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All posts created by jawsWPI

| posted 28 May, 2024 18:08
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).
Posted in: Functional AnnotationGG cluster DNA primse/helicase
| posted 30 Apr, 2024 18:39
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.".
Posted in: PECAANHHPred not updating in PECAAN
| posted 29 Apr, 2024 15:22
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.
Posted in: PECAANHHPred not updating in PECAAN
| posted 04 Aug, 2023 20:36
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?
Posted in: Cluster F Annotation TipsImmunity Repressor and CRO starts
| posted 04 Jun, 2023 19:53
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
Posted in: Cluster AS Annotation TipsTerminase, small subunit in right arm
| posted 04 Jun, 2023 19:40
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.
Posted in: Cluster AS Annotation TipsTerminase, large subunit
| posted 26 Feb, 2023 19:16
Yes.
See Feb. 23 revision to the Guiding principles point 12.f.
Posted in: Cluster CS Annotation TipsTTG followed by ATG
| posted 26 Feb, 2023 19:09
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
Posted in: Choosing Start SitesTwo consecutive ATG start sites
| posted 21 Mar, 2022 19:09
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".
Posted in: Functional AnnotationHicA toxin without antitoxin
| posted 04 Feb, 2022 20:16
A new function has been added to the official function list: Phosphoribosyl transferase. Example genes are Phelipe_64 and Bosnia_40.
Do not confuse with the phosphoribosyl pyrophosphate transferase function–these are two different enzymes in the nucleotide synthesis pathway.

Evidence and rational can be found in the attached document.
Posted in: AnnotationPhosphoribosyl transferase new function: Phelipe_64 and Bosnia_40