I am currently trying to homology model the PAR1 receptor with the P2Y12 receptor as my template structure, but for some reason I believe that parts of my sequence are being altered/removed, namely the loop regions.
For example, the original PAR1 sequence is as follows:
>sp|P25116|PAR1_HUMAN Proteinase-activated receptor 1 OS=Homo sapiens OX=9606 GN=F2R PE=1 SV=2
Post-threading, my sequence is this:
I've bolded the part of the sequence I first noticed this in, the ECL2 region. I was trying to incorporate the disulfide bond (as I have with three previous successful modeling runs of other receptors) when I noticed that the loop cysteine wasn't modeled into the post-threaded model for some reason. I haven't run into this issue before and haven't changed any settings from the previous successful runs except for pdb names when need be.