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Recent Activity
DNA double-strand break repair protein
| Link to this post | posted 03 Jun, 2018 16:54 | |
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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 |
| Link to this post | posted 04 Jun, 2018 00:07 | |
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Which DSB repair gene does it hit on? It seems like there are a number of proteins that are involved in dsb repair. |
| Link to this post | posted 04 Jun, 2018 00:57 | |
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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 |
| Link to this post | posted 04 Jun, 2018 01:41 | |
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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 Stéphane 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…. |
| Link to this post | posted 05 Jun, 2018 16:23 | |
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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? |
| Link to this post | posted 05 Jun, 2018 16:26 | |
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Yes - so the question is go with generic "DNA ds break repair protein" or no function call? |
| Link to this post | posted 05 Jun, 2018 16:28 | |
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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. |
| Link to this post | posted 06 Jun, 2018 21:01 | |
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I think that the functional call for this particular instance could be nuclease. |