Link to this post | posted 30 Mar, 2022 17:50
debbie	Hi Ann, No, I don't believe that sequence is a tRNA in the phage, but if you integrate it into smeg (you will find that it completes a tRNA gene in M. smegmatis (tRNA Thr (Msmeg_6152)). It is picked up by tRNAScanSE because it is likely half of a tRNA that is made when the phage is integrated as a prophage. There is nothing to call in the phage annotation for this. Make sense? debbie

Link to this post | posted 29 Mar, 2022 20:24

debbie

Hi Allison, There are a lot of routes that our phages take to integrate, and close to the integrase is a good way to address it. We - I mean Graham, has spent a lot of time looking for integration sites in the Mycobacteria and proving them biochemically. He is writing a review article that gives a great summary, so when it is available it will help a lot. In the meantime, the first thing you want to know is what kind of integrase you have. The large serine integrases can have an attachment site that is but 3 bases in length. so without some bench work, that is going to be difficult. The tyrosine integrases have arm extensions that make it more readily identifiable. You can look up Bxb1 integration (first author is Pallavi Ghosh). Some of our best data published is in M. abscessus (Dedrick, 2021) because we found the prophages and could see the sequences of the attL and attR in the hosts. Those reads should help to get you started. Some of our phages like to integrate into tRNAs. Being able to match the attP to an attB is also needed, so know in the host sequence will be needed. After you read the Dedrick papers, I think you will see why the answer to your questions are not simple. Having said all that, another paper in the works is a prophage finder, that will help identify attL and attR. So much to do!

Link to this post | posted 29 Mar, 2022 12:37
debbie	Kathleen, Yep. It is rule based on a small data set from some mass spec data. Choose the second one. debbie

Link to this post | posted 25 Mar, 2022 12:33
debbie	I agree with Steve. This may be one of the only places where I rely on that particluar pFam hit. debbie

Link to this post | posted 20 Mar, 2022 14:31
debbie	Hi Sally, I think I can call a toxin or antitoxin without its partner because the host may carry it. Curious if others agree. debbie Edited 20 Mar, 2022 14:31

Link to this post | posted 15 Mar, 2022 13:23
debbie	Vicky, Yes, the hierarchy of what to believe is convoluted. We got tail assembly chaperone calls wrong in this cluster. So Blast data - whether at ncbi or phagesdb - will just regurgitate what we got wrong. BUT, if we got it correct, it would be a good source of info. We are steadily working at correcting the 'wrongs', but it just takes time. debbie

Link to this post | posted 15 Mar, 2022 13:16
debbie	Shima, What you need to provide is one best explanation for each gene call. Since i don't use PECAAN this way, I can't answer your question. You are correct, Claire set up PECAAN so there is an output that works. But whatever you pick, be sure to identify the problem areas and the thinking process. debbie

Link to this post | posted 15 Mar, 2022 13:03
debbie	There is another string of forum posts in the cluster specific annotation tips. I just looked at a set of these genes (see the post) and I am worried that the wrong genes are being implicated. Use your phage's HHpred data to make your decisions. https://seaphages.org/forums/topic/5009/ Best, debbie

Link to this post | posted 07 Mar, 2022 20:56

debbie

Hi Vicky, Here is my 2 cents. I don't think that gene 21 and 22 are tail assembly chaperones. Using the HHPred info in PECAAN. Gene 21 (16902 - 1722 hits the MuF-like protein that we don't quite understand and are currently calling it a Hypothetical Protein. Gene 22 (17225 - 17635) Significantly hits minor capsid genes, and tail genes. In particular it hits HK07-gp10. That phage was well studied at Pitt and those researchers did not know the function of gp10, so it too is a hypothetical protein, Gene 23 (17682-18221) DOES have a significant hit to a tail assembly chaperone (pfam hit). BUT it is in the right place, so I would consider it. This is my first pass on this. If you read the Cluster specific annotation tip on this subject, you can see others have struggled with this also. https://seaphages.org/forums/topic/5009/ Next step, please run all HHpred at HHPred. IGNORE ALL PREVIOUS SEA-PHAGES ANNOTATIONS. When this first of this Cluster (CloverMinnie and Sour) we thought the TAC HAD TO BE THERE. We now know that is not true. As you re-evaluate this, let me know if you need additional help. Good luck! debbie

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