gi_545778205_gb_U000_361

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:

65.3

E-value:

6.3e-12

From sequence:

75610

To sequence:

75511

Alignments:

                                                                      v         v                                  NC
                             :::::[[[[[((((,,<<<<<___...__>>>.>>,,,,,<<<<<<_>>>>>>,,)))),,,,,<<<<--<<<<______>>>>- CS
               RF00059     1 aaauaccacuaGGGGuGCcccuau...aaggg.GCUGAGAugggccuggcccaaACCCuUuGAACCUgAUCcGGaUAAUaCCgGC 81   
                                U+C:::::GGGGUGCC:C        G:G GCUGAGA:+          : ACCC:U GAACCU:AUCCGGAUAA +CCGGC
  gi_545778205_gb_U000 75610 CCGUUCUCAACGGGGUGCCACGCGuacGCGUGcGCUGAGAAA----------AUACCCGUCGAACCUGAUCCGGAUAACGCCGGC 75536
                             ******************888766666667777********8..........9******************************** PP

                                                       NC
                             ->>>>,,.]]]]]:::::::::::: CS
               RF00059    82 GuAGGGA.aguggauauauauuuuu 105  
                             G:AGGGA ::::G  +  U+ U ++
  gi_545778205_gb_U000 75535 GAAGGGAuUUGAGGCUCCUUCUCAA 75511
                             ************************* PP

RNAfold
>gi_545778205_gb_U000_361
ACUUGAGAAGGAGCCUCAAAUCCCUUCGCCGGCGUUAUCCGGAUCAGGUU
CGACGGGUAUUUUCUCAGCGCACGCGUACGCGUGGCACCCCGUUGAGAAC
GGCGU
...((((((((.((((......(((...((((......))))...)))......)))).))))))))((.(((((....)))))))((.(((((...))))).)) (-35.60)

Length sequence

: 105

Length match:

98