Link to this post | posted 21 Apr, 2022 17:55

debbie

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
debbie	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

debbie

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

debbie

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

debbie

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
debbie	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 Edited 18 Apr, 2022 19:26

Link to this post | posted 15 Apr, 2022 02:31
debbie	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
debbie	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.

Link to this post | posted 12 Apr, 2022 02:28
debbie	Ann, I ran into this yesterday. Thee is nothing wrong on your end. we just need to reset the privilege. I'll make sure it gets done tomorrow. debbie

Link to this post | posted 11 Apr, 2022 15:39
debbie	There is a human element in the processing of Starterator reports. It should appear soon. Thank you for your patience. debbie