Open Access Research article

An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92

Pep Charusanti1*, Sadhana Chauhan2, Kathleen McAteer3, Joshua A Lerman1, Daniel R Hyduke1, Vladimir L Motin24, Charles Ansong3, Joshua N Adkins3 and Bernhard O Palsson1

Author Affiliations

1 Department of Bioengineering, University of California, San Diego, La Jolla, California, USA

2 Departments of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA

3 Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington, USA

4 Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA

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BMC Systems Biology 2011, 5:163  doi:10.1186/1752-0509-5-163

Published: 13 October 2011

Additional files

Additional file 1:

Model details. A. Table of contents. B. Gene list. C. Metabolites. D. Reactions and their associated genes (if any). E. Biomass objective functions. F. Comparison between iPC815 and the YP 91001 model of Navid, et al. G. Growth simulations on different carbon sources. H. Growth simulations on different nitrogen sources. I. Growth simulations on different phosphorus sources. J. Growth simulations on different sulfur sources. K. Individual components in BCS growth medium. L. Substrate uptake and secretion rates used to constrain model simulations.

Format: XLSX Size: 330KB Download file

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Additional file 2:

Gene essentiality. A. List of genes predicted to be essential in YP CO92. Homologous genes in E. coli and Salmonella Typhimurium LT2 that were predicted to be essential by the E. coli iAF1260 model [8] and the Salmonella Typhimurium LT2 consensus model [9] have been listed as well. B. List of genes predicted to be essential in E. coli only (from [8]). C. List of genes predicted to be essential in S. Typhimurium only [9].

Format: XLSX Size: 51KB Download file

Open Data

Additional File 3:

The iPC815 model in SBML format.

Format: XML Size: 2.9MB Download file

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