MetaCyc Metabolic Pathway Database

MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2526 pathways from 2844 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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  • 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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  • 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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  • 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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  • Beer is the world's oldest and most widely consumed alcoholic drink, dating back to 9500 BC. Did the ancient Egyptians know all about bitter acids?

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  • We all know about the A, B, and O blood types, but did you know that a single glycosyltransferase is responsible for all of this diversity?

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  • Chitin is the second most common polymer in the world, after cellulose. Our understanding of its degradation was significantly boosted with the discovery of LPMOs. And what are LPMOs?

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  • When oil companies started adding MTBE to gasoline, it seemed like a good idea. Now it is banned in the US, and it is up to the bacteria to degrade the remaining contamination.

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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 2016, "The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases," Nucleic Acids Research 44:D471-D480

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.