gi_545778205_gb_U000_59

cmsearch-Rfam

Family :

FMN

Id:

RF00050

Type:

Cis-reg; riboswitch;

Taxonomy:

Eukaryota; Bacteria; Archaea;

Ontology:

GO:0010181 FMN binding

Description:

The RFN element is a highly conserved domain that is found frequently in the 5'-untranslated regions
of prokaryotic mRNAs that encode for flavin mononucleotide (FMN) biosynthesis and transport proteins. This element
is a metabolite-dependent riboswitch that directly binds FMN in the absence of proteins. In Bacillus
subtilis, the riboswitch most likely controls gene expression by causing premature transcription termination within the
5' untranslated region of the ribDEAHT operon and precluding access to the ribosome-binding site of
ypaA mRNA [3].

Score:

127.0

E-value:

6.7e-31

From sequence:

3184718

To sequence:

3184570

Alignments:

                                                                                                                 NC
                               ::((((((((,,,,,,<<<_______>>>,,,,,<<<<_______________..____>>>>,,,,,,,,,,,,...... CS
               RF00050       1 aaucguccUCaGGGCaGGGUGaAAUUCCCuACCGGCGGUAAuuaauuaaauuu..aAGcCCGCGAgCguuuaaaa...... 73     
                                 U::::CUCAGGGC+GGG GAAAUUCCC ACCGGCGGUAA+U A+ + A UU  AAGCCCGCGAGCG+UU+         
  gi_545778205_gb_U000 3184718 GCUUAUUCUCAGGGCGGGGCGAAAUUCCCCACCGGCGGUAAAUCAACUCAGUUgaAAGCCCGCGAGCGCUUUGGGugcgaa 3184638
                               *****************************************99999888888888***************999999****9 PP

                                                                                                    NC
                               ,,,,,,,,,,,,,,,,<<<<<_______>>>>>,,,,,<<<.______>>>,,,,,,,)))))))):: CS
               RF00050      74 uuuuaaagucagcaGAuccGGUGaaAuUCCggaGCCGACgG.UAuAGUCcGGAUGgaAGAggacgaaa 140    
                                U +AA+G+CAGCAGA:CCGGUG+AAUUCCGG:GCCGACGG UA AGUCCGGAUGG+AGAG::::A +
  gi_545778205_gb_U000 3184637 CUCAAAGGACAGCAGAUCCGGUGUAAUUCCGGGGCCGACGGuUAGAGUCCGGAUGGGAGAGAGUAACG 3184570
                               99999*************************************************************** PP

RNAfold
>gi_545778205_gb_U000_59
GUUACUCUCUCCCAUCCGGACUCUAACCGUCGGCCCCGGAAUUACACCGG
AUCUGCUGUCCUUUGAGUUCGCACCCAAAGCGCUCGCGGGCUUUCAACUG
AGUUGAUUUACCGCCGGUGGGGAAUUUCGCCCCGCCCUGAGAAUAAGC
.(((.((((.......(((((((.....(.((((.((((.......))))....)))).)....)))))))..............((((....(((((...)))))....)))).(((((((.......)))))))..)))).))).. (-45.00)

Length sequence

: 148

Length match:

147