gi_545778205_gb_U000_280

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:

1023.7

E-value:

0

From sequence:

2731152

To sequence:

2729618

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 2731152 GAAGAGUUUGAUCAUGGCUCAGAUUgAACGCUGGCGGCA-GGC-CUAACACAUGCAAGUCGAAC*[34]*GUGGCGGACGG 2731046
                               ************************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         UG
  gi_545778205_gb_U000 2731045 GUGAGUAAUGUCUGGG-AAGCUGCCUGAUGGAGGGGGAUAACUACUGGAAACGGUAGCUAAUACCGCAUAA--------UG 2730974
                               ****************.68****************************************************........68 PP

                                                                                          v                      NC
                               <______>>>>>>>>>>,,,,,,<<.......____.........>>,)))))))--))))))))))<<<--<-<<<--<< CS
               RF01959     170 CUGGAAuGcgcccccccugAAAuGc.......uccg.........gCGCccgaGGAUggggCcgCGcCcgAUcAGGcaGuc 234    
                               : G AA :C        + AA +                        GCC::: GAUG G:CC::: ::GAU:AG::+GU:
  gi_545778205_gb_U000 2730973 UCGCAAGAC--------CAAAGAGGgggaccu----ucgggccucUUGCCAUCGGAUGUGCCCAGAUGGGAUUAGCUUGUU 2730905
                               888888887........544443446777663....23467777899************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 2730904 GGUGGGGUAACGGCUCACCAAGGCGACGAUCCCUAGCUGGUCUGAGAGGAUGACCAGCCACACUGGAACUGAGACACGGUC 2730824
                               ********************************************************************************* 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 2730823 CAGACUCCUACGGGAGGCAGCAGUGGGGAAUAUUGCACAAUGGGCGCAAGCCUGAUGCAGCCAUGCCGCGUGUA*[25]*U 2730724
                               ************************************************************************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 2730723 ACUUUCAGCGGG*[41]*CCCGCAGAAGAAGCACC-GGCUAACUCCGUGCCAGCAGCCGCGGUAAUACGGAGGGUGCAAGC 2730609
                               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 2730608 GUUAAUCGGAAUUACUGGGCGUAAAGCGCACGCAGGCGGUUUGUUAAGUCAGAUGUGAAAUCCCCGGGCUCAACCUGGGAA 2730528
                               ****************************************************************************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 2730527 C-UGCAUCUGAUACUGGCAAGCUUGAGUCUCGUAGAGGGGGGUAGAAUUCCAGGUGUAGCGGUGAAAUGCGUAGAGAUCUG 2730448
                               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 2730447 GAGGAAUACCGGUGGCGAAGGCGGCCCCCUGGACGAAGACUGACGCUCAGGUGCGAAAGCGUGGGGAGCAAACAGGAUUAG 2730367
                               ********************************************************************************* 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 2730366 AUACCCUGGUAGUCCACGCCGUAAACGAUGUCGACUUGGAGGU--UGUGCCCUUGAGGCGUG--GCUUCCGGAGCUAACGC 2730290
                               **************************************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 2730289 GUUAAGUCGACCGCCUGGGGAGUACGGCCGCAAGGUUAAAACUCAAAUGAAUUGACGGGGGCCCGC-ACAAGCGGUGGAGC 2730210
                               *****************************************************************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 2730209 AUGUGGUUUAAUUCGAUGCAACGCGAAGAACCUUACCUGGUCuUGACAUCcaCGGAAGUUUUCAGAGAUG*[9]*CUUCGG 2730125
                               ******************************************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 2730124 GAACCGUGA-GACAGGUGCUGCAUGGCUGUCGUCAGCUCGUGUUGUGAAAUGUUGGGUUAAGUCCCGCAACGAGCGCAACC 2730045
                               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 2730044 CUUAUCCUUUGUUGCCAGCGGU----CCG---GCCGGGAACUCAAAGGAGACUGCCAGUGAUAAACUGGAGGAAGGUGGGG 2729971
                               *********************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 2729970 AUGACGUCAAGUCAUCAUGGCCCUUACGACCAGGGCUACACACGUGCUACAAUGGCGCAUACAAAGAGAAGCGACCUCGCG 2729890
                               ********************************************************************************* 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 2729889 AGAGCAAGCGGACCUCAUAAAGUGCGUCGUAGUCCGGAUUGGAGUCUGCAACUCGACUCCAUGAAGUCGGAAUCGCUAGUA 2729809
                               ********************************************************************************* 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 2729808 AUCGUGGAUCAGAAUGCCACGGUGAAUACGUUCCCGGGCCUUGUACACACCGCCCGUCACACCAUGGGAGUGGGUUGCAAA 2729728
                               ******************************************************************************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 2729727 AGAaGUAGG*[22]*CUUACCACUUUGUGAUUCAUGACUGGGGUGAAGUCGUAACAAGGUAACCGUAGGGGAACCUGCGGU 2729631
                               654144444...6..44444566899******************************************************* PP

                                             NC
                               >>::::::::::: CS
               RF01959    1465 cgGAUCACCUCcu 1477   
                               ::GAUCACCUCCU
  gi_545778205_gb_U000 2729630 UGGAUCACCUCCU 2729618
                               ************* PP

>>

RNAfold

>gi_545778205_gb_U000_280
GGAGGUGAUCCAACCGCAGGUUCCCCUACGGUUACCUUGUUACGACUUCA
CCCCAGUCAUGAAUCACAAAGUGGUAAGCGCCCUCCCGAAGGUUAAGCUA
CCUACUUCUUUUGCAACCCACUCCCAUGGUGUGACGGGCGGUGUGUACAA
GGCCCGGGAACGUAUUCACCGUGGCAUUCUGAUCCACGAUUACUAGCGAU
UCCGACUUCAUGGAGUCGAGUUGCAGACUCCAAUCCGGACUACGACGCAC
UUUAUGAGGUCCGCUUGCUCUCGCGAGGUCGCUUCUCUUUGUAUGCGCCA
UUGUAGCACGUGUGUAGCCCUGGUCGUAAGGGCCAUGAUGACUUGACGUC
AUCCCCACCUUCCUCCAGUUUAUCACUGGCAGUCUCCUUUGAGUUCCCGG
CCGGACCGCUGGCAACAAAGGAUAAGGGUUGCGCUCGUUGCGGGACUUAA
CCCAACAUUUCACAACACGAGCUGACGACAGCCAUGCAGCACCUGUCUCA
CGGUUCCCGAAGGCACAUUCUCAUCUCUGAAAACUUCCGUGGAUGUCAAG
ACCAGGUAAGGUUCUUCGCGUUGCAUCGAAUUAAACCACAUGCUCCACCG
CUUGUGCGGGCCCCCGUCAAUUCAUUUGAGUUUUAACCUUGCGGCCGUAC
UCCCCAGGCGGUCGACUUAACGCGUUAGCUCCGGAAGCCACGCCUCAAGG
GCACAACCUCCAAGUCGACAUCGUUUACGGCGUGGACUACCAGGGUAUCU
AAUCCUGUUUGCUCCCCACGCUUUCGCACCUGAGCGUCAGUCUUCGUCCA
GGGGGCCGCCUUCGCCACCGGUAUUCCUCCAGAUCUCUACGCAUUUCACC
GCUACACCUGGAAUUCUACCCCCCUCUACGAGACUCAAGCUUGCCAGUAU
CAGAUGCAGUUCCCAGGUUGAGCCCGGGGAUUUCACAUCUGACUUAACAA
ACCGCCUGCGUGCGCUUUACGCCCAGUAAUUCCGAUUAACGCUUGCACCC
UCCGUAUUACCGCGGCUGCUGGCACGGAGUUAGCCGGUGCUUCUUCUGCG
GGUAACGUCAAUGAGCAAAGGUAUUAACUUUACUCCCUUCCUCCCCGCUG
AAAGUACUUUACAACCCGAAGGCCUUCUUCAUACACGCGGCAUGGCUGCA
UCAGGCUUGCGCCCAUUGUGCAAUAUUCCCCACUGCUGCCUCCCGUAGGA
GUCUGGACCGUGUCUCAGUUCCAGUGUGGCUGGUCAUCCUCUCAGACCAG
CUAGGGAUCGUCGCCUUGGUGAGCCGUUACCCCACCAACAAGCUAAUCCC
AUCUGGGCACAUCCGAUGGCAAGAGGCCCGAAGGUCCCCCUCUUUGGUCU
UGCGACAUUAUGCGGUAUUAGCUACCGUUUCCAGUAGUUAUCCCCCUCCA
UCAGGCAGCUUCCCAGACAUUACUCACCCGUCCGCCACUCGUCAGCGAAG
CAGCAAGCUGCUUCCUGUUACCGUUCGACUUGCAUGUGUUAGGCCUGCCG
CCAGCGUUCAAUCUGAGCCAUGAUCAAACUCUUC
((.(((((.......((((((..((....))..))).))).......))))))).((((((........(((((...(((.........((((......))))........)))...)))))....(((((.((((((.(((((((((((((((((((((....))).))).)))....(((((...)))))..((((((.(.(((((((((((((.(.((((.((..(((.....))))).)))).)))))))))))))).)(((((....)))))))))))....))))))))))))......(((((.((((((((((((((.....))))).((((((.....)))))).........(((((((.....))))).))..(((((((.....(((((......)))))...)))))))...))))))))).)).)))(((......)))............((((((((((.((((((((((((((.(.((((...((((....((((((.......(((((.((........)).)))))....((((......))))(((((.((((.............((((.((......)).))))(((....)))((((.....))))............(((((((.((....)))))))))......((.((((((((((..(((((((((...(((......)))....((.(((...))).))))))))).))..((((((.....))))))..........((((((........)))))).(((((.(((..(((((((((..........)))......(((((.....((.((........))))...))))).......))))))..))))))))......(((((((((((((((.(((((((.(((...))).)))))))...)))))))...........((..((((.((..((((.....))))...))....))))..)).....((((......)))).))))))))))))))))))))((((((..((.(((((..........(((.((((.......)))).)))........))))).))))))))....)))).))))))))))).....)).)).)))).))))))))..)))((((((.....))))))...(((..(((.((((.....)))).)))..)))...)))))))))))..)))(((((((((.........)))))))))(((((....((.((((((...........))))))...))..))))).((((((.....(((((((...((((((.(((((......)))))))))))((........))((...(((((((........)))))))...))..))))).))......)))))).........))))))))))).....(((.(((((((....)))))))))).....(((((..(((.((((....((....))....)))).)))..))))))))))).......... (-495.50)

Length sequence

: 1534

Length match:

1533