How to get conservation of vaccine candidates between hundreds of bacterial strains?
This website will allow you to blast all sequenced microbial genomes:
http://www.ncbi.nlm.nih.gov/sutils/genom_table.cgi

Recovering the full gene sequence might be a bit of a hassle, since BLAST will only allow you to recover the region that matched your query. You may need to set up your own pipeline for this. You may also be able to identify a "protein family" or "cluster of orthologous genes" using the BLAST results.

Once you have the full sequence, you can perform a multiple sequence alignment with CLUSTAL, Muscle, or another program. This will help you to identify the conserved regions.