SEA-PHAGES | 2015 Functional Call List - Tail Protein Functional Calls

Link to this post \| posted 14 Apr, 2016 15:53
GregFrederick@letu.edu	We are trying to finish up our final annotation files. We just noted the following: 1. Minor Tail Protein - identified 2. Tail Sheath Protein - identified 3. Third tail protein - every homolog lists only "tail protein". Pham 17521 We assume this third protein is the "Major Tail Protein" which simply must not have been called in any recent sub-cluster A6 phages yet. Should we list its function as such? Or should we follow the existing pattern in the database, and ignore the 2015 Functional Name List? Is there a "Best Practice" approach to addressing this? Ideas?

Link to this post | posted 14 Apr, 2016 15:53

We are trying to finish up our final annotation files. We just noted the following:

1. Minor Tail Protein - identified
2. Tail Sheath Protein - identified
3. Third tail protein - every homolog lists only "tail protein". Pham 17521

We assume this third protein is the "Major Tail Protein" which simply must not have been called in any recent sub-cluster A6 phages yet. Should we list its function as such? Or should we follow the existing pattern in the database, and ignore the 2015 Functional Name List?

Is there a "Best Practice" approach to addressing this? Ideas?

Link to this post \| posted 22 Apr, 2016 18:22
debbie	Greg, I assume you are speaking of the Cluster A6 mycobacteriophage WonderPhul, gp6. I don't think it is the major tail protein. I believe that gp26, pham 19254 is the major tail protein. In addition, Cluster A6 phages are siphoviridae, and I don't believe they have a tail sheath. I am not sure what you are calling there. Mycobacteriophages can have many minor tail genes, so calling more than one if you have evidence is predictable. When I HHPred gp 6 (pham 17521), the best hits are to collagen. Phages won't have collagen, but this protein is aligning with collagen because of the GPX motif that is present. We are assuming that has to be a minor tail protein. Prudently, I would not assign a function. But as you can see others have.

Link to this post | posted 22 Apr, 2016 18:22

debbie

Greg,
I assume you are speaking of the Cluster A6 mycobacteriophage WonderPhul, gp6. I don't think it is the major tail protein. I believe that gp26, pham 19254 is the major tail protein. In addition, Cluster A6 phages are siphoviridae, and I don't believe they have a tail sheath. I am not sure what you are calling there. Mycobacteriophages can have many minor tail genes, so calling more than one if you have evidence is predictable.

When I HHPred gp 6 (pham 17521), the best hits are to collagen. Phages won't have collagen, but this protein is aligning with collagen because of the GPX motif that is present. We are assuming that has to be a minor tail protein. Prudently, I would not assign a function. But as you can see others have.

Link to this post \| posted 05 Mar, 2019 03:21
scaruso	A follow up on this old post, if you don't mind. There is a recent post in the Cluster Specific Tips that continues this conversation. See: Forum Home / Science / Cluster-Specific Annotation Tips / Cluster A Annotation Tips / minor tail proteins Welkin Pope posted 03 Apr, 2018 14:11 "Unlike many other clusters, the Cluster A phages have some minor tail proteins at the left end of their genome, upstream of the lysins and terminase genes (around gene 4-6ish). You can recognize these proteins due to their size. Some of them may have structural motifs that suggest long, extended proteins, like collagen-repeats, or coiled-coils." So I would like to get a little feedback if I can. Heather gp18 (a BB2) has BlastP hits to lots of "minor tail protein" calls, as well as some "tail fiber" and other similar calls. But I don't think they are justified. HHPred actually hits to collagen, not to any identified tail proteins. I think it's a rabbit hole. And then there's: The Collagen-like Protein gp12 Is a Temperature-dependent Reversible Binder of SPP1 Viral Capsids. Mohamed Zairi, Asita C. Stiege, Naima Nhiri, Eric Jacquet, and Paulo Tavares http://www.jbc.org/content/289/39/27169.full Which shows that these hits might be for other structural components, like parts of the capsid. My inclination is to leave it NKF, unless I am missing something. Any thoughts? >Heather_gp18 MTQPVETFPLPPSIETVKVHGHYRGPDGRGLQGTVTFTGPGLLTFPDADLFIAGPVVARLDEFGAFEVTLPATDNEGMNPSDWSYTVKENL TGVTGARTFALLLPKDTAEIDLADVAPADPLTPNYVPVPGPQGEPGPQGVKGDPGATGPAGANGAPGAPGAAGAPGVIQSVNGKSAASVTL VPADLGAVPTSDKGVANGVASLGADGKVPAGQLPATSNAVTSVNTKTGAVVLSASDVSAVPTSDKGAANGVATLDASTKVPTAQIPSLTST YVAVSTRGAANGVATLDGTTRLPVAQVPATLPKNTWTPQALGFQAWSCDPGGVANPGAKYLTPQRLYMTGFNITEPTTVSNVVMFARGYGG VGTNRYMAGIYKEDGTRVVASAAVALSMAGQESGALPGMVTNHIGAVPLPITSTTLQPGRYWVAWVLTVGAASDFAFYHVQNEAPVSTANF FMPTTPFARAWYLAGQSTLPTTVSQTAAGVLADHDIPIVALA Edited 05 Mar, 2019 03:24

Link to this post | posted 05 Mar, 2019 03:21

scaruso

A follow up on this old post, if you don't mind.

There is a recent post in the Cluster Specific Tips that continues this conversation.
See: Forum Home / Science / Cluster-Specific Annotation Tips / Cluster A Annotation Tips / minor tail proteins

Welkin Pope posted 03 Apr, 2018 14:11
"Unlike many other clusters, the Cluster A phages have *some* minor tail proteins at the
left end of their genome, upstream of the lysins and terminase genes (around gene 4-6ish).
You can recognize these proteins due to their size. Some of them may have structural motifs
that suggest long, extended proteins, like collagen-repeats, or coiled-coils."

So I would like to get a little feedback if I can. Heather gp18 (a BB2) has BlastP hits to lots
of "minor tail protein" calls, as well as some "tail fiber" and other similar calls. But I don't
think they are justified. HHPred actually hits to collagen, not to any identified tail proteins.
I think it's a rabbit hole. And then there's:

The Collagen-like Protein gp12 Is a Temperature-dependent Reversible Binder of SPP1 Viral
Capsids. Mohamed Zairi, Asita C. Stiege, Naima Nhiri, Eric Jacquet, and Paulo Tavares
http://www.jbc.org/content/289/39/27169.full

Which shows that these hits might be for other structural components, like parts of the
capsid. My inclination is to leave it NKF, unless I am missing something. Any thoughts?

>Heather_gp18
MTQPVETFPLPPSIETVKVHGHYRGPDGRGLQGTVTFTGPGLLTFPDADLFIAGPVVARLDEFGAFEVTLPATDNEGMNPSDWSYTVKENL
TGVTGARTFALLLPKDTAEIDLADVAPADPLTPNYVPVPGPQGEPGPQGVKGDPGATGPAGANGAPGAPGAAGAPGVIQSVNGKSAASVTL
VPADLGAVPTSDKGVANGVASLGADGKVPAGQLPATSNAVTSVNTKTGAVVLSASDVSAVPTSDKGAANGVATLDASTKVPTAQIPSLTST
YVAVSTRGAANGVATLDGTTRLPVAQVPATLPKNTWTPQALGFQAWSCDPGGVANPGAKYLTPQRLYMTGFNITEPTTVSNVVMFARGYGG
VGTNRYMAGIYKEDGTRVVASAAVALSMAGQESGALPGMVTNHIGAVPLPITSTTLQPGRYWVAWVLTVGAASDFAFYHVQNEAPVSTANF
FMPTTPFARAWYLAGQSTLPTTVSQTAAGVLADHDIPIVALA

Edited 05 Mar, 2019 03:24

Link to this post \| posted 05 Mar, 2019 19:06
debbie	Steve, Most minor tail proteins are called by synteny. Sometimes there is no HHPred info to support the call. It is common to call the 4-5 genes "big" downstream of the tape measure "minor tail proteins". In addition, I think the phage genes that hit collagen are commonly minor tail proteins. So there has to be some similarity in the protein structure, but I don't know what that is. I would easily call Heather_gp18 a minor tail protein.

Link to this post | posted 05 Mar, 2019 19:06

debbie

Steve,
Most minor tail proteins are called by synteny. Sometimes there is no HHPred info to support the call. It is common to call the 4-5 genes "big" downstream of the tape measure "minor tail proteins". In addition, I think the phage genes that hit collagen are commonly minor tail proteins. So there has to be some similarity in the protein structure, but I don't know what that is. I would easily call Heather_gp18 a minor tail protein.

Link to this post \| posted 05 Mar, 2019 19:12
scaruso	Excellent. That's very helpful. Thank you! Steve

Link to this post \| posted 05 Mar, 2019 20:43
lhughes	Most of the members of that phamily are called that way now. Steve, I don't know if your original BLAST analysis included the more recent BB1 and BB2 phages since most of those just went live within the last month, but they are updated in Phamerator now. (PECAAN doesn't update automatically unless you ask it to rerun the analysis). Lee

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2015 Functional Call List - Tail Protein Functional Calls