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
All posts created by debbie
| Link to this post | posted 21 Aug, 2023 16:35 | |
|---|---|
|
I agree with your student. I would not call it. From my collegue, Christian Gauthier, "It looks to have an extremely poor D-loop and a weird anticodon loop. Acceptor stem and pseudouridine stem/loop both look OK. If I were a gambling man, I’d speculate that there used to be a tRNA there, but it has undergone some mutational decay and is almost certainly defective. I wouldn’t be inclined to annotate it." Best, debbie |
Posted in: tRNAs → tRNA enigma in Enygma
| Link to this post | posted 08 Aug, 2023 13:24 | |
|---|---|
|
|
The immunity repressor (pham 99175) from cluster A is present in other cluster genomes along with their own cluster specific immunity repressor– specifically C1 (LittleE) , K (, and F1(DLane), CA (Phrankenstein), J(Courthouse), and K (SamScheppers). Graham described this “immunity theft” in Pope et al 2011 in PLoS One https://pubmed.ncbi.nlm.nih.gov/21298013/ From Rick Pollenz: Some of the cluster F1 (and the others Debbie mentioned) have TWO “immunity repressors”, one that is grouped to those mostly from cluster A (Pham 99175) and a second one that is specific to the cluster phage. These rogue one is typically found in a set of 2-3 reverse genes upstream of the integrase. The 2nd repressor is found downstream of the integrase in a 2nd set of reverse genes and groups to a different PHAM. Both sets of reverse genes are on during lysogeny and this is nicely illustrated in the RNA seq figure 4 for phage Fruitloop in the gp52 Wag paper (https://onlinelibrary.wiley.com/doi/10.1111/mmi.13946) where gp37 is the “rogue” hetroimmunity repressor and gp44 is the putative immunity repressor. |
| Link to this post | posted 08 Aug, 2023 13:22 | |
|---|---|
|
|
The immunity repressor (pham 99175) from cluster A is present in other cluster genomes along with their own cluster specific immunity repressor– specifically C1 (LittleE) , K (, and F1(DLane), CA (Phrankenstein), J(Courthouse), and K (SamScheppers). Graham described this “immunity theft” in Pope et al 2011 in PLoS One https://pubmed.ncbi.nlm.nih.gov/21298013/ From Rick Pollenz: Some of the cluster F1 (and the others Debbie mentioned) have TWO “immunity repressors”, one that is grouped to those mostly from cluster A (Pham 99175) and a second one that is specific to the cluster phage. These rogue one is typically found in a set of 2-3 reverse genes upstream of the integrase. The 2nd repressor is found downstream of the integrase in a 2nd set of reverse genes and groups to a different PHAM. Both sets of reverse genes are on during lysogeny and this is nicely illustrated in the RNA seq figure 4 for phage Fruitloop in the gp52 Wag paper (https://onlinelibrary.wiley.com/doi/10.1111/mmi.13946) where gp37 is the “rogue” hetroimmunity repressor and gp44 is the putative immunity repressor. |
| Link to this post | posted 03 Aug, 2023 20:20 | |
|---|---|
|
|
Hi Steve, Will you record? Thanks, debbie |
Posted in: General Message Board → Observable Office Hours
| Link to this post | posted 31 Jul, 2023 19:31 | |
|---|---|
|
|
The approved function list says you have to have a transposon to have a transposase. I don’t know the answer to that. I would ask that you looks as well as you can and if you don’t find something that looks like a transposon, just call the transposase and make note on your cover sheet. Another thing to consider is the types of transposons – papers will define the ends and that may help you find the transposon. |
Posted in: Functional Annotation → Identify transposons
| Link to this post | posted 31 Jul, 2023 14:22 | |
|---|---|
|
|
Kathleen, Yep. debbie |
Posted in: Functional Annotation → WhiB family transcription factors
| Link to this post | posted 11 Jul, 2023 18:17 | |
|---|---|
|
|
Hi! The server is down. Please refer to this post for updates. https://seaphages.org/forums/topic/5569/ |
Posted in: DNA Master → DNA master server down?
| Link to this post | posted 11 Jul, 2023 18:15 | |
|---|---|
|
|
Liz, i just inquired today. It is still not available. debbie |
Posted in: Bioinformatic Tools and Analyses → DNA Master not updating
| Link to this post | posted 29 Jun, 2023 01:49 | |
|---|---|
|
|
Hi all, Still working on it. Likely will not be available until the week of July 9. if you are a SEA-PHAGES faculty member and if you have an URGENT needed for a very tricky workaround, contact Kristen Butela KAB340@pitt.edu. There are no new updates to DNA Master (last build is 2705, but even 2701 will work), so they can ignore update errors. Their programs will work just fine without any need to update for the time being. If people are just getting the update error on existing installs, then they should just turn off automatic updates for now. Only faculty who need a fresh installation need to contact Kristen for a manual update. debbie |
Posted in: Bioinformatic Tools and Analyses → DNA Master not updating
| Link to this post | posted 28 Jun, 2023 20:17 | |
|---|---|
|
|
Hi Marie, I agree,141 is Hypothetical Protein for now and you can assign ADP-ribosyltransferase to 142. interesting, GeneMark seems to include the preceding gene in a frameshift like thing….. (not that we are calling any of that…  Thanks for including the data. debbie |