RegulonDB RegulonDB 11.2:Regulon Page
   

OmpR DNA-binding transcriptional dual regulator

Synonyms: OmpR-phosphorylated, OmpR


Transcription factor      
TF conformation(s):
Name Conformation Type TF-Effector Interaction Type Apo/Holo Conformation Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
OmpR Functional   Apo nd nd nd
OmpR-phosphorylated Functional Covalent Holo nd nd nd
TFBs length: 20
TFBs symmetry: direct-repeat
Sensing class: External-Two-component systems
Connectivity class: Local Regulator
Gene name: ompR
  Genome position: 3535865-3536584
  Length: 720 bp / 239 aa
Operon name: ompR-envZ
TU(s) encoding the TF:
Transcription unit        Promoter
ompR-envZ
ompRp1
ompR-envZ
ompRp2
ompR-envZ
ompRp3
ompR-envZ
ompRp4


Regulon       
Regulated gene(s) bolA, cadA, cadB, cadC, csgD, csgE, csgF, csgG, dtpA, ecnB, fadL, feoA, feoB, feoC, flhC, flhD, micF, nmpC, ompC, ompF, omrA, omrB, pgaA, pgaB, pgaC, pgaD, sra
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
Transcription related (5)
activator (5)
repressor (4)
membrane (4)
Beta barrel porins (The Outer Membrane Porin (OMP) Functional Superfamily) (4)
Read more >
Regulated operon(s) bdm-sra, bolA, cadBA, cadC, csgDEFG, dtpA, ecnAB, fadL, feoABC, flhDC, micF, nmpC, ompC, ompF, omrA, omrB, pgaABCD
First gene in the operon(s) bolA, cadB, cadC, csgD, ecnB, fadL, feoA, flhD, micF, ompC, ompF, omrA, omrB, pgaA, sra, dtpA
Simple and complex regulons AcrR,CRP,FliZ,Fur,H-NS,HdfR,IHF,LrhA,MatA,OmpR,QseB,RcsAB,YjjQ
AcrR,H-NS,HU,IHF,Lrp,MarA,OmpR,Rob,SoxS
ArcA,CRP,FadR,OmpR,PhoP,Rob,ppGpp
ArcA,CadC,GadE-RcsB,GadX,H-NS,Lrp,OmpR
BasR,BolA,BtsR,CRP,CpxR,Cra,CsgD,FliZ,H-NS,IHF,MlrA,MqsA,OmpR,RcdA,RcsAB,RstA,ppGpp
Read more >
Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[OmpR,-](12)
[OmpR,+](11)


Transcription factor regulation    


Transcription factor binding sites (TFBSs) arrangements
      

  Functional conformation Function Promoter Sigma factor Central Rel-Pos Distance to first Gene Genes Sequence
 LeftPos RightPos Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
  OmpR-phosphorylated repressor bolAp Sigma38 -47.5 -85.5 bolA
aggacgaaacCTAAATATTTGTTGTTAAGCtgcaatggaa
 454377 454396 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1]
  OmpR-phosphorylated repressor bolAp1 Sigma70 -47.5 -85.5 bolA
aggacgaaacCTAAATATTTGTTGTTAAGCtgcaatggaa
 454377 454396 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [1], [1]
  OmpR repressor cadBp Sigma70 nd nd cadB, cadA
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2]
  OmpR repressor cadCp Sigma70 nd nd cadC
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2]
  OmpR-phosphorylated activator csgDp1 Sigma70 -49.5 -197.5 csgD, csgE, csgF, csgG
aatataacgaGTTACATTTAGTTACATGTTtaacacttga
 1103384 1103403 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [3], [3], [4], [4], [5], [6], [7]
  OmpR-phosphorylated activator csgDp3 Sigma38 -49.5 -197.5 csgD, csgE, csgF, csgG
aatataacgaGTTACATTTAGTTACATGTTtaacacttga
 1103384 1103403 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [3], [3], [4], [4], [5], [6], [7]
  OmpR-phosphorylated repressor ecnBp Sigma38 18.5 -26.5 ecnB
tttgctatagGCAAACATAAATAACATTACctaaaaggaa
 4376517 4376536 [COMP-HINF-SIMILAR-TO-CONSENSUS] W [8], [8]
  OmpR-phosphorylated repressor fadLp Sigma38 -149.5 -250.5 fadL
gataagtgacCGAAATCACACTTAAAAATGatctaaaaca
 2461046 2461065 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] S [9], [10]
  OmpR-phosphorylated repressor fadLp Sigma38 -60.5 -161.5 fadL
atcgcgtttcTTAGATCATATTTGAAAAAAgatagaaaca
 2461135 2461154 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [10], [10]
  OmpR-phosphorylated repressor fadLp Sigma38 69.5 -32.5 fadL
gttacagcacGTAACATAGTTTGTATAAAAataaatcatt
 2461264 2461283 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [10], [10]
  OmpR-phosphorylated repressor fadLp Sigma38 119.5 18.5 fadL
tcatgagccaGAAAACCCTGTTTACAAAGTctgctctcgc
 2461314 2461333 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [10], [10]
  OmpR-phosphorylated activator feoAp Sigma70 -178.0 -284.0 feoA, feoB, feoC
ccggcaatatTTATCATTTCATTAACAACTgaaaccttaa
 3539869 3539888 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [11], [11]
  OmpR-phosphorylated repressor flhDp Sigma70 -145.5 -343.5 flhD, flhC
caaagtcatcGGGCATTATCTGAACATAAAacactatcaa
 1978531 1978550 [COMP-HINF-SIMILAR-TO-CONSENSUS] W [12]
  OmpR-phosphorylated repressor flhDp Sigma70 18.5 -180.5 flhD, flhC
tcgatttaggAAAAATCTTAGATAAGTGTAaagacccatt
 1978368 1978387 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-DAP-SEQ] W [6], [7], [12]
  OmpR-phosphorylated activator micFp1 Sigma70 -206.5 -206.5 micF
atccaacacgAATATGATACTAAAACTTTTaagatgtttc
 2312868 2312887 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [13], [14], [14], [15], [16], [17], [17]
  OmpR-phosphorylated activator micFp1 Sigma70 -186.5 -186.5 micF
taaaacttttAAGATGTTTCATTTATCGCTatagatgttt
 2312888 2312907 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [7], [13], [14], [14], [15], [17], [17], [18]
  OmpR-phosphorylated activator micFp1 Sigma70 -165.5 -165.5 micF
tttatcgctaTAGATGTTTCAAAATGTAAAtgcaagggaa
 2312909 2312928 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [7], [11], [11], [13], [14], [14], [15], [17], [18]
  OmpR-phosphorylated activator micFp2 Sigma38 -206.5 -206.5 micF
atccaacacgAATATGATACTAAAACTTTTaagatgtttc
 2312868 2312887 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [13], [14], [14], [15], [16], [17], [17]
  OmpR-phosphorylated activator micFp2 Sigma38 -186.5 -186.5 micF
taaaacttttAAGATGTTTCATTTATCGCTatagatgttt
 2312888 2312907 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [7], [13], [14], [14], [15], [17], [17], [18]
  OmpR-phosphorylated activator micFp2 Sigma38 -165.5 -165.5 micF
tttatcgctaTAGATGTTTCAAAATGTAAAtgcaagggaa
 2312909 2312928 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [7], [11], [11], [13], [14], [14], [15], [17], [18]
  OmpR-phosphorylated repressor nmpCp nd -45.5 nd nmpC
aatcaaacgaGAAACCAAAACTTACATCTTgaaataatca
 576906 576925 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-DAP-SEQ], [EXP-IMP-SITE-MUTATION] S [6], [7], [19], [19]
  OmpR-phosphorylated activator ompCp1 Sigma70 -88.5 -169.5 ompC
ttcccttgcaTTTACATTTTGAAACATCTAtagcgataaa
 2312909 2312928 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [7], [11], [11], [13], [14], [14], [15], [17], [18], [20]
  OmpR-phosphorylated activator ompCp1 Sigma70 -67.5 -148.5 ompC
aaacatctatAGCGATAAATGAAACATCTTaaaagtttta
 2312888 2312907 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [7], [13], [14], [14], [15], [17], [17], [18], [20]
  OmpR-phosphorylated activator ompCp1 Sigma70 -47.5 -128.5 ompC
gaaacatcttAAAAGTTTTAGTATCATATTcgtgttggat
 2312868 2312887 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [13], [14], [14], [15], [16], [17], [17], [20]
  OmpR-phosphorylated repressor ompFp Sigma70 -370.5 -480.5 ompF
cgatcatcctGTTACGGAATATTACATTGCaacatttacg
 987453 987472 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [6], [17], [17], [20], [21], [21], [22], [22], [23], [23]
  OmpR-phosphorylated activator ompFp Sigma70 -90.5 -200.5 ompF
ttccttaaatTTTACTTTTGGTTACATATTttttcttttt
 987173 987192 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [7], [14], [14], [16], [17], [17], [18], [24], [25], [26], [27]
  OmpR-phosphorylated activator ompFp Sigma70 -70.5 -180.5 ompF
gttacatattTTTTCTTTTTGAAACCAAATctttatcttt
 987153 987172 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [7], [14], [14], [16], [17], [17], [18], [18], [20], [24], [25], [26], [27], [28], [28], [29]
  OmpR-phosphorylated repressor ompFp Sigma70 -70.5 -180.5 ompF
gttacatattTTTTCTTTTTGAAACCAAATctttatcttt
 987153 987172 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [7], [14], [14], [16], [17], [17], [18], [18], [20], [24], [25], [26], [27], [28], [28], [29]
  OmpR-phosphorylated activator ompFp Sigma70 -50.5 -160.5 ompF
gaaaccaaatCTTTATCTTTGTAGCACTTTcacggtagcg
 987133 987152 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [14], [14], [16], [17], [17], [18], [18], [21], [21], [22], [22], [23], [23], [24], [25], [26], [27], [28], [28]
  OmpR-phosphorylated repressor ompFp Sigma70 -50.5 -160.5 ompF
gaaaccaaatCTTTATCTTTGTAGCACTTTcacggtagcg
 987133 987152 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [14], [14], [16], [17], [17], [18], [18], [21], [21], [22], [22], [23], [23], [24], [25], [26], [27], [28], [28]
  OmpR-phosphorylated repressor ompFp2 Sigma38 -370.5 -480.5 ompF
cgatcatcctGTTACGGAATATTACATTGCaacatttacg
 987453 987472 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [6], [17], [17], [20], [21], [21], [22], [22], [23], [23]
  OmpR-phosphorylated activator ompFp2 Sigma38 -90.5 -200.5 ompF
ttccttaaatTTTACTTTTGGTTACATATTttttcttttt
 987173 987192 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [7], [14], [14], [16], [17], [17], [18], [24], [25], [26], [27]
  OmpR-phosphorylated activator ompFp2 Sigma38 -70.5 -180.5 ompF
gttacatattTTTTCTTTTTGAAACCAAATctttatcttt
 987153 987172 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [7], [14], [14], [16], [17], [17], [18], [18], [20], [24], [25], [26], [27], [28], [28], [29]
  OmpR-phosphorylated repressor ompFp2 Sigma38 -70.5 -180.5 ompF
gttacatattTTTTCTTTTTGAAACCAAATctttatcttt
 987153 987172 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [7], [14], [14], [16], [17], [17], [18], [18], [20], [24], [25], [26], [27], [28], [28], [29]
  OmpR-phosphorylated activator ompFp2 Sigma38 -50.5 -160.5 ompF
gaaaccaaatCTTTATCTTTGTAGCACTTTcacggtagcg
 987133 987152 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [14], [14], [16], [17], [17], [18], [18], [21], [21], [22], [22], [23], [23], [24], [25], [26], [27], [28], [28]
  OmpR-phosphorylated repressor ompFp2 Sigma38 -50.5 -160.5 ompF
gaaaccaaatCTTTATCTTTGTAGCACTTTcacggtagcg
 987133 987152 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [6], [14], [14], [16], [17], [17], [18], [18], [21], [21], [22], [22], [23], [23], [24], [25], [26], [27], [28], [28]
  OmpR-phosphorylated activator omrAp nd -70.5 -70.5 omrA
accgacaattTACACACCTCGTTGCATTTCccttcattcc
 2976250 2976269 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [6], [30], [30]
  OmpR-phosphorylated activator omrBp nd -71.5 -71.5 omrB
aaagagattgCAAACCTTTGGTTACACTTTgcgaaacgct
 2976447 2976466 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-CHIP-SEQ] S [6], [30], [30]
  OmpR-phosphorylated repressor pgaAp nd -31.5 -265.5 pgaA, pgaB, pgaC, pgaD
tgcatcggaaTTTACTGATTTAATTATTTTaatcctaatt
 1092545 1092564 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [31], [31]
  OmpR-phosphorylated repressor srap Sigma38 nd nd sra
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [32]
  OmpR-phosphorylated activator tppBp Sigma70 -45.5 -143.5 dtpA
tcagttatatGTAACAGATTATTACAAAGGacttgtctga
 1712616 1712635 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-CHIP-SEQ], [EXP-DAP-SEQ], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] C [6], [7], [33], [33]



High-throughput Transcription factor binding sites (TFBSs)
      

  Functional conformation Function Object name Object type Distance to first Gene Sequence LeftPos RightPos Center Position Growth Condition Evidence Confidence level (C: Confirmed, S: Strong, W: Weak) References
  OmpR repressor speF-potE Transcription-Unit nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [2]
  OmpR-phosphorylated activator sstT Gene nd
aaacactttgTTACATCCTGAAAGATGCGTCgacagaacgc
3239875 3239895 3239884.5 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ], [EXP-DAP-SEQ], [EXP-GSELEX] S [34]
  OmpR-phosphorylated activator rob Gene nd
gtaatagataAAAATGGTAACAATATGAAATacaagcattt
4635507 4635527 4635516.5 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-GSELEX] S [34]
  OmpR-phosphorylated activator fadE Gene nd
gtggatgtaaAAACATTTAGCAATATGTTTAcaatataatt
243369 243389 243378.5 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ], [EXP-GSELEX] S [34]
  OmpR-phosphorylated activator acrR Gene nd
acatacattcACAAATGTATGTAAATCTAACgcctgtaaat
485720 485740 485729.5 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-GSELEX] S [34]
  OmpR-phosphorylated activator rhtA Gene nd
gagtttcccaTTAATTTTTGATATATTTAAAacttaggact
850394 850414 850403.5 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ], [EXP-GSELEX] S [34]
  OmpR-phosphorylated activator pdhR Gene nd
ctttgaaacgTTATATATGTCAAGTTGTTAAaatgtgcaca
121941 121961 121950.5 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-GSELEX] S [34]
  OmpR-phosphorylated activator ompX Gene nd
gagtttcccaTTAATTTTTGATATATTTAAAacttaggact
850394 850414 850403.5 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ], [EXP-GSELEX] S [34]
  OmpR-phosphorylated activator gmhA Gene nd
gtggatgtaaAAACATTTAGCAATATGTTTAcaatataatt
243369 243389 243378.5 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ], [EXP-GSELEX] S [34]
  OmpR-phosphorylated activator tolC Gene nd
taatttctacATCGTTTTTGCCAAATGTAACgggcaggttg
3177866 3177886 3177875.5 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-GSELEX] S [34]
  OmpR-phosphorylated activator tsgA Gene nd
tacctaatttTACGTATCTGAAATATATGTAacctgacgat
3492387 3492407 3492396.5 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-GSELEX] S [34]
  OmpR-phosphorylated activator narU Gene nd
aagtagccagATATGTGTTACTAAATGTAACtaacaagcta
1544223 1544243 1544232.5 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-CHIP-SEQ], [EXP-DAP-SEQ], [EXP-GSELEX] S [34]
  OmpR-phosphorylated repressor lpp Gene nd
tcaacataaaAAACTTTGTGTAATACTTGTAacgctacatg
1757360 1757380 1757369.5 nd [EXP-IEP-MICROARRAY], [COMP-AINF-PATTERN-DISCOVERY], [EXP-GSELEX] S [34]
Other High-throughput regulatory interactions with weak evidence


Alignment and PSSM for OmpR TFBSs    

Aligned TFBS of OmpR   
  Sequence
  AATATGTAACCAAAAGTAAAAT
  AACATGTAACTAAATGTAACTC
  AACGAGAAACCAAAACTTACAT
  AAAGTGTAACCAAAGGTTTGCA
  AATATGATACTAAAACTTTTAA
  TATATGTAACAGATTATTACAA
  TAGATGTTTCAAAATGTAAATG
  ATCCTGTTACGGAATATTACAT
  GAAATGCAACGAGGTGTGTAAA
  AAAGTGCTACAAAGATAAAGAT
  TATAGGCAAACATAAATAACAT
  ATTTGGTTTCAAAAAGAAAAAA
  AGCACGTAACATAGTTTGTATA
  TACACTTATCTAAGATTTTTCC
  TATCTTTTTTCAAATATGATCT
  TGACCGAAATCACACTTAAAAA
  GCAGCTTAACAACAAATATTTA
  TTAAAATAATTAAATCAGTAAA
  ACTTTGTAAACAGGGTTTTCTG
  GGGCATTATCTGAACATAAAAC
  TCTATAGCGATAAATGAAACAT

Position weight matrix (PWM). OmpR matrix-quality result    
A	10	12	6	11	3	2	3	14	15	3	6	17	16	15	8	6	4	10	13	8	13	9
C	0	3	5	4	4	0	3	1	0	15	7	0	2	0	2	3	0	0	0	7	3	3
G	3	3	2	4	2	15	1	0	1	0	2	3	2	5	2	7	0	4	0	2	0	2
T	8	3	8	2	12	4	14	6	5	3	6	1	1	1	9	5	17	7	8	4	5	7

Consensus    
;	consensus.strict             	aatatGtaaCcaaatgtaacaa
;	consensus.strict.rc          	TTGTTACATTTGGTTACATATT
;	consensus.IUPAC              	wayatGtaaCcaarwgtwwmaw
;	consensus.IUPAC.rc           	WTKWWACWYTTGGTTACATRTW
;	consensus.regexp             	[at]a[ct]atGtaaCcaa[ag][at]gt[at][at][ac]a[at]
;	consensus.regexp.rc          	[AT]T[GT][AT][AT]AC[AT][CT]TTGGTTACAT[AG]T[AT]

PWM logo   


 


Evolutionary conservation of regulatory elements    
     Note: Evolutionary conservation of regulatory interactions and promoters is limited to gammaproteobacteria.
TF-target gene evolutionary conservation
Promoter-target gene evolutionary conservation


Evidence    

 [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

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

 [EXP-CHIP-SEQ] high throughput ChIP-seq evidence

 [EXP-DAP-SEQ] high throughput DNA Affinity Purification (DAP) Sequencing

 [EXP-IMP-SITE-MUTATION] Site mutation

 [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] Binding of cellular extracts

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

 [EXP-IEP-MICROARRAY] high throughput expression microarray evidence

 [COMP-AINF-PATTERN-DISCOVERY] Automated inference based on sequence pattern discovery

 [EXP-GSELEX] high throughput Genomic SELEX-chip evidence


Reference(s)    

 [1] Yamamoto K., Nagura R., Tanabe H., Fujita N., Ishihama A., Utsumi R., 2000, Negative regulation of the bolA1p of Escherichia coli K-12 by the transcription factor OmpR for osmolarity response genes., FEMS Microbiol Lett 186(2):257-62

 [2] Chakraborty S., Winardhi RS., Morgan LK., Yan J., Kenney LJ., 2017, Non-canonical activation of OmpR drives acid and osmotic stress responses in single bacterial cells., Nat Commun 8(1):1587

 [3] Jubelin G., Vianney A., Beloin C., Ghigo JM., Lazzaroni JC., Lejeune P., Dorel C., 2005, CpxR/OmpR interplay regulates curli gene expression in response to osmolarity in Escherichia coli., J Bacteriol 187(6):2038-49

 [4] Ogasawara H., Yamada K., Kori A., Yamamoto K., Ishihama A., 2010, Regulation of the Escherichia coli csgD promoter: interplay between five transcription factors., Microbiology 156(Pt 8):2470-83

 [5] Prigent-Combaret C., Brombacher E., Vidal O., Ambert A., Lejeune P., Landini P., Dorel C., 2001, Complex regulatory network controls initial adhesion and biofilm formation in Escherichia coli via regulation of the csgD gene., J Bacteriol 183(24):7213-23

 [6] Aquino P., Honda B., Jaini S., Lyubetskaya A., Hosur K., Chiu JG., Ekladious I., Hu D., Jin L., Sayeg MK., Stettner AI., Wang J., Wong BG., Wong WS., Alexander SL., Ba C., Bensussen SI., Bernstein DB., Braff D., Cha S., Cheng DI., Cho JH., Chou K., Chuang J., Gastler DE., Grasso DJ., Greifenberger JS., Guo C., Hawes AK., Israni DV., Jain SR., Kim J., Lei J., Li H., Li D., Li Q., Mancuso CP., Mao N., Masud SF., Meisel CL., Mi J., Nykyforchyn CS., Park M., Peterson HM., Ramirez AK., Reynolds DS., Rim NG., Saffie JC., Su H., Su WR., Su Y., Sun M., Thommes MM., Tu T., Varongchayakul N., Wagner TE., Weinberg BH., Yang R., Yaroslavsky A., Yoon C., Zhao Y., Zollinger AJ., Stringer AM., Foster JW., Wade J., Raman S., Broude N., Wong WW., Galagan JE., 2017, Coordinated regulation of acid resistance in Escherichia coli., BMC Syst Biol 11(1):1

 [7] Baumgart LA, Lee JE, Salamov A, Dilworth DJ, Na H, Mingay M, Blow MJ, Zhang Y, Yoshinaga Y, Daum CG, O'Malley RC, 2021, Persistence and plasticity in bacterial gene regulation., Nat Methods, 18(12):1499 10.1038/s41592-021-01312-2

 [8] Bishop RE., Leskiw BK., Hodges RS., Kay CM., Weiner JH., 1998, The entericidin locus of Escherichia coli and its implications for programmed bacterial cell death., J Mol Biol 280(4):583-96

 [9] Black PN., 1991, Primary sequence of the Escherichia coli fadL gene encoding an outer membrane protein required for long-chain fatty acid transport., J Bacteriol 173(2):435-42

 [10] Higashitani A., Nishimura Y., Hara H., Aiba H., Mizuno T., Horiuchi K., 1993, Osmoregulation of the fatty acid receptor gene fadL in Escherichia coli., Mol Gen Genet 240(3):339-47

 [11] Gerken H., Vuong P., Soparkar K., Misra R., 2020, Roles of the EnvZ/OmpR Two-Component System and Porins in Iron Acquisition in Escherichia coli., mBio 11(3)

 [12] Shin S., Park C., 1995, Modulation of flagellar expression in Escherichia coli by acetyl phosphate and the osmoregulator OmpR., J Bacteriol 177(16):4696-702

 [13] Coyer J., Andersen J., Forst SA., Inouye M., Delihas N., 1990, micF RNA in ompB mutants of Escherichia coli: different pathways regulate micF RNA levels in response to osmolarity and temperature change., J Bacteriol 172(8):4143-50

 [14] Mattison K., Oropeza R., Byers N., Kenney LJ., 2002, A phosphorylation site mutant of OmpR reveals different binding conformations at ompF and ompC., J Mol Biol 315(4):497-511

 [15] Miyake Y., Yamamoto K., 2020, Epistatic Effect of Regulators to the Adaptive Growth of Escherichia coli., Sci Rep 10(1):3661

 [16] Qin L., Yoshida T., Inouye M., 2001, The critical role of DNA in the equilibrium between OmpR and phosphorylated OmpR mediated by EnvZ in Escherichia coli., Proc Natl Acad Sci U S A 98(3):908-13

 [17] Yoshida T., Qin L., Egger LA., Inouye M., 2006, Transcription regulation of ompF and ompC by a single transcription factor, OmpR., J Biol Chem 281(25):17114-23

 [18] Tsung K., Brissette RE., Inouye M., 1989, Identification of the DNA-binding domain of the OmpR protein required for transcriptional activation of the ompF and ompC genes of Escherichia coli by in vivo DNA footprinting., J Biol Chem 264(17):10104-9

 [19] Coll JL., Heyde M., Portalier R., 1994, Expression of the nmpC gene of Escherichia coli K-12 is modulated by external pH. Identification of cis-acting regulatory sequences involved in this regulation., Mol Microbiol 12(1):83-93

 [20] Oshima T., Aiba H., Masuda Y., Kanaya S., Sugiura M., Wanner BL., Mori H., Mizuno T., 2002, Transcriptome analysis of all two-component regulatory system mutants of Escherichia coli K-12., Mol Microbiol 46(1):281-91

 [21] Huang KJ., Schieberl JL., Igo MM., 1994, A distant upstream site involved in the negative regulation of the Escherichia coli ompF gene., J Bacteriol 176(5):1309-15

 [22] Rampersaud A., Harlocker SL., Inouye M., 1994, The OmpR protein of Escherichia coli binds to sites in the ompF promoter region in a hierarchical manner determined by its degree of phosphorylation., J Biol Chem 269(17):12559-66

 [23] Slauch JM., Silhavy TJ., 1991, cis-acting ompF mutations that result in OmpR-dependent constitutive expression., J Bacteriol 173(13):4039-48

 [24] Forst SA., Delgado J., Inouye M., 1989, DNA-binding properties of the transcription activator (OmpR) for the upstream sequences of ompF in Escherichia coli are altered by envZ mutations and medium osmolarity., J Bacteriol 171(6):2949-55

 [25] Lan CY., Igo MM., 1998, Differential expression of the OmpF and OmpC porin proteins in Escherichia coli K-12 depends upon the level of active OmpR., J Bacteriol 180(1):171-4

 [26] Rampersaud A., Norioka S., Inouye M., 1989, Characterization of OmpR binding sequences in the upstream region of the ompF promoter essential for transcriptional activation., J Biol Chem 264(31):18693-700

 [27] Sato M., Machida K., Arikado E., Saito H., Kakegawa T., Kobayashi H., 2000, Expression of outer membrane proteins in Escherichia coli growing at acid pH., Appl Environ Microbiol 66(3):943-7

 [28] Forst S., Kalve I., Durski W., 1995, Molecular analysis of OmpR binding sequences involved in the regulation of ompF in Escherichia coli., FEMS Microbiol Lett 131(2):147-51

 [29] Ramani N., Huang L., Freundlich M., 1992, In vitro interactions of integration host factor with the ompF promoter-regulatory region of Escherichia coli., Mol Gen Genet 231(2):248-55

 [30] Guillier M., Gottesman S., 2006, Remodelling of the Escherichia coli outer membrane by two small regulatory RNAs., Mol Microbiol 59(1):231-47

 [31] Oropeza R., Salgado-Bravo R., Calva E., 2015, Deletion analysis of RcsC reveals a novel signalling pathway controlling poly-N-acetylglucosamine synthesis and biofilm formation in Escherichia coli., Microbiology 161(Pt 4):903-13

 [32] Izutsu K., Wada C., Komine Y., Sako T., Ueguchi C., Nakura S., Wada A., 2001, Escherichia coli ribosome-associated protein SRA, whose copy number increases during stationary phase., J Bacteriol 183(9):2765-73

 [33] Goh EB., Siino DF., Igo MM., 2004, The Escherichia coli tppB (ydgR) gene represents a new class of OmpR-regulated genes., J Bacteriol 186(12):4019-24

 [34] Shimada T., Takada H., Yamamoto K., Ishihama A., 2015, Expanded roles of two-component response regulator OmpR in Escherichia coli: genomic SELEX search for novel regulation targets., Genes Cells 20(11):915-31


RegulonDB