The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases
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The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible database describing metabolic pathways and enzymes from all domains of life. MetaCyc pathways are experimentally determined, mostly small-molecule metabolic pathways and are curated from the primary scientific literature. MetaCyc contains >2100 pathways derived from >37,000 publications, and is the largest curated collection of metabolic pathways currently available. BioCyc (BioCyc.org) is a collection of >3000 organism-specific Pathway/Genome Databases (PGDBs), each containing the full genome and predicted metabolic network of one organism, including metabolites, enzymes, reactions, metabolic pathways, predicted operons, transport systems and pathway-hole fillers. Additions to BioCyc over the past 2 years include YeastCyc, a PGDB for Saccharomyces cerevisiae, and 891 new genomes from the Human Microbiome Project. The BioCyc Web site offers a variety of tools for querying and analysis of PGDBs, including Omics Viewers and tools for comparative analysis. New developments include atom mappings in reactions, a new representation of glycan degradation pathways, improved compound structure display, better coverage of enzyme kinetic data, enhancements of the Web Groups functionality, improvements to the Omics viewers, a new representation of the Enzyme Commission system and, for the desktop version of the software, the ability to save display states.
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Both orders Bacteroidales and Clostridiales, identified in this study, are involved in short chain fatty acid metabolism.
“Both orders Bacteroidales and Clostridiales, identified in our study, are involved in short chain fatty acid metabolism.41”
From The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids (2015) · cites this paper as [41]
Order Bacteroidales and family Clostridiaceae are known to be involved in bile acid metabolism.
“In particular, order Bacteroidales (phylum Bacteroidetes) and family Clostridiaceae (phylum Firmicutes) are both negatively correlated with BMI and triglycerides and known to be involved in bile acid metabolism.41”
From The Gut Microbiome Contributes to a Substantial Proportion of the Variation in Blood Lipids (2015) · cites this paper as [41]
Clostridium hathewayi carries genes encoding proteins predicted to be involved in cholic acid metabolism that were not detected in members of the "core plus C. sporogenes" community.
“Genome analysis for members of the “core plus all” community, using the curated database for metabolic pathways MetaCyc, disclosed that Clostridium hathewayi carries genes that encode proteins (3-α-hydroxysteroid dehydrogenase/carbonyl reductase and 3-oxo-cholyl-coenzyme A [CoA] oxidoreductase) predicted to be involved in the metabolism of cholic acid that were not detected in members of the “core”
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- Authors
- Caspi, R., Altman, T., Billington, R., Dreher, K., Foerster, H., Fulcher, C. A., Holland, T. A., Keseler, I. M., Kothari, A., Kubo, A., Krummenacker, M., Latendresse, M., Mueller, L. A., Ong, Q., Paley, S., Subhraveti, P., Weaver, D. S., Weerasinghe, D., Zhang, P., & Karp, P. D.
- Affiliations
- SRI International (US)
- Corresponding author
- Karp, Peter D.
- ORCID
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-11-12
- Volume
- 42
- Issue
- D1
- Pages
- D459-D471
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC3964957
- OpenAlex
- W4230770774
- Cited by
- 1,204
- References
- 75
- Citations by year
- 2026: 71 · 2025: 83 · 2024: 78 · 2023: 85 · 2022: 94 · 2021: 75 · 2020: 68 · 2019: 73 · 2018: 77 · 2017: 146 · 2016: 155 · 2015: 154 · 2014: 42 · 2013: 2
- FWCI
- 52.55
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nucleic Acids Research (publishedVersion, cc-by)
- Europe PMC (PubMed Central) (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
- Funders
- U.S. Department of Energy (DESC0004878)
- National Institute of General Medical Sciences (GM080746, GM077678, GM75742, R01GM080746, R01GM077678, U24GM077678, R01GM075742, U24GM088849, GM088849)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- MetaCyc, BioCyc, pathway/genome databases, metabolic pathways, metabolic enzymes, metabolic networks, genome-scale metabolic models, pathway curation, Saccharomyces cerevisiae, Human Microbiome Project, atom mapping, comparative genomics, metabolites, transport systems, operon
- MeSH terms
- Enzymes, Kinetics, Polysaccharides, Software, Genome, Internet, Metabolic Networks and Pathways, Databases, Chemical, Gene Ontology
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
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