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All posts created by welkin

| posted 13 Apr, 2018 22:22
welkin avatar
welkin
Lysin B is not adjacent to lysin A in cluster DG, instead it is at the end of the right arm of the genome.
Posted in: Cluster DG Annotation Tips → lysin B in right arm
| posted 13 Apr, 2018 22:19
welkin avatar
welkin
Cluster DF phages contain a recombinase in the right arm that is related to the integrase genes of temperate phages. However, these phages do not appear to contain any of the rest of the necessary machinery for lysogeny (attP, immunity repressor, etc); and so we believe these are not integrases, but rather recombinases, and should be labeled as such.
Posted in: Cluster DF Annotation Tips → not an integrase
| posted 13 Apr, 2018 22:17
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 DF. 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 DF Annotation Tips → lysin A in two parts
| posted 13 Apr, 2018 22:15
welkin avatar
welkin
Cluster DF contains some phages that were not isolated and sequenced by the SEA-PHAGES program. Their finders chose a different bp1 than we did, and annotated their genomes differently. We do not curate, update, or QC these genomes.

These phages are:
Gmala1, GordDuk1, GordTnk2, and GMA3
Posted in: Cluster DF Annotation Tips → non SEA-PHAGES genomes
| posted 13 Apr, 2018 22:11
welkin avatar
welkin
Cluster DE contains a phage that was not isolated and sequenced by the SEA-PHAGES program. Its finders annotated their genomes differently. We do not curate, update, or QC this genome.

This phage is:
GTE6
Edited 13 Apr, 2018 22:11
Posted in: Cluster DE Annotation Tips → non SEA-PHAGES genomes
| posted 13 Apr, 2018 22:08
welkin avatar
welkin
Some Cluster DC phages, like Twister6, contain two integrase genes in the central portion of the genome.
Posted in: Cluster DC Annotation Tips → two integrases
| posted 13 Apr, 2018 22:02
welkin avatar
welkin
Cluster DB phages are very plastic in the middle of the genome, near the integration cassette. Some, like Bowser, contain two integrase genes in this region.
Posted in: Cluster DB Annotation Tips → two integrases
| posted 13 Apr, 2018 21:58
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 SOME members of cluster CZ. 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 CZ Annotation Tips → lysin A in two parts SOMETIMES
| posted 13 Apr, 2018 21:55
welkin avatar
welkin
There is a final HNH endonuclease gene at the end of CY genomes that is not predicted by the gene prediction programs.
Posted in: Cluster CY Annotation Tips → Final HNH
| posted 13 Apr, 2018 21:52
welkin avatar
welkin
Cluster CZ phages are very plastic in the middle of the genome, near the integration cassette. Some, like Howe, contain two integrase genes in this region.
Posted in: Cluster CZ Annotation Tips → two integrases