(A) Workflow for identification and analysis of toxin and immunity domains in bacterial polymorphic toxin systems. (B) General domain architecture template for polymorphic toxins along with representative architectures seen in different secretory systems. Trafficking domains are colored grey, repeats light green, pre-toxin domains (PT-domain) yellow, releasing peptidases blue, and toxin domains pink. Newly identified domains are encircled in dashed lines in all figures in this paper. Proteins are not drawn to scale. Note, only repeats automatically detected by profiles are shown in all figures; the proteins usually have much longer repeat units than shown due to repeats being below the detection threshold. Toxins are grouped based on their secretion pathways that are defined by their canonical trafficking domains (Table 1). Proteins are denoted by their gene name, species abbreviations and GI (Genbank Index) numbers separated by underscores. (C) General gene-neighborhoods template for polymorphic toxin operons. Individual genes are represented as arrows pointing from the 5′ to the 3′-end of the coding frame. Genes are labeled by their domain architectures. The gene neighborhood is labeled by the gene name, species abbreviation and GI number of the SUKH gene marked with an asterisk. Toxins are colored pink, immunity proteins orange, and other trafficking related proteins grey. For species abbreviations refer to supplementary material.