Open Access Highly Accessed Research article

Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacterium

Arnau Montagud13*, Emilio Navarro2, Pedro Fernández de Córdoba1, Javier F Urchueguía1 and Kiran Raosaheb Patil3

Author Affiliations

1 Instituto Universitario de Matemática Pura y Aplicada, Universidad Politécnica de Valencia, Camino de Vera 14, 46022 Valencia, Spain

2 Departamento de Lenguajes y Ciencias de la Computación, Campus de Teatrinos, Universidad de Málaga, 29071 Málaga, Spain

3 Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, D-69117 Heidelberg, Germany

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BMC Systems Biology 2010, 4:156  doi:10.1186/1752-0509-4-156

Published: 17 November 2010

Additional files

Additional file 1:

iSyn669 reactions to gene connections. Excel file with the list of iSyn669 reactions and its cognate list of genes.

Format: XLS Size: 78KB Download file

This file can be viewed with: Microsoft Excel Viewer

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Additional file 2:

iSyn669 genome-scale metabolic model in OptGene format. Text file with the stoichiometric model, in OptGene [37] format, with all the constraints needed for its simulation with FBA algorithm.

Format: TXT Size: 79KB Download file

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Additional file 3:

Most connected metabolites with filtered cofactors. Supplementary table with most connected metabolites once the cofactors have been filtered.

Format: DOC Size: 38KB Download file

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Additional file 4:

iSyn669 metabolic fluxes simulated under four conditions. Excel file with all the reactions simulations and resulting flux ranges from the model simulated under four growth conditions: autotrophy, dark o pure heterotrophy, light-activated heterotrophy and mixotrophy.

Format: XLS Size: 253KB Download file

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Additional file 5:

Fluxes of reactions around pyruvate. Flux values (in mmol/g DCW/h) for reactions that produce or drain pyruvate in Synechocystis sp. PCC6803 metabolism. Negative sign in bidirectional reactions means pyruvate consumption. Reactions names can be traced in reaction list in Additional files 2 and fluxes can be found in Additional file 4.

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Additional file 6:

FBA and MOMA simulation values for biomass growth in Synechocystis sp. PCC6803, Escherichia coli and Saccharomyces cerevisiae genome-scale metabolic models. Excel file with the growth values under MOMA simulation for Synechocystis sp. PCC6803, Escherichia coli and Saccharomyces cerevisiae. Data for Synechocystis is original from present work, data for Escherichia coli has been obtained from metabolic model from reference 18 and data for Saccharomyces cerevisiae is from reference 30.

Format: XLS Size: 613KB Download file

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Additional file 7:

iSyn669 groups of correlated genes in the three sets of arrays of light shift experiments. Word file with the list of iSyn669 correlated genes in "All time points", "Dark to light" and "Light to dark" analyses.

Format: DOC Size: 38KB Download file

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