Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2018 Jan 4;46(D1):D633-D639.
doi: 10.1093/nar/gkx935.

The MetaCyc database of metabolic pathways and enzymes

Ron Caspi  1 , Richard Billington  1 , Carol A Fulcher  1 , Ingrid M Keseler  1 , Anamika Kothari  1 , Markus Krummenacker  1 , Mario Latendresse  1 , Peter E Midford  1 , Quang Ong  1 , Wai Kit Ong  1 , Suzanne Paley  1 , Pallavi Subhraveti  1 , Peter D Karp  1
Affiliations

The MetaCyc database of metabolic pathways and enzymes

Ron Caspi et al. Nucleic Acids Res. .

Abstract

MetaCyc (https://MetaCyc.org) is a comprehensive reference database of metabolic pathways and enzymes from all domains of life. It contains more than 2570 pathways derived from >54 000 publications, making it the largest curated collection of metabolic pathways. The data in MetaCyc is strictly evidence-based and richly curated, resulting in an encyclopedic reference tool for metabolism. MetaCyc is also used as a knowledge base for generating thousands of organism-specific Pathway/Genome Databases (PGDBs), which are available in the BioCyc (https://BioCyc.org) and other PGDB collections. This article provides an update on the developments in MetaCyc during the past two years, including the expansion of data and addition of new features.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
A typical MetaCyc pathway. A short pathway was selected for this figure; the average number of metabolites in a MetaCyc pathway is 12.8, with the largest pathway containing 204 metabolites. The enzymes in this pathway have not yet been classified by the Enzyme Commission and were assigned M-numbers (see text). The green captions are links to the upstream pathways that produce the inputs for this pathway.
Figure 2.
Figure 2.
Redesigned compound pages use a tabbed interface to reduce clutter on information pages.
Figure 3.
Figure 3.
MetaCyc contains a number of pre-formed SmartTables that provide access to results of popular searches.
See this image and copyright information in PMC

References

    1. Caspi R., Billington R., Ferrer L., Foerster H., Fulcher C.A., Keseler I.M., Kothari A., Krummenacker M., Latendresse M., Mueller L.A. et al. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res. 2016; 44:D471–480. - PMC - PubMed
    1. Karp P.D., Paley S.M., Krummenacker M., Latendresse M., Dale J.M., Lee T.J., Kaipa P., Gilham F., Spaulding A., Popescu L. et al. Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief. Bioinform. 2010; 11:40–79. - PMC - PubMed
    1. Karp P.D., Latendresse M., Paley S.M., Krummenacker M., Ong Q.D., Billington R., Kothari A., Weaver D., Lee T., Subhraveti P. et al. Pathway Tools version 19.0 update: software for pathway/genome informatics and systems biology. Brief. Bioinform. 2016; 17:877–890. - PMC - PubMed
    1. Karp P.D., Latendresse M., Caspi R.. The pathway tools pathway prediction algorithm. Standards Genomic Sci. 2011; 5:424–429. - PMC - PubMed
    1. Karp P.D., Billington R., Caspi R., Fulcher C.A., Latendresse M., Kothari A., Keseler I.M., Krummenacker M., Midford P.E., Ong Q. et al. The BioCyc collection of microbial genomes and metabolic pathways. Brief. Bioinformatics. 2017; doi:10.1093/bib/bbx085. - PMC - PubMed

Publication types