SEA-PHAGES | head tail connector synteny in Gordonia cluster DJ

head tail connector synteny in Gordonia cluster DJ

Link to this post \| posted 28 Jun, 2018 00:51
anders	A gene next to lysinA and holin has been annotated as head-to-tail connector complex protein in the singleton Camille (gene 8 ) and Gordonia DJ phages Kerry (gene 11) and Gravy (gene 11). 33 other pham members have been annotated NKF, and one as structural protein. Two things make me wonder about the evidence for this function, abnormal synteny and a small fraction of the protein matching by HHPred. 1. In DJ genomes, this gene is not in-between capsid and major tail genes, as they usually are. It is upstream of capsid and is downstream of lysinA and holin. Is this a feature of Gordonia phages? 2. When I look at the HHPred evidence, I only see two alpha helices in these proteins matching to gp6 of HK97, which is a small fraction of the DJ protein and a small fraction of gp6-HK97. HHPred predictions are 40-75%, less than 90%. I have attached some screenshots of the HHPred output and the region of gp6 on PDB. Are there other pieces of evidence that makes this function call stronger? Edited 28 Jun, 2018 00:52 242Kb

Link to this post | posted 28 Jun, 2018 00:51

A gene next to lysinA and holin has been annotated as head-to-tail connector complex protein in the singleton Camille (gene 8 ) and Gordonia DJ phages Kerry (gene 11) and Gravy (gene 11). 33 other pham members have been annotated NKF, and one as structural protein.

Two things make me wonder about the evidence for this function, abnormal synteny and a small fraction of the protein matching by HHPred.

1. In DJ genomes, this gene is not in-between capsid and major tail genes, as they usually are. It is upstream of capsid and is downstream of lysinA and holin. Is this a feature of Gordonia phages?

2. When I look at the HHPred evidence, I only see two alpha helices in these proteins matching to gp6 of HK97, which is a small fraction of the DJ protein and a small fraction of gp6-HK97. HHPred predictions are 40-75%, less than 90%. I have attached some screenshots of the HHPred output and the region of gp6 on PDB.

Are there other pieces of evidence that makes this function call stronger?

Edited 28 Jun, 2018 00:52

Link to this post \| posted 28 Jun, 2018 12:29
welkin	Not that I am aware. I think this one should be NKF. good catch Kirk!

Link to this post \| posted 28 Jun, 2018 17:41
anders	thanks, Welkin. I will post an annotation tip in Cluster DJ.

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head tail connector synteny in Gordonia cluster DJ