The protein sequence that I have has a solved structure in the PDB from the rat, covering 812 of 861 residues. The missing residues are modeled as a disordered loop residues 429-448- which seems fair enough since the crystallographers couldn't do it either, plus a 608-620 and also the very C terminal 846-861.
My question is this:
There are many sequences from all major groups that have a higher C score and TM score than does the rat sequence. Is this because the torsion is less using these other sequences than they are using the rat sequence?
The primary homology between the rat and other species sequences is ~50%. The rat C score was 0.42 and TM score 0.77±0.10, the best scores were with a Leishmania sequence where the C score was 1.91 and the TM score 0.99±0.04 which is about the best score I have seen.
However can someone explain why the prediction is that the Leishmania protein is more confidently predicted to be structurally similar to the rat crystal structure than is the rat sequence from whence the structure was derived? Can it totally be that the Leishmania primary structure folds with less torsion?
Thanks