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smg366 posted in PhamNexus on SEA-VM

Debbie Jacobs-Sera posted in Assignment of gp28 as holin

nietof posted in Assignment of gp28 as holin

nietof posted in Assignment of gp28 as holin

Debbie Jacobs-Sera posted in Capsid maturation protease and MuF-like fusion protein

All posts created by welkin

| posted 28 Jun, 2018 12:29
welkin avatar
welkin
Not that I am aware.

I think this one should be NKF. good catch Kirk!
Posted in: Functional Annotation → head tail connector synteny in Gordonia cluster DJ
| posted 19 Jun, 2018 14:02
welkin avatar
welkin
Hi ARturo,
Any of those are possible— can you post the .dnam5 file and then we'll take a look?

thanks so much!

Welkin
Posted in: Cluster EC Annotation Tips → Tail Assembly Chaperone in KaiHaiDragon
| posted 18 Jun, 2018 12:12
welkin avatar
welkin
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.
Posted in: Functional Annotation → fushigi_draft 52 homing endonuclease + primase
| posted 11 Jun, 2018 21:45
welkin avatar
welkin
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
| posted 11 Jun, 2018 21:40
welkin avatar
welkin
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?
| posted 11 Jun, 2018 21:39
welkin avatar
welkin
see:

https://seaphages.org/forums/topic/4348/
Posted in: Request a new function on the SEA-PHAGES official list → phage replisome organizer
| posted 11 Jun, 2018 19:02
welkin avatar
welkin
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?
| posted 07 Jun, 2018 12:28
welkin avatar
welkin
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?
| posted 05 Jun, 2018 16:28
welkin avatar
welkin
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
| posted 05 Jun, 2018 16:26
welkin avatar
welkin
I guess my questions here is what is the difference between BrnT and RelE, and can HHPred actually distinguish the difference between the two?
Posted in: Request a new function on the SEA-PHAGES official list → Ribonuclease toxin BrnT