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DNA double-strand break repair protein

| posted 03 Jun, 2018 16:54
In Gordonia phage Fryberger for gp 115 (5651-57652), I have a number of nice HHPred matches (over 99% probability, 68-73% coverage, low E values) with a common theme of DNA double-strand break repair protein, all in bactria. Can we add this function or is there an alternative function call to use
| posted 04 Jun, 2018 00:07
Which DSB repair gene does it hit on? It seems like there are a number of proteins that are involved in dsb repair.
| posted 04 Jun, 2018 00:57
It does not appear to be the same gene in all matches. In order of pperance in HHpred

archeal DNA polymerase II, small subunit, C-terminal metallophosphatase domain
DNA double-strand break repair protein mre11
Exonuclease subunit SbcD
Probable DNA double-strand break repair Rad50 ATPase

| posted 04 Jun, 2018 01:41
I wonder if it is a nuclease ? What is strange is that Rad50 and Mre11 form a complex in yeast, but one is a nuclease (mre11) and the other is an ATPase that helps hold the ends of DNA together (Mre11-Rad50 Promotes Rapid Repair of DNA Damage in the Polyploid Archaeon Haloferax volcanii by Restraining Homologous Recombination
St├ęphane Delmas, Lee Shunburne, Hien-Ping Ngo, Thorsten Aller, PLOS Genetics 2009 https://doi.org/10.1371) and references therein. This paper also has analignment of Mre11 and sbcD that might be useful

It also appears that SbcD usually has a partner sbcC. Does your protein have a partner that is homologous to sbcC? The Mre11 does have a metallophosphatase domain that is associated with the exonuclease.

I am probably not helping much here….
| posted 05 Jun, 2018 16:23
So it sounds to me like the results are listing a number of things that we can't clearly distinguish from each other at this time. Is that true?
| posted 05 Jun, 2018 16:26
Yes - so the question is go with generic "DNA ds break repair protein" or no function call?
| posted 05 Jun, 2018 16:28
doesn't sound to me like you can clearly demonstrate DNA ds break repair. From Dave's post, all of those listed require a partner to actually do the repair.

I vote NKF for now.
| posted 06 Jun, 2018 21:01
I think that the functional call for this particular instance could be nuclease.
 
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