SEA-PHAGES | All posts created by debbie

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Link to this post \| posted 05 May, 2021 01:02
debbie	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
debbie	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 Edited 04 May, 2021 20:48

Link to this post | posted 04 May, 2021 20:47

debbie

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

Edited 04 May, 2021 20:48

Posted in: Functional Annotation → acyltransferase and SGNH domains

Link to this post \| posted 04 May, 2021 19:59
debbie	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

Link to this post | posted 04 May, 2021 19:59

debbie

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
debbie	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
debbie	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
debbie	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
debbie	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 23 Apr, 2021 00:07

debbie

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

Posted in: Functional Annotation → New function call proposal: UDP-galactopyranose mutase

Link to this post \| posted 19 Apr, 2021 20:36
debbie	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 19 Apr, 2021 20:36

debbie

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

Posted in: Choosing Start Sites → Second opinion Cluster F1 Gene Start Site

Link to this post \| posted 14 Apr, 2021 23:22
debbie	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
debbie	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

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All posts created by debbie