Computational identification of the selenocysteine tRNA (tRNASec) in genomes
Fig 7
“Redox-active disulfide protein 2” selenoproteins in Brachyspira.
(A) Multiple sequence alignment containing amino acid sequences obtained from UniRef90 (top four) and from Brachyspira genomes using Selenoprofiles [24]. In the Brachyspira sequences, the Sec position (column 26) is coloured according to the codon found in the genome: Cys in red; and Sec in green. The thioredoxin domain spans from column 53 to the C-terminus. (B) Genomic arrangement of the three “Redox-active disulfide protein 2” genes, all of them found in a gene cluster in each of the Brachyspira genomes (rows). The genes are coloured according to the codon in the Sec position (marked in black), following the same colouring scheme as panel A. Selenoproteins were either missed or truncated in the annotations provided by NCBI, here represented in darker color and labeled with the NCBI gene name. No annotation was found in NCBI for B. innocent and B. hyodysenteriae. All genes are represented 5’ to 3’; the scale measures nucleotides and is centered on the start codon of the “Sec.1” gene. (C) Structure alignments of the putative SECIS found downstream the TGA codon (underlined in red) in the two selenoproteins, “Sec.1” (left) and “Sec.2” (right). Alignments produced using Infernal [31] and visualized with RALEE [61]. See Fig 6 for RALEE colouring scheme.