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Recent Activity
All posts created by delesall
| Link to this post | posted 28 Jun, 2018 18:43 | |
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The answer - state both functions: major capsid & capsid maturation protease |
Posted in: Cluster AN Annotation Tips → capsid fusion
| Link to this post | posted 22 Jun, 2018 00:42 | |
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And how should this be labeled? major capsid & capsid maturation protease or capsid morphogenesis protein or? |
Posted in: Cluster AN Annotation Tips → capsid fusion
| Link to this post | posted 13 Jun, 2018 19:26 | |
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Check under help and About! |
Posted in: DNA Master → Important DNA Master Update
| Link to this post | posted 05 Jun, 2018 16:45 | |
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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 | |
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Yes - so the question is go with generic "DNA ds break repair protein" or no function call? |
Posted in: Request a new function on the SEA-PHAGES official list → DNA double-strand break repair protein
| Link to this post | posted 04 Jun, 2018 17:42 | |
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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 | |
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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 |
Posted in: Request a new function on the SEA-PHAGES official list → 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 |
Posted in: Request a new function on the SEA-PHAGES official list → DNA double-strand break repair protein
| Link to this post | posted 02 Jun, 2018 17:38 | |
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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 | |
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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 |