Link to this post | posted 05 Nov, 2019 15:55

debbie

Hi Jordan, If I were calling this genome, I would label both of these proteins as membrane proteins. Neither are great matches to known holins, phages can have more than one holin, and while I may not know which one is a holin, I am confident that they are both membrane proteins. If you are compelled to call a holin, 32 is in a 'more canonical' place. Historically, we called the small protein after lysin A the holin. Now that we are moving away from relying on the location as the sole reason for calling a holin, I am most willing to call these proteins 'membrane proteins'. (Because I can't tell which is the holin, although they both may be holins.) The best writing about holins is from Ry Young, Texas A&M. I don't know if there is a definitive article that he has written that helps, becuase he has written a lot. I kinda liked his J Mol Microbiol, Biotechnol (2002) paper, "Bacteriophage Holins: Deadly Diversity". debbie

Link to this post | posted 01 Nov, 2019 01:06
debbie	Done!

Link to this post | posted 30 Oct, 2019 01:12
debbie	Iain, This is all up to GenBank. They have many folks working through the submissions and they get assigned in ways not know to us. I have files posted in 1 day and I have seen them posted 6 months later. debbie

Link to this post | posted 19 Oct, 2019 00:17
debbie	That would be great! debbie

Link to this post | posted 18 Oct, 2019 01:19
debbie	Hi! Yes, ArV1 is the phage of that paper. Why do you say that AR phages are siphoviridae? debbie

Link to this post | posted 03 Oct, 2019 15:57
debbie	Amy, I am the one QCing this genome and I have not gotten to it yet. Welkin, would you respond to the intron question? I think that info that may be helpful is found here https://seaphages.org/forums/topic/4926/?page=1#post-7336 Thanks, debbie Edited 03 Oct, 2019 17:06

Link to this post | posted 27 Sep, 2019 05:14

debbie

Hi all, Recently Krista Freeman, a post doc in the Hatfull lab, and Julia Kovalski, an undergrad designed primers for 60 cluster/subclusters of mycobacteriophages. These primers were designed for verification of phage lysates in the Hatfull lab (and not to prematurely assign cluster designations to unsequenced phages). Attached is an Excel sheet of the primers/phages. Krista thought having the fasta files of the phages would be helpful. I thought adding a picture of Julia and Krista would be fun! Edited 27 Sep, 2019 05:15 27Kb 2.80Mb 1.17Mb

Link to this post | posted 25 Sep, 2019 20:50
debbie	A lot of Cluster EA1s have a tRNA in the middle of a middle tail gene. since you can only call one or the other, call the minor tail gene!

Link to this post | posted 25 Sep, 2019 18:40

debbie

If one looks at the immunity repressor of Cluster F1s like Mycobacteriophage Strokeseat, the coding potential data is confusing. The Starterator data clearly shows only 1 start that is found in all pham members. The start in Strokeseat is at position 34251 (stop is at 33682).(gene length is 570bp). This then provides adequate (just barely) space for promoters for this gene (CRO) and the next one (because they are transcribed in opposite directions). The start of this gene is at 34358 (stop is at 34651). Hope you find this helpful! Unfortunately, as is the nature of Cluster F1s, not all F1s have these phams. Edited 08 Aug, 2023 13:20 152Kb

Link to this post | posted 31 Jul, 2019 20:07

debbie

Jordan (and anyone else who reads this terrific post, I asked Chris Shaffer if I was correct in thinking that start 1 and 2 in the phamerator report 19534 were basically the same. He explained that they ARE the same. Check it out! chris just showed me that I am smarter than a computer! lol! Deb, what an interesting case, TL,DR: no starts 1 and 2 are not really different even though starterator says they are. Long version if interested: this is a weird corner case where the starterator program is giving the literally correct answer which is really "wrong". So no the 1 and 2 should not be considered different. Looking very closely at the diagram you can see all the 1 starts have a tiny white sliver on the right edge while all the 2 starts do not. Here is the actual multiple sequence alignment (MSA) and you can see the single A base insertion in some sequence and not others (the while sliver represents the gap), I highlighted the start codon in yellow (attached): When you ask a computer are those starts "the same" the answer is no, so Starterator considers the top 3 sequences as start 2 and the bottom 4 as start 1. What we have run across is one of the fundamental problems of MSA's, multiple sequence aligners like clustal just doesn't have any way to know if it should align as -A or A-. This is why people "hand tweek" alignments when they want the best possible alignments (for publishing conserved domains for example) because it just isn't possible to code in the external evidence needed to decide between "A-" and "-A". There might be a way to fix this in starterator, not sure, I will have to think on it. As for recommendation I typically consider starts that are clearly that close on a starterator diagram as "the same" even if the computer gives them different numbers. Chris Edited 31 Jul, 2019 20:11 43Kb