Fig 2. Example model of bacterial metabolism supports the utility of RIPTiDe for identifying most likely context-specific strategies.

(A) General topology of simplified GENRE that consists of 16 reactions and 14 metabolites in total (S2 Table). The objective of ATP generation can be achieved through two separate means: either the catabolism of glucose via glycolysis or through the paired fermentation of proline and glycine. Glycolysis is the more parsimonious pathway for generating ATP, which is reflected in the pFBA solution fluxes to the right of the diagram (outlined in red). (B) RIPTiDe is able to correctly identify a likely route of flux when provided a transcriptome. (C) When provided with transcriptomic evidence, RIPTiDe is able to identify a less parsimonious, but more concordant solution (Lower weighted sum of fluxes). Despite very low transcription, RIPTiDe still identifies the necessity for carbon dioxide efflux during fermentation to maintain mass balance.