Figure 6

Multiple-sequence alignments for each of the four pfam families of the variable core genome with known functions. Dots represent conserved positions relative to the first sequence, topologies of sequence-similarity groupings are shown to the left of each alignment. Alignments illustrate distinct sequence types defined by sequence variation and major deletions/insertions within each gene for A) PF01520/COG0860, N-acetylmuramoyl-L-alanine amidase, B) PF10145/COG5412, tape measure protein, C) PF02511/COG1351, thymidylate synthase, and D) PF11651, P22 coat protein. Whole genome relationships of host C. perfringens as determined by rep-PCR are shown in (E). Scale represents % dissimiliarity. For each gene, topologies of neighbor-joining trees are outlined to the left of the alignment. For A and C, alignments of entire protein are shown; for B, the entire protein was 780 AA, not shown is 220 AA N-terminal deletion for ΦCP13O and ΦCP34O which is encoded by another ORF immediately upstream. Alignments were done using MUSCLE with default parameters as described in the text. Inferred EAD (N-terminal) and CBD (C-terminal) domains of the amidase joined by a linker region are designated by boxes in (A).