Fig. 4

Alignment of the OmpA proteins in association with the predicted OmpA structure. Logo plot summarising the multiple sequence alignment of the partial OmpA sequences of 186 bovine and porcine isolates of P. multocida in Thailand using the WebLogo program (a). The height of the stack indicates the sequence conservation level at that position. The symbol height also indicates the relative frequency of amino acids at that position. The alignment was mapped onto the homology-predicted OmpA structure (b) using the Chimera program to identify substructures of the OmpA protein. These substructures were mapped back onto the alignments as loop 1, loop 2, loop 3, and loop 4. The ompA structures were predicted based on the templates of the OmpA-like domain from Acinetobacter baumannii (4g4x_A) and the OmpA transmembrane domain from Escherichia coli (1qjp) using the HHPRED and MODELLER programs. The domain shown in yellow is the partial C-terminal peptidoglycan-binding domain, and the domain shown in green is the transmembrane ß-barrel N-terminal domain. The model was visualised using the Chimera program