Welcome to the forums at seaphages.org. Please feel free to ask any questions related to the SEA-PHAGES program. Any logged-in user may post new topics and reply to existing topics. If you'd like to see a new forum created, please contact us using our form or email us at info@seaphages.org.
Recent Activity
JustinA posted in Plaques appear on spot test, don't appear in titer
Viknesh Sivanathan posted in Plaques appear on spot test, don't appear in titer
JustinA posted in Plaques appear on spot test, don't appear in titer
Viknesh Sivanathan posted in Plaques appear on spot test, don't appear in titer
RyanWheeler posted in Plaques appear on spot test, don't appear in titer
All posts created by debbie
Link to this post | posted 22 Apr, 2022 12:34 | |
---|---|
|
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 11:22 | |
---|---|
|
Fred, Terrific. I think the note is there. https://seaphagesbioinformatics.helpdocsonline.com/article-40 The 're-look' was a good thing. I am glad we took the time and weighed the evidence. debbie |
Link to this post | posted 21 Apr, 2022 17:55 | |
---|---|
|
Fred, I would delete this gene. The coding potential is "greatest" in the open reading frame in question, is closer to 93100 - so there really is no coding potential in the space between where the tRNAs reside. If you BlastN the sequence in question, it is VERY well conserved across the C1s, but my money is on some kind of RNA thing and not a protein coding gene. This area was well reviewed by an RNA guy back in the day, and for now, without additional data, I think I would like to refrain from calling this a gene. And yes, others called it, but I would disagree. What do you think? debbie |
Link to this post | posted 20 Apr, 2022 20:46 | |
---|---|
|
But as the 2022 Davidson paper shows, T4's TAC were finally elucidated and they go in opposite directions. Check it out. https://pubmed.ncbi.nlm.nih.gov/34826709/ |
Link to this post | posted 19 Apr, 2022 21:22 | |
---|---|
|
Mitch, I agree. I would call the tail assembly chaperones in Morkie (that is the phage you are annotating, right?) The tail assembly chaperones are in the 'right place' and the slippage is cannonical. However, not all slippages in the DNs are cannonical and I would shy away from calling them. Cool! PS I consulted Dr. Hatfull about this and he agreed that the slippage is the compelling piece of data. debbie |
Link to this post | posted 19 Apr, 2022 19:24 | |
---|---|
|
Hi! Did you protein also hit HK97 gp10? If so, the folks that studied that phage for decades could not assign a function to it. Does it also hit minor tail or any kind of tail proteins? So, for me, it is hard to know if it is part of the head or the tail. In addition, our friends at the University of Connecticut have been doing cryo-EM and in at least one phage with that protein, and they have detected no evidence of it in the capsid structure. then if you read the literature, MuF-like domains are associated with toxin/anti-toxin systems, so maybe it is not structural at all. So for me, Hypothetical Protein sounds like the best fit for now. Let me know what you think! debbie |
Link to this post | posted 19 Apr, 2022 18:10 | |
---|---|
|
Mitch, I started to look at this and found what you did and it is believable. But before we go forward. There are 2 caveats that I find troubling: 1. There is no homology to tail assembly chaperones other than what we called. And we called those because of their position. So is there any evidence that these proteins have homology to anything else called a tail assembly chaperone? 2. Would you take a look at Whitney and reconcile our predictions there? very interesting! debbie |
Link to this post | posted 18 Apr, 2022 19:26 | |
---|---|
|
Fred, The tRNAs that I would like to be sure I keep are the ones that are called in Spud and ScottMcG. Would you provide the DNA Master file so i can take a closer look? Thanks, debbie |
Link to this post | posted 15 Apr, 2022 02:31 | |
---|---|
|
Hi Fred, I have to look into this. What Welkin wrote was our best prediction at the time. However, we can show examples of exceptions of every 'rule' we make. We have found an example of a tRNA in the same region as a protein coding gene. BOTH are expressed. However, the tRNA is in the opposite direction. More to come. debbie |
Link to this post | posted 13 Apr, 2022 14:37 | |
---|---|
|
It was pointed out to me (Thanks Mitch!) that the motif needed to include "metallo" in your gene call of a metalloprotease is HEXXH. Sorry for the confusion. |