gi_545778205_gb_U000_103

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:

0.0045

From sequence:

2418515

To sequence:

2418633

Alignments:

                                  v            vvvvv                  v                      v           v vvvv  NC
                               :::<-<<<<<.....-<<<<<<<.......------<<<<<<<<<<----~~~~~~>>>>>>>>>>------>>>.>>>>- CS
               RF00512       1 CuggAgcugg.....uuucaugc.......cuCauacCGuccgcuaaauu*[40]*uggcggaCGgaAUUCAgca.ugaau 102    
                               CUG AG:U G           :C           U C G :::::A++U+      U::::: C G   UCAG:  ++   
  gi_545778205_gb_U000 2418515 CUGAAGGUGGgcgcg------ACccuacuuGGACUGCUGUUUAUUAUGUC*[ 8]*UAGUGAUCGGCGCUCAGUUgAUGGG 2418591
                               **********55443......34111113344445566666666655554...7..9999999999999999776356788 PP

                                     v                   v      v             NC
                               >>>>>->----------<<<<<<<<<<<____>>>>>>>>>>>::: CS
               RF00512     103 ccagcccacauuAaaaaaAAacCCGCGCuauUGCGCGGguUUuUUU 148    
                               C A:C  ++A++A+ ++AA:A:CCGC+  AUU  GCGG:U:UUUUU
  gi_545778205_gb_U000 2418592 CUACCACUAAAAAUGUUAAGAGCCGCA--AUU--GCGGCUCUUUUU 2418633
                               ***********************9985..555..899********* PP

>>

RNAfold
>gi_545778205_gb_U000_103
ACUUCCGUAACUGGCUGAAGGUGGGCGCGACCCUACUUGGACUGCUGUUU
AUUAUGUCCAGCGUCGUAGUGAUCGGCGCUCAGUUGAUGGGCUACCACUA
AAAAUGUUAAGAGCCGCAAUUGCGGCUCUUUUUUCAUUCUGCCGUUUC
........(((.(((.(((((((((......))))))(((((.............)))))((((((.......))))))....(((.(((....))).))).......(((((((((....)))))))))......))).)))))).. (-48.70)

Length sequence

: 148

Length match:

117