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. 2006 Jan 1;34(Database issue):D511-6.
doi: 10.1093/nar/gkj128.

MetaCyc: a multiorganism database of metabolic pathways and enzymes

Ron Caspi  1 , Hartmut Foerster, Carol A Fulcher, Rebecca Hopkinson, John Ingraham, Pallavi Kaipa, Markus Krummenacker, Suzanne Paley, John Pick, Seung Y Rhee, Christophe Tissier, Peifen Zhang, Peter D Karp
Affiliations

MetaCyc: a multiorganism database of metabolic pathways and enzymes

Ron Caspi et al. Nucleic Acids Res. .

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.

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Figures

Figure 1
Figure 1
A representative example of a pathway in MetaCyc. Pathways can be displayed at varying levels of detail. This pathway display depicts an intermediate level of detail including enzymes, EC numbers, genes and chemical structures of the main compounds. Notice the brown arrows that provide hyperlinks to related upstream and downstream pathways.
See this image and copyright information in PMC

References

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