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

Genes
Genes Synonyms Direction Genome position Function COG ID Genus clusters
ptb yqiS, bkd - 2502957..2503856 phosphate butyryltransferase COG0280 x0587-CLO  
bcd bkd, yqiT - 2501851..2502945 leucine dehydrogenase COG0334  
buk yqiU, bkd - 2500741..2501832 branched-chain fatty-acid kinase (butyrate kinase) COG3426 x0742-CLO  
lpdV yqiV, bkd - 2499347..2500720 branched-chain alpha-keto acid dehydrogenase E3 subunit (dihydrolipoamide dehydrogenase) COG1249  
bkdAA bfmBAA, bfmB1a, bkd - 2498281..2499273 branched-chain alpha-keto acid dehydrogenase E1 subunit (2-oxoisovalerate dehydrogenase alpha subunit) COG1071 x0194-BAC bfmBAA-STA x0194-BAC  
bkdAB bfmBAB, bfmB1b, bkd - 2497284..2498267 branched-chain alpha-keto acid dehydrogenase E1 subunit (2-oxoisovalerate dehydrogenase beta subunit) COG0022 bkdAB-BAC bkdAB-BAC  
bkdB bfmBB, bfmB2, bkd - 2495987..2497261 branched-chain alpha-keto acid dehydrogenase E2 subunit (lipoamide acyltransferase) COG0508 bkdB-BAC 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 2503979..2504012 AATATGGCCTTGCAAATGAAGGCATGCAATAATT Debarbouille M, et al. (1999): DB
BkdR Positive -114:-81 2503965..2503998 AATGAAGGCATGCAATAATTTGCAGAATAAACGC Debarbouille M, et al. (1999): DB
BkdR Positive -93:-60 2503944..2503977 GCAGAATAAACGCAAACATCTGCACGAATGTTTC Debarbouille M, et al. (1999): DB
CodY Negative ND ND ND Debarbouille M, et al. (1999): RG
SigL Promoter -34:+8 2503877..2503918 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
 >>>>>>>>>>>>>>>>>>>>     <<<<<<<<<<<<<<<<<<<<
2495936..2495980
7..51
-27.3
bkdB

Overview



Upper Region






Copyright: Human Genome Center, Inst. Med. Sci., Univ. Tokyo; 1999-2006
Contact: Kenta Nakai