Ensembl Bacteria

<!DOCTYPE html> <html lang="en-gb"> <head> <title>Ensembl Bacteria</title> <link rel="stylesheet" type="text/css" media="all" href="/minified/626fdf3f8e1eae27680b56af5e25ecc2.css"/><link rel="stylesheet" type="text/css" media="all" href="/minified/e5de71fba654a9457bc43f860824901a.image.css"/> <link href="/i/ensembl-favicon.png" rel="icon" type="image/png" /> <link href="/apple-touch-icon.png" type="image/png" rel="apple-touch-icon" /> <link href="//bacteria.ensembl.org/opensearch/all.xml" type="application/opensearchdescription+xml" rel="search" title="Ensembl (All)" /> <meta name="description" content="Ensembl Bacteria is a genome-centric portal for bacterial species of scientific interest" /> <meta name="viewport" content="target-densitydpi=device-dpi, width=device-width, initial-scale=1.0, maximum-scale=2.0, user-scalable=yes" /> <script>var prefetch = [];</script> </head> <body class="ie ie7 ie67 no_tabs static" data-pace="2" id="ensembl-webpage"> <div id="min_width_container"> <div id="min_width_holder">   <div id="masthead" class="js_panel"> <input type="hidden" class="panel_type" value="Masthead" /> <div class="logo_holder"><a href="/"><img src="/i/e.png" alt="Ensembl Genomes Home" title="Ensembl Genomes Home" class="print_hide" style="width:43px;height:40px" /></a><a href="/"><img src="/i/ensemblBacteria.png" alt="Ensembl Bacteria Home" title="Ensembl Bacteria Home" class="print_hide" style="width:195px;height:40px" /></a><img src="/i/e-ensembl_print.gif" alt="Ensembl Bacteria Home" title="Ensembl Bacteria Home" class="screen_hide_inline" style="width:195px;height:40px" /> <span class="print_hide"> <span id="site_menu_button">▼</span> <ul id="site_menu" style="display:none"> <li><a href="http://www.ensemblgenomes.org">Ensembl Genomes</a></li> <li><a href="http://bacteria.ensembl.org">Ensembl Bacteria</a></li> <li><a href="http://protists.ensembl.org">Ensembl Protists</a></li> <li><a href="http://fungi.ensembl.org">Ensembl Fungi</a></li> <li><a href="http://plants.ensembl.org">Ensembl Plants</a></li> <li><a href="http://metazoa.ensembl.org">Ensembl Metazoa</a></li> <li><a href="http://www.ensembl.org">Ensembl (vertebrates)</a></li> </ul> </span> </div> <div class="mh print_hide"> <div class="account_holder"><div class="_account_holder"><div class="account-loading">Loading…</div><form action="/Ajax/accounts_dropdown"></form></div></div> <div class="tools_holder"><ul class="tools"><li><a class="constant" href="/hmmer">HMMER</a></li><li><a class="constant" href="/Multi/Tools/Blast">BLAST</a></li><li><a class="constant" href="/tools.html">Tools</a></li><li><a class="constant" href="/info/data/ftp/index.html">Downloads</a></li><li><a class="constant" href="/info/">Help & Docs</a></li><li class="last"><a class="constant" target="_blank" href="http://www.ensembl.info">Blog</a></li></ul><div class="more"><a href="#">More <span class="arrow">▼</span></a></div></div> <div class="search_holder print_hide"> <div id="searchPanel" class="js_panel"> <input type="hidden" class="panel_type" value="SearchBox" /> <form action="/Multi/Psychic"> <div class="search print_hide"> <div class="sites button"> <img class="search_image no-sprite badge-16" src="/i/search/ensemblunit.gif" alt="" /> <img src="/i/search/down.gif" style="width:7px" alt="" /> <input type="hidden" name="site" value="ensemblunit" /> </div> <div> <label class="hidden" for="se_q">Search terms</label> <input class="query inactive" id="se_q" type="text" name="q" value="Search Ensembl Bacteria…" data-role="none" onkeydown="if (event.keyCode == 13) { $(this).closest('form').submit(); 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margin: 0; padding-left:3px" title="Start typing the name of a genome..." value="Start typing the name of a genome..."> </div> </form> <p style="margin-bottom:0"> e.g. type esc to find Escherichia </p> </div> </div> </div> <div class="plain-box access-box"> <ul> <li><em>Search for a gene</em> - type the name of a gene or other identifier into the search box above </li> <li><em>Find a genome</em> - click in the 'browse a genome' box above and start typing your genome name to find matching genomes </li> <li><a href="/species.html">View full list of all Ensembl Bacteria species</a> </li> <li><a href="/info/data/api.html">Access Ensembl Bacteria programmatically</a> </li> </ul> </div> <div class="plain-box"> <h2>What's New in Release 60</h2> <div class="info-box embedded-box float-right"> <h3>Did you know...?</h3> <p><img alt="Ensembl Genomes REST Service" src="/img/rest_service_0.png" style="float:left; height:62px; width:119px; padding:0 8px 2px 0" title="Ensembl Genomes REST Service" /></p> <p>To access Ensembl Genomes data from any programming language, try our <a href="http://rest.ensembl.org">REST service</a>. For full documentation, including examples from a wide range of languages, visit <a href="http://rest.ensembl.org">http://rest.ensembl.org</a></p> </div> <p>In June 2023, Ensembl Bacteria released new gene predictions for almost all of the genomes it hosts. This was done in collaboration with the EMBL-EBI metagenomics team and utlised a pipeline using <a href="https://doi.org/10.1093/bioinformatics/btu153">Prokka</a>, combined with results from <a href="https://www.ebi.ac.uk/Tools/rna/infernal_cmscan/">cmscan</a>, <a href="https://doi.org/10.1093/nar/gky1085">EggNOG</a> and <a href="https://www.ebi.ac.uk/interpro/about/interproscan/">InterProScan</a>. We have retained the community-submitted annotation for 115 species that are in our pan-taxonomic comparative analysis.</p> <ul> <li><p>Genomes</p> <ul> <li>A total of 31,332 <a href="https://www.ensembl.info/2020/09/21/ensembl-bacteria-updates/">non-redundant</a> bacterial and archaeal genomes </li> </ul></li> <li><p>Data </p> <ul> <li>Updated annotation of molecular interactions involving bacterial genes </li> <li>Updated protein features for all species using <a href="https://www.ebi.ac.uk/interpro/search/sequence/">InterProScan</a> </li> <li>Updated pan-taxonomic compara (which includes key bacterial species) </li> </ul></li> </ul> <div id="rapidbox"> <h2>Ensembl Rapid Release</h2> <p><b>New genome assemblies are now being released to the <a target="_blank" href="http://beta.ensembl.org">Ensembl Beta site</a> </b>.</p> <p>All Rapid Release data, including release 65, has been uploaded into the new Ensembl Beta site.</p> <p>The Ensembl Rapid Release website will remain active for the foreseeable future, however, the data and species set will no longer be updated.</p> <p class="right">Find out more on our <a href="https://www.ensembl.info/2024/11/14/we-will-be-freezing-ensembl-rapid-release/" target="_blank">blog</a></p> </div> </div> </div> </div> <div class="column-two"><div class="column-padding no-right-margin"> <div class="plain-box"> <h2 id="archivesites">Archive sites</h2> <p>The following archive sites are available to access previous versions of data: - Release 59, May 2024 <a href="https://eg59-bacteria.ensembl.org">eg59-bacteria.ensembl.org</a> - Release 56, February 2023 <a href="https://eg56-bacteria.ensembl.org">eg56-bacteria.ensembl.org</a> - Release 52, December 2021 <a href="https://eg52-bacteria.ensembl.org">eg52-bacteria.ensembl.org</a> - Release 49, December 2020 <a href="https://eg49-bacteria.ensembl.org">eg49-bacteria.ensembl.org</a> - Release 45, September 2019 <a href="https://eg45-bacteria.ensembl.org">eg45-bacteria.ensembl.org</a></p> </div> <div class="plain-box"> <h2 id="ensemblbacteria">Ensembl Bacteria</h2> <p>Ensembl Bacteria is a browser for bacterial and archaeal genomes. The assemblies for these are taken from the databases of the <a href="http://www.insdc.org/">International Nucleotide Sequence Database Collaboration</a>, the European Nucleotide Archive at the EBI, GenBank at the NCBI, and the DNA Database of Japan).</p> <h3 id="dataaccess">Data access</h3> <p>Data can be visualised through the Ensembl genome browser and accessed programmatically via our Perl and RESTful APIs. Data is also accessible through public MySQL databases and our FTP site containing full data dumps in FASTA, EMBL, GTF, GFF3, JSON and RDF formats. A selection of over 100 key bacterial genomes have been included in the pan-taxonomic compara, and genes from all genomes have been classified into families using HAMAP and PANTHER <a href="/info/docs/compara/index.html">more details</a>.</p> </div> <div class="plain-box"> <p><a href="http://ensemblgenomes.org/">Ensembl Genomes</a> is developed by <a href="http://www.ebi.ac.uk">EMBL-EBI</a> and is powered by the <a href="http://www.ensembl.org">Ensembl</a> software system for the analysis and visualisation of genomic data. For details of our funding please <a href="/info/about/credits.html">click here</a>.</p> <p class="rtecenter"> <a href="http://www.ebi.ac.uk/"><img alt="EMBL-EBI logo" src="/img/ebi_logo.png" style="height:30px; vertical-align:middle" /></a> <a href="http://www.ensembl.org" style="padding-left: 20px;"><img alt="Ensembl logo" src="/img/empowered.png" style="height:20px; vertical-align:middle" /></a> <a href="https://globalbiodata.org/scientific-activities/global-core-biodata-resources"><img alt="Global Bio Data logo" src="/img/GCBR-Logo-RGB.svg" style="width:100px;height:73px;padding-left: 12px;vertical-align:middle"/></a> <a href="https://www.elixir-europe.org/platforms/data/core-data-resources" style="padding-left: 12px;"><img alt="Elixir Logo" src="/img/Elixir_CDR-mini.png" style="vertical-align:middle" /></a> </p> </div> </div> </div> </div> </div> <div id="wide-footer"> <div class="column-wrapper"> <div class="column-two left"> <p> Ensembl Bacteria release 60 - October 2024 © <span class="print_hide"><a href="http://www.ebi.ac.uk/" style="white-space:nowrap">EMBL-EBI</a></span> <span class="screen_hide_inline">EMBL-EBI</span> </p> </div> <p class="invisible">.</p> </div> <div class="column-wrapper"><hr /><div id="fat-footer"> <div class="column-four left"> <h3>About Us</h3> <p><a href="/info/about/">About us</a></p> <p><a href="/info/about/contact/">Contact us</a></p> <p><a href="/info/about/publications.html">Citing Ensembl Genomes</a></p> <p><a href="https://www.ebi.ac.uk/data-protection/ensembl/privacy-notice">Privacy policy</a></p> <p><a href="/info/about/legal/">Disclaimer</a></p> </div> <div class="column-four left"> <h3>Get help</h3> <p><a href="/info/website/">Using this website</a></p> <p><a href="/info/">Documentation</a></p> <p><a href="/info/website/upload/">Adding custom tracks</a></p> <p><a href="/info/data/">Downloading data</a></p> </div> <div class="column-four left"> <h3>Our sister sites</h3> <p><a href="http://www.ensembl.org">Ensembl</a></p><p><a href="http://fungi.ensembl.org">Ensembl Fungi</a></p><p><a href="http://plants.ensembl.org">Ensembl Plants</a></p><p><a href="http://protists.ensembl.org">Ensembl Protists</a></p><p><a href="http://metazoa.ensembl.org">Ensembl Metazoa</a></p> </div> <div class="column-four left"> <h3>Follow us</h3> <p><a class="media-icon" href="http://www.ensembl.info/"> <img alt="[RSS logo]" title="Ensembl blog" src="/i/rss_icon_16.png"></a> <a href="http://www.ensembl.info/">Blog</a></p> <p><a class="media-icon" href="https://twitter.com/ensemblgenomes"> <img alt="[twitter logo]" title="Follow us on Twitter!" src="/i/twitter.png"></a> <a href="https://twitter.com/ensemblgenomes">Twitter</a></p> </div> </div> <p class="invisible">.</p> </div> </div> </div> </div> </div> <form id="core_params" action="#" style="display:none"> <fieldset><input type="hidden" name="db" value="core" /></fieldset> </form> <input type="hidden" id="species_path" name="species_path" value="" /> <input type="hidden" id="gdpr_version" name="gdpr_version" value="2.0.0" /> <input type="hidden" id="gdpr_policy_url" name="gdpr_policy_url" value="https://www.ensembl.org/info/about/legal/privacy.html" /> <input type="hidden" id="gdpr_terms_url" name="gdpr_terms_url" value="https://www.ebi.ac.uk/about/terms-of-use" /> <input type="hidden" id="gdpr_cookie_name" name="gdpr_cookie_name" value="ENSEMBL_PRIVACY_POLICY" /> <input type="hidden" id="species_common_name" name="species_common_name" value="Escherichia coli str. 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