SEA-PHAGES | Frameshift in DR phages?

Link to this post \| posted 13 Mar, 2022 14:39
susannepfeifer	Hello, We have a question about annotating a programmed frameshift. In BiggityBass, two genes (genes 21 (stop: 19523; pham 99210) and 22 (stop: 19933; pham 97251)) near the tape measure protein COULD be in a programmed frameshift but the DR phage Phamerator maps are not very consistent: 1. AnClar - NO programmed frameshift 2. AnarQue - NO programmed frameshift 3. CloverMinnie - YES programmed frameshift (different phams) 4. Ligma - NO programmed frameshift 5. Mariokart - NO programmed frameshift 6. NHagos - YES programmed frameshift 7. Yago84 - NO programmed frameshift 8. Sour - YES programmed frameshift In short, 5/8 annotated DR phages did not call a programmed frameshift(including AnClar and Yago84 which are the most similar to BiggityBass based on our BLAST hits) 2/8 annotated DR phages called a programmed frameshift on their corresponding genes 21 and 22 1/8 annotated DR phage called a programmed frameshift but the genes were part of a different pham The 5/8 annotated DR phages without programmed frameshifts were submitted fairly recently (2019-2022), while the 2/8 annotated DR phages with programmed frameshifts were submitted earlier (2018-2019). Since majority of the DR phages do not have it annotated, would it be a fair assessment that it is okay to leave genes 21 and 22 in BiggityBass as is (i.e., NO programmed frameshift)? Thank you in advance for your help! Susanne

Link to this post | posted 13 Mar, 2022 14:39

Hello,

We have a question about annotating a programmed frameshift. In BiggityBass, two genes (genes 21 (stop: 19523; pham 99210) and 22 (stop: 19933; pham 97251)) near the tape measure protein COULD be in a programmed frameshift but the DR phage Phamerator maps are not very consistent:

1. AnClar - NO programmed frameshift
2. AnarQue - NO programmed frameshift
3. CloverMinnie - YES programmed frameshift (different phams)
4. Ligma - NO programmed frameshift
5. Mariokart - NO programmed frameshift
6. NHagos - YES programmed frameshift
7. Yago84 - NO programmed frameshift
8. Sour - YES programmed frameshift

In short,
5/8 annotated DR phages did not call a programmed frameshift(including AnClar and Yago84 which are the most similar to BiggityBass based on our BLAST hits)
2/8 annotated DR phages called a programmed frameshift on their corresponding genes 21 and 22
1/8 annotated DR phage called a programmed frameshift but the genes were part of a different pham

The 5/8 annotated DR phages without programmed frameshifts were submitted fairly recently (2019-2022), while the 2/8 annotated DR phages with programmed frameshifts were submitted earlier (2018-2019). Since majority of the DR phages do not have it annotated, would it be a fair assessment that it is okay to leave genes 21 and 22 in BiggityBass as is (i.e., NO programmed frameshift)?

Thank you in advance for your help!
Susanne

Link to this post \| posted 14 Mar, 2022 14:25
stpage	Hi, we had this discussion when we annotated MarioKart a little over a year ago. I am not sure that there is not a frameshift but just felt like there wasn't enough evidence to call it. Nhagos and Sours have 4 Gs around the end of gene 21 that is the region identified as the slippery sequence. Does yours have Pham 113375 or 115039? It might be worth tracking it by Pham rather than by cluster.

Link to this post \| posted 15 Mar, 2022 13:03
debbie	There is another string of forum posts in the cluster specific annotation tips. I just looked at a set of these genes (see the post) and I am worried that the wrong genes are being implicated. Use your phage's HHpred data to make your decisions. https://seaphages.org/forums/topic/5009/ Best, debbie

Recent Activity

Frameshift in DR phages?