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Cluster BE - terminase, small subunit

| 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:



For reference, NEHalo gp3 in HHPred and PCOILS:


Let me know what you think. Thanks!

Edited 12 Aug, 2019 00:49
| posted 12 Aug, 2019 18:19
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.
| posted 12 Aug, 2019 18:34

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.


| posted 11 Aug, 2022 18:53
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
| posted 12 Aug, 2022 15:33
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.)
| posted 12 Aug, 2022 16:07
Hi Debbie,

Got it! I figured synteny was the reason the other pham members had been assigned that function.

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