Link to this post | posted 16 Mar, 2019 13:58
delesall	Can you have both a gene for "capsid maturation protease and MuF-like fusion protein" and for a "capsid maturation protease" (e.g., Genes 14 and 18 in KimmyK)in the same genome? Both have been called in DC phages but there is better evidence (good HHPred matches) for the former.

Link to this post | posted 17 Mar, 2019 14:09
welkin	Seems unlikely to me, but who knows. Just look really carefully through the HHPred data to make sure the relevant catalytic domains are present in the right places. MuF and the protease can certainly be separate.

Link to this post | posted 17 Mar, 2019 14:44

delesall

When I annotated Danyall (another DC phage) last year, I went with capsid morphogenesis protein and capsid maturation protease for these genes (genes 14 and 18 in KimmyK, genes 12 and 18 in Danyall) due to past annotations and to synteny (genes are between portal amd major capsid protein. The change of function call from "capsid morphogenesis protein" to "capsid maturation protease and MuF-like fusion protein" made me look more closely at these two genes. Only the early gene (the capsid maturation protease and MuF-like fusion protein) has HHPred matches that suggest a capsid maturation function (one 110 aa region with match to gp7 of SPP1 and another region at C-terminus with lots of matches to ribosyltransferase - see attached), while the other gene (gene 1 only has HHPred matches with less than 50% probability. I would thus be inclined to call a function for the first gene but not the second. What say Pittsburgh? :-) 29Kb

Link to this post | posted 18 Mar, 2019 18:45
debbie	Veronique, I agree, I see no function to call for the second gene in question. and I would call the first one the "capsid maturation protease and MuF-like fusion protein".

Link to this post | posted 18 Mar, 2019 21:42

dbolliva

We are looking at our phage Sucha and comparing with the previously annotated Goodman. Gene 5 in Goodman is called as a capsid maturation protease, and Sucha has a gene that shares similarity but is much shorter and only has HHpred results with minor capsid protein. In Appa a member of the same Pham as the Sucha gene has been called as a head assembly protein, which I believe you want called something different? I guess my question is whether to just call it as a minor capsid protein? It is notable theat the alignment with the capsid maturation protease is to the amino terminus but only covers a third of the protein.

Link to this post | posted 19 Mar, 2019 13:24
welkin	I think minor capsid protein is probably the best call for the Appa gene.