Genome-scale models represent the link from genotype to phenotype, but they also serve as an adaptable platform for discovering: (i) the metabolic potentials of an organism, (ii) metabolic flux distribution in response to stress or changing environment and (iii) targets for metabolic engineering. A genome-scale model consisting of more than 400 metabolites, involved in greater than 500 biochemical reactions (including 30 membrane transport reactions), has been constructed for Clostridium acetobutylicum ATCC 824, a strict anaerobe producing butanol, acetone, ethanol, butyrate and acetate. Model simulations have identified the importance of specific proton flux states during vegetative growth of this bacterium. Additionally, the incorporation of a complex pH model led to not only correct predictions of substrate uptake, byproduct production and growth, but also that of the extracellular medium pH. Thus, the specific molar proton efflux was found to greatly exceed that of combined lactate, acetate and butyrate during the acidogenic-phase of culture growth. Techniques were also developed for the identification of numerically-defined subsystems within an underdetermined metabolic network. Analysis of these subsystems proved useful in determining intracellular flux directions and constraints.