Proteins whose concentration and the k_cat value were integrated in the enzyme-constrained models of <i>R</i>. <i>toruloides</i> representing batch cultivations on three different carbon substrates–glucose (G), xylose (X) and acetate (A)—during exponential growth (exp) and nitrogen limitation (Nlim) phases.

Proteins required EC numbers to allow the algorithm to query their kcat values, therefore the existing and new EC numbers were provided to the input file (uniprot.tab) for the GECKO algorithm (columns J-K). In case of multiple EC numbers found for the same gene in rhto-GEM, EC numbers were combined. For further details on how the algorithm selected the kcat values based on their EC numbers, see [17]. (XLSX)