Link to this post | posted 12 Aug, 2019 00:47

scaruso

Hello all, I think I might have the 'terminase, small subunit' in the BE2 IchabodCrane, which hasn't yet been identified. It looks very similar to gp3 from NEHalo in terms of coverage and the coiled-coils hits using PCOILS described in the forum post: https://seaphages.org/forums/topic/4736/. IchabodCrane_gp121 MKECPICGKDKELDEFGRQITNPSKFYKWCRDCRLSMARRKKNNFDEGRALRSKTVQLRRLTDAQVTEVRLLAEWNTPYTEIAQQYGVSATTISKVVNRGYANVY HHPred https://toolkit.tuebingen.mpg.de/#/jobs/Ichabod_g121 PCOILS https://toolkit.tuebingen.mpg.de/#/jobs/ICH121 For reference, NEHalo gp3 in HHPred and PCOILS: HHPred https://toolkit.tuebingen.mpg.de/#/jobs/NEHALO3b PCOILS https://toolkit.tuebingen.mpg.de/#/jobs/NEHALO3 Let me know what you think. Thanks! Steve Edited 12 Aug, 2019 00:49

Link to this post | posted 12 Aug, 2019 18:19
welkin	Hi Steve, I think 121 is located too far away from the other called terminase gene to be a viable candidate— unless we demonstrate it at the bench. so not for now.

Link to this post | posted 12 Aug, 2019 18:34
scaruso	Welkin, The thing that worries us about both this and Nehal 03 was that it looked a lot like we were seeing just the DNA binding part of a gene, like with the many anti-toxin hits we get that are really just HTH-domains. But it was similar enough to the previous call to merit a look. Thanks! Steve

Link to this post | posted 11 Aug, 2022 18:53

afreise

Hello! I have a follow-up question about another potential small terminase gene, GalacticEye_Draft_6. I've attached a summary of the analysis I ran based on other forum posts on this topic. Key points below: Evidence FOR: Downstream gene is terminase, large subunit. (Synteny) A few other genes in this pham have called terminase, small subunit (all CS phages); they have e-value of 0 on PhagesDB BLAST. PCOILS appears to predict some coil-coil (I’m not sure if I’m interpreting this correctly DNABIND predicts DNA-binding function Evidence AGAINST: NO HHpred hits of significance for this gene when searching thru PECAAN (SCOPE, PDB, PFam). NO evidence of HTH-binding function 84Kb

Link to this post | posted 12 Aug, 2022 15:33
debbie	Hi Amanda, I see no clear evidence for calling this one anything but a Hypothetical Protein. (My best explanation for why some members of the pham are called terminase, small subunit is there was a moment in time when we thought we could call by synteny. But I would not recommend that today.) Best, debbie

Link to this post | posted 12 Aug, 2022 16:07
afreise	Hi Debbie, Got it! I figured synteny was the reason the other pham members had been assigned that function. Thanks, Amanda