TMHMM instead of UniProt and Phobius,

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Willy Yoo

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Aug 23, 2020, 12:34:25 PM8/23/20
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Hi, there!

Eventually, I'm so glad that I found out wonderful application for visualizing transmembrane.

Unfortunately, several proteins of my interest do not exist in the UniProt database and also show inconsistency between Phobius and other publications (that they used TMHMM).

Is there anyone who knows how to visualize TMHMM output via Protter?
Or I'm really hoping to get a little tips.

Best regards,

Willy

Ilnam Kang

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Aug 10, 2021, 9:59:20 PM8/10/21
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Hi,

I'm not sure, but I think I've figured out a way how to do what you want.
"Listing S2" in the supplementary information of the original Protter publication was helpful.


Below is an example for a heliorhodopsin. (https://www.nature.com/articles/s41586-018-0225-9)

The protein sequence is available at https://www.ncbi.nlm.nih.gov/protein/AVZ43932.1

First, run the protein sequence at TMHMM 2.0 server, with "One line per protein" as output format.

Then, you can get the result as below. 
AVZ43932.1 len=256 ExpAA=152.38 First60=22.70 PredHel=7 Topology=i21-43o58-80i101-123o128-147i160-182o192-211i232-254o

Second, using the protein sequence and TMHMM output, build a kind of web address to access Protter web service.

http://wlab.ethz.ch/protter/create?seq=MAKPTVKEIKSLQNFNRIAGVFHLLQMLAVLALANDFALPMTGTYLNGPPGTTFSAPVVILETPVGLAVALFLGLSALFHFIVSSGNFFKRYSASLMKNQNIFRWVEYSLSSSVMIVLIAQICGIADIVALLAIFGVNASMILFGWLQEKYTQPKDGDLLPFWFGCIAGIVPWIGLLIYVIAPGSTSDVAVPGFVYGIIISLFLFFNSFALVQYLQYKGKGKWSNYLRGERAYIVLSLVAKSALAWQIFSGTLIPA&format=pdf&numbers&nterm=intra&tm=21-43,58-80,101-123,128-147,160-182,192-211,232-254

(1) seq: the full protein sequence (the same as TMHMM input)
(2) nterm: "intra" if the TMHMM result topology starts with "i". Else (starts with "o"), then "extra".
(3) tm: use the TMHMM result topology after editing. (Delete starting and trailing i or o. Replace all internal i or o with comma.)

Third, copy and paste the above web address into the address bar of your web browser, and then press enter. You will get a pdf file (in this case).

For other options and more detailed instructions, refer to https://wlab.ethz.ch/protter/help/ ("Parameters for API access")

Best regards,

Ilnam

2020년 8월 24일 월요일 오전 1시 34분 25초 UTC+9에 wong...@gmail.com님이 작성:
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