SEA-PHAGES | Singleton FuzzBuster Frameshift

Singleton FuzzBuster Frameshift

Link to this post \| posted 03 Jun, 2019 19:25
mdgainey	I am finishing up the new Micro singleton FuzzBuster that has some similarities to the cluster EI phages. The tail assembly chaperone genes are orphams, but do have some blast hits to those found in the EI phages,EC phages, and one singleton Hendrix. None of the EI's or EC's call a frame shift but Hendrix does. I have attached a powerpoint with some screen shots of Fuzzbuster, Hendrix, and an EI. The EI's don't have a glycine in the same area as FuzzBuster and Hendrix. My question is would you call a frameshift here, and if so how would you call it -1? Thanks, Maria 130Kb

Link to this post | posted 03 Jun, 2019 19:25

I am finishing up the new Micro singleton FuzzBuster that has some similarities to the cluster EI phages. The tail assembly chaperone genes are orphams, but do have some blast hits to those found in the EI phages,EC phages, and one singleton Hendrix.
None of the EI's or EC's call a frame shift but Hendrix does. I have attached a powerpoint with some screen shots of Fuzzbuster, Hendrix, and an EI. The EI's don't have a glycine in the same area as FuzzBuster and Hendrix.

My question is would you call a frameshift here, and if so how would you call it -1?

Thanks,

Maria

Link to this post \| posted 03 Jun, 2019 19:48
debbie	Maria, If there is a frameshift, it is a -1 because the second gene is -1 from the first. However, I don't see a slippery sequence to call in FuzzBuster. My quick look at HHPred in PECAAN, says you might not even want to call these things TAC. If you are using PECAAN, you might want to re-run your HHPred in PECAAN because it is dated Jan, 2019. I believe the databases used around that time were not complete. debbie

Link to this post | posted 03 Jun, 2019 19:48

debbie

Maria,
If there is a frameshift, it is a -1 because the second gene is -1 from the first. However, I don't see a slippery sequence to call in FuzzBuster. My quick look at HHPred in PECAAN, says you might not even want to call these things TAC. If you are using PECAAN, you might want to re-run your HHPred in PECAAN because it is dated Jan, 2019. I believe the databases used around that time were not complete.
debbie

Link to this post \| posted 03 Jun, 2019 19:56
mdgainey	Thanks Debbie, I will rerun HHPRED, I was just going to call them assembly chaperones based on synteny.

Link to this post \| posted 03 Jun, 2019 20:11
debbie	Recently, we learned that all siphos do not need to have one or both of the TACs. So it would not be wrong to omit the call without evidence.

Link to this post \| posted 03 Jun, 2019 20:12
mdgainey	Okay, I think I will go with NKF.

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Singleton FuzzBuster Frameshift