I am interested to find protein X in bacteria A. We hypothesized some of the strains of bacteria A have protein X, while others haven't. We also assume protein X is missing within species of this particular genus A. I have downloaded the protein sequences of bacteria A from NCBI. Now, I want to compare the genomes to find out which proteins are missing/present in particular strains/species to find out my novel protein. How can I do that? Please suggest me a methodology/software for this particular analysis.