Link to this post | posted 04 Aug, 2017 02:32
clfleischacker	For the B1 subcluster phage Lulumae, for gene 19 it has the queuine tRNA ribosyltransferase as a function which is not on the official function list. Can this be added to the list?

Link to this post | posted 31 Oct, 2017 15:36
welkin	YEs! That should be on the list. Thanks for pointing that out.

Link to this post | posted 05 Aug, 2020 21:25
scaruso	I noticed that this is not on the list, though it is on PECAAN. Has there been a change in its status? Steve

Link to this post | posted 06 Aug, 2020 15:34
debbie	Steve, This has just been revised. Check out the Pre-Qo pathway case study just posted in the Bioinformatics Guide. The revised functional assignments are listed on the approved functions Google doc. August 6, 2020.

Link to this post | posted 10 Mar, 2021 17:09
stukey	The function queuine tRNA-ribosyltransferase - which I do not believe is any of the newly defined Pre-Qo pathway functions - is NOT on the official functions list? PenguinLover67_2 shows almost all pham members with this function? The alternative would be to label it is NKF. Joe

Link to this post | posted 10 Mar, 2021 17:09
stukey	The function queuine tRNA-ribosyltransferase - which I do not believe is any of the newly defined Pre-Qo pathway functions - is NOT on the official functions list? PenguinLover67_2 shows almost all pham members with this function? The alternative would be to label it is NKF. Joe

Link to this post | posted 11 Mar, 2021 02:17
debbie	Joe, I think we have some revision work to do. I would follow the case study in the Bioinformatics Guide. Gene 2 should be named "dpdA-like tRNA-guanine transglycosylase". This in accordance with the biochemical analyses from this paper. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6884629/ debbie

Link to this post | posted 02 Mar, 2022 18:47
erin.windsor	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?

Link to this post | posted 02 Mar, 2022 18:56
debbie	Hi Erin, Did you check out the case study in the Bioinformatics Guide? https://seaphagesbioinformatics.helpdocsonline.com/article-1596481355 I can't quite answer a general question, but if you give me the specifics, I can try to help. Thanks, debbie

Link to this post | posted 02 Mar, 2022 19:56

erin.windsor

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.