Link to this post | posted 26 Jun, 2024 16:23

jawsWPI

My class annotated the cluster B1 phage Schueller. We too saw the odd genome organization immediately upstream of the tape measure protein: forward, forward, reverse. Analysis of both forward genes match what was seen in Usavi (see previous posts). Additionally, I used alphafold 3 and ChimeraX to fold and display one of the reference TACs (3D8I.pdb) and schueller gp_25 (2nd forward gene with partial hits to TACs), and then to merge the structures. Photos are attached showing little structural similarity and virtually no overlap when the predicted structures are merged; Blue is the pdb reference tan is schueller. Conclusion: these genes with partial hits to TACs are not TACs, and no TACs should be called. Edited 26 Jun, 2024 16:34 81Kb 124Kb

Link to this post | posted 28 May, 2024 18:08

jawsWPI

If you click the "phages" dropdown on PhagesDB, scroll to the bottom of the list and click "phams" you will be brought to the 'find a pham' search page where the last option is to Search gene notes–that will let you search "DNA primase/polymerase/helicase". Be aware that some of the DNA primase/polymerase/helicase annotations only have two domains where the primase/polymerase domain hits (CDD) to the bi-functional Prim-pol domain (should show up as an N-terminal domain with helicase as a C-terminal domain).

Link to this post | posted 30 Apr, 2024 18:39
jawsWPI	2:38PM 4-30-24. Just tried HHPred again with job grayed out and queued: "We are addressing a Denial of Service attack by a user who is continually changing IP addresses to submit an excessively high number of jobs, significantly impacting our system’s performance. We regret any inconvenience caused and are actively working to resolve this issue.".

Link to this post | posted 29 Apr, 2024 15:22
jawsWPI	It's possible that HHPred was choked–I setup a manual query around the time you were having issues in PECAAN that was also queued up for a long time and was still 'running' just now but had reached an error stage. Just deleted the request and resent–it ran and came back in a couple of minutes even with a 4-database search. So, if you are still having issues try again.

Link to this post | posted 04 Aug, 2023 20:36
jawsWPI	I'm QCing an F1 phage (Rialto) that also seems to have two immunity repressors: the first at 32973-33485 (rev) current pham 96090 is found primarily in A phages and a few others (including a handful of C1), and 36289-36855 (Rev) that is clearly the cluster F repressor. My question is this: do we assign hypothetical to the first (A phage immunity repressor) until wet bench data is available?

Link to this post | posted 04 Jun, 2023 19:53

jawsWPI

The terminase small subunit is in the right-hand arm of the genome. Example is gene 57 in TaylorSipht (cluster AS1). This gene has a strong hit to PDB 6Z6E_C, with 99.79 probability, 3.8e-18, and 100 columns aligned out of 160. Alignment is to the helix-turn-helix-turn-helix structure of "Terminase small subunit; genome packaging, bacteriophage, DNA binding, VIRAL PROTEIN; 1.4A {Enterobacteria phage HK97}". Do not call two small terminases, nor assign terminase small subunit function to the early gene (example, gene 2 in TaylorSipht). Edited 19 Jul, 2023 19:49

Link to this post | posted 04 Jun, 2023 19:40
jawsWPI	The AS genomes are being assigned a large terminase subunit due to a small subunit that is found in the right arm. Example is gene 3 in TaylorSipht (AS1). See Terminase, small subunit topic for additional information.

Link to this post | posted 26 Feb, 2023 19:16
jawsWPI	Yes. See Feb. 23 revision to the Guiding principles point 12.f.

Link to this post | posted 26 Feb, 2023 19:09
jawsWPI	The Guiding Principles point 12 has been updated to choose the second of any two tandem (i.e. back-to-back) start sites based on the mass spec data and consideration of basic biology principles. guiding principles, point 12 subpoint f. Edited 26 Feb, 2023 19:10

Link to this post | posted 21 Mar, 2022 19:09
jawsWPI	Hi all, I'm seeing exactly the same thing in a K4 phage (Ruthiejr): very strong HHPred hit to HicA toxin (99+% probability and 90% coverage) with no sign of an antitoxin. My recollection is the same as Debbie's: we can call either without the partner because it may not need it or the host may carry it. I'm leaving mine as "toxin in toxin/antitoxin system, HicA-like".