The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities
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It was shown that based on stoichiometric and capacity constraints the in silico analysis was able to qualitatively predict the growth potential of mutant strains in 86% of the cases examined.Abstract:
The Escherichia coli MG1655 genome has been completely sequenced. The annotated sequence, biochemical information, and other information were used to reconstruct the E. coli metabolic map. The stoichiometric coefficients for each metabolic enzyme in the E. coli metabolic map were assembled to construct a genome-specific stoichiometric matrix. The E. coli stoichiometric matrix was used to define the system's characteristics and the capabilities of E. coli metabolism. The effects of gene deletions in the central metabolic pathways on the ability of the in silico metabolic network to support growth were assessed, and the in silico predictions were compared with experimental observations. It was shown that based on stoichiometric and capacity constraints the in silico analysis was able to qualitatively predict the growth potential of mutant strains in 86% of the cases examined. Herein, it is demonstrated that the synthesis of in silico metabolic genotypes based on genomic, biochemical, and strain-specific information is possible, and that systems analysis methods are available to analyze and interpret the metabolic phenotype.read more
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References
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Escherichia coli and Salmonella :cellular and molecular biology
TL;DR: The Enteric Bacterial Cell and the Age of Bacteria Variations on a Theme by Escherichia is described.
“Bioinformatics” 특집을 내면서
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Functional Characterization of the S. cerevisiae Genome by Gene Deletion and Parallel Analysis
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Exploring the new world of the genome with DNA microarrays
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TL;DR: Exploration of the genome using DNA microarrays and other genome–scale technologies should narrow the gap in the knowledge of gene function and molecular biology between the currently–favoured model organisms and other species.