gi_545778205_gb_U000_44

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:

376.7

E-value:

1.4e-110

From sequence:

2924515

To sequence:

2924156

Alignments:

                                                                                                                 NC
                               ::::::::::::::::::::<<<_______>>>,,,,,,,,,,,,,,,<<<<<_____>>>>>,,,,,,,,,,,<<<<<__ CS
               RF00018       1 gAgucggagaaagaaGauaacauCAGGAUGaugacgcuUCugaAGGAcccgcCAGGAuGgcgguaCAagGaaAGgcuUcAG 81     
                               GAGUC+GA AA GAAG++AACAUCAGGAUGAUGAC+CUUCUG+AGGAC:C:CCAGGAUGG:G:U CA+GGAAAGGCUUC G
  gi_545778205_gb_U000 2924515 GAGUCAGACAACGAAGUGAACAUCAGGAUGAUGACACUUCUGCAGGACACACCAGGAUGGUGUUUCAGGGAAAGGCUUCUG 2924435
                               ********************************************************************************* PP

                                                                                                                 NC
                               ___>>>>>,,,,..,,,<<<<<_____>>>>>,,,,,,,,,<<<<_____>>>>,,,,,,,<<<<<<_______>.>>>>> CS
               RF00018      82 GAugAagcaaaG..GAugccgCAGGAUGcggcaAaGGACACCUCCAGGAuGGAGAauGAGAgCCggucAGGAuga.ccGGc 159    
                               GAUGAAGC AAG  GAU::CGCAGGA GCG::AAAGGACACCUCCAGGAUGGAGAAUGAGA:CCG:UCAGGAUGA :CGG:
  gi_545778205_gb_U000 2924434 GAUGAAGCGAAGagGAUGACGCAGGACGCGUUAAAGGACACCUCCAGGAUGGAGAAUGAGAACCGGUCAGGAUGAuUCGGU 2924354
                               ***************************************************************************9***** PP

                                                                                                                 NC
                               ,<<<_______>>>,,,.,,,<<<<_____>>>>,,,,,,,,,,,,,,,,,,,,,<<_____>>,,,,,,,,,,,,,,,,, CS
               RF00018     160 GGGccAGGAuggCCAgG.AcgcuucAGGAUgaaguaucAcAuCgGGaUGgUGugagCAGGAaGcaauuGuuaaggAuGAau 239    
                               GGG:CAGGA+G:CCAGG AC+CUUCAGGAUGAAGUAUCACAUCGGG+UGGUGUGAGCAGGAAGCAAU+GUU+AGGAUGAA+
  gi_545778205_gb_U000 2924353 GGGUCAGGAAGGCCAGGgACACUUCAGGAUGAAGUAUCACAUCGGGGUGGUGUGAGCAGGAAGCAAUAGUUCAGGAUGAAC 2924273
                               *****************9*************************************************************** PP

                                                                                                                 NC
                               ,,,,,,,,,,,,,,,,,,,,,,,,,,,,,<<______>>,,,,,,,,,,,,,,,,<<<<<______>>>>>,,,,,,,,,, CS
               RF00018     240 guugGucaGgAugaCcaaAGGAAAAGUUuUCAaGGAUGAGCAGGGAGCAuaAAauguAGCuGGAuuGCUacgAAACGAACC 320    
                               G+U+G C+G A+G+CCA AGGAAAAGUU+UCAAGGAUGAGCAGGGAGCA++AAA+G:AGCUGGA+UGCU:CGAAACGAACC
  gi_545778205_gb_U000 2924272 GAUUGGCCGCAAGGCCAGAGGAAAAGUUGUCAAGGAUGAGCAGGGAGCAACAAAAGUAGCUGGAAUGCUGCGAAACGAACC 2924192
                               ********************************************************************************* PP

                                                                    NC
                               <<<<<<<<<<______>>>>>>>>>>:::::::::: CS
               RF00018     321 GGGgGcACUGuuuAuACAGUgCcCCCUUUUUUUuuu 356    
                               GGG:GC:CUGU++AUACAG:GC:CCCUUUUUUU+UU
  gi_545778205_gb_U000 2924191 GGGAGCGCUGUGAAUACAGUGCUCCCUUUUUUUAUU 2924156
                               ************************************ PP

>>

RNAfold
>gi_545778205_gb_U000_44
AUAAAAAAAGGGAGCACUGUAUUCACAGCGCUCCCGGUUCGUUUCGCAGC
AUUCCAGCUACUUUUGUUGCUCCCUGCUCAUCCUUGACAACUUUUCCUCU
GGCCUUGCGGCCAAUCGUUCAUCCUGAACUAUUGCUUCCUGCUCACACCA
CCCCGAUGUGAUACUUCAUCCUGAAGUGUCCCUGGCCUUCCUGACCCACC
GAAUCAUCCUGACCGGUUCUCAUUCUCCAUCCUGGAGGUGUCCUUUAACG
CGUCCUGCGUCAUCCUCUUCGCUUCAUCCAGAAGCCUUUCCCUGAAACAC
CAUCCUGGUGUGUCCUGCAGAAGUGUCAUCAUCCUGAUGUUCACUUCGUU
GUCUGACUC
.........((((((.((((....)))).))))))............((((....(((.((....)).)))...)))).......((((((........(((((....)))))...(((((...)))))....((.....))..(((((.((..((((.(((((((((...)))))))))...((.(.....).)).((((..(((...))).))))..........))))..)).)))))......((((.....))))..........(((((.....)))))........((.((((((...)))))).)).....((((((.(((((...)))))..))))))))))))...... (-98.10)

Length sequence

: 359

Length match:

358