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

Link to this post | posted 20 Feb, 2019 17:05

debbie

Hi all, I can weigh in on this. In the papers that we wrote about Cluster O, J, and M, we did some mass spec. The data showed that where there were 2 starts in a row, no methionine was present in that mass spec data. The interpretation of that is likely that post-translational chopping of the initiation methionine occurred. (So there could only be one present to chop.) I just scanned the papers to see if we wrote that in one of them but couldn't find it. So by all means take a look to see if it is there. But that is why we suggest that the second start codon (1 base overlap) be called. It is hard to do, when you are progammed (like me) to look for the 4-base pair overlap and all other data - usually the SD score - points to the first start codon as the better call. But you can do it! It also was not done on lots of files and it is difficult to pinpoint to fix.

Link to this post | posted 11 Feb, 2019 22:12
debbie	I believe that GeneMark is now working! Back in business! debbie

Link to this post | posted 11 Feb, 2019 11:20
debbie	Dana, Hi. I believe that the issue is a licensing issue that we need to do on our end. It should be fixed later today. debbie

Link to this post | posted 05 Feb, 2019 20:00
debbie	Rick, You are right, because Emporer and the prophage in G. westfalica are identical sequences, the Emporer hit is buried. Check out the alignment, you will see +2 more titles. You will find Emporer there.

Link to this post | posted 05 Feb, 2019 17:53
debbie	Rick, I believe the simple explanation is that the BLASTp database(s) have not incorporated the Emperor submission yet. Which, I agree seems odd.