Link to this post | posted 11 Dec, 2019 01:44
scaruso	Been using it, and it's great! Steve

Link to this post | posted 01 Dec, 2019 20:21
scaruso	If I can make sure I am perfectly clear? This is generalizable, correct? If we see GTGATG or ATGATG, go with the second as a rule, and not just in clusters O, J, and M. I presume it is also true with TTGATG? Steve

Link to this post | posted 01 Oct, 2019 15:34
scaruso	Hello, I hesitate to ask this question because I don't want to imply impatience. But I want to know what to tell students who are asking me questions. So, here goes. How often are phages entries checked in to PhagesDB? I am hoping to give students some sort of estimate, if possible, and prevent some of the double entries I know you get. Thanks! Steve

Link to this post | posted 18 Aug, 2019 20:03
scaruso	I see you added Topcons now, too. Cool! Steve

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 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 09 Aug, 2019 21:47

scaruso

Hello all, I think I have the 'terminase, small subunit' in IchabodCrane, a BE2, in which it hasn't yet been identified. It looks very similar to gp3 from NEHalo in terms of coverage and the coiled-coils hits using PCOILS. Could you take a look and see if you agree? I think it is a reasonable call. 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 Thanks! Steve I created a fresh post of this labeled BE - terminase, small subunit, here: https://seaphages.org/forums/topic/4942/?page=1#post-7410 Edited 12 Aug, 2019 00:51

Link to this post | posted 03 Aug, 2019 21:15
scaruso	Welkin, Should we use D family protein or protein D family? I think that's all we need, then can submit. Thanks! Steve

Link to this post | posted 16 Jul, 2019 12:51
scaruso	We found a homolog in a Bacillus phage we just annotated, I believe, and called it: DNA mimic domain containing protein, since the coding sequence was larger than the domain you describe above, but contained it. But if it is the right size, perhaps DNA mimic protein might be a good choice? Steve Edited 16 Jul, 2019 13:49

Link to this post | posted 15 Jul, 2019 17:07
scaruso	Excellent, thanks! Steve