GENOME Database
KEGG GENOME is a collection of KEGG organisms, 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 KEGG Viruses generated from RefSeq data and each identified by the virus taxonomy (vtax) identifier (see KEGG Virus for more details).
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 KEGG Web Apps.
Furthermore, a new genome alignment tool has been developed by treating the genome as a sequence of genes represented by KOs or VOGs.
Category | DBGET (genome) |
Identifiers | DBGET (genes) |
Annotation |
KEGG organisms (Complete genomes) |
GENOME | T0 or T1 numbers / three- or four-letter organism codes |
GENES | KOALA/manual |
KEGG viruses (Vtax category) |
Taxonomy IDs |
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 KEGG Web Apps.
Furthermore, a new genome alignment tool has been developed by treating the genome as a sequence of genes represented by KOs or VOGs.
KEGG Organism and Organism Group
Currently available KEGG organisms are listed in the following Brite table file:
Each organism code (such as hsa for Homo sapiens) is linked to organism-specific pathway maps, Brite hierarchies and KEGG modules. Each organism is also linked to Genome Browser through the "KGB" link.
The category name in this table file represents an organism group. Select any group for viewing, for example, combined pathway maps of Mammals.
The category name in this table file represents an organism group. Select any group for viewing, for example, combined pathway maps of Mammals.
NCBI Taxonomy
KEGG organisms are organized in a simple hierarchy of taxonomic classification. KEGG organisms are also shown in the hierarchy of the NCBI taxonomy with the taxonomic ranks in its abbreviated lineage. The ordering of KEGG organisms is manually defined and is identical in both hierarchies (see also: KEGG Syntax).
- KEGG organisms
- KEGG organisms in the NCBI taxonomy (including addendum)
- KEGG organisms in taxonomic ranks
KEGG Mapping for Genome Comparison and Combination
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.
(Genome comparison) hsa eco Homo sapiens (human) vs. Escherichia coli K-12 strain
such as Terpenoid backbone biosynthesis
where green for human, red for E.coli, and split for both(Host-microbiome relationship) hsa+SRS011061 Homo sapiens (human) + gut microbiome (stool sample SRS011061 from HMP)
KEGG Mapper Reconstruct tool generates combined pathways such as Global metabolism map with the coloring of green for human, red for gut microbiome, and blue for both(Host-symbiont relationship) lja+mlo Lotus japonicus (lotus) + Mesorhizobium loti api+buc Acyrthosiphon pisum (pea aphid) + Buchnera aphidicola bmy+wbm Brugia malayi (filaria) + Wolbachia (Host-vector-pathogen relationship) hsa+aga+pfa Homo sapiens (human) + Anopheles gambiae (mosquito) + Plasmodium falciparum
There are predefined organism group names that can be used to view, for example, combined pathway maps. See the category field of br08606.
(Combined pathway maps, etc.) Vertebrates Escherichia Genus-level pangenome Escherichia coli Species-level pangenome
Last updated: September 24, 2024