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 selected viruses with relevance to diseases, as well as a collection of KEGG Viruses computaionally generated from RefSeq and corresponding to the vg (viral gene) category of the GENES database. KEGG GENOME is supplemented by MGENOME, a collection of metagenome sequences from environmental and organismal samples.
| Category | DBGET (genome) |
Identifiers | DBGET (genes) |
Annotation |
| KEGG organisms (Complete genomes) |
GENOME | T0 numbers / three- or four- letter organism codes |
GENES | KOALA/manual |
| Selected viruses | T4 numbers | |||
| KEGG viruses (Vtax category) |
Taxonomy IDs | |||
| Metagenomes | MGENOME | T3 numbers | MGENES | GhostKOALA |
KEGG Organism and Genome Browser
Currently available KEGG organisms are listed in:
Each organism code (such as hsa for Homo sapiens) is linked to organism-specific pathway maps and other information. Each organism is also linked to KEGG Genome Browser (through "KGB" link), a newly developed browser for viewing and analyzing chromosomal positions of genes (see: KEGG Synteny).
Organism Group
The taxonomic classification of KEGG organisms such as shown below allows search and analysis of specific organism groups. Select any group for viewing, for example, combined pathway maps.
KEGG organism groups include genus or species level pangenomes, which are linked from the following lists.
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 Taxonomy).
- 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+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) T10018+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 groups in KEGG, such as shown below:
(Taxonomic group) Vertebrates Vertebrates (defined in KEGG organisms) (Genus-level pangenome) Escherichia Escherichia pangenome (defined in KEGG genus list) (Species-level pangenome) Escherichia coli Escherichia coli pangenome (defined in KEGG species list)
Last updated: August 12, 2022