Welcome to the forums at seaphages.org. Please feel free to ask any questions related to the SEA-PHAGES program. Any logged-in user may post new topics and reply to existing topics. If you'd like to see a new forum created, please contact us using our form or email us at info@seaphages.org.
Recent Activity
anti-CBASS type III-C protein
| Link to this post | posted 06 May, 2024 19:37 | |
|---|---|
|
Hi! This is an investigation of function for Balomoji protein #102 (Pecaan) or 102 (final DNAMaster file), genome coordinates 60991-61688, pham 163488. We answer the required questions and make a pitch in this google doc for consideration of function related to cyclic trinucleotide binding anti-CBASS proteins, inspired by Dr. Bondy-Denomy's SEA Symposium presentation. Allison and two fantastic students who did this work, Harshini and Mariya |
529Kb| Link to this post | posted 10 May, 2024 01:15 | |
|---|---|
|
Alison and your students, Thank you for your awesome work on this. Maria Gainey presented this and her similar protein at our SMART meeting today and a discussion ensued. For now, we recommend that you call this protein "cyclic nucleotide inhibitor". best, debbie |
| Link to this post | posted 10 May, 2024 16:18 | |
|---|---|
|
Hi Alison, great work! I am going to contact you to share some additional information and then we can post additional details here. I think a more specific name than the one I suggested yesterday, would be "cyclic nucleotide sequestering protein" that is what I am going to go with for now. |
| Link to this post | posted 11 May, 2024 14:01 | |
|---|---|
|
|
Awesome thank you!! |
| Link to this post | posted 09 Jul, 2024 14:08 | |
|---|---|
|
|
Upon further reflection, I am going to go with cyclic oligonucleotide sequestering protein. I think that gives us some flexiblity while being clear on what we think the function is. If you have good HHPRED hits to Vs.4 from T4 and anti-CBASS protein (Acb2) P26 from pseudomonas phage PaP2, and your protein models well as a hexamer (using AlphaFold) I think that we should call these. |
| Link to this post | posted 09 Jul, 2024 14:32 | |
|---|---|
|
|
Maria, What gene is your example? I'll add this to the approved function list! debbie |
| Link to this post | posted 09 Jul, 2024 15:01 | |
|---|---|
|
|
Thank you Debbie! I am finalizing my genome this week and will post the final gene # for Wolfstar as an example, once I am sure it will not change. |
| Link to this post | posted 09 Jul, 2024 17:43 | |
|---|---|
|
|
Woohoo!! "good HHPRED hits to Vs.4 from T4 and anti-CBASS protein (Acb2) P26 from pseudomonas phage PaP2"- definitely. We could post a couple of instructions on using AlphaFold3 server here, and link it to the approved function listing. The webserver makes it as trivial as an HHPred search, but the unknown might feel like a barrier to some. See if I put enough in the attachment? Webserver link: https://alphafoldserver.com/ Settings: molecule type is protein, copies is 6 for hexamer See attachment for screenshots. [The sequence percent identities are quite wide for these phams (there are at least 3). If you're going to list a gene as a guideline as homology, proteins from the other phams won't have much homology to Wolfstar gp30-ish.] |
| Link to this post | posted today, 17:36 | |
|---|---|
|
|
Hi Alison, I think this looks nice. Debbie for the example, you can use Wolfstar gp30. Thank you! Maria |