<p>How to derive <strong>pan proteome</strong> of 28 microbial species? <br />
I already have <strong>core genes /  orthologs</strong> between all the species. <br />
I also have <strong>unique genes</strong> of all species. <br />
I only had problem with getting accessory genes/ proteins. <br />
I am not willing to do blast 784 times. <br />
help pls</p>

First, pan-proteome is not a widely-used term, nor is it very well defined. I assume you mean it in the sense used in <a href='http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2890568/'>this article</a>:

    core (found in all) + accessory (found in > 2) + unique (found in 1)

I don't think the 3 sets together are interesting or useful ; pan-proteome is just a term used to describe those 3 sets.

Second, why are you "not willing" to run 784 BLAST searches? Perhaps you mean "not able"? If you're able but not willing, perhaps consider another career ;)

Third, BLAST is not necessarily the best tool. You may find it more useful to cluster the protein sequences using e.g. <a href='http://weizhong-lab.ucsd.edu/cd-hit/'>CD-HIT</a>. In fact, the output from that may come close to giving you the groupings that you need.