Fig. 3.

Bioinformatics analysis of type III CoA-transferases from bacteria. a Sequence alignment of selected PtmU4 homologs from bacteria. Aligned residues are colored based on the level of conservation (red box with white character and red character show strict identity and similarity, respectively). The conserved catalytic residue, aspartic acid (D430), is shown with blue asterisks. A full sequence alignment was included in Supplementary Fig. 27. b Phylogenetic analysis of the selected type III CoA-transferase from bacteria. The sequences used in the phylogenetic tree include selected one-domain and two-domain type III CoA-transferases (Supplementary Methods). c A sequence similarity network (SSN) of thioacid group. The BLAST e-value threshold is 10^–140 with median 58% sequence identity over 500 residues. All PtmU4 homologs in the thioacid group are from three classes of bacteria: Actinobacteria, Betaproteobacteria, and Gammaproteobacteria. Each node represents protein sequences sharing 100% sequence identity. Colors represent different classes in bacteria. Shapes in c represent the thiocarboxylic acid biosynthesis related type III CoA-transferases discussed in the paper. A complete SSN including all 2401 two-domain type III CoA-transferases in bacteria is shown in Supplementary Fig. 49