Hello everyone I am trying to clone some domains of a transmembrane protein. I have used an online server "Phobius" for the prediction of sequences which is showing it to be a membrane protein with cytoplasmic, non cytoplasmic and transmembrane regions. Attached is the image of that prediction. Regions from 100-200 amino acid residues which I am more concerned about is predicted to be cytoplasmic in nature while other servers have predicted it to be non cytoplasmic in nature. I am having problems in expressing this domain. Sometimes the prediction may go wrong for such a short stretch of amino acid residues.
My question is to know about any technique or any classical experiment which can actually tell me the exact location of this domain across the membrane. I mean real experiments not predictions. Regards Firdous Graduate student Delhi University India
