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

Link to this post | posted 07 Apr, 2022 17:06
debbie	Eric, Your version of DNA Master needs to be updated. You must update to get that "secure connections" box in preferences. I believe the problem is that you must run DNA Master as administrator even when you are updating. Check on that and try again. My latest version is 5.23.6, Build 2705, 14 October 2021.

Link to this post | posted 06 Apr, 2022 17:49

debbie

In many clusters, there is now cryoEM data that identifies that 2 different genes are needed to make the capsid, one that forms the pentamers and another forming the hexamers. this has been best worked out in Rosebush, a Cluster B2 phage. The hexamer gene is part of pham (102634) that has members in 358 phages that include 4 singletons, and Clusters AD, AP, B, BG, DC, DE, DR, EC, EG, EI, GC, and W. The pentamer gene is part of pham 20839, but there is sequence similarity to 2 other phams - 21303 and 102541.Work is being done to verify whether these proteins fold in a similar manner. We won't call them…yet. But cool.

Link to this post | posted 06 Apr, 2022 17:34
debbie	Experimental work (CryoEM) done with phage Patience (gp4) has identified a capsid accessory protein that has a homolog in the Cluster Hs. an example is Barnyard gp 3.

Link to this post | posted 06 Apr, 2022 17:30
debbie	Gene 4 in Patience is a capsid accessory protein. Experimental work done by Simon White (UConn) to be published soon!

Link to this post | posted 06 Apr, 2022 17:27
debbie	Experimental data using cryo EM (by Simon White, UConn) shows that gp 4 of Adjutor is a capsid accessory protein. A paper describing this is in the works.

Link to this post | posted 06 Apr, 2022 16:44
debbie	Yes please! They should be identical to whatever is the beginning of the genome.

Link to this post | posted 06 Apr, 2022 16:32

debbie

Amaya, That is because I recently removed MuF from the function list because it does not describe a function. Originally we thought MuF was a minor capsid protein, but we have a bit of experimental evidence that it doesn't show up in the capsid. There are some papers about how rampant this gene (and its homologues) are found, but still haven't found ay good evidence of what it is. If you have evidence of the portal, please call it. I hope that helps, debbie