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
cdshaffer posted in Whole phage starterator reports
cdshaffer posted in Fin anti-sigmaF factor
uOttawaPHAGE posted in Fin anti-sigmaF factor
Debbie Jacobs-Sera posted in Weird domain distribution over "cytosine methyltransferase" hits in an AS3 phage
nic.vega posted in Weird domain distribution over "cytosine methyltransferase" hits in an AS3 phage
All posts created by welkin
| Link to this post | posted 28 Jun, 2018 12:29 | |
|---|---|
|
Not that I am aware. I think this one should be NKF. good catch Kirk! |
| Link to this post | posted 19 Jun, 2018 14:02 | |
|---|---|
|
|
Hi ARturo, Any of those are possible— can you post the .dnam5 file and then we'll take a look? thanks so much! Welkin |
| Link to this post | posted 18 Jun, 2018 12:12 | |
|---|---|
|
|
Cool! I wonder if we can use this one to figure out the boundaries of the others? I think DNA primase with intein is appropriate here. |
| Link to this post | posted 11 Jun, 2018 21:45 | |
|---|---|
|
|
So at this point, June 2018, we are going to stay with the generic toxin/antitoxin labels for these proteins. |
Posted in: Request a new function on the SEA-PHAGES official list → Death on Curing (DOC) toxin/antitoxin in Gordonia terrae cluster DL
| Link to this post | posted 11 Jun, 2018 21:40 | |
|---|---|
|
|
We have no wet bench data for any frameshifts in anything other than the tail assembly chaperones. So while this is cool, we are not going to annotation this with a frameshift between the two pieces. |
Posted in: Frameshifts and Introns → New frameshift in an A1 phage?
| Link to this post | posted 11 Jun, 2018 21:39 | |
|---|---|
|
|
see: https://seaphages.org/forums/topic/4348/ |
| Link to this post | posted 11 Jun, 2018 19:02 | |
|---|---|
|
|
can you give more information about how exactly a replisome organizer is different from the other functions that we have on the official list that are involved in replication? |
Posted in: Request a new function on the SEA-PHAGES official list → phage replisome organizer found in Cluster T; add to Master List?
| Link to this post | posted 07 Jun, 2018 12:28 | |
|---|---|
|
|
As a follow up from Graham: How long is a piece of string?! If [a new MPME] is 1 aa different, that is not enough for it to be MPME3. If it is a truncated version of MPME1, that does not make it MPME3. If there is a new MPME, full length with all of the features, and it is ~75% DNA identity to 1 and 2, then that would be 3. |
Posted in: Cluster F Annotation Tips → MPMEs--which one?
| Link to this post | posted 05 Jun, 2018 16:28 | |
|---|---|
|
|
doesn't sound to me like you can clearly demonstrate DNA ds break repair. From Dave's post, all of those listed require a partner to actually do the repair. I vote NKF for now. |
Posted in: Request a new function on the SEA-PHAGES official list → DNA double-strand break repair protein
| Link to this post | posted 05 Jun, 2018 16:26 | |
|---|---|
|
|
I guess my questions here is what is the difference between BrnT and RelE, and can HHPred actually distinguish the difference between the two? |