Link to this post | posted 01 Jun, 2022 18:30
debbie	PineapplePizza is the first Microbacterium phage that is like phi29 (a Bacillus phage) and P68 (a Staphylococcus phage). I have used a new set of structural gene names for its various parts that are unique to phages like this. See the attached map for specifics. Cool little phage! debbie 60Kb

Link to this post | posted 01 Jun, 2022 15:40
debbie	Annotate it as the data shows. New data is available all of the time, and we will try to keep up with it. This post is most helpful. I would recommend that you draw attention to this in your cover sheet, so that the reviewer doesn't take it out. Help them to benefit from what you investigated. Thanks! debbie Edited 01 Jun, 2022 15:40

Link to this post | posted 24 May, 2022 15:28
debbie	Hi all. Seems that the TAC ribosomal slippage is difficult to locate. Do not call the slippage at CCCGGAA. It is not a canonical choice. However, recognize that there are some members in Subcluster DN3 and DN4 (Apricot, for example) that do have a canonical slippage, namely G_GG.G_GA.A (where _ separates codons in the original frame, and . separates them in the new frame).

Link to this post | posted 22 May, 2022 22:03
debbie	Tammy, The corrected file has been uploaded to phagesDB and sent to GenBank. Thanks, debbie

Link to this post | posted 22 May, 2022 01:50
debbie	Nope. Thanks for checking. We can correct this. debbie

Link to this post | posted 20 May, 2022 19:48
debbie	Nice!

Link to this post | posted 20 May, 2022 14:05
debbie	Yep. Please call them. Thanks, debbie

Link to this post | posted 19 May, 2022 17:21
debbie	Awesome. Do you log in to do your work? Just fyi - I always copy over input under a new id to submit my next sequence (then I don't have to pick the databases. debbie

Link to this post | posted 18 May, 2022 13:18
debbie	Hi Sean, It should be back up this morning sometime. Steve Cresawn is aware of the problem. Thanks for checking in. debbie

Link to this post | posted 18 May, 2022 00:53

debbie

This bacteriophage is very much like 2 well studied podoviridae, phi29 and P68 both with Cryo EM data. One of the genes described in these phages is a "DNA encapsidation protein". When reading about a DNA encapsidation protein , it functions like a terminase protein. Chris Shaffer (Washington University at St. Louis) answered the question of what to call this gene this way: "I always like gathering more data, so the question I had was: how is the term "Encapsidation" used in general. So I did a quick search of the term "Encapsidation" on swissprot (the manually annotated subset of uniprot), the results show a bit over 600 hits. Scrolling through, I am seeing about 95+% are hits to Eukaryotic RNA viruses. If you sort the data by taxonomy there are only 8 entries out of 615 where this term has been applied to Caudovirales. So it looks to me, (if you take the swissprot professional annotators as your source) that encapsidation is a term mostly used for single stranded RNA viruses but has been applied rarely to a few phage proteins. Interestingly, these including the SSP1 protein 2, more commonly known as "Terminase, large subunit". So when encapsidation was applied to this phage it has been used as a synonym for Terminase. So I too think we should avoid using this term, we could even put it on the approved list in the "do not use" column. Here is the link to all 615 entries." So I think we can easily call gene 15 of PineapplePizza "terminase".