What’s The Answer? (ghost domains)

BioStar is a site for asking, answering and discussing bioinformatics questions and issues. We are members of the community and find it very useful. Often questions and answers arise at BioStar that are germane to our readers (end users of genomics resources). Every Thursday we will be highlighting one of those items or discussions here in this thread. You can ask questions in this thread, or you can always join in at BioStar.

This week’s highlighted question was intriguing–I loved the idea of the ghost domains–but it was the new answer with the link to many transmembrane predicting software tools that was quite handy. So I wanted to store that in my memory banks.

Question: Real or ghost TM domains

This is a Ciona savignyi Ur-BACE ORF from Ensembl

[removed sequence, as it borks the post here]

When I run this through TM prediction at http://www.cbs.dtu.dk/services/TMHMM/ , in addtion to the expected score at the signal peptide and the C-terminal TM I see another high score segment at 339-359.
Could this “cryptic TM” be real and significant in protein function/location terms ?

As we know these TMs don’t show high sequence conservation so homology comparison is not that useful.


Just to keep a copy of that handy list of tools over in my notes here, this is it: http://wiki.bio.dtu.dk/teaching/index.php/Prediction_of_membrane_proteins#Transmembrane_.CE.B1-helix_prediction_servers