gi_545778205_gb_U000_285

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:

4208152

To sequence:

4209686

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 4208152 GAAGAGUUUGAUCAUGGCUCAGAUUgAACGCUGGCGGCA-GGC-CUAACACAUGCAAGUCGAAC*[34]*GUGGCGGACGG 4208258
                               ************************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 4208259 GUGAGUAAUGUCUGGG-AAACUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAA--------CG 4208330
                               ****************.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 4208331 UCGCAAGAC--------CAAAGAGGgggaccu----ucgggccucUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUAGUA 4208399
                               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 4208400 GGUGGGGUAACGGCUCACCUAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUC 4208480
                               ********************************************************************************* 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 4208481 CAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUA*[25]*U 4208580
                               ************************************************************************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 4208581 ACUUUCAGCGGG*[41]*CCCGCAGAAGAAGCACC-GGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGC 4208695
                               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 4208696 GUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAA 4208776
                               ****************************************************************************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 4208777 C-UGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUG 4208856
                               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 4208857 GAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAG 4208937
                               ********************************************************************************* 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 4208938 AUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGU--UGUGCCCUUGAGGCGUG--GCUUCCGGAGCUAACGC 4209014
                               **************************************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 4209015 GUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGC-ACAAGCGGUGGAGC 4209094
                               *****************************************************************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 4209095 AUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCuUGACAUCcaCGGAAGUUUUCAGAGAUG*[9]*CUUCGG 4209179
                               ******************************************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 4209180 GAACCGUGA-GACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACC 4209259
                               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 4209260 CUUAUCCUUUGUUGCCAGCGGU----CCG---GCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGG 4209333
                               *********************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 4209334 AUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCG 4209414
                               ********************************************************************************* 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 4209415 AGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUA 4209495
                               ********************************************************************************* 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 4209496 AUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAA 4209576
                               ******************************************************************************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 4209577 AGAaGUAGG*[22]*CUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGU 4209673
                               654144444...6..44444566899******************************************************* PP

                                             NC
                               >>::::::::::: CS
               RF01959    1465 cgGAUCACCUCcu 1477   
                               ::GAUCACCUCCU
  gi_545778205_gb_U000 4209674 UGGAUCACCUCCU 4209686
                               ************* PP

>>

RNAfold

>gi_545778205_gb_U000_285
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