Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014
Metabolic Modeling Tutorial
discounted EARLY registration ends Dec 31, 2014

MetaCyc Metabolic Pathway Database

MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains 2260 pathways from 2600 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
  • Prediction of 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?

    Learn More
  • Aspirin

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

    Aspirin

    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?

    Learn More
  • Sulfur

    Mount sulfur by akahawkeyefan. Used under creative commons license.

    DMSP Degradation

    The main input of sulfur to the atmoshphere is in the form of dimethyl sulfide, a volatille compound formed by microbial degradation of dimethylsulfoniopropanoate (DMSP). This is an example of how biological processes can influence geochemical cycles.

    Learn More
  • 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!

    Learn More
  • 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 72 pathways for biosynthesis of natural antibiotics.

    Learn More
  • 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.

    Learn More
  • 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?

    Learn More
  • 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.

    Learn More
  • 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.

    Learn More
  • 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.

    Learn More
  • Crested Pool

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

    Using MetaCyc for Metabolic Reconstruction for Metagenomes

    The first step in predicting metabolic pathways for metagenomes is to map metagenome sequences to biochemical reactions. To facilitate this process we make available a file that associates UniProt sequences with MetaCyc reaction IDs.

    Learn More

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.