Open Access Research article

Metabolic modeling and analysis of the metabolic switch in Streptomyces coelicolor

Mohammad T Alam1, Maria E Merlo12, The STREAM Consortium, David A Hodgson3, Elizabeth MH Wellington3, Eriko Takano2 and Rainer Breitling14*

Author Affiliations

1 Groningen Bioinformatics Center, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands

2 Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Kerklaan 30, 9751 NN Haren, The Netherlands

3 Department of Biological Sciences, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, UK

4 Integrative and Systems Biology, Faculty of Biomedical and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK

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BMC Genomics 2010, 11:202  doi:10.1186/1471-2164-11-202

Published: 26 March 2010

Additional files

Additional file 1:

Expression clustering plots. PDF file depicting the expression clustering of 231 enzyme-coding genes for which the catalyzed reaction had zero predicted flux at all time points of the flux balance analysis of our model. The majority of genes are members of clusters that show highly consistent dynamics across the time course, e.g. the purple, red and pink clusters, indicating that they are indeed expressed and the corresponding reactions likely to be active.

Format: PDF Size: 174KB Download file

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Additional file 2:

Stoichiometric metabolic model. SBML file describing the metabolic model of Streptomyces coelicolor.

Format: XML Size: 729KB Download file

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Additional file 3:

Table of metabolites. Excel table defining all metabolites used in the metabolic model.

Format: XLS Size: 79KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 4:

Table of reactions. Excel table defining all reactions used in the metabolic model.

Format: XLS Size: 246KB Download file

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Additional file 5:

Table of zero-flux reactions. Excel table of reactions that show consistent zero predicted flux, including their membership in the expression clusters depicted in Additional file 1.

Format: XLS Size: 55KB Download file

This file can be viewed with: Microsoft Excel Viewer

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