Link to this post | posted 19 Aug, 2018 22:44
dbolliva	Steve, Just my two cents. In looking at the catalytic activity of Lysin B, it appears to be an esterase, hydrolysing an ester bond. This domain seems to be a transglycosylase, which may lead to the cleavage of glycan strands but it is not a hydrolysis like the Lysin B. Thus I would suggest that the glycosyltransferase call is more appropriate. Dave

Link to this post | posted 19 Aug, 2018 22:30
dbolliva	Steve, I have yet to look at the function aspect, but I would recommend you use the GenemarkS that you can run from phagesdb to look for coding potential. It has much more information to offer than what I see uploaded to PECAAN. Dave

Link to this post | posted 21 Jul, 2018 15:05
dbolliva	Cluster J phages can have introns in the major capsid or one of the minor tail proteins. Examples of these are found in LittleE and Baka so it is a good idea to compare your phage with these two and Thibault on phamerator

Link to this post | posted 18 Jul, 2018 19:11

dbolliva

In the genome of Girr that I am Qcing it appears that there is a MPME similar to that seen by Sarah in Zerg. The alignment below is with fruitloop 71 and does not align the C-terminus Alignment statistics for match #1 Score Expect Method Identities Positives Gaps 151 bits(382) 3e-54 Compositional matrix adjust. 66/82(80%) 73/82(89%) 0/82(0%) Query 14 MPTTEHGSDVQHLSPEHRDRAWRDRFNARWHHDYGGWIRTRPQDDASTFALIPDERYGPF 73 M + G+D+ HLS EHRDRAWRDRFNARWHHDYGGWIRTRPQDDASTFALIPDERYGPF Sbjct 1 MKASTQGTDIPHLSSEHRDRAWRDRFNARWHHDYGGWIRTRPQDDASTFALIPDERYGPF 60 Query 74 TEDHSCPYCLVVHPPEDCPVLN 95 EDHSCPYCL +H P++CPVL+ Sbjct 61 VEDHSCPYCLAIHQPQECPVLS 82 I also tried with BPs58 uery 1 MFPITDTRREMTTMPTTEHGSDVQHLSPEHRDRAWRDRFNARWHHDYGGWIRTRPQDDAS 60 MFPITDTRREMTTMPTTEHGSDVQHLSPEHRDRAWRDRFNARWH+DYGGWIRTRPQD+AS Sbjct 1 MFPITDTRREMTTMPTTEHGSDVQHLSPEHRDRAWRDRFNARWHYDYGGWIRTRPQDEAS 60 Query 61 TFALIPDERYGPFTEDHSCPYCLVVHPPEDCPVLNWREQEL 101 TFALIP + YGPFTEDHSCP CLVVHPPEDCPVL+ L Sbjct 61 TFALIPTKHYGPFTEDHSCPACLVVHPPEDCPVLSGNTDML 101 Just for fun, here is the alignment between Girr (Query) and Zerg (Subject) Alignment statistics for match #1 Score Expect Method Identities Positives Gaps 163 bits(412) 8e-59 Compositional matrix adjust. 76/88(86%) 80/88(90%) 0/88(0%) Query 14 MPTTEHGSDVQHLSPEHRDRAWRDRFNARWHHDYGGWIRTRPQDDASTFALIPDERYGPF 73 MPTTEHGSDVQHLSPEHRDRAWRDRFNARWH+DYGGWIRTRPQD+ASTFALIP + YGPF Sbjct 1 MPTTEHGSDVQHLSPEHRDRAWRDRFNARWHYDYGGWIRTRPQDEASTFALIPTKHYGPF 60 Query 74 TEDHSCPYCLVVHPPEDCPVLNWREQEL 101 TEDHSCP CLVVHPPEDCPVL+ L Sbjct 61 TEDHSCPACLVVHPPEDCPVLSGNTDML 88 Edited 18 Jul, 2018 19:12

Link to this post | posted 28 Jun, 2018 18:00
dbolliva	After discussing with Welkin, there are no currently approved holin calls in the B1 phages. The gene in question is too far from the lysins combined with the relatively low hit. The gene from DonSanchon does have several predicted transmembrane domains so can be called as a membrane protein

Link to this post | posted 28 Jun, 2018 16:59
dbolliva	Currently there is no holin identified in B1 phages? There are a few calls present (Xavier14) but in the homolog DonSanchon 14 the best hit was an HHpred to holin at 75% probability and 33% coverage. Thoughts on this?

Link to this post | posted 22 Jun, 2018 03:11

dbolliva

I spent some time looking at the Catfish genes later in the genome. One of the first questions I ask when considering excise is whether there is evidence for an integrase. It is also great if there is lab evidence of lysogeny. Catfish has a strong hit to integrase in gp38 followed by a repressor at gp 40 followed by a strong hit to excise at gp41. Gp41 is likely to be the escise based on its position relative to the repressor and integrase. Although not impossible, it is pretty unlikely for there to be a second excise. Given this combination of evidence, I think the call for gp32 as a helix turn helix DNA binding protein makes more sense in the total context of the genome.

Link to this post | posted 11 Jun, 2018 21:59
dbolliva	see: https://www.seaphages.org/forums/topic/4412/?page=1#post-5706

Link to this post | posted 11 Jun, 2018 21:36
dbolliva	Frokostdame gene 73 (see PECAAN) has a very good HHpred result to a Pfam for N-terminal phage replisome organiser with 98% probability and 48 percent coverage. Currently there are only two pham members for this gene. There are also HHpred hits to RepA proteins. Edited 11 Jun, 2018 21:37

Link to this post | posted 04 Jun, 2018 01:41

dbolliva

I wonder if it is a nuclease ? What is strange is that Rad50 and Mre11 form a complex in yeast, but one is a nuclease (mre11) and the other is an ATPase that helps hold the ends of DNA together (Mre11-Rad50 Promotes Rapid Repair of DNA Damage in the Polyploid Archaeon Haloferax volcanii by Restraining Homologous Recombination Stéphane Delmas, Lee Shunburne, Hien-Ping Ngo, Thorsten Aller, PLOS Genetics 2009 https://doi.org/10.1371) and references therein. This paper also has analignment of Mre11 and sbcD that might be useful It also appears that SbcD usually has a partner sbcC. Does your protein have a partner that is homologous to sbcC? The Mre11 does have a metallophosphatase domain that is associated with the exonuclease. I am probably not helping much here….