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All posts created by welkin

| posted 24 Apr, 2018 13:24
The tape measure protein is not the largest gene in AT phages, instead there appears to be a multi-minor tail fusion gene downstream of the tape measure that is longer.
Posted in: Cluster AT Annotation Tipstape measure
| posted 24 Apr, 2018 13:23
Cluster AT phages have two large terminase genes (not just a large and small subunit).
Posted in: Cluster AT Annotation Tipstwo large terminases
| posted 24 Apr, 2018 13:19
What is a "capsid morphogenesis protein"? Inquiring minds want to know, so I am writing y'all a post about it.

The F protein in phage Mu is a small protein involved in capsid morphogenesis. From the little I can get from poking around and/or pestering phage assembly people, it is probably some kind of small stabilization protein, or a decoration protein. Deleting F from the Mu genome still gives you intact particles under the microscope. It is unclear from what I have read as to whether or not these virions are infectious.

The presence of this domain is what yields the “capsid morphogenesis” functional label in our actinobacteriophage annotations. The MuF domain appears in a number of actinobacteriophage, notably the Cluster Bs, and it appears fused to different things— the protease, the portal, and I think even to the capsid itself.
So yes— you can have both a protease and a morphogenesis protein as they may or may not be fused together.
Posted in: Functional AnnotationCapsid morphogenesis protein
| posted 24 Apr, 2018 13:08
Cluster AR phages have a endolysin gene adjacent to the minor tail proteins, and then another gene with a lysin domain in the right arm. This second smaller gene should be labeled "endolysin domain"
Edited 19 Feb, 2020 17:23
Posted in: Cluster AR Annotation Tipsendolysin domain
| posted 24 Apr, 2018 13:07
AR phages have contractile tails, and so it is appropriate to use the terms "tail sheath" and "tail tube"
Posted in: Cluster AR Annotation Tipstail sheath
| posted 24 Apr, 2018 13:02
AQ phages encode tRNAs, which will not be displayed on Phamerator maps. If your AQ phage has a gap in the map and a jump in gene numbering flanking the gap, that may be why.
Posted in: Cluster AQ Annotation TipstRNAs
| posted 24 Apr, 2018 13:00
The ParB protein in the AP phages is not involved in partiioning the prophage genome, and these phages are not temperate. These genes should be labeled "ParB-like nuclease domain"
Posted in: Cluster AP Annotation TipsParB proteins
| posted 24 Apr, 2018 12:58
It appears that a number of minor tail proteins are fused in the AP phages, yielding a single gene that is actually longer than the tape measure protein.
Posted in: Cluster AP Annotation Tipstape measure
| posted 24 Apr, 2018 12:57
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 TIpstail sheath
| posted 24 Apr, 2018 12:56
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 TIpsParB proteins