The capability of utilizing 14 different carbon sources for cell growth was qualitatively predicted by the model iCY1106 using FBA (Additional file 4). Each substance was the sole carbon source and the rate of uptake was 1.0 mmol gDW−1 h−1. Initially, there were four types of carbon source (ethanol, xylose, maltose, and rhamnose), and the model could not achieve growth with any individual carbon source. For ethanol, the reaction catalyzed by alcohol dehydrogenase (EC: 1.1.1.1) was irreversible, but should be reversible according to the MetaCyc database. For rhamnose, the lack of L-rhamnulose-1-phosphate lactaldehyde-lyase (EC: 4.1.2.19) meant that rhamnose could not generate glycerone phosphate, which could otherwise be used by the glycolysis pathway. After elimination of initial discrepancies using the continuous gap filling process, a 100% match was acquired. This indicated that model iCY1106 could predict catabolic pathways of various carbon sources including common sugars and alcohols. A similar FBA simulation of nitrogen sources (ammonium, nitrate, urea, and amino acids) also generated results that were consistent with experimental fermentation data. Both glutamate and glycine supported M. alpina growth, confirming that the model performed well for predicting the utilization of different carbon and nitrogen sources.