gi_545778205_gb_U000_359

cmsearch-Rfam

Family :

TPP

Id:

RF00059

Type:

Cis-reg; riboswitch;

Taxonomy:

Eukaryota; Bacteria; Archaea;

Ontology:

GO:0030976 thiamine pyrophosphate binding

Description:

Vitamin B(1) in its active form thiamin pyrophosphate (TPP) is an essential coenzyme that is synthesised
by coupling of pyrimidine and thiazole moieties in bacteria. The previously detected thiamin-regulatory element, thi
box [1] was extended, resulting in a new, highly conserved RNA secondary structure, the THI
element, which is widely distributed in eubacteria and also occurs in some archaea. Analysis of
operon structures identified a large number of new candidate thiamin-regulated genes, mostly transporters, in various
prokaryotic organisms [2]. The THI element is a riboswitch [3] that directly binds to TPP
to regulate gene expression through a variety of mechanisms in archaea, bacteria and eukaryotes [4,5].

Score:

66.9

E-value:

2.6e-12

From sequence:

2185432

To sequence:

2185336

Alignments:

                                    v             v          v                                                   NC
                               :::::[[[[[((((,,<<<<<___...__>>>>>,,,,,<<<<<<_>>>>>>,,)))),,,,,<<<<--<<<<______>> CS
               RF00059       1 aaauaccacuaGGGGuGCcccuau...aagggGCUGAGAugggccuggcccaaACCCuUuGAACCUgAUCcGGaUAAUaCC 78     
                                 A+A :ACU:GGGGUGCC :U U     : GGCUGAGA:           : ACCC:U+  ACCUGAUC:GGAUAAU+CC
  gi_545778205_gb_U000 2185432 CCAAACGACUCGGGGUGCCCUUCUgcgUGAAGGCUGAGAA-----------AUACCCGUAUCACCUGAUCUGGAUAAUGCC 2185363
                               *******************999888887799*********...........899*************************** PP

                                             v             NC
                               >>-->>>>,,]]]]]:::::::::::: CS
               RF00059      79 gGCGuAGGGAaguggauauauauuuuu 105    
                               :GCGUAGGGAAGU:  + +  A    +
  gi_545778205_gb_U000 2185362 AGCGUAGGGAAGUCACGGACCACCAGG 2185336
                               *************************** PP

>>

RNAfold
>gi_545778205_gb_U000_359
UGACCUGGUGGUCCGUGACUUCCCUACGCUGGCAUUAUCCAGAUCAGGUG
AUACGGGUAUUUCUCAGCCUUCACGCAGAAGGGCACCCCGAGUCGUUUGG
UUGC
.((((....))))((((.......))))((((......))))((((((((((.((((..........(((((.....)))))....)))).))))))))))... (-28.10)

Length sequence

: 104

Length match:

95