SEA-PHAGES | Head-tail connectors

Link to this post \| posted 04 Feb, 2018 19:08
delesall	First, sharing/repeating instructions from Welkin "We have been reviewing our functional assignments for the head-to-tail connector proteins due to some feedback we've received from a reviewer. We've decided to proceed in two ways: 1) We will not use the functional assignment "head-to-tail connector" anymore. Instead we will be switching to "head-to-tail connector complex protein". 2) Only genes that have HHPred alignments to crystal structures (so must be a PDB hit) to a known connector complex protein can be assigned this function. This includes phage SPP1 genes 15 and 16; phage HK97 gene 6, and Bacillus protein yqbG." So, I'm looking at Gordonia phage Eviarto (CZ1), I've got HHPred alignments with PDB support for genes 8 and 9, but not PDB support for gene 10. However, that gene has nice matches to minor capsid protein. So, call minor capsid?

Link to this post | posted 04 Feb, 2018 19:08

First, sharing/repeating instructions from Welkin

"We have been reviewing our functional assignments for the head-to-tail connector proteins due to some feedback we've received from a reviewer. We've decided to proceed in two ways:
1) We will not use the functional assignment "head-to-tail connector" anymore. Instead we will be switching to "head-to-tail connector complex protein".
2) Only genes that have HHPred alignments to crystal structures (so must be a PDB hit) to a known connector complex protein can be assigned this function. This includes phage SPP1 genes 15 and 16; phage HK97 gene 6, and Bacillus protein yqbG."

So, I'm looking at Gordonia phage Eviarto (CZ1), I've got HHPred alignments with PDB support for genes 8 and 9, but not PDB support for gene 10. However, that gene has nice matches to minor capsid protein. So, call minor capsid?

Link to this post \| posted 08 Feb, 2018 18:33
QUPhage	Hi Veronique, Quick question regarding points one and two. Our phage's gene 9 function would not qualify for option two. Blast functions are listing either head-to-tail connector proteins or NKF. When checking HHpred Head-to-tail connector is called with Pfam, but not PDB. The other HHpred functions don't correspond to the blast results. Phamerator also shows 100% alignment with a head-to-tail connector protein. In this situation do we assign NKF even though we have ample support in assigning head-to-tail connector function.

Link to this post | posted 08 Feb, 2018 18:33

QUPhage

Hi Veronique,

Quick question regarding points one and two. Our phage's gene 9 function would not qualify for option two. Blast functions are listing either head-to-tail connector proteins or NKF. When checking HHpred Head-to-tail connector is called with Pfam, but not PDB. The other HHpred functions don't correspond to the blast results. Phamerator also shows 100% alignment with a head-to-tail connector protein. In this situation do we assign NKF even though we have ample support in assigning head-to-tail connector function.

Link to this post \| posted 08 Feb, 2018 20:29
delesall	Yes - the word from Pitt is that we need crystal structures data to call the HT connector complex protein. This is a change from what we did previously.

Link to this post \| posted 17 Apr, 2018 15:14
shockran	We are having a similar issue with two of our genes with not having HHPred results. Would we now call the genes called head to tail connector proteins initially and do not have HHPred results, NKF? We also have two other genes called head to tail connector protein. Although, with the new approved function list, the portal protein is used for Head to Tail connector but is only called by HHPred but not by blast and synteny so is it assumed that we use portal protein or also call this NKF beings blast and synteny call Head to Tail connector?

Link to this post | posted 17 Apr, 2018 15:14

shockran

We are having a similar issue with two of our genes with not having HHPred results. Would we now call the genes called head to tail connector proteins initially and do not have HHPred results, NKF? We also have two other genes called head to tail connector protein. Although, with the new approved function list, the portal protein is used for Head to Tail connector but is only called by HHPred but not by blast and synteny so is it assumed that we use portal protein or also call this NKF beings blast and synteny call Head to Tail connector?

Link to this post \| posted 17 Apr, 2018 15:31
delesall	If in the HHPred alignments, there is no match with a PDB file, then yes NKF is the proper call. I am not sure what you are asking about the portal…

Link to this post \| posted 17 Apr, 2018 18:48
welkin	I think there are several issues here. some misguided phage biologists call the portal protein a "head to tail connector". The portal is not a head to tail connector. There are other smaller proteins that make a complex that binds to the portal and bottom of the capsid in the "neck" region; and these proteins we call the "head-to-tail connector complex" proteins. There are several different ones and we are using a catch-all term for now to address them. However, in some of the crystal structure papers, the portal has been crystallized with several of the head-to-tail connector complex proteins in a big complex. When you align a true httcc protein with HHPred to the PDB, you may retrieve these records, which may include a portal. This can be confusing, because it looks like your result is a portal. it isn't. So: 1) if you already have a portal upstream of the terminase, that's your portal. you don't have another one. 2) you have to have a crystal structure alignment with HHPred to use the term "head-to-tail connector complex". We have changed our criteria for this assignment in the past year, so the database is currently riddled with genes that do not meet this criteria, and need to be corrected. BLAST on phagesdb is not enough, because we know there are things in there that are not correct and need to be fixed.

Link to this post | posted 17 Apr, 2018 18:48

welkin

I think there are several issues here.
some misguided phage biologists call the portal protein a "head to tail connector". The portal is not a head to tail connector.
There are other smaller proteins that make a complex that binds to the portal and bottom of the capsid in the "neck" region; and these proteins we call the "head-to-tail connector complex" proteins. There are several different ones and we are using a catch-all term for now to address them.

However, in some of the crystal structure papers, the portal has been crystallized with several of the head-to-tail connector complex proteins in a big complex. When you align a true httcc protein with HHPred to the PDB, you may retrieve these records, which may include a portal. This can be confusing, because it looks like your result is a portal. it isn't.

So:
1) if you already have a portal upstream of the terminase, that's your portal. you don't have another one.
2) you have to have a crystal structure alignment with HHPred to use the term "head-to-tail connector complex". We have changed our criteria for this assignment in the past year, so the database is currently riddled with genes that do not meet this criteria, and need to be corrected. BLAST on phagesdb is not enough, because we know there are things in there that are not correct and need to be fixed.

Link to this post \| posted 25 Jul, 2018 15:10
smichael	What should we call proteins that have Blast (either phagesdb or NCBI) evidence for head-to-tail connector complex, but do not have HHPRED evidence?

Link to this post \| posted 25 Jul, 2018 16:37
debbie	I am not sure exactly how to answer this without seeing data. Know that we made a decision about 1 1/2 years ago, to call every small gene between the major capsid and the major tail a -head-to-tail connector protein. Those calls should be ignored without HHPred info. If your BLAST hits our phages, you should be able to tell the difference because when we were calling 'everything', the label was "head-to-tail connector". Once we made the change we are labeling true hits to head-to-tail proteins "head-to-tail connector complex proteins". I hope that helps. it is a bit confusing. debbie

Link to this post | posted 25 Jul, 2018 16:37

debbie

I am not sure exactly how to answer this without seeing data. Know that we made a decision about 1 1/2 years ago, to call every small gene between the major capsid and the major tail a -head-to-tail connector protein. Those calls should be ignored without HHPred info.

If your BLAST hits our phages, you should be able to tell the difference because when we were calling 'everything', the label was "head-to-tail connector". Once we made the change we are labeling true hits to head-to-tail proteins "head-to-tail connector complex proteins".

I hope that helps. it is a bit confusing.
debbie

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