RegulonDB RegulonDB 10.9: Gene Form
   

phoP gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

phoQ purB roxA phoP PurR PhoP terminator phoPp2 phoPp2 phoPp3 phoPp3 phoPp1 phoPp1 TSS_1474 (cluster) TSS_1474 (cluster) TSS_1473 TSS_1473 TSS_1472 TSS_1472 TSS_1471 TSS_1471 TSS_1470 TSS_1470 phoQp5 phoQp5 TSS_1469 TSS_1469 TSS_1468 TSS_1468 ycfDp5 ycfDp5 ycfDp4 ycfDp4 TSS_1466 (cluster) TSS_1466 (cluster)

Gene      
Name: phoP    Texpresso search in the literature
Synonym(s): ECK1116, EG10731, b1130
Genome position(nucleotides): 1189776 <-- 1190447 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
47.77
External database links:  
ASAP:
ABE-0003807
CGSC:
31919
ECHOBASE:
EB0724
ECOLIHUB:
phoP
OU-MICROARRAY:
b1130
STRING:
511145.b1130
COLOMBOS: phoP


Shine dalgarno      
Sequence: aattaagacaGGGAGAaataaaAAT


Product      
Name: DNA-binding transcriptional dual regulator PhoP
Synonym(s): PhoP, PhoP response regulator
Sequence: Get amino acid sequence Fasta Format
Regulator Family: OmpR
Cellular location: cytosol
Molecular weight: 25.535
Isoelectric point: 4.889
Motif(s):
 
Type Positions Sequence
3 -> 112 VLVVEDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYLNEHIPDIAIVDLGLPDEDGLSLIRRWRSNDVSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIEEVMARM
2 -> 116 RVLVVEDNALLRHHLKVQIQDAGHQVDDAEDAKEADYYLNEHIPDIAIVDLGLPDEDGLSLIRRWRSNDVSLPILVLTARESWQDKVEVLSAGADDYVTKPFHIEEVMARMQALM
124 -> 222 SQVISLPPFQVDLSRRELSINDEVIKLTAFEYTIMETLIRNNGKVVSKDSLMLQLYPDAELRESHTIDVLMGRLRKKIQAQYPQEVITTVRGQGYLFEL
146 -> 220 EVIKLTAFEYTIMETLIRNNGKVVSKDSLMLQLYPDAELRESHTIDVLMGRLRKKIQAQYPQEVITTVRGQGYLF

 

Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.2 - activator
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.4 - complex regulation --> 3.1.2.4.3 - two component regulatory systems (external signal)
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.1 - operon
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0032993 - protein-DNA complex
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
GO:0000156 - phosphorelay response regulator activity
GO:0042802 - identical protein binding
GO:0000976 - transcription regulatory region sequence-specific DNA binding
GO:0001216 - DNA-binding transcription activator activity
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0045893 - positive regulation of transcription, DNA-templated
GO:0000160 - phosphorelay signal transduction system
Note(s): Note(s): ...[more].
Evidence: [AIFS] Automated inference of function from sequence
Reference(s): [1] Groisman EA., et al., 1992
[2] Pao GM., et al., 1995
[3] Parkinson JS. 1993
[4] Parkinson JS., et al., 1992
[5] Stock JB., et al., 1990
[6] Zwir I., et al., 2005
External database links:  
DIP:
DIP-10500N
ECOCYC:
PHOP-MONOMER
ECOLIWIKI:
b1130
INTERPRO:
IPR001789
INTERPRO:
IPR039420
INTERPRO:
IPR036388
INTERPRO:
IPR011006
INTERPRO:
IPR001867
MODBASE:
P23836
PANTHER:
PTHR26402
PDB:
2PKX
PDB:
2PL1
PFAM:
PF00072
PFAM:
PF00486
PRIDE:
P23836
PRODB:
PRO_000023544
PROSITE:
PS50110
PROSITE:
PS51755
REFSEQ:
NP_415648
SMART:
SM00448
SMART:
SM00862
SMR:
P23836
UNIPROT:
P23836


Operon      
Name: phoPQ         
Operon arrangement:
Transcription unit        Promoter
phoQ
phoPQ
phoPQ
phoPQ


Transcriptional Regulation      
Display Regulation             
Activated by: PhoP
Repressed by: PhoP


Elements in the selected gene context region unrelated to any object in RegulonDB      

  Type Name Post Left Post Right Strand Notes Evidence (Confirmed, Strong, Weak) References
  promoter TSS_1466 (cluster) 1188265 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [7]
  promoter ycfDp4 1188267 reverse Similarity to the consensus
Read more >
[ICWHO], [RS-EPT-CBR] [7], [8]
  promoter ycfDp5 1188270 reverse Similarity to the consensus
Read more >
[ICWHO] [8]
  promoter TSS_1468 1189078 reverse nd [RS-EPT-CBR] [7]
  promoter TSS_1469 1189096 reverse nd [RS-EPT-CBR] [7]
  promoter TSS_1470 1189968 reverse nd [RS-EPT-CBR] [7]
  promoter TSS_1471 1190330 forward nd [RS-EPT-CBR] [7]
  promoter TSS_1472 1190342 forward nd [RS-EPT-CBR] [7]
  promoter TSS_1473 1190470 reverse nd [RS-EPT-CBR] [7]
  promoter TSS_1474 (cluster) 1190474 reverse For this promoter, there
Read more >
[RS-EPT-CBR] [7]


Evidence    

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

 [ICWHO] Inferred computationally without human oversight



Reference(s)    

 [1] Groisman EA., Heffron F., Solomon F., 1992, Molecular genetic analysis of the Escherichia coli phoP locus., J Bacteriol 174(2):486-91

 [2] Pao GM., Saier MH., 1995, Response regulators of bacterial signal transduction systems: selective domain shuffling during evolution., J Mol Evol 40(2):136-54

 [3] Parkinson JS., 1993, Signal transduction schemes of bacteria., Cell 73(5):857-71

 [4] Parkinson JS., Kofoid EC., 1992, Communication modules in bacterial signaling proteins., Annu Rev Genet 26:71-112

 [5] Stock JB., Stock AM., Mottonen JM., 1990, Signal transduction in bacteria., Nature 344(6265):395-400

 [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] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

 [8] 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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