# STOCKHOLM 1.0
#=GF ID NiCo-AnGGAG
#=GF AC RF03164
#=GF DE NiCo-AnGGAG riboswitch aptamer
#=GF AU Weinberg Z; 0000-0002-6681-3624
#=GF GA 64.5
#=GF NC 64.3
#=GF TC 69.7
#=GF SE Published; PMID:28265071
#=GF SS Published; PMID:28265071
#=GF TP Cis-reg; riboswitch;
#=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 CL CL00122
#=GF DR SO; 0000035; riboswitch;
#=GF DR GO; 0046872; metal ion binding;
#=GF RN [1]
#=GF RM 28265071
#=GF RT Bioinformatic analysis of riboswitch structures uncovers variant classes
#=GF RT with altered ligand specificity.
#=GF RA Weinberg Z, Nelson JW, Lunse CE, Sherlock ME, Breaker RR
#=GF RL Proc Natl Acad Sci U S A. 2017;114:E2077.
#=GF RN [2]
#=GF RM 25794617
#=GF RT Bacterial riboswitches cooperatively bind Ni(2+) or Co(2+) ions and
#=GF RT control expression of heavy metal transporters.
#=GF RA Furukawa K, Ramesh A, Zhou Z, Weinberg Z, Vallery T, Winkler WC, Breaker
#=GF RA RR
#=GF RL Mol Cell. 2015;57:1088-1098.
#=GF CC Nico riboswitches are selective metalloregulatory riboswitches that
#=GF CC recognice Ni2+ and Co2+ metals [2]. NiCo-AnGGAG is a variant of Nico
#=GF CC riboswitch [2], with a change in position 87, from G to A [1].
#=GF WK NiCo_riboswitch
#=GF SQ 13

URS0000D69F34_883113/1-89   AAU--UUGAGCAAGUGGAAGAC--AGAC---G-UCUUC-U-GCCCGGUUGAAC--CGUGAGAA--GUUCGACAGCAGAU------------CUAAUGAACAC------------AUCUGUGAGACAG
URS0000D683A2_908337/1-92   AAUAAACGAACAAGCGGUGG----AAAC------CCAUGCAGCCGGAUGAUUGGCUAGUC---GCCAAUCAUAGCAGUU-CGC--------CCAAGA-------------GCGCAAUUGUGAGACGU
URS0000D6724E_698758/1-94   AAU--CUGAGCAAGCUGCACAUUAUUUCUUA-CUAUGC-A-GCCCGGUCAC----GAUU--------GUGACAGCAGA-GUAUACCUA---UCC-----------UAGG-GUACAUCUGUGAGACAG
URS0000D66085_1123308/1-91  AAG--AUGAACAAGCGGUGGU---CUG------ACCAUGCAGCCGGGCCUUCA--AGUC------UGAAGGCAGCAGUAUAAGUAC-----GAUGA-----------GUGCGUAU-CUGUGAGACAG
URS0000D6A6BE_1123309/1-103 AAU--AUGAACAAGCGGUAAAUC-GUGA--GA-UUUAUGCAGCCGGGUCCUCA--AGUG------UGAGGACAGCAGACCACUGCA-UCUAAUUG-------UAGAGUGC-GUGC-CUGUGAGACAG
URS0000D69A4C_12908/1-76    AAU--CUGAACAAGCUGUGCA---UUA------UGCAUGAAGCCGGGUUAUCC--AAGCA-----GGAUAACAGCGGA-------------GAUA--------------------UCCGUGAGACAG
URS0000D67B3D_12908/1-78    AAU--CUGAACAAGCUGUGCA---UUA------UGCAUGAAGCCGGGUUAUUC--GCAGGAA---GAAUAACAGCGGA-------------GAUA--------------------UCCGUGAGACAG
URS0000D6A437_883111/1-83   AAU--CUGAACAAGCGGUAAA---UUUA-----UUUACGCAGCUGGGUUACAU--GAAAA-----AUGUAACAGCAGAGC-----------CAGAGC----------------GCACUGUGAGACAG
URS0000D659FB_883114/1-89   UAU--CUGAGCAAGCGGUGGAA--AUU----U-UCCAUGCAGCCCGGCUAUA---GUAAA------UAUAGCAGCAGAAGCGU--------AAUUAACA-----------ACGCA-CUGUGAGACAG
URS0000D6AE33_12908/1-88    AAU--CUGAGCAAGCGGUGAAUAGGUGA-CUA-UUCAUGCAGCCCGGCUAC----UAAAC-------GUAGCAGCAGAGUGU---------UAAGGU--------------ACA-UCUGUGAGACAG
URS0000D65DF6_12908/1-88    AAU--CUGAGCAAGCGGUGAAUAGGUGA-CUA-UUCAUGCAGCCCGGCUAC----UAAAC-------GUAGCAGCAGA-GUGU--------UAAG---------------GCACAUCUGUGAGACAG
URS0000D6B8B5_12908/1-89    AAU--CUGAGCAAGCGGUGAAUAGGUGA-CUAUUUCAUGCAGCCCGGCUAC----UAAAC-------GUAGCAGCAGA-GUGU--------UAAG---------------GCACAUCUGUGAGACAG
URS0000D65DF6_883103/1-88   AAU--CUGAGCAAGCGGUGAAUAGGUGA-CUA-UUCAUGCAGCCCGGCUAC----UAAAC-------GUAGCAGCAGA-GUGU--------UAAG---------------GCACAUCUGUGAGACAG
#=GC SS_cons                :::..(((,,,,,<<<<<<<<_..____.....>>>>>->->>,,,<<<<<<<.._____.....>>>>>>>,<<<<<<<<<<........_____..............>>>>>>>>>>,,,,)))
#=GC RF                     AAU..cuGAaCAAGCgguGgau..auaa.....ucCacGcAGCCgGGccaccc..uaaaa.....ggguggCAgCaGaggcgc........uaaaa..............gcgccuCuGuGAGACag
#=GC CORE                   ........x...................................xxx..........................................................................xx....
//
