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Recent Activity

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 17 Dec, 2018 16:09
welkin avatar
welkin
I agree! I coulnd't find any strong evidence of the head-to-tail connectors in any of the genes in the DJs.
Posted in: Cluster DJ Annotation Tips → head-to-tail connector complex
| posted 12 Dec, 2018 20:54
welkin avatar
welkin
sounds good to me!
Posted in: Request a new function on the SEA-PHAGES official list → adenylosuccinate lyase for Hiyaa gene 75 @55288
| posted 03 Dec, 2018 13:12
welkin avatar
welkin
Hi Evan,
So here's some questions:
How big are these types of enzymes in general? Does the phage gene encompass the entire enzyme or just the N-terminal domain? Is the N-terminal domain where the catalytic activity is, or is it just a binding region?

Best,
Welkin
Posted in: Functional Annotation → Proposed function alpha-L-arabinofuranosidase
| posted 15 Nov, 2018 13:05
welkin avatar
welkin
Hi Ruth,
Only if there is a specific function. Thanks for checking.
Posted in: Functional Annotation → marking HHpred for unknown function
| posted 19 Oct, 2018 19:11
welkin avatar
welkin
yep– totally agree with Debbie— there isn't enough of it left to warrant "immunity repressor, truncated".
Posted in: Functional Annotation → Truncated Immunity Repressor
| posted 25 Sep, 2018 17:06
welkin avatar
welkin
Cluster S phages have an unusual structural gene organization— some of the minor tail proteins are way over in the right arm.
see:

https://www.ncbi.nlm.nih.gov/pubmed/22357284
Posted in: Cluster S Annotation Tips → minor tail proteins in the right arm
| posted 23 Aug, 2018 18:13
welkin avatar
welkin
sounds good. I'll add both.
Posted in: Request a new function on the SEA-PHAGES official list → new type of nucleotide pyrophosphohydrolase
| posted 23 Aug, 2018 13:44
welkin avatar
welkin
so we already have ADP-ribosyltransferase— how is this different, other than the name?
Posted in: Request a new function on the SEA-PHAGES official list → rifampin ADP-ribosyltransferase
| posted 21 Aug, 2018 17:31
welkin avatar
welkin
There appears to be a predicted tRNA within the boundaries of the predicted tail sheath protein in some of the Cs. In this case, the tRNA should be removed from the annotation.
Posted in: Cluster C Annotation Tips → tRNA vs tail sheath
| posted 20 Aug, 2018 15:57
welkin avatar
welkin
Thanks guys– I left the "2" out of the starting post. You are all correct: B1s do have lysin B.
Posted in: Cluster B Annotation Tips → Lysin B