# STOCKHOLM 1.0 #=GF ID c-di-GMP-I-GGC #=GF AC RF03167 #=GF DE c-di-GMP-I-GGC riboswitch aptamer #=GF AU Ontiveros-Palacios N; 0000-0001-8457-4455 #=GF GA 59.0 #=GF NC 58.9 #=GF TC 59.0 #=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 CL00126 #=GF DR GO; 0035438; cyclic-di-GMP binding; #=GF DR SO; 0000035; riboswitch; #=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 19898478 #=GF RT Recognition of the bacterial second messenger cyclic diguanylate by its #=GF RT cognate riboswitch. #=GF RA Kulshina N, Baird NJ, Ferre-D'Amare AR #=GF RL Nat Struct Mol Biol. 2009;16:1212-1217. #=GF RN [3] #=GF RM 22148472 #=GF RT Structural and biochemical characterization of linear dinucleotide #=GF RT analogues bound to the c-di-GMP-I aptamer. #=GF RA Smith KD, Lipchock SV, Strobel SA #=GF RL Biochemistry. 2012;51:425-432. #=GF RN [4] #=GF RM 20690679 #=GF RT Structural and biochemical determinants of ligand binding by the c-di-GMP #=GF RT riboswitch . #=GF RA Smith KD, Lipchock SV, Livingston AL, Shanahan CA, Strobel SA #=GF RL Biochemistry. 2010;49:7351-7359. #=GF RN [5] #=GF RM 19898477 #=GF RT Structural basis of ligand binding by a c-di-GMP riboswitch. #=GF RA Smith KD, Lipchock SV, Ames TD, Wang J, Breaker RR, Strobel SA #=GF RL Nat Struct Mol Biol. 2009;16:1218-1223. #=GF CC c-di-MP-I-GGC is a variant of c-di-GMPI riboswitch RF01051, that includes #=GF CC CORESEQ GGC. The structure of c-di-MP-I-GGC riboswitch has been reported #=GF CC in PDB: 3IRW, 3MXH, 3UCU, 3UCZ, 3IWN [2, 3, 4, 5]. #=GF WK Cyclic_di-GMP-I_riboswitch #=GF SQ 40 URS0000D66F14_12908/1-152 ---CACGACAAAGGCAAAUCCGUCGAAAGA-CG-GAGACGCGC--AGCCC-U-UG-----------ACGCGUCGGCGUUGCGCUGAUGCGUCUGGUACUCUAGAUACUGCAUAUCUGCUCGCUCGCACUCUCCACAUGACGCAUUGGGAUGCCCAA-----------AGCAA-AGCUGCUGUU-U- URS0000D670CA_12908/1-90 ---GGUUCAGUGGGCGCACUCAUCGAAAGA-UG-AGGGCGCGA--AGCCG-A-AUGUCCUCCGGGUUGGACA------------------------------------------------------------------------------------ACCCAAGG-ACAGCUUAGGUUGCCACC-C- URS0000D6A7FB_12908/1-138 ---UUCGAUAAAGCCGAACCCAUCGAAAGA-UG-GGGACGGGA--AACCA-C-AAGUUUCAGAUAGUUUCGUUGAUUCAAGCUCCUAGUUUUUUUGGCGCUUCCUUAAGAUCUUGAUUCUCUACU------------------------------------AAACAGUAUUG-AGCUGCAGCG-C- URS0000D66689_12908/1-76 ---GUCCGAAAGGGCAGACUGUCGGCGACG-GC-AGGACGCGA--AGCCU-C-CGGGC------UCGCAA--------------------------------------------------------------------------------------GA-----G-CUAGCGG-GGCCGCCAGG-A- URS0000D67EE2_12908/1-83 ---AAUAAAAAAGGUACAUCUGUCGAAAGU-UU-GGGGCGCGA--AGCCG-C-GGAUU--------UAAUACGACAGCUGC----------------------------------------------------------------------------------G-AUGAGCG-GGCUACCGUG-G- URS0000D69D4A_12908/1-80 ---UCUGCCAGAGGCACACUCGUCGCCAGG-CG-AGGGCGCGA--AGCUA-C-CCGUC----C---CGAUCGUGAC-----------------------------------------------------------------------------------G---G-ACAGUGG-GGUUGCCGCG-G- URS0000D6955D_12908/1-88 ---GUUGAAAAAGGUACACUAUCCCAAAGG-GU-AGGCCGCGA--AGUUU-U-GGGUCUAAAUCACUUUUA-------------------------------------------------------------------------------------GUGACAUG-AUUGCCA-AGCUGCCGAU-U- URS0000D68578_12908/1-91 ---UUGCUGAAGGACAAACCUUCCGAAAGG-UU-GGGACGCGA--AGCUU-C-CGAUCUAAGUCCGUUUUAAG-----------------------------------------------------------------------------------CGGAUAAG-AUAACGGGAGUUACUACG-C- URS0000D6C268_12908/1-85 ---AUAGCCUUCGGUAAACCCUCUGAAAGGAGG-GGGGCACGA--AGCCA-U-GGGUCUAAAGU--AUUCA---------------------------------------------------------------------------------------GCUAUG-AUCGCCG-GGCUGCAGCA-A- URS0000D6C9B1_12908/1-89 ---ACCGAAAAAGG-AAACAACCCGAAAGG-GU-UGGACGCGA--AGCAA-C-UGACCUAAGUCCGGAUUUUA-----------------------------------------------------------------------------------AGGAUACG-GUAGCAG-GGCUGCCGGA-C- URS0000D65E51_12908/1-76 ---AAUAUUCUCGGCAAAACAGUCGAAAGG-CU-GUGACGCGA--AGCUA-CAGGGCCUGUA----AA---------------------------------------------------------------------------------------------AUG-GCAGCC--AGCUGCUUCU-C- URS0000D6B4D3_1262879/1-76 ---CGAAUUAUGGGCAGAUCAGUCGAGAGU-CU-GAGACGCGA--AGCUA-GAGCGCC--------UGUAACAU-----------------------------------------------------------------------------------------G-GCAGUA--AGCCGCUACG-U- URS0000D6C163_12908/1-89 ---CUCAAAAAUGGCAAACCCAGCGAAAGC-UG-GGGCUGCGA--AGCUG-A-UGAUCUAAGGUGUCUUAUG------------------------------------------------------------------------------------GCACUAUG-AUGGUCU-GGCUGCUAAA-A- URS0000D69746_12908/1-92 ---UGACGAAACGCCACACCCGGAGCAAUC-CG-GGGCCGGGA--AGCUA-C-GGGCUC---CACCACGGGCUUUCAAUCU---------------------------------------------------------------------------GGUG---G-GCCGCCG-AGCCGCCGAA-C- URS0000D6BB36_12908/1-79 ---UUUUGUUGUGCCAAACUUGCUGUGAAG-CA-AGGACGGGA--AGCUA-U-GGGUC----UUA-GAUAA--------------------------------------------------------------------------------------UAA---G-AUUGCCA-GGUUGCCAAA-A- URS0000D693CF_12908/1-89 ---CCCGACCAAGGCACACCGCUCGAAAGG-GC-GGCUCGCGA--AGCCA-C-GGGCCUUCCACCGCAACCG------------------------------------------------------------------------------------CGGUCACG-GCAGCCG-GGCCACCGCA-G- URS0000D66693_12908/1-91 ---GCCGAUAAAGGCUAACCUCUCGAAAGA-GA-GGAGAGCGCAAAGCCA-C-GGGUCUAAGGCUCCGAUUU------------------------------------------------------------------------------------GAGCUAUG-GCUACCG-GGUUGCCGAA-G- URS0000D6B29D_12908/1-77 ---UGCGACAAAGGCAACCCCGUCGCAAGA-UG-GGUGAGCGCAAAGCCA-C-GGGCC--------UCUAAGA------------------------------------------------------------------------------------------G-GCAGCCG-GGAUACCGAA-C- URS0000D6B429_12908/1-77 ---UGCGACAAAGGCAACCCCGCCGCAAGG-CG-GGUGAGCGCAAAGCCA-C-GGGCC--------UCAAAGA------------------------------------------------------------------------------------------G-GCAGCCG-GGCUACCGAA-C- URS0000D6571B_12908/1-77 ---UGCGACAAAGGCAACCCCGCCGCGAGG-CG-GGUGAGCGCAAAGCCA-C-GGGCC--------UCAAAGA------------------------------------------------------------------------------------------G-GCAGCCG-GGUUACCGAA-C- URS0000D667CA_12908/1-88 ---CCUCGAAAUGGCAAACCCGGCGAAAGC-CG-GGGACGCGA--AGCCA-C-GGUCCCUCACUCUACUUG-------------------------------------------------------------------------------------AGAGACGG-GAAGCCG-AGCUACCGAA-A- URS0000D6C0F5_12908/1-78 ---UUUGCUAGAGCCAAAUCUUUUGUAAAGCAG-GGGAAGGGA--AACCA-C-AGGUC--------UUAAAUGAA----------------------------------------------------------------------------------------G-AUAGCUG-GGUUGCCAUA-A- URS0000D67D5C_12908/1-88 ---ACCGCCCAGGGCAAACCCGGCGUGAGU-CG-GGGACGCGA--AGCCA-G-GGAUC----UUCGAGAAGGAAUGUU------------------------------------------------------------------------------CGAA---G-ACCGCCC-GGUUGCCGGA-G- URS0000D699CD_12908/1-73 ---CAAGAUAAAGCCAAACCUGCCGUGAGA-CA-GGG-CGGGA--AGCAA-C-GGGUC--------UCAAUA-------------------------------------------------------------------------------------------G-AUAGCCG-AGUUGCCUCU-U- URS0000D6CE47_12908/1-74 ---CAAGGUAAAGCCAAACUUGUCGUAAGG-CA-GGGACGGGA--AGCUA-C-GGGUC--------UCAACU-------------------------------------------------------------------------------------------G-AUAGCCG-AGCUACCUUG-G- URS0000D6858C_12908/1-76 ---CGAGGAUAAGCCAAAUCUGCCGAAAGA-CA-UGGACGGGG--AAUUA-C-GGGUC--------UUAUCGGA-----------------------------------------------------------------------------------------G-AUAACUG-GAUUGCCUUA-A- URS0000D66165_12908/1-75 ---CAAGAGAAAGCCAAACCUGCCGUAAGG-UA-GGGACGAGG--AAUCA-C-AGAUU--------UCUUUGA------------------------------------------------------------------------------------------A-AUAGCCG-AGUUGCCUUG-A- URS0000D67A64_12908/1-75 ---CAAGAAAAAGCCAAACCUGCCGCAAGA-CA-GGGACGAGG--AAUCA-CAGGUUU--------CUUUGA-------------------------------------------------------------------------------------------A-AUAGCCG-AGUUGCCUUG-A- URS0000D6A3DC_12908/1-77 ---AAAGAAAAAGCCAAACCUGCCGCAAGA-CA-GGGACGGGG--AAUUA-C-GGGUC--------UUAUAAAAA----------------------------------------------------------------------------------------U-AUUGCCG-GUUUGCCUUG-A- URS0000D674D6_12908/1-78 ---CCCGACAAAGCCAAACCCUCCGAGAGA-AG-GGGGCGGGA--AGCGG-C-GGGCU----UUA-ACAA---------------------------------------------------------------------------------------UAA---G-AUGGCCG-AGCUGCCGAA-G- URS0000D6C2A1_12908/1-109 ---AACGACAAAGCCAAACCCGUCGAGAGA-CG-GGAAAGGGA--AACUA-C-GGGUG----UUCGCAUCCUCGGCGACGUUCUAUCGCC----------------------------------------------------------ACGAAGGACGCAA--G-AUCGCCC-GGCUGCCGAA-G- URS0000D69DD4_12908/1-106 ---AGCGAAAAGGGCAAACCCGGCGAAAGC-CG-GGGACGCGAA-AGCCG-U-GAGUCUAAGGCAUUCGUGCACCGCUUCGGGCACGG--------------------------------------------------------------------GUGCUAUG-ACCGUCA-GGUUGCCGCU-C- URS0000D65DAE_12908/1-84 ---AGCUACAAGGCCAAACCCGUCGUGAGA-CGGGGGACGGGAA-AACCA-U-GGGUC----UCCAGCUUGC------------------------------------------------------------------------------------UGGA---G-AUCGCCA-GGUUGCCGGU-U- URS0000D65EEA_12908/1-79 ---CCUGACAAAGCUAACCUUUCCGUGUGA-AG-GGGAUAGGA--AGUAU-U-GGGUU--------UUAUGAAGGUA--------------------------------------------------------------------------------------G-AUGGCCG-AACUGCCGAA-A- URS0000D660DF_12908/1-89 ---CCCAUCAAGGGUAAGCCCGGCAAAAUC-CG-GGGGAGCGA--AGCUAAG-GGAUCUGAGACGGUUAAU-------------------------------------------------------------------------------------CUGCUAUG-GUAGCCC-GGCUGCUGGG-A- URS0000D69479_12908/1-85 ---CCACGAUUAGGCAAACCCUGCAAAAGC-AG-GGGGCGCGA--AGCUA-AAGGGCCUAAGGGC-AAAA---------------------------------------------------------------------------------------GCCUAUG-GCAGCC--AGUUGCCGAC-G- URS0000D683BF_12908/1-150 ---CCUCGAAGAGGCAAACUCCGGGUCACC-GG-AGGACGCGA--AGCCA-C-GGGCU--------CUCAAAGACAGUGGAACGUUGACAGUGGAACGUUGAACGUCAAACGCCUUCCACUGAAACGUUCAACGUUCCACUGUGUUCC---------------G-GAAGCCG-GGCUGCCGAA-A- URS0000D67B5A_12908/1-97 ---CCUCGAAAAGGCAAACUGCGCGAAAGU-GC-AGGACGCGA--AGGAA-C-GGGUC--------CUCAUCUAGUGGGAAAAGCGCUCGG---------------------------------------------------------------------CGCG-AGCGCCCCUUCUACCUAA-G- URS000080E2D1_666/1-92 GGUCACGCACAGGGCAAACCAUUCGAAAGA-GU-GGGACGCAA--AGCCU-C-CGGCCUA----AA----CCA---UUGCAC--------------------------------------------------------------------------UCCGGUAG-GUAGCGG-GGUUACCGA-UGG #=GR URS000080E2D1_666/1-92 3IRW_R_SS ...((((......((...((((((....)).)).))..{)).....(((..(.(((((((..........((.......................................................................................))))).)).}))).))))..))..)). #=GR URS000080E2D1_666/1-92 3MXH_R_SS ...((((......((...((((((....)).)).))..{)).....(((..(.(((((((..........((.......................................................................................))))).)).}))).)))...))...)) #=GR URS000080E2D1_666/1-92 3UCU_R_SS ...((((......((...((((((....)).)).))..{)).....(((..(.(((((((..........((.......................................................................................))))).)).}))).)))...))...)) #=GR URS000080E2D1_666/1-92 3UCZ_R_SS ...((((......((...((((((....)).)).))..{)).....(((..(.(((((((..........((.......................................................................................))))).)).}))).)))...))...)) URS000080DFCB_666/1-93 ---CACGCACAGGGCAAACCAUUCGAAAGA-GU-GGGACGCAA--AGCCU-C-CGGCCUAA-ACGGC----------AUUGCAC----------------------------------------------------------------------UCCGCCGUAG-GUAGCGG-GGUUACCGA-UGG #=GR URS000080DFCB_666/1-93 3IWN_A_SS ...((((......((...((((((....)).)).))..{)).....(((..(.(((((((...((((..........................................................................................))))))).)).}))).)))...))...)) #=GR URS000080DFCB_666/1-93 3IWN_B_SS ...((((......((...((((((....)).)).))..{)).....(((..(.(((((((...((((..........................................................................................))))))).)).}))).)))...))..)). #=GC SS_cons ...(-((,,,,,,<<---<<<<<<____>>.>>.>>--A>>,,..<<<<-.<.<<<<<....___._______...................................................................................._._...>.>>-a>>>.>>>>,,))--.). #=GC RF ...cacgaaAAAGGCAAACCcgcCGAAAGg.cg.GGGACGCGA..AgCcA.c.GGguC....ucc.uuaaaaa....................................................................................g.a...G.acAGCCg.gGcUGCcgaa.g. #=GC RNA_ligand_c-di-GMP =========XXXX===========================XXX=======================================================================================================================================X======= #=GC RNA_structural_elements ==[P1a]======[===========P1b============]====[==========================================================P2=====================================================================]===[P1a]== //