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All posts created by scaruso

| posted 12 Aug, 2019 00:47
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
Posted in: Functional AnnotationCluster BE - terminase, small subunit
| posted 09 Aug, 2019 21:47
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
Posted in: Functional AnnotationCluster A1 terminase, small subunit
| posted 03 Aug, 2019 21:15
Welkin,

Should we use D family protein or protein D family? I think that's all we need, then can submit.

Thanks!

Steve
Posted in: Request a new function on the SEA-PHAGES official listTerD, tellurium resistance protein
| posted 16 Jul, 2019 12:51
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
Posted in: Request a new function on the SEA-PHAGES official listnew antirestriction protein type
| posted 15 Jul, 2019 17:07
Excellent, thanks!

Steve
Posted in: Request a new function on the SEA-PHAGES official listTerD, tellurium resistance protein
| posted 14 Jul, 2019 21:22
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
    Posted in: Request a new function on the SEA-PHAGES official listTerD, tellurium resistance protein
    | posted 01 Jul, 2019 21:02
    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

    Posted in: General Message BoardPhagesdb Entry Question
    | posted 28 Jun, 2019 15:58
    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
    Posted in: tRNAsAragorn Issue
    | posted 25 Jun, 2019 15:41
    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
    Posted in: tRNAsAragorn Issue
    | posted 19 Jun, 2019 13:32
    Has anyone been having trouble accessing Aragorn? We have not been able to access it for a couple days now.

    Steve
    Posted in: tRNAsAragorn Issue