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KEGG Syntax

Taxonomy-based analysis of conserved genes and gene sets
Syntax Genome alignment KO composition Synteny analysis Taxonomy analysis

About KEGG Syntax

KEGG Syntax (Synteny and taxonomy) is a new resource for using KOs (K numbers) and modules (M numbers), as well as computationally generated ortholog groups such as VOGs, in the taxonomy-based analysis of conserved genes, conserved gene sets and conserved gene orders (conserved synteny) in cellular organisms and viruses.

An example of using KEGG Mapper and KEGG Syntax
  1. Use BlastKOALA or GhostKOALA to assign KOs to the gene set in the user's genome.
  2. Use KEGG Mapper Reconstruct tool to obtain functional implications from reconstucted pathways, etc.
  3. KO assignment and functional inference may be improved by using KEGG Syntax tools, especially when the gene set is ordered according to the chromosomal position.

Conserved genes

Manually defined KOs

In KEGG conserved genes are represented by KOs (KEGG Orthology groups) for both cellular organisms and viruses. KOs are manually defined from functionally characterized genes and proteins in specific organisms, but they are expanded to other organisms based on sequence similarity.

Computationally generated ortholog groups

For selected sets of proteins, ortholog grouping is computationally performed using the SSEARCH comparison results in order to verify, improve and expand manually defined KO grouping. For viruses, VOGs (virus ortholog groups) are made available.

Conserved gene sets

Manually defined KO sets (modules)

KEGG modules are conserved functional units of genes. They are manually defined sets of KOs that are involved, for example, in successive reactions steps in conserved subpathways of metabolic pathways. They sometimes contain positionally correlated genes, called gene clusters, as in operon structures of prokaryotic genomes.

Computationally generated KO clusters

Here "KO clusters" represent conserved gene sets along chromosomal positions, implying conserved synteny. As the result of KO assignment to genes in the genome, similar gene orders can be found by a sequence alignment method by considering the genome as a sequence of KO identifiers. A new genome comparison method has been developed using the Goad-Kanehisa algorithm, enabling a comprehensive analysis of syntenic regions.

Computationally generated VOG clusters

Furthermore, this algorithm can be used to analyze VOG clusters by considring the genome as a sequence of VOG identifiers for better understanding of gene set transfer between viruses and cellular organisms.

Last updated: January 1, 2026