> I tried downloading the protein sequences for the organism: Agrobacterium
> Tumefaciens C58 strain and I found that there are around 10000 entries. I
> remember that previously (before 1.5 months) when I tried the same query and
> I got only 461 genes. My suspicion is that I am doing something wrong while
> querying. Can you please let me know how shall I query the swissprot database
> so that I can obtain genes for only "Agrobacterium Tumefaciens C58" organism.
I think the problem here is that if you search only in the uniprot/swissprot databank you get 482 entries for the query, if you search in the uniprot/trembl databank you find 9812 entries, as data is moved from uniprot/trembl to uniprot/swissprot, I suspect what you've been doing is searching the uniprot/swissprot databank only and missed all the entires is the uniprot/trembl data.
without knowing which SRS site you have been using, it might be that the site originally had swissprot meaning just the curated version) and sptrembl as separate databanks and they now have swissprot as a virtual library where both swissprot and sptrembl are combined, so whereas before you were searching a relatively small set of all the proteins out there you are now searching the whole set
hope that helps