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KEGG Organisms

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, and selected viruses with relevance to diseases. KEGG GENOME is supplemented by MGENOME, a collection of metagenome sequences from environmental samples (ecosystems).

Category DBGET
(genome)
Identifiers DBGET
(genes)
Annotation
KEGG Organisms
(Complete genomes)
GENOME GENOMES T0 numbers / three- or four-
letter organism codes
GENES KOALA/manual
Viruses T4 numbers
Metagenomes MGENOME T3 numbers MGENES GhostKOALA

Organism Groups and Pangenomes

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.


KEGG Taxonomy and NCBI Taxonomy

KEGG organisms are organized in a simple hierarchy of taxonomic classification, here called the KEGG taxonomy. 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 identical in both hierarchies because the KEGG taxonomy is created in a manner consistent with the NCBI taxonomy. 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.

Taxonomy Mapping

The interface below allows mapping of KEGG organisms to the NCBI taxonomy or the KEGG taxonomy according to the three- or four-letter KEGG organism codes. Given a set of NCBI taxonomy IDs, the following interface generates a taxonomy tree.

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+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: September 21, 2016
KEGG GenomeNet Kanehisa Laboratories