--EQEDDEEGEQEAVVPESRPRRRRPTRPPEAAAKVEPEEKFRGKRQKDFDISEQKESSDEESQKKDRTRAAEEPWTQSQQKLLELALQQYPKGSSDRWDKIAKCVPSKSKE DL L +++ FP GT RWE IA+ + ++ SSG+ R ++ D+I + + ++ +++D ++ D+ ++ VVP+ A P E+F G DF P T QKL E AL YP + +RW IA VP + KE 48 gi|73948750|ref|XP_849482.1| PREDICTED: similar to DnaJ (Hsp40) homolog, subfamily C, member 1 isoform 1 [Canis familiaris] XP_849482 561 1 43.8986 102 0.00284789 1 399 337 540 1 0 48 76 75 206 DLQLLIKAVNLFPAGTNSRWEVIANYM----------------NIHSSSGVKRTAK-------------------DVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQ--------------ADNATPSERFXGP-YTDFT-----------------------PXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE DLSQLTRSMVKFPGGTPGRWEKIAHELGRSVTDVTTKAKQLKDSVTCSSGMVRLSELKSTAQNSRPTKAPTALPDDIITQREDAKQAREEEEED--EQEDDEEGEQEAVVPESRPRRRRPTRPPEAAAKVEPEEKFRGKRQKDFDISEQKESSDEESQKKDRTRAAEEPWTQSQQKLLELALQQYPKGSSDRWDKIAKCVPSKSKE DL L +++ FP GT RWE IA+ + ++ SSG+ R ++ D+I + + ++ +++D ++ D+ ++ VVP+ A P E+F G DF P T QKL E AL YP + +RW IA VP + KE 49 gi|66514203|ref|XP_624533.1| PREDICTED: similar to ENSANGP00000012466 [Apis mellifera] XP_624533 431 1 43.5134 101 0.00371946 1 399 298 411 1 0 40 59 21 134 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNT-XERWXXIAVAVPGRXKE DILELIKLVKKYPSGTSERWDKIADAMN--------RTVFEVTHMAKKI-------KDEGLKPG---TSVEETVVEERSKKTKTR--AEIVDNISEWSQQQQRALEAALIKYPKGTSTDRWEKIANCVEGKSKD D+ LIK V +P+GT+ RW+ IA+ MN RT +V AK + KD+ K E VV + T + + + + + Q+ E AL YP T +RW IA V G+ K+ 50 gi|9758732|dbj|BAB09170.1| unnamed protein product [Arabidopsis thaliana] BAB09170 352 1 42.3578 98 0.00828609 1 396 207 330 1 0 37 60 18 137 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQ-----ALNTYPVNTXERWXXIAVAVPGRXK EIEILKKQLIKHPAGKPGRWETVA------SAFGGRYKTENVIKKAKEIGEKKIYESDDYAQFLKNRKASDPRLVDE------NEENSGAGGD-AEGTKEIWSNGEDIALLNALKAFPKEAAMRWEKIAAAVPGKSK ++++L K + PAG RWE +A S+ G + ++VI KAK + + ++ DD + ++ + +V + +E G D T E E AL +P RW IA AVPG+ K 51 gi|13605893|gb|AAK32932.1| AT5g45420/MFC19_9 [Arabidopsis thaliana] >gi|18491137|gb|AAL69537.1| AT5g45420/MFC19_9 [Arabidopsis thaliana] >gi|26450023|dbj|BAC42132.1| unknown protein [Arabidopsis thaliana] >gi|18422552|ref|NP_568645.1| myb family transcription factor [Arabidopsis thaliana] AAK32932 309 1 42.3578 98 0.00828609 1 396 164 287 1 0 37 60 18 137 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQ-----ALNTYPVNTXERWXXIAVAVPGRXK EIEILKKQLIKHPAGKPGRWETVA------SAFGGRYKTENVIKKAKEIGEKKIYESDDYAQFLKNRKASDPRLVDE------NEENSGAGGD-AEGTKEIWSNGEDIALLNALKAFPKEAAMRWEKIAAAVPGKSK ++++L K + PAG RWE +A S+ G + ++VI KAK + + ++ DD + ++ + +V + +E G D T E E AL +P RW IA AVPG+ K 52 gi|76683316|gb|AAK26135.2| Hypothetical protein F54F2.9 [Caenorhabditis elegans] AAK26135 300 1 41.5874 96 0.0141339 34 399 184 279 1 0 30 54 26 122 FPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE YPAGTPNRWEQMGRVLN--------RSAEDVIAMAGKMKQM---KQEDYTKLLMTTIQQSVPVEEKSED---------------DWSQAEQKAFETALQKYPKGTDERWERISEEIGSKTKK +PAGT +RWE + +N R+A+DVI A ++++ +++D K ++ V ++++ + QK E AL YP T ERW I+ + + K+ 53 gi|17553612|ref|NP_498949.1| F54F2.9 [Caenorhabditis elegans] >gi|465911|sp|P34454|YMA9_CAEEL Hypothetical protein F54F2.9 in chromosome III NP_498949 275 1 41.5874 96 0.0141339 34 399 159 254 1 0 30 54 26 122 FPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE YPAGTPNRWEQMGRVLN--------RSAEDVIAMAGKMKQM---KQEDYTKLLMTTIQQSVPVEEKSED---------------DWSQAEQKAFETALQKYPKGTDERWERISEEIGSKTKK +PAGT +RWE + +N R+A+DVI A ++++ +++D K ++ V ++++ + QK E AL YP T ERW I+ + + K+ 54 gi|7293551|gb|AAF48924.1| CG7556-PA [Drosophila melanogaster] >gi|21428836|gb|AAM50137.1| GH07340p [Drosophila melanogaster] >gi|24643180|ref|NP_573354.1| CG7556-PA [Drosophila melanogaster] AAF48924 522 1 41.2022 95 0.0184595 1 399 308 438 1 0 38 59 16 140 DLQLLIKAVNLFPAGTNSRWEVIANYMN------IHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNT-XERWXXIAVAVPGRXKE DLTELIRLVKKYPGGAGSRWNTIAESMNRSVQEVTFMAAKMKENGYRIPGQTDSVAEALVQESQQAQRK--EKVKK----AAANAGASAEKSMLIPETNW---TQEQQRALEAAIVKYRKTAGGDRWQKIANSVPEKTKE DL LI+ V +P G SRW IA MN ++ +K + G+ S+ + + +K +K KK A+ + P T++ T E Q+ E A+ Y +RW IA +VP + KE 55 gi|39585088|emb|CAE62739.1| Hypothetical protein CBG06902 [Caenorhabditis briggsae] CAE62739 535 1 41.2022 95 0.0184595 34 399 420 515 1 0 31 52 26 122 FPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE YPAGTPNRWEQMGRVLN--------RTPEDVIAMAGKMKQM---KQEDYTKLLMSSIQQS---VPSEEKSEDD------------WSQSEQKAFELALQKYPKGTDERWERISEEIGTKTKK +PAGT +RWE + +N RT +DVI A ++++ +++D K ++ VP + + + QK E AL YP T ERW I+ + + K+ 56 gi|54643310|gb|EAL32054.1| GA20437-PA [Drosophila pseudoobscura] EAL32054 529 1 41.2022 95 0.0184595 1 399 302 440 1 0 40 59 12 142 DLQLLIKAVNLFPAGTNSRWEVIANYMN------IHSSSGVKRTAKDVIGKAKSL-QKLDPHQKDDINKKAFDKFKKEHGVVPQADNAT-PSERFXGPYTDFTPXTTEXQKLXEQAL-NTYPVNTXERWXXIAVAVPGRXKE DLTELIRLVKKHPGGAGSRWNTIAESMNRSVQEVTFMAAKMKENGYRIPGQTESVAENLVQESQEAVRK---EKVKKSASVTATAAPGTVTSSSEKSMLIPETNWTQEQQRALEAAIVKNRKAASGDRWQKIANSVPEKTKE DL LI+ V P G SRW IA MN ++ +K + G+ +S+ + L ++ + K +K KK V A T S T T E Q+ E A+ + +RW IA +VP + KE 57 gi|49119322|gb|AAH73404.1| MGC80867 protein [Xenopus laevis] AAH73404 534 1 40.4318 93 0.0314871 304 399 482 513 1 0 19 20 0 32 QKLXEQALNTYPVNTXERWXXIAVAVPGRXKE QKLLELALQQYPKGTGERWDKIAKCVPGKSKE QKL E AL YP T ERW IA VPG+ KE 2 32.3426 72 8.57476 1 150 316 357 1 0 19 25 8 50 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQ DLSQLTRNMTKFPGGTPGRWEKIAHELG--------RSVTDVTTKAKQLK DL L + + FP GT RWE IA+ + R+ DV KAK L+ 58 gi|16507118|gb|AAL24046.1| DnaJ-like protein [Homo sapiens] AAL24046 275 1 40.0466 92 0.0411235 133 399 165 254 1 0 27 43 1 90 KAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATP-SERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE RRKPARLLEATAKPEPEEKSRAKRQKDFDIAEQNESSDEESLRKERARSAEEPWTQNQQKLLELALQQYPRGSSDRWDKIARCVPSKSKE + K + L+ K + +K+ K +K+ + Q +++ S R + P T QKL E AL YP + +RW IA VP + KE 2 32.3426 72 8.57476 1 150 55 96 1 0 19 26 8 50 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQ DLSQLTRSMVKFPGGTPGRWEKIAHELG--------RSVTDVTTKAKQLK DL L +++ FP GT RWE IA+ + R+ DV KAK L+ 59 gi|10438787|dbj|BAB15343.1| unnamed protein product [Homo sapiens] BAB15343 340 1 40.0466 92 0.0411235 133 399 230 319 1 0 27 43 1 90 KAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATP-SERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE RRKPARLLEATAKPEPEEKSRAKRQKDFDIAEQNESSDEESLRKERARSAEEPWTQNQQKLLELALQQYPRGSSDRWDKIARCVPSKSKE + K + L+ K + +K+ K +K+ + Q +++ S R + P T QKL E AL YP + +RW IA VP + KE 2 32.3426 72 8.57476 1 150 120 161 1 0 19 26 8 50 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQ DLSQLTRSMVKFPGGTPGRWEKIAHELG--------RSVTDVTTKAKQLK DL L +++ FP GT RWE IA+ + R+ DV KAK L+ 60 gi|21361912|ref|NP_071760.2| DnaJ (Hsp40) homolog, subfamily C, member 1 [Homo sapiens] >gi|55960003|emb|CAI13668.1| DnaJ (Hsp40) homolog, subfamily C, member 1 (DNAJC1)(DNAJL1) [Homo sapiens] >gi|55664633|emb|CAH73412.1| DnaJ (Hsp40) homolog, subfamily C, member 1 (DNAJC1)(DNAJL1) [Homo sapiens] >gi|37904711|gb|AAP50497.1| MTJ1-like protein [Homo sapiens] >gi|14041831|dbj|BAB55004.1| unnamed protein product [Homo sapiens] >gi|27805464|sp|Q96KC8|DNJC1_HUMAN DnaJ homolog subfamily C member 1 NP_071760 554 1 40.0466 92 0.0411235 133 399 444 533 1 0 27 43 1 90 KAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATP-SERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE RRKPARLLEATAKPEPEEKSRAKRQKDFDIAEQNESSDEESLRKERARSAEEPWTQNQQKLLELALQQYPRGSSDRWDKIARCVPSKSKE + K + L+ K + +K+ K +K+ + Q +++ S R + P T QKL E AL YP + +RW IA VP + KE 2 32.3426 72 8.57476 1 150 334 375 1 0 19 26 8 50 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQ DLSQLTRSMVKFPGGTPGRWEKIAHELG--------RSVTDVTTKAKQLK DL L +++ FP GT RWE IA+ + R+ DV KAK L+ 61 gi|55633547|ref|XP_507688.1| PREDICTED: similar to DnaJ (Hsp40) homolog, subfamily C, member 1 [Pan troglodytes] XP_507688 171 1 40.0466 92 0.0411235 133 399 61 150 1 0 27 43 1 90 KAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATP-SERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE RRKPARLLEATAKPEPEEKSRAKRQKDFDIAEQNESSDEESLRKERARSAEEPWTQNQQKLLELALQQYPRGSSDRWDKIARCVPSKSKE + K + L+ K + +K+ K +K+ + Q +++ S R + P T QKL E AL YP + +RW IA VP + KE 62 gi|34905190|ref|NP_913942.1| myb-like protein [Oryza sativa (japonica cultivar-group)] >gi|51964708|ref|XP_507138.1| PREDICTED P0498E12.114 gene product [Oryza sativa (japonica cultivar-group)] >gi|28812079|dbj|BAC65017.1| myb-like protein [Oryza sativa (japonica cultivar-group)] NP_913942 325 1 39.6614 91 0.0537089 1 396 177 300 1 0 38 60 18 137 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFX-----GPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXK EMDILRRQMVKHPAGEPQRWEKIA------AAFGGRRTPESVIRAAKS------GGGAAAAGASFDQFLRKRKPLDPRSEATDAGSGNAGGGGGESGDGSWSAGDDRALLN-ALKEFPKDTAMRWEKVAVAVPGKTK ++ +L + + PAG RWE IA ++ G +RT + VI AKS +FD+F ++ + AT + G D + + + L AL +P +T RW +AVAVPG+ K 63 gi|50732383|ref|XP_418609.1| PREDICTED: similar to DnaJ homolog subfamily C member 1 (DnaJ protein homolog MTJ1) [Gallus gallus] XP_418609 1580 1 39.6614 91 0.0537089 292 396 1187 1221 1 0 18 20 0 35 TTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXK TQNQQKLLEMALQQYPKGTSDRWDKIAKCVPGKSK T QKL E AL YP T +RW IA VPG+ K 64 gi|76632251|ref|XP_587525.2| PREDICTED: similar to DnaJ (Hsp40) homolog, subfamily C, member 1, partial [Bos taurus] XP_587525 501 1 39.2762 90 0.070146 250 399 431 480 1 0 20 25 0 50 SERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE SQQRERPRASEEPWTQNQQKLLELALQQYPRGSSDRWDKIAKCVPSKSKE S++ P P T QKL E AL YP + +RW IA VP + KE 2 32.3426 72 8.57476 1 150 288 329 1 0 19 26 8 50 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQ DLSQLTRSMVKFPGGTPGRWEKIAHELG--------RSVTDVTTKAKQLK DL L +++ FP GT RWE IA+ + R+ DV KAK L+ 65 gi|33358308|gb|AAQ16626.1| GlsA-related protein [Chlamydomonas reinhardtii] AAQ16626 760 1 37.7354 86 0.204094 1 153 491 541 1 0 19 27 0 51 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQK ELRLLDKACNKFPMGTPKRWEAVAGFVRTRTLEEVLLMVKDRQGASATRMK +L+LL KA N FP GT RWE +A ++ + V KD G + + K 66 gi|4633127|gb|AAD26632.1| GlsA [Volvox carteri f. nagariensis] >gi|4633129|gb|AAD26633.1| GlsA [Volvox carteri f. nagariensis] AAD26632 748 1 37.7354 86 0.204094 1 192 485 548 1 0 22 30 0 64 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKA ELRLLDKACNKFPMGTPKRWEAVAAFVRTRTLDEVLLMVKDRQGASATRMKAQEDWKGAQKKPA +L+LL KA N FP GT RWE +A ++ + V KD G + + K K K A 67 gi|7106295|ref|NP_031895.1| DnaJ (Hsp40) homolog, subfamily C, member 1 [Mus musculus] >gi|51330487|gb|AAH80300.1| Dnajc1 protein [Mus musculus] >gi|2494160|sp|Q61712|DNJC1_MOUSE DnaJ homolog subfamily C member 1 (DnaJ protein homolog MTJ1) >gi|473847|gb|AAA66349.1| dnaJ-like protein NP_031895 552 1 36.5798 83 0.454673 292 399 496 531 1 0 17 19 0 36 TTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE TQSQQKLLELALQQYPKGASDRWDKIAKCVPSKSKE T QKL E AL YP +RW IA VP + KE 68 gi|62663943|ref|XP_214522.3| PREDICTED: similar to dnaJ-like protein [Rattus norvegicus] XP_214522 565 1 36.5798 83 0.454673 292 399 509 544 1 0 17 19 0 36 TTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKE TQSQQKLLELALQQYPKGASDRWDKIAKCVPSKSKE T QKL E AL YP +RW IA VP + KE 2 32.3426 72 8.57476 1 150 343 384 1 0 19 26 8 50 DLQLLIKAVNLFPAGTNSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQ DLSQLTRSMVKFPGGTPGRWEKIAHELG--------RSVTDVTTKAKELK DL L +++ FP GT RWE IA+ + R+ DV KAK L+ 69 gi|23487909|gb|EAA21175.1| hypothetical protein [Plasmodium yoelii yoelii] EAA21175 2172 1 34.6538 78 1.72776 49 357 918 1022 1 0 27 43 2 105 NSRWEVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNAT--PSERFXGPYTDFTPXTTEXQKLXEQALNTYPVNTXER NSEVEAISTNGTKETEEDVELSLDDELVKNTKYLKLELESKEDIRNKIIEELIETNGNLPNYEMYPNLPAQCFFLLYYDFTPFIQNNLMGIENVINTLKNTTLGR NS E I+ + V+ + D + K KL+ K+DI K ++ + +G +P + P++ F Y DFTP E +NT T R 70 gi|6688529|emb|CAB65169.1| I-box binding factor [Lycopersicon esculentum] CAB65169 191 1 34.2686 77 2.25652 292 405 8 45 1 0 15 21 0 38 TTEXQKLXEQALNTYPVNTXERWXXIAVAVPGRXKEGL TRDDDKLFEHGLVLYPENSADRWQLIADHVPGKTADDI T + KL E L YP N+ +RW IA VPG+ + + 71 gi|53729175|ref|ZP_00134015.2| COG0556: Helicase subunit of the DNA excision repair complex [Actinobacillus pleuropneumoniae serovar 1 str. 4074] ZP_00134015 673 1 33.4982 75 3.84904 103 336 542 625 1 0 25 39 10 86 VKRTAKDVIGKA--------KSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTTEXQKLXEQALNTY IGRAARNLNGKAILYGDRITNSMQKAITETERRREKQ--QKYNEEHGITPQALNKKVGELLDIGQTDKPKRGKQAVKVEEKSANTY + R A+++ GKA S+QK + K+ K+ +EHG+ PQA N E TD + K+ E++ NTY 72 gi|56605378|emb|CAI30890.1| putative MYB transcription factor [Cucumis sativus] CAI30890 295 1 32.7278 73 6.56547 283 390 23 58 1 0 14 19 0 36 TPXTTEXQKLXEQALNTYPVNTXERWXXIAVAVPGR TKWTKEENKMFESALAIYDKETPDRWFKVAALIPGK T T E K+ E AL Y T +RW +A +PG+ 73 gi|55621752|ref|XP_516961.1| PREDICTED: similar to hypothetical protein FLJ35155 [Pan troglodytes] XP_516961 2330 1 32.7278 73 6.56547 345 530 1984 2045 -3 0 20 25 0 62 KKEHPNKKXXXPXPNLHPAXXPGTSFLWLYPXRQSPLXPXXCXPSFXLPGTATAIXXHLSXV RHENPQTRVGGPPPEGLPGFNSGVMLLNLEAMRQSPLYSRLLEPAQSCQGSAMAIRPHTRAV + E+P + P P P G L L RQSPL P+ G+A AI H V 74 gi|62662768|ref|XP_214365.3| PREDICTED: similar to testis protein TEX15 [Rattus norvegicus] XP_214365 3081 1 32.7278 73 6.56547 115 252 2209 2259 1 0 18 29 5 51 AKDVIGKAKSLQKLDPHQK-----DDINKKAFDKFKKEHGVVPQADNATPS AKSLVWKEKSCSLLKAHSEKTREAEEINECAFSKLKKIYGVLSKGLNSEPT AK ++ K KS L H + ++IN+ AF K KK +GV+ + N+ P+ 75 gi|56560951|ref|YP_161369.1| hypothetical protein BGP084 [Borrelia garinii PBi] >gi|52696592|gb|AAU85934.1| hypothetical protein BGP084 [Borrelia garinii PBi] YP_161369 188 1 32.3426 72 8.57476 61 186 72 113 1 0 15 23 0 42 EVIANYMNIHSSSGVKRTAKDVIGKAKSLQKLDPHQKDDINK EALSNIKNWVNSAKTKDNINSIIQKISFIQKIDPNNVDDIKK E ++N N +S+ K +I K +QK+DP+ DDI K 76 gi|65304064|emb|CAI76443.1| DNA-binding chaperone, putative [Theileria annulata] CAI76443 655 1 32.3426 72 8.57476 1 81 529 555 1 0 14 18 0 27 DLQLLIKAVNLFPAGTNSRWEVIANYM DLKRLSKGVEINPAGTPGRWNLIAKYV DL+ L K V + PAGT RW +IA Y+ 77 gi|76657489|ref|XP_593354.2| PREDICTED: similar to Dr1 associated protein 1 (negative cofactor 2 alpha) isoform 1 [Bos taurus] XP_593354 185 1 32.3426 72 8.57476 94 297 96 161 1 0 23 29 2 68 SSGVKRTAKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQADNATPSERFXGPYTDFTPXTT SSGRKNGGMGSKGKDKKLSGTDSEQEDESEDTDSDGEEETPQVPPQASH--PPAHFQSPPTPFMPFTS SSG K GK K L D Q+D+ D ++ V PQA + P F P T F P T+ 78 gi|72081091|ref|XP_800619.1| PREDICTED: hypothetical protein XP_795526 [Strongylocentrotus purpuratus] XP_800619 337 1 32.3426 72 8.57476 40 231 106 172 1 0 21 37 3 67 AGTNSRWEVIANYMNI--HSSSGVKRT-AKDVIGKAKSLQKLDPHQKDDINKKAFDKFKKEHGVVPQ SSSNSSSKASASSSNVGASSSSGTKKSDSKSSNESSKSKRDKEDHKEGSINRSKDEKVSKEHRVVKE + +NS + A+ N+ SSSG K++ +K +KS + + H++ IN+ +K KEH VV + 2934173 1011751523 0 0 0.041 0.267 0.14 weblogo-3.8.0/tests/data/ssearch/xbt004.xml000066400000000000000000006755261467613320200204570ustar00rootroot00000000000000 tblastn TBLASTN 2.2.12 [Aug-07-2005] Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. nr gi|729325|sp|P39483|DHG2_BACME Glucose 1-dehydrogenase II (GLCDH-II) 261 BLOSUM62 0.001 11 1 L; 1 gi|729325|sp|P39483|DHG2_BACME Glucose 1-dehydrogenase II (GLCDH-II) 261 1 gi|58264321|ref|XM_569317.1| Filobasidiella neoformans glucose 1-dehydrogenase, putative (CNB05760) mRNA, complete cds XM_569317 904 1 148.288 373 1.46834e-35 5 250 16 762 0 1 84 143 9 252 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSH---ELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKG-NVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGM LQGKVVAITGCSTGIGRAIAIGAAKNGANVVLHHLGDSTASDIAQVQEECKQAGAKTVVVPGDIAEAKTANEIVSAAVSSFSRIDVLISNAGI---CPFHSFLDLPHPLWKRVQDVNLNGSFYVVQAVANQMAKQEPKGGSIVAVSSISALMGGGEQCHYTPTKAGIKSLMESCAIALGPMGIRCNSVLPGTIETNINKEDLSNPEKRADQIRRVPLGRLGKPEDLVGPTLFFASDLSNYCTGASVLVDGGM L+ KVV +TG S G+GRA+A+ + + VV+++ + + + + E +AG + ++V GD+ + + +V AV F +DV+I+NAG+ P H +L W +V D NL G+F + + + KG +++ +SS+ ++ HY +K G+K + E+ A+ P GIR N++ PG I+T IN E ++PE+RAD +P+G +GKPE++ F AS ++Y TG ++ DGGM 2 gi|46110768|ref|XM_382442.1| Gibberella zeae PH-1 strain PH-1; NRRL 31084 chromosome 1 XM_382442 822 1 147.517 371 2.50461e-35 3 251 19 813 0 1 100 151 18 266 TDLKDKVVVVTGGSKGLGRAMAVRFGQEQSKVV-------VNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGV--ENPVPS---HELSLENWNQVIDTNLTGAFLGSREAIKYFVENDI-----KGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMT TRLKDKVCIVTGSSSGFGRAIALGYSLEGALVVCADLQQGARADVNGEQAISTHELIKQKGGKAIFVQTDVSKNDAVENLVYRAVAEFSRVDVVVNNAGISIESGKPSRRIHDTPEEWWNTTMAVNLKSIFLLSKHAITQMLKQEKNEAGDRGWIINIASIFGLVGGYALPSYVASKGGAQNLTRSIALDYAKDGIHCNAICPGFAETALLADAVKIHDKEA-IRSKHPLHGLGTAEDIVGAAIFLASAEARWITGVRLPVDGGYT T LKDKV +VTG S G GRA+A+ + E + VV N E+A+ + I++ GG+AI V+ DV+K + V NLV AV EF +DV++NNAG+ E+ PS H+ E WN + NL FL S+ AI ++ + +G +IN++S+ ++ Y ASKGG + +T ++AL+YA GI N I PG +T + A+ ++ A + S P+ +G E+I A FLAS++A ++TG+ L DGG T 3 gi|49654999|emb|CR382137.1| Debaryomyces hansenii chromosome E of strain CBS767 of Debaryomyces hansenii CR382137 2037969 1 142.895 359 6.16907e-34 1 250 89764 90510 0 -1 82 139 1 250 MYTDLKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGM MYGLLEGKTVAITGGVTGIGRAIAIGMAKNGANVVVNHLPNQLELVKSLQEEIGED-KFLGVAGDISKPENCEELIVRTVEKFHEINVFVSNAGICEFKEFTEIEPETYYKTIDINLNGAFFSIQAAAKQMKKQGKGGSIIGISSISALVGGAYQAHYTPTKAGILSIIQSTACALGPYGIRCNALLPGTIKTALNGEDLSNDEKKKYMENRIPLTRLGEPEDMAGPSVFLASDLSKYVNGAQLLVDGGL MY L+ K V +TGG G+GRA+A+ + + VVVN+ N+ E ++ +E + + V GD++K E+ L+ V++F ++V ++NAG+ E+ E + + ID NL GAF + A K + G++I +SS+ ++ HY +K G+ + ++ A P GIR N + PG I T +N E ++ E++ +E+ IP+ +G+PE++A + FLAS + YV G L DGG+ 2 100.523 249 3.51114e-21 5 249 692690 693421 0 2 76 124 7 248 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVE-NPVPSHELS-LENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWP-LFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LKGKVASVTGSSGGIGWAVAEAYAQAGADVAVWYNSKNADAKAEYLTKTY-GVKSKAYKCNISDPEDVEKVIGQIEKDFGTIDVFVANAGVPWTEGRSIEADGYDAWKKIVDLDLSGVYYCAKTVGKIFKKHGKGSLVLTASMSGHIVNVPQMQAPYNAAKAGVLHLGKSLAIEWAPFA-RVNTISPGYIATEIS--DFVPAEVKAKWWQLIPLGREALAQELVGAYLYFASDASTYTTGSDLLVDGG LK KV VTG S G+G A+A + Q + V V Y S +A G ++ + +++ EDV ++ K+FG++DV + NAGV S E + W +++D +L+G + ++ K F ++ V+ S ++ P + Y A+K G+ + ++LA+E+AP RVN I PG I T I+ F E +A +IP+G +E+ + AS ++Y TG L DGG 3 99.7525 247 5.9891e-21 5 251 70288 71025 0 1 76 126 9 251 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNY-RSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSL---ENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMT LKGKVALITGGSAGLGAAVARQLAAEGVNLAINYNNSEERALKVAESLASEFGIKTVIIKGDIFDTSVGSKLVSETVNKLGGLDIVISNAGWTKIVPYDDLEALDDELWDGCFNVNVKAHFYLFKAAKKIFDQNEDGGTFIVSASVAGRIVYGSSIPYAVSKAALIHLVKMLSKTQGPK-VRMHAVCPGLLMTEW-GQRFS-PERIEDTKNMSPINTLADVDETA--AQFVLLSKLTTTTGSIVSMDGGIS LK KV ++TGGS GLG A+A + E + +NY S E + E G + +I++GD+ LV V + G LD++I+NAG VP +L E W+ + N+ F + A K F +N+ G I +SV I + + YA SK + + + L+ PK +R++ + PG + T ++F+ PE+ D ++M P+ + +E A A F+ S+ + TG + DGG++ 4 97.0561 240 3.88202e-20 5 251 2008532 2009287 0 2 74 124 11 255 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYR-SNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGN------VINMSSVHEMIPWPLF-VHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMT LKGKVSLITGGSRGIGLAVALGLAEAGSDIAITYNTSGSNYIADIEKQFIGLGVKFKAYQCNVSNKEQITTCVDQVFADFERLDVVIPNSGVTSQGPAEKFSEQDYRNTMSVNLDGAFFTAQAAANSFKKQKAEGKLDQGRIVFTTSVSSQIVNIPQSQAPYNASKAGLVRLAKCLSVEWVDFA-RVNCVSPGFIATDMLDS--LPNEWRDKWMSMVPAQRFCSPYELKGVYVYLASDASSYMTGAELVVGGGYT LK KV ++TGGS+G+G A+A+ + S + + Y S +++K+ G + + +V+ +E + V+ +F LDV+I N+GV + P+ + S +++ + NL GAF ++ A F + +G V S +++ P Y ASK G+ + + L++E+ RVN + PG I T + E R SM+P P E+ V +LAS +SY+TG L GG T 5 81.6481 200 1.68781e-15 5 249 688221 688955 0 3 66 118 10 250 LKDKVVVVTGGSKGLGRAMAVRFGQE--QSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGV--ENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWP-LFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LTGKSAVVTGGISGIGFCISEGYCQAGLAKLAIIDYAENQLVLEKLQQKYPKT--QINFYNCDVRKAEQVKNVIEQIHSDFTEVDIFVANAGIAWTSGAMIDQDDDDEWHNVMNVDLNGVYYCAKHIGRVFRQQGRGSLVMTASMSAHIVNVPQLQAAYNAAKAGVLHLGKSLAAEWAPFA-RVNTVSPGYIATELS--DFVPDDIKNVWYSMTPKGRQGLPRELVGAYLYLGSDASSFTTGTDIIVDGG L K VVTGG G+G ++ + Q +++Y N+ +++++ + Q DV K E V N++E +F +D+ + NAG+ + + + W+ V++ +L G + ++ + F + V+ S ++ P L Y A+K G+ + ++LA E+AP RVN + PG I T ++ F + + SM P G G P E+ +L S +S+ TG + DGG 4 gi|50421638|ref|XM_459373.1| Debaryomyces hansenii CBS767, DEHA0E01474g predicted mRNA XM_459373 765 1 142.895 359 6.16907e-34 1 250 1 747 0 1 82 139 1 250 MYTDLKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGM MYGLLEGKTVAITGGVTGIGRAIAIGMAKNGANVVVNHLPNQLELVKSLQEEIGED-KFLGVAGDISKPENCEELIVRTVEKFHEINVFVSNAGICEFKEFTEIEPETYYKTIDINLNGAFFSIQAAAKQMKKQGKGGSIIGISSISALVGGAYQAHYTPTKAGILSIIQSTACALGPYGIRCNALLPGTIKTALNGEDLSNDEKKKYMENRIPLTRLGEPEDMAGPSVFLASDLSKYVNGAQLLVDGGL MY L+ K V +TGG G+GRA+A+ + + VVVN+ N+ E ++ +E + + V GD++K E+ L+ V++F ++V ++NAG+ E+ E + + ID NL GAF + A K + G++I +SS+ ++ HY +K G+ + ++ A P GIR N + PG I T +N E ++ E++ +E+ IP+ +G+PE++A + FLAS + YV G L DGG+ 5 gi|70996099|ref|XM_747712.1| 2-deoxy-D-gluconate 3-dehydrogenase (Afu1g14350) mRNA, complete cds XM_747712 798 1 141.354 355 1.79492e-33 5 249 31 783 0 1 82 135 8 252 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDI-------KGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LSGKTAIVTGGTRGIGQAMAIALAEAGADIVLIQRDESNTQTRDEIVNRV-GRKAWIHVAELSKREEVKSIIPAVTSQGLKPEILLNCAGIQRRHPSEKFPDEDWDEVIEVNLTSVFTLCREFGAYLLARDASDFPSGRRGSIINVASLLSFQGGITVPAYAASKGGIAQLTKALSNEWASKGINVNAIAPGYIDTDMNVALINDANRNAGIMARIPAGRWGKPDDFKGVIVFLASEASNYVSGEVVCVDGG L K +VTGG++G+G+AMA+ + + +V+ R + G +A I +++K E+V +++ + ++++N AG++ PS + E+W++VI+ NLT F RE Y + D +G++IN++S+ YAASKGG+ +T+ L+ E+A KGI VN I PG IDT +N D + A + + IP G GKP++ V FLAS ++YV+G + DGG 6 gi|71006163|ref|XM_752655.1| Ustilago maydis 521 hypothetical protein (UM01601.1), mRNA XM_752655 1419 1 139.813 351 5.22243e-33 5 249 649 1398 0 1 80 133 5 250 LKDKVVVVTGGSKGLGRAMAVRFGQEQSK-VVVNYRSNXXXXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKG-NVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LPGKVVAITGASRGIGRACALACAAHGARGVIVHYFGDATTTTEAQSLQIELAQLGANAVLVAGDIADAAVGQSIADAAETEFGRLDVFVSNAGICPFMGFLEMQASTWRKVQDVNLNGAFFATQAAARLMARQTPQGGSIIAIASISALVGGEFQSHYTPTKAGLKSMMDSAAIGLGPLGIRCNSVLPGTIETAINQDDLKDTRKRARMMDRHPLKRLGTPDDIAGPVVFLASDLAKFMTGSSVLVDGG L KVV +TG S+G+GRA A+ ++ V+V+Y + E + + G A++V GD+ ++ + A EFG LDV ++NAG+ + E+ W +V D NL GAF ++ A + +G ++I ++S+ ++ HY +K G+K M ++ A+ P GIR N++ PG I+T IN + D +RA + P+ +G P++IA FLAS A ++TG ++ DGG 7 gi|67902797|ref|XM_676563.1| Aspergillus nidulans FGSC A4 hypothetical protein (AN8386.2), mRNA XM_676563 1770 1 139.428 350 6.8207e-33 5 251 979 1761 0 1 90 135 14 261 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVV-----NYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVE----NPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDI-----KGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMT LYNKVAIVTGASSGLGRAIATRYAREGAKVVCADVSPTARSLEESDITTHDLILKHGGEALFIQTDVGDAAQMESLVKATVQHYGRLDILVNNAGISLEARKPAVLHLTDEETWDTTMRVNAKSVFLGCKYGLAQMLRQEPHPSGDRGWIVNISSIMGMIVGPENPSYCASKGAVSQLTRQIALDYAPHRIYANALCPGYTQTAIFKETTTHLTPWEDLNRRHPLKGPGLPDDVARMAVVLASEDASWVTGVCLPVDGGYT L +KV +VTG S GLGRA+A R+ +E +KVV RS EE + I + GG+A+ ++ DV + +LV+ V+ +G LD+++NNAG+ P H E W+ + N FLG + + + + +G ++N+SS+ MI P Y ASKG + +T +AL+YAP I N + PG T I E D+ P+ G P+++A +A LAS AS+VTG+ L DGG T 8 gi|70985099|ref|XM_742963.1| oxidoreductase short chain dehydrogenase/reductase family (Afu5g02870) mRNA, complete cds XM_742963 774 1 138.272 347 1.51949e-32 5 249 28 762 0 1 86 132 26 258 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVE-NPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGP------------GAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LQGKVAIVTGGGSGFGAAISRRFGEEGAKVIVA----DINVENGEKIAAQNPENLVFYKMDVTSASDWDEVMDLAFAKFGRLDVLVNNAGTTYRNKPTLEVTEEEWERVFNVNVRSIFLGSKALMGRLIQQGQGGSMINISSTGASRPRPGLVWYNASKGAVSNATKGLAAEYGPHNIRVNTVSPLLSGTGLFSMFTGMEDTPENREKFI---------GNVPLGRLTDPNDVANMCLYLASDEGSFINGAEMIVDGG L+ KV +VTGG G G A++ RFG+E +KV+V + +K + + + DVT D +++ A +FG LDV++NNAG P+ E++ E W +V + N+ FLGS+ + ++ G++IN+SS P P V Y ASKG + T+ LA EY P IRVN + P G DTP N EKF +P+G + P ++A++ +LAS + S++ G + DGG 9 gi|6594234|emb|AL133522.1|SPAC922 S.pombe chromosome I cosmid c922 AL133522 19999 1 133.265 334 4.88804e-31 5 250 14718 15425 0 3 76 135 16 249 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSV--HEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKF-ADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGM VEGRVVLITGAAGGIGKVLCKMFTELGDRVA----------GIDIVDPSKVQDAALALQADVSKADQIETAIEKVIQTLGPIDVLINNAGLADDTPFEQLSHESWDHDVSLVLRGNYLTQRYVIPHMAKQGKGGSIVNIGSVNGHIYLGSPA---YSAAKAGLENLTKALAVRYGPLGIRVNVCAPGTIWSPAWDERFKKHPDVGDRMKRWYPVGRLGTPEDVARAVIFLADSKNSFITGTTLYVDGGL ++ +VV++TG + G+G+ + F + +V + + A+ ++ DV+K + + +E ++ G +DV+INNAG+ + P +LS E+W+ + L G +L R I + + G+++N+ SV H + P Y+A+K G++ +T+ LA+ Y P GIRVN PG I +P E+F P+ ++ P+G +G PE++A FLA S+ S++TG TL+ DGG+ 10 gi|68006187|ref|NM_001020437.1| Schizosaccharomyces pombe 972h- hypothetical protein (SPAC922.06), partial mRNA NM_001020437 777 1 133.265 334 4.88804e-31 5 250 7 714 0 1 76 135 16 249 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSV--HEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKF-ADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGM VEGRVVLITGAAGGIGKVLCKMFTELGDRVA----------GIDIVDPSKVQDAALALQADVSKADQIETAIEKVIQTLGPIDVLINNAGLADDTPFEQLSHESWDHDVSLVLRGNYLTQRYVIPHMAKQGKGGSIVNIGSVNGHIYLGSPA---YSAAKAGLENLTKALAVRYGPLGIRVNVCAPGTIWSPAWDERFKKHPDVGDRMKRWYPVGRLGTPEDVARAVIFLADSKNSFITGTTLYVDGGL ++ +VV++TG + G+G+ + F + +V + + A+ ++ DV+K + + +E ++ G +DV+INNAG+ + P +LS E+W+ + L G +L R I + + G+++N+ SV H + P Y+A+K G++ +T+ LA+ Y P GIRVN PG I +P E+F P+ ++ P+G +G PE++A FLA S+ S++TG TL+ DGG+ 11 gi|70987186|ref|XM_743980.1| alcohol dehydrogenase (Afu7g04360) mRNA, complete cds XM_743980 1104 1 132.494 332 8.33774e-31 5 250 19 786 0 1 83 135 10 256 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSN-------XXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFV--ENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQAS-YVTGITLFADGGM LVGKVAAITGGLTGIGRAIALEYLRHGARVAVNHLGRPDEEPLLEAMLKDVGEITGSEGGRFITIAGDVSQPETGRDFVAKTVEAFGRLDIFVSNAGVCKFEEFLEVDPPLLGHTVNTNLCGAFYATQAAARQMALAQSPPGGSIIGISSISALVGGGQQTHYTPTKAGVLSLMQSTAVALGKYGIRCNALLPGTIRTQLNDEDMSDPVKRTYMEGRIPLGRLGQPPDLAGPAVFLACDELSGYVTGAQLLVDGGL L KV +TGG G+GRA+A+ + + ++V VN+ E +V + GG+ I + GDV++ E + V V+ FG LD+ ++NAGV E+ ++TNL GAF ++ A + ++ G++I +SS+ ++ HY +K G+ + ++ A+ GIR N + PG I T +N E +DP +R +E IP+G +G+P ++A A FLA + S YVTG L DGG+ 12 gi|67526862|ref|XM_656401.1| Aspergillus nidulans FGSC A4 hypothetical protein (AN3889.2), mRNA XM_656401 1185 1 131.339 329 1.85745e-30 5 249 28 798 0 1 81 132 12 257 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRS----NXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKY--------FVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LSGKTALVTGGTRGIGAAMAIALAEAGADIILIQLTCDAQRDTSNTTTRDQITRLGRKATIHAAELSDRSAVKAIIPTLVSQGHNPTILLNCAGIQRRHPSERFPDEDWDEVLNVNLTSVFTLCREFGAYILSLPESSFTPNKKKGSIINVASLLSYQGGITVPAYAASKGGVAQLTKALSNEWVSKGINVNAIAPGYIDTDMNVALINDANRNAGIMARIPAGRWGRPEDFKGPVVFLASEASSYVSGELVTVDGG L K +VTGG++G+G AMA+ + + +++ + + + +I G +A I +++ V ++ T V + + +++N AG++ PS E+W++V++ NLT F RE Y F N KG++IN++S+ YAASKGG+ +T+ L+ E+ KGI VN I PG IDT +N D + A + + IP G G+PE+ FLAS +SYV+G + DGG 13 gi|1184013|emb|Z69380.1|SPAC4H3 S.pombe chromosome I cosmid c4H3 Z69380 34635 1 131.339 329 1.85745e-30 5 249 19771 20496 0 1 80 136 7 247 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVN-YRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHE-LSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LAEKKTLLTGGDSGIGKAAAVMFAREGSDLVISCLPEERDDAEVTRDLIEREGRNCWIWEGKLDKSDNCRDLVDFALKKLGWIDVLVNNIAYQQVAQSIEDIDDEQWDLTFKTNIFSFFWVTKAAISHMKSGS---SIVNCSSINAYVGRPDLLDYTSTKGAITAFTRGLSNQYAQHGIRVNAVAPGPIYTPLVSSTF--PKEKIELSDQVPLGRMGQPVEVASCYLFLACSDGGYMTGQTLHPNGG L +K ++TGG G+G+A AV F +E S +V++ ++A + IE G I G + K ++ +LV+ A+K+ G +DV++NN + S E + E W+ TN+ F ++ AI + +++N SS++ + P + Y ++KG + T L+ +YA GIRVN + PG I TP+ + F P+++ ++ +P+G +G+P E+AS FLA S Y+TG TL +GG 14 gi|68000400|ref|NM_001019765.1| Schizosaccharomyces pombe 972h- hypothetical protein (SPAC4H3.08), partial mRNA NM_001019765 861 1 131.339 329 1.85745e-30 5 249 118 843 0 1 80 136 7 247 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVN-YRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHE-LSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LAEKKTLLTGGDSGIGKAAAVMFAREGSDLVISCLPEERDDAEVTRDLIEREGRNCWIWEGKLDKSDNCRDLVDFALKKLGWIDVLVNNIAYQQVAQSIEDIDDEQWDLTFKTNIFSFFWVTKAAISHMKSGS---SIVNCSSINAYVGRPDLLDYTSTKGAITAFTRGLSNQYAQHGIRVNAVAPGPIYTPLVSSTF--PKEKIELSDQVPLGRMGQPVEVASCYLFLACSDGGYMTGQTLHPNGG L +K ++TGG G+G+A AV F +E S +V++ ++A + IE G I G + K ++ +LV+ A+K+ G +DV++NN + S E + E W+ TN+ F ++ AI + +++N SS++ + P + Y ++KG + T L+ +YA GIRVN + PG I TP+ + F P+++ ++ +P+G +G+P E+AS FLA S Y+TG TL +GG 15 gi|50552367|ref|XM_503594.1| Yarrowia lipolytica CLIB99, YALI0E05643g predicted mRNA XM_503594 876 1 130.954 328 2.42591e-30 5 251 127 867 0 1 84 138 6 250 LKDKVVVVTGGSKGLGRAMAVRFGQEQSK-VVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVH-EMIPWPL-FVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMT LDGKVAIVTGGARGLGFSMAEGLCSVGLKGIAILDVQQDLGLDAIEKLHKAYGVQAQFYKADVRDEESVNEIIDRVVHDLGSVDVVVNSAGVADLVHAAEYPADKFRRVIDINLNGSFLVTQAAARHMIKQGTGGTVVFIASMSGSIVNWPQPQSAYNASKAAVKHLSKSLAAEWAVHNIRCNSISPGYMDTALNRAYNTLFEEWKD---RTPLGRLGDPDELTGACIYLASDASSYVTGSDIIIDGGYT L KV +VTGG++GLG +MA K + + + ++K + G QA + DV EE V +++ V + GS+DV++N+AGV + V + E + + +VID NL G+FL ++ A ++ ++ G V+ ++S+ ++ WP Y ASK +K ++++LA E+A IR N+I PG +DT +N E+ D P+G +G P+E+ +LAS +SYVTG + DGG T 16 gi|49649227|emb|CR382131.1| Yarrowia lipolytica chromosome E of strain CLIB99 of Yarrowia lipolytica CR382131 4224103 1 130.954 328 2.42591e-30 5 251 628208 628948 0 2 84 138 6 250 LKDKVVVVTGGSKGLGRAMAVRFGQEQSK-VVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVH-EMIPWPL-FVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMT LDGKVAIVTGGARGLGFSMAEGLCSVGLKGIAILDVQQDLGLDAIEKLHKAYGVQAQFYKADVRDEESVNEIIDRVVHDLGSVDVVVNSAGVADLVHAAEYPADKFRRVIDINLNGSFLVTQAAARHMIKQGTGGTVVFIASMSGSIVNWPQPQSAYNASKAAVKHLSKSLAAEWAVHNIRCNSISPGYMDTALNRAYNTLFEEWKD---RTPLGRLGDPDELTGACIYLASDASSYVTGSDIIIDGGYT L KV +VTGG++GLG +MA K + + + ++K + G QA + DV EE V +++ V + GS+DV++N+AGV + V + E + + +VID NL G+FL ++ A ++ ++ G V+ ++S+ ++ WP Y ASK +K ++++LA E+A IR N+I PG +DT +N E+ D P+G +G P+E+ +LAS +SYVTG + DGG T 2 85.5001 210 1.16884e-16 6 248 1830555 1831220 0 -3 77 119 21 243 KDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADG KDQVVIVTGAGAGIGRAYSHLLAKLGAKVVVNDFGNPQKVVDEIKAL---GGIAVADKNNVIHGEKVV---QTAIDAFGAVHAVVNNAGILRDKSFANMDDEMWQLIFDVHLNGTYSVTKAAWPHFLKQKY-GRVINTTSTSGIYGNFGQANYSAAKAGILGFSRALAREGEKYNILVNTIAPNA-GTAMTASVFTE-----------EMLELFKPDFIAPITVLLASDQAP-VTG-DLFETG KD+VV+VTG G+GRA + + +KVVVN N ++ ++ K + GG A+ + +V E VV +TA+ FG++ ++NNAG+ + E W + D +L G + ++ A +F++ G VIN +S + +Y+A+K G+ + LA E I VN I P A T + A F + M + KP+ IA + LAS QA VTG LF G 3 64.6994 156 2.13508e-10 56 252 1831416 1831958 0 -3 56 92 16 197 GGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMTK GGKAVANYDSV---ENGDKIVETAVKAFGSVHIVINNAGILRDISFKKMTDKDWDLVYKVHVFGAYKVTRAAWPYFRKQKY-GRVISTSSAAGLYGNFGQTNYSAAKLALVGFGETLAKEGAKYNITSNVI------APLAASRMTETVMPEDILKLL------KPEYVVPLVGYLTHDSVTESYGIYEVGAGYMAK GG+A+ V E+ +VETAVK FGS+ ++INNAG+ + +++ ++W+ V ++ GA+ +R A YF + G VI+ SS + +Y+A+K + ETLA E A I N I P+ A + + D+ ++ KPE + + +L + GI G M K 4 63.929 154 3.6419e-10 82 251 2364786 2365313 0 3 47 94 14 180 EFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVEN-------DIKGN--VINMSSVHEMIP-WPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMT DFAAVDILVNGAGIAQGGFLPDMEVELIDKIVATNLTGAIKLTKYALEAWVERHENSPRPKSRGNGVIINLASVQGLRPIIPVLSVYSTTKAALNMFTKAVAVEGGAYAIRSNSVCPGYVPTNM-TDGMEVPERPSLVEDDDDVGWVSRDSIARAVYYFATNLQ---VSGAILAVDKAMS +F ++D+++N AG+ ++ +E ++++ TNLTGA ++ A++ +VE +GN +IN++SV + P P+ Y+ +K + + T+ +A+E IR N++ PG + T + + PE+ + VE +G++ + +V F + Q V+G L D M+ 17 gi|39968318|ref|XM_365550.1| Magnaporthe grisea 70-15 chromosome II XM_365550 852 1 129.028 323 9.21845e-30 5 249 79 840 0 1 88 137 15 257 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSV-HEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPI----------NAEKFADPE-QRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LEGKVALVTGAGRGIGREMAMELGRRGCKVIVNYANSTESAEEVVAAIKKNGSDAACVKANVGVVEDIVRMFEEAVKIFGKLDIVCSNSGVVSFGHVKDVTPEEFDRVFTINTRGQFFVAREAYKHL---EIGGRLILMGSITGQAKAVPKHAVYSGSKGAIETFARCMAIDMADKKITVNVVAPGGIKTDMYHAVCREYIPNGENLSNEEVDEYAASAWSPLHRVGLPIDIARVVCFLASNDGGWVTGKVIGIDGG L+ KV +VTG +G+GR MA+ G+ KV+VNY ++ E A EV I++ G A V+ +V ED+V + E AVK FG LD++ +N+GV + +++ E +++V N G F +REA K+ +I G +I M S+ + P Y+ SKG ++ +A++ A K I VN + PG I T + N E ++ E + P+ +G P +IA V FLAS+ +VTG + DGG 18 gi|58262735|ref|XM_568778.1| Filobasidiella neoformans fatty acid beta-oxidation-related protein, putative (CNB00370) mRNA, complete cds XM_568778 920 1 129.028 323 9.21845e-30 5 252 63 842 0 3 86 140 16 262 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVV---NYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLEN--WNQVIDTNLTGAFLGSREAIKYFVEND--------IKGNVINMSSVHEMIPWPL-FVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMTK LEHKVAIITGAGSGIGLETALQFAAEGARLVISDINLRNVEAAAQLINTHFPECG--AVAIKCDVSKEEEVKAMVDKAVEVFGRLDVLFNNAGIMHPADDNAITTEEKVWDLTQNINVKGVWFGCKYGILAMKKNKPDPSKGLGIGGSIINVASFVAILGAATPQLAYTASKGAVLAMTRELAMVHAREGIRFNSLCPGPIRTPLLMDFLNTPEKLNRRMVHVPMGRFGEAVEQAKAVVFLASDDSSFINGTDFLVDGGLHK L+ KV ++TG G+G A++F E +++V+ N R+ E A + E G A+ ++ DV+KEE+V +V+ AV+ FG LDV+ NNAG+ +P + ++ E W+ + N+ G + G + I +N I G++IN++S ++ + Y ASKG + MT LA+ +A +GIR N++ PG I TP+ + PE+ +PMG G+ E A FLAS +S++ G DGG+ K 19 gi|431102|gb|L22309.1|MGNPORE Magnaporthe grisea polyhydroxynaphthalene reductase mRNA, complete cds L22309 1005 1 129.028 323 9.21845e-30 5 249 136 897 0 1 88 137 15 257 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSV-HEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPI----------NAEKFADPE-QRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LEGKVALVTGAGRGIGREMAMELGRRGCKVIVNYANSTESAEEVVAAIKKNGSDAACVKANVGVVEDIVRMFEEAVKIFGKLDIVCSNSGVVSFGHVKDVTPEEFDRVFTINTRGQFFVAREAYKHL---EIGGRLILMGSITGQAKAVPKHAVYSGSKGAIETFARCMAIDMADKKITVNVVAPGGIKTDMYHAVCREYIPNGENLSNEEVDEYAASAWSPLHRVGLPIDIARVVCFLASNDGGWVTGKVIGIDGG L+ KV +VTG +G+GR MA+ G+ KV+VNY ++ E A EV I++ G A V+ +V ED+V + E AVK FG LD++ +N+GV + +++ E +++V N G F +REA K+ +I G +I M S+ + P Y+ SKG ++ +A++ A K I VN + PG I T + N E ++ E + P+ +G P +IA V FLAS+ +VTG + DGG 20 gi|67901637|ref|XM_675983.1| Aspergillus nidulans FGSC A4 versicolorin reductase (AN7806.2), mRNA XM_675983 795 1 127.487 319 2.68216e-29 5 249 25 783 0 1 86 135 14 256 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPW-PLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPI----------NAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LDGKVALVTGAGRGIGAAIAVALGQRGAKVVVNYANSREAAEKVVDEIKSNGSDAISIQADVGDPDAVTKLMDQAVEHFGYLDIVSSNAGIVSFGHVKDVTPDEFDRVFRVNTRGQFFVAREAYRHLREG---GRIILTSSNTASVKGVPRHAVYSGSKGAIDTFVRCLAIDCGDKKITVNAVAPGAIKTDMFLSVSREYIPNGETFTDEQVDECAAWLSPLNRVGLPVDVARVVSFLASDAAEWISGKIIGVDGG L KV +VTG +G+G A+AV GQ +KVVVNY ++ E A +V EI+ G AI ++ DV + V L++ AV+ FG LD++ +NAG+ + +++ + +++V N G F +REA ++ E G +I SS + P Y+ SKG + LA++ K I VN + PGAI T + N E F D + + P+ +G P ++A V +FLAS A +++G + DGG 21 gi|46126246|ref|XM_387677.1| Gibberella zeae PH-1 strain PH-1; NRRL 31084 chromosome 4 XM_387677 798 1 126.331 316 5.97523e-29 9 249 19 783 0 1 79 139 20 258 VVVVTGGSKGLGRAMAVRFGQEQSKVVV------NYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGV-ENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVEND----------IKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG IALVTGAASGIGRATAISFARERCLRLVLADRDADKLKDTQKTIIDMSKNQNQNIQVIAIPTDISKENDIENLYDTTIEKFGRVDYVVNGAGVLSNNKRSHESTIEEFDLINNVNYRGCWLSSRAAIRQMLKQEPLPTHDGRPGSRGSIINIASQLGVVGRPAAPAYCGSKAAVINMTRCDAIDYSKDLIRVNAVCPGVIDTAMTRPQ---ADVLAPAVNIAPMGRMGTAQEVADCVLFLASSKASFVQGSAMMVDGG + +VTG + G+GRA A+ F +E+ +V + + ++ + + + Q I + D++KE D+ NL +T +++FG +D ++N AGV N SHE ++E ++ + + N G +L SR AI+ ++ + +G++IN++S ++ P Y SK + MT A++Y+ IRVN + PG IDT + + + A ++ PMG +G +E+A FLASS+AS+V G + DGG 22 gi|46116185|ref|XM_384111.1| Gibberella zeae PH-1 strain PH-1; NRRL 31084 chromosome 2 XM_384111 750 1 125.946 315 7.80389e-29 5 249 10 738 0 1 90 134 10 249 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLEN-WNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESM---IPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LDGKVAIVTGAASGFGQGIAEHFAEEGAKVLI-CDINEEAGEKVAAHSEAFAFQAM----NVTKAADWQAAVAKAVQIWGHIDILVNNAGTSYENKSTNLVTEDEFDKVMSVNVKSVFLGSNAFTTQVKKQGTKGSMINIASVGAHRPRPGLVWYNASKGAITNATMGLAAEYGPDGIRVNSICPLATMTGL-LPKFIGKEITPEVQKALGNVPLGRMGEIRDVTKAAVFLASEESSFITGVNLDVDGG L KV +VTG + G G+ +A F +E +KV++ NEE +V E QA+ +VTK D V AV+ +G +D+++NNAG S L E+ +++V+ N+ FLGS + KG++IN++SV P P V Y ASKG + T LA EY P GIRVN+I P A T + KF E +V+ +P+G +G+ ++ A FLAS ++S++TG+ L DGG 23 gi|67527874|ref|XM_656698.1| Aspergillus nidulans FGSC A4 hypothetical protein (AN4186.2), mRNA XM_656698 804 1 125.176 313 1.33114e-28 5 250 19 786 0 1 80 130 16 259 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKY--FVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGM LNGKVAAITGGLTGIGRAIALEYLRHGAYVAVNHLGGSNDEPLLTAMKKDVSELLQQTSQTDKERFITVSGDISKPETGTEFIEKTVQAFGRLDVFVSNAGVCRFEEFLDVTPQLLNHTITTNLTGAFYAVQAAARQMAFSQSPPGGSIIGISSISALVGGGQQTHYTPTKAGVLSLMQSTAVALGKYGIRCNALLPGTIRTQLNDEDMSDPVKRKYMEGRIPLGRLGQPPDLAGPAVFLACEGLS---GYVILVDGGL L KV +TGG G+GRA+A+ + + + V VN+ + + + + I V GD++K E +E V+ FG LDV ++NAGV +++ + N I TNLTGAF + A + F ++ G++I +SS+ ++ HY +K G+ + ++ A+ GIR N + PG I T +N E +DP +R +E IP+G +G+P ++A A FLA S G + DGG+ 24 gi|12745774|gb|AF317668.1| Ophiostoma floccosum reductase gene, complete cds AF317668 1444 1 124.405 311 2.27058e-28 5 249 480 1238 0 3 81 132 14 256 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPW-PLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPI----------NAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LAGKVALVTGAGRGIGREMALELGRRGAKVIVNYANSDSSAQEVVDAIKAAGSDAAAIKANVSDVDQIVTLFEKTKQQWGKLDIVCSNSGVVSFGHVKDVTPEEFDRVFSVNTRGQFFVAREAYKHL---EIGGRLILMGSITGQAKMVPRHAVYSASKGAIETFVRCMAVDFGDKKITVNAVAPGGIKTDMYHAVCREYIPNGLTLNDDETDEYAAGWSPIHRVGLPIDVARVVAFLASQDGQWINGKVLGVDGG L KV +VTG +G+GR MA+ G+ +KV+VNY +++ A EV I+ AG A ++ +V+ + +V L E +++G LD++ +N+GV + +++ E +++V N G F +REA K+ +I G +I M S+ P Y+ASKG ++ +A+++ K I VN + PG I T + N D E P+ +G P ++A V AFLAS ++ G L DGG 25 gi|67522612|ref|XM_654275.1| Aspergillus nidulans FGSC A4 hypothetical protein (AN1763.2), mRNA XM_654275 774 1 123.25 308 5.05833e-28 5 249 34 762 0 1 81 133 24 256 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAI-------IVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVE-NPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADP---EQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LHGKVAIVTGAGSGFGYGIAKKFVEEGAKVIV-------------ADISEKNGQAVAAELGSKFIYTDVTRRDDWQALLQATLDEYKTLDIVVNNAGATYSNKPTTEVTDADFDLCVNVNVRSIYLSTSVIVPYFLEHNRPGCFIQVSSTAALRPRPGLTWYNASKAAVSNATKTMAVEYGPKKIRFNCVCPVVGSTGMTHLFLGKPDTEENRAAFVSTIPLGRPSTPADVANTCSFLASDEAGFITGVELEIDGG L KV +VTG G G +A +F +E +KV+V +I E GQA+ + DVT+ +D L++ + E+ +LD+++NNAG + P+ E++ +++ ++ N+ +L + + YF+E++ G I +SS + P P Y ASK + T+T+A+EY PK IR N + P T + P E RA S IP+G P ++A+ +FLAS +A ++TG+ L DGG 26 gi|67525604|ref|XM_655772.1| Aspergillus nidulans FGSC A4 hypothetical protein (AN3260.2), mRNA XM_655772 1665 1 122.865 307 6.60639e-28 5 242 34 750 0 1 80 129 5 241 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVE-NPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRAD--VESMIPMGYIGKPEEIASVAAFLASSQASYVTGI LKDKVAIVTGGAQGMGKATASVFLRAGAKVVI--ADIKAEQGEQVASELSSLGEVRFVKTDISKSEDVQNLVAQTVGFFGRLDVAINNAAMTPDKTVLIETDEEYWRRLVDVNLTGTALCCKYEMQQMRKQGSKGSIVNITSINAFMPQPNMPAYTSTKHALLGLTKHAATEGGPLGIRVNAVAPGAIFSEMSAKALEIMGTTHDEFAPKVSSLNRFGQPHEVAQASLWLASDSSSLSNGL LKDKV +VTGG++G+G+A A F + +KVV+ + E E + G+ V+ D++K EDV NLV V FG LDV INNA + + E E W +++D NLTG L + ++ + KG+++N++S++ +P P Y ++K + +T+ A E P GIRVN + PGAI + ++A+ D + + G+P E+A + +LAS +S G+ 27 gi|71002819|ref|XM_750998.1| 1,3,6,8-tetrahydroxynaphthalene reductase (Afu2g17560) mRNA, complete cds XM_750998 822 1 120.553 301 3.27872e-27 2 241 19 762 0 1 79 130 14 251 YTDLKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPI---NAEKFAD--------PEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTG YLPLSGKVALVTGGGRGIGAGIALELARRGASVAINYGHSAKSAQEVVEAIQAIGRQAVAIQADLTCVPNIESLIQEVVRHFGRLDIVVSNSGMEKFKPLEETTLEDFNEVFNLNTRAQMFVARYAYDHIQPG---GRVILMSSIAAGLGVPGHALYAGSKAAIEGFTRCLAADFGRKGCTVNAIAPAGVKSDMWRENAWRYAPGCDKSSSLEEIETALASGSPLKRCGVPEDIGKVVSFLASPDAEWVNG Y L KV +VTGG +G+G +A+ + + V +NY + + A EV + I+ G QA+ ++ D+T ++ +L++ V+ FG LD++++N+G+E P E +LE++N+V + N +R A + G VI MSS+ + P YA SK ++ T LA ++ KG VN I P + + + NA ++A E + S P+ G PE+I V +FLAS A +V G 28 gi|5689603|emb|Y19033.1|ASF19033 Aspergillus fumigatus thnR gene for 1,3,6,8-tetrahydroxynaphthalene reductase Y19033 1136 1 120.553 301 3.27872e-27 2 241 222 965 0 3 79 130 14 251 YTDLKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPI---NAEKFAD--------PEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTG YLPLSGKVALVTGGGRGIGAGIALELARRGASVAINYGHSAKSAQEVVEAIQAIGRQAVAIQADLTCVPNIESLIQEVVRHFGRLDIVVSNSGMEKFKPLEETTLEDFNEVFNLNTRAQMFVARYAYDHIQPG---GRVILMSSIAAGLGVPGHALYAGSKAAIEGFTRCLAADFGRKGCTVNAIAPAGVKSDMWRENAWRYAPGCDKSSSLEEIETALASGSPLKRCGVPEDIGKVVSFLASPDAEWVNG Y L KV +VTGG +G+G +A+ + + V +NY + + A EV + I+ G QA+ ++ D+T ++ +L++ V+ FG LD++++N+G+E P E +LE++N+V + N +R A + G VI MSS+ + P YA SK ++ T LA ++ KG VN I P + + + NA ++A E + S P+ G PE+I V +FLAS A +V G 29 gi|6090728|gb|AF099736.1|AF099736 Aspergillus fumigatus 1,3,6,8-tetrahydroxynaphthalene reductase (arp2) gene, complete cds AF099736 1624 1 120.553 301 3.27872e-27 2 241 349 1092 0 1 79 130 14 251 YTDLKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPI---NAEKFAD--------PEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTG YLPLSGKVALVTGGGRGIGAGIALELARRGASVAINYGHSAKSAQEVVEAIQAIGRQAVAIQADLTCVPNIESLIQEVVRHFGRLDIVVSNSGMEKFKPLEETTLEDFNEVFNLNTRAQMFVARYAYDHIQPG---GRVILMSSIAAGLGVPGHALYAGSKAAIEGFTRCLAADFGRKGCTVNAIAPAGVKSDMWRENAWRYAPGCDKSSSLEEIETALASGSPLKRCGVPEDIGKVVSFLASPDAEWVNG Y L KV +VTGG +G+G +A+ + + V +NY + + A EV + I+ G QA+ ++ D+T ++ +L++ V+ FG LD++++N+G+E P E +LE++N+V + N +R A + G VI MSS+ + P YA SK ++ T LA ++ KG VN I P + + + NA ++A E + S P+ G PE+I V +FLAS A +V G 30 gi|70991906|ref|XM_745709.1| oxidoreductase short chain dehydrogenase/reductase family (Afu6g09140) mRNA, complete cds XM_745709 786 1 119.783 299 5.59264e-27 5 249 13 774 0 1 76 131 21 260 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVE-NPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGP-----GAID---------TPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LEEKVAIVTGAGSGFGYGIAKKFVEEGANVIIAELSQQSGEKAAAEL------NCKFVLTDVTRRESWQALLQATLDAYGKLDIVVNNAGATYSNKPTVEVTDADFDLCMNVNIKSIYLSTSVIVPYFLQNNRPGSFIQISSTAALRPRPGLTWYNASKAAVSNATKTMAVEYGPKQIRFNCVCPVVGSTGILESDSPCYVFRTHLFLGKPDTEENRAAFVSTVPLGRPSTPRDVANTCCFLASDEAEFITGVNLEVDGG L++KV +VTG G G +A +F +E + V++ S + + V DVT+ E L++ + +G LD+++NNAG + P+ E++ +++ ++ N+ +L + + YF++N+ G+ I +SS + P P Y ASK + T+T+A+EY PK IR N + P G ++ T + K E RA S +P+G P ++A+ FLAS +A ++TG+ L DGG 31 gi|67525708|ref|XM_655824.1| Aspergillus nidulans FGSC A4 hypothetical protein (AN3312.2), mRNA XM_655824 750 1 119.398 298 7.30422e-27 4 251 46 741 0 1 78 125 18 249 DLKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQ-RADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMT DLTGKVAAVTGGARGIGLEVSRGLAEAGANVAIIYNSSPTAIETAAEIAAANNVTARAYRANVTDQAEIEKTVQQIKKDFGHLDIIVVNSGITSNIPAEDYSVEEWRKIMGVNLDGAFYSAQAAAKIFKEQG-RGNVIFTAS------------YNASKAAVVQLARCLSVEWV-DFCRVNCISPGFIETEI---LDAHPQEWRAKWHSMIPAQRMAQAYELKGAYVFCASDASSYMTGADIVIDGGYT DL KV VTGG++G+G ++ + + V + Y S+ + A R +VT + ++ V+ K+FG LD+++ N+G+ + +P+ + S+E W +++ NL GAF ++ A K F E +GNVI +S Y ASK + + L++E+ RVN I PG I+T I A P++ RA SMIP + + E+ F AS +SY+TG + DGG T 32 gi|46107389|ref|XM_380754.1| Gibberella zeae PH-1 strain PH-1; NRRL 31084 chromosome 1 XM_380754 897 1 119.013 297 9.5396e-27 5 249 154 879 0 1 82 132 9 248 LKDKVVVVTGGSKGLGRAMAVRFGQE-QSKVVVNYRSNXXXXXXXXXXXXXXGGQAI-IVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPS-HELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LKGKRALITGGDSGIGAASALLFGREGTSDIVIAYLPEEEKDAQDTKKQVEGEGAKVHLISLDLSKQENCRKLVDFAVEKMKGIDILFNNAAYQMVVKDIKDLPEEQWIHTFNINIHSFFYVSKYALPHMKEG---ATIINNASINAYIGRPDLLDYTSTKGAIVSFTRGLSNQYVSKGIRVNAVAPGPVWTPLIPATMDDEAQK---NFTAPMGRPAQPSEIATCIVFLASSDSSCVSGQTIHCNGG LK K ++TGG G+G A A+ FG+E S +V+ Y EE+ + K+ E G + ++ D++K+E+ LV+ AV++ +D++ NNA + V +L E W + N+ F S+ A+ + E +IN +S++ I P + Y ++KG + T L+ +Y KGIRVN + PG + TP+ D Q+ PMG +P EIA+ FLASS +S V+G T+ +GG 33 gi|32417231|ref|XM_329093.1| Neurospora crassa strain OR74A XM_329093 798 1 119.013 297 9.5396e-27 5 249 37 783 0 1 72 125 8 251 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDI------KGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LEGHTALITGATRGIGQAVAIALAEAGADILLVQRDETSTTTLQAIQSL--GRHAQIYKADLSSPTDVSSLVPRILSDGHTIRILVNCAGIQRRHPSHLFPDSDFAEVMQVNLNAVFTLCRDVGAHMLGLDPHPVTRRKGSVINFASLLTFQGGLTVPAYAASKGAVGQLTKSFANEWTSKGVTVNAIAPGYIETEMNEALLKDEERLKSISARIPAGRWGSPEDFKGTAVYLASKASGYVSGHVLVVDGG L+ ++TG ++G+G+A+A+ + + +++ R + G A I + D++ DV +LV + + ++ +++N AG++ PSH ++ +V+ NL F R+ + + D KG+VIN +S+ YAASKG + +T++ A E+ KG+ VN I PG I+T +N D E+ + + IP G G PE+ A +LAS + YV+G L DGG 34 gi|32423288|ref|XM_332081.1| Neurospora crassa strain OR74A XM_332081 849 1 117.857 294 2.1252e-26 5 249 79 837 0 1 78 132 14 256 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSV-HEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPI----------NAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LGGKVALVTGAGRGIGREMALELGRRGAKVVVNYANSDISANEVVQAIKKIGSDAVAIKANVSDVSQIERLFREAKQRFGKLDIVCSNSGVVSFGHIKDVTPEEYDRVFNINTRGQFFVAREAYKNL---EVGGRLILMGSITGQAKAVPKHTVYSASKGAIETFVRCMAIDFGDKKITVNAVAPGGIKTDMYHAVCREYIPGGDKLDNQGVDEYAAGWSPLHRVGLPIDIARVACFLASQDGEWINGKVIGVDGG L KV +VTG +G+GR MA+ G+ +KVVVNY +++ A EV + I++ G A+ ++ +V+ + L A + FG LD++ +N+GV + +++ E +++V + N G F +REA K ++ G +I M S+ + P Y+ASKG ++ +A+++ K I VN + PG I T + +K + P+ +G P +IA VA FLAS ++ G + DGG 35 gi|67902351|ref|XM_676340.1| Aspergillus nidulans FGSC A4 hypothetical protein (AN8163.2), mRNA XM_676340 1032 1 117.087 292 3.62505e-26 5 239 10 840 0 1 90 132 86 299 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRG---------DVTKEEDVVNLVETAVKEFGSLDVMINNAGVE-----NPVPSHELSLE--------------NWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGM------------------------KLMTETLALEYAPKGIRVNNIGP------------GAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYV LNNKVAIVTGGGSGFGAAIATRFAEEGAKVIV-------------ADINAAGGESVAAQNPENLVFQKVDVTSPSDWAALVETAVTKFGKLDILVNNAGTTYRNKVQPSPASQLLLDMANSVQPTLEVTEAEWERVFNVNVKGIFHGTQAVIARLLEQGHGGSVINISSTGASRPRPGLVWYNASKGAVSNVRSFLSNFALSFLEGKRKAHSHRQATKGLAAEYGPHNIRVNTVSPLLSGTGLFSMFTGMEDTEENRQKFI---------GNVPLGRLTDPADVANMCLYLASDEGSFI L +KV +VTGG G G A+A RF +E +KV+V +I AGG+++ + DVT D LVETAV +FG LD+++NNAG P P+ +L L+ W +V + N+ G F G++ I +E G+VIN+SS P P V Y ASKG + + T+ LA EY P IRVN + P G DT N +KF +P+G + P ++A++ +LAS + S++ 36 gi|70994919|ref|XM_747144.1| oxidoreductase short-chain dehydrogenase/reductase family (Afu4g05870) mRNA, complete cds XM_747144 927 1 117.087 292 3.62505e-26 5 250 184 912 0 1 79 133 7 248 LKDKVVVVTGGSKGLGRAMAVRFGQE-QSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPS-HELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGM LAGKRAIITGGDSGIGRAVAILFAMEGASSLIVYLPEEEIDAQETKRRVQETGKECHCLAVDIRKRENCQKVVDVALRCLGGIDILVNNAAFQNMVQDISELDEDQWHRTFDTNIHPYYYLSKYSLPHMRSG---ATIINCSSVNHYIGRGDLLDYTSTKGAIIAFTRGLSNQQIGKGIRVNCVCPGPIWTPLIPSTM--DTSAMEQFSSVPMGRPGQPSEVATCFVFLASHDSSYISGQSLHPNGGV L K ++TGG G+GRA+A+ F E S ++V E +A E K+ ++E G + + D+ K E+ +V+ A++ G +D+++NNA +N V EL + W++ DTN+ + S+ ++ + +IN SSV+ I + Y ++KG + T L+ + KGIRVN + PG I TP+ + S +PMG G+P E+A+ FLAS +SY++G +L +GG+ 37 gi|70996761|ref|XM_748043.1| short chain dehydrogenase or 3-ketoacyl-CoA reductase (Afu1g17700) mRNA, complete cds XM_748043 840 1 117.087 292 3.62505e-26 1 250 79 828 0 1 79 128 14 257 MYTDLKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPK-GIRVNNIGPGAIDTPINAEKF--ADPEQRADVESMIPMGYIG----KPEEIASVAAFLASSQASYVTGITLFADGGM METSLRDKVAIVSGSSSGIGAAIVRELSSRGANTVVNYPFPSLRAEADTLVASLPS-PAIAVEADMSRADAPQKLVDAAVSQWGRVDIVVNSVALAVNKPFEEQTLEDWDTLVNINGRGTFLLTQASLKYLTKG--SGRIVNIASISARGPPPNQTIYAGTKGMVDSFTKCWAKELPPKYGCTVNAVSPG----PTMTEGFAAAGKEQMKILQPIIDQTPVGPRMAQPDEIAYAVAFLCEERARWINGAHLIASGGL M T L+DKV +V+G S G+G A+ + VVNY A AI V D+++ + LV+ AV ++G +D+++N+ + P E +LE+W+ +++ N G FL ++ ++KY + G ++N++S+ P P YA +KG + T+ A E PK G VN + PG P E F A EQ ++ +I +G +P+EIA AFL +A ++ G L A GG+ 38 gi|67515728|ref|XM_652658.1| Aspergillus nidulans FGSC A4 hypothetical protein (AN0146.2), mRNA XM_652658 798 1 116.701 291 4.73446e-26 5 249 31 789 0 1 83 136 14 256 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSS-VHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPI----------NAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LEGKVALVTGSGRGIGAAMALELGRLGAKVVVNYANSREPAEKLVQEIKELGTDAIALQANIRNVSEIVRVMDDAVAHFGGLDIVCSNAGVVSFGHLGEVTEEEFDRVFSLNTRAQFFVAREAYRHL---NTHGRIILMSSNTAKEFSVPRHSVYSGSKGAIESFVRVMAKDCGDKQITVNAVAPGGTVTDMFYDVAQHYIPNGEKHSAEELQKMAATVSPLKRNGFPVDIAKVVGFLASREAEWVNGKIITVDGG L+ KV +VTG +G+G AMA+ G+ +KVVVNY ++ E A ++ +EI+E G AI ++ ++ ++V +++ AV FG LD++ +NAGV + E++ E +++V N F +REA ++ + G +I MSS + P Y+ SKG ++ +A + K I VN + PG T + N EK + E + ++ P+ G P +IA V FLAS +A +V G + DGG 39 gi|50310038|ref|XM_455033.1| Kluyveromyces lactis NRRL Y-1140, KLLA0E24046g predicted mRNA XM_455033 843 1 116.701 291 4.73446e-26 5 248 82 825 0 1 82 122 10 251 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGV---ENPVPSHELS---LENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWP-LFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADG LKGKVAVVTGASSGIGYAVAEGLAQAGASLAVWYNSNAALVERAVELSAKYNVKVVAYQCPVTEEAKVKKTIEDVIQEFGKIDVFIANAGVPWTKGPLVEAAESGTDTDEWNKVIHTDFNGVYYCAKYVGAQFKRQGSGSMVITASMSGHIVNIPQLQACYNAAKAGVIHFAKSLAVEWAGFA-RVNTVSPGYIATPIS--NFVDEDLKNKWHSLIPMGREGLPQELVGAYLYFASDASTYTTGSDLLVDG LK KV VVTG S G+G A+A Q + + V Y SN + + + + + VT+E V +E ++EFG +DV I NAGV + P+ S + WN+VI T+ G + ++ F VI S ++ P L Y A+K G+ ++LA+E+A RVN + PG I TPI+ F D + + S+IPMG G P+E+ + AS ++Y TG L DG 40 gi|49643087|emb|CR382125.1| Kluyveromyces lactis strain NRRL Y-1140 chromosome E of strain NRRL Y-1140 of Kluyveromyces lactis CR382125 2234072 1 116.701 291 4.73446e-26 5 248 2136601 2137344 0 -3 82 122 10 251 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGV---ENPVPSHELS---LENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWP-LFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADG LKGKVAVVTGASSGIGYAVAEGLAQAGASLAVWYNSNAALVERAVELSAKYNVKVVAYQCPVTEEAKVKKTIEDVIQEFGKIDVFIANAGVPWTKGPLVEAAESGTDTDEWNKVIHTDFNGVYYCAKYVGAQFKRQGSGSMVITASMSGHIVNIPQLQACYNAAKAGVIHFAKSLAVEWAGFA-RVNTVSPGYIATPIS--NFVDEDLKNKWHSLIPMGREGLPQELVGAYLYFASDASTYTTGSDLLVDG LK KV VVTG S G+G A+A Q + + V Y SN + + + + + VT+E V +E ++EFG +DV I NAGV + P+ S + WN+VI T+ G + ++ F VI S ++ P L Y A+K G+ ++LA+E+A RVN + PG I TPI+ F D + + S+IPMG G P+E+ + AS ++Y TG L DG 2 92.8189 229 7.32118e-19 6 251 1997004 1997762 0 3 77 129 19 259 KDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFG--SLDVMINNAGV---ENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVI---NMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYA----PKG-IRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMT KGKLTVITGGAGAIGGALCEGFASCGSDVIILDRT--FQPELSVHLSKTYGIESKSYQVDITNADDVKFVFERILEDFPGRAINTFIANAGIAWTNGSILNDGSTPEMWRRVMDVNVQGTYHCSRYAAEVF-KNQGHGNLILTASMSSYISNVP-NYQTCYNASKAAVRHMAKGFAVEFSGLTSPAGKIRCNSVSPGYTDTLLSS--FVPTEQRAHWWGLTPVGREALPQELVGAYLYLASDAASYTNGCDIQVDGGYT K K+ V+TGG+ +G A+ F S V++ R+ + + G ++ + D+T +DV + E +++F +++ I NAG+ + + + E W +V+D N+ G + SR A + F +N GN+I +MSS +P Y ASK ++ M + A+E++ P G IR N++ PG DT +++ F EQRA + P+G P+E+ +LAS ASY G + DGG T 3 90.8929 224 2.78204e-18 1 248 1219430 1220131 0 2 74 118 18 250 MYTDLKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGK--PEEIASVAAFLASSQASYVTGITLFADG MSLEFKDRVVIITGAGGGLGRVYALEYAKRGGKVVVNDLGRSAADSVVQEIKKL-GGEGDAVANYDSVSDNGAAIVETAISNFGRVDILINNAGILRDSSFAKMSEKQFQQVIDVHLNGAFKLTRAAWPHMRKQKF-GRIINTCSPAGLYGNFGQANYSAAKLGLLGFGESLAKEGYKYNINVNSIAPLA--------------RSAMTENVIPANILKELGPEKIAPLILYLTHENTKVTNNIFELAAG M + KD+VV++TG GLGR A+ + + KVVVN V++ + GG+ V + ++ +VETA+ FG +D++INNAG+ ++S + + QVID +L GAF +R A + + G +IN S + +Y+A+K G+ E+LA E I VN+I P A + A E++IP + + PE+IA + +L I A G 4 88.1965 217 1.80327e-17 5 261 1220360 1221100 0 2 74 124 10 257 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMTKYPSFQAGRG LRGKVVIITGSGSGLGKSHAQWFARYGAKVVIN-DIRDPSAVVDEINKKYGSGSAVADTHDIVKEAQQV--VQTAVDKFGRVDILVNNAGILRDRSFAKMTEDEWNAVINVHLFSTFALSKAVWPIFLKQK-SGYIINTTSTSGIYGNFGQCNYAAAKAAILGFSRTLALEGTKRGITVNVIAPHA-ETAMTKTIFSSKE----LNNHFDPGFV-SPFVVLLCSDELQELGKNRVKGLLFEVGGGWCGLTRWQRSRG L+ KVV++TG GLG++ A F + +KVV+N + A+ + + G A+ D+ KE V V+TAV +FG +D+++NNAG+ +++ + WN VI+ +L F S+ F++ G +IN +S + +YAA+K + + TLALE +GI VN I P A +T + F+ E + + G++ P + + L + V G+ GG +Q RG 5 72.0182 175 1.33733e-12 5 204 873119 873694 0 -2 56 96 12 202 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVE-NPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPI-NAEKFADPE MKKQVILITGASTGIGLSIAETLRSAGYEVFGTSRKGSIPGKEYSFK---------MIKLDITDEESVKSAVNEVIEKAGRIDVLVNNAGIAFKWAAVEECSTDLAKTIFETNFFGVHRMTRAVLPHMREQR-HGKIINISSMGGIMPIPYGALYCSSKHALEGYTESLDYEVKKFGIHVSTIDPHIIKTGMANSNSPADEE +K +V+++TG S G+G ++A +V R E + +++ D+T EE V + V +++ G +DV++NNAG+ E S + + +TN G +R + + E G +IN+SS+ ++P P Y +SK ++ TE+L E GI V+ I P I T + N+ AD E 6 46.9802 110 4.60701e-05 8 145 726382 726786 0 -3 37 72 7 140 KVVVVTGGSKGLGRAMAVRFGQ-EQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPS-HELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSS KVFLVTGVSRGIGSSIVEKLCSIETTKIVIGIARSKDKLEELKTQYS---GKFDYICGDVSDEETITEAVNFIESKYKRLDGIVANAGVLDPVEDVNNIHISKWKQLFDINFFSVVSLVGHALPLLKQSN--GNIVLVSS KV +VTG S+G+G ++ + E +K+V+ ++++ E+K + G+ + GDV+ EE + V ++ LD ++ NAGV +PV + + + W Q+ D N A+ +++ GN++ +SS 41 gi|68480915|ref|XM_710518.1| Candida albicans SC5314 3-oxoacyl-(acyl carrier protein) reductase (CaO19_10417), mRNA XM_710518 789 1 116.316 290 6.18339e-26 1 249 1 765 0 1 77 139 10 257 MYTDLKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVN---YRSNXXXXXXXXXXXXXXGGQAI-IVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENP--VPSHEL-SLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAID-TPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG MSYNLANKIAIVTGGLTGIGLATTIKLLKQGSKVIVGDFLHEHEIDTVLNHIHKQVPENNRNIKFLRINIANYQDNVNLVDFALDEYLDLHYVVTNTAITTTTAIASNKTETIDQFKDVIDTNLNGVFALNKLAINYWEEFHKPGSIVNVSNILGLTTTKGLTSYRVCQGGVQSLTQSLALPYANKDIRLNSVIPGYVEISPMLGQ--INQHIATTAIKQHPMARLGNPDEIANAIAFLLSDEASFVNGTSLVVDGG M +L +K+ +VTGG G+G A ++ ++ SKV+V + + L + + I +R ++ +D VNLV+ A+ E+ L ++ N + + S++ +++ + VIDTNL G F ++ AI Y+ E G+++N+S++ + Y +GG++ +T++LAL YA K IR+N++ PG ++ +P+ + + PM +G P+EIA+ AFL S +AS+V G +L DGG 42 gi|68481026|ref|XM_710462.1| Candida albicans SC5314 3-oxoacyl-(acyl carrier protein) reductase (CaO19_2899), mRNA XM_710462 789 1 116.316 290 6.18339e-26 1 249 1 765 0 1 77 139 10 257 MYTDLKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVN---YRSNXXXXXXXXXXXXXXGGQAI-IVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENP--VPSHEL-SLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAID-TPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG MSYNLANKIAIVTGGLTGIGLATTIKLLKQGSKVIVGDFLHEHEIDTVLNHIHKQVPENNRNIKFLRINIANYQDNVNLVDFALDEYLDLHYVVTNTAITTTTAIASNKTETIDQFKDVIDTNLNGVFALNKLAINYWEEFHKPGSIVNVSNILGLTTTKGLTSYRVCQGGVQSLTQSLALPYANKDIRLNSVIPGYVEISPMLGQ--INQHIATTAIKQHPMARLGNPDEIANAIAFLLSDEASFVNGTSLVVDGG M +L +K+ +VTGG G+G A ++ ++ SKV+V + + L + + I +R ++ +D VNLV+ A+ E+ L ++ N + + S++ +++ + VIDTNL G F ++ AI Y+ E G+++N+S++ + Y +GG++ +T++LAL YA K IR+N++ PG ++ +P+ + + PM +G P+EIA+ AFL S +AS+V G +L DGG 43 gi|6491839|emb|AL021817.2|SPAC8E11 S.pombe chromosome I cosmid c8E11 AL021817 15350 1 116.316 290 6.18339e-26 5 249 1176 1910 0 -1 85 128 8 249 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGS-LDVMINNAGVENPVPSHELSLEN-WNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIP-WPL-FVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LKGKTTLITGGSGGIGFSIAKAFAAAGSNVGLLYGRNKKALEYAAELRDKHGVQAKAYSCPIENRSAVIETTNQAVEELGGRLDVMIANAGIAIPHLSLEDKNEDIWTKVVGINLNGAYYTAQAAGHHFKKQG-KGSLIFTASMSGHIANWPQQWASYHATKAAVKHLARALAVEWAPFA-RVNSVSPGYIDTDLTL--YADENLRKKWKEYTPQARIGLPDELPGAYLYLASDASSYCTGSDIIVDGG LK K ++TGGS G+G ++A F S V + Y N++ + ++ G QA + V+ AV+E G LDVMI NAG+ P S E E+ W +V+ NL GA+ ++ A +F + KG++I +S+ I WP + Y A+K +K + LA+E+AP RVN++ PG IDT + +AD R + P IG P+E+ +LAS +SY TG + DGG 44 gi|68000215|ref|NM_001019585.1| Schizosaccharomyces pombe 972h- hypothetical protein (SPAC8E11.10), partial mRNA NM_001019585 768 1 116.316 290 6.18339e-26 5 249 19 753 0 1 85 128 8 249 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGS-LDVMINNAGVENPVPSHELSLEN-WNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIP-WPL-FVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LKGKTTLITGGSGGIGFSIAKAFAAAGSNVGLLYGRNKKALEYAAELRDKHGVQAKAYSCPIENRSAVIETTNQAVEELGGRLDVMIANAGIAIPHLSLEDKNEDIWTKVVGINLNGAYYTAQAAGHHFKKQG-KGSLIFTASMSGHIANWPQQWASYHATKAAVKHLARALAVEWAPFA-RVNSVSPGYIDTDLTL--YADENLRKKWKEYTPQARIGLPDELPGAYLYLASDASSYCTGSDIIVDGG LK K ++TGGS G+G ++A F S V + Y N++ + ++ G QA + V+ AV+E G LDVMI NAG+ P S E E+ W +V+ NL GA+ ++ A +F + KG++I +S+ I WP + Y A+K +K + LA+E+AP RVN++ PG IDT + +AD R + P IG P+E+ +LAS +SY TG + DGG 45 gi|39971098|ref|XM_366940.1| Magnaporthe grisea 70-15 chromosome VII XM_366940 819 1 115.931 289 8.07576e-26 5 251 13 810 0 1 83 131 19 266 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVN-------YRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSL------ENWNQVIDTNLTGAFLGSREAIKYFVENDI------KGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMT LANKVAIITGASSGIGRATALLMAREGAAVVCSDIRQGPPTDSNSSSSISTHEEIQRLGGRATFVSCDTSDSAQVQALVKSAVAEFGRLDIMFNNAGVGKEGDNYPDTMIWQYDEDDFDLTMAVNVKGVFLGCKYAAAQMKDQEPLVPGGDRGWIVNTGSILGVNAIKGVTAYAASKHAVLGITKAAALDCAPFNIHVNAVNPGFVKTVMTKNMLEDSVGSEALAARHPFKGIGNVEDIAKTVLFLVSDDASWITGTSLCVDGGYT L +KV ++TG S G+GRA A+ +E + VV + SN ++ +EI+ GG+A V D + V LV++AV EFG LD+M NNAGV ++ ++ ++++ + N+ G FLG + A + + +G ++N S+ + YAASK + +T+ AL+ AP I VN + PG + T + D + + P IG E+IA FL S AS++TG +L DGG T 46 gi|39946385|ref|XM_362730.1| Magnaporthe grisea 70-15 chromosome I XM_362730 816 1 115.931 289 8.07576e-26 5 250 19 798 0 1 75 126 14 260 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRS---------NXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGS--LDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIK--GNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQAS-YVTGITLFADGGM LAGKTAIITGGTTGIGRSIALEFLRQGCSVAVNHLGLESDRAHLESLVAEAEAISSSSATAGRLTHLPGDVREPATGTALVSHALTALSSSRLDICVSNAGICTFAEFLDLDAALYDKTARTNLDGCFYVVQAAARQMARGQTPPGGSIIGVSSISALVGGGLQTHYTPTKAGVLSLMQSTAVALGRYGIRCNSLLPGTVRTQLNEEDLRDDKKREYMEGRIPLGRTGEPKDLAGPAVFLACEELSGYVTGAQLLVDGGL L K ++TGG+ G+GR++A+ F ++ V VN+ + E G+ + GDV + LV A+ S LD+ ++NAG+ +L +++ TNL G F + A + G++I +SS+ ++ L HY +K G+ + ++ A+ GIR N++ PG + T +N E D ++R +E IP+G G+P+++A A FLA + S YVTG L DGG+ 47 gi|68480909|ref|XM_710515.1| Candida albicans SC5314 hypothetical protein (CaO19_10414), mRNA XM_710515 846 1 115.546 288 1.05473e-25 5 251 97 837 0 1 79 127 6 250 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVE-NPVPSHELS-LENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWP-LFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMT LKGKVASVTGSSGGIGWAVAEAFAQAGADVAIWYNSKPADAKAEYLTEKY-GVKAKAYKCNVTDPNDVSKVINEIEKDFGTIDIFVANAGVAWTDGPEIDVQGYDQWKKIVDCDLNGVYYCAHTVGQIFKKNKSGSLIITSSMSGTIVNIPQLQAPYNAAKAACTHLAKSLSVEWASFGARVNSISPGYILTDI--ADFADPEMKKKWWQLTPLGREGLPQELVGAYLYLASNASTYTTGSNIAVDGGYT LK KV VTG S G+G A+A F Q + V + Y S +A + G +A + +VT DV ++ K+FG++D+ + NAGV P ++ + W +++D +L G + + + F +N +I S ++ P L Y A+K + ++L++E+A G RVN+I PG I T I FADPE + + P+G G P+E+ +LAS+ ++Y TG + DGG T 48 gi|68481020|ref|XM_710459.1| Candida albicans SC5314 hypothetical protein (CaO19_2896), mRNA XM_710459 846 1 115.546 288 1.05473e-25 5 251 97 837 0 1 79 127 6 250 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVE-NPVPSHELS-LENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWP-LFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMT LKGKVASVTGSSGGIGWAVAEAFAQAGADVAIWYNSKPADAKAEYLTEKY-GVKAKAYKCNVTDPNDVSKVINEIEKDFGTIDIFVANAGVAWTDGPEIDVQGYDQWKKIVDCDLNGVYYCAHTVGQIFKKNKSGSLIITSSMSGTIVNIPQLQAPYNAAKAACTHLAKSLSVEWASFGARVNSISPGYILTDI--ADFADPEMKKKWWQLTPLGREGLPQELVGAYLYLASNASTYTTGSNIAVDGGYT LK KV VTG S G+G A+A F Q + V + Y S +A + G +A + +VT DV ++ K+FG++D+ + NAGV P ++ + W +++D +L G + + + F +N +I S ++ P L Y A+K + ++L++E+A G RVN+I PG I T I FADPE + + P+G G P+E+ +LAS+ ++Y TG + DGG T 49 gi|2183241|gb|AF002134.1|AF002134 Candida albicans Sou2p (SOU2), Sou1p (SOU1) and Vma8p (VMA8) genes, complete cds AF002134 4293 1 115.546 288 1.05473e-25 5 251 2159 2899 0 2 79 127 6 250 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVE-NPVPSHELS-LENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWP-LFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMT LKGKVASVTGSSGGIGWAVAEAFAQAGADVAIWYNSKPADAKAEYLTEKY-GVKAKAYKCNVTDPNDVSKVINEIEKDFGTIDIFVANAGVAWTDGPEIDVQGYDQWKKIVDCDLNGVYYCAHTVGQIFKKNKSGSLIITSSMSGTIVNIPQLQAPYNAAKAACTHLAKSLSVEWASFGARVNSISPGYILTDI--ADFADPEMKKKWWQLTPLGREGLPQELVGAYLYLASNASTYTTGSNIAVDGGYT LK KV VTG S G+G A+A F Q + V + Y S +A + G +A + +VT DV ++ K+FG++D+ + NAGV P ++ + W +++D +L G + + + F +N +I S ++ P L Y A+K + ++L++E+A G RVN+I PG I T I FADPE + + P+G G P+E+ +LAS+ ++Y TG + DGG T 2 110.153 274 4.43132e-24 5 251 452 1189 0 2 80 132 11 252 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVE-NPVPSHELS-LENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVI---NMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMT LKGKVASVTGSSGGIGWAVAEGYAQAGADVAIWYNSHPADDKAEYLTKTY-GVKSKAYKCNVTDFQDVEKVVKQIELDFGTIDIFVANAGVAWTEGPKFDVKGVDKWNKVVDVDLNSVYYCAHVVGPIFRKKG-KGSFIFTASMSASIVNVP-QLQAAYNARKAGVKHLSKSFTVEWAPFA-RVNSVSPGYIATHLS--EFADPDVKSKWLQLTPLGREAKPRELVGAYLYLASDAASYTTGADLAVDGGYT LK KV VTG S G+G A+A + Q + V + Y S+ + G ++ + +VT +DV +V+ +FG++D+ + NAGV P ++ ++ WN+V+D +L + + F + KG+ I +MS+ +P L Y A K G+K ++++ +E+AP RVN++ PG I T ++ +FADP+ ++ + P+G KP E+ +LAS ASY TG L DGG T 50 gi|37813448|gb|AY340666.1| Cochliobolus lunatus StcQ-like protein and 17beta-hydroxysteroid dehydrogenase (17HSDcl) genes, complete cds; and ABC transporter-like protein gene, partial cds AY340666 5200 1 114.005 284 3.06878e-25 5 249 1778 2536 0 2 75 128 12 255 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPI----------NAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LDGKVALVTGSGRGIGAAVAVHLGRLGAKVVVNYANSTKDAEKVVSEIKALGSDAIAIKADIRQVPEIVKLFDQAVAHFGHLDIAVSNSGVVSFGHLKDVTEEEFDRVFSLNTRGQFFVAREAYRHLTEGG--RIVLTSSNTSKDFSVPKHSLYSGSKGAVDSFVRIFSKDCGDKKITVNAVAPGGTVTDMFHEVSHHYIPNGTSYTAEQRQQMAAHASPLHRNGWPQDVANVVGFLVSKEGEWVNGKVLTLDGG L KV +VTG +G+G A+AV G+ +KVVVNY ++ ++A +V EI+ G AI ++ D+ + ++V L + AV FG LD+ ++N+GV + +++ E +++V N G F +REA ++ E V+ S+ + P Y+ SKG + + + K I VN + PG T + N + +++ P+ G P+++A+V FL S + +V G L DGG 51 gi|39971800|ref|XM_367291.1| Magnaporthe grisea 70-15 chromosome I XM_367291 825 1 114.005 284 3.06878e-25 5 249 55 816 0 1 77 136 15 257 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHE-MIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPI---NAEKFAD------PEQRAD--VESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LAGKVALVTGAGRGIGRGIAIELGRRGASVVVNYGSSSKAAEEVVAELKKLGAQGVAIQADISKPSEVVALFDKAVSHFGGLDFVMSNSGMEVWCDELEVTQELFDKVFNLNTRGQFFVAQQGLKHCRRG---GRIILTSSIAAVMTGIPNHALYAGSKAAVEGFCRAFAVDCGAKGVTVNCIAPGGVKTDMFDENSWHYAPGGYKGMPQEKIDEGLANMNPLKRIGYPADIGRAVSALCQEESEWINGQVIKLTGG L KV +VTG +G+GR +A+ G+ + VVVNY S+ + A EV E+++ G Q + ++ D++K +VV L + AV FG LD +++N+G+E E++ E +++V + N G F +++ +K+ G +I SS+ M P YA SK ++ A++ KG+ VN I PG + T + N+ +A P+++ D + +M P+ IG P +I + L ++ ++ G + GG 52 gi|39970290|ref|XM_366536.1| Magnaporthe grisea 70-15 chromosome VII XM_366536 843 1 114.005 284 3.06878e-25 5 252 13 771 0 1 82 132 7 254 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVV-NYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSL-EN-WNQVIDTNLTGAFLGSREAIKYFVEND-IKGNVINMSSVHEMIPWPL-FVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPE-QRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMTK LAGKNAVITGAAGGIGLETSILFAKEGAHVLMADISLDALAKALDKVKSLVPGAQVETVKCDVSKEAEVKAMIEH-VDAWGGLDIIFNNAGIMHADDADAVDTPENIWNLTQDINVKGVWYGSKHAVLALRRHKKTKGSIINTASVVALVGSATPQLAYTASKGAVLAMTRELAIVHAREGFRFNNLCPAPLNTPLLQDWLGDDQAKRHRREVHFPTGRFGEAVEQAQAVLFLASDESSFVNGHDFVVDGGMTK L K V+TG + G+G ++ F +E + V++ + + K + G Q V+ DV+KE +V ++E V +G LD++ NNAG+ + + + EN WN D N+ G + GS+ A+ + KG++IN +SV ++ + Y ASKG + MT LA+ +A +G R NN+ P ++TP+ + D + +R E P G G+ E A FLAS ++S+V G DGGMTK 53 gi|13570026|gb|AF290182.2|AF290182 Pyricularia grisea tetrahydroxynaphthalene reductase mRNA, complete cds AF290182 825 1 114.005 284 3.06878e-25 5 249 55 816 0 1 77 136 15 257 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHE-MIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPI---NAEKFAD------PEQRAD--VESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LAGKVALVTGAGRGIGRGIAIELGRRGASVVVNYGSSSKAAEEVVAELKKLGAQGVAIQADISKPSEVVALFDKAVSHFGGLDFVMSNSGMEVWCDELEVTQELFDKVFNLNTRGQFFVAQQGLKHCRRG---GRIILTSSIAAVMTGIPNHALYAGSKAAVEGFCRAFAVDCGAKGVTVNCIAPGGVKTDMFDENSWHYAPGGYKGMPQEKIDEGLANMNPLKRIGYPADIGRAVSALCQEESEWINGQVIKLTGG L KV +VTG +G+GR +A+ G+ + VVVNY S+ + A EV E+++ G Q + ++ D++K +VV L + AV FG LD +++N+G+E E++ E +++V + N G F +++ +K+ G +I SS+ M P YA SK ++ A++ KG+ VN I PG + T + N+ +A P+++ D + +M P+ IG P +I + L ++ ++ G + GG 54 gi|4210941|gb|AF069518.1|AF069518 Cochliobolus lunatus 17beta-hydroxysteroid dehydrogenase mRNA, complete cds AF069518 1044 1 114.005 284 3.06878e-25 5 249 103 861 0 1 75 128 12 255 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPI----------NAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LDGKVALVTGSGRGIGAAVAVHLGRLGAKVVVNYANSTKDAEKVVSEIKALGSDAIAIKADIRQVPEIVKLFDQAVAHFGHLDIAVSNSGVVSFGHLKDVTEEEFDRVFSLNTRGQFFVAREAYRHLTEGG--RIVLTSSNTSKDFSVPKHSLYSGSKGAVDSFVRIFSKDCGDKKITVNAVAPGGTVTDMFHEVSHHYIPNGTSYTAEQRQQMAAHASPLHRNGWPQDVANVVGFLVSKEGEWVNGKVLTLDGG L KV +VTG +G+G A+AV G+ +KVVVNY ++ ++A +V EI+ G AI ++ D+ + ++V L + AV FG LD+ ++N+GV + +++ E +++V N G F +REA ++ E V+ S+ + P Y+ SKG + + + K I VN + PG T + N + +++ P+ G P+++A+V FL S + +V G L DGG 55 gi|46139490|ref|XM_391436.1| Gibberella zeae PH-1 strain PH-1; NRRL 31084 chromosome linkage group 14 XM_391436 813 1 113.62 283 4.00796e-25 11 252 22 807 0 1 81 138 24 264 VVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXX------GGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGV--ENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDI-----------KGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPI---NAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMTK LITGGASGIGRACARAFARDGSAGIALIDLNLEALQAVKSEIEQEKLSPNNNFRIELYPADVTDETRINEIVNDMVQKFGRIDYVVNAAGIAIKHQGGAAFAQTADWNRVLNINLNGTFFVLRAAARVMLKQDPIKSSINGRDLQRGSIINFSSIQGVVGIPLSTSYTAAKHAIIGLTRSASEDYAKDGLRINAICPGYTETPMTTKNPDVLKAMQER--ISTAVPMHRMGQPEEIADGVLYLAGGRSSFVTGSALAVDGGYTQ ++TGG+ G+GRA A F ++ S + N E VK EIE+ + + DVT E + +V V++FG +D ++N AG+ ++ + +WN+V++ NL G F R A + ++ D +G++IN SS+ ++ PL Y A+K + +T + + +YA G+R+N I PG +TP+ N + ++R + + +PM +G+PEEIA +LA ++S+VTG L DGG T+ 56 gi|58258290|ref|XM_566558.1| Filobasidiella neoformans LSDR, putative (CNA01160) mRNA, complete cds XM_566558 1161 1 113.62 283 4.00796e-25 5 249 82 867 0 1 77 124 21 264 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFG-SLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIK------------------GNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LTGKTALITGATRGIGARMALALAKAGADIILVQRNTSNTATRDDIIAA--GGKADIVVCDLGDAASVAKLIPHVTKELGRTLDIVVNCGGIQRRHPVENFPENDWNDVLQVNLNTVFTITRDAGRHMLESRGGVAGEPVPEGGAAGNPRGFGKIINISSLVAYQGGLNVVAYAAAKHGVQGIVKSFSNGWASKGVCVNAIAPGYIATDMNEALIADKDRARQILERIPAGRWGSPEDFEGAIVFLASRASDYVTGECLVVDGG L K ++TG ++G+G MA+ + + +++ R+ A GG+A IV D+ V L+ KE G +LD+++N G++ P +WN V+ NL F +R+A ++ +E+ G +IN+SS+ V YAA+K G++ + ++ + +A KG+ VN I PG I T +N AD ++ + IP G G PE+ FLAS + YVTG L DGG 57 gi|70989290|ref|XM_744402.1| oxidoreductase short chain dehydrogenase/reductase family (Afu2g03620) mRNA, complete cds XM_744402 1290 1 113.235 282 5.23455e-25 5 244 469 1182 0 1 82 129 6 242 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKV-VVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSH-ELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITL LKDKKVLITGGDSGIGRAVAILMAREGADITIVHLPEEIDDAEETKRAIEHEKRSCLLVAGDLRAHNMCRRAVEEHMNKFQRLNVLINNASKQYMNKNFADIDLNKVEDIFRTNIIQMMALTKYALPFLSKGD---SIINTTSVVTFRGSSSMVDYAATKGAVVGFTRSLASQLLPKGIRVNAVAPGAIYTPIQVDT-RDAEQMANWGSRTPLGRPGEPSEVATTFVFLASADASLYCKCTI LKDK V++TGG G+GRA+A+ +E + + +V+ ++A E K+ IE ++V GD+ VE + +F L+V+INNA + + ++ L + TN+ ++ A+ + + D ++IN +SV V YAA+KG + T +LA + PKGIRVN + PGAI TPI + D EQ A+ S P+G G+P E+A+ FLAS+ AS T+ 58 gi|71023772|ref|XM_757023.1| Ustilago maydis 521 hypothetical protein (UM05969.1), mRNA XM_757023 960 1 112.849 281 6.83654e-25 5 251 16 900 0 1 86 140 50 296 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVV---VNYRS--NXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLEN--WNQVIDTNLTGAFLGSREAIKYFVEN--------DIKGNVINMSSVHEM--IPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAF--------------------------------LASSQASYVTGITLFADGGMT LPHRVAVITGGGSGIGRECAILFASEGANLILADINLEACQQTADIVNERFSNAELPVKAIAVKCDVSKEDEVAAIVKRAVDEFGRLDVMFNNAGIMHPADDNALNTDEKIWDLTQAINVKGVWYGCKHAILAMRNNATDEAKKLHVGGSIINTASFVALRGAATPQ-IAYTASKGAVLAMTRELAMVHAREGIRVNSLCPGPLQTPLLMDFLNTPEKLNRRLTHLPLGRFGEAVEQAKAVLFRKLIPPHSHLVYVDNATDKLDSLRTLLRIRCTVATDESSYVLGHDLLVDGGLS L +V V+TGG G+GR A+ F E + ++ +N + + + + E +AI V+ DV+KE++V +V+ AV EFG LDVM NNAG+ +P + L+ + W+ N+ G + G + AI N + G++IN +S + P + Y ASKG + MT LA+ +A +GIRVN++ PG + TP+ + PE+ + +P+G G+ E A F +A+ ++SYV G L DGG++ 59 gi|46130677|ref|XM_389119.1| Gibberella zeae PH-1 strain PH-1; NRRL 31084 chromosome 2 XM_389119 864 1 112.849 281 6.83654e-25 2 238 13 735 0 1 70 123 8 243 YTDLKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDI------KGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASY FFSLQGQTALVTGGTRGIGQAVAIGLAEAGSDIILVQRDTTSQSTKESIEKL--GRKAFIYTADLSSQESVAALVPKVLADGHEIRILINCAGIQRRHPCEVFPDSDFNEVIQVNLNSVFTLCRDVGAHMLNLEPSPVTGRRGSIINFGSLLTFQGGFTVPAYAASKGAVGQMTKSFANEWTAKGITVNAIAPGYIETDMNEALLNNPERLASITSRIPAGNWGSPDDFKGTSVYLASKASGY + L+ + +VTGG++G+G+A+A+ + S +++ R ++ + E G +A I D++ +E V LV + + + ++IN AG++ P ++N+VI NL F R+ + + + +G++IN S+ YAASKG + MT++ A E+ KGI VN I PG I+T +N +PE+ A + S IP G G P++ + +LAS + Y 60 gi|68480911|ref|XM_710516.1| Candida albicans SC5314 hypothetical protein (CaO19_10415), mRNA XM_710516 843 1 112.464 280 8.9288e-25 5 251 97 834 0 1 82 135 13 253 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGV---ENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVI---NMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMT LKGKVASVTGSSGGIGWAVAEGYAQAGADVAIWYNSHPADDKAEYLTKTY-GVKSKAYKCNVTDFQDVEKVVKQIELDFGTIDIFVANAGVAWTEGPEIDVK-GVDKWNKVVDVDLNSVYYCAHVVGPIFRKKG-KGSFIFTASMSASIVNVP-QLQAAYNAAKAGVKHLSKSLSVEWAPFA-RVNSVSPGYIATHLS--EFADPDVKSKWLQLTPLGREAKPRELVGAYLYLASDAASYTTGADLAVDGGYT LK KV VTG S G+G A+A + Q + V + Y S+ + G ++ + +VT +DV +V+ +FG++D+ + NAGV E P + ++ WN+V+D +L + + F + KG+ I +MS+ +P L Y A+K G+K ++++L++E+AP RVN++ PG I T ++ +FADP+ ++ + P+G KP E+ +LAS ASY TG L DGG T 61 gi|68481022|ref|XM_710460.1| Candida albicans SC5314 hypothetical protein (CaO19_2897), mRNA XM_710460 843 1 112.464 280 8.9288e-25 5 251 97 834 0 1 82 135 13 253 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGV---ENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVI---NMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMT LKGKVASVTGSSGGIGWAVAEGYAQAGADVAIWYNSHPADDKAEYLTKTY-GVKSKAYKCNVTDFQDVEKVVKQIELDFGTIDIFVANAGVAWTEGPEIDVK-GVDKWNKVVDVDLNSVYYCAHVVGPIFRKKG-KGSFIFTASMSASIVNVP-QLQAAYNAAKAGVKHLSKSLSVEWAPFA-RVNSVSPGYIATHLS--EFADPDVKSKWLQLTPLGREAKPRELVGAYLYLASDAASYTTGADLAVDGGYT LK KV VTG S G+G A+A + Q + V + Y S+ + G ++ + +VT +DV +V+ +FG++D+ + NAGV E P + ++ WN+V+D +L + + F + KG+ I +MS+ +P L Y A+K G+K ++++L++E+AP RVN++ PG I T ++ +FADP+ ++ + P+G KP E+ +LAS ASY TG L DGG T 62 gi|46136732|ref|XM_390058.1| Gibberella zeae PH-1 strain PH-1; NRRL 31084 chromosome 1 XM_390058 819 1 112.079 279 1.16614e-24 5 250 22 801 0 1 77 125 14 260 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRS---------NXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGS--LDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFV--ENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQAS-YVTGITLFADGGM LANKTAIITGGTTGIGRAICLEFLRQGANVVVNHLGLEKDQTHLDSLIVEADEIRKASPTAGHLDHQAGDVRDPATATELVKKAVEHSPKKRLDICVSNAGICTFADFLTLEPDLLHSTVRTNLDGAFYVTQAAARQMALHQEPKGGSIIGVSSISALVGGGQQTHYTPTKAGVLSLMQSTACALGEHGIRCNALLPGTIRTQLNDADLADDTKRAYMEGRIPLGRTGSPSDMAGPAVFLACPELSGYVTGAQLLVDGGL L +K ++TGG+ G+GRA+ + F ++ + VVVN+ + + ++ G GDV LV+ AV+ LD+ ++NAG+ L + + + TNL GAF ++ A + + G++I +SS+ ++ HY +K G+ + ++ A GIR N + PG I T +N AD +RA +E IP+G G P ++A A FLA + S YVTG L DGG+ 63 gi|46115191|ref|XM_383614.1| Gibberella zeae PH-1 strain PH-1; NRRL 31084 chromosome 2 XM_383614 786 1 112.079 279 1.16614e-24 2 253 19 783 0 1 79 137 13 260 YTDLKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXG----GQAIIVRGDVTKEEDVVNLVETAVKEFGS-LDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFAD-PEQRADVE-SMIPMG-YIGKPEEIASVAAFLASSQASYVTGITLFADGGMTKY FQTLKGKVAIITGASRGLGAGFAFELARRGAKIVATYTSPSSEKLVSELSEKIASLDPSSQCIGVKADLKEESAPAEIVHQAVAIFGTQIDILINNAGMEIVKPHTDLTISDFDSIFYLNVRAPLL-LLQAVKPFLPSSGGGRIINISSVGARCGFKNLSLYCASKAALEGLTRSWAAELGVEGHTVNAVNPG----PVQSDLLDNIPKEIVDMQKKQTPAGNRLGEVDDIAQIVAWLASEESRWITGQALSASGGLEMY + LK KV ++TG S+GLG A + +K+V Y S E L + + A Q I V+ D+ +E +V AV FG+ +D++INNAG+E P +L++ +++ + N+ L +A+K F+ + G +IN+SSV + Y ASK ++ +T + A E +G VN + PG P+ ++ + P++ D++ P G +G+ ++IA + A+LAS ++ ++TG L A GG+ Y 64 gi|57639515|gb|AY846877.1| Magnaporthe grisea 1,3,6,8-tetrahydroxynaphthalene reductase gene, complete cds AY846877 915 1 111.694 278 1.52302e-24 5 241 55 792 0 1 75 133 15 249 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHE-MIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPI---NAEKFAD------PEQRAD--VESMIPMGYIGKPEEIASVAAFLASSQASYVTG LAGKVALVTGAGRGIGRGIAIELGRRGASVVVNYGSSSKAAEEVVAELKKLGAQGVAIQADISKPSEVVALFDKAVSHFGGLDFVMSNSGMEVWCDELEVTQELFDKVFNLNTRGQFFVAQQGLKHCRRG---GRIILTSSIAAVMTGIPNHALYAGSKAAVEGFCRAFAVDCGAKGVTVNCIAPGGVKTDMFDENSWHYAPGGYKGMPQEKIDEGLANMNPLKRIGYPADIGRAVSALCQEESEWING L KV +VTG +G+GR +A+ G+ + VVVNY S+ + A EV E+++ G Q + ++ D++K +VV L + AV FG LD +++N+G+E E++ E +++V + N G F +++ +K+ G +I SS+ M P YA SK ++ A++ KG+ VN I PG + T + N+ +A P+++ D + +M P+ IG P +I + L ++ ++ G 65 gi|67904029|ref|XM_677179.1| Aspergillus nidulans FGSC A4 hypothetical protein (AN9002.2), mRNA XM_677179 891 1 110.923 276 2.59788e-24 5 241 154 858 0 1 76 131 6 239 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRS-NXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPS-HELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTG LQGKKALITGGDSGIGRSVAALYAKEGADITIVYLPVEEEDAQETKRLVEAEGRQCLLLSGDLRDRGFCKQAVDSHVQKYGHINILVNNASQQFSCPDLAQINLDTVTDVFQTNIIQMFAMTKFSLPHMSKGD---SIINNTSVTAFRGTGSMVDYASTKGAIVGFTRSAALQLIPKGIRVNAVAPGSTYTPIQVDT-RDAEQMQGWASSKPLGRPGQPSEVATSFVFLASSDASLFYG L+ K ++TGG G+GR++A + +E + + + Y EE+A E K+ +E G Q +++ GD+ V++ V+++G +++++NNA + P +++L+ V TN+ F ++ ++ + + D ++IN +SV V YA++KG + T + AL+ PKGIRVN + PG+ TPI + D EQ S P+G G+P E+A+ FLASS AS G 66 gi|67540559|ref|XM_658962.1| Aspergillus nidulans FGSC A4 hypothetical protein (AN6450.2), mRNA XM_658962 744 1 110.923 276 2.59788e-24 5 250 7 738 0 1 78 130 10 250 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFL--GSREAIKYFVENDIKGNVINMSSVHEMIP--WPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGM LAGKVALITGASKGIGRATAQRLASEGASLVINY--NTDAASAQALVDEIGQDRALAVQADASKLADIDRLVDAAVAKFGKIDILIPNAGILPMRDLEHTTEEDFDFTYNLMVKGPYFLAQAQKAAKHIPAG---GRIILVSTGVTVLSNIAPAYLLYASAKAAVEQMARVMAKDLARNGILVNCVAPGPTTTGLFLNGKSDQMLKM-VAGFSPFNRIGEPEEIANAVYFLCSKDSSWVSGQTLRVNGGM L KV ++TG SKG+GRA A R E + +V+NY N + A E +A+ V+ D +K D+ LV+ AV +FG +D++I NAG+ + E+++ + + G + +++A K+ G +I +S+ ++ P ++ YA++K ++ M +A + A GI VN + PG T + +D + V P IG+PEEIA+ FL S +S+V+G TL +GGM 67 gi|14333985|gb|AF285781.1|AF285781 Ophiostoma floccosum hydroxynaphthalene reductase gene, complete cds AF285781 1756 1 110.923 276 2.59788e-24 5 241 710 1447 0 2 69 128 15 249 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPW-PLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEK--------FADPEQRADVESMI---PMGYIGKPEEIASVAAFLASSQASYVTG LAGKVAIITGAGRGIGRGIATELGRRGANVIVNYGSSSAAAEEVVADLKALGTDAVAMQADISKPDEVVKLFDRAVAHFGGIDIVVSNSGMEVWSSELDVTQELFDKVFNLNCRGQFFVAQQGLKHCRRG---GSIILTSSVAASLSGIPNHALYAGSKAAVEGFTRAFSVDCGEKGVTVNAIAPGGVKTDMYDENSWHYVPGGYKGMSQDVIDEGILKACPLKRVGTPSDIGKAVALLVSEEGEWING L KV ++TG +G+GR +A G+ + V+VNY S+ A EV +++ G A+ ++ D++K ++VV L + AV FG +D++++N+G+E +++ E +++V + N G F +++ +K+ G++I SSV + P YA SK ++ T +++ KG+ VN I PG + T + E + Q E ++ P+ +G P +I A L S + ++ G 68 gi|50307534|ref|XM_453747.1| Kluyveromyces lactis NRRL Y-1140, KLLA0D15521g predicted mRNA XM_453747 771 1 110.538 275 3.39294e-24 8 249 25 756 0 1 75 128 8 247 KVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPS--HELSLENWNQVIDTNLTGAFLGSREAIKYFVEN---DIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG KIALVTGASTGVGEGIARALFVRGATVVITSR-HLSEVQETAGNIDPSGSRVIGKEVDVTVAKAVEDLIQEIREEFGALHYLVNNAGITGPHQTGIEDYDIDSWRQVIDTNINGTFYTLKYALPLMESSSSPDSEAAVVNLSAVNGLVGIPGISPYTATKHAVIGITQSVALEYAERNVRVNAVAPGYVSTP--KIQALPKETQQWMSSQHPMKRMATMTEVSNTVLFLLSPLTGFTTGSVYPIDGG K+ +VTG S G+G +A + VV+ R + E E I+ +G + I DVT + V +L++ +EFG+L ++NNAG+ P + + +++W QVIDTN+ G F + A+ + D + V+N+S+V+ ++ P Y A+K + +T+++ALEYA + +RVN + PG + TP + E + + S PM + E+++ FL S + TG DGG 69 gi|49642208|emb|CR382124.1| Kluyveromyces lactis strain NRRL Y-1140 chromosome D of strain NRRL Y-1140 of Kluyveromyces lactis CR382124 1715506 1 110.538 275 3.39294e-24 8 249 1311625 1312356 0 1 75 128 8 247 KVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPS--HELSLENWNQVIDTNLTGAFLGSREAIKYFVEN---DIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG KIALVTGASTGVGEGIARALFVRGATVVITSR-HLSEVQETAGNIDPSGSRVIGKEVDVTVAKAVEDLIQEIREEFGALHYLVNNAGITGPHQTGIEDYDIDSWRQVIDTNINGTFYTLKYALPLMESSSSPDSEAAVVNLSAVNGLVGIPGISPYTATKHAVIGITQSVALEYAERNVRVNAVAPGYVSTP--KIQALPKETQQWMSSQHPMKRMATMTEVSNTVLFLLSPLTGFTTGSVYPIDGG K+ +VTG S G+G +A + VV+ R + E E I+ +G + I DVT + V +L++ +EFG+L ++NNAG+ P + + +++W QVIDTN+ G F + A+ + D + V+N+S+V+ ++ P Y A+K + +T+++ALEYA + +RVN + PG + TP + E + + S PM + E+++ FL S + TG DGG 2 90.1225 222 4.74545e-18 65 249 1592706 1593254 0 -3 56 88 2 185 DVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG DVRNVDQLHEAVKVAIQKFGRLDYVIAGAAGNFLADFTHLSSNAFKSVVSIDLLGSFNTVKACFPELVKT--KGSVLFVSSTLHYYGVPFQSHVGAAKAGIDALSNALAVEMGPLGLRFNCVAPGAIANTEGLARLTKNDSSSDLSEMIPLQRLGTTVDIANTTVFLFSPAASYITGTIHVVDGG DV + + V+ A+++FG LD +I A LS + V+ +L G+F + V+ KG+V+ +SS P H A+K G+ ++ LA+E P G+R N + PGAI + + +D+ MIP+ +G +IA+ FL S ASY+TG DGG 3 82.4185 202 9.89486e-16 7 211 1696573 1697157 0 -2 62 100 12 206 DKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVE-NPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVES NKVVLITGASSGIGLDIAEKLQLDGYEVFGTSRKGAQPNTNYSFK---------MVELDVTKDGSVATAVAEVMKNAGKIDVLINNAGVGISWAAAEESSIEQSKFIFDTNLFGVMRMTQAVLPHMREQG-SGRIINIGSISGIVPVAFGAIYSASKHALEAYTEALDHEVRNQGIRVSVIDPHLIKTPM-FSKDLEPDRPLSIYS +KVV++TG S G+G +A + + +V R + + +V DVTK+ V V +K G +DV+INNAGV + + E S+E + DTNL G ++ + + E G +IN+ S+ ++P Y+ASK ++ TE L E +GIRV+ I P I TP+ K +P++ + S 70 gi|32405197|ref|XM_323211.1| Neurospora crassa strain OR74A XM_323211 1095 1 110.538 275 3.39294e-24 8 253 346 1092 0 1 74 139 5 250 KVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAI-IVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGV-ENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVH-EMIPWPLFVH-YAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMTKY KVIIITGGARGLGNYMARACAEAGAKAIVIFDANQDLGDESAAELHQKTGLPVSFFKVDVRDGSAINAAVQNVVDLYGAPDVLVNSAGIADSNIPAEKYDAAMFRRLIDINLNGSFLMSQAVGRAMMAAGKPGSIILVASMSGTIVNYPQEQSCYNASKAGVIQLGKSLAAEWAKYNIRVNCISPGYMDTALNKVPALDAQKKI-WKSLTPQERLGAVDDLNGLCVFLASDASSFMTGSNVIIDGGYTLY KV+++TGG++GLG MA + +K +V + +N++ E E+ + G + + DV + V+ V +G+ DV++N+AG+ ++ +P+ + + ++ID NL G+FL S+ + + G++I ++S+ ++ +P Y ASK G+ + ++LA E+A IRVN I PG +DT +N D +++ +S+ P +G +++ + FLAS +S++TG + DGG T Y 71 gi|71003148|ref|XM_751162.1| Ustilago maydis 521 hypothetical protein (UM00108.1), mRNA XM_751162 1122 1 110.153 274 4.43132e-24 5 251 325 1113 0 1 72 142 16 263 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVV----VNYRSNXXXXXXXXXXXXXXGGQA---IIVRG---DVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVH-EMIPWPLF-VHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADP----EQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMT MEGKVCVVTGAARGIGNLIARTFVESGANHVAIVDLDEGESQHAAKEVDEWFTNHGGVKPGELDIQGYGCDISDEVQVQDVINRIHQRFGKINVAVNSAGIVENFPATEYPTAKLKKLFDININGSYFVAREVAKRMMQDKVQGSIVMIASMSASVVNVPQAQAPYNASKAAVKHLAKSMAVEWAKAGIRVNSLSPGYMLTSLSRAVLENSPNGKELRTNWENMTPMGRLGNPEDLKGAVVYLSSDASAFTTGADLIVDGGYT ++ KV VVTG ++G+G +A F + + V ++ ++ A EV + GG + ++G D++ E V +++ + FG ++V +N+AG+ P+ E ++ D N+ G++ +RE K +++ ++G+++ ++S+ ++ P Y ASK +K + +++A+E+A GIRVN++ PG + T ++ + E R + E+M PMG +G PE++ +L+S +++ TG L DGG T 72 gi|32420054|ref|XM_330470.1| Neurospora crassa strain OR74A XM_330470 903 1 109.768 273 5.78748e-24 5 249 157 885 0 1 83 128 12 250 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAI-IVRGDVTKEEDVVNLVETAVKEF-GSLDVMINNAGVENPVPS-HELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPI--NAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LKGKKAIITGGDSGIGRASAILFAMEGADSVIAYLPEEEEDAQETKRRVEAYGQKCHLVSTDLRDRENCKKLVDEAVKIFNGQIDILFNNAAYQMVVDDIKDLSEDQWINTFNTNIHPYFYLAKYSLPYMKRGS---TIINNASINAYIGRPDLLDYTSTKGAIVAFTRGLSNQQAGKGIRVNAVAPGPVWTPLIPSTMKRENQEQFGST----PLGRPAQPSEVATAVVFLASEDSSAFSGQTLHPNMG LK K ++TGG G+GRA A+ F E + V+ Y EEE + K EA GQ +V D+ E+ LV+ AVK F G +D++ NNA + V +LS + W +TN+ F ++ ++ Y +IN +S++ I P + Y ++KG + T L+ + A KGIRVN + PG + TP+ + K + EQ P+G +P E+A+ FLAS +S +G TL + G 73 gi|32413422|ref|XM_327190.1| Neurospora crassa strain OR74A XM_327190 807 1 109.768 273 5.78748e-24 5 252 28 804 0 1 76 132 17 262 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHE-MIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKF------ADPEQRAD-VESMI----PMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMTK LEGKVALVTGAGRGIGRGVALELARRGASVIVNYVSSAGPANEVVKEIESLHNGARAIAIQADVRRVSEIDRLFAEAKRAFGRIDIVMSNSGTESWDKTEDVTEEKYDYVFDLNAKAQFFVGQAAYKHLERN---GRVILMTSIAAGLMGVRNHALYNASKMAVQGFVKAFATDFGDKGITVNGVAPGGIKSDMFAENAWHYIPGGTPDLGKDKIEKMMAEHCPLGRCAVPEDVARVVAFLASEDGGWVNGQIITISGGSSQ L+ KV +VTG +G+GR +A+ + + V+VNY S+ + + E G +AI ++ DV + ++ L A + FG +D++++N+G E+ + +++ E ++ V D N F + A K+ N G VI M+S+ ++ Y ASK ++ + A ++ KGI VN + PG I + + AE P+ D +E M+ P+G PE++A V AFLAS +V G + GG ++ 74 gi|67538933|ref|XM_658149.1| Aspergillus nidulans FGSC A4 hypothetical protein (AN5637.2), mRNA XM_658149 789 1 109.383 272 7.55868e-24 4 249 22 765 0 1 80 120 8 251 DLKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAF----LGSREAIKYFVENDIKGNVINMSSVHEM-IPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG DVKGKVVLVTGGAKGIGRMISEGYVTNGATVYISSRDAKACEQAVKELNALGKGKAHAIPADFYKEEDVKKLAEELAKRESKLHVLVNNSGSNWGAPYDEYPSSAWTRVLTLNLHRVFDLTKLVTPLLEKAAAPND-PARIINIGSIDGLRVPALETFAYSASKAGLHHMSRVLANHLGKRNITSNTLACGPFQSKMMAATLKN--FREQIESGIPLKRIGTPEDVAGACLFLSSRAGAYVNGSTIAVDGG D+K KVV+VTGG+KG+GR ++ + + V ++ R + VK+ G+A + D KEEDV L E K L V++NN+G P E W +V+ NL F L + K ND +IN+ S+ + +P Y+ASK G+ M+ LA + I N + G + + A + R +ES IP+ IG PE++A FL+S +YV G T+ DGG 75 gi|46111894|ref|XM_383005.1| Gibberella zeae PH-1 strain PH-1; NRRL 31084 chromosome 2 XM_383005 795 1 109.383 272 7.55868e-24 5 249 52 780 0 1 76 117 6 247 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVV-VNYRSNXXXXXXXXXXXXXXGGQAIIVR-GDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LAGKVAVITGGSSGIGREMAIALGRAGCRIVLIARRPKPLQDTIDHLADLHVTAEAIVADLGNPASVRDAIQAIKATV---GSPDILINAAAVNYRPHMNDLSQGAWDETIAVNLTAPFALGQAFGPKMAENGW-GRIINIISQQAFRCYGNSGAYGASKAGLLGLTRSQAEAWSRHGVLCNAIAPGVVDTPMTRVAFNDPAKAEAHAARTMVGRNGLPRDFAGIAVYLASDASATVTGQTIFVDGG L KV V+TGGS G+GR MA+ G+ ++V + R + +AI+ G+ D + ++ V GS D++IN A V ++LS W++ I NLT F + EN G +IN+ S + Y ASK G+ +T + A ++ G+ N I PG +DTP+ F DP + + +G G P + A +A +LAS ++ VTG T+F DGG 76 gi|39970894|ref|XM_366838.1| Magnaporthe grisea 70-15 chromosome VII XM_366838 783 1 108.997 271 9.87194e-24 2 249 13 768 0 1 67 120 8 254 YTDLKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDI------KGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG FFSLKDHTALITGGTRGIGAAVAIGLAEAGADVLLVQRDESSTTTRDAILAL--GRKSQIYVADLSSPESVAALTPKVLADGHQVRILVNCGGIQRRHKCEVFPDSDFNEVMQVNLGAVFTLTRDVGAHMLSLEPHPVTGRRGSVVNYASLLSFQGGLTVPAYAASKGAVAQLTKSFANEWTSRGVTVNAIAPGYIATDMNEALLKDEERLASISARIPAGRWGDPEDFKGTTVYLASKASGYVSGHVLVVDGG + LKD ++TGG++G+G A+A+ + + V++ R G ++ I D++ E V L + + + +++N G++ ++N+V+ NL F +R+ + + + +G+V+N +S+ YAASKG + +T++ A E+ +G+ VN I PG I T +N D E+ A + + IP G G PE+ +LAS + YV+G L DGG 77 gi|71023680|ref|XM_756977.1| Ustilago maydis 521 hypothetical protein (UM05923.1), mRNA XM_756977 837 1 108.612 270 1.28932e-23 4 249 61 822 0 1 69 123 10 255 DLKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEF--GSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG NLSGKTALLTGGTRGIGQACAVALVEAGASVILAVRPGTATSGAHPALAPLTAVANQSCSQKHSTVDADLSDLSQVKTLFDRALSQSPTSAIDILVNCGGIQRRHPSVDFPESDWDEVLNVNLKAVWLVSQAAGRHMVARR-SGKIINFGSLLTFQGGLTVPAYASAKGAVGQLTKALSNEWAKHNVQVNGIAPGYIATDMNEKLLADPTRLRQISERIPAGRWGDPADFKGPLLFLASQASQYVSGEMLVVDGG +L K ++TGG++G+G+A AV + + V++ R + + + V D++ V L + A+ + ++D+++N G++ PS + +W++V++ NL +L S+ A ++ V G +IN S+ YA++KG + +T+ L+ E+A ++VN I PG I T +N + ADP + + IP G G P + FLAS + YV+G L DGG 78 gi|49651994|emb|CR382133.1| Debaryomyces hansenii chromosome A of strain CBS767 of Debaryomyces hansenii CR382133 1249565 1 108.612 270 1.28932e-23 5 253 393280 394041 0 -3 81 129 9 256 LKDKVVVVTGGSKGLGRAMAVRFGQEQ-SKVVVNYRSNXXXXXXXXXXXXXXGGQAII-VRGD--VTKEEDVVNLVET-AVKEF--GSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMTKY LEGQVALITGGTNGIGLGMAKGLADANIDQIILTYRSEKPLENTIKVLQEVNPKVKISSIEADFGTGNEDDLVAKIATEAFKKSVSGKIDILINNAGINNRFPFDEFPQDKFDEVLRVNLNIPVKLTKAIGCKMLETKTKGKIVFTASLCSFQGGVDSTAYAITKGGIKQFTAALSNDWSLKGIRVNSIAPGYIST--NLTEQIDPKRRETLISRIPIGRWGNMDDFQGPAVFLCSEASRYVTGETLVVDGGWLGY L+ +V ++TGG+ G+G MA ++++ YRS + +K E I + D E+D+V + T A K+ G +D++INNAG+ N P E + +++V+ NL ++ +E KG ++ +S+ YA +KGG+K T L+ +++ KGIRVN+I PG I T N + DP++R + S IP+G G ++ A FL S + YVTG TL DGG Y 2 108.612 270 1.28932e-23 5 251 1048363 1049103 0 1 79 125 10 252 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVE----NPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPL-FVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMT LKGKVAVVTGAARGIGLAIAETFAEAGAAVALVDYTDCSEQALKLATRLKVCTKAF--QCDVADLKRVEGTVQAIEKEFGTIDVFVANAGIVWKTGNIIDEVNRDGKTWQTIMDVNLNGAYYCAQAVGRIFKKNGKGSFIVTSSMSASIVNIPMNLTPYNVSKAGVKHLAKSLAIEWAGFA-RANSISPGYCDTGLNDH--LPRESRGKMWALIPAGREALPYEIASAYLYLASDAASYITGSDIAIDGGYT LK KV VVTG ++G+G A+A F + + V + ++ E + +A + DV + V V+ KEFG++DV + NAG+ N + + W ++D NL GA+ ++ + F +N ++ S ++ P+ Y SK G+K + ++LA+E+A R N+I PG DT +N E R + ++IP G P EIAS +LAS ASY+TG + DGG T 3 97.8265 242 2.27586e-20 5 251 1198503 1199237 0 -1 73 119 6 249 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVE-NPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLF-VHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMT LSGKVASITGSSAGIGLAVAESYAQAGANIAIWYNSTPADDIAERLSKTY-NITAKAYKCAVDNFEEVEKTVNQIVKDFGTIDIFVANAGVGWKSCPVSESSLDAYHNVMKVNLDGVYYAAKCIGPIFEKNGKGSFIITASQAGHIVTVPIAQAAYNASKAALIQLGKSLAIEWV-RFARVNTISPGYILTEI--AKHVPFDVKSKWWPLIPMGREGSPQELVGAFLYFASDASTFTTGADLIIDGGYT L KV +TG S G+G A+A + Q + + + Y S + + + A + V E+V V VK+FG++D+ + NAGV P E SL+ ++ V+ NL G + ++ F +N +I S ++ P+ Y ASK + + ++LA+E+ + RVN I PG I T I K + ++ +IPMG G P+E+ + AS +++ TG L DGG T 4 92.4337 228 9.56175e-19 5 249 1200138 1200869 0 3 73 130 17 253 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVV-NYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGV---ENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLF-VHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADP---EQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LKNKVSVITGAAGDIGGAIAEGFAQAGSDIVILDYKFNPGISERLSKTY---GIKSKSYQVDVSKCEEVKATIKQIEEDFGTIDVFIANAGIAWNRGSILNQDSTPEEWARVYEVDVHGVFYCAKYAGEIFKKNGKGSFIITASISAHIVNVPNYQTCYNSAKAAVLHMGKCLAVEFAGFA-RVNTVSPGYTNTSLS-----DPVPTHERAKWWGLTPLGREALPEELVGAYLYLASDASSFTTGTDIRVDGG LK+KV V+TG + +G A+A F Q S +V+ +Y+ N + + K G ++ + DV+K E+V ++ ++FG++DV I NAG+ + + + + E W +V + ++ G F ++ A + F +N +I S ++ P + Y ++K + M + LA+E+A RVN + PG +T ++ DP +RA + P+G PEE+ +LAS +S+ TG + DGG 5 90.1225 222 4.74545e-18 5 261 703358 704071 0 2 76 131 19 257 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMTKYPSFQAGRG LKGKVVLITGAGAGLGRDYALWFAKYGAKVVVN---DFKDPSKVVDEIIKSGGEAHGDKHDVASDSQAI--IDNVINKYGTIDVLVNNAGVLRDKSFAKMSDADWEIVQKVHLFGTFNLVRLAWPHFLEKK-SGRVINITSTSGIYGNFGQANYASAKAAIIGLSRTLAIEGAKNNIKVNAVAPHA-ETAMTLTIFNEDDKN-----------LFHPDQVAPLLVYLASDDVP-VTGELFEVGGGWIGNTRWQRAKG LK KVV++TG GLGR A+ F + +KVVVN + ++ +V EI ++GG+A + DV + + ++ + ++G++DV++NNAGV ++S +W V +L G F R A +F+E G VIN++S + +YA++K + ++ TLA+E A I+VN + P A +T + F + ++ + P+++A + +LAS VTG GG +Q +G 6 85.8853 211 8.94953e-17 6 188 702419 702979 0 2 66 101 12 191 KDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRS--------NXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGP KDKVVVVTGAGGGLGKQYCLEYAKRGAKVVVNDLGGSLKGDGGNSSAADDVVEEIKKAGGIAV---ADYNNVLDGAKIIETAVKSFGTVHIIVNNAGVLRDASFKKMQEKDFKFVIDVHLNGAYKVTQAAWPYFRKQQY-GRVLNTASPAGLYGNFGQANYSAAKLGLASFAETLAKEGEKYNIKANTIAP KDKVVVVTG GLG+ + + + +KVVVN N A +V +EI++AGG A+ D D ++ETAVK FG++ +++NNAGV ++ +++ VID +L GA+ ++ A YF + G V+N +S + +Y+A+K G+ ETLA E I+ N I P 7 80.1073 196 4.91077e-15 87 249 1027364 1027864 0 -2 56 85 6 168 DVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMI---PWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADV-ESMIPMGYIGKPEEIASVAAFLAS-SQASYVTGITLFADGG DLLINTAGYCENFPAEEYPSANAEGILKVNGLGAFYVSQAFARPLISSNKKGSIILVGSMSGTIVNDPQPQCM-YNMSKAGVIHLTRSLACEWAKFNIRVNTLSPGYILTPLTRNVISGHSDMKEAWESKVPMKRMAEPKEFVGSILYLASESASSYTTGHNLVVDGG D++IN AG P+ E N ++ N GAF S+ + + ++ KG++I + S+ I P P + Y SK G+ +T +LA E+A IRVN + PG I TP+ + + ES +PM + +P+E +LAS S +SY TG L DGG 79 gi|50405794|ref|XM_456538.1| Debaryomyces hansenii CBS767, DEHA0A05016g predicted mRNA XM_456538 783 1 108.612 270 1.28932e-23 5 253 19 780 0 1 81 129 9 256 LKDKVVVVTGGSKGLGRAMAVRFGQEQ-SKVVVNYRSNXXXXXXXXXXXXXXGGQAII-VRGD--VTKEEDVVNLVET-AVKEF--GSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMTKY LEGQVALITGGTNGIGLGMAKGLADANIDQIILTYRSEKPLENTIKVLQEVNPKVKISSIEADFGTGNEDDLVAKIATEAFKKSVSGKIDILINNAGINNRFPFDEFPQDKFDEVLRVNLNIPVKLTKAIGCKMLETKTKGKIVFTASLCSFQGGVDSTAYAITKGGIKQFTAALSNDWSLKGIRVNSIAPGYIST--NLTEQIDPKRRETLISRIPIGRWGNMDDFQGPAVFLCSEASRYVTGETLVVDGGWLGY L+ +V ++TGG+ G+G MA ++++ YRS + +K E I + D E+D+V + T A K+ G +D++INNAG+ N P E + +++V+ NL ++ +E KG ++ +S+ YA +KGG+K T L+ +++ KGIRVN+I PG I T N + DP++R + S IP+G G ++ A FL S + YVTG TL DGG Y 80 gi|50409388|ref|XM_456869.1| Debaryomyces hansenii CBS767, DEHA0A12837g predicted mRNA XM_456869 870 1 108.612 270 1.28932e-23 5 251 121 861 0 1 79 125 10 252 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVE----NPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPL-FVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMT LKGKVAVVTGAARGIGLAIAETFAEAGAAVALVDYTDCSEQALKLATRLKVCTKAF--QCDVADLKRVEGTVQAIEKEFGTIDVFVANAGIVWKTGNIIDEVNRDGKTWQTIMDVNLNGAYYCAQAVGRIFKKNGKGSFIVTSSMSASIVNIPMNLTPYNVSKAGVKHLAKSLAIEWAGFA-RANSISPGYCDTGLNDH--LPRESRGKMWALIPAGREALPYEIASAYLYLASDAASYITGSDIAIDGGYT LK KV VVTG ++G+G A+A F + + V + ++ E + +A + DV + V V+ KEFG++DV + NAG+ N + + W ++D NL GA+ ++ + F +N ++ S ++ P+ Y SK G+K + ++LA+E+A R N+I PG DT +N E R + ++IP G P EIAS +LAS ASY+TG + DGG T 81 gi|3869275|gb|AF053764.1|AF053764 Agaricus bisporus NADP-dependent mannitol dehydrogenase (MtDH) mRNA, complete cds AF053764 870 1 108.612 270 1.28932e-23 7 249 64 807 0 1 77 123 9 250 DKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLF-------VHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG NKTIIVTGGNRGIGLAFTRAVAAAGANVAVIYRSAKDAVEVTEKVGKEFGVKTKAYQCDVSNTDIVTKTIQQIDADLGAISGLIANAGVSVVKPATELTHEDFKFVYDVNVFGVFNTCRAVAKLWLQKQQKGSIVVTSSMSSQIINQSSLNGSLTQVFYNSSKAACSNLVKGLAAEWASAGIRVNALSPGYVNTDQTAHM--DKKIRDHQASNIPLNRFAQPEEMTGQAILLLSDHATYMTGGEYFIDGG +K ++VTGG++G+G A + V V YRS ++ +K +E G + + DV+ + V ++ + G++ +I NAGV P+ EL+ E++ V D N+ G F R K +++ KG+++ SS+ I V Y +SK + + LA E+A GIRVN + PG ++T A D + R S IP+ +PEE+ A L S A+Y+TG F DGG 82 gi|46124280|ref|XM_386694.1| Gibberella zeae PH-1 strain PH-1; NRRL 31084 chromosome 4 XM_386694 807 1 108.227 269 1.6839e-23 4 251 7 786 0 1 75 133 18 263 DLKDKVVVVTGGSK------GLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEM--IPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPIN---AEKFADP----EQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMT NLKNKVALVIGLGQTNTEGWGIGAASAVTLAR-QGAIIFGGNRTIASTTKTKETIQQQGGQCDVVATNATDSASVKAVVDACMEKHGRIDILLTSVGQSQPGDPASMTEDVWDSQMDINLKSVYLACHHVLP-IMESQGSGSIICISSIAGLRYIGKPQ-IAYNTSKAAILQFVKATAVIYAPKGIRLNTVVPGLMDTPYTKSLAQRFATPGGYDEFCSMREGQVPMGRMGDAWDVANTVVFLAADETRYITGQKIVVDGGIT +LK+KV +V G + G+G A AV + Q ++ + K+ I++ GGQ +V + T V +V+ +++ G +D+++ + G P ++ + W+ +D NL +L + +E+ G++I +SS+ + I P + Y SK + + A+ YAPKGIR+N + PG +DTP A++FA P E + E +PMG +G ++A+ FLA+ + Y+TG + DGG+T 83 gi|44889964|emb|BX649607.1| Aspergillus fumigatus BAC pilot project supercontig; segment 3/3 BX649607 227448 1 95.5153 236 1.73273e-23 112 249 191293 191727 0 -1 56 79 7 145 VIDTNLTGAFLGSREAIKYFVENDI-------KGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG VIEVNLTSVFTLCREFGAYLLARDASDFPSGRRGSIINVASLLSFQGGITVPAYAASKGGIAQLTKALSNEWASKGINVNAIAPGYIDTDMNVALINDANRNAGIMARIPAGRWGKPDDFKGVIVFLASEASNYVSGEVVCVDGG VI+ NLT F RE Y + D +G++IN++S+ YAASKGG+ +T+ L+ E+A KGI VN I PG IDT +N D + A + + IP G GKP++ V FLAS ++YV+G + DGG 2 60.8474 146 3.08305e-09 147 250 196959 197255 0 3 41 58 7 105 HEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAI-DTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGM HE*LADAYQIDYAASKGGMTGMMKNLATRLAEYNISVNDVAPAMIGDTGMIPSAQAIPE----VAAGIPLGRLGTPEEVANVVSMLVTT--GYMTGQSLLLAGGL HE + + YAASKGGM M + LA A I VN++ P I DT + A PE V + IP+G +G PEE+A+V + L ++ Y+TG +L GG+ 3 40.0466 92 1.73273e-23 5 112 191790 192194 0 -2 28 61 27 135 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVV-VNYRS--------------------------NXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQV LSGKTAIVTGGTRGIGQAMAIALAEAGADIVLIQVRALDLTLLLARRGLHYMWQGVLIAIM*RDESNTQTRDEIVNRVGRKAWIHVAELSKREEVKSIIPAVTSQGLKPEILLNCAGIQRRHPSEKFPDEDWDEV L K +VTGG++G+G+AMA+ + + +V + R+ +E + + G +A I +++K E+V +++ + ++++N AG++ PS + E+W++V 84 gi|67900787|ref|XM_675558.1| Aspergillus nidulans FGSC A4 hypothetical protein (AN7381.2), mRNA XM_675558 1728 1 107.842 268 2.19924e-23 4 249 886 1638 0 1 79 132 11 254 DLKDKVVVVTG------GSKGLGRAMAVRFGQEQSKV-VVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPV-PSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG DFTDEVAIVTGAGSRLAGEIGNGRATAILLARQGAKVALVDY--NVDWAQETKRMIDLDGGQSIVIQADVTDEESCKKAVAQTIGAFGTVNILVNIVGVGGAMGDATRLDLAAWDRDFRINVTSMVLMSRYVIPEMRKNG-RGAIVNMSSVSGLLGGNPSLLYPTTKGAIIQMTRAMAAQHGPENIRVNCVCPGMVFTPMVRGRGMTDEMRQARINQNLLKQEGTGWDVGYAILFLCSKEAKWITGLIMPVDGG D D+V +VTG G G GRA A+ ++ +KV +V+Y N + A E K+ I+ GGQ+I+++ DVT EE V + FG++++++N GV + + L L W++ N+T L SR I +N +G ++NMSSV ++ + Y +KG + MT +A ++ P+ IRVN + PG + TP+ + E R + + G ++ FL S +A ++TG+ + DGG 85 gi|46140082|ref|XM_391732.1| Gibberella zeae PH-1 strain PH-1; NRRL 31084 chromosome linkage group 10 XM_391732 738 1 107.842 268 2.19924e-23 58 251 100 690 0 1 64 105 3 197 QAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSH-ELSLENWNQVIDTNLTGAFLGSREAIKYFVEND--IKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMT KAIPAQGNVTNEDDCEKSVNLAMKEFGRVDILVNNVGIAGALGTAVDVDMAKWTMGLEVNVSSMVLMAKYAIPAMAKNDGEIKGSIVNMGSVAGLKGGTPHLLYPTAKGAVVNMTRAMAAHHAKDGIRVNCVCPGMLYTPMMYAKGMSEESREARKARSLLGTEGTAWDAACAVVFLASNHARWITGAILPVDAGTT +AI +G+VT E+D V A+KEFG +D+++NN G+ + + ++ + W ++ N++ L ++ AI +ND IKG+++NM SV + + Y +KG + MT +A +A GIRVN + PG + TP+ K E R ++ +G G + A FLAS+ A ++TG L D G T 86 gi|67522858|ref|XM_654398.1| Aspergillus nidulans FGSC A4 hypothetical protein (AN1886.2), mRNA XM_654398 741 1 107.071 266 3.75133e-23 57 250 139 723 0 1 64 100 1 195 GQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQAS-YVTGITLFADGGM GEVLEIVGDVTDLKTSTALIDEAVKRWGKLDAFVANAGVFRQAELFELEPDLLNHSLDVNVKGTFYSCRSAARQMVKRGHGGSIIAISSVSALVGGRLQTPYTPTKAAVLSLMQSRAIALGKHKIRCNALLPGTIITQLADHDIKDPAKKAYLEARIPLGRVGEPEGMTGPAVFLASEEMSRFVNWSGLLEDGGM G+ + + GDVT + L++ AVK +G LD + NAGV EL + N +D N+ G F R A + V+ G++I +SSV ++ L Y +K + + ++ A+ IR N + PG I T + DP ++A +E+ IP+G +G+PE + A FLAS + S +V L DGGM 87 gi|70992820|ref|XM_746166.1| oxidoreductase short chain dehydrogenase/reductase family (Afu6g13830) mRNA, complete cds XM_746166 792 1 107.071 266 3.75133e-23 4 251 46 783 0 1 71 123 6 250 DLKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVH-EMIPWP-LFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMT DLTGKVAAITGGARGIGLEVSRALAEAGANVALIYNSSKTADTTAAEIASANNVRAAAYQANVSNKAEIERTIQQIASDFGGLDIIVVNSGITSNVAAEDYTAEQWKEVMQVNLDGAFYTAQAAAQIFKAQG-RGNVIFTASVSATLVNVPQKQAAYNASKAGVVQLAKCLSVEWV-DFCRVNCISPGFIETDI--LDIHPKEWRERWYSMVPAQRFADAYELKGAYVFCASDASSYMTGANIVIDGGYT DL KV +TGG++G+G ++ + + V + Y S++ + +A + +V+ + ++ ++ +FG LD+++ N+G+ + V + + + E W +V+ NL GAF ++ A + F +GNVI +SV ++ P Y ASK G+ + + L++E+ RVN I PG I+T I E R SM+P E+ F AS +SY+TG + DGG T 88 gi|67903147|ref|XM_676738.1| Aspergillus nidulans FGSC A4 hypothetical protein (AN8561.2), mRNA XM_676738 897 1 106.686 265 4.89939e-23 65 251 304 891 0 1 63 104 11 197 DVTKEEDVVNLVETAVKEFGSLDVMINNAGVENP-VPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDI------KGNVINMSSVHEMIPWPLFVH---YAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMT NVTKEEEISAAVQCAAHRFGRIDISIHGAGITGTGAHTHELDLKEWQRVIDVNQTGVMLCDKWMVKQMLSQELITGYRGRGIIVNISSIYGVVAPDGRLGAAAYAASKHAVIGLTKLDAKNYAKDGVRINAVCPGFVDTPLTHRNLEEGVLSPEIENTV-LKRPARPEEIADAVLFLTSRMGSYMCAAALVVDGGYT +VTKEE++ V+ A FG +D+ I+ AG+ +HEL L+ W +VID N TG L + +K + ++ +G ++N+SS++ ++ + YAASK + +T+ A YA G+R+N + PG +DTP+ + ++E+ + + +PEEIA FL S SY+ L DGG T 89 gi|67526442|ref|XM_656191.1| Aspergillus nidulans FGSC A4 hypothetical protein (AN3679.2), mRNA XM_656191 789 1 106.686 265 4.89939e-23 56 250 202 774 0 1 61 105 6 196 GGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPS-HELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGM GQKCYLLATDLRRKENCKKVVETALEKLGGIDILVNNAGTQTMLPDISDLDESQWESTFDTNIHPVFYLSKYTMPHLKSGS---SIINCASVNPYIGRPDLLDYTSTKGAMVAFTRGLSNQQCSKGIRVNAVCPGPVWTPLIPATMT--TEAIEQFSGTPMGRAGQPSEIATCFVFLASQDSSFISGQCLHPNGGV G + ++ D+ ++E+ +VETA+++ G +D+++NNAG + +P +L W DTN+ F S+ + + ++IN +SV+ I P + Y ++KG M T L+ + KGIRVN + PG + TP+ + + S PMG G+P EIA+ FLAS +S+++G L +GG+ 90 gi|12657576|dbj|AB036927.1| Candida magnoliae crs1 gene for carbonyl reductase S1, complete cds AB036927 852 1 106.686 265 4.89939e-23 5 251 91 843 0 1 76 129 12 255 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSH--ELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGN-----VINMSSVHEMIPWPLF-VHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMT LNGKVASITGSSSGIGYALAEAFAQVGADVAIWYNSHDATGKAEALAKKY-GVKVKAYKANVSSSDAVKQTIEQQIKDFGHLDIVVANAGIPWTKGAYIDQDDDKHFDQVVDVDLKGVGYVAKHAGRHFRERFEKEGKKGALVFTASMSGHIVNVPQFQATYNAAKAGVRHFAKSLAVEFAPFA-RVNSVSPGYINTEIS--DFVPQETQNKWWSLVPLGRGGETAELVGAYLFLASDAGSYATGTDIIVDGGYT L KV +TG S G+G A+A F Q + V + Y S++ + G + + +V+ + V +E +K+FG LD+++ NAG+ ++ + ++++QV+D +L G ++ A ++F E K V S ++ P F Y A+K G++ ++LA+E+AP RVN++ PG I+T I+ F E + S++P+G G+ E+ FLAS SY TG + DGG T 91 gi|46132997|ref|XM_389204.1| Gibberella zeae PH-1 strain PH-1; NRRL 31084 chromosome 4 XM_389204 897 1 106.301 264 6.39881e-23 5 246 154 879 0 1 80 131 6 245 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYR-SNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSH-ELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPIN-AEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFA LENAKAFITGGDSGIGRAVAVLFAREGADVTIVYLPEEQEDAEETKKMVEKEGRKCVLFPGNLMDNETCKNAVQKHVDEFGKIDVLVNNAAKQIMCEDFKDIDLENVESTFRSNILQIFAITKYALHH-MEKGGSCSIINSTSVVAFRGTAAMVDYASTKGAIVAFTRSLSKQLVKKGIRVNAVAPGPVHTPLQPASRPADQMEGFGKQSQ--LGRVGQPSEIATSFVFLASKDATLFHGQILHA L++ +TGG G+GRA+AV F +E + V + Y +E+A E KK +E+ G + ++ G++ E N V+ V EFG +DV++NNA + ++ LEN +N+ F ++ A+ + +E ++IN +SV V YA++KG + T +L+ + KGIRVN + PG + TP+ A + AD + +S +G +G+P EIA+ FLAS A+ G L A 92 gi|32419289|ref|XM_330107.1| Neurospora crassa strain OR74A XM_330107 819 1 106.301 264 6.39881e-23 4 251 4 801 0 1 79 127 22 268 DLKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVV----NYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSH--ELSLENWNQVIDTNLTGAFLGSREAIKYFVEND-------------IKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFAD-PEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMT DLTGSAFVI--GASGIGKACALAFARYGVRGIVIADLTLEAASAVAAECKSQATHPHFLAEAVAIDVTKEESVYQAIAYAHQVLGRIDYAVNSAGVGVQLANEIAEASVSEFEKMFKVNVTGTFIVTRALSALMKTQDPVPVDEAVPARGVSRGSIVNVGSASGFVATPGMVQYTAAKHAVVGITKNAALDNAKHGIRVNSVCPSWVDTPMIRKAMDDIPELGEMIQKAVPLGRIALAEEVADAVMFLSSPKASYATGCNMILDGGTT DL V+ G+ G+G+A A+ F + + +V + A E K + A V DVTKEE V + A + G +D +N+AGV + + E S+ + ++ N+TG F+ +R D +G+++N+ S + P V Y A+K + +T+ AL+ A GIRVN++ P +DTP+ + D PE ++ +P+G I EE+A FL+S +ASY TG + DGG T 93 gi|23451228|gb|AF419330.1| Cochliobolus lunatus hydroxynaphthalene reductase mRNA, complete cds AF419330 1001 1 105.916 263 8.3571e-23 5 248 102 863 0 3 77 124 16 257 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRS--NXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPW-PLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPI----------NAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADG LAGKVAVVTGSGRGIGKAMAIELAKRGAKVAVNYANAVEGAEQVVKEIKALNNGSDAHAFKANVGNVEESEKLMDDVVKHFGKLDICCSNSGVVSFGHFKDVTPEEFDRVFNINTRGQFFVAKAAYKR-MEN--YGRIILMGSITGQAKGVPKHAVYSGSKGAIETFTRCMAIDAGEKKITVNCVAPGGIKTDMYHAVCREYIPGGEKLSDDQVDEYACTWSPHNRVGQPVDIARVVCFLASQDGEWVNGKVIGIDG L KV VVTG +G+G+AMA+ + +KV VNY + E + + + G A + +V E+ L++ VK FG LD+ +N+GV + +++ E +++V + N G F ++ A K +EN G +I M S+ P Y+ SKG ++ T +A++ K I VN + PG I T + EK +D + + P +G+P +IA V FLAS +V G + DG 94 gi|70995419|ref|XM_747373.1| oxidoreductase short chain dehydrogenase/reductase family superfamily (Afu1g11010) mRNA, complete cds XM_747373 768 1 105.916 263 8.3571e-23 5 250 7 756 0 1 73 135 14 255 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNY--RSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGS--LDVMINNAGVENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPK-GIRVNNIGPGAIDTPINAEKFADPEQRADVESM---IPMGY-IGKPEEIASVAAFLASSQASYVTGITLFADGGM LQGKVAIVTGGARGIGAGIVRSLSKEGAKVSFNYVSASSKAAADALVQELRNENKEALAIQADMTDIDAPSRIVQATLAEFKTEQIDILVNNAGAGDNRPLEEVTVDVYQNLMDVNVRAVIFMTKAILSYIPRN---GRIINLSSISARGGYATQSVYAATKAAVEGLTRVWATELGHKYGVTVNAINPGPVNT--DMYRAAGPVHLARMEEQNKKVPAGQRCGTVDDIADIVTFLAQERSRWVTGDVICANGGM L+ KV +VTGG++G+G + +E +KV NY S++ A + +E+ +A+ ++ D+T + +V+ + EF + +D+++NNAG + P E++++ + ++D N+ ++ + Y N G +IN+SS+ + YAA+K ++ +T A E K G+ VN I PG ++T + + A P A +E +P G G ++IA + FLA ++ +VTG + A+GGM 95 gi|58266237|ref|XM_570275.1| Filobasidiella neoformans oxidoreductase, putative (CND02280) mRNA, complete cds XM_570275 1123 1 105.916 263 8.3571e-23 5 249 254 988 0 2 79 125 6 248 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQ-AIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPS-HELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPIN-AEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG LKGKKAIVTGGDSGIGRAAAQMFAREGADVTIVYLPEEEQDAQRVKKAIEQDGQQCLTIAHDLMQADLAADVVKQHMDKFGKLDILVNNASKQIMSQSIAEIELENVESTFRSNILAMFALTKAAVPHLKRGS---TIINTSSVTAFKGSVAMVDYASTKGAIVSYTRSLAVQLAPQGIRVNGVCPGPVYTPLQPASRPPDNMEGWSVGGPPLHGRASMPAEMGPAYVFLASSDANAMTGHFLHLNNG LK K +VTGG G+GRA A F +E + V + Y EE+ + K+ E GQ + + D+ + + ++V+ + +FG LD+++NNA + S E+ LEN +N+ F ++ A+ + +IN SSV V YA++KG + T +LA++ AP+GIRVN + PG + TP+ A + D + V G P E+ FLASS A+ +TG L + G 96 gi|46105097|ref|XM_380353.1| Gibberella zeae PH-1 strain PH-1; NRRL 31084 chromosome 1 XM_380353 852 1 105.145 261 1.42551e-22 5 252 22 783 0 1 76 131 8 255 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXX--GGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGVENPVPSHELSL-EN-WNQVIDTNLTGAFLGSREAIKYFVEND-IKGNVINMSSVHEMIPWPL-FVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPE-QRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMTK LAGKNAVITGAGGGIGLETSILFAKEGASILMSDISQPALEKAAAKVKQLVPDAPRVEILKVDVSKESEVQAMIES-LDSWGGIDVLFNNAGIMHAQDDDAVNTPENIWDLTQNINVKGVWFGCKHAVLSLRRNKKSKASIINTASVVALVGAATPQLAYTASKGAVLALTRELAMVHAREGFRFNNLCPAPLNTPLLQDWLGDDQAKRHRREVHFPMGRFGEAIEQAHAVVFLASDESSFVNGHDFAVDGGMTK L K V+TG G+G ++ F +E + ++++ S K + + I++ DV+KE +V ++E+ + +G +DV+ NNAG+ + ++ EN W+ + N+ G + G + A+ N K ++IN +SV ++ + Y ASKG + +T LA+ +A +G R NN+ P ++TP+ + D + +R E PMG G+ E A FLAS ++S+V G DGGMTK 97 gi|39977182|ref|XM_369979.1| Magnaporthe grisea 70-15 XM_369979 1110 1 105.145 261 1.42551e-22 8 253 361 1107 0 1 72 137 5 250 KVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAI-IVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGV-ENPVPSHELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVH-EMIPWPLFVH-YAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGMTKY KTIIITGGARGLGNYMARACAEAGAKAIIIFDANQELGDESAAELHQKTGLPVTFFKVDVRDGAAINAAVDRVVELFGAPDVLVNSAGIADSNIKAETYDPAMFRRLIDINLTGSFLMSQAVGRAMMAAGKPGSIVLVASMSGSIVNYPQEQSCYNASKAGVIQLGKSLAAEWAKYDIRVNCISPGYMDTALNKVPALDAQKKI-WKSLTPQQRLGNVDDLNGLCIFLASDSSGFMTGSNVIIDGGYTCY K +++TGG++GLG MA + +K ++ + +N+E E E+ + G + + DV + V+ V+ FG+ DV++N+AG+ ++ + + + ++ID NLTG+FL S+ + + G+++ ++S+ ++ +P Y ASK G+ + ++LA E+A IRVN I PG +DT +N D +++ +S+ P +G +++ + FLAS + ++TG + DGG T Y 98 gi|57223396|gb|AE017342.1| Cryptococcus neoformans var. neoformans JEC21 chromosome 2, complete sequence AE017342 1632307 1 100.523 249 3.51114e-21 75 250 1615062 1615706 0 3 64 102 45 218 LVETAVKEFGSLDVMINNAGVENPVPSH---ELSLENWNQVIDTNLTGAFLGSREAIKYFVENDIKG-NVINMSSVHEMIPWPLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGP--------------------------------------GAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGITLFADGGM IVSAAVSSFSRIDVLISNAGI---CPFHSFLDLPHPLWKRVQDVNLNGSFYVVQAVANQMAKQEPKGGSIVAVSSISALMGGGEQCHYTPTKAGIKSLMESCAIALGPMGIRCNSVLPGTSYFLVLALVLFPFPITLLLIVPCG*ECWLNHIKSEIGTIETNINKEDLSNPEKRADQIRRVPLGRLGKPEDLVGPTLFFASDLSNYCTGASVLVDGGM +V AV F +DV+I+NAG+ P H +L W +V D NL G+F + + + KG +++ +SS+ ++ HY +K G+K + E+ A+ P GIR N++ P G I+T IN E ++PE+RAD +P+G +GKPE++ F AS ++Y TG ++ DGGM 2 50.0618 118 5.4421e-06 160 243 106150 106398 0 1 31 45 1 84 ASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPINAEKFADPEQRADVESMIPMGYIGKPEEIASVAAFLASSQASYVTGIT ASKGAVLAMTRELAMVHAREGIRFNSLCPGPIRTPLLMDFLNTPEKLNRRMVHVPMGRFGEAVEQAKAVVFCMWSSSS-IQGMT ASKG + MT LA+ +A +GIR N++ PG I TP+ + PE+ +PMG G+ E A F S +S + G+T 3 45.0542 105 0.000175066 8 124 535540 535968 0 -2 36 62 26 143 KVVVVTGGSKGLGRAMAVRFGQ------EQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMIN------------------NAGVENPVPS--HELSLENWNQVIDTNLTGAFLGS RVILVTGASGGIGRASSIALSNTFPSTAQPEQLVLVLVGRRQAELEETGRQCRDGTLIEVATGDASNEEDVKRIFETVKSKYGRLDVLFNVSVVNHFGRELQLIWMMKNAGINDKSPGEFEDQDMDVFRKVLDINIMSAVLVS +V++VTG S G+GRA ++ + ++V+ + LE G + GD + EEDV + ET ++G LDV+ N NAG+ + P + ++ + +V+D N+ A L S 99 gi|1235618|gb|U34740.1|ENU34740 Emericella nidulans sterigmatocystin biosynthetic gene cluster: (stcA), (stcB), (stcC), (stcE), (aflR), (stcF), (stcI), (stcJ), (stcK), (stcL), (stcO), (stcQ), (stcS), (stcT), (stcU), (stcV) and (stcW) genes, complete cds U34740 59725 1 91.2781 225 1.26737e-20 5 204 49686 50360 0 -3 76 113 31 228 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGV-----------ENPVPS-HELSLE-----NWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPW-PLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPI----------NAEKFADPE LDGKVALVTGAGRGIGAAIAVALGQRGAKVVVNYANSREAAEKVVDEIKSNAQTAISIQADVGDPDAVTKLMDQAVEHFGYLDIVSSNAGIVSFGHVKDVTPDVCVPSPYESPVEL*PQQEFDRVFRVNTRGQFFVAREAYRHLREG---GRIILTSSNTASVKGVPRHAVYSGSKGAIDTFVRCLAIDCGDKKITVNAVAPGAIKTDMFLSVSREYIPNGETFTDEQ L KV +VTG +G+G A+AV GQ +KVVVNY ++ E A +V EI+ AI ++ DV + V L++ AV+ FG LD++ +NAG+ + VPS +E +E +++V N G F +REA ++ E G +I SS + P Y+ SKG + LA++ K I VN + PGAI T + N E F D + 2 34.6538 78 1.26737e-20 214 249 49502 49609 0 -1 14 23 0 36 PMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG PLNRVGLPVDVARVVSFLASDAAEWISGKIIGVDGG P+ +G P ++A V +FLAS A +++G + DGG 100 gi|450259|gb|L27825.1|EMEVERA1AA Emericella nidulans (verA) gene, complete cds, ORF 1 gene, complete cds, and ORF 2 gene, 5' end L27825 4310 1 91.2781 225 1.31998e-20 5 204 579 1253 0 3 76 113 31 228 LKDKVVVVTGGSKGLGRAMAVRFGQEQSKVVVNYRSNXXXXXXXXXXXXXXGGQAIIVRGDVTKEEDVVNLVETAVKEFGSLDVMINNAGV-----------ENPVPS-HELSLE-----NWNQVIDTNLTGAFLGSREAIKYFVENDIKGNVINMSSVHEMIPW-PLFVHYAASKGGMKLMTETLALEYAPKGIRVNNIGPGAIDTPI----------NAEKFADPE LDGKVALVTGAGRGIGAAIAVALGQPGAKVVVNYANSREAAEKVVDEIKSNAQSAISIQADVGDPDAVTKLMDQAVEHFGYLDIVSSNAGIVSFGHVKDVTPDVCVPSPYESPVEL*PQQEFDRVFRVNTRGQFFVAREAYRHLREG---GRIILTSSNTASVKGVPRHAVYSGSKGAIDTFVRCLAIDCGDKKITVNAVAPGAIKTDMFLSVSREYIPNGETFTDEQ L KV +VTG +G+G A+AV GQ +KVVVNY ++ E A +V EI+ AI ++ DV + V L++ AV+ FG LD++ +NAG+ + VPS +E +E +++V N G F +REA ++ E G +I SS + P Y+ SKG + LA++ K I VN + PGAI T + N E F D + 2 34.6538 78 1.31998e-20 214 249 1330 1437 0 1 14 23 0 36 PMGYIGKPEEIASVAAFLASSQASYVTGITLFADGG PLNRVGLPVDVARVVSFLASDAAEWISGKIIGVDGG P+ +G P ++A V +FLAS A +++G + DGG 251887 438542399 0 0 0.041 0.267 0.14 weblogo-3.8.0/tests/data/ssearch/xbt005.xml000066400000000000000000003111051467613320200204340ustar00rootroot00000000000000 tblastx TBLASTX 2.2.12 [Aug-07-2005] Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer, Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), "Gapped BLAST and PSI-BLAST: a new generation of protein database search programs", Nucleic Acids Res. 25:3389-3402. nr gi|1348853|gb|G26621.1|G26621 human STS STS_D12006, sequence tagged site 615 BLOSUM80 1 10 1 L; 1 gi|1348853|gb|G26621.1|G26621 human STS STS_D12006, sequence tagged site 615 1 gi|18072170|gb|AC010333.7| Homo sapiens chromosome 16 clone CTD-3037G24, complete sequence AC010333 159870 1 329.561 661 5.29552e-90 2 355 44324 44677 -3 -3 117 117 0 118 ECXFIMLYIFPARIWST*VICPPEQWL*RRKLSSGQKLLRRCGKTGYIKNNAGLK*PMRFCQGILH*CI*SKSGPIQRMWLKAPFWPFLFLLRALHTFPLFLSKWTK*RVS*VEGHSD ECCFIMLYIFPARIWST*VICPPEQWL*RRKLSSGQKLLRRCGKTGYIKNNAGLK*PMRFCQGILH*CI*SKSGPIQRMWLKAPFWPFLFLLRALHTFPLFLSKWTK*RVS*VEGHSD EC FIMLYIFPARIWST*VICPPEQWL*RRKLSSGQKLLRRCGKTGYIKNNAGLK*PMRFCQGILH*CI*SKSGPIQRMWLKAPFWPFLFLLRALHTFPLFLSKWTK*RVS*VEGHSD 2 329.561 661 4.10767e-89 1 354 44323 44676 -1 -1 117 117 0 118 SAXS*CCIFFLPGFGVPRLFVHQNNGCKGEN*AVVRSC*EDAVKQVT*KTMLV*NNLCAFVKGFCISAFSPSQGQFRGCG*RHRFGLFCFF*ELCIHSHFSCQSGQNEESHEWRGILI SAVS*CCIFFLPGFGVPRLFVHQNNGCKGEN*AVVRSC*EDAVKQVT*KTMLV*NNLCAFVKGFCISAFSPSQGQFRGCG*RHRFGLFCFF*ELCIHSHFSCQSGQNEESHEWRGILI SA S*CCIFFLPGFGVPRLFVHQNNGCKGEN*AVVRSC*EDAVKQVT*KTMLV*NNLCAFVKGFCISAFSPSQGQFRGCG*RHRFGLFCFF*ELCIHSHFSCQSGQNEESHEWRGILI 3 317.685 637 2.67963e-86 1 354 44323 44676 1 1 117 117 0 118 DQNAPPLMRLFILSTLTGKVGMYAELSKETKKAKTVPSATSSELALTWTKCTNAKSLDKSA*VISNQHCFLCNLFYRIFSAASDHCSIFSFTAIVLVDK*PRYSKSWQEKYTAL*XST DQNAPPLMRLFILSTLTGKVGMYAELSKETKKAKTVPSATSSELALTWTKCTNAKSLDKSA*VISNQHCFLCNLFYRIFSAASDHCSIFSFTAIVLVDK*PRYSKSWQEKYTAL*NST DQNAPPLMRLFILSTLTGKVGMYAELSKETKKAKTVPSATSSELALTWTKCTNAKSLDKSA*VISNQHCFLCNLFYRIFSAASDHCSIFSFTAIVLVDK*PRYSKSWQEKYTAL* ST 4 316.696 635 8.18857e-85 3 356 44325 44678 -2 -2 117 117 0 118 *VLXHNAVYFSCQDLEYLGYLSTRTMAVKEKIEQWSEAAEKMR*NRLHKKQCWFEITYALLSRDFALVHLVQVRANSEDVAEGTVLAFFVSFESSAYIPTFPVKVDKMKSLMSGGAF* *VLFHNAVYFSCQDLEYLGYLSTRTMAVKEKIEQWSEAAEKMR*NRLHKKQCWFEITYALLSRDFALVHLVQVRANSEDVAEGTVLAFFVSFESSAYIPTFPVKVDKMKSLMSGGAF* *VL HNAVYFSCQDLEYLGYLSTRTMAVKEKIEQWSEAAEKMR*NRLHKKQCWFEITYALLSRDFALVHLVQVRANSEDVAEGTVLAFFVSFESSAYIPTFPVKVDKMKSLMSGGAF* 5 315.706 633 2.26637e-84 2 355 44324 44677 2 2 117 117 0 118 IRMPLHS*DSSFCPL*QEKWECMXXXXXXXXRPKRCLQPHPLNWP*LGLNALMQNPLTKAHRLFQTSIVFYVTCFTASSQQLLTTAQFSPLQPLFWWTNNLGTPNPGRKNIQHYEXAL IRMPLHS*DSSFCPL*QEKWECMQSSQKKQKRPKRCLQPHPLNWP*LGLNALMQNPLTKAHRLFQTSIVFYVTCFTASSQQLLTTAQFSPLQPLFWWTNNLGTPNPGRKNIQHYETAL IRMPLHS*DSSFCPL*QEKWECMQSSQKKQKRPKRCLQPHPLNWP*LGLNALMQNPLTKAHRLFQTSIVFYVTCFTASSQQLLTTAQFSPLQPLFWWTNNLGTPNPGRKNIQHYE AL 6 206.85 413 2.23367e-68 3 224 44325 44546 3 3 74 74 0 74 SECPSTHETLHFVHFDRKSGNVCRALKRNKKGQNGAFSHIL*IGPDLD*MH*CKIP*QKRIGYFKPALFFM*PV SECPSTHETLHFVHFDRKSGNVCRALKRNKKGQNGAFSHIL*IGPDLD*MH*CKIP*QKRIGYFKPALFFM*PV SECPSTHETLHFVHFDRKSGNVCRALKRNKKGQNGAFSHIL*IGPDLD*MH*CKIP*QKRIGYFKPALFFM*PV 7 75.7282 148 2.23367e-68 273 356 44595 44678 3 3 27 27 0 28 YSHCSGGQIT*VLQILAGKIYSIMXQHS YSHCSGGQIT*VLQILAGKIYSIMKQHS YSHCSGGQIT*VLQILAGKIYSIM QHS 8 28.7222 53 5.29552e-90 371 400 44691 44720 -3 -2 8 9 0 10 RAMCNQLWKS QVMCNQLWKS + MCNQLWKS 9 28.2274 52 2.67963e-86 372 395 44692 44715 3 1 8 8 0 8 DFQSWLHM DFQSWLHM DFQSWLHM 10 25.7534 47 4.10767e-89 372 398 44692 44718 -2 -1 9 9 0 9 GHV*PALEI GHV*PALEI GHV*PALEI 11 24.269 44 8.18857e-85 367 393 44687 44713 -1 -3 8 8 0 9 CVTSFGNPF CVTSFGNHF CVTSFGN F 12 23.7742 43 2.26637e-84 367 399 44687 44719 1 2 9 9 0 11 KWISKAGYTWP KMISKAGYT*P K ISKAGYT P 13 22.2898 40 2.23367e-68 374 394 44694 44714 2 3 7 7 0 7 FPKLVTH FPKLVTH FPKLVTH 2 gi|33991096|gb|BC006289.2| Homo sapiens hypothetical protein FLJ11151, mRNA (cDNA clone MGC:10278 IMAGE:3959701), complete cds BC006289 2865 1 329.561 661 5.39099e-90 2 355 1846 2199 -3 -1 117 117 0 118 ECXFIMLYIFPARIWST*VICPPEQWL*RRKLSSGQKLLRRCGKTGYIKNNAGLK*PMRFCQGILH*CI*SKSGPIQRMWLKAPFWPFLFLLRALHTFPLFLSKWTK*RVS*VEGHSD ECCFIMLYIFPARIWST*VICPPEQWL*RRKLSSGQKLLRRCGKTGYIKNNAGLK*PMRFCQGILH*CI*SKSGPIQRMWLKAPFWPFLFLLRALHTFPLFLSKWTK*RVS*VEGHSD EC FIMLYIFPARIWST*VICPPEQWL*RRKLSSGQKLLRRCGKTGYIKNNAGLK*PMRFCQGILH*CI*SKSGPIQRMWLKAPFWPFLFLLRALHTFPLFLSKWTK*RVS*VEGHSD 2 329.561 661 4.18241e-89 1 354 1845 2198 -1 -2 117 117 0 118 SAXS*CCIFFLPGFGVPRLFVHQNNGCKGEN*AVVRSC*EDAVKQVT*KTMLV*NNLCAFVKGFCISAFSPSQGQFRGCG*RHRFGLFCFF*ELCIHSHFSCQSGQNEESHEWRGILI SAVS*CCIFFLPGFGVPRLFVHQNNGCKGEN*AVVRSC*EDAVKQVT*KTMLV*NNLCAFVKGFCISAFSPSQGQFRGCG*RHRFGLFCFF*ELCIHSHFSCQSGQNEESHEWRGILI SA S*CCIFFLPGFGVPRLFVHQNNGCKGEN*AVVRSC*EDAVKQVT*KTMLV*NNLCAFVKGFCISAFSPSQGQFRGCG*RHRFGLFCFF*ELCIHSHFSCQSGQNEESHEWRGILI 3 317.685 637 2.72986e-86 1 354 1845 2198 1 3 117 117 0 118 DQNAPPLMRLFILSTLTGKVGMYAELSKETKKAKTVPSATSSELALTWTKCTNAKSLDKSA*VISNQHCFLCNLFYRIFSAASDHCSIFSFTAIVLVDK*PRYSKSWQEKYTAL*XST DQNAPPLMRLFILSTLTGKVGMYAELSKETKKAKTVPSATSSELALTWTKCTNAKSLDKSA*VISNQHCFLCNLFYRIFSAASDHCSIFSFTAIVLVDK*PRYSKSWQEKYTAL*NST DQNAPPLMRLFILSTLTGKVGMYAELSKETKKAKTVPSATSSELALTWTKCTNAKSLDKSA*VISNQHCFLCNLFYRIFSAASDHCSIFSFTAIVLVDK*PRYSKSWQEKYTAL* ST 4 316.696 635 8.34456e-85 3 356 1847 2200 -2 -3 117 117 0 118 *VLXHNAVYFSCQDLEYLGYLSTRTMAVKEKIEQWSEAAEKMR*NRLHKKQCWFEITYALLSRDFALVHLVQVRANSEDVAEGTVLAFFVSFESSAYIPTFPVKVDKMKSLMSGGAF* *VLFHNAVYFSCQDLEYLGYLSTRTMAVKEKIEQWSEAAEKMR*NRLHKKQCWFEITYALLSRDFALVHLVQVRANSEDVAEGTVLAFFVSFESSAYIPTFPVKVDKMKSLMSGGAF* *VL HNAVYFSCQDLEYLGYLSTRTMAVKEKIEQWSEAAEKMR*NRLHKKQCWFEITYALLSRDFALVHLVQVRANSEDVAEGTVLAFFVSFESSAYIPTFPVKVDKMKSLMSGGAF* 5 315.706 633 2.30975e-84 2 355 1846 2199 2 1 117 117 0 118 IRMPLHS*DSSFCPL*QEKWECMXXXXXXXXRPKRCLQPHPLNWP*LGLNALMQNPLTKAHRLFQTSIVFYVTCFTASSQQLLTTAQFSPLQPLFWWTNNLGTPNPGRKNIQHYEXAL IRMPLHS*DSSFCPL*QEKWECMQSSQKKQKRPKRCLQPHPLNWP*LGLNALMQNPLTKAHRLFQTSIVFYVTCFTASSQQLLTTAQFSPLQPLFWWTNNLGTPNPGRKNIQHYETAL IRMPLHS*DSSFCPL*QEKWECMQSSQKKQKRPKRCLQPHPLNWP*LGLNALMQNPLTKAHRLFQTSIVFYVTCFTASSQQLLTTAQFSPLQPLFWWTNNLGTPNPGRKNIQHYE AL 6 206.85 413 2.33615e-68 3 224 1847 2068 3 2 74 74 0 74 SECPSTHETLHFVHFDRKSGNVCRALKRNKKGQNGAFSHIL*IGPDLD*MH*CKIP*QKRIGYFKPALFFM*PV SECPSTHETLHFVHFDRKSGNVCRALKRNKKGQNGAFSHIL*IGPDLD*MH*CKIP*QKRIGYFKPALFFM*PV SECPSTHETLHFVHFDRKSGNVCRALKRNKKGQNGAFSHIL*IGPDLD*MH*CKIP*QKRIGYFKPALFFM*PV 7 75.7282 148 2.33615e-68 273 356 2117 2200 3 2 27 27 0 28 YSHCSGGQIT*VLQILAGKIYSIMXQHS YSHCSGGQIT*VLQILAGKIYSIMKQHS YSHCSGGQIT*VLQILAGKIYSIM QHS 8 28.7222 53 5.39099e-90 371 400 2213 2242 -3 -3 8 9 0 10 RAMCNQLWKS QVMCNQLWKS + MCNQLWKS 9 28.2274 52 2.72986e-86 372 395 2214 2237 3 3 8 8 0 8 DFQSWLHM DFQSWLHM DFQSWLHM 10 25.7534 47 4.18241e-89 372 398 2214 2240 -2 -2 9 9 0 9 GHV*PALEI GHV*PALEI GHV*PALEI 11 24.269 44 8.34456e-85 367 393 2209 2235 -1 -1 8 8 0 9 CVTSFGNPF CVTSFGNHF CVTSFGN F 12 23.7742 43 2.30975e-84 367 399 2209 2241 1 1 9 9 0 11 KWISKAGYTWP KMISKAGYT*P K ISKAGYT P 13 22.2898 40 2.33615e-68 374 394 2216 2236 2 2 7 7 0 7 FPKLVTH FPKLVTH FPKLVTH 3 gi|21752798|dbj|AK093854.1| Homo sapiens cDNA FLJ36535 fis, clone TRACH2004521 AK093854 2608 1 329.561 661 5.39325e-90 2 355 1608 1961 -3 -3 117 117 0 118 ECXFIMLYIFPARIWST*VICPPEQWL*RRKLSSGQKLLRRCGKTGYIKNNAGLK*PMRFCQGILH*CI*SKSGPIQRMWLKAPFWPFLFLLRALHTFPLFLSKWTK*RVS*VEGHSD ECCFIMLYIFPARIWST*VICPPEQWL*RRKLSSGQKLLRRCGKTGYIKNNAGLK*PMRFCQGILH*CI*SKSGPIQRMWLKAPFWPFLFLLRALHTFPLFLSKWTK*RVS*VEGHSD EC FIMLYIFPARIWST*VICPPEQWL*RRKLSSGQKLLRRCGKTGYIKNNAGLK*PMRFCQGILH*CI*SKSGPIQRMWLKAPFWPFLFLLRALHTFPLFLSKWTK*RVS*VEGHSD 2 329.561 661 4.18418e-89 1 354 1607 1960 -1 -1 117 117 0 118 SAXS*CCIFFLPGFGVPRLFVHQNNGCKGEN*AVVRSC*EDAVKQVT*KTMLV*NNLCAFVKGFCISAFSPSQGQFRGCG*RHRFGLFCFF*ELCIHSHFSCQSGQNEESHEWRGILI SAVS*CCIFFLPGFGVPRLFVHQNNGCKGEN*AVVRSC*EDAVKQVT*KTMLV*NNLCAFVKGFCISAFSPSQGQFRGCG*RHRFGLFCFF*ELCIHSHFSCQSGQNEESHEWRGILI SA S*CCIFFLPGFGVPRLFVHQNNGCKGEN*AVVRSC*EDAVKQVT*KTMLV*NNLCAFVKGFCISAFSPSQGQFRGCG*RHRFGLFCFF*ELCIHSHFSCQSGQNEESHEWRGILI 3 317.685 637 2.73105e-86 1 354 1607 1960 1 2 117 117 0 118 DQNAPPLMRLFILSTLTGKVGMYAELSKETKKAKTVPSATSSELALTWTKCTNAKSLDKSA*VISNQHCFLCNLFYRIFSAASDHCSIFSFTAIVLVDK*PRYSKSWQEKYTAL*XST DQNAPPLMRLFILSTLTGKVGMYAELSKETKKAKTVPSATSSELALTWTKCTNAKSLDKSA*VISNQHCFLCNLFYRIFSAASDHCSIFSFTAIVLVDK*PRYSKSWQEKYTAL*NST DQNAPPLMRLFILSTLTGKVGMYAELSKETKKAKTVPSATSSELALTWTKCTNAKSLDKSA*VISNQHCFLCNLFYRIFSAASDHCSIFSFTAIVLVDK*PRYSKSWQEKYTAL* ST 4 316.696 635 8.34826e-85 3 356 1609 1962 -2 -2 117 117 0 118 *VLXHNAVYFSCQDLEYLGYLSTRTMAVKEKIEQWSEAAEKMR*NRLHKKQCWFEITYALLSRDFALVHLVQVRANSEDVAEGTVLAFFVSFESSAYIPTFPVKVDKMKSLMSGGAF* *VLFHNAVYFSCQDLEYLGYLSTRTMAVKEKIEQWSEAAEKMR*NRLHKKQCWFEITYALLSRDFALVHLVQVRANSEDVAEGTVLAFFVSFESSAYIPTFPVKVDKMKSLMSGGAF* *VL HNAVYFSCQDLEYLGYLSTRTMAVKEKIEQWSEAAEKMR*NRLHKKQCWFEITYALLSRDFALVHLVQVRANSEDVAEGTVLAFFVSFESSAYIPTFPVKVDKMKSLMSGGAF* 5 315.706 633 2.31078e-84 2 355 1608 1961 2 3 117 117 0 118 IRMPLHS*DSSFCPL*QEKWECMXXXXXXXXRPKRCLQPHPLNWP*LGLNALMQNPLTKAHRLFQTSIVFYVTCFTASSQQLLTTAQFSPLQPLFWWTNNLGTPNPGRKNIQHYEXAL IRMPLHS*DSSFCPL*QEKWECMQSSQKKQKRPKRCLQPHPLNWP*LGLNALMQNPLTKAHRLFQTSIVFYVTCFTASSQQLLTTAQFSPLQPLFWWTNNLGTPNPGRKNIQHYETAL IRMPLHS*DSSFCPL*QEKWECMQSSQKKQKRPKRCLQPHPLNWP*LGLNALMQNPLTKAHRLFQTSIVFYVTCFTASSQQLLTTAQFSPLQPLFWWTNNLGTPNPGRKNIQHYE AL 6 206.85 413 2.33861e-68 3 224 1609 1830 3 1 74 74 0 74 SECPSTHETLHFVHFDRKSGNVCRALKRNKKGQNGAFSHIL*IGPDLD*MH*CKIP*QKRIGYFKPALFFM*PV SECPSTHETLHFVHFDRKSGNVCRALKRNKKGQNGAFSHIL*IGPDLD*MH*CKIP*QKRIGYFKPALFFM*PV SECPSTHETLHFVHFDRKSGNVCRALKRNKKGQNGAFSHIL*IGPDLD*MH*CKIP*QKRIGYFKPALFFM*PV 7 75.7282 148 2.33861e-68 273 356 1879 1962 3 1 27 27 0 28 YSHCSGGQIT*VLQILAGKIYSIMXQHS YSHCSGGQIT*VLQILAGKIYSIMKQHS YSHCSGGQIT*VLQILAGKIYSIM QHS 8 28.7222 53 5.39325e-90 371 400 1975 2004 -3 -2 8 9 0 10 RAMCNQLWKS QVMCNQLWKS + MCNQLWKS 9 28.2274 52 2.73105e-86 372 395 1976 1999 3 2 8 8 0 8 DFQSWLHM DFQSWLHM DFQSWLHM 10 25.7534 47 4.18418e-89 372 398 1976 2002 -2 -1 9 9 0 9 GHV*PALEI GHV*PALEI GHV*PALEI 11 24.269 44 8.34826e-85 367 393 1971 1997 -1 -3 8 8 0 9 CVTSFGNPF CVTSFGNHF CVTSFGN F 12 23.7742 43 2.31078e-84 367 399 1971 2003 1 3 9 9 0 11 KWISKAGYTWP KMISKAGYT*P K ISKAGYT P 13 22.2898 40 2.33861e-68 374 394 1978 1998 2 1 7 7 0 7 FPKLVTH FPKLVTH FPKLVTH 4 gi|34364932|emb|BX640805.1|HSM806909 Homo sapiens mRNA; cDNA DKFZp686M14237 (from clone DKFZp686M14237) BX640805 2003 1 329.561 661 5.39962e-90 2 355 1402 1755 -3 -3 117 117 0 118 ECXFIMLYIFPARIWST*VICPPEQWL*RRKLSSGQKLLRRCGKTGYIKNNAGLK*PMRFCQGILH*CI*SKSGPIQRMWLKAPFWPFLFLLRALHTFPLFLSKWTK*RVS*VEGHSD ECCFIMLYIFPARIWST*VICPPEQWL*RRKLSSGQKLLRRCGKTGYIKNNAGLK*PMRFCQGILH*CI*SKSGPIQRMWLKAPFWPFLFLLRALHTFPLFLSKWTK*RVS*VEGHSD EC FIMLYIFPARIWST*VICPPEQWL*RRKLSSGQKLLRRCGKTGYIKNNAGLK*PMRFCQGILH*CI*SKSGPIQRMWLKAPFWPFLFLLRALHTFPLFLSKWTK*RVS*VEGHSD 2 329.561 661 4.18917e-89 1 354 1401 1754 -1 -1 117 117 0 118 SAXS*CCIFFLPGFGVPRLFVHQNNGCKGEN*AVVRSC*EDAVKQVT*KTMLV*NNLCAFVKGFCISAFSPSQGQFRGCG*RHRFGLFCFF*ELCIHSHFSCQSGQNEESHEWRGILI SAVS*CCIFFLPGFGVPRLFVHQNNGCKGEN*AVVRSC*EDAVKQVT*KTMLV*NNLCAFVKGFCISAFSPSQGQFRGCG*RHRFGLFCFF*ELCIHSHFSCQSGQNEESHEWRGILI SA S*CCIFFLPGFGVPRLFVHQNNGCKGEN*AVVRSC*EDAVKQVT*KTMLV*NNLCAFVKGFCISAFSPSQGQFRGCG*RHRFGLFCFF*ELCIHSHFSCQSGQNEESHEWRGILI 3 317.685 637 2.7344e-86 1 354 1401 1754 1 3 117 117 0 118 DQNAPPLMRLFILSTLTGKVGMYAELSKETKKAKTVPSATSSELALTWTKCTNAKSLDKSA*VISNQHCFLCNLFYRIFSAASDHCSIFSFTAIVLVDK*PRYSKSWQEKYTAL*XST DQNAPPLMRLFILSTLTGKVGMYAELSKETKKAKTVPSATSSELALTWTKCTNAKSLDKSA*VISNQHCFLCNLFYRIFSAASDHCSIFSFTAIVLVDK*PRYSKSWQEKYTAL*NST DQNAPPLMRLFILSTLTGKVGMYAELSKETKKAKTVPSATSSELALTWTKCTNAKSLDKSA*VISNQHCFLCNLFYRIFSAASDHCSIFSFTAIVLVDK*PRYSKSWQEKYTAL* ST 4 316.696 635 8.35867e-85 3 356 1403 1756 -2 -2 117 117 0 118 *VLXHNAVYFSCQDLEYLGYLSTRTMAVKEKIEQWSEAAEKMR*NRLHKKQCWFEITYALLSRDFALVHLVQVRANSEDVAEGTVLAFFVSFESSAYIPTFPVKVDKMKSLMSGGAF* *VLFHNAVYFSCQDLEYLGYLSTRTMAVKEKIEQWSEAAEKMR*NRLHKKQCWFEITYALLSRDFALVHLVQVRANSEDVAEGTVLAFFVSFESSAYIPTFPVKVDKMKSLMSGGAF* *VL HNAVYFSCQDLEYLGYLSTRTMAVKEKIEQWSEAAEKMR*NRLHKKQCWFEITYALLSRDFALVHLVQVRANSEDVAEGTVLAFFVSFESSAYIPTFPVKVDKMKSLMSGGAF* 5 315.706 633 2.31368e-84 2 355 1402 1755 2 1 117 117 0 118 IRMPLHS*DSSFCPL*QEKWECMXXXXXXXXRPKRCLQPHPLNWP*LGLNALMQNPLTKAHRLFQTSIVFYVTCFTASSQQLLTTAQFSPLQPLFWWTNNLGTPNPGRKNIQHYEXAL IRMPLHS*DSSFCPL*QEKWECMQSSQKKQKRPKRCLQPHPLNWP*LGLNALMQNPLTKAHRLFQTSIVFYVTCFTASSQQLLTTAQFSPLQPLFWWTNNLGTPNPGRKNIQHYETAL IRMPLHS*DSSFCPL*QEKWECMQSSQKKQKRPKRCLQPHPLNWP*LGLNALMQNPLTKAHRLFQTSIVFYVTCFTASSQQLLTTAQFSPLQPLFWWTNNLGTPNPGRKNIQHYE AL 6 206.85 413 2.34553e-68 3 224 1403 1624 3 2 74 74 0 74 SECPSTHETLHFVHFDRKSGNVCRALKRNKKGQNGAFSHIL*IGPDLD*MH*CKIP*QKRIGYFKPALFFM*PV SECPSTHETLHFVHFDRKSGNVCRALKRNKKGQNGAFSHIL*IGPDLD*MH*CKIP*QKRIGYFKPALFFM*PV SECPSTHETLHFVHFDRKSGNVCRALKRNKKGQNGAFSHIL*IGPDLD*MH*CKIP*QKRIGYFKPALFFM*PV 7 75.7282 148 2.34553e-68 273 356 1673 1756 3 2 27 27 0 28 YSHCSGGQIT*VLQILAGKIYSIMXQHS YSHCSGGQIT*VLQILAGKIYSIMKQHS YSHCSGGQIT*VLQILAGKIYSIM QHS 8 28.7222 53 5.39962e-90 371 400 1769 1798 -3 -2 8 9 0 10 RAMCNQLWKS QVMCNQLWKS + MCNQLWKS 9 28.2274 52 2.7344e-86 372 395 1770 1793 3 3 8 8 0 8 DFQSWLHM DFQSWLHM DFQSWLHM 10 25.7534 47 4.18917e-89 372 398 1770 1796 -2 -1 9 9 0 9 GHV*PALEI GHV*PALEI GHV*PALEI 11 24.269 44 8.35867e-85 367 393 1765 1791 -1 -3 8 8 0 9 CVTSFGNPF CVTSFGNHF CVTSFGN F 12 23.7742 43 2.31368e-84 367 399 1765 1797 1 1 9 9 0 11 KWISKAGYTWP KMISKAGYT*P K ISKAGYT P 13 22.2898 40 2.34553e-68 374 394 1772 1792 2 2 7 7 0 7 FPKLVTH FPKLVTH FPKLVTH 5 gi|8922900|ref|NM_018340.1| Homo sapiens hypothetical protein FLJ11151 (FLJ11151), mRNA NM_018340 2845 1 322.633 647 6.42287e-88 2 355 1845 2198 -3 -3 115 115 0 118 ECXFIMLYIFPARIWST*VICPPEQWL*RRKLSSGQKLLRRCGKTGYIKNNAGLK*PMRFCQGILH*CI*SKSGPIQRMWLKAPFWPFLFLLRALHTFPLFLSKWTK*RVS*VEGHSD ECCFIMLYIFPARIWST*VICPPEQWL*RRKLSSGQKLLRRCGKTGYIKNNAGLK*PMRFCQGISH*CI*SKSGPIQRMWLKAPFWPFLFLLRALHTFPLFLSKWTKWRVS*VEGHSD EC FIMLYIFPARIWST*VICPPEQWL*RRKLSSGQKLLRRCGKTGYIKNNAGLK*PMRFCQGI H*CI*SKSGPIQRMWLKAPFWPFLFLLRALHTFPLFLSKWTK RVS*VEGHSD 2 318.675 639 7.64846e-86 1 354 1844 2197 -1 -1 115 115 0 118 SAXS*CCIFFLPGFGVPRLFVHQNNGCKGEN*AVVRSC*EDAVKQVT*KTMLV*NNLCAFVKGFCISAFSPSQGQFRGCG*RHRFGLFCFF*ELCIHSHFSCQSGQNEESHEWRGILI SAVS*CCIFFLPGFGVPRLFVHQNNGCKGEN*AVVRSC*EDAVKQVT*KTMLV*NNLCAFVKGFRISAFSPSQGQFRGCG*RHRFGLFCFF*ELCIHSHFSCQSGQNGESHEWRGILI SA S*CCIFFLPGFGVPRLFVHQNNGCKGEN*AVVRSC*EDAVKQVT*KTMLV*NNLCAFVKGF ISAFSPSQGQFRGCG*RHRFGLFCFF*ELCIHSHFSCQSGQN ESHEWRGILI 3 314.717 631 3.26925e-84 3 356 1846 2199 -2 -2 116 117 0 118 *VLXHNAVYFSCQDLEYLGYLSTRTMAVKEKIEQWSEAAEKMR*NRLHKKQCWFEITYALLSRDFALVHLVQVRANSEDVAEGTVLAFFVSFESSAYIPTFPVKVDKMKSLMSGGAF* *VLFHNAVYFSCQDLEYLGYLSTRTMAVKEKIEQWSEAAEKMR*NRLHKKQCWFEITYALLSRDFALVHLVQVRANSEDVAEGTVLAFFVSFESSAYIPTFPVKVDKMESLMSGGAF* *VL HNAVYFSCQDLEYLGYLSTRTMAVKEKIEQWSEAAEKMR*NRLHKKQCWFEITYALLSRDFALVHLVQVRANSEDVAEGTVLAFFVSFESSAYIPTFPVKVDKM+SLMSGGAF* 4 313.232 628 5.89585e-85 1 354 1844 2197 1 2 116 116 0 118 DQNAPPLMRLFILSTLTGKVGMYAELSKETKKAKTVPSATSSELALTWTKCTNAKSLDKSA*VISNQHCFLCNLFYRIFSAASDHCSIFSFTAIVLVDK*PRYSKSWQEKYTAL*XST DQNAPPLMRLSILSTLTGKVGMYAELSKETKKAKTVPSATSSELALTWTKCTNAKSLDKSA*VISNQHCFLCNLFYRIFSAASDHCSIFSFTAIVLVDK*PRYSKSWQEKYTAL*NST DQNAPPLMRL ILSTLTGKVGMYAELSKETKKAKTVPSATSSELALTWTKCTNAKSLDKSA*VISNQHCFLCNLFYRIFSAASDHCSIFSFTAIVLVDK*PRYSKSWQEKYTAL* ST 5 310.263 622 9.87037e-83 2 355 1845 2198 2 3 115 116 0 118 IRMPLHS*DSSFCPL*QEKWECMXXXXXXXXRPKRCLQPHPLNWP*LGLNALMQNPLTKAHRLFQTSIVFYVTCFTASSQQLLTTAQFSPLQPLFWWTNNLGTPNPGRKNIQHYEXAL IRMPLHS*DSPFCPL*QEKWECMQSSQKKQKRPKRCLQPHPLNWP*LGLNALMRNPLTKAHRLFQTSIVFYVTCFTASSQQLLTTAQFSPLQPLFWWTNNLGTPNPGRKNIQHYETAL IRMPLHS*DS FCPL*QEKWECMQSSQKKQKRPKRCLQPHPLNWP*LGLNALM+NPLTKAHRLFQTSIVFYVTCFTASSQQLLTTAQFSPLQPLFWWTNNLGTPNPGRKNIQHYE AL 6 204.871 409 9.07322e-68 3 224 1846 2067 3 1 73 74 0 74 SECPSTHETLHFVHFDRKSGNVCRALKRNKKGQNGAFSHIL*IGPDLD*MH*CKIP*QKRIGYFKPALFFM*PV SECPSTHETLHFVHFDRKSGNVCRALKRNKKGQNGAFSHIL*IGPDLD*MH*CEIP*QKRIGYFKPALFFM*PV SECPSTHETLHFVHFDRKSGNVCRALKRNKKGQNGAFSHIL*IGPDLD*MH*C+IP*QKRIGYFKPALFFM*PV 7 75.7282 148 9.07322e-68 273 356 2116 2199 3 1 27 27 0 28 YSHCSGGQIT*VLQILAGKIYSIMXQHS YSHCSGGQIT*VLQILAGKIYSIMKQHS YSHCSGGQIT*VLQILAGKIYSIM QHS 8 28.7222 53 6.42287e-88 371 400 2212 2241 -3 -2 8 9 0 10 RAMCNQLWKS QVMCNQLWKS + MCNQLWKS 9 28.2274 52 5.89585e-85 372 395 2213 2236 3 2 8 8 0 8 DFQSWLHM DFQSWLHM DFQSWLHM 10 25.7534 47 7.64846e-86 372 398 2213 2239 -2 -1 9 9 0 9 GHV*PALEI GHV*PALEI GHV*PALEI 11 24.269 44 3.26925e-84 367 393 2208 2234 -1 -3 8 8 0 9 CVTSFGNPF CVTSFGNHF CVTSFGN F 12 23.7742 43 9.87037e-83 367 399 2208 2240 1 3 9 9 0 11 KWISKAGYTWP KMISKAGYT*P K ISKAGYT P 13 22.2898 40 9.07322e-68 374 394 2215 2235 2 1 7 7 0 7 FPKLVTH FPKLVTH FPKLVTH 6 gi|7023636|dbj|AK002013.1| Homo sapiens cDNA FLJ11151 fis, clone PLACE1006883 AK002013 2845 1 322.633 647 6.42287e-88 2 355 1845 2198 -3 -3 115 115 0 118 ECXFIMLYIFPARIWST*VICPPEQWL*RRKLSSGQKLLRRCGKTGYIKNNAGLK*PMRFCQGILH*CI*SKSGPIQRMWLKAPFWPFLFLLRALHTFPLFLSKWTK*RVS*VEGHSD ECCFIMLYIFPARIWST*VICPPEQWL*RRKLSSGQKLLRRCGKTGYIKNNAGLK*PMRFCQGISH*CI*SKSGPIQRMWLKAPFWPFLFLLRALHTFPLFLSKWTKWRVS*VEGHSD EC FIMLYIFPARIWST*VICPPEQWL*RRKLSSGQKLLRRCGKTGYIKNNAGLK*PMRFCQGI H*CI*SKSGPIQRMWLKAPFWPFLFLLRALHTFPLFLSKWTK RVS*VEGHSD 2 318.675 639 7.64846e-86 1 354 1844 2197 -1 -1 115 115 0 118 SAXS*CCIFFLPGFGVPRLFVHQNNGCKGEN*AVVRSC*EDAVKQVT*KTMLV*NNLCAFVKGFCISAFSPSQGQFRGCG*RHRFGLFCFF*ELCIHSHFSCQSGQNEESHEWRGILI SAVS*CCIFFLPGFGVPRLFVHQNNGCKGEN*AVVRSC*EDAVKQVT*KTMLV*NNLCAFVKGFRISAFSPSQGQFRGCG*RHRFGLFCFF*ELCIHSHFSCQSGQNGESHEWRGILI SA S*CCIFFLPGFGVPRLFVHQNNGCKGEN*AVVRSC*EDAVKQVT*KTMLV*NNLCAFVKGF ISAFSPSQGQFRGCG*RHRFGLFCFF*ELCIHSHFSCQSGQN ESHEWRGILI 3 314.717 631 3.26925e-84 3 356 1846 2199 -2 -2 116 117 0 118 *VLXHNAVYFSCQDLEYLGYLSTRTMAVKEKIEQWSEAAEKMR*NRLHKKQCWFEITYALLSRDFALVHLVQVRANSEDVAEGTVLAFFVSFESSAYIPTFPVKVDKMKSLMSGGAF* *VLFHNAVYFSCQDLEYLGYLSTRTMAVKEKIEQWSEAAEKMR*NRLHKKQCWFEITYALLSRDFALVHLVQVRANSEDVAEGTVLAFFVSFESSAYIPTFPVKVDKMESLMSGGAF* *VL HNAVYFSCQDLEYLGYLSTRTMAVKEKIEQWSEAAEKMR*NRLHKKQCWFEITYALLSRDFALVHLVQVRANSEDVAEGTVLAFFVSFESSAYIPTFPVKVDKM+SLMSGGAF* 4 313.232 628 5.89585e-85 1 354 1844 2197 1 2 116 116 0 118 DQNAPPLMRLFILSTLTGKVGMYAELSKETKKAKTVPSATSSELALTWTKCTNAKSLDKSA*VISNQHCFLCNLFYRIFSAASDHCSIFSFTAIVLVDK*PRYSKSWQEKYTAL*XST DQNAPPLMRLSILSTLTGKVGMYAELSKETKKAKTVPSATSSELALTWTKCTNAKSLDKSA*VISNQHCFLCNLFYRIFSAASDHCSIFSFTAIVLVDK*PRYSKSWQEKYTAL*NST DQNAPPLMRL ILSTLTGKVGMYAELSKETKKAKTVPSATSSELALTWTKCTNAKSLDKSA*VISNQHCFLCNLFYRIFSAASDHCSIFSFTAIVLVDK*PRYSKSWQEKYTAL* ST 5 310.263 622 9.87037e-83 2 355 1845 2198 2 3 115 116 0 118 IRMPLHS*DSSFCPL*QEKWECMXXXXXXXXRPKRCLQPHPLNWP*LGLNALMQNPLTKAHRLFQTSIVFYVTCFTASSQQLLTTAQFSPLQPLFWWTNNLGTPNPGRKNIQHYEXAL IRMPLHS*DSPFCPL*QEKWECMQSSQKKQKRPKRCLQPHPLNWP*LGLNALMRNPLTKAHRLFQTSIVFYVTCFTASSQQLLTTAQFSPLQPLFWWTNNLGTPNPGRKNIQHYETAL IRMPLHS*DS FCPL*QEKWECMQSSQKKQKRPKRCLQPHPLNWP*LGLNALM+NPLTKAHRLFQTSIVFYVTCFTASSQQLLTTAQFSPLQPLFWWTNNLGTPNPGRKNIQHYE AL 6 204.871 409 9.07322e-68 3 224 1846 2067 3 1 73 74 0 74 SECPSTHETLHFVHFDRKSGNVCRALKRNKKGQNGAFSHIL*IGPDLD*MH*CKIP*QKRIGYFKPALFFM*PV SECPSTHETLHFVHFDRKSGNVCRALKRNKKGQNGAFSHIL*IGPDLD*MH*CEIP*QKRIGYFKPALFFM*PV SECPSTHETLHFVHFDRKSGNVCRALKRNKKGQNGAFSHIL*IGPDLD*MH*C+IP*QKRIGYFKPALFFM*PV 7 75.7282 148 9.07322e-68 273 356 2116 2199 3 1 27 27 0 28 YSHCSGGQIT*VLQILAGKIYSIMXQHS YSHCSGGQIT*VLQILAGKIYSIMKQHS YSHCSGGQIT*VLQILAGKIYSIM QHS 8 28.7222 53 6.42287e-88 371 400 2212 2241 -3 -2 8 9 0 10 RAMCNQLWKS QVMCNQLWKS + MCNQLWKS 9 28.2274 52 5.89585e-85 372 395 2213 2236 3 2 8 8 0 8 DFQSWLHM DFQSWLHM DFQSWLHM 10 25.7534 47 7.64846e-86 372 398 2213 2239 -2 -1 9 9 0 9 GHV*PALEI GHV*PALEI GHV*PALEI 11 24.269 44 3.26925e-84 367 393 2208 2234 -1 -3 8 8 0 9 CVTSFGNPF CVTSFGNHF CVTSFGN F 12 23.7742 43 9.87037e-83 367 399 2208 2240 1 3 9 9 0 11 KWISKAGYTWP KMISKAGYT*P K ISKAGYT P 13 22.2898 40 9.07322e-68 374 394 2215 2235 2 1 7 7 0 7 FPKLVTH FPKLVTH FPKLVTH 7 gi|55727364|emb|CR858200.1| Pongo pygmaeus mRNA; cDNA DKFZp469A2228 (from clone DKFZp469A2228) CR858200 2470 1 245.445 491 1.97657e-84 95 355 1955 2215 2 2 83 84 0 87 RPKRCLQPHPLNWP*LGLNALMQNPLTKAHRLFQTSIVFYVTCFTASSQQLLTTAQFSPLQPLFWWTNNLGTPNPGRKNIQHYEXAL RPKRCLQPHPLNWP*LGLNALMQNPLTKAHRLFQISIVFYVTCFTASSQQLLTIAQFSPLQPLFWWTNNLGTPNPGRKNVQHYETAL RPKRCLQPHPLNWP*LGLNALMQNPLTKAHRLFQ SIVFYVTCFTASSQQLLT AQFSPLQPLFWWTNNLGTPNPGRKN+QHYE AL 2 237.528 475 5.94739e-83 86 355 1946 2215 -3 -1 83 84 0 90 ECXFIMLYIFPARIWST*VICPPEQWL*RRKLSSGQKLLRRCGKTGYIKNNAGLK*PMRFCQGILH*CI*SKSGPIQRMWLKAPFWPFLF ECCFIMLYVFPARIWST*VICPPEQWL*RRKLSNGQKLLRRCSKTGYIKNNADLK*PMRFCQGILH*SI*SKSGPIQRMWLKAPFWPFCF EC FIMLY+FPARIWST*VICPPEQWL*RRKLS GQKLLRRC KTGYIKNNA LK*PMRFCQGILH* I*SKSGPIQRMWLKAPFWPF F 3 229.116 458 2.5863e-76 82 354 1942 2214 -1 -2 83 85 0 91 SAXS*CCIFFLPGFGVPRLFVHQNNGCKGEN*AVVRSC*EDAVKQVT*KTMLV*NNLCAFVKGFCISAFSPSQGQFRGCG*RHRFGLFCFF SAVS*CCTFFLPGFGVPRLFVHQNNGCKGEN*AMVRSC*EDAVKQVT*KTMLI*NNLCAFVKGFCIRAFNPSQGQFRGCG*RHRFGLFVSF SA S*CC FFLPGFGVPRLFVHQNNGCKGEN*A+VRSC*EDAVKQVT*KTML+*NNLCAFVKGFCI AF PSQGQFRGCG*RHRFGLF F 4 224.168 448 9.95534e-75 82 354 1942 2214 1 1 84 85 0 91 KETKKAKTVPSATSSELALTWTKCTNAKSLDKSA*VISNQHCFLCNLFYRIFSAASDHCSIFSFTAIVLVDK*PRYSKSWQEKYTAL*XST KRNKKAKTVPSATSSELALTWIKCSNAKSLDKSA*VISNQHCFLCNLFYCIFSAASDHCSIFSFTAIVLVDK*PRYSKSWQEKRTAL*NST K KKAKTVPSATSSELALTW KC+NAKSLDKSA*VISNQHCFLCNLFY IFSAASDHCSIFSFTAIVLVDK*PRYSKSWQEK TAL* ST 5 220.21 440 8.67164e-55 30 356 1890 2216 -2 -3 86 91 0 109 *VLXHNAVYFSCQDLEYLGYLSTRTMAVKEKIEQWSEAAEKMR*NRLHKKQCWFEITYALLSRDFALVHLVQVRANSEDVAEGTVLAFFVSFESSAYIPTFPVKVDKMK *VLFHNAVRFSCQDLEYLGYLSTRTMAVKEKIEQWSEAAEKMQ*NRLHKKQC*FEITYALLSRDFALEHLIQVRANSEDVAEGTVLAFLFLLKALHTFPLFLSKWTKQR *VL HNAV FSCQDLEYLGYLSTRTMAVKEKIEQWSEAAEKM+*NRLHKKQC FEITYALLSRDFAL HL+QVRANSEDVAEGTVLAF ++ P F K K + 6 112.343 222 1.37884e-51 72 224 1932 2084 3 3 42 47 0 51 RALKRNKKGQNGAFSHIL*IGPDLD*MH*CKIP*QKRIGYFKPALFFM*PV QSFQKKQKGQNGAFSHIL*IGPDLD*ML*CKIP*QKRIGYFKSALFFM*PV ++ ++ +KGQNGAFSHIL*IGPDLD*M *CKIP*QKRIGYFK ALFFM*PV 7 87.6034 172 5.94739e-83 1 93 1862 1954 -1 -1 28 30 0 31 FCFF*ELCIHSHFSCQSGQNEESHEWRGILI FCFF*KLCIHSHFFCQSGQNKESHEWRGILI FCFF*+LCIHSHF CQSGQN+ESHEWRGILI 8 85.1294 167 1.97657e-84 3 101 1864 1962 3 1 29 30 0 33 SECPSTHETLHFVHFDRKSGNVCRALKRNKKGQ SECPSTHETLCFVHFDRKSGNVCRAFKRNKKAK SECPSTHETL FVHFDRKSGNVCRA KRNKK + 9 83.1502 163 9.95534e-75 1 102 1862 1963 1 2 30 32 0 34 DQNAPPLMRLFILSTLTGKVGMYAELSKETKKAK DQNAPPLMRLFVLSTLTEKVGMYAELSKETKRPK DQNAPPLMRLF+LSTLT KVGMYAELSKETK+ K 10 77.7074 152 2.5863e-76 2 94 1863 1955 -3 -3 29 30 0 31 FLFLLRALHTFPLFLSKWTK*RVS*VEGHSD FLFLLKALHTFPLFLSKWTKQRVS*VEGHSD FLFLL+ALHTFPLFLSKWTK RVS*VEGHSD 11 73.749 144 1.06464e-10 3 92 1864 1953 -2 -2 28 28 0 30 FVSFESSAYIPTFPVKVDKMKSLMSGGAF* FVSFESSAYIPTFSVKVDKTKSLMSGGAF* FVSFESSAYIPTF VKVDK KSLMSGGAF* 12 72.7594 142 1.37884e-51 273 356 2133 2216 3 3 26 26 0 28 YSHCSGGQIT*VLQILAGKIYSIMXQHS YSHCSGGQIT*VLQILAGKTYSIMKQHS YSHCSGGQIT*VLQILAGK YSIM QHS 13 63.3582 123 1.37884e-51 2 70 1863 1931 2 3 21 22 0 23 IRMPLHS*DSSFCPL*QEKWECM IRMPLHS*DSLFCPL*QKKWECM IRMPLHS*DS FCPL*Q+KWECM 14 28.7222 53 5.94739e-83 371 400 2229 2258 -3 -3 8 9 0 10 RAMCNQLWKS QVMCNQLWKS + MCNQLWKS 15 28.2274 52 1.97657e-84 372 395 2230 2253 3 1 8 8 0 8 DFQSWLHM DFQSWLHM DFQSWLHM 16 24.7638 45 2.5863e-76 372 398 2230 2256 -2 -2 8 9 0 9 GHV*PALEI GHV*PALEV GHV*PALE+ 8 gi|10434264|dbj|AK022710.1| Homo sapiens cDNA FLJ12648 fis, clone NT2RM4002018 AK022710 1890 1 82.6554 162 2.21876e-13 1 78 1811 1888 -1 -3 26 26 0 26 ELCIHSHFSCQSGQNEESHEWRGILI ELCIHSHFSCQSGQNEESHEWRGILI ELCIHSHFSCQSGQNEESHEWRGILI 2 79.1918 155 2.43296e-12 3 80 1813 1890 3 1 26 26 0 26 SECPSTHETLHFVHFDRKSGNVCRAL SECPSTHETLHFVHFDRKSGNVCRAL SECPSTHETLHFVHFDRKSGNVCRAL 3 72.7594 142 2.10126e-10 1 78 1811 1888 1 2 26 26 0 26 DQNAPPLMRLFILSTLTGKVGMYAEL DQNAPPLMRLFILSTLTGKVGMYAEL DQNAPPLMRLFILSTLTGKVGMYAEL 4 71.275 139 5.91498e-10 3 80 1813 1890 -2 -1 26 26 0 26 ESSAYIPTFPVKVDKMKSLMSGGAF* ESSAYIPTFPVKVDKMKSLMSGGAF* ESSAYIPTFPVKVDKMKSLMSGGAF* 5 71.275 139 5.91498e-10 2 79 1812 1889 -3 -2 26 26 0 26 RALHTFPLFLSKWTK*RVS*VEGHSD RALHTFPLFLSKWTK*RVS*VEGHSD RALHTFPLFLSKWTK*RVS*VEGHSD 6 69.7906 136 1.64505e-09 2 70 1812 1880 2 3 23 23 0 23 IRMPLHS*DSSFCPL*QEKWECM IRMPLHS*DSSFCPL*QEKWECM IRMPLHS*DSSFCPL*QEKWECM 9 gi|13897305|emb|AL391749.4|CNS06C8I Human chromosome 14 DNA sequence BAC R-233L14 of library RPCI-11 from chromosome 14 of Homo sapiens (Human), complete sequence AL391749 195007 1 41.0922 78 0.716571 167 250 8833 8916 2 1 13 19 0 28 PLTKAHRLFQTSIVFYVTCFTASSQQLL PLNKYHTIFQISLCFYLFCYNMAQKQLL PL K H +FQ S+ FY+ C+ + +QLL 10 gi|4309961|gb|AC005993.2|AC005993 Homo sapiens PAC clone RP6-114E22 from 14, complete sequence AC005993 143943 1 41.0922 78 0.716571 167 250 43680 43763 2 3 13 19 0 28 PLTKAHRLFQTSIVFYVTCFTASSQQLL PLNKYHTIFQISLCFYLFCYNMAQKQLL PL K H +FQ S+ FY+ C+ + +QLL 3533718 -1496331888 0 0 0.177051 0.342969 0.656794 weblogo-3.8.0/tests/data/stride/000077500000000000000000000000001467613320200165315ustar00rootroot00000000000000weblogo-3.8.0/tests/data/stride/stride_test_1.txt000066400000000000000000000022601467613320200220430ustar00rootroot00000000000000SEQ 1 QIVNSVDTMTLTNANVSPDGFTRAGILVNGVHGPLIRGGKNDNFELNVVN 50 1A65 STR EETTEEEEEEEEEEETTTT EEEEEETTBTTTEEEEETTT EEEEEEE 1A65 REM --------------- Detailed secondary structure assignment------------- 1A65 REM 1A65 REM |---Residue---| |--Structure--| |-Phi-| |-Psi-| |-Area-| 1A65 ASG GLN A 1 1 C Coil 360.00 157.13 95.4 1A65 ASG ILE A 2 2 E Strand -123.71 140.44 52.6 1A65 ASG VAL A 3 3 E Strand -107.57 132.67 0.8 1A65 ASG ASN A 4 4 T Turn -88.63 171.80 82.8 1A65 ASG SER A 5 5 T Turn -67.82 -20.25 20.9 1A65 ASG VAL A 6 6 E Strand -122.49 116.13 88.1 1A65 ASG ASP A 7 7 E Strand -171.42 177.50 48.2 1A65 ASG THR A 8 8 E Strand -111.06 136.75 56.7 1A65 ASG MET A 9 9 E Strand -116.98 98.04 0.0 1A65 ASG THR A 10 10 E Strand -91.78 123.05 38.1 1A65 weblogo-3.8.0/tests/data/stride/stride_test_2.txt000066400000000000000000000016771467613320200220570ustar00rootroot00000000000000REM . . . . . 1A59 SEQ 1 EPTIHKGLAGVTADVTAISKVNSDTNSLLYRGYPVQELAAKCSFEQVAYL 50 1A59 STR GGGTTT TTTEEEETTTTEEEETTEEHHHHHHH HHHHHHH 1A59 REM 1A59 REM --------------- Detailed secondary structure assignment------------- 1A59 REM 1A59 REM |---Residue---| |--Structure--| |-Phi-| |-Psi-| |-Area-| 1A59 ASG GLU - 2 1 C Coil 360.00 144.02 202.6 1A59 ASG PRO - 3 2 C Coil -78.20 165.31 85.3 1A59 ASG THR - 4 3 C Coil -87.10 122.31 111.1 1A59 ASG ILE - 5 4 C Coil -86.35 130.53 108.9 1A59 ASG HIS - 6 5 C Coil -113.24 69.79 103.0 1A59weblogo-3.8.0/tests/data/stride/stride_test_3.txt000066400000000000000000000015571467613320200220550ustar00rootroot00000000000000REM . . . . . 1A59 SEQ 1 EPTIHKGLAGVTADVTAISKVNSDTNSLLYRGYPVQELAAKCSFEQVAYL 50 1A59 STR GGGTTT TTTEEEETTTTEEEETTEEHHHHHHH HHHHHHH 1A59 REM --------------- Detailed secondary structure assignment------------- 1A59 REM 1A59 REM |---Residue---| |--Structure--| |-Phi-| |-Psi-| |-Area-| 1A59 ASG VAL - 12 11 T Turn -91.52 122.86 57.7 1A59 ASG THR - 13 12 C Coil -86.65 105.28 129.6 1A59 ASG ALA - 14 13 C Coil -77.28 -27.45 50.1 1A59 ASG ASP - 15 14 C Coil -172.70 -176.68 60.4 1A59 ASG VAL - 16 15 C Coil -103.84 157.33 106.2 1A59weblogo-3.8.0/tests/data/transfac_matrix.txt000066400000000000000000000014361467613320200211710ustar00rootroot00000000000000AC M00001 XX ID V$MYOD_01 XX DT 19.10.1992 (created); ewi. DT 22.10.1997 (updated); dbo. CO Copyright (C), Biobase GmbH. XX NA MyoD XX DE myoblast determination gene product XX BF T00526 MyoD; Species: mouse, Mus musculus. XX PO A C G T 01 1 2 2 0 S 02 2 1 2 0 R 03 3 0 1 1 A 04 0 5 0 0 C 05 5 0 0 0 A 06 0 0 4 1 G 07 0 1 4 0 G 08 0 0 0 5 T 09 0 0 5 0 G 10 0 1 2 2 K 11 0 2 0 3 Y 12 1 0 3 1 G XX BA 5 functional elements in 3 genes XX CC no comment XX // weblogo-3.8.0/tests/data/transfac_matrix2.txt000066400000000000000000000023711467613320200212520ustar00rootroot00000000000000AC M00252 XX ID V$TATA_01 XX DT 25.09.1996 (created); ewi. DT 25.09.1996 (updated); ewi. XX NA TATA XX DE cellular and viral TATA box elements XX BF T00794; TBP; Species: human, Homo sapiens. BF T00796; TBP; Species: mouse, Mus musculus. BF T00797; TBP; Species: fruit fly, Drosophila melanogaster. XX P0 A C G T 01 61 145 152 31 S 02 16 46 18 309 T 03 352 0 2 35 A 04 3 10 2 374 T 05 354 0 5 30 A 06 268 0 0 121 A 07 360 3 20 6 A 08 222 2 44 121 W 09 155 44 157 33 R 10 56 135 150 48 N 11 83 147 128 31 N 12 82 127 128 52 N 13 82 118 128 61 N 14 68 107 139 75 N 15 77 101 140 71 N XX BA 389 TATA box elements XX CC selected sequences from 502 promoters of EPD, mainly from vertebrates XX RN [1] RX MEDLINE; 90230299. RA Bucher P. RT Weight matrix descriptions of four eukaryotic RNA RT polymerase II promoter elements derived from 502 unrelated RT promoter sequences RL J. Mol. Biol. 212:563-578 (1990). XX // weblogo-3.8.0/tests/data/transfac_matrix3.txt000066400000000000000000000037621467613320200212600ustar00rootroot00000000000000NA motif0 XX ID motif0 XX P0 A C G T P1 0.932636 0.015597 0.040003 0.011764 P2 0.014199 0.055045 0.004670 0.926086 P3 0.006510 0.557389 0.018640 0.417460 P4 0.009817 0.792327 0.015285 0.182571 P5 0.156092 0.040077 0.233746 0.570085 P6 0.009985 0.945853 0.004484 0.039678 P7 0.015397 0.924484 0.018236 0.041883 P8 0.017029 0.398577 0.012075 0.572319 P9 0.209142 0.034380 0.730386 0.026092 P10 0.013183 0.910396 0.016204 0.060217 P11 0.015700 0.929544 0.006752 0.048004 P12 0.004595 0.024338 0.005668 0.965399 P13 0.006707 0.835210 0.021020 0.137063 P14 0.605453 0.029404 0.345947 0.019196 P15 0.082114 0.003541 0.905070 0.009275 P16 0.013315 0.940515 0.005037 0.041133 P17 0.002267 0.939790 0.007338 0.050605 P18 0.005566 0.007000 0.004046 0.983389 P19 0.011039 0.937713 0.012110 0.039138 P20 0.003923 0.925944 0.004251 0.065882 P21 0.031939 0.778715 0.038562 0.150784 P22 0.676909 0.013948 0.304103 0.005041 P23 0.947903 0.006608 0.023211 0.022278 P24 0.502281 0.002120 0.492464 0.003136 P25 0.033340 0.018195 0.465667 0.482798 P26 0.467192 0.010706 0.018913 0.503189 P27 0.033983 0.028621 0.912787 0.024609 P28 0.003262 0.953524 0.004641 0.038573 P29 0.025245 0.016791 0.014373 0.943591 P30 0.067571 0.002301 0.922626 0.007502 P31 0.055525 0.007650 0.932031 0.004793 P32 0.020766 0.013152 0.958521 0.007561 P33 0.960393 0.008288 0.029220 0.002099 P34 0.005831 0.266106 0.007526 0.720537 P35 0.004315 0.079776 0.020167 0.895742 P36 0.956005 0.014198 0.025262 0.004535 P37 0.018617 0.916719 0.012026 0.052637 P38 0.951831 0.012525 0.030472 0.005172 P39 0.049290 0.008406 0.925078 0.017227 P40 0.045570 0.031012 0.915851 0.007567 P41 0.010633 0.728891 0.017718 0.242758 P42 0.314015 0.048977 0.602085 0.034923 P43 0.003449 0.324195 0.024849 0.647507 P44 0.125199 0.261031 0.591490 0.022279 P45 0.509795 0.252862 0.026296 0.211047 P46 0.170155 0.027907 0.793878 0.008061 P47 0.025962 0.878464 0.034795 0.060779 P48 0.033195 0.911856 0.008576 0.046373 P49 0.919727 0.054315 0.018635 0.007323 P50 0.013073 0.918043 0.036830 0.032054 XX // weblogo-3.8.0/tests/test_array_io.py000077500000000000000000000044751467613320200175610ustar00rootroot00000000000000#!/usr/bin/env python # Copyright (c) 2005 Gavin E. Crooks # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # import unittest from io import StringIO from weblogo.seq_io import array_io, fasta_io class test_array_io(unittest.TestCase): def test_read_example(self) -> None: f = StringIO(array_io.example) seqs = array_io.read(f) # print(seqs) self.assertEqual(len(seqs), 8) self.assertEqual(seqs[0].name, "") self.assertEqual(len(seqs[1]), 60) def test_write_seq(self) -> None: f = StringIO(array_io.example) seqs = array_io.read(f) fout = StringIO() array_io.write(fout, seqs) fout.seek(0) seqs2 = array_io.read(fout) self.assertEqual(seqs, seqs2) def test_fail(self) -> None: # Lengths differ example = """ -SPC-MLETETLNKYVVIIAYALVFLLSLLGNSLVMLVILYSRVGRSVTDVYLLNLALAD -EPC-RDEN """ f = StringIO(example) self.assertRaises(ValueError, array_io.read, f) def test_read_fasta(self) -> None: f = StringIO(fasta_io.example) self.assertRaises(ValueError, array_io.read, f) if __name__ == "__main__": unittest.main() weblogo-3.8.0/tests/test_cli.py000066400000000000000000000054531467613320200165150ustar00rootroot00000000000000import shutil from subprocess import PIPE, Popen from typing import List, Optional, TextIO import pytest from . import data_stream def _exec( args: List[str], outputtext: List[str], returncode: int = 0, stdin: Optional[TextIO] = None, ) -> None: if not stdin: stdin = data_stream("cap.fa") args = ["weblogo"] + args p = Popen(args, stdin=stdin, stdout=PIPE, stderr=PIPE) (out, err) = p.communicate() if returncode == 0 and p.returncode > 0: print(err) assert returncode == p.returncode if returncode == 0: assert len(err) == 0 if outputtext: outs = out.decode() for item in outputtext: assert item in outs stdin.close() def test_malformed_options() -> None: _exec(["--notarealoption"], [], 2) _exec(["extrajunk"], [], 2) _exec(["-I"], [], 2) def test_help_option() -> None: _exec(["-h"], ["options"]) _exec(["--help"], ["options"]) # def test_version_option(): # _exec(['--version'], weblogo.__version__[0:5]) def test_default_build() -> None: _exec([], ["%%Title: Sequence Logo:"]) # Format options def test_width() -> None: _exec(["-W", "1234"], ["/stack_width 1234"]) _exec(["--stack-width", "1234"], ["/stack_width 1234"]) def test_height() -> None: _exec(["-W", "1000"], ["/stack_height 5000"]) _exec(["-W", "1000", "--aspect-ratio", "2"], ["/stack_height 2000"]) def test_stacks_per_line() -> None: _exec(["-n", "7"], ["/stacks_per_line 7 def"]) _exec(["--stacks-per-line", "7"], ["/stacks_per_line 7 def"]) def test_title() -> None: _exec( ["-t", "3456"], ["/logo_title (3456) def", "/show_title True def"], ) _exec(["-t", ""], ["/logo_title () def", "/show_title False def"]) _exec( ["--title", "3456"], ["/logo_title (3456) def", "/show_title True def"], ) def test_annotate() -> None: _exec(["--annotate", "1,2,3,4"], [], 2) _exec(["--annotate", "1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,,"], []) def test_color() -> None: _exec(["--color", "black", "AG", "Purine"], []) _exec(["--color", "not_a_color", "AG", "Purine"], [], 2) def test_reverse_complement() -> None: _exec(["--complement"], []) _exec(["--reverse"], []) _exec(["--revcomp"], []) def test_formats() -> None: _exec(["--format", "eps"], []) _exec(["--format", "png"], []) _exec(["--format", "png_print"], []) _exec(["--format", "pdf"], []) _exec(["--format", "jpeg"], []) _exec(["--format", "logodata"], []) _exec(["--format", "csv"], []) @pytest.mark.skipif(shutil.which("pdf2svg") is None, reason="requires pdf2svg") def test_formats_svg() -> None: _exec(["--format", "svg"], []) weblogo-3.8.0/tests/test_clustal_io.py000077500000000000000000000104161467613320200201020ustar00rootroot00000000000000#!/usr/bin/env python # Copyright (c) 2005 Gavin E. Crooks # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # import unittest from io import StringIO from weblogo.seq import nucleic_alphabet, protein_alphabet from weblogo.seq_io import clustal_io, fasta_io, table_io from . import data_stream class test_clustal_parser(unittest.TestCase): def test_parse_clustal(self) -> None: f = data_stream("clustal.aln") seqs = clustal_io.read(f) self.assertEqual(len(seqs), 7) self.assertEqual(seqs[1].name, "CATH_HUMAN") self.assertEqual(len(seqs[1]), 395) f.close() def test_parse_clustal2_newline(self) -> None: # Bug regession test. Clustal barfed on windows line endings, sometimes f = data_stream("clustalw2.aln") s = f.read() import re s = re.sub("\n", "\r\n", s) # Change to windows line endings clustal_io.read(StringIO(s)) f.close() def test_parse_headerless(self) -> None: f = data_stream("clustal_headerless.aln") seqs = clustal_io.read(f) self.assertEqual(len(seqs), 21) self.assertEqual(seqs[2].name, "O16386_CAEEL") self.assertEqual(len(seqs[1]), 137) f.close() """ Wrong alphabet should throw a parsing error """ def test_parse_error(self) -> None: f = data_stream("clustal.aln") self.assertRaises(ValueError, clustal_io.read, f, nucleic_alphabet) f.close() def test_parse_clustal181(self) -> None: f = data_stream("clustal181.aln") clustal_io.read(f) f.close() def test_parse_clustal_glualign(self) -> None: f = data_stream("clustal_glualign.aln") clustal_io.read(f, nucleic_alphabet) f.close() def test_parse_clustalw182(self) -> None: f = data_stream("clustalw182.aln") clustal_io.read(f, protein_alphabet) f.close() def test_parse_fasta_fail(self) -> None: # should fail with parse error f = StringIO(fasta_io.example) self.assertRaises(ValueError, clustal_io.read, f, protein_alphabet) self.assertRaises(ValueError, clustal_io.read, f) def test_parse_fasta_fail2(self) -> None: # should fail with parse error f = data_stream("globin.fa") self.assertRaises(ValueError, clustal_io.read, f) f.close() def test_parse_clustal_example(self) -> None: f = StringIO(clustal_io.example) clustal_io.read(f) f.close() def test_write(self) -> None: f = StringIO(clustal_io.example) seqs = clustal_io.read(f) fout = StringIO() clustal_io.write(fout, seqs) fout.seek(0) seqs2 = clustal_io.read(fout) self.assertEqual(seqs, seqs2) f.close() def test_parse_table_fail(self) -> None: # should fail with parse error f = StringIO(table_io.example) self.assertRaises(ValueError, clustal_io.read, f) f.close() def test_iterseq(self) -> None: f = StringIO(clustal_io.example) for s in clustal_io.iterseq(f): pass if __name__ == "__main__": unittest.main() weblogo-3.8.0/tests/test_data.py000077500000000000000000000011351467613320200166530ustar00rootroot00000000000000#!/usr/bin/env python import unittest from weblogo.data import ( amino_acid_composition, data_filename, data_stream, data_string, resource_names, ) class test_data(unittest.TestCase): def test_amino_acid_composition(self) -> None: cl = [amino_acid_composition[k] for k in "ARNDCQEGHILKMFPSTWYV"] self.assertAlmostEqual(sum(cl), 1) def test_resources(self) -> None: for n in resource_names: data_string(n) f = data_stream(n) f.close() data_filename(n) if __name__ == "__main__": unittest.main() weblogo-3.8.0/tests/test_fasta_io.py000077500000000000000000000132571467613320200175370ustar00rootroot00000000000000#!/usr/bin/env python # Copyright (c) 2005 Gavin E. Crooks # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # import unittest from io import StringIO from weblogo.seq import nucleic_alphabet, protein_alphabet from weblogo.seq_io import clustal_io, fasta_io, plain_io from . import data_stream example_with_optional_comments = """ >SEQUENCE_1 ;comment line 1 (optional) MTEITAAMVKELRESTGAGMMDCKNALSETNGDFDKAVQLLREKGLGKAAKKADRLAAEG LVSVKVSDDFTIAAMRPSYLSYEDLDMTFVENEYKALVAELEKENEERRRLKDPNKPEHK IPQFASRKQLSDAILKEAEEKIKEELKAQGKPEKIWDNIIPGKMNSFIADNSQLDSKLTL MGQFYVMDDKKTVEQVIAEKEKEFGGKIKIVEFICFEVGEGLEKKTEDFAAEVAAQL >SEQUENCE_2 ;comment line 1 (optional) ;comment line 2 (optional) SATVSEINSETDFVAKNDQFIALTKDTTAHIQSNSLQSVEELHSSTINGVKFEEYLKSQI ATIGENLVVRRFATLKAGANGVVNGYIHTNGRVGVVIAAACDSAEVASKSRDLLRQICMH """ example3 = """ > AAAGTG > AAAGCG > TGCCCT > TGCCTT """ example4 = """ > AAAGTG > AAAGCG TGCCCT > TGCCTT """ class test_fasta_io(unittest.TestCase): def test_read(self) -> None: f = StringIO(fasta_io.example) seqs = fasta_io.read(f) # print seqs self.assertEqual(len(seqs), 3) self.assertEqual(seqs[0].description, "Lamprey GLOBIN V - SEA LAMPREY") self.assertEqual(seqs[0].name, "Lamprey") self.assertEqual(len(seqs[1]), 231) # def test_read_long(self) -> None: # f = data_stream("NC_000913.ffn") # count = 0 # start = time.time() # for s in seq_io.fasta_io.read_seq(f): # count +=1 # end = time.time() # t = end-start # # self.assertEqual(count, 4243) # # # Timing is 3s 1.67 GHz G4 # # print t def test_read_fail(self) -> None: f = StringIO(fasta_io.example) # Wrong alphabet self.assertRaises(ValueError, fasta_io.read, f, nucleic_alphabet) def test_parse_globin(self) -> None: # f = open_resource(__file__, "test_data", "globin.fa") f = data_stream("globin.fa") seqs = fasta_io.read(f, protein_alphabet) self.assertEqual(len(seqs), 56) f.close() def test_parse_clustal_fail(self) -> None: # should fail with parse error f = StringIO(clustal_io.example) self.assertRaises(ValueError, fasta_io.read, f, protein_alphabet) def test_parse_plain_fail(self) -> None: # should fail with parse error f = StringIO(plain_io.example) self.assertRaises(ValueError, fasta_io.read, f) def test_write_seq(self) -> None: f = StringIO(fasta_io.example) seqs = fasta_io.read(f) fout = StringIO() fasta_io.write(fout, seqs) fout.seek(0) seqs2 = fasta_io.read(fout) self.assertEqual(seqs, seqs2) def test_write_with_header(self) -> None: f = StringIO(fasta_io.example) seqs = fasta_io.read(f) seqs.description = "A description\nMore description" fout = StringIO() fasta_io.write(fout, seqs) def test_read_comments(self) -> None: f = StringIO(example_with_optional_comments) seqs = fasta_io.read(f) self.assertEqual(len(seqs), 2) self.assertEqual(seqs[1].startswith("SATVSEI"), True) self.assertEqual( seqs[1].description.splitlines()[1], ("comment line 1 (optional)") ) def test_write_comments(self) -> None: f = StringIO(example_with_optional_comments) seqs = fasta_io.read(f) fout = StringIO() fasta_io.write(fout, seqs) fout.seek(0) seqs2 = fasta_io.read(fout) self.assertEqual(seqs, seqs2) self.assertEqual(seqs[1].description, seqs2[1].description) def test_read_headerless(self) -> None: # This example has blank headers. f = StringIO(example3) seqs = fasta_io.read(f) self.assertEqual(len(seqs), 4) # print seqs fout = StringIO() fasta_io.write(fout, seqs) def test_read_empty(self) -> None: f = StringIO() seqs = fasta_io.read(f) assert len(seqs) == 0 def test_isaligned(self) -> None: seqs = fasta_io.read(StringIO()) assert seqs.isaligned() seqs = fasta_io.read(StringIO(fasta_io.example)) assert seqs.isaligned() seqs = fasta_io.read(StringIO(example4)) assert not seqs.isaligned() def test_read_with_blank_line(self) -> None: f = StringIO(example4) seqs = fasta_io.read(f) assert not seqs.isaligned() self.assertEqual(len(seqs), 3) if __name__ == "__main__": unittest.main() weblogo-3.8.0/tests/test_genbank_io.py000077500000000000000000000056511467613320200200450ustar00rootroot00000000000000#!/usr/bin/env python # Copyright (c) 2005 Gavin E. Crooks # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # import unittest from weblogo import seq_io from weblogo.seq_io import genbank_io from . import data_stream def examples(): # type: ignore return ( data_stream("genbank/NT_019265.gb"), data_stream("genbank/cox2.gb"), data_stream("genbank/iro.gb"), data_stream("genbank/pri1.gb"), data_stream("genbank/dbsource_wrap.gb"), data_stream("genbank/noref.gb"), data_stream("genbank/protein_refseq.gb"), data_stream("genbank/cor6_6.gb"), data_stream("genbank/origin_line.gb"), # These files are too large to include in the distribution # data_stream('genbank/arab1.gb'), # data_stream('genbank/NC_005213.gbk'), # data_stream('genbank/NC_003888.gbk'), ) class test_genbank_io(unittest.TestCase): # Useful for debugging # def test_scan(self) : # for f in examples(): # for t in genbank_io._scan(f): # print t # print # print def test_parse(self) -> None: for f in examples(): # print f.name genbank_io.read(f) f.close() # print seqs def test_read(self) -> None: f = data_stream("genbank/cox2.gb") seqs = genbank_io.read(f) self.assertEqual(len(seqs), 5) self.assertEqual(len(seqs[1]), 210) f.seek(0) seqs = seq_io.read(f) self.assertEqual(len(seqs), 5) self.assertEqual(len(seqs[1]), 210) f.close() f = data_stream("genbank/NT_019265.gb") seqs = genbank_io.read(f) self.assertEqual(len(seqs), 0) f.close() if __name__ == "__main__": unittest.main() weblogo-3.8.0/tests/test_intelligenetics_io.py000077500000000000000000000045511467613320200216200ustar00rootroot00000000000000# Copyright (c) 2005 Gavin E. Crooks # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # from io import StringIO import pytest import weblogo.seq_io.intelligenetics_io as ig_io from weblogo.seq import rna_alphabet from . import data_stream def test_read() -> None: f = StringIO(ig_io.example) seqs = ig_io.read(f) assert len(seqs) == 2 assert seqs[0].description == "H.sapiens fau mRNA, 518 bases" assert seqs[1].name == "HSFAU1" assert len(seqs[1]) == 299 def test_read2() -> None: f = data_stream("intelligenetics.txt") seqs = ig_io.read(f) assert len(seqs[0]) == 518 assert len(seqs[1]) == 2016 f.close() def test_write_seq() -> None: f = StringIO(ig_io.example) seqs = ig_io.read(f) fout = StringIO() ig_io.write(fout, seqs) fout.seek(0) seqs2 = ig_io.read(fout) assert seqs == seqs2 def test_read_fail() -> None: with pytest.raises(ValueError): f = data_stream("intelligenetics.txt") ig_io.read(f, alphabet=rna_alphabet) def test_write_seq_fail() -> None: f = StringIO(ig_io.example) seqs = ig_io.read(f) seqs[0].name = "" fout = StringIO() with pytest.raises(ValueError): ig_io.write(fout, seqs) weblogo-3.8.0/tests/test_matrix.py000077500000000000000000000060541467613320200172530ustar00rootroot00000000000000#!/usr/bin/env python import unittest import numpy as np from weblogo.matrix import AlphabeticArray, Motif from weblogo.seq import protein_alphabet from . import data_stream class test_AlphabeticArray(unittest.TestCase): def test_create(self) -> None: matrix = AlphabeticArray((protein_alphabet, protein_alphabet)) matrix["A", "C"] = 10 assert matrix[0, 1] == 10.0 class test_Motif(unittest.TestCase): def test_read_transfac_alphabet_superset(self) -> None: with data_stream("transfac_matrix.txt") as f: Motif.read_transfac(f, alphabet="TCGA") # Supplied alphabet can be superset of defacto alphabet. # Reverts to defacto alphabet with data_stream("transfac_matrix.txt") as f: Motif.read_transfac(f, alphabet="TCGAXYZ") def test_read_transfac(self) -> None: f = data_stream("transfac_matrix.txt") m = Motif.read_transfac(f) f.close() assert m[3, "A"] == 0.0 assert m[0, "G"] == 2.0 assert np.shape(m.array) == (12, 4) f.close() f = data_stream("transfac_matrix2.txt") m = Motif.read_transfac(f) f.close() assert m[3, "A"] == 3.0 assert m[0, "G"] == 152.0 assert np.shape(m.array) == (15, 4) # this one has extra Ps on start of each line f = data_stream("transfac_matrix3.txt") m = Motif.read_transfac(f) f.close() def test_reindex(self) -> None: f = data_stream("transfac_matrix.txt") m = Motif.read_transfac(f) f.close() m2 = m.reindex("TCGA") assert str(m2.alphabet) == "TCGA" for k in range(0, 12): for i, a in enumerate("AGCT"): assert m[k, a] == m2[k, a] def test_reverse(self) -> None: f = data_stream("transfac_matrix.txt") m = Motif.read_transfac(f) f2 = data_stream("transfac_matrix.txt") m2 = Motif.read_transfac(f2) m2.reverse() (K, N) = np.shape(m2) for k in range(0, K): for n in range(0, N): assert m[k, n] == m2[K - k - 1, n] f.close() f2.close() def test_complement(self) -> None: f = data_stream("transfac_matrix.txt") m = Motif.read_transfac(f) f2 = data_stream("transfac_matrix.txt") m2 = Motif.read_transfac(f2) m2.complement() (K, N) = np.shape(m2) for k in range(0, K): assert m[k, "A"] == m2[k, "T"] assert m[k, "G"] == m2[k, "C"] assert m[k, "C"] == m2[k, "G"] assert m[k, "T"] == m2[k, "A"] f.close() f2.close() def test_reverse_complement(self) -> None: f = data_stream("transfac_matrix.txt") m = Motif.read_transfac(f) f2 = data_stream("transfac_matrix.txt") m2 = Motif.read_transfac(f2) m.complement() m.reverse() m2.reverse_complement() assert (m.array == m2.array).all() f.close() f2.close() if __name__ == "__main__": unittest.main() weblogo-3.8.0/tests/test_msf_io.py000077500000000000000000000074661467613320200172330ustar00rootroot00000000000000#!/usr/bin/env python # Copyright (c) 2006, The Regents of the University of California, through # Lawrence Berkeley National Laboratory (subject to receipt of any required # approvals from the U.S. Dept. of Energy). All rights reserved. # This software is distributed under the new BSD Open Source License. # # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions are met: # # (1) Redistributions of source code must retain the above copyright notice, # this list of conditions and the following disclaimer. # # (2) Redistributions in binary form must reproduce the above copyright # notice, this list of conditions and the following disclaimer in the # documentation and or other materials provided with the distribution. # # (3) Neither the name of the University of California, Lawrence Berkeley # National Laboratory, U.S. Dept. of Energy nor the names of its contributors # may be used to endorse or promote products derived from this software # without specific prior written permission. # # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" # AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE # IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE # ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE # LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR # CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF # SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS # INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN # CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE # POSSIBILITY OF SUCH DAMAGE. import unittest from io import StringIO from weblogo.seq import nucleic_alphabet from weblogo.seq_io import msf_io, plain_io from . import data_stream class test_msf_io(unittest.TestCase): def test_parse_msf(self) -> None: f = data_stream("dna.msf") seqs = msf_io.read(f) self.assertEqual(len(seqs), 10) self.assertEqual(seqs[1].name, "Carp") self.assertEqual(len(seqs[1]), 705) self.assertEqual(str(seqs[2][0:10]), "ATGGCCAACC") f.close() def test_parse_msf2(self) -> None: f = data_stream("cox2.msf") seqs = msf_io.read(f) self.assertEqual(len(seqs), 5) self.assertEqual(seqs[1].name, "cox2_crifa") self.assertEqual(len(seqs[1]), 166) self.assertEqual(str(seqs[2][0:10]), "MSFILTFWMI") f.close() def test_parse_1beo(self) -> None: f = data_stream("1beo.msf") msf_io.read(f) f.close() """ Wrong alphabet should throw a parsing error """ def test_parse_error(self) -> None: f = data_stream("cox2.msf") self.assertRaises(ValueError, msf_io.read, f, nucleic_alphabet) f.close() def test_parse_fasta_fail2(self) -> None: # should fail with parse error f = data_stream("globin.fa") self.assertRaises(ValueError, msf_io.read, f) f.close() def test_parse_plain_fail(self) -> None: # should fail with parse error f = StringIO(plain_io.example) self.assertRaises(ValueError, msf_io.read, f) f.close() def test_parse_phylip_fail(self) -> None: # should fail with parse error f = data_stream("phylip_test_2.phy") self.assertRaises(ValueError, msf_io.read, f) f.close() def test_iter(self) -> None: f = data_stream("1beo.msf") for seq in msf_io.iterseq(f): pass f.close() if __name__ == "__main__": unittest.main() weblogo-3.8.0/tests/test_nbrf_io.py000077500000000000000000000115011467613320200173560ustar00rootroot00000000000000#!/usr/bin/env python # Copyright (c) 2006, The Regents of the University of California, through # Lawrence Berkeley National Laboratory (subject to receipt of any required # approvals from the U.S. Dept. of Energy). All rights reserved. # This software is distributed under the new BSD Open Source License. # # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions are met: # # (1) Redistributions of source code must retain the above copyright notice, # this list of conditions and the following disclaimer. # # (2) Redistributions in binary form must reproduce the above copyright # notice, this list of conditions and the following disclaimer in the # documentation and or other materials provided with the distribution. # # (3) Neither the name of the University of California, Lawrence Berkeley # National Laboratory, U.S. Dept. of Energy nor the names of its contributors # may be used to endorse or promote products derived from this software # without specific prior written permission. # # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" # AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE # IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE # ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE # LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR # CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF # SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS # INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN # CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE # POSSIBILITY OF SUCH DAMAGE. import unittest from io import StringIO from weblogo.seq import dna_alphabet, protein_alphabet from weblogo.seq_io import clustal_io, nbrf_io, plain_io from . import data_stream class test_nbrf_io(unittest.TestCase): def test_parse_cox2(self) -> None: f = data_stream("cox2.nbrf") seqs = nbrf_io.read(f) self.assertEqual(len(seqs), 5) self.assertEqual(len(seqs[1]), 210) self.assertEqual( str(seqs[0]), "MAFILSFWMIFLLDSVIVLLSFVCFVCVWICALLFSTVLLVSKLNNIYCTWDFTASKFIDVYWFTIGGMFSLG" "LLLRLCLLLYFGHLNFVSFDLCKVVGFQWYWVYFIFGETTIFSNLILESDYMIGDLRLLQCNHVLTLLSLVIY" "KLWLSAVDVIHSFAISSLGVKVENLVAVMK", ) self.assertEqual(seqs[0].alphabet, protein_alphabet) f.close() def test_parse_crab(self) -> None: f = data_stream("crab.nbrf") seqs = nbrf_io.read(f) self.assertEqual(seqs[0].alphabet, protein_alphabet) self.assertEqual(len(seqs), 9) self.assertEqual(seqs[2].name, "CRAB_CHICK") self.assertEqual( seqs[2].description, "ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN)." ) f.close() def test_parse_dna(self) -> None: f = data_stream("dna.pir") seqs = nbrf_io.read(f) self.assertEqual(seqs[0].alphabet, dna_alphabet) self.assertEqual(len(seqs), 10) f.close() def test_parse_examples(self) -> None: f = data_stream("rhod.pir") seqs = nbrf_io.read(f) self.assertEqual(seqs[0].alphabet, protein_alphabet) self.assertEqual(len(seqs), 3) f.close() def test_parse_protein(self) -> None: f = data_stream("protein.pir") seqs = nbrf_io.read(f) self.assertEqual(seqs[0].alphabet, protein_alphabet) self.assertEqual(len(seqs), 10) f.close() def test_parse_clustal_fail(self) -> None: # should fail with parse error f = StringIO(clustal_io.example) self.assertRaises(ValueError, nbrf_io.read, f, protein_alphabet) def test_parse_plain_fail(self) -> None: # should fail with parse error f = StringIO(plain_io.example) self.assertRaises(ValueError, nbrf_io.read, f) def test_pir_file_from_clustal(self) -> None: f = data_stream("clustalw.pir") seqs = nbrf_io.read(f) self.assertEqual(len(seqs), 2) self.assertEqual( seqs[1].endswith( "C-AATC-G-CAATG-G--CTTGAACCGGGTAAAAGTCGT-A----------------------------------------" "-----------------------------------------" ), True, ) f.close() def test_parse_examples_alphabet(self) -> None: f = data_stream("rhod.pir") seqs = nbrf_io.read(f, alphabet=protein_alphabet) self.assertEqual(seqs[0].alphabet, protein_alphabet) self.assertEqual(len(seqs), 3) f.close() if __name__ == "__main__": unittest.main() weblogo-3.8.0/tests/test_nexus.py000077500000000000000000000031731467613320200171100ustar00rootroot00000000000000#!/usr/bin/env python import unittest from weblogo.seq_io._nexus import Nexus from . import data_stream class test_nexus(unittest.TestCase): def test_create(self) -> None: n = Nexus() self.assertNotEqual(n, None) def test_parse_f0(self) -> None: f = data_stream("nexus/test_Nexus_input.nex") n = Nexus(f) # self.output_basics(n) expected = [ "t1", "t2 the name", "isn'that [a] strange name?", "one should be punished, for (that)!", "t5", "t6", "t7", "t8", "t9", ] taxa = n.taxlabels self.assertEqual(taxa, expected) f.close() def test_parse_protein(self) -> None: f = data_stream("nexus/protein.nex") Nexus(f) f.close() def test_parse_dna(self) -> None: f = data_stream("nexus/dna.nex") n = Nexus(f) taxa = n.taxlabels taxa.sort() self.assertEqual(len(taxa), 10) self.assertEqual(taxa[0], "Carp") self.assertEqual(taxa[-1], "Whale") f.close() def test_TreeTest1(self) -> None: """Test Tree module.""" f = data_stream("nexus/test_Nexus_input.nex") n = Nexus(f) t3 = n.trees[2] n.trees[2] t3.root_with_outgroup(["t1", "t5"]) # Return node_id of common ancestor if # taxon_list is monophyletic, -1 otherwise. self.assertEqual(t3.is_monophyletic(["t1", "t5"]), 13) t3.split(parent_id=t3.search_taxon("t9")) f.close() if __name__ == "__main__": unittest.main() weblogo-3.8.0/tests/test_nexus_io.py000077500000000000000000000026331467613320200175770ustar00rootroot00000000000000from io import StringIO import pytest from weblogo.seq import protein_alphabet from weblogo.seq_io import clustal_io, nexus_io, plain_io from . import data_stream def test_read() -> None: f = data_stream("nexus/protein.nex") seqs = nexus_io.read(f) # print seqs assert len(seqs) == 10 assert seqs[0].name == "Cow" assert len(seqs[1]) == 234 assert str(seqs[0][0:10]) == "MAYPMQLGFQ" f.close() def test_parse_StringIO() -> None: # Bio.Nexus cannot read from a StringIO object. f0 = data_stream("nexus/protein.nex") f = StringIO(f0.read()) nexus_io.read(f) f0.close() def test_parse_fasta_fail() -> None: with pytest.raises(ValueError): with data_stream("globin.fa") as f: nexus_io.read(f) def test_parse_clustal_fail() -> None: # should fail with parse error with pytest.raises(ValueError): f = StringIO(clustal_io.example) nexus_io.read(f, protein_alphabet) def test_parse_plain_fail() -> None: # should fail with parse error f = StringIO(plain_io.example) with pytest.raises(ValueError): nexus_io.read(f) def test_iterseq() -> None: f = data_stream("nexus/protein.nex") for seq in nexus_io.iterseq(f): pass def test_read_alphabet() -> None: f = data_stream("nexus/protein.nex") seqs = nexus_io.read(f, alphabet=protein_alphabet) # print seqs assert len(seqs) == 10 weblogo-3.8.0/tests/test_null_io.py000077500000000000000000000033141467613320200174040ustar00rootroot00000000000000#!/usr/bin/env python # Copyright (c) 2005 Gavin E. Crooks # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # from io import StringIO from weblogo.seq_io import null_io, plain_io def test_read() -> None: f = StringIO(plain_io.example) null_io.read(f) def test_write() -> None: f = StringIO(plain_io.example) seqs = plain_io.read(f) fout = StringIO() null_io.write(fout, seqs) fout.seek(0) assert fout.read() == "" def test_iterseq() -> None: f = StringIO(plain_io.example) for seq in null_io.iterseq(f): pass weblogo-3.8.0/tests/test_phylip_io.py000077500000000000000000000121371467613320200177420ustar00rootroot00000000000000#!/usr/bin/env python # Copyright (c) 2006, The Regents of the University of California, through # Lawrence Berkeley National Laboratory (subject to receipt of any required # approvals from the U.S. Dept. of Energy). All rights reserved. # This software is distributed under the new BSD Open Source License. # # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions are met: # # (1) Redistributions of source code must retain the above copyright notice, # this list of conditions and the following disclaimer. # # (2) Redistributions in binary form must reproduce the above copyright # notice, this list of conditions and the following disclaimer in the # documentation and or other materials provided with the distribution. # # (3) Neither the name of the University of California, Lawrence Berkeley # National Laboratory, U.S. Dept. of Energy nor the names of its contributors # may be used to endorse or promote products derived from this software # without specific prior written permission. # # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" # AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE # IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE # ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE # LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR # CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF # SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS # INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN # CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE # POSSIBILITY OF SUCH DAMAGE. import unittest from io import StringIO from weblogo.seq import protein_alphabet from weblogo.seq_io import clustal_io, phylip_io, plain_io from . import data_stream class test_phylip_io(unittest.TestCase): def test_read(self) -> None: f = data_stream("phylip_test_1.phy") seqs = phylip_io.read(f) # print seqs self.assertEqual(len(seqs), 10) self.assertEqual(seqs[0].name, "Cow") self.assertEqual(len(seqs[1]), 234) f.close() def test_iterseq(self) -> None: f = data_stream("phylip_test_1.phy") n = 0 for seq in phylip_io.iterseq(f): n += 1 assert n == 10 f.close() def test_parse_plain_fail(self) -> None: # should fail with parse error f = StringIO(plain_io.example) self.assertRaises(ValueError, phylip_io.read, f) def test_parse_phylip_test_2(self) -> None: f = data_stream("phylip_test_2.phy") seqs = phylip_io.read(f) self.assertEqual(len(seqs), 6) self.assertEqual(len(seqs[0]), 20) self.assertEqual(str(seqs[1]), "CGTTACTCGTTGTCGTTACT") self.assertEqual(seqs[1].name, "Hesperorni") f.close() def test_parse_clustal_fail(self) -> None: # should fail with parse error f = StringIO(clustal_io.example) self.assertRaises(ValueError, phylip_io.read, f, protein_alphabet) def test_parse_phylip_test_3(self) -> None: f = data_stream("phylip_test_3.phy") seqs = phylip_io.read(f) self.assertEqual(len(seqs), 6) self.assertEqual(len(seqs[0]), 20) self.assertEqual(str(seqs[1]), "CGTTACTCGTTGTCGTTACT") self.assertEqual(seqs[1].name, "Hesperorni") f.close() def test_parse_phylip_test_4(self) -> None: f = data_stream("phylip_test_4.phy") seqs = phylip_io.read(f) self.assertEqual(len(seqs), 6) self.assertEqual(len(seqs[0]), 25) self.assertEqual(str(seqs[1]), "GTGGTGGTGGGCGCCGGCCGTGTGG") self.assertEqual(seqs[2].name, "ddrasa") f.close() def test_parse_phylip_test_5(self) -> None: f = data_stream("phylip_test_5.phy") seqs = phylip_io.read(f) self.assertEqual(len(seqs), 6) self.assertEqual(len(seqs[0]), 50) self.assertEqual( str(seqs[1]), "GTGGTGGTGGGCGCCGGCCGTGTGGGTGGTGGTGGGCGCCGGCCGTGTGG" ) self.assertEqual(seqs[2].name, "ddrasa") f.close() def test_parse_wrong_phylip_codes_1(self) -> None: f = data_stream("phylip_test_6.corrupt.phy") self.assertRaises(ValueError, phylip_io.read, f, protein_alphabet) f.close() def test_parse_wrong_phylip_codes_2(self) -> None: f = data_stream("phylip_test_7.corrupt.phy") self.assertRaises(ValueError, phylip_io.read, f, protein_alphabet) f.close() def test_parse_phylip_dna(self) -> None: f = data_stream("dna.phy") seqs = phylip_io.read(f) self.assertEqual(len(seqs), 10) self.assertEqual(len(seqs[0]), 705) self.assertEqual(str(seqs[1][0:10]), "ATGGCACACC") self.assertEqual(seqs[2].name, "Chicken") f.close() if __name__ == "__main__": unittest.main() weblogo-3.8.0/tests/test_plain_io.py000077500000000000000000000044031467613320200175350ustar00rootroot00000000000000#!/usr/bin/env python # Copyright (c) 2005 Gavin E. Crooks # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # from io import StringIO import pytest from weblogo.seq import protein_alphabet, rna_alphabet from weblogo.seq_io import fasta_io, plain_io def test_read_example() -> None: f = StringIO(plain_io.example) seqs = plain_io.read(f) # print seqs assert len(seqs) == 1 assert not seqs[0].name # print seqs[0] assert len(seqs[0]) == 450 def test_write_seq() -> None: f = StringIO(plain_io.example) seqs = plain_io.read(f) fout = StringIO() plain_io.write(fout, seqs) fout.seek(0) seqs2 = plain_io.read(fout) # print seqs[0].alphabet !=seqs2[0].alphabet assert seqs[0].alphabet == seqs2[0].alphabet assert seqs[0] == seqs2[0] assert seqs == seqs2 def test_parse_fasta_fail() -> None: # should fail with parse error with pytest.raises(ValueError): f = StringIO(fasta_io.example) plain_io.read(f, protein_alphabet) with pytest.raises(ValueError): f = StringIO(plain_io.example) plain_io.read(f, rna_alphabet) weblogo-3.8.0/tests/test_seq.py000077500000000000000000000360231467613320200165360ustar00rootroot00000000000000#!/usr/bin/env python # Copyright (c) 2005 Gavin E. Crooks # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # import unittest import pytest from weblogo import seq_io from weblogo.seq import ( Alphabet, Seq, SeqList, dna, dna_alphabet, generic_alphabet, nucleic_alphabet, protein, protein_alphabet, rna, unambiguous_dna_alphabet, unambiguous_protein_alphabet, ) from . import data_stream class test_alphabet(unittest.TestCase): def test_create_alphabet(self) -> None: # Alphabet contains repeated character self.assertRaises(ValueError, Alphabet, "alphabet") # Alphabet contains null character self.assertRaises(ValueError, Alphabet, "alph\x00") Alphabet("alphbet") def test_alphabet_alphabetic(self) -> None: a = Alphabet("alphbet") self.assertTrue(a.alphabetic("alphbet")) self.assertTrue(not a.alphabetic("alphbetX")) def test_alphabet_ord(self) -> None: a = generic_alphabet for i, c in enumerate(a): self.assertEqual(a.ord(c), i) a = Alphabet("alph") self.assertEqual(2, a.ord("p")) def test_alphabet_chr(self) -> None: a = generic_alphabet for i, c in enumerate(a): self.assertEqual(ord(a.chr(i)), i + 32) a = Alphabet("alph") self.assertEqual("h", a.chr(3)) def test_alphabet_ords(self) -> None: a = Alphabet("alph") self.assertEqual(0, a.ords("alphalph")[4]) a = generic_alphabet o = a.ords(str(a)) for i, c in enumerate(o): self.assertEqual(c, i) def test_alphabet_chrs(self) -> None: a = Alphabet("alph") self.assertEqual(Seq("ppla", a), a.chrs((2, 2, 1, 0))) def test_none(self) -> None: a1 = Alphabet(None) self.assertEqual(a1, generic_alphabet) def test_create_from_alphabet(self) -> None: """If we pass an alphabet to the constuctor, it's passed right back""" a1 = Alphabet("kjdahf") a2 = Alphabet(str(a1)) self.assertTrue(a1 == a2) self.assertFalse(a1 == "not an alphabet") def test_repr(self) -> None: a = Alphabet("kjdahf") repr(a) str(a) def test_str(self) -> None: self.assertEqual(str(Alphabet("kjdahf")), "kjdahf") def test_letters(self) -> None: self.assertEqual(Alphabet("kjdahf").letters(), "kjdahf") def test_normalize(self) -> None: a = Alphabet("ABCDE") s = "aBbc" n = a.normalize(s) self.assertEqual(str(n), "ABBC") self.assertRaises(ValueError, a.normalize, "aslkfdnnr33") def test_alt(self) -> None: alt = tuple(zip("12345", "ABCED")) alpha = Alphabet("ABCDE", alt) assert alpha.ord("A") == 0 for a, c in alt: assert alpha.ord(a) == alpha.ord(c) def test_which_alphabet(self) -> None: a = Alphabet.which(Seq("ARNDCQEGHILKMFPSTWYVX")) assert a == unambiguous_protein_alphabet f1 = data_stream("cap.fa") f2 = data_stream("cox2.msf") f3 = data_stream("Rv3829c.fasta") f4 = data_stream("chain_B.fasta") tests = ( (seq_io.read(f1), unambiguous_dna_alphabet), (seq_io.read(f2), unambiguous_protein_alphabet), (seq_io.read(f3), unambiguous_protein_alphabet), (seq_io.read(f4), unambiguous_protein_alphabet), ) for t in tests: self.assertEqual(Alphabet.which(t[0]), t[1]) f1.close() f2.close() f3.close() f4.close() class test_seq(unittest.TestCase): def test_create_seq(self) -> None: self.assertTrue(Seq("alphabet", Alphabet("alphbet"))) self.assertRaises(ValueError, Seq, "not alphabetic", "alphabet") a = ( "Any printable Ascii character `1234567890-=~!@#$%^&*()_+{}|[]\\:;'<>?,./QWERTYUIOPASD" "FGHJKLZXCVBNMqwertyuiopasdfghjklzxcvbnm " ) for x in a: self.assertTrue(x in generic_alphabet) self.assertTrue(Seq(a, generic_alphabet)) self.assertRaises(ValueError, Seq, "Not zero. \x00", generic_alphabet) def test_std_alphabets(self) -> None: s = Seq("dskjjfskdjbfKJJSJKSKJDjk123u768erbm", generic_alphabet) s = Seq("ARNDCQEGHILKMFPSTWYVX", protein_alphabet) self.assertRaises(ValueError, Seq, "1234", protein_alphabet) s = Seq("AGTCAGCTACGACGCGC", dna_alphabet) self.assertEqual(str(s[1]), "G") def test_ords(self) -> None: a = Alphabet("ABC") s = Seq("ABCCBA", a) self.assertEqual(list(s.ords()), [0, 1, 2, 2, 1, 0]) def test_tally(self) -> None: s = Seq("AGTCAGCTACGACGCGC", unambiguous_dna_alphabet) c = s.tally() self.assertEqual(len(unambiguous_dna_alphabet), len(c)) self.assertEqual(list(c), [4, 6, 5, 2]) def test_tally_nonalphabetic(self) -> None: s = Seq("AGTCAGCTACGACGCGC", dna_alphabet) c = s.tally(Alphabet("AC")) self.assertEqual(2, len(c)) self.assertEqual(list(c), [4, 6]) def test_words(self) -> None: s = Seq("AGTCAGCTACGACGcgcx", dna_alphabet) w = list(s.words(2, unambiguous_dna_alphabet)) self.assertEqual(len(w), len(s) - 2) self.assertEqual( w, [ "AG", "GT", "TC", "CA", "AG", "GC", "CT", "TA", "AC", "CG", "GA", "AC", "CG", "GC", "CG", "GC", ], ) self.assertEqual(list(s.words(len(s), unambiguous_dna_alphabet)), []) self.assertEqual( list(s.words(len(s) - 1, unambiguous_dna_alphabet)), [ "AGTCAGCTACGACGCGC", ], ) w = list(s.words(200, unambiguous_dna_alphabet)) def test_words2(self) -> None: s = Seq("AGTCAGCTACGACGCGC", unambiguous_dna_alphabet) wc = s.word_count(2) count = list(zip(*wc))[1] self.assertEqual(count, (2, 2, 1, 3, 1, 1, 3, 1, 1, 1)) def test_getslice(self) -> None: s = Seq("AGTCAGCTACGACGCGC", dna_alphabet) slice = s[2:4] self.assertEqual(s.alphabet, slice.alphabet) def test_create_annotated(self) -> None: s = "ACGTURYSWKMBDHVNACGTURYSWKMBDHVNAAAAA" a = Seq(s, nucleic_alphabet, name="ID", description="DESCRIPTION") self.assertEqual(a.name, "ID") self.assertEqual(a.description, "DESCRIPTION") self.assertEqual(s, str(a)) def test_add(self) -> None: s1 = Seq("AAAA", dna_alphabet) s2 = Seq("TTTT", dna_alphabet) s3 = s1 + s2 self.assertEqual(s3.alphabet, dna_alphabet) self.assertEqual(s3, Seq("AAAATTTT", dna_alphabet)) assert s3 == Seq("AAAATTTT", dna_alphabet) assert s3 != Seq("AAAATTTT", protein_alphabet) assert s3 != "not a seq" s4 = "AA" s5 = s4 + s1 s6 = s1 + s4 self.assertEqual(s5.alphabet, s6.alphabet) self.assertEqual(s5, s6) assert s5 == s6 assert not (s5 != s6) def test_join(self) -> None: s1 = Seq("AAAA", dna_alphabet) s2 = Seq("TTTT", dna_alphabet) s3 = Seq("GGGG") s0 = Seq("", dna_alphabet) j = s0.join([s1, s2, s3]) self.assertEqual(j, Seq("AAAATTTTGGGG", dna_alphabet)) def test_repr(self) -> None: s1 = Seq("AAAA", dna_alphabet) repr(s1) def test_str(self) -> None: s1 = Seq("AGCTA", dna_alphabet) self.assertEqual(str(s1), "AGCTA") # Uncased alpahebt self.assertEqual(str(Seq("AgcTA", dna_alphabet)), "AgcTA") def test_tostring(self) -> None: self.assertEqual(Seq("AgcTAAAA", dna_alphabet).tostring(), "AgcTAAAA") def test_reverse(self) -> None: s = Seq("ACGT", dna_alphabet) self.assertEqual(s, s.reverse().reverse()) self.assertEqual(s.reverse(), Seq("TGCA", dna_alphabet)) def test_translate(self) -> None: s = dna("GCCATTGTAATGGGCCGCTGAAAGGGTGCCCGA") p = s.translate() self.assertEqual(str(p), "AIVMGR*KGAR") p.back_translate() def test_reverse_complement(self) -> None: s = dna("GGGGaaaaaaaatttatatat") rc = s.reverse_complement() self.assertEqual(rc, dna("atatataaattttttttCCCC")) self.assertEqual( dna("ACGTRYSWKMBDHVN").reverse_complement(), dna("NBDHVKMWSRYACGT") ) self.assertRaises(ValueError, protein("G").reverse_complement) def test_ungap(self) -> None: s = Seq("T-T", dna_alphabet).ungap() self.assertEqual(str(s), "TT") s = Seq("T-~---T...~~~--", dna_alphabet).ungap() self.assertEqual(str(s), "TT") def test_mask(self) -> None: s = dna("AAaaaaAAA").mask() self.assertEqual(str(s), "AAXXXXAAA") def test_shortcuts(self) -> None: protein("gGGGGG-PPPPP") dna("ACGTRYSWKMBDHVN") dna("t") dna("actgta") dna("acgtrysw-kmb-dhvn") rna("ACUUUUU") def test_casechange(self) -> None: s1 = dna("ACGTRYSWKMBDHVN") s2 = s1.lower().upper() self.assertEqual(s1, s2) def test_slice(self) -> None: s1 = dna("ACGTRYSWKMBDHVN") s2 = s1[4:6] assert s2 == dna("RY") class test_seqlist(unittest.TestCase): def test_create(self) -> None: # 1234567890123456789012345678 s0 = Seq("ACGTURYBDHVNACGTURYSWKMBDHVN", nucleic_alphabet) s1 = Seq("ACGTURYSWKMBDHVNACGTURYSWKMBDHVN", nucleic_alphabet) s2 = Seq("ACGTURSWKMBDHVNACGTURKMBDHVN", nucleic_alphabet) seqs = SeqList([s0, s1, s2]) self.assertEqual(len(seqs), 3) def test_create_annotated(self) -> None: s0 = Seq("ACGTURYBDHVNACGTURYSWKMBDHVN", nucleic_alphabet) s1 = Seq("ACGTURYSWKMBDHVNACGTURYSWKMBDHVN", nucleic_alphabet) s2 = Seq("ACGTURSWKMBDHVNACGTURKMBDHVN", nucleic_alphabet) seqs = SeqList( [s0, s1, s2], alphabet=nucleic_alphabet, name="alsdf", description="a" ) self.assertEqual(seqs.name, "alsdf") self.assertEqual(seqs.description, "a") self.assertEqual(seqs.alphabet, nucleic_alphabet) def test_ords(self) -> None: s0 = Seq("ACGTURYBDHVNACGTURYSWKMBDHVN", nucleic_alphabet) s1 = Seq("ACGTURYSDHVNACGTURYSWKMBDHVN", nucleic_alphabet) s2 = Seq("ACGTURSWKMBDHVNACGTURKMBDHVN", nucleic_alphabet) seqs = SeqList([s0, s1, s2], nucleic_alphabet) seqs.ords() # self.assertEqual( a.shape, (3, 28) ) # Fails if seqs are of different lengths # FIXME? # s3 = Seq("ACGTUR", nucleic_alphabet ) # seqs2 = SeqList( [ s0,s1,s3,s2], nucleic_alphabet) # self.assertRaises(ValueError, seqs2.ords ) # Use a different alphabet seqs.ords(nucleic_alphabet) # No alphabet seqs3 = SeqList([s0, s1, s2]) seqs3.ords(alphabet=Alphabet("ABC")) # Fail if no alphabet self.assertRaises(ValueError, seqs3.ords) def test_isaligned(self) -> None: a = Alphabet("ABCD") s0 = Seq("ABCDD", a) s1 = Seq("AAAAD", a) s2 = Seq("AAABD", a) s3 = Seq("AAACD", a) seqs = SeqList([s0, s1, s2, s3], a) assert seqs.isaligned() seqs = SeqList([s0, s1, s2, s3], Alphabet("ABCDE")) assert not seqs.isaligned() def test_profile(self) -> None: a = Alphabet("ABCD") s0 = Seq("ABCDD", a) s1 = Seq("AAAAD", a) s2 = Seq("AAABD", a) s3 = Seq("AAACD", a) seqs = SeqList([s0, s1, s2, s3], a) tally = seqs.profile() self.assertEqual(list(tally[0]), [4, 0, 0, 0]) self.assertEqual(list(tally[1]), [3, 1, 0, 0]) self.assertEqual(list(tally[2]), [3, 0, 1, 0]) self.assertEqual(list(tally[3]), [1, 1, 1, 1]) self.assertEqual(list(tally[4]), [0, 0, 0, 4]) self.assertEqual(tally[4, "D"], 4) seqs = SeqList([Seq("AAACD", a), Seq("AAACDA", a)], a) self.assertRaises(ValueError, seqs.profile) seqs = SeqList([Seq("AAACD", a), Seq("AAACD", a)]) self.assertRaises(ValueError, seqs.profile) def test_tally(self) -> None: # 1234567890123456789012345678 s0 = Seq("ACTTT", nucleic_alphabet) s1 = Seq("ACCCC", nucleic_alphabet) s2 = Seq("GGGG", nucleic_alphabet) seqs = SeqList([s0, s1, s2], nucleic_alphabet) counts = seqs.tally() assert counts == [2, 5, 4, 3, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0] seqs = SeqList([Seq("AAACD", nucleic_alphabet), Seq("AAACD", nucleic_alphabet)]) self.assertRaises(ValueError, seqs.tally) def test_create_empty(self) -> None: s0 = Seq("ACGTURYBDHVNACGTURYSWKMBDHVN", nucleic_alphabet) s1 = Seq("ACGTURYSWKMBDHVNACGTURYSWKMBDHVN", nucleic_alphabet) s2 = Seq("ACGTURSWKMBDHVNACGTURKMBDHVN", nucleic_alphabet) seqs = SeqList() seqs.append(s0) seqs.extend((s1, s2)) self.assertEqual(len(seqs), 3) self.assertEqual(type(seqs), SeqList) def test_repr(self) -> None: s0 = Seq("ACGTURYBDHVNACGTURYSWKMBDHVN", nucleic_alphabet) s1 = Seq("ACGTURYSWKMBDHVNACGTURYSWKMBDHVN", nucleic_alphabet) s2 = Seq("ACGTURSWKMBDHVNACGTURKMBDHVN", nucleic_alphabet) seqs = SeqList([s0, s1, s2]) repr(seqs) def test_str(self) -> None: s0 = Seq("ACGTURYBDHVNACGTURYSWKMBDHVN", nucleic_alphabet) s1 = Seq("ACGTURYSWKMBDHVNACGTURYSWKMBDHVN", nucleic_alphabet) s2 = Seq("ACGTURSWKMBDHVNACGTURKMBDHVN", nucleic_alphabet) seqs = SeqList([s0, s1, s2]) str(seqs) def test_bad_mask() -> None: with pytest.raises(ValueError): dna("AAaaaaAAA").mask(mask="ABC") if __name__ == "__main__": unittest.main() weblogo-3.8.0/tests/test_seq_io.py000077500000000000000000000162751467613320200172340ustar00rootroot00000000000000#!/usr/bin/env python # Copyright (c) 2005 Gavin E. Crooks # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # import unittest from io import StringIO from weblogo import seq_io from weblogo.seq import nucleic_alphabet, protein_alphabet from weblogo.seq_io import ( array_io, clustal_io, fasta_io, genbank_io, msf_io, nbrf_io, nexus_io, phylip_io, plain_io, stockholm_io, table_io, ) from . import data_stream, test_genbank_io class test_seq_io(unittest.TestCase): def test_attr(self) -> None: f = seq_io.formats for i in f: i.names[0] # Ensure every format has a name. seq_io.format_names() seq_io.format_extensions() def test_parse_clustal(self) -> None: with data_stream("clustal.aln") as f: seqs = seq_io.read(f) self.assertEqual(len(seqs), 7) self.assertEqual(seqs[1].name, "CATH_HUMAN") self.assertEqual(len(seqs[1]), 395) def test_parse_error(self) -> None: """Wrong alphabet should throw a parsing error""" with data_stream("clustal.aln") as f: self.assertRaises(ValueError, seq_io.read, f, nucleic_alphabet) def test_parse_clustal181(self) -> None: with data_stream("clustal181.aln") as f: seq_io.read(f, protein_alphabet) def test_parse_clustal_glualign(self) -> None: with data_stream("clustal_glualign.aln") as f: seq_io.read(f, nucleic_alphabet) def test_parse_clustalw182(self) -> None: with data_stream("clustalw182.aln") as f: seq_io.read(f, protein_alphabet) def test_read_example_array(self) -> None: f = StringIO(array_io.example) seqs = seq_io.read(f) # print seqs self.assertEqual(len(seqs), 8) self.assertEqual(seqs[0].name, "") self.assertEqual(len(seqs[1]), 60) def test_read_fasta(self) -> None: f = StringIO(fasta_io.example) seqs = seq_io.read(f) # print seqs self.assertEqual(len(seqs), 3) self.assertEqual(seqs[0].description, "Lamprey GLOBIN V - SEA LAMPREY") self.assertEqual(len(seqs[1]), 231) def test_parse_globin_fasta(self) -> None: with data_stream("globin.fa") as f: seqs = seq_io.read(f) self.assertEqual(len(seqs), 56) def test_parser_extensions(self) -> None: # Test that the list of extension is a list. # Very easy with one extension list to write ('txt') rather than ('txt',) for p in seq_io._parsers: self.assertTrue(type(p.extensions) is tuple) def test_parser_names(self) -> None: # Same for names for p in seq_io._parsers: self.assertTrue(type(p.names) is tuple) def test_parsers(self) -> None: # seq_io._parsers is an ordered list of sequence parsers that are # tried, in turn, on files of unknown format. Each parser must raise # an exception when fed a format further down the list. # We may include examples here for parsers that are not currently in # seq_io._parsers # TODO: Refactor these examples as with test_genbank_io.examples() # TODO: Then test that each example works with read() and iterseq() # TODO: Also autotest Write and writeseq, where available. fasta_examples = (StringIO(fasta_io.example), data_stream("globin.fa")) clustal_examples = ( StringIO(clustal_io.example), data_stream("clustal.aln"), data_stream("clustal181.aln"), data_stream("clustal_glualign.aln"), data_stream("clustalw182.aln"), ) plain_examples = (StringIO(plain_io.example),) phylip_examples = ( data_stream("phylip_test_1.phy"), data_stream("phylip_test_2.phy"), data_stream("phylip_test_3.phy"), data_stream("phylip_test_4.phy"), data_stream("phylip_test_5.phy"), data_stream("dna.phy"), ) msf_examples = ( data_stream("dna.msf"), data_stream("cox2.msf"), data_stream("1beo.msf"), ) nbrf_examples = ( data_stream("cox2.nbrf"), data_stream("crab.nbrf"), data_stream("dna.pir"), data_stream("rhod.pir"), data_stream("protein.pir"), ) nexus_examples = ( data_stream("nexus/protein.nex"), data_stream("nexus/dna.nex"), ) stockholm_examples = ( StringIO(stockholm_io.example), data_stream("pfam_example.txt"), data_stream("pfam.txt"), ) table_examples = (StringIO(table_io.example),) array_examples = (StringIO(array_io.example),) examples = { fasta_io: fasta_examples, clustal_io: clustal_examples, plain_io: plain_examples, phylip_io: phylip_examples, msf_io: msf_examples, nbrf_io: nbrf_examples, nexus_io: nexus_examples, stockholm_io: stockholm_examples, table_io: table_examples, array_io: array_examples, genbank_io: test_genbank_io.examples(), } parsers = seq_io._parsers for i in range(0, len(parsers)): for j in range(i + 1, len(parsers)): # Check that parser[i] cannot read files intended for parser[j] (where j>i) for f in examples[parsers[j]]: # print parsers[i].names[0], parsers[j].names[0] f.seek(0) self.assertRaises(ValueError, parsers[i].read, f) # When fed an empty file, the parser should either raise a ValueError # or return an empty SeqList e = StringIO() for p in seq_io._parsers: try: s = p.read(e) self.assertEqual(len(s), 0) except ValueError: pass for e in examples.values(): for f in e: f.close() if __name__ == "__main__": unittest.main() weblogo-3.8.0/tests/test_stockholm_io.py000077500000000000000000000104641467613320200204410ustar00rootroot00000000000000#!/usr/bin/env python # Copyright (c) 2006, The Regents of the University of California, through # Lawrence Berkeley National Laboratory (subject to receipt of any required # approvals from the U.S. Dept. of Energy). All rights reserved. # This software is distributed under the new BSD Open Source License. # # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions are met: # # (1) Redistributions of source code must retain the above copyright notice, # this list of conditions and the following disclaimer. # # (2) Redistributions in binary form must reproduce the above copyright # notice, this list of conditions and the following disclaimer in the # documentation and or other materials provided with the distribution. # # (3) Neither the name of the University of California, Lawrence Berkeley # National Laboratory, U.S. Dept. of Energy nor the names of its contributors # may be used to endorse or promote products derived from this software # without specific prior written permission. # # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" # AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE # IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE # ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE # LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR # CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF # SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS # INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN # CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE # POSSIBILITY OF SUCH DAMAGE. import unittest from io import StringIO from weblogo.seq import nucleic_alphabet, protein_alphabet, rna_alphabet from weblogo.seq_io import clustal_io, fasta_io, stockholm_io from . import data_stream class test_stockholm_io(unittest.TestCase): def test_parse1(self) -> None: with data_stream("pfam.txt") as f: seqs = stockholm_io.read(f) # self.assertEqual(len(seqs), 7) self.assertEqual(seqs[1].name, "O61132/1-232") self.assertEqual(len(seqs[1]), 265) def test_parse2(self) -> None: f = StringIO(stockholm_io.example) seqs = stockholm_io.read(f) self.assertEqual(len(seqs), 5) self.assertEqual(seqs[1].name, "O83071/259-312") self.assertEqual(len(seqs[1]), 43) def test_iterseq(self) -> None: with data_stream("pfam.txt") as f: for seq in stockholm_io.iterseq(f): pass # 12345678901234567890123456789012345678901234567890 # 12*50 +6 = 606 # QYVTVFYGVPAWRNATIPLFCATKNR.......DTWGTTQCLPDNDDYSE def test_parse3(self) -> None: with data_stream("pfam_example.txt") as f: seqs = stockholm_io.read(f) self.assertEqual(len(seqs), 24) self.assertEqual(seqs[5].name, "ENV_HV2BE/24-510") self.assertEqual(len(seqs[1]), 606) self.assertEqual(str(seqs[0][-6:]), "TSRNKR") def test_parse_error(self) -> None: """Wrong alphabet should throw a parsing error""" f = StringIO(stockholm_io.example) self.assertRaises(ValueError, clustal_io.read, f, nucleic_alphabet) def test_parse_fasta_fail(self) -> None: # should fail with parse error f = StringIO(stockholm_io.example) self.assertRaises(ValueError, stockholm_io.read, f, rna_alphabet) def test_parse_alphabet_fail(self) -> None: # should fail with parse error f = StringIO(fasta_io.example) self.assertRaises(ValueError, stockholm_io.read, f, protein_alphabet) def test_parse_fasta_fail2(self) -> None: # should fail with parse error with data_stream("globin.fa") as f: self.assertRaises(ValueError, stockholm_io.read, f) def test_parse_fail(self) -> None: # should fail with parse error examples = (StringIO(clustal_io.example),) for f in examples: self.assertRaises(ValueError, stockholm_io.read, f) if __name__ == "__main__": unittest.main() weblogo-3.8.0/tests/test_table_io.py000077500000000000000000000041171467613320200175230ustar00rootroot00000000000000#!/usr/bin/env python # Copyright (c) 2005 Gavin E. Crooks # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # import unittest from io import StringIO from weblogo.seq_io import plain_io, table_io class test_table_io(unittest.TestCase): def test_read(self) -> None: f = StringIO(table_io.example) seqs = table_io.read(f) self.assertEqual(len(seqs), 10) self.assertEqual(seqs[2].name, "EC0003") self.assertEqual(len(seqs[1]), 50) def test_read_fail(self) -> None: f = StringIO(plain_io.example) # Wrong alphabet self.assertRaises(ValueError, table_io.read, f) def test_write_seq(self) -> None: f = StringIO(table_io.example) seqs = table_io.read(f) fout = StringIO() table_io.write(fout, seqs) fout.seek(0) seqs2 = table_io.read(fout) self.assertEqual(seqs, seqs2) if __name__ == "__main__": unittest.main() weblogo-3.8.0/tests/test_transform.py000077500000000000000000000131271467613320200177610ustar00rootroot00000000000000#!/usr/bin/env python # Copyright (c) 2006 John Gilman # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. import unittest from weblogo.seq import ( Seq, dna_alphabet, nucleic_alphabet, protein_alphabet, reduced_protein_alphabet, ) from weblogo.transform import ( GeneticCode, Transform, mask_low_complexity, reduced_protein_alphabets, ) class test_mask_low_complexity(unittest.TestCase): def test_segging(self) -> None: before = ( "mgnrafkshhghflsaegeavkthhghhdhhthfhvenhggkvalkthcgkylsigdhkqvylshhlhgdhslfhlehhg" "gkvsikghhhhyisadhhghvstkehhdhdttfeeiii".upper() ) after = ( "MGNRAFKSHHGHFLSAEGEAVxxxxxxxxxxxxxxxENHGGKVALKTHCGKYLSIGDHKQVYLSHHLHGDHSLFHLEHHGG" "KVSIKGHHHHYISADHHGHVSTKEHHDHDTTFEEIII".upper() ) bseq = Seq(before, protein_alphabet) aseq = Seq(after, protein_alphabet) xseq = Seq("X" * len(bseq), protein_alphabet) sseq = mask_low_complexity(bseq) self.assertEqual(aseq, sseq) # Nothing should be segged sseq = mask_low_complexity(bseq, 12, 0, 0) self.assertEqual(bseq, sseq) # Everthing should be segged sseq = mask_low_complexity(bseq, 12, 4.3, 4.3) self.assertEqual(sseq, xseq) mask_low_complexity(bseq, 100000, 4.3, 4.3) def test_seg_invalid(self) -> None: seq = Seq("KTHCGKYLSIGDHKQVYLSHH", protein_alphabet) self.assertRaises(ValueError, mask_low_complexity, seq, 12, -1, 0) self.assertRaises(ValueError, mask_low_complexity, seq, -1, 0, 0) self.assertRaises(ValueError, mask_low_complexity, seq, 12, 1, 10) self.assertRaises(ValueError, mask_low_complexity, seq, 6, 12, 13) self.assertRaises(ValueError, mask_low_complexity, seq, 6, 2.0, 1.9) class test_transform(unittest.TestCase): def test_transform(self) -> None: trans = Transform( Seq("ACGTURYSWKMBDHVN", nucleic_alphabet), Seq("ACGTTNNNNNNNNNNN", dna_alphabet), ) s0 = Seq("AAAAAR", nucleic_alphabet) s1 = trans(s0) # Callable ob self.assertEqual(s1.alphabet, dna_alphabet) self.assertEqual(s1, Seq("AAAAAN", dna_alphabet)) s2 = Seq(str(protein_alphabet), protein_alphabet) self.assertRaises(ValueError, trans, s2) # def test_translations(self) -> None: # s = Seq("ACGTURYSWKMBDHVNACGTURYSWKMBDHVN", nucleic_alphabet) # s2 = dna_ext_to_std(s) # s3 = Seq("ACGTTNNNNNNNNNNNACGTTNNNNNNNNNNN", dna_alphabet) # self.assertEqual(s2, s3) def test_reduced_protein_alphabets(self) -> None: seq = Seq( "ENHGGKVALKTHCGKYLSIGDHKQVYLSHHLHGDHSLFHLEHHGGKVSIKGHHHHYISADHHGHVSTKEHHDHDT" "TFEEIII", reduced_protein_alphabet, ) for t in reduced_protein_alphabets.values(): t(seq) class test_geneticcode(unittest.TestCase): def test_repr(self) -> None: for t in GeneticCode.std_list(): r = repr(t) gc = eval(r) self.assertEqual(r, repr(gc)) self.assertEqual(str(gc), str(t)) # print r # print t # print gc def test_translate_std(self) -> None: dna = Seq("GCCATTGTAATGGGCCGCTGAAAGGGTGCCCGA") t = GeneticCode.std() s = t.translate(dna) self.assertEqual(str(s), "AIVMGR*KGAR") for t in GeneticCode.std_list(): t.translate(dna) def test_translate(self) -> None: # Ref: http://lists.open-bio.org/pipermail/biopython/2006-March/002960.html cft = ( ( "Vertebrate Mitochondrial", "GCCATTGTAATGGGCCGCTGAAAGGGTGCCCGA", "AIVMGRWKGAR", ), (11, "CAAGGCGTCGAAYAGCTTCAGGAACAGGAC", "QGVE?LQEQD"), (1, "GCCATTGTAATGGGCCGCTGAAAGGGTGCCCGA", "AIVMGR*KGAR"), ) for code, dna, protein in cft: c = GeneticCode.by_name(code) # type: ignore trans = c.translate(Seq(dna)) self.assertEqual(str(trans), protein) self.assertRaises(ValueError, GeneticCode.by_name, "not_a_name") def test_back_translate(self) -> None: prot = Seq("ACDEFGHIKLMNPQRSTVWY*") t = GeneticCode.std() t.table["CGA"] # type: ignore s = t.back_translate(prot) self.assertEqual(str(prot), str(t.translate(s))) GeneticCode.std().back_table if __name__ == "__main__": unittest.main() weblogo-3.8.0/tests/test_transformseq.py000066400000000000000000000024731467613320200204710ustar00rootroot00000000000000from subprocess import PIPE, Popen import weblogo._transformseq from . import data_stream def _exec(args, outputtext, returncode=0, stdin=None): # type: ignore if not stdin: stdin = data_stream("cap.fa") args = ["transformseq"] + args p = Popen(args, stdin=stdin, stdout=PIPE, stderr=PIPE) (out, err) = p.communicate() if returncode == 0 and p.returncode > 0: print(err) assert returncode == p.returncode if returncode == 0: assert len(err) == 0 out = out.decode() for item in outputtext: assert item in out stdin.close() def test_malformed_options() -> None: _exec(["--notarealoption"], [], 2) _exec(["extrajunk"], [], 2) _exec(["-I"], [], 2) def test_help_option() -> None: _exec(["-h"], ["options"]) _exec(["--help"], ["options"]) def test_version_option() -> None: _exec(["--version"], weblogo._transformseq.__version__) def test_clustal() -> None: _exec(["-F", "clustal"], ["TCTTGTGATGTGGTTAACCAAT"]) def test_reverse() -> None: _exec(["--reverse"], ["TAACCAATTGGTGTAGTGTTCT"]) def test_complement() -> None: _exec(["--complement"], ["AGAACACTACACCAATTGGTTA"]) def test_seg() -> None: _exec(["--seg"], ["XXXXXXXXXXXXXXXXXXXXXX"]) def test_subsample() -> None: _exec(["--subsample", "0.4"], []) weblogo-3.8.0/tests/test_utils.py000077500000000000000000000127101467613320200171030ustar00rootroot00000000000000#!/usr/bin/env python # Copyright (c) 2006, The Regents of the University of California, through # Lawrence Berkeley National Laboratory (subject to receipt of any required # approvals from the U.S. Dept. of Energy). All rights reserved. # This software is distributed under the new BSD Open Source License. # # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions are met: # # (1) Redistributions of source code must retain the above copyright notice, # this list of conditions and the following disclaimer. # # (2) Redistributions in binary form must reproduce the above copyright # notice, this list of conditions and the following disclaimer in the # documentation and or other materials provided with the distribution. # # (3) Neither the name of the University of California, Lawrence Berkeley # National Laboratory, U.S. Dept. of Energy nor the names of its contributors # may be used to endorse or promote products derived from this software # without specific prior written permission. # # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" # AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE # IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE # ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE # LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR # CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF # SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS # INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN # CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE # POSSIBILITY OF SUCH DAMAGE. import unittest from weblogo.utils import ( ArgumentError, Token, crc32, crc64, group_count, invert_dict, isblank, isfloat, isint, remove_whitespace, resource_filename, resource_stream, resource_string, ) class test_utils(unittest.TestCase): def test_isfloat(self) -> None: self.assertTrue(isfloat("0.5")) self.assertTrue(isfloat(" 0")) self.assertTrue(isfloat("+1000000000 ")) self.assertTrue(isfloat("2")) self.assertTrue(isfloat("0000.2323")) self.assertTrue(isfloat("0.1e-23")) self.assertTrue(isfloat(" -0.5e+23")) self.assertFalse(isfloat(None)) self.assertFalse(isfloat("")) self.assertFalse(isfloat("asdad")) self.assertFalse(isfloat("q34sd")) self.assertFalse(isfloat("92384.kjdfghiksw")) self.assertFalse(isfloat("adf!@#nn")) def test_isint(self) -> None: self.assertTrue(isint("0")) self.assertTrue(isint("-1")) self.assertTrue(isint("10")) self.assertTrue(isint("100101012234")) self.assertTrue(isint("000")) self.assertFalse(isint(None)) self.assertFalse(isint("")) self.assertFalse(isint("asdad")) self.assertFalse(isint("q34sd")) self.assertFalse(isint("0.23")) self.assertFalse(isint("adf!@#nn")) def test_remove_whitespace(self) -> None: self.assertEqual( remove_whitespace(" kjashd askjdh askjdh\tasdf"), "kjashdaskjdhaskjdhasdf" ) def test_isblank(self) -> None: blank = ("", " ", "\n", "\t \n\n") not_blank = (" a",) for s in blank: self.assertTrue(isblank(s)) for s in not_blank: self.assertFalse(isblank(s)) self.assertFalse(isblank(123)) def test_group_count(self) -> None: test = "aaabbbbcccddea" out = group_count(test) self.assertEqual( tuple(out), (("a", 3), ("b", 4), ("c", 3), ("d", 2), ("e", 1), ("a", 1)) ) def test_token(self) -> None: t = Token("kind", "some data", 4, 3) str(t) r = repr(t) t2 = eval(r) self.assertEqual(t2.typeof, "kind") def test_invert_dict(self) -> None: d = dict(a=3, b=4) invd = invert_dict(d) self.assertTrue(3 in invd) self.assertEqual(invd[3], "a") def test_crc64(self) -> None: self.assertEqual(crc64("IHATEMATH"), "E3DCADD69B01ADD1") def test_crc32(self) -> None: self.assertEqual(crc32("Test the CRC-32 of this string."), "%08X" % 1571220330) def test_ArgumentValueError(self) -> None: message = "Some message" component = "whatsit" try: raise ArgumentError(message, component) except ArgumentError as err: self.assertEqual(err.msg, message) self.assertEqual(err.key, component) try: raise ArgumentError(message, component, 10) except ArgumentError as err: self.assertEqual(err.msg, message) self.assertEqual(err.key, component) self.assertEqual(err.value, 10) def test_resource(self) -> None: fn = resource_filename(__name__, "data/cap.fa", __file__) self.assertTrue(fn.endswith("data/cap.fa")) f = resource_stream(__name__, "data/cap.fa", __file__) f.close() s = resource_string(__name__, "data/cap.fa", __file__).decode() self.assertTrue(s.startswith(">aldB")) tfile = """line 0 line 1 Blah line 3 line 4 """ if __name__ == "__main__": unittest.main() weblogo-3.8.0/tests/test_weblogo.py000077500000000000000000000613121467613320200174030ustar00rootroot00000000000000#!/usr/bin/env python # Copyright (c) 2006, The Regents of the University of California, through # Lawrence Berkeley National Laboratory (subject to receipt of any required # approvals from the U.S. Dept. of Energy). All rights reserved. # This software is distributed under the new BSD Open Source License. # # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions are met: # # (1) Redistributions of source code must retain the above copyright notice, # this list of conditions and the following disclaimer. # # (2) Redistributions in binary form must reproduce the above copyright # notice, this list of conditions and the following disclaimer in the # documentation and or other materials provided with the distribution. # # (3) Neither the name of the University of California, Lawrence Berkeley # National Laboratory, U.S. Dept. of Energy nor the names of its contributors # may be used to endorse or promote products derived from this software # without specific prior written permission. # # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" # AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE # IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE # ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE # LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR # CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF # SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS # INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN # CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE # POSSIBILITY OF SUCH DAMAGE. import typing import unittest from math import log, sqrt from typing import Tuple import pytest from numpy import all, array, float64, ones, zeros from pkg_resources import resource_stream from scipy.stats import entropy from weblogo import ( GhostscriptAPI, LogoData, LogoFormat, LogoOptions, equiprobable_distribution, parse_prior, ) from weblogo.color import Color from weblogo.colorscheme import ColorScheme, IndexColor, RefSeqColor, SymbolColor from weblogo.logomath import Dirichlet, Gamma from weblogo.seq import ( Alphabet, unambiguous_dna_alphabet, unambiguous_protein_alphabet, unambiguous_rna_alphabet, ) from weblogo.utils import ArgumentError def data_stream(name: str) -> typing.IO[bytes]: return resource_stream(__name__, "data/" + name) class test_logoformat(unittest.TestCase): def test_options(self) -> None: LogoOptions() def test_logoformat_errors() -> None: logodata = LogoData() logodata.length = 100 # Negactive logo_margin with pytest.raises(ArgumentError): logooptions = LogoOptions() logooptions.logo_margin = -1 LogoFormat(logodata, logooptions) # logo_start before start of sequecne with pytest.raises(ArgumentError): logooptions = LogoOptions() logooptions.first_index = 10 logooptions.logo_start = -10 LogoFormat(logodata, logooptions) # logo_end before logo_staRT with pytest.raises(ArgumentError): logooptions = LogoOptions() logooptions.first_index = 1 logooptions.logo_start = 10 logooptions.logo_end = -10 LogoFormat(logodata, logooptions) # logo_end past lenght of sequence with pytest.raises(ArgumentError): logooptions = LogoOptions() logooptions.first_index = 1 logooptions.logo_start = 10 logooptions.logo_end = 200 LogoFormat(logodata, logooptions) # No alphabet with pytest.raises(ArgumentError): logooptions = LogoOptions() logooptions.first_index = 1 logooptions.logo_start = 10 logooptions.logo_end = 20 LogoFormat(logodata, logooptions) with pytest.raises(ArgumentError): logooptions = LogoOptions() logooptions.yaxis_scale = -1 LogoFormat(logodata, logooptions) def test_logoformats() -> None: # Make sure all different logo option code gets run logodata = LogoData() logodata.alphabet = unambiguous_rna_alphabet logodata.length = 100 logooptions = LogoOptions() logooptions.fineprint = "" logooptions.xaxis_label = "" logooptions.yaxis_label = "Label" LogoFormat(logodata, logooptions) logooptions.yaxis_label = "" logooptions.unit_name = "probability" LogoFormat(logodata, logooptions) logooptions.show_yaxis = False LogoFormat(logodata, logooptions) logooptions.yaxis_label = "Label" logooptions.show_ends = True logooptions.show_xaxis = True LogoFormat(logodata, logooptions) logooptions.rotate_numbers = True LogoFormat(logodata, logooptions) logooptions.show_xaxis = False LogoFormat(logodata, logooptions) logodata.alphabet = Alphabet("ABCD") LogoFormat(logodata, logooptions) class test_ghostscript(unittest.TestCase): def test_version(self) -> None: GhostscriptAPI().version() class test_parse_prior(unittest.TestCase): def test_parse_prior_none(self) -> None: self.assertEqual(None, parse_prior(None, unambiguous_protein_alphabet)) self.assertEqual(None, parse_prior("none", unambiguous_protein_alphabet)) def test_parse_prior_equiprobable(self) -> None: self.assertTrue( all( 20.0 * equiprobable_distribution(20) == parse_prior( "equiprobable", unambiguous_protein_alphabet, weight=20.0 ) ) ) self.assertTrue( all( 1.2 * equiprobable_distribution(3) == parse_prior(" equiprobablE ", Alphabet("123"), 1.2) ) ) def test_parse_prior_percentage(self) -> None: # print(parse_prior('50%', unambiguous_dna_alphabet, 1.)) self.assertTrue( all( equiprobable_distribution(4) == parse_prior("50%", unambiguous_dna_alphabet, 1.0) ) ) self.assertTrue( all( equiprobable_distribution(4) == parse_prior(" 50.0 % ", unambiguous_dna_alphabet, 1.0) ) ) self.assertTrue( all( array((0.3, 0.2, 0.2, 0.3), float64) == parse_prior(" 40.0 % ", unambiguous_dna_alphabet, 1.0) ) ) def test_parse_prior_float(self) -> None: self.assertTrue( all( equiprobable_distribution(4) == parse_prior("0.5", unambiguous_dna_alphabet, 1.0) ) ) self.assertTrue( all( equiprobable_distribution(4) == parse_prior(" 0.500 ", unambiguous_dna_alphabet, 1.0) ) ) self.assertTrue( all( array((0.3, 0.2, 0.2, 0.3), float64) == parse_prior(" 0.40 ", unambiguous_dna_alphabet, 1.0) ) ) def test_auto(self) -> None: self.assertTrue( all( 2.0 * equiprobable_distribution(4) == parse_prior("auto", unambiguous_dna_alphabet) ) ) self.assertTrue( all( 2.0 * equiprobable_distribution(4) == parse_prior("automatic", unambiguous_dna_alphabet) ) ) parse_prior("automatic", unambiguous_protein_alphabet) parse_prior("E. coli", unambiguous_dna_alphabet) def test_weight(self) -> None: self.assertTrue( all( 2.0 * equiprobable_distribution(4) == parse_prior("automatic", unambiguous_dna_alphabet) ) ) self.assertTrue( all( 123.123 * equiprobable_distribution(4) == parse_prior("auto", unambiguous_dna_alphabet, 123.123) ) ) def test_explicit(self) -> None: s = "{'A':10, 'C':40, 'G':40, 'T':10}" p = array((10, 40, 40, 10), float64) * 2.0 / 100.0 self.assertTrue(all(p == parse_prior(s, unambiguous_dna_alphabet))) def test_parse_prior_error() -> None: with pytest.raises(ValueError): parse_prior("0.5", unambiguous_protein_alphabet, weight=-10000.0) with pytest.raises(ValueError): s = "{'A':10, 'C':40, 'G':40, 'T':10}" parse_prior(s, unambiguous_protein_alphabet) with pytest.raises(ValueError): s = "{'A':'ljkasd', 'C':40, 'G':40, 'T':10}" parse_prior(s, unambiguous_dna_alphabet) with pytest.raises(ValueError): s = "asjnd" parse_prior(s, unambiguous_dna_alphabet) class test_logooptions(unittest.TestCase): def test_create(self) -> None: opt = LogoOptions() opt.small_fontsize = 10 repr(opt) opt = LogoOptions(logo_title="sometitle") # type: ignore self.assertEqual(opt.logo_title, "sometitle") class test_colorscheme(unittest.TestCase): def test_symbol_color(self) -> None: sc = SymbolColor("ABC", "black", "Because") self.assertEqual(sc.description, "Because") self.assertEqual(sc.symbol_color(0, "A", 0), Color.by_name("black")) self.assertEqual(sc.symbol_color(1, "D", 0), None) def test_index_color(self) -> None: ic = IndexColor([1, 3], "black", "Because") self.assertEqual(ic.description, "Because") self.assertEqual(ic.symbol_color(0, "A", 0), None) self.assertEqual(ic.symbol_color(1, "A", 0), Color.by_name("black")) def test_ref_seq_color(self) -> None: rc = RefSeqColor("ABC", "black", "Because") self.assertEqual(rc.description, "Because") self.assertEqual(rc.symbol_color(0, "A", 0), Color.by_name("black")) self.assertEqual(rc.symbol_color(1, "A", 0), None) self.assertEqual(rc.symbol_color(2, "A", 0), None) self.assertEqual(rc.symbol_color(0, "B", 0), None) self.assertEqual(rc.symbol_color(1, "B", 0), Color.by_name("black")) self.assertEqual(rc.symbol_color(2, "B", 0), None) self.assertEqual(rc.symbol_color(0, "C", 0), None) self.assertEqual(rc.symbol_color(1, "C", 0), None) self.assertEqual(rc.symbol_color(2, "C", 0), Color.by_name("black")) def test_colorscheme(self) -> None: cs = ColorScheme( [ SymbolColor("G", "orange"), SymbolColor("TU", "red"), SymbolColor("C", "blue"), SymbolColor("A", "green"), ], title="title", description="description", ) self.assertEqual(cs.symbol_color(1, "G", 1), Color.by_name("orange")) self.assertEqual(cs.symbol_color(1, "T", 1), Color.by_name("red")) self.assertEqual(cs.symbol_color(1, "C", 1), Color.by_name("blue")) self.assertEqual(cs.symbol_color(1, "A", 1), Color.by_name("green")) self.assertEqual(cs.symbol_color(1, "X", 1), cs.default_color) cs = ColorScheme( [ SymbolColor("G", "orange"), SymbolColor("TU", "red"), SymbolColor("C", "blue"), SymbolColor("A", "green"), ], title="title", description="description", alphabet=Alphabet("GTUCA"), ) self.assertRaises(KeyError, cs.symbol_color, 1, "X", 1) class test_color(unittest.TestCase): def test_color_names(self) -> None: names = Color.names() self.assertEqual(len(names), 147) for n in names: c = Color.by_name(n) self.assertTrue(c is not None) def test_color_components(self) -> None: white = Color.by_name("white") self.assertEqual(1.0, white.red) self.assertEqual(1.0, white.green) self.assertEqual(1.0, white.blue) c = Color(0.3, 0.4, 0.2) self.assertEqual(0.3, c.red) self.assertEqual(0.4, c.green) self.assertEqual(0.2, c.blue) c = Color(0, 128, 0) self.assertEqual(0.0, c.red) self.assertEqual(128.0 / 255.0, c.green) self.assertEqual(0.0, c.blue) def test_color_from_rgb(self) -> None: white = Color.by_name("white") self.assertEqual(white, Color(1.0, 1.0, 1.0)) self.assertEqual(white, Color(255, 255, 255)) self.assertEqual(white, Color.from_rgb(1.0, 1.0, 1.0)) self.assertEqual(white, Color.from_rgb(255, 255, 255)) def test_color_from_hsl(self) -> None: red = Color.by_name("red") lime = Color.by_name("lime") saddlebrown = Color.by_name("saddlebrown") darkgreen = Color.by_name("darkgreen") blue = Color.by_name("blue") Color.by_name("green") self.assertEqual(red, Color.from_hsl(0, 1.0, 0.5)) self.assertEqual(lime, Color.from_hsl(120, 1.0, 0.5)) self.assertEqual(blue, Color.from_hsl(240, 1.0, 0.5)) self.assertEqual(Color.by_name("gray"), Color.from_hsl(0, 0, 0.5)) self.assertEqual(saddlebrown, Color.from_hsl(25, 0.76, 0.31)) self.assertEqual(darkgreen, Color.from_hsl(120, 1.0, 0.197)) def test_color_by_name(self) -> None: white = Color.by_name("white") self.assertEqual(white, Color.by_name("white")) self.assertEqual(white, Color.by_name("WHITE")) self.assertEqual(white, Color.by_name(" wHiTe \t\n\t")) self.assertEqual(Color(255, 255, 240), Color.by_name("ivory")) self.assertEqual(Color(70, 130, 180), Color.by_name("steelblue")) self.assertEqual(Color(0, 128, 0), Color.by_name("green")) def test_color_from_invalid_name(self) -> None: self.assertRaises(ValueError, Color.by_name, "not_a_color") def test_color_clipping(self) -> None: red = Color.by_name("red") self.assertEqual(red, Color(255, 0, 0)) self.assertEqual(red, Color(260, -10, 0)) self.assertEqual(red, Color(1.1, -0.0, -1.0)) self.assertEqual(Color(1.0001, 213.0, 1.2).red, 1.0) self.assertEqual(Color(-0.001, -2183.0, -1.0).red, 0.0) self.assertEqual(Color(1.0001, 213.0, 1.2).green, 1.0) self.assertEqual(Color(-0.001, -2183.0, -1.0).green, 0.0) self.assertEqual(Color(1.0001, 213.0, 1.2).blue, 1.0) self.assertEqual(Color(-0.001, -2183.0, -1.0).blue, 0.0) def test_color_fail_on_mixed_type(self) -> None: self.assertRaises(TypeError, Color.from_rgb, 1, 1, 1.0) self.assertRaises(TypeError, Color.from_rgb, 1.0, 1, 1.0) def test_color_red(self) -> None: # Check Usage comment in Color red = Color.by_name("red") self.assertEqual(red, Color(255, 0, 0)) self.assertEqual(red, Color(1.0, 0.0, 0.0)) self.assertEqual(red, Color.from_rgb(1.0, 0.0, 0.0)) self.assertEqual(red, Color.from_rgb(255, 0, 0)) self.assertEqual(red, Color.from_hsl(0.0, 1.0, 0.5)) self.assertEqual(red, Color.from_string("red")) self.assertEqual(red, Color.from_string("RED")) self.assertEqual(red, Color.from_string("#F00")) self.assertEqual(red, Color.from_string("#FF0000")) self.assertEqual(red, Color.from_string("rgb(255, 0, 0)")) self.assertEqual(red, Color.from_string("rgb(100%, 0%, 0%)")) self.assertEqual(red, Color.from_string("hsl(0, 100%, 50%)")) def test_color_from_string(self) -> None: Color(128, 0, 128) # purple red = Color(255, 0, 0) skyblue = Color(135, 206, 235) red_strings = ( "red", "ReD", "RED", " Red \t", "#F00", "#FF0000", "rgb(255, 0, 0)", "rgb(100%, 0%, 0%)", "hsl(0, 100%, 50%)", ) for s in red_strings: self.assertEqual(red, Color.from_string(s)) skyblue_strings = ( "skyblue", "SKYBLUE", " \t\n SkyBlue \t", "#87ceeb", "rgb(135,206,235)", ) for s in skyblue_strings: self.assertEqual(skyblue, Color.from_string(s)) self.assertRaises(ValueError, Color.from_string, "#not_a_color") self.assertRaises(ValueError, Color.from_string, "rgb(not_a_color)") self.assertRaises(ValueError, Color.from_string, "hsl(not_a_color)") self.assertRaises(ValueError, Color.from_string, "not_a_color") def test_color_equality(self) -> None: c1 = Color(123, 99, 12) c2 = Color(123, 99, 12) self.assertEqual(c1, c2) self.assertNotEqual(c1, "not_a_color") class test_gamma(unittest.TestCase): def test_create(self) -> None: a = 1.213 b = 3.210 g = Gamma(a, b) self.assertEqual(g.alpha, a) self.assertEqual(g.beta, b) def test_mean_variance(self) -> None: g = Gamma.from_mean_variance(2.0, 3.0) self.assertEqual(g.mean(), 2.0) self.assertEqual(g.variance(), 3.0) g = Gamma.from_mean_variance(2.0123, 3.01283) self.assertEqual(g.mean(), 2.0123) self.assertEqual(g.variance(), 3.01283) def test_from_shape_scale(self) -> None: g = Gamma.from_shape_scale(1.0, 8.0) self.assertEqual(g.alpha, 1.0) self.assertEqual(g.beta, 1.0 / 8.0) def test_invalid_args(self) -> None: self.assertRaises(ValueError, Gamma, 1.0, -1.0) self.assertRaises(ValueError, Gamma, 0.0, 1.0) self.assertRaises(ValueError, Gamma, 1.0, 0.0) def test_sample(self) -> None: m = 10.0 v = 2.0 g = Gamma.from_mean_variance(m, v) # print(g.alpha, g.beta) S = 1000 total = 0.0 for s in range(S): total += g.sample() mean = total / S # The estimated mean will differ from true mean by a small amount error = 4.0 * sqrt(g.variance() / S) # print(mean, m, error) self.assertTrue(abs(mean - m) < error) def test_pdf(self) -> None: m = 3.0 v = 2.0 g = Gamma.from_mean_variance(m, v) upper = 30.0 norm = integrate(g.pdf, 0, upper) self.assertAlmostEqual(norm, 1.0) def fx(x: float) -> float: return x * g.pdf(x) mean = integrate(fx, 0, upper) self.assertAlmostEqual(mean, m) def fx2(x: float) -> float: return x * x * g.pdf(x) x2 = integrate(fx2, 0, upper) var = x2 - mean**2 self.assertAlmostEqual(var, v) def test_cdf(self) -> None: m = 3.0 v = 2.0 g = Gamma.from_mean_variance(m, v) # Numerical integration S = 1000 M = 10.0 total_p = 0.0 epsilon = 1e-4 last = 0.0 for s in range(S): x = s * M / S p = g.pdf(x) * M / S total_p += (last - p) / 2.0 last = p # print(x, total_p, g.cdf(x)) self.assertTrue((total_p - g.cdf(x)) < epsilon) def test_inverse_cdf(self) -> None: g = Gamma.from_mean_variance(2.34, 4) self.assertAlmostEqual(3.9, g.inverse_cdf(g.cdf(3.9))) self.assertAlmostEqual(1.92, g.inverse_cdf(g.cdf(1.92))) g = Gamma.from_mean_variance(10.34, 2) self.assertAlmostEqual(3.9, g.inverse_cdf(g.cdf(3.9))) self.assertAlmostEqual(10.92, g.inverse_cdf(g.cdf(10.92))) g = Gamma.from_mean_variance(10.34, 2) self.assertAlmostEqual(0.975, g.cdf(g.inverse_cdf(0.975))) self.assertAlmostEqual(0.025, g.cdf(g.inverse_cdf(0.025))) g = Gamma.from_mean_variance(1.34, 4) self.assertAlmostEqual(0.975, g.cdf(g.inverse_cdf(0.975))) self.assertAlmostEqual(0.025, g.cdf(g.inverse_cdf(0.025))) class test_Dirichlet(unittest.TestCase): def test_init(self) -> None: Dirichlet( ( 1, 1, 1, 1, ) ) def test_random(self) -> None: def do_test(alpha: Tuple[float, ...], samples: int = 1000) -> None: ent = zeros((samples,), float64) # alpha = ones( ( K,), Float64 ) * A/K # pt = zeros( (len(alpha) ,), Float64) d = Dirichlet(alpha) for s in range(samples): p = d.sample() # print(p) # pt +=p ent[s] = entropy(p) # print(pt/samples) m = mean(ent) v = var(ent) dm = d.mean_entropy() dv = d.variance_entropy() # print(alpha, ':', m, v, dm, dv) error = 4.0 * sqrt(v / samples) self.assertTrue(abs(m - dm) < error) self.assertTrue(abs(v - dv) < error) # dodgy error estimate do_test((1.0, 1.0)) do_test((2.0, 1.0)) do_test((3.0, 1.0)) do_test((4.0, 1.0)) do_test((5.0, 1.0)) do_test((6.0, 1.0)) do_test((1.0, 1.0)) do_test((20.0, 20.0)) do_test((1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0, 1.0)) do_test((0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1, 0.1)) do_test((0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01, 0.01)) do_test((2.0, 6.0, 1.0, 1.0)) def test_mean(self) -> None: alpha = ones((10,), float64) * 23.0 d = Dirichlet(alpha) m = d.mean() self.assertAlmostEqual(m[2], 1.0 / 10) self.assertAlmostEqual(sum(m), 1.0) def test_covariance(self) -> None: alpha = ones((4,), float64) d = Dirichlet(alpha) cv = d.covariance() self.assertEqual(cv.shape, (4, 4)) self.assertAlmostEqual(cv[0, 0], 1.0 * (1.0 - 1.0 / 4.0) / (4.0 * 5.0)) self.assertAlmostEqual(cv[0, 1], -1 / (4.0 * 4.0 * 5.0)) def test_mean_x(self) -> None: alpha = (1.0, 2.0, 3.0, 4.0) xx = (2.0, 2.0, 2.0, 2.0) m = Dirichlet(alpha).mean_x(xx) self.assertEqual(m, 2.0) xx2 = (2.0, 2.0, 2.0, 2.0, 2.0) self.assertRaises(ValueError, Dirichlet(alpha).mean_x, xx2) alpha = (1.0, 1.0, 1.0, 1.0) xx = (2.0, 3.0, 4.0, 3.0) m = Dirichlet(alpha).mean_x(xx) self.assertEqual(m, 3.0) def test_variance_x(self) -> None: alpha = (1.0, 1.0, 1.0, 1.0) xx = (2.0, 2.0, 2.0, 2.0) v = Dirichlet(alpha).variance_x(xx) self.assertAlmostEqual(v, 0.0) alpha = (1.0, 2.0, 3.0, 4.0) xx = (2.0, 0.0, 1.0, 10.0) v = Dirichlet(alpha).variance_x(xx) # print(v) # TODO: Don't actually know if this is correct xx2 = (2.0, 2.0, 2.0, 2.0, 2.0) self.assertRaises(ValueError, Dirichlet(alpha).variance_x, xx2) def test_relative_entropy(self) -> None: alpha = (2.0, 10.0, 1.0, 1.0) d = Dirichlet(alpha) pvec = (0.1, 0.2, 0.3, 0.4) rent = d.mean_relative_entropy(pvec) vrent = d.variance_relative_entropy(pvec) low, high = d.interval_relative_entropy(pvec, 0.95) # print() # print('> ', rent, vrent, low, high) # This test can fail randomly, but the precision from a few # thousand samples is low. Increasing samples, 1000->2000 samples = 2000 sent = zeros((samples,), float64) for s in range(samples): post = d.sample() e = -entropy(post) for k in range(4): e += -post[k] * log(pvec[k]) sent[s] = e sent.sort() self.assertTrue(abs(sent.mean() - rent) < 4.0 * sqrt(vrent)) self.assertAlmostEqual(sent.std(), sqrt(vrent), 1) self.assertTrue(abs(low - sent[int(samples * 0.025)]) < 0.2) self.assertTrue(abs(high - sent[int(samples * 0.975)]) < 0.2) class _from_URL_fileopen_Tests(unittest.TestCase): def test_URLscheme(self) -> None: """test for http, https, or ftp scheme""" from weblogo.logo import _from_URL_fileopen broken_url = "file://foo.txt" self.assertRaises(ValueError, _from_URL_fileopen, (broken_url)) def mean(a) -> float: # type: ignore return sum(a) / len(a) def var(a) -> float: # type: ignore return (sum(a * a) / len(a)) - mean(a) ** 2 def integrate(f, a, b, n=1000): # type: ignore """ Numerically integrate the function 'f' from 'a' to 'b' using a discretization with 'n' points. Args: - f -- A function that eats a float and returns a float. - a -- Lower integration bound (float) - b -- Upper integration bound (float) - n -- number of sample points (int) Status : Alpha (very primitive.) """ h = (b - a) / (n - 1.0) total = 0.0 for i in range(n): total += f(a + (i) * h) result = h * (total - 0.5 * f(a) - 0.5 * f(b)) return result if __name__ == "__main__": unittest.main() weblogo-3.8.0/weblogo/000077500000000000000000000000001467613320200146225ustar00rootroot00000000000000weblogo-3.8.0/weblogo/__init__.py000066400000000000000000000005711467613320200167360ustar00rootroot00000000000000from pkg_resources import DistributionNotFound, get_distribution try: __version__: str = get_distribution(__name__).version except DistributionNotFound: # pragma: no cover __version__ = "?.?.?" from .logo import * # noqa: F401, F403 from .logo_formatter import * # noqa: F401, F403 from .seq import * # noqa: F401, F403 from .seq_io import * # noqa: F401, F403 weblogo-3.8.0/weblogo/_cgi.py000077500000000000000000000462431467613320200161110ustar00rootroot00000000000000# Copyright (c) 2003-2004 The Regents of the University of California. # Copyright (c) 2005 Gavin E. Crooks # Copyright (c) 2006-2015, The Regents of the University of California, through # Lawrence Berkeley National Laboratory (subject to receipt of any required # approvals from the U.S. Dept. of Energy). All rights reserved. # This software is distributed under the new BSD Open Source License. # # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions are met: # # (1) Redistributions of source code must retain the above copyright notice, # this list of conditions and the following disclaimer. # # (2) Redistributions in binary form must reproduce the above copyright # notice, this list of conditions and the following disclaimer in the # documentation and or other materials provided with the distribution. # # (3) Neither the name of the University of California, Lawrence Berkeley # National Laboratory, U.S. Dept. of Energy nor the names of its contributors # may be used to endorse or promote products derived from this software # without specific prior written permission. # # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" # AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE # IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE # ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE # LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR # CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF # SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS # INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN # CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE # POSSIBILITY OF SUCH DAMAGE. import cgi as cgilib import cgitb import os.path import shutil import sys from io import BytesIO, StringIO, TextIOWrapper from string import Template from typing import Any, Callable, List, Optional, Union import weblogo from weblogo.colorscheme import ColorScheme, SymbolColor cgitb.enable() # TODO: Check units # TODO: In WebLogo2: why slash create.cgi? I think this was a workaround # for some browser quirk #
# Should replace with weblogo.utils? def resource_string(resource: str, basefilename: str) -> str: import os fn = os.path.join(os.path.dirname(basefilename), resource) return open(fn).read() mime_type = { "eps": "application/postscript", "pdf": "application/pdf", "svg": "image/svg+xml", "png": "image/png", "png_print": "image/png", "logodata": "text/plain", "csv": "text/plain", "jpeg": "image/jpeg", } extension = { "eps": "eps", "pdf": "pdf", "png": "png", "svg": "svg", "png_print": "png", "logodata": "txt", "csv": "csv", "jpeg": "jpeg", } alphabets = { "alphabet_auto": None, "alphabet_protein": weblogo.unambiguous_protein_alphabet, "alphabet_rna": weblogo.unambiguous_rna_alphabet, "alphabet_dna": weblogo.unambiguous_dna_alphabet, } color_schemes = {} for k in weblogo.std_color_schemes.keys(): color_schemes["color_" + k.replace(" ", "_")] = weblogo.std_color_schemes[k] composition = { "comp_none": "none", "comp_auto": "auto", "comp_equiprobable": "equiprobable", "comp_CG": "percentCG", "comp_Celegans": "C. elegans", "comp_Dmelanogaster": "D. melanogaster", "comp_Ecoli": "E. coli", "comp_Hsapiens": "H. sapiens", "comp_Mmusculus": "M. musculus", "comp_Scerevisiae": "S. cerevisiae", } class Field: """A representation of an HTML form field.""" def __init__( self, name: str, default: Optional[Any] = None, conversion: Optional[Callable] = None, options: Optional[List[Any]] = None, errmsg: str = "Illegal value.", ) -> None: self.name = name self.default = default self.value = default self.conversion = conversion self.options = options self.errmsg = errmsg def get_value(self) -> Any: if self.options: if self.value not in self.options: raise ValueError(str((self.name, self.errmsg))) if self.conversion: try: return self.conversion(self.value) except ValueError: raise ValueError(str((self.name, self.errmsg))) else: return self.value def string_or_none(value: Any) -> Optional[str]: if value is None or value == "auto": return None return str(value) def truth(value: Any) -> bool: if value == "true": return True return bool(value) def int_or_none(value: Any) -> Optional[int]: if value == "" or value is None or value == "auto": return None return int(value) def float_or_none(value: Any) -> Optional[float]: if value == "" or value is None or value == "auto": return None return float(value) def main(htdocs_directory: Optional[str] = None) -> None: logooptions = weblogo.LogoOptions() # A list of form fields. # The default for checkbox values must be False (irrespective of # the default in logooptions) since a checked checkbox returns 'true' # but an unchecked checkbox returns nothing. controls = [ Field("sequences", ""), Field("sequences_url", ""), Field( "format", "png", weblogo.formatters.get, options=[ "png_print", "png", "jpeg", "eps", "pdf", "svg", "logodata", "csv", ], # TODO: Should copy list from __init__.formatters errmsg="Unknown format option.", ), Field( "stacks_per_line", logooptions.stacks_per_line, int, errmsg="Invalid number of stacks per line.", ), Field( "stack_width", "medium", weblogo.std_sizes.get, options=["small", "medium", "large"], errmsg="Invalid logo size.", ), Field( "alphabet", "alphabet_auto", alphabets.get, options=[ "alphabet_auto", "alphabet_protein", "alphabet_dna", "alphabet_rna", ], errmsg="Unknown sequence type.", ), Field( "unit_name", "bits", options=["probability", "bits", "nats", "kT", "kJ/mol", "kcal/mol"], ), Field("first_index", 1, int_or_none), Field("logo_start", "", int_or_none), Field("logo_end", "", int_or_none), Field( "composition", "comp_auto", composition.get, options=[ "comp_none", "comp_auto", "comp_equiprobable", "comp_CG", "comp_Celegans", "comp_Dmelanogaster", "comp_Ecoli", "comp_Hsapiens", "comp_Mmusculus", "comp_Scerevisiae", ], errmsg="Illegal sequence composition.", ), Field("percentCG", "", float_or_none, errmsg="Invalid CG percentage."), Field("show_errorbars", False, truth), Field("logo_title", logooptions.logo_title), Field("logo_label", logooptions.logo_label), Field("show_xaxis", False, truth), Field("xaxis_label", logooptions.xaxis_label), Field("show_yaxis", False, truth), Field("yaxis_label", logooptions.yaxis_label, string_or_none), Field( "yaxis_scale", logooptions.yaxis_scale, float_or_none, errmsg="The yaxis scale must be a positive number.", ), Field("yaxis_tic_interval", logooptions.yaxis_tic_interval, float_or_none), Field("show_ends", False, truth), Field("show_fineprint", False, truth), Field( "color_scheme", "color_auto", color_schemes.get, options=list(color_schemes.keys()), errmsg="Unknown color scheme", ), Field("color0", ""), Field("symbols0", ""), Field("desc0", ""), Field("color1", ""), Field("symbols1", ""), Field("desc1", ""), Field("color2", ""), Field("symbols2", ""), Field("desc2", ""), Field("color3", ""), Field("symbols3", ""), Field("desc3", ""), Field("color4", ""), Field("symbols4", ""), Field("desc4", ""), Field("ignore_lower_case", False, truth), Field("scale_width", False, truth), ] form = {} for c in controls: form[c.name] = c form_values = cgilib.FieldStorage() # Send default form? if len(form_values) == 0 or "cmd_reset" in form_values: # Load default truth values now. form["show_errorbars"].value = logooptions.show_errorbars form["show_xaxis"].value = logooptions.show_xaxis form["show_yaxis"].value = logooptions.show_yaxis form["show_ends"].value = logooptions.show_ends form["show_fineprint"].value = logooptions.show_fineprint form["scale_width"].value = logooptions.scale_width send_form(controls, htdocs_directory=htdocs_directory) return # Get form content for c in controls: c.value = form_values.getfirst(c.name, c.default) options_from_form = [ "format", "stacks_per_line", "stack_width", "alphabet", "unit_name", "first_index", "logo_start", "logo_end", "composition", "show_errorbars", "logo_title", "logo_label", "show_xaxis", "xaxis_label", "show_yaxis", "yaxis_label", "yaxis_scale", "yaxis_tic_interval", "show_ends", "show_fineprint", "scale_width", ] errors = [] for optname in options_from_form: try: value = form[optname].get_value() if value is not None: setattr(logooptions, optname, value) except ValueError as err: errors.append(err.args) # Construct custom color scheme custom = ColorScheme() for i in range(0, 5): color = form["color%d" % i].get_value() symbols = form["symbols%d" % i].get_value() desc = form["desc%d" % i].get_value() if color: try: custom.rules.append(SymbolColor(symbols, color, desc)) except ValueError: errors.append(("color%d" % i, "Invalid color: %s" % color)) if form["color_scheme"].value == "color_custom": logooptions.color_scheme = custom else: try: logooptions.color_scheme = form["color_scheme"].get_value() except ValueError as err: errors.append(err.args) # FIXME: Ugly fix: Must check that sequence_file key exists # FIXME: Sending malformed or missing form keys should not cause a crash # sequences_file = form["sequences_file"] sequences_from_file = None if "sequences_file" in form_values: sequences_from_file = form_values.getvalue("sequences_file") sequences_from_textfield = form["sequences"].get_value() sequences_url = form["sequences_url"].get_value() sequences = None seq_file: Union[StringIO, TextIOWrapper, None] = None if sequences_from_file: if sequences_from_textfield or sequences_url: errors.append(("sequences_file", "Cannot upload, sequence source conflict")) else: sequences = sequences_from_file seq_file = TextIOWrapper(BytesIO(sequences), encoding="utf-8") elif sequences_from_textfield: if sequences_url: errors.append(("sequences", "Cannot upload, sequence source conflict")) else: # check SEQUENCES_MAXLENGT # If a user tries to paste a very large file into sequence textarea, # then WebLogo runs very slow for no apparently good reason. (Might be client side bug?) # So we limit the maximum sequence size. # Form field also limits size, but not necessarly respected. Also can truncate data # without warning, so we'll set textarea maximum to be larger than MAX_SEQUENCE_SIZE SEQUENCES_MAXLENGTH = 100000 if len(sequences_from_textfield) > SEQUENCES_MAXLENGTH: errors.append( ( "sequences", "Sequence data too large for text input. Use file upload instead.", ) ) controls[0] = Field("sequences", "") else: sequences = sequences_from_textfield seq_file = StringIO(sequences) elif sequences_url: from .logo import _from_URL_fileopen try: seq_file = _from_URL_fileopen(sequences_url) except ValueError: errors.append(("sequences_url", "Cannot parse URL")) except IOError: errors.append(("sequences_url", "Cannot load sequences from URL")) else: errors.append( ( "sequences", "Please enter a multiple-sequence alignment in the box above, or select a " "file to upload.", ) ) # If we have uncovered errors or we want the chance to edit the logo # ("cmd_edit" command from examples page) then we return the form now. # We do not proceed to the time consuming logo creation step unless # required by a 'create' or 'validate' command, and no errors have been # found yet. if errors or "cmd_edit" in form_values: send_form(controls, errors, htdocs_directory) return try: comp = form["composition"].get_value() percentCG = form["percentCG"].get_value() ignore_lower_case = "ignore_lower_case" in form_values if comp == "percentCG": comp = str(percentCG / 100) from .matrix import Motif try: # Try reading data in transfac format first. # TODO Refactor this code motif = Motif.read_transfac(seq_file, alphabet=logooptions.alphabet) # type: ignore # FIXME prior = weblogo.parse_prior(comp, motif.alphabet) data = weblogo.LogoData.from_counts(motif.alphabet, motif.array, prior) except ValueError: seqs = weblogo.read_seq_data( seq_file, alphabet=logooptions.alphabet, ignore_lower_case=ignore_lower_case, ) alpha = seqs.alphabet assert alpha is not None prior = weblogo.parse_prior(comp, alpha) data = weblogo.LogoData.from_seqs(seqs, prior) logoformat = weblogo.LogoFormat(data, logooptions) format = str(form["format"].value) logo = weblogo.formatters[format](data, logoformat) except ValueError as err: errors.append(err.args) except IOError as err: errors.append(err.args) except RuntimeError as err: errors.append(err.args) if errors or "cmd_validate" in form_values: send_form(controls, errors, htdocs_directory) return # # RETURN LOGO OVER HTTP # print("Content-Type:", mime_type[format]) # Content-Disposition: inline Open logo in browser window # Content-Disposition: attachment Download logo if "download" in form_values: print( "Content-Disposition: attachment; " 'filename="logo.%s"' % extension[format] ) else: print("Content-Disposition: inline; " 'filename="logo.%s"' % extension[format]) # Separate header from data print() sys.stdout.flush() # Finally, and at last, send the logo. sys.stdout.buffer.write(logo) def send_form( controls: List[Field], errors: Optional[List[tuple]] = None, htdocs_directory: Optional[str] = None, ) -> None: if errors is None: errors = [] if htdocs_directory is None: htdocs_directory = os.path.join(os.path.dirname(__file__), "htdocs") substitutions = {} substitutions["version"] = weblogo.release_description # Bug fix. Not sure why this default substitution isn't added automatically like everything else substitutions["color_custom"] = "" for c in controls: if c.options: for opt in c.options: substitutions[opt.replace("/", "_")] = "" substitutions[str(c.value).replace("/", "_")] = "selected" else: value = c.value if value is None: value = "auto" if value == "true": substitutions[c.name] = "checked" elif type(value) is bool: if value: substitutions[c.name] = "checked" else: substitutions[c.name] = "" else: substitutions[c.name] = str(value) substitutions[c.name + "_err"] = "" substitutions["logo_range_err"] = "" # Disable graphics options if necessary auxiliary programs are not installed. if shutil.which("gs") is None and shutil.which("gswin32c.exe") is None: substitutions["png_print"] = 'disabled="disabled"' substitutions["png"] = 'disabled="disabled"' substitutions["jpeg"] = 'disabled="disabled"' substitutions["pdf"] = 'disabled="disabled"' substitutions["svg"] = 'disabled="disabled"' substitutions["eps"] = 'selected="selected"' if shutil.which("pdf2svg") is None: substitutions["svg"] = 'disabled="disabled"' if errors: print(errors, file=sys.stderr) error_message: List[str] = [] for e in errors: if type(e) is str: msg = e elif len(e) == 2: substitutions[e[0] + "_err"] = "class='error'" msg = e[1] else: msg = e[0] error_message += "ERROR: " error_message += msg error_message += "
" error_message += ( " " ) substitutions["error_message"] = "".join(error_message) else: substitutions["error_message"] = "" template = resource_string("create_html_template.html", htdocs_directory) html = Template(template).safe_substitute(substitutions) # FIXME print("Content-Type: text/html\n\n") print(html) # DEBUG # keys = substitutions.keys() # keys.sort() # for k in keys : # print(k, "=", substitutions[k], "
") # print("
") # print("
") # for k in controls : # print(k.name, "=", k.get_value(), "
") if __name__ == "__main__": from . import _cli _cli.main() weblogo-3.8.0/weblogo/_cli.py000077500000000000000000000677431467613320200161260ustar00rootroot00000000000000#!/usr/bin/env python # -------------------------------- WebLogo -------------------------------- # Copyright (c) 2003-2004 The Regents of the University of California. # Copyright (c) 2005 Gavin E. Crooks # Copyright (c) 2006-2011, The Regents of the University of California, through # Lawrence Berkeley National Laboratory (subject to receipt of any required # approvals from the U.S. Dept. of Energy). All rights reserved. # This software is distributed under the new BSD Open Source License. # # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions are met: # # (1) Redistributions of source code must retain the above copyright notice, # this list of conditions and the following disclaimer. # # (2) Redistributions in binary form must reproduce the above copyright # notice, this list of conditions and the following disclaimer in the # documentation and or other materials provided with the distribution. # # (3) Neither the name of the University of California, Lawrence Berkeley # National Laboratory, U.S. Dept. of Energy nor the names of its contributors # may be used to endorse or promote products derived from this software # without specific prior written permission. # # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" # AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE # IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE # ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE # LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR # CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF # SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS # INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN # CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE # POSSIBILITY OF SUCH DAMAGE. # WebLogo Command Line Interfaceg import os import sys from io import StringIO from optparse import OptionGroup from os import PathLike from typing import Any, Union from . import ( LogoData, LogoFormat, LogoOptions, default_formatter, description, formatters, parse_prior, read_seq_data, release_description, seq_io, std_alphabets, std_color_schemes, std_sizes, std_units, ) from .colorscheme import ColorScheme, SymbolColor from .logo import _seq_formats, _seq_names from .seq import Seq, SeqList, nucleic_alphabet from .utils import resource_filename from .utils.deoptparse import DeOptionParser # ====================== Main: Parse Command line ============================= def main() -> None: """WebLogo command line interface""" # ------ Parse Command line ------ parser = _build_option_parser() (opts, args) = parser.parse_args(sys.argv[1:]) if args: parser.error("Unparsable arguments: %s " % args) if opts.serve: httpd_serve_forever(opts.port) # Never returns? # pragma: no cover sys.exit(0) # pragma: no cover # ------ Create Logo ------ try: data = _build_logodata(opts) format = _build_logoformat(data, opts) formatter = opts.formatter logo = formatter(data, format) # logo = logo.encode() opts.fout.buffer.write(logo) except ValueError as err: print("Error:", err, file=sys.stderr) sys.exit(2) except KeyboardInterrupt: # pragma: no cover sys.exit(0) # End main() def httpd_serve_forever(port: int = 8080) -> None: """Start a webserver on a local port.""" import http.server as server import http.server as cgiserver class __HTTPRequestHandler(cgiserver.CGIHTTPRequestHandler): # Modify CGIHTTPRequestHandler so that it will run the cgi script directly, # instead of exec'ing # This bypasses the need for the cgi script to have execute permissions set, # since distutils install does not preserve permissions. def is_cgi(self) -> bool: self.have_fork = False # Prevent CGIHTTPRequestHandler from using fork if self.path == "/create.cgi": self.cgi_info = "", "create.cgi" return True return False def is_python( self, path: Union[str, PathLike] ) -> bool: # Let CGIHTTPRequestHandler know that cgi script is python return True # Add current directory to PYTHONPATH. This is # so that we can run the standalone server # without having to run the install script. pythonpath = os.getenv("PYTHONPATH", "") pythonpath += os.pathsep + os.path.abspath(sys.path[0]) # .split()[0] os.environ["PYTHONPATH"] = pythonpath htdocs = resource_filename(__name__, "htdocs", __file__) os.chdir(htdocs) HandlerClass = __HTTPRequestHandler ServerClass = server.HTTPServer httpd = ServerClass(("", port), HandlerClass) print("WebLogo server running at http://localhost:%d/" % port) try: httpd.serve_forever() except KeyboardInterrupt: sys.exit(0) # end httpd_serve_forever() def _build_logodata(options: Any) -> LogoData: motif_flag = False fin = options.fin if options.upload is None: if fin is None: fin = StringIO(sys.stdin.read()) else: if fin is None: from .logo import _from_URL_fileopen fin = _from_URL_fileopen(options.upload) else: raise ValueError("error: options --fin and --upload are incompatible") try: # Try reading data in transfac format first. from .matrix import Motif motif = Motif.read_transfac(fin, alphabet=options.alphabet) motif_flag = True except ValueError as motif_err: # Failed reading Motif, try reading as multiple sequence data. if options.input_parser == "transfac": raise motif_err # Adding transfac as str insted of parser is a bit of a ugly kludge seqs = read_seq_data( fin, options.input_parser.read, alphabet=options.alphabet, ignore_lower_case=options.ignore_lower_case, ) if motif_flag: if options.ignore_lower_case: raise ValueError( "error: option --ignore-lower-case incompatible with matrix input" ) if options.reverse or options.revcomp: motif.reverse() if options.complement or options.revcomp: motif.complement() prior = parse_prior(options.composition, motif.alphabet, options.weight) data = LogoData.from_counts(motif.alphabet, motif.array, prior) else: if options.reverse or options.revcomp: seqs = SeqList([s.reverse() for s in seqs], seqs.alphabet) if options.complement or options.revcomp: if not nucleic_alphabet.alphabetic(str(seqs.alphabet)): raise ValueError( "non-nucleic sequence cannot be complemented" ) # pragam: no cover aaa = seqs.alphabet seqs.alphabet = nucleic_alphabet seqs = SeqList( [Seq(s, seqs.alphabet).complement() for s in seqs], seqs.alphabet ) seqs.alphabet = aaa a = seqs.alphabet assert a is not None prior = parse_prior(options.composition, a, options.weight) data = LogoData.from_seqs(seqs, prior) return data def _build_logoformat(logodata: LogoData, opts: Any) -> LogoFormat: """Extract and process relevant option values and return a LogoFormat object.""" args = {} direct_from_opts = [ # Logo Data Options. "alphabet", "unit_name", "first_index", "logo_start", "logo_end", # Logo Format Options. "stack_width", "stacks_per_line", "logo_title", "logo_label", "show_xaxis", "xaxis_label", "annotate", "rotate_numbers", "number_interval", "yaxis_scale", "show_yaxis", "yaxis_label", "show_ends", "fineprint", "yaxis_tic_interval", "show_errorbars", "reverse_stacks", # Color Options. "color_scheme", "default_color", # Font Format Options. "fontsize", "title_fontsize", "small_fontsize", "number_fontsize", "text_font", "logo_font", "title_font", # Advanced Format Options. "stack_aspect_ratio", "show_boxes", "resolution", "scale_width", "debug", "errorbar_fraction", "errorbar_width_fraction", "errorbar_gray", ] for k in direct_from_opts: args[k] = opts.__dict__[k] # logo_size = copy.copy(opts.__dict__['logo_size']) # size_from_opts = ["stack_width", "stack_height"] # for k in size_from_opts : # length = getattr(opts, k) # if length : # setattr( logo_size, k, length ) # args["size"] = logo_size if opts.colors: color_scheme = ColorScheme() for color, symbols, desc in opts.colors: try: # c = Color.from_string(color) color_scheme.rules.append(SymbolColor(symbols, color, desc)) except ValueError: raise ValueError("error: option --color: invalid value: '%s'" % color) args["color_scheme"] = color_scheme if opts.annotate: args["annotate"] = opts.annotate.split(",") logooptions = LogoOptions() for a, v in args.items(): setattr(logooptions, a, v) theformat = LogoFormat(logodata, logooptions) return theformat # ========================== OPTIONS ========================== def _build_option_parser() -> DeOptionParser: defaults = LogoOptions() parser = DeOptionParser( usage="%prog [options] < sequence_data.fa > sequence_logo.eps", description=description, version=release_description, add_verbose_options=False, ) io_grp = OptionGroup( parser, "Input/Output Options", ) data_grp = OptionGroup( parser, "Logo Data Options", ) trans_grp = OptionGroup( parser, "Transformations", "Optional transformations of the sequence data." ) format_grp = OptionGroup( parser, "Logo Format Options", "These options control the format and display of the logo.", ) color_grp = OptionGroup( parser, "Color Options", "Colors can be specified using CSS2 syntax. e.g. 'red', '#FF0000', etc", ) font_grp = OptionGroup( parser, "Font Format Options", "These options provide control over the font sizes and types.", ) advanced_grp = OptionGroup( parser, "Advanced Format Options", "These options provide fine control over the display of the logo.", ) server_grp = OptionGroup( parser, "WebLogo Server", "Run a standalone webserver on a local port." ) parser.add_option_group(io_grp) parser.add_option_group(data_grp) parser.add_option_group(trans_grp) parser.add_option_group(format_grp) parser.add_option_group(color_grp) parser.add_option_group(font_grp) parser.add_option_group(advanced_grp) parser.add_option_group(server_grp) # ========================== IO OPTIONS ========================== io_grp.add_option( "-f", "--fin", dest="fin", action="store", type="file_in", default=None, help="Sequence input file (default: stdin)", metavar="FILENAME", ) io_grp.add_option( "", "--upload", dest="upload", action="store", default=None, help="Upload input file from URL", metavar="URL", ) io_grp.add_option( "-D", "--datatype", dest="input_parser", action="store", type="dict", default=seq_io, choices=_seq_formats(), help="Type of multiple sequence alignment or position" " weight matrix file: (%s)" % ", ".join(_seq_names()), metavar="FORMAT", ) io_grp.add_option( "-o", "--fout", dest="fout", type="file_out", default=sys.stdout, help="Output file (default: stdout)", metavar="FILENAME", ) io_grp.add_option( "-F", "--format", dest="formatter", action="store", type="dict", choices=formatters, metavar="FORMAT", help="Format of output: eps (default), png, png_print, pdf, jpeg, svg, " "logodata, csv", default=default_formatter, ) # ========================== Data OPTIONS ========================== data_grp.add_option( "-A", "--sequence-type", dest="alphabet", action="store", type="dict", choices=std_alphabets, help="The type of sequence data: 'protein', 'rna' or 'dna'.", metavar="TYPE", ) data_grp.add_option( "-a", "--alphabet", dest="alphabet", action="store", help="The set of symbols to count, e.g. 'AGTC'. " "All characters not in the alphabet are ignored. " "If neither the alphabet nor sequence-type are specified then weblogo " "will examine the input data and make an educated guess. " "See also --sequence-type, --ignore-lower-case", ) data_grp.add_option( "-U", "--units", dest="unit_name", action="store", choices=list(std_units.keys()), type="choice", default=defaults.unit_name, help="A unit of entropy ('bits' (default), 'nats', 'digits'), or a unit of" "free energy ('kT', 'kJ/mol', 'kcal/mol'), or 'probability' for" " probabilities", metavar="UNIT", ) data_grp.add_option( "", "--composition", dest="composition", action="store", type="string", default="auto", help="The expected composition of the sequences: 'auto' (default), " "'equiprobable', 'none' (do not perform any compositional " "adjustment), a CG percentage, a species name (e.g. 'E. coli', " "'H. sapiens'), or an explicit distribution (e.g. \"{'A':10, 'C':40," " 'G':40, 'T':10}\"). The automatic option uses a typical " "distribution for proteins and equiprobable distribution for " "everything else. ", metavar="COMP.", ) data_grp.add_option( "", "--weight", dest="weight", action="store", type="float", default=None, help="The weight of prior data. Default depends on alphabet length", metavar="NUMBER", ) data_grp.add_option( "-i", "--first-index", dest="first_index", action="store", type="int", default=1, help="Index of first position in sequence data (default: 1)", metavar="INDEX", ) data_grp.add_option( "-l", "--lower", dest="logo_start", action="store", type="int", help="Lower bound of sequence to display", metavar="INDEX", ) data_grp.add_option( "-u", "--upper", dest="logo_end", action="store", type="int", help="Upper bound of sequence to display", metavar="INDEX", ) # ========================== Transformation OPTIONS ========================== # FIXME Add test? trans_grp.add_option( "", "--ignore-lower-case", dest="ignore_lower_case", action="store_true", default=False, help="Disregard lower case letters and only count upper case letters" " in sequences.", ) trans_grp.add_option( "", "--reverse", dest="reverse", action="store_true", default=False, help="reverse sequences", ) trans_grp.add_option( "", "--complement", dest="complement", action="store_true", default=False, help="complement nucleic sequences", ) trans_grp.add_option( "", "--revcomp", dest="revcomp", action="store_true", default=False, help="reverse complement nucleic sequences", ) # ========================== FORMAT OPTIONS ========================== format_grp.add_option( "-s", "--size", dest="stack_width", action="store", type="dict", choices=std_sizes, metavar="LOGOSIZE", default=defaults.stack_width, help="Specify a standard logo size (small, medium (default), large)", ) format_grp.add_option( "-n", "--stacks-per-line", dest="stacks_per_line", action="store", type="int", help="Maximum number of logo stacks per logo line. (default: %default)", default=defaults.stacks_per_line, metavar="COUNT", ) format_grp.add_option( "-t", "--title", dest="logo_title", action="store", type="string", help="Logo title text.", default=defaults.logo_title, metavar="TEXT", ) format_grp.add_option( "", "--label", dest="logo_label", action="store", type="string", help="A figure label, e.g. '2a'", default=defaults.logo_label, metavar="TEXT", ) format_grp.add_option( "-X", "--show-xaxis", action="store", type="boolean", default=defaults.show_xaxis, metavar="YES/NO", help="Display sequence numbers along x-axis? (default: %default)", ) format_grp.add_option( "-x", "--xlabel", dest="xaxis_label", action="store", type="string", default=defaults.xaxis_label, help="X-axis label", metavar="TEXT", ) format_grp.add_option( "", "--annotate", dest="annotate", action="store", type="string", default=None, help="A comma separated list of custom stack annotations, " "e.g. '1,3,4,5,6,7'. Annotation list must be same length as " "sequences.", metavar="TEXT", ) format_grp.add_option( "", "--rotate-numbers", dest="rotate_numbers", action="store", type="boolean", default=defaults.rotate_numbers, help="Draw X-axis numbers with vertical orientation (default: %default).", metavar="YES/NO", ) format_grp.add_option( "", "--number-interval", dest="number_interval", action="store", type="float", default=defaults.number_interval, help="Distance between numbers on X-axis (default: %s)" % defaults.number_interval, metavar="NUMBER", ) format_grp.add_option( "-S", "--yaxis", dest="yaxis_scale", action="store", type="float", help="Height of yaxis in units. (Default: Maximum value with " "uninformative prior.)", metavar="NUMBER", ) format_grp.add_option( "-Y", "--show-yaxis", action="store", type="boolean", dest="show_yaxis", default=defaults.show_yaxis, metavar="YES/NO", help="Display entropy scale along y-axis? (default: %default)", ) format_grp.add_option( "-y", "--ylabel", dest="yaxis_label", action="store", type="string", help="Y-axis label (default depends on plot type and units)", metavar="TEXT", ) format_grp.add_option( "-E", "--show-ends", action="store", type="boolean", default=defaults.show_ends, metavar="YES/NO", help="Label the ends of the sequence? (default: %default)", ) format_grp.add_option( "-P", "--fineprint", dest="fineprint", action="store", type="string", default=defaults.fineprint, help="The fine print (default: weblogo version)", metavar="TEXT", ) format_grp.add_option( "", "--ticmarks", dest="yaxis_tic_interval", action="store", type="float", default=defaults.yaxis_tic_interval, help="Distance between ticmarks (default: %default)", metavar="NUMBER", ) format_grp.add_option( "", "--errorbars", dest="show_errorbars", action="store", type="boolean", default=defaults.show_errorbars, metavar="YES/NO", help="Display error bars? (default: %default)", ) format_grp.add_option( "", "--reverse-stacks", dest="reverse_stacks", action="store", type="boolean", default=defaults.show_errorbars, metavar="YES/NO", help="Draw stacks with largest letters on top? (default: %default)", ) # ========================== Color OPTIONS ========================== # TODO: Future Feature # color_grp.add_option( "-K", "--color-key", # dest= "show_color_key", # action="store", # type = "boolean", # default= defaults.show_color_key, # metavar = "YES/NO", # help="Display a color key (default: %default)") color_scheme_choices = list(std_color_schemes.keys()) color_scheme_choices.sort() color_grp.add_option( "-c", "--color-scheme", dest="color_scheme", action="store", type="dict", choices=std_color_schemes, metavar="SCHEME", default=None, # Auto help="Specify a standard color scheme (%s)" % ", ".join(color_scheme_choices), ) color_grp.add_option( "-C", "--color", dest="colors", action="append", metavar="COLOR SYMBOLS DESCRIPTION ", nargs=3, default=[], help="Specify symbol colors, e.g. --color black AG 'Purine' " "--color red TC 'Pyrimidine' ", ) color_grp.add_option( "", "--default-color", dest="default_color", action="store", metavar="COLOR", default=defaults.default_color, help="Symbol color if not otherwise specified.", ) # ========================== Font options ========================= font_grp.add_option( "", "--fontsize", dest="fontsize", action="store", type="float", default=defaults.fontsize, help="Regular text font size in points (default: %s)" % defaults.fontsize, metavar="POINTS", ) font_grp.add_option( "", "--title-fontsize", dest="title_fontsize", action="store", type="float", default=defaults.title_fontsize, help="Title text font size in points (default: %s)" % defaults.title_fontsize, metavar="POINTS", ) font_grp.add_option( "", "--small-fontsize", dest="small_fontsize", action="store", type="float", default=defaults.small_fontsize, help="Small text font size in points (default: %s)" % defaults.small_fontsize, metavar="POINTS", ) font_grp.add_option( "", "--number-fontsize", dest="number_fontsize", action="store", type="float", default=defaults.number_fontsize, help="Axis numbers font size in points (default: %s)" % defaults.number_fontsize, metavar="POINTS", ) font_grp.add_option( "", "--text-font", dest="text_font", action="store", type="string", default=defaults.text_font, help="Specify font for labels (default: %s)" % defaults.text_font, metavar="FONT", ) font_grp.add_option( "", "--logo-font", dest="logo_font", action="store", type="string", default=defaults.text_font, help="Specify font for logo (default: %s)" % defaults.logo_font, metavar="FONT", ) font_grp.add_option( "", "--title-font", dest="title_font", action="store", type="string", default=defaults.title_font, help="Specify font for title (default: %s)" % defaults.title_font, metavar="FONT", ) # ========================== Advanced options ========================= advanced_grp.add_option( "-W", "--stack-width", dest="stack_width", action="store", type="float", default=defaults.stack_width, help="Width of a logo stack (default: %s)" % defaults.stack_width, metavar="POINTS", ) advanced_grp.add_option( "", "--aspect-ratio", dest="stack_aspect_ratio", action="store", type="float", default=defaults.stack_aspect_ratio, help="Ratio of stack height to width (default: %s)" % defaults.stack_aspect_ratio, metavar="POINTS", ) advanced_grp.add_option( "", "--box", dest="show_boxes", action="store", type="boolean", default=False, metavar="YES/NO", help="Draw boxes around symbols? (default: no)", ) advanced_grp.add_option( "", "--resolution", dest="resolution", action="store", type="float", default=96, help="Bitmap resolution in dots per inch (DPI). (Default: 96 DPI," " except png_print, 600 DPI) Low resolution bitmaps (DPI<300)" " are antialiased.", metavar="DPI", ) advanced_grp.add_option( "", "--scale-width", dest="scale_width", action="store", type="boolean", default=True, metavar="YES/NO", help="Scale the visible stack width by the fraction of symbols in the" " column? (I.e. columns with many gaps of unknowns are narrow.) " "(Default: yes)", ) advanced_grp.add_option( "", "--debug", action="store", type="boolean", default=defaults.debug, metavar="YES/NO", help="Output additional diagnostic information. (Default: %default)", ) advanced_grp.add_option( "", "--errorbar-fraction", dest="errorbar_fraction", action="store", type="float", default=defaults.errorbar_fraction, help="Sets error bars display proportion (default: %s)" % defaults.errorbar_fraction, metavar="NUMBER", ) advanced_grp.add_option( "", "--errorbar-width-fraction", dest="errorbar_width_fraction", action="store", type="float", default=defaults.errorbar_width_fraction, help="Sets error bars width display proportion (default: %s)" % defaults.errorbar_width_fraction, metavar="NUMBER", ) advanced_grp.add_option( "", "--errorbar-gray", dest="errorbar_gray", action="store", type="float", default=defaults.errorbar_gray, help="Sets error bars' gray scale percentage (default: %s)" % defaults.errorbar_gray, metavar="NUMBER", ) # ========================== Server options ========================= server_grp.add_option( "", "--serve", dest="serve", action="store_true", default=False, help="Start a standalone WebLogo server for creating sequence logos.", ) server_grp.add_option( "", "--port", dest="port", action="store", type="int", default=8080, help="Listen to this local port. (Default: %default)", metavar="PORT", ) return parser # END _build_option_parser ############################################################## weblogo-3.8.0/weblogo/_transformseq.py000077500000000000000000000107671467613320200200750ustar00rootroot00000000000000#!/usr/bin/env python # Copyright (c) 2006, The Regents of the University of California, through # Lawrence Berkeley National Laboratory (subject to receipt of any required # approvals from the U.S. Dept. of Energy). All rights reserved. # This software is distributed under the new BSD Open Source License. # # Please see the LICENSE.txt file that should have been included # as part of this package. """ A tool for converting multiple sequence alignments from one format to another. """ import sys from optparse import OptionGroup from weblogo import seq_io from weblogo.seq import Seq, SeqList, nucleic_alphabet from weblogo.transform import mask_low_complexity from weblogo.utils.deoptparse import DeOptionParser __version__ = "1.0.0" description = """ A tool for converting multiple sequence alignments from one format to another. """ def main() -> None: # ------ Parse Command line ------ parser = _build_option_parser() (opts, args) = parser.parse_args(sys.argv[1:]) if args: parser.error("Unparsable arguments: %s " % args) seqs = opts.reader.read(opts.fin) if opts.trans_seg: seqs = SeqList([mask_low_complexity(s) for s in seqs]) if opts.subsample is not None: from random import random frac = opts.subsample ss = [] for s in seqs: if random() < frac: ss.append(s) seqs = SeqList(ss) if opts.reverse: seqs = SeqList([s.reverse() for s in seqs]) if opts.complement: seqs = SeqList([Seq(s, alphabet=nucleic_alphabet) for s in seqs]) seqs = SeqList([s.complement() for s in seqs]) opts.writer.write(opts.fout, seqs) def _build_option_parser() -> DeOptionParser: parser = DeOptionParser( usage="%prog [options] < sequence_data.fa > sequence_logo.eps", description=description, version=__version__, add_verbose_options=False, ) io_grp = OptionGroup( parser, "Input/Output Options", ) parser.add_option_group(io_grp) io_grp.add_option( "-f", "--fin", dest="fin", action="store", type="file_in", default=sys.stdin, help="Sequence input file (default: stdin)", metavar="FILENAME", ) io_grp.add_option( "", "--format-in", dest="reader", action="store", type="dict", default=seq_io, choices=seq_io.format_names(), help="Multiple sequence alignment format: (%s)" % ", ".join([f.names[0] for f in seq_io.formats]), # type: ignore metavar="FORMAT", ) io_grp.add_option( "-o", "--fout", dest="fout", type="file_out", default=sys.stdout, help="Output file (default: stdout)", metavar="FILENAME", ) trans_grp = OptionGroup( parser, "Transformations", ) parser.add_option_group(trans_grp) trans_grp.add_option( "", "--seg", dest="trans_seg", action="store_true", default=False, help="Mask low complexity regions in protein sequences.", metavar="TRUE/FALSE", ) trans_grp.add_option( "", "--subsample", dest="subsample", action="store", type="float", default=None, help="Return a random subsample of the sequences.", metavar="FRACTION", ) trans_grp.add_option( "", "--reverse", dest="reverse", action="store_true", default=False, help="reverse sequences", metavar="TRUE/FALSE", ) trans_grp.add_option( "", "--complement", dest="complement", action="store_true", default=False, help="complement DNA sequences", metavar="TRUE/FALSE", ) # Writers out_formats = [] for f in seq_io.formats: if hasattr(f, "write"): out_formats.append(f) out_choices = {} for f in out_formats: out_choices[f.names[0]] = f # type: ignore out_names = [f.names[0] for f in out_formats] # type: ignore io_grp.add_option( "-F", "--format-out", dest="writer", action="store", type="dict", default=seq_io.fasta_io, choices=out_choices, help="Multiple sequence alignment output format: (%s) (Default: fasta)" % ", ".join(out_names), metavar="FORMAT", ) return parser weblogo-3.8.0/weblogo/color.py000077500000000000000000000316111467613320200163170ustar00rootroot00000000000000# Copyright (c) 2005 Gavin E. Crooks # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. """ Color specifications using CSS2 (Cascading Style Sheet) syntax.""" from typing import Any, List class Color(object): """Color specifications using CSS2 (Cascading Style Sheet) syntax. http://www.w3.org/TR/REC-CSS2/syndata.html#color-units Usage: red = Color(255,0,0) red = Color(1., 0., 0.) red = Color.by_name("red") red = Color.from_rgb(1.,0.,0.) red = Color.from_rgb(255,0,0) red = Color.from_hsl(0.,1., 0.5) red = Color.from_string("red") red = Color.from_string("RED") red = Color.from_string("#F00") red = Color.from_string("#FF0000") red = Color.from_string("rgb(255, 0, 0)") red = Color.from_string("rgb(100%, 0%, 0%)") red = Color.from_string("hsl(0, 100%, 50%)") """ def __init__(self, red: float, green: float, blue: float) -> None: if not (type(red) is type(green) is type(blue)): raise TypeError("Mixed floats and integers?") # Convert integer RBG values in [0, 255] to floats in [0, 1] if isinstance(red, int): red /= 255.0 if isinstance(green, int): green /= 255.0 if isinstance(blue, int): blue /= 255.0 # Clip RBG values to [0, 1] self.red = max(0.0, min(red, 1.0)) self.green = max(0.0, min(green, 1.0)) self.blue = max(0.0, min(blue, 1.0)) @staticmethod def names() -> List[str]: "Return a list of standard color names." return list(_std_colors.keys()) @classmethod def from_rgb(cls, r: float, g: float, b: float) -> "Color": return cls(r, g, b) @classmethod def from_hsl(cls, hue_angle: float, saturation: float, lightness: float) -> "Color": def hue_to_rgb(v1: float, v2: float, vH: float) -> float: if vH < 0.0: vH += 1.0 if vH > 1.0: vH -= 1.0 # pragma: no cover (Grandfathered in) if vH * 6.0 < 1.0: return v1 + (v2 - v1) * 6.0 * vH if vH * 2.0 < 1.0: return v2 if vH * 3.0 < 2.0: return v1 + (v2 - v1) * ((2.0 / 3.0) - vH) * 6.0 # pragma: no cover return v1 hue = (((hue_angle % 360.0) + 360.0) % 360.0) / 360.0 if not (saturation >= 0.0 and saturation <= 1.0): raise ValueError( "Out-of-range saturation %f" % saturation ) # pragma: no cover if not (lightness >= 0.0 and lightness <= 1.0): raise ValueError( "Out-of-range lightness %f" % lightness ) # pragma: no cover if saturation == 0: # greyscale return cls.from_rgb(lightness, lightness, lightness) if lightness < 0.5: v2 = lightness * (1.0 + saturation) else: v2 = (lightness + saturation) - (saturation * lightness) v1 = 2.0 * lightness - v2 r = hue_to_rgb(v1, v2, hue + (1.0 / 3.0)) g = hue_to_rgb(v1, v2, hue) b = hue_to_rgb(v1, v2, hue - (1.0 / 3.0)) return cls(r, g, b) @staticmethod def by_name(string: str) -> "Color": s = string.strip().lower().replace(" ", "") try: return _std_colors[s] except KeyError: raise ValueError("Unknown color name: %s" % s) @classmethod def from_string(cls, string: str) -> "Color": def to_frac(string: str) -> float: # string can be "255" or "100%" if string[-1] == "%": return float(string[0:-1]) / 100.0 else: return float(string) / 255.0 s = string.strip().lower().replace(" ", "").replace("_", "") if s in _std_colors: # "red" return _std_colors[s] if s[0] == "#": # "#fef" if len(s) == 4: r = int(s[1] + s[1], 16) g = int(s[2] + s[2], 16) b = int(s[3] + s[3], 16) return cls(r, g, b) elif len(s) == 7: # "#ff00aa" r = int(s[1:3], 16) g = int(s[3:5], 16) b = int(s[5:7], 16) return cls(r, g, b) else: raise ValueError("Cannot parse string: %s" % s) if s[0:4] == "rgb(" and s[-1] == ")": rgb = s[4:-1].split(",") if len(rgb) != 3: raise ValueError("Cannot parse string a: %s" % s) return cls(to_frac(rgb[0]), to_frac(rgb[1]), to_frac(rgb[2])) if s[0:4] == "hsl(" and s[-1] == ")": hsl = s[4:-1].split(",") if len(hsl) != 3: raise ValueError("Cannot parse string a: %s" % s) return cls.from_hsl(int(hsl[0]), to_frac(hsl[1]), to_frac(hsl[2])) raise ValueError("Cannot parse string: %s" % s) def __eq__(self, other: Any) -> bool: if not isinstance(other, self.__class__): return False req = int(0.5 + 255.0 * self.red) == int(0.5 + 255.0 * other.red) beq = int(0.5 + 255.0 * self.blue) == int(0.5 + 255.0 * other.blue) geq = int(0.5 + 255.0 * self.green) == int(0.5 + 255.0 * other.green) return req and beq and geq def __repr__(self) -> str: return "Color(%f,%f,%f)" % (self.red, self.green, self.blue) _std_colors = dict( aliceblue=Color(240, 248, 255), # f0f8ff antiquewhite=Color(250, 235, 215), # faebd7 aqua=Color(0, 255, 255), # 00ffff aquamarine=Color(127, 255, 212), # 7fffd4 azure=Color(240, 255, 255), # f0ffff beige=Color(245, 245, 220), # f5f5dc bisque=Color(255, 228, 196), # ffe4c4 black=Color(0, 0, 0), # 000000 blanchedalmond=Color(255, 235, 205), # ffebcd blue=Color(0, 0, 255), # 0000ff blueviolet=Color(138, 43, 226), # 8a2be2 brown=Color(165, 42, 42), # a52a2a burlywood=Color(222, 184, 135), # deb887 cadetblue=Color(95, 158, 160), # 5f9ea0 chartreuse=Color(127, 255, 0), # 7fff00 chocolate=Color(210, 105, 30), # d2691e coral=Color(255, 127, 80), # ff7f50 cornflowerblue=Color(100, 149, 237), # 6495ed cornsilk=Color(255, 248, 220), # fff8dc crimson=Color(220, 20, 60), # dc143c cyan=Color(0, 255, 255), # 00ffff darkblue=Color(0, 0, 139), # 00008b darkcyan=Color(0, 139, 139), # 008b8b darkgoldenrod=Color(184, 134, 11), # b8860b darkgray=Color(169, 169, 169), # a9a9a9 darkgreen=Color(0, 100, 0), # 006400 darkgrey=Color(169, 169, 169), # a9a9a9 darkkhaki=Color(189, 183, 107), # bdb76b darkmagenta=Color(139, 0, 139), # 8b008b darkolivegreen=Color(85, 107, 47), # 556b2f darkorange=Color(255, 140, 0), # ff8c00 darkorchid=Color(153, 50, 204), # 9932cc darkred=Color(139, 0, 0), # 8b0000 darksalmon=Color(233, 150, 122), # e9967a darkseagreen=Color(143, 188, 143), # 8fbc8f darkslateblue=Color(72, 61, 139), # 483d8b darkslategray=Color(47, 79, 79), # 2f4f4f darkslategrey=Color(47, 79, 79), # 2f4f4f darkturquoise=Color(0, 206, 209), # 00ced1 darkviolet=Color(148, 0, 211), # 9400d3 deeppink=Color(255, 20, 147), # ff1493 deepskyblue=Color(0, 191, 255), # 00bfff dimgray=Color(105, 105, 105), # 696969 dimgrey=Color(105, 105, 105), # 696969 dodgerblue=Color(30, 144, 255), # 1e90ff firebrick=Color(178, 34, 34), # b22222 floralwhite=Color(255, 250, 240), # fffaf0 forestgreen=Color(34, 139, 34), # 228b22 fuchsia=Color(255, 0, 255), # ff00ff gainsboro=Color(220, 220, 220), # dcdcdc ghostwhite=Color(248, 248, 255), # f8f8ff gold=Color(255, 215, 0), # ffd700 goldenrod=Color(218, 165, 32), # daa520 gray=Color(128, 128, 128), # 808080 green=Color(0, 128, 0), # 008000 greenyellow=Color(173, 255, 47), # adff2f grey=Color(128, 128, 128), # 808080 honeydew=Color(240, 255, 240), # f0fff0 hotpink=Color(255, 105, 180), # ff69b4 indianred=Color(205, 92, 92), # cd5c5c indigo=Color(75, 0, 130), # 4b0082 ivory=Color(255, 255, 240), # fffff0 khaki=Color(240, 230, 140), # f0e68c lavender=Color(230, 230, 250), # e6e6fa lavenderblush=Color(255, 240, 245), # fff0f5 lawngreen=Color(124, 252, 0), # 7cfc00 lemonchiffon=Color(255, 250, 205), # fffacd lightblue=Color(173, 216, 230), # add8e6 lightcoral=Color(240, 128, 128), # f08080 lightcyan=Color(224, 255, 255), # e0ffff lightgoldenrodyellow=Color(250, 250, 210), # fafad2 lightgray=Color(211, 211, 211), # d3d3d3 lightgreen=Color(144, 238, 144), # 90ee90 lightgrey=Color(211, 211, 211), # d3d3d3 lightpink=Color(255, 182, 193), # ffb6c1 lightsalmon=Color(255, 160, 122), # ffa07a lightseagreen=Color(32, 178, 170), # 20b2aa lightskyblue=Color(135, 206, 250), # 87cefa lightslategray=Color(119, 136, 153), # 778899 lightslategrey=Color(119, 136, 153), # 778899 lightsteelblue=Color(176, 196, 222), # b0c4de lightyellow=Color(255, 255, 224), # ffffe0 lime=Color(0, 255, 0), # 00ff00 limegreen=Color(50, 205, 50), # 32cd32 linen=Color(250, 240, 230), # faf0e6 magenta=Color(255, 0, 255), # ff00ff maroon=Color(128, 0, 0), # 800000 mediumaquamarine=Color(102, 205, 170), # 66cdaa mediumblue=Color(0, 0, 205), # 0000cd mediumorchid=Color(186, 85, 211), # ba55d3 mediumpurple=Color(147, 112, 219), # 9370db mediumseagreen=Color(60, 179, 113), # 3cb371 mediumslateblue=Color(123, 104, 238), # 7b68ee mediumspringgreen=Color(0, 250, 154), # 00fa9a mediumturquoise=Color(72, 209, 204), # 48d1cc mediumvioletred=Color(199, 21, 133), # c71585 midnightblue=Color(25, 25, 112), # 191970 mintcream=Color(245, 255, 250), # f5fffa mistyrose=Color(255, 228, 225), # ffe4e1 moccasin=Color(255, 228, 181), # ffe4b5 navajowhite=Color(255, 222, 173), # ffdead navy=Color(0, 0, 128), # 000080 oldlace=Color(253, 245, 230), # fdf5e6 olive=Color(128, 128, 0), # 808000 olivedrab=Color(107, 142, 35), # 6b8e23 orange=Color(255, 165, 0), # ffa500 orangered=Color(255, 69, 0), # ff4500 orchid=Color(218, 112, 214), # da70d6 palegoldenrod=Color(238, 232, 170), # eee8aa palegreen=Color(152, 251, 152), # 98fb98 paleturquoise=Color(175, 238, 238), # afeeee palevioletred=Color(219, 112, 147), # db7093 papayawhip=Color(255, 239, 213), # ffefd5 peachpuff=Color(255, 218, 185), # ffdab9 peru=Color(205, 133, 63), # cd853f pink=Color(255, 192, 203), # ffc0cb plum=Color(221, 160, 221), # dda0dd powderblue=Color(176, 224, 230), # b0e0e6 purple=Color(128, 0, 128), # 800080 red=Color(255, 0, 0), # ff0000 rosybrown=Color(188, 143, 143), # bc8f8f royalblue=Color(65, 105, 225), # 4169e1 saddlebrown=Color(139, 69, 19), # 8b4513 salmon=Color(250, 128, 114), # fa8072 sandybrown=Color(244, 164, 96), # f4a460 seagreen=Color(46, 139, 87), # 2e8b57 seashell=Color(255, 245, 238), # fff5ee sienna=Color(160, 82, 45), # a0522d silver=Color(192, 192, 192), # c0c0c0 skyblue=Color(135, 206, 235), # 87ceeb slateblue=Color(106, 90, 205), # 6a5acd slategray=Color(112, 128, 144), # 708090 slategrey=Color(112, 128, 144), # 708090 snow=Color(255, 250, 250), # fffafa springgreen=Color(0, 255, 127), # 00ff7f steelblue=Color(70, 130, 180), # 4682b4 tan=Color(210, 180, 140), # d2b48c teal=Color(0, 128, 128), # 008080 thistle=Color(216, 191, 216), # d8bfd8 tomato=Color(255, 99, 71), # ff6347 turquoise=Color(64, 224, 208), # 40e0d0 violet=Color(238, 130, 238), # ee82ee wheat=Color(245, 222, 179), # f5deb3 white=Color(255, 255, 255), # ffffff whitesmoke=Color(245, 245, 245), # f5f5f5 yellow=Color(255, 255, 0), # ffff00 yellowgreen=Color(154, 205, 50), # 9acd32 ) weblogo-3.8.0/weblogo/colorscheme.py000077500000000000000000000166641467613320200175170ustar00rootroot00000000000000# Copyright (c) 2003-2005 The Regents of the University of California. # Copyright (c) 2005 Gavin E. Crooks # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. """ Popular color codings for nucleic and amino acids. Classes: ColorScheme -- A color scheme SymbolColor IndexColor RefSeqColor Generic monochrome Nucleotides nucleotide base pairing Amino Acid hydrophobicity chemistry charge taylor Status : Beta - Needs documentation. """ # Good online references include bioruby and the JalView alignment editor. # Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), # "The Jalview Java Alignment Editor," Bioinformatics, 12, 426-7 # http://www.jalview.org from typing import List, Optional, Sequence from . import seq from .color import Color from .seq import Alphabet # TODO: Make as abstract class ColorRule: """ Define an interface for coloring individual symbols based on their position and identity. Subclasses should reimplement the symbol_color() method to return a Color object based on the given parameters. """ def symbol_color(self, seq_index: int, symbol: str, rank: int) -> Optional[Color]: raise NotImplementedError # pragma: no cover class ColorScheme(ColorRule): """ Specify which color each symbol in a sequence logo should be. A color scheme is primarily a container of color rules. These rules would be along the lines of "hydrophobic residues are blue" or "indices 5-10 are red" or "the wildtype sequence is black". When a color is requested for a particular symbol, each rule is consulted in turn until one provides a color. If no rule provides a color, the given default color will be used. """ def __init__( self, rules: List[ColorRule] = [], title: str = "", description: str = "", default_color: str = "black", alphabet: Alphabet = seq.generic_alphabet, ) -> None: self.rules = rules self.title = title self.description = description self.default_color = Color.from_string(default_color) self.alphabet = alphabet def symbol_color(self, seq_index: int, symbol: str, rank: int) -> Color: if symbol not in self.alphabet: raise KeyError("Colored symbol '%s' does not exist in alphabet." % symbol) for rule in self.rules: color = rule.symbol_color(seq_index, symbol, rank) if color is not None: return color return self.default_color class SymbolColor(ColorRule): """ Represent the given set of symbols (e.g. "DEHKR" for charged residues) with a single color. """ def __init__( self, symbols: str, color: str, description: Optional[str] = None ) -> None: self.symbols = symbols self.color = Color.from_string(color) self.description = description def symbol_color(self, seq_index: int, symbol: str, rank: int) -> Optional[Color]: if symbol in self.symbols: return self.color return None class IndexColor(ColorRule): """ Represent the given set of indices (e.g. range(10) for the first ten residues) with a single color. """ def __init__( self, indices: Sequence[int], color: str, description: Optional[str] = None ) -> None: self.indices = indices self.color = Color.from_string(color) self.description = description def symbol_color(self, seq_index: int, symbol: str, rank: int) -> Optional[Color]: if seq_index in self.indices: return self.color return None class RefSeqColor(ColorRule): """ Color the given reference sequence in its own color, so you can easily see which positions match that sequence and which don't. """ def __init__( self, ref_seq: str, color: str, description: Optional[str] = None ) -> None: self.ref_seq = ref_seq self.color = Color.from_string(color) self.description = description def symbol_color(self, seq_index: int, symbol: str, rank: int) -> Optional[Color]: if symbol == self.ref_seq[seq_index]: return self.color return None monochrome = ColorScheme([]) # This list intentionally left blank # From makelogo nucleotide = ColorScheme( [ SymbolColor("G", "orange"), SymbolColor("TU", "red"), SymbolColor("C", "blue"), SymbolColor("A", "green"), ], ) base_pairing = ColorScheme( [ SymbolColor("TAU", "darkorange", "Weak (2 Watson-Crick hydrogen bonds)"), SymbolColor("GC", "blue", "Strong (3 Watson-Crick hydrogen bonds)"), ], ) # From Crooks2004c-Proteins-SeqStr.pdf hydrophobicity = ColorScheme( [ SymbolColor("RKDENQ", "blue", "hydrophilic"), SymbolColor("SGHTAP", "green", "neutral"), SymbolColor("YVMCLFIW", "black", "hydrophobic"), ], alphabet=seq.unambiguous_protein_alphabet, ) # from makelogo chemistry = ColorScheme( [ SymbolColor("GSTYC", "green", "polar"), SymbolColor("NQ", "purple", "neutral"), SymbolColor("KRH", "blue", "basic"), SymbolColor("DE", "red", "acidic"), SymbolColor("PAWFLIMV", "black", "hydrophobic"), ], alphabet=seq.unambiguous_protein_alphabet, ) charge = ColorScheme( [SymbolColor("KRH", "blue", "Positive"), SymbolColor("DE", "red", "Negative")], alphabet=seq.unambiguous_protein_alphabet, ) taylor = ColorScheme( [ SymbolColor("A", "#CCFF00"), SymbolColor("C", "#FFFF00"), SymbolColor("D", "#FF0000"), SymbolColor("E", "#FF0066"), SymbolColor("F", "#00FF66"), SymbolColor("G", "#FF9900"), SymbolColor("H", "#0066FF"), SymbolColor("I", "#66FF00"), SymbolColor("K", "#6600FF"), SymbolColor("L", "#33FF00"), SymbolColor("M", "#00FF00"), SymbolColor("N", "#CC00FF"), SymbolColor("P", "#FFCC00"), SymbolColor("Q", "#FF00CC"), SymbolColor("R", "#0000FF"), SymbolColor("S", "#FF3300"), SymbolColor("T", "#FF6600"), SymbolColor("V", "#99FF00"), SymbolColor("W", "#00CCFF"), SymbolColor("Y", "#00FFCC"), ], title="Taylor", description="W. Taylor, Protein Engineering, Vol 10 , 743-746 (1997)", alphabet=seq.unambiguous_protein_alphabet, ) weblogo-3.8.0/weblogo/data.py000077500000000000000000000330331467613320200161120ustar00rootroot00000000000000# Copyright (c) 2006, The Regents of the University of California, through # Lawrence Berkeley National Laboratory (subject to receipt of any required # approvals from the U.S. Dept. of Energy). All rights reserved. # This software is distributed under the new BSD Open Source License. # # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions are met: # # (1) Redistributions of source code must retain the above copyright notice, # this list of conditions and the following disclaimer. # # (2) Redistributions in binary form must reproduce the above copyright # notice, this list of conditions and the following disclaimer in the # documentation and or other materials provided with the distribution. # # (3) Neither the name of the University of California, Lawrence Berkeley # National Laboratory, U.S. Dept. of Energy nor the names of its contributors # may be used to endorse or promote products derived from this software # without specific prior written permission. # # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" # AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE # IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE # ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE # LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR # CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF # SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS # INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN # CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE # POSSIBILITY OF SUCH DAMAGE. """ Standard data used in computational biology. To convert a property dictionary to a list : >>> comp = [ amino_acid_composition[k] for k in amino_acid_letters] Resources: Various standard data files are included in the weblogo distribution. These may be loaded with the data_string, data_stream or data_filename methods. A complete set of names is stored in 'resource_names' BLOSUM Scoring Matrices Source: ftp://ftp.ncbi.nih.gov/repository/blocks/unix/blosum These are all new blast style with 1/3 bit scaling - blosum35 - blosum45 - blosum62 - blosum40 - blosum50 - blosum80 - blosum100 Other substitution scoring matrices: - dist20_comp - pam250 - pam120 - vtml160 Description of database cross references : - dbxref.txt (http://www.expasy.org/cgi-bin/lists?dbxref.txt) Attributes: - amino_acid_letters -- Standard codes for the 20 canonical amino acids, in alphabetic order. - amino_acid_alternative_letters -- Amino acid one letter codes, alphabetic by three letter codes. - amino_acid_extended_letters - dna_letters - dna_extended_letters - rna_letters - rna_extended_letters - dna_ambiguity - rna_ambiguity - amino_acid_ambiguity - amino_acid_mass -- Monomer isotopically averaged molecular mass - dna_mass - rna_mass - one_to_three -- Map from standard 1 letter amino acid codes to standard three letter codes. Ref: http://www.ebi.ac.uk/RESID/faq.html - standard_three_to_one -- Map from standard 3 letter amino acid codes to standard 1 letter codes. - extended_three_to_one -- Map between three letter amino acid codes (first letter capitalized) and standard one letter codes. This map contains many nonstandard three letter codes, used, for example, to specify chemically modified amino acids in PDB files. Ref: http://astral.berkeley.edu/ Ref: http://www.ebi.ac.uk/RESID/faq.html - amino_acid_names - amino_acid_composition -- Average amino acid composition of proteins. Ref: McCaldon P., Argos P. Proteins 4:99-122 (1988). - kyte_doolittle_hydrophobicity -- Kyte-Doolittle hydrophobicity scale. Ref: Kyte J., Doolittle R.F. J. Mol. Biol. 157:105-132 (1982) - nucleotide_names Status: Beta (Data needs to be proof checked.) """ # FIXME: Proof check data # FIXME: Add __all__ # The ExPasy ProtScale tool is a great source of amino acid properties. # http://au.expasy.org/cgi-bin/protscale.pl from typing import ByteString, TextIO from . import utils from .utils import resource_filename, resource_stream, resource_string # Explicitly list set of available data resources. We want to be able to access # these resources in, for example, a webapp, without inadvertently allowing # unrestricted read access to the local file system. resource_names = [ "blosum35", "blosum45", "blosum62", "blosum40", "blosum50", "blosum80", "blosum100", "dist20_comp", "pam250", "pam120", "dbxref.txt", "vtml160", ] _resource_filenames = { "blosum35": "data/blosum35.mat", "blosum45": "data/blosum45.mat", "blosum62": "data/blosum62.mat", "blosum40": "data/blosum40.mat", "blosum50": "data/blosum50.mat", "blosum80": "data/blosum80.mat", "blosum100": "data/blosum100.mat", "dist20_comp": "data/dist20_comp.mat", "pam250": "data/pam250.mat", "pam120": "data/pam120.mat", "dbxref.txt": "data/dbxref.txt", "vtml160": "data/vtml160", } # TODO: Substitution matrix parser, SeqMatrix.read # _resource_parsers = {} def data_string(name: str) -> ByteString: """Load the specified resource as a string.""" fn = _resource_filenames[name] return resource_string(__name__, fn, __file__) def data_stream(name: str) -> TextIO: """Provide an open file handle to the specified resource.""" fn = _resource_filenames[name] return resource_stream(__name__, fn, __file__) def data_filename(name: str) -> str: """Provide a filename for the given resource in the local filesystem.""" fn = _resource_filenames[name] return resource_filename(__name__, fn, __file__) # def data_object( name, parser = None) : # if parser is None : # if name in _resource_parsers : # parser = _resource_parsers[name] # else : # parser = str # return parser( data_stream(name) ) amino_acid_letters = "ACDEFGHIKLMNPQRSTVWY" amino_acid_alternative_letters = "ARNDCQEGHILKMFPSTWYV" amino_acid_extended_letters = "ACDEFGHIKLMNOPQRSTUVWYBJZX*-" dna_letters = "GATC" dna_extended_letters = "GATCRYWSMKHBVDN" rna_letters = "GAUC" rna_extended_letters = "GAUCRYWSMKHBVDN" dna_ambiguity = { "A": "A", "C": "C", "G": "G", "T": "T", "M": "AC", "R": "AG", "W": "AT", "S": "CG", "Y": "CT", "K": "GT", "V": "ACG", "H": "ACT", "D": "AGT", "B": "CGT", "X": "GATC", "N": "GATC", } rna_ambiguity = { "A": "A", "C": "C", "G": "G", "U": "U", "M": "AC", "R": "AG", "W": "AU", "S": "CG", "Y": "CU", "K": "GU", "V": "ACG", "H": "ACU", "D": "AGU", "B": "CGU", "X": "GAUC", "N": "GAUC", } amino_acid_ambiguity = { "A": "A", "B": "ND", "C": "C", "D": "D", "E": "E", "F": "F", "G": "G", "H": "H", "I": "I", "K": "K", "L": "L", "M": "M", "N": "N", "P": "P", "Q": "Q", "R": "R", "S": "S", "T": "T", "V": "V", "W": "W", "X": "ACDEFGHIKLMNPQRSTVWY", "Y": "Y", "Z": "QE", "J": "IL", "U": "U", "O": "O", } # Monomer isotopically averaged molecular mass # Data Checked GEC Nov 2006 amino_acid_mass = { "A": 89.09, "B": 132.66, # Averaged proportional to amino_acid_composition "C": 121.16, "D": 133.10, "E": 147.13, "F": 165.19, "G": 75.07, "H": 155.16, "I": 131.18, "J": 131.18, "K": 146.19, "L": 131.18, "M": 149.21, "N": 132.12, # "O" : ???, # TODO "P": 115.13, "Q": 146.15, "R": 174.20, "S": 105.09, "T": 119.12, "U": 168.05, "V": 117.15, "W": 204.23, "X": 129.15, # Averaged proportional to amino_acid_composition "Y": 181.19, "Z": 146.76, # Averaged proportional to amino_acid_composition } dna_mass = { "A": 347.0, "C": 323.0, "G": 363.0, "T": 322.0, } rna_mass = { "A": 363.0, "C": 319.0, "G": 379.0, "U": 340.0, } one_to_three = { "A": "Ala", "B": "Asx", "C": "Cys", "D": "Asp", "E": "Glu", "F": "Phe", "G": "Gly", "H": "His", "I": "Ile", "K": "Lys", "L": "Leu", "M": "Met", "N": "Asn", "P": "Pro", "Q": "Gln", "R": "Arg", "S": "Ser", "T": "Thr", "V": "Val", "W": "Trp", "Y": "Tyr", "Z": "Glx", "X": "Xaa", "U": "Sec", "J": "Xle", "O": "Pyl", } standard_three_to_one = utils.invert_dict(one_to_three) extended_three_to_one = { "2as": "D", "3ah": "H", "5hp": "E", "Acl": "R", "Agm": "R", "Aib": "A", "Ala": "A", "Alm": "A", "Alo": "T", "Aly": "K", "Arg": "R", "Arm": "R", "Asa": "D", "Asb": "D", "Ask": "D", "Asl": "D", "Asn": "N", "Asp": "D", "Asq": "D", "Asx": "B", "Aya": "A", "Bcs": "C", "Bhd": "D", "Bmt": "T", "Bnn": "A", "Buc": "C", "Bug": "L", "C5c": "C", "C6c": "C", "Ccs": "C", "Cea": "C", "Cgu": "E", "Chg": "A", "Cle": "L", "Cme": "C", "Csd": "A", "Cso": "C", "Csp": "C", "Css": "C", "Csw": "C", "Csx": "C", "Cxm": "M", "Cy1": "C", "Cy3": "C", "Cyg": "C", "Cym": "C", "Cyq": "C", "Cys": "C", "Dah": "F", "Dal": "A", "Dar": "R", "Das": "D", "Dcy": "C", "Dgl": "E", "Dgn": "Q", "Dha": "A", "Dhi": "H", "Dil": "I", "Div": "V", "Dle": "L", "Dly": "K", "Dnp": "A", "Dpn": "F", "Dpr": "P", "Dsn": "S", "Dsp": "D", "Dth": "T", "Dtr": "W", "Dty": "Y", "Dva": "V", "Efc": "C", "Fla": "A", "Fme": "M", "Ggl": "E", "Gl3": "G", "Gln": "Q", "Glu": "E", "Glx": "Z", "Gly": "G", "Glz": "G", "Gma": "E", "Gsc": "G", "Hac": "A", "Har": "R", "Hic": "H", "Hip": "H", "His": "H", "Hmr": "R", "Hpq": "F", "Htr": "W", "Hyp": "P", "Iil": "I", "Ile": "I", "Iyr": "Y", "Kcx": "K", "Leu": "L", "Llp": "K", "Lly": "K", "Ltr": "W", "Lym": "K", "Lys": "K", "Lyz": "K", "Maa": "A", "Men": "N", "Met": "M", "Mhs": "H", "Mis": "S", "Mle": "L", "Mpq": "G", "Msa": "G", "Mse": "M", "Mva": "V", "Nem": "H", "Nep": "H", "Nle": "L", "Nln": "L", "Nlp": "L", "Nmc": "G", "Oas": "S", "Ocs": "C", "Omt": "M", "Paq": "Y", "Pca": "E", "Pec": "C", "Phe": "F", "Phi": "F", "Phl": "F", "Pr3": "C", "Pro": "P", "Prr": "A", "Ptr": "Y", "Pyl": "O", "Sac": "S", "Sar": "G", "Sch": "C", "Scs": "C", "Scy": "C", "Sec": "U", "Sel": "U", "Sep": "S", "Ser": "S", "Set": "S", "Shc": "C", "Shr": "K", "Smc": "C", "Soc": "C", "Sty": "Y", "Sva": "S", "Ter": "*", "Thr": "T", "Tih": "A", "Tpl": "W", "Tpo": "T", "Tpq": "A", "Trg": "K", "Tro": "W", "Trp": "W", "Tyb": "Y", "Tyq": "Y", "Tyr": "Y", "Tys": "Y", "Tyy": "Y", "Unk": "X", "Val": "V", "Xaa": "X", "Xer": "X", "Xle": "J", } # Initial table is from the ASTRAL RAF release notes. # added UNK # Extra IUPAC: Xle, Xaa, Sec, Pyl # The following have been seen in biopython code. # Ter : '*' Termination # Sel : 'U' A typo for Sec, selenocysteine? # Xer : 'X' Another alternative for unknown? amino_acid_names = { "A": "alanine", "M": "methionine", "C": "cysteine", "N": "asparagine", "D": "aspartic acid", "P": "proline", "E": "glutamic acid", "Q": "glutamine", "F": "phenylalanine", "R": "arginine", "G": "glycine", "S": "serine", "H": "histidine", "T": "threonine", "I": "isoleucine", "V": "valine", "K": "lysine", "W": "tryptophan", "L": "leucine", "Y": "tyrosine", "B": "aspartic acid or asparagine", "J": "leucine or isoleucine", "X": "unknown", "Z": "glutamic acid or glutamine", "U": "selenocysteine", "O": "pyrrolysine", "*": "translation stop", "-": "gap", } amino_acid_composition = dict( A=0.082, R=0.057, N=0.044, D=0.053, C=0.017, Q=0.040, E=0.062, G=0.072, H=0.022, I=0.052, # noqa: E741 L=0.090, K=0.057, M=0.024, F=0.039, P=0.051, S=0.069, T=0.058, W=0.013, Y=0.032, V=0.066, ) kyte_doolittle_hydrophobicity = dict( A=1.8, R=-4.5, N=-3.5, D=-3.5, C=2.5, Q=-3.5, E=-3.5, G=-0.4, H=-3.2, I=4.5, # noqa: E741 L=3.8, K=-3.9, M=1.9, F=2.8, P=-1.6, S=-0.8, T=-0.7, W=-0.9, Y=-1.3, V=4.2, ) nucleotide_names = { "A": "Adenosine", "C": "Cytidine", "G": "Guanine", "T": "Thymidine", "U": "Uracil", "R": "G A (puRine)", "Y": "T C (pYrimidine)", "K": "G T (Ketone)", "M": "A C (aMino group)", "S": "G C (Strong interaction)", "W": "A T (Weak interaction)", "B": "G T C (not A) (B comes after A)", "D": "G A T (not C) (D comes after C)", "H": "A C T (not G) (H comes after G)", "V": "G C A (not T, not U) (V comes after U)", "N": "A G C T (aNy)", "-": "gap", } weblogo-3.8.0/weblogo/data/000077500000000000000000000000001467613320200155335ustar00rootroot00000000000000weblogo-3.8.0/weblogo/data/blosum100.mat000066400000000000000000000042001467613320200177540ustar00rootroot00000000000000# Matrix made by matblas from blosum100_3.iij # * column uses minimum score # BLOSUM Clustered Scoring Matrix in 1/3 Bit Units # Blocks Database = /data/blocks_5.0/blocks.dat # Cluster Percentage: >= 100 # Entropy = 1.4516, Expected = -1.0948 A R N D C Q E G H I L K M F P S T W Y V B Z X * A 8 -3 -4 -5 -2 -2 -3 -1 -4 -4 -4 -2 -3 -5 -2 1 -1 -6 -5 -2 -4 -2 -2 -10 R -3 10 -2 -5 -8 0 -2 -6 -1 -7 -6 3 -4 -6 -5 -3 -3 -7 -5 -6 -4 -1 -3 -10 N -4 -2 11 1 -5 -1 -2 -2 0 -7 -7 -1 -5 -7 -5 0 -1 -8 -5 -7 5 -2 -3 -10 D -5 -5 1 10 -8 -2 2 -4 -3 -8 -8 -3 -8 -8 -5 -2 -4 -10 -7 -8 6 0 -4 -10 C -2 -8 -5 -8 14 -7 -9 -7 -8 -3 -5 -8 -4 -4 -8 -3 -3 -7 -6 -3 -7 -8 -5 -10 Q -2 0 -1 -2 -7 11 2 -5 1 -6 -5 2 -2 -6 -4 -2 -3 -5 -4 -5 -2 5 -2 -10 E -3 -2 -2 2 -9 2 10 -6 -2 -7 -7 0 -5 -8 -4 -2 -3 -8 -7 -5 0 7 -3 -10 G -1 -6 -2 -4 -7 -5 -6 9 -6 -9 -8 -5 -7 -8 -6 -2 -5 -7 -8 -8 -3 -5 -4 -10 H -4 -1 0 -3 -8 1 -2 -6 13 -7 -6 -3 -5 -4 -5 -3 -4 -5 1 -7 -2 -1 -4 -10 I -4 -7 -7 -8 -3 -6 -7 -9 -7 8 2 -6 1 -2 -7 -5 -3 -6 -4 4 -8 -7 -3 -10 L -4 -6 -7 -8 -5 -5 -7 -8 -6 2 8 -6 3 0 -7 -6 -4 -5 -4 0 -8 -6 -3 -10 K -2 3 -1 -3 -8 2 0 -5 -3 -6 -6 10 -4 -6 -3 -2 -3 -8 -5 -5 -2 0 -3 -10 M -3 -4 -5 -8 -4 -2 -5 -7 -5 1 3 -4 12 -1 -5 -4 -2 -4 -5 0 -7 -4 -3 -10 F -5 -6 -7 -8 -4 -6 -8 -8 -4 -2 0 -6 -1 11 -7 -5 -5 0 4 -3 -7 -7 -4 -10 P -2 -5 -5 -5 -8 -4 -4 -6 -5 -7 -7 -3 -5 -7 12 -3 -4 -8 -7 -6 -5 -4 -4 -10 S 1 -3 0 -2 -3 -2 -2 -2 -3 -5 -6 -2 -4 -5 -3 9 2 -7 -5 -4 -1 -2 -2 -10 T -1 -3 -1 -4 -3 -3 -3 -5 -4 -3 -4 -3 -2 -5 -4 2 9 -7 -5 -1 -2 -3 -2 -10 W -6 -7 -8 -10 -7 -5 -8 -7 -5 -6 -5 -8 -4 0 -8 -7 -7 17 2 -5 -9 -7 -6 -10 Y -5 -5 -5 -7 -6 -4 -7 -8 1 -4 -4 -5 -5 4 -7 -5 -5 2 12 -5 -6 -6 -4 -10 V -2 -6 -7 -8 -3 -5 -5 -8 -7 4 0 -5 0 -3 -6 -4 -1 -5 -5 8 -7 -5 -3 -10 B -4 -4 5 6 -7 -2 0 -3 -2 -8 -8 -2 -7 -7 -5 -1 -2 -9 -6 -7 6 0 -4 -10 Z -2 -1 -2 0 -8 5 7 -5 -1 -7 -6 0 -4 -7 -4 -2 -3 -7 -6 -5 0 6 -2 -10 X -2 -3 -3 -4 -5 -2 -3 -4 -4 -3 -3 -3 -3 -4 -4 -2 -2 -6 -4 -3 -4 -2 -3 -10 * -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 -10 1 weblogo-3.8.0/weblogo/data/blosum35.mat000066400000000000000000000041141467613320200177070ustar00rootroot00000000000000# Matrix made by matblas from blosum35.iij # * column uses minimum score # BLOSUM Clustered Scoring Matrix in 1/4 Bit Units # Blocks Database = /data/blocks_5.0/blocks.dat # Cluster Percentage: >= 35 # Entropy = 0.2111, Expected = -0.1550 A R N D C Q E G H I L K M F P S T W Y V B Z X * A 5 -1 -1 -1 -2 0 -1 0 -2 -1 -2 0 0 -2 -2 1 0 -2 -1 0 -1 -1 0 -5 R -1 8 -1 -1 -3 2 -1 -2 -1 -3 -2 2 0 -1 -2 -1 -2 0 0 -1 -1 0 -1 -5 N -1 -1 7 1 -1 1 -1 1 1 -1 -2 0 -1 -1 -2 0 0 -2 -2 -2 4 0 0 -5 D -1 -1 1 8 -3 -1 2 -2 0 -3 -2 -1 -3 -3 -1 -1 -1 -3 -2 -2 5 1 -1 -5 C -2 -3 -1 -3 15 -3 -1 -3 -4 -4 -2 -2 -4 -4 -4 -3 -1 -5 -5 -2 -2 -2 -2 -5 Q 0 2 1 -1 -3 7 2 -2 -1 -2 -2 0 -1 -4 0 0 0 -1 0 -3 0 4 -1 -5 E -1 -1 -1 2 -1 2 6 -2 -1 -3 -1 1 -2 -3 0 0 -1 -1 -1 -2 0 5 -1 -5 G 0 -2 1 -2 -3 -2 -2 7 -2 -3 -3 -1 -1 -3 -2 1 -2 -1 -2 -3 0 -2 -1 -5 H -2 -1 1 0 -4 -1 -1 -2 12 -3 -2 -2 1 -3 -1 -1 -2 -4 0 -4 0 -1 -1 -5 I -1 -3 -1 -3 -4 -2 -3 -3 -3 5 2 -2 1 1 -1 -2 -1 -1 0 4 -2 -3 0 -5 L -2 -2 -2 -2 -2 -2 -1 -3 -2 2 5 -2 3 2 -3 -2 0 0 0 2 -2 -2 0 -5 K 0 2 0 -1 -2 0 1 -1 -2 -2 -2 5 0 -1 0 0 0 0 -1 -2 0 1 0 -5 M 0 0 -1 -3 -4 -1 -2 -1 1 1 3 0 6 0 -3 -1 0 1 0 1 -2 -2 0 -5 F -2 -1 -1 -3 -4 -4 -3 -3 -3 1 2 -1 0 8 -4 -1 -1 1 3 1 -2 -3 -1 -5 P -2 -2 -2 -1 -4 0 0 -2 -1 -1 -3 0 -3 -4 10 -2 0 -4 -3 -3 -1 0 -1 -5 S 1 -1 0 -1 -3 0 0 1 -1 -2 -2 0 -1 -1 -2 4 2 -2 -1 -1 0 0 0 -5 T 0 -2 0 -1 -1 0 -1 -2 -2 -1 0 0 0 -1 0 2 5 -2 -2 1 -1 -1 0 -5 W -2 0 -2 -3 -5 -1 -1 -1 -4 -1 0 0 1 1 -4 -2 -2 16 3 -2 -3 -1 -1 -5 Y -1 0 -2 -2 -5 0 -1 -2 0 0 0 -1 0 3 -3 -1 -2 3 8 0 -2 -1 -1 -5 V 0 -1 -2 -2 -2 -3 -2 -3 -4 4 2 -2 1 1 -3 -1 1 -2 0 5 -2 -2 0 -5 B -1 -1 4 5 -2 0 0 0 0 -2 -2 0 -2 -2 -1 0 -1 -3 -2 -2 5 0 -1 -5 Z -1 0 0 1 -2 4 5 -2 -1 -3 -2 1 -2 -3 0 0 -1 -1 -1 -2 0 4 0 -5 X 0 -1 0 -1 -2 -1 -1 -1 -1 0 0 0 0 -1 -1 0 0 -1 -1 0 -1 0 -1 -5 * -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1 weblogo-3.8.0/weblogo/data/blosum40.mat000066400000000000000000000041141467613320200177030ustar00rootroot00000000000000# Matrix made by matblas from blosum40.iij # * column uses minimum score # BLOSUM Clustered Scoring Matrix in 1/4 Bit Units # Blocks Database = /data/blocks_5.0/blocks.dat # Cluster Percentage: >= 40 # Entropy = 0.2851, Expected = -0.2090 A R N D C Q E G H I L K M F P S T W Y V B Z X * A 5 -2 -1 -1 -2 0 -1 1 -2 -1 -2 -1 -1 -3 -2 1 0 -3 -2 0 -1 -1 0 -6 R -2 9 0 -1 -3 2 -1 -3 0 -3 -2 3 -1 -2 -3 -1 -2 -2 -1 -2 -1 0 -1 -6 N -1 0 8 2 -2 1 -1 0 1 -2 -3 0 -2 -3 -2 1 0 -4 -2 -3 4 0 -1 -6 D -1 -1 2 9 -2 -1 2 -2 0 -4 -3 0 -3 -4 -2 0 -1 -5 -3 -3 6 1 -1 -6 C -2 -3 -2 -2 16 -4 -2 -3 -4 -4 -2 -3 -3 -2 -5 -1 -1 -6 -4 -2 -2 -3 -2 -6 Q 0 2 1 -1 -4 8 2 -2 0 -3 -2 1 -1 -4 -2 1 -1 -1 -1 -3 0 4 -1 -6 E -1 -1 -1 2 -2 2 7 -3 0 -4 -2 1 -2 -3 0 0 -1 -2 -2 -3 1 5 -1 -6 G 1 -3 0 -2 -3 -2 -3 8 -2 -4 -4 -2 -2 -3 -1 0 -2 -2 -3 -4 -1 -2 -1 -6 H -2 0 1 0 -4 0 0 -2 13 -3 -2 -1 1 -2 -2 -1 -2 -5 2 -4 0 0 -1 -6 I -1 -3 -2 -4 -4 -3 -4 -4 -3 6 2 -3 1 1 -2 -2 -1 -3 0 4 -3 -4 -1 -6 L -2 -2 -3 -3 -2 -2 -2 -4 -2 2 6 -2 3 2 -4 -3 -1 -1 0 2 -3 -2 -1 -6 K -1 3 0 0 -3 1 1 -2 -1 -3 -2 6 -1 -3 -1 0 0 -2 -1 -2 0 1 -1 -6 M -1 -1 -2 -3 -3 -1 -2 -2 1 1 3 -1 7 0 -2 -2 -1 -2 1 1 -3 -2 0 -6 F -3 -2 -3 -4 -2 -4 -3 -3 -2 1 2 -3 0 9 -4 -2 -1 1 4 0 -3 -4 -1 -6 P -2 -3 -2 -2 -5 -2 0 -1 -2 -2 -4 -1 -2 -4 11 -1 0 -4 -3 -3 -2 -1 -2 -6 S 1 -1 1 0 -1 1 0 0 -1 -2 -3 0 -2 -2 -1 5 2 -5 -2 -1 0 0 0 -6 T 0 -2 0 -1 -1 -1 -1 -2 -2 -1 -1 0 -1 -1 0 2 6 -4 -1 1 0 -1 0 -6 W -3 -2 -4 -5 -6 -1 -2 -2 -5 -3 -1 -2 -2 1 -4 -5 -4 19 3 -3 -4 -2 -2 -6 Y -2 -1 -2 -3 -4 -1 -2 -3 2 0 0 -1 1 4 -3 -2 -1 3 9 -1 -3 -2 -1 -6 V 0 -2 -3 -3 -2 -3 -3 -4 -4 4 2 -2 1 0 -3 -1 1 -3 -1 5 -3 -3 -1 -6 B -1 -1 4 6 -2 0 1 -1 0 -3 -3 0 -3 -3 -2 0 0 -4 -3 -3 5 0 -1 -6 Z -1 0 0 1 -3 4 5 -2 0 -4 -2 1 -2 -4 -1 0 -1 -2 -2 -3 0 5 -1 -6 X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 0 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -6 * -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1 weblogo-3.8.0/weblogo/data/blosum45.mat000066400000000000000000000041141467613320200177100ustar00rootroot00000000000000# Matrix made by matblas from blosum45.iij # * column uses minimum score # BLOSUM Clustered Scoring Matrix in 1/3 Bit Units # Blocks Database = /data/blocks_5.0/blocks.dat # Cluster Percentage: >= 45 # Entropy = 0.3795, Expected = -0.2789 A R N D C Q E G H I L K M F P S T W Y V B Z X * A 5 -2 -1 -2 -1 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -2 -2 0 -1 -1 0 -5 R -2 7 0 -1 -3 1 0 -2 0 -3 -2 3 -1 -2 -2 -1 -1 -2 -1 -2 -1 0 -1 -5 N -1 0 6 2 -2 0 0 0 1 -2 -3 0 -2 -2 -2 1 0 -4 -2 -3 4 0 -1 -5 D -2 -1 2 7 -3 0 2 -1 0 -4 -3 0 -3 -4 -1 0 -1 -4 -2 -3 5 1 -1 -5 C -1 -3 -2 -3 12 -3 -3 -3 -3 -3 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1 -2 -3 -2 -5 Q -1 1 0 0 -3 6 2 -2 1 -2 -2 1 0 -4 -1 0 -1 -2 -1 -3 0 4 -1 -5 E -1 0 0 2 -3 2 6 -2 0 -3 -2 1 -2 -3 0 0 -1 -3 -2 -3 1 4 -1 -5 G 0 -2 0 -1 -3 -2 -2 7 -2 -4 -3 -2 -2 -3 -2 0 -2 -2 -3 -3 -1 -2 -1 -5 H -2 0 1 0 -3 1 0 -2 10 -3 -2 -1 0 -2 -2 -1 -2 -3 2 -3 0 0 -1 -5 I -1 -3 -2 -4 -3 -2 -3 -4 -3 5 2 -3 2 0 -2 -2 -1 -2 0 3 -3 -3 -1 -5 L -1 -2 -3 -3 -2 -2 -2 -3 -2 2 5 -3 2 1 -3 -3 -1 -2 0 1 -3 -2 -1 -5 K -1 3 0 0 -3 1 1 -2 -1 -3 -3 5 -1 -3 -1 -1 -1 -2 -1 -2 0 1 -1 -5 M -1 -1 -2 -3 -2 0 -2 -2 0 2 2 -1 6 0 -2 -2 -1 -2 0 1 -2 -1 -1 -5 F -2 -2 -2 -4 -2 -4 -3 -3 -2 0 1 -3 0 8 -3 -2 -1 1 3 0 -3 -3 -1 -5 P -1 -2 -2 -1 -4 -1 0 -2 -2 -2 -3 -1 -2 -3 9 -1 -1 -3 -3 -3 -2 -1 -1 -5 S 1 -1 1 0 -1 0 0 0 -1 -2 -3 -1 -2 -2 -1 4 2 -4 -2 -1 0 0 0 -5 T 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -1 -1 2 5 -3 -1 0 0 -1 0 -5 W -2 -2 -4 -4 -5 -2 -3 -2 -3 -2 -2 -2 -2 1 -3 -4 -3 15 3 -3 -4 -2 -2 -5 Y -2 -1 -2 -2 -3 -1 -2 -3 2 0 0 -1 0 3 -3 -2 -1 3 8 -1 -2 -2 -1 -5 V 0 -2 -3 -3 -1 -3 -3 -3 -3 3 1 -2 1 0 -3 -1 0 -3 -1 5 -3 -3 -1 -5 B -1 -1 4 5 -2 0 1 -1 0 -3 -3 0 -2 -3 -2 0 0 -4 -2 -3 4 0 -1 -5 Z -1 0 0 1 -3 4 4 -2 0 -3 -2 1 -1 -3 -1 0 -1 -2 -2 -3 0 4 -1 -5 X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 0 -2 -1 -1 -1 -1 -1 -5 * -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1 weblogo-3.8.0/weblogo/data/blosum50.mat000066400000000000000000000040301467613320200177010ustar00rootroot00000000000000# Matrix made by matblas from blosum50.iij # * column uses minimum score # BLOSUM Clustered Scoring Matrix in 1/3 Bit Units # Blocks Database = /data/blocks_5.0/blocks.dat # Cluster Percentage: >= 50 # Entropy = 0.4808, Expected = -0.3573 A R N D C Q E G H I L K M F P S T W Y V B Z X * 5 -2 -1 -2 -1 -1 -1 0 -2 -1 -2 -1 -1 -3 -1 1 0 -3 -2 0 -2 -1 -1 -5 -2 7 -1 -2 -4 1 0 -3 0 -4 -3 3 -2 -3 -3 -1 -1 -3 -1 -3 -1 0 -1 -5 -1 -1 7 2 -2 0 0 0 1 -3 -4 0 -2 -4 -2 1 0 -4 -2 -3 4 0 -1 -5 -2 -2 2 8 -4 0 2 -1 -1 -4 -4 -1 -4 -5 -1 0 -1 -5 -3 -4 5 1 -1 -5 -1 -4 -2 -4 13 -3 -3 -3 -3 -2 -2 -3 -2 -2 -4 -1 -1 -5 -3 -1 -3 -3 -2 -5 -1 1 0 0 -3 7 2 -2 1 -3 -2 2 0 -4 -1 0 -1 -1 -1 -3 0 4 -1 -5 -1 0 0 2 -3 2 6 -3 0 -4 -3 1 -2 -3 -1 -1 -1 -3 -2 -3 1 5 -1 -5 0 -3 0 -1 -3 -2 -3 8 -2 -4 -4 -2 -3 -4 -2 0 -2 -3 -3 -4 -1 -2 -2 -5 -2 0 1 -1 -3 1 0 -2 10 -4 -3 0 -1 -1 -2 -1 -2 -3 2 -4 0 0 -1 -5 -1 -4 -3 -4 -2 -3 -4 -4 -4 5 2 -3 2 0 -3 -3 -1 -3 -1 4 -4 -3 -1 -5 -2 -3 -4 -4 -2 -2 -3 -4 -3 2 5 -3 3 1 -4 -3 -1 -2 -1 1 -4 -3 -1 -5 -1 3 0 -1 -3 2 1 -2 0 -3 -3 6 -2 -4 -1 0 -1 -3 -2 -3 0 1 -1 -5 -1 -2 -2 -4 -2 0 -2 -3 -1 2 3 -2 7 0 -3 -2 -1 -1 0 1 -3 -1 -1 -5 -3 -3 -4 -5 -2 -4 -3 -4 -1 0 1 -4 0 8 -4 -3 -2 1 4 -1 -4 -4 -2 -5 -1 -3 -2 -1 -4 -1 -1 -2 -2 -3 -4 -1 -3 -4 10 -1 -1 -4 -3 -3 -2 -1 -2 -5 1 -1 1 0 -1 0 -1 0 -1 -3 -3 0 -2 -3 -1 5 2 -4 -2 -2 0 0 -1 -5 0 -1 0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1 2 5 -3 -2 0 0 -1 0 -5 -3 -3 -4 -5 -5 -1 -3 -3 -3 -3 -2 -3 -1 1 -4 -4 -3 15 2 -3 -5 -2 -3 -5 -2 -1 -2 -3 -3 -1 -2 -3 2 -1 -1 -2 0 4 -3 -2 -2 2 8 -1 -3 -2 -1 -5 0 -3 -3 -4 -1 -3 -3 -4 -4 4 1 -3 1 -1 -3 -2 0 -3 -1 5 -4 -3 -1 -5 -2 -1 4 5 -3 0 1 -1 0 -4 -4 0 -3 -4 -2 0 0 -5 -3 -4 5 0 -1 -5 -1 0 0 1 -3 4 5 -2 0 -3 -3 1 -1 -4 -1 0 -1 -2 -2 -3 0 5 -1 -5 -1 -1 -1 -1 -2 -1 -1 -2 -1 -1 -1 -1 -1 -2 -2 -1 0 -3 -1 -1 -1 -1 -1 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 -5 1 weblogo-3.8.0/weblogo/data/blosum62.mat000077500000000000000000000041161467613320200177140ustar00rootroot00000000000000# Matrix made by matblas from blosum62_3.iij # * column uses minimum score # BLOSUM Clustered Scoring Matrix in 1/3 Bit Units # Blocks Database = /data/blocks_5.0/blocks.dat # Cluster Percentage: >= 62 # Entropy = 0.6979, Expected = -0.5209 A R N D C Q E G H I L K M F P S T W Y V B Z X * A 6 -2 -2 -3 -1 -1 -1 0 -2 -2 -2 -1 -1 -3 -1 2 0 -4 -3 0 -2 -1 -1 -6 R -2 8 -1 -2 -5 1 0 -3 0 -4 -3 3 -2 -4 -3 -1 -2 -4 -3 -4 -2 0 -2 -6 N -2 -1 8 2 -4 0 0 -1 1 -5 -5 0 -3 -4 -3 1 0 -6 -3 -4 5 0 -2 -6 D -3 -2 2 9 -5 0 2 -2 -2 -5 -5 -1 -5 -5 -2 0 -2 -6 -5 -5 6 1 -2 -6 C -1 -5 -4 -5 13 -4 -5 -4 -4 -2 -2 -5 -2 -4 -4 -1 -1 -3 -4 -1 -5 -5 -3 -6 Q -1 1 0 0 -4 8 3 -3 1 -4 -3 2 -1 -5 -2 0 -1 -3 -2 -3 0 5 -1 -6 E -1 0 0 2 -5 3 7 -3 0 -5 -4 1 -3 -5 -2 0 -1 -4 -3 -4 1 6 -1 -6 G 0 -3 -1 -2 -4 -3 -3 8 -3 -6 -5 -2 -4 -5 -3 0 -2 -4 -5 -5 -1 -3 -2 -6 H -2 0 1 -2 -4 1 0 -3 11 -5 -4 -1 -2 -2 -3 -1 -3 -4 3 -5 -1 0 -2 -6 I -2 -4 -5 -5 -2 -4 -5 -6 -5 6 2 -4 2 0 -4 -4 -1 -4 -2 4 -5 -5 -2 -6 L -2 -3 -5 -5 -2 -3 -4 -5 -4 2 6 -4 3 1 -4 -4 -2 -2 -2 1 -5 -4 -2 -6 K -1 3 0 -1 -5 2 1 -2 -1 -4 -4 7 -2 -5 -2 0 -1 -4 -3 -3 -1 1 -1 -6 M -1 -2 -3 -5 -2 -1 -3 -4 -2 2 3 -2 8 0 -4 -2 -1 -2 -1 1 -4 -2 -1 -6 F -3 -4 -4 -5 -4 -5 -5 -5 -2 0 1 -5 0 9 -5 -4 -3 1 4 -1 -5 -5 -2 -6 P -1 -3 -3 -2 -4 -2 -2 -3 -3 -4 -4 -2 -4 -5 11 -1 -2 -5 -4 -4 -3 -2 -2 -6 S 2 -1 1 0 -1 0 0 0 -1 -4 -4 0 -2 -4 -1 6 2 -4 -3 -2 0 0 -1 -6 T 0 -2 0 -2 -1 -1 -1 -2 -3 -1 -2 -1 -1 -3 -2 2 7 -4 -2 0 -1 -1 -1 -6 W -4 -4 -6 -6 -3 -3 -4 -4 -4 -4 -2 -4 -2 1 -5 -4 -4 16 3 -4 -6 -4 -3 -6 Y -3 -3 -3 -5 -4 -2 -3 -5 3 -2 -2 -3 -1 4 -4 -3 -2 3 10 -2 -4 -3 -2 -6 V 0 -4 -4 -5 -1 -3 -4 -5 -5 4 1 -3 1 -1 -4 -2 0 -4 -2 6 -5 -4 -1 -6 B -2 -2 5 6 -5 0 1 -1 -1 -5 -5 -1 -4 -5 -3 0 -1 -6 -4 -5 5 0 -2 -6 Z -1 0 0 1 -5 5 6 -3 0 -5 -4 1 -2 -5 -2 0 -1 -4 -3 -4 0 5 -1 -6 X -1 -2 -2 -2 -3 -1 -1 -2 -2 -2 -2 -1 -1 -2 -2 -1 -1 -3 -2 -1 -2 -1 -2 -6 * -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 -6 1 weblogo-3.8.0/weblogo/data/blosum80.mat000077500000000000000000000041161467613320200177140ustar00rootroot00000000000000# Matrix made by matblas from blosum80_3.iij # * column uses minimum score # BLOSUM Clustered Scoring Matrix in 1/3 Bit Units # Blocks Database = /data/blocks_5.0/blocks.dat # Cluster Percentage: >= 80 # Entropy = 0.9868, Expected = -0.7442 A R N D C Q E G H I L K M F P S T W Y V B Z X * A 7 -3 -3 -3 -1 -2 -2 0 -3 -3 -3 -1 -2 -4 -1 2 0 -5 -4 -1 -3 -2 -1 -8 R -3 9 -1 -3 -6 1 -1 -4 0 -5 -4 3 -3 -5 -3 -2 -2 -5 -4 -4 -2 0 -2 -8 N -3 -1 9 2 -5 0 -1 -1 1 -6 -6 0 -4 -6 -4 1 0 -7 -4 -5 5 -1 -2 -8 D -3 -3 2 10 -7 -1 2 -3 -2 -7 -7 -2 -6 -6 -3 -1 -2 -8 -6 -6 6 1 -3 -8 C -1 -6 -5 -7 13 -5 -7 -6 -7 -2 -3 -6 -3 -4 -6 -2 -2 -5 -5 -2 -6 -7 -4 -8 Q -2 1 0 -1 -5 9 3 -4 1 -5 -4 2 -1 -5 -3 -1 -1 -4 -3 -4 -1 5 -2 -8 E -2 -1 -1 2 -7 3 8 -4 0 -6 -6 1 -4 -6 -2 -1 -2 -6 -5 -4 1 6 -2 -8 G 0 -4 -1 -3 -6 -4 -4 9 -4 -7 -7 -3 -5 -6 -5 -1 -3 -6 -6 -6 -2 -4 -3 -8 H -3 0 1 -2 -7 1 0 -4 12 -6 -5 -1 -4 -2 -4 -2 -3 -4 3 -5 -1 0 -2 -8 I -3 -5 -6 -7 -2 -5 -6 -7 -6 7 2 -5 2 -1 -5 -4 -2 -5 -3 4 -6 -6 -2 -8 L -3 -4 -6 -7 -3 -4 -6 -7 -5 2 6 -4 3 0 -5 -4 -3 -4 -2 1 -7 -5 -2 -8 K -1 3 0 -2 -6 2 1 -3 -1 -5 -4 8 -3 -5 -2 -1 -1 -6 -4 -4 -1 1 -2 -8 M -2 -3 -4 -6 -3 -1 -4 -5 -4 2 3 -3 9 0 -4 -3 -1 -3 -3 1 -5 -3 -2 -8 F -4 -5 -6 -6 -4 -5 -6 -6 -2 -1 0 -5 0 10 -6 -4 -4 0 4 -2 -6 -6 -3 -8 P -1 -3 -4 -3 -6 -3 -2 -5 -4 -5 -5 -2 -4 -6 12 -2 -3 -7 -6 -4 -4 -2 -3 -8 S 2 -2 1 -1 -2 -1 -1 -1 -2 -4 -4 -1 -3 -4 -2 7 2 -6 -3 -3 0 -1 -1 -8 T 0 -2 0 -2 -2 -1 -2 -3 -3 -2 -3 -1 -1 -4 -3 2 8 -5 -3 0 -1 -2 -1 -8 W -5 -5 -7 -8 -5 -4 -6 -6 -4 -5 -4 -6 -3 0 -7 -6 -5 16 3 -5 -8 -5 -5 -8 Y -4 -4 -4 -6 -5 -3 -5 -6 3 -3 -2 -4 -3 4 -6 -3 -3 3 11 -3 -5 -4 -3 -8 V -1 -4 -5 -6 -2 -4 -4 -6 -5 4 1 -4 1 -2 -4 -3 0 -5 -3 7 -6 -4 -2 -8 B -3 -2 5 6 -6 -1 1 -2 -1 -6 -7 -1 -5 -6 -4 0 -1 -8 -5 -6 6 0 -3 -8 Z -2 0 -1 1 -7 5 6 -4 0 -6 -5 1 -3 -6 -2 -1 -2 -5 -4 -4 0 6 -1 -8 X -1 -2 -2 -3 -4 -2 -2 -3 -2 -2 -2 -2 -2 -3 -3 -1 -1 -5 -3 -2 -3 -1 -2 -8 * -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1 weblogo-3.8.0/weblogo/data/dbxref.txt000066400000000000000000000604141467613320200175530ustar00rootroot00000000000000---------------------------------------------------------------------------- UniProt Knowledgebase: Swiss-Prot Protein Knowledgebase TrEMBL Protein Database Swiss Institute of Bioinformatics (SIB); Geneva, Switzerland European Bioinformatics Institute (EBI); Hinxton, United Kingdom Protein Information Resource (PIR); Washington DC, USA ---------------------------------------------------------------------------- Description: List of databases cross-referenced in Swiss-Prot Name: DBXREF.TXT Release: 50.5 of 22-Aug-2006 ---------------------------------------------------------------------------- This document lists the databases that are cross-referenced in Swiss-Prot. It does not list WWW resources or databases specifically mentionned in the "DATABASE" comment topic of Swiss-Prot entries. It lists both the databases that are explicitly linked (in the DR lines and in rare cases in the FT lines) and those to which implicit links can be automatically generated by programs based on simple rules. For more details on Swiss-Prot cross-references, implicit and explicit links, you can read: Gasteiger E., Jung E., Bairoch A. SWISS-PROT: connecting biological knowledge via a protein database. Curr. Issues Mol. Biol. 3:47-55(2001) Abbrev: AGD Name : Ashbya genome database LinkTp: Explicit Server: http://agd.unibas.ch/ Db_URL: agd.unibas.ch/Ashbya_gossypii/geneview?gene=%s Cat : Organism-specific gene databases Abbrev: ANU-2DPAGE Name : Australian National University 2-DE database LinkTp: Explicit Server: http://semele.anu.edu.au Cat : 2D gel databases Abbrev: AraC-XylS Name : AraC-XylS; a database on a family of Helix-Turn-Helix transcription factors from bacteria LinkTp: Implicit; All bacterial Swiss-Prot entries with a cross-reference to PROSITE PS01124 Server: http://www.eez.csic.es/arac-xyls/ Db_URL: www.eez.csic.es/arac-xyls/wfichas/%s.HTM Cat : Protein family/group databases Abbrev: BioCyc Name : Collection of Pathway/Genome Databases LinkTp: Explicit. Server: http://www.biocyc.org/ Db_URL: biocyc.org/getid?id=%s Cat : Enzyme and pathway databases Abbrev: BLOCKS Name : BLOCKS; a protein domain database LinkTp: Implicit; All Swiss-Prot entries Server: http://blocks.fhcrc.org/ Db_URL: blocks.fhcrc.org/blocks-bin/getblock.sh?%s Cat : Family and domain databases Abbrev: CleanEx Name : CleanEx database of gene expression profiles LinkTp: Implicit; all human and mouse entries with >= HGNC or MGI X-ref Server: http://www.cleanex.isb-sib.ch/ Db_URL: www.cleanex.isb-sib.ch/cgi-bin/cleanex_query_result.pl?out_format=NICE&Entry_0=HGNC:%s Cat : Gene expression databases Abbrev: CMR Name : Comprehensive Microbial Resource LinkTp: Implicit; all entries from completely sequenced microbial genomes which don't have an explicit link to TIGR Server: http://cmr.tigr.org/ Cat : Genome annotation databases Abbrev: COMPLUYEAST-2DPAGE Name : 2-DE database at Universidad Complutense de Madrid LinkTp: Explicit Server: http://babbage.csc.ucm.es/2d/2d.html Cat : 2D gel databases Abbrev: dbSNP Name : Database of single nucleotide polymorphism LinkTp: Explicit Server: http://www.ncbi.nlm.nih.gov/SNP/ Db_URL: www.ncbi.nlm.nih.gov/SNP/snp_ref.cgi?type=rs&rs=%s Cat : Polymorphism databases Abbrev: DDBJ Name : DNA Data Bank of Japan; a nucleotide sequence database LinkTp: Implicit; All Swiss-Prot entries with >=1 EMBL Xref. Server: http://www.ddbj.nig.ac.jp/ Cat : Sequence databases Abbrev: DictyBase Name : Dictyostelium discoideum online informatics resource LinkTp: Explicit Server: http://dictybase.org/ Db_URL: dictybase.org/db/cgi-bin/dictyBase/locus.pl?locus=%s Cat : Organism-specific gene databases Abbrev: DIP Name : Database of interacting proteins LinkTp: Implicit; All Swiss-Prot entries Server: http://dip.doe-mbi.ucla.edu/ Db_URL: dip.doe-mbi.ucla.edu/dip/Search.cgi?SM=3&AC=%s&Search2=Query+DIP&GE= Cat : Protein-protein interaction databases Abbrev: EchoBASE Name : EchoBASE - an integrated post-genomic database for E. coli LinkTp: Explicit Server: http://www.biolws1.york.ac.uk/echobase/ Db_URL: www.biolws1.york.ac.uk/echobase/Gene.cfm?recordID=%s Cat : Organism-specific gene databases Abbrev: EcoGene Name : Escherichia coli strain K12 genome database LinkTp: Explicit Server: http://www.ecogene.org/ Db_URL: www.ecogene.org/geneInfo.php?eg_id=%s Cat : Organism-specific gene databases Abbrev: EMBL Name : EMBL nucleotide sequence database LinkTp: Explicit Server: http://www.ebi.ac.uk/embl/ Db_URL: www.ebi.ac.uk/htbin/expasyfetch?%s Cat : Sequence databases Abbrev: Ensembl Name : Ensembl eukaryotic genome annotation project LinkTp: Explicit Server: http://www.ensembl.org/ Cat : Genome annotation databases Abbrev: ENZYME Name : Enzyme nomenclature database LinkTp: Implicit; All Swiss-Prot entries that contain >=1 EC numbers in their description lines Server: http://www.expasy.org/enzyme/ Cat : Enzyme and pathway databases Abbrev: FlyBase Name : Drosophila genome database LinkTp: Explicit Server: http://flybase.bio.indiana.edu/ Db_URL: flybase.bio.indiana.edu/.bin/fbidq.html?%s Note : Obsolete abbreviation: DMAP Cat : Organism-specific gene databases Abbrev: GenAtlas Name : GenAtlas: human gene database LinkTp: Implicit; Human sequence entries with >=1 gene name and >=1 HGNC X-ref. Server: http://www.dsi.univ-paris5.fr/genatlas/ Db_URL: www.dsi.univ-paris5.fr/genatlas/fiche.php?symbol=%s Cat : Organism-specific gene databases Abbrev: GenBank Name : GenBank nucleotide sequence database LinkTp: Implicit; All Swiss-Prot entries with >=1 EMBL Xref. Server: http://www.ncbi.nlm.nih.gov/ Cat : Sequence databases Abbrev: Gene3D Name : Gene3D Structural and Functional Annotation of Protein Families LinkTp: Explicit Server: http://cathwww.biochem.ucl.ac.uk:8080/Gene3D/ Db_URL: www.biochem.ucl.ac.uk/cgi-bin/grant/gene3d.pl?domainchoice=%s Cat : Family and domain databases Abbrev: GeneCards Name : GeneCards: human genes, protein and diseases LinkTp: Implicit; Human sequence entries with >=1 gene name and >=1 HGNC X-ref. Server: http://www.genecards.org/ Db_URL: www.genecards.org/cgi-bin/carddisp?%s Cat : Organism-specific gene databases Abbrev: GeneDB_Spombe Name : Schizosaccharomyces pombe GeneDB LinkTp: Explicit Server: http://www.genedb.org/genedb/pombe/ Db_URL: www.genedb.org/genedb/Search?submit=Search+for&name=%s&organism=pombe&desc=yes Cat : Organism-specific gene databases Abbrev: GeneFarm Name : Structural and functional annotation of Arabidopsis thaliana gene and protein families. LinkTp: Explicit Server: http://urgi.infobiogen.fr/Genefarm/ Db_URL: urgi.infobiogen.fr/Genefarm/Gene/display_gene.htpl?GENE_ID=%s Cat : Organism-specific gene databases Abbrev: GeneLynx Name : GeneLynx; a portal to the human, mouse and rat genomes LinkTp: Implicit; Human sequence entries with >=1 gene name and >=1 HGNC X-ref or mouse sequence with >=1 MGI X-ref or rat sequence with >=1 RGD X-ref. Server: http://www.genelynx.org/ Cat : Organism-specific gene databases Abbrev: GenomeReviews Name : Genome Reviews; an annotated view of completely sequenced genomes LinkTp: Explicit Server: http://www.ebi.ac.uk/GenomeReviews/ Cat : Genome annotation databases Abbrev: GermOnline Name : GermOnline - a gateway for gametogenesis LinkTp: Explicit Server: http://germonline.unibas.ch Db_URL: germonline.unibas.ch/gene_page.php?orf_id=%s Cat : Protein family/group databases Abbrev: GlycoSuiteDB Name : GlycoSuiteDB; an annotated and curated relational database of glycan structures LinkTp: Explicit Server: https://tmat.proteomesystems.com/glycosuite/ Cat : PTM databases Abbrev: GO Name : Gene Ontology LinkTp: Explicit Server: http://www.geneontology.org/ Db_URL: www.ebi.ac.uk/ego/QuickGO?mode=display&entry=%s Cat : Ontologies Abbrev: GPCRDB Name : Information system for G protein-coupled receptors (GPCRs) LinkTp: Implicit; All Swiss-Prot entries that contains a CC line of the type: "-!- SIMILARITY: Belongs to the G-protein coupled receptor ..." Server: http://www.gpcr.org/7tm/ Cat : Protein family/group databases Abbrev: Gramene Name : Gramene; a comparative mapping resource for grains LinkTp: Explicit Server: http://www.gramene.org/ Db_URL: www.gramene.org//db/protein/protein_search?acc=%s Cat : Organism-specific gene databases Abbrev: H-InvDB Name : H-Invitational Database, human transcriptome db LinkTp: Explicit Server: http://www.h-invitational.jp/ Db_URL: www.jbirc.aist.go.jp/hinv/soup/pub_Locus.pl?locus_id=%s Cat : Organism-specific gene databases Abbrev: HAMAP Name : HAMAP database of microbial protein families LinkTp: Explicit Server: http://www.expasy.org/sprot/hamap/ Db_URL: www.expasy.org/cgi-bin/hamap/nicemf.cgi?%s Cat : Family and domain databases Abbrev: HGNC Name : Human Gene Nomenclature Database LinkTp: Explicit Server: http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl Db_URL: www.gene.ucl.ac.uk/cgi-bin/nomenclature/get_data.pl?hgnc_id=%s Note : Obsolete abbreviation: Genew Cat : Organism-specific gene databases Abbrev: HIV Name : HIV sequence database LinkTp: Explicit Server: http://hiv-web.lanl.gov/ Cat : Organism-specific gene databases Abbrev: HOGENOM Name : Homologous Sequences from Complete Genomes database LinkTp: Implicit; entries from Bacteria and Archaea except fragments of <100 AA Server: http://pbil.univ-lyon1.fr/databases/hogenom.html Db_URL: pbil.univ-lyon1.fr/cgi-bin/acnuc-link-ac2fam?db=Hogenprot&query=%s Cat : Organism-specific gene databases Abbrev: HOVERGEN Name : Homologous vertebrate genes database LinkTp: Implicit; entries from Vertebrata except fragments of <100 AA Server: http://pbil.univ-lyon1.fr/databases/hovergen.html Db_URL: pbil.univ-lyon1.fr/cgi-bin/acnuc-link-ac2fam?db=Hoverprot&query=%s Cat : Organism-specific gene databases Abbrev: HSC-2DPAGE Name : 2-DE gel protein databases at Harefield LinkTp: Explicit Server: http://www.doc.ic.ac.uk/vip/hsc-2dpage/ Cat : 2D gel databases Abbrev: HSSP Name : Homology-derived secondary structure of proteins database LinkTp: Explicit Server: http://www.sander.ebi.ac.uk/hssp/ Db_URL: srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?[PDB-Id:%s]+-e Cat : 3D structure databases Abbrev: HUGE Name : Human Unidentified Gene-Encoded large proteins database LinkTp: Implicit; Human sequence entries with KIAAnnnn in a GN line Server: http://www.kazusa.or.jp/huge/ Cat : Organism-specific gene databases Abbrev: IMGT Name : ImMunoGeneTics db LinkTp: Implicit; All entries with a KW "Immunoglobulin [CV] region" and >=1 EMBL X-ref. Server: http://imgt.cines.fr/ Cat : Protein family/group databases Abbrev: IntAct Name : Protein interaction database and analysis system LinkTp: Explicit Server: http://www.ebi.ac.uk/intact/ Db_URL: www.ebi.ac.uk/intact/search/do/hvWelcome?searchClass=Interactor&searchString=%s Cat : Protein-protein interaction databases Abbrev: InterPro Name : Integrated resource of protein families, domains and functional sites LinkTp: Explicit Server: http://www.ebi.ac.uk/interpro/ Db_URL: www.ebi.ac.uk/interpro/IEntry?ac=%s Cat : Family and domain databases Abbrev: LegioList Name : Legionella pneumophila genome database LinkTp: Explicit Server: http://genolist.pasteur.fr/LegioList/ Cat : Organism-specific gene databases Abbrev: Leproma Name : Mycobacterium leprae genome database LinkTp: Explicit Server: http://genolist.pasteur.fr/Leproma/ Cat : Organism-specific gene databases Abbrev: LinkHub Name : LinkHub; links to different genomics and protein resources LinkTp: Explicit Server: http://hub.gersteinlab.org/ Db_URL: hub.gersteinlab.org/id/%s/link_origin/UNIPROT Cat : Other Abbrev: ListiList Name : Listeria innocua and Listeria monocytogenes genomes database LinkTp: Explicit Server: http://genolist.pasteur.fr/ListiList/ Cat : Organism-specific gene databases Abbrev: MaizeDB Name : Maize genome database LinkTp: Explicit Server: http://www.agron.missouri.edu/ Cat : Organism-specific gene databases Abbrev: MEROPS Name : MEROPS protease database LinkTp: Explicit Server: http://merops.sanger.ac.uk/ Db_URL: merops.sanger.ac.uk/cgi-bin/make_frame_file?id=%s Cat : Protein family/group databases Abbrev: MGI Name : Mouse genome database (MGD) from Mouse Genome Informatics (MGI) LinkTp: Explicit Server: http://www.informatics.jax.org/ Db_URL: www.informatics.jax.org/searches/accession_report.cgi?id=%s Note : Obsolete abbreviation: MGD Cat : Organism-specific gene databases Abbrev: Micado Name : Microbial advanced database LinkTp: Implicit; All Swiss-Prot entries with >=1 SubtiList Xref where the gene name does not start with "Y" Server: http://genome.jouy.inra.fr/cgi-bin/micado/index.cgi Db_URL: genome.jouy.inra.fr/micado/gene.cgi?species=Bacillus+subtilis&gene=%2 Cat : Organism-specific gene databases Abbrev: MIM Name : Online Mendelian Inheritance in Man (OMIM) LinkTp: Explicit Server: http://www.ncbi.nlm.nih.gov/omim/ Db_URL: www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=OMIM&dopt=Detailed&tmpl=dispomimTemplate&list_uids=%s Cat : Organism-specific gene databases Abbrev: ModBase Name : Database of comparative protein structure models LinkTp: Implicit; All Swiss-Prot and TrEMBL entries Server: http://alto.compbio.ucsf.edu/modbase-cgi/index.cgi Cat : 3D structure databases Abbrev: MypuList Name : Mycoplasma pulmonis genome database LinkTp: Explicit Server: http://genolist.pasteur.fr/MypuList/ Cat : Organism-specific gene databases Abbrev: NIEHS-SNPs Name : NIEHS SNPs Program at the University of Washington LinkTp: Implicit; all entries with >= HGNC X-ref and an RT line starting with "NIEHS-SNPs" Server: http://egp.gs.washington.edu/ Db_URL: egp.gs.washington.edu/data/%s/ Cat : Polymorphism databases Abbrev: NucleaRDB Name : Information system for nuclear receptors LinkTp: Implicit; All Swiss-Prot entries that contain a CC line of the type: "-!- SIMILARITY: Belongs to the nuclear hormone receptor family." Server: http://www.receptors.org/NR/ Cat : Protein family/group databases Abbrev: OGP Name : Oxford GlycoProteomics 2-DE database, Oxford University, England LinkTp: Explicit Server: http://proteomewww.bioch.ox.ac.uk/2d/2d.html Db_URL: proteomewww.bioch.ox.ac.uk/cgi-bin/get-2d-entry?%s Cat : 2D gel databases Abbrev: PANTHER Name : The PANTHER Classification System LinkTp: Explicit Server: http://www.pantherdb.org/ Db_URL: www.pantherdb.org/panther/family.do?clsAccession=%s Cat : Family and domain databases Abbrev: PDB Name : Protein Data Bank; a repository for 3D biological macromolecular structure data LinkTp: Explicit Server: http://www.rcsb.org/pdb/ Db_URL: srs.ebi.ac.uk/srs6bin/cgi-bin/wgetz?[PDB-Id:%s]+-e Cat : 3D structure databases Abbrev: Pfam Name : Pfam protein domain database LinkTp: Explicit Server: http://www.sanger.ac.uk/Software/Pfam/ http://pfam.wustl.edu/ Db_URL: www.sanger.ac.uk/cgi-bin/Pfam/getacc?%s Cat : Family and domain databases Abbrev: PHCI-2DPAGE Name : Parasite host cell interaction 2D-PAGE database LinkTp: Explicit Server: http://www.gram.au.dk/2d/2d.html Cat : 2D gel databases Abbrev: PhosSite Name : Phosphorylation site database for Archaea and Bacteria LinkTp: Explicit Server: http://vigen.biochem.vt.edu/xpd/xpd.htm Db_URL: vigen.biochem.vt.edu/xpd/xpd2.cfm?extf=swissprot&extref=%s Cat : PTM databases Abbrev: PhotoList Name : Photorhabdus luminescens genome database LinkTp: Explicit Server: http://genolist.pasteur.fr/PhotoList/ Cat : Organism-specific gene databases Abbrev: PIR Name : Protein sequence database of the Protein Information Resource LinkTp: Explicit Server: http://pir.georgetown.edu/ Db_URL: pir.georgetown.edu/cgi-bin/nbrfget?uid=%s Cat : Sequence databases Abbrev: PIRSF Name : PIR superfamilies, an integrated protein classification database LinkTp: Explicit Server: http://pir.georgetown.edu/iproclass/ Db_URL: pir.georgetown.edu/cgi-bin/ipcSF?id=%s Cat : Family and domain databases Abbrev: PMMA-2DPAGE Name : Purkyne Military Medical Academy 2D-PAGE database LinkTp: Explicit Server: http://www.pmma.pmfhk.cz/2d/2d.html Cat : 2D gel databases Abbrev: PptaseDB Name : Prokaryotic Protein Phosphatase Database LinkTp: Explicit Server: http://vigen.biochem.vt.edu/p3d/p3d.htm Db_URL: http://vigen.biochem.vt.edu/p3d/p3d2.cfm?extf=swissprot&extref=swissprot&extref=%s Cat : Protein family/group databases Abbrev: PRINTS Name : Protein Motif fingerprint database; a protein domain database LinkTp: Explicit Server: http://umber.sbs.man.ac.uk/dbbrowser/PRINTS/ Db_URL: umber.sbs.man.ac.uk/cgi-bin/dbbrowser/sprint/searchprintss.cgi?display_opts=Prints&category=None&queryform=false&prints_accn=%s Note : Obsolete abbreviation: PRINT Cat : Family and domain databases Abbrev: ProDom Name : ProDom; a protein domain database LinkTp: Explicit Server: http://protein.toulouse.inra.fr/prodom/current/html/home.php Db_URL: protein.toulouse.inra.fr/cgi-bin/ReqProdomII.pl?acc_seq0=%s Cat : Family and domain databases Abbrev: PROSITE Name : PROSITE; a protein domain and family database LinkTp: Explicit Server: http://www.expasy.org/prosite/ Db_URL: www.expasy.org/cgi-bin/get-prosite-raw.pl?%s Cat : Family and domain databases Abbrev: ProtoNet Name : ProtoNet; Automatic hierarchical classification of proteins LinkTp: Implicit; All Swiss-Prot entries Server: http://www.protonet.cs.huji.ac.il/ Db_URL: www.protonet.cs.huji.ac.il/protonet/sp.jsp?prot=%s Cat : Other Abbrev: Rat-heart-2DPAGE Name : 2-DE database of rat heart, at German Heart Institute Berlin, Germany LinkTp: Explicit Server: http://www.mpiib-berlin.mpg.de/2D-PAGE/RAT-HEART/2d/ Db_URL: www.mpiib-berlin.mpg.de/mpiib-cgi/RAT-HEART/get-2d-entry?%s Cat : 2D gel databases Abbrev: Reactome Name : Reactome - a knowledgebase of biological processes LinkTp: Explicit Server: http://www.reactome.org/ Db_URL: www.reactome.org/cgi-bin/search?QUERY_CLASS=DatabaseIdentifier&QUERY=SPTREMBL:%s Note : Obsolete abbreviation: GK Cat : Enzyme and pathway databases Abbrev: REBASE Name : Restriction enzymes and methylases database LinkTp: Explicit Server: http://rebase.neb.com/ Db_URL: rebase.neb.com/rebase/enz/%s.html Cat : Protein family/group databases Abbrev: RGD Name : Rat genome database LinkTp: Explicit Server: http://rgd.mcw.edu/ Db_URL: rgd.mcw.edu/tools/genes/genes_view.cgi?id=%s Cat : Organism-specific gene databases Abbrev: Rouge Name : Rodent Unidentified Gene-Encoded large proteins database LinkTp: Implicit; Mouse sequence entries with KIAAnnnn in a GN line Server: http://www.kazusa.or.jp/rouge/ Cat : Organism-specific gene databases Abbrev: RZPD-ProtExp Name : RZPDs collection of validated ORF protein expression clones LinkTp: Explicit Server: http://www.rzpd.de/products/orfclones/ Db_URL: www.rzpd.de/gene?productId=%s Cat : Other Abbrev: SagaList Name : Streptococcus agalactiae NEM316 / Serotype III genome database LinkTp: Explicit Server: http://genolist.pasteur.fr/SagaList/ Cat : Organism-specific gene databases Abbrev: SeattleSNPs Name : UW-FHCRC Variation Discovery Resource LinkTp: Implicit; all entries with >= HGNC X-ref and an RT line starting with "SeattleSNPs" Server: http://pga.gs.washington.edu/ Db_URL: pga.gs.washington.edu/data/%s/ Cat : Polymorphism databases Abbrev: SGD Name : Saccharomyces Genome Database LinkTp: Explicit Server: http://www.yeastgenome.org/ Db_URL: db.yeastgenome.org/cgi-bin/SGD/locus.pl?locus=%s Cat : Organism-specific gene databases Abbrev: Siena-2DPAGE Name : 2D-PAGE database from the Department of Molecular Biology, University of Siena, Italy LinkTp: Explicit Server: http://www.bio-mol.unisi.it/2d/2d.html Cat : 2D gel databases Abbrev: SMART Name : Simple Modular Architecture Research Tool; a protein domain database LinkTp: Explicit Server: http://smart.embl.de/ Db_URL: http://smart.embl.de/smart/do_annotation.pl?DOMAIN=%s Cat : Family and domain databases Abbrev: SMR Name : SWISS-MODEL Repository LinkTp: Explicit Server: http://swissmodel.expasy.org/repository/ Db_URL: swissmodel.expasy.org/repository/smr.php?sptr_ac=%s Cat : 3D structure databases Abbrev: SOURCE Name : The Stanford Online Universal Resource for Clones and ESTs LinkTp: Implicit; All human and mouse entries with >=1 gene name and >= 1 MIM or MGI X-ref. Server: http://genome-www5.stanford.edu/cgi-bin/SMD/source/sourceSearch Cat : Other Abbrev: SubtiList Name : Bacillus subtilis strain 168 genome database LinkTp: Explicit Server: http://genolist.pasteur.fr/SubtiList/ Db_URL: genolist.pasteur.fr/SubtiList/genome.cgi?external_query+%s Cat : Organism-specific gene databases Abbrev: SWISS-2DPAGE Name : Two-dimensional polyacrylamide gel electrophoresis database from the Geneva University Hospital LinkTp: Explicit Server: http://www.expasy.org/ch2d/ Db_URL: www.expasy.org/cgi-bin/ch2d-search-ac?%s Cat : 2D gel databases Abbrev: TAIR Name : The Arabidopsis Information Resource LinkTp: Explicit Server: http://www.arabidopsis.org/ Db_URL: www.arabidopsis.org/servlets/TairObject?type=locus&name=%s Cat : Organism-specific gene databases Abbrev: TIGR Name : The bacterial database(s) of 'The Institute of Genome Research' LinkTp: Explicit Server: http://www.tigr.org/tdb/ Db_URL: cmr.tigr.org/tigr-scripts/CMR/shared/GenePage.cgi?locus=%s Cat : Genome annotation databases Abbrev: TIGRFAMs Name : TIGRFAMs; a protein family database LinkTp: Explicit Server: http://www.tigr.org/TIGRFAMs/ Db_URL: cmr.tigr.org/tigr-scripts/CMR/HmmReport.cgi?hmm_acc=%s Cat : Family and domain databases Abbrev: TRANSFAC Name : Transcription factor database LinkTp: Explicit Server: http://www.gene-regulation.com/ Cat : Protein family/group databases Abbrev: TubercuList Name : Mycobacterium tuberculosis strain H37Rv genome database LinkTp: Explicit Server: http://genolist.pasteur.fr/TubercuList/ Cat : Organism-specific gene databases Abbrev: UniGene Name : UniGene gene-oriented nucleotide sequence clusters LinkTp: Explicit Server: http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=UniGene Db_URL: www.ncbi.nlm.nih.gov/UniGene/clust.cgi?ORG=%s1&CID=%s2 Cat : Sequence databases Abbrev: UniRef Name : UniProt Non-redundant Reference (UniRef) Databases LinkTp: Implicit; all Swiss-Prot and TrEMBL (UniProt knowledgebase) entries Server: http://www.uniprot.org/database/nref.shtml Cat : Other Abbrev: WorfDB Name : The C.elegans ORFeome cloning project LinkTp: Implicit; all C.elegans entries with an explicit cross-reference to WormPep Server: http://worfdb.dfci.harvard.edu/ Db_URL: worfdb.dfci.harvard.edu/search.pl?form=1&search=%2 Cat : Organism-specific gene databases Abbrev: WormBase Name : WormBase LinkTp: Explicit Server: http://www.wormbase.org/ Db_URL: www.wormbase.org/db/gene/gene?name=%s Cat : Organism-specific gene databases Abbrev: WormPep Name : Caenorhabditis elegans genome sequencing project protein database LinkTp: Explicit Server: http://www.sanger.ac.uk/Projects/C_elegans/WORMBASE/current/wormpep.shtml Db_URL: www.sanger.ac.uk/cgi-bin/Projects/C_elegans/wormpep_fetch.pl?entry=%s&what=protein&type=exact Cat : Organism-specific gene databases Abbrev: Yeast-GFP Name : Yeast GFP fusion localization database LinkTp: Implicit; All Swiss-Prot entries from Saccharomyces cerevisiae with Y[A-Z]{2}[0-9]{3}[A-Z] in the GN line Server: http://yeastgfp.ucsf.edu Db_URL: yeastgfp.ucsf.edu/getOrf.php?orf=%s Cat : Organism-specific gene databases Abbrev: ZFIN Name : Zebrafish Information Network genome database LinkTp: Explicit Server: http://zfin.org/ Db_URL: zfin.org/cgi-bin/webdriver?MIval=aa-markerview.apg&OID=%s Cat : Organism-specific gene databases Abbrev: Aarhus/Ghent-2DPAGE Name : Human keratinocyte 2D gel protein database from Aarhus and Ghent universities LinkTp: Explicit Server: None Cat : 2D gel databases Abbrev: ECO2DBASE Name : Escherichia coli gene-protein database; a 2-DE gel database LinkTp: Explicit Server: None Note : Obsolete abbreviation: EC-2D-GEL Cat : 2D gel databases Abbrev: StyGene Name : Salmonella typhimurium LT2 genome database LinkTp: Explicit Server: None Cat : Organism-specific gene databases ----------------------------------------------------------------------- Copyrighted by the UniProt Consortium, see http://www.uniprot.org/terms Distributed under the Creative Commons Attribution-NoDerivs License ----------------------------------------------------------------------- weblogo-3.8.0/weblogo/data/dist20_comp.mat000066400000000000000000000042601467613320200203630ustar00rootroot00000000000000#TOTAL: 1.000000 # entropy = 0.404334 A 4 -2 -2 -2 0 -1 -1 -1 -2 -2 -2 -2 -1 -2 -1 0 -1 -3 -2 -1 -2 -1 -1 R -2 6 -1 -1 -4 1 0 -3 0 -3 -3 2 -2 -3 -2 -1 -1 -2 -2 -3 3 -1 -1 N -2 -1 7 1 -3 0 0 -1 0 -5 -4 0 -3 -4 -2 0 -1 -3 -2 -4 3 -1 -1 D -2 -1 1 7 -4 0 1 -1 -1 -6 -5 0 -4 -5 -1 0 -1 -4 -3 -5 0 -2 -2 C 0 -4 -3 -4 12 -3 -4 -3 -3 -1 -2 -4 -1 -2 -3 -2 -1 -2 -2 0 -3 5 -2 Q -1 1 0 0 -3 6 1 -2 0 -3 -3 1 -2 -3 -1 0 -1 -2 -2 -3 0 1 -1 E -1 0 0 1 -4 1 5 -2 -1 -4 -4 1 -3 -4 -1 -1 -1 -3 -3 -4 0 -1 -1 G -1 -3 -1 -1 -3 -2 -2 7 -2 -6 -5 -2 -4 -5 -2 -1 -2 -4 -4 -5 -2 -2 -2 H -2 0 0 -1 -3 0 -1 -2 9 -3 -3 -1 -2 -1 -2 -1 -1 0 0 -3 0 -1 -1 I -2 -3 -5 -6 -1 -3 -4 -6 -3 5 2 -4 1 0 -4 -4 -2 -1 -1 3 -4 -2 -2 L -2 -3 -4 -5 -2 -3 -4 -5 -3 2 5 -3 2 1 -3 -3 -2 -1 -1 1 -4 -2 -2 K -2 2 0 0 -4 1 1 -2 -1 -4 -3 5 -2 -4 -1 -1 -1 -3 -3 -3 1 -1 -1 M -1 -2 -3 -4 -1 -2 -3 -4 -2 1 2 -2 7 1 -3 -2 -1 0 0 1 -3 -2 -1 F -2 -3 -4 -5 -2 -3 -4 -5 -1 0 1 -4 1 7 -3 -3 -2 3 3 0 -3 -2 -1 P -1 -2 -2 -1 -3 -1 -1 -2 -2 -4 -3 -1 -3 -3 8 -1 -2 -3 -3 -3 -2 -2 -2 S 0 -1 0 0 -2 0 -1 -1 -1 -4 -3 -1 -2 -3 -1 4 1 -3 -2 -3 0 -1 -1 T -1 -1 -1 -1 -1 -1 -1 -2 -1 -2 -2 -1 -1 -2 -2 1 5 -2 -2 -1 -1 -1 -1 W -3 -2 -3 -4 -2 -2 -3 -4 0 -1 -1 -3 0 3 -3 -3 -2 12 3 -2 -3 -2 -1 Y -2 -2 -2 -3 -2 -2 -3 -4 0 -1 -1 -3 0 3 -3 -2 -2 3 8 -2 -2 -2 -1 V -1 -3 -4 -5 0 -3 -4 -5 -3 3 1 -3 1 0 -3 -3 -1 -2 -2 5 -4 -2 -2 B -2 3 3 0 -3 0 0 -2 0 -4 -4 1 -3 -3 -2 0 -1 -3 -2 -4 3 -1 -1 Z -1 -1 -1 -2 5 1 -1 -2 -1 -2 -2 -1 -2 -2 -2 -1 -1 -2 -2 -2 -1 3 -1 X -1 -1 -1 -2 -2 -1 -1 -2 -1 -2 -2 -1 -1 -1 -2 -1 -1 -1 -1 -2 -1 -1 -1 weblogo-3.8.0/weblogo/data/pam120.mat000077500000000000000000000036021467613320200172420ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 120 substitution matrix, scale = ln(2)/2 = 0.346574 # # Expected score = -1.64, Entropy = 0.979 bits # # Lowest score = -8, Highest score = 12 # A R N D C Q E G H I L K M F P S T W Y V B Z X A 3 -3 -1 0 -3 -1 0 1 -3 -1 -3 -2 -2 -4 1 1 1 -7 -4 0 0 -1 -1 R -3 6 -1 -3 -4 1 -3 -4 1 -2 -4 2 -1 -5 -1 -1 -2 1 -5 -3 -2 -1 -2 N -1 -1 4 2 -5 0 1 0 2 -2 -4 1 -3 -4 -2 1 0 -4 -2 -3 3 0 -1 D 0 -3 2 5 -7 1 3 0 0 -3 -5 -1 -4 -7 -3 0 -1 -8 -5 -3 4 3 -2 C -3 -4 -5 -7 9 -7 -7 -4 -4 -3 -7 -7 -6 -6 -4 0 -3 -8 -1 -3 -6 -7 -4 Q -1 1 0 1 -7 6 2 -3 3 -3 -2 0 -1 -6 0 -2 -2 -6 -5 -3 0 4 -1 E 0 -3 1 3 -7 2 5 -1 -1 -3 -4 -1 -3 -7 -2 -1 -2 -8 -5 -3 3 4 -1 G 1 -4 0 0 -4 -3 -1 5 -4 -4 -5 -3 -4 -5 -2 1 -1 -8 -6 -2 0 -2 -2 H -3 1 2 0 -4 3 -1 -4 7 -4 -3 -2 -4 -3 -1 -2 -3 -3 -1 -3 1 1 -2 I -1 -2 -2 -3 -3 -3 -3 -4 -4 6 1 -3 1 0 -3 -2 0 -6 -2 3 -3 -3 -1 L -3 -4 -4 -5 -7 -2 -4 -5 -3 1 5 -4 3 0 -3 -4 -3 -3 -2 1 -4 -3 -2 K -2 2 1 -1 -7 0 -1 -3 -2 -3 -4 5 0 -7 -2 -1 -1 -5 -5 -4 0 -1 -2 M -2 -1 -3 -4 -6 -1 -3 -4 -4 1 3 0 8 -1 -3 -2 -1 -6 -4 1 -4 -2 -2 F -4 -5 -4 -7 -6 -6 -7 -5 -3 0 0 -7 -1 8 -5 -3 -4 -1 4 -3 -5 -6 -3 P 1 -1 -2 -3 -4 0 -2 -2 -1 -3 -3 -2 -3 -5 6 1 -1 -7 -6 -2 -2 -1 -2 S 1 -1 1 0 0 -2 -1 1 -2 -2 -4 -1 -2 -3 1 3 2 -2 -3 -2 0 -1 -1 T 1 -2 0 -1 -3 -2 -2 -1 -3 0 -3 -1 -1 -4 -1 2 4 -6 -3 0 0 -2 -1 W -7 1 -4 -8 -8 -6 -8 -8 -3 -6 -3 -5 -6 -1 -7 -2 -6 12 -2 -8 -6 -7 -5 Y -4 -5 -2 -5 -1 -5 -5 -6 -1 -2 -2 -5 -4 4 -6 -3 -3 -2 8 -3 -3 -5 -3 V 0 -3 -3 -3 -3 -3 -3 -2 -3 3 1 -4 1 -3 -2 -2 0 -8 -3 5 -3 -3 -1 B 0 -2 3 4 -6 0 3 0 1 -3 -4 0 -4 -5 -2 0 0 -6 -3 -3 4 2 -1 Z -1 -1 0 3 -7 4 4 -2 1 -3 -3 -1 -2 -6 -1 -1 -2 -7 -5 -3 2 4 -1 X -1 -2 -1 -2 -4 -1 -1 -2 -2 -1 -2 -2 -2 -3 -2 -1 -1 -5 -3 -1 -1 -1 -2 weblogo-3.8.0/weblogo/data/pam250.mat000077500000000000000000000036031467613320200172470ustar00rootroot00000000000000# # This matrix was produced by "pam" Version 1.0.6 [28-Jul-93] # # PAM 250 substitution matrix, scale = ln(2)/3 = 0.231049 # # Expected score = -0.844, Entropy = 0.354 bits # # Lowest score = -8, Highest score = 17 # A R N D C Q E G H I L K M F P S T W Y V B Z X A 2 -2 0 0 -2 0 0 1 -1 -1 -2 -1 -1 -3 1 1 1 -6 -3 0 0 0 0 R -2 6 0 -1 -4 1 -1 -3 2 -2 -3 3 0 -4 0 0 -1 2 -4 -2 -1 0 -1 N 0 0 2 2 -4 1 1 0 2 -2 -3 1 -2 -3 0 1 0 -4 -2 -2 2 1 0 D 0 -1 2 4 -5 2 3 1 1 -2 -4 0 -3 -6 -1 0 0 -7 -4 -2 3 3 -1 C -2 -4 -4 -5 12 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3 0 -2 -8 0 -2 -4 -5 -3 Q 0 1 1 2 -5 4 2 -1 3 -2 -2 1 -1 -5 0 -1 -1 -5 -4 -2 1 3 -1 E 0 -1 1 3 -5 2 4 0 1 -2 -3 0 -2 -5 -1 0 0 -7 -4 -2 3 3 -1 G 1 -3 0 1 -3 -1 0 5 -2 -3 -4 -2 -3 -5 0 1 0 -7 -5 -1 0 0 -1 H -1 2 2 1 -3 3 1 -2 6 -2 -2 0 -2 -2 0 -1 -1 -3 0 -2 1 2 -1 I -1 -2 -2 -2 -2 -2 -2 -3 -2 5 2 -2 2 1 -2 -1 0 -5 -1 4 -2 -2 -1 L -2 -3 -3 -4 -6 -2 -3 -4 -2 2 6 -3 4 2 -3 -3 -2 -2 -1 2 -3 -3 -1 K -1 3 1 0 -5 1 0 -2 0 -2 -3 5 0 -5 -1 0 0 -3 -4 -2 1 0 -1 M -1 0 -2 -3 -5 -1 -2 -3 -2 2 4 0 6 0 -2 -2 -1 -4 -2 2 -2 -2 -1 F -3 -4 -3 -6 -4 -5 -5 -5 -2 1 2 -5 0 9 -5 -3 -3 0 7 -1 -4 -5 -2 P 1 0 0 -1 -3 0 -1 0 0 -2 -3 -1 -2 -5 6 1 0 -6 -5 -1 -1 0 -1 S 1 0 1 0 0 -1 0 1 -1 -1 -3 0 -2 -3 1 2 1 -2 -3 -1 0 0 0 T 1 -1 0 0 -2 -1 0 0 -1 0 -2 0 -1 -3 0 1 3 -5 -3 0 0 -1 0 W -6 2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4 0 -6 -2 -5 17 0 -6 -5 -6 -4 Y -3 -4 -2 -4 0 -4 -4 -5 0 -1 -1 -4 -2 7 -5 -3 -3 0 10 -2 -3 -4 -2 V 0 -2 -2 -2 -2 -2 -2 -1 -2 4 2 -2 2 -1 -1 -1 0 -6 -2 4 -2 -2 -1 B 0 -1 2 3 -4 1 3 0 1 -2 -3 1 -2 -4 -1 0 0 -5 -3 -2 3 2 -1 Z 0 0 1 3 -5 3 3 0 2 -2 -3 0 -2 -5 0 0 -1 -6 -4 -2 2 3 -1 X 0 -1 0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1 0 0 -4 -2 -1 -1 -1 -1 weblogo-3.8.0/weblogo/data/vtml160000066400000000000000000000062731467613320200166770ustar00rootroot00000000000000# # VTML160 # # This matrix was produced by scripts written by # Kai Kneutgen and Tobias Mueller [Mai-2002] # # VTML160 substitution matrix, Units = Third-Bits # # Expected Score = -1.490 Third-Bits # Lowest Score = -7.833 # Highest Score = 15.821 # Entropy H = 0.610 Bits # # # For further information on the VTML substitution model, see # # Estimating Amino Acid Substitution Models: # A Comparison of Dayhoff's Estimator, the Resolvent Approach and a Maximum Likelihood Method. # T. Mueller, R. Spang and M. Vingron # Mol Biol Evol 19(1): 8-13. 2002. # # or mail to # Tobias.Mueller@molgen.mpg.de # # The latest version of this perl script can be downloaded at # http://www.molgen.mpg.de/~muelle_t A R N D C Q E G H I L K M F P S T W Y V B Z X * A 5 -2 -1 -1 1 -1 -1 0 -2 -2 -2 -1 -1 -3 0 1 1 -5 -4 0 -1 -1 -1 -8 R -2 8 -1 -3 -3 2 -2 -3 1 -4 -4 4 -2 -5 -2 -1 -2 -4 -3 -4 -2 0 -2 -8 N -1 -1 7 3 -3 0 0 0 1 -5 -5 0 -3 -5 -2 1 0 -6 -2 -4 5 0 -1 -8 D -1 -3 3 8 -6 0 3 -1 0 -6 -7 0 -5 -8 -2 0 -1 -7 -6 -5 5 2 -2 -8 C 1 -3 -3 -6 13 -5 -5 -3 -2 -1 -4 -5 -1 -4 -4 1 -1 -7 -1 1 -4 -5 -2 -8 Q -1 2 0 0 -5 6 3 -3 2 -4 -3 2 -1 -4 -1 0 -1 -7 -4 -3 0 4 -1 -8 E -1 -2 0 3 -5 3 6 -2 -1 -5 -4 1 -4 -6 -1 0 -1 -8 -4 -3 2 4 -2 -8 G 0 -3 0 -1 -3 -3 -2 8 -3 -7 -7 -3 -5 -6 -3 0 -3 -5 -6 -5 -1 -2 -3 -8 H -2 1 1 0 -2 2 -1 -3 10 -4 -3 0 -4 0 -2 -1 -1 -2 3 -4 0 0 -1 -8 I -2 -4 -5 -6 -1 -4 -5 -7 -4 6 3 -4 2 0 -5 -4 -1 -2 -2 4 -5 -4 -2 -8 L -2 -4 -5 -7 -4 -3 -4 -7 -3 3 6 -4 4 2 -3 -4 -2 -2 -1 2 -6 -3 -2 -8 K -1 4 0 0 -5 2 1 -3 0 -4 -4 6 -2 -6 -1 -1 -1 -5 -4 -3 0 2 -1 -8 M -1 -2 -3 -5 -1 -1 -4 -5 -4 2 4 -2 8 1 -4 -3 -1 -4 -3 1 -4 -2 -1 -8 F -3 -5 -5 -8 -4 -4 -6 -6 0 0 2 -6 1 9 -5 -3 -3 3 6 -1 -6 -5 -2 -8 P 0 -2 -2 -2 -4 -1 -1 -3 -2 -5 -3 -1 -4 -5 10 0 -1 -5 -6 -3 -2 -1 -2 -8 S 1 -1 1 0 1 0 0 0 -1 -4 -4 -1 -3 -3 0 5 2 -4 -2 -2 0 0 -1 -8 T 1 -2 0 -1 -1 -1 -1 -3 -1 -1 -2 -1 -1 -3 -1 2 6 -7 -3 0 0 -1 -1 -8 W -5 -4 -6 -7 -7 -7 -8 -5 -2 -2 -2 -5 -4 3 -5 -4 -7 16 4 -5 -6 -7 -3 -8 Y -4 -3 -2 -6 -1 -4 -4 -6 3 -2 -1 -4 -3 6 -6 -2 -3 4 10 -3 -4 -4 -2 -8 V 0 -4 -4 -5 1 -3 -3 -5 -4 4 2 -3 1 -1 -3 -2 0 -5 -3 5 -4 -3 -2 -8 B -1 -2 5 5 -4 0 2 -1 0 -5 -6 0 -4 -6 -2 0 0 -6 -4 -4 5 1 -2 -8 Z -1 0 0 2 -5 4 4 -2 0 -4 -3 2 -2 -5 -1 0 -1 -7 -4 -3 1 4 -1 -8 X -1 -2 -1 -2 -2 -1 -2 -3 -1 -2 -2 -1 -1 -2 -2 -1 -1 -3 -2 -2 -2 -1 -2 -8 * -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 -8 1 weblogo-3.8.0/weblogo/htdocs/000077500000000000000000000000001467613320200161065ustar00rootroot00000000000000weblogo-3.8.0/weblogo/htdocs/create.cgi000077500000000000000000000041651467613320200200460ustar00rootroot00000000000000#!/usr/bin/env python3 # Copyright (c) 2003-2004 The Regents of the University of California. # Copyright (c) 2005 Gavin E. Crooks # Copyright (c) 2006, The Regents of the University of California, through # Lawrence Berkeley National Laboratory (subject to receipt of any required # approvals from the U.S. Dept. of Energy). All rights reserved. # This software is distributed under the new BSD Open Source License. # # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions are met: # # (1) Redistributions of source code must retain the above copyright notice, # this list of conditions and the following disclaimer. # # (2) Redistributions in binary form must reproduce the above copyright # notice, this list of conditions and the following disclaimer in the # documentation and or other materials provided with the distribution. # # (3) Neither the name of the University of California, Lawrence Berkeley # National Laboratory, U.S. Dept. of Energy nor the names of its contributors # may be used to endorse or promote products derived from this software # without specific prior written permission. # # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" # AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE # IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE # ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE # LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR # CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF # SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS # INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN # CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE # POSSIBILITY OF SUCH DAMAGE. import cgi import cgitb import weblogo cgitb.enable() if __name__ == "__main__": weblogo.cgi(__file__) weblogo-3.8.0/weblogo/htdocs/create_html_template.html000066400000000000000000000626051467613320200231670ustar00rootroot00000000000000 WebLogo 3 - Create WebLogo Create Layout Template

WebLogo 3: Create


Sequence Data Input:



-
or % CG

Label:
Label:

weblogo-3.8.0/weblogo/htdocs/examples.html000066400000000000000000002742041467613320200206230ustar00rootroot00000000000000 WebLogo 3 - Examples

WebLogo 3 Gallery

The Edit Logo buttons will transfer the relevant sequence data to the Logo creation form. There you can examine the sequence data and recreate the logo for yourself. Additional examples can be found at the Sequence Logo Gallery.

Catobolite Activator Protein (CAP)

Catobolite Activator Protein
The helix-turn-helix motif from the CAP family of homodimeric DNA binding proteins. CAP (Catabolite Activator Protein, also known as CRP for cAMP Receptor Protein) is a transcription promoter that binds at more than 100 sites within the E. coli genome. Residues 1-7 form the first helix, 8-11 the turn and 12-20 the DNA recognition helix. The glycine at position 9 appears to be critical in forming the turn. Positions 4, 8, 10, 15 and 19 are partially or completely buried, and therefore tend to be populated by hydrophobic amino acids, which are colored black. Positions 11-14, 17 and 20 interact directly with bases in the major groove and are critical to the sequence specific binding of the protein. The data for this logo consists of 100 sequences from the full Pfam alignment of this family (Accession number PF00325). A few sequences with rare insertions were removed for convenience.
DNA-binding helix-turn-helix motif of the CAP family
CAP Binding Site Logo
The two DNA recognition helixes of the CAP homodimer insert themselves into consecutive turns of the major groove. Several consequences can be observed in this CAP binding site logo. The logo is approximately palindromic, which provides two very similar recognition sites, one for each subunit of the dimer. However, the binding site is not perfectly symmetric, possible due to the inherent asymmetry of the operon promoter region.

The displacement of the two parts is 11 base pairs, or approximately one full turn of the DNA helix. Additional interactions between the protein and the first and last two bases occur within the DNA minor groove, where it is difficult for the protein to distinguish A from T, or G from C.

The data for this logo consists of 59 binding sites determined by DNA footprinting:

Robison, K., McGuire, A. M., Church, G. M. A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K12 genome. Journal of Molecular Biology (1998) 284, 241-254.

58 CAP Binding Sites

E. coli Transcription Factor Binding Sites

LexA repressor
The following logos (along with the CAP logo above) display a selection of E. coli transcription factor binding sites determined by DNA footprinting. This data has been collated in the DPInteract database and has been used to search for additional binding sites within the E. coli genome. Robison, K., McGuire, A. M., Church, G. M. A comprehensive library of DNA-binding site matrices for 55 proteins applied to the complete Escherichia coli K12 genome. Journal of Molecular Biology (1998) 284, 241-254.
LexA repressor is closely related to CAP, and has similar DNA protein interactions.
H-NS: Histone like, nucleoid-associated DNA-binding protein.
DNA biosynthesis initiation binding protein.
Arginine Repressor

E. coli Promoters (Transcription Start Signals)

E. coli Promotor logo
In prokaryotes the DNA sequence just upstream of the transcription start point contains two important conserved regions. The first such region is centered at around 35bp upstream and is involved in the initial recognition of the gene by RNA polymerase.

The second region, sometimes referred to as the Pribnow box, is centered at about 10bp upstream. The typical separation between the -35 and -10 sites is 15-18 bp.

baseflip: Strong Minor Groove Base Conservation in Sequence Logos implies DNA Distortion or Base Flipping during Replication and Transcription Initiation for more information. This sequence data was kindly provided by Prof. Julia Brettschneider <juliab@stat.berkeley.edu>
The -10 region of 350 E. coli promoters

Globins

Responsive image
The end of the B helix through the beginning of the D helix of 34 globins. This sequence data was taken from Sequence Logos: A New Way to Display Consensus Sequences.

Globins

HTH Proteins

Responsive image
Helix-Turn-Helix DNA binding motifs found by the Gibbs sampling system. Compared to the CAP HTH logo there is much less sequence conservation within the DNA binding helix (11-17), as might be expected for a diverse sample of proteins.
HTH Proteins

Human Splice Sites

These logos show a small sample of Human intron-exon splice boundaries. Sequences of experimentally confirmed genes were extracted from EID: the Exon-Intron database.

Additional discussion of the features in this logo can be found in the paper Features of spliceosome evolution...

exon-intron image
Exon-Intron (Donor) Sites
Responsive image

Intron-Exon (Acceptor) Sites
weblogo-3.8.0/weblogo/htdocs/examples/000077500000000000000000000000001467613320200177245ustar00rootroot00000000000000weblogo-3.8.0/weblogo/htdocs/examples/build_examples.sh000077500000000000000000000030461467613320200232630ustar00rootroot00000000000000#!/bin/bash cd "$(dirname "${BASH_SOURCE[0]}")" echo -n '.' weblogo --format png_print --size large \ -i -5 -l 1 -u 20 \ --title "The DNA-binding helix-turn-helix motif of the CAP family" \ < cap_hth.fa \ > cap_hth.png || exit echo -n '.' weblogo --format png_print --size large \ --title "58 CAP Binding Sites" \ -i -10 \ < cap_dna.fa \ > cap_dna.png || exit echo -n '.' weblogo --format png_print --size large \ --title "19 LexA Binding Sites" \ -i -9 \ < lexA.fa \ > lexA.png || exit echo -n '.' weblogo --format png_print --size large \ --title "-10 region of E. coli promoters" \ -i -21 --lower 0 -u 7 \ < ecoli10.fa \ > ecoli10.png || exit echo -n '.' weblogo --format png_print --size large \ -l 63 -u 83 \ < globins.fa \ > globins.png || exit #echo -n '.' #weblogo --format PNG --size large \ # -l 31 -u 150 \ # < globins.fa \ # > more_globins.png || exit echo -n '.' weblogo --format png_print --size large \ --title "Helix-Turn-Helix Motifs" \ -i -11 -l 1 -u 17 --yaxis 3.5 \ < hth.fa \ > hth.png || exit echo -n '.' weblogo --format png_print --size large \ --title "exon|intron" \ -i -11 -l -6 -u 8 \ < exon-intron.fa \ > exon-intron.png || exit echo -n '.' weblogo --format png_print --size large \ --title "intron | exon" \ -i -21 -l -20 -u 3 \ < intron-exon.fa \ > intron-exon.png || exit echo weblogo-3.8.0/weblogo/htdocs/examples/cap_dna.fa000066400000000000000000000036561467613320200216330ustar00rootroot00000000000000>aldB -18->4 attcgtgatagctgtcgtaaag >ansB 103->125 ttttgttacctgcctctaactt >araB1 109->131 aagtgtgacgccgtgcaaataa >araB2 147->169 tgccgtgattatagacactttt >cdd 1 107->129 atttgcgatgcgtcgcgcattt >cdd 2 57->79 taatgagattcagatcacatat >crp 1 115->137 taatgtgacgtcctttgcatac >crp 2 gaaggcgacctgggtcatgctg >cya 151->173 aggtgttaaattgatcacgttt >cytR 1 125->147 cgatgcgaggcggatcgaaaaa >cytR 2 106->128 aaattcaatattcatcacactt >dadAX 1 95->117 agatgtgagccagctcaccata >dadAX 2 32->54 agatgtgattagattattattc >deoP2 1 75->97 aattgtgatgtgtatcgaagtg >deoP2 2 128->150 ttatttgaaccagatcgcatta >fur 136->158 aaatgtaagctgtgccacgttt >gal 56->78 aagtgtgacatggaataaatta >glpACB (glpTQ) 1 54->76 ttgtttgatttcgcgcatattc >glpACB (glpTQ) 2 94->116 aaacgtgatttcatgcgtcatt >glpACB (glpTQ) 144->166 atgtgtgcggcaattcacattt >glpD (glpE) 95->117 taatgttatacatatcactcta >glpFK 1 120->142 ttttatgacgaggcacacacat >glpFK 2 95->117 aagttcgatatttctcgttttt >gut (srlA) 72->94 ttttgcgatcaaaataacactt >ilvB 87->109 aaacgtgatcaacccctcaatt >lac 1 (lacZ) 88->110 taatgtgagttagctcactcat >lac 2 (lacZ) 16->38 aattgtgagcggataacaattt >malEpKp1 110->132 ttgtgtgatctctgttacagaa >malEpKp2 139->161 TAAtgtggagatgcgcacaTAA >malEpKp3 173->195 TTTtgcaagcaacatcacgAAA >malEpKp4 205->227 GACctcggtttagttcacaGAA >malT 121->143 aattgtgacacagtgcaaattc >melR 52->74 aaccgtgctcccactcgcagtc >mtl 302->324 TCTTGTGATTCAGATCACAAAG >nag 156->178 ttttgtgagttttgtcaccaaa >nupG2 97->119 aaatgttatccacatcacaatt >nupG1 47->69 ttatttgccacaggtaacaaaa >ompA 166->188 atgcctgacggagttcacactt >ompR 161->183 taacgtgatcatatcaacagaa >ptsH A 316->338 Ttttgtggcctgcttcaaactt >ptsH B 188->210 ttttatgatttggttcaattct >rhaS (rhaB) 161->183 aattgtgaacatcatcacgttc >rot 1 (ppiA) 182->204 ttttgtgatctgtttaaatgtt >rot 2 (ppiA) 129->151 agaggtgattttgatcacggaa >tdcA 60->82 atttgtgagtggtcgcacatat >tnaL 73->95 gattgtgattcgattcacattt >tsx 2 146->168 gtgtgtaaacgtgaacgcaatc >tsx 1 107->129 aactgtgaaacgaaacatattt >uxuAB 165->187 TCTTGTGATGTGGTTAACCAAT weblogo-3.8.0/weblogo/htdocs/examples/cap_dna.png000066400000000000000000001072641467613320200220310ustar00rootroot00000000000000‰PNG  IHDR Óà-yL× 2iCCPdefault_rgb.iccH‰••gP“YÇïó<é…@B‡PC‘*%€”Z(Ò«¨@èPElˆ¸+Šˆ4EE\•"kE ‹‚tƒ,ʺqQAYpß÷?¼ÿ™{ÏoþsæÞsÏùp ˆƒeÁË{bRºÀÛÉŽÌß(ŒŸ–ÂñôtßÕ»­Ä{ºßÏù®‘iü常¼rù)‚t ìeÖÌJOYá£ËLÿÂgWX°\à2ßXáèyìKο,ú’ãëÍ]~ 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“­€c²5pL¶Žý«Â“´éR¦IEND®B`‚weblogo-3.8.0/weblogo/htdocs/examples/ecoli10.fa000066400000000000000000000442361467613320200215010ustar00rootroot00000000000000> The -10 hexamers of 350 E.coli promoters gatgacgtggtttacgaccccaTTTAGTagtcaaccgcagtgagtgagtc > ttgaaaccagacgtttcgccccTATTACagactcacaaccacatgatgac > ctggcggcgtagcgatgcgctgGTTACTctgaaaacggtctatgcaaatt > tgacttttagcgcccatatctcCAGAATgccgccgtttgccagaaattcg > gatttacgtcatcattgtgaatTAATATgcaaataaagtgagtgaatatt > agaatacagcttattgaataccCATTATgagttagccattaacgcgtcca > cgacgacggtttacgctttacgTATAGTggcgacaattttttttatcggg > ctgacgctttttatcgcaactcTCTACTgtttctccatacccgttttttt > atccgtttttgtatccagtaacTCTAAAagcatatcgcattcatctggag > ttttttattgaatgtagaatttTATTCTgaatgtgtgggctctctatttt > tattctgaatgtgtgggctctcTATTTTaggattaattaaaaaaatagag > tcttttcacctttcctcctgttTATTCTtattaccccgtgtttatgtctc > attgcttaagcaagatcggacgGTTAATgtgttttacacattttttccgt > gcgccacactaaggtaattcctTATGCTggcaatgtcgtgaccagtgata > tgcagcctgtgctcagcgcgtgTTTCATacgcaagtgcgtatcggcgcgc > tgcattcgctgccgcataccatTATTCTtgatctgacggaagtctttttg > ggacataaggtgaatactttgtTACTTTagcgtcacagacatgaaattgg > ttattgagctttccggcgagagTTCAATgggacaggttccagaaaactca > ttaaaaattgttaacaattttgTAAAATaccgacggatagaacgacccgg > taacacctcgtcaaaatcctgcTATTCTgcccgttgcggtactgggcatt > tctattttatattattccctgtTTTAATtaactctatcagggatggttta > gacagaggccctcaatccaaacGATAAAgggtgatgtgtttactgatatg > tgctatctcgctgacggacaggCAAATTgatgaccagcttttaaaccgac > tttgacatttcttttgcactggTAAACTaaatcacttttttttgtcccag > ttttctcgcgtccgcgatagcgTAAAATagcgccgtaacccccaggtcct > aatttctacctgtttaagcatcTCTGGTagacttcctgtaattgaatcga > tgcagtgctcatagcggtcattTATGTCagacttgtcgttttacagttcg > aacatatctcgcaagcctgtctTGTGTTgacaacattttctgctaaccct > ctctccctgacgcgggataaagTGGTATtctcaaacatatctcgcaagcc > tatatctttaacaatctcaggtTAAAAActttcctgttttcaacgggact > gttgcaaatgaataattacacaTATAAAgtgaattttaattcaataagtg > tgaacgtccaatcaataaccgcTTTAATagataaacaccgctgatgaatg > ttgctttttatcttcagatgaaTAGAATgcggcggattttttgggtttca > gtcataaggtaaaagtctcattTATGATgagttccattggatttacttat > ttaccttatgacaatcggcgagTAGTCTgcctctcattccagagacagac > tacactttatgcttccggctcgTATGTTgtgtggaattgtgagcggataa > cgcaaaacctttcgcggtatggCATGATagcgcccggaagagagtcaatt > taaagttgtcacggccgagactTATAGTcgctttgtttttattttttaat > ttcattcttgaatatttattggTATAGTaaggggtgtattgagattttca > atctcttggccttgctggtcgtTATCCTgcaagctatcactttattggct > taaatctgtcataaatctgacgCATAATgacgtcgcattaatgatcgcaa > tgcagggagagcgccccggcacTAGACTacccgcctcttattttagtctg > acatatttttgtgagcaatgatTTTTATaataggctcctctgtatacgaa > ttacagtaatgtaaccttcccgTAAAATgcccacacactttaaacgccac > tagcgtaacaacaaaagattgtTATGCTtgaaatatggtgatgccgtacc > tcccttgtccccatctctcccaCATCCTgtttttaaccttaaaatggcat > tgaggcaatcgcctgttggtggTATCGTttatcgctttttcaaaaaattc > gattgcagaaatatattgataaTATTATtgataactatttgcatttgcaa > aaatgcaaatagttatcaataaTATTATcaatatatttctgcaatcaatg > tgctggaaaattaatgtgctttTATAGTggcgcttattgttgtcaatatt > attatcactcccttttactggcTAAACCagaaaacttattttatcattca > tcacacactctgtagcagatgaTCTAACaatctgattacagaacatcggc > tgtcagcctgtcccgcttataaGATCATacgccgttatacgttgtttacg > tttcatttaggcgtggcaattcTATAATgatacgcattatctcaagagca > acagttattagtggtagacaagTTTAATaattcggattgctaagtacttg > acaaacattaccaggaaaagcaTATAATgcgtaaaagttatgaagtcggt > tgtaatgattttgtgaacagccTATACTgccgccaggtctccggaacacc > tgggcagcttcttcgtcaaattTATCATgtggggcatccttaccgctctg > ctttaaaaactgcccctgacacTAAGACagtttttaaaggttccttcgcg > ggaaatgggcatcaaaaagagaTAAATTgttctcgatcaaattggctgaa > ttacacattctgacggaagataTAGATTggaagtattgcattcactaaga > gtcacacttttcgcatctttgtTATGCTatggttatttcataccataagc > gtcacacttttcgcatctttgtTATGCTatggttatttcataccataagc > gttttttgttgttaattcggtgTAGACTtgtaaacctaaatcttttcaat > tgtaaaccaaattgaaaagattTAGGTTtacaagtctacaccgaattaac > caaaactggcacgattttttcaTATATGtgaatgtcacgcaggggatcgt > tttttcatcaggttttacgctaAATAATcactgtgttgagtgcacaattt > ttgacggctcgccctaattctcTAAATTgtatttctagagttggcgaggt > cgtgttacaaaaattcttttctTATGATgtagaacgtgcaacgcaattga > caaaaattcttttcttatgatgTAGAACgtgcaacgcaattgatgctcgc > gatggtgaacaagtacgcgaggGAGAATgagcatccattgctgtgtacgc > actcctcacttacacgtaatacTACTTTcgagtgaaaatctacctatctc > ggtggtggtttgttggttgggtTGACATactgggtcatttacctgcgtga > tatggtgctgccggtcgcgatgTTTGTTgccagcggttttgagcacagta > gcaaacctgatggtatgtctggCAGTATggatgagttattctggccgcag > tttctcatctataatgctttgtTAGTATctcgtcgccgacttaataaaga > tttctcatctataatgctttgtTAGTATctcgtcgccgacttaataaaga > tgataaaaccgatagccacaggAATAATgtattacctgtggtcgcaatcg > gagcaagtgattgaaaaagcgcTACAATacgcgcgccagaaattggctct > tggaattttgtaaatctcccgtTACCCTgatagcggacttcccttctgta > ttcaataaattgcgaaacaaggTATACTccagcagttcctgaagatgttt > acgcagcagtagcaaactaagcTATAAAttgcagcgcgaactggagcagc > tgttcagcgtacacgtgttagcTATCCTgcgtgcttcaataaaataaggc > ttgtaagttttcaactacgttgTAGACTttacatcgccaggggtgctcgg > ttcacacttgtaagttttcaacTACGTTgtagactttacatcgccagggg > gttgatctttgttgtcactggaTGTACTgtacatccatacagtaactcac > attagcatcgcatcaggcaatcAATAATgtcagatatgaaaagcggaaac > tggcatatgaaattttgaggatTACCCTacacttataggagttaccttac > acatggttgcacaaagttgcaaCATCATggatatttcacgataacgttaa > aaaatttaatgtaaatggtgtgTTAAATcgattgtgaataaccagcgctt > aaaatttaatgtaaatggtgtgTTAAATcgattgtgaataaccagcgctt > tgtgaataaccagcgcttccggCAGGATacggtcgccctggtaaaacata > aacggcaagtttcgacattgccGATAATaattttttggagactttagatg > catcactctgtcatctttccagTAGAAActaatgtcactgaaatggtgtt > gtcggaatggctggttatccatTAAAATagatcggatcgatataagcaca > tgcaaaggaaaacgtttccgctTATCCTttgtgtccggcaaaaacatccc > tgactctatgacgttacaaagtTAATATgcgcgccctatgcaaaaggtaa > tttcagagattatgaattgccgCATTATagcctaataacgcgcatctttc > ttcatgacggcaaacaatagggTAGTATtgacaagccaattacaaatcat > tgatctgctggcaagaacagacTACTGTatataaaaacagtataacttca > tgaataatattttcaactgagtTATCAAgatgtgattagattattattct > gatcatgcagctagtgcgatccTGAACTaaggttttctgatacttgaata > gatgcggtgctttcctggctgtTAGAATacgccccgtcgcgcctgactgg > agcgttaccgtccgctatcgtcTATGTTcaagttgtcttaattgccagaa > tttattgatcttacgcatcctgTATGATgcaagcagactaaccctatcaa > catcaaattgcctttagctacaGACACTaaggtggcagacatcgaaacga > gtttcagagcgttaccttgcccTTAAACattagcaatgtcgatttatcag > tgcacaactgaatttaaggctcTATTATtacctcaacaaaccaccccaat > taatgtagccaccaaatcatacTACAATttattaactgttagctataatg > tgctgaagaataattgaaatgaTATTATtaattccactgcctttggtaga > gaatatgattgctatttgcattTAAAATcgagacctggtttttctactga > cgtgacattttaacacgtttgtTACAAGgtaaaggcgacgccgcccatga > tgacaattaatcatcgaactagTTAACTagtacgcaagttcacgtaaaaa > ttgcgtatcggattttatcaggTACAGTgtgacgctttcgtcaatctggc > gacgctttcgtcaatctggcaaTAGATTtgcttgacattcgaccaaaatt > acattcgaccaaaattccgtcgTGCTATagcgcctgtaggccaagacctg > ggtgaaccccttctcgttatggCAAAATaagccaatacagaaccagcatt > gacagatttgtgccattccgtgAACGATcgacgcgtcgtgattaggtgaa > tttcaccagacttattcttagcTATTATagttatagagagcttacttccg > tcctgctatccaaatagtgtcaTATCATcatattaattgttcttttttca > gctgtgttattgacagttagcaTAAACTaggtgtgacgttaactatatgt > cgattccgtctctctgatgattGATGTTaattaacaatgtattcaccgaa > tgtccttgttcgataaacacaaTAAACTtgatcatgaaattgccagaaag > tatcctcgtgctgtttctcacgTAGTCTataatttcctttttaagcccac > tttgttaaaaaagtgtgtaggaTATTGTtactcgcttttaacagggcaac > ttacttcccgtaggattcttgcTTTAATagtgggattaatttccacatta > attacgcaacgataatagcgggTATAAGataaataaaaggtaaaacgttt > tttgtctcaccttttaatttgcTACCCTatccatacgcacaataaggcta > tccccttttcgtcaagatcggcCAAAATtccacgcttacactatttgcgt > attctcaacataaaaaactttgTGTAATacttgtaacgctacatggagat > ttcatccggttaaatatgcaaaGATAAAtgcgcagaaatgtgtttctcaa > gtgcattagcttatttttttgtTATCATgctaaccacccggcgaggtgtg > tgacttttatcgccgtagccttTTCAATaaaggtcttttgaagagtacca > ttaacgtttttaactttttaatTAGAATatagatacaggagagcacatat > taacggatgtatccgtttagtcTATGATatgtacagcacttttggcttcg > tcactttccgctgattcggtgcCAGACTgaaatcagcctataggaggaaa > gggcttgaaaaagcgcccaatgTATTCCaggcttatctaacacgctgata > cttaccgtcacattcttgatggTATAGTcgaaaactgcaaaagcacatga > accaactggcaaaattttgtccTAAACTtgatctcgacgaaatggctgca > catttttatcgtaattgcccttTAAAATtcggggcgccgaccccatgtgg > aaaattcggggcgccgaccccaTGTGGTctcaagcccaaaggaagagtga > ttgacgctgcgtaaggtttttgTAATTTtacaggcaaccttttattcact > ataaaataattttttcgatatcTAAAATaaatcgcgaaacgcaggggttt > ttgaaaatagtcgcgtaacccaTACGATgtgggtatcgcatattgcgttt > tttcgcaagctcgtaaaagcagTACAGTgcaccgtaagaaaattacaagt > tcttcatccttcgctggatatcTATCCAgcatttttttatcatacagcat > gacgagtacagttgcgtcgattTAGGAAaaatcttagataagtgtaaaga > cttcatgaccgtgaatagagtcCATCGTccctcctcaaaaaaagcctagc > tgacgaagcagccgttatgcctTAACCTgcgccgcagatatcactcataa > tgaaacattgatgtctctgtagCAACATaggggtaatcttactgacaaca > tgtctgaacgtgaattgcagatTATGCTgatgatcaccaagggccagaag > tcaaagttgcaataaaaaccgcTAATATacgaatgactaactatcagtag > gattaaaaaccctgcagaaacgGATAATcatgccgataactcatataacg > ctttgttgcgctcaagacgcagGATAATtagccgataagcagtagcgaca > tactttaagacaattccaggcaAATTATacaacactttacgggatagtaa > tttgtttcacatttctgtgacaTACTATcggatgtgcggtaattgtatgg > ttcacatttctgtgacatactaTCGGATgtgcggtaattgtatggaacag > ttcacatttctgtgacatactaTCGGATgtgcggtaattgtatggaacag > tgtgacatactatcggatgtgcGGTAATtgtatggaacaggagacacaca > tgtgacatactatcggatgtgcGGTAATtgtatggaacaggagacacaca > gctgattagcacggtgatatttGATACTctggcagacagcagaaataacg > taataaatagttaattaacgctCATCATtgtacaatgaactgtacaaaag > ttaaatctttgtgggatcagggCATTATcttacgtgatcagaataaacaa > ttatactttaataagtactttgTATACTtatttgcgaacattccaggccg > atataaagccacaacgggttcgTAAACTgttatcccattacatgattatg > gaagtcctgtattcagtgctgaCAAAATagccgccagcaagcagtcattt > tgataattgttatcgtttgcatTATCGTtacgccgcaatcaaaaaaggct > taacatttggattgataattgtTATCGTttgcattatcgttacgccgcaa > tggattattctgcatttttgggGAGAATggacttgccgactgattaatga > acctcaaactgcgcggctgtgtTATAATttgcgacctttgaatccgggat > tgcaagagggtcattttcacacTATCTTgcagtgaatcccaaacataccc > atttaatttatgaatgttttctTAACATcgcggcaactcaagaaacggca > aaatcacgtttcactttcgaatTATGAGcgaatatgcgcgaaatcaaaca > attagctgtataaaagaatttcTACAGTgattgtaaggttttttttattc > ccaaagtttcgggctgttatgtTTTAATgtgcaacattcatggtctgttg > acgagagttaaccggacaagtgTGCCATaatctcgcggccaggcatactt > tgttcggcgtacaagtgtacgcTATTGTgcattcgaaacttactctatgt > caacattccagctggtccgaccTATACTctcgccactggtctgatttcta > ggcgctacgctcaatgaaacatTTAAATactatacgacagcgacatttat > ttgaggaatcaggcgggagtgaTAGAATatcgcccacttaatttttccag > tgtcaacgaaaacaataatgcgTAAGGTagaaacccgaactacattgagg > tgcgcaatttgtcaacgaaaacAATAATgcgtaaggtagaaacccgaact > ttccgcatattctctgagcgggTATGCTacctgttgtatcccaatttcat > attcagcctgtcggaactggtaTTTAACcagactaattattttgatgcgc > attcagcctgtcggaactggtaTTTAACcagactaattattttgatgcgc > ggttcaattcttcctttagcggCATAATgtttaatgacgtacgaaacgtc > ttcttcctttagcggcataatgTTTAATgacgtacgaaacgtcagcggtc > tggcagttgaccgtggtaatgaTATGATttcacacctttaccagccaatg > gcttttaatgccataccaaacgTACCATtgagacacttgtttgcacagag > attgttgtatgcatgtttttttTATGCTttccttaagaacaactcacccc > cagaactcaatgcacaaggcagTATTAAcgtcgtcaattattcccaacat > ttgccgccttgaagaaaggaggTATAATccgtcgattttttttgtggctg > cgcaaacgtttgctttccctgtTAGAATtgcgccgaattttatttttcta > ccggaagctggttgcgtgaaatTAGAAAtttcgccgctgatccaaacctg > gggaagcgcctcgcttcccgtgTATGATtgaacccgcatggctcccgaaa > ttcccttcgccatttccttgagCAAACTttagctattcttatcaattatg > tgttatcgcacaatgattcggtTATACTgttcgccgttgtccaacaggac > ggaatgaattggcgttatgtgtTACGTTtagcagatcaaaagacaggcga > ggggcgcaaccggacagaatttTATAAActgctttcccgacacgagctgg > ttcgtcagcgcatcagattcttTATAATgacgcccgtttcccccccttgg > ttgtagtgtagaatgcggcgttTCTATTaatacagacgttaagctcagaa > gaataattgagggatgacctcaTTTAATctccagtagcaactttgatccg > gacagcgtgaaaacagtacgggTACTGTactaaagtcacttaaggaaaca > ttgaaaactttactttatgtgtTATCGTtacgtcatcctcgctgaggatc > ttgaaaccctgaaactgatcccCATAATaagcgaagttagcgagatgaat > ggaaatataataagtgatcgctTACACTacgcgacgaaatactttttttg > acgcaaataatttgtggtgatcTACACTgatactctgttgcattattcgc > tgcattattcgcctgaaaccacAATATTcaggcgttttttcgctatcttt > ttgcctcagattctcagtatgtTAGGGTagaaaaaagtgactatttccat > ttactttatttgtcactgtcgtTACTATatcggctgaaattaatgaggtc > taccttcccagtcaagaaaactTATCTTattcccacttttcagttaccag > ttgatactgtatgagcatacagTATAATtgcttcaacagaacatattgac > cttttaaatctttcaatctgatTAGATTaggttgccgtttggtaataaaa > gcggcagcgtggcggaaggttgTAAACTgcacctcgaagaacaagaggcc > tgcgtcgcaaccgacaattacgTATTCTgagtcttcgggtgaacagagtg > gttattttgccgcaggtcagcgTATCGTgaacatcttttccagtgttcag > tcattcgttctcttacgctcccTATAGTcgaaacatctgatggcaagaaa > taatccacaccgtttgccccgtTAACCTtaccttctcttctgttttatgg > tgtggcacaggtcatgttcgggTATACTgctttcccgtcttggttattcc > aaaacatttaccccaaaggggcTATTTTctcactcctgatttcaatagtg > tattacagagcgttttttatttGAAAATgaatccatgagttcatttcaga > ggtagaagctcaacggacaattTATAATggctcagattaaaaaaactaat > tgcgcaatctatccgcttacttTATGATgcgcaccagtcacggactgatg > acacctgcgtgagttgttcacgTATTTTttcactatgtcttactctctgc > tccttttattccacgtttcgctTATCCTagctgaagcgtttcagtcgatt > gttcgaggcaggtttgtacggtTATACTtatcttgaagatgagtaagtcc > aatttcccatacagagctaaggGATAATgcgtagcgttcacgtaactgga > tctccaaaatatattcacgttgTAAATTgtttaacgtcaaatttcccata > taacaaaaaaccagtccgcgaaGTTGATagaatcccatcatctcgcacgg > acaacagtaaaatcagagcgttTCTGCTtttactgatgtctggcggtcgg > ttacatcaacccgcattggtccTACACTgcgcggtaataaagcgaggtaa > cgcccctggagaaagcctcgtgTATACTcctcacccttataaaagtccct > tacaaagcagcagcaattgcagTAAAATtccgcaccattttgaaataagc > caccgggcaacttttagagcacTATCGTggtacaaataatgctgccaccc > aaaaactgtcgatgtgggacgaTATAGCagataagaatattgctgagcaa > gcacatatcctgttcatttcatTTTGATacacttcatgccgtcaatgagg > gtcttttgtactcgtgtactggTACAGTgcaatgcataacaacgcagtcg > tgcgataacaggtcgctacgagTAGAATactgccgcttaacgtcgcgtaa > tgcattttttacccaaaacgagTAGAATttgccacgtttcaggcgcgggg > tgacctgtatcagctttcccgaTAAGTTggaaatccgctggaagctttct > gtttctcaataacgaaatttgaTAAAATcccgctctttcataacattatt > ataaaaattcatctgtatgcacAATAATgttgtatcaaccaccatatcgg > tgattatcttccctgataagacCAGTATttagctgccaattgctacgaaa > acccatatccttgaagcggtgtTATAATgccgcgccctcgatatggggat > ttgcgttcggtggttaagtatgTATAATgcgcgggcttgtcgtagttgac > tgacaccttttcggcatcgcccTAAAATtcggcgtcctcatattgtgtga > agacacaaagcgaaagctatgcTAAAACagtcaggatgctacagtaatac > gccaaacccgctggagtattgaGATAATtttcagtctgactctcgcaata > tgacgcgcgcaggtatttagcaTACAAGgagtaccgatttgagagttggt > acacctaaaatgctatttctgcGATAATagcaaccgtttcgtgacaggaa > attgtatacttaagctgctgttTAATATgctttgtaacaatttaggctga > ggaaggtcaacatcgagcctggCAAACTagcgataacgttgtgttgaaaa > taacgccacgcttgaggtaacaGAGATTgttttacctgctggggagtggc > tttttctgtaattcgagcatgtCATGTTaccccgcgagcataaaacgcgt > tgtcatctttctgacaccttacTATCTTacaaatgtaacaaaaaagttat > ttttatgctgacaaaggcacttTTTTCTgtttatctatcaataaattcag > ttccaatatcataaaaatcgggTATGTTttagcagagtatgctgctaaag > ggtctgataaaacagtgaatgaTAACCTcgttgctcttaagctctggcac > gaacttgtggataaaatcacggTCTGATaaaacagtgaatgataacctcg > gaacttgtggataaaatcacggTCTGATaaaacagtgaatgataacctcg > cgcctgaataataaaagcgtgtTATACTctttccctgcaatgggttccgt > attgacggatcatccgggtcgcTATAAGgtaaggatggtcttaacactga > tgacttatccgcttcgaagagaGACACTacctgcaacaatcaggagcgca > tgacgttttcacattctgttgaCAGATTgtaggtcacgaggggcatttta > tgcatcacccgccaatgcgtggCTTAATgcacatcaacggtttgacgtac > gttttgtttggcttatcgctggCAAACTgtctgaaatcgcagcaataagg > ggacagttaaccgattcagtgcCAGATTtcgcagtatctacaaggtccgg > tgcggaaaaaacgcgcgcgaggCAGCATtgactttactaggtcgtgcacg > cgtcgcgacctataagtttgggTAATATgtgctggaatttgccctgtctg > atctcaggcctgatttgctgctGATTTTtacaatgcatgcctcacgcagg > ttgaaaagttcatttccagaccCATTTTtacatcgtagccgatgaggacg > agatgtttaccgtggaaaagggTAAAATaacggattaacccaagtataaa > gcatcaggacgttcgctattacTTAAATggtatgctgtttgaaaccgaag > tatgaaatttaccgtagaacgtGAGCATttattaaaaccgctacaacagg > tcagaagacggtggcggagtacTACAAGatcaaagtcgcggatctccttt > gcaggaaaaactggtcaccatcGACAATattcagaagacggtggcggagt > gcgttctttatcgccaagcgtcTACGATctaacgtacgtgagctggaagg > cccgcctcgcggcaggatcgttTACACTtagcgagttctggaaagtcctg > agacaaaaattggcttaatcgaTCTAATaaagatccaggacgatccttgc > ttgcgctttacccatcagcccgTATAATcctccacccggcgcgccatgct > tgactccggagtgtacaattatTACAATccggcctctttaatcacccatg > gttttttcaaggtgaagcggttTAAATTcgttctcaaattacagtcagga > gacaaaaggcgtgacgatggtcGAAAATggcgctttcgtcagcggggata > tggcagtctttctgcctaacgtTTTGTTtatgatatttgcctggcgtcac > ttgaaatcacgggggcgcaccgTATAATttgaccgctttttgatgcttga > gttttcccaactcagtcaggatTAAACTgtgggtcagcgaaacgtttcgc > ttatttttaaaaaacaacaattTATATTgaaattattaaacgcatcataa > ttgccagcccacggtcggtcgaCTTACTgtttagtcagttaaataaactg > ggaaatttattgcggaaattgaTATATTcacaacgtcacattgcaatttt > atatatcaatttccgcaataaaTTTCCTgtcatatagtgaattcaatctc > tcacattcaaatgcgattctgcTACAATcctccccccgttcgaagattga > ggacgcccggcgtgagtcatgcTAACTTagtgttgacttcgtattaaaca > ttacggtcaatcagcaaggtgtTAAATTgatcacgttttagaccattttt > ttggcatctctgacctcgctgaTATAATcagcaaatctgtatatataccc > gaaaaaatgttaaacccttcggTAAAGTgtctttttgcttcttctgacta > tgcatatttttaacacaaaataCACACTtcgactcatctggtacgaccag > gcgctttttatccgtaaaaagcTATAATgcactaaaatggtgcaacctgt > gcaccaacatggtgcttaatgtTTCCATtgaagcactatattggtgcaac > ggtaagaacctgacctcgtgatTACTATttcgccgtgttgacgacatcag > ttttcaatatcatttaattaacTATAATgaaccaactgcttacgcggcat > tctcgtttttgctcgttaacgaTAAGTTtacagcatgcctacaagcatcg > attgacgtccattaacacaatgTTTACTctggtgcctgacatttcaccga > tttcggttgacgcccttcggctTTTCCTtcatctttacatctggacgtct > gttgacacacctctggtcatgaTAGTATcaatattcatgcagtatttatg > tttattacgctcaacgttagtgTATTTTtattcataaatactgcatgaat > gcgctgaaacagtcaaagcggtTATGTTcatatgcggatggcgatttaca > gatagggataatcgttcattgcTATTCTacctatcgccatgaactatcgt > tggacatctgatgagcaatcccTACAATcgccgcgtactttaatttttca > gacagtaacttgttacaacctgTAGCATccacttgccggtcctgtgagtt > tgcatgaactcgcatgtctccaTAGAATgcgcgctacttgatgccgactt > gacgcaatgcgcactaaaagggCATCATttgatgccctttttgcacgctt > tgcacaaggcgtgagattggaaTACAATttcgcgccttttgtttttatgg > ttacgtgggcggtgattttgtcTACAATcttacccccacgtataatgctt > tttgactactgctgtgcctttcAATGCTtgtttctatcgacgacttaata > ttcgcgagcgttgcgcaaacgtTTTCGTtacaatgcgggcgaaaaataag > cgacattggcaaattttctggtTATCTTcagctatctggatgtctaaacg > ttgattttgcattttaaatgagTAGTCTtagttgtgctgaacgaaaagag > accacagatgcgtttatgccagTATGGTttgttgaatttttattaaatct > ttgacaaccgccccgctcacccTTTATTtataaatgtactacctgcgcta > tggaaagaggttgccgtataaaGAAACTagagtccgtttaggtgttttca > tttaagccatctcctgatgacgCATAGTcagcccatcatgaatgttgctg > tccaaaatcgccttttgctgtaTATACTcacagcataactgtatatacac > attcattcaggtcaatttgtgtCATAATtaaccgtttgtgatcgccggta > gaatgcattacccggagtgttgTGTAACaatgtctggccaggtttgtttc > ggtaatggtacaatcgcgcgttTACACTtattcagaacgatttttttcag > acctcaagttaacttgaggaatTATACTccccaacagatgaattaacgaa > ataaaatgtggcataaaagatgCATACTgtagtcgagagcgcgtatgcgt > tgatcacaaatttaaacactggTAGGGTaaaaaggtcattaactgcccaa > agtcatcctccctcactcctgcCATAATtctgatattccaggaaagagag > ctgtgatctattcagcaaaaatTTAAATaggattatcgcgagggttcaca > gtaagcgttagtttcgataagaTAAACTgagttactaatagtcgaggcag > ttgaggtaagcgttagtttcgaTAAGATaaactgagttactaatagtcga > ggattaatccttttttcgtgagTAATCTtatcgccagtttggtctggtca > cggtagaaatcctcaagcagcaTATGATctcgggtattcggtcgatgcag > ttgtcacgctgattggtgtcgtTACAATctaacgcatcgccaatgtaaat > gtcatgaatccatggcagtgacCATACTaatggtgactgccattgatgga > ttttcaaagcgtaaaattgtggCATTCTtcactgttctataagtaagacg > ggcattcacaaatgcgcaggggTAAAACgtttcctgtagcaccgtgagtt > tttcctgtagcaccgtgagttaTACTTTgtataacttaaggaggtgcaga > ttgcgccgcttctgacgatgagTATAATgccggacaatttgccgggagga > gccaccgctttcacagaagtggTAGACTtcgttccttatgaagattctct > taaggaaaataattcttatttcGATTGTcctttttacccttctcgttcga > tggaaacaattttatttccaatTGTAATgataaccattctcatattaata > ggcgtttgtatggcaacgttatTATAATtaacagttgctactccatttaa > gaacatcgatctcgtcttgtgtTAGAATtctaacatacggttgcaacaac > aagtgtgttgcggagtagatgtTAGAATactaacaaactcgcaaggtgaa > tcgccgtatcagcgaataacggTATACTgatctgatcatttaaatttgaa > ttgcttctggcaacattaagtcTCAAATtttcaaagggtggaagatggct > gccagaagcaatggatacaaggTAGCCTcatgcgttattttccctgcttc > ttactgatccgcacgtttatgaTATGCTatcgtactctttagcgagtacaweblogo-3.8.0/weblogo/htdocs/examples/ecoli10.png000066400000000000000000000450231467613320200216720ustar00rootroot00000000000000‰PNG  IHDRpà[À 2iCCPdefault_rgb.iccH‰••gP“YÇïó<é…@B‡PC‘*%€”Z(Ò«¨@èPElˆ¸+Šˆ4EE\•"kE ‹‚tƒ,ʺqQAYpß÷?¼ÿ™{ÏoþsæÞsÏùp ˆƒeÁË{bRºÀÛÉŽÌß(ŒŸ–ÂñôtßÕ»­Ä{ºßÏù®‘iü常¼rù)‚t ìeÖÌJOYá£ËLÿÂgWX°\à2ßXáèyìKο,ú’ãëÍ]~ )úÿ†ÿsïŠT8‚ôبÈl¦OrTzV˜ ’™¶Ò —Ëô$GÅ&D~Sðÿ•ü¥Gf§¯DnrÊ&AltL:ó5204_gñÆëK!FÿÏgE_½äzØs 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AATCTCCATTCgtaagtacc > 45330_AB001517 ACTGGACGCTGgtaaggact > 45331_AB001517 TCGCTTACCGGgtgagcgcg > 45331_AB001517 GACCTTAAAAAgtaagtatg > 45331_AB001517 CGTCGATGAAGgtacttgcc > 45331_AB001517 CCTGATGGCAGgtaaggggg > 45331_AB001517 GATGACTCCAGgtgcggcct > 45331_AB001517 ACAGCCTGGACgtatgtccc > 45331_AB001517 CGGCTGGCCAAgtaggtctc > 45331_AB001517 CACTCCCTGAGgtaagcctt > 45331_AB001517 TGGCTGTTCAGgtttgtccc > 45331_AB001517 ACGACGGCAAGgtaggctcc > 45331_AB001517 GACCTTCACAGgtgatgttt > 45331_AB001517 GGCTCCTTGATgtaagcacc > 45331_AB001517 GACCTCTGATGgtgagcacg > 45331_AB001517 GCCAAGGGGAAgtgagtgtc > 45331_AB001517 ACGCCATGGAGgtgagccgc > 45331_AB001517 CGTCAGGAAAGgtgagcaga > 45331_AB001517 CTCTCCCACTGgtgagcact > 45331_AB001517 CAGGGGCGAGAgtgagttgg > 45331_AB001517 CTGAAGTCCAGgtagagggt > 45331_AB001517 CTGTCGAAACTgtacgtgtg > 45332_AB001517 GGGTCGCGCTGgtgagtgga > 45332_AB001517 GAGGCCTCGGCgtaagtcct > 45332_AB001517 GGCGAGAGCAGgtgtggggg > 45332_AB001517 GCTAAAAACCTgtgcgtatt > 45332_AB001517 AAGCCCATCGGgtgtgtaca > 45333_AB001517 GGGTCGCGCTGgtgagtgga > 45333_AB001517 GAGGCCTCGGCgtaagtcct > 45333_AB001517 GGCGAGAGCAGgtgtggggg > 45333_AB001517 GCTAAAAACCTgtgcgtatt > 45334_AB001523 CATCGTCACCTgtgagtgcc > 45334_AB001523 GAATGGAGAAGgtatgagtt > 45334_AB001523 CAGAGTGCTGTgtgagtacc > 45334_AB001523 CAGAGTGACAGgtaagtgta > 45334_AB001523 TCATGGTTCAGgtacttgac > 45334_AB001523 CGGGGCCGGGGgtgagtagt > 45334_AB001523 AGCTCTTAGAAgtgagtcgg > 45334_AB001523 CCACAGAAAAGgtgcctacc > 45334_AB001523 ACCAGAAACAGgtacttttt > 45334_AB001523 AACACTACTTAgtaagtatt > 45334_AB001523 GAGTTTTACATgtaattgat > 45334_AB001523 CAAATTGAAAAgtatccttt > 45334_AB001523 AGACAGCCCAGgtaagacca > 45334_AB001523 TCAGGACTCAGgtatgcgtt > 45334_AB001523 GCCGCTGGCTGgtgagtggg > 45334_AB001523 CAACACGAGAGgtgaggtgc > 45334_AB001523 CAGACCACAAAgtgagtagg > 45334_AB001523 TCAGGAACACGgtaacggag > 45334_AB001523 AGTCCCAGCAGgtaaacatt > 45334_AB001523 AAAATTTTTTTgtaagtgat > 45334_AB001523 TATGTATGAAGgtaggtggt > 45334_AB001523 ACTGGACGCTGgtaaggact > 45335_AB001523 TCGCTTACCGGgtgagcgcg > 45337_AB00189S TGTGGTACCTGgtgagtagg > 45337_AB00189S CCCCAAATTATgtaagtcaa > 45337_AB00189S AATGAAAATAAgtacgtcac > 45338_AB00189S TGTGGTACCTGgtgagtagg > 45338_AB00189S CCCCAAATTATgtaagtcaa > 45338_AB00189S AATGAAAATAAgtacgtcac > 45338_AB00189S GGAGAAGCAAGgtcagtggc > 45339_AB00189S TGTGGTACCTGgtgagtagg > 45339_AB00189S CCCCAAATTATgtaagtcaa > 45339_AB00189S AATGAAAATAAgtacgtcac > 45339_AB00189S GGAGAAGCAAGgtcagtggc > 45340_AB00189S TGTGGTACCTGgtgagtagg > 45340_AB00189S CCCCAAATTATgtaagtcaa > 45340_AB00189S AATGAAAATAAgtacgtcac > 45341_AB00189S TGTGGTACCTGgtgagtagg > 45341_AB00189S CCCCAAATTATgtaagtcaa > 45341_AB00189S AATGAAAATAAgtacgtcac > 45341_AB00189S AAGACCAGCAGgtaatgcat > 45342_AB00189S TGTGGTACCTGgtgagtagg > 45342_AB00189S CCCCAAATTATgtaagtcaa > 45342_AB00189S AATGAAAATAAgtacgtcac > 45342_AB00189S AGATTACACAGgtaatgagc > 45342_AB00189S AAGACCAGCAGgtaatgcat > 45342_AB00189S GTGTGTCGAAGgtacggtcc > 45342_AB00189S GTGCAGCAACGgtgagcagc > 45343_AB00189S TGTGGTACCTGgtgagtagg > 45343_AB00189S CCCCAAATTATgtaagtcaa > 45343_AB00189S AATGAAAATAAgtacgtcac > 45343_AB00189S AAGACCAGCAGgtaatgcat > 45343_AB00189S GTGTGTCGAAGgtacggtcc > 45343_AB00189S GTGCAGCAACGgtgagcagc > 45344_AB00189S TGTGGTACCTGgtgagtagg > 45344_AB00189S CCCCAAATTATgtaagtcaa > 45344_AB00189S AATGAAAATAAgtacgtcac > 45344_AB00189S AGATTACACAGgtaatgagc > 45344_AB00189S AAGACCAGCAGgtaatgcat > 45345_AB002059 TATGTGGTAGGgtaagagag > 45345_AB002059 AGCCACCTCAGgtgggggcc > 45345_AB002059 GATGCCCAGAGgtgagttta > 45345_AB002059 ACACAGCCACGgtaactgtg > 45345_AB002059 GTTGTGCCCTCgtaagtgtc > 45345_AB002059 AACTTCTCTAAgtaagcaga > 45345_AB002059 TGGCGTTGCTGgtgggtccc weblogo-3.8.0/weblogo/htdocs/examples/exon-intron.png000066400000000000000000000616051467613320200227220ustar00rootroot00000000000000‰PNG  IHDR &àªK§H 2iCCPdefault_rgb.iccH‰••gP“YÇïó<é…@B‡PC‘*%€”Z(Ò«¨@èPElˆ¸+Šˆ4EE\•"kE ‹‚tƒ,ʺqQAYpß÷?¼ÿ™{ÏoþsæÞsÏùp 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----------S------------------LSDKDKAAVKIAWAKISPKA---DDIGAEALGRMLTVYPQTKTYFAHWADL SP----------GSG---PVKHGK-KVIMGAVGDAVSKIDDLVGGL--ASL-SELHASK----LRVDPANFKILANHIVV GIMFYL-PG-DFPPEVH-MSVDKFFQN------L---ALALS----E-----K-----YR----------- >Bullfrog HEMOGLOBIN ALPHA CHAIN - BULLFROG TADPOLE ----------S------------------LSASEKAAVLSIVGKIGSQG---SALGSEALTRLFLSFPQTKTYFPHF-DL TP----------GSA---DLNTHG-GKIINALAGAANHLDDLAGNL--SSL-SDLHAYN----LRVDPGNFPLLAHIIQV VLATHF-PG-DFTAEVQ-AAWDKFLAL------V---SAVLT----S-----K-----YR----------- >Nile Crocodile HEMOGLOBIN ALPHA CHAIN - NILE CROCODILE ----------V------------------LSSDDKCNVKAVWSKVAGHL---EEYGAEALERMFCAYPQTKIYFPHF-DL SH----------GSA---QIRAHG-KKVFAALHEAVNHIDDLPGAL--CRL-SELHAHS----LRVDPVNFKFLAQCVLV VVAIHH-PG-SLTPEVH-ASLDKFLCA------V---SSVLT----S-----K-----YR----------- >Ostrich HEMOGLOBIN ALPHA CHAIN - OSTRICH ----------V------------------LSGTDKTNVKGIFSKISSHA---EEYGAETLERMFITYPQTKTYFPHF-DL HH----------GSA---QIKAHG-KKVANALIEAVNHIDDISGAL--SKL-SDLHAQK----LRVDPVNFKLLGQCFLV VVAIHH-PS-ALTPEVH-ASLDKFLCA------V---GAVLT----A-----K-----YR----------- >Kangaroo HEMOGLOBIN ALPHA CHAIN - EASTERN GRAY KANGAROO ----------V------------------LSAADKGHVKAIWGKVGGHA---GEYAAEGLERTFHSFPTTKTYFPHF-DL SH----------GSA---QIQAHG-KKIADALGQAVEHIDDLPGTL--SKL-SDLHAHK----LRVDPVNFKLLSHCLLV TFAAHL-GD-AFTPEVH-ASLDKFLAA------V---STVLT----S-----K-----YR----------- >Armadillo HEMOGLOBIN ALPHA CHAIN - NINE-BANDED ARMADILLO ----------V------------------LSAADKTHVKAFWGKVGGHA---AEFGAEALERMFASFPPTKTYFSHM-DL SH----------GSA---QVKAHG-KKVADALTLAVGHLDDLPGAL--STL-SDLHAHK----LRVDPVNFKFLSHCLLV TLACHL-PD-DFTPAVH-ASMDKFMAG------V---STVLV----S-----K-----YR----------- >Horse HEMOGLOBIN ALPHA CHAINS - HORSE ----------V------------------LSAADKTNVKAAWSKVGGHA---GEYGAEALERMFLGFPTTKTYFPHF-DL SH----------GSA---QVKAHG-KKVGDALTLAVGHLDDLPGAL--SNL-SDLHAHK----LRVDPVNFKLLSHCLLS TLAVHL-PN-DFTPAVH-ASLDKFLSS------V---STVLT----S-----K-----YR----------- >Primate HEMOGLOBIN ALPHA CHAIN - HUMAN AND CHIMPANZEES ----------V------------------LSPADKTNVKAAWGKVGAHA---GEYGAEALERMFLSFPTTKTYFPHF-DL SH----------GSA---QVKGHG-KKVADALTNAVAHVDDMPNAL--SAL-SDLHAHK----LRVDPVNFKLLSHCLLV TLAAHL-PA-EFTPAVH-ASLDKFLAS------V---STVLT----S-----K-----YR----------- >Macaque HEMOGLOBIN ALPHA CHAIN - RHESUS MACAQUE AND JAPANESE MACAQUE ----------V------------------LSPADKSNVKAAWGKVGGHA---GEYGAEALERMFLSFPTTKTYFPHF-DL SH----------GSA---QVKGHG-KKVADALTLAVGHVDDMPNAL--SAL-SDLHAHK----LRVDPVNFKLLSHCLLV TLAAHL-PA-EFTPAVH-ASLDKFLAS------V---STVLT----S-----K-----YR----------- >Badger HEMOGLOBIN ALPHA CHAIN - EURASIAN BADGER ----------V------------------LSPADKANIKATWDKIGGHA---GEYGGEALERTFASFPTTKTYFPHF-DL SH----------GSA---QVKGHG-KKVADALTNAVAHLDDLPGAL--SAL-SDLHAYK----LRVDPVNFKLLSHCLLV TLACHH-PA-EFTPAVH-ASLDKFLSS------V---STVLT----S-----K-----YR----------- >Ind Elephant HEMOGLOBIN ALPHA CHAIN - INDIAN ELEPHANT ----------V------------------LSDKDKTNVKATWSKVGDHA---SDYVAEALERMFFSFPTTKTYFPHF-DL SH----------GSG---QVKGHG-KKVGEALTQAVGHLDDLPSAL--SAL-SDLHAHK----LRVDPVNFKLLSHCLLV TLSSHQ-PT-EFTPEVH-ASLDKFLSN------V---STVLT----S-----K-----YR----------- >Hyrax HEMOGLOBIN ALPHA CHAIN - ABYSSINIAN HYRAX ----------V------------------LSAADKNNVKGAWEKVGTHA---GEYGAEALERMFLSFPTTKTYFPHF-DL TH----------GSA---QVKAHG-QKVGAALTKAVGHLDDLPNAL--SDL-SDLHAHK----LRVDPVNFKLLSHCLLV TLSRHL-PEQEFTPAVH-ASLDKFFSN------V---STVLT----S-----K-----YR----------- >Tuna MYOGLOBIN - YELLOWFIN TUNA ----------A----------------------DFDAVLKCWGPVEADY---TTMGGLVLTRLFKEHPETQKLFPKFAGI -A-----QADIAGNA---AISAHG-ATVLKKLGELLKAKGSHAAIL--KPL-ANSHATK----HKIPINNFKLISEVLVK VMHEK---A-GLDAGGQ-TALRNVMGI------I---IADLE----ANYKELG-----FSG---------- >Shark MYOGLOBIN - PORT JACKSON SHARK ----------T----------------------EWEHVNKVWAVVEPDI---PAVGLAILLRLFKEHKETKDLFPKFKEI -P-----VQQLGNNE---DLRKHG-VTVLRALGNILKQKGKHSTNV--KEL-ADTHINK----HKIPPKNFVLITNIAVK VLTEMY-PS-DMTGPMQ-ESFSKVFTV------I---CSDLE----TLYKEAN-----FQG---------- >Turtle MYOGLOBIN - MAP TURTLE ----------G------------------LSDDEWHHVLGIWAKVEPDL---SAHGQEVIIRLFQVHPETQERFAKFKNL KT-----IDELRSSE---EVKKHG-TTVLTALGRILKLKNNHEPEL--KPL-AESHATK----HKIPVKYLEFICEIIVK VIAEKH-PS-DFGADSQ-AAMRKALEL------F---RNDMA----SKYKEFG-----FQG---------- >Chicken MYOGLOBIN - CHICKEN ----------G------------------LSDQEWQQVLTIWGKVEADI---AGHGHEVLMRLFHDHPETLDRFDKFKGL KT-----EPDMKGSE---DLKKHG-QTVLTALGAQLKKKGHHEADL--KPL-AQTHATK----HKIPVKYLEFISEVIIK VIAEKH-AA-DFGADSQ-AAMKKALEL------F---RDDMA----SKYKEFG-----FQG---------- >Dog MYOGLOBIN - DOG, BAT-EARED FOX, AFRICAN HUNTING DOG, AND CAPE FOX ----------G------------------LSDGEWQIVLNIWGKVETDL---AGHGQEVLIRLFKNHPETLDKFDKFKHL KT-----EDEMKGSE---DLKKHG-NTVLTALGGILKKKGHHEAEL--KPL-AQSHATK----HKIPVKYLEFISDAIIQ VLQSKH-SG-DFHADTE-AAMKKALEL------F---RNDIA----AKYKELG-----FQG---------- >Badger MYOGLOBIN - EURASIAN BADGER ----------G------------------LSDGEWQLVLNVWGKVEADL---AGHGQEVLIRLFKGHPETLEKFDKFKHL KS-----EDEMKGSE---DLKKHG-NTVLTALGGILKKKGHQEAEL--KPL-AQSHATK----HKIPVKYLEFISDAIAQ VLQSKH-PG-NFAAEAQ-GAMKKALEL------F---RNDIA----AKYKELG-----FQG---------- >Dolphin MYOGLOBIN - SADDLEBACK DOLPHIN ----------G------------------LSDGEWQLVLNVWGKVEADV---AGHGQDILIRLFKGHPETLEKFDKFKHL KT-----EADMKASE---DLKKHG-DTVLTALGAILKKKGHHDAEL--KPL-AQSHATK----HKIPIKYLEFISEAIIH VLHSRH-PA-QFGADAQ-GAMNKALEL------F---RKDIA----AKYKELG-----FHG---------- >Horse, Zebra MYOGLOBIN - HORSE AND PLAINS ZEBRA ----------G------------------LSDGEWQQVLNVWGKVEADI---AGHGQEVLIRLFTGHPETLEKFDKFKHL KT-----EAEMKASE---DLKKHG-TVVLTALGGILKKKGHHEAEL--KPL-AQSHATK----HKIPIKYLEFISDAIIH VLHSKH-PG-NFGADAQ-GAMTKALEL------F---RNDIA----AKYKELG-----FQG---------- >African Elephant MYOGLOBIN - AFRICAN ELEPHANT ----------G------------------LSDGEWELVLKTWGKVEADI---PGHGEFVLVRLFTGHPETLEKFDKFKHL KT-----EGEMKASE---DLKKQG-VTVLTALGGILKKKGHHEAEI--QPL-AQSHATK----HKIPIKYLEFISDAIIH VLQSKH-PA-EFGADAQ-AAMKKALEL------F---RNDIA----AKYKELG-----FQG---------- >Aardvark MYOGLOBIN - AARDVARK ----------G------------------LSDAEWQLVLNVWGKVEADI---PGHGQDVLIRLFKGHPETLEKFDRFKHL KT-----EDEMKASE---DLKKHG-TTVLTALGGILKKKGQHEAEI--QPL-AQSHATK----HKIPVKYLEFISEAIIQ VIQSKH-SG-DFGADAQ-GAMSKALEL------F---RNDIA----AKYKELG-----FQG---------- >Human MYOGLOBIN - HUMAN ----------G------------------LSDGEWQLVLNVWGKVEADI---PGHGQEVLIRLFKGHPETLEKFDKFKHL KS-----EDEMKASE---DLKKHG-ATVLTALGGILKKKGHHEAEI--KPL-AQSHATK----HKIPVKYLEFISECIIQ VLQSKH-PG-DFGADAQ-GAMNKALEL------F---RKDMA----SNYKELG-----FQG---------- >Macaque MYOGLOBIN - CRAB-EATING MACAQUE (TENTATIVE SEQUENCE) ----------G------------------LSDGEWQLVLNVWGKVEADI---PSHGQEVLIRLFKGHPETLEKFDKFKHL KS-----EDEMKASE---DLKKHG-VTVLTALGGILKKKGHHEAEI--KPL-AQSHATK----HKIPVKYLELISESIIQ VLQSKH-PG-DFGADAQ-GAMNKALEL------F---RNDMA----AKYKELG-----FQG---------- >NA Opossum MYOGLOBIN - NORTH AMERICAN OPOSSUM ----------G------------------LSDGEWQLVLNAWGKVEADI---PGHGQEVLIRLFKGHPETLEKFDKFKHL KS-----EDEMKASE---DLKKHG-ATVLTALGNILKKKGNHEAEL--KPL-AQSHATK----HKISVQFLEFISEAIIQ VIQSKH-PG-DFGGDAQ-AAMGKALEL------F---RNDMA----AKYKELG-----FQG---------- >Earthworm GLOBIN AIII - COMMON EARTHWORM ---------KK------------------QCGVLEGLKVKSEWGRAYGS---GHDREAFSQAIWRATFAQVPESRSLFKR VH-----GDH-TSDP---AFIAHA-ERVLGGLDIAISTLDQPATLK--EEL-DHLQVQHEG--RKIPDNYFDAFKTAILH VVAAQL-GE-RCYSNN--EEIHDAIACDGFARVL---PQVLE----R-----G-----IKGHH-------- > SMALL CHAIN - TYLORRHYNCHUS HETEROCHAETUS ----------T------------------DCGILQRIKVKQQWAQVYSV---GESRTDFAIDVFNNFFRTNPD-RSLFNR VN-----GDN-VYSP---EFKAHM-VRVFAGFDILISVLDDKPVLD--QAL-AHYAAFH----KQFGTIPFKAFGQTMFQ TIAEHI--------HG--ADIGAWRAC------Y---AEQIV----T-----G-----ITA---------- >BloodwormGLOBIN, MAJOR MONOMERIC COMPONENT - BLOODWORM ----------G------------------LSAAQRQVIAATWKDIAGND---NGAGVGKDCLI--KHLSAHPQMAAVFGF SG-----ASD-PAVA---DLGAKV-LAIGVAVSHLGDGKMVAQMKA--VGV-RHKGYGN----KHIKGQYFEPLGASLLS AMEHRI-GG-KMNAAA-KDAWAAAYAD------I---SGALI----S-----G-----LQS---------- >Whelk GLOBIN - WHELK ----------G------------------LDGAQKTALKESWKVLGADGPTMMKNGSLLFGLLFKTYPDTKKHFKHFDDA TF-----AAM-DTTG---VGKAHG-VAVFSGLGSMICSIDDDDCV---GLA-KKLSRNH--LARGVSAADF-KLLEAVFK FLDEAT-QR-KATDAQ-KDADGALLTM------L---IKA------------H-----V------------ >Snail GLOBIN - WATER SNAIL ----------S------------------LQPASKSALASSWKTLAKDAATIQNNGATLFSLLFKQFPDTRNYFTHFGNM SD-----AEM-KTTG---VGKAHS-MAVFAGIGSMIDSMDDADCMN--GLA-LKLSRNH--IQRKIGASRFGEMRQVFPN FLDEAL-GG-GASGDV-KGAWDALLAY------LQDNKQA------------Q-----A----L------- >Clam GLOBIN I - BLOOD CLAM ----------P--------SVQGAAAQ--LTADVKKDLRDSWKVIGSDK---KGNGVALMTTLFADNQETIGYFKRLGNV SQ-----GM---AND---KLRGHS-ITLMYALQNFIDQLDNTDDLV--CVV-EKFAVNH--ITRKISAAEFGKINGP--- -IKKVL-AS-KNFGDK-YANAWAKLVA------V---VQA------------A-----L------------ >Midge larvaGLOBIN CTT-II BETA - MIDGE LARVA ----------A------------------PLSADEASLV---RGSWAQV---KHSEVDILYYIFKANPDIMAKFPQFAGK DL-----ETL-KGTGQFATHAGRI-VGFVSEIVALMGNSANMPAME--TLI-KDMAANH--KARGIPKAQFNEFRASLVS YLQSKV----SWNDSL-GAAWTQGLDN------V---FNMMF----S-----Y-----L------------ >Midge larva GLOBINS CTT-I AND CTT-IA - MIDGE LARVA ----------G------------------P-SGDQIAAA---KASWNTV---KNNQVDILYAVFKANPDIQTAFSQFAGK DL-----DSI-KGTPDFSKHAGRV-VGLFSEVMDLLGNDANTPTIL--AKA-KDFGKSH--KSRASP-AQLDNFRKSLVV YLKGAT----KWDSAV-ESSWAPVLDF------V---FSTLK----N-----E-----L------------ >Bacteria BACTERIAL HEMOGLOBIN - VITREOSCILLA SP -----------------------------MLDQQTINII---KATVPVL---KEHGVTITTTFYKNLFAKHPEVRPLFDM GR-----Q---ESLEQ-------P-KALAMTVLAAAQNIENLPAIL--PAV-KKIAVKH--CQAGVAAAHYPIVGQELLG AIKEVL-GD-AATDDI-LDAWGKAYGV------I---ADVFI----Q-----VEADLYA-----Q-AVE-- >P andersonii ONLEGUME HEMOGLOBIN I - PARASPONIA ANDERSONII ----------V----------------NKVFTEEQEALV---VKAWAVM---KKNSAELGLQFLK-IFEIAPSAKNLFSY 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–ïÑà–”H“%X€U‚ÉÍ-É9±†ÍG (ë9ñ(¢Ná3O2!¬GÔ àßè |&ê ê ê êðžÕøn,öIEND®B`‚weblogo-3.8.0/weblogo/htdocs/examples/hth.fa000066400000000000000000000062611467613320200210240ustar00rootroot00000000000000>A25944 DNA-directed RNA polymerase sigma-37 chain - Bacillu 223-240 iidltyiqnk SQKETGDILGISQMHVSR lqrkavkklr >A28627 spoIIIC protein - Bacillus subtilis 94-111 rfgldlkkek TQREIAKELGISRSYVSR iekralmkmf >A32837 *Transcriptional activator nahR - Pseudomonas putida 22-39 vvfnqllvdr RVSITAENLGLTQPAVSN alkrlrtslq >A23450 Antennapedia homeotic protein - Fruit fly (Drosophil 326-343 fhfnryltrr RRIEIAHALCLTERQIKI wfqnrrmkwk >B26499 Regulatory protein ntrC - Bradyrhizobium sp. 449-466 ltaalaatrg NQIRAADLLGLNRNTLRK kirdldiqvy >BVECDA dicA protein - Escherichia coli | 1551.0 1.0 1.0 1.0 22-39 iryrrknlkh TQRSLAKALKISHVSVSQ wergdseptg >C29010 Mercuric resistance operon regulatory merD protein - 5-22 ------mnay TVSRLALDAGVSVHIVRD yllrgllrpv >DNECFS DNA-binding protein fis - Escherichia coli | 928.0 1 73-90 ldmvmqytrg NQTRAALMMGINRGTLRK klkkygmn-- >JEBY1 Mating hormone a1 - Yeast (Saccharomyces cerevisiae) 99-116 frrkqslnsk EKEEVAKKCGITPLQVRV wfinkrmrsk >QCBP2L Regulatory protein cII - Phage lambda | 1559.0 2.0 1 25-42 sallnkiaml GTEKTAEAVGVDKSQISR wkrdwipkfs >QRECC cAMP receptor protein (CAP) - Escherichia coli | 1507 169-186 thpdgmqiki TRQEIGQIVGCSRETVGR ilkmledqnl >RCBPL Regulatory protein cro - Phage lambda | 1555.0 1.0 1. 15-32 itlkdyamrf GQTKTAKDLGVYQSAINK aihagrkifl >RGBP22 Regulatory protein cro - Phage P22 | 1556.0 1.0 1.0 12-29 ykkdvidhfg TQRAVAKALGISDAAVSQ wkevipekda >RGECA Arabinose operon regulatory protein - Escherichia col 196-213 isdhladsnf DIASVAQHVCLSPSRLSH lfrqqlgisv >RGECF Regulatory protein fnr - Escherichia coli | 1507.0 1. 196-213 fsprefrltm TRGDIGNYLGLTVETISR llgrfqksgm >RGECH Heat shock regulatory protein - Escherichia coli | 30 252-269 arwldednks TLQELADRYGVSAERVRQ leknamkklr >RGKBCP Nitrogen assimilation regulatory protein - Klebsiell 444-461 lttalrhtqg HKQEAARLLGWGRNTLTR klkelgme-- >RPECCT cyt repressor - Escherichia coli | 1291.0 3.0 1.0 1. 11-28 mkakkqetaa TMKDVALKAKVSTATVSR almnpdkvsq >RPECDO Deo operon repressor - Escherichia coli | 1536.0 1.0 23-40 lqelkrsdkl HLKDAAALLGVSEMTIRR dlnnhsapvv >RPECG gal repressor - Escherichia coli | 1291.0 4.0 1.0 1.0 3-20 --------ma TIKDVARLAGVSVATVSR vinnspkase >RPECL lac repressor - Escherichia coli | 1291.0 2.0 1.0 1.0 5-22 ------mkpv TLYDVAEYAGVSYQTVSR vvnqashvsa >RPECTN TetR repressor - Escherichia coli transposon Tn10 | 26-43 llnevgiegl TTRKLAQKLGVEQPTLYW hvknkralld >RPECW trp repressor - Escherichia coli | 1534.0 1.0 1.0 1.0 67-84 iveellrgem SQRELKNELGAGIATITR gsnslkaapv >S02513 Regulatory protein nifA - Klebsiella pneumoniae 495-512 liaalekagw VQAKAARLLGMTPRQVAY riqimditmp >S07337 *spoIIG protein - Bacillus subtilis 205-222 rfglvgeeek TQKDVADMMGISQSYISR lekriikrlr >S07958 *DNA-invertase - Escherichia coli 160-177 qagrliaagt PRQKVAIIYDVGVSTLYK tfpagdk--- >S08477 Regulatory protein purR - 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Ð;É_‡}”2ÇâôL 0€ÏÈ-g~ól›£‰]ñ¢Ç™ÓgËÄn—b%mØÎ˪îö$y,4@FÌÕª‡Ž×¨çû²„ˆ¯2¢FIâiH ð,IdAîøµ–!²ÌœFÝ‘¯Û™ˆvn9þÔMè‡8‘žL pO'c¿£‹~WQCṠv7Ȭ%¢™VMçÒЗY¾+Ñc\–ì€~I£ÚOëÀͬ¿ ÷`†4!ÒpÙó¡÷70šÑ ¤ Ö,WÞɤ¿ÆÕ0Ï€«åϦGsfH@¸£é²4š{˜œÊps£y44°L¦%wÜ@€ž! @4!Ò„HB @ˆÿ±„½Û kU+IEND®B`‚weblogo-3.8.0/weblogo/htdocs/examples/intron-exon.fa000066400000000000000000000132501467613320200225150ustar00rootroot00000000000000> 19082_AF115399 ttctctgaaatatgaatttagACTGGTACTTATCATGGAG > 45328_AB000381 gcctgctttctcccctctcagGGACTTACAGTTTGAGATG > 45328_AB000381 cattgctgcttctttttttagGCATAAATTCTCGTGAACT > 45330_AB001517 aacttcctgtgtgttttgcagACAGCTGGATAGAAAACGA > 45331_AB001517 acaattttgttttcttcacagTTTTCAAATTTGCTGGGTA > 45331_AB001517 tgtggtttttgtctttatcagCAACAAATCTGACACGCTG > 45331_AB001517 gtgacctctggcgtcctgcagGGGGCGATGCGCTGCTGGT > 45331_AB001517 atgtccgcgttccttccatagGAAGTTTGTTGTCACAAAG > 45331_AB001517 tgccatctccctcttttccagGTGCTTTGTGGTTGGGAGC > 45331_AB001517 accctgtgcttccccttgcagCTGTACTCACTCAGCCAGG > 45331_AB001517 tcttctctctcgtcaattcagGTACTTCTTCAATAAAGAA > 45331_AB001517 ttacaggcccgttctctgcagCATTTCAGATCAGAGCATC > 45331_AB001517 cagcttcccccgtgtgcacagGCCTGGGCCAGCTGCTGGT > 45331_AB001517 gcccctcctgtcctgcctcagGTCAAGGTGTGGAACACCC > 45331_AB001517 gaccttgcctcttctctgcagGTACCGAAACTTCCGCACC > 45331_AB001517 cgcctccttgctctacggtagGTTTTGTCTGGACACGAAG > 45331_AB001517 ttactttgcatctctgtttagCTCTGGCTGTGACTTTTCG > 45331_AB001517 ccatgtctcctctccacccagGGCCTTCACCGCCCTGTGC > 45331_AB001517 ccactgcttttgctgttctagGAATTTTTGAACCGAAGAA > 45331_AB001517 taacggttcttttttccccagGTGACATGAGTTCTCGGCA > 45331_AB001517 aagcactgcttaatttcccagGGCGCTGCTGGGCGGCCAC > 45331_AB001517 tgattttttctccttttgcagTTGAAGTGGTCACCTCCTC > 45331_AB001517 cttagggagtctccctttcagAGCCGGGACGCTGCTGCCT > 45331_AB001517 catcccctgtgtgattgacagCTGTAGCTGGAACCACTAT > 45332_AB001517 cagctcccgctcctctcgcagGTGCTGTCTGGATGCGGAG > 45332_AB001517 ctctggttttcccccgtgcagGATCCTGGTGCACCTGAGC > 45332_AB001517 ttgccctgtgctctttcccagGAATGTTTTGACCGAGTCT > 45332_AB001517 aggccttttgtctcccggtagGAGCACGTTTGCCGTGGAC > 45332_AB001517 cgtgttcttttcgcctttcagCTTGTGCTGCATTGCACCT > 45333_AB001517 cagctcccgctcctctcgcagGTGCTGTCTGGATGCGGAG > 45333_AB001517 ctctggttttcccccgtgcagGATCCTGGTGCACCTGAGC > 45333_AB001517 ttgccctgtgctctttcccagGAATGTTTTGACCGAGTCT > 45333_AB001517 cgtgttcttttcgcctttcagCTTGTGCTGCATTGCACCT > 45334_AB001523 atttctttcttcccttcatagGTGCTGGAGATCAGAATTT > 45334_AB001523 acttcaaacaattgtttacagGTCCTATGGCCGGGCTCCG > 45334_AB001523 cagtgacttgtttgtttttagGATACCGAAGTGTATAAAG > 45334_AB001523 agtctgttcatgtctttgcagGTGTGTTGTGCTCTCCGAC > 45334_AB001523 aaacgtatcttgggcgaatagGAGGAGCTTGCCTTTGTTT > 45334_AB001523 tcatgatgtgtgtttgtttagATGGTGCCAACTGGCTGAC > 45334_AB001523 ttcgcatttgcacccccacagGTCTCTGTCCCACCTGGTG > 45334_AB001523 attgtggatttatcttaacagTTAAAGTCCTTGGGCTATC > 45334_AB001523 tctcgtttctttctgtttaagCCAACACAGCTCAGAGTCC > 45334_AB001523 tgtgtttttacttccccacagGATTTGTCCCATGCCACCA > 45334_AB001523 actgtttgttgactttgcaagGAGGAAAAAGGCTCCACAA > 45334_AB001523 ctccttacctctccgctccagCTACCTGCAGACCAGCAGC > 45334_AB001523 tacgataatgtctatttacagGTCATAAGATAGTGCTACC > 45334_AB001523 tgcctgattctttgactctagGCCAAGGAACCTGGAACGT > 45334_AB001523 ccacgatctcttttcctttagATAGCCTTCTGGCAGGCAT > 45334_AB001523 gactttttctgtccttcgtagAACAGTCTTCTGAGGCCGC > 45334_AB001523 gtctttgtgcttcctcctcagGTGTCGATTGACTGCCCGT > 45334_AB001523 ctttttgtttttccactttagGAAATATGTTCAAGTTTGT > 45334_AB001523 gacccccaactctctttccagCCCATCTACAGCAAGCAGT > 45334_AB001523 ttctctccctttcctgcccagACATTATACAACGTGAAGG > 45334_AB001523 catcgcttcctctcgtttcagTTGTCGACAACAGTAGCAA > 45334_AB001523 aacttcctgtgtgttttgcagACAGCTGGATAGAAAACGA > 45335_AB001523 acaattttgttttcttcacagTTTTCAAATTTGCTGGGTA > 45337_AB00189S ttgtgtctttcgtgcttacagCATTGTGGCGACAAGAACA > 45337_AB00189S caccacgattccatttcttagGATTCCTACGCCAGCTACG > 45337_AB00189S tggttttttcctttgtttcagACACGGCACTCGTTGTGCG > 45338_AB00189S ttgtgtctttcgtgcttacagCATTGTGGCGACAAGAACA > 45338_AB00189S caccacgattccatttcttagGATTCCTACGCCAGCTACG > 45338_AB00189S tggttttttcctttgtttcagACACGGCACTCGTTGTGCG > 45338_AB00189S aatgcattctttacccattagGTGATCTTGAGACTCCTGT > 45339_AB00189S ttgtgtctttcgtgcttacagCATTGTGGCGACAAGAACA > 45339_AB00189S caccacgattccatttcttagGATTCCTACGCCAGCTACG > 45339_AB00189S tggttttttcctttgtttcagACACGGCACTCGTTGTGCG > 45339_AB00189S aatgcattctttacccattagGTGATCTTGAGACTCCTGT > 45340_AB00189S ttgtgtctttcgtgcttacagCATTGTGGCGACAAGAACA > 45340_AB00189S caccacgattccatttcttagGATTCCTACGCCAGCTACG > 45340_AB00189S tggttttttcctttgtttcagACACGGCACTCGTTGTGCG > 45341_AB00189S ttgtgtctttcgtgcttacagCATTGTGGCGACAAGAACA > 45341_AB00189S caccacgattccatttcttagGATTCCTACGCCAGCTACG > 45341_AB00189S tggttttttcctttgtttcagACACGGCACTCGTTGTGCG > 45341_AB00189S ctcctgcctttgctcctacagGAAGTGCGTGAGTGTGTGC > 45342_AB00189S ttgtgtctttcgtgcttacagCATTGTGGCGACAAGAACA > 45342_AB00189S caccacgattccatttcttagGATTCCTACGCCAGCTACG > 45342_AB00189S tggttttttcctttgtttcagACACGGCACTCGTTGTGCG > 45342_AB00189S -ggcaatttgcactcacacagCTCAATCCACCCCAGGCTC > 45342_AB00189S ctcctgcctttgctcctacagGAAGTGCGTGAGTGTGTGC > 45342_AB00189S aggaacggtatcttcccacagGTGTGACGAGAACTGCTTG > 45342_AB00189S tttcctgatgcggggccccagCTGACGAGACATTCTGCGA > 45343_AB00189S ttgtgtctttcgtgcttacagCATTGTGGCGACAAGAACA > 45343_AB00189S caccacgattccatttcttagGATTCCTACGCCAGCTACG > 45343_AB00189S tggttttttcctttgtttcagACACGGCACTCGTTGTGCG > 45343_AB00189S ctcctgcctttgctcctacagGAAGTGCGTGAGTGTGTGC > 45343_AB00189S aggaacggtatcttcccacagGTGTGACGAGAACTGCTTG > 45343_AB00189S tttcctgatgcggggccccagCTGACGAGACATTCTGCGA > 45344_AB00189S ttgtgtctttcgtgcttacagCATTGTGGCGACAAGAACA > 45344_AB00189S caccacgattccatttcttagGATTCCTACGCCAGCTACG > 45344_AB00189S tggttttttcctttgtttcagACACGGCACTCGTTGTGCG > 45344_AB00189S -ggcaatttgcactcacacagCTCAATCCACCCCAGGCTC > 45344_AB00189S ctcctgcctttgctcctacagGAAGTGCGTGAGTGTGTGC > 45345_AB002059 tgcccgacttctcctccccagGTGGGCGCTCCTCGCCAAA > 45345_AB002059 accttgagacttgcctcctagGGAGAGAACGTGTTCTTCT > 45345_AB002059 ctgctctctctcccacctcagCACCCGTCCGTCCCACTGG > 45345_AB002059 agttcatcttttgttttctagGTGTAAAAACAGGCCAGTG > 45345_AB002059 tcacctcccttccacctgcagGAGGCCCCTGCTGGCCCAG > 45345_AB002059 gacctttcccactcctcccagGTCCAATGCCTTGGAGACC > 45345_AB002059 aaagctatgtgctatgtgcagGGTGGCTCTGTAGGCATCA > 45345_AB002059 agccttctttcctgcccacagGACAGCCACTCACTGGTGG weblogo-3.8.0/weblogo/htdocs/examples/intron-exon.png000066400000000000000000000772411467613320200227250ustar00rootroot00000000000000‰PNG  IHDR Þà § 2iCCPdefault_rgb.iccH‰••gP“YÇïó<é…@B‡PC‘*%€”Z(Ò«¨@èPElˆ¸+Šˆ4EE\•"kE ‹‚tƒ,ʺqQAYpß÷?¼ÿ™{ÏoþsæÞsÏùp ˆƒeÁË{bRºÀÛÉŽÌß(ŒŸ–ÂñôtßÕ»­Ä{ºßÏù®‘iü常¼rù)‚t ìeÖÌJOYá£ËLÿÂgWX°\à2ßXáèyìKο,ú’ãëÍ]~ )úÿ†ÿsïŠT8‚ôبÈl¦OrTzV˜ ’™¶Ò —Ëô$GÅ&D~Sðÿ•ü¥Gf§¯DnrÊ&AltL:ó5204_gñÆëK!FÿÏgE_½äzØs û¾zá•tî@úÑWOm¹¯”|:îð3™ÿz¨• €è@(U  t0–À8à|AØø $ȹ`(E`8ª@-hM œà<¸®ƒÛà.L‚—@Þ‚°¢A2¤é@F²† 7È ‚B¡h( Ê€r¡PT UAuPô tºÝ„¡‡Ð84ý }„˜ÓaXÖ‡Ù0v…}áõp4œ çÀùð^¸®‡OÂðø6< á—ð"Â@”]„p$‰BÈV¤)Gê‘V¤éCî!Bdù€Â h(&Je‰rFù¡ø¨TÔVT1ª uÕêEÝC£D¨Ïh2Z­ƒ¶@óÐèhtº]ŽnD·£¯¡‡Ñ“èw †aaÌ0Θ Lf3¦sÓ†¹ŒÄL`æ°X¬ Vk…õÀ†aÓ±ØJìIì%ìvûGÄ)áŒpŽ¸`\.WŽkÆ]Ä á¦p 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Introduction

WebLogo is a web-based application designed to make the generation of sequence logos easy and painless. WebLogo has been featured in over 12000 scientific publications.

A sequence logo is a graphical representation of an amino acid or nucleic acid multiple sequence alignment. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. In general, a sequence logo provides a richer and more precise description of, for example, a binding site, than would a consensus sequence.

WebLogo is a web-based application designed to make the generation of sequence logos easy and painless. WebLogo has featured in over 10000 scientific publications.

Responsive image

References

Crooks GE, Hon G, Chandonia JM, Brenner SE WebLogo: A sequence logo generator, Genome Research, 14:1188-1190, (2004) [Full Text ]

Schneider TD, Stephens RM. 1990. Sequence Logos: A New Way to Display Consensus Sequences. Nucleic Acids Res. 18:6097-6100

Warning

Please do not abuse our server. If you need to create large numbers of logos then you are welcome to download the code and run WebLogo on your own machine. If a request flood compromises the WebLogo server then your IP address will be unceremoniously blocked.

Disclaimer

While no permanent records are kept of submitted sequences, we cannot undertake to guarantee that data sent to WebLogo remains secure. Moreover, no guarantees whatsoever are provided about data generated by WebLogo.

Feedback

Please report bugs and other issues at github.com/WebLogo/weblogo/.

weblogo-3.8.0/weblogo/htdocs/logo.css000066400000000000000000000111511467613320200175570ustar00rootroot00000000000000 /* Logo Cascading Style Sheet */ /*original WebLogo CSS*/ body { font-family: sans-serif; color: black; background: white; } a:link { color: #369; background: transparent } a:visited { color: #066; background: transparent } a:active { color: #C00; background: transparent } a.selected:visited { color: #000; background: #EEE; text-decoration: none; } th, td { /* ns 4 */ font-family: sans-serif; } h1, h2, h3, h4, h5, h6 { text-align: left } h1 { color: #900 } h1 { text-align: left ; padding-top: 50px} h1 { font: 170% sans-serif} h2 { font: bold 140% sans-serif } h3 { font: bold 120% sans-serif } h4 { font: bold 100% sans-serif; padding-top: 15px } h5 { font: italic 100% sans-serif } h6 { font: small-caps 100% sans-serif } h2 { margin-top: 2em} h4 { margin-bottom: 0.2em} .discourse { font-size: small } p {text-align: justify; margin-top: 0em} p.copyright { font-size: small; text-align: center } pre { margin-left: 2em ; } dt, dd { margin-top: 0; margin-bottom: 0 } /* opera 3.50 */ dt { font-weight: bold } /* navigator 4 requires this */ pre, code { font-family: monospace ; } /*bootstrap CSS*/ html, body { height: 100% } #wrap { min-height: 100% overflow: hidden; } #thumbnail-2, #thumbnail-3 { height: 580px } body { padding-top: 25px; font-family: sans-serif; color: black; background: white; } /* .thumbnail:hover { background-color: rgba(204,204,204,.85); } */ .thumbnail { display: inline-flex } .btn-sm{ width: 100% } #sequence-data { height: 100px } option { font-size: 12px } h1 { padding: 20px } table: { cell-padding: 5; } form { font-size: 12px } img { padding: 2px; border-style: solid; } #introduction { padding-top: 150px } #spacing-row { height: 50px; } #padding-div { height: 7px } .edit-logo-btn { padding-top: 5px } .image-div { padding: 5px; } .code { text-color: black; } #last-button { width: 100% } .button { padding-bottom: 5px; } #sequence-data { height: 100px } #url-upload{ width: 80% } #title { width: 80% } option { font-size: 12px } h1 { padding: 35px } #Gallery-header { text-align: center; } #CAP-header { text-align: center; } table: { cell-padding: 5; } code { color: black; } /*fluidbox css*/ @-webkit-keyframes fluidboxLoading { 0% { -webkit-transform: translate(-50%, -50%) rotateX(0) rotateY(0); } 50% { -webkit-transform: translate(-50%, -50%) rotateX(-180deg) rotateY(0); } 100% { -webkit-transform: translate(-50%, -50%) rotateX(-180deg) rotateY(-180deg); } } @keyframes fluidboxLoading { 0% { transform: translate(-50%, -50%) rotateX(0) rotateY(0); } 50% { transform: translate(-50%, -50%) rotateX(-180deg) rotateY(0); } 100% { transform: translate(-50%, -50%) rotateX(-180deg) rotateY(-180deg); } } .fluidbox { outline: none; } .fluidbox-overlay { background-color: rgba(255, 255, 255, 0.85); cursor: pointer; cursor: -webkit-zoom-out; cursor: -moz-zoom-out; cursor: zoom-out; opacity: 0; position: fixed; top: 0; left: 0; bottom: 0; right: 0; /* Transition time for overlay is halved to ensure that flickering doesn't happen */ transition: all 0.125s ease-in-out 0.125s; } .fluidbox-wrap { background-position: center center; background-size: cover; margin: 0 auto; position: relative; transition: all 0.25s ease-in-out; /* To prevent flickering, we delay the showing of the image */ } .fluidbox-closed .fluidbox-wrap img { transition: opacity 0s ease-in-out 0.25s; } .fluidbox-ghost { background-size: 100% 100%; background-position: center center; position: absolute; -webkit-transition-property: opacity, -webkit-transform; -moz-transition-property: opacity, -moz-transform; -o-transition-property: opacity, -o-transform; transition-property: opacity, transform; transition-duration: 0s, 0.25s; transition-delay: 0.25s, 0s; } .fluidbox-opened .fluidbox-ghost { transition-delay: 0s, 0s; } .fluidbox-loader { perspective: 200px; position: absolute; top: 0; left: 0; bottom: 0; right: 0; } .fluidbox-loader::before { /* You can replace this with any color you want, or even a loading gif if desired */ background-color: rgba(255, 255, 255, 0.85); content: ''; transform-style: preserve-3d; transition: all 0.25s ease-in-out; opacity: 0; position: absolute; top: 50%; left: 50%; width: 20%; padding-bottom: 20%; } .fluidbox-loading .fluidbox-loader::before { -webkit-animation: fluidboxLoading 1s 0s infinite ease-in-out forwards; animation: fluidboxLoading 1s 0s infinite ease-in-out forwards; opacity: 1; }weblogo-3.8.0/weblogo/htdocs/manual.html000066400000000000000000001511151467613320200202550ustar00rootroot00000000000000 WebLogo 3 - User's Manual


WebLogo 3: User's Manual

Contents

Web Logo example

Release Notes and Known Bugs

The WebLogo release notes detail changes to WebLogo and known issues with particular versions.

Introduction

WebLogo is a web based application designed to make the generation of sequence logos as easy and painless as possible.

A sequence logo is a graphical representation of an amino acid or nucleic acid multiple sequence alignment. Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino or nucleic acid at that position. The width of the stack is proportional to the fraction of valid symbols in that position. (Positions with many gaps have thin stacks.)In general, a sequence logo provides a richer and more precise description of, for example,a binding site, than would a consensus sequence.

References

Crooks GE, Hon G, Chandonia JM, Brenner SE WebLogo: A sequence logo generator, Genome Research, 14:1188-1190, (2004) [ Full Text ]

Schneider TD, Stephens RM. 1990. Sequence Logos: A New Way to Display Consensus Sequences. Nucleic Acids Res. 18:6097-6100


Creating Sequences Logos using the Web interface

Sequence Data
Enter your multiple sequence alignment or position weight matrix file, or select a file to upload. Supported file formats include CLUSTALW, FASTA, plain flatfile, MSF, NBRF, PIR, NEXUS and PHYLIP for multiple sequence alignments, and transfac for position weight matrices. All sequences must be the same length, else WebLogo will return an error and report the first sequence that differed in length from previous sequences.

Output format
Generally speaking, vector formats (EPS and PDF) are better for print, while bitmaps (JPEG and PNG) are more suitable for displaying on the screen or embedding into a web page.
PNG: (600 DPI) Print resolution bitmap
PNG: (low res, 96 DPI) Screen resolution bitmap
JPEG: Screen resolution bitmap
EPS: Encapsulated postscript
PDF: Portable Document Format
SVG: Scalable Vector Graphics

Logo size
The physical dimensions of the generated logo. Specifically, Logo Size controls the size of individual symbols stacks.
small: 5.4 points wide (same as 9pt Courier), aspect ratio 5:1
medium: Double the width and height of small.
large: Triple the width and height of small.
The choices have been limited to promote inter-logo consistency. Small logos can fit 80 stacks across a printed page, or 40 across a half page column. The command line interface provides greater control, if so desired.

Stacks per line
If the length of the sequences is greater than this maximum number of stacks per line, then the logo will be split across multiple lines.

Sequence Type
Selects the type of biological molecule.
auto: Automatically guess sequence type from the data
protein
dna
rna

Ignore Lower Case
Disregard lower case letters and only count upper case letters in sequences

Units
The units used for the y-axis.
probability: Show residue probabilities, rather than information content. If compositional adjustment is disabled, then these are the raw residue frequencies.
bits: Information content in bits
nats: Natural units, 1 bit = ln 2 (0.69) nats
kT: Thermal energy units in natural units (numerically the same as nats)
kJ/mol: Thermal energy (assuming T = 300 K)
kcal/mol: Thermal energy (assuming T = 300 K)

First position number
The numerical label of the first position in the sequence data in the input file. The label must be an integer. Residue labels for the logo will be relative to this number. (See also: Logo range.)

Logo range
By default, all sequence data from the input file is displayed in the Sequence Logo. With this option, you can instead show a subrange of the sequence data. The numbering of Start and End Positions is relative to the First Position Number. Thus, if the First Position Number is "2", Start is "5" and End is "10", then the 4th through 9th (inclusive) sequence positions of the input file will be displayed, and they will be numbered "5", "6", "7", "8", "9" and "10".

Composition

The background composition of the genome or proteome from which the sequences have been drawn. The default, automatic option is to use equiprobable background for nucleic acids and a typical amino acid usage pattern for proteins. However, you may also explicitly set the expected CG content for nucleic acid sequences, insist on equiprobable background distributions, or turn off composition adjustment altogether.

Compositional adjustment has two effects. First, the information content of a site is defined as the relative entropy of the monomers at that site to the background distribution. Consequentially, rare monomers have higher information content (when they occur) than relatively common monomers.

Secondly, the background composition is used in the small sample correction of information content. Briefly, if only a few sequences are available in the multiple sequence alignment, then sites typically appear more conserved than they really are. Small samples bias the relative entropy upwards. To compensate, we add pseudocounts to the actual counts, proportional to the expected background composition. These pseudocounts smooth the data for small samples, but become irrelevant for large samples. The proportionality constant is set to 4 for nucleic acid sequences, and 20 for proteins (these numbers have been found to give reasonable results in practice).

Behind the scenes, things are more complex. We do a full Bayesian calculation, starting with explicit Dirichlet priors based on the background composition, to which we add the data and then calculate both the posterior mean relative entropy (the stack height) and Bayesian 95% confidence intervals for error bars. These interesting details will be explained elsewhere.


Scale stack width
Scale the visible stack width by the fraction of symbols in the column.(I.e. columns with many gaps or unknown residues are narrow.)

Error bars
Display error bars. These indicate an approximate Bayesian 95% confidence interval.

Title
Give your logo a title.

Figure label
An optional figure label, added to the top left (e.g. '(a)').

X-axis
Add a label to the x-axis, or hide axis altogether.

Y-axis
The vertical axis indicates the information content of a sequence position. Use this option to toggle the y-axis and override the default axis label.

Y-axis scale
The height of the y-axis in designated units. The automatic option will pick reasonable defaults based on the sequence type and axis unit.

Y-axis tic spacing
The distance between major tic marks on the y-axis.

Sequence end labels
Choose this option to label the 5' & 3' ends of nucleic acid or the N & C termini of amino acid sequences.

Version fineprint
Toggle display of the WebLogo version information in the lower right corner. Optional, but we appreciate the acknowledgment.

Color Scheme
Auto:
Use Base Pairing for nucleic acids (NA), Hydrophobicity for amino acids (AA).

Monochrome:
All symbols black

Base Pairing
(NA default):
2 Watson-Crick hydrogen bonds TAU dark orange
3 Watson-Crick hydrogen bonds GC blue

Classic (NA):
G orange
TU red
C blue
A green
WebLogo (version 1 and 2) and makelogo default color scheme for nucleic acids: G, orange; T & U, red; C, blue; and A, green.

Hydrophobicity
(AA default):
Hydrophilic RKDENQ blue
Neutral SGHTAP green
Hydrophobic YVMCLFIW black

Chemistry (AA):
Color amino acids according to chemical properties.
Polar G,S,T,Y,C green
Neutral Q,N purple
Basic K,R,H blue
Acidic D,E red
Hydrophobic A,V,L,I,P,W,F,M black
WebLogo (version 1 and 2) and makelogo default color. (Note that the WebLogo 2 documentation erroneously lists Q and N under green.)

Charge (AA) :
Positive KRH blue
Negative DE red

Custom:
A custom color scheme can be specified in the input field below. Specify colors on the left and associated symbols on the right. Colors are entered using CSS2 (Cascading Style Sheet) syntax. (E.g. 'red', '#F00', '#FF0000', 'rgb(255, 0, 0)', 'rgb(100%, 0%, 0%)' or 'hsl(0, 100%, 50%)' for the color red.)


More Options
The weblogo command line client, weblogo, provides many more options and greater control over the final logo appearance.

Installing WebLogo

Dependencies

WebLogo version 3 is written in python. It is necessary to have Python 3.8 or later and the extension package numpy installed before WebLogo will run. WebLogo also requires a recent version of ghostscript to create PNG and PDF output, and pdf2svg to generate SVG output.

Download and Installation

WebLogo and its dependencies can be downloaded and installed with pip, 
                pip install weblogo
or conda. 
                conda install -c conda-forge weblogo
Alternatively, weblogo and its dependencies can be installed manually. The WebLogo source code can be downloaded from Weblogo's Github repository. This code is distributed under various open source licenses. Please consult the LICENSE.txt file in the source distribution for details.

After unpacking the WebLogo tarfile, it should be possible to immediately create logos using the command line client (provided that python, numpy and ghostscript have already been installed). 

                ./weblogo --format PNG < cap.fa > cap.png

Please consult the file build_examples.sh for more examples.

To run WebLogo as a stand alone web service, run the logo server command : 

                ./weblogo --serve

It should now be possible to access WebLogo at http://localhost:8080/.

Web App

To use WebLogo as a web application, first install the weblogo dependencies and libraries as above, then place (or link) the weblogo/htdocs directory somewhere within the document root of your webserver. The webserver must be able to execute the CGI script create.cgi. For Apache, you may have to add an ExecCGI option and add a cgi handler in the httpd.conf configuration file. Something like this: 
                    DocumentRoot "/home/ec2-user/weblogo/weblogo/htdocs"

                    # Further relax access to the default document root:
                    <Directory "/home/ec2-user/weblogo/weblogo/htdocs">
                        Options Indexes FollowSymLinks ExecCGI MultiViews
                        AddHandler cgi-script .cgi
                        AllowOverride All
                        Require all granted
                    </Directory>
It may also be necessary to set the PATH and PYTHONPATH environment variables. 
                    SetEnv PYTHONPATH /path/to/weblogo/libraries
The cgi script also has to be able to find the 'gs' ghostscript executable. The maximum bytes of uploaded sequence data can be controlled with the WEBLOGO_MAX_FILE_SIZE environment variable. 
                    SetEnv WEBLOGO_MAX_FILE_SIZE 1000000

weblogo, The WebLogo Command Line Interface (CLI)

The command line client has many options not available through the web interface. Please consult the bundled build_examples.sh script for inspiration. 
Usage: weblogo [options]  < sequence_data.fa > sequence_logo.eps

Create sequence logos from biological sequence alignments.

Options:
     --version                  show program's version number and exit
  -h --help                     show this help message and exit

  Input/Output Options:
    -f --fin FILENAME           Sequence input file (default: stdin)
       --upload URL             Upload input file from URL
    -D --datatype FORMAT        Type of multiple sequence alignment or
                                position weight matrix file: (clustal, fasta,
                                msf, genbank, nbrf, nexus, phylip, stockholm,
                                intelligenetics, table, array, transfac)
    -o --fout FILENAME          Output file (default: stdout)
    -F --format FORMAT          Format of output: eps (default), png,
                                png_print, pdf, jpeg, svg, logodata

  Logo Data Options:
    -A --sequence-type TYPE     The type of sequence data: 'protein', 'rna' or
                                'dna'.
    -a --alphabet ALPHABET      The set of symbols to count, e.g. 'AGTC'. All
                                characters not in the alphabet are ignored. If
                                neither the alphabet nor sequence-type are
                                specified then weblogo will examine the input
                                data and make an educated guess. See also
                                --sequence-type, --ignore-lower-case
    -U --units UNIT             A unit of entropy ('bits' (default), 'nats',
                                'digits'), or a unit of free energy ('kT',
                                'kJ/mol', 'kcal/mol'), or 'probability' for
                                probabilities
       --composition COMP.      The expected composition of the sequences:
                                'auto' (default), 'equiprobable', 'none' (do
                                not perform any compositional adjustment), a
                                CG percentage, a species name (e.g. 'E. coli',
                                'H. sapiens'), or an explicit distribution
                                (e.g. "{'A':10, 'C':40, 'G':40, 'T':10}"). The
                                automatic option uses a typical distribution
                                for proteins and equiprobable distribution for
                                everything else.
       --weight NUMBER          The weight of prior data.  Default depends on
                                alphabet length
    -i --first-index INDEX      Index of first position in sequence data
                                (default: 1)
    -l --lower INDEX            Lower bound of sequence to display
    -u --upper INDEX            Upper bound of sequence to display

  Transformations:
    Optional transformations of the sequence data.

       --ignore-lower-case      Disregard lower case letters and only count
                                upper case letters in sequences.
       --reverse                reverse sequences
       --complement             complement nucleic sequences
       --revcomp                reverse complement nucleic sequences

  Logo Format Options:
    These options control the format and display of the logo.

    -s --size LOGOSIZE          Specify a standard logo size (small, medium
                                (default), large)
    -n --stacks-per-line COUNT  Maximum number of logo stacks per logo line.
                                (default: 40)
    -t --title TEXT             Logo title text.
       --label TEXT             A figure label, e.g. '2a'
    -X --show-xaxis YES/NO      Display sequence numbers along x-axis?
                                (default: True)
    -x --xlabel TEXT            X-axis label
       --annotate TEXT          A comma separated list of custom stack
                                annotations, e.g. '1,3,4,5,6,7'.  Annotation
                                list must be same length as sequences.
       --rotate-numbers YES/NO  Draw X-axis numbers with vertical orientation
                                (default: False).
       --number-interval NUMBER
                                Distance between numbers on X-axis (default:
                                5)
    -S --yaxis NUMBER           Height of yaxis in units. (Default: Maximum
                                value with uninformative prior.)
    -Y --show-yaxis YES/NO      Display entropy scale along y-axis? (default:
                                True)
    -y --ylabel TEXT            Y-axis label (default depends on plot type and
                                units)
    -E --show-ends YES/NO       Label the ends of the sequence? (default:
                                False)
    -P --fineprint TEXT         The fine print (default: weblogo version)
       --ticmarks NUMBER        Distance between ticmarks (default: 1.0)
       --errorbars YES/NO       Display error bars? (default: True)
       --reverse-stacks YES/NO  Draw stacks with largest letters on top?
                                (default: True)

  Color Options:
    Colors can be specified using CSS2 syntax. e.g. 'red', '#FF0000', etc.

    -c --color-scheme SCHEME    Specify a standard color scheme (auto, base
                                pairing, charge, chemistry, classic,
                                hydrophobicity, monochrome)
    -C --color COLOR SYMBOLS DESCRIPTION 
                                Specify symbol colors, e.g. --color black AG
                                'Purine' --color red TC 'Pyrimidine'
       --default-color COLOR    Symbol color if not otherwise specified.

  Font Format Options:
    These options provide control over the font sizes and types.

       --fontsize POINTS        Regular text font size in points (default: 10)
       --title-fontsize POINTS  Title text font size in points (default: 12)
       --small-fontsize POINTS  Small text font size in points (default: 6)
       --number-fontsize POINTS
                                Axis numbers font size in points (default: 8)
       --text-font FONT         Specify font for labels (default: ArialMT)
       --logo-font FONT         Specify font for logo (default: Arial-BoldMT)
       --title-font FONT        Specify font for title (default: ArialMT)

  Advanced Format Options:
    These options provide fine control over the display of the logo.

    -W --stack-width POINTS     Width of a logo stack (default: 10.8)
       --aspect-ratio POINTS    Ratio of stack height to width (default: 5)
       --box YES/NO             Draw boxes around symbols? (default: no)
       --resolution DPI         Bitmap resolution in dots per inch (DPI).
                                (Default: 96 DPI, except png_print, 600 DPI)
                                Low resolution bitmaps (DPI<300) are
                                antialiased.
       --scale-width YES/NO     Scale the visible stack width by the fraction
                                of symbols in the column?  (I.e. columns with
                                many gaps of unknowns are narrow.)  (Default:
                                yes)
       --debug YES/NO           Output additional diagnostic information.
                                (Default: False)
       --errorbar-fraction NUMBER
                                Sets error bars display proportion (default:
                                0.9)
       --errorbar-width-fraction NUMBER
                                Sets error bars width display proportion
                                (default: 0.25)
       --errorbar-gray NUMBER   Sets error bars' gray scale percentage
                                (default: 0.75)

  WebLogo Server:
    Run a standalone webserver on a local port.

       --serve                  Start a standalone WebLogo server for creating
                                sequence logos.
       --port PORT              Listen to this local port. (Default: 8080)

WebLogo Application Programmer Interface (API)

The WebLogo python libraries provide even greater flexibility than the command line client. Please consult the code documentation at readthedocs.

WebLogo Development and Future Features

The development project is hosted at https://github.com/WebLogo/weblogo. If you wish to extend WebLogo or to contribute code, then you should download the full source code development package directly from the Github repository. 

                > git clone https://github.com/WebLogo/weblogo
                > pip install -e .

                
                > cd weblogo

Please consult the developer notes, DEVELOPERS.txt and software license LICENSE.txt

Outstanding bugs and feature requests are listed on the WebLogo issue tracker.


Miscellanea

WebLogo 2

The legacy WebLogo 2 sever can be found here.

Acknowledgments

WebLogo was created by Gavin E. Crooks, Liana Lareau, Gary Hon, John-Marc Chandonia and Steven E. Brenner. Many others have provided suggestions, bug fixes and moral support.

WebLogo was originally based upon the programs alpro and makelogo, both of which are part of Tom Schneider's delila package. Many thanks are due to him for making this software freely available and for encouraging its use.

Disclaimer

While no permanent records are kept of submitted sequences, we cannot undertake to guarantee that data sent to WebLogo remains secure. Moreover, no guarantees whatsoever are provided about data generated by WebLogo.

Feedback

Suggestions on how to improve WebLogo are heartily welcomed! Please direct questions to WebLogo's issue tracker.

weblogo-3.8.0/weblogo/htdocs/test.html000066400000000000000000000342361467613320200177630ustar00rootroot00000000000000 WebLogo 3 - Tests

WebLogo 3: Tests

 · about · create · examples · manual ·
 
Various tests of the WebLogo webapp.
Relative Entropy Test
The entropy should be 2 bits, 1 bit, 0 bits (The small sample correction should be turned off.)
Title And Labels Test
Replace and display x-label, y-label and title.
Same, but do not show axes
Format Test
Ensure that this logo can be created in each of the available formats
Format:
Test Alphabetic Order
Each character in each stack has the same entropy. The letters should be alphabetized, top down.
(NA)
(AA)
One Single Column
Should not die just because there is only 1 stack.
Small Sample Correction Test
The samples per column decrease from 32 (left) to 1 (right). Before the small sample correction the relative entropy of each stack is 2 bits.
Test Graceful Failure
Each of these tests should result in a polite and informative error message.
Logo Sizes
Same sequences, three different sizes.
Size:
Transfac test

weblogo-3.8.0/weblogo/htdocs/weblogo_changelog.txt000066400000000000000000000225411467613320200223200ustar00rootroot00000000000000WebLogo Release Notes 3.8 (2024-03-03) [Gavin Crooks, Melissa Fabros] * fixes for Ghostscript deprecation * remove support for python 3.8 Weblogo 3.8 runs under python 3.9, 3.10, 3.11, 3.12 3.7.11 (2022-05-26) [Gavin Crooks, Melissa Fabros] * enable typehints * updated examples for website * `conda` installation enabled with `conda-forge` * remove support for python 3.6 * Weblogo 3.7 runs under python 3.7, 3.8, 3.9 and 3.10 3.7 (2019-03-04) [Gavin Crooks] * Refactor and cleanup code, removing python 2.7 support * Extend API documentation * WebLogo python package is now 'weblogo', rather than 'weblogolib', matching pip install name. The 'corebio' package has been merged into 'weblogo'. * Miscellaneous minor bug fixes and refactoring * Weblogo 3.7 runs under python 3.6 and 3.7 3.6 (2017-12-29) [Gavin Crooks, Melissa Fabros] * refactor version string creation * update testing framework for use with tox and pytest * weblogo is centered in it's png file (Kudos: Gert Huselmans) * Miscellaneous minor bug fixes and refactoring (Kudos: Jerry Caskey, Coby Viner) * fix headings in README.md * Weblogo 3.6 runs under python 2.7, 3.4, 3.5 & 3.6 3.5 (2016-07-24) [Gavin Crooks, Melissa Fabros] * Moved source control from GoogleCode to GitHub * Switched from Subversion as version control method to Git * Refactor html to optimize WebLogo use on mobile computing devices * Add feature to open sequence files via file sharing URL link from Web application and command line * Updated documentation * PEP8ify all python files to solve formatting issues. (Kudos:Gert Hulselmans) * Expose additonal LogoOptions via CLI options (Kudos:Gert Hulselmans) * Fixed performance issue by limiting size of data that can be pasted into html form Use file upload instead. (Kudos: Peter Cherepanov) * Add ability to custom color every stack (Kudos: Kale Kundert) * Weblogo 3.5 runs under python 2.6, 2.7, 3.2, 3.3, 3.4 & 3.5 * Fixed bugs for compatible with Python 3 (Kudos: Gert Hulselmans, Teshome Mulugeta) * Miscellaneous minor bug fixes and refactoring (Kudos: David Kelley) 3.4 (2014-06-03) [Gavin Crooks, Eric Talevich] * Python 3 Weblogo now runs under python 2.6, 2.7, 3.2, 3.3 & 3.4 (Python 2.5 is no longer supported.) Note that the api for creating a logo has changed. See docs. (Kudos: Eric Talevic) * Fix bug with using Ghostscript 9.10 (Issue 36) (Kudos: Michael Imbeault, Estienne Swart, FiReaNG3L) * Fix various bugs in transfac parsing. (Kudos: Promita Bose, Christopher Lamantia) * Fix --complement of gapped sequences, added --revcomp option (Issue 36) (Kudos: Jacob Engelbrecht) * Miscellaneous minor bug fixes and refactoring. (Kudos: Kamil Slowikowski, Jacob Engelbrecht) 3.3 (2012-07-02) [Gavin Crooks, David Sivak] * Improved the algorithm that guesses the sequence type (DNA, RNA or protein) (Kudos: Bug report, Roland Pache) * Fixed an issue with reading transfac matrices with alternative alphabets (Kudos: Bug report, Nima Emami) * Fixed Motif.reindex() * Implemented Motif.reverse() and Motif.complement() (Can now reverse complement transfac matrix input on the command line.) (Kudos: Feature request, Seth P Boudreaux) * Command line interface now automagically recognizes transfac files. * Add command line option "--reverse-stacks NO" which inverts the logo stacks so that the most conserved monomers are at the bottom of the stack, rather than the top. This ordering is consistent with the standard ordering for histograms, and is arguably a better representation. (Kudos: Luke Hutchison) * Fixed an issue so that the correct color scheme is chosen for the specified sequence type. * Miscellaneous minor bug fixes and refactoring. 3.2 (2012-01-30) [Gavin Crooks, David Sivak] * Graphical interface now accepts transfac format motif files. * New output format option: SVG (Scalable Vector Graphics) * Miscellaneous minor bug fixes and refactoring. 3.1 (2011-08-16) [Gavin Crooks, David Sivak] Mostly bug fixes, code improvements and minor user enhancements. * Command line: Add parsing of transfac PWM files * Command line: Add reverse and complement transformations * Improve clustal file parsing * Currently compatible with python 2.5, 2.6 and 2.7 * Deprecate support for python 2.3 and 2.4 * Migrate corebio library into weblogo for easier maintenance and development. * Add new annotate option for custom annotation line * Miscellaneous minor bug fixes and refactoring. * Incorporates bug fixes and feedback from Gavin Crooks, John Gilman, Kevin Schutz and Perry Evan. 3.0 (2008-10-14) [GEC] A significant update of WebLogo. New and improved feature include: * Simplified GUI. More useful options, less obscure options that are rarely used. * Several choices of unit including bits and nats, and corresponding energy measures such as kJ/mol. * Error bars are smaller and more discrete. * The size of logo stacks is consistent (Does not change with sequence length.) * The width of the characters in a stack are scaled by the fraction of non-gaps. Therefore gappy columns are visually less important than columns with gaps. * Three standard logo sizes. * Can now read many multiple sequence alignment formats, including CLUSTALW, FASTA, plain flatfile, MSF, NBRF, PIR, NEXUS and PHYLIP. * High resolution PNG output. * New, rational, easy to use command line client. * Python based API library. * New color schemes, including Watson-Crick pairing, hydrophobicity and charge. * I (Isolucine) now shows crossbars, so that the letter is distinguishable from a line. * Colors can be specified using CSS2 syntax. * Optional figure label. * Conservation is now calculated as the Bayesian posterior mean relative entropy. (This is the most significant change scientifically. The math needed to get this right is very interesting.) * Similarly, we now display Bayesian 95% confidence intervals for error bars. * Compositional adjustment. * Includes contributions from Clare Gollnick, David Ding, John Gilman. * Incorporates bug fixes and feedback from John Reid, Gordon Robertson, Eric Odell, Krisztina Gabor, ... * Incorporates or adapts ideas and code from Gary Hon, Steven Brenner, John-Marc Chandonia, Liana Lareau, Ed Green, James Casbon, Jeffrey Chang, Frank Kauff, Cymon J. Cox, ... ----------------------------------------------------------------------- 2.8.2 (2005-09-08) [LL, GEC] Various Bug fixes: * Fixed Yellow (Was orange) * Various improvements in handling malformed input. * Fixed the fineprint checkbox option, which was stuck on. * Renamed "Uniform Height Logo" option to a more descriptive "Frequency Plot", and removed deceptive y-axis. 2.8.1 (2004-10-18) (Minor bug fix release) [GEC] Bug fixes: * Made weblogo compatibly with ghostscript version 8.1x. This release is known to work with ghostscript version 7.05, 8.00 & 8.14 Kudos for bug reports and suggestions to: * Lei Shen 2.8 (2004-10-01) [GEC] Bug fixes: * Fixed another form data parsing bug whose only apparent effect was to fill up the webserver's error log. * Fixed an issue with using double slashes in weblogo's url. Kudos for bug reports and suggestions to: * Eric Odell * Scot Wolfe * Alban Mancheron * Ed Green 2.7 (2004-06-09) [GEC] Bug fixes : * Fixed logo.cgi's parsing of checkbox form data. Kudos for bug reports and suggestions to: * Eric Odell 2.6 (2004-03-15) [GEC, GH] Bug fixes: * Resolved an issue with hard coded paths within the seqlogo command line client * Improved the parsing of clustalw files Kudos for bug reports and suggestions to: * Allen Liu * Guo Anyaun * Harald Weber 2.5 (2004-02-19) [GEC, GH] New features and enhancements : * Added multiline logos. 2.4 (2004-01-29) [GEC, GH] New features and enhancements : * Added file upload for sequence data. * Updated main page to reflect updated publication status 2.3 (2003-11-03) [GEC, GH] New features and enhancements * Added ability to parse CLUSTALW and flat file multiple sequence alignment formats. Bug fixes: * Antialiasing PNGs now works with recent versions of ghostscript * Can now change output file type when using Mozilla. Kudos for bug reports and suggestions to: * Stefanie Lager * Ed Green * Michael Galperin 2.2 (2003-08-01) [GEC, GH] Several minor bug fixes and changes to the web pages. * Fixed various buggy command line options * A request for an empty yaxis label is now respected * Fixed a major bug in temporary file name assignment that prevented weblogo from running on some unix variants New features and enhancements * Made error bars darker * Added option to control distance between tic marks Kudos for bug reports and suggestions to * Stefanie Lager * Arlin Stoltzfus * JP Cartailler * Peter G. Warren 2.1 (2003-01-08) [GEC] Several minor bug fixes and changes to the web pages. 2.0 (2002) [GEC, GH, JMC, SEB] This second version of WebLogo is a complete rewrite of both the user interface and the backend. Many new features and options have been provided. 1.0 (1995) [SEB] The original version of WebLogo was written in 1995 by Steven Brenner, and was hosted by the School of Biological Science, University of Cambridge WebLogo change log ----------------------- + New feature * Changed/Improved feature ! Fixed bug - Removed feature Versions : major.minor.patch. The WebLogo Team ------------------ LL: Liana Lareau GEC: Gavin E. Crooks GH: Gary Hon JMC: John-Marc Chandonia SEB: Steven E. Brenner weblogo-3.8.0/weblogo/logo.py000077500000000000000000001070221467613320200161410ustar00rootroot00000000000000# -------------------------------- WebLogo -------------------------------- # Copyright (c) 2003-2004 The Regents of the University of California. # Copyright (c) 2005 Gavin E. Crooks # Copyright (c) 2006-2015, The Regents of the University of California, through # Lawrence Berkeley National Laboratory (subject to receipt of any required # approvals from the U.S. Dept. of Energy). All rights reserved. # This software is distributed under the new BSD Open Source License. # # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions are met: # # (1) Redistributions of source code must retain the above copyright notice, # this list of conditions and the following disclaimer. # # (2) Redistributions in binary form must reproduce the above copyright # notice, this list of conditions and the following disclaimer in the # documentation and or other materials provided with the distribution. # # (3) Neither the name of the University of California, Lawrence Berkeley # National Laboratory, U.S. Dept. of Energy nor the names of its contributors # may be used to endorse or promote products derived from this software # without specific prior written permission. # # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" # AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE # IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE # ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE # LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR # CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF # SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS # INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN # CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE # POSSIBILITY OF SUCH DAMAGE. """ """ import os import sys from datetime import datetime from io import StringIO, TextIOWrapper from math import log, sqrt from typing import Any, Callable, Dict, List, Optional, Union from urllib.parse import urlparse, urlunparse from urllib.request import Request, urlopen import numpy as np # Avoid 'from numpy import *' since numpy has lots of names defined from numpy import any, array, asarray, float64, ones, zeros from scipy.stats import entropy from . import __version__, seq_io from .color import Color from .colorscheme import ( ColorScheme, SymbolColor, base_pairing, charge, chemistry, hydrophobicity, monochrome, ) from .data import amino_acid_composition from .logomath import Dirichlet from .seq import ( Alphabet, SeqList, unambiguous_dna_alphabet, unambiguous_protein_alphabet, unambiguous_rna_alphabet, ) from .utils import ArgumentError, isfloat, stdrepr # Shorten development version string of the form weblogo-3.6.1.dev43+g64d9f12.d20190304 if __version__.find("+") != -1: __version__ = __version__[: __version__.find("+")] # pragma: no cover # from .logo_formatter import (GhostscriptAPI, pdf_formatter, jpeg_formatter, png_formatter, # png_print_formatter, # txt_formatter, eps_formatter, formatters, default_formatter) # ------ META DATA ------ # __all__ = ['LogoOptions', # 'description', # '__version__', # 'LogoFormat', # 'LogoData', # 'GhostscriptAPI', # 'std_color_schemes', # 'default_color_schemes', # 'classic', # 'std_units', # 'std_sizes', # 'std_alphabets', # 'std_percentCG', # 'pdf_formatter', # 'jpeg_formatter', # 'png_formatter', # 'png_print_formatter', # 'txt_formatter', # 'eps_formatter', # 'formatters', # 'default_formatter', # 'base_distribution', # 'equiprobable_distribution', # 'read_seq_data', # 'Color', # 'ColorScheme', # 'parse_prior', # 'release_description', # 'description' # ] description = "Create sequence logos from biological sequence alignments." release_description = "WebLogo %s" % (__version__) def cgi(htdocs_directory: str) -> None: # pragma: no cover import weblogo._cgi weblogo._cgi.main(htdocs_directory) aa_composition = [amino_acid_composition[_k] for _k in unambiguous_protein_alphabet] # ------ DATA ------ classic = ColorScheme( [ SymbolColor("G", "orange"), SymbolColor("TU", "red"), SymbolColor("C", "blue"), SymbolColor("A", "green"), ] ) std_color_schemes = { "auto": None, # Depends on sequence type "monochrome": monochrome, "base pairing": base_pairing, "classic": classic, "hydrophobicity": hydrophobicity, "chemistry": chemistry, "charge": charge, } default_color_schemes = { unambiguous_protein_alphabet: hydrophobicity, unambiguous_rna_alphabet: base_pairing, unambiguous_dna_alphabet: base_pairing, } std_units = { "bits": 1.0 / log(2), "nats": 1.0, "digits": 1.0 / log(10), "kT": 1.0, "kJ/mol": 8.314472 * 298.15 / 1000.0, "kcal/mol": 1.987 * 298.15 / 1000.0, "probability": None, } # The base stack width is set equal to 9pt Courier. # (Courier has a width equal to 3/5 of the point size.) # Check that can get 80 characters in journal page @small # 40 characters in a journal column std_sizes = {"small": 5.4, "medium": 5.4 * 2, "large": 5.4 * 3} std_alphabets = { "protein": unambiguous_protein_alphabet, "rna": unambiguous_rna_alphabet, "dna": unambiguous_dna_alphabet, } std_percentCG = { "H. sapiens": 40.0, "E. coli": 50.5, "S. cerevisiae": 38.0, "C. elegans": 36.0, "D. melanogaster": 43.0, "M. musculus": 42.0, "T. thermophilus": 69.4, } # Thermus thermophilus: Henne A, Bruggemann H, Raasch C, Wiezer A, Hartsch T, # Liesegang H, Johann A, Lienard T, Gohl O, Martinez-Arias R, Jacobi C, # Starkuviene V, Schlenczeck S, Dencker S, Huber R, Klenk HP, Kramer W, # Merkl R, Gottschalk G, Fritz HJ: The genome sequence of the extreme # thermophile Thermus thermophilus. # Nat Biotechnol 2004, 22:547-53 class LogoOptions: """A container for all logo formatting options. Not all of these are directly accessible through the CLI or web interfaces. To display LogoOption defaults:: >>> from weblogo import * >>> LogoOptions() All physical lengths are measured in points. (72 points per inch, 28.3 points per cm) Args: creator_text: Embedded as comment in figures. logo_title: Creates title for the sequence logo logo_label: An optional figure label, added to the top left (e.g. '(a)'). unit_name: See std_units for options. (Default 'bits') yaxis_label: Defaults to unit_name xaxis_label: Add a label to the x-axis, or hide x-axis altogether. fineprint: Defaults to WebLogo name and version show_yaxis: Display entropy scale along y-axis (default: True) show_xaxis: Display sequence numbers along x-axis (default: True) show_ends: Display label at the ends of the sequence (default: False) show_fineprint: Toggle display of the WebLogo version information in the lower right corner. Optional, but we appreciate the acknowledgment. show_errorbars: Draw errorbars (default: False) show_boxes: Draw boxes around stack characters (default: True) debug: Draw extra graphics debugging information. rotate_numbers: Draw xaxis numbers with vertical orientation? scale_width: boolean, scale width of characters proportional to ungaps pad_right: Make a single line logo the same width as multiline logos (default: False) stacks_per_line: Maximum number of logo stacks per logo line. (Default: 40) yaxis_tic_interval: Distance between ticmarks on y-axis(default: 1.0) yaxis_minor_tic_ratio: Distance between minor tic ratio yaxis_scale: Sets height of the y-axis in designated units xaxis_tic_interval: Distance between ticmarks on x-axis(default: 1.0) number_interval: Distance between ticmarks (default: 1.0) shrink_fraction: Proportional shrinkage of characters if show_boxes is true. errorbar_fraction: Sets error bars display proportion errorbar_width_fraction: Sets error bars display errorbar_gray: Sets error bars' gray scale percentage (default .75) resolution: Dots per inch (default: 96). Used for bitmapped output formats default_color: Symbol color if not otherwise specified color_scheme: A custom color scheme can be specified using CSS2 (Cascading Style Sheet) syntax. E.g. 'red', '#F00', '#FF0000', 'rgb(255, 0, 0)', 'rgb(100%, 0%, 0%)' or 'hsl(0, 100%, 50%)' for the color red. stack_width: Scale the visible stack width by the fraction of symbols in the column (I.e. columns with many gaps of unknowns are narrow.) (Default: yes) stack_aspect_ratio: Ratio of stack height to width (default: 5) logo_margin: Default: 2 pts stroke_width: Default: 0.5 pts tic_length: Default: 5 pts stack_margin: Default: 0.5 pts small_fontsize: Small text font size in points fontsize: Regular text font size in points title_fontsize: Title text font size in points number_fontsize: Font size for axis-numbers, in points. text_font: Select font for labels logo_font: Select font for Logo title_font: Select font for Logo's title first_index: Index of first position in sequence data logo_start: Lower bound of sequence to display logo_end: Upper bound of sequence to display """ def __init__(self, **kwargs: dict) -> None: """Create a new LogoOptions instance. >>> logooptions = LogoOptions(logo_title = "Some Title String") >>> logooptions.show_yaxis = False >>> repr(logooptions) """ self.alphabet: Optional[Alphabet] = None self.creator_text = release_description self.logo_title = "" self.logo_label = "" self.stacks_per_line = 40 self.unit_name = "bits" self.show_yaxis = True # yaxis_lable default depends on other settings. See LogoFormat self.yaxis_label: Optional[str] = None self.yaxis_tic_interval = 1.0 self.yaxis_minor_tic_ratio = 5 self.yaxis_scale: Optional[float] = None self.show_xaxis = True self.xaxis_label = "" self.xaxis_tic_interval = 1 self.rotate_numbers = False self.number_interval = 5 self.show_ends = False self.annotate = None self.show_fineprint = True self.fineprint: str = "WebLogo " + ".".join(__version__.split(".")[0:3]) self.show_boxes = False self.shrink_fraction = 0.5 self.show_errorbars = True self.errorbar_fraction = 0.90 self.errorbar_width_fraction = 0.25 self.errorbar_gray = 0.75 self.resolution: int = 96 # Dots per inch self.default_color = Color.by_name("black") self.color_scheme: Optional[ColorScheme] = None # self.show_color_key = False # NOT yet implemented self.debug = False self.logo_margin = 2 self.stroke_width = 0.5 self.tic_length = 5 self.stack_width = std_sizes["medium"] self.stack_aspect_ratio = 5 self.stack_margin = 0.5 self.pad_right = False self.small_fontsize = 6 self.fontsize = 10 self.title_fontsize = 12 self.number_fontsize = 8 self.text_font = "ArialMT" self.logo_font = "Arial-BoldMT" self.title_font = "ArialMT" self.first_index = 1 self.logo_start: Optional[int] = None self.logo_end: Optional[int] = None self.scale_width = True self.reverse_stacks = True # If true, draw stacks with largest letters on top. for k, v in kwargs.items(): setattr(self, k, v) def __repr__(self) -> str: attributes = list(vars(self).keys()) attributes.sort() return stdrepr(self, attributes) # End class LogoOptions class LogoFormat(LogoOptions): """Specifies the format of the logo. Requires LogoData and LogoOptions objects. >>> logodata = LogoData.from_seqs(seqs) >>> logooptions = LogoOptions() >>> logooptions.title = "A Logo Title" >>> format = LogoFormat(logodata, logooptions) Raises: ArgumentError: if arguments are invalid. """ def __init__( self, logodata: "LogoData", logooptions: Optional[LogoOptions] = None ) -> None: """Create a new LogoFormat instance.""" if logooptions is not None: self.__dict__.update(logooptions.__dict__) self.alphabet: Optional[Alphabet] = logodata.alphabet self.seqlen: Optional[int] = logodata.length # Derived parameters. self.show_title = False self.show_xaxis_label = False self.yaxis_minor_tic_interval = None self.lines_per_logo = None self.char_width = None # Maximum character width. Stack width minus margins. self.line_margin_left = None self.line_margin_right = None self.line_margin_bottom = None self.line_margin_top = None self.title_height = None self.xaxis_label_height = None self.line_height = None self.line_width = None self.logo_height: Optional[int] = None self.logo_width: Optional[int] = None self.creation_date = None self.end_type = None self.stack_height = self.stack_width * self.stack_aspect_ratio # Attribute to test, test, error message arg_conditions = ( ("stacks_per_line", lambda x: x > 0, "Stacks per line must be positive."), ( "stack_width", lambda x: x > 0.0, "Stack width must be greater than zero.", ), ( "stack_aspect_ratio", lambda x: x > 0, "Stack aspect ratio must be greater than zero.", ), ("fontsize", lambda x: x > 0, "Font sizes must be positive."), ("small_fontsize", lambda x: x > 0, "Font sizes must be positive."), ("title_fontsize", lambda x: x > 0, "Font sizes must be positive."), ( "errorbar_fraction", lambda x: x >= 0.0 and x <= 1.0, "The visible fraction of the error bar must be between zero and one.", ), ( "yaxis_tic_interval", lambda x: x >= 0.0, "The yaxis tic interval cannot be negative.", ), ( "yaxis_minor_tic_interval", lambda x: not (x and x < 0.0), "Distances cannot be negative.", ), ( "xaxis_tic_interval", lambda x: x > 0.0, "Tic interval must be greater than zero.", ), ("number_interval", lambda x: x > 0.0, "Invalid interval between numbers."), ( "shrink_fraction", lambda x: x >= 0.0 and x <= 1.0, "Invalid shrink fraction.", ), ("stack_margin", lambda x: x > 0.0, "Invalid stack margin."), ("logo_margin", lambda x: x > 0.0, "Invalid logo margin."), ("stroke_width", lambda x: x > 0.0, "Invalid stroke width."), ("tic_length", lambda x: x > 0.0, "Invalid tic length."), ) # Run arguments tests. The second, attribute argument to the ArgumentError is # used by the UI to provide user feedback. # FIXME: More validation for test in arg_conditions: if not test[1](getattr(self, test[0])): raise ArgumentError(test[2], test[0]) # Inclusive upper and lower bounds # FIXME: Validate here. Move from eps_formatter # asserts checks that defaults that were initialized to None have been set assert self.first_index is not None assert self.seqlen is not None if self.logo_start is None: self.logo_start = self.first_index assert self.logo_start is not None if self.logo_end is None: self.logo_end = self.seqlen + self.first_index - 1 assert self.logo_end is not None assert self.logo_start is not None self.total_stacks = self.logo_end - self.logo_start + 1 if self.total_stacks <= 0: raise ArgumentError("Logo must contain at least one stack", "logo_end") if self.logo_start - self.first_index < 0: raise ArgumentError( "Logo range extends before start of available sequence.", "logo_range" ) if self.logo_end - self.first_index >= self.seqlen: raise ArgumentError( "Logo range extends beyond end of available sequence.", "logo_range" ) if self.logo_title: self.show_title = True if not self.fineprint: self.show_fineprint = False if self.xaxis_label: self.show_xaxis_label = True if self.yaxis_label is None: self.yaxis_label = self.unit_name assert self.yaxis_label is not None if self.yaxis_label: self.show_yaxis_label = True else: self.show_yaxis_label = False self.show_ends = False if not self.yaxis_scale: conversion_factor = std_units[self.unit_name] if conversion_factor: if self.alphabet is None: raise ArgumentError("Need an alphabet", "alphabet") assert self.alphabet is not None self.yaxis_scale = log(len(self.alphabet)) * conversion_factor else: self.yaxis_scale = 1.0 # probability units if self.yaxis_scale <= 0.0: raise ArgumentError( "Invalid yaxis scale", "yaxis_scale", ) if self.yaxis_tic_interval >= self.yaxis_scale: self.yaxis_tic_interval /= 2.0 self.yaxis_minor_tic_interval = ( float(self.yaxis_tic_interval) / self.yaxis_minor_tic_ratio ) if self.color_scheme is None: if self.alphabet in default_color_schemes: self.color_scheme = default_color_schemes[self.alphabet] else: self.color_scheme = monochrome self.lines_per_logo = 1 + ((self.total_stacks - 1) // self.stacks_per_line) if self.lines_per_logo == 1 and not self.pad_right: self.stacks_per_line = min(self.stacks_per_line, self.total_stacks) self.char_width = self.stack_width - 2 * self.stack_margin if self.show_yaxis: self.line_margin_left = self.fontsize * 3.0 else: if self.show_ends and self.show_xaxis: self.line_margin_left = self.fontsize * 1.5 else: self.line_margin_left = 4 if self.show_ends and self.show_xaxis: self.line_margin_right = self.fontsize * 1.5 else: self.line_margin_right = 4 if self.show_xaxis: if self.rotate_numbers: self.line_margin_bottom = self.number_fontsize * 2.5 else: self.line_margin_bottom = self.number_fontsize * 1.5 else: self.line_margin_bottom = 4 self.line_margin_top = 4 if self.show_title: self.title_height = self.title_fontsize else: self.title_height = 0 self.xaxis_label_height = 0.0 if self.show_xaxis_label: self.xaxis_label_height += self.fontsize if self.show_fineprint: if len(self.fineprint) != 0: self.xaxis_label_height += self.small_fontsize self.line_height = ( self.stack_height + self.line_margin_top + self.line_margin_bottom ) self.line_width = ( self.stack_width * self.stacks_per_line + self.line_margin_left + self.line_margin_right ) self.logo_height = int( 2 * self.logo_margin + self.title_height + self.xaxis_label_height + self.line_height * self.lines_per_logo ) self.logo_width = int(2 * self.logo_margin + self.line_width) self.creation_date = datetime.now().isoformat(" ") end_type = "-" end_types = { unambiguous_protein_alphabet: "p", unambiguous_rna_alphabet: "-", unambiguous_dna_alphabet: "d", } if self.show_ends and self.alphabet in end_types: end_type = end_types[self.alphabet] self.end_type = end_type if self.annotate is None: self.annotate: list = [] for i in range(self.seqlen): index = i + self.first_index if index % self.number_interval == 0: self.annotate.append("%d" % index) else: self.annotate.append("") if len(self.annotate) != self.seqlen: raise ArgumentError( "Annotations must be same length as sequences.", "annotate" ) # End __init__ # End class LogoFormat def parse_prior( composition: Any, alphabet: Alphabet, weight: Optional[float] = None ) -> Optional[np.ndarray]: """Parse a description of the expected monomer distribution of a sequence. Valid compositions: * None or 'none' No composition specified * 'auto' or 'automatic' Use the typical average distribution for proteins and an equiprobable distribution for everything else. * 'equiprobable' All monomers have the same probability. * a percentage, e.g. '45%' or a fraction '0.45' The fraction of CG bases for nucleotide alphabets * a species name, e.g. 'E. coli', 'H. sapiens', Use the average CG percentage for the species's genome. * An explicit distribution e.g. {'A':10, 'C':40, 'G':40, 'T':10} returns a dict of {monomer: probability} pairs. """ if composition is None: return None comp = composition.strip() if comp.lower() == "none": return None if weight is None and alphabet is not None: weight = sqrt(float(len(alphabet))) if weight < 0: raise ValueError("Weight cannot be negative.") if comp.lower() == "equiprobable": prior: np.ndarray prior = weight * equiprobable_distribution(len(alphabet)) elif comp.lower() == "auto" or comp.lower() == "automatic": if alphabet == unambiguous_protein_alphabet: prior = weight * asarray(aa_composition, float64) else: prior = weight * equiprobable_distribution(len(alphabet)) elif comp in std_percentCG: prior = weight * base_distribution(std_percentCG[comp]) elif comp[-1] == "%": prior = weight * base_distribution(float(comp[:-1])) elif isfloat(comp): prior = weight * base_distribution(float(comp) * 100.0) elif composition[0] == "{" and composition[-1] == "}": explicit = composition[1:-1] explicit = ( explicit.replace(",", " ") .replace("'", " ") .replace('"', " ") .replace(":", " ") .split() ) if len(explicit) != len(alphabet) * 2: raise ValueError("Explicit prior does not match length of alphabet") prior = -ones(len(alphabet), float64) try: for r in range(len(explicit) // 2): letter = explicit[r * 2] index = alphabet.ord(letter) value = float(explicit[r * 2 + 1]) prior[index] = value except ValueError: raise ValueError("Cannot parse explicit composition") if any(prior == -1.0): raise ValueError( "Explicit prior does not match alphabet" ) # pragma: no cover prior /= sum(prior) prior *= weight else: raise ValueError("Unknown or malformed composition: %s" % composition) if len(prior) != len(alphabet): raise ValueError( "The sequence alphabet and composition are incompatible." ) # pragma: no cover return prior def base_distribution(percentCG: float) -> np.ndarray: A = (1.0 - (percentCG / 100.0)) / 2.0 C = (percentCG / 100.0) / 2.0 G = (percentCG / 100.0) / 2.0 T = (1.0 - (percentCG / 100)) / 2.0 return asarray((A, C, G, T), float64) def equiprobable_distribution(length: int) -> np.ndarray: return ones((length), float64) / length def _seq_formats() -> Dict[str, str]: """Return a dictionary mapping between the names of formats for the sequence data and the corresponding parsers. """ # Add position weight matrix formats to input parsers by hand fin_choices = dict(seq_io.format_names()) fin_choices["transfac"] = "transfac" del fin_choices["plain"] return fin_choices def _seq_names() -> List[str]: """Returns a list of the names of accepted sequence data formats.""" fin_names = [f.names[0] for f in seq_io.formats] # type: ignore fin_names.remove("plain") fin_names.append("transfac") return fin_names def read_seq_data( fin: Union[StringIO, TextIOWrapper, None], input_parser: Callable = seq_io.read, alphabet: Optional[Alphabet] = None, ignore_lower_case: bool = False, max_file_size: int = 0, ) -> SeqList: """Read sequence data from the input stream and return a seqs object. The environment variable WEBLOGO_MAX_FILE_SIZE overides the max_file_size argument. Used to limit the load on the WebLogo webserver. """ max_file_size = int(os.environ.get("WEBLOGO_MAX_FILE_SIZE", max_file_size)) # If max_file_size is set, or if fin==stdin (which is non-seekable), we # read the data and replace fin with a StringIO object. assert fin is not None if max_file_size > 0: data = fin.read(max_file_size) more_data = fin.read(2) if more_data != "": raise IOError("File exceeds maximum allowed size: %d bytes" % max_file_size) fin = StringIO(data) elif fin == sys.stdin: fin = StringIO(fin.read()) fin.seek(0) seqs = input_parser(fin) if seqs is None or len(seqs) == 0: raise ValueError("Please provide a multiple sequence alignment") if ignore_lower_case: # Case is significant. Do not count lower case letters. for i, s in enumerate(seqs): seqs[i] = s.mask() # Add alphabet to seqs. if alphabet: seqs.alphabet = Alphabet(str(alphabet)) else: seqs.alphabet = Alphabet.which(seqs) return seqs class LogoData: """The data needed to generate a sequence logo. Args: alphabet: The set of symbols to count. See also --sequence-type, --ignore-lower-case length: All sequences must be the same length, else WebLogo will return an error counts: An array of character counts entropy: The relative entropy of each column entropy_interval: entropy confidence interval """ def __init__( self, length: Optional[int] = None, alphabet: Optional[Alphabet] = None, counts: Optional[np.ndarray] = None, entropy: Optional[np.ndarray] = None, entropy_interval: Optional[np.ndarray] = None, weight: Optional[np.ndarray] = None, ) -> None: """Creates a new LogoData object""" self.length = length self.alphabet = alphabet self.counts = counts self.entropy = entropy self.entropy_interval = entropy_interval self.weight = weight @classmethod def from_counts( cls, alphabet: Optional[Alphabet], counts: np.ndarray, prior: Optional[np.ndarray] = None, ) -> "LogoData": """Build a LogoData object from counts.""" # Counts is a Motif object? # counts = counts.array seq_length, A = counts.shape if prior is not None: prior = array(prior, float64) if prior is None or sum(prior) == 0.0: R = log(A) ent = zeros(seq_length, float64) entropy_interval = None for i in range(0, seq_length): C = sum(counts[i]) # FIXME: fixup .moremath.entropy()? if C == 0: ent[i] = 0.0 else: ent[i] = R - entropy(counts[i]) else: ent = zeros(seq_length, float64) entropy_interval = zeros((seq_length, 2), float64) R = log(A) for i in range(0, seq_length): alpha = array(counts[i], float64) alpha += prior posterior = Dirichlet(alpha) ent[i] = posterior.mean_relative_entropy(prior / sum(prior)) ( entropy_interval[i][0], entropy_interval[i][1], ) = posterior.interval_relative_entropy(prior / sum(prior), 0.95) weight = array(np.sum(counts, axis=1), float) max_weight = max(weight) if max_weight == 0.0: raise ValueError("No counts.") weight /= max_weight return cls(seq_length, alphabet, counts, ent, entropy_interval, weight) @classmethod def from_seqs(cls, seqs: SeqList, prior: Optional[np.ndarray] = None) -> "LogoData": """Build a LogoData object from a SeqList, a list of sequences.""" # --- VALIDATE DATA --- # check that at least one sequence of length at least 1 long if len(seqs) == 0 or len(seqs[0]) == 0: raise ValueError("No sequence data found.") # Check sequence lengths seq_length = len(seqs[0]) for i, s in enumerate(seqs): # print(i, s, len(s)) # TODO: Redundant? Should be checked in SeqList? if seq_length != len(s): raise ArgumentError( "Sequence number %d differs in length from the previous sequences" % (i + 1), "sequences", ) # FIXME: Check seqs.alphabet? counts = seqs.profile() return cls.from_counts(seqs.alphabet, counts, prior) def __str__(self) -> str: out = StringIO() print("## LogoData", file=out) print("# First column is position number, counting from zero", file=out) print("# Subsequent columns are raw symbol counts", file=out) print("# Entropy is mean entropy measured in nats.", file=out) print("# Low and High are the 95% confidence limits.", file=out) print("# Weight is the fraction of non-gap symbols in the column.", file=out) print("#\t", file=out) # Show column names print("#", end="\t", file=out) # asserts checks that defaults that were initialized to None have been set assert self.alphabet is not None assert self.length is not None assert self.counts is not None assert self.entropy is not None for a in self.alphabet: print(a, end=" \t", file=out) print("Entropy\tLow\tHigh\tWeight", file=out) # Write the data table for i in range(self.length): print(i + 1, end=" \t", file=out) for c in self.counts[i]: print(c, end=" \t", file=out) print("%6.4f" % self.entropy[i], end=" \t", file=out) if self.entropy_interval is not None: print("%6.4f" % self.entropy_interval[i][0], end=" \t", file=out) print("%6.4f" % self.entropy_interval[i][1], end=" \t", file=out) else: print("\t", "\t", end="", file=out) if self.weight is not None: print("%6.4f" % self.weight[i], end="", file=out) print("", file=out) print("# End LogoData", file=out) return out.getvalue() def csv(self) -> str: """Return logodata as a csv formatted string""" out = StringIO() # asserts checks that defaults that were initialized to None have been set assert self.alphabet is not None assert self.length is not None assert self.counts is not None assert self.entropy is not None # Show column names print("Position", end=",", file=out) for a in self.alphabet: print(a, end=",", file=out) print("Entropy,Low,High,Weight", file=out) # Write the data table for i in range(self.length): print(i + 1, end=",", file=out) for c in self.counts[i]: print(c, end=",", file=out) print("%6.4f" % self.entropy[i], end=",", file=out) if self.entropy_interval is not None: print("%6.4f" % self.entropy_interval[i][0], end=",", file=out) print("%6.4f" % self.entropy_interval[i][1], end=",", file=out) else: print(",", ",", end="", file=out) if self.weight is not None: print("%6.4f" % self.weight[i], end="", file=out) print("", file=out) return out.getvalue() def _from_URL_fileopen(target_url: str) -> StringIO: # pragma: no cover """opens files from a remote URL location""" # parsing url in component parts (scheme, net_location, path, param, query, frag) = urlparse(target_url) # checks if string is URL link if scheme != "http" and scheme != "https" and scheme != "ftp": raise ValueError("Cannot open url: %s", target_url) # checks for dropbox link if net_location == "www.dropbox.com": # changes dropbox http link into download link if query == "dl=0": query2 = "dl=1" # rebuild download URL, with new query2 variable target_url = urlunparse((scheme, net_location, path, param, query2, "")) # checks for google drive link if net_location == "drive.google.com": # link configuration for direct download instead of html frame google_directdl_frag = "https://docs.google.com/uc?export=download&id=" # pull file id (scheme, net_location, path_raw, param, query, frag) = urlparse(target_url) id_file = path_raw.split("/")[3] # rebuild URL for direct download target_url = google_directdl_frag + id_file # save url to temporary file req = Request(target_url) res = urlopen(req) return StringIO(str(res.read())) weblogo-3.8.0/weblogo/logo_formatter.py000066400000000000000000000315701467613320200202250ustar00rootroot00000000000000""" Logo formatting. Each formatter is a function f(data, format) that draws a representation of the logo. The main graphical formatter is eps_formatter. A mapping 'formatters' containing all available formatters . Each formatter returns binary data. The eps and data formats can decoded to strings, e.g. eps_as_string = eps_data.decode() """ import os import shutil from math import log from string import Template from subprocess import PIPE, Popen from typing import Optional from .color import Color from .logo import LogoData, LogoFormat from .utils import resource_string __all__ = [ "pdf_formatter", "jpeg_formatter", "svg_formatter", "png_print_formatter", "txt_formatter", "eps_formatter", "formatters", "default_formatter", "GhostscriptAPI", ] std_units = { "bits": 1.0 / log(2), "nats": 1.0, "digits": 1.0 / log(10), "kT": 1.0, "kJ/mol": 8.314472 * 298.15 / 1000.0, "kcal/mol": 1.987 * 298.15 / 1000.0, "probability": None, } """Some text""" def pdf_formatter(logodata: LogoData, logoformat: LogoFormat) -> bytes: """Generate a logo in PDF format.""" eps = eps_formatter(logodata, logoformat).decode() gs = GhostscriptAPI() assert logoformat.logo_height is not None assert logoformat.logo_width is not None return gs.convert("pdf", eps, logoformat.logo_width, logoformat.logo_height) def _bitmap_formatter(logodata: LogoData, logoformat: LogoFormat, device: str) -> bytes: eps = eps_formatter(logodata, logoformat).decode() gs = GhostscriptAPI() return gs.convert( device, eps, logoformat.logo_width, logoformat.logo_height, logoformat.resolution, ) def jpeg_formatter(logodata: LogoData, logoformat: LogoFormat) -> bytes: """Generate a logo in JPEG format.""" return _bitmap_formatter(logodata, logoformat, device="jpeg") def svg_formatter(logodata: LogoData, logoformat: LogoFormat) -> bytes: """Generate a logo in Scalable Vector Graphics (SVG) format. Requires the program 'pdf2svg' be installed. """ pdf = pdf_formatter(logodata, logoformat) command = shutil.which("pdf2svg") if command is None: raise EnvironmentError( "Scalable Vector Graphics (SVG) format requires the program" "'pdf2svg'." ) # pragma: no cover import tempfile fpdfi, fname_pdf = tempfile.mkstemp(suffix=".pdf") fsvgi, fname_svg = tempfile.mkstemp(suffix=".svg") try: fpdf2 = open(fname_pdf, "w") fpdf2.buffer.write(pdf) fpdf2.seek(0) args = [command, fname_pdf, fname_svg] p = Popen(args) (out, err) = p.communicate() fsvg = open(fname_svg) return fsvg.read().encode() finally: os.remove(fname_svg) os.remove(fname_pdf) # def png_formatter(logodata: LogoData, logoformat: LogoFormat) -> bytes: # """Generate a logo in PNG format.""" # return _bitmap_formatter(logodata, logoformat, device="png") def png_print_formatter(logodata: LogoData, logoformat: LogoFormat) -> bytes: """Generate a logo in PNG format with print quality (600 DPI) resolution.""" logoformat.resolution = 600 return _bitmap_formatter(logodata, logoformat, device="png") def txt_formatter(logodata: LogoData, logoformat: LogoFormat) -> bytes: """Create a text representation of the logo data.""" return str(logodata).encode() def csv_formatter(logodata: LogoData, logoformat: LogoFormat) -> bytes: """Create a csv representation of the logo data.""" return logodata.csv().encode() def eps_formatter(logodata: LogoData, logoformat: LogoFormat) -> bytes: """Generate a logo in Encapsulated Postscript (EPS)""" substitutions = {} from_format = [ "creation_date", "logo_width", "logo_height", "lines_per_logo", "line_width", "line_height", "line_margin_right", "line_margin_left", "line_margin_bottom", "line_margin_top", "title_height", "xaxis_label_height", "creator_text", "logo_title", "logo_margin", "stroke_width", "tic_length", "stacks_per_line", "stack_margin", "yaxis_label", "yaxis_tic_interval", "yaxis_minor_tic_interval", "xaxis_label", "xaxis_tic_interval", "number_interval", "fineprint", "shrink_fraction", "errorbar_fraction", "errorbar_width_fraction", "errorbar_gray", "small_fontsize", "fontsize", "title_fontsize", "number_fontsize", "text_font", "logo_font", "title_font", "logo_label", "yaxis_scale", "end_type", "debug", "show_title", "show_xaxis", "show_xaxis_label", "show_yaxis", "show_yaxis_label", "show_boxes", "show_errorbars", "show_fineprint", "rotate_numbers", "show_ends", "stack_height", "stack_width", ] for sf in from_format: substitutions[sf] = getattr(logoformat, sf) substitutions["shrink"] = str(logoformat.show_boxes).lower() def format_color(color: Color) -> str: # (no fold) return " ".join(("[", str(color.red), str(color.green), str(color.blue), "]")) substitutions["default_color"] = format_color(logoformat.default_color) data = [] # Unit conversion. 'None' for probability units conv_factor = std_units[logoformat.unit_name] data.append("StartLine") # assert checks for logoformat attributes that are intialized to None assert logoformat.logo_start is not None assert logoformat.first_index is not None assert logoformat.logo_end is not None seq_from = logoformat.logo_start - logoformat.first_index seq_to = logoformat.logo_end - logoformat.first_index + 1 # seq_index : zero based index into sequence data # logo_index : User visible coordinate, first_index based # stack_index : zero based index of visible stacks for seq_index in range(seq_from, seq_to): # logo_index = seq_index + logoformat.first_index stack_index = seq_index - seq_from if stack_index != 0 and (stack_index % logoformat.stacks_per_line) == 0: data.append("") data.append("EndLine") data.append("StartLine") data.append("") data.append("(%s) StartStack" % logoformat.annotate[seq_index]) if conv_factor: assert logodata.entropy is not None assert logoformat.unit_name is not None stack_height = logodata.entropy[seq_index] * std_units[logoformat.unit_name] else: stack_height = 1.0 # probability # pragma: no cover # Sort by frequency. If equal frequency then reverse alphabetic # (So sort reverse alphabetic first, then frequency) # TODO: doublecheck this actual works assert logodata.alphabet is not None assert logodata.counts is not None s = list(zip(logodata.counts[seq_index], logodata.alphabet)) s.sort(key=lambda x: x[1]) s.reverse() s.sort(key=lambda x: x[0]) if not logoformat.reverse_stacks: s.reverse() # pragma: no cover C = float(sum(logodata.counts[seq_index])) if C > 0.0: fraction_width = 1.0 assert logoformat.scale_width is not None if logoformat.scale_width: assert logodata.weight is not None fraction_width = float(logodata.weight[seq_index]) for rank, c in enumerate(s): assert logoformat.color_scheme is not None color = logoformat.color_scheme.symbol_color(seq_index, c[1], rank) data.append( " %f %f %s (%s) ShowSymbol" % ( fraction_width, c[0] * stack_height / C, format_color(color), c[1], ) ) # Draw error bar on top of logo. Replaced by DrawErrorbarFirst above. if logodata.entropy_interval is not None and conv_factor and C > 0.0: low, high = logodata.entropy_interval[seq_index] assert logodata.entropy is not None center = logodata.entropy[seq_index] low *= conv_factor high *= conv_factor center *= conv_factor if high > logoformat.yaxis_scale: high = logoformat.yaxis_scale # pragma: no cover down = center - low up = high - center data.append(" %f %f DrawErrorbar" % (down, up)) data.append("EndStack") data.append("") data.append("EndLine") substitutions["logo_data"] = "\n".join(data) # Create and output logo template = resource_string(__name__, "template.eps", __file__).decode() logo = Template(template).substitute(substitutions) return logo.encode() formatters = { "eps": eps_formatter, "pdf": pdf_formatter, "png": png_print_formatter, "png_print": png_print_formatter, "jpeg": jpeg_formatter, "svg": svg_formatter, "logodata": txt_formatter, "csv": csv_formatter, } """Map between output format names and corresponding logo formatter""" default_formatter = eps_formatter """The default logo formatter.""" class GhostscriptAPI: """Interface to the command line program Ghostscript ('gs')""" formats = ("png", "pdf", "jpeg") def __init__(self, path: Optional[os.PathLike] = None) -> None: """ Raises: EnvironmentError: If cannot find Ghostscript executable on path """ command = shutil.which("gs", path=path) if command is None: command = shutil.which("gswin64c.exe", path=path) # pragma: no cover if command is None: command = shutil.which("gswin32c.exe", path=path) # pragma: no cover if command is None: raise EnvironmentError( "Could not find Ghostscript on path. " "There should be either a gs executable or a gswin32c.exe on " "your system's path" ) # pragma: no cover self.command = command def version(self) -> bytes: """Returns: The ghostscript version string""" args = [self.command, "--version"] try: p = Popen(args, stdout=PIPE) (out, err) = p.communicate() except OSError: # pragma: no cover raise RuntimeError( "Cannot communicate with ghostscript." ) # pragma: no cover return out.strip() def convert( self, format: str, postscript: str, width: Optional[int], height: Optional[int], resolution: int = 300, ) -> bytes: """Convert a string of postscript into a different graphical format Supported formats are 'png', 'pdf', and 'jpeg'. Raises: ValueError: For an unrecognized format. """ device_map = {"png": "png16m", "pdf": "pdfwrite", "jpeg": "jpeg"} try: device = device_map[format] except KeyError: # pragma: no cover raise ValueError("Unsupported format.") args = [ self.command, "-sDEVICE=%s" % device, "-dPDFSETTINGS=/printer", # "-q", # Quite: Do not dump messages to stdout. "-sstdout=%stderr", # Redirect messages and errors to stderr # fix issue 36, problems with ghostscript 9.10 "-dColorConversionStrategy=/LeaveColorUnchanged", "-sOutputFile=-", # Stdout "-dDEVICEWIDTHPOINTS=%s" % str(width), "-dDEVICEHEIGHTPOINTS=%s" % str(height), "-dSAFER", # For added security "-dNOPAUSE", ] if device != "pdf": args.append("-r%s" % str(resolution)) assert resolution is not None if resolution < 300: # Antialias if resolution is Less than 300 DPI args.append("-dGraphicsAlphaBits=4") args.append("-dTextAlphaBits=4") args.append("-dAlignToPixels=0") args.append("-") # Read from stdin. Must be last argument. error_msg = ( "Unrecoverable error : Ghostscript conversion failed " "(Invalid postscript?). %s" % " ".join(args) ) try: p = Popen(args, stdin=PIPE, stdout=PIPE, stderr=PIPE) (out, err) = p.communicate(postscript.encode()) except OSError: # pragma: no cover raise RuntimeError(error_msg) # pragma: no cover if p.returncode != 0: # pragma: no cover error_msg += "\nReturn code: %i\n" % p.returncode if err is not None: error_msg += str(err) raise RuntimeError(error_msg) return out # end class Ghostscript weblogo-3.8.0/weblogo/logomath.py000077500000000000000000000235321467613320200170160ustar00rootroot00000000000000# -------------------------------- WebLogo -------------------------------- # Copyright (c) 2003-2004 The Regents of the University of California. # Copyright (c) 2005 Gavin E. Crooks # Copyright (c) 2006-2011, The Regents of the University of California, through # Lawrence Berkeley National Laboratory (subject to receipt of any required # approvals from the U.S. Dept. of Energy). All rights reserved. # This software is distributed under the new BSD Open Source License. # # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions are met: # # (1) Redistributions of source code must retain the above copyright notice, # this list of conditions and the following disclaimer. # # (2) Redistributions in binary form must reproduce the above copyright # notice, this list of conditions and the following disclaimer in the # documentation and or other materials provided with the distribution. # # (3) Neither the name of the University of California, Lawrence Berkeley # National Laboratory, U.S. Dept. of Energy nor the names of its contributors # may be used to endorse or promote products derived from this software # without specific prior written permission. # # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" # AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE # IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE # ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE # LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR # CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF # SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS # INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN # CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE # POSSIBILITY OF SUCH DAMAGE. import random from math import exp, log, sqrt from typing import Tuple import numpy as np import scipy.optimize from numpy import asarray, float64, shape, zeros from numpy.typing import ArrayLike # pragma: no cover from scipy.special import digamma, gamma, gammaincc, polygamma class Dirichlet(object): """The Dirichlet probability distribution. The Dirichlet is a continuous multivariate probability distribution across non-negative unit length vectors. In other words, the Dirichlet is a probability distribution of probability distributions. It is conjugate to the multinomial distribution and is widely used in Bayesian statistics. The Dirichlet probability distribution of order K-1 is p(theta_1,...,theta_K) d theta_1 ... d theta_K = (1/Z) prod_i=1,K theta_i^{alpha_i - 1} delta(1 -sum_i=1,K theta_i) The normalization factor Z can be expressed in terms of gamma functions: Z = {prod_i=1,K Gamma(alpha_i)} / {Gamma( sum_i=1,K alpha_i)} The K constants, alpha_1,...,alpha_K, must be positive. The K parameters, theta_1,...,theta_K are nonnegative and sum to 1. Status: Alpha """ __slots__ = ( "alpha", "_total", "_mean", ) def __init__(self, alpha: "ArrayLike") -> None: """ Args: - alpha -- The parameters of the Dirichlet prior distribution. A vector of non-negative real numbers. """ # TODO: Check that alphas are positive # TODO: what if alpha's not one dimensional? self.alpha = asarray(alpha, float64) self._total = sum(alpha) self._mean: np.ndarray = self.alpha / self._total def sample(self) -> np.ndarray: """Return a randomly generated probability vector. Random samples are generated by sampling K values from gamma distributions with parameters a=\alpha_i, b=1, and renormalizing. Ref: A.M. Law, W.D. Kelton, Simulation Modeling and Analysis (1991). Authors: Gavin E. Crooks (2002) """ alpha = self.alpha K = len(alpha) theta = zeros((K,), float64) for k in range(K): theta[k] = random.gammavariate(alpha[k], 1.0) theta /= sum(theta) return theta def mean(self) -> np.ndarray: return self._mean def covariance(self) -> np.ndarray: alpha = self.alpha A = sum(alpha) # A2 = A * A K = len(alpha) cv = zeros((K, K), float64) for i in range(K): cv[i, i] = alpha[i] * (1.0 - alpha[i] / A) / (A * (A + 1.0)) for i in range(K): for j in range(i + 1, K): v = -alpha[i] * alpha[j] / (A * A * (A + 1.0)) cv[i, j] = v cv[j, i] = v return cv def mean_x(self, x: "ArrayLike") -> float: x = asarray(x, float64) if shape(x) != shape(self.alpha): raise ValueError("Argument must be same dimension as Dirichlet") return sum(x * self.mean()) def variance_x(self, x: "ArrayLike") -> float: x = asarray(x, float64) if shape(x) != shape(self.alpha): raise ValueError("Argument must be same dimension as Dirichlet") cv = self.covariance() var = np.dot(np.dot(np.transpose(x), cv), x) return var def mean_entropy(self) -> float: """Calculate the average entropy of probabilities sampled from this Dirichlet distribution. Returns: The average entropy. Ref: Wolpert & Wolf, PRE 53:6841-6854 (1996) Theorem 7 (Warning: this paper contains typos.) Status: Alpha Authors: GEC 2005 """ # TODO: Optimize alpha = self.alpha A = float(sum(alpha)) ent = 0.0 for a in alpha: if a > 0: ent += -1.0 * a * digamma(1.0 + a) # FIXME: Check ent /= A ent += digamma(A + 1.0) return ent def variance_entropy(self) -> float: """Calculate the variance of the Dirichlet entropy. Ref: Wolpert & Wolf, PRE 53:6841-6854 (1996) Theorem 8 (Warning: this paper contains typos.) """ alpha = self.alpha A = float(sum(alpha)) A2 = A * (A + 1) L = len(alpha) dg1 = zeros((L), float64) dg2 = zeros((L), float64) tg2 = zeros((L), float64) for i in range(L): dg1[i] = digamma(alpha[i] + 1.0) dg2[i] = digamma(alpha[i] + 2.0) tg2[i] = polygamma(1, alpha[i] + 2.0) dg_Ap2 = digamma(A + 2.0) tg_Ap2 = polygamma(1, A + 2.0) mean = self.mean_entropy() var = 0.0 for i in range(L): for j in range(L): if i != j: var += ( ((dg1[i] - dg_Ap2) * (dg1[j] - dg_Ap2) - tg_Ap2) * (alpha[i] * alpha[j]) / A2 ) else: var += ( ((dg2[i] - dg_Ap2) ** 2 + (tg2[i] - tg_Ap2)) * (alpha[i] * (alpha[i] + 1.0)) / A2 ) var -= mean**2 return var def mean_relative_entropy(self, pvec: "ArrayLike") -> float: pvec = asarray(pvec) ln_p = np.log(pvec) return -self.mean_x(ln_p) - self.mean_entropy() def variance_relative_entropy(self, pvec: "ArrayLike") -> float: pvec = asarray(pvec) ln_p = np.log(pvec) return self.variance_x(ln_p) + self.variance_entropy() def interval_relative_entropy( self, pvec: "ArrayLike", frac: float ) -> Tuple[float, float]: pvec = asarray(pvec) mean = self.mean_relative_entropy(pvec) variance = self.variance_relative_entropy(pvec) sd = sqrt(variance) # If the variance is small, use the standard 95% # confidence interval: mean +/- 1.96 * sd if mean / sd > 3.0: return max(0.0, mean - sd * 1.96), mean + sd * 1.96 g = Gamma.from_mean_variance(mean, variance) low_limit = g.inverse_cdf((1.0 - frac) / 2.0) high_limit = g.inverse_cdf(1.0 - (1.0 - frac) / 2.0) return low_limit, high_limit class Gamma(object): """The gamma probability distribution. (Not to be confused with the gamma function.) """ __slots__ = "alpha", "beta" def __init__(self, alpha: float, beta: float) -> None: if alpha <= 0.0: raise ValueError("alpha must be positive") if beta <= 0.0: raise ValueError("beta must be positive") self.alpha = alpha self.beta = beta @classmethod def from_shape_scale(cls, shape: float, scale: float) -> "Gamma": return cls(shape, 1.0 / scale) @classmethod def from_mean_variance(cls, mean: float, variance: float) -> "Gamma": alpha = mean**2 / variance beta = alpha / mean return cls(alpha, beta) def mean(self) -> float: return self.alpha / self.beta def variance(self) -> float: return self.alpha / (self.beta**2) def sample(self) -> float: return random.gammavariate(self.alpha, 1.0 / self.beta) def pdf(self, x: float) -> float: if x == 0.0: return 0.0 a = self.alpha b = self.beta return (x ** (a - 1.0)) * exp(-b * x) * (b**a) / gamma(a) def cdf(self, x: float) -> float: return 1.0 - gammaincc(self.alpha, self.beta * x) def inverse_cdf(self, p: float) -> float: def rootof(x: float) -> float: return self.cdf(exp(x)) - p root = scipy.optimize.newton(rootof, log(self.mean())) return exp(root) weblogo-3.8.0/weblogo/matrix.py000077500000000000000000000365561467613320200165220ustar00rootroot00000000000000# Copyright (c) 2005 Gavin E. Crooks # Copyright (c) 2006 John Gilman # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING # FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS # IN THE SOFTWARE. """ Arrays indexed by alphabetic strings. """ from array import array from typing import Any, List, Optional, TextIO, Tuple, Union import numpy as np from numpy.typing import ArrayLike, DTypeLike from .seq import ( Alphabet, Seq, unambiguous_dna_alphabet, unambiguous_protein_alphabet, unambiguous_rna_alphabet, ) from .utils import ischar, isint __all__ = "AlphabeticArray", "Motif" class AlphabeticArray(object): """An alphabetic array. Wraps a numpy array so that each dimension can be associated with an alphabet and indexed with characters or strings. Attributes : - alphabets -- A sequence of alphabets used to index the array - array -- The underlying array object that is indexed. Examples : >>> from weblogo.seq import * >>> from weblogo.matrix import AlphabeticArray >>> >>> str(protein_alphabet) 'ACDEFGHIKLMNOPQRSTUVWYBJZX*-' >>> matrix = AlphabeticArray( (protein_alphabet, protein_alphabet) ) >>> >>> # Index by character or integer: >>> matrix['A', 'C'] = 10 >>> matrix[0,1] 10 >>> >>> # Different alphabets on each dimension: >>> import numpy as na >>> a234 = zeros( shape = (2,3,4) ) >>> alpha = ( "AB", "ABC", "ABCD") >>> aa = AlphabeticArray(alpha,a234) >>> aa['A', 'B', 'C'] = 22 >>> >>> # String indices are converted to integer index arrays: ... >>> aa['A', 'B', 'ABCD'] array([ 0, 0, 22, 0]) Authors: o GEC 2005, JXG 2006 """ # Design note: Subclassing numpy arrays is hard, so instead we # build this proxy wrapper. __slots__ = ["alphabets", "array"] def __init__( self, alphabets: Union[Alphabet, Tuple[Union[Alphabet, None], ...], str], values: Optional["ArrayLike"] = None, dtype: Optional["DTypeLike"] = None, ): """ Args: - alphabets -- a list of alphabets (as string or Alphabet objects) to be used to convert strings into indices. The lengths of the alphabets match the shape of the indexed array. Alternatively, an integer or None in the list indicate a non-alphabetic dimension. If None the dimension length is taken from values argument. - values -- An array of values to be indexed. If None a new array is created. If this argument is not a numpy array then the alphabet list must be explicit (cannot contain None.) - dtype -- An optional numpy type code. """ # A dummy object to be used in place of None in the alphabets list # so that we get meaningful error messages if we try to index a # nonalphabetic dimension with a string. class NullAlphabet(Alphabet): def ord(self, key: str) -> int: raise IndexError( "This dimension does not have an alphabet" ) # pragma: no cover def ords(self, string: Union["Seq", str]) -> array: raise IndexError( "This dimension does not have an alphabet" ) # pragma: no cover alpha: List[Union[Alphabet, None]] = [] shape: List[Union[int, None]] = [] for a in alphabets: if isinstance(a, str): a = Alphabet(a) if a is None: shape.append(None) alpha.append(NullAlphabet(letters="")) elif isinstance(a, Alphabet): shape.append(len(a)) alpha.append(a) else: shape.append(int(a)) # pragma: no cover alpha.append(None) # pragma: no cover # shape = tuple(shape) # CHECKME, line not needed? if values is None: values = np.zeros(shape=shape, dtype=dtype) else: values = np.asarray(values, dtype=dtype) vshape = values.shape if len(shape) != len(vshape): raise ValueError( "The values array is the wrong shape." ) # pragma: no cover for s1, s2 in zip(shape, vshape): if s1 is not None and s1 != s2: raise ValueError( "The values array is the wrong shape." ) # pragma: no cover self.array = values self.alphabets = tuple(alpha) def __getitem__(self, key: Any) -> Any: return self.array.__getitem__(self._ordkey(key)) def __setitem__(self, key: Any, value: Any) -> None: self.array.__setitem__(self._ordkey(key), value) def _ordkey(self, key: Any) -> Union[int, np.ndarray, slice, Tuple, Alphabet]: """Convert string indices into integers. Handles characters, strings slices with strings, and tuples of the same. Anything else is unchanged. """ def norm( key: Any, alpha: Alphabet ) -> Union[int, np.ndarray, slice, Tuple, Alphabet, None]: if key is None: return None elif isinstance(key, str) or isinstance(key, Alphabet): assert alpha is not None key = str(key) if len(key) == 1: return alpha.ord(key) if len(key) == 0: return None # pragma: no cover return np.asarray(alpha.ords(key)) elif isinstance(key, slice): start = norm(key.start, alpha) # pragma: no cover stop = norm(key.stop, alpha) # pragma: no cover step = key.step # pragma: no cover return slice(start, stop, step) # pragma: no cover else: return key if isinstance(key, tuple): return tuple([norm(k, a) for k, a in zip(key, self.alphabets)]) # type: ignore else: return norm(key, self.alphabets[0]) # type: ignore # FIXME def index(self, keys: Any) -> np.ndarray: """Return an array of shape (len(key1), len(key2), ...) whose values are indexed by keys. a.outerindex( (I,J,K) )[i,j,k] == a.array[I[i],J[j],K[k]] """ # TODO: Above docstring is not very clear. # Deep voodoo using numpy indexing keys = self._ordkey(keys) outerkeys = [] for i, k in enumerate(keys): if k is None: k = range(0, self.array.shape[i]) k = np.asarray(k) for j in range(len(keys) - i - 1): k = k[..., np.newaxis] outerkeys.append(k) return self.array.__getitem__(tuple(outerkeys)) def reindex(self, new_alphabet: Alphabet) -> "AlphabeticArray": """Create a new AlphabeticArray with the given alphabet. The new alphabet must be a subset of the current alphabet. Useful for extracting a submatrix or for permuting the alphabet. """ new_array = self.index(new_alphabet) return AlphabeticArray(new_alphabet, new_array) # The following code is designed to proxy all attributes # of the wrapped array. But I'm not entirely sure that this will work as # intended. def __getattr__(self, name: str) -> str: try: return self.array.__getattr__(self, name) except AttributeError: return getattr(self.array, name) def __setattr__(self, name: str, value: str) -> None: try: return object.__setattr__(self, name, value) except AttributeError: # pragma: no cover return setattr(self.array, name, value) # pragma: no cover # End class AlphabeticArray class Motif(AlphabeticArray): """A two dimensional array where the second dimension is indexed by an Alphabet. Used to represent sequence motifs and similar information. Attr: - alphabet -- An Alphabet - array -- A numpy array - name -- The name of this motif (if any) as a string. - description -- The description, if any. """ _TRANSFAC_DELIM_LINES = ["XX", "//"] def __init__( self, alphabet: Alphabet, array: Optional["ArrayLike"] = None, dtype: Optional["DTypeLike"] = None, name: Optional[str] = None, description: Optional[str] = None, scale: Optional[float] = None, ): AlphabeticArray.__init__(self, (None, alphabet), array, dtype) self.name = name self.description = description self.scale = scale @property def alphabet(self) -> Alphabet: assert self.alphabets[1] is not None return self.alphabets[1] def reindex(self, alphabet: Union[Alphabet, Tuple[Alphabet, ...], str]) -> "Motif": return Motif(alphabet, AlphabeticArray.reindex(self, (None, alphabet))) # type: ignore # These methods alter self, and therefore do not return a value. # (Compare to Seq objects, where the data is immutable and # therefore methods return a new Seq.) # TODO: Should reindex (above) also act on self? # Deprecate? def reverse(self) -> None: """Reverse sequence data""" self.array = self.array[::-1] # view into the original numpy array # Deprecate? def complement(self) -> None: """Complement nucleic acid sequence.""" from weblogo.seq import Alphabet, Seq alphabet = self.alphabet complement_alphabet = Alphabet(Seq(str(alphabet), alphabet).complement()) self.alphabets = (None, complement_alphabet) assert alphabet is not None m = self.reindex(alphabet) self.alphabets = (None, alphabet) self.array = m.array # Deprecate? def reverse_complement(self) -> None: """Complements and reverses nucleic acid sequence (i.e. the other strand of a DNA sequence.) """ self.reverse() self.complement() @classmethod def read_transfac( cls, fin: TextIO, alphabet: Optional[Union[Alphabet, str]] = None ) -> "Motif": """Parse a TRANSFAC-format PWM from a file. Returns a Motif object, representing the provided PWM along with an inferred or provided alphabet. """ items = [] start = False for line in fin: if line.isspace() or line[0] == "#": continue # pragma: no cover stuff = line.split() if stuff[0] == "PO" or stuff[0] == "P0": start = True # 'XX' delimiters may precede the first motif if start: if stuff[0] in cls._TRANSFAC_DELIM_LINES: break else: items.append(stuff) if len(items) < 2: raise ValueError("Vacuous file.") # Is the first line a header line? header = items.pop(0) hcols = len(header) rows = len(items) cols = len(items[0]) if not ( header[0] == "PO" or header[0] == "P0" or hcols == cols - 1 or hcols == cols - 2 ): raise ValueError("Missing header line!") # pragma: no cover # Do all lines (except the first) contain the same number of items? cols = len(items[0]) for i in range(1, len(items)): if cols != len(items[i]): raise ValueError( "Inconsistant length, row: {}".format(i) ) # pragma: no cover # Vertical or horizontal arrangement? if header[0] == "PO" or header[0] == "P0": header.pop(0) position_header = True for h in header: if not ischar(h): raise ValueError( "Expected a single character per header " 'item, but got "{}" as one item'.format(h) ) # pragma: no cover if not isint(h): position_header = False alphabet_header = False if position_header else True # Check row headers if alphabet_header: for i, r in enumerate(items): if not isint(r[0]) and r[0][0] != "P": raise ValueError( "Expected position " "as first item on line {}".format(i) ) # pragma: no cover r.pop(0) defacto_alphabet_str = "".join(header) else: a = [] # pragma: no cover for i, r in enumerate(items): # pragma: no cover if not ischar(r[0]) and r[0][0] != "P": # pragma: no cover raise ValueError( "Expected position " # pragma: no cover "as first item on line {}".format(i) ) # pragma: no cover a.append(r.pop(0)) # pragma: no cover defacto_alphabet_str = "".join(a) # pragma: no cover # Check defacto_alphabet defacto_alphabet = Alphabet(defacto_alphabet_str) if alphabet: alphabet = Alphabet(str(alphabet)) if not defacto_alphabet.alphabetic(str(alphabet)): # Allow alphabet to be a superset of defacto_alphabet alphabet = defacto_alphabet else: alphabets = ( unambiguous_rna_alphabet, unambiguous_dna_alphabet, unambiguous_protein_alphabet, ) for aa in alphabets: if defacto_alphabet.alphabetic(str(aa)): alphabet = aa break if not alphabet: alphabet = defacto_alphabet # pragma: no cover # The last item of each row may be extra cruft. Remove if len(items[0]) == len(header) + 1: for r in items: r.pop() # items should now be a list of lists of numbers (as strings) rows = len(items) cols = len(items[0]) matrix = np.zeros((rows, cols), dtype=np.float64) for rr in range(rows): for cc in range(cols): matrix[rr, cc] = float(items[rr][cc]) if position_header: matrix.transpose() # pragma: no cover return Motif(defacto_alphabet, matrix).reindex(alphabet) weblogo-3.8.0/weblogo/seq.py000077500000000000000000000604651467613320200160020ustar00rootroot00000000000000# Copyright (c) 2005 Gavin E. Crooks # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # """ Alphabetic sequences and associated tools and data. Seq is a subclass of a python string with additional annotation and an alphabet. The characters in string must be contained in the alphabet. Various standard alphabets are provided. Classes :: Alphabet -- A subset of non-null ascii characters Seq -- An alphabetic string SeqList -- A collection of Seq's Alphabets :: o generic_alphabet -- A generic alphabet. Any printable ASCII character. o protein_alphabet -- IUCAP/IUB Amino Acid one letter codes. o nucleic_alphabet -- IUPAC/IUB Nucleic Acid codes 'ACGTURYSWKMBDHVN-' o dna_alphabet -- Same as nucleic_alphabet, with 'U' (Uracil) an alternative for 'T' (Thymidine). o rna_alphabet -- Same as nucleic_alphabet, with 'T' (Thymidine) an alternative for 'U' (Uracil). o reduced_nucleic_alphabet -- All ambiguous codes in 'nucleic_alphabet' are alternative to 'N' (aNy) o reduced_protein_alphabet -- All ambiguous ('BZJ') and non-canonical amino acids codes ( 'U', Selenocysteine and 'O', Pyrrolysine) in 'protein_alphabet' are alternative to 'X'. o unambiguous_dna_alphabet -- 'ACGT' o unambiguous_rna_alphabet -- 'ACGU' o unambiguous_protein_alphabet -- The twenty canonical amino acid one letter codes, in alphabetic order, 'ACDEFGHIKLMNPQRSTVWY' Amino Acid Codes:: Code Alt. Meaning ----------------- A Alanine B Aspartic acid or Asparagine C Cysteine D Aspartate E Glutamate F Phenylalanine G Glycine H Histidine I Isoleucine J Leucine or Isoleucine K Lysine L Leucine M Methionine N Asparagine O Pyrrolysine P Proline Q Glutamine R Arginine S Serine T Threonine U Selenocysteine V Valine W Tryptophan Y Tyrosine Z Glutamate or Glutamine X ? any * translation stop - .~ gap Nucleotide Codes:: Code Alt. Meaning ------------------------------ A Adenosine C Cytidine G Guanine T Thymidine U Uracil R G A (puRine) Y T C (pYrimidine) K G T (Ketone) M A C (aMino group) S G C (Strong interaction) W A T (Weak interaction) B G T C (not A) (B comes after A) D G A T (not C) (D comes after C) H A C T (not G) (H comes after G) V G C A (not T, not U) (V comes after U) N X? A G C T (aNy) - .~ A gap Refs: http://www.chem.qmw.ac.uk/iupac/AminoAcid/A2021.html http://www.chem.qmw.ac.uk/iubmb/misc/naseq.html Authors: GEC 2004,2005 """ # TODO: Add this to docstring somewhere. # To replace all ambiguous nucleic code by 'N', replace alphabet and then n # normalize. # # >>> Seq( 'ACGT-RYKM', reduced_nucleic_alphabet).normalized() # 'ACGT-NNNN' import codecs from array import array from typing import Any, Generator, Iterator, List, Optional, Sequence, Tuple, Union __all__ = [ "Alphabet", "Seq", "rna", "dna", "protein", "SeqList", "generic_alphabet", "protein_alphabet", "nucleic_alphabet", "dna_alphabet", "rna_alphabet", "reduced_nucleic_alphabet", "reduced_protein_alphabet", "unambiguous_dna_alphabet", "unambiguous_dna_alphabet", "unambiguous_rna_alphabet", "unambiguous_protein_alphabet", "generic_alphabet", ] class Alphabet(object): """An ordered subset of printable ascii characters. Status: Beta Authors: - GEC 2005 """ _letters: str _alternatives: Tuple[str, str] _ord_table: bytes _chr_table: str __slots__ = ["_letters", "_alternatives", "_ord_table", "_chr_table"] # We're immutable, so use __new__ not __init__ def __new__( cls, letters: Optional[Union["Alphabet", str]] = None, alternatives: Optional[Tuple[Tuple[str, str], ...]] = None, ) -> "Alphabet": """Create a new, immutable Alphabet. e.g. Alphabet( 'ACDEFGHIKLMNPQRSTVUWY', zip('acdefghiklmnpqrstvuwy', 'ACDEFGHIKLMNPQRSTVUWY') ) arguments: - letters -- the letters in the alphabet. The ordering determines the ordinal position of each character in this alphabet. - alt -- A list of (alternative, canonical) letters. The alternatives are given the same ordinal position as the canonical characters. e.g. (('?','X'),('x', 'X')) states that '?' and 'x' are synonomous with 'X'. Values that are not in 'letters' are ignored. Alternatives that are already in 'letters' are also ignored. If the same alternative character is used twice then the alternative is assigned to the canonical character that occurs first in 'letters'. The default is to assume that upper and lower case characters are equivalent, unless both cases are included in 'letters'. raises: ValueError : Repetitive or otherwise illegal set of letters. """ self = object.__new__(cls) # Printable Ascii characters ascii_letters = "".join([chr(__i) for __i in range(32, 128)]) if letters is None: letters = ascii_letters else: letters = str(letters) self._letters = letters equivalent_by_case = zip( "abcdefghijklmnopqrstuvwxyz", "ABCDEFGHIJKLMNOPQRSTUVWXYZ" ) if alternatives is None: alternatives = tuple(equivalent_by_case) # The ord_table maps between the ordinal position of a character in ascii # and the ordinal position in this alphabet. Characters not in the # alphabet are given a position of 255. The ord_table is stored as a # string. ord_table = bytearray( [ 0xFF, ] * 256 ) for i, a in enumerate(letters): n = ord(a) if n == 0: raise ValueError("Alphabet cannot contain null character \\0") if ord_table[n] != 0xFF: raise ValueError("Repetitive alphabet") ord_table[n] = i # Add alternatives _from = [] _to = [] for e, c in alternatives: if c in letters: n = ord(e) if ord_table[n] == 0xFF: # empty ord_table[n] = ord_table[ord(c)] _from.append(e) _to.append(c) self._alternatives = ("".join(_from), "".join(_to)) assert ord_table[0] == 0xFF self._ord_table = ord_table # The chr_table maps between ordinal position in the alphabet letters # and the ordinal position in ascii. This map is not the inverse of # ord_table if there are alternatives. chr_table = bytearray( [ 0x00, ] * 256 ) for i, a in enumerate(letters): chr_table[i] = ord(a) self._chr_table = chr_table.decode() return self def alphabetic(self, string: str) -> bool: """True if all characters of the string are in this alphabet.""" table = self._ord_table for s in str(string): if table[ord(s)] == 0xFF: return False return True def chr(self, n: int) -> str: """The n'th character in the alphabet (zero indexed) or \\0""" return self._chr_table[n] def ord(self, c: str) -> int: """The ordinal position of the character c in this alphabet, or 255 if no such character. """ return self._ord_table[ord(c)] def chrs(self, sequence_of_ints: Sequence[int]) -> "Seq": """Convert a sequence of ordinals into an alphabetic string.""" c = [self.chr(n) for n in sequence_of_ints] s = "".join(c) return Seq(s, self) def ords(self, string: Union["Seq", str]) -> array: """Convert an alphabetic string into a byte array of ordinals.""" s = str(string) s = s.translate(self._ord_table) a = array("B", codecs.latin_1_encode(s)[0]) # type: ignore # TESTME FIXME? return a def normalize(self, string: str) -> "Seq": """Normalize an alphabetic string by converting all alternative symbols to the canonical equivalent in 'letters'. """ if not self.alphabetic(string): raise ValueError("Not an alphabetic string.") return self.chrs(self.ords(string)) def letters(self) -> str: """Letters of the alphabet as a string.""" return str(self) # def _all_letters(self): # """ All allowed letters, including alternatives.""" # let = [] # let.append(self._letters) # for key, value in self._alternatives: # let.append(value) # return ''.join(let) def __repr__(self) -> str: return ( "Alphabet( '" + self._letters + "', zip" + repr(self._alternatives) + " )" ) def __str__(self) -> str: return str(self._letters) def __len__(self) -> int: return len(self._letters) def __eq__(self, other: Any) -> bool: if not hasattr(other, "_ord_table"): return False return self._ord_table == other._ord_table def __ne__(self, other: Any) -> bool: return not self.__eq__(other) def __iter__(self) -> Iterator[str]: return iter(self._letters) # def __getitem__(self, key: Any) -> str: # return self._letters[key] def __hash__(self) -> int: return hash(tuple(self._ord_table)) @staticmethod def which( seqs: Union["Seq", "SeqList"], alphabets: Optional[List["Alphabet"]] = None ) -> "Alphabet": """Returns the most appropriate unambiguous protein, RNA or DNA alphabet for a Seq or SeqList. If a list of alphabets is supplied, then the best alphabet is selected from that list. The heuristic is to count the occurrences of letters for each alphabet and downweight longer alphabets by the log of the alphabet length. Ties go to the first alphabet in the list. """ if alphabets is None: alphabets = [ unambiguous_dna_alphabet, unambiguous_rna_alphabet, unambiguous_protein_alphabet, ] import math score = [sum(seqs.tally(a)) / math.log(len(a)) for a in alphabets] best = score.index(max(score)) a = alphabets[best] return a # End class Alphabet # ------------------- Standard ALPHABETS ------------------- # Standard alphabets are defined here, after Alphabet class. generic_alphabet = Alphabet(None, None) protein_alphabet = Alphabet( "ACDEFGHIKLMNOPQRSTUVWYBJZX*-", tuple(zip("acdefghiklmnopqrstuvwybjzx?.~", "ACDEFGHIKLMNOPQRSTUVWYBJZXX--")), ) nucleic_alphabet = Alphabet( "ACGTURYSWKMBDHVN-", tuple(zip("acgturyswkmbdhvnXx?.~", "ACGTURYSWKMBDHVNNNN--")) ) dna_alphabet = Alphabet( "ACGTRYSWKMBDHVN-", tuple(zip("acgtryswkmbdhvnXx?.~Uu", "ACGTRYSWKMBDHVNNNN--TT")) ) rna_alphabet = Alphabet( "ACGURYSWKMBDHVN-", tuple(zip("acguryswkmbdhvnXx?.~Tt", "ACGURYSWKMBDHVNNNN--UU")) ) reduced_nucleic_alphabet = Alphabet( "ACGTN-", tuple(zip("acgtryswkmbdhvnXx?.~TtRYSWKMBDHV", "ACGTNNNNNNNNNNNNNN--TTNNNNNNNNNN")), ) reduced_protein_alphabet = Alphabet( "ACDEFGHIKLMNPQRSTVWYX*-", tuple(zip("acdefghiklmnpqrstvwyx?.~BbZzUu", "ACDEFGHIKLMNPQRSTVWYXX--XXXXCC")), ) unambiguous_dna_alphabet = Alphabet("ACGT", tuple(zip("acgt", "ACGT"))) unambiguous_rna_alphabet = Alphabet("ACGU", tuple(zip("acgu", "ACGU"))) unambiguous_protein_alphabet = Alphabet( "ACDEFGHIKLMNPQRSTVWY", tuple(zip("acdefghiklmnopqrstuvwy", "ACDEFGHIKLMNOPQRSTUVWY")), ) _complement_table = str.maketrans( "ACGTRYSWKMBDHVN-acgtUuryswkmbdhvnXx?.~", "TGCAYRSWMKVHDBN-tgcaAayrswmkvhdbnXx?.~" ) class Seq(str): """An alphabetic string. A subclass of "str" consisting solely of letters from the same alphabet. Attributes: alphabet -- A string or Alphabet of allowed characters. name -- A short string used to identify the sequence. description -- A string describing the sequence Authors : GEC 2005 """ # TODO: need a method to return a copy of the string with a new alphabet, # preserving the sequence, name and alphabet? name: str description: str _alphabet: Alphabet def __new__( cls, obj: str, alphabet: Optional[Alphabet] = generic_alphabet, name: Optional[str] = None, description: Optional[str] = None, ) -> "Seq": self = str.__new__(cls, obj) if alphabet is None: alphabet = generic_alphabet if name is None: name = "" if description is None: description = "" if not isinstance(alphabet, Alphabet): alphabet = Alphabet(alphabet) if not alphabet.alphabetic(self): raise ValueError("Sequence not alphabetic %s, '%s'" % (alphabet, self)) self._alphabet = alphabet self.name = name self.description = description return self # BEGIN PROPERTIES # Make alphabet constant @property def alphabet(self) -> Alphabet: return self._alphabet # END PROPERTIES def ords(self) -> array: """Convert sequence to an array of integers in the range [0, len(alphabet) ) """ return self.alphabet.ords(self) def tally(self, alphabet: Optional[Alphabet] = None) -> List[int]: """Counts the occurrences of alphabetic characters. Arguments: - alphabet -- an optional alternative alphabet Returns : A list of character counts in alphabetic order. """ # Renamed from count() since this conflicts with str.count(). if not alphabet: alphabet = self.alphabet L = len(alphabet) counts = [ 0, ] * L ords = alphabet.ords(self) for n in ords: if n < L: counts[n] += 1 return counts def __getitem__(self, key: Any) -> "Seq": cls = self.__class__ return cls(str.__getitem__(self, key), self.alphabet) def __add__(self, other: Any) -> "Seq": # called for "self + other" cls = self.__class__ return cls(str.__add__(self, other), self.alphabet) def __radd__(self, other: Any) -> "Seq": # Called when "other + self" and other is superclass of self cls = self.__class__ return cls(str.__add__(self, other), self.alphabet) def join(self, str_list: List["Seq"]) -> "Seq": # type: ignore # Incorrectly overrides superclass join cls = self.__class__ return cls(super(Seq, self).join(str_list), self.alphabet) def __eq__(self, other: Any) -> bool: if not hasattr(other, "alphabet"): return False if self.alphabet != other.alphabet: return False return str.__eq__(self, other) def __ne__(self, other: Any) -> bool: return not self.__eq__(other) def tostring(self) -> "str": """Converts Seq to a raw string.""" # Compatibility with biopython return str(self) # ---- Transformations of Seq ---- def reverse(self) -> "Seq": """Return the reversed sequence. Note that this method returns a new object, in contrast to the in-place reverse() method of list objects. """ cls = self.__class__ return cls(self[::-1], self.alphabet) def ungap(self) -> "Seq": # FIXME: Gap symbols should be specified by the Alphabet? return self.remove("-.~") def remove(self, delchars: str) -> "Seq": """Return a new alphabetic sequence with all characters in 'delchars' removed. """ cls = self.__class__ cleanseq = "".join(char for char in str(self) if char not in set(delchars)) return cls(cleanseq.translate(str.maketrans("", "")), self.alphabet) def lower(self) -> "Seq": """Return a lower case copy of the sequence.""" cls = self.__class__ trans = str.maketrans( "ABCDEFGHIJKLMNOPQRSTUVWXYZ", "abcdefghijklmnopqrstuvwxyz" ) return cls(str(self).translate(trans), self.alphabet) def upper(self) -> "Seq": """Return a lower case copy of the sequence.""" cls = self.__class__ trans = str.maketrans( "abcdefghijklmnopqrstuvwxyz", "ABCDEFGHIJKLMNOPQRSTUVWXYZ" ) return cls(str(self).translate(trans), self.alphabet) def mask( self, letters: str = "abcdefghijklmnopqrstuvwxyz", mask: str = "X" ) -> "Seq": """Replace all occurrences of letters with the mask character. The default is to replace all lower case letters with 'X'. """ LL = len(letters) if len(mask) != 1: raise ValueError("Mask should be single character") to = mask * LL trans = str.maketrans(letters, to) cls = self.__class__ return cls(str(self).translate(trans), self.alphabet) def translate(self) -> "Seq": # type: ignore # RENAME: Incorrectly overrides superclass translate. """Translate a nucleotide sequence to a polypeptide using full IUPAC ambiguities in DNA/RNA and amino acid codes, using the standard genetic code. See weblogo.transform.GeneticCode for details and more options. """ # Note: masks str.translate from .transform import GeneticCode return GeneticCode.std().translate(self) def back_translate(self) -> "Seq": """Translate a protein sequence back into coding DNA, using the standard genetic code. See weblogo.transform.GeneticCode for details and more options. """ from .transform import GeneticCode return GeneticCode.std().back_translate(self) def reverse_complement(self) -> "Seq": """Returns reversed complementary nucleic acid sequence (i.e. the other strand of a DNA sequence.) """ return self.reverse().complement() def complement(self) -> "Seq": """Returns complementary nucleic acid sequence.""" if not nucleic_alphabet.alphabetic(str(self.alphabet)): raise ValueError("Incompatibly alphabets") s = str.translate(self, _complement_table) cls = self.__class__ return cls(s, self.alphabet, self.name, self.description) def words( self, k: int, alphabet: Optional[Alphabet] = None ) -> Generator[str, None, None]: """Return an iteration over all subwords of length k in the sequence. If an optional alphabet is provided, only words from that alphabet are returned. >>> list(Seq("abcabc").words(3)) ['abc', 'bca', 'cab', 'abc'] """ if len(self) < k: return # An optimization. Chopping up strings is faster. seq = self.alphabet.normalize(self).tostring() # seq = self.tostring() for i in range(0, len(seq) - k + 1): word = seq[i : i + k] if alphabet is None or alphabet.alphabetic(word): yield word def word_count(self, k: int, alphabet: Optional[Alphabet] = None) -> List: """Return a count of all subwords in the sequence. >>> from weblogo.seq import * >>> Seq("abcabc").word_count(3) [('abc', 2), ('bca', 1), ('cab', 1)] """ from .utils import group_count words = sorted(self.words(k, alphabet)) return group_count(words) # end class Seq class SeqList(list): """A list of sequences.""" __slots__ = ["alphabet", "name", "description"] def __init__( self, alist: List[Seq] = [], alphabet: Optional[Alphabet] = None, name: Optional[str] = None, description: Optional[str] = None, ): list.__init__(self, alist) self.alphabet = alphabet self.name = name self.description = description # TOOWTDI. Replicates seq_io.read() # @classmethod # def read(cls, afile, alphabet = None): # return weblogo.seq_io.read(afile, alphabet) def isaligned(self) -> bool: """Are all sequences of the same length and alphabet?""" if len(self) == 0: return True A = self.alphabet if A is None: A = self[0].alphabet L = len(self[0]) for s in self: if len(s) != L: return False if s.alphabet != A: return False return True def ords(self, alphabet: Optional[Alphabet] = None) -> List[array]: """Convert sequence list into a 2D array of ordinals.""" if not alphabet: alphabet = self.alphabet if not alphabet: raise ValueError("No alphabet") k = [] for s in self: k.append(alphabet.ords(s)) return k def tally(self, alphabet: Optional[Alphabet] = None) -> List[int]: """Counts the occurrences of alphabetic characters. Arguments: - alphabet -- an optional alternative alphabet Returns : A list of character counts in alphabetic order. """ if not alphabet: alphabet = self.alphabet if not alphabet: raise ValueError("No alphabet") counts = [sum(c) for c in zip(*[s.tally(alphabet) for s in self])] return counts def profile(self, alphabet: Optional[Alphabet] = None): # type: ignore # Nasty circular import """Counts the occurrences of characters in each column. Returns: Motif(counts, alphabet) """ if not alphabet: alphabet = self.alphabet if not alphabet: raise ValueError("No alphabet") N = len(alphabet) ords = self.ords(alphabet) L = len(ords[0]) counts = [ [ 0, ] * N for x in range(0, L) ] for o in ords: if len(o) != L: raise ValueError( "Sequences are of incommensurate lengths. Cannot tally." ) for j, n in enumerate(o): if n < N: counts[j][n] += 1 from .matrix import Motif return Motif(alphabet, counts) # end class SeqList def dna(string: str) -> Seq: """Create an alphabetic sequence representing a stretch of DNA.""" return Seq(string, alphabet=dna_alphabet) def rna(string: str) -> Seq: """Create an alphabetic sequence representing a stretch of RNA.""" return Seq(string, alphabet=rna_alphabet) def protein(string: str) -> Seq: """Create an alphabetic sequence representing a stretch of polypeptide.""" return Seq(string, alphabet=protein_alphabet) weblogo-3.8.0/weblogo/seq_io/000077500000000000000000000000001467613320200161015ustar00rootroot00000000000000weblogo-3.8.0/weblogo/seq_io/__init__.py000077500000000000000000000220311467613320200202130ustar00rootroot00000000000000# Copyright (c) 2005 Gavin E. Crooks # Copyright (c) 2006, The Regents of the University of California, through # Lawrence Berkeley National Laboratory (subject to receipt of any required # approvals from the U.S. Dept. of Energy). All rights reserved. # This software is distributed under the new BSD Open Source License. # # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions are met: # # (1) Redistributions of source code must retain the above copyright notice, # this list of conditions and the following disclaimer. # # (2) Redistributions in binary form must reproduce the above copyright # notice, this list of conditions and the following disclaimer in the # documentation and or other materials provided with the distribution. # # (3) Neither the name of the University of California, Lawrence Berkeley # National Laboratory, U.S. Dept. of Energy nor the names of its contributors # may be used to endorse or promote products derived from this software # without specific prior written permission. # # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" # AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE # IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE # ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE # LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR # CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF # SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS # INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN # CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE # POSSIBILITY OF SUCH DAMAGE. """ Sequence file reading and writing --------------------------------- Biological sequence data is stored and transmitted using a wide variety of different file formats. This package provides convenient methods to read and write several of these file fomats. WebLogo is often capable of guessing the correct file type, either from the file extension or the structure of the file:: >>> import weblogo.seq_io >>> afile = open("test_weblogo/data/cap.fa") >>> seqs = weblogo.seq_io.read(afile) Alternatively, each sequence file type has a separate module named FILETYPE_io (e.g. fasta_io, clustal_io):: >>> import weblogo.seq_io.fasta_io >>> afile = open("test_weblogo/data/cap.fa") >>> seqs = weblogo.seq_io.fasta_io.read(afile) Sequence data can also be written back to files:: >>> fout = open("out.fa", "w") >>> weblogo.seq_io.fasta_io.write(fout, seqs) Supported File Formats ---------------------- :: Module Name Extension read write features --------------------------------------------------------------------------- array_io array, flatfile yes yes none clustal_io clustalw aln yes yes fasta_io fasta, Pearson fa yes yes none genbank_io genbank gb yes intelligenetics_io intelligenetics ig yes yes msf_io msf msf yes nbrf_io nbrf, pir pir yes nexus_io nexus nexus yes phylip_io phylip phy yes plain_io plain, raw yes yes none table_io table tbl yes yes none Each IO module defines one or more of the following functions and variables: read(afile, alphabet=None) Read a file of sequence data and return a SeqList, a collection of Seq's (Alphabetic strings) and features. read_seq(afile, alphabet=None) Read a single sequence from a file. iter_seq(afile, alphabet =None) Iterate over the sequences in a file. index(afile, alphabet = None) Instead of loading all of the sequences into memory, scan the file and return an index map that will load sequences on demand. Typically not implemented for formats with interleaved sequences. write(afile, seqlist) Write a collection of sequences to the specified file. write_seq(afile, seq) Write one sequence to the file. Only implemented for non-interleaved, headerless formats, such as fasta and plain. example A string containing a short example of the file format names A list of synonyms for the file format. E.g. for fasta_io, ( 'fasta', 'pearson', 'fa'). The first entry is the preferred format name. extensions A list of file name extensions used for this file format. e.g. fasta_io.extensions is ('fa', 'fasta', 'fast', 'seq', 'fsa', 'fst', 'nt', 'aa','fna','mpfa'). The preferred or standard extension is first in the list. Attributes : * formats: Available seq_io format parsers * format_names: A map between format names and format parsers. * format_extensions: A map between filename extensions and parsers. """ # Dev. References : # # - http://iubio.bio.indiana.edu/soft/molbio/readseq/java/Readseq2-help.html # - http://www.ebi.ac.uk/help/formats_frame.html # - http://www.cmbi.kun.nl/bioinf/tools/crab_pir.html # - http://bioperl.org/HOWTOs/html/SeqIO.html # - http://emboss.sourceforge.net/docs/themes/SequenceFormats.html # - http://www.cse.ucsc.edu/research/compbio/a2m-desc.html (a2m) # - http://www.genomatix.de/online_help/help/sequence_formats.html from types import ModuleType from typing import List, Optional, TextIO from ..seq import Alphabet, SeqList from . import genbank_io # null_io, from . import ( array_io, clustal_io, fasta_io, intelligenetics_io, msf_io, nbrf_io, nexus_io, phylip_io, plain_io, stockholm_io, table_io, ) __all__ = [ "clustal_io", "fasta_io", "msf_io", "nbrf_io", "nexus_io", "plain_io", "phylip_io", "null_io", "stockholm_io", "intelligenetics_io", "table_io", "array_io", "genbank_io", "read", "formats", "format_names", "format_extensions", ] """Available seq_io formats""" formats = ( clustal_io, fasta_io, plain_io, msf_io, genbank_io, nbrf_io, nexus_io, phylip_io, stockholm_io, intelligenetics_io, table_io, array_io, ) def format_names() -> dict: """Return a map between format names and format modules""" global formats fnames = {} for f in formats: for name in f.names: # type: ignore assert name not in fnames # Insanity check fnames[name] = f return fnames def format_extensions() -> dict: """Return a map between filename extensions and sequence file types""" global formats fext = {} for f in formats: for ext in f.extensions: # type: ignore assert ext not in fext # Insanity check fext[ext] = f return fext # seq_io._parsers is an ordered list of sequence parsers that are tried, in # turn, on files of unknown format. Each parser must raise an exception when # fed a format further down the list. # # The general trend is most common to least common file format. However, # 'nbrf_io' is before 'fasta_io' because nbrf looks like fasta with extras, and # 'array_io' is last, since it is very general. _parsers = ( nbrf_io, fasta_io, clustal_io, phylip_io, genbank_io, stockholm_io, msf_io, nexus_io, table_io, array_io, ) def _get_parsers(fin: TextIO) -> List[ModuleType]: global _parsers fnames = format_names() fext = format_extensions() parsers = list(_parsers) best_guess = parsers[0] # If a filename is supplied use the extension to guess the format. if hasattr(fin, "name") and "." in fin.name: extension = fin.name.split(".")[-1] if extension in fnames: best_guess = fnames[extension] elif extension in fext: best_guess = fext[extension] if best_guess in parsers: parsers.remove(best_guess) parsers.insert(0, best_guess) return parsers def read(fin: TextIO, alphabet: Optional[Alphabet] = None) -> SeqList: """Read a sequence file and attempt to guess its format. First the filename extension (if available) is used to infer the format. If that fails, then we attempt to parse the file using several common formats. Note, fin cannot be unseekable stream such as sys.stdin returns : SeqList Raises : ValueError: If the file cannot be parsed. ValueError: Sequence do not conform to the alphabet. """ alphabet = Alphabet(alphabet) parsers = _get_parsers(fin) for p in parsers: fin.seek(0) try: return p.read(fin, alphabet) # type: ignore except ValueError: pass names = ", ".join([p.names[0] for p in parsers]) # type: ignore raise ValueError("Cannot parse sequence file: Tried %s " % names) weblogo-3.8.0/weblogo/seq_io/_nexus/000077500000000000000000000000001467613320200174025ustar00rootroot00000000000000weblogo-3.8.0/weblogo/seq_io/_nexus/Nodes.py000077500000000000000000000125531467613320200210350ustar00rootroot00000000000000# Copyright 2005-2008 by Frank Kauff & Cymon J. Cox. All rights reserved. # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. """Provides functionality of a linked list. Each node has one (or none) predecessor, and an arbitrary number of successors. Nodes can store arbitrary data in a NodeData class. Subclassed by Trees to store phylogenetic trees. """ # type: ignore class ChainException(Exception): pass class NodeException(Exception): pass class Chain(object): """Stores a list of nodes that are linked together.""" def __init__(self): """Initiates a node chain.""" self.chain = {} self.id = -1 def _get_id(self): """Gets a new id for a node in the chain.""" self.id += 1 return self.id def all_ids(self): """Return a list of all node ids.""" return list(self.chain.keys()) def add(self, node, prev=None): """Attaches node to another.""" if prev is not None and prev not in self.chain: raise ChainException("Unknown predecessor: " + str(prev)) else: id = self._get_id() node.set_id(id) node.set_prev(prev) if prev is not None: self.chain[prev].add_succ(id) self.chain[id] = node return id def collapse(self, id): """Deletes node from chain and relinks successors to predecessor.""" if id not in self.chain: raise ChainException("Unknown ID: " + str(id)) prev_id = self.chain[id].get_prev() self.chain[prev_id].remove_succ(id) succ_ids = self.chain[id].get_succ() for i in succ_ids: self.chain[i].set_prev(prev_id) self.chain[prev_id].add_succ(succ_ids) node = self.chain[id] self.kill(id) return node def kill(self, id): """Kills a node from chain without caring to what it is connected.""" if id not in self.chain: raise ChainException("Unknown ID: " + str(id)) else: del self.chain[id] def unlink(self, id): """Disconnects node from his predecessor.""" if id not in self.chain: raise ChainException("Unknown ID: " + str(id)) else: prev_id = self.chain[id].prev if prev_id is not None: self.chain[prev_id].succ.pop(self.chain[prev_id].succ.index(id)) self.chain[id].prev = None return prev_id def link(self, parent, child): """Connects son to parent.""" if child not in self.chain: raise ChainException("Unknown ID: " + str(child)) elif parent not in self.chain: raise ChainException("Unknown ID: " + str(parent)) else: self.unlink(child) self.chain[parent].succ.append(child) self.chain[child].set_prev(parent) def is_parent_of(self, parent, grandchild): """Check if grandchild is a subnode of parent.""" if grandchild == parent or grandchild in self.chain[parent].get_succ(): return True else: for sn in self.chain[parent].get_succ(): if self.is_parent_of(sn, grandchild): return True else: return False def trace(self, start, finish): """Returns a list of all node_ids between two nodes (excluding start, including end).""" if start not in self.chain or finish not in self.chain: raise NodeException("Unknown node.") if not self.is_parent_of(start, finish) or start == finish: return [] for sn in self.chain[start].get_succ(): if self.is_parent_of(sn, finish): return [sn] + self.trace(sn, finish) class Node(object): """A single node.""" def __init__(self, data=None): """Represents a node with one predecessor and multiple successors.""" self.id = None self.data = data self.prev = None self.succ = [] def set_id(self, id): """Sets the id of a node, if not set yet.""" if self.id is not None: raise NodeException("Node id cannot be changed.") self.id = id def get_id(self): """Returns the node's id.""" return self.id def get_succ(self): """Returns a list of the node's successors.""" return self.succ def get_prev(self): """Returns the id of the node's predecessor.""" return self.prev def add_succ(self, id): """Adds a node id to the node's successors.""" if isinstance(id, type([])): self.succ.extend(id) else: self.succ.append(id) def remove_succ(self, id): """Removes a node id from the node's successors.""" self.succ.remove(id) def set_succ(self, new_succ): """Sets the node's successors.""" if not isinstance(new_succ, type([])): raise NodeException("Node successor must be of list type.") self.succ = new_succ def set_prev(self, id): """Sets the node's predecessor.""" self.prev = id def get_data(self): """Returns a node's data.""" return self.data def set_data(self, data): """Sets a node's data.""" self.data = data weblogo-3.8.0/weblogo/seq_io/_nexus/Trees.py000077500000000000000000001154711467613320200210520ustar00rootroot00000000000000# Copyright 2005-2008 by Frank Kauff & Cymon J. Cox. All rights reserved. # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. """Tree class to handle phylogenetic trees. Provides a set of methods to read and write newick-format tree descriptions, get information about trees (monphyly of taxon sets, congruence between trees, common ancestors,...) and to manipulate trees (reroot trees, split terminal nodes). """ # type: ignore import random from . import Nodes PRECISION_BRANCHLENGTH = 6 PRECISION_SUPPORT = 6 NODECOMMENT_START = "[&" NODECOMMENT_END = "]" class TreeError(Exception): pass class NodeData(object): """Stores tree-relevant data associated with nodes (e.g. branches or otus).""" def __init__(self, taxon=None, branchlength=0.0, support=None, comment=None): self.taxon = taxon self.branchlength = branchlength self.support = support self.comment = comment class Tree(Nodes.Chain): """Represents a tree using a chain of nodes with on predecessor (=ancestor) and multiple successors (=subclades). """ # A newick tree is parsed into nested list and then converted to a node list in two stages # mostly due to historical reasons. This could be done in one swoop). Note: parentheses ( ) and # colon : are not allowed in taxon names. This is against NEXUS standard, but makes life much # easier when parsing trees. ## NOTE: Tree should store its data class in something like self.dataclass=data, ## so that nodes that are generated have easy access to the data class ## Some routines use automatically NodeData, this needs to be more concise def __init__( self, tree=None, weight=1.0, rooted=False, name="", data=NodeData, values_are_support=False, max_support=1.0, ): """Ntree(self,tree).""" Nodes.Chain.__init__(self) self.dataclass = data self.__values_are_support = values_are_support self.max_support = max_support self.weight = weight self.rooted = rooted self.name = name root = Nodes.Node(data()) self.root = self.add(root) if tree: # use the tree we have # if Tree is called from outside Nexus parser, we need to get rid of linebreaks, etc tree = tree.strip().replace("\n", "").replace("\r", "") # there's discrepancy whether newick allows semicolons et the end tree = tree.rstrip(";") subtree_info, base_info = self._parse(tree) root.data = self._add_nodedata(root.data, [[], base_info]) self._add_subtree(parent_id=root.id, tree=subtree_info) def _parse(self, tree): """Parses (a,b,c...)[[[xx]:]yy] into subcomponents and travels down recursively.""" # Remove any leading/trailing white space - want any string starting # with " (..." should be recognised as a leaf, "(..." tree = tree.strip() if tree.count("(") != tree.count(")"): raise TreeError("Parentheses do not match in (sub)tree: " + tree) if tree.count("(") == 0: # a leaf # check if there's a colon, or a special comment, or both after the taxon name nodecomment = tree.find(NODECOMMENT_START) colon = tree.find(":") if colon == -1 and nodecomment == -1: # none return [tree, [None]] elif colon == -1 and nodecomment > -1: # only special comment return [tree[:nodecomment], self._get_values(tree[nodecomment:])] elif colon > -1 and nodecomment == -1: # only numerical values return [tree[:colon], self._get_values(tree[colon + 1 :])] elif ( colon < nodecomment ): # taxon name ends at first colon or with special comment return [tree[:colon], self._get_values(tree[colon + 1 :])] else: return [tree[:nodecomment], self._get_values(tree[nodecomment:])] else: closing = tree.rfind(")") val = self._get_values(tree[closing + 1 :]) if not val: val = [None] subtrees = [] plevel = 0 prev = 1 for p in range(1, closing): if tree[p] == "(": plevel += 1 elif tree[p] == ")": plevel -= 1 elif tree[p] == "," and plevel == 0: subtrees.append(tree[prev:p]) prev = p + 1 subtrees.append(tree[prev:closing]) subclades = [self._parse(subtree) for subtree in subtrees] return [subclades, val] def _add_subtree(self, parent_id=None, tree=None): """Adds leaf or tree (in newick format) to a parent_id.""" if parent_id is None: raise TreeError("Need node_id to connect to.") for st in tree: nd = self.dataclass() nd = self._add_nodedata(nd, st) if isinstance(st[0], list): # it's a subtree sn = Nodes.Node(nd) self.add(sn, parent_id) self._add_subtree(sn.id, st[0]) else: # it's a leaf nd.taxon = st[0] leaf = Nodes.Node(nd) self.add(leaf, parent_id) def _add_nodedata(self, nd, st): """Add data to the node parsed from the comments, taxon and support.""" if isinstance(st[1][-1], str) and st[1][-1].startswith(NODECOMMENT_START): nd.comment = st[1].pop(-1) # if the first element is a string, it's the subtree node taxon elif isinstance(st[1][0], str): nd.taxon = st[1][0] st[1] = st[1][1:] if len(st) > 1: if ( len(st[1]) >= 2 ): # if there's two values, support comes first. Is that always so? nd.support = st[1][0] if st[1][1] is not None: nd.branchlength = st[1][1] elif ( len(st[1]) == 1 ): # otherwise it could be real branchlengths or support as branchlengths if not self.__values_are_support: # default if st[1][0] is not None: nd.branchlength = st[1][0] else: nd.support = st[1][0] return nd def _get_values(self, text): """Extracts values (support/branchlength) from xx[:yyy], xx.""" if text == "": return None nodecomment = None if NODECOMMENT_START in text: # if there's a [&....] comment, cut it out nc_start = text.find(NODECOMMENT_START) nc_end = text.find(NODECOMMENT_END) if nc_end == -1: raise TreeError( "Error in tree description: Found %s without matching %s" % (NODECOMMENT_START, NODECOMMENT_END) ) nodecomment = text[nc_start : nc_end + 1] text = text[:nc_start] + text[nc_end + 1 :] # pase out supports and branchlengths, with internal node taxa info values = [] taxonomy = None for part in [t.strip() for t in text.split(":")]: if part: try: values.append(float(part)) except ValueError: assert taxonomy is None, "Two string taxonomies?" taxonomy = part if taxonomy: values.insert(0, taxonomy) if nodecomment: values.append(nodecomment) return values def _walk(self, node=None): """Return all node_ids downwards from a node.""" if node is None: node = self.root for n in self.node(node).succ: yield n for sn in self._walk(n): yield sn def node(self, node_id): """Return the instance of node_id. node = node(self,node_id) """ if node_id not in self.chain: raise TreeError("Unknown node_id: %d" % node_id) return self.chain[node_id] def split(self, parent_id=None, n=2, branchlength=1.0): """Speciation: generates n (default two) descendants of a node. [new ids] = split(self,parent_id=None,n=2,branchlength=1.0): """ if parent_id is None: raise TreeError("Missing node_id.") ids = [] parent_data = self.chain[parent_id].data for i in range(n): node = Nodes.Node() if parent_data: node.data = self.dataclass() # each node has taxon and branchlength attribute if parent_data.taxon: node.data.taxon = parent_data.taxon + str(i) node.data.branchlength = branchlength ids.append(self.add(node, parent_id)) return ids def search_taxon(self, taxon): """Returns the first matching taxon in self.data.taxon. Not restricted to terminal nodes. node_id = search_taxon(self,taxon) """ for id, node in self.chain.items(): if node.data.taxon == taxon: return id return None def prune(self, taxon): """Prunes a terminal taxon from the tree. id_of_previous_node = prune(self,taxon) If taxon is from a bifurcation, the connectiong node will be collapsed and its branchlength added to remaining terminal node. This might be no longer a meaningful value' """ id = self.search_taxon(taxon) if id is None: raise TreeError("Taxon not found: %s" % taxon) elif id not in self.get_terminals(): raise TreeError("Not a terminal taxon: %s" % taxon) else: prev = self.unlink(id) self.kill(id) if len(self.node(prev).succ) == 1: if ( prev == self.root ): # we deleted one branch of a bifurcating root, then we have to move the root upwards self.root = self.node(self.root).succ[0] self.node(self.root).branchlength = 0.0 self.kill(prev) else: succ = self.node(prev).succ[0] new_bl = ( self.node(prev).data.branchlength + self.node(succ).data.branchlength ) self.collapse(prev) self.node(succ).data.branchlength = new_bl return prev def get_taxa(self, node_id=None): """Return a list of all otus downwards from a node. nodes = get_taxa(self,node_id=None) """ if node_id is None: node_id = self.root if node_id not in self.chain: raise TreeError("Unknown node_id: %d." % node_id) if self.chain[node_id].succ == []: if self.chain[node_id].data: return [self.chain[node_id].data.taxon] else: return None else: list = [] for succ in self.chain[node_id].succ: list.extend(self.get_taxa(succ)) return list def get_terminals(self): """Return a list of all terminal nodes.""" return [i for i in self.all_ids() if self.node(i).succ == []] def is_terminal(self, node): """Returns True if node is a terminal node.""" return self.node(node).succ == [] def is_internal(self, node): """Returns True if node is an internal node.""" return len(self.node(node).succ) > 0 def is_preterminal(self, node): """Returns True if all successors of a node are terminal ones.""" if self.is_terminal(node): return False not in [self.is_terminal(n) for n in self.node(node).succ] else: return False def count_terminals(self, node=None): """Counts the number of terminal nodes that are attached to a node.""" if node is None: node = self.root return len([n for n in self._walk(node) if self.is_terminal(n)]) def collapse_genera(self, space_equals_underscore=True): """Collapses all subtrees which belong to the same genus (i.e share the same first word in their taxon name.)""" while True: for n in self._walk(): if self.is_terminal(n): continue taxa = self.get_taxa(n) genera = [] for t in taxa: if space_equals_underscore: t = t.replace(" ", "_") try: genus = t.split("_", 1)[0] except: genus = "None" if genus not in genera: genera.append(genus) if len(genera) == 1: self.node(n).data.taxon = genera[0] + " " # now we kill all nodes downstream nodes2kill = [kn for kn in self._walk(node=n)] for kn in nodes2kill: self.kill(kn) self.node(n).succ = [] break # break out of for loop because node list from _walk will be inconsistent else: # for loop exhausted: no genera to collapse left break # while def sum_branchlength(self, root=None, node=None): """Adds up the branchlengths from root (default self.root) to node. sum = sum_branchlength(self,root=None,node=None) """ if root is None: root = self.root if node is None: raise TreeError("Missing node id.") blen = 0.0 while node is not None and node is not root: blen += self.node(node).data.branchlength node = self.node(node).prev return blen def set_subtree(self, node): """Return subtree as a set of nested sets. sets = set_subtree(self,node) """ if self.node(node).succ == []: return self.node(node).data.taxon else: try: return frozenset(self.set_subtree(n) for n in self.node(node).succ) except: print(node) print(self.node(node).succ) for n in self.node(node).succ: print("%s %s" % (n, self.set_subtree(n))) print([self.set_subtree(n) for n in self.node(node).succ]) raise def is_identical(self, tree2): """Compare tree and tree2 for identity. result = is_identical(self,tree2) """ return self.set_subtree(self.root) == tree2.set_subtree(tree2.root) def is_compatible(self, tree2, threshold, strict=True): """Compares branches with support>threshold for compatibility. result = is_compatible(self,tree2,threshold) """ # check if both trees have the same set of taxa. strict=True enforces this. missing2 = set(self.get_taxa()) - set(tree2.get_taxa()) missing1 = set(tree2.get_taxa()) - set(self.get_taxa()) if strict and (missing1 or missing2): if missing1: print( "Taxon/taxa %s is/are missing in tree %s" % (",".join(missing1), self.name) ) if missing2: print( "Taxon/taxa %s is/are missing in tree %s" % (",".join(missing2), tree2.name) ) raise TreeError("Can't compare trees with different taxon compositions.") t1 = [ (set(self.get_taxa(n)), self.node(n).data.support) for n in self.all_ids() if self.node(n).succ and ( self.node(n).data and self.node(n).data.support and self.node(n).data.support >= threshold ) ] t2 = [ (set(tree2.get_taxa(n)), tree2.node(n).data.support) for n in tree2.all_ids() if tree2.node(n).succ and ( tree2.node(n).data and tree2.node(n).data.support and tree2.node(n).data.support >= threshold ) ] conflict = [] for st1, sup1 in t1: for st2, sup2 in t2: if not st1.issubset(st2) and not st2.issubset( st1 ): # don't hiccup on upstream nodes intersect, notin1, notin2 = ( st1 & st2, st2 - st1, st1 - st2, ) # all three are non-empty sets # if notin1==missing1 or notin2==missing2 <==> st1.issubset(st2) or st2.issubset(st1) ??? if intersect and not ( notin1.issubset(missing1) or notin2.issubset(missing2) ): # omit conflicts due to missing taxa conflict.append( (st1, sup1, st2, sup2, intersect, notin1, notin2) ) return conflict def common_ancestor(self, node1, node2): """Return the common ancestor that connects two nodes. node_id = common_ancestor(self,node1,node2) """ l1 = [self.root] + self.trace(self.root, node1) l2 = [self.root] + self.trace(self.root, node2) return [n for n in l1 if n in l2][-1] def distance(self, node1, node2): """Add and return the sum of the branchlengths between two nodes. dist = distance(self,node1,node2) """ ca = self.common_ancestor(node1, node2) return self.sum_branchlength(ca, node1) + self.sum_branchlength(ca, node2) def is_monophyletic(self, taxon_list): """Return node_id of common ancestor if taxon_list is monophyletic, -1 otherwise. result = is_monophyletic(self,taxon_list) """ if isinstance(taxon_list, str): taxon_set = set([taxon_list]) else: taxon_set = set(taxon_list) node_id = self.root while True: subclade_taxa = set(self.get_taxa(node_id)) if subclade_taxa == taxon_set: # are we there? return node_id else: # check subnodes for subnode in self.chain[node_id].succ: if set(self.get_taxa(subnode)).issuperset( taxon_set ): # taxon_set is downstream node_id = subnode break # out of for loop else: return -1 # taxon set was not with successors, for loop exhausted def is_bifurcating(self, node=None): """Return True if tree downstream of node is strictly bifurcating.""" if node is None: node = self.root if ( node == self.root and len(self.node(node).succ) == 3 ): # root can be trifurcating, because it has no ancestor return ( self.is_bifurcating(self.node(node).succ[0]) and self.is_bifurcating(self.node(node).succ[1]) and self.is_bifurcating(self.node(node).succ[2]) ) if len(self.node(node).succ) == 2: return self.is_bifurcating(self.node(node).succ[0]) and self.is_bifurcating( self.node(node).succ[1] ) elif len(self.node(node).succ) == 0: return True else: return False def branchlength2support(self): """Move values stored in data.branchlength to data.support, and set branchlength to 0.0 This is necessary when support has been stored as branchlength (e.g. paup), and has thus been read in as branchlength. """ for n in self.chain: self.node(n).data.support = self.node(n).data.branchlength self.node(n).data.branchlength = 0.0 def convert_absolute_support(self, nrep): """Convert absolute support (clade-count) to rel. frequencies. Some software (e.g. PHYLIP consense) just calculate how often clades appear, instead of calculating relative frequencies.""" for n in self._walk(): if self.node(n).data.support: self.node(n).data.support /= float(nrep) def has_support(self, node=None): """Returns True if any of the nodes has data.support is not None.""" for n in self._walk(node): if self.node(n).data.support: return True else: return False def randomize( self, ntax=None, taxon_list=None, branchlength=1.0, branchlength_sd=None, bifurcate=True, ): """Generates a random tree with ntax taxa and/or taxa from taxlabels. new_tree = randomize(self,ntax=None,taxon_list=None,branchlength=1.0,branchlength_sd=None,bifurcate=True) Trees are bifurcating by default. (Polytomies not yet supported). """ if not ntax and taxon_list: ntax = len(taxon_list) elif not taxon_list and ntax: taxon_list = ["taxon" + str(i + 1) for i in range(ntax)] elif not ntax and not taxon_list: raise TreeError("Either numer of taxa or list of taxa must be specified.") elif ntax != len(taxon_list): raise TreeError("Length of taxon list must correspond to ntax.") # initiate self with empty root self.__init__() terminals = self.get_terminals() # bifurcate randomly at terminal nodes until ntax is reached while len(terminals) < ntax: newsplit = random.choice(terminals) new_terminals = self.split(parent_id=newsplit, branchlength=branchlength) # if desired, give some variation to the branch length if branchlength_sd: for nt in new_terminals: bl = random.gauss(branchlength, branchlength_sd) if bl < 0: bl = 0 self.node(nt).data.branchlength = bl terminals.extend(new_terminals) terminals.remove(newsplit) # distribute taxon labels randomly random.shuffle(taxon_list) for node, name in zip(terminals, taxon_list): self.node(node).data.taxon = name def display(self): """Quick and dirty lists of all nodes.""" table = [ ("#", "taxon", "prev", "succ", "brlen", "blen (sum)", "support", "comment") ] # Sort this to be consistent across CPython, Jython, etc for i in sorted(self.all_ids()): n = self.node(i) if not n.data: table.append( (str(i), "-", str(n.prev), str(n.succ), "-", "-", "-", "-") ) else: tx = n.data.taxon if not tx: tx = "-" blength = "%0.2f" % n.data.branchlength if blength is None: blength = "-" sum_blength = "-" else: sum_blength = "%0.2f" % self.sum_branchlength(node=i) support = n.data.support if support is None: support = "-" else: support = "%0.2f" % support comment = n.data.comment if comment is None: comment = "-" table.append( ( str(i), tx, str(n.prev), str(n.succ), blength, sum_blength, support, comment, ) ) print("\n".join("%3s %32s %15s %15s %8s %10s %8s %20s" % l for l in table)) print("\nRoot: %s" % self.root) def to_string( self, support_as_branchlengths=False, branchlengths_only=False, plain=True, plain_newick=False, ladderize=None, ignore_comments=True, ): """Return a paup compatible tree line.""" # if there's a conflict in the arguments, we override plain=True if support_as_branchlengths or branchlengths_only: plain = False self.support_as_branchlengths = support_as_branchlengths self.branchlengths_only = branchlengths_only self.ignore_comments = ignore_comments self.plain = plain def make_info_string(data, terminal=False): """Creates nicely formatted support/branchlengths.""" # CHECK FORMATTING if self.plain: # plain tree only. That's easy. info_string = "" elif ( self.support_as_branchlengths ): # support as branchlengths (eg. PAUP), ignore actual branchlengths if terminal: # terminal branches have 100% support info_string = ":%1.2f" % self.max_support elif data.support: info_string = ":%1.2f" % (data.support) else: info_string = ":0.00" elif self.branchlengths_only: # write only branchlengths, ignore support info_string = ":%1.5f" % (data.branchlength) else: # write suport and branchlengths (e.g. .con tree of mrbayes) if terminal: info_string = ":%1.5f" % (data.branchlength) else: if ( data.branchlength is not None and data.support is not None ): # we have blen and suppport info_string = "%1.2f:%1.5f" % (data.support, data.branchlength) elif data.branchlength is not None: # we have only blen info_string = "0.00000:%1.5f" % (data.branchlength) elif data.support is not None: # we have only support info_string = "%1.2f:0.00000" % (data.support) else: info_string = "0.00:0.00000" if not ignore_comments and hasattr(data, "nodecomment"): info_string = str(data.nodecomment) + info_string return info_string def ladderize_nodes(nodes, ladderize=None): """Sorts node numbers according to the number of terminal nodes.""" if ladderize in ["left", "LEFT", "right", "RIGHT"]: succnode_terminals = sorted( (self.count_terminals(node=n), n) for n in nodes ) if ladderize == "right" or ladderize == "RIGHT": succnode_terminals.reverse() if succnode_terminals: succnodes = zip(*succnode_terminals)[1] else: succnodes = [] else: succnodes = nodes return succnodes def newickize(node, ladderize=None): """Convert a node tree to a newick tree recursively.""" if not self.node(node).succ: # terminal return self.node(node).data.taxon + make_info_string( self.node(node).data, terminal=True ) else: succnodes = ladderize_nodes(self.node(node).succ, ladderize=ladderize) subtrees = [newickize(sn, ladderize=ladderize) for sn in succnodes] return "(%s)%s" % ( ",".join(subtrees), make_info_string(self.node(node).data), ) treeline = ["tree"] if self.name: treeline.append(self.name) else: treeline.append("a_tree") treeline.append("=") if self.weight != 1: treeline.append("[&W%s]" % str(round(float(self.weight), 3))) if self.rooted: treeline.append("[&R]") succnodes = ladderize_nodes(self.node(self.root).succ) subtrees = [newickize(sn, ladderize=ladderize) for sn in succnodes] treeline.append("(%s)" % ",".join(subtrees)) if plain_newick: return treeline[-1] else: return " ".join(treeline) + ";" def __str__(self): """Short version of to_string(), gives plain tree""" return self.to_string(plain=True) def unroot(self): """Defines a unrooted Tree structure, using data of a rooted Tree.""" # travel down the rooted tree structure and save all branches and the nodes they connect def _get_branches(node): branches = [] for b in self.node(node).succ: branches.append( [node, b, self.node(b).data.branchlength, self.node(b).data.support] ) branches.extend(_get_branches(b)) return branches self.unrooted = _get_branches(self.root) # if root is bifurcating, then it is eliminated if len(self.node(self.root).succ) == 2: # find the two branches that connect to root rootbranches = [b for b in self.unrooted if self.root in b[:2]] b1 = self.unrooted.pop(self.unrooted.index(rootbranches[0])) b2 = self.unrooted.pop(self.unrooted.index(rootbranches[1])) # Connect them two each other. If both have support, it should be identical (or one set to None?). # If both have branchlengths, they will be added newbranch = [b1[1], b2[1], b1[2] + b2[2]] if b1[3] is None: newbranch.append( b2[3] ) # either None (both rootbranches are unsupported) or some support elif b2[3] is None: newbranch.append(b1[3]) # dito elif b1[3] == b2[3]: newbranch.append(b1[3]) # identical support elif b1[3] == 0 or b2[3] == 0: newbranch.append(b1[3] + b2[3]) # one is 0, take the other else: raise TreeError( "Support mismatch in bifurcating root: %f, %f" % (float(b1[3]), float(b2[3])) ) self.unrooted.append(newbranch) def root_with_outgroup(self, outgroup=None): def _connect_subtree(parent, child): """Hook subtree starting with node child to parent.""" for i, branch in enumerate(self.unrooted): if parent in branch[:2] and child in branch[:2]: branch = self.unrooted.pop(i) break else: raise TreeError( "Unable to connect nodes for rooting: nodes %d and %d are not connected" % (parent, child) ) self.link(parent, child) self.node(child).data.branchlength = branch[2] self.node(child).data.support = branch[3] # now check if there are more branches connected to the child, and if so, connect them child_branches = [b for b in self.unrooted if child in b[:2]] for b in child_branches: if child == b[0]: succ = b[1] else: succ = b[0] _connect_subtree(child, succ) # check the outgroup we're supposed to root with if outgroup is None: return self.root outgroup_node = self.is_monophyletic(outgroup) if outgroup_node == -1: return -1 # if tree is already rooted with outgroup on a bifurcating root, # or the outgroup includes all taxa on the tree, then we're fine if ( len(self.node(self.root).succ) == 2 and outgroup_node in self.node(self.root).succ ) or outgroup_node == self.root: return self.root self.unroot() # now we find the branch that connects outgroup and ingroup # print(self.node(outgroup_node).prev) for i, b in enumerate(self.unrooted): if outgroup_node in b[:2] and self.node(outgroup_node).prev in b[:2]: root_branch = self.unrooted.pop(i) break else: raise TreeError("Unrooted and rooted Tree do not match") if outgroup_node == root_branch[1]: ingroup_node = root_branch[0] else: ingroup_node = root_branch[1] # now we destroy the old tree structure, but keep node data. Nodes will be reconnected according to new outgroup for n in self.all_ids(): self.node(n).prev = None self.node(n).succ = [] # now we just add both subtrees (outgroup and ingroup) branch for branch root = Nodes.Node(data=NodeData()) # new root self.add(root) # add to tree description self.root = root.id # set as root self.unrooted.append( [root.id, ingroup_node, root_branch[2], root_branch[3]] ) # add branch to ingroup to unrooted tree self.unrooted.append( [root.id, outgroup_node, 0.0, 0.0] ) # add branch to outgroup to unrooted tree _connect_subtree(root.id, ingroup_node) # add ingroup _connect_subtree(root.id, outgroup_node) # add outgroup # if theres still a lonely node in self.chain, then it's the old root, and we delete it oldroot = [ i for i in self.all_ids() if self.node(i).prev is None and i != self.root ] if len(oldroot) > 1: raise TreeError( "Isolated nodes in tree description: %s" % ",".join(oldroot) ) elif len(oldroot) == 1: self.kill(oldroot[0]) return self.root def merge_with_support( self, bstrees=None, constree=None, threshold=0.5, outgroup=None ): """Merges clade support (from consensus or list of bootstrap-trees) with phylogeny. tree=merge_bootstrap(phylo,bs_tree=) or tree=merge_bootstrap(phylo,consree=consensus_tree with clade support) """ if bstrees and constree: raise TreeError( "Specify either list of bootstrap trees or consensus tree, not both" ) if not (bstrees or constree): raise TreeError("Specify either list of bootstrap trees or consensus tree.") # no outgroup specified: use the smallest clade of the root if outgroup is None: try: succnodes = self.node(self.root).succ smallest = min((len(self.get_taxa(n)), n) for n in succnodes) outgroup = self.get_taxa(smallest[1]) except: raise TreeError("Error determining outgroup.") else: # root with user specified outgroup self.root_with_outgroup(outgroup) if bstrees: # calculate consensus constree = consensus(bstrees, threshold=threshold, outgroup=outgroup) else: if not constree.has_support(): constree.branchlength2support() constree.root_with_outgroup(outgroup) # now we travel all nodes, and add support from consensus, if the clade is present in both for pnode in self._walk(): cnode = constree.is_monophyletic(self.get_taxa(pnode)) if cnode > -1: self.node(pnode).data.support = constree.node(cnode).data.support def consensus(trees, threshold=0.5, outgroup=None): """Compute a majority rule consensus tree of all clades with relative frequency>=threshold from a list of trees.""" total = len(trees) if total == 0: return None # shouldn't we make sure that it's NodeData or subclass?? dataclass = trees[0].dataclass max_support = trees[0].max_support clades = {} # countclades={} alltaxa = set(trees[0].get_taxa()) # calculate calde frequencies c = 0 for t in trees: c += 1 # if c % 100 == 0: # print(c) if alltaxa != set(t.get_taxa()): raise TreeError("Trees for consensus must contain the same taxa") t.root_with_outgroup(outgroup=outgroup) for st_node in t._walk(t.root): subclade_taxa = sorted(t.get_taxa(st_node)) subclade_taxa = str(subclade_taxa) # lists are not hashable if subclade_taxa in clades: clades[subclade_taxa] += float(t.weight) / total else: clades[subclade_taxa] = float(t.weight) / total # if subclade_taxa in countclades: # countclades[subclade_taxa]+ = t.weight # else: # countclades[subclade_taxa] = t.weight # weed out clades below threshold delclades = [ c for c, p in clades.items() if round(p, 3) < threshold ] # round can be necessary for c in delclades: del clades[c] # create a tree with a root node consensus = Tree(name="consensus_%2.1f" % float(threshold), data=dataclass) # each clade needs a node in the new tree, add them as isolated nodes for c, s in clades.items(): node = Nodes.Node(data=dataclass()) node.data.support = s node.data.taxon = set(eval(c)) consensus.add(node) # set root node data consensus.node(consensus.root).data.support = None consensus.node(consensus.root).data.taxon = alltaxa # we sort the nodes by no. of taxa in the clade, so root will be the last consensus_ids = consensus.all_ids() consensus_ids.sort( lambda x, y: len(consensus.node(x).data.taxon) - len(consensus.node(y).data.taxon) ) # now we just have to hook each node to the next smallest node that includes all taxa of the current for i, current in enumerate( consensus_ids[:-1] ): # skip the last one which is the root # print('----') # print('current: %s' % consensus.node(current).data.taxon) # search remaining nodes for parent in consensus_ids[i + 1 :]: # print('parent: %s' % consensus.node(parent).data.taxon) if consensus.node(parent).data.taxon.issuperset( consensus.node(current).data.taxon ): break else: raise TreeError("corrupt tree structure?") # internal nodes don't have taxa if len(consensus.node(current).data.taxon) == 1: consensus.node(current).data.taxon = consensus.node( current ).data.taxon.pop() # reset the support for terminal nodes to maximum # consensus.node(current).data.support=max_support else: consensus.node(current).data.taxon = None consensus.link(parent, current) # eliminate root taxon name consensus.node(consensus_ids[-1]).data.taxon = None if alltaxa != set(consensus.get_taxa()): raise TreeError("FATAL ERROR: consensus tree is corrupt") return consensus weblogo-3.8.0/weblogo/seq_io/_nexus/__init__.py000077500000000000000000002333571467613320200215330ustar00rootroot00000000000000# Nexus.py - a NEXUS parser # # Copyright 2005-2008 by Frank Kauff & Cymon J. Cox. All rights reserved. # This code is part of the Biopython distribution and governed by its # license. Please see the LICENSE file that should have been included # as part of this package. # # Bug reports welcome: fkauff@biologie.uni-kl.de or the Biopython issue tracker # at http://github.com/biopython/biopython. """Parse the contents of a NEXUS file. Based upon 'NEXUS: An extensible file format for systematic information' Maddison, Swofford, Maddison. 1997. Syst. Biol. 46(4):590-621 Authors: Frank Kauff and Cymon J. Cox """ # type: ignore import contextlib import copy import math import random import sys from collections import namedtuple from functools import reduce from ... import data from ...seq import Alphabet, Seq, protein_alphabet # --- Changes from Bio.Nexus --- # Renamed Nexus.py to __init__.py. Helps with api documentation. # from Bio import File # from Bio.Alphabet import IUPAC # from Bio.Data import IUPACData # from Bio.Seq import Seq _IUPACData = dict( ambiguous_dna_letters=data.dna_extended_letters, ambiguous_rna_letters=data.rna_extended_letters, ambiguous_dna_values=data.dna_ambiguity, ambiguous_rna_values=data.rna_ambiguity, protein_letters=data.amino_acid_letters, unambiguous_dna_letters=data.dna_letters, unambiguous_rna_letters=data.rna_letters, ) IUPACData = namedtuple("IUPACDataTuple", _IUPACData.keys())(**_IUPACData) _IUPAC = dict( ambiguous_dna=Alphabet(data.dna_extended_letters + "-?"), ambiguous_rna=Alphabet(data.rna_extended_letters + "-?"), protein=protein_alphabet, # Alphabet(IUPACData.protein_letters+'-?') ) IUPAC = namedtuple("IUPATuple", _IUPAC.keys())(**_IUPAC) @contextlib.contextmanager def as_handle(handleish, mode="r"): """Treat a filename or file-like object as an open file handle.""" if isinstance(handleish, str): with open(handleish, mode) as fp: yield fp else: yield handleish # Not bundling cnexus def _get_command_lines(file_contents): lines = _kill_comments_and_break_lines(file_contents) commandlines = _adjust_lines(lines) return commandlines # --- End Changes --- from .Trees import Tree INTERLEAVE = 70 SPECIAL_COMMANDS = [ "charstatelabels", "charlabels", "taxlabels", "taxset", "charset", "charpartition", "taxpartition", "matrix", "tree", "utree", "translate", "codonposset", "title", ] KNOWN_NEXUS_BLOCKS = ["trees", "data", "characters", "taxa", "sets", "codons"] PUNCTUATION = "()[]{}/\\,;:=*'\"`+-<>" MRBAYESSAFE = "abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ1234567890_" WHITESPACE = " \t\n" # SPECIALCOMMENTS = ['!', '&', '%', '/', '\\', '@'] # original list of special comments SPECIALCOMMENTS = [ "&" ] # supported special comment ('tree' command), all others are ignored CHARSET = "chars" TAXSET = "taxa" CODONPOSITIONS = "codonpositions" DEFAULTNEXUS = ( "#NEXUS\nbegin data; dimensions ntax=0 nchar=0; format datatype=dna; end; " ) class NexusError(Exception): pass class CharBuffer(object): """Helps reading NEXUS-words and characters from a buffer (semi-PRIVATE). This class is not intended for public use (any more). """ def __init__(self, string): if string: self.buffer = list(string) else: self.buffer = [] def peek(self): if self.buffer: return self.buffer[0] else: return None def peek_nonwhitespace(self): b = "".join(self.buffer).strip() if b: return b[0] else: return None def __next__(self): if self.buffer: return self.buffer.pop(0) else: return None if sys.version_info[0] < 3: def next(self): """Deprecated Python 2 style alias for Python 3 style __next__ method.""" return self.__next__() def next_nonwhitespace(self): while True: p = next(self) if p is None: break if p not in WHITESPACE: return p return None def skip_whitespace(self): while self.buffer[0] in WHITESPACE: self.buffer = self.buffer[1:] def next_until(self, target): for t in target: try: pos = self.buffer.index(t) except ValueError: pass else: found = "".join(self.buffer[:pos]) self.buffer = self.buffer[pos:] return found else: return None def peek_word(self, word): return "".join(self.buffer[: len(word)]) == word def next_word(self): """Return the next NEXUS word from a string. This deals with single and double quotes, whitespace and punctuation. """ word = [] quoted = False first = self.next_nonwhitespace() # get first character if not first: # return empty if only whitespace left return None word.append(first) if first == "'": # word starts with a quote quoted = "'" elif first == '"': quoted = '"' elif first in PUNCTUATION: # if it's punctuation, return immediately return first while True: c = self.peek() if c == quoted: # a quote? word.append(next(self)) # store quote if self.peek() == quoted: # double quote skip = next(self) # skip second quote elif quoted: # second single quote ends word break elif quoted: word.append(next(self)) # if quoted, then add anything elif not c or c in PUNCTUATION or c in WHITESPACE: # if not quoted and special character, stop break else: word.append(next(self)) # standard character return "".join(word) def rest(self): """Return the rest of the string without parsing.""" return "".join(self.buffer) class StepMatrix(object): """Calculate a stepmatrix for weighted parsimony. See Wheeler (1990), Cladistics 6:269-275. """ def __init__(self, symbols, gap): self.data = {} self.symbols = sorted(symbols) if gap: self.symbols.append(gap) for x in self.symbols: for y in [s for s in self.symbols if s != x]: self.set(x, y, 0) def set(self, x, y, value): if x > y: x, y = y, x self.data[x + y] = value def add(self, x, y, value): if x > y: x, y = y, x self.data[x + y] += value def sum(self): return reduce(lambda x, y: x + y, self.data.values()) def transformation(self): total = self.sum() if total != 0: for k in self.data: self.data[k] = self.data[k] / float(total) return self def weighting(self): for k in self.data: if self.data[k] != 0: self.data[k] = -math.log(self.data[k]) return self def smprint(self, name="your_name_here"): matrix = "usertype %s stepmatrix=%d\n" % (name, len(self.symbols)) matrix += " %s\n" % " ".join(self.symbols) for x in self.symbols: matrix += "[%s]".ljust(8) % x for y in self.symbols: if x == y: matrix += " . " else: if x > y: x1, y1 = y, x else: x1, y1 = x, y if self.data[x1 + y1] == 0: matrix += "inf. " else: matrix += "%2.2f".ljust(10) % (self.data[x1 + y1]) matrix += "\n" matrix += ";\n" return matrix def safename(name, mrbayes=False): """Return a taxon identifier according to NEXUS standard. Wrap quotes around names with punctuation or whitespace, and double single quotes. mrbayes=True: write names without quotes, whitespace or punctuation for the mrbayes software package. """ if mrbayes: safe = name.replace(" ", "_") safe = "".join(c for c in safe if c in MRBAYESSAFE) else: safe = name.replace("'", "''") if set(safe).intersection(set(WHITESPACE + PUNCTUATION)): safe = "'" + safe + "'" return safe def quotestrip(word): """Remove quotes and/or double quotes around identifiers.""" if not word: return None while (word.startswith("'") and word.endswith("'")) or ( word.startswith('"') and word.endswith('"') ): word = word[1:-1] return word def get_start_end(sequence, skiplist=["-", "?"]): """Return position of first and last character which is not in skiplist. Skiplist defaults to ['-','?']).""" length = len(sequence) if length == 0: return None, None end = length - 1 while end >= 0 and (sequence[end] in skiplist): end -= 1 start = 0 while start < length and (sequence[start] in skiplist): start += 1 if start == length and end == -1: # empty sequence return -1, -1 else: return start, end def _sort_keys_by_values(p): """Returns a sorted list of keys of p sorted by values of p.""" return sorted((pn for pn in p if p[pn]), key=lambda pn: p[pn]) def _make_unique(l): """Check that all values in list are unique and return a pruned and sorted list.""" return sorted(set(l)) def _unique_label(previous_labels, label): """Returns a unique name if label is already in previous_labels.""" while label in previous_labels: if label.split(".")[-1].startswith("copy"): label = ( ".".join(label.split(".")[:-1]) + ".copy" + str(eval("0" + label.split(".")[-1][4:]) + 1) ) else: label += ".copy" return label def _seqmatrix2strmatrix(matrix): """Converts a Seq-object matrix to a plain sequence-string matrix.""" return dict((t, str(matrix[t])) for t in matrix) def _compact4nexus(orig_list): """Transform [1 2 3 5 6 7 8 12 15 18 20] (baseindex 0, used in the Nexus class) into '2-4 6-9 13-19\\3 21' (baseindex 1, used in programs like Paup or MrBayes.). """ if not orig_list: return "" orig_list = sorted(set(orig_list)) shortlist = [] clist = orig_list[:] clist.append(clist[-1] + 0.5) # dummy value makes it easier while len(clist) > 1: step = 1 for i, x in enumerate(clist): if x == clist[0] + i * step: # are we still in the right step? continue elif i == 1 and len(clist) > 3 and clist[i + 1] - x == x - clist[0]: # second element, and possibly at least 3 elements to link, # and the next one is in the right step step = x - clist[0] else: # pattern broke, add all values before current position to new list sub = clist[:i] if len(sub) == 1: shortlist.append(str(sub[0] + 1)) else: if step == 1: shortlist.append("%d-%d" % (sub[0] + 1, sub[-1] + 1)) else: shortlist.append("%d-%d\\%d" % (sub[0] + 1, sub[-1] + 1, step)) clist = clist[i:] break return " ".join(shortlist) def combine(matrices): """Combine matrices in [(name,nexus-instance),...] and return new nexus instance. combined_matrix=combine([(name1,nexus_instance1),(name2,nexus_instance2),...] Character sets, character partitions and taxon sets are prefixed, readjusted and present in the combined matrix. """ if not matrices: return None name = matrices[0][0] combined = copy.deepcopy(matrices[0][1]) # initiate with copy of first matrix mixed_datatypes = len(set(n[1].datatype for n in matrices)) > 1 if mixed_datatypes: # dealing with mixed matrices is application specific. # You take care of that yourself! combined.datatype = "None" # raise NexusError('Matrices must be of same datatype') combined.charlabels = None combined.statelabels = None combined.interleave = False combined.translate = None # rename taxon sets and character sets and name them with prefix for cn, cs in combined.charsets.items(): combined.charsets["%s.%s" % (name, cn)] = cs del combined.charsets[cn] for tn, ts in combined.taxsets.items(): combined.taxsets["%s.%s" % (name, tn)] = ts del combined.taxsets[tn] # previous partitions usually don't make much sense in combined matrix # just initiate one new partition parted by single matrices combined.charpartitions = {"combined": {name: list(range(combined.nchar))}} for n, m in matrices[1:]: # add all other matrices both = [t for t in combined.taxlabels if t in m.taxlabels] combined_only = [t for t in combined.taxlabels if t not in both] m_only = [t for t in m.taxlabels if t not in both] for t in both: # concatenate sequences and unify gap and missing character symbols combined.matrix[t] += Seq( str(m.matrix[t]) .replace(m.gap, combined.gap) .replace(m.missing, combined.missing), combined.alphabet, ) # replace date of missing taxa with symbol for missing data for t in combined_only: combined.matrix[t] += Seq(combined.missing * m.nchar, combined.alphabet) for t in m_only: combined.matrix[t] = Seq( combined.missing * combined.nchar, combined.alphabet ) + Seq( str(m.matrix[t]) .replace(m.gap, combined.gap) .replace(m.missing, combined.missing), combined.alphabet, ) combined.taxlabels.extend(m_only) # new taxon list for cn, cs in m.charsets.items(): # adjust character sets for new matrix combined.charsets["%s.%s" % (n, cn)] = [x + combined.nchar for x in cs] if m.taxsets: if not combined.taxsets: combined.taxsets = {} # update taxon sets combined.taxsets.update( dict(("%s.%s" % (n, tn), ts) for tn, ts in m.taxsets.items()) ) # update new charpartition combined.charpartitions["combined"][n] = list( range(combined.nchar, combined.nchar + m.nchar) ) # update charlabels if m.charlabels: if not combined.charlabels: combined.charlabels = {} combined.charlabels.update( dict((combined.nchar + i, label) for (i, label) in m.charlabels.items()) ) combined.nchar += m.nchar # update nchar and ntax combined.ntax += len(m_only) # some prefer partitions, some charsets: # make separate charset for ecah initial dataset for c in combined.charpartitions["combined"]: combined.charsets[c] = combined.charpartitions["combined"][c] return combined def _kill_comments_and_break_lines(text): r"""Delete []-delimited comments out of a file and break into lines separated by ';'. stripped_text=_kill_comments_and_break_lines(text): Nested and multiline comments are allowed. [ and ] symbols within single or double quotes are ignored, newline ends a quote, all symbols with quotes are treated the same (thus not quoting inside comments like [this character ']' ends a comment]) Special [&...] and [\...] comments remain untouched, if not inside standard comment. Quotes inside special [& and [\ are treated as normal characters, but no nesting inside these special comments allowed (like [& [\ ]]). ';' ist deleted from end of line. NOTE: this function is very slow for large files, and obsolete when using C extension cnexus """ if not text: # Empty file/stream return [] contents = iter(text) newtext = [] newline = [] quotelevel = "" speciallevel = False commlevel = 0 # Parse with one character look ahead (for special comments) t2 = next(contents) while True: t = t2 try: t2 = next(contents) except StopIteration: t2 = None if t is None: break if t == quotelevel and not (commlevel or speciallevel): # matching quote ends quotation quotelevel = "" elif ( not quotelevel and not (commlevel or speciallevel) and (t == '"' or t == "'") ): # single or double quote starts quotation quotelevel = t elif not quotelevel and t == "[": # opening bracket outside a quote if t2 in SPECIALCOMMENTS and commlevel == 0 and not speciallevel: speciallevel = True else: commlevel += 1 elif not quotelevel and t == "]": # closing bracket ioutside a quote if speciallevel: speciallevel = False else: commlevel -= 1 if commlevel < 0: raise NexusError("Nexus formatting error: unmatched ]") continue if commlevel == 0: # copy if we're not in comment if t == ";" and not quotelevel: newtext.append("".join(newline)) newline = [] else: newline.append(t) # level of comments should be 0 at the end of the file if newline: newtext.append("\n".join(newline)) if commlevel > 0: raise NexusError("Nexus formatting error: unmatched [") return newtext def _adjust_lines(lines): """Adjust linebreaks to match ';', strip leading/trailing whitespace. list_of_commandlines=_adjust_lines(input_text) Lines are adjusted so that no linebreaks occur within a commandline (except matrix command line) """ formatted_lines = [] for l in lines: # Convert line endings l = l.replace("\r\n", "\n").replace("\r", "\n").strip() if l.lower().startswith("matrix"): formatted_lines.append(l) else: l = l.replace("\n", " ") if l: formatted_lines.append(l) return formatted_lines def _replace_parenthesized_ambigs(seq, rev_ambig_values): """Replaces ambigs in xxx(ACG)xxx format by IUPAC ambiguity code.""" opening = seq.find("(") while opening > -1: closing = seq.find(")") if closing < 0: raise NexusError("Missing closing parenthesis in: " + seq) elif closing < opening: raise NexusError("Missing opening parenthesis in: " + seq) ambig = "".join(sorted(seq[opening + 1 : closing])) ambig_code = rev_ambig_values[ambig.upper()] if ambig != ambig.upper(): ambig_code = ambig_code.lower() seq = seq[:opening] + ambig_code + seq[closing + 1 :] opening = seq.find("(") return seq class Commandline(object): """Represent a commandline as command and options.""" def __init__(self, line, title): self.options = {} options = [] self.command = None try: # Assume matrix (all other command lines have been stripped of \n) self.command, options = line.strip().split("\n", 1) except ValueError: # Not matrix # self.command,options=line.split(' ',1) # no: could be tab or spaces (translate...) self.command = line.split()[0] options = " ".join(line.split()[1:]) self.command = self.command.strip().lower() if self.command in SPECIAL_COMMANDS: # special command that need newlines and order of options preserved self.options = options.strip() else: if len(options) > 0: try: options = options.replace("=", " = ").split() valued_indices = [ (n - 1, n, n + 1) for n in range(len(options)) if options[n] == "=" and n != 0 and n != len((options)) ] indices = [] for sl in valued_indices: indices.extend(sl) token_indices = [n for n in range(len(options)) if n not in indices] for opt in valued_indices: # self.options[options[opt[0]].lower()] = options[opt[2]].lower() self.options[options[opt[0]].lower()] = options[opt[2]] for token in token_indices: self.options[options[token].lower()] = None except ValueError: raise NexusError("Incorrect formatting in line: %s" % line) class Block(object): """Represent a NEXUS block with block name and list of commandlines.""" def __init__(self, title=None): self.title = title self.commandlines = [] class Nexus(object): def __init__(self, input=None): self.ntax = 0 # number of taxa self.nchar = 0 # number of characters self.unaltered_taxlabels = ( [] ) # taxlabels as the appear in the input file (incl. duplicates, etc.) self.taxlabels = [] # labels for taxa, ordered by their id self.charlabels = None # ... and for characters self.statelabels = None # ... and for states self.datatype = "dna" # (standard), dna, rna, nucleotide, protein self.respectcase = False # case sensitivity self.missing = "?" # symbol for missing characters self.gap = "-" # symbol for gap self.symbols = None # set of symbols self.equate = None # set of symbol synonyms self.matchchar = None # matching char for matrix representation self.labels = None # left, right, no self.transpose = False # whether matrix is transposed self.interleave = False # whether matrix is interleaved self.tokens = False # unsupported self.eliminate = None # unsupported self.matrix = None # ... self.unknown_blocks = [] # blocks we don't care about self.taxsets = {} self.charsets = {} self.charpartitions = {} self.taxpartitions = {} self.trees = [] # list of Trees (instances of Tree class) self.translate = None # Dict to translate taxon <-> taxon numbers self.structured = [] # structured input representation self.set = {} # dict of the set command to set various options self.options = {} # dict of the options command in the data block self.codonposset = ( None # name of the charpartition that defines codon positions ) # some defaults self.options["gapmode"] = "missing" if input: self.read(input) else: self.read(DEFAULTNEXUS) def get_original_taxon_order(self): """Included for backwards compatibility (DEPRECATED).""" return self.taxlabels def set_original_taxon_order(self, value): """Included for backwards compatibility (DEPRECATED).""" self.taxlabels = value original_taxon_order = property(get_original_taxon_order, set_original_taxon_order) def read(self, input): """Read and parse NEXUS input (a filename, file-handle, or string).""" # 1. Assume we have the name of a file in the execution dir or a # file-like object. # Note we need to add parsing of the path to dir/filename try: with as_handle(input) as fp: file_contents = fp.read() self.filename = getattr(fp, "name", "Unknown_nexus_file") except (TypeError, IOError, AttributeError): # 2 Assume we have a string from a fh.read() if isinstance(input, str): file_contents = input self.filename = "input_string" else: print(input.strip()[:50]) raise NexusError("Unrecognized input: %s ..." % input[:100]) file_contents = file_contents.strip() if file_contents.startswith("#NEXUS"): file_contents = file_contents[6:] commandlines = _get_command_lines(file_contents) # get rid of stupid 'NEXUS token - in merged treefiles, this might appear multiple times' for i, cl in enumerate(commandlines): try: if cl[:6].upper() == "#NEXUS": commandlines[i] = cl[6:].strip() except: pass # now loop through blocks (we parse only data in known blocks, thus ignoring non-block commands nexus_block_gen = self._get_nexus_block(commandlines) while True: try: title, contents = next(nexus_block_gen) except StopIteration: break if title in KNOWN_NEXUS_BLOCKS: self._parse_nexus_block(title, contents) else: self._unknown_nexus_block(title, contents) def _get_nexus_block(self, file_contents): """Generator for looping through Nexus blocks.""" inblock = False blocklines = [] while file_contents: cl = file_contents.pop(0) if cl.lower().startswith("begin"): if not inblock: inblock = True title = cl.split()[1].lower() else: raise NexusError("Illegal block nesting in block %s" % title) elif cl.lower().startswith("end"): if inblock: inblock = False yield title, blocklines blocklines = [] else: raise NexusError("Unmatched 'end'.") elif inblock: blocklines.append(cl) def _unknown_nexus_block(self, title, contents): block = Block() block.commandlines.append(contents) block.title = title self.unknown_blocks.append(block) def _parse_nexus_block(self, title, contents): """Parse a known Nexus Block (PRIVATE).""" # attached the structered block representation self._apply_block_structure(title, contents) # now check for taxa,characters,data blocks. If this stuff is defined more than once # the later occurences will override the previous ones. block = self.structured[-1] for line in block.commandlines: try: getattr(self, "_" + line.command)(line.options) except AttributeError: raise NexusError("Unknown command: %s " % line.command) def _title(self, options): pass def _link(self, options): pass def _dimensions(self, options): if "ntax" in options: self.ntax = eval(options["ntax"]) if "nchar" in options: self.nchar = eval(options["nchar"]) def _format(self, options): # print options # we first need to test respectcase, then symbols (which depends on respectcase) # then datatype (which, if standard, depends on symbols and respectcase in order to generate # dicts for ambiguous values and alphabet if "respectcase" in options: self.respectcase = True # adjust symbols to for respectcase if "symbols" in options: self.symbols = options["symbols"] if (self.symbols.startswith('"') and self.symbols.endswith('"')) or ( self.symbols.startswith("'") and self.symbols.endswith("'") ): self.symbols = self.symbols[1:-1].replace(" ", "") if not self.respectcase: self.symbols = self.symbols.lower() + self.symbols.upper() self.symbols = list(set(self.symbols)) if "datatype" in options: self.datatype = options["datatype"].lower() # TODO: Create a fresh instance of each object for self.alphabet if self.datatype == "dna" or self.datatype == "nucleotide": self.alphabet = IUPAC.ambiguous_dna self.ambiguous_values = IUPACData.ambiguous_dna_values.copy() self.unambiguous_letters = IUPACData.unambiguous_dna_letters elif self.datatype == "rna": self.alphabet = IUPAC.ambiguous_rna self.ambiguous_values = IUPACData.ambiguous_rna_values.copy() self.unambiguous_letters = IUPACData.unambiguous_rna_letters elif self.datatype == "protein": # TODO - Should this not be ExtendedIUPACProtein? self.alphabet = IUPAC.protein self.ambiguous_values = { "B": "DN", "Z": "EQ", "X": IUPACData.protein_letters, } # that's how PAUP handles it self.unambiguous_letters = IUPACData.protein_letters + "*" # stop-codon elif self.datatype == "standard": raise NexusError("Datatype standard is not yet supported.") # self.alphabet = None # self.ambiguous_values = {} # if not self.symbols: # self.symbols = '01' # if nothing else defined, then 0 and 1 are the default states # self.unambiguous_letters = self.symbols else: raise NexusError("Unsupported datatype: " + self.datatype) self.valid_characters = ( "".join(self.ambiguous_values) + self.unambiguous_letters ) if not self.respectcase: self.valid_characters = ( self.valid_characters.lower() + self.valid_characters.upper() ) # we have to sort the reverse ambig coding dict key characters: # to be sure that it's 'ACGT':'N' and not 'GTCA':'N' rev = dict( (i[1], i[0]) for i in self.ambiguous_values.items() if i[0] != "X" ) self.rev_ambiguous_values = {} for k, v in rev.items(): key = sorted(c for c in k) self.rev_ambiguous_values["".join(key)] = v # overwrite symbols for datype rna,dna,nucleotide if self.datatype in ["dna", "rna", "nucleotide"]: self.symbols = self.alphabet.letters if self.missing not in self.ambiguous_values: self.ambiguous_values[self.missing] = ( self.unambiguous_letters + self.gap ) self.ambiguous_values[self.gap] = self.gap elif self.datatype == "standard": if not self.symbols: self.symbols = ["1", "0"] if "missing" in options: self.missing = options["missing"][0] if "gap" in options: self.gap = options["gap"][0] if "equate" in options: self.equate = options["equate"] if "matchchar" in options: self.matchchar = options["matchchar"][0] if "labels" in options: self.labels = options["labels"] if "transpose" in options: raise NexusError("TRANSPOSE is not supported!") self.transpose = True if "interleave" in options: if options["interleave"] is None or options["interleave"].lower() == "yes": self.interleave = True if "tokens" in options: self.tokens = True if "notokens" in options: self.tokens = False def _set(self, options): self.set = options def _options(self, options): self.options = options def _eliminate(self, options): self.eliminate = options def _taxlabels(self, options): """Get taxon labels (PRIVATE). As the taxon names are already in the matrix, this is superfluous except for transpose matrices, which are currently unsupported anyway. Thus, we ignore the taxlabels command to make handling of duplicate taxon names easier. """ pass # self.taxlabels = [] # opts = CharBuffer(options) # while True: # taxon = quotestrip(opts.next_word()) # if not taxon: # break # self.taxlabels.append(taxon) def _check_taxlabels(self, taxon): """Check for presence of taxon in self.taxlabels.""" # According to NEXUS standard, underscores shall be treated as spaces..., # so checking for identity is more difficult nextaxa = dict((t.replace(" ", "_"), t) for t in self.taxlabels) nexid = taxon.replace(" ", "_") return nextaxa.get(nexid) def _charlabels(self, options): self.charlabels = {} opts = CharBuffer(options) while True: # get id and state w = opts.next_word() if ( w is None ): # McClade saves and reads charlabel-lists with terminal comma?! break identifier = self._resolve(w, set_type=CHARSET) state = quotestrip(opts.next_word()) self.charlabels[identifier] = state # check for comma or end of command c = opts.next_nonwhitespace() if c is None: break elif c != ",": raise NexusError("Missing ',' in line %s." % options) def _charstatelabels(self, options): # warning: charstatelabels supports only charlabels-syntax! self._charlabels(options) def _statelabels(self, options): # self.charlabels = options # print 'Command statelabels is not supported and will be ignored.' pass def _matrix(self, options): if not self.ntax or not self.nchar: raise NexusError("Dimensions must be specified before matrix!") self.matrix = {} taxcount = 0 first_matrix_block = True # eliminate empty lines and leading/trailing whitespace lines = [l.strip() for l in options.split("\n") if l.strip() != ""] lineiter = iter(lines) while True: try: l = next(lineiter) except StopIteration: if taxcount < self.ntax: raise NexusError("Not enough taxa in matrix.") elif taxcount > self.ntax: raise NexusError("Too many taxa in matrix.") else: break # count the taxa and check for interleaved matrix taxcount += 1 ##print taxcount if taxcount > self.ntax: if not self.interleave: raise NexusError( "Too many taxa in matrix - should matrix be interleaved?" ) else: taxcount = 1 first_matrix_block = False # get taxon name and sequence linechars = CharBuffer(l) id = quotestrip(linechars.next_word()) l = linechars.rest().strip() chars = "" if self.interleave: # interleaved matrix # print 'In interleave' if l: chars = "".join(l.split()) else: chars = "".join(next(lineiter).split()) else: # non-interleaved matrix chars = "".join(l.split()) while len(chars) < self.nchar: l = next(lineiter) chars += "".join(l.split()) iupac_seq = Seq( _replace_parenthesized_ambigs(chars, self.rev_ambiguous_values), self.alphabet, ) # first taxon has the reference sequence if matchhar is used if taxcount == 1: refseq = iupac_seq else: if self.matchchar: while True: p = str(iupac_seq).find(self.matchchar) if p == -1: break iupac_seq = Seq( str(iupac_seq)[:p] + refseq[p] + str(iupac_seq)[p + 1 :], self.alphabet, ) # check for invalid characters for i, c in enumerate(str(iupac_seq)): if ( c not in self.valid_characters and c != self.gap and c != self.missing ): raise NexusError( "Taxon %s: Illegal character %s in sequence %s " "(check dimensions/interleaving)" % (id, c, iupac_seq) ) # add sequence to matrix if first_matrix_block: self.unaltered_taxlabels.append(id) id = _unique_label(list(self.matrix.keys()), id) self.matrix[id] = iupac_seq self.taxlabels.append(id) else: # taxon names need to be in the same order in each interleaved block id = _unique_label(self.taxlabels[: taxcount - 1], id) taxon_present = self._check_taxlabels(id) if taxon_present: self.matrix[taxon_present] += iupac_seq else: raise NexusError( "Taxon %s not in first block of interleaved " "matrix. Check matrix dimensions and interleave." % id ) # check all sequences for length according to nchar for taxon in self.matrix: if len(self.matrix[taxon]) != self.nchar: raise NexusError( "Matrix Nchar %d does not match data length (%d) for taxon %s" % (self.nchar, len(self.matrix[taxon]), taxon) ) # check that taxlabels is identical with matrix.keys. If not, it's a problem matrixkeys = sorted(self.matrix) taxlabelssort = sorted(self.taxlabels[:]) assert matrixkeys == taxlabelssort, ( "ERROR: TAXLABELS must be identical with MATRIX. " + "Please Report this as a bug, and send in data file." ) def _translate(self, options): self.translate = {} opts = CharBuffer(options) while True: try: # get id and state identifier = int(opts.next_word()) label = quotestrip(opts.next_word()) self.translate[identifier] = label # check for comma or end of command c = opts.next_nonwhitespace() if c is None: break elif c != ",": raise NexusError("Missing ',' in line %s." % options) except NexusError: raise except: raise NexusError("Format error in line %s." % options) def _utree(self, options): """Some software (clustalx) uses 'utree' to denote an unrooted tree.""" self._tree(options) def _tree(self, options): opts = CharBuffer(options) if opts.peek_nonwhitespace() == "*": # a star can be used to make it the default tree in some software packages dummy = opts.next_nonwhitespace() name = opts.next_word() if opts.next_nonwhitespace() != "=": raise NexusError("Syntax error in tree description: %s" % options[:50]) rooted = False weight = 1.0 while opts.peek_nonwhitespace() == "[": open = opts.next_nonwhitespace() symbol = next(opts) if symbol != "&": raise NexusError( "Illegal special comment [%s...] in tree description: %s" % (symbol, options[:50]) ) special = next(opts) value = opts.next_until("]") closing = next(opts) if special == "R": rooted = True elif special == "U": rooted = False elif special == "W": weight = float(value) tree = Tree(name=name, weight=weight, rooted=rooted, tree=opts.rest().strip()) # if there's an active translation table, translate if self.translate: for n in tree.get_terminals(): try: tree.node(n).data.taxon = safename( self.translate[int(tree.node(n).data.taxon)] ) except (ValueError, KeyError): raise NexusError( "Unable to substitute %s using 'translate' data." % tree.node(n).data.taxon ) self.trees.append(tree) def _apply_block_structure(self, title, lines): block = Block("") block.title = title for line in lines: block.commandlines.append(Commandline(line, title)) self.structured.append(block) def _taxset(self, options): name, taxa = self._get_indices(options, set_type=TAXSET) self.taxsets[name] = _make_unique(taxa) def _charset(self, options): name, sites = self._get_indices(options, set_type=CHARSET) self.charsets[name] = _make_unique(sites) def _taxpartition(self, options): taxpartition = {} quotelevel = False opts = CharBuffer(options) name = self._name_n_vector(opts) if not name: raise NexusError("Formatting error in taxpartition: %s " % options) # now collect thesubbpartitions and parse them # subpartitons separated by commas - which unfortunately could be part of a quoted identifier... # this is rather unelegant, but we have to avoid double-parsing and potential change of special nexus-words sub = "" while True: w = next(opts) if w is None or (w == "," and not quotelevel): subname, subindices = self._get_indices( sub, set_type=TAXSET, separator=":" ) taxpartition[subname] = _make_unique(subindices) sub = "" if w is None: break else: if w == "'": quotelevel = not quotelevel sub += w self.taxpartitions[name] = taxpartition def _codonposset(self, options): """Read codon positions from a codons block as written from McClade. Here codonposset is just a fancy name for a character partition with the name CodonPositions and the partitions N,1,2,3 """ prev_partitions = list(self.charpartitions.keys()) self._charpartition(options) # mcclade calls it CodonPositions, but you never know... codonname = [n for n in self.charpartitions if n not in prev_partitions] if codonname == [] or len(codonname) > 1: raise NexusError("Formatting Error in codonposset: %s " % options) else: self.codonposset = codonname[0] def _codeset(self, options): pass def _charpartition(self, options): charpartition = {} quotelevel = False opts = CharBuffer(options) name = self._name_n_vector(opts) if not name: raise NexusError("Formatting error in charpartition: %s " % options) # now collect thesubbpartitions and parse them # subpartitons separated by commas - which unfortunately could be part of a quoted identifier... sub = "" while True: w = next(opts) if w is None or (w == "," and not quotelevel): subname, subindices = self._get_indices( sub, set_type=CHARSET, separator=":" ) charpartition[subname] = _make_unique(subindices) sub = "" if w is None: break else: if w == "'": quotelevel = not quotelevel sub += w self.charpartitions[name] = charpartition def _get_indices(self, options, set_type=CHARSET, separator="="): """Parse the taxset/charset specification (PRIVATE). e.g. '1 2 3 - 5 dog cat 10 - 20 \\ 3' --> [0,1,2,3,4,'dog','cat',9,12,15,18] """ opts = CharBuffer(options) name = self._name_n_vector(opts, separator=separator) indices = self._parse_list(opts, set_type=set_type) if indices is None: raise NexusError("Formatting error in line: %s " % options) return name, indices def _name_n_vector(self, opts, separator="="): """Extract name and check that it's not in vector format.""" rest = opts.rest() name = opts.next_word() # we ignore * before names if name == "*": name = opts.next_word() if not name: raise NexusError("Formatting error in line: %s " % rest) name = quotestrip(name) if opts.peek_nonwhitespace == "(": open = opts.next_nonwhitespace() qualifier = open.next_word() close = opts.next_nonwhitespace() if qualifier.lower() == "vector": raise NexusError("Unsupported VECTOR format in line %s" % (opts)) elif qualifier.lower() != "standard": raise NexusError("Unknown qualifier %s in line %s" % (qualifier, opts)) if opts.next_nonwhitespace() != separator: raise NexusError("Formatting error in line: %s " % rest) return name def _parse_list(self, options_buffer, set_type): """Parse a NEXUS list (PRIVATE). e.g. [1, 2, 4-8\\2, dog, cat] --> [1,2,4,6,8,17,21], (assuming dog is taxon no. 17 and cat is taxon no. 21). """ plain_list = [] if options_buffer.peek_nonwhitespace(): try: # capture all possible exceptions and treat them as formatting # errors, if they are not NexusError while True: identifier = options_buffer.next_word() # next list element if not identifier: # end of list? break start = self._resolve(identifier, set_type=set_type) if options_buffer.peek_nonwhitespace() == "-": # followd by - end = start step = 1 # get hyphen and end of range hyphen = options_buffer.next_nonwhitespace() end = self._resolve( options_buffer.next_word(), set_type=set_type ) if set_type == CHARSET: if ( options_buffer.peek_nonwhitespace() == "\\" ): # followd by \ backslash = options_buffer.next_nonwhitespace() step = int( options_buffer.next_word() ) # get backslash and step plain_list.extend(range(start, end + 1, step)) else: if isinstance(start, list) or isinstance(end, list): raise NexusError( "Name if character sets not allowed in range definition: %s" % identifier ) start = self.taxlabels.index(start) end = self.taxlabels.index(end) taxrange = self.taxlabels[start : end + 1] plain_list.extend(taxrange) else: if isinstance( start, list ): # start was the name of charset or taxset plain_list.extend(start) else: # start was an ordinary identifier plain_list.append(start) except NexusError: raise except: return None return plain_list def _resolve(self, identifier, set_type=None): """Translate identifier in list into character/taxon index. Characters (which are referred to by their index in Nexus.py): Plain numbers are returned minus 1 (Nexus indices to python indices) Text identifiers are translated into their indices (if plain character identifiers), the first hit in charlabels is returned (charlabels don't need to be unique) or the range of indices is returned (if names of character sets). Taxa (which are referred to by their unique name in Nexus.py): Plain numbers are translated in their taxon name, underscores and spaces are considered equal. Names are returned unchanged (if plain taxon identifiers), or the names in the corresponding taxon set is returned. """ identifier = quotestrip(identifier) if not set_type: raise NexusError("INTERNAL ERROR: Need type to resolve identifier.") if set_type == CHARSET: try: n = int(identifier) except ValueError: if self.charlabels and identifier in self.charlabels.values(): for k in self.charlabels: if self.charlabels[k] == identifier: return k elif self.charsets and identifier in self.charsets: return self.charsets[identifier] else: raise NexusError("Unknown character identifier: %s" % identifier) else: if n <= self.nchar: return n - 1 else: raise NexusError( "Illegal character identifier: %d>nchar (=%d)." % (identifier, self.nchar) ) elif set_type == TAXSET: try: n = int(identifier) except ValueError: taxlabels_id = self._check_taxlabels(identifier) if taxlabels_id: return taxlabels_id elif self.taxsets and identifier in self.taxsets: return self.taxsets[identifier] else: raise NexusError("Unknown taxon identifier: %s" % identifier) else: if n > 0 and n <= self.ntax: return self.taxlabels[n - 1] else: raise NexusError( "Illegal taxon identifier: %d>ntax (=%d)." % (identifier, self.ntax) ) else: raise NexusError("Unknown set specification: %s." % set_type) def _stateset(self, options): # Not implemented pass def _changeset(self, options): # Not implemented pass def _treeset(self, options): # Not implemented pass def _treepartition(self, options): # Not implemented pass def write_nexus_data_partitions( self, matrix=None, filename=None, blocksize=None, interleave=False, exclude=[], delete=[], charpartition=None, comment="", mrbayes=False, ): """Writes a nexus file for each partition in charpartition. Only non-excluded characters and non-deleted taxa are included, just the data block is written. """ if not matrix: matrix = self.matrix if not matrix: return if not filename: filename = self.filename if charpartition: pfilenames = {} for p in charpartition: total_exclude = [] + exclude total_exclude.extend( c for c in range(self.nchar) if c not in charpartition[p] ) total_exclude = _make_unique(total_exclude) pcomment = comment + "\nPartition: " + p + "\n" dot = filename.rfind(".") if dot > 0: pfilename = filename[:dot] + "_" + p + ".data" else: pfilename = filename + "_" + p pfilenames[p] = pfilename self.write_nexus_data( filename=pfilename, matrix=matrix, blocksize=blocksize, interleave=interleave, exclude=total_exclude, delete=delete, comment=pcomment, append_sets=False, mrbayes=mrbayes, ) return pfilenames else: fn = self.filename + ".data" self.write_nexus_data( filename=fn, matrix=matrix, blocksize=blocksize, interleave=interleave, exclude=exclude, delete=delete, comment=comment, append_sets=False, mrbayes=mrbayes, ) return fn def write_nexus_data( self, filename=None, matrix=None, exclude=[], delete=[], blocksize=None, interleave=False, interleave_by_partition=False, comment=None, omit_NEXUS=False, append_sets=True, mrbayes=False, codons_block=True, ): """Writes a nexus file with data and sets block to a file or handle. Character sets and partitions are appended by default, and are adjusted according to excluded characters (i.e. character sets still point to the same sites (not necessarily same positions), without including the deleted characters. filename - Either a filename as a string (which will be opened, written to and closed), or a handle object (which will be written to but NOT closed). interleave_by_partition - Optional name of partition (string) omit_NEXUS - Boolean. If true, the '#NEXUS' line normally at the start of the file is omitted. Returns the filename/handle used to write the data. """ if not matrix: matrix = self.matrix if not matrix: return if not filename: filename = self.filename if [t for t in delete if not self._check_taxlabels(t)]: raise NexusError( "Unknown taxa: %s" % ", ".join(set(delete).difference(set(self.taxlabels))) ) if interleave_by_partition: if not interleave_by_partition in self.charpartitions: raise NexusError("Unknown partition: %r" % interleave_by_partition) else: partition = self.charpartitions[interleave_by_partition] # we need to sort the partition names by starting position before we exclude characters names = _sort_keys_by_values(partition) newpartition = {} for p in partition: newpartition[p] = [c for c in partition[p] if c not in exclude] # how many taxa and how many characters are left? undelete = [ taxon for taxon in self.taxlabels if taxon in matrix and taxon not in delete ] cropped_matrix = _seqmatrix2strmatrix( self.crop_matrix(matrix, exclude=exclude, delete=delete) ) ntax_adjusted = len(undelete) nchar_adjusted = len(cropped_matrix[undelete[0]]) if not undelete or (undelete and undelete[0] == ""): return with as_handle(filename, mode="w") as fh: if not omit_NEXUS: fh.write("#NEXUS\n") if comment: fh.write("[" + comment + "]\n") fh.write("begin data;\n") fh.write( "\tdimensions ntax=%d nchar=%d;\n" % (ntax_adjusted, nchar_adjusted) ) fh.write("\tformat datatype=" + self.datatype) if self.respectcase: fh.write(" respectcase") if self.missing: fh.write(" missing=" + self.missing) if self.gap: fh.write(" gap=" + self.gap) if self.matchchar: fh.write(" matchchar=" + self.matchchar) if self.labels: fh.write(" labels=" + self.labels) if self.equate: fh.write(" equate=" + self.equate) if interleave or interleave_by_partition: fh.write(" interleave") fh.write(";\n") # if self.taxlabels: # fh.write('taxlabels '+' '.join(self.taxlabels)+';\n') if self.charlabels: newcharlabels = self._adjust_charlabels(exclude=exclude) clkeys = sorted(newcharlabels) fh.write( "charlabels " + ", ".join( "%s %s" % (k + 1, safename(newcharlabels[k])) for k in clkeys ) + ";\n" ) fh.write("matrix\n") if not blocksize: if interleave: blocksize = 70 else: blocksize = self.nchar # delete deleted taxa and ecxclude excluded characters... namelength = max(len(safename(t, mrbayes=mrbayes)) for t in undelete) if interleave_by_partition: # interleave by partitions, but adjust partitions with regard to excluded characters seek = 0 for p in names: fh.write("[%s: %s]\n" % (interleave_by_partition, p)) if len(newpartition[p]) > 0: for taxon in undelete: fh.write( safename(taxon, mrbayes=mrbayes).ljust(namelength + 1) ) fh.write( cropped_matrix[taxon][ seek : seek + len(newpartition[p]) ] + "\n" ) fh.write("\n") else: fh.write("[empty]\n\n") seek += len(newpartition[p]) elif interleave: for seek in range(0, nchar_adjusted, blocksize): for taxon in undelete: fh.write(safename(taxon, mrbayes=mrbayes).ljust(namelength + 1)) fh.write(cropped_matrix[taxon][seek : seek + blocksize] + "\n") fh.write("\n") else: for taxon in undelete: if blocksize < nchar_adjusted: fh.write(safename(taxon, mrbayes=mrbayes) + "\n") else: fh.write(safename(taxon, mrbayes=mrbayes).ljust(namelength + 1)) taxon_seq = cropped_matrix[taxon] for seek in range(0, nchar_adjusted, blocksize): fh.write(taxon_seq[seek : seek + blocksize] + "\n") del taxon_seq fh.write(";\nend;\n") if append_sets: if codons_block: fh.write( self.append_sets( exclude=exclude, delete=delete, mrbayes=mrbayes, include_codons=False, ) ) fh.write( self.append_sets( exclude=exclude, delete=delete, mrbayes=mrbayes, codons_only=True, ) ) else: fh.write( self.append_sets( exclude=exclude, delete=delete, mrbayes=mrbayes ) ) return filename def append_sets( self, exclude=[], delete=[], mrbayes=False, include_codons=True, codons_only=False, ): """Returns a sets block.""" if not self.charsets and not self.taxsets and not self.charpartitions: return "" if codons_only: setsb = ["\nbegin codons"] else: setsb = ["\nbegin sets"] # - now if characters have been excluded, the character sets need to be adjusted, # so that they still point to the right character positions # calculate a list of offsets: for each deleted character, the following character position # in the new file will have an additional offset of -1 offset = 0 offlist = [] for c in range(self.nchar): if c in exclude: offset += 1 offlist.append( -1 ) # dummy value as these character positions are excluded else: offlist.append(c - offset) # now adjust each of the character sets if not codons_only: for n, ns in self.charsets.items(): cset = [offlist[c] for c in ns if c not in exclude] if cset: setsb.append( "charset %s = %s" % (safename(n), _compact4nexus(cset)) ) for n, s in self.taxsets.items(): tset = [safename(t, mrbayes=mrbayes) for t in s if t not in delete] if tset: setsb.append("taxset %s = %s" % (safename(n), " ".join(tset))) for n, p in self.charpartitions.items(): if not include_codons and n == CODONPOSITIONS: continue elif codons_only and n != CODONPOSITIONS: continue # as characters have been excluded, the partitions must be adjusted # if a partition is empty, it will be omitted from the charpartition command # (although paup allows charpartition part=t1:,t2:,t3:1-100) names = _sort_keys_by_values(p) newpartition = {} for sn in names: nsp = [offlist[c] for c in p[sn] if c not in exclude] if nsp: newpartition[sn] = nsp if newpartition: if include_codons and n == CODONPOSITIONS: command = "codonposset" else: command = "charpartition" setsb.append( "%s %s = %s" % ( command, safename(n), ", ".join( "%s: %s" % (sn, _compact4nexus(newpartition[sn])) for sn in names if sn in newpartition ), ) ) # now write charpartititions, much easier than charpartitions for n, p in self.taxpartitions.items(): names = _sort_keys_by_values(p) newpartition = {} for sn in names: nsp = [t for t in p[sn] if t not in delete] if nsp: newpartition[sn] = nsp if newpartition: setsb.append( "taxpartition %s = %s" % ( safename(n), ", ".join( "%s: %s" % ( safename(sn), " ".join(safename(x) for x in newpartition[sn]), ) for sn in names if sn in newpartition ), ) ) # add 'end' and return everything setsb.append("end;\n") if len(setsb) == 2: # begin and end only return "" else: return ";\n".join(setsb) def export_fasta(self, filename=None, width=70): """Writes matrix into a fasta file.""" if not filename: if "." in self.filename and self.filename.split(".")[-1].lower() in [ "paup", "nexus", "nex", "dat", ]: filename = ".".join(self.filename.split(".")[:-1]) + ".fas" else: filename = self.filename + ".fas" with open(filename, "w") as fh: for taxon in self.taxlabels: fh.write(">" + safename(taxon) + "\n") for i in range(0, len(str(self.matrix[taxon])), width): fh.write(str(self.matrix[taxon])[i : i + width] + "\n") return filename def export_phylip(self, filename=None): """Writes matrix into a PHYLIP file. Note that this writes a relaxed PHYLIP format file, where the names are not truncated, nor checked for invalid characters.""" if not filename: if "." in self.filename and self.filename.split(".")[-1].lower() in [ "paup", "nexus", "nex", "dat", ]: filename = ".".join(self.filename.split(".")[:-1]) + ".phy" else: filename = self.filename + ".phy" with open(filename, "w") as fh: fh.write("%d %d\n" % (self.ntax, self.nchar)) for taxon in self.taxlabels: fh.write("%s %s\n" % (safename(taxon), str(self.matrix[taxon]))) return filename def constant(self, matrix=None, delete=[], exclude=[]): """Return a list with all constant characters.""" if not matrix: matrix = self.matrix undelete = [t for t in self.taxlabels if t in matrix and t not in delete] if not undelete: return None elif len(undelete) == 1: return [x for x in range(len(matrix[undelete[0]])) if x not in exclude] # get the first sequence and expand all ambiguous values constant = [ (x, self.ambiguous_values.get(n.upper(), n.upper())) for x, n in enumerate(str(matrix[undelete[0]])) if x not in exclude ] for taxon in undelete[1:]: newconstant = [] for site in constant: # print '%d (paup=%d)' % (site[0],site[0]+1), seqsite = matrix[taxon][site[0]].upper() # print seqsite,'checked against',site[1],'\t', if ( seqsite == self.missing or ( seqsite == self.gap and self.options["gapmode"].lower() == "missing" ) or seqsite == site[1] ): # missing or same as before -> ok newconstant.append(site) elif ( seqsite in site[1] or site[1] == self.missing or ( self.options["gapmode"].lower() == "missing" and site[1] == self.gap ) ): # subset of an ambig or only missing in previous -> take subset newconstant.append( (site[0], self.ambiguous_values.get(seqsite, seqsite)) ) elif seqsite in self.ambiguous_values: # is it an ambig: check the intersection with prev. values intersect = set(self.ambiguous_values[seqsite]).intersection( set(site[1]) ) if intersect: newconstant.append((site[0], "".join(intersect))) # print 'ok' # else: # print 'failed' # else: # print 'failed' constant = newconstant cpos = [s[0] for s in constant] return cpos def cstatus(self, site, delete=[], narrow=True): """Summarize character. narrow=True: paup-mode (a c ? --> ac; ? ? ? --> ?) narrow=false: (a c ? --> a c g t -; ? ? ? --> a c g t -) """ undelete = [t for t in self.taxlabels if t not in delete] if not undelete: return None cstatus = [] for t in undelete: c = self.matrix[t][site].upper() if self.options.get("gapmode") == "missing" and c == self.gap: c = self.missing if narrow and c == self.missing: if c not in cstatus: cstatus.append(c) else: cstatus.extend(b for b in self.ambiguous_values[c] if b not in cstatus) if self.missing in cstatus and narrow and len(cstatus) > 1: cstatus = [c for c in cstatus if c != self.missing] cstatus.sort() return cstatus def weighted_stepmatrix(self, name="your_name_here", exclude=[], delete=[]): """Calculates a stepmatrix for weighted parsimony. See Wheeler (1990), Cladistics 6:269-275 and Felsenstein (1981), Biol. J. Linn. Soc. 16:183-196 """ m = StepMatrix(self.unambiguous_letters, self.gap) for site in [s for s in range(self.nchar) if s not in exclude]: cstatus = self.cstatus(site, delete) for i, b1 in enumerate(cstatus[:-1]): for b2 in cstatus[i + 1 :]: m.add(b1.upper(), b2.upper(), 1) return m.transformation().weighting().smprint(name=name) def crop_matrix(self, matrix=None, delete=[], exclude=[]): """Return a matrix without deleted taxa and excluded characters.""" if not matrix: matrix = self.matrix if [t for t in delete if not self._check_taxlabels(t)]: raise NexusError( "Unknown taxa: %s" % ", ".join(set(delete).difference(self.taxlabels)) ) if exclude != []: undelete = [t for t in self.taxlabels if t in matrix and t not in delete] if not undelete: return {} m = [str(matrix[k]) for k in undelete] sitesm = [s for i, s in enumerate(zip(*m)) if i not in exclude] if sitesm == []: return dict((t, Seq("", self.alphabet)) for t in undelete) else: m = [Seq(s, self.alphabet) for s in ("".join(x) for x in zip(*sitesm))] return dict(zip(undelete, m)) else: return dict( (t, matrix[t]) for t in self.taxlabels if t in matrix and t not in delete ) def bootstrap(self, matrix=None, delete=[], exclude=[]): """Return a bootstrapped matrix.""" if not matrix: matrix = self.matrix seqobjects = isinstance( matrix[list(matrix.keys())[0]], Seq ) # remember if Seq objects cm = self.crop_matrix(delete=delete, exclude=exclude) # crop data out if not cm: # everything deleted? return {} elif not cm[list(cm.keys())[0]]: # everything excluded? return cm undelete = [t for t in self.taxlabels if t in cm] if seqobjects: sitesm = list(zip(*[str(cm[t]) for t in undelete])) alphabet = matrix[list(matrix.keys())[0]].alphabet else: sitesm = list(zip(*[cm[t] for t in undelete])) bootstrapsitesm = [ sitesm[random.randint(0, len(sitesm) - 1)] for i in range(len(sitesm)) ] bootstrapseqs = ["".join(x) for x in zip(*bootstrapsitesm)] if seqobjects: bootstrapseqs = [Seq(s, alphabet) for s in bootstrapseqs] return dict(zip(undelete, bootstrapseqs)) def add_sequence(self, name, sequence): """Adds a sequence (string) to the matrix.""" if not name: raise NexusError("New sequence must have a name") diff = self.nchar - len(sequence) if diff < 0: self.insert_gap(self.nchar, -diff) elif diff > 0: sequence += self.missing * diff if name in self.taxlabels: unique_name = _unique_label(self.taxlabels, name) # print "WARNING: Sequence name %s is already present. Sequence was added as %s." % (name,unique_name) else: unique_name = name assert ( unique_name not in self.matrix ), "ERROR. There is a discrepancy between taxlabels and matrix keys. Report this as a bug." self.matrix[unique_name] = Seq(sequence, self.alphabet) self.ntax += 1 self.taxlabels.append(unique_name) self.unaltered_taxlabels.append(name) def insert_gap(self, pos, n=1, leftgreedy=False): """Add a gap into the matrix and adjust charsets and partitions. pos=0: first position pos=nchar: last position """ def _adjust(set, x, d, leftgreedy=False): """Adjusts character sets if gaps are inserted, taking care of new gaps within a coherent character set.""" # if 3 gaps are inserted at pos. 9 in a set that looks like 1 2 3 8 9 10 11 13 14 15 # then the adjusted set will be 1 2 3 8 9 10 11 12 13 14 15 16 17 18 # but inserting into position 8 it will stay like 1 2 3 11 12 13 14 15 16 17 18 set.sort() addpos = 0 for i, c in enumerate(set): if c >= x: set[i] = c + d # if we add gaps within a group of characters, we want the gap position included in this group if c == x: if leftgreedy or (i > 0 and set[i - 1] == c - 1): addpos = i if addpos > 0: set[addpos:addpos] = list(range(x, x + d)) return set if pos < 0 or pos > self.nchar: raise NexusError("Illegal gap position: %d" % pos) if n == 0: return sitesm = list(zip(*[str(self.matrix[t]) for t in self.taxlabels])) sitesm[pos:pos] = [["-"] * len(self.taxlabels)] * n mapped = ["".join(x) for x in zip(*sitesm)] listed = [ (taxon, Seq(mapped[i], self.alphabet)) for i, taxon in enumerate(self.taxlabels) ] self.matrix = dict(listed) self.nchar += n # now adjust character sets for i, s in self.charsets.items(): self.charsets[i] = _adjust(s, pos, n, leftgreedy=leftgreedy) for p in self.charpartitions: for sp, s in self.charpartitions[p].items(): self.charpartitions[p][sp] = _adjust(s, pos, n, leftgreedy=leftgreedy) # now adjust character state labels self.charlabels = self._adjust_charlabels(insert=[pos] * n) return self.charlabels def _adjust_charlabels(self, exclude=None, insert=None): """Return adjusted indices of self.charlabels if characters are excluded or inserted.""" if exclude and insert: raise NexusError("Can't exclude and insert at the same time") if not self.charlabels: return None labels = sorted(self.charlabels) newcharlabels = {} if exclude: exclude.sort() exclude.append(sys.maxsize) excount = 0 for c in labels: if not c in exclude: while c > exclude[excount]: excount += 1 newcharlabels[c - excount] = self.charlabels[c] elif insert: insert.sort() insert.append(sys.maxsize) icount = 0 for c in labels: while c >= insert[icount]: icount += 1 newcharlabels[c + icount] = self.charlabels[c] else: return self.charlabels return newcharlabels def invert(self, charlist): """Returns all character indices that are not in charlist.""" return [c for c in range(self.nchar) if c not in charlist] def gaponly(self, include_missing=False): """Return gap-only sites.""" gap = set(self.gap) if include_missing: gap.add(self.missing) sitesm = zip(*[str(self.matrix[t]) for t in self.taxlabels]) return [i for i, site in enumerate(sitesm) if set(site).issubset(gap)] def terminal_gap_to_missing(self, missing=None, skip_n=True): """Replaces all terminal gaps with missing character. Mixtures like ???------??------- are properly resolved.""" if not missing: missing = self.missing replace = [self.missing, self.gap] if not skip_n: replace.extend(["n", "N"]) for taxon in self.taxlabels: sequence = str(self.matrix[taxon]) length = len(sequence) start, end = get_start_end(sequence, skiplist=replace) if start == -1 and end == -1: sequence = missing * length else: sequence = sequence[: end + 1] + missing * (length - end - 1) sequence = start * missing + sequence[start:] assert length == len(sequence), ( "Illegal sequence manipulation in Nexus.terminal_gap_to_missing in taxon %s" % taxon ) self.matrix[taxon] = Seq(sequence, self.alphabet) weblogo-3.8.0/weblogo/seq_io/array_io.py000077500000000000000000000111461467613320200202660ustar00rootroot00000000000000#!/usr/bin/env python # Copyright (c) 2005 Gavin E. Crooks # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # """Read and write a rectangular array of sequence data. One sequence per line and nothing else. Each line must contain the same number of characters. Blank lines and white space are ignored. --- Example Array --- --------------------------LENSTSPYDYGENESD-------FSDSPPCPQDF --------------------------LENLEDLF-WELDRLD------NYNDTSLVENH- --------------------------MSNITDPQMWDFDDLN-------FTGMPPADEDY -----------------------------------YTSDN---------YSGSGDYDSNK -SL-------NFDRTFLPALYSLLFLLGLLGNGAVAAVLLSQRTALSSTDTFLLHLAVAD --LC-PATMASFKAVFVPVAYSLIFLLGVIGNVLVLVILERHRQTRSSTETFLFHLAVAD -SPC-MLETETLNKYVVIIAYALVFLLSLLGNSLVMLVILYSRVGRSVTDVYLLNLALAD -EPC-RDENVHFNRIFLPTIYFIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHLSVAD """ from typing import Generator, Optional, TextIO from ..seq import Alphabet, Seq, SeqList from ..utils import remove_whitespace example = """ --------------------------LENSTSPYDYGENESD-------FSDSPPCPQDF --------------------------LENLEDLF-WELDRLD------NYNDTSLVENH- --------------------------MSNITDPQMWDFDDLN-------FTGMPPADEDY -----------------------------------YTSDN---------YSGSGDYDSNK -SL-------NFDRTFLPALYSLLFLLGLLGNGAVAAVLLSQRTALSSTDTFLLHLAVAD --LC-PATMASFKAVFVPVAYSLIFLLGVIGNVLVLVILERHRQTRSSTETFLFHLAVAD -SPC-MLETETLNKYVVIIAYALVFLLSLLGNSLVMLVILYSRVGRSVTDVYLLNLALAD -EPC-RDENVHFNRIFLPTIYFIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHLSVAD """ names = ("array", "flatfile") extensions = () def read(fin: TextIO, alphabet: Optional[Alphabet] = None) -> SeqList: """Read a file of raw sequence alignment data. Args: fin -- A stream or file to read alphabet -- The expected alphabet of the data, if given Returns: SeqList -- A list of sequences Raises: ValueError -- If the file is unparsable """ seqs = [s for s in iterseq(fin, alphabet)] return SeqList(seqs) def iterseq(fin: TextIO, alphabet: Optional[Alphabet] = None) -> Generator: """Read one line of sequence data and yield the sequence. Args: fin -- A stream or file to read alphabet -- The expected alphabet of the data, if given Yields: Seq -- One alphabetic sequence at a time. Raises: ValueError -- If the file is unparsable """ alphabet = Alphabet(alphabet) line_length = 0 for linenum, line in enumerate(fin): if line.isspace(): continue # Blank line line = line.strip() if line[0] == ">": # probably a fasta file. Fail. raise ValueError("Parse Error on input line: %d " % linenum) line = remove_whitespace(line) if not alphabet.alphabetic(line): raise ValueError( "Character on line: %d not in alphabet: %s : %s" % (linenum, alphabet, line) ) if line_length and line_length != len(line): raise ValueError("Line %d has an incommensurate length." % linenum) line_length = len(line) yield Seq(line, alphabet) def write(afile: TextIO, seqs: SeqList) -> None: """Write raw sequence data, one line per sequence. arguments: afile -- A writable stream. seqs -- A list of Seq's """ for s in seqs: writeseq(afile, s) def writeseq(afile: TextIO, seq: SeqList) -> None: """Write a single sequence in raw format. arguments: afile -- A writable stream. seq -- A Seq instance """ print(seq, file=afile) weblogo-3.8.0/weblogo/seq_io/clustal_io.py000077500000000000000000000174301467613320200206210ustar00rootroot00000000000000# Copyright (c) 2005 Gavin E. Crooks # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # """ Read and write the CLUSTAL sequence file format. See : - http://www.cmpharm.ucsf.edu/~goh/Treecorr/sampleAlignment.html - http://www.bioperl.org/wiki/ClustalW_multiple_alignment_format Ref : - Higgins D., Thompson J., Gibson T., Thompson J.D., Higgins D.G., Gibson T.J. (1994). CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680. """ # TODO: What happens if CLUSTAL is not the first line of the file? import re from typing import Iterator, Optional, TextIO from ..seq import Alphabet, Seq, SeqList from ..utils import Token __all__ = ("example", "names", "extensions", "read") example = """ CLUSTAL W (1.81) multiple sequence alignment CXCR3_MOUSE --------------------------LENSTSPYDYGENESD-------FSDSPPCPQDF BLR_HUMAN --------------------------LENLEDLF-WELDRLD------NYNDTSLVENH- CXCR1_HUMAN --------------------------MSNITDPQMWDFDDLN-------FTGMPPADEDY CXCR4_MURINE -----------------------------------YTSDN---------YSGSGDYDSNK : : :.. .. CXCR3_MOUSE -SL-------NFDRTFLPALYSLLFLLGLLGNGAVAAVLLSQRTALSSTDTFLLHLAVAD BLR_HUMAN --LC-PATMASFKAVFVPVAYSLIFLLGVIGNVLVLVILERHRQTRSSTETFLFHLAVAD CXCR1_HUMAN -SPC-MLETETLNKYVVIIAYALVFLLSLLGNSLVMLVILYSRVGRSVTDVYLLNLALAD CXCR4_MURINE -EPC-RDENVHFNRIFLPTIYFIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHLSVAD :. .: * ::** .::** * :: : * *: : ::*::** CXCR3_MOUSE VLLVLTLPLWAVDAA-VQWVFGPGLCKVAGALFNINFYAGAFLLACISFDRYLSIVHATQ BLR_HUMAN LLLVFILPFAVAEGS-VGWVLGTFLCKTVIALHKVNFYCSSLLLACIAVDRYLAIVHAVH CXCR1_HUMAN LLFALTLPIWAASKV-NGWIFGTFLCKVVSLLKEVNFYSGILLLACISVDRYLAIVHATR CXCR4_MURINE LLFVITLPFWAVDAM-ADWYFGKFLCKAVHIIYTVNLYSSVLILAFISLDRYLAIVHATN :*:.: **: ... * :* ***.. : :*:*.. ::** *:.****:****.. """ names = ( "clustal", "clustalw", ) extensions = ("aln",) header_line = re.compile(r"(CLUSTAL.*)$") # (sequence_id) (Sequence) (Optional sequence number) seq_line = re.compile(r"(\s*\S+\s+)(\S+)\s*(\d*)\s*$") # Saved group includes variable length leading space. # Must consult a seq_line to figure out how long the leading space is since # the maximum CLUSTAL ids length (normally 10 characters) can be changed. match_line = re.compile(r"([\s:\.\*]*)$") def iterseq(fin: TextIO, alphabet: Optional[Alphabet] = None) -> Iterator[Seq]: """Iterate over the sequences in the file.""" # Default implementation return iter(read(fin, alphabet)) def read(fin: TextIO, alphabet: Optional[Alphabet] = None) -> SeqList: alphabet = Alphabet(alphabet) seq_ids = [] seqs: list = [] block_count = 0 data_len = 0 for token in _scan(fin): if token.typeof == "begin_block": block_count = 0 elif token.typeof == "seq_id": if len(seqs) <= block_count: seq_ids.append(token.data) seqs.append([]) elif token.typeof == "seq": data = token.data assert data is not None if not alphabet.alphabetic(data): raise ValueError( "Character on line: %d not in alphabet: %s : %s" % (token.lineno, alphabet, data) ) seqs[block_count].append(data) if block_count == 0: data_len = len(data) elif data_len != len(data): raise ValueError("Inconsistent line lengths") block_count += 1 seqs = [Seq("".join(s), alphabet, name=i) for s, i in zip(seqs, seq_ids)] return SeqList(seqs) # 1) The word "CLUSTAL" should be the first word on the first line of the file. # (But sometimes isn't.) # 2) The alignment is displayed in blocks of fixed length. # 3) Each line in the block corresponds to one sequence. # 4) Each sequence line starts with a sequence name followed by at least one # space and then the sequence. def _scan(fin: TextIO) -> Iterator[Token]: """Scan a clustal format MSA file and yield tokens. The basic file structure is begin_document header? (begin_block (seq_id seq seq_index?)+ match_line? end_block)* end_document Usage: for token in scan(clustal_file): do_something(token) """ header, body, block = range(3) yield Token("begin") leader_width = -1 state = header for L, line in enumerate(fin): if state == header: if line.isspace(): continue m = header_line.match(line) state = body if m is not None: yield Token("header", m.group()) continue # Just keep going and hope for the best. # else: # raise ValueError("Cannot find required header") if state == body: if line.isspace(): continue yield Token("begin_block") state = block # fall through to block if state == block: if line.isspace(): yield Token("end_block") state = body continue m = match_line.match(line) if m is not None: yield Token("match_line", line[leader_width:-1]) continue m = seq_line.match(line) if m is None: raise ValueError("Parse error on line: %d (%s)" % (L, line)) leader_width = len(m.group(1)) yield Token("seq_id", m.group(1).strip()) yield Token("seq", m.group(2).strip()) if m.group(3): yield Token("seq_num", m.group(3)) continue # END state blocks. If I ever get here something has gone terrible wrong raise RuntimeError() # pragma: nocover if state == block: yield Token("end_block") yield Token("end") def write(fout: TextIO, seqs: SeqList) -> None: """Write 'seqs' to 'fout' as text in clustal format""" header = "CLUSTAL W (1.81) multiple sequence alignment" name_width = 17 seq_width = 60 print(header, end="\n\n", file=fout) L = max(len(s) for s in seqs) for block in range(0, L, seq_width): for s in seqs: start = min(block, len(s)) end = min(start + seq_width, len(s)) print(s.name.ljust(name_width), end="", file=fout) print(s[start:end], file=fout) print(file=fout) weblogo-3.8.0/weblogo/seq_io/fasta_io.py000077500000000000000000000167141467613320200202540ustar00rootroot00000000000000#!/usr/bin/env python # Copyright (c) 2005 Gavin E. Crooks # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # """Read and write sequence information in FASTA format. This is a very common format for unannotated biological sequence data, accepted by many multiple sequence alignment programs. Each sequence consists of a single-line description, followed by lines of sequence data. The first character of the description line is a greater-than (">") symbol in the first column. The first word of the description is often the name or ID of the sequence. Fasta files containing multiple sequences have one sequence listed right after another. Example Fasta File :: >Lamprey GLOBIN V - SEA LAMPREY PIVDTGSVA-P------------------LSAAEKTKIRSAWAPVYSTY---ETSGVDILVKFFTSTPAAQEFFPKFKGL TT-----ADQLKKSA---DVRWHA-ERIINAVNDAVASMDDTEKMS--MKL-RDLSGKH----AKSFQV-----DPQYFK VLAAVI-AD-TVAAGD--AGFEKLMSM------I---CILLR----S-----A-----Y------------ >Hagfish GLOBIN III - ATLANTIC HAGFISH PITDHGQPP-T------------------LSEGDKKAIRESWPQIYKNF---EQNSLAVLLEFLKKFPKAQDSFPKFSAK KS-------HLEQDP---AVKLQA-EVIINAVNHTIGLMDKEAAMK--KYL-KDLSTKH----STEFQV-----NPDMFK ELSAVF-VS-TMG-GK--AAYEKLFSI------I---ATLLR----S-----T-----YDA---------- >Frog HEMOGLOBIN BETA CHAIN - EDIBLE FROG ----------GS-----------------------DLVSGFWGKV--DA---HKIGGEALARLLVVYPWTQRYFTTFGNL GSADAIC-----HNA---KVLAHG-EKVLAAIGEGLKHPENLKAHY--AKL-SEYHSNK----LHVDPANFRLLGNVFIT VLARHF-QH-EFTPELQ-HALEAHFCA------V---GDALA----K-----A-----YH----------- """ from typing import Iterator, List, Optional, TextIO from ..seq import Alphabet, Seq, SeqList names = ("fasta", "pearson", "fa") extensions = ( "fa", "fasta", "fast", "seq", "fsa", "fst", "nt", "aa", "fna", "mpfa", "faa", "fnn", "mfasta", "tfa", "pfa", ) example = """ >Lamprey GLOBIN V - SEA LAMPREY PIVDTGSVA-P------------------LSAAEKTKIRSAWAPVYSTY---ETSGVDILVKFFTSTPAAQEFFPKFKGL TT-----ADQLKKSA---DVRWHA-ERIINAVNDAVASMDDTEKMS--MKL-RDLSGKH----AKSFQV-----DPQYFK VLAAVI-AD-TVAAGD--AGFEKLMSM------I---CILLR----S-----A-----Y------------ >Hagfish GLOBIN III - ATLANTIC HAGFISH PITDHGQPP-T------------------LSEGDKKAIRESWPQIYKNF---EQNSLAVLLEFLKKFPKAQDSFPKFSAK KS-------HLEQDP---AVKLQA-EVIINAVNHTIGLMDKEAAMK--KYL-KDLSTKH----STEFQV-----NPDMFK ELSAVF-VS-TMG-GK--AAYEKLFSI------I---ATLLR----S-----T-----YDA---------- >Frog HEMOGLOBIN BETA CHAIN - EDIBLE FROG ----------GS-----------------------DLVSGFWGKV--DA---HKIGGEALARLLVVYPWTQRYFTTFGNL GSADAIC-----HNA---KVLAHG-EKVLAAIGEGLKHPENLKAHY--AKL-SEYHSNK----LHVDPANFRLLGNVFIT VLARHF-QH-EFTPELQ-HALEAHFCA------V---GDALA----K-----A-----YH----------- """ def read(fin: TextIO, alphabet: Optional[Alphabet] = None) -> SeqList: """Read and parse a fasta file. Args: fin -- A stream or file to read alphabet -- The expected alphabet of the data, if given Returns: SeqList -- A list of sequences Raises: ValueError -- If the file is unparsable """ seqs = [s for s in iterseq(fin, alphabet)] name = names[0] if hasattr(fin, "name"): name = fin.name return SeqList(seqs, name=name) # def readseq(fin: TextIO, alphabet: Alphabet = None) -> Seq: # """Read one sequence from the file, starting # from the current file position.""" # return next(iterseq(fin, alphabet)) def iterseq(fin: TextIO, alphabet: Optional[Alphabet] = None) -> Iterator[Seq]: """Parse a fasta file and generate sequences. Args: fin -- A stream or file to read alphabet -- The expected alphabet of the data, if given Yields: Seq -- One alphabetic sequence at a time. Raises: ValueError -- If the file is unparsable """ alphabet = Alphabet(alphabet) seqs = [] comments: List[str] = [] # FIXME: comments before first sequence are lost. header = None header_lineno = -1 def build_seq( seqs: List[str], alphabet: Alphabet, header: str, header_lineno: int, comments: List[str], ) -> Seq: try: name = header.split(" ", 1)[0] if comments: header += "\n" + "\n".join(comments) s = Seq("".join(seqs), alphabet, name=name, description=header) except ValueError: raise ValueError( "Parse failed with sequence starting at line %d: " "Character not in alphabet: %s" % (header_lineno, alphabet) ) return s for lineno, line in enumerate(fin): line = line.strip() if line == "": continue if line.startswith(">"): if header is not None: yield build_seq(seqs, alphabet, header, header_lineno, comments) header = None seqs = [] header = line[1:] header_lineno = lineno comments = [] elif line.startswith(";"): # Optional (and unusual) comment line comments.append(line[1:]) else: if header is None: raise ValueError( "Parse failed on line %d: sequence before header" % (lineno) ) seqs.append(line) if not seqs: return assert header is not None yield build_seq(seqs, alphabet, header, header_lineno, comments) def write(fout: TextIO, seqs: SeqList) -> None: """Write a fasta file. Args: fout -- A writable stream. seqs -- A list of Seq's """ if seqs.description: for line in seqs.description.splitlines(): print(";" + line, file=fout) for s in seqs: writeseq(fout, s) def writeseq(afile: TextIO, seq: Seq) -> None: """Write a single sequence in fasta format. Args: afile -- A writable stream. seq -- A Seq instance """ header = seq.description or seq.name or "" # We prepend '>' to the first header line # Additional lines start with ';' to indicate comment lines if header: headings = header.splitlines() print(">" + headings[0], file=afile) if len(headings) > 1: for h in headings[1:]: print(";" + h, file=afile) else: print(">", file=afile) L = len(seq) line_length = 80 for n in range(1 + L // line_length): print(seq[n * line_length : (n + 1) * line_length], file=afile) print(file=afile) weblogo-3.8.0/weblogo/seq_io/genbank_io.py000077500000000000000000000033661467613320200205620ustar00rootroot00000000000000#!/usr/bin/env python """Read GenBank flat files. Currently only reads sequence data and not annotations. """ from typing import Iterator, Optional, TextIO from ..seq import Alphabet, Seq, SeqList from ..utils import isblank names = ("genbank",) extensions = ("gb", "genbank", "gbk") def read(fin: TextIO, alphabet: Optional[Alphabet] = None) -> SeqList: """Read and parse a file of genbank records. Args: fin -- A stream or file to read alphabet -- The expected alphabet of the data, if given Returns: SeqList -- A list of sequences Raises: ValueError -- If the file is unparsable """ seqs = [s for s in iterseq(fin, alphabet)] return SeqList(seqs) def iterseq(fin: TextIO, alphabet: Optional[Alphabet] = None) -> Iterator[Seq]: """Iterate over genbank records Args: fin -- A stream or file to read alphabet -- The expected alphabet of the data, if given Yields: Seq -- One alphabetic sequence at a time. Raises: ValueError -- If the file is unparsable """ alphabet = Alphabet(alphabet) header, block, data = range(3) state = header seq: list = [] for L, line in enumerate(fin): if isblank(line): continue if state == header: if not line.startswith("LOCUS"): raise ValueError("Cannot find start of record at line %d" % L) state = block elif state == block: if line.startswith("ORIGIN") or line.startswith("//"): state = data elif state == data: if line.startswith("//"): yield Seq("".join(seq), alphabet) seq = [] state = block else: seq.extend(line.split()[1:]) weblogo-3.8.0/weblogo/seq_io/intelligenetics_io.py000077500000000000000000000141521467613320200223320ustar00rootroot00000000000000#!/usr/bin/env python # Copyright (c) 2005 Gavin E. Crooks # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # """Read and write sequence information in IntelliGenetics format. A sequence file in IG format can contain several sequences, each consisting of a number of comment lines that must begin with a semicolon (";"), a line with the sequence name and the sequence itself terminated with the termination character '1' for linear or '2' for circular sequences. The termination character is defacto optional. --- Example IG File --- ;H.sapiens fau mRNA, 518 bases HSFAU ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtc actcttaagtcttttgtaattctggctttctctaataaaaaagccactta gttcagtcaaaaaaaaaa1 ;H.sapiens fau 1 gene, 2016 bases HSFAU1 ctaccattttccctctcgattctatatgtacactcgggacaagttctcct gatcgaaaacggcaaaactaaggccccaagtaggaatgccttagttttcg gggttaacaatgattaacactgagcctcacacccacgcgatgccctcagc tcctcgctcagcgctctcaccaacagccgtagcccgcagccccgctggac accggttctccatccccgcagcgtagcccggaacatggtagctgccatct ttacctgctacgccagccttctgtgcgcgcaactgtctggtcccgcccc2 """ from typing import Iterator, List, Optional, TextIO from ..seq import Alphabet, Seq, SeqList from ..utils import remove_whitespace names = ( "intelligenetics", "ig", "stanford", ) extensions = ("ig",) example = """ ;H.sapiens fau mRNA, 518 bases HSFAU ttcctctttctcgactccatcttcgcggtagctgggaccgccgttcagtc actcttaagtcttttgtaattctggctttctctaataaaaaagccactta gttcagtcaaaaaaaaaa1 ;H.sapiens fau 1 gene, 2016 bases HSFAU1 ctaccattttccctctcgattctatatgtacactcgggacaagttctcct gatcgaaaacggcaaaactaaggccccaagtaggaatgccttagttttcg gggttaacaatgattaacactgagcctcacacccacgcgatgccctcagc tcctcgctcagcgctctcaccaacagccgtagcccgcagccccgctggac accggttctccatccccgcagcgtagcccggaacatggtagctgccatct ttacctgctacgccagccttctgtgcgcgcaactgtctggtcccgcccc2 """ def read(fin: TextIO, alphabet: Optional[Alphabet] = None) -> SeqList: """Read and parse an IG file. Args: fin -- A stream or file to read alphabet -- The expected alphabet of the data, if given Returns: SeqList -- A list of sequences Raises: ValueError -- If the file is unparsable """ seqs = [s for s in iterseq(fin, alphabet)] return SeqList(seqs) def iterseq(fin: TextIO, alphabet: Optional[Alphabet] = None) -> Iterator[Seq]: """Parse an IG file and generate sequences. Args: fin -- A stream or file to read alphabet -- The expected alphabet of the data, if given Yields: Seq -- One alphabetic sequence at a time. Raises: ValueError -- If the file is unparsable """ alphabet = Alphabet(alphabet) seqs: list = [] header: list = [] start_lineno = -1 name = None def build_seq( seqs: List[str], alphabet: Alphabet, name: Optional[str], comments: List[str], lineno: int, ) -> Seq: try: desc = "\n".join(comments) s = Seq("".join(seqs), alphabet, name=name, description=desc) except ValueError: raise ValueError( "Parse failed with sequence starting at line %d: " "Character not in alphabet: %s" % (lineno, alphabet) ) return s for lineno, line in enumerate(fin): line = line.strip() if line == "": continue if line.startswith(";"): if seqs: # end of sequence yield build_seq(seqs, alphabet, name, header, start_lineno) header = [] seqs = [] name = None header.append(line[1:]) start_lineno = lineno elif not name: name = line elif line[-1] == "1" or line[-1] == "2": # End of sequence seqs.append(remove_whitespace(line[0:-1])) yield build_seq(seqs, alphabet, name, header, start_lineno) header = [] seqs = [] name = None else: seqs.append(remove_whitespace(line)) if seqs: yield build_seq(seqs, alphabet, name, header, start_lineno) return def write(fout: TextIO, seqs: SeqList) -> None: """Write an IG file. Args: fout -- A writable stream. seqs -- A list of Seq's Raises: ValueError -- If a sequence is missing a name """ for s in seqs: writeseq(fout, s) def writeseq(fout: TextIO, seq: Seq) -> None: """Write a single sequence in IG format. Args: fout -- A writable stream. seq -- A Seq instance Raises: ValueError -- If a sequence is missing a name """ desc = seq.description or "" # We prepend ';' to each line for h in desc.splitlines(): print(";" + h, file=fout) if not seq.name: raise ValueError("Write failed with missing sequence name: %s" % str(seq)) print(seq.name, file=fout) L = len(seq) line_length = 80 for n in range(1 + L // line_length): print(seq[n * line_length : (n + 1) * line_length], file=fout) print(file=fout) weblogo-3.8.0/weblogo/seq_io/msf_io.py000077500000000000000000000133021467613320200177310ustar00rootroot00000000000000#!/usr/bin/env python # Copyright (c) 2005 Clare Gollnick # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # """Read sequence information in MSF format. This is a file format for biological sequence data. The sequences are interweaved and each line is labeled with the sequence name. The MSF format can be identified in one or more of the following ways: 1. The word PileUp on the first line (optional) 2. the word !!AA_MULTIPLE_ALIGNMENT or !!NA_MULTIPLE_ALIGNMENT at the start of the file (optional) 3. the word MSF on the first line of the file, and the characters ".." at the end of this line (optional) 4. A header containing sequence information followed by a line with the characters "//" """ import re from typing import Iterator, Optional, TextIO from ..seq import Alphabet, Seq, SeqList from ..utils import Token example = """ PileUp MSF: 64 Type: P Check: 767 .. Name: Cow Len: 100 Check: 3761 Weight: 1.00 Name: Carp Len: 100 Check: 1550 Weight: 1.00 Name: Chicken Len: 100 Check: 2397 Weight: 1.00 Name: Human Len: 100 Check: 9021 Weight: 1.00 Name: Loach Len: 100 Check: 984 Weight: 1.00 Name: Mouse Len: 100 Check: 2993 Weight: 1.00 // Cow MAYPMQLGFQ DATSPIMEEL LHFHDHTLMI VFLISSLVLY IISLMLTTKL Carp MAHPTQLGFK DAAMPVMEEL LHFHDHALMI VLLISTLVLY IITAMVSTKL Chicken MANHSQLGFQ DASSPIMEEL VEFHDHALMV ALAICSLVLY LLTLMLMEKL Human MAHAAQVGLQ DATSPIMEEL ITFHDHALMI IFLICFLVLY ALFLTLTTKL Loach MAHPTQLGFQ DAASPVMEEL LHFHDHALMI VFLISALVLY VIITTVSTKL Mouse MAYPFQLGLQ DATSPIMEEL MNFHDHTLMI VFLISSLVLY IISLMLTTKL Cow THTSTMDAQE VETIWTILPA IILILIALPS LRILYMMDEI NNPSLTVKTM Carp TNKYILDSQE IEIVWTILPA VILVLIALPS LRILYLMDEI NDPHLTIKAM Chicken S.SNTVDAQE VELIWTILPA IVLVLLALPS LQILYMMDEI DEPDLTLKAI Human TNTNISDAQE METVWTILPA IILVLIALPS LRILYMTDEV NDPSLTIKSI Loach TNMYILDSQE IEIVWTVLPA LILILIALPS LRILYLMDEI NDPHLTIKAM Mouse THTSTMDAQE VETIWTILPA VILIMIALPS LRILYMMDEI NNPVLTVKTM """ names = ("msf", "gcg-msf", "gcg", "PileUp") extensions = ("msf",) end_header = re.compile(r"(//)(\s*)$") seq_line = re.compile(r"\s*(\S+)\s+([\S\s.?]+)$") def iterseq(fin: TextIO, alphabet: Optional[Alphabet] = None) -> Iterator[Seq]: """Iterate over the sequences in the file.""" # Default implementation return iter(read(fin, alphabet)) def read(fin: TextIO, alphabet: Optional[Alphabet] = None) -> SeqList: alphabet = Alphabet(alphabet) seq_ids = [] seqs: list = [] block_count = 0 for token in _line_is(fin): if token.typeof == "begin_block": block_count = 0 elif token.typeof == "seq_id": if len(seqs) <= block_count: seq_ids.append(token.data) seqs.append([]) elif token.typeof == "seq": data = token.data assert data is not None if not alphabet.alphabetic(data): raise ValueError( "Character on line: %d not in alphabet: %s : %s" % (token.lineno, alphabet, token.data) ) seqs[block_count].append(data) block_count += 1 if seq_ids == []: raise ValueError("Parse error, possible wrong format") seqs = [Seq("".join(s), alphabet, name=i) for s, i in zip(seqs, seq_ids)] return SeqList(seqs) def _line_is(fin: TextIO) -> Iterator[Token]: header, body, block = range(3) yield Token("begin") state = header for L, line in enumerate(fin): if state == header: if line.isspace(): continue m = end_header.match(line) if m is not None: yield Token("end_header") state = body continue else: continue # pragma: no cover if state == body: if line.isspace(): continue yield Token("begin_block") state = block # skips to a block of sequences if state == block: if line.isspace(): yield Token("end_block") state = body continue m = seq_line.match(line) if m is None: raise ValueError("Parse error on line: %d" % L) # pragma: no cover if m.group(1).isdigit() and m.group(2).strip().isdigit(): continue yield Token("seq_id", m.group(1).strip()) data = m.group(2) data = "".join((data.split())) yield Token("seq", data.strip()) weblogo-3.8.0/weblogo/seq_io/nbrf_io.py000077500000000000000000000135661467613320200201070ustar00rootroot00000000000000# Copyright (c) 2006, The Regents of the University of California, through # Lawrence Berkeley National Laboratory (subject to receipt of any required # approvals from the U.S. Dept. of Energy). All rights reserved. # This software is distributed under the new BSD Open Source License. # # # Redistribution and use in source and binary forms, with or without # modification, are permitted provided that the following conditions are met: # # (1) Redistributions of source code must retain the above copyright notice, # this list of conditions and the following disclaimer. # # (2) Redistributions in binary form must reproduce the above copyright # notice, this list of conditions and the following disclaimer in the # documentation and or other materials provided with the distribution. # # (3) Neither the name of the University of California, Lawrence Berkeley # National Laboratory, U.S. Dept. of Energy nor the names of its contributors # may be used to endorse or promote products derived from this software # without specific prior written permission. # # THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" # AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE # IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE # ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE # LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR # CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF # SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS # INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN # CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) # ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE # POSSIBILITY OF SUCH DAMAGE. """Sequence IO for NBRF/PIR format. The format is similar to fasta. The header line consistins of '>', a two- letter sequence type (P1, F1, DL, DC, RL, RC, or XX), a semicolon, and a sequence ID. The next line is a textual description of the sequence, followed by one or more lines containing the sequence data. The end of the sequence is marked by a "*" (asterisk) character. type_code -- A map between NBRF two letter type codes and Alphabets. see: http://www.cmbi.kun.nl/bioinf/tools/crab_pir.html --- Example NBRF File --- >P1;CRAB_ANAPL ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN). MDITIHNPLI RRPLFSWLAP SRIFDQIFGE HLQESELLPA SPSLSPFLMR SPIFRMPSWL ETGLSEMRLE KDKFSVNLDV KHFSPEELKV KVLGDMVEIH GKHEERQDEH GFIAREFNRK YRIPADVDPL TITSSLSLDG VLTVSAPRKQ SDVPERSIPI TREEKPAIAG AQRK* >P1;CRAB_BOVIN ALPHA CRYSTALLIN B CHAIN (ALPHA(B)-CRYSTALLIN). MDIAIHHPWI RRPFFPFHSP SRLFDQFFGE HLLESDLFPA STSLSPFYLR PPSFLRAPSW IDTGLSEMRL EKDRFSVNLD VKHFSPEELK VKVLGDVIEV HGKHEERQDE HGFISREFHR KYRIPADVDP LAITSSLSSD GVLTVNGPRK QASGPERTIP ITREEKPAVT AAPKK* """ from typing import Iterator, Optional, TextIO from ..seq import ( Alphabet, Seq, SeqList, dna_alphabet, generic_alphabet, protein_alphabet, rna_alphabet, ) names = ( "nbrf", "pir", ) extensions = ("nbrf", "pir", "ali") type_code = { "P1": protein_alphabet, # Protein (complete) "F1": protein_alphabet, # Protein (fragment) "DL": dna_alphabet, # DNA (linear) "DC": dna_alphabet, # DNA (circular) "RC": rna_alphabet, # RNA (linear) "RL": rna_alphabet, # RNA (circular) "N3": rna_alphabet, # tRNA "N1": rna_alphabet, # other functional RNA "XX": generic_alphabet, } def read(fin: TextIO, alphabet: Optional[Alphabet] = None) -> SeqList: """Read and parse a NBRF sequence file. Args: fin -- A stream or file to read alphabet -- The expected alphabet of the data. If not supplied, then an appropriate alphabet will be inferred from the data. Returns: SeqList -- A list of sequences Raises: ValueError -- If the file is unparsable """ seqs = [s for s in iterseq(fin, alphabet)] return SeqList(seqs) def iterseq(fin: TextIO, alphabet: Optional[Alphabet] = None) -> Iterator[Seq]: """Generate sequences from an NBRF file. arguments: fin -- A stream or file to read alphabet -- yields : Seq raises : ValueError -- On a parse error. """ body, header, sequence = range(3) # Internal states state = body seq_id = None seq_desc = None seq_alpha = None seqs = [] for lineno, line in enumerate(fin): if state == body: if line == "" or line.isspace(): continue if line[0] == ">": seq_type, seq_id = line[1:].split(";") if alphabet: seq_alpha = alphabet else: seq_alpha = type_code[seq_type] state = header continue raise ValueError("Parse error on line: %d" % lineno) elif state == header: seq_desc = line.strip() state = sequence continue elif state == sequence: data = "".join(line.split()) # Strip out white space if data[-1] == "*": # End of sequence data seqs.append(data[:-1]) seq = Seq( "".join(seqs), name=seq_id.strip(), # type: ignore description=seq_desc, alphabet=seq_alpha, ) yield seq state = body seq_id = None seq_desc = None seqs = [] continue else: seqs.append(data) continue else: # If we ever get here something has gone terrible wrong assert False # pragma: no cover # end for weblogo-3.8.0/weblogo/seq_io/nexus_io.py000077500000000000000000000047601467613320200203160ustar00rootroot00000000000000#!/usr/bin/env python # Copyright 2005 Gavin E. Crooks # Copyright 2005-2006 The Regents of the University of California. # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # """Read the sequence data from a nexus file. This IO code only gives read access to the sequence data. Reference: 'NEXUS: An extensible file format for systematic information' Maddison, Swofford, Maddison. 1997. Syst. Biol. 46(4):590-621 """ from typing import Iterator, Optional, TextIO from ..seq import Alphabet, Seq, SeqList from ._nexus import Nexus, safename names = ("nexus", "paup") extensions = ("nex", "nexus", "paup", "nxs") def iterseq(fin: TextIO, alphabet: Optional[Alphabet] = None) -> Iterator[Seq]: """Iterate over the sequences in the file.""" # Default implementation return iter(read(fin, alphabet)) def read(fin: TextIO, alphabet: Optional[Alphabet] = None) -> SeqList: """Extract sequence data from a nexus file.""" n = Nexus(fin) seqs = [] for taxon in n.taxlabels: name = safename(taxon) r = n.matrix[taxon] if alphabet is None: s = Seq(r, name=name, alphabet=r.alphabet) else: s = Seq(r, name=name, alphabet=alphabet) seqs.append(s) if len(seqs) == 0: # Something went terrible wrong. raise ValueError("Cannot parse file") return SeqList(seqs) weblogo-3.8.0/weblogo/seq_io/null_io.py000077500000000000000000000041251467613320200201210ustar00rootroot00000000000000#!/usr/bin/env python # Copyright (c) 2005 Gavin E. Crooks # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # """ Null sequence IO. Acts like /dev/null. Read returns empty sequences or sequence lists, writes do nothing. """ from typing import Iterator, Optional, TextIO from ..seq import Alphabet, Seq, SeqList names = () extensions = () def read(fin: TextIO, alphabet: Optional[Alphabet] = None) -> SeqList: assert fin is not None # Do something with arguments to quiet pychecker # if alphabet is not None: # pass return SeqList([]) def iterseq(fin: TextIO, alphabet: Optional[Alphabet] = None) -> Iterator[Seq]: assert fin is not None # if alphabet is not None: # pass yield Seq("") return def write(fout: TextIO, seqs: SeqList) -> None: for s in seqs: writeseq(fout, s) def writeseq(fout: TextIO, seq: SeqList) -> None: assert fout is not None assert seq is not None return weblogo-3.8.0/weblogo/seq_io/phylip_io.py000077500000000000000000000144351467613320200204610ustar00rootroot00000000000000#!/usr/bin/env python # Copyright (c) 2005 David D. Ding # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # """Reads Sequences in interleaved Phylip format (not sequential) and returns a list of sequences. Phylip is a very common phylogeny generating sequence type that has the following traits: 1) First line contains number of species and number of characters in a species' sequence. Options may follow, and they can be spaced or unspaced. Options are simply letters such as A and W after the number of characters. 2) Options don't have to contain U in order for a usertree to appear. 3) If there are options then options appear first, then the sequences. For the first iteration of sequences the first ten spaces are reserved for names of options and species, the rest is for sequences. 4) For the second and following iterations the names are removed, only sequence appears 4) At end of file a usertree may appear. First there is a number that indicts the number of lines the usertree will take, and then the usertrees follow. Examples: 6 50 W W 0101001111 0101110101 01011 dmras1 GTCGTCGTTG GACCTGGAGG CGTGG hschras GTGGTGGTGG GCGCCGGCCG TGTGG ddrasa GTTATTGTTG GTGGTGGTGG TGTCG spras GTAGTTGTAG GAGATGGTGG TGTTG scras1 GTAGTTGTCG GTGGAGGTGG CGTTG scras2 GTCGTCGTTG GTGGTGGTGG TGTTG 0101001111 0101110101 01011 GTCGTCGTTG GACCTGGAGG CGTGG GTGGTGGTGG GCGCCGGCCG TGTGG GTTATTGTTG GTGGTGGTGG TGTCG GTAGTTGTAG GAGATGGTGG TGTTG GTAGTTGTCG GTGGAGGTGG CGTTG GTCGTCGTTG GTGGTGGTGG TGTTG 1 ((dmras1,ddrasa),((hschras,spras),(scras1,scras2))); """ from typing import Iterator, Optional, TextIO from ..seq import Alphabet, Seq, SeqList names = ("phylip",) extensions = ("phy",) def iterseq(fin: TextIO, alphabet: Optional[Alphabet] = None) -> Iterator[Seq]: """Iterate over the sequences in the file.""" # Default implementation return iter(read(fin, alphabet)) # Read takes in a phylip file name, reads it, processes it, and returns a SeqList def read(fin: TextIO, alphabet: Optional[Alphabet] = None) -> SeqList: sequence: list = [] # where sequences are stored idents = [] num_seq = 0 num_total_seq = 0 # length of sequence of 1 species tracker = 0 # track what sequence the line is on usertree_tracker = 0 # track usertree lines options = "" # options num_options = 0 # number/lens of options - U line = fin.readline() while line: s_line = ( line.split() ) # for ease of use, not used in all scenarios, but easier on the eye if s_line == []: # see nothing do nothing pass elif ( s_line[0].isdigit() and len(s_line) == 1 and len(sequence) == num_seq and len(sequence[0]) == num_total_seq ): usertree_tracker = int(s_line[0]) pass elif num_options > 0: if len(sequence) < num_seq: if s_line[0][0] in options: num_options -= 1 pass else: raise ValueError( "Not an option, but it should be one" ) # pragma: no cover else: num_options -= 1 pass elif usertree_tracker > 0: # basically skip usertree if len(sequence[num_seq - 1]) == num_total_seq: usertree_tracker -= 1 # pragma: no cover else: raise ValueError("User Tree in Wrong Place") # problems parse error unexpected elif s_line[0].isdigit(): if len(s_line) >= 2 and len(sequence) == 0: # identifies first line of file num_seq = int(s_line[0]) # get number of sequences num_total_seq = int(s_line[1]) # get length of sequences if len(s_line) > 2: # takes care of the options options = "".join(s_line[2:]) num_options = len(options) - options.count("U") else: raise ValueError("parse error") # when options end, this takes care of the sequence elif num_options == 0: if num_seq == 0: raise ValueError("Empty File, or possibly wrong file") elif tracker < num_seq: if num_seq > len(sequence): sequence.append("".join(line[10:].split())) # removes species name idents.append(line[0:10].strip()) tracker += 1 else: sequence[tracker] += "".join(s_line) tracker += 1 if tracker == num_seq: tracker = 0 num_options = len(options) - options.count("U") line = fin.readline() if len(sequence) != len(idents) or len(sequence) != num_seq: raise ValueError("Number of different sequences wrong") # pragma: no cover seqs = [] for i in range(0, len(idents)): if len(sequence[i]) == num_total_seq: seqs.append(Seq(sequence[i], alphabet, idents[i])) else: raise ValueError("extra sequence in list") # pragma: no cover return SeqList(seqs) weblogo-3.8.0/weblogo/seq_io/plain_io.py000077500000000000000000000105771467613320200202620ustar00rootroot00000000000000#!/usr/bin/env python # Copyright (c) 2005 Gavin E. Crooks # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # """Read and write raw, unformatted sequence data. The whole file is read in as a sequence. Whitespace is removed. --- Example Plain/Raw/Text File --- --------------------------LENSTSPYDYGENESD-------FSDSPPCPQDF --------------------------LENLEDLF-WELDRLD------NYNDTSLVENH- --------------------------MSNITDPQMWDFDDLN-------FTGMPPADEDY -----------------------------------YTSDN---------YSGSGDYDSNK -SL-------NFDRTFLPALYSLLFLLGLLGNGAVAAVLLSQRTALSSTDTFLLHLAVAD --LC-PATMASFKAVFVPVAYSLIFLLGVIGNVLVLVILERHRQTRSSTETFLFHLAVAD -SPC-MLETETLNKYVVIIAYALVFLLSLLGNSLVMLVILYSRVGRSVTDVYLLNLALAD -EPC-RDENVHFNRIFLPTIYFIIFLTGIVGNGLVILVMGYQKKLRSMTDKYRLHLSVAD """ from typing import Iterator, List, Optional, TextIO from ..seq import Alphabet, Seq, SeqList from ..utils import remove_whitespace example = """ --------------------------LENSTSPYDYGENESD-------FSDSPPCPQDF --------------------------LENLEDLF-WELDRLD------NYNDTSLVENH- --------------------------MSNITDPQMWDFDDLN-------FTGMPPADEDY -----------------------------------YTSDN---------YSGSGDYDSNK -SL-------NFDRTFLPALYSLLFLLGLLGNGAVAAVLLSQRTALSSTDTFLLHLAVAD --LC-PATMASFKAVFVPVAYSLIFLLGVIGNVLVLVILERHRQTRSSTETFLFHLAVAD -SPC-MLETETLNKYVVIIAYALVFLLSLLGNSLVMLVILYSRVGRSVTDVYLLNLALAD -EPC-RDENVHFNRIFLPTIYFIIFLTGIV """ names = ("plain", "raw") extensions = () def read(fin: TextIO, alphabet: Optional[Alphabet] = None) -> SeqList: """Read a file of raw sequence data. Args: fin -- A stream or file to read alphabet -- The expected alphabet of the data, if given Returns: SeqList -- A list of sequences Raises: ValueError -- If the file is unparsable """ seqs = [s for s in iterseq(fin, alphabet)] return SeqList(seqs) def iterseq(fin: TextIO, alphabet: Optional[Alphabet] = None) -> Iterator[Seq]: """Read the sequence data and yield one (and only one) sequence. Args: fin -- A stream or file to read alphabet -- The expected alphabet of the data, if given Yields: Seq -- One alphabetic sequence at a time. Raises: ValueError -- If the file is unparsable """ alphabet = Alphabet(alphabet) lines = [] for linenum, line in enumerate(fin): if line.isspace(): continue # Blank line line = line.strip() if line[0] == ">": # probably a fasta file. Fail. raise ValueError("Parse Error on input line: %d " % (linenum)) line = remove_whitespace(line) if not alphabet.alphabetic(line): raise ValueError( "Character on line: %d not in alphabet: %s : %s" % (linenum, alphabet, line) ) lines.append(line) yield Seq("".join(lines), alphabet) def write(afile: TextIO, seqs: List[Seq]) -> None: """Write raw sequence data, one line per sequence. arguments: afile -- A writable stream. seqs -- A list of Seq's """ for s in seqs: writeseq(afile, s) def writeseq(afile: TextIO, seq: Seq) -> None: """Write a single sequence in raw format. arguments: afile -- A writable stream. seq -- A Seq instance """ print(seq, file=afile) weblogo-3.8.0/weblogo/seq_io/stockholm_io.py000077500000000000000000000130151467613320200211500ustar00rootroot00000000000000# Copyright (c) 2005 Gavin E. Crooks # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # """Read a multiple sequence alignment in STOCKHOLM format. This file format is used by PFAM and HMMER. At present, all annotation information is ignored. See: - http://www.cgb.ki.se/cgb/groups/sonnhammer/Stockholm.html - HMMER manual """ import re from typing import Iterator, Optional, TextIO from ..seq import Alphabet, Seq, SeqList from ..utils import Token example = """ # STOCKHOLM 1.0 #=GF ID CBS #=GF AC PF00571 #=GF DE CBS domain #=GF AU Bateman A #=GF CC CBS domains are small intracellular modules mostly found #=GF CC in 2 or four copies within a protein. #=GF SQ 67 #=GS O31698/18-71 AC O31698 #=GS O83071/192-246 AC O83071 #=GS O83071/259-312 AC O83071 #=GS O31698/88-139 AC O31698 #=GS O31698/88-139 OS Bacillus subtilis O83071/192-246 MTCRAQLIAVPRASSLAE..AIACAQKM....RVSRVPVYERS #=GR O83071/192-246 SA 999887756453524252..55152525....36463774777 O83071/259-312 MQHVSAPVFVFECTRLAY..VQHKLRAH....SRAVAIVLDEY #=GR O83071/259-312 SS CCCCCHHHHHHHHHHHHH..EEEEEEEE....EEEEEEEEEEE O31698/18-71 MIEADKVAHVQVGNNLEH..ALLVLTKT....GYTAIPVLDPS #=GR O31698/18-71 SS CCCHHHHHHHHHHHHHHH..EEEEEEEE....EEEEEEEEHHH O31698/88-139 EVMLTDIPRLHINDPIMK..GFGMVINN......GFVCVENDE #=GR O31698/88-139 SS CCCCCCCHHHHHHHHHHH..HEEEEEEE....EEEEEEEEEEH #=GC SS_cons CCCCCHHHHHHHHHHHHH..EEEEEEEE....EEEEEEEEEEH O31699/88-139 EVMLTDIPRLHINDPIMK..GFGMVINN......GFVCVENDE #=GR O31699/88-139 AS ________________*__________________________ #=GR_O31699/88-139_IN ____________1______________2__________0____ // """ names = ( "stockholm", "pfam", ) extensions = ("sth", "stockholm", "align") header_line = re.compile(r"#\s+STOCKHOLM\s+1.\d\s+$") def iterseq(fin: TextIO, alphabet: Optional[Alphabet] = None) -> Iterator[Seq]: """Iterate over the sequences in the file.""" # Default implementation return iter(read(fin, alphabet)) def read(fin: TextIO, alphabet: Optional[Alphabet] = None) -> SeqList: alphabet = Alphabet(alphabet) seq_ids = [] seqs: list = [] block_count = 0 for token in _scan(fin): if token.typeof == "begin_block": block_count = 0 elif token.typeof == "seq_id": if len(seqs) <= block_count: seq_ids.append(token.data) seqs.append([]) elif token.typeof == "seq": data = token.data assert data is not None if not alphabet.alphabetic(data): raise ValueError( "Character on line: %d not in alphabet: %s : %s" % (token.lineno, alphabet, data) ) seqs[block_count].append(data) block_count += 1 seqs = [Seq("".join(s), alphabet, name=i) for s, i in zip(seqs, seq_ids)] return SeqList(seqs) def _scan(fin: TextIO) -> Iterator[Token]: header, body, block = range(3) yield Token("begin") state = header for L, line in enumerate(fin): if state == header: if line.isspace(): continue m = header_line.match(line) state = body if m is not None: # print("header: ", m.group()) yield Token("header", m.group()) continue else: raise ValueError("Parse error on line: %d" % L) if state == body: if line.isspace(): continue # pragma: no cover yield Token("begin_block") state = block # fall through to block if state == block: if line.isspace(): yield Token("end_block") state = body continue if line.strip() == "//": yield Token("end_block") return if line[0] == "#": # Comment or annotation line continue name_seq = line.split(None, 1) # Split into two parts at first whitespace if len(name_seq) != 2: raise ValueError("Parse error on line: %d" % L) # pragma: no cover yield Token("seq_id", name_seq[0].strip()) yield Token("seq", name_seq[1].strip()) continue # END state blocks. If I ever get here something has gone terrible wrong raise RuntimeError() # pragma: no cover weblogo-3.8.0/weblogo/seq_io/table_io.py000077500000000000000000000075621467613320200202460ustar00rootroot00000000000000#!/usr/bin/env python # Copyright (c) 2005 Gavin E. Crooks # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # """Read and write sequence information in tab-delimited format. This very simple format has two columns per line. The first column is a sequence name, the second column is the sequence itself. The columns are separated by a single tab ("\\t") character. """ from typing import Iterator, List, Optional, TextIO from ..seq import Alphabet, Seq, SeqList names = ("table", "tab") extensions = ("tbl",) example = """ EC0001 MKRISTTITTTITITTGNGAG EC0002 MRVLKFGGTSVANAERFLRVADILESNARQGQVATVLSAPAKITNHLVAM EC0003 MVKVYAPASSANMSVGFDVLGAAVTPVDGALLGDVVTVEAAETFSLNNLG EC0004 MKLYNLKDHNEQVSFAQAVTQGLGKNQGLFFPHDLPEFSLTEIDEMLKLD EC0005 MKKMQSIVLALSLVLVAPMAAQAAEITLVPSVKLQIGDRDNRGYYWDGGH EC0006 MLILISPAKTLDYQSPLTTTRYTLPELLDNSQQLIHEARKLTPPQISTLM EC0007 MPDFFSFINSVLWGSVMIYLLFGAGCWFTFRTGFVQFRYIRQFGKSLKNS EC0008 MTDKLTSLRQYTTVVADTGDIAAMKLYQPQDATTNPSLILNAAQIPEYRK EC0009 MNTLRIGLVSISDRASSGVYQDKGIPALEEWLTSALTTPFELETRLIPDE EC0010 MGNTKLANPAPLGLMGFGMTTILLNLHNVGYFALDGIILAMGIFYGGIAQ """ def read(fin: TextIO, alphabet: Optional[Alphabet] = None) -> SeqList: """Read and parse file. Args: fin -- A stream or file to read alphabet -- The expected alphabet of the data, if given Returns: SeqList -- A list of sequences Raises: ValueError -- If the file is unparsable """ seqs = [s for s in iterseq(fin, alphabet)] return SeqList(seqs) def iterseq(fin: TextIO, alphabet: Optional[Alphabet] = None) -> Iterator[Seq]: """Parse a file and generate sequences. Args: fin -- A stream or file to read alphabet -- The expected alphabet of the data, if given Yields: Seq -- One alphabetic sequence at a time. Raises: ValueError -- If the file is unparsable """ alphabet = Alphabet(alphabet) for lineno, line in enumerate(fin): line = line.strip() if line == "": continue columns = line.split("\t") if len(columns) != 2: raise ValueError( "Parse failed on line %d: did not find two columns separated by a tab." % lineno ) yield Seq(columns[1], alphabet=alphabet, name=columns[0]) def write(fout: TextIO, seqs: List[Seq]) -> None: """Write a two column, tab-delimited file. Args: fout -- A writable stream. seqs -- A list of Seq's """ for s in seqs: writeseq(fout, s) def writeseq(fout: TextIO, seq: Seq) -> None: """Write a single sequence in fasta format. Args: afile -- A writable stream. seq -- A Seq instance """ name = seq.name or "" print(name, seq, sep="\t", file=fout) weblogo-3.8.0/weblogo/template.eps000066400000000000000000000370661467613320200171620ustar00rootroot00000000000000%!PS-Adobe-3.0 EPSF-3.0 %%Title: Sequence Logo: ${logo_title} %%Creator: ${creator_text} %%CreationDate: ${creation_date} %%BoundingBox: 0 0 ${logo_width} ${logo_height} %%Pages: 0 %%DocumentFonts: %%EndComments % ---- VARIABLES ---- /True true def /False false def /debug ${debug} def /logo_height ${logo_height} def /logo_width ${logo_width} def /logo_title (${logo_title}) def /show_title ${show_title} def /logo_margin ${logo_margin} def /xaxis_label_height ${xaxis_label_height} def /title_height ${title_height} def /stroke_width ${stroke_width} def /tic_length ${tic_length} def /lines_per_logo ${lines_per_logo} def /line_width ${line_width} def /line_height ${line_height} def /line_margin_left ${line_margin_left} def /line_margin_right ${line_margin_right} def /line_margin_bottom ${line_margin_bottom} def /line_margin_top ${line_margin_top} def /stack_width ${stack_width} def /stack_height ${stack_height} def /stacks_per_line ${stacks_per_line} def /stack_margin ${stack_margin} def /show_yaxis ${show_yaxis} def /show_yaxis_label ${show_yaxis_label} def /yaxis_label (${yaxis_label}) def /yaxis_scale ${yaxis_scale} def % height in units /yaxis_tic_interval ${yaxis_tic_interval} def % in units /yaxis_minor_tic_interval ${yaxis_minor_tic_interval} def % in units /show_xaxis_label ${show_xaxis_label} def % True or False /show_xaxis ${show_xaxis} def % True or False /xaxis_label (${xaxis_label}) def /xaxis_tic_interval ${xaxis_tic_interval} def /rotate_numbers ${rotate_numbers} def % True or False /number_interval ${number_interval} def /show_ends ${show_ends} def /end_type (${end_type}) def % d: DNA, p: PROTEIN, -: none /show_fineprint ${show_fineprint} def /fineprint (${fineprint}) def /logo_label (${logo_label}) def /show_boxes ${show_boxes} def % True or False /shrink ${shrink} def % True or False /shrink_fraction ${shrink_fraction} def /show_errorbars ${show_errorbars} def % True or False /errorbar_fraction ${errorbar_fraction} def /errorbar_width_fraction ${errorbar_width_fraction} def /errorbar_gray ${errorbar_gray} def /fontsize ${fontsize} def /small_fontsize ${small_fontsize} def /title_fontsize ${title_fontsize} def /number_fontsize ${number_fontsize} def /UseCIEColor true def % Fix for issue 4 /default_color ${default_color} def % ---- DERIVED PARAMETERS ---- /char_width stack_width 2 stack_margin mul sub def /char_width2 char_width 2 div def /char_width4 char_width 4 div def % movements to place 5'/N and 3'/C symbols /leftEndDeltaX fontsize neg def /leftEndDeltaY fontsize 1.25 mul neg def /rightEndDeltaX fontsize 0.25 mul def /rightEndDeltaY leftEndDeltaY def % ---- PROCEDURES ---- /SetTitleFont {/${title_font} findfont title_fontsize scalefont setfont} bind def /SetLogoFont {/${logo_font} findfont char_width scalefont setfont} bind def /SetStringFont{/${text_font} findfont fontsize scalefont setfont} bind def /SetPrimeFont {/Symbol findfont fontsize scalefont setfont} bind def /SetSmallFont {/${text_font} findfont small_fontsize scalefont setfont} bind def /SetNumberFont {/${text_font} findfont number_fontsize scalefont setfont} bind def /DrawBox { % width height /hh exch def /ww exch def gsave 0.2 setlinewidth %0.5 setgray %0 0 moveto hh 0 rlineto 0 ww rlineto hh neg 0 rlineto 0 ww neg rlineto stroke grestore } bind def /StartLogo { %save gsave debug { logo_margin logo_margin moveto logo_height logo_margin 2 mul sub logo_width logo_margin 2 mul sub DrawBox } if show_title { DrawTitle } if show_xaxis_label { DrawXaxisLable } if show_fineprint { DrawFineprint } if DrawLogoLabel MoveToFirstLine } bind def /DrawLogoLabel { gsave SetTitleFont logo_margin logo_height title_fontsize sub logo_margin sub moveto debug { title_fontsize logo_label stringwidth pop DrawBox } if 0 title_fontsize 4 div rmoveto % Move up to baseline (approximatly) logo_label show grestore } bind def /DrawTitle { gsave SetTitleFont logo_width 2 div logo_title stringwidth pop 2 div sub logo_height title_fontsize sub logo_margin sub moveto debug { title_fontsize logo_title stringwidth pop DrawBox } if 0 title_fontsize 4 div rmoveto % Move up to baseline (approximatly) logo_title show grestore } bind def /DrawXaxisLable { % Print X-axis label, bottom center gsave SetStringFont logo_width 2 div xaxis_label stringwidth pop 2 div sub xaxis_label_height logo_margin add fontsize sub moveto %fontsize 3 div debug { fontsize xaxis_label stringwidth pop DrawBox } if xaxis_label show grestore } bind def /DrawFineprint { gsave SetSmallFont logo_width fineprint stringwidth pop sub logo_margin sub line_margin_right sub logo_margin moveto debug { small_fontsize fineprint stringwidth pop DrawBox } if fineprint show grestore } bind def /MoveToFirstLine { logo_margin logo_height logo_margin sub title_height sub line_height sub moveto } bind def /EndLogo { grestore %showpage %restore } bind def /StartLine{ gsave % Draw outer box debug { line_height line_width DrawBox } if % Move to lower left corner of content area line_margin_left line_margin_bottom rmoveto % Draw inner content box debug { line_height line_margin_bottom sub line_margin_top sub line_width line_margin_left sub line_margin_right sub DrawBox } if show_yaxis { DrawYaxis } if show_xaxis { DrawLeftEnd } if } bind def /EndLine{ show_xaxis { DrawRightEnd } if grestore 0 line_height neg rmoveto } bind def /DrawYaxis { gsave stack_margin neg 0 translate DrawYaxisBar DrawYaxisLabel grestore } bind def /DrawYaxisBar { gsave stack_margin neg 0 rmoveto SetNumberFont stroke_width setlinewidth /str 10 string def % string to hold number /smallgap stack_margin def % Draw first tic and bar gsave tic_length neg 0 rmoveto tic_length 0 rlineto 0 stack_height rlineto stroke grestore % Draw the tics % initial increment limit proc for 0 yaxis_tic_interval yaxis_scale abs {/loopnumber exch def % convert the number coming from the loop to a string % and find its width loopnumber 10 str cvrs /stringnumber exch def % string representing the number stringnumber stringwidth pop /numberwidth exch def % width of number to show /halfnumberheight stringnumber CharBoxHeight 2 div def gsave numberwidth % move back width of number neg loopnumber stack_height yaxis_scale div mul % shift on y axis halfnumberheight sub % down half the digit rmoveto % move back the width of the string tic_length neg smallgap sub % Move back a bit more 0 rmoveto % move back the width of the tic stringnumber show smallgap 0 rmoveto % Make a small gap % now show the tic mark 0 halfnumberheight rmoveto % shift up again tic_length 0 rlineto stroke grestore } for % Draw the minor tics % initial increment limit proc for 0 yaxis_minor_tic_interval yaxis_scale abs {/loopnumber2 exch def gsave 0 loopnumber2 stack_height yaxis_scale div mul rmoveto tic_length 2 div neg 0 rlineto stroke grestore } for grestore } bind def /DrawYaxisLabel { gsave SetStringFont % How far we move left depends on the size of % the tic labels. /str 10 string def % string to hold number yaxis_scale yaxis_tic_interval div cvi yaxis_tic_interval mul str cvs stringwidth pop tic_length 1.25 mul add neg stack_height yaxis_label stringwidth pop sub 2 div rmoveto 90 rotate yaxis_label show grestore } bind def %Take a single character and return the bounding box /CharBox { % CharBox gsave newpath 0 0 moveto % take the character off the stack and use it here: true charpath flattenpath pathbbox % compute bounding box of 1 pt. char => lx ly ux uy % the path is here, but toss it away ... grestore } bind def % The height of a characters bounding box /CharBoxHeight { % CharBoxHeight CharBox exch pop sub neg exch pop } bind def % The width of a characters bounding box /CharBoxWidth { % CharBoxHeight CharBox pop exch pop sub neg } bind def /DrawLeftEnd { gsave SetStringFont leftEndDeltaX leftEndDeltaY rmoveto show_ends { debug { leftEndDeltaY neg leftEndDeltaX neg DrawBox } if end_type (d) eq {(5) show DrawPrime} if end_type (p) eq {(N) show} if } if grestore } bind def /DrawRightEnd { gsave SetStringFont rightEndDeltaX rightEndDeltaY rmoveto show_ends { debug { rightEndDeltaY neg leftEndDeltaX neg DrawBox } if end_type (d) eq {(3) show DrawPrime} if end_type (p) eq {(C) show} if } if grestore } bind def /DrawPrime { gsave SetPrimeFont (\242) show grestore } bind def /StartStack { % startstack show_xaxis {DrawNumber}{pop} ifelse gsave debug { stack_height stack_width DrawBox } if } bind def /EndStack { grestore stack_width 0 rmoveto } bind def /DrawNumber { % number MakeNumber /n exch def gsave %0 stack_margin neg rmoveto stroke_width setlinewidth stack_width 0 rlineto stack_width 2 div neg 0 rmoveto n () eq { 0 tic_length 4 div neg rlineto } { 0 tic_length 2 div neg rlineto } ifelse stroke grestore gsave n SetNumberFont stack_width 2 div tic_length 2 div neg rmoveto rotate_numbers { 90 rotate dup stringwidth pop neg % find the length of the number stack_margin sub % Move down a bit (0) CharBoxHeight 2 div neg % left half height of numbers rmoveto show } { dup stringwidth pop neg 2 div number_fontsize neg rmoveto show } ifelse grestore } bind def % Draw a character whose height is proportional to symbol bits /ShowSymbol{ % interval color character ShowSymbol /char exch def /color exch def /interval exch def /fraction_width exch def /char_height interval yaxis_scale div stack_height mul stack_margin sub dup % if char_height is negative or very small replace with zero % BUG FIX: This used to be '0.0 gt' but it seems that DrawHeight % has a finite, non-zero minimum, which results in a rangecheck error 0.01 gt {}{pop 0.0} ifelse def char_height 0.0 gt { show_boxes { gsave /ww char_height stack_margin add def /hh stack_width def stroke_width setlinewidth hh 0 rlineto 0 ww rlineto hh neg 0 rlineto 0 ww neg rlineto stroke grestore } if gsave stack_margin stack_margin rmoveto debug { char_height char_width DrawBox } if 1 fraction_width sub char_width mul 2 div 0 rmoveto fraction_width char_width mul char_height color char DrawChar grestore } if 0 interval yaxis_scale div stack_height mul rmoveto } bind def /DrawChar { % ShowChar /tc exch def % The character /color exch def % The color of the character /ysize exch def % the y size of the character /xsize exch def % the x size of the character /xmulfactor 1 def /ymulfactor 1 def gsave SetLogoFont color aload pop setrgbcolor % IReplacementHack % Deal with the lack of bars on the letter 'I' in Arial and Helvetica % by replacing with 'I' from Courier. tc (I) eq { /Courier findfont char_width scalefont setfont } if shrink { xsize 1 shrink_fraction sub 2 div mul ysize 1 shrink_fraction sub 2 div mul rmoveto shrink_fraction shrink_fraction scale } if % Calculate the font scaling factors % Loop twice to catch small correction due to first scaling 2 { gsave xmulfactor ymulfactor scale ysize % desired size of character in points tc CharBoxHeight dup 0.0 ne { div % factor by which to scale up the character /ymulfactor exch def } {pop pop} ifelse xsize % desired size of character in points tc CharBoxWidth dup 0.0 ne { div % factor by which to scale up the character /xmulfactor exch def } {pop pop} ifelse grestore } repeat % Draw the character xmulfactor ymulfactor scale % Move lower left corner of character to start point tc CharBox pop pop % llx lly : Lower left corner exch neg exch neg rmoveto tc show grestore } bind def /DrawErrorbar{ % interval_down interval_up DrawErrorbar gsave /points_per_unit stack_height yaxis_scale div def /height_up exch points_per_unit mul def /height_down exch points_per_unit mul def show_errorbars { stroke_width setlinewidth errorbar_gray setgray stack_width 2 div 0 rmoveto /errorbar_width char_width errorbar_width_fraction mul def /errorbar_width2 errorbar_width 2 div def gsave 0 height_down neg rmoveto errorbar_width2 neg 0 rlineto errorbar_width 0 rlineto errorbar_width2 neg 0 rlineto 0 height_down errorbar_fraction mul rlineto stroke grestore gsave 0 height_up rmoveto errorbar_width2 neg 0 rlineto errorbar_width 0 rlineto errorbar_width2 neg 0 rlineto 0 height_up neg errorbar_fraction mul rlineto stroke grestore } if grestore } bind def /DrawErrorbarFirst{ % interval_down interval_up center DrawErrorbarFirst gsave /points_per_unit stack_height yaxis_scale div def /center exch points_per_unit mul def 0 center rmoveto DrawErrorbar grestore } bind def %%EndProlog %%Page: 1 1 % Example Data %StartLogo % StartLine % (1) StartStack % 1.2 [0 0 0] (C) ShowSymbol % 2.2 [0 0 0] (I) ShowSymbol % 0.5 0.5 DrawErrorbar % EndStack % (2) StartStack % 0.5 [0 0 0] (I) ShowSymbol % 0.9 [0 0 0] (L) ShowSymbol % 1.0 [0 0 0] (G) ShowSymbol % 0.5 0.5 DrawErrorbar % EndStack % (234) StartStack % EndStack % (235) StartStack % EndStack % EndLine %EndLogo StartLogo ${logo_data} EndLogo %%EOF weblogo-3.8.0/weblogo/transform.py000077500000000000000000001045671467613320200172270ustar00rootroot00000000000000# Copyright (c) 2006 John Gilman # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. """ Transformations of Seqs (alphabetic sequences). Classes : - Transform -- Simple transforms of alphabetic strings. - GeneticCode -- The genetic mapping of DNA to protein. Functions : - mask_low_complexity -- Implementation of Seg algorithm to remove low complexity regions from protein sequences. Other: - reduced_protein_alphabets -- A dictionary of transforms that reduce the size of the protein alphabet, merging various amino acids into classes. "LiBn" where n is 2 to 19 are from Li et al (2003), table I, 2 to 19 groups. "LiBn" where n is 2 to 19 are from Li et al (2003), table II (no interlacing), 2 to 19 groups. Ref: Li et al Reduction of protein sequence complexity by residue grouping, Prot. Eng. 16 323-330 (2003) """ from typing import Dict, List, Optional, Tuple from numpy import log2 from scipy.stats import entropy from .data import dna_ambiguity, dna_extended_letters from .seq import Alphabet, Seq, dna_alphabet, protein_alphabet from .seq import reduced_protein_alphabet as std_protein_alphabet __all__ = [ "Transform", "mask_low_complexity", "GeneticCode", "reduced_protein_alphabets", ] class Transform(object): """A translation between alphabetic strings. (This class is not called 'Translation' to avoid confusion with the biological translation of RNA to protein.) Example: trans = Transform( Seq("ACGTRYSWKMBDHVN-acgtUuryswkmbdhvnXx?.~", dna_alphabet), Seq("ACGTRYSWKMNNNNN-acgtUuryswkmbnnnnXx?.~", reduced_nucleic_alphabet) ) s0 = Seq("AAAAAV", nucleic_alphabet) s1 = trans(s0) assert(s1.alphabet == reduced_nucleic_alphabet) assert(s2 == Seq("AAAAAN", reduced_nucleic_alphabet) Status : Beta """ __slots__ = ["table", "source", "target", "name", "description"] def __init__( self, source: Seq, target: Seq, name: Optional[str] = None, description: Optional[str] = None, ) -> None: self.table = str.maketrans(source.tostring(), target.tostring()) self.source = source self.target = target self.name = name self.description = description def __call__(self, seq: Seq) -> Seq: """Translate sequence.""" if not self.source.alphabet.alphabetic(seq): raise ValueError("Incompatible alphabets") s = str.translate(seq, self.table) cls = self.target.__class__ return cls(s, self.target.alphabet, seq.name, seq.description) # End class Translation # FIXME: Test, document, add to seq. dna_complement = Transform( Seq("ACGTRYSWKMBDHVN-acgtUuryswkmbdhvnXx?.~", dna_alphabet), Seq("TGCAYRSWMKVHDBN-tgcaAayrswmkvhdbnXx?.~", dna_alphabet), ) def mask_low_complexity( seq: Seq, width: int = 12, trigger: float = 1.8, extension: float = 2.0, mask: str = "X", ) -> Seq: """Mask low complexity regions in protein sequences. Uses the method of Seg [1] by Wootton & Federhen [2] to divide a sequence into regions of high and low complexity. The sequence is divided into overlapping windows. Low complexity windows either have a sequence entropy less than the trigger complexity, or have an entropy less than the extension complexity and neighbor other low-complexity windows. The sequence within a low complexity region is replaced with the mask character (default 'X'), and the masked alphabetic sequence is returned. The default parameters, width=12, trigger=1.8, extension=2.0, mask='X' are suitable for masking protein sequences before a database search. The standard default seg parameters are width=12, trigger=2.2, extension=2.5 Arguments: Seq seq -- An alphabetic sequence int width -- Window width float trigger -- Entropy in bits between 0 and 4.3.. ( =log_2(20) ) float extension -- Entropy in bits between 0 and 4.3.. ( =log_2(20) ) char mask -- The mask character (default: 'X') Returns : Seq -- A masked alphabetic sequence Raises : ValueError -- On invalid arguments Refs: [1] seg man page: http://bioportal.weizmann.ac.il/education/materials/gcg/seg.html [2] Wootton & Federhen (Computers and Chemistry 17; 149-163, (1993)) Authors: GEC 2005 Future : - Optional mask character. - Option to lower case masked symbols. - Remove arbitary restriction to protein. """ lg20 = log2(20) if trigger < 0 or trigger > lg20: raise ValueError("Invalid trigger complexity: %f" % trigger) if extension < 0 or extension > lg20 or extension < trigger: raise ValueError("Invalid extension complexity: %f" % extension) if width < 0: raise ValueError("Invalid width: %d" % width) if width > len(seq): return seq s = seq.ords() X = seq.alphabet.ord(mask) nwindows = len(seq) - width + 1 ent = [0 for x in range(0, nwindows)] count = [0 for x in range(0, len(seq.alphabet))] for c in s[0:width]: count[c] += 1 ent[0] = entropy(count, base=2) for i in range(1, nwindows): count[s[i - 1]] -= 1 count[s[i + width - 1]] += 1 ent[i] = entropy(count, base=2) prev_segged = False for i in range(0, nwindows): if (prev_segged and ent[i] < extension) or ent[i] < trigger: for j in range(0, width): s[i + j] = X prev_segged = True else: prev_segged = False # Redo, only backwards prev_segged = False for i in range(nwindows - 1, -1, -1): if (prev_segged and ent[i] < extension) or ent[i] < trigger: for j in range(0, width): s[i + j] = X prev_segged = True else: prev_segged = False segged = seq.alphabet.chrs(s) segged.name = seq.name segged.description = seq.description return segged # end mask_low_complexity() class GeneticCode(object): """An encoding of amino acids by DNA triplets. Example : Genetic Code [1]: Standard T C A G +---------+---------+---------+---------+ T | TTT F | TCT S | TAT Y | TGT C | T T | TTC F | TCC S | TAC Y | TGC C | C T | TTA L | TCA S | TAA Stop| TGA Stop| A T | TTG L(s)| TCG S | TAG Stop| TGG W | G +---------+---------+---------+---------+ C | CTT L | CCT P | CAT H | CGT R | T C | CTC L | CCC P | CAC H | CGC R | C C | CTA L | CCA P | CAA Q | CGA R | A C | CTG L(s)| CCG P | CAG Q | CGG R | G +---------+---------+---------+---------+ A | ATT I | ACT T | AAT N | AGT S | T A | ATC I | ACC T | AAC N | AGC S | C A | ATA I | ACA T | AAA K | AGA R | A A | ATG M(s)| ACG T | AAG K | AGG R | G +---------+---------+---------+---------+ G | GTT V | GCT A | GAT D | GGT G | T G | GTC V | GCC A | GAC D | GGC G | C G | GTA V | GCA A | GAA E | GGA G | A G | GTG V | GCG A | GAG E | GGG G | G +---------+---------+---------+---------+ See Also : -- http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c -- http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html#7.5 Authors: JXG, GEC """ # TODO: Explain use of '?' in translated sequence. # TODO: Does translate fails with aproriate execption when fed gaps? # TODO: Can back_translate handle gaps? def __init__( self, ident: int, description: str, amino_acid: str, start: str, base1: str, base2: str, base3: str, ) -> None: """Create a new GeneticCode. Args: -- ident - Standard identifier (or zero). An integer -- description -- amino acid - A sequence of amino acids and stop codons. e.g. "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG" -- start - A sequence indicating start codons, e.g., "---M---------------M---------------M----------------------------" -- base1 - The first base of each codon. e.g., "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG" -- base2 - The second base of each codon. e.g., "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG" -- base3 - The last base of each codon. e.g., "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG" """ self.ident = ident self.description = description self.amino_acid = amino_acid self.start = start self.base1 = base1 self.base2 = base2 self.base3 = base3 stop_codons = [] start_codons = [] for i, a in enumerate(amino_acid): codon = base1[i] + base2[i] + base3[i] if a == "*": stop_codons.append(codon) if start[i] == "M": start_codons.append(codon) self.stop_codons = tuple(stop_codons) self.start_codons = tuple(start_codons) # Building the full translation table is expensive, # so we avoid doing so until necessary. self._table: Optional[Dict[str, str]] = None self._back_table: Optional[Dict[str, str]] = None @staticmethod def std_list() -> Tuple[ "GeneticCode", "GeneticCode", "GeneticCode", "GeneticCode", "GeneticCode", "GeneticCode", "GeneticCode", "GeneticCode", "GeneticCode", "GeneticCode", "GeneticCode", "GeneticCode", "GeneticCode", "GeneticCode", "GeneticCode", "GeneticCode", "GeneticCode", ]: "Return a list of standard genetic codes." return _codon_tables @staticmethod def std() -> "GeneticCode": "The standard 'universal' genetic code." return _codon_tables[0] @staticmethod def by_name(name: str) -> "GeneticCode": """Find a genetic code in the code list by name or identifier.""" for t in _codon_tables: if t.ident == name or t.description == name: return t raise ValueError("No such translation table: %s" % str(name)) @property def table(self) -> Optional[Dict[str, str]]: """A map between codons and amino acids""" if self._table is None: self._create_table() # pragma: no cover return self._table @property def back_table(self) -> Optional[Dict[str, str]]: """A map between amino acids and codons""" if self._back_table is None: self._create_table() # pragma: no cover return self._back_table def _create_table(self) -> None: aa = self.amino_acid base1 = self.base1 base2 = self.base2 base3 = self.base3 # Construct a table of unambiguous codon translations table = {} for i, a in enumerate(aa): codon = base1[i] + base2[i] + base3[i] table[codon] = a # Build the back table. back_table = {} items = list(table.items()) items.sort() for codon, aa in items[::-1]: back_table[aa] = codon # Use first codon, alphabetically. back_table["X"] = "NNN" back_table["B"] = "NNN" back_table["Z"] = "NNN" back_table["J"] = "NNN" self._back_table = back_table ltable = {} letters = dna_extended_letters + "U" # include RNA in table # Create a list of all possible codons codons = [] for c1 in letters: for c2 in letters: for c3 in letters: codons.append(c1 + c2 + c3) # For each ambiguous codon, construct all compatible unambiguous codons. # Translate and collect a set of all possible translated amino acids. # If more than one translation look for possible amino acid ambiguity # codes. for C in codons: pre_translate = dict() # Use dict, because no set in py2.3 c = C.replace("U", "T") # Convert RNA codon to DNA for c1 in dna_ambiguity[c[0]]: for c2 in dna_ambiguity[c[1]]: for c3 in dna_ambiguity[c[2]]: aa = table[c1 + c2 + c3] pre_translate[aa] = "" translated = list(pre_translate.keys()) translated.sort() if len(translated) == 1: trans = list(translated)[0] elif translated == ["D", "N"]: trans = "B" elif translated == ["E", "Q"]: trans = "Z" elif translated == ["I", "L"]: trans = "J" elif "*" in translated: trans = "?" else: trans = "X" ltable[C] = trans self._table = ltable # End create tables def translate(self, seq: Seq, frame: int = 0) -> Seq: """Translate a DNA sequence to a polypeptide using full IUPAC ambiguities in DNA/RNA and amino acid codes. Returns : -- Seq - A polypeptide sequence """ # TODO: Optimize. # TODO: Insanity check alphabet. seqs = seq table = self.table assert table is not None trans = [] L = len(seq) for i in range(frame, L - 2, 3): codon = str(seqs[i : i + 3]).upper() trans.append(table[codon]) return Seq("".join(trans), protein_alphabet) def back_translate(self, seq: Seq) -> Seq: """Convert protein back into coding DNA. Args: -- seq - A polypeptide sequence. Returns : -- Seq - A DNA sequence """ # TODO: Optimize # TODO: Insanity check alphabet. table = self.back_table assert table is not None seqs = seq trans = [table[a] for a in seqs] return Seq("".join(trans), dna_alphabet) # TODO: translate_orf(self, seq, start) ? # TODO: translate_to_stop(self, seq, frame) ? # TODO: translate_all_frames(self,seq) -> 6 translations. def __repr__(self) -> str: string: List[str] = [] string += 'GeneticCode( %d, "' % self.ident string += self.description string += '", \n' string += ' amino_acid = "' string += self.amino_acid string += '",\n' string += ' start = "' string += self.start string += '",\n' string += ' base1 = "' string += self.base1 string += '",\n' string += ' base2 = "' string += self.base2 string += '",\n' string += ' base3 = "' string += self.base3 string += '" )' return "".join(string) def __str__(self) -> str: """Returns a text representation of this genetic code.""" # Inspired by http://bugzilla.open-bio.org/show_bug.cgi?id=1963 letters = "TCAG" # Conventional ordering for codon tables. string: List[str] = [] if self.ident: string += "Genetic Code [%d]: " % self.ident else: string += "Genetic Code: " # pragma: no cover string += self.description or "" string += "\n " string += " ".join([" %s " % c2 for c2 in letters]) string += "\n +" string += "+".join(["---------" for c2 in letters]) + "+ " table = self.table assert table is not None for c1 in letters: for c3 in letters: string += "\n " string += c1 string += " |" for c2 in letters: codon = c1 + c2 + c3 string += " " + codon if codon in self.stop_codons: string += " Stop|" else: amino = table.get(codon, "?") if codon in self.start_codons: string += " %s(s)|" % amino else: string += " %s |" % amino string += " " + c3 string += "\n +" string += "+".join(["---------" for c2 in letters]) string += "+ " string += "\n" return "".join(string) # end class GeneticCode # Data from http://www.ncbi.nlm.nih.gov/projects/collab/FT/index.html#7.5 # Aug. 2006 # Genetic Code Tables # # Authority International Sequence Databank Collaboration # Contact NCBI # Scope /transl_table qualifier # URL http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi?mode=c _codon_tables = ( GeneticCode( 1, "Standard", "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "---M---------------M---------------M----------------------------", "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG", "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG", "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG", ), GeneticCode( 2, "Vertebrate Mitochondrial", "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSS**VVVVAAAADDEEGGGG", "--------------------------------MMMM---------------M------------", "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG", "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG", "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG", ), GeneticCode( 3, "Yeast Mitochondrial", "FFLLSSSSYY**CCWWTTTTPPPPHHQQRRRRIIMMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "----------------------------------MM----------------------------", "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG", "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG", "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG", ), GeneticCode( 4, "Mold, Protozoan, Coelenterate Mitochondrial & Mycoplasma/Spiroplasma", "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--MM---------------M------------MMMM---------------M------------", "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG", "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG", "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG", ), GeneticCode( 5, "Invertebrate Mitochondrial", "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSSSVVVVAAAADDEEGGGG", "---M----------------------------MMMM---------------M------------", "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG", "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG", "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG", ), GeneticCode( 6, "Ciliate, Dasycladacean and Hexamita Nuclear", "FFLLSSSSYYQQCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "-----------------------------------M----------------------------", "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG", "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG", "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG", ), GeneticCode( 9, "Echinoderm and Flatworm Mitochondrial", "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG", "-----------------------------------M---------------M------------", "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG", "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG", "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG", ), GeneticCode( 10, "Euplotid Nuclear", "FFLLSSSSYY**CCCWLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "-----------------------------------M----------------------------", "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG", "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG", "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG", ), GeneticCode( 11, "Bacterial and Plant Plastid", "FFLLSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "---M---------------M------------MMMM---------------M------------", "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG", "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG", "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG", ), GeneticCode( 12, "Alternative Yeast Nuclear", "FFLLSSSSYY**CC*WLLLSPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "-------------------M---------------M----------------------------", "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG", "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG", "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG", ), GeneticCode( 13, "Ascidian Mitochondrial", "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNKKSSGGVVVVAAAADDEEGGGG", "-----------------------------------M----------------------------", "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG", "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG", "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG", ), GeneticCode( 14, "Alternative Flatworm Mitochondrial", "FFLLSSSSYYY*CCWWLLLLPPPPHHQQRRRRIIIMTTTTNNNKSSSSVVVVAAAADDEEGGGG", "-----------------------------------M----------------------------", "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG", "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG", "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG", ), GeneticCode( 15, "Blepharisma Nuclear", "FFLLSSSSYY*QCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "-----------------------------------M----------------------------", "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG", "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG", "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG", ), GeneticCode( 16, "Chlorophycean Mitochondrial", "FFLLSSSSYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "-----------------------------------M----------------------------", "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG", "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG", "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG", ), GeneticCode( 21, "Trematode Mitochondrial", "FFLLSSSSYY**CCWWLLLLPPPPHHQQRRRRIIMMTTTTNNNKSSSSVVVVAAAADDEEGGGG", "-----------------------------------M---------------M------------", "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG", "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG", "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG", ), GeneticCode( 22, "Scenedesmus obliquus Mitochondrial", "FFLLSS*SYY*LCC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "-----------------------------------M----------------------------", "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG", "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG", "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG", ), GeneticCode( 23, "Thraustochytrium Mitochondrial", "FF*LSSSSYY**CC*WLLLLPPPPHHQQRRRRIIIMTTTTNNKKSSRRVVVVAAAADDEEGGGG", "--------------------------------M--M---------------M------------", "TTTTTTTTTTTTTTTTCCCCCCCCCCCCCCCCAAAAAAAAAAAAAAAAGGGGGGGGGGGGGGGG", "TTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGGTTTTCCCCAAAAGGGG", "TCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAGTCAG", ), ) reduced_protein_alphabets = { # "LiB2": Transform( Seq("CFYWMLIV-GPATSNHQEDRKX*-", std_protein_alphabet), Seq("IIIIIIII-SSSSSSSSSSSSX*-", Alphabet("ISX*-")), "Li et al (2003), table II, group 2", ), # "LiB3": Transform( Seq("CFYWMLIV-GPATS-NHQEDRKX*-", std_protein_alphabet), Seq("IIIIIIII-SSSSS-EEEEEEEX*-", Alphabet("ISEX*-")), "Li et al (2003), table II, group 3", ), # "LiB4": Transform( Seq("CFYW-MLIV-GPATS-NHQEDRKX*-", std_protein_alphabet), Seq("YYYY-IIII-SSSSS-EEEEEEEX*-", Alphabet("YISEX*-")), "Li et al (2003), table II, group 4", ), # "LiB5": Transform( Seq("CFYW-MLIV-G-PATS-NHQEDRKX*-", std_protein_alphabet), Seq("YYYY-IIII-G-SSSS-EEEEEEEX*-", Alphabet("YIGSEX*-")), "Li et al (2003), table II, group 5", ), # "LiB6": Transform( Seq("CFYW-MLIV-G-P-ATS-NHQEDRKX*-", std_protein_alphabet), Seq("YYYY-IIII-G-P-SSS-EEEEEEEX*-", Alphabet("YIGPSEX*-")), "Li et al (2003), table II, group 6", ), # "LiB7": Transform( Seq("CFYW-MLIV-G-P-ATS-NHQED-RKX*-", std_protein_alphabet), Seq("YYYY-IIII-G-P-SSS-EEEEE-KKX*-", Alphabet("YIGPSEKX*-")), "Li et al (2003), table II, group 7", ), # "LiB8": Transform( Seq("CFYW-MLIV-G-P-ATS-NH-QED-RKX*-", std_protein_alphabet), Seq("YYYY-IIII-G-P-SSS-NN-EEE-KKX*-", Alphabet("YIGPSNEKX*-")), "Li et al (2003), table II, group 8", ), # "LiB9": Transform( Seq("CFYW-ML-IV-G-P-ATS-NH-QED-RKX*-", std_protein_alphabet), Seq("YYYY-LL-II-G-P-SSS-NN-EEE-KKX*-", Alphabet("YLIGPSNEKX*-")), "Li et al (2003), table II, group 9", ), # "LiB10": Transform( Seq("C-FYW-ML-IV-G-P-ATS-NH-QED-RKX*-", std_protein_alphabet), Seq("C-YYY-LL-II-G-P-SSS-NN-EEE-KKX*-", Alphabet("CYLIGPSNEKX*-")), "Li et al (2003), table II, group 10", ), # "LiB11": Transform( Seq("C-FYW-ML-IV-G-P-A-TS-NH-QED-RKX*-", std_protein_alphabet), Seq("C-YYY-LL-II-G-P-A-SS-NN-EEE-KKX*-", Alphabet("CYLIGPASNEKX*-")), "Li et al (2003), table II, group 11", ), # "LiB12": Transform( Seq("C-FYW-ML-IV-G-P-A-TS-NH-QE-D-RKX*-", std_protein_alphabet), Seq("C-YYY-LL-II-G-P-A-SS-NN-EE-D-KKX*-", Alphabet("CYLIGPASNEDKX*-")), "Li et al (2003), table II, group 12", ), # "LiB13": Transform( Seq("C-FYW-ML-IV-G-P-A-T-S-NH-QE-D-RKX*-", std_protein_alphabet), Seq("C-YYY-LL-II-G-P-A-T-S-NN-EE-D-KKX*-", Alphabet("CYLIGPATSNEDKX*-")), "Li et al (2003), table II, group 13", ), # "LiB14": Transform( Seq("C-FYW-ML-IV-G-P-A-T-S-N-H-QE-D-RKX*-", std_protein_alphabet), Seq("C-YYY-LL-II-G-P-A-T-S-N-H-EE-D-KKX*-", Alphabet("CYLIGPATSNHEDKX*-")), "Li et al (2003), table II, group 14", ), # "LiB15": Transform( Seq("C-FYW-ML-IV-G-P-A-T-S-N-H-QE-D-R-KX*-", std_protein_alphabet), Seq("C-YYY-LL-II-G-P-A-T-S-N-H-EE-D-R-KX*-", Alphabet("CYLIGPATSNHEDRKX*-")), "Li et al (2003), table II, group 15", ), # "LiB16": Transform( Seq("C-FY-W-ML-IV-G-P-A-T-S-N-H-QE-D-R-KX*-", std_protein_alphabet), Seq("C-YY-W-LL-II-G-P-A-T-S-N-H-EE-D-R-KX*-", Alphabet("CYWLIGPATSNHEDRKX*-")), "Li et al (2003), table II, group 16", ), # "LiB17": Transform( Seq("C-FY-W-ML-IV-G-P-A-T-S-N-H-Q-E-D-R-KX*-", std_protein_alphabet), Seq( "C-YY-W-LL-II-G-P-A-T-S-N-H-Q-E-D-R-KX*-", Alphabet("CYWLIGPATSNHQEDRKX*-") ), "Li et al (2003), table II, group 17", ), # "LiB18": Transform( Seq("C-FY-W-M-L-IV-G-P-A-T-S-N-H-Q-E-D-R-KX*-", std_protein_alphabet), Seq( "C-YY-W-M-L-II-G-P-A-T-S-N-H-Q-E-D-R-KX*-", Alphabet("CYWMLIGPATSNHQEDRKX*-"), ), "Li et al (2003), table II, group 18", ), # "LiB19": Transform( Seq("C-F-Y-W-M-L-IV-G-P-A-T-S-N-H-Q-E-D-R-KX*-", std_protein_alphabet), Seq( "C-F-Y-W-M-L-II-G-P-A-T-S-N-H-Q-E-D-R-KX*-", Alphabet("CFYWMLIGPATSNHQEDRKX*-"), ), "Li et al (2003), table II, group 19", ), # "LiB20": Transform( Seq("C-F-Y-W-M-L-I-V-G-P-A-T-S-N-H-Q-E-D-R-KX*-", std_protein_alphabet), Seq( "C-F-Y-W-M-L-I-V-G-P-A-T-S-N-H-Q-E-D-R-KX*-", Alphabet("CFYWMLIVGPATSNHQEDRKX*-"), ), "Li et al (2003), table II, group 20", ), # "LiA2": Transform( Seq("CMFILVWY-AGTSNQDEHRKPX*-", std_protein_alphabet), Seq("IIIIIIII-SSSSSSSSSSSSX*-", Alphabet("ISX*-")), "Li et al (2003), table I, group 2", ), # "LiA3": Transform( Seq("CMFILVWY-AGTSP-NQDEHRKX*-", std_protein_alphabet), Seq("IIIIIIII-SSSSS-EEEEEEEX*-", Alphabet("ISEX*-")), "Li et al (2003), table I, group 3", ), # "LiA4": Transform( Seq("CMFWY-ILV-AGTS-NQDEHRKPX*-", std_protein_alphabet), Seq("YYYYY-III-SSSS-EEEEEEEEX*-", Alphabet("YISEX*-")), "Li et al (2003), table I, group 4", ), # "LiA5": Transform( Seq("FWYH-MILV-CATSP-G-NQDERKX*-", std_protein_alphabet), Seq("YYYY-IIII-SSSSS-G-EEEEEEX*-", Alphabet("YISGEX*-")), "Li et al (2003), table I, group 5", ), # "LiA6": Transform( Seq("FWYH-MILV-CATS-P-G-NQDERKX*-", std_protein_alphabet), Seq("YYYY-IIII-SSSS-P-G-EEEEEEX*-", Alphabet("YISPGEX*-")), "Li et al (2003), table I, group 6", ), # "LiA7": Transform( Seq("FWYH-MILV-CATS-P-G-NQDE-RKX*-", std_protein_alphabet), Seq("YYYY-IIII-SSSS-P-G-EEEE-KKX*-", Alphabet("YISPGEKX*-")), "Li et al (2003), table I, group 7", ), # "LiA8": Transform( Seq("FWYH-MILV-CA-NTS-P-G-DE-QRKX*-", std_protein_alphabet), Seq("YYYY-IIII-AA-SSS-P-G-NN-KKKX*-", Alphabet("YIASPGNKX*-")), "Li et al (2003), table I, group 8", ), # "LiA9": Transform( Seq("FWYH-ML-IV-CA-NTS-P-G-DE-QRKX*-", std_protein_alphabet), Seq("YYYY-LL-VV-AA-SSS-P-G-NN-KKKX*-", Alphabet("YLVASPGNKX*-")), "Li et al (2003), table I, group 9", ), # "LiA10": Transform( Seq("FWY-ML-IV-CA-TS-NH-P-G-DE-QRKX*-", std_protein_alphabet), Seq("YYY-LL-VV-AA-TT-NN-P-G-DD-KKKX*-", Alphabet("YLVATNPGDKX*-")), "Li et al (2003), table I, group 10", ), # "LiA11": Transform( Seq("FWY-ML-IV-CA-TS-NH-P-G-D-QE-RKX*-", std_protein_alphabet), Seq("YYY-LL-VV-AA-TT-NN-P-G-D-EE-KKX*-", Alphabet("YLVATNPGDEKX*-")), "Li et al (2003), table I, group 11", ), # "LiA12": Transform( Seq("FWY-ML-IV-C-A-TS-NH-P-G-D-QE-RKX*-", std_protein_alphabet), Seq("YYY-LL-VV-C-A-TT-NN-P-G-D-EE-KKX*-", Alphabet("YLVCATNPGDEKX*-")), "Li et al (2003), table I, group 12", ), # "LiA13": Transform( Seq("FWY-ML-IV-C-A-T-S-NH-P-G-D-QE-RKX*-", std_protein_alphabet), Seq("YYY-LL-VV-C-A-T-S-NN-P-G-D-EE-KKX*-", Alphabet("YLVCATSNPGDEKX*-")), "Li et al (2003), table I, group 13", ), # "LiA14": Transform( Seq("FWY-ML-IV-C-A-T-S-NH-P-G-D-QE-R-KX*-", std_protein_alphabet), Seq("YYY-LL-VV-C-A-T-S-NN-P-G-D-EE-R-KX*-", Alphabet("YLVCATSNPGDERKX*-")), "Li et al (2003), table I, group 14", ), # "LiA15": Transform( Seq("FWY-ML-IV-C-A-T-S-N-H-P-G-D-QE-R-KX*-", std_protein_alphabet), Seq("YYY-LL-VV-C-A-T-S-N-H-P-G-D-EE-R-KX*-", Alphabet("YLVCATSNHPGDERKX*-")), "Li et al (2003), table I, group 15", ), # "LiA16": Transform( Seq("W-FY-ML-IV-C-A-T-S-N-H-P-G-D-QE-R-KX*-", std_protein_alphabet), Seq("W-YY-LL-VV-C-A-T-S-N-H-P-G-D-EE-R-KX*-", Alphabet("WYLVCATSNHPGDERKX*-")), "Li et al (2003), table I, group 16", ), # "LiA17": Transform( Seq("W-FY-ML-IV-C-A-T-S-N-H-P-G-D-Q-E-R-KX*-", std_protein_alphabet), Seq( "W-YY-LL-VV-C-A-T-S-N-H-P-G-D-Q-E-R-KX*-", Alphabet("WYLVCATSNHPGDQERKX*-") ), "Li et al (2003), table I, group 17", ), # "LiA18": Transform( Seq("W-FY-M-L-IV-C-A-T-S-N-H-P-G-D-Q-E-R-KX*-", std_protein_alphabet), Seq( "W-YY-M-L-VV-C-A-T-S-N-H-P-G-D-Q-E-R-KX*-", Alphabet("WYMLVCATSNHPGDQERKX*-"), ), "Li et al (2003), table I, group 18", ), # "LiA19": Transform( Seq("W-F-Y-M-L-IV-C-A-T-S-N-H-P-G-D-Q-E-R-KX*-", std_protein_alphabet), Seq( "W-F-Y-M-L-VV-C-A-T-S-N-H-P-G-D-Q-E-R-KX*-", Alphabet("WFYMLVCATSNHPGDQERKX*-"), ), "Li et al (2003), table I, group 19", ), # "LiA20": Transform( Seq("W-F-Y-M-L-I-V-C-A-T-S-N-H-P-G-D-Q-E-R-KX*-", std_protein_alphabet), Seq( "W-F-Y-M-L-I-V-C-A-T-S-N-H-P-G-D-Q-E-R-KX*-", Alphabet("WFYMLIVCATSNHPGDQERKX*-"), ), "Li et al (2003), table I, group 20", ), } weblogo-3.8.0/weblogo/utils/000077500000000000000000000000001467613320200157625ustar00rootroot00000000000000weblogo-3.8.0/weblogo/utils/__init__.py000077500000000000000000000200571467613320200201020ustar00rootroot00000000000000# Copyright (c) 2005 Gavin E. Crooks # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # """Extra utilities and core classes not in standard python. """ from typing import Any, Iterable, List, Optional, TextIO import pkg_resources __all__ = ( "isblank", "isfloat", "isint", "ischar", "remove_whitespace", "invert_dict", "stdrepr", "Token", "deoptparse", "crc32", "crc64", "ArgumentError", "group_count", "resource_string", "resource_stream", "resource_filename", ) def isblank(s: Any) -> bool: """Is this whitespace or an empty string?""" if isinstance(s, str): if not s: return True else: return s.isspace() else: return False def isfloat(s: Any) -> bool: """Does this object represent a floating point number?""" try: float(s) return True except (ValueError, TypeError): return False def isint(s: Any) -> bool: """Does this object represent an integer?""" try: int(s) return True except (ValueError, TypeError): return False def ischar(s: Any) -> bool: """Does this object represent a character?""" # Adapted from: https://stackoverflow.com/a/14321721 and # https://mail.python.org/pipermail/python-list/2007-March/425058.html return isinstance(s, str) and bool(s) and s == len(s) * s[0] def remove_whitespace(astring: str) -> str: """Remove all whitespace from a string.""" # TODO: Is this horrible slow? return "".join(astring.split()) def invert_dict(dictionary: dict) -> dict: """Constructs a new dictionary with inverted mappings so that keys become values and vice versa. If the values of the original dictionary are not unique then only one of the original keys will be included in the new dictionary. """ return dict((value, key) for key, value in dictionary.items()) def stdrepr( obj: Any, attributes: Optional[List[str]] = None, name: Optional[str] = None ) -> str: """Create a standard representation of an object.""" if name is None: name = obj.__class__.__name__ if attributes is None: attributes = obj.__class__.__slots__ args = [] for a in attributes: if a[0] == "_": continue # pragma: no cover args.append("%s=%s" % (a, repr(getattr(obj, a)))) arg_str = ",\n".join(args).replace("\n", "\n ") return "%s(\n %s\n)" % (name, arg_str) def group_count(i: Iterable) -> list: """An iteration that returns tuples of items and the number of consecutive occurrences. Thus group_count('aabbbc') yields ('a',2), ('b',3), ('c',1) """ from itertools import groupby return [(item, sum(1 for n in group)) for item, group in groupby(i)] class Token: """Represents the items returned by a file scanner, normally processed by a parser. Attributes : o typeof -- a string describing the kind of token o data -- the value of the token o lineno -- the line of the file on which the data was found (if known) o offset -- the offset of the data within the line (if known) """ __slots__ = ["typeof", "data", "lineno", "offset"] def __init__( self, typeof: str, data: Optional[str] = None, lineno: int = -1, offset: int = -1, ) -> None: self.typeof = typeof self.data = data self.lineno = lineno self.offset = offset def __repr__(self) -> str: return stdrepr(self) def __str__(self) -> str: coord = str(self.lineno) if self.offset != -1: coord += ":" + str(self.offset) coord = coord.ljust(7) return (coord + " " + self.typeof + " : ").ljust(32) + str(self.data or "") def crc32(string: str) -> str: """Return the standard CRC32 checksum as a hexidecimal string.""" import binascii return "%08X" % binascii.crc32(string.encode()) _crc64_table = None def crc64(string: str) -> str: """Calculate ISO 3309 standard cyclic redundancy checksum. Used, for example, by SWISS-PROT. Returns : The CRC as a hexadecimal string. Reference: o W. H. Press, S. A. Teukolsky, W. T. Vetterling, and B. P. Flannery, "Numerical recipes in C", 2nd ed., Cambridge University Press. Pages 896ff. """ # Adapted from biopython, which was adapted from bioperl global _crc64_table if _crc64_table is None: # Initialisation of CRC64 table table = [] for i in range(256): k = i part_h = 0 for j in range(8): rflag = k & 1 k >>= 1 if part_h & 1: k |= 1 << 31 # pragma: no cover part_h >>= 1 if rflag: part_h ^= 0xD8000000 table.append(part_h) _crc64_table = tuple(table) crcl = 0 crch = 0 for c in string: shr = (crch & 0xFF) << 24 temp1h = crch >> 8 temp1l = (crcl >> 8) | shr idx = (crcl ^ ord(c)) & 0xFF crch = temp1h ^ _crc64_table[idx] crcl = temp1l return "%08X%08X" % (crch, crcl) # End crc64 class ArgumentError(ValueError): """A subclass of ValueError raised when a function receives an argument that has the right type but an inappropriate value, and the situation is not described by a more precise exception such as IndexError. The name of the argument or component at fault and (optionally) the value are also stored. """ def __init__(self, message: str, key: str, value: Optional[Any] = None) -> None: """Args: - msg -- An error message. - key -- The name of the argument or component at fault. - value -- Optional value of the argument. """ ValueError.__init__(self, key, message) # Changed .message to .msg because of deprecation warning in python 2.6 self.msg = message self.key = key self.value = value # end class ArgumentError # TODO: Replace with direct calls to pkg_resources def resource_string( modulename: str, resource: str, basefilename: Optional[str] = None ) -> bytes: """Locate and return a resource as a string. >>> f = resource_string( __name__, 'somedatafile', __file__) """ return pkg_resources.resource_string(modulename, resource) def resource_stream( modulename: str, resource: str, basefilename: Optional[str] = None ) -> TextIO: """Locate and return a resource as a stream. >>> f = resource_stream( __name__, 'somedatafile', __file__) """ return open(resource_filename(modulename, resource, basefilename)) def resource_filename( modulename: str, resource: str, basefilename: Optional[str] = None ) -> str: """Locate and return a resource filename. >>> f = resource_filename( __name__, 'somedatafile', __file__) """ return pkg_resources.resource_filename(modulename, resource) weblogo-3.8.0/weblogo/utils/deoptparse.py000077500000000000000000000172231467613320200205120ustar00rootroot00000000000000# Copyright (c) 2004 Gavin E. Crooks # # This software is distributed under the MIT Open Source License. # # # Permission is hereby granted, free of charge, to any person obtaining a # copy of this software and associated documentation files (the "Software"), # to deal in the Software without restriction, including without limitation # the rights to use, copy, modify, merge, publish, distribute, sublicense, # and/or sell copies of the Software, and to permit persons to whom the # Software is furnished to do so, subject to the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR # IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE # AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER # LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, # OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN # THE SOFTWARE. # """Custom extensions to OptionParse for parsing command line options.""" # FIXME: Docstring # TODO: Add profiling option # DeOptionParser : # # http://docs.python.org/lib/module-optparse.html # # Random_options : # Set random generator and seed. Use options.random as # source of random numbers # Copyright : # print copyright information # Documentation : # print extended document information # # Additional file_in and file_out types import sys from copy import copy from optparse import IndentedHelpFormatter, Option, OptionParser, OptionValueError from typing import Any, Iterable, Optional, TextIO, Type def _copyright_callback( option: Any, opt: Any, value: Any, parser: "DeOptionParser" ) -> None: if option or opt or value or parser: pass # Shut up lint checker print(parser.copyright) sys.exit() def _doc_callback(option: Any, opt: Any, value: Any, parser: "DeOptionParser") -> None: if option or opt or value or parser: pass # Shut up lint checker print(parser.long_description) sys.exit() class DeHelpFormatter(IndentedHelpFormatter): def __init__( self, indent_increment: int = 2, max_help_position: int = 32, width: int = 78, short_first: int = 1, ): IndentedHelpFormatter.__init__( self, indent_increment, max_help_position, width, short_first ) def format_option_strings(self, option: Option) -> str: """Return a comma-separated list of option strings & metavariables.""" if option.takes_value(): dest = option.dest assert dest is not None metavar = option.metavar or dest.upper() short_opts = option._short_opts long_opts = [lopt + " " + metavar for lopt in option._long_opts] else: short_opts = option._short_opts long_opts = option._long_opts if not short_opts: short_opts = [ " ", ] if self.short_first: opts = short_opts + long_opts else: opts = long_opts + short_opts return " ".join(opts) def _check_file_in(option: Any, opt: Any, value: str) -> TextIO: if option or opt or value: pass # Shut up lint checker try: return open(value, "r") except IOError: raise OptionValueError("option %s: cannot open file: %s" % (opt, value)) def _check_file_out(option: Any, opt: Any, value: str) -> TextIO: if option or opt or value: pass # Shut up lint checker try: return open(value, "w+") except IOError: raise OptionValueError("option %s: cannot open file: %s" % (opt, value)) def _check_boolean(option: Any, opt: Any, value: str) -> bool: if option or opt or value: pass # Shut up lint checker v = value.lower() choices = { "no": False, "false": False, "0": False, "yes": True, "true": True, "1": True, } try: return choices[v] except KeyError: raise OptionValueError( "option %s: invalid choice: '%s' (choose from 'yes' or 'no', 'true' or 'false')" % (opt, value) ) def _check_dict(option: Any, opt: Any, value: str) -> str: if option or opt or value: pass # Shut up lint checker v = value.lower() choices = option.choices try: return choices[v] except KeyError: raise OptionValueError( "option %s: invalid choice: '%s' (choose from '%s')" % (opt, value, "', '".join(choices)) ) class DeOption(Option): TYPES = Option.TYPES + ("file_in", "file_out", "boolean", "dict") TYPE_CHECKER = copy(Option.TYPE_CHECKER) TYPE_CHECKER["file_in"] = _check_file_in TYPE_CHECKER["file_out"] = _check_file_out TYPE_CHECKER["boolean"] = _check_boolean TYPE_CHECKER["dict"] = _check_dict choices = None def _new_check_choice(self) -> None: if self.type == "dict": if self.choices is None: raise OptionValueError( "must supply a dictionary of choices for type 'dict'" ) elif not isinstance(self.choices, dict): raise OptionValueError( "choices must be a dictionary ('%s' supplied)" % str(type(self.choices)).split("'")[1] ) return self._check_choice() # Have to override _check_choices so that we can parse # a dict through to check_dict CHECK_METHODS = Option.CHECK_METHODS CHECK_METHODS[2] = _new_check_choice # type: ignore class DeOptionParser(OptionParser): def __init__( self, usage: Optional[str] = None, option_list: Optional[Iterable[Option]] = None, option_class: Type[Option] = DeOption, version: Optional[str] = None, conflict_handler: str = "error", description: Optional[str] = None, long_description: Optional[str] = None, formatter: IndentedHelpFormatter = DeHelpFormatter(), add_help_option: bool = True, prog: Optional[str] = None, copyright: Optional[str] = None, add_verbose_options: bool = True, ): OptionParser.__init__( self, usage, option_list, option_class, version, conflict_handler, description, formatter, add_help_option, prog, ) if long_description: self.long_description = long_description self.add_option( "--doc", action="callback", callback=_doc_callback, help="Detailed documentation", ) if copyright: self.copyright = copyright self.add_option( "--copyright", action="callback", callback=_copyright_callback, help="" ) if add_verbose_options: self.add_option( "-q", "--quite", action="store_false", dest="verbose", default=False, help="Run quietly (default)", ) self.add_option( "-v", "--verbose", action="store_true", dest="verbose", default=False, help="Verbose output (Not quite)", )