The results from the pepinfo hydropathy plot showed seven highly hydrophobic regions within xlrhodop.pep. Could these be transmembrane domains? We can use the wEMBOSS program tmap to investigate this possibility:

Exercise: tmap

Program: tmap

Displays membrane spanning regions

Sequences file to be read in: xlrhodop.pep

Graph type [png]:

You will see a window that looks like this:

The bars across the top represent areas where transmembrane segments are predicted. Taken in combination with the results from pepinfo, we can see that there may be seven transmembrane helices in this protein.

There are various other programs you can use to analyze your peptide sequence - to find out what is available, try rerunning wossname as we did in the first chapter.