SEA-PHAGES | Help with frameshift annotation in A1 phage

Link to this post \| posted 24 May, 2019 16:34
nietof	Hi We are working on Snazzy. The tail assembly chaperones are genes 20 and 21 both on the forward strand but gene 20 ORF is in the 1 and 21 in the 3 frame. We located a GGGGGAA slippery sequence at 15336 in 20. We thought the ribosome would read the GGG at position 15337-15339 in frame 1 for a G and then slip back and read again GGA in frame 3 for another G. It yields 266 residues. When I blastp the product after the frameshift it aligns 100%, 100% coverage and 99.6% identity(residue 69 is different) to Violet tail assembly chaperone protein with no gaps. The sequence in the region where the shift happens aligns perfectly with that of Violet. Am I looking at this right? Is it a -1 frameshift but the ribosome jumps from frame 1 to 3. Thank you Fernando

Link to this post | posted 24 May, 2019 16:34

Hi
We are working on Snazzy. The tail assembly chaperones are genes 20 and 21 both on the forward strand but gene 20 ORF is in the 1 and 21 in the 3 frame. We located a GGGGGAA slippery sequence at 15336 in 20. We thought the ribosome would read the GGG at position 15337-15339 in frame 1 for a G and then slip back and read again GGA in frame 3 for another G. It yields 266 residues. When I blastp the product after the frameshift it aligns 100%, 100% coverage and 99.6% identity(residue 69 is different) to Violet tail assembly chaperone protein with no gaps. The sequence in the region where the shift happens aligns perfectly with that of Violet. Am I looking at this right?
Is it a -1 frameshift but the ribosome jumps from frame 1 to 3.
Thank you
Fernando

Link to this post \| posted 24 May, 2019 16:39
debbie	Fernando, Please send me your DNA Master file and I can show you. If you make sure each region is divisible by 3 it will show you where to cut it. If this is a -1 frameshift (most certainly it is), the last nucleotide of region 1 is the first nucleotide of region 2. Your frame jumping question is not easy to follow when the ribosome is really slipping backwards. debbie

Link to this post \| posted 24 May, 2019 20:07
nietof	Debbie Jacobs-Sera Fernando, Please send me your DNA Master file and I can show you. If you make sure each region is divisible by 3 it will show you where to cut it. If this is a -1 frameshift (most certainly it is), the last nucleotide of region 1 is the first nucleotide of region 2. Your frame jumping question is not easy to follow when the ribosome is really slipping backwards. debbie Hi Debbie Here is the DNA Master file. Thanks F 223Kb

Link to this post | posted 24 May, 2019 20:07

nietof

Debbie Jacobs-Sera
Fernando,
Please send me your DNA Master file and I can show you. If you make sure each region is divisible by 3 it will show you where to cut it. If this is a -1 frameshift (most certainly it is), the last nucleotide of region 1 is the first nucleotide of region 2. Your frame jumping question is not easy to follow when the ribosome is really slipping backwards.
debbie

Hi Debbie
Here is the DNA Master file.
Thanks
F

Link to this post \| posted 24 May, 2019 20:08
nietof	nietof Debbie Jacobs-Sera Fernando, Please send me your DNA Master file and I can show you. If you make sure each region is divisible by 3 it will show you where to cut it. If this is a -1 frameshift (most certainly it is), the last nucleotide of region 1 is the first nucleotide of region 2. Your frame jumping question is not easy to follow when the ribosome is really slipping backwards. debbie Hi Debbie Here is the DNA Master file. Thanks F Debbie I have also attached my rationale for the shift showing the six frame translation and the protein sequences. thanks F 115Kb

Link to this post | posted 24 May, 2019 20:08

nietof

nietof
Debbie Jacobs-Sera
Fernando,
Please send me your DNA Master file and I can show you. If you make sure each region is divisible by 3 it will show you where to cut it. If this is a -1 frameshift (most certainly it is), the last nucleotide of region 1 is the first nucleotide of region 2. Your frame jumping question is not easy to follow when the ribosome is really slipping backwards.
debbie

Hi Debbie
Here is the DNA Master file.
Thanks
F

Debbie
I have also attached my rationale for the shift showing the six frame translation and the protein sequences.
thanks
F

Link to this post \| posted 28 May, 2019 12:52
debbie	Fernando, You have called the frameshift exactly correctly. It is a -1 frameshift. The "G" gene is annotated as 14986 - 15363, product is "tail assembly chaperone. The "T" gene is annotated as 14986 - 15785, with 2 regions (14986 - 15339, 15339 - 15785), product is tail assembly chaperone. So it sounds like what confused you is that the "g" gene 'happened to be located in the top frame of the six-frame translation output". and you your real question is where would the -1 frame be, in relationship to that. As you can now see, it is the bottom displayed frame. Is that what you were asking? debbie

Link to this post | posted 28 May, 2019 12:52

debbie

Fernando,
You have called the frameshift exactly correctly. It is a -1 frameshift. The "G" gene is annotated as 14986 - 15363, product is "tail assembly chaperone. The "T" gene is annotated as 14986 - 15785, with 2 regions (14986 - 15339, 15339 - 15785), product is tail assembly chaperone.

So it sounds like what confused you is that the "g" gene 'happened to be located in the top frame of the six-frame translation output". and you your real question is where would the -1 frame be, in relationship to that. As you can now see, it is the bottom displayed frame. Is that what you were asking?
debbie

Link to this post \| posted 28 May, 2019 14:47
nietof	Debbie Somehow I had a misconception that a shift between 1 and 3 frames required a two base shift either back or forth(-2 or +2). It took me looking at the closely related genomes to realize that I was wrong. So I think I just needed confirmation on this one. Thank you. F

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Help with frameshift annotation in A1 phage