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KEGG Annotation
<!DOCTYPE html> <html lang="en"> <head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1"> <title>KEGG Annotation</title> <link rel="stylesheet" href="/css/kegg25.css"> <style> #sidebar { background: linear-gradient(#f0e0e4, 40%, white); } </style> <script> <!-- function extract_kid(form,mode){ var ent = form.text.value; var line; ent = ent.replace( /\W/g, " " ); ent = ent.replace( /\s+/g, " " ); ent = ent.replace( /\s+$/, "" ); ent = ent.replace( /^\s+/, "" ); line = ent.split(" "); ent = ""; if (mode == 0) { for(i = 0; i < line.length; i++){ if (line[i].match(/^K\d{5}/i)) { ent = ent + " " + line[i]; } } } else if (mode == 1) { for(i = 0; i < line.length; i++){ if (line[i].match(/^[MK]\d{5}/i)) { ent = ent + " " + line[i]; } } } ent = ent.replace( /^\s/, "" ); form.text.value = ent; } function Launcher(formobj,mode) { var p = formobj.text.value; var param, url; p = p.replace( /\W/g, " " ); p = p.replace( /^\s+/, "" ); p = p.replace( /\s+$/, "" ); param = p.replace( /\s+/g, "+" ); if (p == "") { return false; } url = ''; if (mode == 0) { url = "/kegg-bin/view_ortholog_table?orthology=" + param; } else if (mode == 1) { url = "/kegg-bin/view_module_table?id=" + param; } if (url) { window.open(url,'_blank'); } } //--> </script> </head> <body> <div id="header3"> <div class="logo3"> <a href="/kegg/"><img src="/Fig/keg100R.png" alt="KEGG in Keg"></a> </div> <div class="title"> <h2 class="txt1">KEGG Annotation</h2> <h5>KO-based annotation for linking genomes to phenotypes</h5> </div> </div> <div id="sidebar"> <ul> <li><a href="/kegg/mapper/"><b>KEGG Mapper</b></a></li> <li> <a href="/kegg/mapper/reconstruct.html"><b>Reconstruct</b></a></li> <li> <a href="/kegg/mapper/search.html"><b>Search</b></a></li> <li> <a href="/kegg/mapper/color.html"><b>Color</b></a></li> <li> <a href="/kegg/mapper/join.html"><b>Join</b></a></li> <li> <a href="/kegg/mapper/mwsearch.html"><b>MWsearch</b></a></li> <li style="margin-top:4px;"> <a href="/kegg/mapper/convert_id.html">Convert ID</a></li> </ul> <ul> <li><a href="/kegg/webapp/"><b>KEGG Web Apps</b></a></li> <li> <a href="/kegg/webapp/color_gui.html">Map coloring GUI</a></li> <li> <a href="/kegg/webapp/color_url.html">Map coloring URL</a></li> </ul> <ul> <li><a href="/kegg/syntax/"><b>KEGG Syntax</b></a></li> <li> <a href="/kegg/syntax/taxonomy.html">Taxonomy mapping</a></li> <li> <a href="/kegg/syntax/gnalign.html">Genome alignment</a></li> <li> <a href="/kegg/syntax/synteny.html">Synteny analysis</a></li> </ul> <ul> <li><span class="current"><b>KEGG Annotation</b></span></li> <li> <a href="/kegg/annotation/ko_assign.html">KO assignment</a></li> <li> <a href="https://www.kegg.jp/blastkoala/">BlastKOALA</a></li> <li> <a href="https://www.kegg.jp/ghostkoala/">GhostKOALA</a></li> </ul> <ul> <li><a href="/kegg/kegg2.html">KEGG2</a></li> <li><a href="/kegg/">KEGG</a></li> </ul> </div> <div id="content2"> <hr class="frame1" style="margin-top:0;"> <!-- start --> <div class="main"> <h4 class="txt1">Genome Annotation (KO Assignment)</h4> <div class="indent"> The KEGG database contains three main components for genome/metagenome annotation: <ul> <li>the collection of internally annotated gene catalogs for sequenced genomes, both for cellular organisms (called KEGG organisms) and viruses, and additional publication-based protein sequences in the <a href="/kegg/genes.html">GENES</a> database,</li> <li>the knowledge base of high-level functions represented as molecular interaction, reaction and relation networks in the <a href="/kegg/pathway.html">PATHWAY</a>, <a href="/kegg/brite.html">BRITE</a> and <a href="/kegg/module.html">MODULE</a> databases, and</li> <li>the knowledge base of molecular-level functions associated with ortholog groups in the <a href="/kegg/ko.html">KO</a> database, where most KO entries are defined in a context-dependent manner as nodes of the KEGG molecular networks.</li> </ul> In general, KO entries (identified by K numbers) also represent sequence similarity groups. Thus, the sequence similarity search of a query genome against KEGG GENES is a search for most appropriate K numbers (see <a href="/kegg/ko.html#tool">KO assignment tools</a>). The assigned set of K numbers can then be used to reconstruct KEGG pathway maps, BRITE hierarchies and KEGG modules, enabling interpretation of high-level functions. <br><br> Automatic KO assignment can be done by the following web servers <ul style="list-style:none;"> <li><a href="https://www.kegg.jp/blastkoala/">BlastKOALA</a></li> <li><a href="https://www.kegg.jp/ghostkoala/">GhostKOALA</a></li> </ul> and the result of KO assignment is linked to <a href="/kegg/mapper/reconstruct.html">KEGG Mapper Reconstruct</a> tool. </div> <br> <hr class="frame1"> <h4 class="txt1">Ortholog table</h4> <div class="indent"> The ortholog table (OT) has existed from the beginning of the KEGG project. For a given set of K numbers it displays the current assignment of genes in KEGG organisms and viruses. <br><br> <form name="ot" method="post" enctype="multipart/form-data" action="javascript:Launcher(document.ot);"> <table> <tr><td colspan="2"> Enter K numbers <span class="small">(Example) K22014 K21512 K26964 K26963 K21511 K26962 K26961 K26965 K26966</span> </td></tr> <tr style="vertical-align:bottom;"><td> <textarea name="text" cols="50" rows="2"></textarea> </td> <td> <input type="button" value="Go" onclick="Launcher(document.ot,0);"> <input type="button" value="Filter" onclick="extract_kid(document.ot,0);"> <input type="reset" value="Clear"> </td></tr> </table> </form> <br> The ortholog table additionally displays positional correlations of genes in the chromosome, such as operon structures, by coloring. The same color means that the genes are adjacent. </div> <br> <hr class="frame1"> <h4 class="txt1" id="aguide">Annotation guide</h4> <div class="indent"> The KEGG Annotation Guide is a collection of HTML tables, called BRITE tables, showing summary views of the current annotation of the GENES database, such as how K numbers are defined and assigned for distinguishing related genes and for comparing different subunit structures. <br><br> Comparing subunit structures or gene sets <ul style="list-style:none;"> <li>01610 <a href="/kegg/annotation/br01610.html">Ribosomal proteins</a></li> <li>01611 <a href="/kegg/annotation/br01611.html">RNA polymerases</a></li> <li>01632 <a href="/kegg/annotation/br01612.html">DNA polymerases</a></li> <li>01610 <a href="/kegg/annotation/br01613.html">Aminoacyl-tRNA synthetases</a></li> </ul> Distinguishing related genes <ul style="list-style:none;"> <li>01601 <a href="/kegg/annotation/br01601.html">Enzymes of 2-oxocarboxylic acid metabolism</a></li> <li>01602 <a href="/kegg/annotation/br01602.html">Dioxygenases</a></li> </ul> </div> <hr class="frame1"> <h4 class="txt1" id="signature">Signature KOs and modules</h4> <div class="indent"> Another set of BRITE tables contains signature KOs and/or signature modules, which can be used to infer phenotypic features of organisms. <br><br> Metabolic capacity <ul style="list-style:none;"> <li>01620 <a href="/kegg/annotation/br01620.html">Photosynthetic and chemosynthetic capacities</a></li> </ul> Pathogenicity and drug resistance <ul style="list-style:none;"> <li>01600 <a href="/kegg/annotation/br01600.html">Antimicrobial resistance: KEGG signatures</a></li> </ul> </div> <br> <hr class="frame1"> <i>Last updated: September 23, 2024</i> </div> <!-- end --> </div> </body> </html>