Regulated Operon: ptb-bcd-buk-lpdV-bkdAABB

Genes
Genes Synonyms Direction Genome position Function COG ID Conserved groups
ptb bkd - 2503765..2504664
COG0280C x0587-CLO  
bcd yqiT - 2502659..2503753
COG0334E  
buk bkd - 2501549..2502640
COG3426C x0742-CLO  
lpdV bkd - 2500104..2501528
COG1249C  
bkdAA bkd - 2499090..2500082
COG1071C x0194-BAC  
bkdAB bkd - 2498093..2499076
COG0022C bkdAB-BAC  
bkdB bkd - 2496796..2498070
COG0508C bkdB-BAC  

Operon evidence: Northern blotting (7.9 kb transcript)
Reference: Nickel M, et al. (2004), Wang GF, et al. (1993), Yoshida K, et al. (2003)
Comments: Northern blotting results in BSORF show various transcripts in this region. Northern blotting experiments by Yoshida et al. show a 8.7 kb bkdR-ptb-bcd-buk-lpdV-bkdAA-bkdAB transcript. Nickel also found a 10.2 kb bkdR-ptb-bcd-buk-lpdV-bkdAA-bkdAB-bkdB transcript due to readthrough at the terminator downstream of bkdR.

Promoters

Binding
factor		 Regulation Location Absolute position Binding seq.(cis-element) Experimental evidence
BkdR Positive -128:-95 2504787..2504820 AATATGGCCTTGCAAATGAAGGCATGCAATAATT Debarbouille M, et al. (1999): DB
BkdR Positive -114:-81 2504773..2504806 AATGAAGGCATGCAATAATTTGCAGAATAAACGC Debarbouille M, et al. (1999): DB
BkdR Positive -93:-60 2504752..2504785 GCAGAATAAACGCAAACATCTGCACGAATGTTTC Debarbouille M, et al. (1999): DB
CodY Negative ND ND ND Debarbouille M, et al. (1999): RG
SigL Promoter -34:+8 2504685..2504726 TAAGAGCTGGCATGGAACTTGCATAATAAAAGGCGGAGTCGA Debarbouille M, et al. (1999): PE
TnrA Negative ND ND ND Debarbouille M, et al. (1999): RG

Terminator

Terminator sequence Absolute position Position from stop codon Free energy
[kcal/mol]		 Downstream of
CAAAAAGAGCATTTTTTGAAGTTTTGTTTCAAAAAATGCTCTTTTTCTATGCTTTATT
 >>>>>>>>>>>>>>>>>>>>     <<<<<<<<<<<<<<<<<<<<
2496745..2496789
7..51
-27.3
 bkdB

Overview



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