Blast a sequence against multiple databases
To scan multiple databases:-


Download all the databases that you intend to match against (all databases will have a download option)
Download standalone BLAST executables from NCBI
Pool all the sequences from the different databases and make a BLAST database using the program makeblastdb (it is better to check for redundant sequences and remove them for improved performance)
Run blastp with desired parameters against this database 
The first hit wont mean much. Use cutoffs on E-value or Bit-Scores or precentage identity


Now, if you vaccine targets a protein it is good to study the protein sequence conservation. BLAST isn't a really good option for studying conservation by comparing different orthologs. Use tools for multiple sequence alignment like ClustalW or T-COFFEE. In my opinion it is also better to use BLOSUM for scoring the alignments compared to PAM. 

It might also be important to look at the protein structures. You can try VAST if possible.