RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: bamE
Gene(s): bamE   Genome Browser M3D Gene expression COLOMBOS
Promoter
Name: bamEp
+1: 2753486
Sigma Factor: Sigma24 Sigmulon
Distance from start of the gene: 119
Sequence: ggcgaatgcgaaagaactgcttgcagcgtaaacttttttcctgcttcacggtcagagtaaAcagcaaaacgccgtaagacc
                              -35                   -10     +1                   
Note(s): This promoter appears to be induced in two phases after σE induction. It is induced during the first 5 minutes folowing σE induction, decreased from 5 to 10 minutes, and induced from 10 to 20 minutes Lacoux C,2020.
Evidence: [COMP-AINF]
[COMP-AINF-POSITIONAL-IDENTIFICATION]
[COMP-AINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Huerta AM., et al., 2003
[2] Rezuchova B., et al., 2003
[3] Rhodius VA., et al., 2005
TF binding sites (TFBSs)
[CpxR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
proximal CpxR-phosphorylated repressor bamEp 2753495 2753496 11.0 acagcaaaacGccgtaagacc nd [COMP] nd [4]
[NsrR,-] Phrase
Type Transcription factor Function Promoter Binding Sites Growth Conditions Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) Reference(s)
LeftPos RightPos Central Rel-Pos Sequence
remote NsrR repressor bamEp 2753547 2753558 67.0 gtctattatcATCGGCATATTAcagatgagcc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [5]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-AINF-POSITIONAL-IDENTIFICATION] Automated inference of promoter position

 [COMP-AINF-SIMILAR-TO-CONSENSUS] Automated inference based on similarity to consensus sequences

 [EXP-IDA-TRANSCRIPTION-INIT-MAPPING] Transcription initiation mapping

 [COMP] Inferred by computational analysis

 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis

 [COMP-HINF-SIMILAR-TO-CONSENSUS] A person inferred or reviewed a computer inference of sequence function based on similarity to a consensus sequence.


Reference(s)    

 [1] 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

 [2] Rezuchova B., Miticka H., Homerova D., Roberts M., Kormanec J., 2003, New members of the Escherichia coli sigmaE regulon identified by a two-plasmid system., FEMS Microbiol Lett 225(1):1-7

 [3] Rhodius VA., Suh WC., Nonaka G., West J., Gross CA., 2005, Conserved and variable functions of the sigmaE stress response in related genomes., PLoS Biol 4(1):e2

 [4] De Wulf P., McGuire AM., Liu X., Lin EC., 2002, Genome-wide profiling of promoter recognition by the two-component response regulator CpxR-P in Escherichia coli., J Biol Chem 277(29):26652-61

 [5] Partridge JD., Bodenmiller DM., Humphrys MS., Spiro S., 2009, NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility., Mol Microbiol 73(4):680-94

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