SEA-PHAGES | Frameshift in CZ4 Phage Annalisa

Frameshift in CZ4 Phage Annalisa

Link to this post \| posted 27 Feb, 2024 17:09
Bowen.Meng	Hi, We are currently annotating CZ4 phage Annalisa (https://phagesdb.org/phages/Annalisa/)and have come across a potential programmed frameshift of the Tail Assembly Chaperone (Gene 15 and 16 in the gene list). When I look at other phages in this cluster, it seems the shift occurs with the sequence GGGGACT. Annalisa however, does not have this sequence in the similar location as other CZ4 phages like Oregano and Sekhmet. Instead, it seems like the sequence in Annalisa is GGCGACT. Is the frameshift not present in Annalisa, or is there another possibility for a slippery sequence? I've attached an image of the region for Annalisa. Edited 27 Feb, 2024 17:10 144Kb

Link to this post | posted 27 Feb, 2024 17:09

Hi,

We are currently annotating CZ4 phage Annalisa (https://phagesdb.org/phages/Annalisa/)and have come across a potential programmed frameshift of the Tail Assembly Chaperone (Gene 15 and 16 in the gene list). When I look at other phages in this cluster, it seems the shift occurs with the sequence GGGGACT. Annalisa however, does not have this sequence in the similar location as other CZ4 phages like Oregano and Sekhmet. Instead, it seems like the sequence in Annalisa is GGCGACT. Is the frameshift not present in Annalisa, or is there another possibility for a slippery sequence? I've attached an image of the region for Annalisa.

Edited 27 Feb, 2024 17:10

Link to this post \| posted 27 Feb, 2024 19:09
kbutela	Marcie Warner and I have reviewed the frameshifts currently called in Cluster CZ4, and they are not matching up to any of the wet bench experimentally validated frameshift sequences listed in the Bioinformatics Guide. For now, we do not recommend calling frameshifts in this cluster until a more thorough investigation can be performed. The currently called slippery sequence is suspicious and may be an annotation error that has been propagated over the years.

Link to this post | posted 27 Feb, 2024 19:09

kbutela

Marcie Warner and I have reviewed the frameshifts currently called in Cluster CZ4, and they are not matching up to any of the wet bench experimentally validated frameshift sequences listed in the Bioinformatics Guide. For now, we do not recommend calling frameshifts in this cluster until a more thorough investigation can be performed. The currently called slippery sequence is suspicious and may be an annotation error that has been propagated over the years.

Link to this post \| posted 28 Feb, 2024 15:14
Bowen.Meng	Hi Kristen, Thank you for your input. We will keep the these two genes separate unless there is further evidence to call it with a programmed frameshift.

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Frameshift in CZ4 Phage Annalisa