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KEGG REACTION

Knowledge base for predicting biodegradation and biosynthesis

KEGG2 PATHWAY BRITE MODULE LIGAND COMPOUND GLYCAN REACTION
Enter R/RP/RC numbers

KEGG ENZYME Database

KEGG ENZYME is an implementation of the Enzyme Nomenclature (EC number) produced by the IUBMB/IUPAC Biochemical Nomenclature Committee. KEGG ENZYME is based on the ExplorEnz database at Trinity College Dublin, and is maintained in the KEGG LIGAND relational database with additional annotation of reaction hierarchy, organism information, and sequence data links.

KEGG REACTION Database

KEGG REACTION contains all reactions taken from KEGG ENZYME and additional reactions taken from the metabolic pathway maps in KEGG PATHWAY. Each reaction is identified by the R number, such as R00259 for the acetylation of L-glutamate. Reactions are linked to ortholog groups of enzymes as defined by the KEGG ORTHOLOGY database, enabling integrated analysis genomic (enzyme genes) and chemical (compound pairs) information.

KEGG RPAIR Database

KEGG RPAIR is a collection of substrate-product pairs (reactant pairs) defined for each reaction in KEGG REACTION, together with the chemical structure transformation patterns characterized by the RDM patterns (see below). In general, a reaction consists of multiple reactant pairs, and the one that appears on the KEGG metabolic pathway map is called the main pair, such as RP04458 for the above acetylation reaction.

In order to distinguish functional groups and microenvironments of atoms, atomic species of C, N, O, S, and P are classified into 68 types, called KEGG atom types. They were first introduced for detecting biochemical similarities by graph-based chemical structure comparison [1]. The RDM pattern is defined as KEGG atom type changes at the reaction center (R), the difference region (D), and the matched region (M) for each reactant pair. It characterizes chemical structure transformation patterns associated with enzymatic reactions [2].
RDM

(Example) RDM pattern for RP04458

KEGG RCLASS Database

KEGG RCLASS represents classification of reactions based on the chemical structure transformation patterns of main reactant pairs. The transformation pattern may consist of multiple RDM patterns when more than one reaction center is identified. The reaction class for RP04458 is RC00064. Given a set of RC numbers, similar reaction pathways may be searched using the following tools: KEGG Reaction Modules are a collection of conserved RC number sequences extracted from the analysis of KEGG metabolic pathways.

Reaction Pathway Prediction

The RDM patterns are the basis for predicting reaction types given a pair (or pairs) of chemical compound structures in E-zyme software [3]. Furthermore, based on the observation that specific RDM patterns are uniquely or preferentially found in specific categories of KEGG metabolic pathways [4], new software has been developed for predicting metabolic fate of a given chemical compound [5].
  • E-zyme: automatic assignment of EC numbers
  • PathPred: prediction of biodegradation/biosynthetic pathways

References
  1. Hattori, M., Okuno, Y., Goto, S., and Kanehisa, M.; Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways. J. Am. Chem. Soc. 125, 11853-11865 (2003). [pubmed]
  2. Kotera, M., Okuno, Y., Hattori, M., Goto, S., and Kanehisa, M.; Computational assignment of the EC numbers for genomic-scale analysis of enzymatic reactions. J. Am. Chem. Soc. 126, 16487-16498 (2004). [pubmed]
  3. Yamanishi, Y., Hattori, M., Kotera, M., Goto, S., and Kanehisa, M.; E-zyme: predicting potential EC numbers from the chemical transformation pattern of substrate-product pairs. Bioinformatics 25, i79-i86 (2009). [pubmed]
  4. Oh, M., Yamada, T., Hattori, M., Goto, S., and Kanehisa, M.; Systematic analysis of enzyme-catalyzed reaction patterns and prediction of microbial biodegradation pathways. J. Chem. Inf. Model. 47, 1702-1712 (2007). [pubmed]
  5. Moriya, Y., Shigemizu, D., Hattori, M., Tokimatsu, T., Kotera, M., Goto, S., and Kanehisa, M.; PathPred: an enzyme-catalyzed metabolic pathway prediction server. Nucleic Acids Res. 38, W138-W143 (2010). [pubmed]
  6. 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]

Last updated: May 15, 2013
KEGG GenomeNet Kanehisa Laboratories