To be honest, if you are serious about tackling this problem through bioinformatics, you should get in contact with an expert. Sure, there are tools claiming to address this problem, but none of them is particularly good at that.
There are three principal possibilities here:
- you have an interaction domain
- you have an interaction motif
- this is a 'one-off' interaction -
If there is really 'no conservation' in this region, this would favor the third option. However, some domains and motifs are so poorly conserved that they are hard to spot. I assume that you have already tried Pfam or Interpro on you protein to check for domains. As 'spitshine' suggested, you might also check ELM for a motif (although this rarely works). As far as I know, there are no known ER-alpha interaction domains or motifs.
Assuming that alll of the above fails, I would do the following: First, get a collection of reliable orthologs of your protein from reasonable taxonomic range (wherever you find decent orthologs, it might be advisable to restrict the search to species that are assumed to have ER-alpha). Next, create a multiple alignment of the sequences with a good program (MAFFT, MUSCLE, PROBCONS). Next, use an alignment viewer/editor to look at the alignment and see if there still is 'no consevation' in the region of interest. Set the alignment viewer/editor to a mode where highlighting is based on conservation rather than amino acid properties. If you still don't see anything conserved in this region, there is not much hope. If there is, you could try to derive a consesus sequence and scan this, or if you are really serious, try to go for HMM- or profile-based methods.
If you have come to this point and have further problems, post again!
9.5 years ago by
Lyco • 2.3k