I'm trying to establish if a particular motif at the very C-terminal of any membrane protein (the C-terminal being intracellular) terminates with the residues YKI.
This is obiously a very short sequence and will produce thousands of hits in a search of Swissprot or other protein databases.
Does anyone know how I can set up search parameters to confidently limit my search to membrane proteins, and tell the search engine that I want these residues to be the terminal three residues of the protein? So far without manually trawling through thousands of potential hits I have not found a way to do this in NCBI. A positive control search would be YKV which I know is present in some receptors.
I have also searched PDZbase, but this service is presently limited to only about 300 known interactions.
Any help would be greatly appreciated.