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 13 Apr, 2022 14:37 | |
|---|---|
|
It was pointed out to me (Thanks Mitch!) that the motif needed to include "metallo" in your gene call of a metalloprotease is HEXXH. Sorry for the confusion. |
Posted in: Functional Annotation → Metalloprotease or metallopeptidase
| Link to this post | posted 12 Apr, 2022 02:28 | |
|---|---|
|
|
Ann, I ran into this yesterday. Thee is nothing wrong on your end. we just need to reset the privilege. I'll make sure it gets done tomorrow. debbie |
Posted in: DNA Master → Auto-annotation fix for fall 2017 and later
| Link to this post | posted 11 Apr, 2022 15:39 | |
|---|---|
|
|
There is a human element in the processing of Starterator reports. It should appear soon. Thank you for your patience. debbie |
Posted in: Starterator → Pham not found in Starterator
| Link to this post | posted 10 Apr, 2022 19:29 | |
|---|---|
|
|
We have a systematic approach to revising genomes. Just call what you have well and eventually we can work out the rest. Some phages are not ours to change. Nope, no opinion. I think that all TAC homology stems back to lambda and lambda-like phages. |
Posted in: Annotation → TAC in FM cluster
| Link to this post | posted 08 Apr, 2022 21:31 | |
|---|---|
|
|
We are in Ottawa, right, so the nucleotide both regions share is 17167 and not 17164. sorry, i must have been looking elsewhere before. cool. debbie |
Posted in: Annotation → TAC in FM cluster
| Link to this post | posted 08 Apr, 2022 20:07 | |
|---|---|
|
|
I am going to use the gene numbers on phamerator - and I used phage Ottawa to look a bit closer. I think that the two genes i the same pham - 42 and 42 are major tail proteins. The the next one -gene 44 is the "G" of the TAC. There is an opening reading frame with coding potential (stop is at 17367) that is likely the reading frame that "G" slips into, BUT I could not find the slippage. I would call thought the hit is weak, I would call it a TAC. debbie |
Posted in: Annotation → TAC in FM cluster
| Link to this post | posted 07 Apr, 2022 17:06 | |
|---|---|
|
|
Eric, Your version of DNA Master needs to be updated. You must update to get that "secure connections" box in preferences. I believe the problem is that you must run DNA Master as administrator even when you are updating. Check on that and try again. My latest version is 5.23.6, Build 2705, 14 October 2021. |
Posted in: DNA Master → DNAMaster BLAST failure
| Link to this post | posted 06 Apr, 2022 17:49 | |
|---|---|
|
|
In many clusters, there is now cryoEM data that identifies that 2 different genes are needed to make the capsid, one that forms the pentamers and another forming the hexamers. this has been best worked out in Rosebush, a Cluster B2 phage. The hexamer gene is part of pham (102634) that has members in 358 phages that include 4 singletons, and Clusters AD, AP, B, BG, DC, DE, DR, EC, EG, EI, GC, and W. The pentamer gene is part of pham 20839, but there is sequence similarity to 2 other phams - 21303 and 102541.Work is being done to verify whether these proteins fold in a similar manner. We won't call them…yet. But cool. |
Posted in: Annotation → Capsid genes
| Link to this post | posted 06 Apr, 2022 17:34 | |
|---|---|
|
|
Experimental work (CryoEM) done with phage Patience (gp4) has identified a capsid accessory protein that has a homolog in the Cluster Hs. an example is Barnyard gp 3. |
Posted in: Cluster H Annotation Tips → capsid accessory protein
| Link to this post | posted 06 Apr, 2022 17:30 | |
|---|---|
|
|
Gene 4 in Patience is a capsid accessory protein. Experimental work done by Simon White (UConn) to be published soon! |
Posted in: Cluster U Annotation Tips → capsid accesory protein