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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 Syntax</title> <link rel="stylesheet" href="/css/kegg25.css"> <link rel="stylesheet" href="/css/jquery-ui.css"> <style> #sidebar { background: linear-gradient(#f0e0e4, 40%, white); } </style> </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 Syntax</h2> <h5>Analysis of onserved genes, gene sets and gene orders</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><span class="current"><b>KEGG Syntax</b></span></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><a href="/kegg/annotation/"><b>KEGG Annotation</b></a></li> <li>  <a href="/kegg/annotation/ko_assign.html">KO assignment</a></li> <li>  <a href="/kegg/annotation/ann_stat.html">Current statistics</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;">  <div class="main"> <h4 class="txt1">KEGG Syntax</h4> <b>KEGG Syntax</b> (<b>Syn</b>teny and <b>tax</b>onomy) is a new resource for using KOs (K numbers), as well as VOGs (virus ortholog groups), and modules (M numbers) in the taxonomy-based analysis of conserved genes, conserved gene sets and conserved gene orders (conserved synteny) in cellular organisms and viruses. <br><br> <hr class="frame1"> <h4 class="txt1">Conserved genes</h4> <div class="indent"> In KEGG conserved genes are represented by <a href="/kegg/ko.html"><b>KOs</b> (KEGG Orthology groups)</a> for both cellular organisms and viruses. KOs are manually defined from functionally characterized genes and proteins in specific organisms, but they are expanded to other organisms based on sequence similarity. <br><br> For viruses, <a href="/kegg/genome/virus.html#vog"><b>VOGs</b> (virus ortholog groups)</a> are defined fully computationally to supplement low assignment of KOs. </div> <h4 class="txt1">Conserved gene sets of functional units</h4> <div class="indent"> <a href="/kegg/module.html"><b>KEGG modules</b></a> are examples of conserved functional units of genes. They are manually defined sets of enzyme KOs that are involved in successive reactions steps in conserved subpathways of metabolic pathways. They sometimes contain positionally correlated genes, as in operon structures of prokaryotic genomes. </div> <h4 class="txt1">Conserved gene orders</h4> <div class="indent"> As the result of KO and VOG assignments to genes in the genome, similar gene orders can be found by a sequence alignment method by considering the genome as a sequence of KO identifiers or VOG identifiers. A new <a href="/kegg/syntax/gnalign.html">genome comparison</a> method has been developed using the Goad-Kanehisa algorithm, enabling the development of the KEGG Syntax resouce. <br><br> The dataset of precomputed genome alignment results is now available in the <a href="/kegg/syntax/synteny.html">Synteny analysis</a> page for all cellular organisms compared against viruses using VOGs. </div> <br> <hr class="frame1"> <h4 class="txt1" id="taxonomy">Taxonomy files</h4> <div class="indent"> The KEGG database uses the <a href="https://www.ncbi.nlm.nih.gov/taxonomy">NCBI taxonomy</a> for classification of cellular organisms and viruses. For cellular organisms, the three- or four-letter KEGG organism codes are classified somewhat differently in the following Brite hierarchy files. <div class="list"> <ul> <li>08601 <a href="/brite/br08601">KEGG organisms</a></li> <li>08610 <a href="/brite/br08610">KEGG organisms in the NCBI taxonomy</a></li> <li>08611 <a href="/brite/br08611">KEGG organisms in taxonomic ranks</a></li> </ul> </div> 08601 is a manually created taxonomy file using the simple hierarchy defined in the <a href="/kegg/tables/br08608.html">KEGG organism groups</a> and the predefined order of organism codes with hsa (Homo sapiens) at the top. 08610 is computationally generated using the abbreviated lineage of the NCBI taxonomy keeping the order of organism codes defined in 08601. In addition, 08610 contains taxonomy IDs for GENES Addendum (ag) entries. 08611 is another computationally generated file for the KEGG organisms with fixed levels of taxonomic ranks: phylum, class, order, family, genus and species. <br><br> For viruses, the taxonomy IDs of KEGG Viruses (GENOME vtax category and GENES vg category) are classified according to the NCBI taxonomy, which is based on the <a href="https://ictv.global/taxonomy/">ICTV taxonomy</a>, with the Baltimore classification <a href="/kegg/genome/virus.html">added by KEGG</a>. <div class="list"> <ul> <li>08620 <a href="/brite/br08620">KEGG viruses in the NCBI taxonomy</a></li> <li>08621 <a href="/brite/br08621">KEGG viruses in taxonomic ranks</a></li> </ul> </div> Both of these Brite hierarchy files are computationally generated and the lowest-level taxonomy IDs are linked to GENOME vtax entries. In the 08620 file the taxonomy IDs are shown in the full lineage of NCBI virus taxonomy, while the 08621 file is organized in the fixed levels of taxonomic ranks: realm, kingdom, phylum, class, order, family, genus and species. </div> <br> <hr class="frame1"> <i>Last updated: January 7, 2025</i> </div>  </div> </body> </html>