I have a GPCR that I am working on. I have used a number of databases to classify it by bioinformatics but the webservers seem to be "confused" about it's class. I have used GPCR-CA for example and this predicts it as a CLASS A GPCR, GPCR-GIA on the other hand indicates that it is NOT a GPCR, and PCA-GPCR indicates that it is a CLASS B, Secretin-like receptor. Where do I go on from here? I have used other databases and the trend seem to be the same.
It looks like classic 7TM protein (GPCR orientation) -use biologyworkbench (TMHMM).
I wouldn't say that is Secretin family (since the sectertin family gpcrs have quite conserved aminoacid sequence in their last 14aa of the 7th tm domain. do you know the ligand for the receptor?
Thanks, Danijela. For now we really do not know any ligands for the protein. Initially we used GPCRsclass from Imtech (Raghava's Lab) in India and we had it as a serotonin receptor, but recentlt we can not reproduce the results on the same website. Protein BLAST on UniprotKb however, puts it as an Intimal thickness-related protein and for these I don't know the class of ligands.
I perform PSI and protein to protein blast, against PDB and found the following match:
1. PBD ID: 1PV8 (42% match), 3OLP (30%), 1E51 (42%) and 3NA5 (27%).
All were chain A. Check whether these hits are GPCR or not and to which class they belong.
In determining the classes, I can perform statistical analysis for you, but I need more information. on the frequency of GPCR hits classifications, you got and those that did not see it as a GPCR , still analysis based on decision to classify it under the classes. whether class A or B. Also i need results on the hits within classes as well to give you a decision based on classes.
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