gi_545778205_gb_U000_284

cmsearch-Rfam

Family :

SSU_rRNA_archaea

Id:

RF01959

Type:

Gene; rRNA;

Taxonomy:

Eukaryota; Bacteria; Viruses; Archaea; Viroids;

Ontology:

GO:0003735 structural constituent of ribosomeRF01959

Description:

not description

Score:

1024.8

E-value:

0

From sequence:

4166664

To sequence:

4168198

Alignments:

                                                                      v                                          NC
                               :::<<<<<_______>>>>>,{{{{.{{{{{{,{{{{{{{{{{-----{{{-{{{,,<<<--<<~~~~~~>>>>>,,,,,, CS
               RF01959       1 AuUCcGguUGAUCCUgcCgGAggcc.accgCuAucGGgguccGauUaAGCCAuGcuAGucgagc*[14]*gcggCguAcaG 88     
                                + ::G UUGAUC UG C::AG::: A:CGCU :CGG:: ::: +UAA::CAUGC+AGUCGA:C      G:GGCG AC+G
  gi_545778205_gb_U000 4166664 GAAGAGUUUGAUCAUGGCUCAGAUUgAACGCUGGCGGCA-GGC-CUAACACAUGCAAGUCGAAC*[34]*GUGGCGGACGG 4166770
                               ************************9789***********.555.699***************98...9..89********* PP

                                               v                v      v                v       v                NC
                               [[[,,,,,,((((((((--((---(((((((,<<<<----<<<<<<<____>>>>>>>----->>>>,,,,<<<<<<<<-< CS
               RF01959      89 CucAGUAACgCGcgGccAAccUAcCCucggGacggggAUAccCcCgGGAAACuGgGggUAAUacccgAUAggggggggcug 169    
                               :U:AGUAA  :::GG: AA:CU CC :::GGA: GGGAUA C::C GGAAAC G::G UAAUACC :AUA          G
  gi_545778205_gb_U000 4166771 GUGAGUAAUGUCUGGG-AAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAA--------CG 4166842
                               ****************.689**************************************************9........58 PP

                                                                                          v                      NC
                               <______>>>>>>>>>>,,,,,,<<.......____.........>>,)))))))--))))))))))<<<--<-<<<--<< CS
               RF01959     170 CUGGAAuGcgcccccccugAAAuGc.......uccg.........gCGCccgaGGAUggggCcgCGcCcgAUcAGGcaGuc 234    
                               : G AA :C        + AA +                        GCC::: GAUG:G:CC::: ::GAU:AG::AGU:
  gi_545778205_gb_U000 4166843 UCGCAAGAC--------CAAAGAGGgggaccu----ucgggccucUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUA 4166911
                               888888887........555444446776653....23467777799************9********************* PP

                                                                                                                 NC
                               <<<<<<_______>>>>>>>>>>>----->>>>,,<<<<<<<<____>>>>--->>>>]]],<<<<<<__________>>> CS
               RF01959     235 GGcgGgGUAAcGGcCcgCCgagCCuauaAgcgGUAcGGGccguGAGAgcgggAGCCCggaGAcGGgcuCUGAGACAaGagc 315    
                               GG:G GGUAACGGC C:CC:A::C+A +A:C::UA:::G ::UGAGAG:: GA C::::A:AC:GG::CUGAGACA G::C
  gi_545778205_gb_U000 4166912 GGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUC 4166992
                               ********************************************************************************* PP

                                                                                             v                   NC
                               >>>,<<<<____>>>>,,,}}}}}}-},,,,,<-<<<---<<<<<____>>>>>->>>>,}}}}}}}}},,<<<~~~~~~> CS
               RF01959     316 CCgGGCCCUACGGGGCGCAgCaGGCgCGAAAacUccgCAaugCgcGaaAgcGcgAcgggGggaccCCgaGUGcc*[15]*g 405    
                               C:G ::CCUACGGG::GCAGCAG::G:GAA A:U:C:CAAU::GCG AAGC::GA:G::G::A::CCG:GUG::      :
  gi_545778205_gb_U000 4166993 CAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUA*[25]*U 4167092
                               ************************************************************************98...9..7 PP

                                     v                v           v                                   v          NC
                               >>,,,<<<<<<<~~~~~~>>>>>>--->,,<<<<<<-------<<<<-----<<____>>------->>>>>>>>>>,}}} CS
               RF01959     406 gCUuUcccccgg*[ 9]*ccggggGAAgAAGgGgcGGGcAAGaCcGGUGuCAGCCGCCGCGGUAAuACCgGCgcCcCgaGc 489    
                               :CUUUC :C:GG      CC:G: GAAGAAG:::C GGC A  :C:GUG+CAGC GCCGCGGUAAUAC:G: G:::C+AGC
  gi_545778205_gb_U000 4167093 ACUUUCAGCGGG*[41]*CCCGCAGAAGAAGCACC-GGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGC 4167207
                               888888888887...9..899999*********97.7888889************************************** PP

                                                               v                            v                 v  NC
                               }}}}}}},,,,,,,,,,{{{-----{,[[[[-[-[[[,<<<<<<<-<<<<<<<<<<<----<<<<<<<_____>>>>>>>- CS
               RF01959     490 gguggccauuaUUAuUGGGCcUAAAGcGucCGcAgCcGGcccggcAaGucccccgggAAAuCcgcggGCUcAACccgcgGa 570    
                               G:U:::C+  AUUA UGGGC UAAAGCG::CG AG:CGG:::G :AAGUC::::G::AAAU C:C GGCUCAACC G:G A
  gi_545778205_gb_U000 4167208 GUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAA 4167288
                               ****************************************************************************99988 PP

                                                           v               v                                     NC
                               -->>>>>>>>>-->>>>>>>>>,,,(((((((((--(((((((<<--<<<<<<<<---<<<______>>>------>>>>> CS
               RF01959     571 cgcccgggggauACugccgggCUuGGGgccGgccGAggccggggGUAcucccgGGGUAGggGugAAAccCuaUaAUCCcgg 651    
                               C ::C::::GAUACU: C:::CUUG:G: ::G::GA:G::GG :  A:UCC:G :GUAG::GUGAAA::C +  A : C:G
  gi_545778205_gb_U000 4167289 C-UGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUG 4167368
                               8.******************************************************************************* PP

                                    v                              v          v                                  NC
                               >>>-->>,,,,<--<<____>>>)))))))-))))))-))),,,]]]]--]]]],,,,<<<<<<---<<---<<<<_____ CS
               RF01959     652 gagGACcACCacUGGCGAAaGCgcccggccaggcCggacCCGACgGugAGGgaCGAAAGCcgGGGgagCgAAccGGAUUAG 732    
                               GA:GA :ACC :UGGCGAA+GC: CC::C: ::C:: +:C:GACG:U AGG::CGAAAGC::GGGGA:C+AAC:GGAUUAG
  gi_545778205_gb_U000 4167369 GAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAG 4167449
                               ********************************************************************************* PP

                                                                                                                 NC
                               ____>>>>--->>>>>>>>,,,,,,,,,,((((((,,<<<<<<<<<<<<<<_____>>>>>>>>>>>>>>,,,<<____>> CS
               RF01959     733 AUACCCggGUAGcCCcgGCuGUAAACgaUGcggGcUaggugccgggcgggcuucGagcccgcccggcgccGuAGgGAAGcC 813    
                               AUACCC:GGUAG:CC::GC GUAAACGAUG::G:CU+GG:::      G:C U+GAG:C      :::CCG AG: AA :C
  gi_545778205_gb_U000 4167450 AUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGU--UGUGCCCUUGAGGCGUG--GCUUCCGGAGCUAACGC 4167526
                               **************************************98865..56788999999988765..56889************ PP

                                                                                                                 NC
                               ,,,,,))))))}}}},<<<------<<<<____>>>>---->>>,,,,,,,,{{{{{-{{{{{{{--{{,,{{{{{{{{{{ CS
               RF01959     814 GuuAAgCccgCCGCCUggGgAGUACggcCGCAAGgcuGAAACuuAAAGGAAUuGGCgGgGGaGCaCcaCAAcggguGcaGc 894    
                               GUUAAG:C::CCGCCU:GGGAGUACG CCGCAAGG U AAACU:AAA GAAUUG:CGGGGG::C:C ACAA::GGUG:AGC
  gi_545778205_gb_U000 4167527 GUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGC-ACAAGCGGUGGAGC 4167606
                               *****************************************************************8.************** PP

                                                                              v               v              v   NC
                               {{{{{{{,,,,<<<<________>>>>,,,,,,,,{{{{{{{.,,,<<<<..<<------<<<<<<<___~~~~~>>>>>> CS
               RF01959     895 cuGCGGuUUAAccgGAuUCAACGCcggaaAuCUcACCgGggg.cGACaGc..cgaAUGAagGccaGguUg*[4]*cCuggC 971    
                               :UG:GGUUUAA:::GAU CAACGC:::+AA CU+ACC:GG::  GACA:C  CG+A G +  C ::G UG     C:: G 
  gi_545778205_gb_U000 4167607 AUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCuUGACAUCcaCGGAAGUUUUCAGAGAUG*[9]*CUUCGG 4167691
                               ******************************************5588866545666666665555555555..5..555555 PP

                                        v                   v                                                    NC
                               >--->>->>>>,,,[[-[[[[--[[[[[[[[[,,,((((((<<<____>>>,,<<<<______>>>>,,)))))),,,,,( CS
               RF01959     972 cuGAcgagCuGAGAGGaGGugCAuggCCgcCGuCAGcuCGugCcGUGAgGcGUCCuGUUAAGUCaGGcAaCGagCGAGACC 1052   
                                +  CG+G: GA AGG+G:UGCAUGGC:G CGUCAGCUCGU:::GUGA:::GU ::GUUAAGUC:: CAACGAGCG  ACC
  gi_545778205_gb_U000 4167692 GAACCGUGA-GACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACC 4167771
                               555566554.9********************************************************************** PP

                                                                                                                 NC
                               (((,<<<<<<<---<<--<<<<<<<____>>>>>>>>>---->>>>>>>,,<<<<<<<<_____>>>>>>>>,,,,,)))) CS
               RF01959    1053 CccacccccagUUGCcAucgcggccuuugggccgcggGcAcacugggggGACcgCcggcGcuAAgccgGagGAAGGAggGG 1133   
                               C :A:CC:::GUUGCCA CG:     ++G    :CGGG AC+C:::GG:GAC:GCC:G:G+UAA:C:GGA:GAAGG : GG
  gi_545778205_gb_U000 4167772 CUUAUCCUUUGUUGCCAGCGGU----CCG---GCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGG 4167845
                               *********************7....455...7************************************************ PP

                                     v                                                                   v       NC
                               ,,,,]]]]-]]]---]]]]]]]],,,,}}}}}}},,,}}-}}}}}}}}}},,,<<<<<<<-----<<<--<<--<<<<___ CS
               RF01959    1134 GCaACGgcAGGuCAGcaugCCCCGAAucccCcGGGCuaCACGCgggCugCAAUGgccgggACAauGgGuucCgAcccCGAa 1214   
                                  ACG CA:GUCA CAUG:CCC  A ::CC:GGGCUACAC:CG:GCU:CAAUG:C::: ACAA G:G++:CGA C:CG  
  gi_545778205_gb_U000 4167846 AUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCG 4167926
                               ********************************************************************************* PP

                                   v                                                                             NC
                               _>>>>-->>---->>>----->>>>>>>,,,,,,<---<<<<<<<<________>>>>>>>>--->,,,,,}}}}},,,,, CS
               RF01959    1215 AGgggaaGguAAUCcCuuAAAcccggcCuuAGUugGGAccGaGGgCUGuAACUCGcCCuCggGAAccuGGAauccgUAGUA 1295   
                               AG:G AAG:  A C:C UAAA :::G:C+UAGU :GGA::G::G:CUG+AACUCG:C::C::GAA:  GGAAUC::UAGUA
  gi_545778205_gb_U000 4167927 AGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUA 4168007
                               ********************************************************************************* PP

                                      v       v                                                                  NC
                               <<<<<<<<_______>>>>>>>>,,,,,,}}---}}}}}}}}}}-}},,<-<<-<<-<-<<<<<<<<--<<<<<<<<<<<< CS
               RF01959    1296 acCGCgcgUCAacAucgcGCGguGAAUAcGuCCCuGCuCCuuGCACaCACcGcCCGUCacgcCacccgAGcggggcccggg 1376   
                               A:CG:G: UCA +AU :C:CG:UGAAUACGU CC:G::CCUUG:ACACACCG:CCGUCAC:CCA  :GA::G:::: C:::
  gi_545778205_gb_U000 4168008 AUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAA 4168088
                               ******************************************************************************987 PP

                               v v                 v v                                                           NC
                               <<<.<<<<<~~~~~~>>>>>>>>>>>>>>>>>>>>-->>>>>>>>-->->>-->>-->,<<<<<<<<<<____>>>>>>>> CS
               RF01959    1377 cgc.Ggccc*[14]*gggcCgagcccgggccccgCaAggggGgcgAAGUCGUAgCAAGGcggCCGcaggGGAAccugCGGc 1464   
                                G  G:: :      : ::C A :::G ::::C::+A:  GGG:GAAGUCGUA:CAAGG:::CCG:AGGGGAACCU:CGG:
  gi_545778205_gb_U000 4168089 AGAaGUAGG*[22]*CUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGU 4168185
                               654144444...6..44444566899******************************************************* PP

                                             NC
                               >>::::::::::: CS
               RF01959    1465 cgGAUCACCUCcu 1477   
                               ::GAUCACCUCCU
  gi_545778205_gb_U000 4168186 UGGAUCACCUCCU 4168198
                               ************* PP

>>

RNAfold

>gi_545778205_gb_U000_284
AAGAGUUUGAUCAUGGCUCAGAUUGAACGCUGGCGGCAGGCCUAACACAU
GCAAGUCGAACGGUAACAGGAAGAAGCUUGCUUCUUUGCUGACGAGUGGC
GGACGGGUGAGUAAUGUCUGGGAAACUGCCUGAUGGAGGGGGAUAACUAC
UGGAAACGGUAGCUAAUACCGCAUAACGUCGCAAGACCAAAGAGGGGGAC
CUUCGGGCCUCUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUAGGU
GGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGA
CCAGCCACACUGGAACUGAGACACGGUCCAGACUCCUACGGGAGGCAGCA
GUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUG
UAUGAAGAAGGCCUUCGGGUUGUAAAGUACUUUCAGCGGGGAGGAAGGGA
GUAAAGUUAAUACCUUUGCUCAUUGACGUUACCCGCAGAAGAAGCACCGG
CUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGCGUUAAUC
GGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUG
AAAUCCCCGGGCUCAACCUGGGAACUGCAUCUGAUACUGGCAAGCUUGAG
UCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGA
UCUGGAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGC
UCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAGAUACCCUGGUAGUCC
ACGCCGUAAACGAUGUCGACUUGGAGGUUGUGCCCUUGAGGCGUGGCUUC
CGGAGCUAACGCGUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUA
AAACUCAAAUGAAUUGACGGGGGCCCGCACAAGCGGUGGAGCAUGUGGUU
UAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCUUGACAUCCACGGAAG
UUUUCAGAGAUGAGAAUGUGCCUUCGGGAACCGUGAGACAGGUGCUGCAU
GGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAG
CGCAACCCUUAUCCUUUGUUGCCAGCGGUCCGGCCGGGAACUCAAAGGAG
ACUGCCAGUGAUAAACUGGAGGAAGGUGGGGAUGACGUCAAGUCAUCAUG
GCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGA
AGCGACCUCGCGAGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGA
UUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUAAUCGUGG
AUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGU
CACACCAUGGGAGUGGGUUGCAAAAGAAGUAGGUAGCUUAACCUUCGGGA
GGGCGCUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGU
AACCGUAGGGGAACCUGCGGUUGGAUCACCUCCU
..(((..(((((((((((..........((((.((((..((.........))..))))..))))..((((((((((....))))))).))).....((((((.((((((..(((.(((((((((.(((((((((((((((((....((((((....))))))......(((......(((....)))....((((....))))))).)))))).)))))...((((((((...((((((.(((..((((((((.......)))))))))))...))))))..(((((((.........)))))))....(((((.(((.....)))))))).((((....))))...((((((.....))))))....))))))))(((.((((((((((((((.((..........((((.(((((.((((((..((..((((.(((((..(..((.((((((((.......)))))))).))..)....))))).))))..)).((((.(((.(((((((..(((.((.((......))..)).)))..))).....)))).)))))))((((...)))).(.((((((((((((((.(((((((((....((((.((......)).))))...)))))))))..)))))))).(.((((((((..(((((((((...((((((((.(.(((........)))..).))))))))...)))).((.((....)).)))))))..))).))))).)(((......)))...(((((((..((...((((.........))))))..)))))))..........((((((((((.(((((.((.((.(((((...))))).)).)))))).).)))))))))))))))).)((((..((((....))))...))))...(((((((((.(.(((((((.......)))).)).).).).)))))))).)))))).)))))..))))(((((.(((((...(((.((((.(((((((....)))))....)).)))))))....)))))))))))).))))))))).))))))))...((((((...(((.(((......)))))).....)))))).....(((((((((.((.((......)).)).)))..))))))..((.(((((.....))))).)).)))))).((((((.....)))))).(((((((.......)))))))........((((...(((((((.....(((..((...(((....)))...))....))).....)))))))))))(((((..(((((((........))))))).....)))))..((.((...(((((((.........)))))))...))))))))))))).)))..))).))).))))))((((..((..((((((((((((.(..((((((.((((..((...))..))))))))))..)))))))))))))..))..)))).)))))).......((((((((((....))))))))))))))).))).. (-588.30)

Length sequence

: 1534

Length match:

1533