Link to this post | posted 07 Aug, 2017 04:58
anders	For such enzymes that are not in the RuvC, RusA, or endoVII families of Holliday junction resolvases. Please see Lee's and my discussion in the Function calling section. Thanks :-)

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 06 Aug, 2017 21:26

anders

Phabba_draft_83 HHPred hits many acetyltransferases. The matches are across most of the acetyltransferase domain in each alignment. This link to HHPred results should be live for about 2 weeks: https://toolkit.tuebingen.mpg.de/#/jobs/6362589. I'm attaching the full HHPred output as text. With aa sequence alignments, the alignment is narrowed to just the central acetyl-CoA binding portion on CDD. Edited 06 Aug, 2017 21:30 187Kb

Link to this post | posted 06 Aug, 2017 04:30
anders	Infernal appears to be covariance model search program for RNA homology searches, from Sean Eddy's lab. https://www.ncbi.nlm.nih.gov/pubmed/24008419/ Edited 06 Aug, 2017 04:32

Link to this post | posted 23 Jul, 2015 16:27
anders	TymAbreu_Draft from Actino_Draft causes starterator to stop at gene 24 with "Startstaerator has encountered an error. Please try again". When individual genes are run around 24, it is only 24 that causes the error.