SEA-PHAGES | Another minor tail protein in F1 phage DoRead?

Link to this post \| posted yesterday, 18:24
fbaliraine	Is draft feature 23 of DoRead at position 23627-24265 bp (639 bp long), a minor tail protein? Its aa sequence is: MAYDKQAWQNAPSTETPLSAGALNHMEDGIADAHTLAESKADSEHTHVLADVTDVVASAGEVNVLAGATVSTGELNTLDGVTSNVQTQLDGKAASSHNHSAANVTSGTLDIARIPVGNSGSTVCVGNDSRLSDQRVPVDGSVSSAKIASGSITNTHVSPSAAIAASKMSTGVQASLTKADGSVQKSGTAEGMWMGTTLPGTGTAGVLYVVVPZ Minor tail proteins are typically the 5 big genes (at least1000 bp long) downstream the tape measure…"There are usually not more than 5" (https://genomicsguide.seaphages.org/). We have already identified the other minor tail proteins. We have previously called this NKF, though there are some hits to minor tail proteins in some phages. But I notice a recent deposit in HHPred by Freeman K.G. et al, and this is the is the only significant hit in HHpred, hitting “Minor tail protein; Bacteriophage, tail tip” of Mycobacterium phage Bxb1 with 99.11% probability. Its PDB description at https://www.rcsb.org/structure/9D93 I wanted to cross-check before making the final call. Thanks! Fred Edited yesterday, 20:30 119Kb

Link to this post | posted yesterday, 18:24

Is draft feature 23 of DoRead at position 23627-24265 bp (639 bp long), a minor tail protein? Its aa sequence is:
MAYDKQAWQNAPSTETPLSAGALNHMEDGIADAHTLAESKADSEHTHVLADVTDVVASAGEVNVLAGATVSTGELNTLDGVTSNVQTQLDGKAASSHNHSAANVTSGTLDIARIPVGNSGSTVCVGNDSRLSDQRVPVDGSVSSAKIASGSITNTHVSPSAAIAASKMSTGVQASLTKADGSVQKSGTAEGMWMGTTLPGTGTAGVLYVVVPZ

Minor tail proteins are typically the 5 big genes (at least1000 bp long) downstream the tape measure…"There are usually not more than 5" (https://genomicsguide.seaphages.org/). We have already identified the other minor tail proteins.
We have previously called this NKF, though there are some hits to minor tail proteins in some phages. But I notice a recent deposit in HHPred by Freeman K.G. et al, and this is the is the only significant hit in HHpred, hitting “Minor tail protein; Bacteriophage, tail tip” of Mycobacterium phage Bxb1 with 99.11% probability. Its PDB description at
https://www.rcsb.org/structure/9D93

I wanted to cross-check before making the final call.
Thanks!
Fred

Edited yesterday, 20:30

Link to this post \| posted yesterday, 20:27
debbie	Hi Fred, First, I believe the title of this inquiry is misplaced. There has never been a 5-rule cutoff. The text uses the word "typically" in the description, so, if you don't mind, I am going to change the title of this post. Next, your genome investigations are hitting the excellent work of Krista Freeman from the Hatfull Lab (soon to have her own lab at Case Western), where she has identified the various tail parts found in Mycobacterium phage Bxb1. Final revisions were accepted yesterday so we will have a paper(in Cell) to reference soon. The PDB for the structural proteins of Bxb1, but needs some tidying up. In the meantime, Here a bit of information to help guide: The tail tip project is PDB 9D93. (There are more projects for the tail tube and the capsid of Bxb1. TBD) 9D93_L: (A, B, C, D, E) is related to tail tube. This particular hit is hitting a small portion of a decoration domain of the tail tube, but NOT the important part of that decoration of the tail tube. Therefore, please call this one a Hypothetical Protein. However, the next gene, gp 24, stop at 25086, IS a hit to Bxb1's tail genes it hits Bxb1_gp34, the "tail wing brush". This is part of the PDB project 9D93_Q. Please use that terminology when calling this protein. And if you hit PDB project 9D93_J, you are hitting part of the tail tube (which we have historically called the major tail protein). More to come. The alpha-fold-chimera X views of all of this is extremely informative. Edited yesterday, 20:31

Link to this post | posted yesterday, 20:27

debbie

Hi Fred,
First, I believe the title of this inquiry is misplaced. There has never been a 5-rule cutoff. The text uses the word "typically" in the description, so, if you don't mind, I am going to change the title of this post.

Next, your genome investigations are hitting the excellent work of Krista Freeman from the Hatfull Lab (soon to have her own lab at Case Western), where she has identified the various tail parts found in Mycobacterium phage Bxb1. Final revisions were accepted yesterday so we will have a paper(in Cell) to reference soon.
The PDB for the structural proteins of Bxb1, but needs some tidying up. In the meantime, Here a bit of information to help guide:
The tail tip project is PDB 9D93. (There are more projects for the tail tube and the capsid of Bxb1. TBD)
9D93_L: (A, B, C, D, E) is related to tail tube.
This particular hit is hitting a small portion of a decoration domain of the tail tube, but NOT the important part of that decoration of the tail tube. Therefore, please call this one a Hypothetical Protein.
However, the next gene, gp 24, stop at 25086, IS a hit to Bxb1's tail genes it hits Bxb1_gp34, the "tail wing brush". This is part of the PDB project 9D93_Q. Please use that terminology when calling this protein.
And if you hit PDB project 9D93_J, you are hitting part of the tail tube (which we have historically called the major tail protein). More to come.

The alpha-fold-chimera X views of all of this is extremely informative.

Edited yesterday, 20:31

Link to this post \| posted yesterday, 20:36
fbaliraine	Thank you Debbie for the clarification and congratulations to Krista and the entire Hatfull lab on the new paper in Cell!

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Another minor tail protein in F1 phage DoRead?