I am attempting to predict the structure of a protein which includes a transmembrane domain.
The domain that I am most interested is not transmembrane (corresponding to residues 99 to 226 of the whole protein).
When I run i-TASSER on the whole protein and look at the 99 to 226 region in a viewer, I get several models of interest.
However when I run i-TASSER on just the truncated 99 to 226 region, none of the predicted models have any similarity to the 99 to 226 region of the i-TASSER model of the whole protein.
Can you explain why this is happening? I would have expected high similarity. Links below:
Whole protein:
Job: S138189
Fragment corresponding to 99 to 226 region of whole protein:
Job: S138024
Thanks for your help