rrsB

cmscan-Rfam

Family :

SSU_rRNA_bacteria

Id:

RF00177

Type:

Gene; rRNA;

Taxonomy:

Eukaryota; Bacteria; Viruses; Archaea; Viroids;

Ontology:

GO:0003735 structural constituent of ribosomeRF00177

Description:

not description

Score:

1577.3

E-value:

0

From sequence:

1

To sequence:

1542

Alignments:

                                                                                                                    NC
               ::::::::<<<<<_______>>>>>,{{{{-{{{{{{,{{{{{{{{{----{{{-{{{,,<<<--<<<<<-....<<<<<<<____>>>>>>>...->>- CS
  RF00177    1 uuuauggAGaGuuUGAUCcUggCuCAGggcGaaCGCuGGCGGcgcGcuUaAcaCAuGCAAGuCGagcccca....cggggccuuaaggccccg...aggg 93  
               ++++UG+AGAGUUUGAUC UGGCUCAG:::GAACGCUGGCGGC::GC+UAACACAUGCAAGUCGA:C:::A     ::G::: U++:::C::    +::G
     rrsB    1 AAAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAUGCAAGUCGAACGGUAacagGAAGAAGCUUGCUUCUUUgcuGACG 100 
               **********************************************************************999999999999999999999999999*** PP

                                           v                v      v                v       v                       NC
               >>>>>>,,,,,,[[[,,,,,,((((((((--((---(((((((,<<<<----<<<<<<<____>>>>>>>----->>>>,,,,,<<<<<<<<<<____>> CS
  RF00177   94 ggcGgCGaAcGGGuGAGUAAcgCGcgggcAAccUacCcccgggugcgGgAUAccccccgGAAAcggggggUAAUACcgcAUaaugccccggcccguaugg 193 
               :G:GGCG ACGGGUGAGUAA+::::GGG  A:CU+CC :::GG+G GGGAUA C::C:GGAAAC:G::G UAAUACC CAUAA        ::CG+A+G:
     rrsB  101 AGUGGCGGACGGGUGAGUAAUGUCUGGGA-AACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAAC-------GUCGCAAGA 192 
               *****************************.9*****************************************************.......9******** PP

                                                             v                                                      NC
               >>>>>>>>,,,,<<<..........._____>>>,)))))))--))))))))))<<<--<-<<<--<<<<<<<<_______>>>>>>>>>>>----->>> CS
  RF00177  194 gccggggcuAAAGgc...........auuuagcCGcccgggGAugggcccgCGccccAUcAGcuAGuuGGuggGGUAAuGGCccaCCaaggCgAuGAggg 282 
               :        AAA:::              ++:::GCC::: GAUG: CCC:::::::AU:AGCUAGU:GGUG:GGUAA GGC:CACC:AGGCGA+GA:::
     rrsB  193 C-------CAAAGAGggggaccuucgGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGUGGGGUAACGGCUCACCUAGGCGACGAUCC 285 
               9.......******99****99877655556********************************************************************* PP

                                                                                                                    NC
               >,,<<<<<<<<____>>>>--->>>>]]],<<<<<<__________>>>>>>,<<<<____>>>>,,,}}}}}}-},,,,,<-<<<---<<<<<____>> CS
  RF00177  283 gUAGccGgccuGAGAgggcGauCggCCaCAcuGGgaCUGAGAcACGgcCCagACuCCUACGGGaGGCAGCaGugggGAAUauUgcgCAAugGgcGaAAgc 382 
               :UAGC:G::CUGAGAGG::GA C:GCCACACUGG:ACUGAGACACGG:CCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGC:CAAUGGGCG AAGC
     rrsB  286 CUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGC 385 
               **************************************************************************************************** PP

                                                                      v                                             NC
               >>>->>>>,}}-}}}}}},,<<<<------<<<<____>>>>----->>>>,,,<<<<<<<---<-----<<<___........______>>>----->- CS
  RF00177  383 CugAcgcaGCgAcgCCGCGUGgggGAuGAAggccUUcGggccGUAAAcccCUuUcccggGgGAagAaaaaccgaua........uuuuaucgguuuGAcg 474 
               CUGA:GCAGC:A:GCCGCGUG:::GA+GAA::CCUUCGGG::GUAAA:::CUUUC ::GGGGA GAA   ::G++A          UU+ C::+UUGACG
     rrsB  386 CUGAUGCAGCCAUGCCGCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAG-GGAGUAAaguuaauaCCUUUGCUCAUUGACG 484 
               *****************************************************************998.7888888899988754445558999****** PP

                       v                                                                                        v   NC
               --->>>>>>--->,,<<<<<------<<<<<-----<<____>>------->>>>>>>>>>,}}}}}}}}}},,,,,,,,,,{{{-----{,[[[[-[-[ CS
  RF00177  475 gUAcCccgggAagAAGcccCGGCUAAcuccGUGCCAGCAGCCGCGGUAAuACggagGgggCaaGCGuugccCGGAaUuAuUGGGcGUAAAGgGcgcGcAg 574 
                UACCC:: GAAGAAGC:CCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGG:GCAAGCGUU:::CGGAAUUA+UGGGCGUAAAG GC:CG AG
     rrsB  485 UUACCCGCAGAAGAAGCACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAG 584 
               **************************************************************************************************** PP

                                         v                 v                            v                           NC
               [[,<<<<<<<-<<<<<<<<<<<----<<<<<<<_____>>>>>>>-->>>>>>>>>-->>>>>>>>>,,,(((((((((--(((((((<<--<<<<<<<< CS
  RF00177  575 GcGGcccggcAaGucgggcgcgAAAucccgcgGCUcAACcgcgggaucgcgcccgaaACugccgggCUuGaGuccggccGAgGggggcggAAcucccggu 674 
               GCGG:::G::AAGUC:G::G::AAAU CC: GGCUCAACC :GG A+::C::C:GA+ACU::C:::CUUGAGU ::G::GAGGGGGG::GAA:UCC:GGU
     rrsB  585 GCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGU 684 
               **************************************************************************************************** PP

                                                    v          v             v          v                           NC
               ---<<<______>>>------>>>>>>>>-->>,,,,<--<<____>>>)))))))-))))))-))),,,]]]]--]]]],,,,<<<<<<---<<---<< CS
  RF00177  675 GUAGcgGUGAAAugCGUAGAuaucgggagGAacACCacugGCGAAGGCggccccCuGggccgguaCuGACgCugAggcgCGAAAGCguGGGgAgCaAAcg 774 
               GUAGCGGUGAAAUGCGUAGA AUC:GGA:GAA:ACC+ UGGCGAAGGC :CCCCCUG::C::  ACUGACGCU AGG:GCGAAAGCGUGGGGAGCAAAC:
     rrsB  685 GUAGCGGUGAAAUGCGUAGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACA 784 
               **************************************************************************************************** PP

                                                                                                                    NC
               <<_________>>>>--->>>>>>>>,,,,,,,,,,((((((,,<<<<<<<<<<<<_____>>>>>>>>>>>>,,,<<____>>,,,,,))))))}}}}, CS
  RF00177  775 GGAUUAGAUACCCcgGUAGuCCacGCcgUAAACGAUGggcgCUAGgcgccggggggauuaaccccccggcgcCgaAGcuAAcgCauUAAGcgccCCgCCU 874 
               GGAUUAGAUACCC:GGUAGUCCACGCCGUAAACGAUG::::CU GG:::  : G:: UU A::C :  :::CCG AGCUAACGC+UUAAG::::CCGCCU
     rrsB  785 GGAUUAGAUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUCCGGAGCUAACGCGUUAAGUCGACCGCCU 884 
               **************************************************************************************************** PP

                                                                                                                    NC
               <<<------<<<<____>>>>---->>>,,,,,,,,{{{{{-{{{{{{{-{{,,{{{{{{{{{{{{{{{{{,,,,<<<<________>>>>,,,,,,,,{ CS
  RF00177  875 GgGGAgUACggcCGCAAGgcugAAACuCAAAGGAAUuGaCgGgGgCCCGCaCAAGCGguGgagcauGuGGuUUAAuuCGAuGcaAcgCGaaGAACCUUAC 974 
               GGGGAGUACG:CCGCAAGG:U+AAACUCAAA GAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUAC
     rrsB  885 GGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUAC 984 
               **************************************************************************************************** PP

                                                        v        v                                                  NC
               {{{{{{,,,,,((((((((,,<<<<<<<____>>>>>>>,<<<<____>>>>)))))-))),[[-[[[[--[[[[[[[[[,,,((((((<<<____>>>, CS
  RF00177  975 CcgggcUUGAcgugccgggaaccccccgGAaAcgggggguccccuuaaggggcccggacacAGGUGcugCAuGgcuGuCGUCAGCuCGuguCGUGAGauG 1074
               C:GG:CUUGAC:U:C::GGAA ::::C:GA A:G:::: +: CCUU +GG :CC::GA:A:AGGUGCUGCAUGGCUGUCGUCAGCUCGUGU:GUGA:AUG
     rrsB  985 CUGGUCUUGACAUCCACGGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUG 1084
               **************************************************************************************************** PP

                                                                                                                    NC
               ,<<<<______>>>>,,)))))),,,,,((((,<<<<<<<---<<--<<<______>>>>>---->>>>>>>,,<<<<<<<<_____>>>>>>>>,,,,, CS
  RF00177 1075 UcgGGUUAAGUCCcgcAaCGaGCGCAACCCccgccccuagUUgCcAucgguuuauuccggGcACUcuaggggGACcgCCggcGauAAgccGGagGAAGGu 1174
               U:GGGUUAAGUCCC:CAACGAGCGCAACCC::+:CC:U:GUUGCCA+CGG U  ++CCGGG+ACUC:A:GG:GAC:GCC:G:GAUAA:C:GGA:GAAGGU
     rrsB 1085 UUGGGUUAAGUCCCGCAACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGG-UCCGGCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGU 1183
               **************************************************.88899******************************************** PP

                                                                                                                    NC
               )))),,,,]]]]-]]]---]]]]]]]],,,,}}}}}}},,,}}-}}}}}}}}}},,,<<<<<<<-----<<<--<<---<<<____>>>--->>---->> CS
  RF00177 1175 ggGGAuGACGuCAaguCauCauggCCCUUAugcccgGGGCuaCACaCgugcuaCAAUGgccggcACAaaggGuaGCaAagccGcGAggcggAGCuAAUCc 1274
               ::GGAUGACGUCAAGUCAUCAUGGCCCUUA+G:CC:GGGCUACACACGUGCUACAAUG:C::::ACAAAG:G+AGC+A ::CGCGAG:: +AGC  A C:
     rrsB 1184 GGGGAUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCGAGAGCAAGCGGACCU 1283
               **************************************************************************************************** PP

                                                                                                                    NC
               >----->>>>>>>,,,,,,<---<<<<<<<<________>>>>>>>>--->,,,,,}}}}},,,,,<<<<<<<<_______>>>>>>>>,,,,,,}}--- CS
  RF00177 1275 cauAAAgccggcCucAGUUCGGAcuGgaGgCUGcAAcUCGcCucCagGAAGuuGGAauCGCUAGUAaucGcggcUCAGcAugccgCgguGAAUACGuUCc 1374
               CAUAAA::::G:C +AGU CGGA:UGGAG:CUGCAACUCG:CUCCA:GAAGU+GGAAUCGCUAGUAAUCG:GG:UCAG AU:CC:CGGUGAAUACGUUCC
     rrsB 1284 CAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCC 1383
               **************************************************************************************************** PP

                                                                                                                    NC
               }}}}}}}}}}-}},,<-<<-<<---<<<<<<<<--<<<<<<<<<<<<----<<<<<<-<<<<--<<____>>->>>>>>>>>>--->>>>>>>>>>>>-- CS
  RF00177 1375 CGGGcCuuGuACaCACCGcCCGUCAcgcCacggaAgccggccccgcCcGAAGccgccgcgccAAccuuaaggaggcgggcggCuAaGgcggggccggcgA 1474
               CGGGCCUUGUACACACCGCCCGUCAC:CCA::G+A::::::::C::: GAAG:::::+::::AACCUU  GGA:::::::::C A :::G::::::::GA
     rrsB 1384 CGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGAGGGCGCUUACCACUUUGUGAUUCAUGA 1483
               **************************************************************************************************** PP

                                                                           NC
               >>>>>>>>---->>-->>-->,<<<<<<<<<<____>>>>>>>>>>::::::::::::: CS
  RF00177 1475 ccggGgcgAAGUCGUAaCAAGGuagCcguaccGGAAggugcgGcugGAUcAccUcCUUu 1533
               C::GGG:GAAGUCGUAACAAGGUA:CCGUA::GGAA::UGCGG:UGGAUCACCUCCUU 
     rrsB 1484 CUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA 1542
               *********************************************************** PP

RNAfold

>rrsB
AAUUGAAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAA
CACAUGCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGA
GUGGCGGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUA
ACUACUGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGG
GGGACCUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAG
UAGGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAG
GAUGACCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGG
CAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCC
GCGUGUAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGA
AGGGAGUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAAGAAGC
ACCGGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGU
UAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAG
AUGUGAAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGC
UUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGU
AGAGAUCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACU
GACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGU
AGUCCACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUG
GCUUCCGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAA
GGUUAAAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUG
UGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCAC
GGAAGUUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACAGGUGC
UGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCA
ACGAGCGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAA
AGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCA
UCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAA
AGAGAAGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGU
CCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAU
CGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCG
CCCGUCACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUU
CGGGAGGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAAC
AAGGUAACCGUAGGGGAACCUGCGGUUGGAUCACCUCCUUA
.......(((..(((((((((((..........((((.((((..((.........))..))))..))))..((((((((((....))))))).))).....((((((.((((((..(((.(((((((((.(((((((((((((((((....((((((....))))))......(((......(((....)))....((((....))))))).)))))).)))))...((((((((...((((((.(((..((((((((.......)))))))))))...))))))..(((((((.........)))))))....(((((.(((.....)))))))).((((....))))...((((((.....))))))....))))))))(((.((((((((((((((.((..........((((.(((((.((((((..((..((((.(((((..(..((.((((((((.......)))))))).))..)....))))).))))..)).((((.(((.(((((((..(((.((.((......))..)).)))..))).....)))).)))))))((((...)))).(.((((((((((((((.(((((((((....((((.((......)).))))...)))))))))..)))))))).(.((((((((..(((((((((...((((((((.(.(((........)))..).))))))))...)))).((.((....)).)))))))..))).))))).)(((......)))...(((((((..((...((((.........))))))..)))))))..........((((((((((.(((((.((.((.(((((...))))).)).)))))).).)))))))))))))))).)((((..((((....))))...))))...(((((((((.(.(((((((.......)))).)).).).).)))))))).)))))).)))))..))))(((((.(((((...(((.((((.(((((((....)))))....)).)))))))....)))))))))))).))))))))).))))))))...((((((...(((.(((......)))))).....)))))).....(((((((((.((.((......)).)).)))..))))))..((.(((((.....))))).)).)))))).((((((.....)))))).(((((((.......)))))))........((((...(((((((.....(((..((...(((....)))...))....))).....)))))))))))(((((..(((((((........))))))).....)))))..((.((...(((((((.........)))))))...))))))))))))).)))..))).))).))))))((((..((..((((((((((((.(..((((((.((((..((...))..))))))))))..)))))))))))))..))..)))).)))))).......((((((((((....))))))))))))))).))).... (-588.30)

Length sequence

: 1541

Length match:

1540