Finding an exactly conserved amino acid sequence in a particular protein.

Question

[siddharth.avadhanam]

Hi

I've been trying to find a perfectly conserved region of a particular protein (secY : a membrane translocase ) among all species of Leptospira. I tried using microbial BLAST, but this isn't very helpful, as it gives me alignments that are off by 5 - 10 amino acids. Can someone direct me to a site or tool that can do this for me?

Answer 1

[bioslayer]

The highest scoring sequences in Blast should give you an insight about the degree of conservation for this region.
Try querying your sequence against Pfam http://pfam.xfam.org/ to see if that domain is actually conserved. Another thing you can do is to see which amino acid residues remain conserved in this region and if it has any distant homologs through jackhmmer http://hmmer.janelia.org/search/jackhmmer.

If your region is short enough you may consider writing a script that search for it across several Leptospira species.