Ec_CsrB,

cmscan-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:

376.7

E-value:

2.6e-111

From sequence:

1

To sequence:

360

Alignments:

                                                                                                                     NC
               ::::::::::::::::::::<<<_______>>>,,,,,,,,,,,,,,,<<<<<_____>>>>>,,,,,,,,,,,<<<<<_____>>>>>,,,,..,,,<<< CS
   RF00018   1 gAgucggagaaagaaGauaacauCAGGAUGaugacgcuUCugaAGGAcccgcCAGGAuGgcgguaCAagGaaAGgcuUcAGGAugAagcaaaG..GAugcc 99 
               GAGUC+GA AA GAAG++AACAUCAGGAUGAUGAC+CUUCUG+AGGAC:C:CCAGGAUGG:G:U CA+GGAAAGGCUUC GGAUGAAGC AAG  GAU::C
  Ec_CsrB,   1 GAGUCAGACAACGAAGUGAACAUCAGGAUGAUGACACUUCUGCAGGACACACCAGGAUGGUGUUUCAGGGAAAGGCUUCUGGAUGAAGCGAAGagGAUGAC 101
               ***************************************************************************************************** PP

                                                                                                                     NC
               <<_____>>>>>,,,,,,,,,<<<<_____>>>>,,,,,,,<<<<<<_______>.>>>>>,<<<_______>>>,,,.,,,<<<<_____>>>>,,,,,, CS
   RF00018 100 gCAGGAUGcggcaAaGGACACCUCCAGGAuGGAGAauGAGAgCCggucAGGAuga.ccGGcGGGccAGGAuggCCAgG.AcgcuucAGGAUgaaguaucAc 198
               GCAGGA GCG::AAAGGACACCUCCAGGAUGGAGAAUGAGA:CCG:UCAGGAUGA :CGG:GGG:CAGGA+G:CCAGG AC+CUUCAGGAUGAAGUAUCAC
  Ec_CsrB, 102 GCAGGACGCGUUAAAGGACACCUCCAGGAUGGAGAAUGAGAACCGGUCAGGAUGAuUCGGUGGGUCAGGAAGGCCAGGgACACUUCAGGAUGAAGUAUCAC 202
               *******************************************************9**********************9********************** PP

                                                                                                                     NC
               ,,,,,,,,,,,,,,,<<_____>>,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<______>>,,,,,,,,,,,,,,,,<<<<< CS
   RF00018 199 AuCgGGaUGgUGugagCAGGAaGcaauuGuuaaggAuGAauguugGucaGgAugaCcaaAGGAAAAGUUuUCAaGGAUGAGCAGGGAGCAuaAAauguAGC 299
               AUCGGG+UGGUGUGAGCAGGAAGCAAU+GUU+AGGAUGAA+G+U+G C+G A+G+CCA AGGAAAAGUU+UCAAGGAUGAGCAGGGAGCA++AAA+G:AGC
  Ec_CsrB, 203 AUCGGGGUGGUGUGAGCAGGAAGCAAUAGUUCAGGAUGAACGAUUGGCCGCAAGGCCAGAGGAAAAGUUGUCAAGGAUGAGCAGGGAGCAACAAAAGUAGC 303
               ***************************************************************************************************** PP

                                                                         NC
               ______>>>>>,,,,,,,,,,<<<<<<<<<<______>>>>>>>>>>:::::::::: CS
   RF00018 300 uGGAuuGCUacgAAACGAACCGGGgGcACUGuuuAuACAGUgCcCCCUUUUUUUuuu 356
               UGGA+UGCU:CGAAACGAACCGGG:GC:CUGU++AUACAG:GC:CCCUUUUUUU+UU
  Ec_CsrB, 304 UGGAAUGCUGCGAAACGAACCGGGAGCGCUGUGAAUACAGUGCUCCCUUUUUUUAUU 360
               ********************************************************* PP

RNAfold
>Ec_CsrB,
agucagacaacgaagugaacaucaggaugaugacacuucugcaggacaca
ccaggaugguguuucagggaaaggcuucuggaugaagcgaagaggaugac
gcaggacgcguuaaaggacaccuccaggauggagaaugagaaccggucag
gaugauucggugggucaggaaggccagggacacuucaggaugaaguauca
caucgggguggugugagcaggaagcaauaguucaggaugaacgauuggcc
gcaaggccagaggaaaaguugucaaggaugagcagggagcaacaaaagua
gcuggaaugcugcgaaacgaaccgggagcgcugugaauacagugcucccu
uuuuuuauu
.(((.((((((((((((..(((((...))))).))))))..(..((.((((((...)))))).))..).....(((((.....)))))........((((((.....))))))....(((((.((..((((..........((((((((...))).))))).((((.....))))...((.((((((...)))))).)).))))..)).)))))..((.....))....(((((...)))))..((((((....)))))).......))))))...))).((((...(((.((....)).)))....))))............(((((((((((....))))))))))).......... (-116.10)

Length sequence

: 359

Length match:

358