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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 16 Apr, 2018 17:11
welkin avatar
welkin
Cluster ALs do not have a lysin B.
Posted in: Cluster AL Annotation Tips → no lysin B
| posted 16 Apr, 2018 17:10
welkin avatar
welkin
Cluster AL phages have only one endolysin, it should be labeled "lysin A".
Posted in: Cluster AL Annotation Tips → lysin A
| posted 16 Apr, 2018 17:09
welkin avatar
welkin
Cluster AL has only one major tail protein. There are several phages in the database as of April 2018 that show two, and this is not correct.
Posted in: Cluster AL Annotation Tips → one major tail protein
| posted 16 Apr, 2018 17:06
welkin avatar
welkin
Cluster AK has one endolysin, and it should be labeled as "lysin A".
Posted in: Cluster AK Annotation Tips → lysin A
| posted 16 Apr, 2018 17:05
welkin avatar
welkin
Cluster AK does not have a lysin B.
Posted in: Cluster AK Annotation Tips → no lysin B
| posted 16 Apr, 2018 16:58
welkin avatar
welkin
We do not know where the slippery sequence for the frameshift is in this cluster.
Posted in: Cluster DT Annotation Tips → Tail assembly chaperones?
| posted 16 Apr, 2018 16:56
welkin avatar
welkin
Cluster DS contains a phage that was not isolated and sequenced by the SEA-PHAGES program. Its finders chose a different bp1 than we did, and annotated the genome differently. We do not curate, update, or QC this genome.

This phages is:
GMA2
Posted in: Cluster DS Annotation Tips → non SEA-PHAGES genomes
| posted 16 Apr, 2018 16:52
welkin avatar
welkin
Cluster DQ contains a phage that was not isolated and sequenced by the SEA-PHAGES program. Its finders chose a different bp1 than we did, and annotated the genome differently. We do not curate, update, or QC this genome.

This phage is:
GMA6
Posted in: Cluster DQ Annotation Tips → non SEA-PHAGES genomes
| posted 16 Apr, 2018 16:48
welkin avatar
welkin
cluster DM contains a capsid fusion protein in which the capsid, capsid maturation protease, and scaffolding proteins are all fused together in one long gene.
Posted in: Cluster DM Annotation Tips → capsid fusion
| posted 16 Apr, 2018 16:47
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 DM. The functions should be reported as "lysin A, whatever the domain is" to indicate that each gene does not encode the full lysin A.
Lysin A is also inbetween the portal and capsid fusion which is an unusual place.
Posted in: Cluster DM Annotation Tips → lysin A in two parts