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TAC frameshifts in CF
| Link to this post | posted yesterday, 21:39 | |
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We have a possible Tail Assembly Chaperone frameshift in two new cluster CF phages (CurlyFries and RegnumDei). The only possible slippery sequence is GGATTTC. In two previous CF annotations that have this same sequence (Shagrat and Madraxi), a frameshift was not called. In another CF annotation, Jflix2, the putative slippery sequence is GGGTTTC, and it was called as a frameshift. Seems like the GGATTTC, conserved in 4 phages in the cluster, could also be a slippery sequence. But without stronger evidence, better to not call it as a frameshift? Any opinions out there? Thanks! |
| Link to this post | posted today, 15:16 | |
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Hi Randy, This is going to take a bit of time to check. And i don't have that time, so maybe I can provide enough info' to get you started. Historically, it was thought that all sipho have TACS, canonically directly upstream of the tape measure. There is now reports that the genes are present, and do not have to be beside each other. And that not all sipho have TACs. There is also evidence that the 4 nucleotide sequence of XXXY can constitute a slippage (if they are in the 'right spacing' of the reading frames). That is part of the evaluation that can occur. Having the numerous cluster members to compare will also be informative. I don't know what you meant about a second slippage site. You are correct to look more closely. debbie |