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All posts created by welkin

| posted 13 Apr, 2018 21:47
Cluster CX contains several tRNAs in a small cluster in the right arm. Phamerator does not show tRNAs, so there will be a gap in the protein encoding genes in this area in the Phamerator maps.
Posted in: Cluster CX Annotation TipstRNAs
| posted 13 Apr, 2018 21:43
Lysin A and Lysin B are separated by a number of tail proteins, rather than being adjacent.
Posted in: Cluster CX Annotation Tipslysins not adjacent
| posted 13 Apr, 2018 21:36
We do not know where the tail assembly chaperones are in Cluster CW.
Posted in: Cluster CW Annotation TipsTail assembly chaperones?
| posted 13 Apr, 2018 21:36
In the cluster CW phages, the capsid maturation protease, scaffolding, and major capsid protein genes are fused into one long gene. It is likely translated as a single polypeptide that can assembly into a procapsid, and then self-cleaves.
Posted in: Cluster CW Annotation Tipscapsid fusion
| posted 13 Apr, 2018 21:33
Cluster CW contains some phages that were not isolated and sequenced by the SEA-PHAGES program. Their finders annotated their genomes differently. We do not curate, update, or QC these genomes.

These phages are:
GRU3 and GMA5
Posted in: Cluster CW Annotation Tipsnon SEA-PHAGES genomes
| posted 13 Apr, 2018 19:09
The lysis cassette is found within the group of minor tail proteins, rather than upstream or downstream of all the structural proteins.
Posted in: Cluster CV Annotation Tipslysis cassette amidst tail proteins
| posted 13 Apr, 2018 19:07
Cluster CV is very plastic in the central portion of the genome where the integration cassette is located. At least one CV phage, Utz, has two identifiable integrase genes.
Posted in: Cluster CV Annotation Tipstwo integrases
| posted 13 Apr, 2018 19:06
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 CV. 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 CV Annotation Tipslysin A in two parts
| posted 13 Apr, 2018 19:04
Cluster CU phages do not have an obvious lysin B gene.
Posted in: Cluster CU Annotation Tipsno lysin B
| posted 13 Apr, 2018 19:03
lysin A is found within the group of minor tail protein in the left arm, rather than upstream or downstream of all the structural genes.
Posted in: Cluster CU Annotation Tipslysin A located amidst tail protein