Link to this post | posted 11 May, 2020 11:06
smolloy123	Thanks Debbie! I am actually QCing another DC phage so Ellen's question and your answer helped me as well!

Link to this post | posted 11 May, 2020 00:18

smolloy123

Hi All, We have identified a probably TA pair adjacent to the integrase in the cluster CZ6 phage Moosehead. It looks like the MTb VapBC TA pair. Gp38 with (stop 27,095) has a Pin domain ( PF18478.1) that is typical of the ribonuclease toxin protein and upstream is a gene with good HHPRED matches to VapBC antitoxin of MTb and it also has strong matches to Mer-like HTH DNA binding domains typical of antitoxin proteins. PErmission to add toxin in toxin/antitoxin system, VapBC-like and antitoxin in toxin/antitoxin system, VapBC-like or some other name for this TA system? Here is a paper by the way that describes this TA system in M. smegmatis. Robson J, McKenzie JL, Cursons R, Cook GM, Arcus VL. The vapBC operon from Mycobacterium smegmatis is an autoregulated toxin–antitoxin module that controls growth via inhibition of translation. Journal of molecular biology. 2009 Jul 17;390(3):353-67.

Link to this post | posted 29 Jan, 2020 23:44

smolloy123

Hi All, We didn't have starterator or pham data available on PECAAN early in January when we did a hack-a-thon and it appears that we are still not getting that data the classroom sequences last week. Will these features in PECAAN be available again? For now we are just using the gene list on phagesdb and that works fine but having the starterator reports linked to PECAAN is helpful. Best Sally jawsWPI How long does it take PECAAN to update pham numbers for the Starterator and phageDB links? We are annotating on PECAAN, and over the past 2 days have run into several instances where these links gave the following error message: "Page/Report not found Error 404" for a gene that isn't an orpham. The stand-alone phamerator map pham numbers are accurate (embedded PECAAN pham map numbers are not), and can be used on phagesDB or the stand-along starterator site to get information. So, it looks like this is a PECAAN update issue.

Link to this post | posted 10 Dec, 2019 22:20
smolloy123	you're a genius Chris!

Link to this post | posted 18 Jul, 2019 10:04

smolloy123

Hi Welkkin, There are basically two phams for this small subunit terminase in the Ks. Pham 45539 –> found in all K1, K2, K3, K5, and K6 phage. Pham46057 –> Found in all K4 and K7 phage For Pham 45539, small subunit terminase is called for many phage, a total of 62 call it out of 108 . Many don't call it because they are draft but there are 20 non-draft genomes that do not call it For Pham 46057, there are 15 members total. It is called in only 3 of those genome (of those that do not call it 1 is Malthus and 2 are draft genome). So perhaps those genes need mass corrections?

Link to this post | posted 15 Jul, 2019 09:46

smolloy123

Hi All, I am QCing a cluster K4 phage (Malthus) and am trying to make decisions about calling small and large subunit terminases vs calling a single terminase gene. The authors have called a small subunit terminase for gp8 because it is located upstream of the terminase gene and because a small number of cluster K genomes have called this gene small subunit terminase. In general, cluster K phage have a single terminase gene called. But a few genomes have a large subunit terminase called (typically gp9) and a small subunit called immediately upstream (gp. The HHPRED results do not match any DNA binding proteins but Phyre2 analysis (see attached) brings back a weak match to a ssDNA binding protein but it is the center portion of the protein (around 13-56) and the predicted structure has two anti-parallel alpha helices. From the literature it looks like its hard to determine crystal structure of small subunit terminase but in general they have an N-terminus DNA binding domain, a center oligomerization domain (two anti-parallel alpha helices) plus C-terminus that interacts with large subunit terminase. gp8 in other cluster K genomes (e.g. cluster K1 Pixie_ are of a different pham yet have the same type of matches in Phyre2 (weak matches to ssDNA binding proteins). Can we go ahead and call these upstream gp8 small subunit terminases and gp9 large subunit terminase or should I go with the old consensus of solely calling the gp9 gene "terminase"? Thanks! Sally 268Kb

Link to this post | posted 23 May, 2019 19:25
smolloy123	Hi Welkin, It actually does include a both exonuclease domains and just a smidge of the polymerase domain. I think I need to go the paper for this one. It aligns to residue 604 of the polymerase. Cheers Sally

Link to this post | posted 21 May, 2019 00:43
smolloy123	Hi Debbie, We have this problem every year with certain phage (ironically one phage's name was faintshadow!). Last year, we struggled with a phage called Eden, a cluster EB phage. We were never able to successfully do a restriction digest on it but Dan was able to sequence it. Cheers Sally

Link to this post | posted 19 May, 2019 12:10
smolloy123	Actually there is only the protein map as I could only attach one thing. Attached is the beginning of the HHPRED alignment of gp52 to DNA pol I from E. coli 376Kb

Link to this post | posted 19 May, 2019 12:09

smolloy123

Hi All, I am trying to assign a function to gp52 of NHagos. Nearly every single homologue of this pham has been assigned the function of DNA polymerase I. But gp52 (residues 13-602 out of 602 amino acids total) very precisely aligns only to the 5'-3' exonuclease and the 3'-5' exonuclease domains (residues 4-604 of the DNA polymerase) of DNA polymerase and does not at all align to the polymerase domain. I've attached the HHPRED alignment (in two batches…it was a long one) and a screen shot of the protein feature view of DNA polymerase gene map of E. coli DNA polymerase I. I would not assign a polymerase function to this gene but rather an exonuclease function. Is there a specific exonuclease name I should use for this gene? And if you agree that this is not a polymerase, do we want to change the name of all the homologues? Thanks! Sally 174Kb