gi_545778205_gb_U000_58

cmsearch-Rfam

Family :

DsrA

Id:

RF00014

Type:

Gene; sRNA;

Taxonomy:

Eukaryota; Bacteria;

Ontology:

Not found

Description:

DsrA RNA regulates both transcription, by overcoming transcriptional silencing by the nucleoid-associated H-NS protein, and translation,
by promoting efficient translation of the stress sigma factor, RpoS. These two activities of DsrA
can be separated by mutation: the first of three stem-loops of the 85 nucleotide RNA
is necessary for RpoS translation but not for anti-H-NS action, while the second stem-loop is
essential for antisilencing and less critical for RpoS translation. The third stem-loop, which behaves as
a transcription terminator, can be substituted by the trp transcription terminator without loss of either
DsrA function. The sequence of the first stem-loop of DsrA is complementary with the upstream
leader portion of RpoS messenger RNA, suggesting that pairing of DsrA with the RpoS message
might be important for translational regulation.

Score:

102.8

E-value:

3.4e-20

From sequence:

2025313

To sequence:

2025227

Alignments:

                                                                                                                 NC
                               :::<<<<<<<_____>>>>>>>,,,<<<<<.<<<<<<<<_____>>>>>>>>->>->>>-<<<<<<<-<<____.>>->>> CS
               RF00014       1 aaCaCauCaGAUUUCCuGguGuAACgaauu.uuuaaGugCUUCUugCuuaagCaaGuucaauCCcGacccCuuc.ggGuCg 79     
                               AACACAUCAGAUUUCCUGGUGUAAC:AAUU UUUAAGUGCUUCUUGCUUAAGCAAGUU: AUCCCGACCCC+UC GGGUCG
  gi_545778205_gb_U000 2025313 AACACAUCAGAUUUCCUGGUGUAACGAAUUuUUUAAGUGCUUCUUGCUUAAGCAAGUUUCAUCCCGACCCCCUCaGGGUCG 2025233
                               *****************************99************************************65555544****** PP

                                      NC
                               >>>>:: CS
               RF00014      80 GGauUU 85     
                               GGAUUU
  gi_545778205_gb_U000 2025232 GGAUUU 2025227
                               ****** PP

RNAfold
>gi_545778205_gb_U000_58
AAUCCCGACCCUGAGGGGGUCGGGAUGAAACUUGCUUAAGCAAGAAGCAC
UUAAAAAAUUCGUUACACCAGGAAAUCUGAUGUGUU
.(((((((((((...)))))))))))....(((((....)))))...................((((.(((.....))).)))).. (-29.70)

Length sequence

: 86

Length match:

85