Link to this post | posted 06 Feb, 2018 18:44

delesall

I'm looking at the tail assembly chaperones of a Gordonia CZ1 phage, Eviarto. Four other CZ1 phages have been annotated but I don't see why the frameshift was called the way it was. Two issues: 1) the frameshift in Nymphadora gp 14 and 15 was called at a different place from that in BatStarr, Kita, and Zirinka (see attached document). 2) the sequences were the frameshift is called don't look slippery to me (in Nymphadora (AAGCG; in others CAGGC) and don't look like the ones identified in Xu et al. What am I missing? I do see a region - CCCGAAA - just before the "called" frameshift for Nymphadora that looks slippery to me (starting at bp 9880 in Eviarto)… Any advice? 13Kb

Link to this post | posted 08 Feb, 2018 01:52
dbolliva	Veronique, You probably already know this, but my go to for slippery sequences is the Xu, Hendrix, and Duda paper: https://doi.org/10.1016/j.molcel.2004.09.006 That sequence you list is not represented in any of their tables but still could be one……. I agree with you that those other sequences do not look slippery at all to me. Just my two cents… and it might not be worth that. Dave

Link to this post | posted 08 Feb, 2018 02:08
delesall	Yes I did look at Xu, Hendrix and Duda - I don't see any of the slippery sequences they identify in these phages (at least in the region where I expect frameshift to occur). So I am still perplexed but isn't that the pleasure of phage annotation? :-) Veronique

Link to this post | posted 09 Feb, 2018 19:22
welkin	so i am trying to remember why we picked the sequence we did: i think it had some thing to with stop codons or a lack of conserved sequences across the cluster. our initial choice in phage 1 was proven wrong when examined in the context of phages 2, 3, 4 etc; and the weird sequence was the only choice left. i would have to dig through my notes to recreate it.

Link to this post | posted 09 Feb, 2018 20:14
delesall	So in Eviarto, as mentioned above, I see a region that looks slippery around bp 9875 to 9886. I also see a region of 5 G starting at 9752. I don't see any stop codons that would make frameshifting at these sites not possible…

Link to this post | posted 21 Feb, 2018 15:48
welkin	The problem wasn't the stop codon in Eviarto- it was a stop codon in a closely related phage that meant we couldn't choose the sequence that we wanted to and make the whole cluster congruent.

Link to this post | posted 21 Feb, 2018 18:35
delesall	OK - We will do some more comparative investigations and I will update then!

Link to this post | posted 21 Oct, 2020 16:33

mitchellcc

Hey everybody. We are working on BoyNamedSue from CZ1 and are having similar problems. The slips that are called in Zirinka, Bosnia, or BatStarr do not match up to the appropriate slippery sequences from the Xu, Hendrix, and Duda paper. However, BoyNamedSue does have what looks like a slippery sequence starting at bp9752(GGGGGAG). This is where Eviarto called the slip. Would this be correct for BoyNamedSue? Thanks. Parks 12Kb

Link to this post | posted 21 Oct, 2020 19:12

debbie

Hi Parks, I am not sure, but wanted to give you some more to think about or do. See the attached picture and look at the sequence at 9731. A more canonical slippage, but really upstream of the stop of the "G" part of the G/T gene. What would be helpful is to check out the other CZ1s and see if a consensus sequence is apparent in that place. Alignments are in order! I do like the sequence, but I don't like how upstream it is…. need more info and to think about it. debbie 76Kb