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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 24 Apr, 2018 12:57
welkin avatar
welkin
These phages have contractile tails, and therefore it is appropriate to use the terms "tail sheath" and "tail tube" in the annotation.
Posted in: Cluster AO Annotation TIps → tail sheath
| posted 24 Apr, 2018 12:56
welkin avatar
welkin
The ParB in the AOs should be labeled "ParB-like nuclease domain". These phages are not temperate and there is no ParA partner in the genome to allow for plasmid like partitioning of the prophage genome.
Posted in: Cluster AO Annotation TIps → ParB proteins
| posted 24 Apr, 2018 12:53
welkin avatar
welkin
Lysin A is encoded by two adjacent genes within cluster AN, and each portion should be labeled with its specific domain, for example "lysin A, peptidase domain"
Posted in: Cluster AN Annotation Tips → lysin A in two parts
| posted 24 Apr, 2018 12:51
welkin avatar
welkin
The major capsid protein, scaffolding protein, and protease are all encoded by a single gene.
Posted in: Cluster AN Annotation Tips → capsid fusion
| posted 24 Apr, 2018 12:49
welkin avatar
welkin
The major capsid protein, scaffolding protein, and capsid maturation protein are fused into a single protein and encoded by a single gene.
Edited 24 Apr, 2018 12:50
Posted in: Cluster AU Annotation Tips → capsid fusion
| posted 24 Apr, 2018 12:48
welkin avatar
welkin
The tape measure protein is located amidst the minor tail proteins, rather than upstream of them all.
Posted in: Cluster AU Annotation Tips → tape measure
| posted 24 Apr, 2018 12:48
welkin avatar
welkin
Cluster AU phages have two genes that appear to encode major tail proteins.
Posted in: Cluster AU Annotation Tips → two major tail genes
| posted 24 Apr, 2018 12:46
welkin avatar
welkin
there are many many membrane proteins in the AM phages. this makes it very difficult to identify the holin.
Posted in: Cluster AM Annotation Tips → many membrane proteins
| posted 24 Apr, 2018 12:44
welkin avatar
welkin
The partitioning proteins in the AL phages are the "ParB-like nuclease domain" type, and not the sets that are actually causing plasmid partitioning for the prophage. There is no evidence that the AL phages are temperate.
Posted in: Cluster AL Annotation Tips → ParB proteins
| posted 24 Apr, 2018 12:36
welkin avatar
welkin
AK phages have an extra domain fused to their portal proteins. This domain is similar to the F gene of phage Mu, which is a protein involved in capsid morphogenesis.
This gene should be labeled "portal and MuF-like fusion protein"

Revised: Do not call any of the MuF-like minor capsid proteins for now. (6/16/21)
Edited 16 Jun, 2021 21:27
Posted in: Cluster AK Annotation Tips → Portal and MuF-like