Link to this post | posted 14 Mar, 2019 01:39
debbie	Hari, Basically yes. However, when you add gene "11" in HarperAnne, add the gene only in that frame. If you add a gene that starts at 10 and ends at 11 it will be difficult to see where to slip it. (But if you know that coordinates of the slippage, it won't matter.) Then go back and chagen the start and add regions when you have it figured out. debbie

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.