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).

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.

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). As shown above the NCBI taxonomy is used to represent non-genome entries (addendum category) of the KEGG GENES database. It is also used to compare KEGG organisms and the NCBI reference and representative genomes.

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.
Define organism group (enter organism codes or T numbers):

(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