Link to this post | posted 25 Mar, 2019 16:59

welkin

Hi Steve, At this point we are not differentiating in our function names for other capsid-scaffolding fusions; as this is not uncommon in phages. In the case of HK97, the scaffolding is called the "delta domain" of the major capsid protein, and the literature refers to the procapsid or uncleaved form vs the mature form. So to be consistent, we have not labeled our capsids with delta domains anything other than "major capsid protein"–and so therefore, don't mention specifically it here either.

Link to this post | posted 25 Mar, 2019 16:43
welkin	Hi Greg, We are aware of the new suggestion, but do not plan to change our nomenclature at this time. We will keep you posted should anything change on that front.

Link to this post | posted 25 Mar, 2019 16:03
welkin	there is a tRNA with a low-ish infernal score— we think that it should be included in the annotations.

Link to this post | posted 23 Mar, 2019 16:31
welkin	Hi Chris, It depends on the phage. We've had phages with all possible assortments.

Link to this post | posted 22 Mar, 2019 21:49
welkin	Hi Deb, So I haven't looked at this one closely yet. In general, when I try to decide what/if any function a protein may have, I try to find out more about the possibilities. What do you know about RepA/RecA? Are they both the same size? Does one have a domain that the other doesn't? Are there key catalytic residues that need to be present for either one?

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.

Link to this post | posted 19 Mar, 2019 13:20
welkin	It sound to me like we can add ribonuclease toxin BrnT to the list. Thanks!

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 14 Mar, 2019 13:57
welkin	Hi Hari, IT looks like you are correct to me. Best, Welkin

Link to this post | posted 13 Mar, 2019 16:34
welkin	Hi Cristian, I've never seen the error that you are describing, but I can tell you that I've had difficulty performing simultaneous comparisons with 80 phages. I had to do it in smaller chunks (like 20 at a time) and then collect the answers in a spreadsheet. So it is possible you are maxing it out. Best, Welkin