# STOCKHOLM 1.0
#=GF ID Thr_leader
#=GF AC RF00506
#=GF DE Threonine operon leader
#=GF AU Bateman A; 0000-0002-6982-4660
#=GF GA 55.0
#=GF NC 54.9
#=GF TC 55.0
#=GF SE Bateman A
#=GF SS Published; PMID:6186194
#=GF TP Cis-reg; leader;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 29.45 -Z 2958934 CM SEQDB
#=GF DR GO; 0009088; threonine biosynthetic process;
#=GF DR SO; 0000655; ncRNA;
#=GF RN [1]
#=GF RM 6186194
#=GF RT Attenuation in amino acid biosynthetic operons.
#=GF RA Kolter R, Yanofsky C
#=GF RL Annu Rev Genet 1982;16:113-134.
#=GF CC At least 6 amino acid operons are known to be regulated by attenuation
#=GF CC [1]. In each a leader sequence of 150-200 bp is found upstream of the
#=GF CC first gene in the operon. This leader sequence can assume two different
#=GF CC secondary structures known as the terminator and the anti-terminator
#=GF CC structure. In each case the leader also codes for very short peptide
#=GF CC sequence that is rich in the end product amino acid of the operon. The
#=GF CC terminator structure is recognised as a termination signal for RNA
#=GF CC polymerase and the operon is not transcribed. This structure forms when
#=GF CC the cell has an excess of the regulatory amino acid and ribosome movement
#=GF CC over the leader transcript is not impeded [1]. When there is a deficiency
#=GF CC of the charged tRNA of the regulatory amino acid the ribosome translating
#=GF CC the leader peptide stalls and the antiterminator structure can form. This
#=GF CC allows RNA polymerase to transcribe the operon [1]. In the Rfam alignment
#=GF CC the consensus structure is of the terminator. The alternative consensus
#=GF CC structure is the antiterminator structure.
#=GF WK Threonine_operon_leader
#=GF SQ 25

M10393.1/122-16              -CACC-------ACCAUUACCACCA---CCAUCACCAU------UACC------ACA---GGUAACGGUG-CGGGCUGACGCGUA-CAGCAAAC-ACAGA-AAAAAGCCCGCA-CCUG-A--CAG-UGCGGGCUUUUUUUUU
CR378664.1/249363-249488     UUAUC-------AGCACAACCACAA---CCACAACCAUUAUUAUUACUGGCACGAUUAUUCGUGUUGGUG-CGGGCUGAUACGCA-UAAGAUUC--UAAA-AAAAAGCCCGCA-CUUCUUAUUAGAUGCGGGCUUUUUUUUU
BX950851.1/4357430-4357315   CUAUC-------AGCCUAAUCACCACGAUUAUUACCAU------CACCGAUACAACC---AGUAACGGUG-CGGGCUGACGCAUA-CAAAGAUU-CCAG--AAAAAGCCCGCA-CCGA-A--CAG-UGCGGGCUUUUUUUUU
BX571860.1/286462-286580     UUAUC-------AGCCUGAAAACCACAAUGAUUACCAC------CACCGGGACCACA---GGUUGCGGGG-CGGGCUGACGCAUA-UAUAAAAC-AGAGA-AAAAAGCCCGCA-UCCAAAU-CAGAUGCGGGCUUUUUUUU-
U00096.2/184-310             ACAUCCAUGAAACGCAUUAGCACCA---CCAUUACCACCACCAUCACCAUUACCACA---GGUAACGGUG-CGGGCUGACGCGUA-CAGGAAAC-ACAGA-AAAAAGCCCGCA-CCUG-A--CAG-UGCGGGCUUUUUUUUU
U14003.1/332669-332795       ACAUCCAUGAAACGCAUUAGCACCA---CCAUUACCACCACCAUCACCAUUACCACA---GGUAACGGUG-CGGGCUGACGCGUA-CAGGAAAC-ACAGA-AAAAAGCCCGCA-CCUG-A--CAG-UGCGGGCUUUUUUUUU
V00360.1/26-152              ACAUCCAUGAAACGCAUUAGCACCA---CCAUUACCACCACCAUCACCAUUACCACA---GGUAACGGUG-CGGGCUGACGCGUA-CAGGAAAC-ACAGA-AAAAAGCCCGCA-CCUG-A--CAG-UGCGGGCUUUUUUUUU
J01706.1/44-170              ACAUCCAUGAAACGCAUUAGCACCA---CCAUUACCACCACCAUCACCAUUACCACA---GGUAACGGUG-CGGGCUGACGCGUA-CAGGAAAC-ACAGA-AAAAAGCCCGCA-CCUG-A--CAG-UGCGGGCUUUUUUUUU
AF487900.1/184-310           ACAUCCAUGAAACGCAUUAGCACCA---CCAUUACCACCACCAUCACCAUUACCACA---GGUAACGGUG-CGGGCUGACGCGUA-CAGGAAAC-ACAGA-AAAAAGCCCGCA-CCUG-A--CAG-UGCGGGCUUUUUUUUU
M28570.1/169-295             ACAUCCAUGAAACGCAUUAGCACCA---CCAUUACCACCACCAUCACCAUUACCACA---GGUAACGGUG-CGGGCUGACGCGUA-CAGGAAAC-ACAGA-AAAAAGCCCGCA-CCUG-A--CAG-UGCGGGCUUUUUUUUU
X68872.1/167-293             ACAUCCAUGAAACGCAUUAGCACCA---CCAUUACCACCACCAUCACCAUUACCACA---GGUAACGGUG-CGGGCUGACGCGUA-CAGGAAAC-ACAGA-AAAAAGCCCGCA-CCUG-A--CAG-UGCGGGCUUUUUUUUU
X60821.1/811-927             AUAUC-------AGCCUGACUACCACAAUUAUUACCAC------CACCGAUACCACA---GGUAACGGGG-CGGGCUGACGCGCA-CAGGAAAC-ACAGA-AAAAAGCCCGCA-CCUAAU--CAG-UGCGGGCUUUUUUUU-
D10387.1/811-927             AUAUC-------AGCCUGACUACCACAAUUAUUACCAC------CACCGAUACCACA---GGUAACGGGG-CGGGCUGACGCGCA-CAGGAAAC-ACAGA-AAAAAGCCCGCA-CCUAAU--CAG-UGCGGGCUUUUUUUU-
D10386.1/76-192              AUAUC-------AGCCUGACUACCACAAUUAUUACCAC------CACCGAUACCACA---GGUAACGGGG-CGGGCUGACGCGCA-CAGGAAAC-ACAGA-AAAAAGCCCGCA-CCUAAU--CAG-UGCGGGCUUUUUUUU-
D10385.1/76-192              AUAUC-------AGCCUGACUACCACAAUUAUUACCAC------CACCGAUACCACA---GGUAACGGGG-CGGGCUGACGCGCA-CAGGAAAC-ACAGA-AAAAAGCCCGCA-CCUAAU--CAG-UGCGGGCUUUUUUUU-
AAYV01000002.1/459724-459606 ACAUC-------AGCCUGAACACAA---CGAUUAUUACCAC---CACCGAAACCACA---GGUUACGGGG-CGGGCUGACGCGUA-CAGGAAACAAUAGA-AAAAAGCCCGCA-CCUAGA--CAG-UGCGGGCUUUUUUUUU
AE005174.2/215-328           CCACC-------ACCAUCACCACCA---CCAUCACCAU------UACCAUUACCACA---GGUAACGGUG-CGGGCUGACGCGUA-CAGGAAAC-ACAGA-AAAAAGCCCGCA-CCUG-A--CAG-UGCGGGCUUUUUUUUC
CP000653.1/632784-632902     GCGUU-------AGCACCACCACCA---UUACAACAACCAU---CAUCAUUACCACA---GGUAACGAUG-CGGGCUGACGCGUAACAGGAAAA-ACAGA-AAAAAGCCCGCA-CCUAAA--CAG-UGCGGGCUUUUUUUUC
AP008232.1/715571-715690     GCUUC-------AGCCACAGCACCA---UUAUUACCACCAC---CACCGAUACCACCACGGGUAGCGGCG-CGGGCUGACGCAUA-CAGGAAUC--CAGA-AAAAAGCCCGCA-CCUUGA--UAA-UGCGGGCUUUUUUUUA
CP000627.1/2075691-2075573   GCCUA-------AUCGUAAUGACCA---CCAUUAUUACCAU---UACCGACACGUCG---CAUGUUGGGG-CAGGCUGCUGAGCG-CAAAAUUU-CACAA-AAAAGGCCUGUA-UCCCAAC-CGA-UACAGGCCUUUUUUUA
CP000302.1/3285222-3285104   CUCAG-------AGUAUUACUCUUA---UCACCAUUACAAC---CACCACAAUCAAU---AUUGUGGGGG-CGGGCUAGCGCACC-UAAAAGAU-UUACAAAAAAAGCCCGCU-UCCCAC--UGA-AGCGGGCUUUUUUGUU
CP000746.1/858744-858862     CCGAC-------CGCACUUUUACCA---UGAUGACGAUUAC---CACCAUUAUGAC----CUUUAUAAUGGCGGGGUAGUGCGAA-CGAAAGAU-AUUCA-AUUAAGCCCGCAACCUGAA--AAG-UGCGGGCUUUUUUGCA
AAMK02000025.1/34036-34149   UGAAA-------CGCAUUAGCACCA---CCAUUACCAU------CACCAUUACCACA---GGUAACGGUG-CGGGCUGACGCGUA-CAGGAAAC-ACAGA-AAAAAGCCCGCA-CCUG-A--CAG-UGCGGGCUUUUUUUUU
CP000826.1/750669-750787     AUAUC-------AGCCUGAACACAA---CAAUUAUUACCAC---CACCGAUACCACA---GGUAACGGGG-CGGGCUGACGCGUA-CAGGAAACAAAAGA-AAAAAGCCCGCA-CCUA-AC-CAG-UGCGGGCUUUUUUUUC
CP001235.1/2607111-2606993   GCCUA-------AUCGUAAUGACCA---CCAUUAUUACCAU---UACCGACACGUCG---CAUGUUGGGG-CAGGCUGCUGAGCG-CAAAAUUU-CACAA-AAAAGGCCUGUA-UCCCAAC-CGA-UACAGGCCUUUUUUUA
#=GC SS_cons                 :::<<.......<<<-<<<<<--<<...<<-<<<<<_____..._____________...>>>>>->>>>.--->>>>>->>>--.--->>:::.::<<<.<<<<<<<<<<<<.<_____..__>.>>>>>>>>>>>>>>>:
#=GC RF                      acauc.......cgCaucAgcACca...ccAuuAccAccAc...CACCauuACcACa...ggUaacggug.CGGgcUgacGcguA.CAagaaAc.acagA.AAAAaGCCCGCa.cCuaAa..cAg.uGCGGGCuUUUUUuuu
//
