gi_545778205_gb_U000_177

cmsearch-Rfam

Family :

PrrB_RsmZ

Id:

RF00166

Type:

Gene; sRNA;

Taxonomy:

Bacteria;

Ontology:

GO:0006401 RNA catabolic processRF00166

Description:

PrrB RNA is able to phenotypically complement gacS and gacA mutants and is itself regulated by
the GacS-GacA two-component signal transduction system [1]. Inactivation of the prrB gene in Pseudomonas fluorescens
F113 resulted in a significant reduction of 2, 4-diacetylphloroglucinol (Phl) and hydrogen cyanide (HCN) production,
while increased metabolite production was observed when prrB was overexpressed [1]. The prrB gene sequence
contains a number of imperfect repeats of the consensus sequence 5'-AGGA-3', and sequence analysis predicted
a complex secondary structure featuring multiple putative stem-loops with the consensus sequences predominantly positioned at
the single-stranded regions at the ends of the stem-loops. This structure is similar to the
CsrB and RsmB regulatory RNAs Rfam:RF00018 [1], suggesting this RNA also interacts with a CsrA-like
protein.

Score:

27.4

E-value:

0.00046

From sequence:

4639441

To sequence:

4639572

Alignments:

                                   v          v                              v             v                     NC
                               <<<<<__________>>>>>,<<<<<<______>>>>>>,,,,,,,<<<<<_____>>>>><<<~~~~~~>>>,,,,,,,, CS
               RF00166       1 uGuGcacAcGGAuaugCaCaggCccucAaGGAugaggGcaAgGgacaucGCAGGAaGCgauuCA*[ 9]*UGauuaagGAa 84     
                               : U: A+A+ GA+ +G:A : ::::UCA  G  GA:::: A+ G C ::: AG A  ::: :C:      :G: U  GGAA
  gi_545778205_gb_U000 4639441 CGUA-AUAUCGACUGGUAUGCGUUUUCACUGCCGAAAAUGAAAGCCAGUAAAGAAGUUACAACG*[12]*CGUAUCUGGAA 4639526
                               ***9.568999****9**************************9******999999999999998...5..89999999999 PP

                                             v    v                      v    v  NC
                               ,,,,,,,,,,,,,,<<<<<<---<<<<<<<____>>>>>>>->>>>>>: CS
               RF00166      85 uAaAGGGAcUAgGaaaaaAgUGUGGgcGGgucAacCCgcCCccUuuuuU 133    
                               + AAGG    A  A AAAA    :GGCG :  AA: CGCC: +UUUU U
  gi_545778205_gb_U000 4639527 AUAAGGUUGAAAAAUAAAA---ACGGCGCUAAAAAGCGCCGUUUUUUUU 4639572
                               9999987777644444444...4************************** PP

RNAfold
>gi_545778205_gb_U000_177
CGUAAUAUCGACUGGUAUGCGUUUUCACUGCCGAAAAUGAAAGCCAGUAA
AGAAGUUACAACGGACGAUGAGUUACGUAUCUGGAAAUAAGGUUGAAAAA
UAAAAACGGCGCUAAAAAGCGCCGUUUUUUUUG
.(((((.((.((((((...(((((((......)))))))...))))))...)).))))).((((((.....))).)))((((.......))))........((((((((((((....)))))))))))).... (-40.20)

Length sequence

: 133

Length match:

130