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Recent Activity
All posts created by debbie
Link to this post | posted 03 Jun, 2018 20:09 | |
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I think that we have missed a gene in these genomes. Look at the gap between upstream of the tape measure. I don't (yet) see the slippery sequence, but I think that is the T region of the G-T protein of a tail assembly chaperone. |
Posted in: Cluster AN Annotation Tips → tail assembly chaperone
Link to this post | posted 02 Jun, 2018 15:20 | |
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Sally, Hi. What gene are your questions about? The two functions together a DNA binding protein that sticks to the host membrane is more interesting than either a DNA binding protein or a membrane protein. I would call it as you have decided for now, but just curious. 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". |
Posted in: Cluster AV Annotation Tips → lysin A
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! |
Posted in: DNA Master → Saving Blast Results in DNA Master
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. |
Posted in: DNA Master → Saving Blast Results in DNA Master
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. |
Posted in: Web Phamerator → Pham Number Discrepancy
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? |
Posted in: Cluster DE Annotation Tips → Tail assembly chaperones
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). |
Posted in: Gene or not a Gene → Cluster A1 gene question