SEA-PHAGES | queuine tRNA ribosyltransferase

Link to this post \| posted 02 Mar, 2022 20:47
debbie	The paper about the queuosine pathway found in Rosebush was published in 2019. I was hoping to have curated those phams and gotten it recorded in phamerator in a better way, but that curation is lagging further behind the data than hoped for. The paper contains the empirical bench data that we want to capture in our annotation. So while others could interpret bioinformatic hits diferently, Rosebush genes have empirical bench data to support the calls. Once the paper was published, Dr. Hatfull and I carefully chose the names to call the genes. They are recorded in the case study that I mentioned. A few minutes ago, I sat down with Christian and he updated the annotation of Rosebush in phamerator for the gene names of the first 6 genes. The processing will take a bit of time, and then the data will have to be transferred to the web version. BUT, in a few hours Rosebush will reflect the correct gene functions for these genes. In the meantime, follow the "Gene assignment as per approved function list" in the table about Rosebush in the aforementioned case study. Sorry for the confusion. debbie

Link to this post | posted 02 Mar, 2022 20:47

The paper about the queuosine pathway found in Rosebush was published in 2019. I was hoping to have curated those phams and gotten it recorded in phamerator in a better way, but that curation is lagging further behind the data than hoped for.
The paper contains the empirical bench data that we want to capture in our annotation. So while others could interpret bioinformatic hits diferently, Rosebush genes have empirical bench data to support the calls. Once the paper was published, Dr. Hatfull and I carefully chose the names to call the genes. They are recorded in the case study that I mentioned.
A few minutes ago, I sat down with Christian and he updated the annotation of Rosebush in phamerator for the gene names of the first 6 genes. The processing will take a bit of time, and then the data will have to be transferred to the web version. BUT, in a few hours Rosebush will reflect the correct gene functions for these genes. In the meantime, follow the "Gene assignment as per approved function list" in the table about Rosebush in the aforementioned case study.
Sorry for the confusion.
debbie

Link to this post \| posted 21 Apr, 2022 21:53
amaya.garciacostas	Gene 39 in Aoka also appears to be a DpdA-like tRNA-guanine transglycosylase. BLAST search called it a queuine tRNA ribosyltransferase but of course we didn't see that in the functions list. All of the members of the Pham, for what it is worth, have called it a DpdA-like tRNA-guanine transglycosylase. We tried to do an alignment with Orion20 from the case study, but there is no significant alignment so not great. HHPred also has hits with high coverage and probability and low e value to a Queuine tRNA-ribosyltransferase, so we are ready to call it a DpdA-like tRNA-guanine transglycosylase and just wanted to share this since it seems like you are actively working on this. No gene context is helpful as this gene is surrounded by orphams.

Link to this post | posted 21 Apr, 2022 21:53

amaya.garciacostas

Gene 39 in Aoka also appears to be a DpdA-like tRNA-guanine transglycosylase. BLAST search called it a queuine tRNA ribosyltransferase but of course we didn't see that in the functions list. All of the members of the Pham, for what it is worth, have called it a DpdA-like tRNA-guanine transglycosylase. We tried to do an alignment with Orion20 from the case study, but there is no significant alignment so not great. HHPred also has hits with high coverage and probability and low e value to a Queuine tRNA-ribosyltransferase, so we are ready to call it a DpdA-like tRNA-guanine transglycosylase and just wanted to share this since it seems like you are actively working on this. No gene context is helpful as this gene is surrounded by orphams.

Link to this post \| posted 22 Apr, 2022 12:34
debbie	Amaya, As I look at this gene, I would NOT call it any of the above, but rather a Hypothetical Protein. If it was a hit to the transferase of the cluster B2's Rosebush DNA modification system, using DpdA-like tRNA-guanine transglycosylase would be appropriate. Sonali, a phage with the other queosine pathway genes (I think) suggests that transferase could be the DpdA-like tRNA-guanine transglycosylase. But I haven't looked closely yet. In the case of Aoka, when I HHPred that gene, I do not get a single significant hit. I worked through this with Christian and we agreed to not call it. Here is the caveat, you have a bunch of orphams in the area. Have you been able to assign a function to any of the surrounding genes? Depending on what you have found, I would like to look again.

Link to this post | posted 22 Apr, 2022 12:34

debbie

Amaya,
As I look at this gene, I would NOT call it any of the above, but rather a Hypothetical Protein. If it was a hit to the transferase of the cluster B2's Rosebush DNA modification system, using DpdA-like tRNA-guanine transglycosylase would be appropriate.
Sonali, a phage with the other queosine pathway genes (I think) suggests that transferase could be the DpdA-like tRNA-guanine transglycosylase. But I haven't looked closely yet.
In the case of Aoka, when I HHPred that gene, I do not get a single significant hit. I worked through this with Christian and we agreed to not call it. Here is the caveat, you have a bunch of orphams in the area. Have you been able to assign a function to any of the surrounding genes? Depending on what you have found, I would like to look again.

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queuine tRNA ribosyltransferase