Link to this post | posted 19 Apr, 2018 14:51
welkin	Yes, looks like Squiddly has two integrases, including one of the same ones that appears in several other gordonias with two integrases: Howe, Utz, Bowser. And yes, you can have two tyrosine ones. We talk about it in the Gordonia paper: http://mbio.asm.org/content/8/4/e01069-17.short Good catch!

Link to this post | posted 18 Apr, 2018 15:58
welkin	I think we should be conservative here and not call anything. I have seen some BLAST results between Bs and other clusters, but the gene organization is not conserved: that is, the genes in Bs with BLAST hits don't have a downstream ORF with a substantial overlap in a different frame. There is something else going on in these phages.

Link to this post | posted 18 Apr, 2018 15:55
welkin	We do not know where the capsid maturation protease or scaffolding proteins are for Cluster D.

Link to this post | posted 18 Apr, 2018 15:55
welkin	we do not know where the frameshift is in Cluster D.

Link to this post | posted 18 Apr, 2018 14:36
welkin	Lee Hughes Welkin Pope Crosby is for Sidney, no? Wasn't sure what you were asking until I googled it I just can't even…. You are sentenced to watch play-off hockey for at least another week.

Link to this post | posted 17 Apr, 2018 18:49
welkin	sounds good to me. make it HU-like domain though. Crosby is for Sidney, no? Edited 17 Apr, 2018 18:51

Link to this post | posted 17 Apr, 2018 18:48

welkin

I think there are several issues here. some misguided phage biologists call the portal protein a "head to tail connector". The portal is not a head to tail connector. There are other smaller proteins that make a complex that binds to the portal and bottom of the capsid in the "neck" region; and these proteins we call the "head-to-tail connector complex" proteins. There are several different ones and we are using a catch-all term for now to address them. However, in some of the crystal structure papers, the portal has been crystallized with several of the head-to-tail connector complex proteins in a big complex. When you align a true httcc protein with HHPred to the PDB, you may retrieve these records, which may include a portal. This can be confusing, because it looks like your result is a portal. it isn't. So: 1) if you already have a portal upstream of the terminase, that's your portal. you don't have another one. 2) you have to have a crystal structure alignment with HHPred to use the term "head-to-tail connector complex". We have changed our criteria for this assignment in the past year, so the database is currently riddled with genes that do not meet this criteria, and need to be corrected. BLAST on phagesdb is not enough, because we know there are things in there that are not correct and need to be fixed.

Link to this post | posted 17 Apr, 2018 12:56
welkin	Cluster AR contains a phage that was not isolated and sequenced by the SEA-PHAGES program. Its finders annotated the genome differently. We do not curate, update, or QC this genome. This phage is: ArV1 (edited) Edited 22 Oct, 2019 14:04

Link to this post | posted 17 Apr, 2018 12:54
welkin	AQ phages have only one endolysin, and it should be labeled "lysin A".

Link to this post | posted 17 Apr, 2018 12:53
welkin	some minor tail proteins are upstream of the terminase, instead of after the tape measure.