Regulated Operon: ypuE-ribDEAHT

Genes
Genes Synonyms Direction Genome position Function COG ID Conserved groups
ypuE
- 2430519..2430671

 
ribD ribG - 2430258..2431343
COG1985H ribD-STA ribG-BAC ribG-BAC  
ribE ribB - 2429600..2430247
COG0307H  
ribA
- 2428389..2429585
COG0108H ribA-BAC ribA-STA  
ribH
- 2427892..2428356
COG0054H ribH-BAC-1 ribH-BAC-2 ribH-STA  
ribT ribD, ribD - 2426599..2426973 reductase
ribD-STA ribG-BAC ribD-STA ribG-BAC  

Operon evidence: Northern blotting (4.3 kb transcript); nuclease protection mapping of the 5' and 3' end
Reference: Mironov VN, et al. (1990), Azevedo V, et al. (1993), Mironov VN, et al. (1994), Perkins JB, et al., Mironov AS, et al. (2002), Genbank L09228
Comments: The 3' end of the mRNA was mapped 47 bp downstream of ribT in a T-rich region. Internal promoters in front of ribA and ribT, leading to a 2.4 kb and a 0.4 kb transcript. The original papers do not mention the existence of the ypuE gene, which partly overlaps ribD. The promoter site that was found experimentally for ribD lies upstream of ypuE. Azevedo also finds a 0.16 kb ypuE-specific transcript. Just upstream of ribD is a putative terminator/antiterminator structure. Binding of flavin mononucleotide or flavin adenine dinucleotide to the rfn (riboflavin) box favor transcriptional termination.


Promoters

Binding
factor
Regulation Location Absolute position Binding seq.(cis-element) Experimental evidence
SigA Promoter -43:+9 2431629..2431680 TATTTCATTGCGTACTTTAAAAAGGATCGCTATAATAACCAATAAGGACAAA Mironov VN, et al. (1994): NB S1
Perkins JB, et al. (1999): RG NB

Terminator

Terminator sequence Absolute position Position from stop codon Free energy
[kcal/mol]
Downstream of
TAAAATACCTAAAGCCCCGAATTTTTTATAAATTCGGGGCTTTTTTGACGGTAAA
             >>>>>>>>>>>     <<<<<<<<<<<
2431383..2431409
-890..-864
-19.6
ypuE
ATTAAGCAGAGGCTGTGATCAGTCTCTGCTTTTTTTTCTGCGTT
     >>>>>>>>>>    <<<<<<<<<<
2427381..2427404
488..511
-17.0
ribH

Overview



Upper Region






Copyright: Human Genome Center, Inst. Med. Sci., Univ. Tokyo; 1999-2008
Contact: Kenta Nakai