Dataset Information

Orth2011_E.coli_MetabolicNetwork

ABSTRACT: This model is from the article: A comprehensive genome-scale reconstruction of Escherichia coli metabolism-2011. Orth JD, Conrad TM, Na J, Lerman JA, Nam H, Feist AM, Palsson BØ. Mol Syst Biol. 2011 Oct 11;7:535. doi: 10.1038/msb.2011.65. 21988831 , Abstract: The initial genome-scale reconstruction of the metabolic network of Escherichia coli K-12 MG1655 was assembled in 2000. It has been updated and periodically released since then based on new and curated genomic and biochemical knowledge. An update has now been built, named iJO1366, which accounts for 1366 genes, 2251 metabolic reactions, and 1136 unique metabolites. iJO1366 was (1) updated in part using a new experimental screen of 1075 gene knockout strains, illuminating cases where alternative pathways and isozymes are yet to be discovered, (2) compared with its predecessor and to experimental data sets to confirm that it continues to make accurate phenotypic predictions of growth on different substrates and for gene knockout strains, and (3) mapped to the genomes of all available sequenced E. coli strains, including pathogens, leading to the identification of hundreds of unannotated genes in these organisms. Like its predecessors, the iJO1366 reconstruction is expected to be widely deployed for studying the systems biology of E. coli and for metabolic engineering applications. This model originates from BioModels Database: A Database of Annotated Published Models (http://www.ebi.ac.uk/biomodels/). It is copyright (c) 2005-2011 The BioModels.net Team. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. In summary, you are entitled to use this encoded model in absolutely any manner you deem suitable, verbatim, or with modification, alone or embedded it in a larger context, redistribute it, commercially or not, in a restricted way or not.. To cite BioModels Database, please use: Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, Snoep JL, Hucka M, Le Novère N, Laibe C (2010) BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol., 4:92.

SUBMITTER: Jeffrey Orth

PROVIDER: MODEL1108160000 | BioModels | 2005-01-01

REPOSITORIES: BioModels

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			Action	DRS
	MODEL1108160000?filename=MODEL1108160000-biopax2.owl	Owl
	MODEL1108160000?filename=MODEL1108160000-biopax3.owl	Owl
	MODEL1108160000?filename=MODEL1108160000.m	Other
	MODEL1108160000?filename=MODEL1108160000.pdf	Pdf
	MODEL1108160000?filename=MODEL1108160000.png	Other

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Publications

A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011.

Orth Jeffrey D JD Conrad Tom M TM Na Jessica J Lerman Joshua A JA Nam Hojung H Feist Adam M AM Palsson Bernhard Ø BØ

Molecular systems biology 20111011

The initial genome-scale reconstruction of the metabolic network of Escherichia coli K-12 MG1655 was assembled in 2000. It has been updated and periodically released since then based on new and curated genomic and biochemical knowledge. An update has now been built, named iJO1366, which accounts for 1366 genes, 2251 metabolic reactions, and 1136 unique metabolites. iJO1366 was (1) updated in part using a new experimental screen of 1075 gene knockout strains, illuminating cases where alternative ...[more]

PMID: 21988831

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