SEA-PHAGES | Cluster DZ

Link to this post \| posted 22 May, 2023 19:46
fogartym1	Question about gene 5 in a DZ cluster phage, Morgana - call as minor capsid protein? ? Pham: 81331 This gene comes directly after portal and has 2 HHPRED hits > 90 % for minor head/capsid protein including P = 99.87to GP7_BPSPP Minor head protein GP7 OS=Bacillus phage SPP1 OX=10724 GN=7 PE=1 SV=2. It has been shown to be a minor capsid protein in SPP1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6316719/ This gene was called as a Muf-like minor capsid protein in DZ phage Cafasso, and a minor capsid protein in phage Aleemily and some others. I know to discount the Muf, but is it appropriate to call as minor capsid protein in this area. I don't see any evidence for capsid maturation protease except this is where one would expect it based on synteny. HHPred image attached 221Kb

Link to this post | posted 22 May, 2023 19:46

Question about gene 5 in a DZ cluster phage, Morgana - call as minor capsid protein? ?
Pham: 81331

This gene comes directly after portal and has 2 HHPRED hits > 90 % for minor head/capsid protein including
P = 99.87to GP7_BPSPP Minor head protein GP7 OS=Bacillus phage SPP1 OX=10724 GN=7 PE=1 SV=2. It has been shown to be a minor capsid protein in SPP1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6316719/
This gene was called as a Muf-like minor capsid protein in DZ phage Cafasso, and a minor capsid protein in phage Aleemily and some others. I know to discount the Muf, but is it appropriate to call as minor capsid protein in this area. I don't see any evidence for capsid maturation protease except this is where one would expect it based on synteny.

HHPred image attached

Link to this post \| posted 22 May, 2023 20:06
debbie	Hi Marie, I think we have enough evidence to call this the capsid maturation protease (CMP). It hits a structural protein of a lactobacillus phage. Which then makes debate whether this is a head or tail protein. The next hit is to gp7 of SPP1 - the papers written about that gene are capsid proteins involved in packaging….. that makes me think not quite in the final virion structure…. And then we hit the capsid maturation protease of D29 (gp15). That hit is at 97%, with an e-value of 10-3. So while that hit is not the best, it is the most descriptive for me and jives with the stronger hits. AND then look at where this gene is in the genome. In between portal and scaffolding!! I think I would be OK calling is a CMP. what do you think? debbie

Link to this post | posted 22 May, 2023 20:06

debbie

Hi Marie,
I think we have enough evidence to call this the capsid maturation protease (CMP). It hits a structural protein of a lactobacillus phage. Which then makes debate whether this is a head or tail protein. The next hit is to gp7 of SPP1 - the papers written about that gene are capsid proteins involved in packaging….. that makes me think not quite in the final virion structure….
And then we hit the capsid maturation protease of D29 (gp15). That hit is at 97%, with an e-value of 10-3. So while that hit is not the best, it is the most descriptive for me and jives with the stronger hits. AND then look at where this gene is in the genome. In between portal and scaffolding!! I think I would be OK calling is a CMP. what do you think?
debbie

Link to this post \| posted 23 May, 2023 12:26
fogartym1	debbie Hi Marie, I think we have enough evidence to call this the capsid maturation protease (CMP). It hits a structural protein of a lactobacillus phage. Which then makes debate whether this is a head or tail protein. The next hit is to gp7 of SPP1 - the papers written about that gene are capsid proteins involved in packaging….. that makes me think not quite in the final virion structure…. And then we hit the capsid maturation protease of D29 (gp15). That hit is at 97%, with an e-value of 10-3. So while that hit is not the best, it is the most descriptive for me and jives with the stronger hits. AND then look at where this gene is in the genome. In between portal and scaffolding!! I think I would be OK calling is a CMP. what do you think? debbie Hi Debbie: Yes, this makes sense. The D29 hit to capsid maturation protease along with the synteny does seem like enough evidence. Thanks Marie

Link to this post | posted 23 May, 2023 12:26

fogartym1

debbie
Hi Marie,
I think we have enough evidence to call this the capsid maturation protease (CMP). It hits a structural protein of a lactobacillus phage. Which then makes debate whether this is a head or tail protein. The next hit is to gp7 of SPP1 - the papers written about that gene are capsid proteins involved in packaging….. that makes me think not quite in the final virion structure….
And then we hit the capsid maturation protease of D29 (gp15). That hit is at 97%, with an e-value of 10-3. So while that hit is not the best, it is the most descriptive for me and jives with the stronger hits. AND then look at where this gene is in the genome. In between portal and scaffolding!! I think I would be OK calling is a CMP. what do you think?
debbie

Hi Debbie:

Yes, this makes sense. The D29 hit to capsid maturation protease along with the synteny does seem like enough evidence.
Thanks
Marie

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