Link to this post | posted 24 Apr, 2018 13:45
welkin	Cluster AS phages encode a tail protein called a "tail spike". Tail spike is equivalent in function to a tail fiber, however, is characterized by triple beta-prisms and beta-coils, resulting in a large structure visible in the TEM. Salmonella phage P22 is the most famous tailspike enabled phage.

Link to this post | posted 24 Apr, 2018 13:25
welkin	there is a single endolysin in cluster AT phages, it is found upstream of the capsid maturation protease and should be labeled "lysin A".

Link to this post | posted 24 Apr, 2018 13:24
welkin	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.

Link to this post | posted 24 Apr, 2018 13:23
welkin	Cluster AT phages have two large terminase genes (not just a large and small subunit).

Link to this post | posted 24 Apr, 2018 13:19

welkin

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.

Link to this post | posted 24 Apr, 2018 13:08
welkin	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

Link to this post | posted 24 Apr, 2018 13:07
welkin	AR phages have contractile tails, and so it is appropriate to use the terms "tail sheath" and "tail tube"

Link to this post | posted 24 Apr, 2018 13:02
welkin	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.

Link to this post | posted 24 Apr, 2018 13:00
welkin	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"

Link to this post | posted 24 Apr, 2018 12:58
welkin	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.