RegulonDB RegulonDB 11.2: Operon Form
   

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




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


Transcription unit          
Name: ppiD
Gene(s): ppiD   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: ppiDp2
+1: 461819
Sigma Factor: Sigma70 Sigmulon
Distance from start of the gene: 96
Sequence: ggcgcatctactgatgtgccttttttatttgtattcggtgactttctgcgtcttgtgggcTgacaattgcccccgtttctt
                             -35                   -10      +1                   
Evidence: [COMP-AINF]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Dartigalongue C., et al., 1998
[2] Huerta AM., et al., 2003
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
remote CpxR-phosphorylated activator ppiDp2 461653 461654 -165.0 ccggtaaagaGatcaccatcg nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] nd [1]
remote CpxR-phosphorylated activator ppiDp2 461701 461702 -117.0 caggtaaagcActgaaagacg nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] nd [1]
remote CpxR-phosphorylated activator ppiDp2 461715 461731 -96.5 gaaagacgcgGTAAACTAAGCGTTGTCcccagtgggg nd [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] nd [1]


Transcription unit       
Name: ppiD
Gene(s): ppiD   Genome Browser M3D Gene expression COLOMBOS
Evidence: [COMP-AINF] Inferred computationally without human oversight
Promoter
Name: ppiDp1
+1: 461838
Sigma Factor: Sigma32 Sigmulon
Distance from start of the gene: 77
Sequence: cttttttatttgtattcggtgactttctgcgtcttgtgggctgacaattgcccccgtttcTtgtcacaataggcctttgcg
                                  -35               -10     +1                   
Evidence: [COMP-AINF]
[COMP-HINF-POSITIONAL-IDENTIFICATION]
[COMP-HINF-SIMILAR-TO-CONSENSUS]
[EXP-IDA-TRANSCRIPTION-INIT-MAPPING]
Reference(s): [1] Dartigalongue C., et al., 1998
[2] Huerta AM., et al., 2003


RNA cis-regulatory element    
Regulation, transcriptional elongation  
Attenuator type: Transcriptional
Strand: forward
  Structure type Energy LeftPos RightPos Sequence (RNA-strand)
  terminator -15.7 461756 461788 acgaagttcaAGGGCGCATCTACTGATGTGCCTTTTTTATTTgtattcggtg
  anti-terminator -10.46 461724 461763 gtaaactaagCGTTGTCCCCAGTGGGGATGTGACGAAGTTCAAGGGCGCatctactgat
  anti-anti-terminator -10.6 461701 461738 caggtaaagcACTGAAAGACGCGGTAAACTAAGCGTTGTCCCCAGTGgggatgtgac
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

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

 [EXP-IMP-SITE-MUTATION] Site mutation

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


Reference(s)    

 [1] Dartigalongue C., Raina S., 1998, A new heat-shock gene, ppiD, encodes a peptidyl-prolyl isomerase required for folding of outer membrane proteins in Escherichia coli., EMBO J 17(14):3968-80

 [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

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