The process of reconstructing and analyzing a genome-scale metabolic network model starts with a sequenced genome. Functional annotation of the genome [50] links genes to enzymatic activity and allows the reconstruction of a draft network of metabolic reactions. Further steps include compartmentalization, the addition of exchange and transport reactions, the definition of a biomass equation and the gap filling procedure. Gap filling is needed to complement pathways where enzymes are missing, usually because of incomplete annotation knowledge [22]. Today automated workflows like the Model SEED [51] and KBase [23] allow quick reconstruction of genome-scale metabolic network models, but do not solve yet the eventual need for manual curation. The network of reactions can then be represented mathematically as a stoichiometric matrix and analyzed with CBMs under the steady-state assumption and imposing boundaries on the reaction fluxes. Elementary modes [29] and FBA [31] are widely used methods to study the metabolic flux distributions.