Flux balance analysis (FBA) was used to simulate all experimental conditions to validate the iBsu1103 model. FBA defines the limits on the metabolic capabilities of a model organism under steady-state flux conditions by constraining the net production rate of every metabolite in the system to zero [36 (link)-39 (link)]. This quasi-steady-state constraint on the metabolic fluxes is described mathematically in Equation 1:
In Equation 1, N is the m × r matrix of the stoichiometric coefficients for the r reactions and m metabolites in the model, and v is the r × 1 vector of the steady-state fluxes through the r reactions in the model. Bounds are placed on the reaction fluxes depending on the reversibility of the reactions:
- (CDW = cell dry weight). When simulating a gene knockout, the bounds on the flux through all reactions associated exclusively with the gene being knocked out (or associated exclusively with a protein complex partially encoded by the gene being knocked out) were reset to zero. When simulating media conditions, only nutrients present in the media were allowed to have a net uptake by the cell. All other transportable nutrients were allowed only to be excreted by the cell. Details on conditions for all FBA simulations performed are provided in Table S8 in Additional data files 1 and 2.
In Equation 1, N is the m × r matrix of the stoichiometric coefficients for the r reactions and m metabolites in the model, and v is the r × 1 vector of the steady-state fluxes through the r reactions in the model. Bounds are placed on the reaction fluxes depending on the reversibility of the reactions:
- (CDW = cell dry weight). When simulating a gene knockout, the bounds on the flux through all reactions associated exclusively with the gene being knocked out (or associated exclusively with a protein complex partially encoded by the gene being knocked out) were reset to zero. When simulating media conditions, only nutrients present in the media were allowed to have a net uptake by the cell. All other transportable nutrients were allowed only to be excreted by the cell. Details on conditions for all FBA simulations performed are provided in Table S8 in Additional data files 1 and 2.
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