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,
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.