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All posts created by jparker

| posted 02 Feb, 2020 21:34
I'm QCing the singleton Bluefeather (most closely related to clusters FE and FI), and have found some fairly strong evidence for immunity repressor (gp19 - good reverse strand coding potential), and excise (gp20 - forward), but no integrase. There is another HTH at gp21). Plaques do look bullseye, but could be just large halos.

I'll call them HTH DNA binding for now, but would appreciate feedback on whether these should be called as a lysogeny cassette.
Posted in: Singleton Annotation TipsBluefeather (singleton) lysogeny genes
| posted 02 Nov, 2019 23:28
I am QCing the annotation of DrYang and it looks like it might have two holins. There is a 4 TMD protein (gp_30), then Lysin A, then the officially called holin (3 TMD - gp_32). Some AO phages have the same gp30 pham and name it holin.

DrYang_gp30 (membrane protein)

DrYang_gp32 (holin)
Posted in: Cluster AR Annotation Tipstwo holins in AR?
| posted 31 Jul, 2019 06:24
Hello, kind of a complicated question. Im looking at Tanis gp25 (stop 18226) which is in cluster 19534 as of today (also contains Gravy_25 and Kerry_25); this is directly downstream of the second major tail gene. The most commonly called start is the longest one, but the 4th start in starterator (1773smile is more conserved. When doing a phagesdb BLAST and HHPred on the longest ORF, there aren't any good functional hits. However, when I use the later/most conserved start, I get pretty strong blast and hhpred hits to tail genes.

I'm leaning towards calling the shorter orf and assigning it as a minor tail. Thoughts?

Here are the sequences to check for yourself, if you like.


Posted in: Cluster DJ Annotation Tipsnew minor tail?
| posted 30 Jul, 2019 18:09
Thanks, Debbie! There is an other membrane protein near by. I'll paste the sequences here if you want to take a look, but I'll go with membrane protein for now.

>Helpful_37 (membrane protein)

- TMHMM and SOSUI predict 2 TM domains and phobius predicts a signal peptide and one TM. Mixed results from TOPCONS, but def. signal peptide.

>Helpful_39 (membrane protein)

- 4 TM domains confirmed with TOPCONS, phobius, SOSUI and TMHMM
Posted in: Cluster D Annotation TipsHolin in D1
| posted 30 Jul, 2019 00:26
Has the holin in D1 been identified? There is a 4 transmembrane domain protein only called a holin in one cluster D1 phage (Nova gp37), all the rest call membrane domain or NKF. This is a conserved gene located between the lysin A and lysin B. How much evidence is needed to designate this as the holin?
Posted in: Cluster D Annotation TipsHolin in D1
| posted 12 Jul, 2019 22:26
Thanks for the advice! The deletion is just under 300bp, so I don't think it is a sequencing error (see attached phamerator screenshot). In PHamerator Fireball draft genes 61 and 62 align to Mutzi gene 58, which was also supported by blastn of this region of Fireball having two separate hits to Mutzi_58. Neither the original pham or the two orphams have any evidence of functions, so I'm just trying to decide on starts.
Posted in: AnnotationMid-gene deletion causing frameshift and orphams
| posted 12 Jul, 2019 01:59
I am annotating Fireball (DC) and appear to have a mid-gene deletion resulting in two orphams. The region has sequence conservation with Gene58 in Muzi (pham 45614). The deletion results in a frameshift with parts of the original gene in two different frames which are now orphams. How do I annotate this? The first gene would be truncated, so that makes sense, but should I include the second gene? The possible start sites result in a giant overlap or cutting off of coding potential? Or do I leave the second gene off altogether, since it wouldn't be likely to be expressed?
Posted in: AnnotationMid-gene deletion causing frameshift and orphams
| posted 31 Oct, 2018 02:10
How should we cite Starterator? I want to be sure to give proper credit. smile
Posted in: StarteratorCiting Starterator
| posted 30 Oct, 2018 23:34
Steven Caruso
I see that the web phamerator can make maps, and understand that other features are coming. Is there a way to have it access alternate databases that I don't see (like Bacillus phages), of is that one of the not yet ready for prime time features?



We went out on a limb this quarter and tried to isolate bacillus phages. It worked, woohoo! However, I didn't think it through, and am just realizing that there isn't phamerator set up for bacillus. Is there a work around, or is this in the works?
Posted in: Web PhameratorAre we there yet?
| posted 27 Jan, 2018 00:54
Sorry, it looks like I got my gene numbers muddled. I am proposing this, for lack of a better idea:
gp85: BrnT-like toxin
gp86: RelB-like antitoxin
Posted in: Request a new function on the SEA-PHAGES official listRibonuclease toxin BrnT