Figure 5.

Essential reactions and genes in the methanogenic pathway of M. barkeri. Listed are the enzymes of the methanogenic pathway, the protein encoding genes needed to produce the functional enzymes and the abbreviation for the reaction they perform. Each of the reactions catalyzed by the enzyme listed was removed from the network and growth phenotypes were determined. For each computational prediction, green indicates methanogenic growth, blue indicates acetogenic growth, and red indicates no growth (0 net flux through the BOF). A plus symbol for a given condition indicates an agreement between model predictions and experimental characterization. A negative symbol indicates a disagreement. The colored enzyme and encoding gene sets (pink, yellow and green) indicate equal flux correlated reaction sets that possess the same reaction flux value under all growth conditions since they belong to a linear pathway. The simulation results can be used to determine the growth phenotypes of mutant strains and interpret the active pathways under each given condition.