gi_545778205_gb_U000_45

cmsearch-Rfam

Family :

CsrB

Id:

RF00018

Type:

Gene; sRNA;

Taxonomy:

Eukaryota; Bacteria;

Ontology:

GO:0005515 protein binding

Description:

The CsrB RNA binds to approximately 18 copies of the CsrA protein Pfam:PF02599. Although CsrA proteins
are found in a wide variety of bacteria, CsrB RNAs are only known in enterobacter.
The CsrB RNAs contain a conserved motif CAGGXXG that is found in up to 18
copies and has been suggested to bind CsrA. The Csr regulatory system has a strong
negative regulatory effect on glycogen biosynthesis, glyconeogenesis and glycogen catabolism and a positive regulatory effect
on glycolysis [1]. In other bacteria such as Erwinia caratovara the RsmA protein has been
shown to regulate the production of virulence determinants, such extracellular enzymes [2]. RsmA binds to
RsmB regulatory RNA which is also a member of this family [2].

Score:

35.1

E-value:

9.8e-08

From sequence:

4051045

To sequence:

4051283

Alignments:

                                                   v           v               v             v                   NC
                               ::::::::::::::::::::<<<_______>>>,,,,,,,,,,,,,,,<<<<<_____>>>>>,,,,,,,,,,,<<<<<__ CS
               RF00018       1 gAgucggagaaagaaGauaacauCAGGAUGaugacgcuUCugaAGGAcccgcCAGGAuGgcgguaCAagGaaAGgcuUcAG 81     
                               G      A+ A GAA A  + :UCAGGAUGA:           AGGA  CGCCAGGA GGCG+ A A +GA   :::UCAG
  gi_545778205_gb_U000 4051045 GGACGCUAACAGGAACAAUGACUCAGGAUGAGGGUC-------AGGAG-CGCCAGGA-GGCGA-AGACAGAGGAUUGUCAG 4051115

                                                                                                                 NC
                               ___>>>>>,,,,,,,<<<<<_____>>>>>,,~~~~~~,,,,,,,,,,,,,,,,,,,,,~~~~~~,,,,,,,,,,,,,,,, CS
               RF00018      82 GAugAagcaaaGGAugccgCAGGAUGcggcaA*[79]*uaucAcAuCgGGaUGgUGuga*[65]*GCAGGGAGCAuaAAau 294    
                               GA GA:::       :C::C GGA G::G:AA      +   A A C+GG+UG   UG+      GCA GGA   UAA A 
  gi_545778205_gb_U000 4051116 GAAGACAA-------ACGUCCGGA-GACGUAA*[39]*AGGAAAAACAGGGUGUGUUGG*[ 6]*GCAAGGAUUGUAAGAC 4051221

                               v   v      v   v                                               NC
                               <<<<<______>>>>>,,,,,,,,,,<<<<<<<<<<______>>>>>>>>>>:::::::::: CS
               RF00018     295 guAGCuGGAuuGCUacgAAACGAACCGGGgGcACUGuuuAuACAGUgCcCCCUUUUUUUuuu 356    
                                ::    G  U  :: G  A GAA  ::GG :AC G +UA+ C GU: CC::UUUU UUU  
  gi_545778205_gb_U000 4051222 CCGUUAAGGGUUAUGAGUCAGGAAAAAAGGCGACAGAGUAAUCUGUCGCCUUUUUUCUUUGC 4051283

RNAfold
>gi_545778205_gb_U000_45
CUGAUGGCGGUUGAUUGUUUGUUUAAAGCAAAGGCGUAAAGUAGCACCCA
UAGAGCGAGGACGCUAACAGGAACAAUGACUCAGGAUGAGGGUCAGGAGC
GCCAGGAGGCGAAGACAGAGGAUUGUCAGGAAGACAAACGUCCGGAGACG
UAAUUAAACGGAAAUGGAAUCAACACGGAUUGUUCCGGCUAAAGGAAAAA
CAGGGUGUGUUGGCGGCCUGCAAGGAUUGUAAGACCCGUUAAGGGUUAUG
AGUCAGGAAAAAAGGCGACAGAGUAAUCUGUCGCCUUUUUUCUUUGCUUG
CUUUCUGUUAGAUUCCGCCGCAAAUCUAUACUGAAUAAAACGGCUAAAAG
ACGAAC
((..((((.(((..((((((.....)))))).((.((......)).)).((((((((.(((..(((((((((((((((((((.......))))))....((((....))))...........(((((.....)))))(((((....)))))..(((..((((...(.((((......)))).)))))..)))........((((.(((....))).))))....((((....(((((.....)))))...))))((((((((((((((((((....))))))))))))))))))...))).))))))))))..)))..)))...))))).........))).))))..))...... (-117.50)

Length sequence

: 356

Length match:

237