Link to this post | posted 05 Jun, 2018 16:45
delesall	Based on what I can find http://pfam.xfam.org/family/PF14384 BrnT/BrnA belongs to type I toxin-antitoxin while RelE/RelB is a type II. The HHPred match to BrnT is quite nice (99%, low E, covering 80%,. The HHpred match to RelE is quite poor (48% prob, E value greater that 40, covering 50%)

Link to this post | posted 05 Jun, 2018 16:26
delesall	Yes - so the question is go with generic "DNA ds break repair protein" or no function call?

Link to this post | posted 04 Jun, 2018 17:42
delesall	So the HHPred match with a link to a pdb file does give me repA https://www.rcsb.org/structure/4PT7 the short gene that follows also has nice matches to Bacillus subtilis replisome organizer so this protein may be coded by two genes but I will just call function for the first gene!

Link to this post | posted 04 Jun, 2018 00:57
delesall	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 03 Jun, 2018 16:54
delesall	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 02 Jun, 2018 17:38
delesall	PS In both Gordonia phages Eviarto and TimTam, this gene is followed by the replisome organizer (helicase loader/inhibitor protein) so that function should also be added to the list

Link to this post | posted 02 Jun, 2018 17:36

delesall

I have seen good HHpred matches to this protein in a number of phages. In Gordonia phage TimTam and Eviarto, I see a nice match with 97.2% probability and 36% coverage. Here's the definition This entry represents the N-terminal domain of a small family of phage proteins. The protein contains a region of low-complexity sequence that reflects DNA direct repeats able to function as an origin of phage replication. The region is N-terminal to the low-complexity region. Can call eitehr N-terminal phage replisome organiser or Replication initiator protein A But can also go with more generic HTH DNA Binding domain protein

Link to this post | posted 31 May, 2018 17:57

delesall

Where are we with this? We would like to call BrnT-like toxin for gene 38 in GEazy Gordonia phage GEazy gene 38 (30023- 29697, based on the HHpred database, has been identified as having great similarities with Ribonuclease toxin BrnT from Brucella abortus (3U97_A Ribonuclease toxin BrnT). This hit had a probability of 99.19%, and an E-value of 1.1E-12. Gene 38 is 327bp long, which is characteristic of other documented BrnT proteins. However, no antitoxin could be identified, although there were many flanking genes with no identified functions both before gene 38 and after. A two gene operon of toxin and antitoxin genes is characteristic of this toxin system. BrnT toxins have a RelE-like fold that is essential for interacting with the antitoxin. GEazy gene 38: MQYTYLMRIEIKANAQEHGIEGSEIRTVVSYPALEIPIAARRPGAELVLYIGPASDNEPYIEVIADLADAGMAIVFHAMMLRRQLVANLGLTDLLPTNIYGPQRPQRKZ Citations: Heaton, Brook E., et al. "Molecular structure and function of the novel BrnT/BrnA toxin-antitoxin system of Brucella abortus." Journal of Biological Chemistry 287.15 (2012): 12098-12110. HHpred data: https://toolkit.tuebingen.mpg.de/#/jobs/7676101 https://www.rcsb.org/structure/3U97

Link to this post | posted 31 May, 2018 17:39

delesall

I'd like to request adding this function to the approved list The SPP1 phage helicase loader protein is a well-studies phage protein (see reference below). I have seen good HHPred matches to this protein in a number of phages. In Gordonia phage Rofo, gp 57 shows a couple of HHPred matches with 98% probability; 40-43% coverage and low E-values Structural analysis of Bacillus subtilis SPP1 phage helicase loader protein G39P Bailey, S., Sedelnikova, S.E., Mesa, P., Ayora, S., Waltho, J.P., Ashcroft, A.E., Baron, A.J., Alonso, J.C., Rafferty, J.B. (2003) J.Biol.Chem. 278: 15304-15312

Link to this post | posted 30 May, 2018 17:37
delesall	Will do in future but where do I find this forum? Quick search not successful! :-)