Link to this post | posted 11 Apr, 2019 18:16

GregFrederick@letu.edu

I believe gp2 has both ATPase and endonuclease functions. I am running to a full afternoon of classes. So I will have to check after. The top three hits for gp68 (that in question) range in 18-28% coverage. So they may be hitting domains within these other distally related terminase proteins (and not ours)? Those hits are here to make it easier for you to take a look. Thanks. 1. https://www.rcsb.org/structure/5OE8 2. http://pfam.xfam.org/family/PF04466.13#tabview=tab0 3. https://www.rcsb.org/structure/4ZNK The actual HHPred report is here: https://toolkit.tuebingen.mpg.de/#/jobs/Phalm68 Thanks again. Greg

Link to this post | posted 11 Apr, 2019 17:53
GregFrederick@letu.edu	Super! This makes perfect sense now. I saw the "homohexamer" in the description. I had not stopped to ponder that one monomer would be designated "A" and another "B" and so on…. Thanks for your help on this! Greg Edited 11 Apr, 2019 17:57

Link to this post | posted 11 Apr, 2019 15:31

GregFrederick@letu.edu

Welkin and or Debbie. We are looking at this closely since we are annotating seven phages all in the same subcluster. We are trying to avoid setting incorrect precedent. So thanks in advance for help with this call. The gene in questions is gp13 in Megiddo. The amino acid sequence is here in case you wish to rerun the analysis: Megiddo gp13>> MIELLDREAPPDIRFLRAWLLPVGGGVGAKRETGDPFPFTLIQKFDGWENSHTQYGFYQFDHLAVAADGKSAYTACEDYARTIKRRMLYLRDRPWTEVTVPGWGVATADVVRCTASPRHDPYNNTDVERFIARYSVHLRLVSVASZ The HHPred analysis will be here for another week or so: https://toolkit.tuebingen.mpg.de/#/jobs/4365093 A top HHPred hit includes: https://www.rcsb.org/structure/3FZ2 RCSB PDB - 3FZ2: Crystal structure of the tail terminator protein from phage lambda (gpU-D74A) www.rcsb.org The X-ray crystal structure of the phage lambda tail terminator protein reveals the biologically relevant hexameric ring structure and demonstrates a conserved mechanism of tail termination among diverse long-tailed phages. The Official Function List states that the Tail terminator “must have an HHPRED alignment to one of the following: SPP1 17 (5A21 chain G in the macromolecular complex) or Lambda U (3FZ2_F)” PROBLEM: When we look closely at this identified protein it is actually 3FZ2_B not 3FZ2_F. That protein lists this way: 3FZ2_B Minor tail protein U; Mixed Alpha-Beta fold, VIRAL PROTEIN; HET: MSE, SO4; 2.7A {Enterobacteria phage lambda} SCOP: d.323.1.1, l.1.1.1 However, once the link is clicked, the loaded page reads: 3FZ2 Crystal structure of the tail terminator protein from phage lambda (gpU-D74A) • DOI: 10.2210/pdb3FZ2/pdb QUESTION: We feel that HHPred supports a functional call of “Tail Terminator”. However, we would be breaking guidelines in the Official Functional List by calling the function. What should we do with this info? Thanks. Edited 11 Apr, 2019 15:35

Link to this post | posted 11 Apr, 2019 03:33

GregFrederick@letu.edu

We are finishing annotations of seven P1 subcluster phages this semester. Yes. You read correctly. It's one of those years… We have identified the typical Terminase small subunit in P1s (gp1) and the typical P1 Terminase large subunit (gp2). In finishing gene analysis, we also found a third gene (gp68 in Phalm, Kilkor and Meggido) that hits various 'Terminase large subunit' proteins multiple times, three with a P value of >90%. The HHPred report is here: https://toolkit.tuebingen.mpg.de/#/jobs/Phalm68 1 5OE8_B Large subunit terminase; large terminase, VIRAL PROTEIN; 2.2A {Deep-sea thermophilic phage D6E} 91.72 2.5 7.7 78 430 2 PF04466.13 ; Terminase_3 ; Phage terminase large subunit 90.65 4 6.9 78 202 3 4ZNK_A Phage terminase large subunit; DNA Translocation, VIRAL PROTEIN; HET: SO4; 1.931A {Thermus phage P7426} 90.53 3.9 7.1 77 274 QUESTIONS: I cannot see why a phage might have more than one Terminase large subunit gene. But it looks very real based on HHPred analysis. Can/should we call the function as such? Is there some other explanation? Is there a reason why a phage might benefit from carrying an alternative Terminase presumably with an alternative endonuclease function? To call function or not to call? That is the question. Edited 11 Apr, 2019 03:35

Link to this post | posted 25 Mar, 2019 21:27

GregFrederick@letu.edu

Thanks Graham and Welkin, We are just seeing the name in the literature. It's becoming confusing for our freshman students. But we are already talking about varying nomenclatures for the same proteins depending on which group was studying a specific function or role of the protein. So they can understand and they are learning to look for publications with both genus names. Thanks for the clarification. Greg

Link to this post | posted 23 Mar, 2019 16:04
GregFrederick@letu.edu	It was pointed out to me recently that the genus for many "Mycobacterium sp." organisms has been changed (or at least suggested to be changed). The usage is beginning to show up in the published literature as well. See Mycolicibacterium smegmatis Has there been discussion of changing our nomenclature usage in the SEA-PHAGES program and related publications? Thoughts?

Link to this post | posted 26 Feb, 2019 23:03
GregFrederick@letu.edu	We tried the process described in the link above and still get the database failed error. We are just going back to a previous version and copying our feature notes from the corrupted file into the most recent non-corrupted version. Hopefully that will get us back to where we were.

Link to this post | posted 26 Feb, 2019 22:13
GregFrederick@letu.edu	I found this fix in the new -2019- online annotation guide. We're giving it a try. https://seaphagesbioinformatics.helpdocsonline.com/article-104 Edited 26 Feb, 2019 22:46

Link to this post | posted 26 Feb, 2019 21:53
GregFrederick@letu.edu	We are getting this error on one computer. The files were generated and saved on a student's personal PC. Did we determine a functional solution to this problem? Thanks. Greg

Link to this post | posted 26 Feb, 2019 15:57

GregFrederick@letu.edu

HELP! When we run Starterator from PhagesDB using the "Gene List", the reports that come up do not actually include our viruses. Also, Pham numbers have changed since the beginning of the semester and even in the last day. I understand that updates to the databases may create new Phams occasionally. But the Pham list produced from the gene list function on PhagesDB is not giving us Starterator reports that include our viruses. I hope this is just a temporary outage or database disconnect? Please let us know. Thanks. Greg