TheMetaCycdatabase is one of the largestmetabolic pathwaysandenzymesdatabases currently available. The data in the database is manually curated from the scientific literature, and covers all domains of life. MetaCyc has extensive information about chemical compounds, reactions, metabolic pathways and enzymes. The data have been curated from more than 58,000 publications.[1][2][3]
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| Content | |
|---|---|
| Description | Database ofmetabolic pathwaysand enzymes |
| Contact | |
| Research center | SRI International |
| Authors | R. Caspi, H. Foerster, C.A. Fulcher, L.A. Mueller,Peter Karp |
| Primary citation | Caspi et al. (2014)[1] |
| Release date | 1997 |
| Access | |
| Website | metacyc |
MetaCyc has been designed for multiple types of uses. It is often used as an extensive online encyclopedia of metabolism. In addition, MetaCyc is used as a reference data set for computationally predicting the metabolic network of organisms from their sequenced genomes; it has been used to perform pathway predictions for thousands of organisms, including those in theBioCyc Database Collection.MetaCyc is also used inmetabolic engineeringandmetabolomicsresearch.
MetaCyc includes mini reviews for pathways and enzymes that provide background information as well as relevant literature references. It also provides extensive data on individual enzymes, describing their subunit structure, cofactors, activators and inhibitors, substrate specificity, and, when available, kinetic constants. MetaCyc data onmetabolitesincludes chemical structures, predicted Standard energy of formation, and links to external databases. Reactions in MetaCyc are presented in a visual display that includes the structures of all components. The reactions are balanced and includeEC numbers,reaction direction, predicted atom mappings that describe the correspondence between atoms in the reactant compounds and the product compounds, and computedGibbs free energy.
All objects in MetaCyc are clickable and provide easy access to related objects. For example, the page for L-lysine lists all of the reactions in which L-lysine participates, as well as the enzymes that catalyze them and pathways in which these reactions take place.
References
edit- ^abCaspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA, Holland TA, Keseler IM, Kothari A, Kubo A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Weerasinghe D, Zhang P, Karp PD (January 2014)."The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases".Nucleic Acids Res.38(Database issue): D473–9.doi:10.1093/nar/gkp875.PMC2808959.PMID19850718.
- ^"MetaCyc Publications".
- ^Karp PD, Caspi R (September 2011)."A survey of metabolic databases emphasizing the MetaCyc family".Arch. Toxicol.85(9): 1015–33.doi:10.1007/s00204-011-0705-2.PMC3352032.PMID21523460.