Figure 1From: Flux variability scanning based on enforced objective flux for identifying gene amplification targetsSchematic illustration of the FVSEOF method with GR constraints. Functionally grouped reactions were considered based on genomic context and flux-converging pattern analyses obtained from the STRING database. FVSEOF was then performed under GR constraints to identify gene amplification candidates for the production of a target chemical. The candidates were evaluated based on the model predictions and additional criteria of the flux bias ( V avg ) and the slope of the flux changes (q slope ). Each rectangle containing a C x J y index and a line with different colors defines the reaction groups that are likely on or off simultaneously, as determined by genomic context and flux-converging pattern analyses. The C x J y index for each reaction is determined by flux-converging pattern analysis. C x and J y denote the total number of carbon atoms in metabolites that participate in each reaction and the type of fluxes through the flux-converging metabolites from a carbon source, respectively. The red metabolites indicate flux-converging metabolites. The flux-converging metabolites indicate metabolites at which two pathways split by another metabolite recombine. For example, glyceraldehyde-3-phosphate converges the fluxes split by the fructose-bisphosphate aldolase from the fructose-6-phosphate. The flux-converging metabolites categorize J y into four types, indicated as J A , J B , J C , and J D . Each subscript of J y denotes the number of flux-converging metabolites that are passed zero, one, two, or three times, respectively, for a given flux from a carbon source. The subscript E is specially denoted to indicate the fluxes derived from pyruvate. The values of C x J y for each reaction were assigned based on possible flux routes reaching from glucose, and are partitioned by a slash.Back to article page