# STOCKHOLM 1.0
#=GF ID GcvB
#=GF AC RF00022
#=GF DE GcvB RNA
#=GF AU Daub J; 0000-0001-6022-563X
#=GF GA 42.0
#=GF NC 41.8
#=GF TC 42.1
#=GF SE Bateman A, PMID:17974919, Daub J
#=GF SS Published; PMID:17974919
#=GF TP Gene;
#=GF BM cmbuild -F CM SEED
#=GF CB cmcalibrate --mpi CM
#=GF SM cmsearch --cpu 4 --verbose --nohmmonly -T 25.14 -Z 2958934 CM SEQDB
#=GF DR SO; 0000379; GcvB_RNA;
#=GF DR GO; 0003729; mRNA binding;
#=GF DR GO; 0010468; regulation of gene expression;
#=GF RN [1]
#=GF RM 10972807
#=GF RT The gcvB gene encodes a small untranslated RNA involved in expression of
#=GF RT the dipeptide and oligopeptide transport systems in Escherichia coli.
#=GF RA Urbanowski ML, Stauffer LT, Stauffer GV
#=GF RL Mol Microbiol 2000;37:856-868.
#=GF RN [2]
#=GF RM 17974919
#=GF RT A small RNA regulates multiple ABC transporter mRNAs by targeting C/A-rich
#=GF RT elements inside and upstream of ribosome-binding sites.
#=GF RA Sharma CM, Darfeuille F, Plantinga TH, Vogel J
#=GF RL Genes Dev. 2007;21:2804-2817.
#=GF RN [3]
#=GF RM 19379489
#=GF RT Small noncoding RNA GcvB is a novel regulator of acid resistance in
#=GF RT Escherichia coli.
#=GF RA Jin Y, Watt RM, Danchin A, Huang JD
#=GF RL BMC Genomics. 2009;10:165.
#=GF RN [4]
#=GF RM 27298343
#=GF RT Temperature-responsive in vitro RNA structurome of Yersinia
#=GF RT pseudotuberculosis.
#=GF RA Righetti F, Nuss AM, Twittenhoff C, Beele S, Urban K, Will S, Bernhart SH,
#=GF RA Stadler PF, Dersch P, Narberhaus F
#=GF RL Proc Natl Acad Sci U S A. 2016;113:7237-7242.
#=GF RN [5]
#=GF RM 25630703
#=GF RT Cross talk between ABC transporter mRNAs via a target mRNA-derived sponge
#=GF RT of the  GcvB small RNA.
#=GF RA Miyakoshi M, Chao Y, Vogel J
#=GF RL EMBO J. 2015;34:1478-1492.
#=GF CC The gcvB gene encodes a small untranslated RNA involved in expression of
#=GF CC the dipeptide and oligopeptide transport systems in Escherichia coli.
#=GF CC Included several unknown homologues in alignment (Bateman A pers obs). It
#=GF CC base-pairs with SorC. This interaction triggers the degradation of GcvB by
#=GF CC RNase E, alleviating the GcvB-mediated mRNA repression of other amino
#=GF CC acid-related transport and metabolic genes [5].
#=GF WK GcvB_RNA
#=GF SQ 27

U00096.2/2940718-2940923   ACUUC-CUGAGCC--GGAACGAAAAGUUUU-AUCGGAAU-GCG-U-GUUCUGGUGAA----CUUUU----GGCUUACG-GUUGUGAUGUUGUGUUGUUGUGUUUGCAA----UUGGUCUGCGAU----UCAGACCAUGGUAGCAA--------------------------AGCUACC----------UUUUUUCACUUC
U29581.1/24251-24456       ACUUC-CUGAGCC--GGAACGAAAAGUUUU-AUCGGAAU-GCG-U-GUUCUGGUGAA----CUUUU----GGCUUACG-GUUGUGAUGUUGUGUUGUUGUGUUUGCAA----UUGGUCUGCGAU----UCAGACCAUGGUAGCAA--------------------------AGCUACC----------UUUUUUCACUUC
BX571861.1/50378-50183     ACUUC-CUAAGCC--GGAACGAAAAGUGA--AUCAGCUU-A-----ACGCUAUGAAA----CUUUU----GGCUUUGUGGUUGUGAUG--------UUGUGUUUGCAA----GUUGUCUGGGAA---ACCGGACCCU-GUAGCUC-------------------------AAGCUACU---------GUUUUUUCACUUC
BX950851.1/1137282-1137085 ACUUC-CUGGGCC--GGAACGAAAAGUGCG-GAGGGG--------UGACCUGAGGUG----CUUUU----GGCUUGUG-GUUGUGAUG--------UUGUGUUUGCUAUUUUUUUGUCUGCUUC--UUGCAGAUGU-GGUAGCGA--------------------------GUCUACC---------CUAUU--CACUUC
AL627277.1/14855-15060     ACUUC-CUGAGCC--GGAACGAAAAGUUUU-AUCGGAAU-GCG-U-GUUCUGAUGGG----CUUUU----GGCUUACG-GUUGUGAUGUUGUGUUGUUGUGUUUGCAA----UUGGUCUGCGAU----UCAGACCACGGUAGCGA--------------------------GACUACC----------CUUUUUCACUUC
AAZG01000006.1/28699-28507 UUCUU-AAAAUAC--CGCCAUACUUAAUG--AUUGGUAA-UUC-C-UUACUAGUUAAUGAGUUUCA----GACUUAAG---UAUGAUG--------UUGUGUUUGCAU----AUAGUUCGGGAA---ACCGAACUUGAGUAACAAU------------------------UUGUUACU----------CAUUU--ACUUC
CP000671.1/1207671-1207862 UCCUU-ACAAUAC--AACCAUACUUAAUG--AUUGGUAA-UUC-C-UUACUAGUUAAUGAGUUUCG----GACUUAAG---UAUGAUG--------UUGUGUUUGCAU----AUAGUUCGGGUA---ACCGAACUUGAGUAACAAA-----------------------UAUGUUACU----------CAUUU--ACUUC
AAYT01000006.1/48084-48288 ACUUCCCCUAGCC--GGAACGAAAAGUAGG-UUUGGUAU-CCCAG-GUACUGAAAUG----CUUUU----GGCUUUGUGGUGGUGAUG--------UUGUGUUUGCAA----AUGGUCUGGUAU---GCCAGACAU-AGUAGCUA--------------------------AGCUACUG-------CUUUUUUUCACUUC
CP000647.1/3469834-3470041 ACUUC-CUGAGCC--GGAACGAGAAGCUUUUUUUGGAAU-GCG-U-GUUCCAUCAAG----CUUUU----GGCUUACG-GUUGUGAUGUUGUGUUGUUGUGUUUGCAA----UUGGUCUGUUUU---UGCAGACCCUGGUAGCAA--------------------------AGCUACC----------CCUUUUCACUUC
AE017220.1/3095018-3095215 ACUUC-CUGAGCC--GGAACGAAAAGUUUU-AUCGGAAU-GCG-U-GUUCUGAUGGG----CUUUU----GGCUUACG-GUUGUGAUG--------UUGUGUUUGCAA----UUGGUCUGCGAU----UCAGACCACGGUAGCGA--------------------------GACUACC----------CUUUUUCACUUC
AAZF01000004.1/84336-84525 UCUUA-AAAUAUC--GC-CAUACUUAAUG--AUUGGUAA-UUC-C-UUACUAGUUAAUGAGUUUCA----GACUUAAG---UAUGAUG--------UUGUGUUUGCAU----AUAGUUCGGGAA---ACCGAACUUGAGUAACAAU------------------------UUGUUACU----------CAUUU--ACUUC
CP000653.1/3547890-3548097 ACUUC-CUGAGCC--GGAACGAAAAGCUUUUUUUGGAAU-GCG-U-GUUCUGAAGGG----CUUUU----GGCUUGCG-GUUGUGAUGUUGUGUUGUUGUGUUUGCAA----UUGGUCUGCUAU----UCAGAUCAUGGUAGCAA--------------------------AGCUACC---------CUUUUUUCACUUC
AE016827.1/873502-873689   GCGUA-CUU--------AAUGAUUAAGCAA-UUCCUUUU-UCA-U-AAAGAGUUUCA----UUCUU------AUUAAG---UAUUAUG--------UUGUGUUUGCAU----AUUGUUCGGGAA---ACCGAACGCAAGUAACUU--------------------------AGUUACU----------UAUUUA-ACUUC
CP000746.1/1862334-1862531 ACUUA-AUGACUG--GUAAUUCCUUAAUUG-AUU------AAG-A------GUUGAA----UCUUU----UAGUUAAG---UAUUAUG--------UUGUGUUUGCAU----AUUGUUUGGGUA---ACCAAACAAAAGUAAUUAAUCCUU--------------CUAUUUAAUUACU----------UAUUA--ACUUC
CP000266.1/2950132-2950337 ACUUC-CUGAGCC--GGAACGAAAAGUUUU-AUCGGAAU-GCG-U-AUUCUGGUGAA----CUUUU----GGCUUACG-GUUGUGAUGUUGUGUUGUUGUGUUUGCAA----UUGGUCUGCGAU----UCAGACCAUGGUAGCAA--------------------------AGCUACC----------UUUUUUCACUUC
AE017143.1/818099-817906   ACUGA-AAUAGUUUAGUGUUUAUUCGUGUU-CUUUAAUG-C-----UAUUAAAUCCA----UCUAUUUCAAAUUUAAG---UAUGAUG--------UUGUGUUUGCAU---AUUGGUCUAGGCA---ACUAGACUAGAGUAACAGU-----------------------UAAGUUACU----------CAUUU-CACUUC
BA000037.2/879563-879356   GCAAC-GCUAGCC--UGAACGGCUUGAUUU-CUU----------U------GUAAAU----CAAUU----GGCUUAGUUGUUGCGAUG--------UUGUGUUUGCAA--------ACUCGUAU--UUCGAGU---UAGGUAGAUUUCUACCGUAG----UGUUUUGUCCAACUCCCUGUG---ACAAAACCUAUACUUC
BA000031.2/725281-725072   GCAAC-ACGAGCC--UGAACGGC--------UUGAUUUC-CUU-G-GAAAUCAA----------UU----GGCUUCGUUGUUGCGAUG--------UUGUGUUUGCAA--------ACUCGUAU--UUCGAGU---UAGGUAGAUUUCUACCAUGA---UGUUUUGUCCACACUCCCUGUG---ACAAAACAGAUACUUC
AAND01000021.1/495-707     CAGCA-GCUAGCC--UGAACGGC--------UUGAUUCU-CUC-U-AGAAUCAA----------UU----GGUUUAGCUCCUGCGAUG--------UUGUGUUUGCAA--------ACUCGUUCUUUUCGAGU---UGGGUAGAGUUCUACCAAAUG--UUUUGUUGCAGUUCUAUACUGAAACGAGGCAUGU--ACUUC
AAZW01000011.1/773-985     CAGCA-GCUAGCC--UGGACGGC--------UUGAUUCU-CUC-U-AGAAUCAA----------UU----GGCUUAGCUCCUGCGAUG--------UUGUGUUUGCAA--------ACUCGUACUUUUCGAGU---UGG-GUAGAGUUCUACCAAAUGUUUUGUUGCAGUUAUACACUGAAA-CGAGGCAUCU--ACUUC
CP000826.1/4206206-4206404 ACUUC-CCGGGCC--GGAACGAAAAGGGA--GUGGGUGUCGAG-G-ACGCCGAUGAA----CUUUU----GGCUUGUG-GUUGUGAUG--------UUGUGUUUGCAA----AUUGUCUGGCAA---UCCAGACGU-GGUAGCUA--------------------------AGCUACU----------GUUUUUCACUUC
CP001113.1/3119655-3119860 ACUUC-CUGAGCC--GGAACGAAAAGUUUU-AUCGGAAU-GCG-U-GUUCUGAUGGG----CUUUU----GGCUUACG-GUUGUGAUGUUGUGUUGUUGUGUUUGCAA----UUGGUCUGCGAU----UCAGACCACGGUAGCGA--------------------------GACUACC----------CUUUUUCACUUC
AE004439.1/652195-651997   -CCUCUAAAAUGC--GCGCAUACUUAAUG--AUUGGUAA-UUC-C-UUACUGGUUAAG-AGUUUCG----GACUUAAG---UAUGAUG--------UUGUGUUUGCAU----AUUGUUUGGGAA---ACCAAACAG-AGUAACUUAUC--------------------UUAAGUUACU----------UAUUUUCACUUC
AALD02000009.1/78108-77906 ACUUC-CCAAGCC--GGAACGAAAAGUAGG-UUUAGUAU-CCA-G-GUACUGAAAUG----CUUUU----GGCUUUGUGGUUGUGAUG--------UUGUGUUUGCAA----AUGGUCUGGUGU---GCCAGACAU-AGUAGCUA--------------------------AGCUACUG-------UUUUUUUUCACUUC
FR729477.2/4274443-4274241 ACUUC-CCAAGCC--GGAACGAAAAGUAGG-UUUAGUAU-CCA-G-GUACUGAAUUG----CUUUU----GGCUUUGUGGUUGUGAUG--------UUGUGUUUGCAA----AUGGUCUGGUAU---GCCAGACAU-AGUAGCUA--------------------------AGCUACUGU------UUUUUUU-CACUUC
FM954972.2/2569880-2570092 CAGCA-GCUAGCC--UGAACGGC--------UUGAUUCU-CUC-U-AGAAUCAA----------UU----GGUUUAGCUCCUGCGAUG--------UUGUGUUUGCAA--------ACUCGUUCUUUUCGAGU---UGGGUAGAGUUCUACCAAAUG--UUUUGUUGCAGUUCUAUACUGAAACGAGGCAUGU--ACUUC
AE017042.1/3133288-3133493 ACUUCCCCUAGCC--GGAACGAAAAGUAGG-UUUGGUAUCCCA-G-GUACUGAAAUG----CUUUU----GGCUUUGUGGUGGUGAUG--------UUGUGUUUGCAA----AUGGUCUGGUAU---GCCAGACAU-AGUAGCUA--------------------------AGCUACUG-------CUUUUUUUCACUUC
#=GC SS_cons               :::::.:::<<<<..--<<----<<<<<<-.<<<<<<<<.___._.>>>>>>>>>>>....>>>>>....>>>>::::.:::::::::........::::::::::::....:<<<<<<<<___..._>>>>>>>>:<<<<<<___........................__>>>>>>..........::::::::::::
#=GC RF                    aCuUc.auuAgcC..ggaacGAaaagcucu.uucgguau.uuc.u.auaccgaagag....cuuuu....GgcUUAag.GUUgUGAUG........UUGUGUUUGCAa....augGuCuGggau...acCaGaCcaugGuagcaau........................uagcuaCc..........uaUUUuCACUUC

U00096.2/2940718-2940923   CUGUACAUUUACCCUGUCUGUCCAUAGUGA-UUAAUGU----AGCACCGCCUAAU-------------UGCGGUGCUUUUUUUU
U29581.1/24251-24456       CUGUACAUUUACCCUGUCUGUCCAUAGUGA-UUAAUGU----AGCACCGCCUAAU-------------UGCGGUGCUUUUUUUU
BX571861.1/50378-50183     CUGUACAUUUACCCUGUCUGUCCAUAGUGA-UUUUUUAA---UGCACCGCAG---------------UUGCGGUGCUUUUUUUU
BX950851.1/1137282-1137085 CUGUACAUUUACCCUGUCUGUCUAAAGUGA-UUUUUUAUG-UAGCACCGCAA--------------AUUGCGGUGCUUUUUUU-
AL627277.1/14855-15060     CUGUACAUUUACCCUGUCUGUCCAUAGUGA-UUAAUGU----AGCACCGCCAUAU-------------UGCGGUGCUUUUUUUU
AAZG01000006.1/28699-28507 CUGUAUAUUAUUAAACC-----------GAUUUGGUUAA---AUCGCCGCUCCAU-----------UGAGCGGCGUUUUUUUCA
CP000671.1/1207671-1207862 CUGUAUAUUAUUAAACC-----------GAUUUGGUUAA--ACGCUGCUCUCAUU--------------GAGUGGCGUUUUUUU
AAYT01000006.1/48084-48288 CUGUACAUUUACCCUGUCUGUCCAUAGUGAUUUUAUG-C---AGCACCGU-UAUU-----------UUGGCGGUGCUUUUUUU-
CP000647.1/3469834-3470041 CUGUACAUUUACCCUGUCUGUCCAUAGUGAUUUAAUG-U---AGCACCGC-AACG-------------CGCGGUGCUUUUUUUU
AE017220.1/3095018-3095215 CUGUACAUUUACCCUGUCUGUCCAUAGUGA-UUAAUGU----AGCACCGCCAUAU-------------UGCGGUGCUUUUUUUU
AAZF01000004.1/84336-84525 CUGUAUAUUAUUAAACC-----------GAUUUGGUUAA--ACGCUGCUCUC--------------AUUGAGUGGCGUUUUUUU
CP000653.1/3547890-3548097 CUGUACAUUUACCCUGUCUGUCCAUAGUGA-UUAAUGU----AGCACCGCCUAUU-------------UGCGGUGCUUUUUUUU
AE016827.1/873502-873689   CUGUAUAUUUUUAAACC---UAAUUUUGGG-UUCGUA-A---UGCACCGCUCUUUG---------UG-AGCGGUGUUUUUUUAU
CP000746.1/1862334-1862531 CUGUAUAUUUACUACCU----AAUUUUAGG-UUAUU------GGCACCGCGCUUAAACUCCAAAAAAGUGCGGUGUUU------
CP000266.1/2950132-2950337 CUGUACAUUUACCCUGUCUGUCCAUAGUGA-UUAAUGU----AGCACCGCCUAAU-------------UGCGGUGCUUUUUUUU
AE017143.1/818099-817906   CUGUAUAUUUAAACCUUUU---------GG-UUUAU-U------AACCGCCUAAUU----------UAGGCGGUUUUUUUACUU
BA000037.2/879563-879356   CUGUAUUUAUUUUUGACCUGUCU------G-UCAAAUUUG-UUACACCGCCUAUU------------AGGCGGUGUUUUUUUAU
BA000031.2/725281-725072   CUGUAUUUAUUUUUGACCUGUCU------G-UCAAAUUUG-UUACACCGCCUUUU-----------UAGGCGGUGUUUUUUUAU
AAND01000021.1/495-707     CUGUAUUUAUUUUGACC-UGUCU------G-UCAAAUUUGUUUACACCGCCUUAU------------GGGCGGUGUUUUUUUAU
AAZW01000011.1/773-985     CUGUAUUUAUUUUGACC-UGUCU------G-UCAAAUUUGUUUACACCGCCUAUA------------CGGCGGUGUUUUUUUAU
CP000826.1/4206206-4206404 CUGUACAUUUACCCUGUCUGUCCAUAGUGAUUUUAUG-C---AGCACCGCAA-UC-----------UUUGCGGUGCUUUUUUU-
CP001113.1/3119655-3119860 CUGUACAUUUACCCUGUCUGUCCAUAGUGA-UUAAUGU----AGCACCGCCAUAU-------------UGCGGUGCUUUUUUUU
AE004439.1/652195-651997   CUGUAUAUUUAUUUUAGACCCUU--------UUGGUUA----AACACCGCUCU--A---------UCGAGCGGUGUUUUUUUAU
AALD02000009.1/78108-77906 CUGUACAUUUACCCUGUCUGUCCAUAGUGAUUUUAUG-C---AGCACCGCCA--UU----------UUCGCGGUGCUUUUUUU-
FR729477.2/4274443-4274241 CUGUACAUUUACCCUGUCUGUCCAUAGUGAUUUUAUG-C---AGCACCGCU-AUU-----------UUCGCGGUGCUUUUUUU-
FM954972.2/2569880-2570092 CUGUAUUUAUUUUGACC-UGUCU------G-UCAAAUUUGUUUACACCGCCUUAU------------GGGCGGUGUUUUUUUAU
AE017042.1/3133288-3133493 CUGUACAUUUACCCUGUCUGUCCAUAGUGAUUUUAUG-C---AGCACCGUUAUUU------------UGGCGGUGCUUUUUUUU
#=GC SS_cons               ::::<<<<<_____________________.__>>>>>:...<<<<<<<<_____...........___>>>>>>>>:::::::
#=GC RF                    CUGUacauuUauucuguCUGUCuAUAGUGa.UUaauguu...agCaCCGCcuuuU...........uuuGCGGuGcuUUUUUuU
//
