Fig. 6

Metabolic modules involving amino acid biosynthesis represented in the LBCA core genome. Each reaction is labeled with the corresponding KEGG orthogroup(s) and gene name(s) and is colored by the minimum penalty ratio at which the corresponding orthogroup is present in the LBCA core genome (or maximum of ratios if multiple orthogroups are required). Missing reactions are colored white and spontaneous reactions are colored black. Amino acid inputs and outputs are bold. The biosynthesis pathways of alanine, aspartate, asparagine, glutamate, and glutamine do not have specific KEGG modules and have been added separately. Starred reactions indicate reactions that can be catalyzed by enzymes in unrelated pathways as the standard enzyme is missing from LBCA: In Lysine biosynthesis, K00821 (argD) can catalyze SL2A60 → SL26DA in place of K14267 (dapC), and in Tyrosine/Phenylalanine biosynthesis, K00812 (aspB) can catalyze the final steps in both pathways in place of K00832 (tyrB). For double-starred reactions corresponding to metB and metC, the COG orthogroup COG0626 present at g = 1.3 represents sequences from both genes