MetaCyc Metabolic Pathway Database | SRI International

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MetaCyc Metabolic Pathway Database

MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2500 pathways from 2800 organisms.

metacyc logoMetaCyc is a member of the BioCyc Collection of Pathway/Genome Databases. In contrast to all other members of that collection, which are organism-specific databases (DBs), MetaCyc is a multiorganism DB, meaning that its contents span many organisms. One goal of the MetaCyc project is for MetaCyc to contain a representative example of every experimentally determined metabolic pathway. MetaCyc does not seek to model the complete metabolism of any particular organism, which is the role of individual BioCyc DBs. Instead, MetaCyc serves as a high-quality reference on known metabolic pathways, enzymes, and reactions.

You can access the MetaCyc database at http://metacyc.org.

Support for Scientific Research

Scientists typically use MetaCyc to answer metabolic questions that span multiple domains of life, such as “what are all the pathways for arginine degradation in microbes?” or “what cofactor biosynthesis pathways are known in bacteria?” For questions that require information about the complete genome, proteome, or metabolic network of an organism, instead consult the organism-specific pathway/genome database (PGDB).

The MetaCyc mission is to serve a broad community of researchers from genetics, molecular biology, microbiology, biochemistry, genomics, bioinformatics, metabolic engineering, and systems biology in support of the following tasks:

Support computational metabolic network prediction

One of MetaCyc’s primary applications is to serve as a reference database for computationally predicting the metabolic network of an organism from its annotated genome, such as by the PathoLogic algorithm, part of Pathway Tools.

Provide an encyclopedic reference on pathways and enzymes

MetaCyc is used as a readily accessible source of up-to-date, literature-curated information on metabolic pathways and enzymes by researchers for basic research and genome analysis, and by students and teachers for educational purposes.

Support metabolic engineering

Metabolic engineers use MetaCyc as an encyclopedia of metabolic pathways and enzymes that may be genetically engineered into an organism to alter its metabolism.

MetaCyc Database Content

MetaCyc is a database of non-redundant, experimentally elucidated metabolic pathways and enzymes. It also contains reactions, chemical compounds, and genes. It stores predominantly qualitative information rather than quantitative data, although it does contain some quantitative data such as enzyme kinetics data.

A unique property of MetaCyc is that it is curated from the scientific experimental literature according to an extensive process, such that:

  • MetaCyc contains more than than 2,500 metabolic pathways, with 14,000 enzymatic reactions and 52,000 associated literature citations
  • The majority of pathways occur in microorganisms and plants
  • More than 2,800 different organisms are represented 
  • MetaCyc stores all enzyme-catalyzed reactions that have been assigned EC numbers by the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB), plus thousands of additional enzyme-catalyzed reactions that have not yet been assigned an EC number

The NIH National Institute for General Medical Sciences funds development of the MetaCyc database and the BioCyc collection under grant GM080746. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institute of General Medical Sciences or the National Institutes of Health.