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! :-)

Link to this post | posted 30 May, 2018 17:22
delesall	gp 72 in Gordonia phage Danyall has nice HHPred matches to nicotinamide riboside transporter. This function has been called in Gordonia phage Wizard but is not on the approved function list. Add?

Link to this post | posted 29 May, 2018 20:40
delesall	We are annotating Rofo. In a couple of related phages (Vivi2 and Lennon), homologs of genes 4 and 6 have been called membrane proteins. However, gp 4 has no predicted TMH, so mistake? gp 6 does have 1 TMH but its location - between terminase and portal - makes me think this function call is suspect. Any insights?

Link to this post | posted 29 May, 2018 19:54
delesall	I'm reviewing the annotation of Danyall, a DC phage. There are two rather long genes, 35 and 38, between the tapemeasure and the lysin genes that have been called Minor tail genes in Twister, another DC phage. Besides that and synteny, no other info supports function call. So, call function based on synteny?

Link to this post | posted 17 Apr, 2018 15:31
delesall	If in the HHPred alignments, there is no match with a PDB file, then yes NKF is the proper call. I am not sure what you are asking about the portal…

Link to this post | posted 23 Feb, 2018 20:03
delesall	OK Thanks - I think I just needed to update DNAMaster and my post was supposed to read "asn" files! I love autocorrect, not!

Link to this post | posted 23 Feb, 2018 18:45
delesall	has anybody tried to recently generate ash files in DNAMaster? I get nonsense…

Link to this post | posted 21 Feb, 2018 23:17
delesall	And this is not an issue due to wrong lengths being entered when you entered the start and stop coordinates for each region? Or did those values not transfer after merge? I seem to recall getting weird messages from DNAMaster when that has happened…