# STOCKHOLM 1.0
#=GF ID SAM-III
#=GF AC RF01767
#=GF DE SAM-III riboswitch aptamer (SMK box)
#=GF AU Gardner PP; 0000-0002-7808-1213
#=GF GA 45.0
#=GF NC 44.9
#=GF TC 45.1
#=GF PI SMK_box_riboswitch;
#=GF SE Gardner PP
#=GF SS Published; PMID:18806797; Gardner PP
#=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; 0006446; regulation of translational initiation;
#=GF DR GO; 0004478; methionine adenosyltransferase activity;
#=GF RN [1]
#=GF RM 17360376
#=GF RT S-adenosylmethionine directly inhibits binding of 30S ribosomal subunits
#=GF RT to the SMK box translational riboswitch RNA.
#=GF RA Fuchs RT, Grundy FJ, Henkin TM
#=GF RL Proc Natl Acad Sci U S A. 2007;104:4876-4880.
#=GF RN [2]
#=GF RM 16491091
#=GF RT The S(MK) box is a new SAM-binding RNA for translational regulation of SAM
#=GF RT synthetase.
#=GF RA Fuchs RT, Grundy FJ, Henkin TM
#=GF RL Nat Struct Mol Biol. 2006;13:226-233.
#=GF RN [3]
#=GF RM 18806797
#=GF RT Crystal structures of the SAM-III/S(MK) riboswitch reveal the
#=GF RT SAM-dependent translation inhibition mechanism.
#=GF RA Lu C, Smith AM, Fuchs RT, Ding F, Rajashankar K, Henkin TM, Ke A
#=GF RL Nat Struct Mol Biol. 2008;15:1076-1083.
#=GF RN [4]
#=GF RM 18443629
#=GF RT Riboswitches that sense S-adenosylmethionine and S-adenosylhomocysteine.
#=GF RA Wang JX, Breaker RR
#=GF RL Biochem Cell Biol. 2008;86:157-168.
#=GF RN [5]
#=GF RM 18374645
#=GF RT Riboswitches that sense S-adenosylhomocysteine and activate genes involved
#=GF RT in coenzyme recycling.
#=GF RA Wang JX, Lee ER, Morales DR, Lim J, Breaker RR
#=GF RL Mol Cell. 2008;29:691-702.
#=GF WK SMK_box_riboswitch
#=GF SQ 25

ACHK01000062.1/4026-4119     U--UGUUAC---AA-----GUUCCCGAAAGGAUUUAGCAAGUAAUUGUCGUUACUUAC-UAAAGAUGCCUUGUAACC---GAAA----------CUA----------------------------UUUAGGGGGAAU--AACAUUAUG
ACBD01000055.1/1906-1985     GUUCGUUGC---AA-----GUUCCCGAAAGGAUCCGU-----------------AGGA-CGGAGAUGCCUUGUAACC---GAAU----------UUA----------------------------ACUAGGGGGAAU-CAUUAUAAUG
ACAJ01000030.1/519-601       GUCCGUUGC---AA-----GUUCCCGAAAGGAUUCGC----------------AGCUG-CGAAGAUGCCUUGUAACC---GAAU----------CGA--------------------------AAUUUAGGGGGAAU-ACAAAAAAUG
ACAO01000044.1/534-615       GUCCGUUGC---AA-----GUUCCCGAAAGGAUUCGC----------------AGCUG-CGAAGAUGCCUUGUAACC---GAAA-------CAUAUA-----------------------------UUAGGGGGAAU--ACAAAAAUG
AE017198.1/564018-564088     UUCGGUU-----AA-----GGUCCCGAAAGGAUUCGU---------------UUUUAA-CGAAGAUGCCUUGUAACC---GAAA------------------------------------------GAUGGGGGACU------CUAUG
CP000233.1/487061-487146     AAUAGUUAC---AAUC--CAUUCCCGAAAGGAUUCGU---------------UUUAAA-CGAAGAUGCCUUGUAACC---AAAU-----UACUUAUA---------------------------AUAAUGGGGGAAU---UAAAU---
ACLL01000026.1/19090-19198   CUUCGUUAU--GAAGC-AAAUUCCCGAUAGGAUUCAC--------------UUAAUUG-UGAAGAUGCCUUGUAACC---GCAA----------CUACAAAACUACUACUAGAGUUUCGACUAGAAUAUGGGGGAAU----UAA----
ACGV01000186.1/13246-13351   UCUCGUUAU--AAAGC-AAAUUCCCGAUAGGAUUCAC--------------UUUACUG-UGAAGAUGCCUUGUAACCACUAAAU-GUUUCAAUUGUAAC----------------------UUGCAUAUGGGGGAAUUAACACACAU-
CP000422.1/681467-681547     GUAAGUUAC---UAGU---GUUCCCGAUAGGAUUAGU---------------UAUCCAA--AAGAU-CCUUGUAACC---GAAA----------UUA--------------------------AAUUUAGGGGGAAU----UUACAUG
ACIZ01000041.1/43695-43782   UAGAGUUGC---AAUACA--UUCCCGAUGGGGUUCGUUA-----------GCGAUUAA-CGAACAUGCCUUGUAACC---GAAA----------AUC----------------------------AUGAGGGGGAA--ACAAACGAUG
FM177140.1/914403-914491     UAGAGUUGC---AAAACA--UUCCCGAUGGGGUUCGUCA----------AAGCUAUGA-CGAACAUGCCUUGUAACC---UAAA----------AUA----------------------------AUAAGGGGGAA--ACAAAACAUG
CP000413.1/483009-483080     UUCGGUU-----AA-----GGUCCCGAAAGGAUUCGC--------------UUUUUAA-CGAAGAUGCCUUGUAACC---GAAA------------------------------------------GAUGGGGGACU------CUAUG
CP000517.1/1692576-1692488   UAUCGGUUC---AA------GUCCUGAAAGGAUUCACU------------AUUAUUAG-UGAAGAUGCCUUGUAACC---GAAUA-GCUAAUGUCUA----------------------------UAUGGGGGGAC-----UAUUAUG
ACIL02000003.1/164571-164483 GUCAGUUACAACAAUAAA--UUCCCGAUGGGAUUCAUU-------------UUCUUAA-UGAAGUUGCCUUGUAACC---AAU-----------CUA--------------------------CAAAAUGGGGGAA---AUUACUAUG
CP000033.3/1626537-1626447   UAUCGGUUC---AA------GUCCUGAAAGGAUUCAUUA----------AAUAAUUAG-UGAAGAUGCCUUGUAACC---GAAU-AGCCGAUGUCUA----------------------------UAUAGGGGGAC-----UAAUAUG
ACGH01000133.1/29066-28984   GUAGGUUAU---GAG-----UUCCCGAUAGGAUUCACG-------------CCAGACG-UGAAGAAGCCUUGUAACC---UAAA--------AAAUA----------------------------UAUAGGGGGAA----AUAAAAUG
ACLN01000012.1/57665-57589   UACGGUU-----AA-----GGUCCCGAGAGGAUUCGA-----------------AAUU-CGAAGAUGCCUUGUAACC---GAUU--------UUUUA------------------------------AAGGGGGAC--UUCUAUUAUG
CR954253.1/1355763-1355676   AUUUGUUAC---AA------GUCCUGAUAGGAUUCACC-------------AAAUUGG-UGAAGAUGCCUUGUAACC---GUGUA--------GCUA-------------------------GUCUAUAGGGGGAC-ACAUAUAGAUG
ACKR01000001.1/1180-1268     UAUCGGUUC---AA------GUCCUGAGAGGAUUCACU------------AUGAUUAG-UGAAGAUGCCUUGUAACC---GAAU-AGCCAAUGUCUA----------------------------UAUAGGGGGAC-----UAAUAUG
ABHH01000037.1/13513-13426   GAGGUUUGC---AAUUCGGAUUCCCGAGAGGAUUCACU-------------UUUAAAG-UGGAGAAGCCUUGUAACC---GAAA--------AUUUA------------------------------AAGGGGGAA--CAAAGUAAUG
ACKZ01000012.1/36527-36446   AAAAGUUAA---AAAUGAUAUUCCCGAAAGGAUGCAC-----------------CAUG-UGUAGAUGCCUUGUAACC---GGAA----------UUG-----------------------------AAUGGGGGAA---AAAGAAAUG
AF401669.1/1455-1540         UAGAGUUAU---AAGAAG--UUCCCGAUAGGAUUCAC---------------ACACCG-UGAAGAGGCCUUGUAACC---GACA---------CAUA----------------------------UAUAGGGGGAA-ACAUAGAAAUG
ACGU01000017.1/23671-23581   UAUCGGUUC---AA------GUCCUGAUAGGAUUCAUUA----------CUUAGUUAA-UGAAGAUGCCUUGUAACC---GGAU-AGCCAAUGUCUA----------------------------UAUAGGGGGAC-----UAAUAUG
ADEX01000093.1/3153-3076     AUCGGUU-C---AA------GUCCUGAUAGGAUUCGU-----------------UAUA-CGAAGAUGCCUUGUAACC---GAA------------UAGC---------------------UUGUCUAUAGGGGGAC------AUUAUG
CP003032.1/1501869-1501780   AAGCGUUAC---AACU--CAUUCCCGAUAGGAUUCACG-------------CUUUUAG-UGAAGAUGCCUUGUAACC---ACAA----------AUAU------------------------AAUGAAUGGGGGAAU--UUUAUUAUG
#=GC SS_cons                 :::::::::...:::....:(((((,,<<<<-<<<<<..............______>.>>>>---->>>>,,,,<<...____..........___............................____>>)))))...:::::::::
#=GC RF                      uauaGUUac...AAu....guUCCCGAaAGGAUuCgc..............uuauuag.cGaAGAUGCCUuGUAACC...GAAa..........uUA............................uauaGGGGGAa...aauaauAUG
//
