SEA-PHAGES | All posts created by debbie

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Link to this post \| posted 04 Apr, 2025 17:05
debbie	The server that held DNA Master is down (likely permanently). Please follow Kristen Butela's work-around. https://seaphages.org/forums/topic/5577/ debbie

Posted in: DNA Master → DNA Master on M1 Mac

Link to this post \| posted 04 Apr, 2025 17:03
debbie	I think the best call is "ASCE ATPase", that is the term when you can't call it a RecA or provide more specificity. But you know you have an ATP-ase domain, yes? Seems to be missing the C terminus domain of a RecA. Is that what you are asking? debbie

Posted in: Cluster EA Annotation Tips → AAA ATPase or RecA recombinase?

Link to this post \| posted 27 Mar, 2025 17:16
debbie	Fred, Cluster F1 phages are notorious for the 1-4 base overlaps. The reason I like calling the shorter version of the glycosyltransferase is that it is supported by Starterator AND the HHPred doesn't show alignments in the upstream region of PDB glycosyltransferases. Check out the glycosylation paper about Che8. It should provide more information of best call. https://pubmed.ncbi.nlm.nih.gov/37329881/ debbie Remember that no one piece of data tells the story. It is when we put all of the pieces together that we can see best choices.

Link to this post | posted 27 Mar, 2025 17:16

debbie

Fred,
Cluster F1 phages are notorious for the 1-4 base overlaps.
The reason I like calling the shorter version of the glycosyltransferase is that it is supported by Starterator AND the HHPred doesn't show alignments in the upstream region of PDB glycosyltransferases. Check out the glycosylation paper about Che8. It should provide more information of best call.
https://pubmed.ncbi.nlm.nih.gov/37329881/

debbie

Remember that no one piece of data tells the story. It is when we put all of the pieces together that we can see best choices.

Posted in: Choosing Start Sites → Phage DoRead Start at 52714 bp with 8 bp overlap vs start at 52718 with 4 bp overlap?

Link to this post \| posted 26 Mar, 2025 11:34
debbie	Hi all, The GenBank file will need to include Hypothetical Protein or hypothetical protein. NKF will not be accepted. debbie

Posted in: Functional Annotation → hypothetical or NKF

Link to this post \| posted 24 Mar, 2025 15:21
debbie	Hi Ann, Yes, we can resend and depending on the dates of the MTA, no further paperwork is required. Would you send me an email for this (djs@pitt.edu). Please include your shipping address (and phone number), or confirm that information is on seaphages.org. Best, debbie

Posted in: Arthrobacter → Arthrobacter vanishing plaques 2025

Link to this post \| posted 13 Mar, 2025 12:15
debbie	Have you looked here? https://blast.ncbi.nlm.nih.gov/doc/blast-help/ There is a glossary of terms included there. Best, debbie

Posted in: Bioinformatic Tools and Analyses → % Identity vs % Aligned vs % Coverage

Link to this post \| posted 12 Mar, 2025 16:01
debbie	Hi Kieran, I agree with your assessment. debbie

Posted in: Cluster AU Annotation Tips → Called Gene not a Gene

Link to this post \| posted 11 Mar, 2025 20:27
debbie	Hi Fred, First, I believe the title of this inquiry is misplaced. There has never been a 5-rule cutoff. The text uses the word "typically" in the description, so, if you don't mind, I am going to change the title of this post. Next, your genome investigations are hitting the excellent work of Krista Freeman from the Hatfull Lab (soon to have her own lab at Case Western), where she has identified the various tail parts found in Mycobacterium phage Bxb1. Final revisions were accepted yesterday so we will have a paper(in Cell) to reference soon. The PDB for the structural proteins of Bxb1, but needs some tidying up. In the meantime, Here a bit of information to help guide: The tail tip project is PDB 9D93. (There are more projects for the tail tube and the capsid of Bxb1. TBD) 9D93_L: (A, B, C, D, E) is related to tail tube. This particular hit is hitting a small portion of a decoration domain of the tail tube, but NOT the important part of that decoration of the tail tube. Therefore, please call this one a Hypothetical Protein. However, the next gene, gp 24, stop at 25086, IS a hit to Bxb1's tail genes it hits Bxb1_gp34, the "tail wing brush". This is part of the PDB project 9D93_Q. Please use that terminology when calling this protein. And if you hit PDB project 9D93_J, you are hitting part of the tail tube (which we have historically called the major tail protein). More to come. The alpha-fold-chimera X views of all of this is extremely informative. Edited 11 Mar, 2025 20:31

Link to this post | posted 11 Mar, 2025 20:27

debbie

Hi Fred,
First, I believe the title of this inquiry is misplaced. There has never been a 5-rule cutoff. The text uses the word "typically" in the description, so, if you don't mind, I am going to change the title of this post.

Next, your genome investigations are hitting the excellent work of Krista Freeman from the Hatfull Lab (soon to have her own lab at Case Western), where she has identified the various tail parts found in Mycobacterium phage Bxb1. Final revisions were accepted yesterday so we will have a paper(in Cell) to reference soon.
The PDB for the structural proteins of Bxb1, but needs some tidying up. In the meantime, Here a bit of information to help guide:
The tail tip project is PDB 9D93. (There are more projects for the tail tube and the capsid of Bxb1. TBD)
9D93_L: (A, B, C, D, E) is related to tail tube.
This particular hit is hitting a small portion of a decoration domain of the tail tube, but NOT the important part of that decoration of the tail tube. Therefore, please call this one a Hypothetical Protein.
However, the next gene, gp 24, stop at 25086, IS a hit to Bxb1's tail genes it hits Bxb1_gp34, the "tail wing brush". This is part of the PDB project 9D93_Q. Please use that terminology when calling this protein.
And if you hit PDB project 9D93_J, you are hitting part of the tail tube (which we have historically called the major tail protein). More to come.

The alpha-fold-chimera X views of all of this is extremely informative.

Edited 11 Mar, 2025 20:31

Posted in: Functional Annotation → Another minor tail protein in F1 phage DoRead?

Link to this post \| posted 10 Mar, 2025 18:31
debbie	Hi Christy, Yep. It looks like the DNA Master website is down. (I've made an inquiry.) You can find the program that is needed in this forum post. the program is on Kristen Butela's One Drive. Kristen was posting a work around that is not needed, so get the program from her one drive and then closely follow the installation instructions found oh phagesDB. https://phagesdb.org/DNAMaster/ Best, debbie

Link to this post | posted 10 Mar, 2025 18:31

debbie

Hi Christy,
Yep. It looks like the DNA Master website is down. (I've made an inquiry.)
You can find the program that is needed in this forum post. the program is on Kristen Butela's One Drive. Kristen was posting a work around that is not needed, so get the program from her one drive and then closely follow the installation instructions found oh phagesDB.
https://phagesdb.org/DNAMaster/

Best,
debbie

Posted in: DNA Master → Issue uninstalling DNA Master

Link to this post \| posted 03 Mar, 2025 19:57
debbie	Shallee, in a perfect world. you can take 1ul of the sample, make some dilutions, and plate for single plaques. If that doesn't work, there are some additional considerations. (and of course you can start with more than 1ul.) Second step is to pick a single plaque and make a new working lysate, being sure to verify (maybe by pcr) that you have the phage you are interested in. debbie Edited 03 Mar, 2025 19:59

Link to this post | posted 03 Mar, 2025 19:57

debbie

Shallee,
in a perfect world. you can take 1ul of the sample, make some dilutions, and plate for single plaques. If that doesn't work, there are some additional considerations. (and of course you can start with more than 1ul.)
Second step is to pick a single plaque and make a new working lysate, being sure to verify (maybe by pcr) that you have the phage you are interested in.
debbie

Edited 03 Mar, 2025 19:59

Posted in: Phage Discovery/Isolation → Reviving

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All posts created by debbie