gi_545778205_gb_U000_17

cmsearch-Rfam

Family :

Alpha_RBS

Id:

RF00140

Type:

Cis-reg;

Taxonomy:

Eukaryota; Bacteria;

Ontology:

Not found

Description:

The bacterial alpha operon ribosome binding site is surrounded by this complex pseudoknotted structure. Translation of
the mRNA produces 4 ribosomal protein products, one of which (S4) acts as a translational
repressor by binding to the nested pseudoknot region. The mechanism of repression is thought to
involve a conformational switch in the pseudoknot region and ribosome entrapment [1].

Score:

104.1

E-value:

7e-25

From sequence:

3442550

To sequence:

3442439

Alignments:

                                                                                                                 NC
                               :::<<<<<<<.<<<______________.._________________>>>>>>>>>>:::::::::::::::::::::::: CS
               RF00140       1 uaauggcgcc.cccguuuGaGUAUCCUg..aACGGGCUUUuCaAgaugggggcgccauuUuaAauuauuAGGAGUGcAUAG 78     
                                + UG: ::: :CC UUUGAGUAUCCUG  AACGGGCUUUUCA+ AUGG:::: :CAU+UUAAAU+ U AGGAGUGCAUAG
  gi_545778205_gb_U000 3442550 GUCUGUGCGUuUCCAUUUGAGUAUCCUGaaAACGGGCUUUUCAGCAUGGAACGUACAUAUUAAAUAGU-AGGAGUGCAUAG 3442471
                               **********555589*****************************************99888777666.************ PP

                                                                NC
                               :::::::::::::::::::::::::::::::: CS
               RF00140      79 UGGCCCGUAUuGCaGGCAUUAACAUUCCUGAU 110    
                               UGGCCCGUAU+GCAGGCAUUAACAUUCCUGAU
  gi_545778205_gb_U000 3442470 UGGCCCGUAUAGCAGGCAUUAACAUUCCUGAU 3442439
                               ******************************** PP

RNAfold
>gi_545778205_gb_U000_17
UCAGGAAUGUUAAUGCCUGCUAUACGGGCCACUAUGCACUCCUACUAUUU
AAUAUGUACGUUCCAUGCUGAAAAGCCCGUUUUCAGGAUACUCAAAUGGA
AACGCACAGAC
..((((.(((....(((((.....)))))......))).))))...........(((.((((((((.(((((((.....))))))).)........))).)))).)))... (-26.00)

Length sequence

: 111

Length match:

110