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All posts created by welkin

| posted 13 Apr, 2018 21:51
welkin avatar
welkin
Cluster CY phages are very plastic in the middle of the genome, near the integration cassette. Some contain two integrase genes in this region.
Edited 13 Apr, 2018 21:51
Posted in: Cluster CY Annotation Tips → two integrases
| posted 13 Apr, 2018 21:47
welkin avatar
welkin
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 Tips → tRNAs
| posted 13 Apr, 2018 21:43
welkin avatar
welkin
Lysin A and Lysin B are separated by a number of tail proteins, rather than being adjacent.
Posted in: Cluster CX Annotation Tips → lysins not adjacent
| posted 13 Apr, 2018 21:36
welkin avatar
welkin
We do not know where the tail assembly chaperones are in Cluster CW.
Posted in: Cluster CW Annotation Tips → Tail assembly chaperones?
| posted 13 Apr, 2018 21:36
welkin avatar
welkin
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 Tips → capsid fusion
| posted 13 Apr, 2018 21:33
welkin avatar
welkin
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 Tips → non SEA-PHAGES genomes
| posted 13 Apr, 2018 19:09
welkin avatar
welkin
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 Tips → lysis cassette amidst tail proteins
| posted 13 Apr, 2018 19:07
welkin avatar
welkin
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 Tips → two integrases
| posted 13 Apr, 2018 19:06
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 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 Tips → lysin A in two parts
| posted 13 Apr, 2018 19:04
welkin avatar
welkin
Cluster CU phages do not have an obvious lysin B gene.
Posted in: Cluster CU Annotation Tips → no lysin B