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 13 May, 2019 16:28
is there another candidate for an endolysin/lysin A?
Posted in: Functional AnnotationCluster BI - Endolysin
| posted 13 May, 2019 16:27
sounds like the kinase call is wrong.
Thanks Steve.
Posted in: Functional AnnotationCluster BI - Thymidylate kinase
| posted 13 May, 2019 15:03
Hi Steve,
sO I guess the question is if we can confirm the more specific assignment. I don't know enough about the enzymes to know how closely related they are, and if we are sure of the chitosinase label. are there specific domains or residues we should look for? IF it is not easy to confirm, the more generic is always appropriate.
Posted in: Functional AnnotationCluster BI - Chitosinase
| posted 07 May, 2019 19:50
Hi All,
The frameshift should be in close proximity to the C-terminus of the G protein; the GN-GK one is simply too far away.
We probably should look at all the CZ4s and see if there is a consensus.

W
Posted in: Frameshifts and IntronsCluster CZ4 Frameshift
| posted 30 Apr, 2019 15:07
Depends on how humid the air is. Under vaccuum and with dessicant, months; under humid conditions, maybe a few days tops.
Posted in: Phage Discovery/IsolationEM Sample Stability
| posted 29 Apr, 2019 14:57
I think this has to be a minor tail protein; otherwise there won't be enough proteins to make up the tail tip.
Posted in: Request a new function on the SEA-PHAGES official listAlpha-L-arabinofuranosidase B?
| posted 26 Apr, 2019 18:32
Hi Dave,
Sounds like it to me.

Thanks!
Posted in: Functional Annotationthymidylate synthases versus dihydrofolate reductases
| posted 25 Apr, 2019 22:33
Hi Veronique,
How long is the protein, and how many other minor tail proteins have you identified already?
Posted in: Request a new function on the SEA-PHAGES official listAlpha-L-arabinofuranosidase B?
| posted 25 Apr, 2019 22:25
It is OK to indicate on your coversheet which scoring matrix and spacing matrix you used, as long as you don't change it on a per gene basis. Z-score and final score should still be included with every gene.
Yes/no indicates if it is the best score or not, as compared to the other choices for that gene.

Edited 25 Apr, 2019 22:32
Posted in: DNA MasterRBS Data
| posted 19 Apr, 2019 21:52
The capsid, scaffolding, and protease are fused into a single gene in the EEs and should be annotated as "major capsid and protease fusion protein"
Edited 25 Apr, 2019 22:27
Posted in: Cluster EE Annotation Tipscapsid and protease fusion