There are several approaches and tools. I had a good experience with ConSurf (http://consurf.tau.ac.il) and ConSeq (http://conseq.tau.ac.il). These are two well-established web servers for calculating the evolutionary conservation of amino acid positions in proteins using an empirical Bayesian inference, starting from protein structure and sequence, respectively.
Sherine Saber, comparing the protein across the strains is the short answer. I would begin with NCBI BLAST https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastp&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome