gi_545778205_gb_U000_348

cmsearch-Rfam

Family :

Thr_leader

Id:

RF00506

Type:

Cis-reg; leader;

Taxonomy:

Eukaryota; Bacteria;

Ontology:

GO:0009088 threonine 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:

28.9

E-value:

0.0046

From sequence:

2700538

To sequence:

2700595

Alignments:

                                                                  vv         vv               NC
                               :::<<~~~~~~---->>-----<<<<<<<<<<<<<<<<_______>>>>>>>>>>>>>>>>: CS
               RF00506       1 acauc*[62]*ACAggaaAcacagAAAAAAGCCCGCacCUaaacAguGCGGGCUUUUUUuuu 118    
                               ACA::      A AG:: A A A: AAAA: CCCG  CCU A CAG  CGGG :UUUU :UU
  gi_545778205_gb_U000 2700538 ACAAA*[ 3]*AAAGUU-AAAAAGUAAAACCCCCGUUCCUUACCAGUUCGGGGGUUUUACUU 2700595
                               ***99...6..445555.5569**************************************** PP

>>

RNAfold
>gi_545778205_gb_U000_348
UAAUCGCUGUUGUUGAGGGUGCAUGCUGCACAAAAUUAAAGUUAAAAAGU
AAAACCCCCGUUCCUUACCAGUUCGGGGGUUUUACUUUUUAAAGAGAACG
GUAUUAUUUUUAACUUU
.....((((((.((....(((((...)))))..........(((((((((((((((((((..(.......)..))))))))))))))))))).)).))))))............... (-38.40)

Length sequence

: 117

Length match:

56