gi_545778205_gb_U000_34

cmsearch-Rfam

Family :

Cobalamin

Id:

RF00174

Type:

Cis-reg; riboswitch;

Taxonomy:

Eukaryota; Bacteria; Viruses;

Ontology:

GO:0031419 cobalamin binding

Description:

Riboswitches are metabolite binding domains within certain messenger RNAs that serve as precision sensors for their
corresponding targets. Allosteric rearrangement of mRNA structure is mediated by ligand binding, and this results
in modulation of gene expression [1]. This family represents a cobalamin riboswitch (B12-element) which is
widely distributed in 5' UTRs of vitamin B(12)-related genes in bacteria. Cobalamin in the form
of adenosylcobalamin (Ado-CBL) is known to repress expression of genes for vitamin B(12) biosynthesis and
be transported by a post-transcriptional regulatory mechanism, which involves direct binding of Ado-CBL to 5'
UTRs [2].

Score:

98.3

E-value:

7.2e-26

From sequence:

4163384

To sequence:

4163574

Alignments:

                                                      v              v                                 v    v    NC
                               :::::::::::::::[[[[[[,<<<____________>>>,,,,,(((,,,<<<<<_______>>>>>,,<<<____>>>, CS
               RF00174       1 uuaaauugaaacgaugauGGUuccccuuuaaagugaaggguuAAaaGGGAAcccGGUGaaAaUCCgggGCuGcCCCCgCaA 81     
                                U +A  ++ +   UG::GGU C : U          : GUUAA AGGGAA:CC:GUG++AAUC:GG:GCUG  C C CA+
  gi_545778205_gb_U000 4163384 CUGUAGCAUCCACUUGCCGGU-CCUGU----------GAGUUAAUAGGGAAUCCAGUGCGAAUCUGGAGCUGA-CGCGCAG 4163452
                               *********************.88888..........99**********************************.******* PP

                                        v                                                                        NC
                               <<<---<<<<------<<<<<<-----......<<<-<<<<<<______>>>>>>--->>>>>>>>>----------.... CS
               RF00174      82 CuGUAAgcGgagagcaccccccAauAa......GCCACUggcccgcaagggccGGGAAGGCggggggaaggaaugac.... 152    
                               C:GUAAG:: AG+ ++::::::  + +      G:CACU::C   +++  G::GGGAAG:C::::::   +A+U+ C    
  gi_545778205_gb_U000 4163453 CGGUAAGGAAAGGUGCGAUGAUUGCGUuaugcgGACACUGCC--AUUC--GGUGGGAAGUCAUCAUCUCUUAGUAUCuuag 4163529
                               **************************9***************..5555..***********************9998**** PP

                                     v                                       NC
                               ......>>>>---->>>,,,,)))]]]]]]::::::::::::::: CS
               RF00174     153 ......cCgcgAGcCaGGAGACCuGCCaucaguuuuugaaucucc 191    
                                      ::C+AGCC:G+AGACCUGCC::C ++  U G AUCU  
  gi_545778205_gb_U000 4163530 auacccCUCCAAGCCCGAAGACCUGCCGGCCAACGUCGCAUCUGG 4163574
                               ********************************************* PP

RNAfold
>gi_545778205_gb_U000_34
UGUAGCAUCCACUUGCCGGUCCUGUGAGUUAAUAGGGAAUCCAGUGCGAA
UCUGGAGCUGACGCGCAGCGGUAAGGAAAGGUGCGAUGAUUGCGUUAUGC
GGACACUGCCAUUCGGUGGGAAGUCAUCAUCUCUUAGUAUCUUAGAUACC
CCUCCAAGCCCGAAGACCUGCCGGCCAACGUCGCAUCUGG
...........(((((((...(((((.(((.....((..(((((.......))))).))))).))))))))))))...((((((((((.((((((...)))(((.(((((....)))))...)))...........(((((...)))))........(((.(........).)))))))))))))))).. (-53.50)

Length sequence

: 190

Length match:

189