SEA-PHAGES | All posts created by Hemiparasite

Link to this post \| posted 28 May, 2024 13:02
Hemiparasite	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. Edited 28 May, 2024 13:39 100Kb

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.

Edited 28 May, 2024 13:39

Posted in: Functional Annotation → GG cluster DNA primse/helicase

Link to this post \| posted 04 Apr, 2024 00:41
Hemiparasite	afreise As of Dec 2022, are we leaving off the MuF part, based on this update from Debbie? https://seaphages.org/forums/topic/4628/ So now just: capsid maturation protease? (I am annotating Usavi (B1). The gene is here: https://phagesdb.org/genes/Usavi_CDS_10/) 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/

Link to this post | posted 04 Apr, 2024 00:41

Hemiparasite

afreise
As of Dec 2022, are we leaving off the MuF part, based on this update from Debbie? https://seaphages.org/forums/topic/4628/

So now just: capsid maturation protease?

(I am annotating Usavi (B1). The gene is here: https://phagesdb.org/genes/Usavi_CDS_10/)

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/

Posted in: Cluster B Annotation Tips → Capsid maturation protease and MuF-like fusion protein

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