SEA-PHAGES | New Frameshift in K5 bacteriophage RtcB-ligase ?

Link to this post \| posted 13 Jul, 2018 18:22
mdgainey	Hi I have been annotating Rando14, a K5 bacteriophage and when we go to the area where many of the K5's have an RtcB ligase, there were some weird reverse genes that we needed to delete, and then we found 2 forward ORFs that we think should fill this area nicely with good CP, the first in the +2, and the second in the +1 reading frame that blast up to the N and C terminal portions of the the RtcB ligase respectively. I have attached a power point showing the potential slippery GGGG sequence, where I think the frame shift might occur, and the protein products. Do you think this could possibly be a sequencing error, or perhaps a real frameshift? I know we don't have wet bench data to support frameshifts, other than in the tail assembly chaperones, so I would probably not annotate this as such, but since this one has a predicted function I thought I would post about it to get some advice on how to handle this one. Thank you, Maria 324Kb

Link to this post | posted 13 Jul, 2018 18:22

Hi I have been annotating Rando14, a K5 bacteriophage and when we go to the area where many of the K5's have an RtcB ligase, there were some weird reverse genes that we needed to delete, and then we found 2 forward ORFs that we think should fill this area nicely with good CP, the first in the +2, and the second in the +1 reading frame that blast up to the N and C terminal portions of the the RtcB ligase respectively. I have attached a power point showing the potential slippery GGGG sequence, where I think the frame shift might occur, and the protein products.

Do you think this could possibly be a sequencing error, or perhaps a real frameshift?
I know we don't have wet bench data to support frameshifts, other than in the tail assembly chaperones, so I would probably not annotate this as such, but since this one has a predicted function I thought I would post about it to get some advice on how to handle this one.
Thank you,
Maria

Link to this post \| posted 17 Jul, 2018 15:55
welkin	Hi Maria, It is always worth asking Becky and Dan to double-check the sequence when you find a disruption in a gene with a known function. We do find errors in sequences, especially those that were sequenced with the Ion Torrent technology. It is pretty rare in those sequenced with Illumina. If the sequence is legitimate, you could annotate it is RtcB-like ligase, truncated. As you noted, we don't add frameshifts to the annotations, other than for the tail assembly chaperones.

Link to this post | posted 17 Jul, 2018 15:55

welkin

Hi Maria,
It is always worth asking Becky and Dan to double-check the sequence when you find a disruption in a gene with a known function. We do find errors in sequences, especially those that were sequenced with the Ion Torrent technology. It is pretty rare in those sequenced with Illumina.

If the sequence is legitimate, you could annotate it is RtcB-like ligase, truncated. As you noted, we don't add frameshifts to the annotations, other than for the tail assembly chaperones.

Link to this post \| posted 17 Jul, 2018 20:42
mdgainey	Thanks Welkin, Maria

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New Frameshift in K5 bacteriophage RtcB-ligase ?