Question: Real Or Ghost Tm Domains
0
gravatar for cdsouthan
7.4 years ago by
cdsouthan1.8k
cdsouthan1.8k wrote:

This is a Ciona savignyi Ur-BACE ORF from Ensembl

MVKFLWCLWLGVFIVCSGARIRLKRAATDNLHGTTITGYYVTVKLGNPPQELNVIVDTGSSNFAVAGGPNPVISNFYNKSSSNTSVDTGVRSVKVDYTEGWWMGDVVSDVLSVPSAQLDTSVRVPVADITNSNKFFVNGSNWVGILGLAYSDLVLPKGNGLKSVMHEITHQTSTPDLLSMQLCSTSLQDATYGALLIGEIDLSLAAGPLYWTPIVKQWYYDIIVSGLKIGDKVVDIDCSDINYDRTIVDSGTTNLRFPQKVYDIILPIIKASVVRFYFDQDFYDGKTMFCTTDPAELYGEFPNITIYLPSTNENQTIELTIHSASIPQFTTMLDASKQSCYKFAIFPSAIGTVLGTVLMEEYYVVFNRINSSIGFALSACHKGSTIQVINKWINSTNCRYIPPTKPITYAAYVVLALFCICLLPLCFLLAFNYFRSKSTPCRPRESYDQLDDHHEVSH

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

• 1.8k views
ADD COMMENTlink modified 7.0 years ago by jackuser1979870 • written 7.4 years ago by cdsouthan1.8k

Hi Chris

Have you tried running it through other TM predictors, like Phobius? The signal is much lower there...

Sarah

ADD REPLYlink written 7.4 years ago by sarahhunter600

Your right, thanks. OK so I'll chalk up this particular cryptic TMHMM as an artefact, but this post can ensure it persists in the collective memory bank, just in case it comes up again.

ADD REPLYlink written 7.4 years ago by cdsouthan1.8k
0
gravatar for jackuser1979
7.0 years ago by
jackuser1979870
US
jackuser1979870 wrote:

Whenever you do bioinformatics predictions, it always better to get consensus view by using different predictors and decide if all the predictors give the same TM prediction. See the list of TM predictors

ADD COMMENTlink written 7.0 years ago by jackuser1979870
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