gi_545778205_gb_U000_108

cmsearch-Rfam

Family :

Leu_leader

Id:

RF00512

Type:

Cis-reg; leader;

Taxonomy:

Eukaryota; Bacteria;

Ontology:

GO:0009098 leucine 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. The alternative consensus
structure is the antiterminator structure.

Score:

26.6

E-value:

0.0044

From sequence:

4044210

To sequence:

4044059

Alignments:

                                  v   v v                     vv              vv                     v v   v     NC
                               :::<-<<<<<-<<<<<<<------<<<<<<<<<<------~~~~~~>>>>>>>>>>------>>>>>>>->>>>>->---- CS
               RF00512       1 CuggAgcugguuucaugccuCauacCGuccgcuaaauuag*[38]*uggcggaCGgaAUUCAgcaugaauccagcccacau 113    
                               CU    :+   :U:::::+ ++  C:G::::  :A+++A       :  ::::C:GAAU  A:::::A:U   : + A+ +
  gi_545778205_gb_U000 4044210 CUUACGUA-UCAUAUAAAUAUUCCCUGAUAAAACAGCAAA*[45]*GCAUUAUCAGAAUGUAUUUAUAUUU--AUUAAAUA 4044094
                               **976554.37******************98666655544...9..55689*****************994..45677888 PP

                                                                   NC
                               ------<<<<<<<<<<<____>>>>>>>>>>>::: CS
               RF00512     114 uAaaaaaAAacCCGCGCuauUGCGCGGguUUuUUU 148    
                               + AAAAAAA:CCCG:G   +U C:CGGG:UUU U 
  gi_545778205_gb_U000 4044093 AUAAAAAAAGCCCGUGAAUAUUCACGGGCUUUAUG 4044059
                               888888***************************** PP

>>

RNAfold
>gi_545778205_gb_U000_108
AUAAAGCCCGUGAAUAUUCACGGGCUUUUUUUAUUAUUUAAUAAAUAUAA
AUACAUUCUGAUAAUGCAUCCUGCCGCUGGACAUUAUUUCAGCAUAAGUG
GAUAUUCAAAGUUUUGCUGUUUUAUCAGGGAAUAUUUAUAUGAUACGUAA
G
..(((((((((((....)))))))))))................(((((((((..(((((((((.((((((....((((((......))))))......)))...............))).)))))))))..))))))))).......... (-40.60)

Length sequence

: 151

Length match:

150