Question: Partial Protein Sequence
gravatar for mcc
5.3 years ago by
mcc70 wrote:

I have a partial protein sequence from a western blot of a contaminating protein that co-elutes with my protein of interest. What software or which web tools could I use to determine the possible protein that is confounding my purification. Cheers,

software webservice protein • 1.3k views
ADD COMMENTlink modified 17 months ago by onkarnims20090 • written 5.3 years ago by mcc70

How long is the sequence (number of amino acid residues) ?

ADD REPLYlink written 5.3 years ago by Neilfws46k

approximately 50 AA

ADD REPLYlink written 5.3 years ago by mcc70
gravatar for Larry_Parnell
5.3 years ago by
Boston, MA USA
Larry_Parnell15k wrote:

With 50 amino acids of sequence, you can perform a BLASTP search (protein BLAST). This uses a protein query to search a protein database (you should search against "nr" non-redundant protein sequences). A perfect match will tell you exactly which protein is co-eluting with your protein. If you have a near match then you'll know the type of protein or protein family that is co-eluting.

If you have only moderate to poor matches from this BLASTP search, then you will want to use the 50-aa protein sequence as a query in a TBLASTN search: Search translated nucleotide database using a protein query. I'll bet though that you'll have a good idea of the contaminant after the BLASTP search.

ADD COMMENTlink written 5.3 years ago by Larry_Parnell15k
gravatar for onkarnims2009
17 months ago by
onkarnims20090 wrote:

Can any body tell me what is  partial and non-partial protein sequences? 

ADD COMMENTlink written 17 months ago by onkarnims20090
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