RegulonDB RegulonDB 10.10: Operon Form
   

exbBD operon and associated TUs in Escherichia coli K-12 genome




Operon      
Name: exbBD
This page displays every known transcription unit of this operon and their known regulation.


Transcription unit          
Name: exbD
Gene(s): exbD   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
Reference(s): [1] Ahmer BM., et al., 1995
[2] Eick-Helmerich K., et al., 1989
Promoter
Name: exbDp
+1: 3151390
Distance from start of the gene: 147
Sequence: ttagcaacggcaatcggcctcgtggcagcgattcctgcggtcgttatctataacgtatttGcacgccagattggcggcttt
Evidence: [HIPP]
Reference(s): [2] Eick-Helmerich K., et al., 1989
Terminator(s)
Type: rho-independent
Sequence: gttaaaaaaaTGCCCGGTTGTGAAAAGCAACCGGGcatcattgtg
Reference(s): [2] Eick-Helmerich K., et al., 1989
TF binding sites (TFBSs)
[Fur,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fur-Fe2+ repressor exbDp 3151427 3151445 -46.0 ctctgttagcAACGGCAATCGGCCTCGTGgcagcgattc nd [APIORCISFBSCS] [2]


Transcription unit          
Name: exbBD
Gene(s): exbD, exbB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [BTEI] Boundaries of transcription experimentally identified
[ITCR] Inferred through co-regulation
Reference(s): [1] Ahmer BM., et al., 1995
[2] Eick-Helmerich K., et al., 1989
Promoter
Name: exbBp
+1: 3152014
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 30
Sequence: atgcaaatagtaatgagaacgactatcaattcgacgtcgttttgatattattatgcgcagAttttgtgacttgcgtcctgg
                         -35                  -10           +1                   
Evidence: [HIPP]
[ICWHO]
Reference(s): [2] Eick-Helmerich K., et al., 1989
[3] Huerta AM., et al., 2003
Terminator(s)
Type: rho-independent
Sequence: gttaaaaaaaTGCCCGGTTGTGAAAAGCAACCGGGcatcattgtg
Reference(s): [2] Eick-Helmerich K., et al., 1989
TF binding sites (TFBSs)
[Fur,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence (Confirmed, Strong, Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal Fur-Fe2+ repressor exbBp 3152045 3152063 -40.0 tgcaaatagtAATGAGAACGACTATCAATtcgacgtcgt nd [APIORCISFBSCS], [BPP] [2], [4]
proximal Fur-Fe2+ repressor exbBp 3152051 3152069 -46.0 gcagtatgcaAATAGTAATGAGAACGACTatcaattcga nd [AIBSCS] nd


Evidence    

 [HIPP] Human inference of promoter position

 [APIORCISFBSCS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.

 [ICWHO] Inferred computationally without human oversight

 [BPP] Binding of purified proteins

 [AIBSCS] Automated inference based on similarity to consensus sequences


Reference(s)    

 [1] Ahmer BM., Thomas MG., Larsen RA., Postle K., 1995, Characterization of the exbBD operon of Escherichia coli and the role of ExbB and ExbD in TonB function and stability., J Bacteriol 177(16):4742-7

 [2] Eick-Helmerich K., Braun V., 1989, Import of biopolymers into Escherichia coli: nucleotide sequences of the exbB and exbD genes are homologous to those of the tolQ and tolR genes, respectively., J Bacteriol 171(9):5117-26

 [3] Huerta AM., Collado-Vides J., 2003, Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals., J Mol Biol 333(2):261-78

 [4] Chen Z., Lewis KA., Shultzaberger RK., Lyakhov IG., Zheng M., Doan B., Storz G., Schneider TD., 2007, Discovery of Fur binding site clusters in Escherichia coli by information theory models., Nucleic Acids Res 35(20):6762-77

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