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

Link to this post | posted 14 Jul, 2019 21:22

scaruso

Hello, We would like to propose the addition of TerD or tellurium resistance protein, or the equivalent, to the approved function list. We believe pham 15777, which currently includes: Geostin gene 71 (39028 - 39609) FlowerPower gene 76 (39028 - 39609) Fabian_Draft gene 79 (39358 - 39939) Shows compelling evidence for the functional call. Examination of the protein sequence here: >Geostin gp71 MINLTKGSAPVTLSKAARMSVRITWPAATDYDAGAEILYKDGTTESIATFGARGVDAKLTSLTGKVRHNGDATRGAGTATETIDIDHDDEIVEIRPWAYSAQSNGTGSFRKYAVSMEVSNGTDTVKIDANNASNHDNVYTCVPAVLRFTGDGVQVEYAELYSDPRSEARPAFKKSGLLGKLKFTMDGPRNNYK By HHPred: https://toolkit.tuebingen.mpg.de/#/jobs/SEAGEOSTIN71 And by BlastP: https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Get&RID=JPXJD11B01R Shows high coverage and high confidence matches to the tellurium resistance protein TerD in multiple bacterial species. A brief literature search found that the gene has been found in phages infecting : Salmonella and Cronobacter spp.: https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-14-481 and https://atrium.lib.uoguelph.ca/xmlui/handle/10214/7414, Pseudomona spp https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4178739/, Clostridium spp. https://www.ncbi.nlm.nih.gov/pubmed/17322187, and Bacillus spp.: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4178739/ The domain, as shown in Phamerator is also found by the CDD: https://www.ncbi.nlm.nih.gov/Structure/cdd/wrpsb.cgi?RID=JPXJCJHM01R Thanks, Steve Edited 14 Jul, 2019 21:23

Link to this post | posted 01 Jul, 2019 21:02

scaruso

OK, here's a dumb question. But I figure, someone needs to ask them. I have seen the "Number of Genes" field in Phagesdb where it is a total including tRNA genes and where it doesn't include tRNAs gene and, presumably reflects only protein coding genes. I would assume it is supposed to be the CDS number since at the input it says '# of ORFs' not genes, but the output says 'genes.' Can you clarify, so I know for sure? Thanks, Steve

Link to this post | posted 28 Jun, 2019 15:58

scaruso

Excellent, Question, though. I caught up on the meeting that I had to leave from yesterday and have a question that pertains to this. Perhaps the new version of the virtual machine could include some of these useful tools all put together? The new Starterator from Chris, a standalone Aragorn in case we loose it in the future (or it's down again, or until we can host it somewhere), the new version of the splitstree prep-program, and the newest version of the checker? I'd happily upgrade. Steve

Link to this post | posted 25 Jun, 2019 15:41
scaruso	It won't load for me at all, still. I asked some people to try it at the last SMART meeting, and it didn't load for them either, so there may be something going on. Welkin mentioned she heard there may be a retirement coming up. Steve

Link to this post | posted 19 Jun, 2019 13:32
scaruso	Has anyone been having trouble accessing Aragorn? We have not been able to access it for a couple days now. Steve