Link to this post | posted 07 Apr, 2025 12:43

debbie

Hi! What are ribosomal proteins doing in phage genomes? https://www.nature.com/articles/s43705-022-00111-w And what accompanying factors could the phages encode? so many questions! Once you find a significant hit, refer to the Approved Function List to see if we have seen it before. Compare your hits to those to glean more information (if possible). If you find a differrent ribosomal protein, request a review by SMART and we can help to figure out what to add to the list. We will follow this paper for naming, https://pubmed.ncbi.nlm.nih.gov/24524803/ At present, we have 2 hit: bL12 and uL24. Good luck! debbie

Link to this post | posted 04 Apr, 2025 17:25
debbie	Hi all, updating will no longer work, but it has to be updated. Follow the directions on this forum post: https://seaphages.org/forums/topic/5577/

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

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

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 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

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

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

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

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