Figure 2

Variation with the protein sequence of OmpA is confined to a hypervariable region of loop 3. (a) Phylogenetic relatedness of ompA amongst 16 isolates of Y. ruckeri. Isolates were recovered from rainbow trout (green), Atlantic salmon (red) and European eel (yellow). The tree was constructed using the Jukes–Cantor correction for synonymous changes. Distinct variants are indicated by i–iii and reflect Supplementary Fig. S1. (b) The proposed secondary structure the OmpA protein of Y. ruckeri. The sequence is based on OmpA of strain ATCC29473. The periplasmic turns are shown in red, the β-sheets in grey and the surface exposed loops in green. Variable amino acids are shown in bold red and correspond with the sequence alignment in Supplementary Fig. S1. Domains were predicted using Pred TMBB based on Hidden Markov Models (HMM). Sequences at both N- and C-terminals are truncated. Distribution of polymorphic nucleotide sites among ompA alleles in reference isolates (c). The numbers above the sequences represent the positions of polymorphic nucleotide sites from the 5′ end of the gene. The dots represent sites where the nucleotides match those the first sequence (RD6). The boxes highlight regions of sequence identity that represent proposed recombinant segments.