About KEGG Syntax
KEGG Syntax (Synteny and taxonomy) is a collection of tools for comparison and analysis of organisms, organism groups and viruses, as well as the user’s data, by the conserved gene repertoires, including KOs, modules, VOGs and conserved gene orders (syntenic regions).
One particular example is to characterize an organism group by the combined composition of KOs, define a similarity measure using the composition, and compare KEGG organism groups (see details in Organism group similarity).
The dendrogram for the six top-level groups shows the distinction of eukaryotes and prokaryotes, or the similarity of archaea and bacteria, which presents a different view from the three domains of life.
One particular example is to characterize an organism group by the combined composition of KOs, define a similarity measure using the composition, and compare KEGG organism groups (see details in Organism group similarity).
The dendrogram for the six top-level groups shows the distinction of eukaryotes and prokaryotes, or the similarity of archaea and bacteria, which presents a different view from the three domains of life.
An example of using KEGG Mapper and KEGG Syntax
- Use BlastKOALA or GhostKOALA to assign KOs to the gene set in the user's genome.
- Use KEGG Mapper Reconstruct tool to obtain functional implications from reconstucted pathways, etc.
- 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, and 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: April 1, 2026