# STOCKHOLM 1.0
#=GF ID PreQ1-III
#=GF AC RF02680
#=GF DE PreQ1-III (pre queuosine) riboswitch aptamer
#=GF AU Ontiveros-Palacios N; 0000-0001-8457-4455
#=GF GA 63.0
#=GF NC 54.4
#=GF TC 64.9
#=GF SE Zasha Weinberg, Phillip McCown, Jonathan Liang
#=GF SS Published; PMID:25036777
#=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 DR SO; 0000035; riboswitch;
#=GF DR GO; 0008616; queuosine biosynthetic process;
#=GF RN [1]
#=GF RM 25036777
#=GF RT Structural, functional, and taxonomic diversity of three preQ1 riboswitch
#=GF RT classes.
#=GF RA McCown PJ, Liang JJ, Weinberg Z, Breaker RR
#=GF RL Chem Biol. 2014;21:880-889.
#=GF RN [2]
#=GF RM 26106162
#=GF RT Structural analysis of a class III preQ1 riboswitch reveals an aptamer
#=GF RT distant from a ribosome-binding site regulated by fast dynamics.
#=GF RA Liberman JA, Suddala KC, Aytenfisu A, Chan D, Belashov IA, Salim M,
#=GF RA Mathews DH, Spitale RC, Walter NG, Wedekind JE
#=GF RL Proc Natl Acad Sci U S A. 2015;112:E3485-E3494.
#=GF CC A third preQ1-binding (preQ1-III riboswitch that differs structurally from
#=GF CC preQ1 (RF00522) and preQ1-II (RF01054) was first reported for McCown et
#=GF CC al. 2014 [1]. The structure of preQ1-III has been reported for Mathews et
#=GF CC al. 2015 [2], preQ1-III riboswitch aptamer presents four pairing regions
#=GF CC P1-P4, organised as a HL out-type pseudoknot in its structure. preQ1-II
#=GF CC presents a bipartite architecture, wich permit a dynamic conformational
#=GF CC switch involved in the expression platform accessibility. PreQ1-III
#=GF CC riboswitch structure was reported in PDB: 4RZD_A [2] and 6XKN_A and 6XKO_A
#=GF WK PreQ1-III_riboswitch
#=GF SQ 31

BABG01013292.1/257-357                      GAGCAACUUAGGAUUUUAGGCUCCCCG-GUGCGUCUCGAACCGCGCCGGGCCAAACCC-ACAGGGGCUGGCGG-UCCUGU-GCGGUCAAAAUCUUUCCGCUGGAG
BABD01012433.1/319-419                      GAGAAACUUAGGAUUUUAGGCUCCGCU-GCCGGCUGCUG-GUCGGCAGCGC-AAACCC-CGCAAGGCUGGCGGUCUUGCGCGUGGUCAAAAUCUAUCCGCCGGAG
FP929046.1/562024-562125                    GAGCAACUUAGGAUUUUAGGCUCCCCG-GUGCCACUCGAGCGGCGCUGGGCAAAACCC-ACAGGAGCUGGCGGUUCCUGU-GCGGUCAAAAUCAAACCGCUGGAG
BAAY01013224.1/926-826                      GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCCGGGCCAAACCC-AUAGGG-CUGGCGGUCCCUGU-GCGGUCAAAAUUCAUCCGCCGGAG
FP929045.1/1765647-1765748                  GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCCGGGCCAAACCC-ACGGGGGCUGGCGGUCCCCGC-GCGGUCAAAAUCAAACCGCUGGAG
BAAX01019688.1/382-483                      GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCCGGGCCAAACCC-ACGGGGGCUGGCGGUCCCCGC-GCGGUCAAAAUCAAACCGCUGGAG
BAAY01002983.1/1264-1163                    GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCCGGGCCAAACCC-ACGGGGGCUGGCGGUCCCCGC-GUGGUCAAAAUCAAACCGCUGGAG
ADJS01009939.1/10976-11077                  GAGCAACUUAGGAUUUUAGGCUCCGCC-GUCUCCCCUGCGGGAGGCGGCGC-AAACCC-CGCAAGGCUGGCGGUCUUGCGUGCGGUCAAAAUCUAUCCGCCGGAG
ADJS01012726.1/612-517                      GAGCAACUUAGGAUUUUAGGCUCCACC-GCGGCUU------GCUGCGGUGC-AAACCC-CGCAAGCCUGGCGGUCUUGCGCGCGGUCAAAAUCUAUCCGCCGGAG
BAAZ01007046.1/1247-1147                    --GCAACUUAGGAUUUUAGGCUCCCCGUGCGUGUCUCGAACCAUGCCGGGCCAAACCC-ACGGGGGCUGGCGGUCCCCGU-GCGGUCAAAAUCAAACCGCUGGAG
BABA01010993.1/1076-1176                    GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCCGGGCCAAACCC-ACAGGGGCUGGCGG-CCCUGU-GCGGUCAAAAUCAUCCCGCUGGAG
BAAY01002380.1/1139-1039                    GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCCGGGCCAAACCC-ACAGGGGCUGGCGG-CCCUGU-GCGGUCAAAAUCAUCCCGCUGGAG
BABA01026116.1/736-636                      GAGCAACUUAGGAUUUUAGGCUCCCCG-GUGCGUCUCGAACCGCGCUGGGCCAAACCC-ACAGGGGCUGGCGG-CCCUGU-GCGGUCAAAAUCAAACCGCUGGAG
BABA01018694.1/413-513                      GAGCAACUUAGGAUUUUAGGCUCCGCU-GCCGGCUGCUG-GUCGGCAGCGC-AAACCC-CGCAAGGCUGGCGGUCUUGCGCGUGGUCNAAAUCUAUCCGCCGGAG
AECU01000177.1/7590-7690                    GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCCGGGCCAAACCC-ACAGGGGCUGGCGG-CCCUGU-GCGGUCAAAAUCAUCCCGCUGGAG
ADJS01009870.1/10212-10312                  GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCCGGGCCAAACCC-ACAGGGGCUGGCGG-CCCUGU-GCGGUCAAAAUCAUCCCGCUGGAG
BAAX01000750.1/3091-2990                    GAGCAACUUAGGAUUUUAGGCUCCCCG-GUGCCACUCGAGCGGCGCUGGGCAAAACCC-ACAGGAGCUGGCGGUUCCUGU-GCGGUCAAAAUCAAACCGCUGGAG
ADJS01011583.1/9082-9183                    GAGCAACUUAGGAUUUUAGGCUCCCCG-GUGCCACUCGAGCGGCGCUGGGCAAAACCC-ACAGGAGCUGGCGGUUCCUGU-GCGGUCAAAAUCAAACCGCUGGAG
BAAX01000347.1/2947-2847                    GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCCGGGCCAAACCC-AUAGGG-CUGGCGGUCCCUGU-GCGGUCAAAAUUCAUCCGCCGGAG
BAAV01004919.1/1075-1175                    GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCCGGGCCAAACCC-AUAGGG-CUGGCGGUCCCUGU-GCGGUCAAAAUUCAUCCGCCGGAG
ABED02000027.1/116756-116655                GAGCAACUUAGGAUUUUAGGCUCCCCG-GUGCCACUCGAGCGGCGCUGGGCAAAACCC-ACAGGAGCUGGCGGUUCCUGU-GCGGUCAAAAUCAAACCGCUGGAG
ADJS01012663.1/5165-5065                    GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCCGGGCCAAACCC-AUAGGG-CUGGCGGUCCCUGU-GCGGUCAAAAUUCAUCCGCCGGAG
ACOP02000046.1/22370-22270                  GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCCGGGCCAAACCC-AUAGGG-CUGGCGGUCCCUGU-GCGGUCAAAAUUCAUCCGCCGGAG
ADJT01005830.1/328-228                      GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCUGGGCCAAACCC-AUAGGG-CUGGCGGUCCCUGU-GCGGUCAAAAUUCAUCCGCCGGAG
ACBY02000013.1/114529-114434                GAGCAACUUAGGAUUUUAGGCUCCGCC-GCAG----CUU---CCGCGGCGC-AAACCGGUGUCAGGCUGGCGGUCUGGCAUGCGGUCAAAAUCUAUCCGCCGGAG
BAAU01020333.1/1-83                         ------------------GGCUCCGCU-GUCGGCUGCUG-GUCGGCAGCGC-AAACCC-CGCAAGGCUGGCGGUCUUGCGUGUGGUCAAAAUCUAUCCGCCGGAG
ADJT01007369.1/6381-6474                    GAGCAACUUAGGAUUUUAGGCUCCGCC-UGGU------U---UUCAGGCGCAAACCCA-CCCAAGCCUGGCGGUCUUGGGCGCGGUCAAAAUCUAUCCGCCGGAG
ADJS01013861.1/2134-2227                    GAGCAACUUAGGAUUUUAGGCUCCGCC-UGGU------U---UUCAGGCGCAAACCCA-CCCAAGCCUGGCGGUCUUGGGCGCGGUCAAAAUCUAUCCGCCGGAG
URS0000868518_853/1-101                     GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCCGGGCCAAACCC-AUAGGG-CUGGCGGUCCCUGU-GCGGUCAAAAUUCAUCCGCCGGAG
#=GR URS0000868518_853/1-101      4RZD_A_SS ((((......{{{{{{...))))((((.(((((........)))))))))....((((.(.((((.........)))).).).)))..}}}}}}...........
URS0002311A1C_853/1-101                     GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCCGGGCCGAACCC-AUAGGG-CUGGCGGUCCCUGU-GCGGUCAAAAUUCAUCCGCCGGAG
#=GR URS0002311A1C_853/1-101      6XKN_A_SS ((((......{{{{{{...))))((((.(((((........))))))))).....(((.((((((.........)))))).).))...}}}}}}...........
URS000231199B_853/1-101                     GAGCAACUUAGGAUUUUAGGCUCCCCG-GCGUGUCUCGAACCAUGCCGGGCCAAACCC-AUAGGG-CUGGCGGUCCCUGU-GCGGUCGAAAUUCAUCCGCCGGAG
#=GR URS000231199B_853/1-101      6XKO_A_SS ((((......{{{{{{...))))((((.(((((........)))))))))....((((.((((((.........)))))).).)))..}}}}}}...........
#=GC SS_cons                                <<<<______AAAAAA___>>>><<<<.<<<<<________>>>>>>>>>::::<<<<.<<<<<<<_______>>>>>>>.>->>>::aaaaaa:::::::::::
#=GC RF                                     GaGCAACUUAGGAUUUUAGGCuCCcCg.GcgcgucuCgaaccgcgCcGgGCcAAaCCC.gccggGgCUGGCGGcCccggc.GcGGuCAAAAUcuAuCCGCuGGAG
#=GC RNA_ligand_preQ1                       ======X=========X======================================================================X=================
#=GC RNA_structural_element                 [5p=P1=]=[5p=P2][3p=P1][===========P3============]====[==============P4==============]==[3p=P2]==========
//
