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<!DOCTYPE html> <html lang="en"> <head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1"> <title>KEGG GENOME Database</title> <link rel="stylesheet" href="/css/kegg25.css"> <script>  </script> </head> <body> <div id="topnav" ontouchstart=""> <div class="navlist"> <a href="/kegg/">KEGG</a> </div> <div class="dropdown"> Databases <div class="dropdown-content"> <ul> <li><a href="/kegg/pathway.html">Pathway</a></li> <li><a href="/kegg/brite.html">Brite</a></li> <li><a href="/kegg/ko.html">KO</a></li> <li><a href="/kegg/genes.html">Genes</a></li> <li><a href="/kegg/compound/">Chemical</a></li> <li><a href="/kegg/disease/">Disease</a></li> <li><a href="/kegg/drug/">Drug</a></li> <li><a href="/kegg/medicus.html">Medicus</a></li> </ul> </div> </div> <div class="dropdown"> Tools <div class="dropdown-content"> <ul> <li><a href="/kegg/mapper/">Mapper</a></li> <li><a href="/kegg/webapp/">Web Apps</a></li> <li><a href="/kegg/syntax/">Syntax</a></li> <li><a href="/kegg/annotation/">Annotation</a></li> </ul> </div> </div> <div class="dropdown"> Auto annotation <div class="dropdown-content"> <ul> <li><a href="https://www.kegg.jp/blastkoala/">BlastKOALA</a></li> <li><a href="https://www.kegg.jp/ghostkoala/">GhostKOALA</a></li> </ul> </div> </div> <div class="navlist"> <a href="https://www.kanehisa.jp/">Kanehisa Lab</a> </div> </div> <div id="header"> <div class="logo"> <a href="/kegg/"><img src="/Fig/kegg128.gif" alt="KEGG icon"></a> </div> <div class="title"> <h2 class="txt1">KEGG GENOME Database</h2> <h5>Cellular organisms with complete genome sequences</h5> </div> </div> <div id="dbnav" class="bar1"> <ul> <li><a href="/kegg/kegg2.html">KEGG2</a></li> <li><a href="/kegg/pathway.html">PATHWAY</a></li> <li><a href="/kegg/brite.html">BRITE</a></li> <li><a href="/kegg/module.html">MODULE</a></li> <li><a href="/kegg/ko.html">KO</a></li> <li><a href="/kegg/genes.html">GENES</a></li> <li><span class="current">GENOME</span></li> <li><a href="/kegg/genome/virus.html">Virus</a></li> <li><a href="/kegg/seq/">SeqData</a></li> <li><a href="/kegg/annotation/enzyme.html">Enzyme</a></li> </ul> </div> <div id="content">  <div class="searchbox"> <form method="get" action="/dbget-bin/www_bfind_sub"> <input type="hidden" name="mode" value="bfind"> <input type="hidden" name="max_hit" value="1000"> Search <select name="dbkey"> <option value="kegg">KEGG</option> <option value="pathway">PATHWAY</option> <option value="brite">BRITE</option> <option value="module">MODULE</option> <option value="orthology">KO</option> <option value="genes">GENES</option> <option value="genome" selected="selected">GENOME</option> <option value="compound">COMPOUND</option> <option value="glycan">GLYCAN</option> <option value="reaction">REACTION</option> <option value="rclass">RCLASS</option> <option value="enzyme">ENZYME</option> <option value="network">NETWORK</option> <option value="variant">VARIANT</option> <option value="disease">DISEASE</option> <option value="drug">DRUG</option> <option value="dgroup">DGROUP</option> </select> for <input type="search" size="40" name="keywords"> <input type="submit" value="Go"> </form> </div>  <div class="searchbox"> <form name="show" method="get" action="/kegg-bin/show_genome"> <table style="border-collapse:collapse;"> <tr><td></td><td><span class="small">organism code or vtax number</span></td></tr> <tr><td>Genome browser</td><td>  <input type="text" name="org" size="10" value="">  <input type="submit" value="Launch"> <input type="reset" value="Clear"> </td></tr> </table> </form> </div> <div class="searchbox"> <form name="show" method="get" action="https://www.kegg.jp/ssdb-bin/genome_align"> <table style="border-collapse:collapse;"> <tr><td></td><td><span class="small">organism codes to be compared</span></td></tr> <tr><td>Gene order alignment</td><td>  <input type="text" name="gn1" size="6" value=""> vs <input type="text" name="gn2" size="6" value="">  <input type="submit" value="Align"> <input type="reset" value="Clear"> </td></tr> </table> </form> </div> <div class="main"> <hr class="frame1"> <h4 class="txt1">GENOME Database</h4> <div class="indent"> <b>KEGG GENOME</b> is a collection of <b>KEGG organisms</b>, which are the organisms with complete genome sequences and each of which is identified by the three- or four-letter organism code. The GENOME database also contains a collection of <b>KEGG Viruses</b> generated from RefSeq data and each identified by the virus taxonomy (vtax) identifier (see <a href="/kegg/genome/virus.html">KEGG Virus</a> for more details). <br><br> <div class="frame0"> <table> <tr> <td class="center">Category</td> <td class="center">DBGET<br>(genome)</td> <td class="center">Identifiers</td> <td class="center">DBGET<br>(genes)</td> <td class="center">Annotation</td> </tr> <tr> <td><a href="/kegg/tables/br08606.html">KEGG organisms</a></td> <td rowspan="2" class="center"><a href="/dbget-bin/www_bfind?genome">GENOME</a></td> <td>T0 or T1 numbers / three- or<br>four-letter organism codes</td> <td rowspan="2"><a href="/dbget-bin/www_bfind?genes">GENES</a></td> <td rowspan="2">KOALA/manual</td> </tr> <tr> <td><a href="/brite/br08621">KEGG viruses</a></td> <td>Taxonomy IDs (Vtax numbers)</td> </tr> </table> </div> <br> Most genomes are associated with genome maps showing chromosomal locations of genes, which can be viewed by a graphical interface of KEGG Genome Browse, a part of <a href="/kegg/webapp/#genome">KEGG Web Apps</a>. <br><br> Furthermore, a new <a href="/kegg/syntax/gnalign.html">genome alignment</a> tool has been developed by treating the genome as a sequence of genes represented by <a href="/kegg/ko.html">KOs</a> or <a href="/kegg/genome/virus.html">VOGs</a>. <li><a href="/kegg/annotation/">Annotation</a></li> </div> <br> <hr class="frame1"> <h4 class="txt1">KEGG Organism and Taxonomic Grouping</h4> <div class="indent"> KEGG organisms are manually organized in a simple hierarchy of taxonomic classification with predefined ordering of organisms starting with hsa (Homo sapiens). The hierarchy is shown in the following two Brite files with identical contents. <ul style="list-style:none;"> <li>08601 <a href="/brite/br08601.keg">KEGG organisms</a> (Brite hierarchy file)</li> <li>08606 <a href="/kegg/tables/br08606.html">KEGG organisms</a> (Brite table file)</li> </ul> Each organism code in these files is linked to an organism-specific entry point (such as <a href="/kegg-bin/show_organism?org=hsa">hsa</a>) for viewing pathway maps, Brite hierarchies and KEGG modules, as well as for launching Genome Browser. <br><br> KEGG organisms, as well as KEGG viruses, are also shown in the following Brite hierarchy files, which are computationally generated from the NCBI taxonomy. <ul style="list-style:none;"> <li>08610 <a href="/brite/br08610.keg+-e">KEGG organisms in the NCBI taxonomy</a> (including addendum)</li> <li>08611 <a href="/brite/br08611.keg+-e">KEGG organisms in taxonomic ranks</a></li> <li>08620 <a href="/brite/br08620.keg+-e">KEGG viruses in the NCBI taxonomy</a></li> <li>08621 <a href="/brite/br08621.keg+-e">KEGG viruses in taxonomic ranks</a></li> </ul> The ordering of KEGG organisms defined in 08601 is retained in 08610 and 08611 and the ordering of KEGG viruses in 08620 and 08621 is based on the Baltimore classification (see <a href="/kegg/genome/virus.html#taxonomy">more details</a>). In addition to KEGG organism codes, the 08610 file contains taxonomy IDs of GENES addendum category. The 08611 and 08621 files are created with the fixed levels of taxonomic ranks and used for taxonomy mapping and other purposes as default (see <a href="/kegg/syntax/syntax.html#taxonomy">more details</a>). <li><a href="/kegg/annotation/">Annotation</a></li> <br><br> The category name in this table file represents an organism group. Select any group for viewing, for example, combined pathway maps of <a href="/kegg-bin/show_organism?category=Mammals">Mammals</a>. <ul style="list-style:none;"> </ul> As shown above the NCBI taxonomy is used to represent non-genome entries (addendum category) of the <a href="/kegg/genes.html">KEGG GENES</a> database. It is also used to compare KEGG organisms and the NCBI reference and representative genomes. <ul style="list-style:none;"> <li>08608 <a href="/kegg/tables/br08608.html">KEGG organisms and virus groups</a></li> </ul> </div> <hr class="frame1"> <h4 class="txt1">KEGG Mapping for Genome Comparison and Combination</h4> <div class="indent"> An organism group may be defined to compare or combine KEGG organisms, other organisms and environmental samples, enabling the analysis of combined pathway maps for the group. </div> <blockquote> <form action="/kegg-bin/show_organism"> <table> <tr><td> Define organism group (enter organism codes or T numbers): </td></tr> <tr><td> <input type="search" name="orgs" size="40"> <input type="button" value="Go" onclick="submit_chk(this.form);"> </td></tr> </table> </form> <br> <table> <tr> <td colspan="2">(Genome comparison)</td> </tr> <tr class="top"> <td><a href="/kegg-bin/show_organism?orgs=hsa+eco">hsa eco</a></td> <td>Homo sapiens (human) vs. Escherichia coli K-12 strain<br> such as <a href="/kegg-bin/show_pathway?orgs=hsa+eco&mapno=00900">Terpenoid backbone biosynthesis</a><br> where green for human, red for E.coli, and split for both</td> </tr> <tr> <td colspan="2">(Host-microbiome relationship)</td> </tr> <tr class="top"> <td>hsa+SRS011061</td> <td>Homo sapiens (human) + gut microbiome (stool sample SRS011061 from <a href="https://www.ncbi.nlm.nih.gov/datasets/genome/GCA_900207615.1/">HMP</a>)<br> KEGG Mapper Reconstruct tool generates combined pathways such as <a href="/kegg/mapper/example/map01100_hsa_SRS011061.html">Global metabolism map</a> with the coloring of green for human, red for gut microbiome, and blue for both</td> </tr> <tr> <td colspan="2">(Host-symbiont relationship)</td> </tr> <tr> <td><a href="/kegg-bin/show_organism?orgs=lja+mlo">lja+mlo</a></td> <td>Lotus japonicus (lotus) + Mesorhizobium loti</td> </tr> <tr> <td><a href="/kegg-bin/show_organism?orgs=api+buc">api+buc</a></td> <td>Acyrthosiphon pisum (pea aphid) + Buchnera aphidicola</td> </tr> <tr> <td><a href="/kegg-bin/show_organism?orgs=bmy+wbm">bmy+wbm</a></td> <td>Brugia malayi (filaria) + Wolbachia</td> </tr> <tr> <td colspan="2">(Host-vector-pathogen relationship)</td> </tr> <tr class="top"> <td><a href="/kegg-bin/show_organism?orgs=hsa+aga+pfa">hsa+aga+pfa</a></td> <td>Homo sapiens (human) + Anopheles gambiae (mosquito) + Plasmodium falciparum</td> </tr> </table> </blockquote> <div class="indent"> There are predefined organism group names that can be used to view, for example, combined pathway maps. See the category field of <a href="/kegg/tables/br08606.html">br08606</a>. </div> <blockquote> <table> <tr> <td colspan="2">(Combined pathway maps, etc.) </tr> <tr> <td><a href="/kegg-bin/show_organism?category=Vertebrates">Vertebrates</a></td> <td></td> </tr> <tr> <td><a href="/kegg-bin/show_organism?category=Escherichia">Escherichia</a></td> <td>Genus-level pangenome</td> </tr> <tr> <td><a href="/kegg-bin/show_organism?category=Escherichia%20coli&category_type=species">Escherichia coli</a>  </td> <td>Species-level pangenome</td> </tr> </table> </blockquote> <hr class="frame1"> <i>Last updated: April 8, 2025</i> </div>  </div> </body> </html>