Open Access Highly Accessed Research article

The evolution of metabolic networks of E. coli

David J Baumler1*, Roman G Peplinski1, Jennifer L Reed2, Jeremy D Glasner1 and Nicole T Perna13

Author Affiliations

1 Genome Center of Wisconsin, University of Wisconsin-Madison, Madison, Wisconsin, USA

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

3 Department of Genetics, University of Wisconsin-Madison, USA

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BMC Systems Biology 2011, 5:182  doi:10.1186/1752-0509-5-182

Published: 1 November 2011

Additional files

Additional file 1:

Genome-scale metabolic model for E. coli K-12 strain MG1655. SBML format of iEco1339_MG1655 for distribution and use in other modeling environments.

Format: XML Size: 2.8MB Download file

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Additional file 2:

Gene to protein to reaction (GPR) updates for E. coli K-12 MG1655 in the final version of the reconstruction. This file contains two tables, the first contains all new GPR information added to the previous E. coli K-12 MG1655 GEM (iAF1260), and the second contains the final GPR information for iEco1339_MG1655.

Format: XLS Size: 536KB Download file

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Additional file 3:

Orthologous gene cluster groupings for all ORFs in 16 E. coli genomes and one Salmonella genome. This file contains the mapping of orthologous cluster group identifiers to each ASAP feature identifier and locus tag for all ORFs contained in the genomes of 16 strains of E. coli and one Salmonella genome.

Format: XLS Size: 5.6MB Download file

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Additional file 4:

E. coli pangenome orthologous cluster group identifier (OCG) to protein to reaction information for the E. coli pan-GEM. This file contains four tables, the first contains all gene additions, the second contains all metabolite additions, and the third contains all reaction additions to iEco1339_MG1655 to construct the E. coli pan-GEM (Eco1712_pan). The fourth table contains the final OCG to protein to reaction information for Eco1712_pan.

Format: XLS Size: 703KB Download file

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Additional file 5:

Pangenome-scale metabolic model representing the E. coli pangenome. SBML format of iEco1712_pan for distribution and use in other modeling environments.

Format: XML Size: 2.9MB Download file

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Additional file 6:

Quantitative experimental batch growth data for six E. coli and one Salmonella strain for aerobic and anaerobic conditions. This file contains 3 tables, the first contains the biomass data (g/L), the second contains glucose data (g/L), and the third contains the optical density data (600 nm and 1 cm cuvette path length) for experimental batch growth of six E. coli and one Salmonella strain for aerobic or anaerobic conditions. Values highlighted in yellow reflect the timepoints used to determine lineage-specific glucose uptake rates and strain-specific growth rates.

Format: XLS Size: 57KB Download file

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Additional file 7:

Experimental and in silico carbon source utilization data. This file contains two tables, the first contains experimental and in silico carbon source utilization data during aerobic conditions, and the second contains experimental and in silico carbon source utilization data during anaerobic conditions for six E. coli and a Salmonella strain. Values highlighted in blue represent false negatives and those highlighted in magenta represent false positives.

Format: XLS Size: 59KB Download file

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Additional file 8:

Genome-scale metabolic model representing the ancestral core of E. coli. SBML format of iEco1053_core for distribution and use in other modeling environments.

Format: XML Size: 2.6MB Download file

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Additional file 9:

Necessary orphan reactions required for biomass production. List of metabolic reactions without corresponding genes necessary for each E. coli strain-specific GEM for biomass production in minimal media with glucose added as the sole carbon source.

Format: XLS Size: 18KB Download file

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Additional file 10:

Genome-scale metabolic model for E. coli K-12 strain W3110. SBML format of iEco1335_W3110 for distribution and use in other modeling environments.

Format: XML Size: 2.8MB Download file

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Additional file 11:

Genome-scale metabolic model for enterohemorrhagic E. coli O157:H7 strain EDL933. SBML format of iEco1344_EDL933 for distribution and use in other modeling environments.

Format: XML Size: 2.8MB Download file

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Additional file 12:

Genome-scale metabolic model for enterohemorrhagic E. coli O157:H7 strain Sakai. SBML format of iEco1345_Sakai for distribution and use in other modeling environments.

Format: XML Size: 2.8MB Download file

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Additional file 13:

Genome-scale metabolic model for uropathogenic E. coli strain CFT073. SBML format of iEco1288_CFT073 for distribution and use in other modeling environments.

Format: XML Size: 2.7MB Download file

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Additional file 14:

Genome-scale metabolic model for uropathogenic E. coli strain UTI89. SBML format of iEco1301_UTI89 for distribution and use in other modeling environments.

Format: XML Size: 2.8MB Download file

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Additional file 15:

Deleted reactions for strain-specific E. coli GEMs and the E. coli ancestral core GEM. This file contains three tables; the first contains all gene and corresponding reactions deleted for five E. coli strains in comparison to Eco1339_MG1655, the second contains all deleted genes corresponding to isozymes for five E. coli strains in comparison to Eco1339_MG1655, the third contains all reactions deleted from Eco1339_MG1655 to generate the E. coli ancestral core GEM (iEco1053_core).

Format: XLS Size: 38KB Download file

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Additional file 16:

Reactions corresponding to essential gene predictions for all six strain-specific E. coli GEMs and for the E. coli ancestral core GEM. This file contains three tables, the first contains all predicted essential reactions during both aerobic and anaerobic conditions, the second contains all anaerobic-specific predicted essential reactions, the third contains predicted strain- or core-specific essential reactions for all six strain-specific E. coli GEMs and for the E. coli ancestral core E. coli GEM.

Format: XLS Size: 78KB Download file

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