SEA-PHAGES | Possible translational frameshift in Cluster J

Link to this post \| posted 25 Mar, 2019 22:56
ptsourkas	I have a situation with two overlapping genes in Cluster J phage NihilNomen which looks like it might be a translational frameshift. Gene 123 in forward frame 2 is called by Glimmer and GeneMark, albeit both call it short. However, there is an even longer ORF in frame 1 that is called by the host-trained GeneMark.hmm that has very strong coding potential and full overlaps with gene 123 (se attached figure). Interestingly, the coding potential for the ORF in frame 1 and gene 123 do not overlap: The coding potential for gene 123 starts right where the coding potential for the ORF in frame 1 ends (see attached figure). Furthermore, the coding potential map seems to indicate there is a translational frameshift. The ORF in frame 1 has BLAST matches to phage Thibaut, while gene 123 has matches to phages Omega and Porcelain. In terms of function, both genes have matches to DNA cytosine methyltransferase. I am unsure what to do here? Call both genes? If so, what to do about the potential translational frameshift? Or should I call only one gene, and if so which one? 102Kb

Link to this post | posted 25 Mar, 2019 22:56

I have a situation with two overlapping genes in Cluster J phage NihilNomen which looks like it might be a translational frameshift.

Gene 123 in forward frame 2 is called by Glimmer and GeneMark, albeit both call it short. However, there is an even longer ORF in frame 1 that is called by the host-trained GeneMark.hmm that has very strong coding potential and full overlaps with gene 123 (se attached figure).

Interestingly, the coding potential for the ORF in frame 1 and gene 123 do not overlap: The coding potential for gene 123 starts right where the coding potential for the ORF in frame 1 ends (see attached figure). Furthermore, the coding potential map seems to indicate there is a translational frameshift. The ORF in frame 1 has BLAST matches to phage Thibaut, while gene 123 has matches to phages Omega and Porcelain. In terms of function, both genes have matches to DNA cytosine methyltransferase.

I am unsure what to do here? Call both genes? If so, what to do about the potential translational frameshift? Or should I call only one gene, and if so which one?

Link to this post \| posted 26 Mar, 2019 08:40
debbie	Philippos, Hi. No, I would not call auto-annotated gene 123, but instead call the longer gene you describe (it is a DNA methylase, so that should convince you). In addition, don't miss the next forward gene, because it too is a DNA methylase. See my attached frames window. Check out the differences in the auto-annotation…. 25Kb

Link to this post \| posted 26 Mar, 2019 14:59
ptsourkas	Yes, I got the next forward gene and deleted those short reverse genes (121-125). Thanks for looking into this.

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Possible translational frameshift in Cluster J