I have a sequence of a protein which I have put into several disorder predictors like PONDR, psipred and iupred. I know that there is an intrinsically disordered region in the middle of the sequence. I wish to clone only that disordered section into a vector. For this I need to make a decision as to what are the amino acids that mark the boundaries for this IDD.
As with most prediction algorithms there is a zone of haziness and no predictor will agree 100% on a particular amino acid from which disorder starts. This may reflect on reality as disorder is a plastic phenomenon. But I need to make a definition in order to make clones.
How does one go about this? Are there certain amino acids that make good boundaries for IDD's?
You can use the consensus of may predictors. Check out D2P2. It gives you exactly what you want - at the bottom of the page for your protein (after you've searched by sequence or ID) you can look at the disordered regions tab and D2P2 gives you the disordered regions as agreed upon by 75% of predictors.
http://d2p2.pro/
An orthogonal approach for finding the boundaries of a disordered region is sequence conservation.
Try to use homologous proteins- a solved structure of a homolog can help you determine the location of the boundaries of the disordered region. In case you do not have a crystal-solved homolog, you can generate a multiple sequence alignment of several orthologs and judge where some consistency of conservation is achieved. Typically, disordered regions are not conserved (the type, rather than the order of the residues is conserved…)
Good luck...
Thanks, I think d2p2 worked best!
The BLAST option did not work because there weren't any other proteins that seemed to match this one. All results were isoforms or from different species. So the protein of one unique superfamily.
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