RegulonDB RegulonDB 11.1: Gene Form
   

arcA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

creD arcA yjjY terminator arcAp3 arcAp3 TSS_5194 TSS_5194 arcAp2 arcAp2 arcAp1 arcAp1 TSS_5192 TSS_5192 TSS_5191 TSS_5191 TSS_5190 (cluster) TSS_5190 (cluster) yjjYp6 yjjYp6 TSS_5189 TSS_5189 TSS_5188 TSS_5188 TSS_5187 TSS_5187

Gene      
Name: arcA    Texpresso search in the literature
Synonym(s): ECK4393, EG10061, b4401, cpxC, dye, fexA, msp, seg, sfrA
Genome position(nucleotides): 4639590 <-- 4640306
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 51.05
External database links:  
ASAP:
 ABE-0014434
CGSC:
 831
ECHOBASE:
 EB0059
ECOLIHUB:
 arcA
OU-MICROARRAY:
 b4401
STRING:
 511145.b4401
COLOMBOS: arcA


Product      
Name: DNA-binding transcriptional dual regulator ArcA
Synonym(s): ArcA, ArcA response regulator, CpxC, Dye, FexA, Msp, Seg, SfrA, dye resistance protein
Sequence: Get amino acid sequence Fasta Format
Regulator Family: OmpR
Cellular location: cytosol
Molecular weight: 27.292
Isoelectric point: 4.978
Motif(s):
 
Type Positions Sequence Comment
5 -> 118 HILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILSEYDINLVIMDINLPGKNGLLLARELREQANVALMFLTGRDNEVDKILGLEIGADDYITKPFNPRELTIRARNLL UniProt: Response regulatory.
6 -> 113 ILIVEDELVTRNTLKSIFEAEGYDVFEATDGAEMHQILSEYDINLVIMDINLPGKNGLLLARELREQANVALMFLTGRDNEVDKILGLEIGADDYITKPFNPRELTIR
134 -> 234 VESYKFNGWELDINSRSLIGPDGEQYKLPRSEFRAMLHFCENPGKIQSRAELLKKMTGRELKPHDRTVDVTIRRIRKHFESTPDTPEIIATIHGEGYRFCG UniProt: OmpR/PhoB-type.
156 -> 232 GEQYKLPRSEFRAMLHFCENPGKIQSRAELLKKMTGRELKPHDRTVDVTIRRIRKHFESTPDTPEIIATIHGEGYRF

 
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
  5 - cell processes --> 5.5 - adaptations --> 5.5.6 - other (mechanical, nutritional, oxidative stress)
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0032993 - protein-DNA complex
molecular_function GO:0003677 - DNA binding
GO:0005515 - protein binding
GO:0003700 - DNA-binding transcription factor activity
GO:0000156 - phosphorelay response regulator activity
GO:0042802 - identical protein binding
GO:0000976 - transcription cis-regulatory region binding
GO:0001217 - DNA-binding transcription repressor activity
GO:0001216 - DNA-binding transcription activator activity
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0045892 - negative regulation of transcription, DNA-templated
GO:0045893 - positive regulation of transcription, DNA-templated
GO:0000160 - phosphorelay signal transduction system
Evidence: [COMP-AINF-FN-FROM-SEQ] Automated inference of function from sequence
[EXP-IDA-PURIFIED-PROTEIN] Assay of protein purified to homogeneity
[EXP-IEP-GENE-EXPRESSION-ANALYSIS] Gene expression analysis
Reference(s): [1] Alexeeva S., et al., 2003
[2] Cho BK., et al., 2006
[3] Drury LS., et al., 1985
[4] Pao GM., et al., 1995
[5] Parkinson JS. 1993
[6] Parkinson JS., et al., 1992
[7] Stock JB., et al., 1990
External database links:  
ALPHAFOLD:
 P0A9Q1
DIP:
 DIP-36035N
ECOCYC:
 ARCA-MONOMER
ECOLIWIKI:
 b4401
INTERPRO:
 IPR011006
INTERPRO:
 IPR036388
INTERPRO:
 IPR001867
INTERPRO:
 IPR001789
INTERPRO:
 IPR039420
INTERPRO:
 IPR016032
MODBASE:
 P0A9Q1
PANTHER:
 PTHR48111
PDB:
 1XHE
PDB:
 1XHF
PFAM:
 PF00072
PFAM:
 PF00486
PRIDE:
 P0A9Q1
PRODB:
 PRO_000022123
PROSITE:
 PS51755
PROSITE:
 PS50110
REFSEQ:
 NP_418818
SMART:
 SM00862
SMART:
 SM00448
SMR:
 P0A9Q1
UNIPROT:
 P0A9Q1


Operon      
Name: arcA         
Operon arrangement:
Transcription unit        Promoter
arcA
arcA
arcA
arcA
arcA
arcA
arcA


Transcriptional Regulation      
Display Regulation             
Activated by: FNR
Repressed by: FNR


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_5187 4640243 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_5188 4640332 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_5189 4640338 reverse nd [RS-EPT-CBR] [8]
  promoter yjjYp6 4640358 forward nd [COMP-AINF] [9]
  promoter TSS_5190 (cluster) 4640420 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_5191 4640424 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_5192 4640426 reverse nd [RS-EPT-CBR] [8]
  promoter TSS_5194 4640530 reverse nd [RS-EPT-CBR] [8]


Evidence    

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

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Alexeeva S., Hellingwerf KJ., Teixeira de Mattos MJ., 2003, Requirement of ArcA for redox regulation in Escherichia coli under microaerobic but not anaerobic or aerobic conditions., J Bacteriol 185(1):204-9

 [2] Cho BK., Knight EM., Palsson BO., 2006, Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA., Microbiology 152(Pt 8):2207-19

 [3] Drury LS., Buxton RS., 1985, DNA sequence analysis of the dye gene of Escherichia coli reveals amino acid homology between the dye and OmpR proteins., J Biol Chem 260(7):4236-42

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

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

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

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

 [8] 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.

 [9] 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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