KEGG Orthology (KO) System
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The KEGG reference pathway maps and BRITE functional hierarchies are represented in a general way to be applicable to all organisms.
KEGG Orthology (KO) is the basis for this representation, consisting of manually defined ortholog groups that correspond to KEGG pathway nodes and BRITE hierarchy nodes.
Once genes are assigned the KO identifiers, or the K numbers, by the genome annotation procedure described below, the organism-specific pathway maps and BRITE functional hierarchies can be automatically generated.
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Ortholog Annotation in KEGG
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There are two types of annotations in KEGG.
One is a genome based annotation, assigning K numbers to genes in a given genome.
The other is a pathway based annotation, assigning given K numbers (such as in a pathway map) to genes in all organisms.
In order to cope with an increasing number of complete genomes, the first annotation is now automatically performed (except for a selected number of reference organisms) with continuous efforts to manually improve the second cross-species annotation.
The KEGG annotation procedure is as follows:
- Gene information for completely sequenced genomes is computationally generated from RefSeq and other public resources, and stored in the KEGG GENES database.
- Sequence similarity scores and best hit relations are computationally generated from GENES by pairwise genome comparisons using SSEARCH, and stored in the KEGG SSDB database.
- Automatic annotation is performed for a limited number (currently, about 3000-4000) of K numbers, which are considered safe to do so based on the result of SSDB computation and the criteria of the KOALA (KEGG Orthology And Links Annotation) tool.
- Manual annotation is performed across species for other K numbers, using the KOALA and GFIT tools. This step may involve addition/revision of ortholog groups, which is essential to increase the number of safe K numbers.
The read-only version of KEGG annotation tools is available for public view.
- KOALA - linked from each KEGG ORTHOLOGY entry page
- GFIT - linked from each KEGG GENES entry page
The quality of KEGG annotation can be examined by two tools for mapping on the pathway and the genome.
The ortholog table is useful to check completeness of pathways and complexes and the gene cluster is useful to check consistency of annotation for operon-like structures in bacterial genomes.
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Last updated: January 1, 2010
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