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[…] b'somerization catalyzed by \xcf\x88 synthase occurs when the uracil base is rotated 180\xc2\xb0 through an N-3\xe2\x80\x93C-6 diagonal axis. In \xcf\x88, the C-5 position of uracil is linked to the C-1\xe2\x80\xb2 position of the sugar, resulting in an increase in hydrogen bonding capacity compared with that in uridine (). A.\xc2\xa0tyrosinisolvens LL-002T () possesses seven \xcf\x88 synthases according to the genome analysis., The draft genome sequencing of A.\xc2\xa0tyrosinisolvens LL-002T was performed on an Ion Torrent PGM sequencer (Life Technologies) equipped with a 318 chip. Data from the genomic DNA library contained 1,960,572 reads and 532,539,090 nucleotide bases, with an average read length of 271.62\xc2\xa0bp using 400-base chemistry. Assembly using Newbler Ver.2.6 (Roche Diagnostics, USA), which is a software package for de novo DNA sequence assembly, generated 136 contigs with a maximum and minimum contig size of 414,016 bp and 530\xc2\xa0bp, respectively., The draft genome comprising 5,693,818 nucleotides was annotated with the help of the GeneMark S () and the Rapid Annotations using Subsystems Technology (RAST) () servers. These annotation results indicate that strain LL-002T possesses nine genes coding \xcf\x88 synthases: MBEAT2_0006 and MBEAT2_0009 code TruA and TruB, which modify the uridyl residue (nucleotide positions 38, 39, 40, and 55 in Escherichia coli) of the tRNA molecules, and these two genes show 64.6% and 67.6% identity with those of A.\xc2\xa0aneurinilyticus, respectively. As for rRNA modification, three genes coding RsuA (MBEAT2_0001, -0004, and -0008) and four genes coding RluA (MBEAT2_0002, -0003, -0005, and -0007) are found. RsuA modifies the uridyl residue (nucleotide position 516 in E.\xc2\xa0coli) of the 16S rRNA molecules and RluA modifies one (nucleotide position 746 in E.\xc2\xa0coli) of the 23S' […]

Pipeline specifications

Software tools Newbler, GeneMark, RAST