# STOCKHOLM 1.0
#=GF ID RydC
#=GF AC RF00505
#=GF DE RydC RNA
#=GF AU Ontiveros-Palacios N; 0000-0001-8457-4455
#=GF GA 48.0
#=GF NC 39.3
#=GF TC 48.9
#=GF SE PMID:15618228
#=GF SS Published; PMID:15618228
#=GF TP Gene; sRNA;
#=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; 0000370; small_regulatory_ncRNA;
#=GF RN [1]
#=GF RM 15618228
#=GF RT A small bacterial RNA regulates a putative ABC transporter.
#=GF RA Antal M, Bordeau V, Douchin V, Felden B
#=GF RL J Biol Chem. 2005;280:7901-7908.
#=GF RN [2]
#=GF RM 25551292
#=GF RT Recognition of the small regulatory RNA RydC by the bacterial Hfq protein.
#=GF RA Dimastrogiovanni D, Frohlich KS, Bandyra KJ, Bruce HA, Hohensee S, Vogel
#=GF RA J, Luisi BF
#=GF RL Elife. 2014;3:e05375.
#=GF CC This family represents a bacterial non-coding RNA called RydC. RydC is
#=GF CC thought to regulate an mRNA, yejABEF which encodes an ABC transporter
#=GF CC protein. RydC is known to bind the protein Hfq which causes a
#=GF CC conformational change in the RNA molecule. The Hfq/RydC complex is then
#=GF CC thought to bind to the target mRNA and induce its degradation [1]. The
#=GF CC structure of RydC has been reported in PDB 4V2S [2].
#=GF WK RydC_RNA
#=GF SQ 6

U00096.2/1489530-1489467                  CUUCCGAUGUAGACCCGU-AUUCUUCGCCUGUACCACGGGUC-GGUUUUAGUACAGGCGUUUUCUU
AL627270.1/77020-76955                    CUUCCGAUGUAGACCCGUCCUCCUUCGCCUGCGUCACGGGUCCUGGUUAGACGCAGGCGUUUUCUG
CP000038.1/1826318-1826381                CUUCCGAUGUAGACCCGU-AUUCUUCGCCUGUACCACGGGUC-GGUUUUAGUACAGGCAUUUUCUU
CU928161.2/1508420-1508357                CUUCCGAUGUAGGCCCGU-AUUCUUCGCCUGUACCACGGGUC-GGUUUUAGUACAGGCGUUUUCUU
CP001113.1/1726026-1726091                CUUCCGAUGUAGACCCGUCCUCCUUCGCCUGCGUCACGGGUCUUGGUUAGACGCAGGCGUUUUCUG
URS00008FED35_90371/1-65                  -UUCCGAUGUAGACCCGUCCUCCUUCGCCUGCGUCACGGGUCCUGGUUAGACGCAGGCGUUUUCUG
#=GR URS00008FED35_90371/1-65   4V2S_Q_SS ..........{{{{{{{{.......((((((((((}}}}}}}.}.....)))))))))).......
#=GC SS_cons                              ::::::::::<<<<<<<<.______AAAAAAAAA_>>>>>>>.>::::::aaaaaaaaa:::::::
#=GC RF                                   CUUCCGAUGUaGACCCGU.aUuCUUCGCCUGuauCACGGGUC.uGuUUuaauaCAGGCGUUUUCUu
#=GC RNA_structural_elements              ==========[=SI5p=]=======[=SII=5p=][=SI=3p=]=====[=SII=3p=]=======
//
