Question: Partial Protein Sequence
gravatar for mcc
7.1 years ago by
mcc80 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 • 2.1k views
ADD COMMENTlink modified 3.2 years ago by onkarnims20090 • written 7.1 years ago by mcc80

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

ADD REPLYlink written 7.1 years ago by Neilfws48k

approximately 50 AA

ADD REPLYlink written 7.1 years ago by mcc80
gravatar for Larry_Parnell
7.1 years ago by
Boston, MA USA
Larry_Parnell16k 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 7.1 years ago by Larry_Parnell16k
gravatar for onkarnims2009
3.2 years ago by
onkarnims20090 wrote:

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

ADD COMMENTlink written 3.2 years ago by onkarnims20090
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