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Recent Activity
JustinA posted in Plaques appear on spot test, don't appear in titer
Viknesh Sivanathan posted in Plaques appear on spot test, don't appear in titer
JustinA posted in Plaques appear on spot test, don't appear in titer
Viknesh Sivanathan posted in Plaques appear on spot test, don't appear in titer
RyanWheeler posted in Plaques appear on spot test, don't appear in titer
All posts created by debbie
Link to this post | posted 30 May, 2018 00:52 | |
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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 | |
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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 | |
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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 | |
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Thanks Welkin! |
Link to this post | posted 26 Apr, 2018 12:06 | |
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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. |
Link to this post | posted 26 Apr, 2018 11:50 | |
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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 | |
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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 | |
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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 | |
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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. |
Link to this post | posted 01 Mar, 2018 17:25 | |
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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! |