Link to this post | posted 15 May, 2024 23:13
debbie	Hi Dane, From the HHPred results, because of the limited nature of the hits, i would not call anything at this time. best, debbie

Link to this post | posted 10 May, 2024 01:15
debbie	Alison and your students, Thank you for your awesome work on this. Maria Gainey presented this and her similar protein at our SMART meeting today and a discussion ensued. For now, we recommend that you call this protein "cyclic nucleotide inhibitor". best, debbie

Link to this post | posted 09 May, 2024 02:16
debbie	Hi Nikki, Sorry to id the paper as Tweety, when the data is about Fruitloop. Bit I di have the paper right! (Just what you needed, more confusion.) I think your decision is a good as we can get at this point. best, debbie

Link to this post | posted 03 May, 2024 18:42
debbie	Be careful what you say about Fruitloop. Go to the paper and see the mas spec table and the map there. (when I looked, the paper doesn't match the GB file). There is a gene in there that you do want to call. i just don't have time right now to match it correctly. Let's touch base before you submit. best, debbie

Link to this post | posted 03 May, 2024 16:20
debbie	Hi Nikki, Mycobacteriophage Tweety has a paper that includes mass spec data. While the integrase and repressor have less sequence homology, that space in between may have enough similarity that you can draw some inferences that are applicable. Let me know what you think. https://onlinelibrary.wiley.com/doi/full/10.1111/mmi.13946 Best, debbie Edited 03 May, 2024 16:22

Link to this post | posted 24 Apr, 2024 19:04
debbie	You are welcome! debbie

Link to this post | posted 24 Apr, 2024 17:02
debbie	Hi Dane, See the attached picture for why I would call a lot of theses proteins membrane proteins and not holins….. yet. Too many to choose from? debbie 392Kb

Link to this post | posted 12 Apr, 2024 00:24

debbie

Hi Fernando, I think I want to stick with what is written in the Cluster O paper. There are 4 transmembrane proteins in the region downstream of lysin A and lysin B. I would call the 4 genes that hit Deep TMHMM transmembrane proteins - membrane proteins. Deep TMHMM is now the preferred method for transmembrane detection. (See Bioinformatics Guide.) And check out that data on phamerator!!! As to why holins may not be detected in HHPRed, I think that list could include that holins demonstrate a lot of diversity, holin activity may need more than one gene, holins are small proteins and must not be easy to crytallize and study. It is not uncommon to not find a hit to a holin. Best, debbie

Link to this post | posted 10 Apr, 2024 00:42

debbie

Hemiparasite afreise As of Dec 2022, are we leaving off the MuF part, based on this update from Debbie? https://seaphages.org/forums/topic/4628/ So now just: capsid maturation protease? (I am annotating Usavi (B1). The gene is here: https://phagesdb.org/genes/Usavi_CDS_10/) In the final annotation of Usavi, would it be Usavi_9 that is the example of this call, rather than Usavi_10? https://phagesdb.org/genes/Usavi_CDS_9/ YEP!!!

Link to this post | posted 08 Apr, 2024 02:06

debbie

Hi Ombeline, I am not one to say that close enough is good enough, but in this case, I think the resemblance will do. I would call this slippage. The explanation is that for many years we believed that all siphoviridae had to have a programmed frameshift. In 2022 Alan Davidson's group published this paper to counter that. https://www.sciencedirect.com/science/article/pii/S0042682221002221 The sequence identified for the programmed frameshift is just too believable to not annotate it! best, debbie