SEA-PHAGES | Membrane protein

Link to this post \| posted 28 Apr, 2022 17:21
mdgainey	I am working with a cluster DJ phage named Vardy this semester, that seems to have a surprising amount of membrane proteins (they called 16 initially), with many clustered together in the same area of the genome. There are also some with signal peptides in this area (predicted by signal P and topcons). I looked up the past signal peptide post and it seems that these we were not calling, but given that the idea here is just to alert someone about interesting areas of the genome where these membrane and potentially membrane associated proteins are, can I call these membrane proteins as well just to denote their presence for now, or can we add a signal peptide containing protein to the choices on the list? I will have some students look into this area a bit more this summer as it is also chocked full of interesting repeat sequences.

Link to this post | posted 28 Apr, 2022 17:21

I am working with a cluster DJ phage named Vardy this semester, that seems to have a surprising amount of membrane proteins (they called 16 initially), with many clustered together in the same area of the genome. There are also some with signal peptides in this area (predicted by signal P and topcons). I looked up the past signal peptide post and it seems that these we were not calling, but given that the idea here is just to alert someone about interesting areas of the genome where these membrane and potentially membrane associated proteins are, can I call these membrane proteins as well just to denote their presence for now, or can we add a signal peptide containing protein to the choices on the list? I will have some students look into this area a bit more this summer as it is also chocked full of interesting repeat sequences.

Link to this post \| posted 28 Apr, 2022 17:42
debbie	Maria, I think that this is something to investigate. Let's see what your students turn up this ummer and address it then. Will that work? debbie

Link to this post \| posted 20 May, 2022 14:02
smg366	I am doing QC for a DE genome, where there are a number of Membrane Protein functions called. SOSUI, TMHMM and Topcons all support at least 2 transmembrane domains, but no other phages have called membrane proteins for these genes. I just want to check that we are still calling membrane protein as a function if there is evidence for it?

Link to this post \| posted 20 May, 2022 14:05
debbie	Yep. Please call them. Thanks, debbie

Link to this post \| posted 20 May, 2022 14:07
smg366	Thank you for getting back to me so quickly! Susan

Link to this post \| posted 20 May, 2022 14:16
mdgainey	Thanks Debbie, I will leave them in my GenBank submission for now. M

Link to this post \| posted 30 Jan, 2024 22:53
kurt.regner@unlv.edu	Looks like SOSUI no longer exists. Should we use DeepTMHMM and TOPCONS to identify membrane proteins?

Link to this post \| posted 31 Jan, 2024 02:00
debbie	Kurt, only DeepTMHMM is used. Please see the January Faculty Meeting forum post for more information. https://seaphages.org/forums/topic/5612/ debbie

Link to this post \| posted 14 Mar, 2024 21:28
mthomas	Now that DeepTMHMM has replaced other tools membrane to call membrane proteins, I noticed that a call from last year (KillerTomato gene 19) is now predicted to have 2 membrane domains (rather than just one). This gives us evidence consistent with calling the gene a holin (a call made for other genes in Pham 1053), which is supported by HHPred. Could we update the NCBI report for the phage?

Link to this post \| posted 15 Mar, 2024 18:18
scaruso	Though it may no longer be relevant, SOSUI was down for a long time, but it seems to be working right now at this site: https://harrier.nagahama-i-bio.ac.jp/sosui/mobile/ Steve Edited 15 Mar, 2024 18:18

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Membrane protein