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Recent Activity
All posts created by debbie
| Link to this post | posted 04 May, 2021 20:47 | |
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Becky, I wrote this way before Chris posted. So to muddle this a bit. Hi. I think I would like to call this O-acetyltransferase A. I have attached an article that describes this gene as having 2 domains, which I believe I see in LonelyBoi_31, namely an acetyltransferase and a SGNH hydrolase fold. Let me know what you think, debbie https://www.sciencedirect.com/science/article/pii/S0021925817494105?via%3Dihub |
Posted in: Functional Annotation → acyltransferase and SGNH domains
| Link to this post | posted 04 May, 2021 19:59 | |
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Hi folks, I need more info. What is the relationship with the upstream and downstream gene in this genome? Cluster F genomes are chucked full of tiny genes that have the 4 bp overlap with each other. If this gene has that I would call it. Also blastn the sequence to see if this is more highly conserved. If it is, does that influence your call? Looking forward to what you are thinking? Send the .dnam5 file is you want me to look further. Thanks, debbie |
Posted in: Gene or not a Gene → F1 gene needs second opinon
| Link to this post | posted 03 May, 2021 12:56 | |
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Hi, I would use this terminology: RepA-like replication initiator What do you think? debbie |
Posted in: Request a new function on the SEA-PHAGES official list → phage replisome organizer found in Cluster T; add to Master List?
| Link to this post | posted 27 Apr, 2021 13:18 | |
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It could also be that a Visuals Basic package is missing https://www.microsoft.com/en-us/download/details.aspx?id=5555 |
Posted in: DNA Master → Scroll bar in six frame translation
| Link to this post | posted 27 Apr, 2021 13:03 | |
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Hi Fernando, I think you will need to install windows drivers again. I am not sure how to do that. Can you check with your IT people? debbie |
Posted in: DNA Master → Scroll bar in six frame translation
| Link to this post | posted 23 Apr, 2021 00:07 | |
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Hi Kristen, This is not a quick answer. Here is where I have gotten. The top hits seem convincing that this is a UDP-galactopyranose mutase. i am hesitant to call it because that is a very specific assignment. I am worried that this gene is ~100 aa shorter than what the crystal structures of UDP-galactopyranose mutase describe, so is it missing a domain? I was not able to dig deep enough to figure out what the C-terminus domain of a UDP-galactopyranose mutase is. (I am guessing it is the missing the mutase part.) Since this is in the oxidoreductase family, I am inclined to be more generic. If you find all of the domains of a UDP-galactopyranose mutase present, then that would settle it. I just ran out of time. What do you think? debbie |
| Link to this post | posted 19 Apr, 2021 20:36 | |
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Hi Andy, This is a big pham of genes with no easy answers about starts. It is an easy function call, with this gene being the terminase. Starterator was not easily helpful. The conservation of the overlap may just be because that upstream gene is driving that portion of the sequence. There is no good indication for me to push to change what Glimmer and GeneMark agree on. If I recollect correctly, the N-terminus of a terminase gene is its ATPase domain. If you carve out that domain (so that your bioinformatic comparisons don't get overpowered by the rest of the protein) you may be able to align the N-terminus sequence with other ATPase domains and find an alignment that is informative. Without more data, I would stick with the start at 797. Just my two cents on the subject. debbie |
| Link to this post | posted 14 Apr, 2021 23:22 | |
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HI! I think this is just an artifact of programs/databases that are not quite caught up to each other. I think if you wait another day, they'll catch up to one another. debbie |
Posted in: Starterator → Pham not found in Starterator
| Link to this post | posted 08 Apr, 2021 16:46 | |
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Hi Susan, Of the 125 A4 genomes in the database as of this writing, not counting the _Drafts, 3 are miscalled: NorthStar, LeoAvram, and Kingmustik0402. I believe I see a slippery sequence, joining at position 15418 in Lochmonster. I'll get to updating those soon. debbie |
Posted in: Frameshifts and Introns → A4 - no frameshift
| Link to this post | posted 06 Apr, 2021 00:57 | |
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Please use the RNAseq data to call genes in Cluster Q. https://pubmed.ncbi.nlm.nih.gov/23560716/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3641587/ If you don't read this paper, it would easy to over call the genes in this cluster of genomes. In particular, there is experimental evidence for a non-coding RNA between genes 74 and 75. The paper is in direct contrast to coding potential in that region. I will revise Cluster Q genomes soon (I am writing this on April 8,2021 and it is not done yet). Please use Giles and the data in the paper as your guide as you call Cluster Q genomes. |
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