SEA-PHAGES | Gene or not a gene? MrMiyagi

Gene or not a gene? MrMiyagi

Link to this post \| posted 30 Apr, 2020 03:12
fbaliraine	Dear Phage hunters, I am strongly inclined to deleting reverse gene 36 in phage MrMiyagi (SSC: 33325-33185 reverse, RBS z=2.o12, Fs =-5.0722), but perhaps a second opinion might help before I pull the trigger, since this is an orpham with not other data. Here’s the deal. It was called by GM, but not GM. No hits in phagesDb, but Blast via DNA master shows a hit at “extracellular solute-binding protein, NCBI, Roseovarius sp., WP_138933805, 58.70%, e-value 2.24 (13.3% similarity; e-value not significant; https://www.ncbi.nlm.nih.gov/protein/WP_138933805.1/). NB. Roseovarius is a genus of the Rhodobacteraceae. No coding potential in both GeneMark (smeg) & TB, but there is atypical CD in GeneMarkS. This "gene" is in a large gap between forward genes, and I know it is not common for phages to switch between forward and reverse genes. What is your take on this? Is atypical coding potential ever acceptable to be used? see attachment. Thanks! Fred Edited 30 Apr, 2020 03:16 79Kb

Link to this post | posted 30 Apr, 2020 03:12

Dear Phage hunters,
I am strongly inclined to deleting reverse gene 36 in phage MrMiyagi (SSC: 33325-33185 reverse, RBS z=2.o12, Fs =-5.0722), but perhaps a second opinion might help before I pull the trigger, since this is an orpham with not other data. Here’s the deal. It was called by GM, but not GM. No hits in phagesDb, but Blast via DNA master shows a hit at “extracellular solute-binding protein, NCBI, Roseovarius sp., WP_138933805, 58.70%, e-value 2.24 (13.3% similarity; e-value not significant; https://www.ncbi.nlm.nih.gov/protein/WP_138933805.1/). NB. Roseovarius is a genus of the Rhodobacteraceae. No coding potential in both GeneMark (smeg) & TB, but there is atypical CD in GeneMarkS. This "gene" is in a large gap between forward genes, and I know it is not common for phages to switch between forward and reverse genes. What is your take on this? Is atypical coding potential ever acceptable to be used? see attachment.

Thanks!
Fred

Edited 30 Apr, 2020 03:16

Link to this post \| posted 30 Apr, 2020 09:31
debbie	Fred, I too would be inclined to delete this gene. debbie

Link to this post \| posted 04 May, 2020 03:06
fbaliraine	Thank you Debbie! Fred Edited 04 May, 2020 03:07

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Gene or not a gene? MrMiyagi