Hello, I am new to this forum as well to bioinformatics, however I have this project to do and I am completley blank… I am asking for help/advice from any kind people who know more than me about that subject.
My project objective is to find out whether cytoplasmic loops of ‘7-transmembrane helix’ receptor proteins show structural homology/conserved features. I have chosen Class C (or 3) Metabotropic glutamate receptors to work on, I know roughly what genes encode different types of that receptor family proteins but I DO NOT know how to isolate sequences of cytoplasmic loops.
Is there any way I can find this from entire sequence of the protein gene? OR there is some other ways?
You need to determine, which segments are membrane-spanning helices. The rest are the extra-membranous loops. What I remember about 7TM proteins, one of them should be considerably longer and that’s the one you are looking for 😉