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All posts created by welkin

| posted 16 Apr, 2018 16:44
welkin avatar
welkin
Lysin A, which is a single multi-domain protein in many Actinobacteriophages, is split at the domain boundaries encoded by two adjacent genes in cluster DL. The functions should be reported as "lysin A, whatever the domain is" to indicate that each gene does not encode the full lysin A.
Posted in: Cluster DL Annotation Tips → lysin A in two parts
| posted 16 Apr, 2018 16:38
welkin avatar
welkin
Cluster CX phages contain a gene that encodes a protein very similar to the integrases of the temperate phages. However, these phages do not contain any other identifiable integration machinery–immunity repressor, CRO, excise, etc; nor have we been successful in isolating lysogens. Therefore, we've decided that the "integrase" is better off labeled as "recombinase".
Posted in: Cluster CX Annotation Tips → not an integrase
| posted 16 Apr, 2018 16:05
welkin avatar
welkin
sounds like you are making a strong case for including the more specific one. Which way are you leaning on this?
Posted in: Functional Annotation → Phosporibosylpyrophosphate synthetase
| posted 16 Apr, 2018 16:04
welkin avatar
welkin
yep.

I don't really like the name "super -infection immunity protein" because there are too many different types of proteins that can accomplish that phenotype.
Posted in: Functional Annotation → Superinfection immunity proteins
| posted 13 Apr, 2018 22:37
welkin avatar
welkin
Lysin A is near the left end of the genome, Lysin B is two genes upstream from the tape measure protein.
Posted in: Cluster DJ Annotation Tips → lysins not adjacent
| posted 13 Apr, 2018 22:36
welkin avatar
welkin
Cluster DJ phages have two genes that are predicted to encode major tail proteins with good bioinformatic support. This has not been demonstrated at the bench yet, however, we are going to label both with the functional label "major tail protein".
Posted in: Cluster DJ Annotation Tips → two major tail genes
| posted 13 Apr, 2018 22:35
welkin avatar
welkin
The capsid maturation protease, scaffolding, and major capsid protein are fused in cluster DJ phages.
Posted in: Cluster DJ Annotation Tips → capsid fusion
| posted 13 Apr, 2018 22:32
welkin avatar
welkin
Lysin A, which is a single multi-domain protein in many Actinobacteriophages, is split at the domain boundaries encoded by two adjacent genes in members of cluster DI. The functions should be reported as "lysin A, whatever the domain is" to indicate that each gene does not encode the full lysin A.
Posted in: Cluster DI Annotation Tips → lysin A in two parts
| posted 13 Apr, 2018 22:26
welkin avatar
welkin
We do not know where the frameshift is in the DH tail assembly chaperones.
Posted in: Cluster DH Annotation Tips → Tail assembly chaperones?
| posted 13 Apr, 2018 22:23
welkin avatar
welkin
We do not know where the frameshift is in the DG tail assembly chaperones.
Posted in: Cluster DG Annotation Tips → Tail assembly chaperones?