Link to this post | posted 01 Jul, 2017 20:56
lhughes	The official list has RuvC resolvase, but all my HHPRED hits for some of our genes are hitting Holliday Junction Resolvase (which I am assuming, hopefully correctly, is really the same thing by a different name). None of the hits use the RuvC resolvase term. Should I stick with RuvC resolvase or would it be better to start using Holliday junction resolvase? Lee

Link to this post | posted 07 Aug, 2017 04:52

anders

I've got a gene in a C2 that is like this. The HHPred hits are to an archeal Holliday junction resolvase. When I use RuvC or RusA in HHPred, these do not hit this class of Holliday junction resolvases. Here is a paper reports the structure of the top hit: https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkh869. In the introduction, it says that RuvC resolvase and RusA resolvase (from bacteria), and Endonuclease VII (from T4) are also Holliday junction resolvases. All of them are members of the type II endonuclease superfamily. This archael Hj resolvase is similar in structure to the HJ resolvase in Bacillus, RecU. If I understand this right, I feel like if I assign RusA or RuvC or endoVII to this protein, it would certainly indicate that it is a protein that resolves Holliday junctions, but it would not be accurately place the structure into the right structure family. The protein is Phabba_draft_198. These are the HHPred results: https://toolkit.tuebingen.mpg.de/#/jobs/4369808 (available for about 2 weeks, I think). Turns out that Phabba_draft_202 also hits these same structures in HHPred, although it doesn't have an obvious AA match to gp198. 202 hhpred: https://toolkit.tuebingen.mpg.de/#/jobs/9936992 Holliday junction resolvase is an unofficial function that has been assigned to some of its homologs in other phages. Maybe we could have this be an official function and use it when it's not RuvC, RusA, or endoVII. Alternatively, maybe we could name this one, too. HJC Holliday junction cleavage? RecU Holliday junction resolvase? I will make a post in the New functions request area. Edited 07 Aug, 2017 05:08

Link to this post | posted 10 Aug, 2017 17:14
lhughes	Here is some more information: BeardedLady_37 gives hits mostly to the archael HJC on HHPRED (this is a BD1 phage) Sushi23_89 gives one hit to an E.coli HJC and the rest are RuvC (this is a BE1 phage) (data screen shots attached) 265Kb

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 07 Jan, 2021 23:38
anders	Hi Maria, The official function list does have Holliday junction resolvase. I found it near the bottom of the spreadsheet when we annotated some M2s recently. Best, Kirk

Link to this post | posted 08 Jan, 2021 00:33

debbie

Hi all, And remember that Holliday is named after a person, so it is one of the few words that we capitalize. "In 1964, Robin Holliday proposed a model to explain three important events that occur during meiosis in fungi: crossing-over, gene conversion, and postmeiotic segregation." (Holliday Junction Resolvases,Cold Spring Harb Perspect Biol. 2014 Sep; 6(9): a023192. doi: 10.1101/cshperspect.a023192)

Link to this post | posted 23 Jan, 2021 16:19
mdgainey	Thanks Debbie and Kirk,I missed this on the list due to not doing control F with the capital H in holliday. I felt like it should be there, and it is is….. Edited 23 Jan, 2021 16:19