SEA-PHAGES | Tail Assembly Chaperone

Link to this post \| posted 07 Mar, 2022 16:40
vbrownk	See attached image. I am having trouble convincing myself that Fresco_21 / Fresco_22 have the slippage/frameshift in the tail assembly chaperones, because a TGA stop happens too early in the 1st ORF(Fresco_21) making that frameshift at the - gggg - into the 2nd ORF(Fresco_22) unproductive. Both NHagos and Sour align well to Fresco_21 (frame 1) and Fresco_22 (frame 3 only), but that would require a 2-frame shift, and the only viable place I see for slippage (– gggg &ndash is downstream of the TGA. See attached image worth 1,000 poorly written words. Thoughts? -VBK 186Kb

Link to this post | posted 07 Mar, 2022 16:40

See attached image.
I am having trouble convincing myself that Fresco_21 / Fresco_22 have the slippage/frameshift in the tail assembly chaperones, because a TGA stop happens too early in the 1st ORF(Fresco_21) making that frameshift at the - gggg - into the 2nd ORF(Fresco_22) unproductive. Both NHagos and Sour align well to Fresco_21 (frame 1) and Fresco_22 (frame 3 only), but that would require a 2-frame shift, and the only viable place I see for slippage (– gggg &ndash smile

is downstream of the TGA. See attached image worth 1,000 poorly written words. smile

Thoughts?
-VBK

Link to this post \| posted 07 Mar, 2022 20:56
debbie	Hi Vicky, Here is my 2 cents. I don't think that gene 21 and 22 are tail assembly chaperones. Using the HHPred info in PECAAN. Gene 21 (16902 - 1722 hits the MuF-like protein that we don't quite understand and are currently calling it a Hypothetical Protein. Gene 22 (17225 - 17635) Significantly hits minor capsid genes, and tail genes. In particular it hits HK07-gp10. That phage was well studied at Pitt and those researchers did not know the function of gp10, so it too is a hypothetical protein, Gene 23 (17682-18221) DOES have a significant hit to a tail assembly chaperone (pfam hit). BUT it is in the right place, so I would consider it. This is my first pass on this. If you read the Cluster specific annotation tip on this subject, you can see others have struggled with this also. https://seaphages.org/forums/topic/5009/ Next step, please run all HHpred at HHPred. IGNORE ALL PREVIOUS SEA-PHAGES ANNOTATIONS. When this first of this Cluster (CloverMinnie and Sour) we thought the TAC HAD TO BE THERE. We now know that is not true. As you re-evaluate this, let me know if you need additional help. Good luck! debbie

Link to this post | posted 07 Mar, 2022 20:56

debbie

Hi Vicky,
Here is my 2 cents.
I don't think that gene 21 and 22 are tail assembly chaperones.
Using the HHPred info in PECAAN.
Gene 21 (16902 - 1722 smile

hits the MuF-like protein that we don't quite understand and are currently calling it a Hypothetical Protein.

Gene 22 (17225 - 17635) Significantly hits minor capsid genes, and tail genes. In particular it hits HK07-gp10. That phage was well studied at Pitt and those researchers did not know the function of gp10, so it too is a hypothetical protein,

Gene 23 (17682-18221) DOES have a significant hit to a tail assembly chaperone (pfam hit). BUT it is in the right place, so I would consider it.

This is my first pass on this. If you read the Cluster specific annotation tip on this subject, you can see others have struggled with this also.
https://seaphages.org/forums/topic/5009/

Next step, please run all HHpred at HHPred. IGNORE ALL PREVIOUS SEA-PHAGES ANNOTATIONS. When this first of this Cluster (CloverMinnie and Sour) we thought the TAC HAD TO BE THERE. We now know that is not true. As you re-evaluate this, let me know if you need additional help. Good luck!

debbie

Link to this post \| posted 11 Mar, 2022 20:22
vbrownk	Makes sense for Gene 21 For Gene 22 (17225 - 17635): PHAM 97251 has 367 non-draft genomes calling this as 'tail assembly chaperone' for this protein family, in various clusters, and the Phages Frequency Function, the NCBI blast… do we ignore that all to go with the HHPred? Because two HHPred hits down is: Phage_tail_S ; Phage virion morphogenesis family … Prob = 97.9, e-val is ).00048. I get that the 1st couple of annotations in DR cluster may need to be evaluated … but isn't this other evidence from the PHAM annotations in all those clusters also valid? I'm starting to doubt the hierarchy of what trumps what as far as gravid evidence (one HHPred hit versus a lot of non-HHPred data)… so sorry for these questions. Really love how responsive and helpful SEA-PHAGES P.I.s are! I'm on my own here, but not really because you all are so helpful. - VBK Gene 22 (17225 - 17635) Significantly hits minor capsid genes, and tail genes. In particular it hits HK07-gp10. That phage was well studied at Pitt and those researchers did not know the function of gp10, so it too is a hypothetical protein, Gene 23 (17682-18221) DOES have a significant hit to a tail assembly chaperone (pfam hit). BUT it is in the right place, so I would consider it. This is my first pass on this. If you read the Cluster specific annotation tip on this subject, you can see others have struggled with this also. https://seaphages.org/forums/topic/5009/ Next step, please run all HHpred at HHPred. IGNORE ALL PREVIOUS SEA-PHAGES ANNOTATIONS. When this first of this Cluster (CloverMinnie and Sour) we thought the TAC HAD TO BE THERE. We now know that is not true. As you re-evaluate this, let me know if you need additional help. Good luck! debbie

Link to this post | posted 11 Mar, 2022 20:22

vbrownk

Makes sense for Gene 21
For Gene 22 (17225 - 17635): PHAM 97251 has 367 non-draft genomes calling this as 'tail assembly chaperone' for this protein family, in various clusters, and the Phages Frequency Function, the NCBI blast… do we ignore that all to go with the HHPred? Because two HHPred hits down is: Phage_tail_S ; Phage virion morphogenesis family … Prob = 97.9, e-val is ).00048. I get that the 1st couple of annotations in DR cluster may need to be evaluated … but isn't this other evidence from the PHAM annotations in all those clusters also valid? I'm starting to doubt the hierarchy of what trumps what as far as gravid evidence (one HHPred hit versus a lot of non-HHPred data)… so sorry for these questions. Really love how responsive and helpful SEA-PHAGES P.I.s are! I'm on my own here, but not really because you all are so helpful. smile

- VBK

Gene 22 (17225 - 17635) Significantly hits minor capsid genes, and tail genes. In particular it hits HK07-gp10. That phage was well studied at Pitt and those researchers did not know the function of gp10, so it too is a hypothetical protein,

Gene 23 (17682-18221) DOES have a significant hit to a tail assembly chaperone (pfam hit). BUT it is in the right place, so I would consider it.

This is my first pass on this. If you read the Cluster specific annotation tip on this subject, you can see others have struggled with this also.
https://seaphages.org/forums/topic/5009/

Next step, please run all HHpred at HHPred. IGNORE ALL PREVIOUS SEA-PHAGES ANNOTATIONS. When this first of this Cluster (CloverMinnie and Sour) we thought the TAC HAD TO BE THERE. We now know that is not true. As you re-evaluate this, let me know if you need additional help. Good luck!

debbie

Link to this post \| posted 11 Mar, 2022 20:22
vbrownk	Makes sense for Gene 21 For Gene 22 (17225 - 17635): PHAM 97251 has 367 non-draft genomes calling this as 'tail assembly chaperone' for this protein family, in various clusters, and the Phages Frequency Function, the NCBI blast… do we ignore that all to go with the HHPred? Because two HHPred hits down is: Phage_tail_S ; Phage virion morphogenesis family … Prob = 97.9, e-val is ).00048. I get that the 1st couple of annotations in DR cluster may need to be evaluated … but isn't this other evidence from the PHAM annotations in all those clusters also valid? I'm starting to doubt the hierarchy of what trumps what as far as gravid evidence (one HHPred hit versus a lot of non-HHPred data)… so sorry for these questions. Really love how responsive and helpful SEA-PHAGES P.I.s are! I'm on my own here, but not really because you all are so helpful. - VBK Gene 22 (17225 - 17635) Significantly hits minor capsid genes, and tail genes. In particular it hits HK07-gp10. That phage was well studied at Pitt and those researchers did not know the function of gp10, so it too is a hypothetical protein, Gene 23 (17682-18221) DOES have a significant hit to a tail assembly chaperone (pfam hit). BUT it is in the right place, so I would consider it. This is my first pass on this. If you read the Cluster specific annotation tip on this subject, you can see others have struggled with this also. https://seaphages.org/forums/topic/5009/ Next step, please run all HHpred at HHPred. IGNORE ALL PREVIOUS SEA-PHAGES ANNOTATIONS. When this first of this Cluster (CloverMinnie and Sour) we thought the TAC HAD TO BE THERE. We now know that is not true. As you re-evaluate this, let me know if you need additional help. Good luck! debbie

Link to this post | posted 11 Mar, 2022 20:22

vbrownk

Link to this post \| posted 15 Mar, 2022 13:23
debbie	Vicky, Yes, the hierarchy of what to believe is convoluted. We got tail assembly chaperone calls wrong in this cluster. So Blast data - whether at ncbi or phagesdb - will just regurgitate what we got wrong. BUT, if we got it correct, it would be a good source of info. We are steadily working at correcting the 'wrongs', but it just takes time. debbie

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Tail Assembly Chaperone