gi_545778205_gb_U000_483

cmsearch-Rfam

Family :

Trp_leader

Id:

RF00513

Type:

Cis-reg; leader;

Taxonomy:

Eukaryota; Bacteria;

Ontology:

Not found

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:

90.4

E-value:

9.1e-20

From sequence:

1323061

To sequence:

1322968

Alignments:

                                                                                                                 NC
                               ::::::::<<<<-<<<<<-<<<<____>>>>->>>>>-->>>>-----------------------------<<<<<<<<_ CS
               RF00513       1 CuuggUUGGUGgCgCACcUcccgaauucgggCgGUGuaauCACGuaUaucUguaaucAGaaaacagauACCaaGCCCGCua 81     
                                + GGUUGGUGGCGCAC:UCC:GAA  C:GGC:GUGUA+UCAC       UG  +++AG AA CAGAUACC AGCCCGC:+
  gi_545778205_gb_U000 1323061 AAAGGUUGGUGGCGCACUUCCUGAAA-CGGGCAGUGUAUUCACCA-----UGCGUAAAGCAAUCAGAUACCCAGCCCGCCU 1322987
                               **************************.****************99.....******************************* PP

                                                   NC
                               ___>->>>>>>>::::::: CS
               RF00513      82 auuaAGCGGGCuUUUUuaU 100    
                               A+U:AGCGGGCUUUUUU+U
  gi_545778205_gb_U000 1322986 AAUGAGCGGGCUUUUUUUU 1322968
                               ******************* PP

>>

RNAfold
>gi_545778205_gb_U000_483
UCAAAAAAAAGCCCGCUCAUUAGGCGGGCUGGGUAUCUGAUUGCUUUACG
CAUGGUGAAUACACUGCCCGUUUCAGGAAGUGCGCCACCAACCUUUCAG
.........((((((((.....))))))))((((.......(((.....)))(((((....((((..((......)).))))...)))))))))..... (-29.60)

Length sequence

: 99

Length match:

92