SEA-PHAGES | frameshifts

frameshifts

Link to this post \| posted 14 Mar, 2018 14:41
welkin	Cluster F phages can have either +1 or -1 frameshifts in the tail assembly chaperones. Make sure you know which one your phage has.

Link to this post \| posted yesterday, 03:08
uOttawaPHAGE	We are annotating Lordvader (Cluster F) and the sequence and slippery sequence of the tail assembly chaperone matches Frankie (F1): KS to KV (LordVader: 8391..8885,8887..9327; Frankie: 8588..9082,9084..9524), with a slippery sequence of CCAAAAG. This sequence is found on the table in the guide as being used in IS3 as a -1 slip, but this is a +1 slip. I haven't seen any discussion on the forums of evidence to support the +1 slip using this sequence. It seems like others have called it, but I wanted to confirm.

Link to this post | posted yesterday, 03:08

uOttawaPHAGE

We are annotating Lordvader (Cluster F) and the sequence and slippery sequence of the tail assembly chaperone matches Frankie (F1): KS to KV (LordVader: 8391..8885,8887..9327; Frankie: 8588..9082,9084..9524), with a slippery sequence of CCAAAAG. This sequence is found on the table in the guide as being used in IS3 as a -1 slip, but this is a +1 slip. I haven't seen any discussion on the forums of evidence to support the +1 slip using this sequence. It seems like others have called it, but I wanted to confirm.

Link to this post \| posted today, 00:12
debbie	Hi Adam and all, This is indeed a +1 slippage. And it is not in that published paper. However, this is well-conserved sequence and perfectly matches the calls made by G. Hatfull and Roger Hendrix. Roger (and his lab) discovered the ribosomal slippage of the tail assembly chaperones in HK97 and he called the original like sequences (Che8 and Tweety). You can couple that with other published works that have demonstrated that what may only be needed is the first 4 based of the canonical sequence XXXYYYZ to accomplish the slippage, so I think it is wise to call this one. The regions to call are: 8391..8888, 8890..9327. (slipping from a lysine to a valine) debbie

Link to this post | posted today, 00:12

debbie

Hi Adam and all,
This is indeed a +1 slippage. And it is not in that published paper. However, this is well-conserved sequence and perfectly matches the calls made by G. Hatfull and Roger Hendrix. Roger (and his lab) discovered the ribosomal slippage of the tail assembly chaperones in HK97 and he called the original like sequences (Che8 and Tweety). You can couple that with other published works that have demonstrated that what may only be needed is the first 4 based of the canonical sequence XXXYYYZ to accomplish the slippage, so I think it is wise to call this one. The regions to call are: 8391..8888, 8890..9327. (slipping from a lysine to a valine)

debbie

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frameshifts