Open Access Highly Accessed Research article

iRsp1095: A genome-scale reconstruction of the Rhodobacter sphaeroides metabolic network

Saheed Imam156, Safak Yilmaz25, Ugur Sohmen2, Alexander S Gorzalski2, Jennifer L Reed45, Daniel R Noguera25 and Timothy J Donohue35*

Author Affiliations

1 Program in Cellular and Molecular Biology, University of Wisconsin - Madison, USA

2 Department of Civil and Environmental Engineering, University of Wisconsin - Madison, USA

3 Department of Bacteriology, University of Wisconsin - Madison, 5159 Microbial Sciences Building, 1550 Linden Drive, Madison, WI 53706, USA

4 Chemical and Biological Engineering Department, University of Wisconsin - Madison, USA

5 DOE Great Lakes Bioenergy Research Center, University of Wisconsin - Madison, USA

6 BACTER Institute, University of Wisconsin - Madison, USA

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BMC Systems Biology 2011, 5:116  doi:10.1186/1752-0509-5-116

Published: 21 July 2011

Additional files

Additional file 1:

Supplemental materials and methods Additional File 1 contains details of the model reconstruction and refinement process, as well as details of GC/MS and supernatant analysis.

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Additional file 2:

iRsp1095 Metabolic Reconstruction Additional File 2 contains 12 tables. Table S1 list all the reactions in iRsp1095 including official reaction names, reaction stoichiometry, GPR assignments, directionality assignments and localization information. Table S2 contains information about metabolites in the model. Table S3 contains thermodynamic calculations used in the determined reaction directionality. Table S4 lists reactions constrained to eliminate SBCs. Table S5 lists the genes present in the model. Table S6 summarizes simulated growth phenotypes with various carbon sources. Table S7 lists all the references used in curation of iRsp1095. Table S8 lists reactions added to the model based on metaSHARK analysis. Table S9 details the compositions of SIS minimal media. Table S10 lists essential genes identified by FBA analysis. Table S11 list the gap filling reactions added to iRsp1095. Table S12 contains as description of the confidence scores assigned to the reactions in iRsp1095.

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Additional file 3:

Biomass calculations This contains calculations of the coefficients of the biomass precursors based on determined contribution to biomass and genomic information for aerobic and photosynthetic growth.

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Additional file 4:

iRsp1095 in SBML SBML format of iRsp1095 for distribution and use in other modeling environments.

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Additional file 5:

Sensitivity analysis Additional File 5 contains additional sensitivity analysis conducted to assess the effects of light, biomass composition and P/O ratio on growth and metabolite production rates.

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