Link to this post | posted 12 Mar, 2019 17:07
debbie	Claire, It works! Thanks, debbie

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 01 Mar, 2019 22:15
debbie	I think Ry Young (from Texas A&M) has papers written about multiple holins in the phages that he studies. It is just hard to know if a membrane protein is a holin. and if a pfam hit to holin is believable.

Link to this post | posted 26 Feb, 2019 21:27
debbie	Cathy, The owner of the file got hacked which is where that google sheet resided. I just learned of this today, so I am going to need some time to see if this attached list matches what was posted. In the meantime, here is the list I have. 49Kb

Link to this post | posted 26 Feb, 2019 18:04
debbie	Roy, I think this is the same question as yours. https://seaphages.org/forums/topic/4858/ debbie

Link to this post | posted 26 Feb, 2019 16:22
debbie	Answers are here! https://seaphages.org/forums/topic/4858/

Link to this post | posted 25 Feb, 2019 23:24

debbie

This refers specifically to BubbaBear_gp56. A question posed by Dr. Herren (Kansas State U): Isn't this a dihydrofolate reductase rather than a thymidylate synthase. First I scanned this website http://www.ebi.ac.uk/interpro/entry/IPR012262 From this I learned that they often come together. However, when both parts are there, I think it is a much larger protein, with PDB citing residues of 159-384 for the DR crystal structure and 1042 – 2084 residues for the TS structure. It looks like this is aligning with the DR domains and not the TS. So I would call BubbaBear gp 56 a "dihydrofolate reductase"!

Link to this post | posted 25 Feb, 2019 23:00

debbie

Instead , its function can be denoted as “HTH DNA binding protein, MerR-like”. The folks at LeTourneau University did not agree with the funcitonal assignemnt of "peptidase" to Glaske gp65 (coordinates:43072 to 43974). According to Dr. Frederick, Fred Ballraine and students did some investigating. "Thirty one of the 103 hits above 90% probability reference “MerR”. We find nothing in the HHPred results referencing a “peptidase” function or domain. However, there are five references to peptidase function in the NCBI Blast results. All are phages. While I did not dig deeper, most are ours. The first hit “Babsiella” lists the two of you, Dan and Graham as authors on the GenBank submission (201. So I suspect we are missing some evidence you all saw. A local BlastP on PhagesDB with Glaske gp65 hits 16 of our SEA phages identifying the function of this proteins as a “peptidase”. Since HHPred does not reference “peptidase” once for any of the hits and since an NCBI BlastP does not reference any other than our phages and a few other phages, I suggest that someone jumped at the “peptidase” function for this gene. Then once it was in the database and on the “Official Function List” everyone started to “Band-wagon” as one of my student’s likes to put it. We are going to list the function as “HTH DNA binding protein, MerR-like”. Edited 25 Feb, 2019 23:02

Link to this post | posted 25 Feb, 2019 22:38
debbie	Some Cluster EA phages have a tRNA. Right now (2-14-19); it looks like the the Clusters EA3 and EA4 have one.

Link to this post | posted 25 Feb, 2019 22:26
debbie	Susan, Excellent question! I think those tRNAs are missed in Golden and Koji. I will be making some edits soon. Good catch! debbie