gi_545778205_gb_U000_360

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:

77.2

E-value:

9.1e-15

From sequence:

4196280

To sequence:

4196180

Alignments:

                                                  vv     vv           vv   vv                                    NC
                               :::::[[[[[((((,,<<<<<_____>>>>>,,,,,<<<<<<_>>>>>>,,)))),,,,,<<<<--<<<<______>>>>- CS
               RF00059       1 aaauaccacuaGGGGuGCcccuauaagggGCUGAGAugggccuggcccaaACCCuUuGAACCUgAUCcGGaUAAUaCCgGC 81     
                               AA+U+C:::U:GG:GUGCC  +   A  GGCUGAGA::G  : :  C::+A:CC:  GAACCU:AUC:GG UAAUACC:GC
  gi_545778205_gb_U000 4196280 AAUUUCUUGUCGGAGUGCCUUA---ACUGGCUGAGACCGUUU-AUUCGGGAUCCGCGGAACCUGAUCAGGCUAAUACCUGC 4196204
                               *******************975...679************99.9************************************* PP

                                                        NC
                               ->>>>,,]]]]]:::::::::::: CS
               RF00059      82 GuAGGGAaguggauauauauuuuu 105    
                               G:AGGGAA:::GA++UA + U  U
  gi_545778205_gb_U000 4196203 GAAGGGAACAAGAGUUAAUCUGCU 4196180
                               ************************ PP

>>

RNAfold
>gi_545778205_gb_U000_360
UAGCAGAUUAACUCUUGUUCCCUUCGCAGGUAUUAGCCUGAUCAGGUUCC
GCGGAUCCCGAAUAAACGGUCUCAGCCAGUUAAGGCACUCCGACAAGAAA
UUAG
............((((((..(((...(((((....)))))...))).....(((...)))......(((.....(((......)))...)))))))))...... (-22.70)

Length sequence

: 104

Length match:

99