Figure 1.

The amino acid biosynthetic network analyzed in this work. Bipartite amino acid biosynthetic network from multiple species. The 20 standard amino acids (red triangles) are shown as the ends of pathways. Green circles represent the canonical E. coli enzymes. Blue circles represent alternative enzymes (analogs and alternologs) from other species. The size of nodes corresponds to the normalized average taxonomic distribution of orthologs for each enzyme domain (domains in multimeric enzymes) catalyzing the corresponding reaction. The larger a node is the wider the distribution of orthologs for the corresponding enzyme across genomes. Red edges denote steps that could occur in the LCA based on the TDs of their catalyzing enzymes (Figures 2 and 4). Purple EC numbers correspond to reactions without known gene/enzymes. A detailed view of this network, including substrates and products, is provided in Additional data files 1 and 3, and the data for its construction are provided in Additional data files 2 and 4.