The KEGG MODULE database is a collection of KEGG modules, manually defined functional units of gene sets. Each module is identified by the M number and defined by the logical expression of K numbers. There are two types of modules.

• pathway modules – functional units of gene sets in metabolic pathways, including molecular complexes
• signature modules – functional units of gene sets that characterize phenotypic features

Some signature modules are represented in a hierarchical manner, using the logical expression of K numbers and M numbers. A related dataset of reaction modules represents functional units of chemical reaction steps. Each reaction module is identified by the RM number and defined by the logical expression of RC (Raction Class) numbers.

• reaction modules – functional units of successive reaction steps in metabolic pathways

Reactioon modules are treated as part of the KEGG MODULE database in the DBGET system, allowing search and retrieval such as by using the search box above.

Currently available KEGG modules and reaction modules are summarized in the following Brite hierarchy files.

• 00002 KEGG modules
• 00003 KEGG reaction modules

The actual content of each KEGG module can be viewed by a dynamically generated graphical diagram, called the module diagram, such as M00002 for glycolysis core module involving three-carbon compounds. This reference module can be expanded by adding the KEGG organism code in the form of hsa_M00002, for example, for a human-specific module. Similar to organism-specific KEGG pathway maps, organism-specific modules are highlighted green. They are also complete modules detected by the following procedure.

In order to evaluate whether the gene set is complete, i.e., the functional unit is present, in a given genome, the completeness check is performed for organism-specific modules. In the logical expression a space or a plus sign, representing a connection in the pathway or the molecular complex, is treated as an AND operator and a comma, used for alternatives, is treated as an OR operator. A minus sign designates an optional item in the complex. Thus, the completeness check involves identifying individual blocks separated by the AND operator and checking if all blocks are present. The completeness check of all moduels is performed for KEGG organisms and is also made available in KEGG Mapper Reconstruct tool.

Another representation of KEGG modules, called the module entry contains a list of organisms, including addendum and virus categories, with complete modules. Alternatively, each organism or virus may be viewed from Change pathway type button of the module diagram page. Here is an example of naming organism-specific modules.

M00793

Reference module

eco_M00793

Escherichia coli K-12 MG1655 (KEGG organism)

1877_M00793

Micromonospora echinospora (addendum category)

948870_M00793

Escherichia coli phage phi927 (virus category)

It is usually the case that complete modules representing specific biosynthetic pathways, biodegradation pathways, molecular complexes, etc. are found in specific organism groups. The taxonomy analysis tool shows the number of organisms having complete modules and/or KOs in the three pre-defined levels of taxonomic groups. The distribution of complete modules is shown below for the seven top levles: Animals, Plants, Fungi, Protists, Bacteria, Archaea and Viruses.