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

Link to this post | posted 06 Apr, 2022 16:29
debbie	All information is informative. I guess it depends on how you use it! It might be helpful to do a protein alignment. debbie

Link to this post | posted 06 Apr, 2022 16:25
debbie	No, I meant the phage pages, they describe the specific ends type of the phage genome. I am trying to remember a good resource that gives the biology behind this, but I am still thinking about that. Although, there will be some good info concerning this in one of Dan's videos. https://phagesdb.org/workflow/videos/phageterm/ debbie

Link to this post | posted 06 Apr, 2022 16:14

debbie

Hi. Genome organization is something that is worked out during the sequencing of phages. We are keen to make sure we have been precise with the ends of our phage genomes. The type of ends fall into 3 categories: Those with cos ends, meaning there is an overhang of sequence, usually about 10 bases long this 'sticks the genome together Those with no ends - because these phages use a head-full-packaging mechanism that puts in > the genome length, but the start/stop of that length is not the same in every genome Those with direct terminal repeats, meaning that that genome when it circularizes in the host will overlap for the length of the repeat - so even though you see identical genes at the front and back of a genome (and you SHOULD see identical genes because the sequence is identical) there will only be one copy of them in the working phage genome. The phage page is chocked full of information about the phage, check there to see how Ottawa and Kharcho's genomes are described! Best, debbie Edited 06 Apr, 2022 16:21