Model correction examples. Examples of model corrections performed between iAbaylyiv2 (left) and iAbaylyiv3 (right) models. Metabolites are depicted by blue circles and triangles, triangles indicating essential biomass precursors. Reactions are represented by arrows colored in red if they are predicted essential and in green if they are predicted dispensable. Gene names are indicated next to reaction arrows; they are written in red if they are experimentally essential and in green if they are dispensable. Genes with inconsistent predictions are written in bold italic. Dashed boxes indicate components that have been modified. Further evidence for model corrections are shown in main text and Additional file 3. (A) First steps of histidine biosynthesis. Unpredicted essentiality of ACIAD2907 encoding for ribose-phosphate diphosphokinase activity was corrected by removing the alternate gene ACIAD0964 from the reaction GPR. Unpredicted essentialities of ACIAD0661 and ACIAD1257, catalyzing the ATP phosphoribosyltransferase reaction, were corrected by assigning them as complex subunits instead of isozymes in the reaction GPR. (B) Isoprenoids biosynthesis. Unpredicted dispensability of ACIAD2968, catalyzing farnesyl-diphosphate and geranyl-diphosphate synthases activities, was corrected by adding ACIAD1374 (undecaprenyl-diphosphate synthase) and ACIAD2940 (octaprenyl-diphosphate synthase) as isozymes. Unpredicted essentiality of ACIAD1374 was resolved by adding undecaprenyl-PP to the set of essential biomass precursors. (C) Synthesis of charged glutamine-tRNA(gln) and asparagine-tRNA(asn). Unpredicted essentiality of ACIAD1920, encoding for glutaminyl-tRNA synthetase activity, was corrected by removing from the model the alternate pathway using aspartyl/glutamyl-tRNA amidotransferase enzyme (ACIAD0822-0824). (D) Biosynthesis of polysaccharides. Unpredicted dispensabilities of all genes involved in GDP-mannose, UDP-glucose, and dTDP-rhamnose synthesis were corrected by removing these three metabolites from the list of essential biomass precursors.