gi_545778205_gb_U000_350

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:

28.7

E-value:

0.0051

From sequence:

4051336

To sequence:

4051241

Alignments:

                                   vv v  vv                        vv  v v     v      v                          NC
                               :::<<<<<-<<<<<--<<.<<~~~~~~>>>>--->>>>>->>>----->>-----<<<<<<<<<<<<<<<<_______>>> CS
               RF00506       1 acauccGCaucAgcACca.cc*[30]*ggugCGGgcUgacGCguACAggaaAcacagAAAAAAGCCCGCacCUaaacAguG 104    
                                + U  G     ::A :: ::      ::::CGG::     C  A AG AA CA  :AAAAAAG C::CA: U  AC :UG
  gi_545778205_gb_U000 4051336 CUUUUAGCCGUUUUAUUCaGU*[ 8]*GCGGCGGAAUCUAACAGAAAGCAAGCAAAGAAAAAAGGCGACAGAUU-ACUCUG 4051255
                               *****9999999999754255...7..55889*****************************************9.999*** PP

                                           v  NC
                               >>>>>>>>>>>>>: CS
               RF00506     105 CGGGCUUUUUUuuu 118    
                               ::G CUUUUUU: U
  gi_545778205_gb_U000 4051254 UCGCCUUUUUUCCU 4051241
                               ************** PP

>>

RNAfold
>gi_545778205_gb_U000_350
GUUAUGAGUCAGGAAAAAAGGCGACAGAGUAAUCUGUCGCCUUUUUUCUU
UGCUUGCUUUCUGUUAGAUUCCGCCGCAAAUCUAUACUGAAUAAAACGGC
UAAAAGACGAACCAUUA
.....((((.((((((((((((((((((....)))))))))))))))))).))))((((((.((((((((........)))))).)).)))......)))................. (-37.20)

Length sequence

: 117

Length match:

94