Link to this post | posted 07 Jan, 2021 19:59

mdgainey

I am QCing the M3 bacteriophage Nanosmite, I ran into a similar issue and checked the request for new function list and it seems that this issue has not been resolved. The gene is Nanosmite_78 MARNRKSAKAAGARFEAQIAEALRNALGDPNIQRAPRWGAVDKGDIVNVRIDGHDLVIQTKDVTRLDLPKGVGDAKVQAVNAGALAGLFIHKRHGVGDPMKQWVSCTVAELVALITKVPVHPGAEEGIEGRAV All cluster members call holliday junction resolvase which is not on the official functions list, just Ruv-C-like or Ruv-A-like, and endonuclease VII. I am leaning toward just going with the flow and calling it a holliday junction resolvase, even though it it not on the official function list at this time, but would appreciate hearing other's opinions.

Link to this post | posted 10 Dec, 2020 18:14
mdgainey	Thanks Chris, they are going to test out some samples before we purchase one, and if I can get it to work well, I would be happy to share protocols.

Link to this post | posted 05 Dec, 2020 19:03
mdgainey	Hi all, has anyone used an SEM with a TEM detector to image their phages? We are hopefully going to be getting a new SEM with a TEM detector for our new science building next year, and I am hoping to use it to image our phages in house for the first time. We are still deciding on the specs to purchase, so any specific information would be helpful. Edited 05 Dec, 2020 19:04

Link to this post | posted 03 Jun, 2019 20:12
mdgainey	Okay, I think I will go with NKF.

Link to this post | posted 03 Jun, 2019 19:56
mdgainey	Thanks Debbie, I will rerun HHPRED, I was just going to call them assembly chaperones based on synteny.

Link to this post | posted 03 Jun, 2019 19:51

mdgainey

I am finishing up the new Micro singleton FuzzBuster that has some similarities to the cluster EI phages. I have not called a Major Capsid, but about half of other annotators call pham 10363 (FuzzBuster_31) a Major Capsid. I don't see any evidence for this and feel I should get nice HHPRED hits for a Major Capsid. I am not sure if this was called based on synteny alone, but perhaps I am missing something. I am leaning toward NKF.

Link to this post | posted 03 Jun, 2019 19:25

mdgainey

I am finishing up the new Micro singleton FuzzBuster that has some similarities to the cluster EI phages. The tail assembly chaperone genes are orphams, but do have some blast hits to those found in the EI phages,EC phages, and one singleton Hendrix. None of the EI's or EC's call a frame shift but Hendrix does. I have attached a powerpoint with some screen shots of Fuzzbuster, Hendrix, and an EI. The EI's don't have a glycine in the same area as FuzzBuster and Hendrix. My question is would you call a frameshift here, and if so how would you call it -1? Thanks, Maria 130Kb

Link to this post | posted 26 Feb, 2019 16:18
mdgainey	Thanks Chris, I will wait a few hours and try it again=)

Link to this post | posted 26 Feb, 2019 15:19
mdgainey	I am having some trouble with the starterator reports in PECAAN, the phagesdb gene list, and on the WUSTL site. I checked on phamerator and the phams#'s I am using are still correct. Is anyone else having this issue? I was hoping to check my student's gene calls today.

Link to this post | posted 02 Jan, 2019 20:53

mdgainey

Hi all, I am currently working on QCing cluster N BabeRuth from our 2018 faculty hackathon. On the official functions list is says the Xeno_32 is the example for the toxin in toxin/antitoxin system, HicA-like, but this is not called in Phamerator. BabeRuth_40 is in the same pham as Xeno_32 (Pham 3607), we have currently annotated this as a membrane protein but could switch it to HicA-like if this is correct. In the prophage-mediated defense cluster N paper in figure 4 I think they are just labeled these as membrane proteins. Is this an error on the official functions list? I think BabeRuth_37 should be assigned the HicA-like toxin/antitoxin function based on HHPRED data and these are labeled as toxin in figure 4 of the paper, but see no such support for 40. BabeRuth_40 MENVPPSPPPGWYPDPVGSGGQRYWDGQRWTEHYAPPAVAAQIADRRFTVNYGFALLAFFSLLATVGLPLLAMAGGAGADVGPFAILWMLWGGMWTLVWTAFAIQHTLRNRR BabeRuth_37 MNRRIESLGGVQTRQRGSHRRYAVTYTDEMGIVRSAFTTVQQHKSQEIPLGTLRAIQRDLEPAFGKGWLLG