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Tail Assembly Chaperone

| posted 02 Mar, 2020 01:48
Not annotating frameshift in absence of wet bench evidence, GC-rich region but not obvious slippery sequence. Some in cluster have two tail assembly chaperone back to back in same frame (Sour, NHagos), most overlapping in separate frames (Cloverminnie, Mariokart).
| posted 02 Mar, 2020 14:36
Hi Shallee– sounds like a good decision to me.
| posted 02 Mar, 2020 19:09
Hi Shallee,

NHagos annotator here. NHagos and Sour tail assembly chaperones are not in the same frame. They were annotated with frameshifts so it looks back-to-back in phamerator. You cannot tell which frame it is in from phamerator. Download the NHagos minimal file to see our frameshift. You can also look up the genbank entry to see that is was annotated at nucleotide 17143. There are 4 G's in a row. Sour also had these 4 G's in a row. Our complete notes file does not have the frameshift annotated.
| posted 03 Mar, 2020 17:15
Thanks again, Erin. It makes more sense looking at the GenBank entry rather than Phamerator. I don't have that many Gs, but I'll try a mockup of the frameshift and see how it looks in Mariokart.
| posted 03 Mar, 2020 17:50
Hi all,
I am going to chime in here, but my understanding today is that every phage may not have the G/T programmed frameshift. In lots of cases we can only find homologues to G and nothing to T. If the downstream gene of the frameshift does not have homologues and you cannot find a slippery sequence as denoted in the review paper cited in the guide https://seaphagesbioinformatics.helpdocsonline.com/article-54 , do not 'force' a frameshift. I would not call 4Gs, not followed by 3 of something else as a slippery sequence (though we have done it in the past). Is that the case here?
debbie
| posted 03 Mar, 2020 18:00
Ours was identified as CGGGGAG during QC.
| posted 03 Mar, 2020 20:43
Yeah, that location in Mariokart is just AGGGCCG….
Yago84 did not call the frameshift but there is a aagggcct
So maybe I should just follow that.
| posted 03 Mar, 2020 23:40
I think with those sequences I would go with no slip for now.
 
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