Abstract
The Encyclopedia of Genes and Metabolism (EcoCyc) is a database that combines information about the genome and the intermediary metabolism of Escherichia coli. It describes 2970 genes of E.coli, 547 enzymes encoded by these genes, 702 metabolic reactions that occur in E.coli and the organization of these reactions into 107 metabolic pathways. The EcoCyc graphical user interface allows scientists to query and explore the EcoCyc database using visualization tools such as genomic-map browsers and automatic layouts of metabolic pathways. EcoCyc spans the space from sequence to function to allow scientists to investigate an unusually broad range of questions. EcoCyc can be thought of as both an electronic review article because of its copious references to the primary literature, and as an in silicio model of E.coli metabolism that can be probed and analyzed through computational means.
Full Text
The Full Text of this article is available as a PDF (116.7 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Bairoch A. The ENZYME data bank. Nucleic Acids Res. 1994 Sep;22(17):3626–3627. [PMC free article] [PubMed] [Google Scholar]
- Karp P. D. A knowledge base of the chemical compounds of intermediary metabolism. Comput Appl Biosci. 1992 Aug;8(4):347–357. doi: 10.1093/bioinformatics/8.4.347. [DOI] [PubMed] [Google Scholar]
- Karp P. D., Paley S. M. Representations of metabolic knowledge: pathways. Proc Int Conf Intell Syst Mol Biol. 1994;2:203–211. [PubMed] [Google Scholar]
- Karp P. D., Paley S. Integrated access to metabolic and genomic data. J Comput Biol. 1996 Spring;3(1):191–212. doi: 10.1089/cmb.1996.3.191. [DOI] [PubMed] [Google Scholar]
- Riley M. Functions of the gene products of Escherichia coli. Microbiol Rev. 1993 Dec;57(4):862–952. doi: 10.1128/mr.57.4.862-952.1993. [DOI] [PMC free article] [PubMed] [Google Scholar]