Reaction Module

KEGG pathway modules in the metabolic pathways represent functional units defined by a set of KO identifiers (K numbers) for the enzymes involved. In contrast, KEGG reaction modules are defined from purely chemical data without incorporating any enzyme data, i.e., from the analysis of chemical structure transformation patterns along the metabolic pathways. The reaction module is a conserved sequence of chemical structure transformation patterns defined by a set of Reaction Class identifiers (RC numbers).
ko/rc modules
The Reaction Class is like a reaction ortholog accommodating global structural differences of metabolites. Therefore, it is interesting to examine how well reaction modules (RC modules) defined by reaction orthologs correspond to KEGG pathway modules (KO modules) defined by gene orthologs. This is summarized in the following BRITE hierarchy file.
Reaction modules are now part of the MODULE flat file (see KEGG MODULE Database).


Carboxylic acid metabolism

2-Oxocarboxylic acid chain extension

RM001
2-Oxocarboxylic acid chain extension by tricarboxylic acid pathway

2-Oxocarboxylic acid chain modification

RM002
Carboxyl to amino conversion using protective N-acetyl group (basic amino acid synthesis)
RM032
Carboxyl to amino conversion without using protective group
RM033
Branched-chain addition (branched-chain amino acid synthesis)
RM030
Glucosinolate synthesis
RM901
Reductive amination of 2-oxocarboxylic acid (aminotransferase reaction)
RM903
Oxidative decarboxylation of 2-oxoacid to form its CoA derivative

Fatty acid synthsis and degradation

RM018
Beta oxidation in acyl-CoA degradation
RM020
Fatty acid synthesis using acetyl-CoA (reversal of RM018)
RM021
Fatty acid synthesis using malonyl-CoA

Acyl-CoA metabolism

RM019
Acyl-CoA conversion via dicarboxylate semialdehyde

Reaction module variation

RM032 RM002
Carboxyl to amino conversion
RM020 RM021
Fatty acid synthesis
RM018 RM016
Beta oxidation

Reaction module combination

RM001+(RM002,RM032,RM033)
Amino acid synthesis
RM001+RM030
Glucosinolate synthesis

Reaction module map

map01210
2-Oxocarboxylic acid metabolism
map01212
Fatty acid metabolism
map01230
Biosynthesis of amino acids

Nucleotide sugar metabolism

Nucleotide sugar biosynthesis

RM022
Nucleotide sugar biosynthesis, type 1
RM023
Nucleotide sugar biosynthesis, type 2
RM039
Nucleotide sugar biosynthesis, type 3
RM042
Nucleotide sugar biosynthesis, type 4

Deoxy sugar metabolism

RM035
Transamination and N,N-dimethylation in polyketide biosynthesis
RM043
Transamination and N-acetylation in deoxysugar biosynthesis
RM036
Epimerization and reduction in deoxysugar biosynthesis
RM037
Deoxygenation (transamination and deamination) in deoxysugar biosynthesis
RM038
Deoxygenation (dehydration and reduction) in deoxysugar biosynthesis

Sugar conversion

RM040
Sugar activation and nucleotide sugar interconversion
RM041
Inversion of the carbon chain

Reaction module variation

RM022 RM023 RM039
Nucleotide sugar biosynthesis (sugar activation)

Reaction module combination

(RM022,RM039)+(RM040,RM041)
Ascorbate synthesis

Reaction module map

map01250
Biosynthesis of nucleotide sugars

Aromatics degradation

Methyl to carboxyl conversion on aromatic ring (preprocessing module)

RM003
Methyl to carboxyl conversion on aromatic ring
RM015
Methyl to carboxyl conversion on aromatic ring, anaerobic

Dihydroxylation of aromatic ring

RM004
Dihydroxylation of aromatic ring, type 1 (dioxygenase and dehydrogenase reactions)
RM005
Dihydroxylation of aromatic ring, type 1a (dioxygenase and decarboxylating dehydrogenase reactions)
RM902
Dihydroxylation of aromatic ring, type 1b (single dioxygenase reaction)
RM006
Dihydroxylation of aromatic ring, type 2 (two monooxygenase reactions)
RM007
Dihydroxylation of aromatic ring, type 3 (dealkylation and monooxygenase reactions)

Cleavage of aromatic ring

RM008
Ortho-cleavage of dihydroxylated aromatic ring (beta-ketoadipate pathway)
RM009
Meta-cleavage of dihydroxylated aromatic ring
RM013
Ortho-cleavage of halogenated aromatic ring
RM016
Ring cleavage via beta oxidation, anaerobic
RM017
Ring cleavage via Baeyer-Villiger oxidation

Dihydroxylation and cleavage of aromatic ring

RM010
Dihydroxylation and meta-cleavage of aromatic ring, type 1
RM011
Dihydroxylation and meta-cleavage of aromatic ring, type 1b
RM012
Dihydroxylation and meta-cleavage of aromatic ring, type 3a
RM014
Ring removal from polycyclic aromatic ring

Reaction module comparison

RM003 RM015
Methyl to carboxyl conversion of aromatic ring

Reaction module combination

Reaction module map

map01220
Degradation of aromatic compounds

Other

Amino acid metabolism

RM025
Conversion of amino acid moiety to carboxyl group (biogenic amine metabolism)

Nucleotide metabolism

RM024
Pyrimidine degradation

Sugar metabolism

RM034
Sugar degradation to aldehyde and pyruvate

Aromatics metabolism

RM027
Hydroxylation and methylation motif
RM026
Hydroxylation and decarboxylation motif
RM028
Flavonoid synthesis
RM029
Pterocarpan synthesis
RM031
Oxime to acetate conversion

References
  1. Muto, A., Kotera, M., Tokimatsu, T., Nakagawa, Z., Goto, S., and Kanehisa, M.; Modular architecture of metabolic pathways revealed by conserved sequences of reactions. J. Chem. Inf. Model. 53, 613-622 (2013). [pubmed] [pdf]
  2. Kanehisa, M.; Chemical and genomic evolution of enzyme-catalyzed reaction networks. FEBS Lett. 587, 2731-2737 (2013). [pubmed] [pdf]
  3. Kanehisa, M., Goto, S., Sato, Y., Kawashima, M., Furumichi, M., and Tanabe, M.; Data, information, knowledge and principle: back to metabolism in KEGG. Nucleic Acids Res. 42, D199–D205 (2014). [pubmed] [pdf]

Last updated: November 4, 2021