Annotation of the available pARS3 IS26Tn sequence fragment and comparison with pTRACA22. The sequence fragment of the E. coli plasmid pARS3 described by Wachino et al was downloaded from GenBank [AB261016]. Due to the high identity of pTRACA22 ORFs with regions of the pARS3 sequence observed during tBlastn searches, the currently available pARS3 sequence (limited to a 3964 bp region of the 9.1 Kb IS26Tn) was analysed using Glimmer v3, and predicted ORFs annotated. All ORFs described by Wachino et al  were predicted along with five ORFs not originally described or annotated in the GenBank record, * denotes ORFs in pARS3 annotated during this study. Nucleotide sequences of pTRACA22 and pARS3 were compared using the Artemis Comparison Tool (ACT) and shaded areas between sequence maps represent regions of high identity at the nucleotide level. Areas shaded pink range from 95-97% identity, and areas shaded orange exhibited 89% identity. ORFs described previously by Wachino et al follow nomenclature used in that study , and the following functions were originally assigned to these ORFs: Orf4 - putative replication protein, Orf5: hypothetical protein, Orf6 - NpmA aminoglycoside resistance gene, Orf7 - putative ABC transporter substrate binding protein. ORFs are shown as arrows. Open arrows denote ORFs that do not have a homologue in both sequences. Coloured arrows indicate ORFs with homologues present in both pTRACA22 and pARS3, and "paired" ORFs are connected by dashed lines with colours representing % identity at the amino acid level: Red arrows indicate greater than 90% identity between paired ORFs, Orange arrows indicate greater than 80% identity between paired ORFs. Jagged edges indicate truncated ORFs.
Jones et al. BMC Genomics 2010 11:46 doi:10.1186/1471-2164-11-46