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All posts created by welkin

| posted 05 Jul, 2018 20:11
Hi Chris,
All of the mass-spec evidence that we have indicates that when there are two start codons back-to-back, it is the downstream one that is correct.

So sounds like you should go with the ATG in this case.

Best,
Welkin
Posted in: Cluster CS Annotation TipsTTG followed by ATG
| posted 05 Jul, 2018 20:09
Sounds good to me.
Posted in: Functional AnnotationCluster A1 terminase, small subunit
| posted 28 Jun, 2018 16:20
Sorry it took me so long to get back to this— I think the way forward is to call them tail assembly chaperones and not to put in the slip.

We probably need to remove it from the other two, as well– they are all probably using the same site and we can't identify it at this time.

Thanks!
Welkin
Posted in: Cluster EC Annotation TipsTail Assembly Chaperone in KaiHaiDragon
| posted 28 Jun, 2018 12:29
Not that I am aware.

I think this one should be NKF. good catch Kirk!
Posted in: Functional Annotationhead tail connector synteny in Gordonia cluster DJ
| 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
Posted in: Cluster EC Annotation TipsTail Assembly Chaperone in KaiHaiDragon
| 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.
Posted in: Functional Annotationfushigi_draft 52 homing endonuclease + primase
| 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 listDeath on Curing (DOC) toxin/antitoxin in Gordonia terrae cluster DL
| 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 IntronsNew frameshift in an A1 phage?
| posted 11 Jun, 2018 21:39
see:

https://seaphages.org/forums/topic/4348/
Posted in: Request a new function on the SEA-PHAGES official listphage replisome organizer
| 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 listphage replisome organizer found in Cluster T; add to Master List?