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Recent Activity
Tail Assembly Chaperone
| Link to this post | posted 07 Feb, 2024 07:04 | |
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hi We are annotating phage Aikyam. We noted that phages in this cluster with the same TAC pham, phage Isolde, for example, call the programmed frameshift using a slippery sequence CCCTTTTT (a PF to PF -1 slip). CCCTTTTT doesn't appear on any list of validated slippery sequences that I could find, so I wasn't sure why this site has been called. It certainly works as a slippery sequence, but is there any evidence to support this call? Other AY phages, like EvePickles, use CCCAAAAA (PK to PK; a different Pham), which does appear on Sup Table 1 from Xu et al. thanks Adam |
| Link to this post | posted 07 Feb, 2024 12:44 | |
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Adam, In the paper referred to the Bioinformatics Guide, the TAC 'template' is X_XX.Y_YY.Z. You have not provided enough information for me to look quickly, but check the guide to interpret the '_ 'and '.'s If your CCCTTTT lines up correctly for a -1 Frameshift, you have a canonical programmed ribosomal slippage. You also used an abbreviation 'PF' that i don't recognize. debbie |
| Link to this post | posted 07 Feb, 2024 13:04 | |
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Hi Debbie Ok, this was a misunderstanding on my part. I thought we needed to identify a slippery sequence similar to those that have been defined previously (i.e. on the table). CCCTTTTT definitely works as an XXXYYYZ sequence, and is in the correct position for a -1 frameshift. PF to PF referred to the slip as coding proline-phenylalanine to proline-phenylalanine. thanks Adam |