SEA-PHAGES | tRNA enigma in Enygma

tRNA enigma in Enygma

Link to this post \| posted 18 Aug, 2023 00:05
engstrom	Hi Folks, I am looking at a possible (but I am increasingly thinking unlikely) tRNA in Enygma at roughly 88430-88539. Infernal score is low, but just misses the cutoff at 29.8. Size of the tRNA is within 90 nt, but only just. Aragorn, Aragorn 1.2.38 and tRNAscan-SE all draw different conclusions about the anti-codon. Aragorn 1.2.38 wants to put an intron in, which makes the least sense of anything to my mind. There is no syntenic tRNA annotated at this location in any of the most closely related genomes (Bordeaux, SaltySpitoon, PumpkinSpice). Student annotator took it out. I am leaning toward agreeing, but would value a third opinion.

Link to this post | posted 18 Aug, 2023 00:05

Hi Folks,

I am looking at a possible (but I am increasingly thinking unlikely) tRNA in Enygma at roughly 88430-88539. Infernal score is low, but just misses the cutoff at 29.8. Size of the tRNA is within 90 nt, but only just. Aragorn, Aragorn 1.2.38 and tRNAscan-SE all draw different conclusions about the anti-codon. Aragorn 1.2.38 wants to put an intron in, which makes the least sense of anything to my mind. There is no syntenic tRNA annotated at this location in any of the most closely related genomes (Bordeaux, SaltySpitoon, PumpkinSpice). Student annotator took it out. I am leaning toward agreeing, but would value a third opinion.

Link to this post \| posted 21 Aug, 2023 16:35
debbie	I agree with your student. I would not call it. From my collegue, Christian Gauthier, "It looks to have an extremely poor D-loop and a weird anticodon loop. Acceptor stem and pseudouridine stem/loop both look OK. If I were a gambling man, I’d speculate that there used to be a tRNA there, but it has undergone some mutational decay and is almost certainly defective. I wouldn’t be inclined to annotate it." Best, debbie

Link to this post | posted 21 Aug, 2023 16:35

debbie

I agree with your student. I would not call it.
From my collegue, Christian Gauthier, "It looks to have an extremely poor D-loop and a weird anticodon loop. Acceptor stem and pseudouridine stem/loop both look OK. If I were a gambling man, I’d speculate that there used to be a tRNA there, but it has undergone some mutational decay and is almost certainly defective. I wouldn’t be inclined to annotate it."

Best,
debbie

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tRNA enigma in Enygma