# STOCKHOLM 1.0
#=GF ID AAC_AAD_leader
#=GF AC RF02912
#=GF DE putative aminoglycoside riboswitch / attI site
#=GF AU Argasinska J; 0000-0003-2678-2824
#=GF GA 56.0
#=GF NC 52.2
#=GF TC 60.6
#=GF SE Argasinska J
#=GF SS Published; 23332747;
#=GF TP Cis-reg;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 30.00 -Z 2958934 CM SEQDB
#=GF DR SO; 0005836; regulatory region;
#=GF DR GO; 0010468; regulation of gene expression;
#=GF DR GO; 0030647; aminoglycoside antibiotic metabolic process;
#=GF RN [1]
#=GF RM 23332747
#=GF RT Riboswitch control of aminoglycoside antibiotic resistance.
#=GF RA Jia X, Zhang J, Sun W, He W, Jiang H, Chen D, Murchie AI
#=GF RL Cell. 2013;152:68-81.
#=GF RN [2]
#=GF RM 23791167
#=GF RT Integron attI1 sites, not riboswitches, associate with antibiotic
#=GF RT resistance genes.
#=GF RA Roth A, Breaker RR
#=GF RL Cell. 2013;153:1417-1418.
#=GF CC Conserved RNA structure found upstream of the bacterial aminoglycosides
#=GF CC antibiotic-resistant genes: aminoglycoside acetyl transferase (AAC) and
#=GF CC aminoglycoside adenyl transferase (AAD). It has putative short open
#=GF CC reading frame (ORF) that encode leader peptide upstream of the resistance
#=GF CC gene. 75 nucleotide long sequence from the first ribosome binding site
#=GF CC (SD1) up to the coding sequence was shown to have the regulatory role, and
#=GF CC it was considered the minima functional RNA. Aminoglycosides bind to
#=GF CC specific regions of AAC/AAD 5' leader and induce change in the RNA
#=GF CC structure. The drug binding induces expression of the resistance protein.
#=GF CC The leader RNA is widely distributed among antibiotic-resistant bacterial
#=GF CC pathogens.[1]
#=GF WK AAC/AAD_leader
#=GF SQ 4

CP011599.1/36880-36951     GGAGCAGCAACGAUGUUACGCAGCAGGGCAGUCGCCCUAAAACAAAGUUAGGCCGCAUG--GACACA---A-CGCAGG
CP000650.1/38256-38185     GGAGCAGCAACGAUGUUACGCAGCAGGGCAGUCGCCCUAAAACAAGGUUAGGCCGCAUG--GACACA---A-CGCAGG
CP018135.1/1913478-1913552 GGAGCAGCAACGAUGUUACGCAGCAGGGCAGUCGCCCUAAAACAAAGUUAGGCAUCAUGGGUGAAUU---UUUCCCUG
CP018839.1/285461-285385   GGAGCAGCAACGAUGUUACGCAGCAGGGCAGUCGCCCUAAAACAAAGUUA-GCCGAGAGGAGAAACUAUGUCUGCAAA
#=GC SS_cons               :::[,<-<<____>>->,,((-((,<<<<____>>>><<<_______>>>,))-)),,<-<<___>>...->,,]:::
#=GC RF                    GGAGCAGCAACGAUGUUACgcAGCAGGGCAGUCGCCCUAAAACAAAGUUAGGCcgcAugGggAaAcc...ucugCagg
//
