SEA-PHAGES | Minor tail proteins far upstream of the tape measure protein?

Link to this post \| posted 19 Jul, 2021 23:21
fbaliraine	Genes 5, 6, and 7 of phage Mach and gp 6 in phage Duplo (as per current naming in phamerator before annotation) are showing synteny with minor tail proteins in phamerator, and also hitting minor tail proteins in phagesDb and NCBI (q1:s1, 99-100%). However, none of them have any significant hits to minor tail proteins in HHPred. I have tried checking the forum to see if anyone previously asked a specific question about minor tail proteins occurring this far upstream of the tape measure protein, but I have not seen such a direct question or answer in this regard. What I can see from previous posts is that minor tail proteins should typically come after the tape measure (downstream) or just before it (upstream) in some clusters. https://seaphages.org/forums/topic/4872/ and https://seaphages.org/forums/topic/4836/ The official functions list states that “If you have significant hits to either collagen-like or glycine-rich proteins, and are in the syntenic region of minor tail proteins, you can call them minor tail proteins.” But none of this is seen in HHPRED in phage Mach and Duplo. Of note, phages Mach and Duplo are Siphoviridae, and Siphoviridae genes are expected to occur in the following order: Terminase small subunit – Terminase large subunit – Portal – Protease – Capsid – Head-Tail Connectors/adaptors – Major Tail Subunit/major tail protein – Tail assembly Chaperones –Tape measure Protein – Minor Tail Proteins (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0069273). Thus, synteny, per this Pope et al. 2013 does not seem to support minor tail protein in this region (see pg 4 under “Virion structure and assembly genes” in this paper). I need to be sure whether something has changed since this article was published about 8 years ago. Based on the above, I am inclined to call them “NKF” rather than “minor tail proteins,” but since there are several hits to “minor tail proteins” in phagesDB as well as having synteny in phamerator, I am seeking the forum’s informed clarification. Below is a sample sequence, Mach gp 6, is anyone wants to cross-check by BLAST in phagesDB and HHPred: MANIGIVSDADTLVLWKGRDFKWSFENLDENRQPVDFPDGSLFIELQTGGEHNARQRVTITGATGGTYAFDILGETTPPIDYNDVSENPQGLPGDITEALEAAAGVGNVEVYPTLLQPSWILNFNLNSGKPLTEQLVNTINKTANDFFDTFEQLMGVDVSMTVTDALNFQLKVTSRRSFDEVGVVTFAVDVTGTAVKNFFNAVSGLVGAVNTVNVDFYWNRVYEIEFVGELANQPIEAILPDASNLTGYNPWITVEVIDLGKERLTIWPFIIDGTEATIKVESEEADLIPERTVWQLVFLPDGEPAGGDPITYGRVTRLGDZ I have also attached a searchable phamerator map for phage Mach that demostrates what I am seeing. Thanks! Fred Edited 19 Jul, 2021 23:34 1.05Mb

Link to this post | posted 19 Jul, 2021 23:21

Genes 5, 6, and 7 of phage Mach and gp 6 in phage Duplo (as per current naming in phamerator before annotation) are showing synteny with minor tail proteins in phamerator, and also hitting minor tail proteins in phagesDb and NCBI (q1:s1, 99-100%). However, none of them have any significant hits to minor tail proteins in HHPred. I have tried checking the forum to see if anyone previously asked a specific question about minor tail proteins occurring this far upstream of the tape measure protein, but I have not seen such a direct question or answer in this regard. What I can see from previous posts is that minor tail proteins should typically come after the tape measure (downstream) or just before it (upstream) in some clusters. https://seaphages.org/forums/topic/4872/ and https://seaphages.org/forums/topic/4836/

The official functions list states that “If you have significant hits to either collagen-like or glycine-rich proteins, and are in the syntenic region of minor tail proteins, you can call them minor tail proteins.” But none of this is seen in HHPRED in phage Mach and Duplo. Of note, phages Mach and Duplo are Siphoviridae, and Siphoviridae genes are expected to occur in the following order: Terminase small subunit – Terminase large subunit – Portal – Protease – Capsid – Head-Tail Connectors/adaptors – Major Tail Subunit/major tail protein – Tail assembly Chaperones –Tape measure Protein – Minor Tail Proteins (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0069273). Thus, synteny, per this Pope et al. 2013 does not seem to support minor tail protein in this region (see pg 4 under “Virion structure and assembly genes” in this paper).

I need to be sure whether something has changed since this article was published about 8 years ago. Based on the above, I am inclined to call them “NKF” rather than “minor tail proteins,” but since there are several hits to “minor tail proteins” in phagesDB as well as having synteny in phamerator, I am seeking the forum’s informed clarification.

Below is a sample sequence, Mach gp 6, is anyone wants to cross-check by BLAST in phagesDB and HHPred:
MANIGIVSDADTLVLWKGRDFKWSFENLDENRQPVDFPDGSLFIELQTGGEHNARQRVTITGATGGTYAFDILGETTPPIDYNDVSENPQGLPGDITEALEAAAGVGNVEVYPTLLQPSWILNFNLNSGKPLTEQLVNTINKTANDFFDTFEQLMGVDVSMTVTDALNFQLKVTSRRSFDEVGVVTFAVDVTGTAVKNFFNAVSGLVGAVNTVNVDFYWNRVYEIEFVGELANQPIEAILPDASNLTGYNPWITVEVIDLGKERLTIWPFIIDGTEATIKVESEEADLIPERTVWQLVFLPDGEPAGGDPITYGRVTRLGDZ

I have also attached a searchable phamerator map for phage Mach that demostrates what I am seeing.
Thanks!
Fred

Edited 19 Jul, 2021 23:34

Link to this post \| posted 20 Jul, 2021 14:44
debbie	Hi Fred, I HHPred'd Mach genes 5,6,7 (as found on phamerator). I would call all 3 as minor tail proteins. I used these 4 databases to search: PDB, PfamA, CDD, and Uni-Prot-Swiss Protein-viral. I did not use Scope. Because you are calling structural genes in cluster A, A2 in particular, I would want to be sure to not overwrite any historical data (that would include some bench work) that has been derived about well studied phages such as D29. When you include the HHPred results from the Uni-Prot database, you have significant hits to minor tail proteins. In addition, when you phamerator MaCh and Duplo together, gene 7 of MaCh hits gene 34 of Duplo, a much more canonical orientation for a minor tail protein. See what you think! debbie

Link to this post | posted 20 Jul, 2021 14:44

debbie

Hi Fred,
I HHPred'd Mach genes 5,6,7 (as found on phamerator). I would call all 3 as minor tail proteins.
I used these 4 databases to search: PDB, PfamA, CDD, and Uni-Prot-Swiss Protein-viral. I did not use Scope.
Because you are calling structural genes in cluster A, A2 in particular, I would want to be sure to not overwrite any historical data (that would include some bench work) that has been derived about well studied phages such as D29.
When you include the HHPred results from the Uni-Prot database, you have significant hits to minor tail proteins.
In addition, when you phamerator MaCh and Duplo together, gene 7 of MaCh hits gene 34 of Duplo, a much more canonical orientation for a minor tail protein.
See what you think!
debbie

Link to this post \| posted 21 Jul, 2021 22:21
fbaliraine	Hi Debbie, Thank you for helping put this to rest. We have been using PDB, PfamA, CDD, and Scope! We have not been including the Uni-Prot-Swiss Protein-viral database. Now when I exclude scope like you did and use Uni-Prot-Swiss Protein-viral, I can see hits in HHPred to minor tail proteins! Previously there was no significant hits to anything similar. Perhaps it might help to include the use of Uni-Prot-Swiss Protein-viral rather than or besides Scope in the resource guide for HHPred. Case closed! I will go ahead and name them minor tail proteins. Thanks again! Fred

Link to this post | posted 21 Jul, 2021 22:21

fbaliraine

Hi Debbie,
Thank you for helping put this to rest. We have been using PDB, PfamA, CDD, and Scope! We have not been including the Uni-Prot-Swiss Protein-viral database. Now when I exclude scope like you did and use Uni-Prot-Swiss Protein-viral, I can see hits in HHPred to minor tail proteins! Previously there was no significant hits to anything similar. Perhaps it might help to include the use of Uni-Prot-Swiss Protein-viral rather than or besides Scope in the resource guide for HHPred. Case closed! I will go ahead and name them minor tail proteins. Thanks again!
Fred

Link to this post \| posted 21 Jul, 2021 22:38
debbie	Fred, I am just learning about the Uni-Prot-Swiss Protein database, and all data there is not the same. I don't think i have had any significant data reported from Scope, which is why i started using Uni-Prot. I feel like i am beta testing it for now. Try it out and see what you find! debbie

Link to this post \| posted 27 Feb, 2024 18:02
rdejong	Like fbaliraine (Fred) we have a possible minor tail protein called very early (gene 4) in our phage that is called a minor tail protein in a similar gene (JFlix 2). Unlike the previous post, we have no correlation to any gene with any canonical orientation. We ended up calling this gene minor tail protein in Jflix2 last year, but not finding anything in our notes why - it may have occurred during the QC process. Guidance would be appreciated!

Link to this post | posted 27 Feb, 2024 18:02

rdejong

Like fbaliraine (Fred) we have a possible minor tail protein called very early (gene 4) in our phage that is called a minor tail protein in a similar gene (JFlix 2). Unlike the previous post, we have no correlation to any gene with any canonical orientation. We ended up calling this gene minor tail protein in Jflix2 last year, but not finding anything in our notes why - it may have occurred during the QC process. Guidance would be appreciated!

Link to this post \| posted 29 Feb, 2024 02:40
debbie	Check HHPred results. Yes, they are not in the typical synteny. Though it is not common, it is not uncommon. debbie

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Minor tail proteins far upstream of the tape measure protein?