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.
Recent Activity
Viknesh Sivanathan posted in did you know you can do restriction digests in the microwave?
nic.vega posted in did you know you can do restriction digests in the microwave?
nic.vega posted in did you know you can do restriction digests in the microwave?
Viknesh Sivanathan posted in did you know you can do restriction digests in the microwave?
nic.vega posted in did you know you can do restriction digests in the microwave?
All posts created by Hemiparasite
| Link to this post | posted 28 May, 2024 13:02 | |
|---|---|
|
As a follow up to this, I have found more genes with the same architecture. My gene of interest is the Andre gene that has its stop at 49133. It also has the pattern 1) DNA primase/polymerase, 2) Helicase, 3) DNA binding domain. In the process of looking for a way to separate this from the typical DNA primase/helicase architechture, I noticed that the example gene given in the approved function list for "DNA primase/polymerase/helicase" (GreenHearts_47) also has this same architecture. (The approved function list specifies that it is supposed to have three different domains.) So far as I can tell, the difference between the approved function list's example “DNA primase/helicase” and the approved function list's example “DNA primase/polymerase/helicase” does not seem to have anything to do with the presence of an additional polymerase domain. Rather, the second gene includes a C-terminal DNA binding domain. I attached annotated screenshots of these HHPred hits in the same format that Chris used above. The pham containing the Andre gene (with stop 49133) calls a mix of "DNA primase/helicase" and "DNA primase/polymerase/helicase." I assume the genes in the pham generally have a similar architecture to the Andre gene (HHPred screenshot in attachment). The approved function list does not have a call along the lines of “DNA primase/helicase/DNA binding," but I’m wondering if that is the gene architecture that most of the genes currently called “DNA primase/polymerase/helicase” actually have? Is there a way to search PhagesDB genes by the functional annotations they were assigned? I'd be interested in looking at more genes with the "DNA primase/polymerase/helicase" call in other phams. |
100KbPosted in: Functional Annotation → GG cluster DNA primse/helicase
| Link to this post | posted 04 Apr, 2024 00:41 | |
|---|---|
|
|
afreise In the final annotation of Usavi, would it be Usavi_9 that is the example of this call, rather than Usavi_10? https://phagesdb.org/genes/Usavi_CDS_9/ |