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PhoP DNA-binding transcriptional dual regulator

Synonyms: PhoP, PhoP-phosphorylated
Summary:
PhoP is a dual transcriptional regulator that is activated in response to low extracellular levels of divalent cations, e.g., magnesium or calcium [11, 20, 21]. In Escherichia coli K-12, PhoP activates transcription of a large collection of genes involved in Mg2+ homeostasis, resistance to antimicrobial peptides, acid resistance, and LPS modification [3, 11, 22]. PhoP belongs to the OmpR/PhoB subfamily of response regulators characterized by a winged-helix DNA-binding domain. The structure of the N-terminal receiver domain has been solved in the absence and presence of the phosphoryl analog beryllofluoride [23]. PhoP is phosphorylated and thereby activated by its cognate sensor kinase PhoQ at a low extracellular concentration of magnesium. At high levels of magnesium the phospho-PhoP phosphatase activity of the sensor protein is induced [24]. Z nucleotides [ZMP (5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5-monophosphate) and/or ZTP (5-aminoimidazole-4-carboxamide-1-beta-D-ribofuranosyl 5-triphosphate)] can act as direct phosphodonors to PhoP in vivo, activating it in a PhoQ-independent manner when they accumulate [25]. Regulation of the PhoQ/PhoP system is connected to the EvgS/EvgA system through the small inner membrane protein B1500.
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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
PhoP Non-Functional   Apo [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IPI] S [1]
PhoP-phosphorylated Functional Covalent Holo [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IPI] S [1]
Evolutionary Family: OmpR
TFBs length: 17
TFBs symmetry: direct-repeat
Sensing class: External-Two-component systems
Connectivity class: Local Regulator
Gene name: phoP
  Genome position: 1189776-1190447
  Length: 672 bp / 223 aa
Operon name: phoPQ
TU(s) encoding the TF:
Transcription unit        Promoter
phoPQ
phoPp1
phoPQ
phoPp2
phoPQ
phoPp3


Regulon       
Regulated gene(s) acrA, acrB, argD, borD, clpS, cysB, dcuD, fadL, gadE, gadF, gadW, glgA, glgB, glgC, glgP, glgX, hdeA, hdeB, hdeD, hemL, iraM, malS, metB, metL, mgrB, mgrR, mgtA, mgtL, mgtS, nagA, ompT, pagP, phoP, phoQ, purD, purH, rstA, rstB, rutA, rutB, rutC, rutD, rutE, rutF, rutG, safA, slyB, tolC, treR, ybjG, ydeO, ydeP, ygiB, ygiC, yhiD, yrbL
Multifun term(s) of regulated gene(s) MultiFun Term (List of genes associated to the multifun term)
membrane (11)
Transcription related (7)
pH (6)
nitrogen metabolism (6)
activator (5)
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Regulated operon(s) acrAB, argD, borD, clpS, cysB, dcuD, envY-ompT, fadL, gadAXW, gadEF-mdtEF, glgBXCAP, hdeAB-yhiD, hdeD, hemL, iraM, malS, metBL, mgrB, mgrR, mgtLA, mgtS, nagBAC-umpH, pagP, phoPQ, purHD, rstAB, rutABCDEFG, safA-ydeO, slyB, tolC-ygiBC, treR, ybjG, ydeP, yrbL
First gene in the operon(s) acrA, argD, borD, clpS, cysB, dcuD, fadL, gadE, gadW, glgA, glgB, hdeA, hdeD, hemL, iraM, malS, metB, mgrB, mgrR, mgtL, mgtS, nagA, ompT, pagP, phoP, purH, rstA, rutA, safA, slyB, tolC, treR, ybjG, ydeP, yrbL
Simple and complex regulons AcrR,EnvR,MarA,MprA,PhoP,Rob,SoxS
ArcA,CRP,FadR,OmpR,PhoP,Rob,ppGpp
ArcA,FNR,PhoP
ArcA,GadE,PhoP
ArcA,NtrC,PhoP,RutR
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Simple and complex regulatory phrases Regulatory phrase (List of promoters regulated by the phrase)
[PhoP,+](31)
[PhoP,-](10)


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
  PhoP-phosphorylated repressor acrAp Sigma70 32.0 -48.0 acrA, acrB
cgcagcaatgGGTTTATTAACTTTTGAccattgacca
 485659 485675 [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [2], [2]
  PhoP-phosphorylated repressor argDp Sigma70 11.0 -31.0 argD
ttgtggttatAATTTCACATTTGTTTAtgcgtaacag
 3490203 3490219 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2], [2]
  PhoP-phosphorylated activator borDp nd -33.0 -61.0 borD
ttcaactcatTGTTTAGGGTTTGTTTAattttctaca
 578946 578962 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [3], [3]
  PhoP-phosphorylated repressor clpSp nd -7.0 -169.0 clpS
gacaaggggcAGGTATGAATCAAAAATttgaagcagt
 922736 922752 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF], [EXP-IDA-BINDING-OF-CELLULAR-EXTRACTS] S [4], [4]
  PhoP-phosphorylated activator cysBp Sigma70 -43.0 -110.0 cysB
acctatacacTAAGGCTATAAATGATATAGTGGTtatagttagc
 1333734 1333757 [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [5], [5]
  PhoP-phosphorylated repressor dcuDp1 Sigma70 56.5 -47.5 dcuD
ataacatcgtTGTTTTCAATCTGCCGTTTATgggattgacc
 3374812 3374832 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2], [2]
  PhoP-phosphorylated activator fadLp Sigma38 -191.5 -292.5 fadL
ttccggaaagTGCTGCTCCAGTTGTTAATtctgcaaaat
 2461005 2461023 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2], [2]
  PhoP-phosphorylated activator gadEp1 Sigma38 -85.0 -209.0 gadE, gadF
ttttgtttgcTATTTACAAGCTGATAAcaaccaggaa
 3658149 3658165 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [6], [6]
  PhoP-phosphorylated activator gadWp2 nd -28.0 -191.0 gadW
catttttttaTAAACATAAGCTATACGctgtgcgaaa
 3664801 3664817 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [6], [6]
  PhoP-phosphorylated activator glgAp Sigma70 nd nd glgA, glgP
nd
 nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [7]
  PhoP-phosphorylated activator glgBp Sigma70 -34.0 -189.0 glgB, glgX, glgC, glgA, glgP
gatgtttcatGATTTACCGGGAGTTAAatagagcatt
 3573683 3573699 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [7]
  PhoP-phosphorylated activator hdeAp Sigma70 -32.0 -83.0 hdeA, hdeB, yhiD
atattttccaTCAACATGACATATACAgaaaaccagg
 3656815 3656831 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [6], [6]
  PhoP-phosphorylated activator hdeAp2 Sigma38 -32.0 -83.0 hdeA, hdeB, yhiD
atattttccaTCAACATGACATATACAgaaaaccagg
 3656815 3656831 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [6], [6]
  PhoP-phosphorylated activator hdeDp Sigma70 -137.0 -172.0 hdeD
cctggttttcTGTATATGTCATGTTGAtggaaaatat
 3656815 3656831 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [6], [6]
  PhoP-phosphorylated activator hdeDp2 Sigma38 -137.0 -172.0 hdeD
cctggttttcTGTATATGTCATGTTGAtggaaaatat
 3656815 3656831 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [6], [6]
  PhoP-phosphorylated activator hemLp Sigma28 -31.0 -70.0 hemL
agcagcctgaTGTTTGACGAGTATTTAacttgttatg
 174944 174960 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [3], [3]
  PhoP-phosphorylated activator iraMp1 nd -199.5 -286.5 iraM
cataatgtttAGCAAATTGGCACAAAGtagcataaag
 1212282 1212298 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [8], [8]
  PhoP-phosphorylated activator iraMp1 nd -68.0 -155.0 iraM
aatctcatttTGTTTAACATCCATTGAgattccttgc
 1212150 1212166 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [8], [8], [9], [9]
  PhoP-phosphorylated activator iraMp2 Sigma70 -35.0 -155.0 iraM
aatctcatttTGTTTAACATCCATTGAgattccttgc
 1212150 1212166 [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [8], [8], [9], [9]
  PhoP-phosphorylated activator malSp Sigma70 -161.0 -188.0 malS
caaatctgaaACTATGTCACGTGTTAAcgattcagat
 3737301 3737317 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2], [2]
  PhoP-phosphorylated activator metBp Sigma70 -20.0 -56.0 metB, metL
tattgacgtcCATTAACACAATGTTTActctggtgcc
 4128608 4128624 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2], [2]
  PhoP-phosphorylated activator mgrBp nd -33.0 -59.0 mgrB
aatatcgacaTAGTTAGGCGCTGTTTAactaacgcat
 1908817 1908833 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [3], [3], [10], [10], [11], [11]
  PhoP-phosphorylated activator mgrRp Sigma70 -44.0 -44.0 mgrR
tgattaaccgAGTTTAAGCTCCGTTTAacattcattg
 1622950 1622966 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [12], [12]
  PhoP-phosphorylated activator mgtAp1 Sigma70 -34.0 -102.0 mgtL, mgtA
ggtaaagtctGGTTTATCGTTGGTTTAgttgtcagca
 4467321 4467337 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3], [3], [11], [11], [13], [14], [14]
  PhoP-phosphorylated activator mgtSp Sigma70 -35.0 -93.0 mgtS
ataaagatttAATTCAGCCTTCGTTTAggttacctct
 1622545 1622561 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [12], [12]
  PhoP-phosphorylated activator nagAp nd -31.0 -455.0 nagA
aaaattcatcTGTTTATGGGCGGTGTAggtaacgacg
 703198 703214 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [3], [3]
  PhoP-phosphorylated activator ompTp nd -49.0 -81.0 ompT
aaacaaaataTAAACAGTGGAGCAATAtgtaattgac
 585706 585722 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [3], [6], [6]
  PhoP-phosphorylated activator pagPp nd -32.0 -63.0 pagP
atgttgggtcTATTAAGGTTATGTTAAttgtagcttt
 656486 656502 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [10], [10]
  PhoP-phosphorylated repressor phoPp1 nd -33.0 -69.0 phoP, phoQ
cctccccgctGGTTTATTTAATGTTTAcccccataac
 1190508 1190524 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2], [3], [3], [10], [10], [11], [11]
  PhoP-phosphorylated activator phoPp2 nd -8.0 -69.0 phoP, phoQ
cctccccgctGGTTTATTTAATGTTTAcccccataac
 1190508 1190524 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2], [3], [3], [10], [10], [11], [11]
  PhoP-phosphorylated activator purHp Sigma70 -479.0 -574.0 purH, purD
taaacttcgtAATGAATTACGTGTTCActcttgagac
 4208098 4208114 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2], [2]
  PhoP-phosphorylated activator rstAp nd -44.0 -65.0 rstA, rstB
gatgaaaactTGTTTAGAAACGATTGAtagtaagtaa
 1682086 1682102 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2], [3], [3], [15]
  PhoP-phosphorylated activator rutAp Sigma54 -106.0 -121.0 rutA, rutB, rutC, rutD, rutE, rutF, rutG
ttatgtgcaaCTGTTTTGACCGTTTAgtccactttt
 1074125 1074140 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS] W [2], [2]
  PhoP-phosphorylated repressor safAp Sigma70 33.0 -37.0 safA, ydeO
attaagcataCTGATTAACGATTTTTAAcgttatccgc
 1583988 1584005 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] S [16], [16]
  PhoP-phosphorylated repressor safAp Sigma70 53.0 -17.0 safA, ydeO
atttttaacgTTATCCGCTAAATAAACAtatttgaaat
 1583968 1583985 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IMP-SITE-MUTATION] S [16], [16]
  PhoP-phosphorylated activator slyBp1 nd -33.0 -132.0 slyB
atgaatgtttTGTTTATAATTGGTTGAtcctactttc
 1719736 1719752 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [3], [3]
  PhoP-phosphorylated repressor slyBp2 nd -4.0 -132.0 slyB
atgaatgtttTGTTTATAATTGGTTGAtcctactttc
 1719736 1719752 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [3], [3]
  PhoP-phosphorylated activator tolCp2 nd -46.0 -149.0 tolC, ygiB, ygiC
atttcagcgaCGTTTGACTGCCGTTTGAgcagtcatgt
 3177958 3177975 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [17], [17]
  PhoP-phosphorylated repressor treRp3 Sigma70 -50.0 -83.0 treR
tgctgacaacTAAACCAACGATAAACCagactttacc
 4467321 4467337 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3], [3], [11], [14], [14]
  PhoP-phosphorylated repressor treRp4 Sigma70 19.0 -83.0 treR
tgctgacaacTAAACCAACGATAAACCagactttacc
 4467321 4467337 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS], [EXP-IMP-SITE-MUTATION] C [3], [3], [11], [14], [14]
  PhoP-phosphorylated activator ybjGp nd -32.0 -152.0 ybjG
agctacgcttTCTTTAAGTTTTATTTAacctatgccc
 883532 883548 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [10], [10]
  PhoP-phosphorylated repressor ydePp Sigma70 34.5 -144.5 ydeP
ttaacttatcGTATTTAATCTATTGTTTAacgataatag
 1586622 1586640 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-HINF-SIMILAR-TO-CONSENSUS] W [16], [16]
  PhoP-phosphorylated activator yrbLp nd -28.0 -59.0 yrbL
taagaggcatTGTTTAGGTTTTGTTTAagttaatcga
 3348385 3348401 [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [COMP-AINF-SIMILAR-TO-CONSENSUS], [COMP-HINF-SIMILAR-TO-CONSENSUS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] S [2], [2], [3], [3]



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
  PhoP-phosphorylated activator queE Transcription-Unit nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS], [EXP-IDA-BINDING-OF-PURIFIED-PROTEINS] W [18]
  PhoP-phosphorylated activator ryjB Gene nd
nd
nd nd nd nd [EXP-IEP-GENE-EXPRESSION-ANALYSIS] W [19]


Alignment and PSSM for PhoP TFBSs    

Aligned TFBS of PhoP   
  Sequence
  TTGTTTAGGTTTTGTTTA
  TTGTTTAGGGTTTGTTTA
  GAGTTTAAGCTCCGTTTA
  TGGTTTATCGTTGGTTTA
  TGGTTTATTTAATGTTTA
  TTGTTTAACATCCATTGA
  CTGTTTATGGGCGGTGTA
  TTGTTTATAATTGGTTGA
  TAATTTCACATTTGTTTA
  TATTTAATCTATTGTTTA
  GCGTATAGCTTATGTTTA
  CTGTATATGTCATGTTGA
  ATATTGCTCCACTGTTTA
  TTCTTTAAGTTTTATTTA
  ATAGTTAGGCGCTGTTTA
  ATGTTTGACGAGTATTTA
  CTATTAAGGTTATGTTAA
  CTATTTAACTCCCGGTAA
  TAATTCAGCCTTCGTTTA
  TTGTTTAGAAACGATTGA
  GGGTTTATTAACTTTTGA
  TTTTCAATCTGCCGTTTA
  ACGTTTGACTGCCGTTTG
  CCATTAACACAATGTTTA
  ATGTTTATTTAGCGGATA
  CTGATTAACGATTTTTAA
  ATTTATAGCCTTAGTGTA
  AACTGTTTTGACCGTTTA
  CTATTTACAAGCTGATAA
  AACTATGTCACGTGTTAA
  TAATGAATTACGTGTTCA
  GTATGAATCAAAAATTTG
  GTGCTGCTCCAGTTGTTA
  CTACTTTGTGCCAATTTG

Position weight matrix (PWM). PhoP matrix-quality result    
A	8	7	11	1	4	6	26	8	4	9	12	6	3	6	1	1	5	31
C	8	3	3	2	1	1	3	2	16	7	5	13	8	0	0	0	1	0
G	5	3	17	1	3	2	3	9	8	7	5	5	4	25	3	2	5	3
T	13	21	3	30	26	25	2	15	6	11	12	10	19	3	30	31	23	0

Consensus    
;	consensus.strict             	ttgTttatctactGTTtA
;	consensus.strict.rc          	TAAACAGTAGATAAACAA
;	consensus.IUPAC              	ytrTttakskwcyGTTtA
;	consensus.IUPAC.rc           	TAAACRGWMSMTAAAYAR
;	consensus.regexp             	[ct]t[ag]Ttta[gt][cg][gt][at]c[ct]GTTtA
;	consensus.regexp.rc          	TAAAC[AG]G[AT][AC][CG][AC]TAAA[CT]A[AG]

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    

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

 [EXP-IPI] Inferred from physical interaction

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

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

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

 [COMP-HINF] Inferred by a human based on computational evidence

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

 [EXP-IMP-SITE-MUTATION] Site mutation


Reference(s)    

 [1] Yamamoto K., Hirao K., Oshima T., Aiba H., Utsumi R., Ishihama A., 2005, Functional characterization in vitro of all two-component signal transduction systems from Escherichia coli., J Biol Chem 280(2):1448-56

 [2] Monsieurs P., De Keersmaecker S., Navarre WW., Bader MW., De Smet F., McClelland M., Fang FC., De Moor B., Vanderleyden J., Marchal K., 2005, Comparison of the PhoPQ regulon in Escherichia coli and Salmonella typhimurium., J Mol Evol 60(4):462-74

 [3] Minagawa S., Ogasawara H., Kato A., Yamamoto K., Eguchi Y., Oshima T., Mori H., Ishihama A., Utsumi R., 2003, Identification and molecular characterization of the Mg2+ stimulon of Escherichia coli., J Bacteriol 185(13):3696-702

 [4] Yeom J., Gao X., Groisman EA., 2018, Reduction in adaptor amounts establishes degradation hierarchy among protease substrates., Proc Natl Acad Sci U S A 115(19):E4483-E4492

 [5] Kaleta C., Gohler A., Schuster S., Jahreis K., Guthke R., Nikolajewa S., 2010, Integrative inference of gene-regulatory networks in Escherichia coli using information theoretic concepts and sequence analysis., BMC Syst Biol 4:116

 [6] Zwir I., Shin D., Kato A., Nishino K., Latifi T., Solomon F., Hare JM., Huang H., Groisman EA., 2005, Dissecting the PhoP regulatory network of Escherichia coli and Salmonella enterica., Proc Natl Acad Sci U S A 102(8):2862-7

 [7] Montero M., Almagro G., Eydallin G., Viale AM., Munoz FJ., Bahaji A., Li J., Rahimpour M., Baroja-Fernandez E., Pozueta-Romero J., 2011, Escherichia coli glycogen genes are organized in a single glgBXCAP transcriptional unit possessing an alternative suboperonic promoter within glgC that directs glgAP expression., Biochem J 433(1):107-17

 [8] Bougdour A., Cunning C., Baptiste PJ., Elliott T., Gottesman S., 2008, Multiple pathways for regulation of sigmaS (RpoS) stability in Escherichia coli via the action of multiple anti-adaptors., Mol Microbiol 68(2):298-313

 [9] Eguchi Y., Ishii E., Hata K., Utsumi R., 2011, Regulation of acid resistance by connectors of two-component signal transduction systems in Escherichia coli., J Bacteriol 193(5):1222-8

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