Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets

Additional File 1:

Molecular composition of biomass functions. A detailed list of the biomass constituents and their respective coefficients in the biomass function in addition to the references from which this information was found.

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Additional File 7:

Robustness plots for phosphate and sulfate for iNJ661 and iJR904. Plotting the biomass objective function versus phosphate or sulfate uptake rates for in silico strains of M. tb and E. coli.

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Additional File 4:

Comprehensive list of false negatives between OptGro data set and iNJ661 lethal gene deletions. A catalog of the false negative results produced by iNJ661 when compared to the OptGro data set. Each of false negative results is categorized into at least one of four different categories. Specific loci are listed in cases with suggested alternative loci or alternative paths.

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Additional File 2:

HCRs mapped to experimental data sets. The list of HCRs that mapped to the three experimental data, based on gene loci.

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Additional File 6:

Explicit list of references used in the reconstruction process. The list of references used to define particular reactions and GPR relationships.

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Additional File 8:

Amino acid metabolism. A map of the amino acid pathways in iNJ661.

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Additional File 9:

Central metabolism. A map of the central metabolic pathways in iNJ661.

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Additional File 10:

Fatty acid metabolism. A map of the fatty acid pathways in iNJ661.

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Additional File 11:

Membrane metabolism. A map of the membrane metabolism pathways in iNJ661.

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Additional File 12:

Nucleotide metabolism. A map of the nucleotide synthesis and degradation pathways in iNJ661.

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Additional File 13:

Peptidoglycan metabolism. A map of the peptidoglycan pathways in iNJ661.

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Additional File 14:

Transporters. A map of the transport reactions found in iNJ661.

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Additional File 15:

Vitamin and cofactor metabolism. A map of the vitamin and cofactor pathways in iNJ661.

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Additional File 3:

HCRs mapped to reaction and metabolic subsystems. The complete list of HCRs, highlighting those known to be drug targets in M. tb.

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Additional File 5:

Model content for iNJ661. A complete list of the reactions (abbreviations and full names), the associated mass and charge balanced reactions, confidence scores, reaction subsystems, and the list of the Gene-Protein-Reaction relationships, including logical AND/OR relationships, for all of the reactions in the model. A complete list of metabolites appearing in iNJ661, including abbreviation, full name, formula, and charge at pH 7.2 can be found in the second tab in the file.

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