Fig. 3.

Schematic diagram showing Streptomyces TopA regions identified by blast protein sequence search. An ≈600-aa segment corresponding to the TopA domain of multiple bacterial proteins annotated as topoisomerases contains two short segments (amino acid residues 221-264 and 441-498 of the S. coelicolor TopA protein) that are absent in most of these proteins. These segments are conserved in proteins annotated as topoisomerases in the subclass of enzymes shown in B. As shown, the 441-498 segment contains two Asp-Asp doublets. (B) Alignment of the conserved motif regions of the subfamily bacterial topoisomerases. The bold DD in S. coelicolor are the DD doublets that were mutated to Ala doublets. (C) Phylogenetic analysis of proteins annotated from DNA sequences of certain bacterial genomes as topoisomerase I enzymes. The subfamily identified by the analysis is discussed in the text. The Calculation Phylogeny Unweighted Pair Group Method with Arithmetic Mean Analysis (UPGMA) Tree program was used for analysis. The numbers indicate tree distance proportional to the amount of inferred evolutionary change.