EcoCyc: Enyclopedia of Escherichia Coli Genes and Metabolism

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 1997 Jan 1

PMID 9016502

Citations 5

Authors

P D Karp

M Riley

S M Paley

A Pellegrini-Toole

M Krummenacker

Affiliations

Soon will be listed here.

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.

Citing Articles

Cysteine and iron accelerate the formation of ribose-5-phosphate, providing insights into the evolutionary origins of the metabolic network structure.

Piedrafita G, Varma S, Castro C, Messner C, Szyrwiel L, Griffin J PLoS Biol. 2021; 19(12):e3001468.

PMID: 34860829 PMC: 8673631. DOI: 10.1371/journal.pbio.3001468.

Prediction of Selected Biosynthetic Pathways for the Lipopolysaccharide Components in .

Swietnicki W, Caspi R Pathogens. 2021; 10(3).

PMID: 33804654 PMC: 8003790. DOI: 10.3390/pathogens10030374.

Pathway Tools Visualization of Organism-Scale Metabolic Networks.

Paley S, Billington R, Herson J, Krummenacker M, Karp P Metabolites. 2021; 11(2).

PMID: 33499002 PMC: 7911265. DOI: 10.3390/metabo11020064.

The EcoCyc Database.

Karp P, Weaver D, Paley S, Fulcher C, Kubo A, Kothari A EcoSal Plus. 2015; 6(1).

PMID: 26442933 PMC: 4243172. DOI: 10.1128/ecosalplus.ESP-0009-2013.

EcoCyc: Encyclopedia of Escherichia coli genes and metabolism.

Karp P, Riley M, Paley S, Pellegrini-Toole A, Krummenacker M Nucleic Acids Res. 1998; 26(1):50-3.

PMID: 9399798 PMC: 147256. DOI: 10.1093/nar/26.1.50.

References

Karp P . A knowledge base of the chemical compounds of intermediary metabolism. Comput Appl Biosci. 1992; 8(4):347-57. DOI: 10.1093/bioinformatics/8.4.347. View

Riley M . Functions of the gene products of Escherichia coli. Microbiol Rev. 1993; 57(4):862-952. PMC: 372942. DOI: 10.1128/mr.57.4.862-952.1993. View

Karp P, Paley S . Integrated access to metabolic and genomic data. J Comput Biol. 1996; 3(1):191-212. DOI: 10.1089/cmb.1996.3.191. View

Karp P, Paley S . Representations of metabolic knowledge: pathways. Proc Int Conf Intell Syst Mol Biol. 1994; 2:203-11. View

Bairoch A . The ENZYME data bank. Nucleic Acids Res. 1994; 22(17):3626-7. PMC: 308334. View