Link to this post | posted 17 Aug, 2017 16:00

washj

So this has me intrigued and I took another look at the cluster J terminases. Phyre2 analysis reveals that Klein11 is a DNA packaging protein similar to T4 gp17 (large terminase)- 100% confidence, coverage 77%; based on crystal structures. Klein 11 is homologous to Baka6 which is has a much longer ORF. The N terminal region of Baka6 (not in Klein11) is a intein endonuclease (pi-scei homing endonuclease with protein splicing activity) and the C terminal domain has hits to the t4 gp17 atpase domain. Klein2 is also modeled with 100% confidence to T4 dna packaging protein gp17. So it appears that Klein2 and 11 (as well as Baka 2 and 5) are both large terminase subunits. it doesn't seem that they are different domains of the terminase large subunit. Just to make things more interesting, it doesn't appear that Squint has a 2nd large terminase subunit but it has the version of the large terminase without the intein (Squint10). Klein5 appears to be the small terminase. There is another paper refering to the coiled coil motif in small terminases by Kondabagil and Rao Journal of Molecular Biology Vol358 issue 1 (2006)https://doi.org/10.1016/j.jmb.2006.01.078 Edited 18 Aug, 2017 00:34

Link to this post | posted 14 Aug, 2017 14:15
washj	I think ASC-1 transciption coactivator is OK.

Link to this post | posted 14 Aug, 2017 14:13

washj

HI Welkin, The insertion element is identical to IS1096 which is present in smegmatis~ 16 copies (2278 bp in LouisV14 vs 2275bp in smeg - identical blast alignment e0.0; 3 bp diff may be due to sequencing error). The identification of IS10096 is detailed in the following paper from the Jacobs lab http://jb.asm.org/content/173/24/7772.full.pdf I propose the following designations: tnpA transposase tnpR resolvase Jackie

Link to this post | posted 14 Aug, 2017 13:50
washj	Hi Claire, Welkin had given the ok to add MRE11 double-strand break endo/exonuclease. See the post below: https://seaphages.org/forums/topic/4346/?page=1#post-5533 Best, Jackie

Link to this post | posted 28 Jul, 2017 02:48

washj

TnpA and TnpR encode the transposase and resolvase of the ISL3 family of type II transposons. These two genes are flanked inverted repeats - found in LouisV14 gp34/35. This transposon is distinct from others found in the database such as Omega_21. Shound it be distinguished by calling it TnpA transposase or maybe Tn3 transposase? Likewise for the resolvase - TpnR resolvase or Tn3 resolvase? Thanks!

Link to this post | posted 28 Jul, 2017 02:09

washj

Activating Signal Cointegrator is a RNA binding protein which acts as an transcriptional coactivator and plays an important role in gene transactivation by multiple transcription factors. The gene has been previously annotated (unofficially) as ASC-1 like domain in Zombie_38 and activating signal cointegrator (ASC-1) protein in several other genomes - Kita_62/Jane_38. PHYRE2 search using LouisV14_40 returns 100% confidence to crystal structure of activating signal cointegrator (np_814290.1) from Enterococcus faecalis. HHpred and CCD searches also return hits to ASC.

Link to this post | posted 26 Jul, 2017 00:23

washj

Hi Karen, I ran into a similar problem in trying to identify the small terminase in a K2 phage and so I did some digging and found a paper by Shen et al "Functional Identification of the DNA Packaging Terminase from Pseudomonas.." Archives of Virology 2012 Nov. 157 (11) in which they explained that most terminase small subunits have HTH DNA binding motifs but some don't. They used the program COILS2 (http://www.ch.embnet.org/software/COILS_form.html) to identify the small terminase as it reveals the presence of a coiled coil motif (CCM) which is need for protein dimerization. Based on this, I ran both Baka_2 and Baka_5 and it appears that Baka_5 is the small terminase as it has a CCM motif. Baka_2 does not. Jackie

Link to this post | posted 24 May, 2017 23:59
washj	Should we add HAD superfamily hydrolase to the approved list? Found in K1, supported by HHpred and CD. Thanks, Jackie Edited 25 May, 2017 00:05 59Kb

Link to this post | posted 24 May, 2017 20:17
washj	Hi Veronique, Re the toxin/antitoxin the approved names are as follows: toxin in toxin/antitoxin system, HicA-like antitoxin in toxin/antitoxin system, HicB-like Best, Jackie Edited 24 May, 2017 20:17

Link to this post | posted 23 May, 2017 23:56
washj	Is head morphogenesis protein on the approved list? CD 99.8% to head morphogenesis protein, SPP1 gp7 family.