Link to this post | posted 30 May, 2018 00:52

debbie

I think that when I called this, I decided that thymidylate synthase is a generic enough term that it would be best until more is known. I unfortunately didn't put the more generic term "thymidylate synthase" on the approved list (until today). I didn't use dihydrofolate reductase because it wasn't on the list; it surely could be. Neither are very specific or satisfying, using both seems to be too much. We could add ThyA-like thymidylate synthase, but until someone wants to look at all thymidylate synthases more closely, I think it could be problematic. Chris - thank you for your investigation on this, it was very helpful.

Link to this post | posted 23 May, 2018 16:24
debbie	Unless of course there are 2 genes that have different domains that are part of a lysin (not unlike the Gordonia phages). That is the case in the Cluster AV genomes. The functional assignment for Jasmine gp 22 is best called as "lysin A, amidase domain"; while Jasmine gp 30 is best called as "lysin A, peptidase domain".

Link to this post | posted 27 Apr, 2018 02:28
debbie	Megan, I agree in your assessment. If I am right in the Golden annotation of the slippery sequence, then Adromedas shows a point mutation obliterating the slippage with a stop codon. While I believe that is where the slippage occurs, it is unclear how that works or what the slippage is. So I am confident calling both genes the TAC genes, but no slippage should be annotated.

Link to this post | posted 26 Apr, 2018 17:03
debbie	Thanks Welkin!

Link to this post | posted 26 Apr, 2018 12:06

debbie

Kayla, Hi. I have fixed the file. I believe the issue involves not providing DNA master enough time to build he database correctly. I used a DNA master utility to repack the file (which has no value until I show you what that means). I couldn't quickly find a protocol to this on the on-line bioinformatics guide. i will get it posted soon. If you are coming to the symposium/faculty meeting, let's chat. 1.39Mb

Link to this post | posted 26 Apr, 2018 11:50
debbie	Andrea, The databases need a moment to talk to one another. Once data is updated in Phamerator, phagesDB will follow. You just caught them in the middle.

Link to this post | posted 26 Apr, 2018 11:38
debbie	Hi. My supporting data is: Sitar_31 has a Pfam hit to TAC (90.6%/40% coverage). It is in the right location for a TAC. The G protein most typically hits homologs (vs T). I could not find the slippery sequence when I checked this genome. Could it be a +1 at position 24240, 24242?

Link to this post | posted 13 Apr, 2018 14:40
debbie	I think that this is a gene and the coding potential says to use the longest start. I did not find Starterator helpful. Blast at PhagesDB and NCBI along with HHpred results did not show any functions. CLUSTALW does show the 'insert' you mention, but i don't believe there is anything to say about it at this point (not knowing function or relevance).

Link to this post | posted 27 Mar, 2018 01:40
debbie	I think that at this time, we can only call the G of the G/T frameshift because, there is no start codon in the frame of the T gene nor can I find a slippery sequence as per published literature. So for now, I recommend that we only call the G gene as a tail assembly chaperone if you have supporting evidence. Continue to look for a slippery sequence. Edited 27 Mar, 2018 01:42 35Kb

Link to this post | posted 01 Mar, 2018 17:25
debbie	The last gene in these genomes is an HNH endonuclease. The auto-annotated gene in that space is not it and it is usually on the opposite strand!