Link to this post | posted 29 Dec, 2017 18:17

dbolliva

Hi, I have been reviewing the annotation of our phage Tesla in the S cluster. At the very end of the genome genes 109 and 110 both appear to be involved in nitrogen metabolism potentially. Gene 110 has hits in both the conserved domain database and hhpred to glutamine amidotransferases. The blast hits are to glucosamine -6 phosphate synthetases in the DNA Master file There are two classes of this enzyme and this is the class II which unfortunately does not have diagnostic conserved residues. It is known that these domains can be present in a wide variety of enzymes and are usually only a part of the whole enzyme. In this case the first 100 amino acids of the predicted polypeptide shows this domain in the CDD figure. I would like to propose a function that is glutamine amidotransferase domain for this polypeptide. gene 109 has hits in Blast seen in the DNA master file to amidoligases from Mycobacterial species, and the HHpred result hits to a protein called YbdK from both Salmonella and E. coli. YbdK is an enzyme that is involved in glutathione biosynthesis and attaches the nitrogen from glutamine to cysteine. In the absence of wet bench evidence for the role in glutathione biosynthesis, I think it is still possible to indicate this enzyme is involved in transferring amido groups. Edited 29 Dec, 2017 18:51 702Kb 160Kb 162Kb 151Kb 160Kb

Link to this post | posted 29 Dec, 2017 16:47
dbolliva	Sally, Steve has made it so you can shift genomes left and right relative to each other so you can line it up. Pretty cool. Dave

Link to this post | posted 28 Dec, 2017 19:16
dbolliva	Hi Sally, It has also been misbehaving for me. Dave

Link to this post | posted 17 Aug, 2017 14:31
dbolliva	Cluster B1s definitely have lysinB calls. As far as I can tell the Holin has not been identified in B1s. It most assuredly has one but it is not clear which gene it is.

Link to this post | posted 17 Aug, 2017 14:22
dbolliva	Thomas, The server that stores DNAMaster and does updates has been offline due to some reconstruction at the university where it is housed. Others might be able to tell you when this might be fixed. Dave

Link to this post | posted 16 Aug, 2017 20:55

dbolliva

I(n reviewing a cluster C phage I found a pham that has been called as a Zn-finger binding domain protein ex. (Ava3_101) when I just did HHpred I received results sugesting there is a domain that is hared with an endodeoxyribonuclease from the phage T7 that is involved in resolving Holliday junctions. (https://toolkit.tuebingen.mpg.de/#/jobs/2374445). Currently there are two classes of resolvases we can call, but this deos not seem to beither of those. What does everyone think? Many of the calls are also endodeoxyribonuclease I that is also not an approved function. Dave

Link to this post | posted 16 Aug, 2017 16:58
dbolliva	I thought we were calling it NKF because it is unlikely to be a terminase?

Link to this post | posted 15 Aug, 2017 19:47

dbolliva

Hi Veronique and Karen, Just to muddy the waters a bit about ribonucleotide reductases is that are two classes that are found in bacteriophages (Ribonucleotide reductases: essential enzymes for bacterial life Eduard Torrents in Frontiers in Cellular and Infection Microbiology) One does not care if oxygen is around and uses B12 (adenosylcobalamin)(class II) at the active site and the other one is considered anaerobic and uses Adenosylmethionine at the active site (class III). There are also two other subclasses (Ia and Ib) of ribonucleotide reductases found in the eubacteria that have not yet been associated with bacteriophages. The three main classes do not really have any sequence similarity. The hits for the Redrock_53 protein are all to class II RNR's. The one BLAST hit I see for RNR is from a phage and I don't see any HHPred results for RNR's. The HHPred really seems to argue for the PAPS reductase PAPS reductase seems like the better call based on all the information together. Dave

Link to this post | posted 14 Aug, 2017 22:43

dbolliva

In pham3247 (for example Kugel_77 there are calls for repressor and immunity repressor, but in the cluster J phages it appears to be called mostly as function unknown. It is pretty far on the right in the cluster J phages (Squint_188 ) that I called as a helix-turn-helix DNA binding domain. Without wet bench evidence in the cluster J's how should we be calling this? The best hit for the gene I am looking at right now is for an RNA polymerase sigma factor and then a number of HTH containg proteins. Ideas? best, Dave Edited 21 Feb, 2018 16:12

Link to this post | posted 10 Aug, 2017 14:46
dbolliva	Karen, That is indeed the "holin" I am looking at in Dmpstrdiver. It does not really seem like one to me based on all the evidence we have but I was wondering if there was evidence I don't know about for why this has been called a holin. Best, Dave