KEGG MODULE is a collection of functional units that are classified into:

• pathway modules – representing tighter functional units than KEGG pathway maps, such as M00002 (Glycolysis, core module involving three-carbon compounds)
• structural complexes – often forming molecular machineries, such as M00072 (Oligosaccharyltransferase)
• functinal sets – for other types of essential sets, such as M00360 (Aminoacyl-tRNA synthases, prokaryotes)
• signature modules – as markers of phenotypes, such as M00363 (EHEC pathogenicity signature, Shiga toxin)

The entire list of KEGG modules can be viewed from the BRITE hierarchy file:

KEGG Modules

Each module is defined by the combination of KEGG ORTHOLOGY (KO) identifiers or K numbers, so that it can be used for annotation and interpretation purposes in individual genomes. Notations for this definition include:

• space delimited items for pathway elements
• comma separated items in parentheses for alternatives
• plus sign to define a complex
• minus sign for an optional item

KEGG modules are associated with graphical diagrams called module maps. For example, M00002 represents glycolysis core module involving three-carbon compounds and its organism specific module can be selected from the pop-up menu or directly specified in the form of hsa_M00002. While KEGG pathway maps are all manually drawn, KEGG module maps are computationally generated from the text definition describe above. There is also a difference of how organism-specific versions are generated. Organism specific modules are generated only when consituent components are present in the genome.

The KEGG Mapper interface now allows KEGG MODULE mapping in a similar way to KEGG PATHWAY mapping.

• Search Module - basic module mapping tool

The ortholog table is a useful tool to check completeness and consistency of genome annotations. It shows currently annotated genes in individual genomes for a given set of K numbers, together with coloring of adjacent genes on the chromosome. Each KEGG module contains a link to the corresponding ortholog table.

Each KEGG module also contains a link to KEGG taxonomy mapping, which indicates the presence or absence of the module in all KEGG organisms under a taxonomic classification.