SEA-PHAGES | Kikiko

Link to this post \| posted 24 Mar, 2023 20:18
uOttawaPHAGE	Kikiko_42 (46820-49244) is in a pham that has been called NKF in all other annotations, but it has very strong HHpred hits to gp12 in T7 (and other phages) that is part of the DNA ejection machinery. On Alphafold it also has very high probability to have a similar structure to gp12. I'm trying to understand why it has no approved function despite - is it because unlike T7, which has a contractile tail, this gene is found in podoviridaes? Without experimental data do we leave it as an NKF? Given that this pham has many members, I assume you have answered this question before…. Adam

Link to this post | posted 24 Mar, 2023 20:18

Kikiko_42 (46820-49244) is in a pham that has been called NKF in all other annotations, but it has very strong HHpred hits to gp12 in T7 (and other phages) that is part of the DNA ejection machinery. On Alphafold it also has very high probability to have a similar structure to gp12. I'm trying to understand why it has no approved function despite - is it because unlike T7, which has a contractile tail, this gene is found in podoviridaes? Without experimental data do we leave it as an NKF?

Given that this pham has many members, I assume you have answered this question before….
Adam

Link to this post \| posted 24 Mar, 2023 21:28
debbie	Hi Adam, My answer is I don't know. This cluster of genomes is not like the others. It is a podo and I am not sure it fits the canonical features of podos. In order to answer this question, a review of podovirus structures is warranted. What are the canonical featured of them? So a deep dive into the literature is warranted here. Next, the cryoEM data is pouring in to the PDB, so what we have access to now vs when this cluster first appeared has grown. Next, in the literature you can find good reviews about podos and myos tails(and learn that the tail structures of siphos is a bit more elusive). We'll need to apply that to this. Next, your are cherry-picking one gene is a very non-canonical place in the genome. Structural genes frequently hit heads and tails and until we can clearly determine what we have going on here, I recommend that we prudently wait on jumping the gun. Finally, the same terminology doesn't always cross from sipho, myo and podo. So some thought will be required. Keep us posted as you do your investigations. debbie

Link to this post | posted 24 Mar, 2023 21:28

debbie

Hi Adam,
My answer is I don't know.
This cluster of genomes is not like the others. It is a podo and I am not sure it fits the canonical features of podos.
In order to answer this question, a review of podovirus structures is warranted. What are the canonical featured of them? So a deep dive into the literature is warranted here.
Next, the cryoEM data is pouring in to the PDB, so what we have access to now vs when this cluster first appeared has grown.
Next, in the literature you can find good reviews about podos and myos tails(and learn that the tail structures of siphos is a bit more elusive). We'll need to apply that to this.
Next, your are cherry-picking one gene is a very non-canonical place in the genome. Structural genes frequently hit heads and tails and until we can clearly determine what we have going on here, I recommend that we prudently wait on jumping the gun.
Finally, the same terminology doesn't always cross from sipho, myo and podo. So some thought will be required.
Keep us posted as you do your investigations.
debbie

Link to this post \| posted 28 Mar, 2023 20:04
uOttawaPHAGE	thanks Debbie. We will leave it NKF and I'll suggest the students see what they can learn from published work or if any of the foldseek matches are cryoEMs from a podo. I also suggested they see if some of the other T4 proteins (gp11?) is present in the genome. I was mainly struck by the alphafold/HHpred similarity, but it sounds like there is currently insufficient data to give it a specific call. Have you gotten similar questions from all annotators of this pham? Adam

Link to this post | posted 28 Mar, 2023 20:04

uOttawaPHAGE

thanks Debbie. We will leave it NKF and I'll suggest the students see what they can learn from published work or if any of the foldseek matches are cryoEMs from a podo. I also suggested they see if some of the other T4 proteins (gp11?) is present in the genome.

I was mainly struck by the alphafold/HHpred similarity, but it sounds like there is currently insufficient data to give it a specific call. Have you gotten similar questions from all annotators of this pham?

Adam

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