title: PathPred: an enzyme-catalyzed metabolic pathway prediction server.
abstract: The KEGG RPAIR database is a collection of biochemical structure transformation patterns, called RDM patterns, and chemical structure alignments of substrate-product pairs (reactant pairs) in all known enzyme-catalyzed reactions taken from the Enzyme Nomenclature and the KEGG PATHWAY database. Here, we present PathPred (http://www.genome.jp/tools/pathpred/), a web-based server to predict plausible pathways of muti-step reactions starting from a query compound, based on the local RDM pattern match and the global chemical structure alignment against the reactant pair library. In this server, we focus on predicting pathways for microbial biodegradation of environmental compounds and biosynthesis of plant secondary metabolites, which correspond to characteristic RDM patterns in 947 and 1397 reactant pairs, respectively. The server provides transformed compounds and reference transformation patterns in each predicted reaction, and displays all predicted multi-step reaction pathways in a tree-shaped graph.
authors.affiliation: Bioinformatics Center, Institute for Chemical Research, Kyoto University, Gokasho, Uji, Kyoto 611-0011, Japan.
authors.forename: Yuki
authors.initials: Y
authors.lastname: Moriya
authors.forename: Daichi
authors.initials: D
authors.lastname: Shigemizu
authors.forename: Masahiro
authors.initials: M
authors.lastname: Hattori
authors.forename: Toshiaki
authors.initials: T
authors.lastname: Tokimatsu
authors.forename: Masaaki
authors.initials: M
authors.lastname: Kotera
authors.forename: Susumu
authors.initials: S
authors.lastname: Goto
authors.forename: Minoru
authors.initials: M
authors.lastname: Kanehisa
mesh_terms: D055162:Biocatalysis; D053898:Biosynthetic Pathways; D004785:Environmental Pollutants / Q000378:metabolism; D004798:Enzymes / Q000378:metabolism*; D020407:Internet; D053858:Metabolic Networks and Pathways; D012984:Software
chemical_list: D004785:Environmental Pollutants; D004798:Enzymes