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Cluster A1 terminase, small subunit
| Link to this post | posted 02 Jul, 2018 20:37 | |
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NEHalo gp3 (http://phagesdb.org/genes/NEHALO_DRAFT_3/) currently Pham 37118 ) is called in several phages as "terminase, small subunit" or "tail protein" in four other phages. The sole HHPred match at 94% probability is to PF05119.11 Terminase_4, phage terminase, small subunit but is not linked to a crystal structure in the PDB. This match has an E-value of 0.17 with coverage of 47%. All other matches show low probability scores of 40% or below. COILS did not reveal the coil-coiled domain that is typically found in many small subunit terminase sequences in gp3. I ran the sequence through Phyre2 (output attached) and got low confidence matches to the regulatory domain of mycobacterial adenylyl cyclase rv1264 (80; 12% id) and a phage tail protein (40.6, 22% id). No other evidence of the call for terminase, small subunit was found other than Blast matches to previously annotated phages and that one HHPred hit with low e-value. Should this call of "terminase, small subunit" be changed to NKF? Gp10 is annotated as "terminase, large subunit" and has well supported HHPred matches to other large terminases. There are a few NKF genes located in between the putative "terminase, small subunit" gp3 and gp10 from a synteny perspective. |
282Kb| Link to this post | posted 03 Jul, 2018 15:45 | |
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Hi Kristen, The small terminases are very diverse which is probably why it is not linked to a crystal structure although it has a high probability match in HHpred to a terminase small subunit. Nehalo gp3 has the hallmarks of a small terminase subunit in that it is predicted by DNAbind as a DNA binding protein, it is predicted to have a HTH motif and the COILS2 output is similar to T4 gp16, one of the most well studied small terminases - see attached document. COILS2 uses an algorithm that compares the sequence of interest to known two strand coiled coils, so low probabilities don't necessarily mean that the protein of interest does not have coiled coil domains. I think that there is enough evidence to call Nehalo gp3 as a small terminase subunit but of course the final word lies with the Pitt team. |
| Link to this post | posted 05 Jul, 2018 20:09 | |
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Sounds good to me. |
| Link to this post | posted 05 Jul, 2018 20:23 | |
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Thanks Jackie and Welkin! Should this be added to the "Cluster Specific Annotation Tips" forum for Cluster A phages? |
| Link to this post | posted 09 Aug, 2019 21:47 | |
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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 |