General steps for the reconstruction of genome-scale metabolic models of P. stipitis and P. pastoris. Draft models were automatically generated by the RAVEN Toolbox, which also included the primary subcellular localization and transport reactions. Manual curation work was then performed based on known metabolic functions. Gene annotation in the curated model was improved by using functional genomics tools in the third step. The subcellular localization was improved in the fourth step, where the biomass reaction was also added. In this step, the ability of the model to produce all the components to synthesize a cell was checked, and this involved gap filling. In the last step, results from simulations were compared with experimental data. Knockout studies were also done in order to study model robustness.