How KEGG can be used for genome/metagenome annotation
The KEGG database contains three main components for genome/metagenome annotation:
Continuous efforts are being made to expand the repertoire of KO entries and the improved collection of KEGG modules (identified by M numbers) for automated interpretation of high-level funtions.
- the collection of internally annotated gene catalogs for the complete genomes (called KEGG organisms) and additional protein sequences in the KEGG GENES database
- the knowledge base of high-level functions represented as the molecular interaction, reaction and relation networks in the KEGG PATHWAY, BRITE and MODULE databases, and
- the knowledge base of molecular-level functions associated with ortholog groups in the KO database, where most KO entries are defined in a context-dependent manner as nodes of the KEGG molecular networks.
Continuous efforts are being made to expand the repertoire of KO entries and the improved collection of KEGG modules (identified by M numbers) for automated interpretation of high-level funtions.
Ortholog Table
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.
Taxonomic Distribution
The taxonomic distribution of each KO or module can be viewed from its entry page through the "Taxonomy" or "Virus taxonomy" button linked to the NCBI taxonomy for cellular organsims (br08610) or viruses (br08620).
The taxonomic distribution of a combination of KOs and modules in cellular organisms can be examined with the taxonomy mapping tool in the KEGG Taxonomy page.
The taxonomic distribution of a combination of KOs and modules in cellular organisms can be examined with the taxonomy mapping tool in the KEGG Taxonomy page.
Module Table
The module table (MT) is another way of showing the taxonomic distribution of a combination of modules and KOs. For a given set of M and/or K numbers it identifies organisms that contain complete modules and/or KO groups. The list of organisms may be collapsed into broader organism groups.
Annotation Guide
The KEGG Annotation Guide is a collection of HTML tables, called BRITE tables, showing summary views of the current annotation of the KEGG GENES database, such as how K numbers are defined and assigned for distinguishing related genes and for comparing different subunit structures.
Comparing subunit structures or gene sets Distinguishing related genes
Comparing subunit structures or gene sets Distinguishing related genes
Signature KOs and Modules
Another set of BRITE tables contains signature KOs and/or signature modules, which can be used to infer phenotypic features of organisms.
Metabolic capacity Pathogenicity and drug resistance
Metabolic capacity Pathogenicity and drug resistance
Last updated: July 1, 2022