RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: aldB
Synonym(s): OP00186
Gene(s): aldB   Genome Browser M3D Gene expression COLOMBOS
Evidence: [EXP-IEP] Inferred from expression pattern
[EXP-IEP-COREGULATION] Inferred through co-regulation
Reference(s): [1] Xu J., et al., 1995
Promoter
Name: aldBp
+1: 3756535
Sigma Factor: Sigma38 Sigmulon
Distance from start of the gene: 24
Sequence: gctgtcgtaaagctgttaccgactggcgaagatttcgccagtcacgtctacccttgttatAcctcacaccgcaaggagacg
                               -35                    -10   +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
[EXP-IEP]
Reference(s): [2] Huerta AM., et al., 2003
[1] Xu J., et al., 1995
Terminator(s)
Type: rho-independent
Sequence: tcaggttcccGTAGGCATGATAAGACGCGTAAGCGTCGCATCAGGCaatgaatacc
Note(s): A sequence with characteristics of a rho-independent transcription terminator within 54 bp downstream of the aldB stop codon is not present, although a repeated extragenic palindromic sequence is located 32 bp downstream of the stop codon.
Reference(s): [1] Xu J., et al., 1995
TF binding sites (TFBSs)
[CRP,+] 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 CRP-cyclic-AMP activator aldBp 3756585 3756606 -60.5 cttgcccgtaAATTCGTGATAGCTGTCGTAAAgctgttaccg nd [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [1]
[Fis,-] 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 Fis repressor aldBp 3756557 3756571 -29.0 gttaccgactGGCGAAGATTTCGCCagtcacgtct nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [3]
proximal Fis repressor aldBp 3756576 3756590 -48.0 tgatagctgtCGTAAAGCTGTTACCgactggcgaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [3]
remote Fis repressor aldBp 3756641 3756655 -113.0 cacaacggctGGCAAATTGTTAGCCgctttttcaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [3]
remote Fis repressor aldBp 3756663 3756677 -135.0 gcagcgatgtAATCATCATTTCCACaacggctggc nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [3]
remote Fis repressor aldBp 3756686 3756700 -158.0 aagaaattgtGGCGATTTATCGCGCagcgatgtaa nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [1], [3]


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: reverse
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -11.4 3756633 3756660 atttccacaaCGGCTGGCAAATTGTTAGCCGCTTTTTcaactatctc
  anti-terminator -13.84 3756654 3756724 ctaacccgatCCAGGCAACTCACGAAGAAATTGTGGCGATTTATCGCGCAGCGATGTAATCATCATTTCCACAACGGCTGgcaaattgtt
  anti-anti-terminator -5.2 3756684 3756704 cacgaagaaaTTGTGGCGATTTATCGCGCAgcgatgtaat
Notes: "The provided "Sequence" is that of the RNA strand, i.e. U's are shown instead of T's and regulators on the reverse strand will appear as the reverse complement of the sequence delimited by LeftPos-RigtPos"


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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

 [EXP-IEP] Inferred from expression pattern

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

 [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] Binding of purified proteins

 [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] Xu J., Johnson RC., 1995, aldB, an RpoS-dependent gene in Escherichia coli encoding an aldehyde dehydrogenase that is repressed by Fis and activated by Crp., J Bacteriol 177(11):3166-75

 [2] 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

 [3] Xu J., Johnson RC., 1995, Identification of genes negatively regulated by Fis: Fis and RpoS comodulate growth-phase-dependent gene expression in Escherichia coli., J Bacteriol 177(4):938-47

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