SEA-PHAGES Logo

The official website of the HHMI Science Education Alliance-Phage Hunters Advancing Genomics and Evolutionary Science program.

Welcome to the forums at seaphages.org. Please feel free to ask any questions related to the SEA-PHAGES program. Any logged-in user may post new topics and reply to existing topics. If you'd like to see a new forum created, please contact us using our form or email us at info@seaphages.org.

All posts created by welkin

| posted 25 Mar, 2019 16:59
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.
Posted in: Cluster BI Annotation Tipscapsid fusion
| posted 25 Mar, 2019 16:43
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.

Posted in: General Message BoardMycolicibacterium rename...
| posted 25 Mar, 2019 16:03
there is a tRNA with a low-ish infernal score— we think that it should be included in the annotations.
Posted in: Cluster EJ Annotation TipstRNA
| posted 23 Mar, 2019 16:31
Hi Chris,
It depends on the phage. We've had phages with all possible assortments.
Posted in: Cluster CY Annotation Tipstwo integrases
| posted 22 Mar, 2019 21:49
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?

Posted in: Functional AnnotationIs pham 23434 a DNA recombinase or a helicase?
| posted 19 Mar, 2019 13:24
I think minor capsid protein is probably the best call for the Appa gene.
Posted in: Functional Annotationcapsid maturation protease
| posted 19 Mar, 2019 13:20
It sound to me like we can add ribonuclease toxin BrnT to the list. Thanks!
Posted in: Request a new function on the SEA-PHAGES official listRibonuclease toxin BrnT
| posted 17 Mar, 2019 14:09
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.
Posted in: Functional Annotationcapsid maturation protease
| posted 14 Mar, 2019 13:57
Hi Hari,
IT looks like you are correct to me.

Best,
Welkin
Posted in: AnnotationAnnotations of Microbacterium foliorum
| posted 13 Mar, 2019 16:34
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
Posted in: DNA MasterGenome Comparison