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".

Link to this post | posted 11 May, 2022 15:21
debbie	Shallee, Hi. I think this is important to investigate. Would you consider contacting them and explaining what you were doing? My guess is that they confused you all with a robot or something. Thanks, debbie

Link to this post | posted 06 May, 2022 17:51
debbie	Fred, I would not call this gene a minor tail protein. It is at the end of a string of minor tail proteins and the next genes change directions. In my mind, these genes could be anything. debbie

Link to this post | posted 28 Apr, 2022 19:17
debbie	Great idea! I just added that! debbie

Link to this post | posted 28 Apr, 2022 17:57
debbie	We keep bumping into the IrrE protein. I have added "IrrE-like protein" to the Approved Function List. Will that work? debbie

Link to this post | posted 28 Apr, 2022 17:42
debbie	Maria, I think that this is something to investigate. Let's see what your students turn up this ummer and address it then. Will that work? debbie

Link to this post | posted 28 Apr, 2022 00:55
debbie	Hi all, I just updated SEA-PHAGES phages shared with SEA-PHAGES schools. Thanks for making your phages available to others! April 27, 2022 Edited 28 Apr, 2022 00:55 84Kb

Link to this post | posted 25 Apr, 2022 19:55
debbie	function assignment being used is "major capsid and protease fusion protein".

Link to this post | posted 25 Apr, 2022 19:40
debbie	Any time one transmembrane domain is found, it is questionable. So we recommend using a second program. that usually takes care of the discrepancy. Thanks for doing the quick experiment.