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 defined by the logical expression of RC numbers:

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

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

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.

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.

The following is a daily updated list of complete modules for KEGG organisms and viruses categorized into seven groups: Animals, Plants, Fungi, Protists, Bacteria, Archaea and Viruses. Each organism or virus may be viewed from Change pathway type button of the module diagram page.