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Recent Activity
All posts created by debbie
| Link to this post | posted 07 May, 2021 20:42 | |
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You too! Terrific that you contacted Kirk! Thanks, debbie |
| Link to this post | posted 07 May, 2021 20:03 | |
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Hi Andrea, i do not know how to do this in PECAAN, but in following Kirk's explanation for Coco12, i would annotate it the same way he did. debbie |
| Link to this post | posted 07 May, 2021 19:23 | |
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Hi Kristen and all, This is one of those genes that needs a dig deep. Here are some of what i have been thinking. I am reluctant to call a RecE without a RecT. I don't know how to differentiate between a RecE, a generic exonuclease or the Cas4 family exonuclease. I am looking forward to what we can figure out about these. Good question, sorry to not be of much help. debbie |
Posted in: Functional Annotation → Refining the call for Cas4 family exonuclease vs. RecE-like exonuclease
| Link to this post | posted 05 May, 2021 01:02 | |
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I would delete this gene because we don't believe that 2 genes exist in the same space of a genome. Genes can overlap a bit, but this is completely covered by the forward genes 35 and 37. they are better choices because it is unlikely that a gene would be in the opposite direction 'for no good reason'. What do you think? debbie |
Posted in: Gene or not a Gene → F1 gene needs second opinon
| 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 |