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Membrane proteins

| posted 10 Apr, 2023 07:19
smg366 avatar
smg366
I am a little confused with our current calling of membrane proteins. Should we be calling membrane proteins as functions within our annotations? From PhagesDB and Phamerator it looks like there is a move away from that.
| posted 10 Apr, 2023 12:15
debbie avatar
debbie
The current position is to call membrane proteins found by DeepTMHMM.
https://dtu.biolib.com/DeepTMHMM
See the powerpoint at this forum post for current details.
https://seaphages.org/forums/topic/5438/

debbie
| posted 20 Jan, 2024 00:51
kurt.regner@unlv.edu avatar
kurt.regner@unlv.edu
Hello: I would like to receive feedback on TOPCONS for identifying α-helical transmembrane proteins. At UNLV, we've used DeepTMHMM and SOSUI but only recently became aware of TOPCONS. TOPCONS is found at doi: 10.1093/nar/gkv485. Thanks, Kurt Regner, UNLV
| posted 20 Jan, 2024 01:09
debbie avatar
debbie
Others can give more specifics, but we have found TopCons to be confusing. It runs 5 (ish) different programs that contradict each other. DeepTMHMM has shown to be most reliable. results from DeepTmHmm are incorporated in phamerator.
debbie
| posted 22 Jan, 2024 17:38
afreise avatar
afreise
The approved function list still lists the old evidence requirements (TmHmm, TOPCONS) for membrane proteins - could this be updated?
https://docs.google.com/spreadsheets/d/e/2PACX-1vToasuRfxx_yfLa9ECFN4_6okwNI_5AJGWZ3NCy53Gz0QfoNrhAQ48HnBuSD1hsrY0zUTTn6EP3MGK_/pubhtml?gid=0&single=true
| posted 30 Jan, 2024 16:57
hnance@ccga.edu avatar
hnance@ccga.edu
I'm having trouble finding another program besides TMHMM to run online to predict membrane proteins. I've got evidence of one domain with TMHMM, but it sounds like I need another prediction program to call this a membrane protein. I can't find how to access SOSUI online.
Thanks!
Holly
| posted 30 Jan, 2024 23:18
kurt.regner@unlv.edu avatar
kurt.regner@unlv.edu
I agree, SOSUI is offline. Any recommendations on the following: CCTOP (https://cctop.ttk.hu/), Phobius (https://phobius.sbc.su.se/), and SMART (http://smart.embl-heidelberg.de/). An abstract by LeTourneau University (https://seaphages.org/abstracts/summary/1153/)mentions their use.
| posted 31 Jan, 2024 02:04
debbie avatar
debbie
afreise
The approved function list still lists the old evidence requirements (TmHmm, TOPCONS) for membrane proteins - could this be updated?
https://docs.google.com/spreadsheets/d/e/2PACX-1vToasuRfxx_yfLa9ECFN4_6okwNI_5AJGWZ3NCy53Gz0QfoNrhAQ48HnBuSD1hsrY0zUTTn6EP3MGK_/pubhtml?gid=0&single=true

Not anymore. Approved Function now states to use DeepTMHMM.
| posted 31 Jan, 2024 10:54
hnance@ccga.edu avatar
hnance@ccga.edu
Thanks for clarifying this. So we only need one domain identified by TMHMM to call a membrane protein?
Thanks again!
Holly
| posted 07 Feb, 2024 03:03
debbie avatar
debbie
Holly,
Sorry for the confusion. The only program to use is DeepTMHMM. And only 1 transmembrane protein needs to be found to call a membrane protein. take care to interpret DeepTMHMM hits because some will identify signal proteins. At this time, we are not calling signal proteins.
The Bioinformatics Guide is updated.
debbie
 
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