gi_545778205_gb_U000_73

cmsearch-Rfam

Family :

His_leader

Id:

RF00514

Type:

Cis-reg; leader;

Taxonomy:

Eukaryota; Bacteria;

Ontology:

GO:0000105 histidine biosynthetic process

Description:

At least 6 amino acid operons are known to be regulated by attenuation [1]. In each
a leader sequence of 150-200 bp is found upstream of the first gene in the
operon. This leader sequence can assume two different secondary structures known as the terminator and
the anti-terminator structure. In each case the leader also codes for very short peptide sequence
that is rich in the end product amino acid of the operon. The terminator structure
is recognised as a termination signal for RNA polymerase and the operon is not transcribed.
This structure forms when the cell has an excess of the regulatory amino acid and
ribosome movement over the leader transcript is not impeded [1]. When there is a deficiency
of the charged tRNA of the regulatory amino acid the ribosome translating the leader peptide
stalls and the antiterminator structure can form. This allows RNA polymerase to transcribe the operon
[1]. In the Rfam alignment the consensus structure is of the terminator structure.

Score:

131.6

E-value:

7.4e-24

From sequence:

2090022

To sequence:

2090145

Alignments:

                                                                                                                 NC
                               :::::::<<<<<<<--<<<<<________>>>>>->>>>-->>><<<<<<<<________>>>>>>>>------------- CS
               RF00514       1 uCAUCAccAccAucAuCCuGacUAGUCUUuCaGGagaUguugUgcuGGaAGgcaauuAuacCUuCCagagugauauaaaAA 81     
                               +CAUCA+CACCAUCAUCCUGACUAGUCUUUCAGG+GAUGU GUGCUGGAAG:CA+U+A A:CUUCCAG  UG+U+ A++AA
  gi_545778205_gb_U000 2090022 CCAUCAUCACCAUCAUCCUGACUAGUCUUUCAGGCGAUGU-GUGCUGGAAGACAUUCAGAUCUUCCAG--UGGUGCAUGAA 2090099
                               ****************************************.***************************..*********** PP

                                                                              NC
                               ------<<<<<<<<<<<<<<<<_____>>>>>>>>>>>>>>>>::: CS
               RF00514      82 caaAuuaaaaAaCCCuCGGgaGAucAuCucCCGaGGGuUuuuuuuU 127    
                               C+ AU A:AAA:CCC:CGG:AGAUCA CU:CCG:GGG:UUU:UU+U
  gi_545778205_gb_U000 2090100 CGCAUGAGAAAGCCCCCGGAAGAUCACCUUCCGGGGGCUUUUUUAU 2090145
                               ********************************************** PP

>>

RNAfold
>gi_545778205_gb_U000_73
ACCAUCAUCACCAUCAUCCUGACUAGUCUUUCAGGCGAUGUGUGCUGGAA
GACAUUCAGAUCUUCCAGUGGUGCAUGAACGCAUGAGAAAGCCCCCGGAA
GAUCACCUUCCGGGGGCUUUUUUAUUG
((((....(((((((..(((((........))))).)))).)))((((((((........))))))))))))((......))(((((((((((((((((((.....))))))))))))))))))).. (-59.60)

Length sequence

: 127

Length match:

122