SEA-PHAGES | All posts created by tbouklas

Link to this post \| posted 24 Jan, 2023 00:09
tbouklas	Posting on behalf of a phage hunter at UCLA: Hey Y’all, I am a student at UCLA and we are annotating phage JulietS (C1). One of the genes I am annotating is stop @48994 F and I am having some problems with it. Attached are screenshots of the results. There is coding potential in both the host trained (start site around 48600) and Self trained (start site around 48500). Glimmer and GeneMark call the start site at 48518 but this provides a gap of 297. The smallest gap is 84 with a start site of 48305 but that isn't covered in the coding potential. Moreover, there are only 2 non-draft genomes in this pham (54797 1/23/23). One of these phages, Rabinovish, called the function as Holliday junction resolvase. This phage has a gene downstream which isn’t found in JulietS and has an overlap of -91 bp. The other phage, ScottMcG, does not call a function and has a gap of 328 bp. Where this gets extra complicated is looking at Phagesdb BLAST on PECAAN. There are several non-draft phages (EmmaElysia C1, Melpomini C1, Napoleon13 C1) and called the function as Holliday Junction resolvase but have the pham as 3757. Changing the start site does not change the pham sadly. I was hoping to get some help on figuring out this tricky gene. All help is appreciated and thank you for your time! – Tejas Bouklas Lecturer, UCLA 112Kb

Link to this post | posted 24 Jan, 2023 00:09

Posting on behalf of a phage hunter at UCLA:

Hey Y’all,

I am a student at UCLA and we are annotating phage JulietS (C1). One of the genes I am annotating is stop @48994 F and I am having some problems with it. Attached are screenshots of the results.

There is coding potential in both the host trained (start site around 48600) and Self trained (start site around 48500). Glimmer and GeneMark call the start site at 48518 but this provides a gap of 297. The smallest gap is 84 with a start site of 48305 but that isn't covered in the coding potential. Moreover, there are only 2 non-draft genomes in this pham (54797 1/23/23). One of these phages, Rabinovish, called the function as Holliday junction resolvase. This phage has a gene downstream which isn’t found in JulietS and has an overlap of -91 bp. The other phage, ScottMcG, does not call a function and has a gap of 328 bp.

Where this gets extra complicated is looking at Phagesdb BLAST on PECAAN. There are several non-draft phages (EmmaElysia C1, Melpomini C1, Napoleon13 C1) and called the function as Holliday Junction resolvase but have the pham as 3757. Changing the start site does not change the pham sadly.

I was hoping to get some help on figuring out this tricky gene. All help is appreciated and thank you for your time!

–
Tejas Bouklas
Lecturer, UCLA

Posted in: Functional Annotation → JulietS (C1): Holliday junction resolvase?

Link to this post \| posted 21 Dec, 2022 21:19
tbouklas	Thank you for your quick response! – Tejas Bouklas Lecturer, UCLA

Posted in: Functional Annotation → Usavi_draft_70: potentially ribbon-helix-helix?

Link to this post \| posted 21 Dec, 2022 05:41
tbouklas	Hello all, I am annotating phage Usavi (B1). The gene at stop 57734 (Usavi_draft_70) has some pretty good hits in HHpred to entries that mention ribbon helix helix, but I'm not sure if they are sufficient to call anything related to a RHH. None of the hits mention anything specifically about RHH, the currently approved function. But the hits were strong enough, and apppeared to cover enough of the sequence from Usavi, that I am curious. I've summarized the data I found in the attachment and also copied some key info below. I would appreciate any advice on this one? Usavi_draft_70: MLPIKCPPDVRQRLKIAAAEDGLTYAQLLVSLLDLRDDRHRRQRAAQASPLHRPRAETA Currently 7 members of pham call ribbon-helix-helix DNA binding domain protein. Phages DB: https://phagesdb.org/genes/Usavi_CDS_70/ HHpred results: https://toolkit.tuebingen.mpg.de/jobs/Usavi__69 Both 2BNW and 1IRQ link to manuscripts that discuss RHH. PDB: https://www.rcsb.org/structure/2BNW PDB: https://www.rcsb.org/structure/1IRQ *I don't see any HHpred hits that line up with the evidence entries for the example RHH genes, Chorkpop_70 and Pharaoh_67. Chorkpop_70 HHpred: https://toolkit.tuebingen.mpg.de/jobs/Chorkpop_70 Phareon_67 HHpred: https://toolkit.tuebingen.mpg.de/jobs/Chorkpop_71 Thank you, Tejas – Tejas Bouklas Lecturer, UCLA 636Kb

Link to this post | posted 21 Dec, 2022 05:41

tbouklas

Hello all,

I am annotating phage Usavi (B1). The gene at stop 57734 (Usavi_draft_70) has some pretty good hits in HHpred to entries that mention ribbon helix helix, but I'm not sure if they are sufficient to call anything related to a RHH. None of the hits mention anything specifically about RHH, the currently approved function. But the hits were strong enough, and apppeared to cover enough of the sequence from Usavi, that I am curious.

I've summarized the data I found in the attachment and also copied some key info below. I would appreciate any advice on this one?

Usavi_draft_70:
MLPIKCPPDVRQRLKIAAAEDGLTYAQLLVSLLDLRDDRHRRQRAAQASPLHRPRAETA

Currently 7 members of pham call ribbon-helix-helix DNA binding domain protein.

Phages DB: https://phagesdb.org/genes/Usavi_CDS_70/

HHpred results: https://toolkit.tuebingen.mpg.de/jobs/Usavi__69

Both 2BNW and 1IRQ link to manuscripts that discuss RHH.
PDB: https://www.rcsb.org/structure/2BNW
PDB: https://www.rcsb.org/structure/1IRQ

*I don't see any HHpred hits that line up with the evidence entries for the example RHH genes, Chorkpop_70 and Pharaoh_67.
Chorkpop_70 HHpred: https://toolkit.tuebingen.mpg.de/jobs/Chorkpop_70
Phareon_67 HHpred: https://toolkit.tuebingen.mpg.de/jobs/Chorkpop_71

Thank you,
Tejas

–
Tejas Bouklas
Lecturer, UCLA

Posted in: Functional Annotation → Usavi_draft_70: potentially ribbon-helix-helix?

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