Figure 2.

Average taxonomic distribution of amino acid biosynthetic enzymes widely distributed across the three domains of life. The TDs for enzymes catalyzing the amino acid biosynthetic pathways (vertical labels) were computed by searching for their ortholog distribution across diverse taxonomic groups (horizontal labels). The plot shows enzymes with an average normalized distribution ≥ 50% (see Materials and methods). Amino acid three letter codes in red denote amino acids whose biosynthesis probably occurred in the LCA (detailed in the main text). Four types of seeds were used to look for TDs: the canonical E. coli enzymes (gray scale); homolog enzymes - paralogs and orthologs - from other species showing a higher distribution than E. coli counterparts (yellow scale); analog enzymes - catalyzing the same reaction and coming from a different structural superfamily - (red scale); and alternolog enzymes and branches - converging in the same end compound, but proceeding via different metabolites - in other species (blue scale). In the vertical labels, subunits of multimeric enzymes are denoted with 'S', analog enzyme machinery is denoted with 'A' and isoenzymes are denoted with 'I'. For example, the annotation 'EC:3.5.1.1(Eco_Ans-AnsB)(A:1/2-I:1/2)' indicates that there are two analog EC:3.5.1.1 enzymes and this annotation corresponds to the first type (A:1/2). In turn, this type has two isoenzymes and this annotation corresponds to the first one (I:1/2), formed by AnsA and AnsB proteins in E. coli. The average distribution of orthologs for each route is shown in parentheses following amino acid three letter codes. Biosynthetic enzymes for each amino acid were sorted as they appear downstream in the metabolic flux.