iCHO2441 genome-scale metabolic model

For auxotrophy and gene essentiality predictions, a generic IgG structure was used to add secretory reactions to the model (Table S1). As per the recommendation by Hart et al., genes with transformed values less than -3 were classed as ‘not expressed/ negative confidence’ (class -1). Genes with transformed values between -3 and -1.5 were classed as ‘low confidence expressed’ (class 1).

Genes with transformed values between -1.5 and 0 were classed as ‘medium confidence expressed’ (class 2). Genes with transformed values greater than 0 were classed as ‘expressed/high confidence’ (class 3). These classifications were mapped to reactions within iCHO2441 using the method described above, where unclassified reactions were given a class of 0.

Reconstructions were generated per experiment using the CORDA function for python which took iCHO2441 constrained with experimental uptakes (Table S2) as a base model and the gene confidence classifications as inputs. An in-depth rationale behind this novel approach is presented in supplementary material 1.