Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function

Figure 5

Conservation of metabolic reactions. A map showing the extent of conservation for the reactions of the M. acetivorans model iST807 (as encoded in the gene-protein-reaction associations (GPRs) of the model). Nodes represent either a metabolite or reaction and edges indicate the dependencies between reactions and metabolites. Reactions on the blue end of the spectrum are facilitated by enzymes that are conserved in relatively few of the 221 archaea in the database while reactions in red are facilitated by highly conserved enzymes. Reactions with thin grey lines are not associated with genes. To assess conservation, the db_evaluateReactionsFromGpr.py functionality of the ITEP software [45] was used. It computes homologous genes to those in the GPRs of each reaction in iST807. The ITEP function was executed with the “or” option enabled to identify whether any of the enzymes (or enzymatic subunits) annotated as facilitating the reactions were encoded in the organism.