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KEGG GENOME Database

Organisms and ecosystems with genome sequence information

KEGG2 PATHWAY BRITE MODULE KO GENOME GENES SSDB Organisms
Enter KEGG organism code or use Organism button to select
     (Examples) hsa  mmu  dme  cel  ath  sce  eco  bsu  syn  mja

KEGG Organisms

KEGG GENOME has been a collection of KEGG organisms (see release history), which are the organisms with known complete genome sequences supplemented by those with massive EST datasets (see also KEGG GENES). KEGG GENOME is being extended in three ways. First, it now contains metagenomes representing environmental samples (ecosystems) of genome sequences for multiple species. Second, KEGG organisms with high-quality KOALA annotation can now be combined computationally to examine, for example, reconstructed pathways for pangenomes and organism groups. Third, virus genomes will be integrated and virus genes will be annotated.

Category Genome Identifiers Gene
catalog		 Annotation
Organisms Complete
genomes		 GENOME GENOMES T0 numbers or three-letter
organism codes		 GENES KOALA
T1 numbers or four-letter
organism codes starting with "d"		 DGENES KAAS
EST datasets EGENOME T2 numbers EGENES KAAS
Metagenomes MGENOME T3 numbers MGENES KAAS
Pangenomes     Generic species names GENES KOALA
Viruses VGENOME   RefSeq identifiers VGENES None

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KEGG Mapping for Genome Comparison and Combination

An organism group may be defined to compare or combine KEGG organisms, 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+T30003 Homo sapiens (human) + gut microbiome
such as Global metabolism map
where green for human, red for gut microbiome, and blue for both
(Host-symbiont relationship)
dlja+mlo Lotus japonicus (lotus) + Mesorhizobium loti
api+buc Acyrthosiphon pisum (pea aphid) + Buchnera aphidicola
bmy+wbm Brugia malayi (filaria) + Wolbachia
(Host-pathogen relationship)
hsa+pfa Homo sapiens (human) + Plasmodium falciparum
aga+pfa Anopheles gambiae (mosquito) + Plasmodium falciparum
There are predefined organism groups in KEGG, such as shown below:
(Taxonomic group)
Vertebrates Vertebrates (defined in KEGG organisms)
(Pangenome)
Escherichia coli Escherichia coli pangenome (defined in KEGG pangenomes)

KEGG Taxonomy

KEGG organisms are organized in a simple hierarchy of taxonomic classification. Animals and plants are classified in somewhat more detailed hierarchies. These hierarchies are maintained as part of the KEGG BRITE database. The interface below allows mapping of KEGG organisms to these hierarchies according to the three- or four-letter KEGG organism codes.

NCBI Taxonomy

KEGG organisms, as well as viruses, can be viewed in the NCBI taxonomy. Given a set of NCBI taxonomy IDs, the following interface generates a taxonomy tree.
Last updated: February 1, 2012
KEGG GenomeNet Bioinformatics Japan Kanehisa Laboratories