gi_545778205_gb_U000_240

cmsearch-Rfam

Family :

SgrS

Id:

RF00534

Type:

Gene; antisense;

Taxonomy:

Eukaryota; Bacteria;

Ontology:

GO:0032057 negative regulation of translational initiation in response to stressRF00534

Description:

In sugar transport-related sRNA (SgrS) is induced under conditions of glucose phosphate stress in E.coli. This
small RNA acts to negatively regulate the translation and stability of the ptsG mRNA, which
encodes the major glucose transporter in E. coli [2]. SgrS forms a specific ribonucleoprotein complex
with RNAse E and the chaperone Hfq and acts by base pairing with the ptsG
mRNA. The crucial base-pairs for action of SgrS are confined to the 6 nt region
overlapping the Shine-Dalgarno sequence of the ptsG mRNA [3].

Score:

224.9

E-value:

2.3e-65

From sequence:

77367

To sequence:

77593

Alignments:

                                                                                                                   NC
                             [[[[--[[[[[,,,,,,,,,,,,((((((((((((((((-((((((,,,,,,,,,,,<<<<<<<<______>>>>->>>>,,,<< CS
               RF00534     1 gAUGAAgCaagcaaaagaGgUcccCCaugcguCaGuucuaucagcgaUaCUuuuCcgCGaCcgcuAaauCGagcgGGuUGcGcug 85   
                             GAUGAAGCAAG     G GGU CCCCAUGCGUCAGU:::AUCAGC:+UA+UUU CCGCGAC:GC:AA U+G:GC:GGUUGCG+UG
  gi_545778205_gb_U000 77367 GAUGAAGCAAG-----GGGGUGCCCCAUGCGUCAGUUUUAUCAGCACUAUUUUACCGCGACAGCGAAGUUGUGCUGGUUGCGUUG 77446
                             ***********.....********************************************************************* PP

                                                                                                                   NC
                             <<<<<-<<<______>>>->>>>>>>)))-)))))))))))))))-)))),,,,,,,,,,,<<________>>]]]]]---]]]] CS
               RF00534    86 ccugagCgcccaACAgcGAucaggcacgcUugaggaaCuGaugcaGuGGgaaGugAccaccuCcGaAuGCuGacuuGcaGACAUc 170  
                             ::U:AGCG:CC+ACA:CGAU:A::CA:GCUUGA:::ACUGAUGCAGUGGGA G + +CA++UC+GAA G+UGACUUGC   CAUC
  gi_545778205_gb_U000 77447 GUUAAGCGUCCCACAACGAUUAACCAUGCUUGAAGGACUGAUGCAGUGGGAUGACCGCAAUUCUGAAAGUUGACUUGCCUGCAUC 77531
                             ************************************************************************************* PP

                                                                                            NC
                             --------------------------------<<<<<<<<_______>>>>>>>>::::::: CS
               RF00534   171 AuGUGgguCUGAGUAuUGGUGUaAuaucaCCCgcCagCggaauuUcuccGcuGgcuUUUUUu 232  
                             AUGUG+G+CUGAGUAUUGGUGUAA+AUCACCC:CCAGC:GA+U+U+ C:GCUGG:UUUUUUU
  gi_545778205_gb_U000 77532 AUGUGUGACUGAGUAUUGGUGUAAAAUCACCCGCCAGCAGAUUAUACCUGCUGGUUUUUUUU 77593
                             ************************************************************** PP

RNAfold
>gi_545778205_gb_U000_240
ACGAUGAAGCAAGGGGGUGCCCCAUGCGUCAGUUUUAUCAGCACUAUUUU
ACCGCGACAGCGAAGUUGUGCUGGUUGCGUUGGUUAAGCGUCCCACAACG
AUUAACCAUGCUUGAAGGACUGAUGCAGUGGGAUGACCGCAAUUCUGAAA
GUUGACUUGCCUGCAUCAUGUGUGACUGAGUAUUGGUGUAAAAUCACCCG
CCAGCAGAUUAUACCUGCUGGUUUUUUUUAUU
(((((((.(((.((.(((..((((((((((((((((((((((((.((((...(((....))))))).)))))))).((((.((((((.(((......))).))))))))))....)))))))))))).))))...))).(((.((........)).)))))))).)))).)))...........((((......)))).((((((((.......)))))))).......... (-78.70)

Length sequence

: 232

Length match:

225