gi_545778205_gb_U000_25

cmsearch-Rfam

Family :

beta_tmRNA

Id:

RF01850

Type:

Gene;

Taxonomy:

Bacteria;

Ontology:

GO:0006401 RNA catabolic process

Description:

Bacterial tmRNA, also known as 10Sa RNA or SsrA, is named for its dual tRNA and
mRNA-like properties. Its role is to liberate the mRNA from a stalled ribosome. To accomplish
this part of the tmRNA is used as a reading frame that ends in a
translation stop signal. The broken mRNA is replaced in the ribosome by the tmRNA and
translation of the tmRNA leads to addition of a proteolysis tag to the incomplete protein
enabling recognition by a protease. Recently a number of permuted tmRNA genes have been found
encoded in two parts. tmRNAs have been identified in eubacteria and some chloroplasts but are
absent from archaeal and eukaryote nuclear genomes.

Score:

28.9

E-value:

6.4e-07

From sequence:

2755528

To sequence:

2755766

Alignments:

                                                                                   v v v        v   v            NC
                               :::::::::::::::::::::::::::::::::::::::::::.::::::::(((((----((-((-((((-----((((( CS
               RF01850       1 acacgcAaauugaCUUGAagcugacggCagcgcgCgUAuAAUc.uagAgCAUgGUUGUauuCCggcaaccuGgAGGCgUUC 80     
                                +ACG  AA+  + UUGA GCUG      GCGC C UA+A  +   + +C U   U UA +C +:  :: U      ::UC
  gi_545778205_gb_U000 2755528 UAACGAUAACGCCAUUGAGGCUGGUCAUGGCGCUCAUAAAUCUgGUAUACUUACCUUUACACAUUGGGGCU-----GAUUC 2755603
                               **********************9998888888888888776440445556777777788899988887777.....89999 PP

                                                           v    v    v v v                                       NC
                               ((,,,~~~~~~,,,,)))))))-----))))--))-)))))))<<<<______~~~~~>>>>,,,,,,,,,,,,,,,,,,, CS
               RF01850      81 UGGAC*[71]*UCGACAGGGcGgGcaAaggugagcAGGCAACcCGucAGgcgA*[2]*gaCGUuAauaauacAaauccaUA 223    
                                GGA       UCGAC GG::  GC AA :: A :  G A   CG:: GGCG      ::CGU+AA+A++   AA ++AUA
  gi_545778205_gb_U000 2755604 UGGAU*[ 0]*UCGACGGGAUUUGCGAAACCCAAGGUGCAUGCCGAGGGGCGG*[5]*CUCGUAAAAAGCCGCAAAAAAUA 2755678
                               99999......7999*****9999999999999999999*******9998765..5..9**********999999****** PP

                                                                                      v        v           NC
                               ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,~~~~~~,,<<<<<<<<<____>>>>>>>>>.::: CS
               RF01850     224 AAuGCcAAcGAuGAgcauUUCGCaaUgGCCGCcUAAaAaCg*[40]*CggcgggggccUCGGggcccccgc.UCA 331    
                                 +GC AACGA+GA++A U CGC++U+GC GC+UAA AAC       C  C:::: C:U   :G ::::G  UCA
  gi_545778205_gb_U000 2755679 GUCGCAAACGACGAAAACUACGCUUUAGCAGCUUAAUAACC*[23]*CCUCCGCU-CUU---AGGACGGGGaUCA 2755766
                               ************************************98874...5..55555554.344...4444444445*** PP

>>

RNAfold
>gi_545778205_gb_U000_25
AUUGCUUAAUCGAAUAAAAAUCAGGCUACAUGGGUGCUAAAUCUUUAACG
AUAACGCCAUUGAGGCUGGUCAUGGCGCUCAUAAAUCUGGUAUACUUACC
UUUACACAUUGGGGCUGAUUCUGGAUUCGACGGGAUUUGCGAAACCCAAG
GUGCAUGCCGAGGGGCGGUUGGCCUCGUAAAAAGCCGCAAAAAAUAGUCG
CAAACGACGAAAACUACGCUUUAGCAGCUUAAUAACCUGCUUAGAGCCCU
CUCUCCCUAGCCUCCGCUCUUAGGACGGGGAUCAAGAGAGGUCAAACCCA
AAAGAGAUCGCGUGGAAGCCCUGCCUGGGG
....................((((((.....(((.(((...(((....((((..((((((.((......))))))))...........((((....))))........(((((((.(((((((.......))))))).))....(((..(((....)))..)))((((((............))))))........((((....)))).........((((((((((.........)))).))))))(((((((((((..(((........)))..)))))....)))))).....))))).....))))...))))))))))))))).. (-97.20)

Length sequence

: 330

Length match:

237