MetaCyc Metabolic Pathway Database

MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2453 pathways from 2788 different organisms.

MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway.

MetaCyc applications include:

  • Online encyclopedia of metabolism
  • Predict metabolic pathways in sequenced genomes
  • Support metabolic engineering via enzyme database
  • Metabolite database aids metabolomics research

Guide To MetaCyc

  • Vitamin D

    Paradise waiting by .craig. Used under creative commons license.

    Vitamin D

    It is well known that vitamin D is produced in our skin during exposure to the sun. But did you know it is made from cholesterol?

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  • Aspirin

    Image of 1950's Bayer Aspirin by Roadsidepictures. Used under creative commons license.


    Aspirin is a well known nonsteroidal anti-inflammatory (NSAID) drug used to relieve minor aches and pains. Would you like to know how it actually works?

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  • Sulfur

    Mount sulfur by akahawkeyefan. Used under creative commons license.

    DMSP Degradation

    Biological processes influence geochemical cycles. The main input of sulfur to the atmosphere is dimethyl sulfide, which is formed by microbial degradation of marine algae biomass.

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  • Books

    Book 6 by Brenda Clarke. Used under creative commons license.

    Commentary in MetaCyc

    Pathways, enzymes, and many compounds in MetaCyc contain summaries curated from a wealth of sources. The cumulative commentary in MetaCyc 18.5 equals 6,300 textbook pages!

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  • Petri Dish

    Photograph of colonies on a Petri dish by Michael Alan Smith. Used under creative commons license.

    Antibiotic Biosythesis in MetaCyc

    Antibiotics have transformed modern medicine. MetaCyc currently contains 86 pathways for biosynthesis of natural antibiotics.

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  • Field

    Image of a field by Chris Lindsay. Used under creative commons license.

    Engineered Pathways in MetaCyc

    Although most of the pathways in MetaCyc are naturally-occurring, the database also includes a growing number of synthetic pathways from the metabolic engineering literature.

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  • Glycan Pathways

    Image generated by Pathway Tools.

    Glycan Pathways and Compounds in MetaCyc

    It is often easier to comprehend the structures of complex glycans using symbolic representation. Did you know that MetaCyc can represent glycan molecules using symbols for the glycan monomers?

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  • Super Pathways

    Image generated by Pathway Tools.

    Superpathways in MetaCyc

    MetaCyc superpathways are larger pathways constructed by combining and connecting other pathways to depict relationships between them. They provide a more complete overview of a metabolic process.

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  • Reaction Atom Mappings

    Image generated by Pathway Tools.

    Reaction Atom Mappings Indicate Atom Flow

    The compounds in MetaCyc reactions are color labeled to make it easy to follow the atom flow. You can cause the atoms to be numbered to more clearly identify corresponding atoms in reactants and products.

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  • Locally Installed Omics Viewer Image

    Run MetaCyc on Your Own Computer

    Install SRI's Pathway Tools software locally to predict metabolic pathways from sequenced genomes, generate metabolic models, and analyze omics data.

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  • Crested Pool

    Image of a crested pool by Chuck Martin. Used under creative commons license.

    Using MetaCyc of Metabolic Reconstruction for Metagenomes

    A file that associates UniProt sequences with MetaCyc reaction IDs facilitates the prediction of metabolic pathways for metagenomes by mapping of metagenome sequences to biochemical reactions.

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  • So what killed this guy?

    Napoleon at Sainte-Helene by Francois Joseph Sandmann. Public domain.

    So what killed this guy?

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  • Maxinne Sentinna by Dame Gothel

    Maxinne Sentinna by Dame Gothel. Used under creative commons license.

    Twenty people were executed around Salem, MA for using witchcraft to afflict young girls. Were the victims bewitched, or could it be something they ate?

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  • Coral Reef by Susan Hazlett, USGS

    Coral Reef, taken by Susan Hazlett, USGS. Public domain.

    Have you ever swum in the ocean and started to itch? Care to know why?

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  • So what killed this guy?

    Exodus by Dennis Jarvis. Used under creative commons license.

    The bible tells us that the ancient Israelites were fed manna that fell from the sky while crossing the Sinai desert. But what is manna?

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Accessing MetaCyc Data

MetaCyc data can be accessed in several ways:

How to Cite MetaCyc

Please cite MetaCyc as Caspi et al 2014, "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases," Nucleic Acids Research 42:D459-D471

Funding Sources

The development of MetaCyc is funded by grant GM080746 from the NIH National Institute of General Medical Sciences.

Video Tutorials

The BioCyc webinar series introduces users to the basic and advanced features of the BioCyc website and the Pathway Tools software and covers:

  • BioCyc site contents, including EcoCyc, MetaCyc, and our extensive database collection
  • How to search, browse, and find what you need in the BioCyc collection
  • How we represent metabolism, transcription, and all their parts

A complete list of videos in additional download formats are available on the Video and Podcast page.