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phage justbecause tRNA @ 88542

| posted 29 Jun, 2018 17:22
Online aragorn call the reverse strand tRNA from 88542-88627 as a Pyl amino acid and an anti-codon of cta (which pairs with the amber stop codon UAG). Pyl (pyrrolysine) is one of the noncanonical amino acids which have been described but are fairly rare. A pubmed search of Pyrrolysine in streptomyces only found examples of using a system cloned out of an archaea into streptomyces for use in amber supression. online tRNA scan calls this with an infernal score of 55.7, type undet and anti-codon of NNN.

So, are we calling these specialized amino acids and anti-codons if called by Aragorn 1.2.38? Or should we go to a less specific designation of a tRNA with unknown aa and anti-codon?
Edited 29 Jun, 2018 20:46
| posted 01 Jul, 2018 14:53
Hi Chris,

We encountered something very similar in the Rhodococcus cluster CA phages and decided to call those tRNA-other and not specify the anti-codon (this is allowed in GenBank). If it looks like a legitimate tRNA otherwise, that seems like a reasonable option here.

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