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

Link to this post | posted 10 Apr, 2022 19:29
debbie	We have a systematic approach to revising genomes. Just call what you have well and eventually we can work out the rest. Some phages are not ours to change. Nope, no opinion. I think that all TAC homology stems back to lambda and lambda-like phages.

Link to this post | posted 08 Apr, 2022 21:31
debbie	We are in Ottawa, right, so the nucleotide both regions share is 17167 and not 17164. sorry, i must have been looking elsewhere before. cool. debbie

Link to this post | posted 08 Apr, 2022 20:07

debbie

I am going to use the gene numbers on phamerator - and I used phage Ottawa to look a bit closer. I think that the two genes i the same pham - 42 and 42 are major tail proteins. The the next one -gene 44 is the "G" of the TAC. There is an opening reading frame with coding potential (stop is at 17367) that is likely the reading frame that "G" slips into, BUT I could not find the slippage. I would call thought the hit is weak, I would call it a TAC. debbie