title: MetaCyc: a multiorganism database of metabolic pathways and enzymes.
abstract: MetaCyc is a database of metabolic pathways and enzymes located at http://MetaCyc.org/. Its goal is to serve as a metabolic encyclopedia, containing a collection of non-redundant pathways central to small molecule metabolism, which have been reported in the experimental literature. Most of the pathways in MetaCyc occur in microorganisms and plants, although animal pathways are also represented. MetaCyc contains metabolic pathways, enzymatic reactions, enzymes, chemical compounds, genes and review-level comments. Enzyme information includes substrate specificity, kinetic properties, activators, inhibitors, cofactor requirements and links to sequence and structure databases. Data are curated from the primary literature by curators with expertise in biochemistry and molecular biology. MetaCyc serves as a readily accessible comprehensive resource on microbial and plant pathways for genome analysis, basic research, education, metabolic engineering and systems biology. Querying, visualization and curation of the database is supported by SRI's Pathway Tools software. The PathoLogic component of Pathway Tools is used in conjunction with MetaCyc to predict the metabolic network of an organism from its annotated genome. SRI and the European Bioinformatics Institute employed this tool to create pathway/genome databases (PGDBs) for 165 organisms, available at the BioCyc.org website. These PGDBs also include predicted operons and pathway hole fillers.
authors.affiliation: SRI International 333 Ravenswood, Menlo Park, CA 94025, USA.
authors.forename: Ron
authors.initials: R
authors.lastname: Caspi
authors.forename: Hartmut
authors.initials: H
authors.lastname: Foerster
authors.forename: Carol A
authors.initials: CA
authors.lastname: Fulcher
authors.forename: Rebecca
authors.initials: R
authors.lastname: Hopkinson
authors.forename: John
authors.initials: J
authors.lastname: Ingraham
authors.forename: Pallavi
authors.initials: P
authors.lastname: Kaipa
authors.forename: Markus
authors.initials: M
authors.lastname: Krummenacker
authors.forename: Suzanne
authors.initials: S
authors.lastname: Paley
authors.forename: John
authors.initials: J
authors.lastname: Pick
authors.forename: Seung Y
authors.initials: SY
authors.lastname: Rhee
authors.forename: Christophe
authors.initials: C
authors.lastname: Tissier
authors.forename: Peifen
authors.initials: P
authors.lastname: Zhang
authors.forename: Peter D
authors.initials: PD
authors.lastname: Karp
mesh_terms: D000818:Animals; D001419:Bacteria / Q000201:enzymology / Q000378:metabolism; D016208:Databases, Factual; D004785:Environmental Pollutants / Q000378:metabolism; D004798:Enzymes / Q000032:analysis / Q000737:chemistry* / Q000235:genetics; D006801:Humans; D020407:Internet; D008660:Metabolism; D010944:Plants / Q000201:enzymology / Q000378:metabolism; D012984:Software; D014584:User-Computer Interface
chemical_list: D004785:Environmental Pollutants; D004798:Enzymes