SEA-PHAGES | 4 bp overlaps

Link to this post \| posted 14 Mar, 2018 14:40
welkin	The right arms of cluster F genes are characterized by TONS of tiny genes. These genes are sometimes so small that the gene prediction programs have a really difficult time predicting them. You can usually identify them easily though, as their start and stop codons will overlap with the flanking genes in a 4bp overlap.

Link to this post \| posted 26 Jun, 2020 21:54
ClaireRinehart	Welkin, I am struggling with the evidence for OfUltron and Sebastian gene 103. The -4 gap start is at 54324 and has a Z-score of 3 and Final score of -2.6 which looks like very compelling evidence for this start site. When I look at Starterator results I find that all 109 Cluster F1 hits call the start at 54471 which has a Z-score of 2.255 and a Final score of -4.458. When I look at the secondary structure potential for the RBS at start 54471 I find that 5 of the seven bases are in a very strong stem of a local stem-loop with a final Free Energy of -1200, which is very high (6 of the 7 bp in the stem are G-C bp). Wow, this makes the -4 gap look even better. However, if translation starts at the -4 start site there is no coding capacity for about 70 bases and then there is atypical coding capacity for about 50 bases before the start at 54471. I searched this non-coding capacity range and found 4 rare codons in this region. My initial instinct is to go with start 54324 with the -4 gap with the hope that some of the ribosomes would be able to navigate the rare codon domain, even though that may be at a slower rate. Is there Mass Spec data for Cluster F1 phages or other evidence (besides herd instinct) that has pointed everyone else to call the start at 54471?

Link to this post | posted 26 Jun, 2020 21:54

ClaireRinehart

Welkin,
I am struggling with the evidence for OfUltron and Sebastian gene 103.
The -4 gap start is at 54324 and has a Z-score of 3 and Final score of -2.6 which looks like very compelling evidence for this start site. When I look at Starterator results I find that all 109 Cluster F1 hits call the start at 54471 which has a Z-score of 2.255 and a Final score of -4.458. When I look at the secondary structure potential for the RBS at start 54471 I find that 5 of the seven bases are in a very strong stem of a local stem-loop with a final Free Energy of -1200, which is very high (6 of the 7 bp in the stem are G-C bp). Wow, this makes the -4 gap look even better. However, if translation starts at the -4 start site there is no coding capacity for about 70 bases and then there is atypical coding capacity for about 50 bases before the start at 54471. I searched this non-coding capacity range and found 4 rare codons in this region. My initial instinct is to go with start 54324 with the -4 gap with the hope that some of the ribosomes would be able to navigate the rare codon domain, even though that may be at a slower rate. Is there Mass Spec data for Cluster F1 phages or other evidence (besides herd instinct) that has pointed everyone else to call the start at 54471?

Link to this post \| posted 27 Jun, 2020 13:32
ClaireRinehart	Only 8 of the 109 have the -4 start site at Starterator location 12. As you can see from the Starterator map, all of these belong to the family of longest ORFs. All of the closest nucleotide BLAST relatives to OfUltron and Seabastion (Llama, Modragons and Ochi17) have this -4 start. I am going to call the -4 start because the data is consistent for these longer ORFs and may be a new evolving pham.

Link to this post | posted 27 Jun, 2020 13:32

ClaireRinehart

Only 8 of the 109 have the -4 start site at Starterator location 12. As you can see from the Starterator map, all of these belong to the family of longest ORFs. All of the closest nucleotide BLAST relatives to OfUltron and Seabastion (Llama, Modragons and Ochi17) have this -4 start. I am going to call the -4 start because the data is consistent for these longer ORFs and may be a new evolving pham.

Link to this post \| posted 27 Jun, 2020 13:48
debbie	Claire, The Starterator data for the shorter start is quite compelling. I just looked at a different scenario where the -4bp overlap was on a portal gene. In this case, the thought was that the structural studies for the portal protein out-weighed the convenient -4bp overlap. In this case -with such a tiny gene and in a place where the -4bp overlap is common - I can't blame you for picking it. We need experiments! About your 'evolving pham' comment, maybe this is an older version…… debbie

Link to this post | posted 27 Jun, 2020 13:48

debbie

Claire,
The Starterator data for the shorter start is quite compelling. I just looked at a different scenario where the -4bp overlap was on a portal gene. In this case, the thought was that the structural studies for the portal protein out-weighed the convenient -4bp overlap. In this case -with such a tiny gene and in a place where the -4bp overlap is common - I can't blame you for picking it. We need experiments!
About your 'evolving pham' comment, maybe this is an older version……
debbie

Link to this post \| posted 17 Mar, 2023 22:50
seaphages_usc	Working on the end of Cluster FF phage Gusanita and am wondering what criteria I should use to add a gene here. I could insert a gene at start site 41673 with a -4 overlap. There is decent BLAST and HHPred matches here, so I am comfortable with that. There is potential for another gene at 41974, also with a -4 overlap. This one doesn't have good HHPred or BLAST matches. Should I leave it out or go with the notion that it's an orphan with its attractive overlap. Lastly, a potential start at 42293 with a -4 overlap and a single BLAST match. Any help would be appreciated with these gaps at the end with lovely potential ORFs. welkin The right arms of cluster F genes are characterized by TONS of tiny genes. These genes are sometimes so small that the gene prediction programs have a really difficult time predicting them. You can usually identify them easily though, as their start and stop codons will overlap with the flanking genes in a 4bp overlap.

Link to this post | posted 17 Mar, 2023 22:50

seaphages_usc

Working on the end of Cluster FF phage Gusanita and am wondering what criteria I should use to add a gene here.
I could insert a gene at start site 41673 with a -4 overlap. There is decent BLAST and HHPred matches here, so I am comfortable with that.
There is potential for another gene at 41974, also with a -4 overlap. This one doesn't have good HHPred or BLAST matches. Should I leave it out or go with the notion that it's an orphan with its attractive overlap.
Lastly, a potential start at 42293 with a -4 overlap and a single BLAST match.
Any help would be appreciated with these gaps at the end with lovely potential ORFs.

welkin
The right arms of cluster F genes are characterized by TONS of tiny genes. These genes are sometimes so small that the gene prediction programs have a really difficult time predicting them. You can usually identify them easily though, as their start and stop codons will overlap with the flanking genes in a 4bp overlap.

Link to this post \| posted 17 Mar, 2023 23:59
debbie	Hi! I could call 41673-41810. There is a nib of coding potential and that if fits with 4bp overlaps at both ends is compelling. I think the coding potential is there for 41974-42225. However, I am not sure about the last one 42293-42394. I don't think that i would call it. debbie

Link to this post \| posted 18 Mar, 2023 00:07
seaphages_usc	Thank you! debbie Hi! I could call 41673-41810. There is a nib of coding potential and that if fits with 4bp overlaps at both ends is compelling. I think the coding potential is there for 41974-42225. However, I am not sure about the last one 42293-42394. I don't think that i would call it. debbie

Link to this post \| posted 23 Apr, 2023 23:05
ooduniyi@purdue.edu	Hi Debbie, We seem to be having an issue with AlpineSix. While trying to the work on the frameshift, the "Validate" button is giving us an error code "join(8535. .9033;9033. .9086) Not In Frame 1 In-frame Stop Codon" it says there is a stop codon within the frame region and that is what is causing the error. We believe we have taken the right steps so far, but we have never encountered this problem in annotation. Can you let us know what you think about it? we believe it is a +2 frameshift which is something we have never seen either. Most are either -1,+1, or -2. Thank you for your help!

Link to this post | posted 23 Apr, 2023 23:05

ooduniyi@purdue.edu

Hi Debbie,

We seem to be having an issue with AlpineSix. While trying to the work on the frameshift, the "Validate" button is giving us an error code "join(8535. .9033;9033. .9086)
Not In Frame
1 In-frame Stop Codon" it says there is a stop codon within the frame region and that is what is causing the error. We believe we have taken the right steps so far, but we have never encountered this problem in annotation. Can you let us know what you think about it? we believe it is a +2 frameshift which is something we have never seen either. Most are either -1,+1, or -2.

Thank you for your help!

Link to this post \| posted 23 Apr, 2023 23:06
ooduniyi@purdue.edu	Hi Debbie, We seem to be having an issue with AlpineSix. While trying to the work on the frameshift, the "Validate" button is giving us an error code "join(8535. .9033;9033. .9086) Not In Frame 1 In-frame Stop Codon" it says there is a stop codon within the frame region and that is what is causing the error. We believe we have taken the right steps so far, but we have never encountered this problem in annotation. Can you let us know what you think about it? we believe it is a +2 frameshift which is something we have never seen either. Most are either -1,+1, or -2. Thank you for your help!

Link to this post | posted 23 Apr, 2023 23:06

ooduniyi@purdue.edu

Link to this post \| posted 23 Apr, 2023 23:58
debbie	Hi! AlpineSix's programmed frame shift has to be a +1. Check out the relationship of the "G" gene to the "T" gene. It does not appear to have a canoninical frameshift, BUT was called by the researcher who did the research on frameshifts, so we will do the same. Check out the frame-shift in Che8. I have attached a photo of the DNA Master annotation of AlpineSix. Let me know if you have any further questions. debbie 87Kb

Link to this post | posted 23 Apr, 2023 23:58

debbie

Hi!
AlpineSix's programmed frame shift has to be a +1. Check out the relationship of the "G" gene to the "T" gene. It does not appear to have a canoninical frameshift, BUT was called by the researcher who did the research on frameshifts, so we will do the same. Check out the frame-shift in Che8. I have attached a photo of the DNA Master annotation of AlpineSix.
Let me know if you have any further questions.
debbie

Recent Activity

4 bp overlaps