RegulonDB RegulonDB 11.1: Operon Form
   

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




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


Transcription unit          
Name: paaXY
Gene(s): paaX, paaY   Genome Browser M3D Gene expression COLOMBOS
Note(s): Based on the improved computational program DTI (Direct Information criterion), which is an extension of the concept of MI that allows investigators to measure the direction of information flow between two random variables, and DTInfer, a new R-package for the inference of gene regulatory networks from microarrays based on directed information, the paaY gene was identified as a new target of PaaX based on a high Z-score Kaleta C,2010 The paaABCDEFGHIJK and paaXY operons might be cotranscribed Kaleta C,2010
Evidence: [EXP-IDA-BOUNDARIES-DEFINED] Boundaries of transcription experimentally identified
[EXP-IDA-TRANSCRIPT-LEN-DETERMINATION] Length of transcript experimentally determined
Reference(s): [1] Fernandez C., et al., 2014
[2] Ferrandez A., et al., 1998
Promoter
Name: paaXp
+1: 1463509
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 30
Sequence: ggccctggtggggtaaagcgccagggccagaagtcgatacgacctgtgctatgattcataAatcacaacaataacaacaga
                        -35                       -10       +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [2] Ferrandez A., et al., 1998
[3] Huerta AM., et al., 2003
TF binding sites (TFBSs)
[PaaX,-] 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 PaaX repressor paaXp 1463500 1463538 10.5 acctgtgctaTGATTCATAAATCACAACAATAACAACAGACTGAAGCGAatgagtaaac nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] nd [1]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [COMP-HINF-POSITIONAL-IDENTIFICATION] Human inference of promoter position

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

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

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


Reference(s)    

 [1] Fernandez C., Diaz E., Garcia JL., 2014, Insights on the regulation of the phenylacetate degradation pathway from Escherichia coli., Environ Microbiol Rep 6(3):239-50

 [2] Ferrandez A., Minambres B., Garcia B., Olivera ER., Luengo JM., Garcia JL., Diaz E., 1998, Catabolism of phenylacetic acid in Escherichia coli. Characterization of a new aerobic hybrid pathway., J Biol Chem 273(40):25974-86

 [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

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