Fig. 4: Polymorphic toxin systems in Ca. B. vickermanii.

Schematic diagrams of the organization of the three predicted polymorphic toxin systems in Ca. B. vickermanii (A–C). In each case, the putative, alternative orphan toxin modules are shown downstream of the main multi-domain toxin. Beneath each is a protein multiple sequence alignment of the main toxin C-terminus and the alternative orphan sequences, generated using MAFFT program under default parameters as implemented in Geneious software v6.7. Grey scale gradient represents identical (black), similar (dark grey) and dissimilar (light grey) residues in the alignment based on the Blosum62 score matrix. Note that the specification of orphan modules is least certain for PTS III. Although CPBP_00970 resembles the N-terminus of CPBP_00960, its coding sequence is abbreviated. This, and the metalloprotease (PF03410) match of CPBP_00971 that would, by expected PTS gene positioning encode an antitoxin, argue against this pair of genes representing an orphan module. Another pair of genes that should, by the PTS gene positioning scheme, be an orphan module are CPBP_00964 and CPBP_00965. However, these two sequences are short (75 and 67 residues respectively), homologous (around 34% identical) and CPBP_00964 lacks any homology to the N-terminus of CPBP_00960, arguing against these genes constituting an orphan module.