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All posts created by erin.windsor

| posted 10 Mar, 2023 19:47
We are annotating Olgasclover. Our 3 most closely related phages, Jodelie19, Aflac, and Figliar, call gene 4 in the second frame. They all had genemark call a gene in that frame, based on the genemark maps. Glimmer called a reverse gene there for us. We have no coding potential in frame 2 despite high homology in that area. Frame 3, where we have some coding potential, would cause a 69bp overlap. See attachment for genemark screenshots of Olgasclover and Aflac and the phamerator map of closely related phages. Any tips?
Posted in: Cluster DJ Annotation TipsNo coding potential where others call a gene
| posted 02 Mar, 2022 19:56
Yes, I saw the case study. We are working on gene 2 in Blocker23. There are 50 members in the pham and all but two of the annotated phages call it queuine tRNA-ribosyltransferase. Calamitous and Lars call it dpdA-like tRNA-guanine transglycosylase. queuine tRNA-ribosyltransferase is not listed in the case study and it is not on the official function list. Per this thread it looks like it was added in 2017 and removed around 2020. March 11, 2021 you said there were many revisions to make. I assumed you were talking about changing the queuine tRNA-ribosyltransferase calls to dpdA-like tRNA-guanine transglycosylase because of the new paper found.
Posted in: Request a new function on the SEA-PHAGES official listqueuine tRNA ribosyltransferase
| posted 02 Mar, 2022 18:47
Hi Debbie,

Just to confirm, if we think we have queuine tRNA-ribosyltransferase, based on new evidence, we should instead call it dpdA-like tRNA-guanine transglycosylase?
Posted in: Request a new function on the SEA-PHAGES official listqueuine tRNA ribosyltransferase
| posted 19 Nov, 2020 18:06
The only enzyme that cuts well for us in Gordonia rubripertincta is NspI. See attached.
Posted in: GordoniaGordonia DNA not cutting
| posted 03 Mar, 2020 18:00
Ours was identified as CGGGGAG during QC.
Posted in: Cluster DR Annotation TipsTail Assembly Chaperone
| posted 02 Mar, 2020 19:09
Hi Shallee,

NHagos annotator here. NHagos and Sour tail assembly chaperones are not in the same frame. They were annotated with frameshifts so it looks back-to-back in phamerator. You cannot tell which frame it is in from phamerator. Download the NHagos minimal file to see our frameshift. You can also look up the genbank entry to see that is was annotated at nucleotide 17143. There are 4 G's in a row. Sour also had these 4 G's in a row. Our complete notes file does not have the frameshift annotated.
Posted in: Cluster DR Annotation TipsTail Assembly Chaperone
| posted 11 Mar, 2019 18:36

SOSUI is down. We contacted the host, and we do not know when it will be back up. We see that TMHMM predicts one transmembrane domain. The Official Function list says we need two domains called by TMHMM. This means we cannot call it a membrane protein, correct? Why does it have to have two domains?
Posted in: Functional AnnotationMembrane protein