RegulonDB RegulonDB 11.2: Gene Form
   

fimZ gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

fimZ sfmF argU Fis terminator argUp argUp fimZp3 fimZp3 TSS_681 TSS_681

Gene      
Name: fimZ    Texpresso search in the literature
Synonym(s): ECK0528, EG11103, b0535, ybcA
Genome position(nucleotides): 563848 <-- 564480
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 36.65
External database links:  
ASAP:
 ABE-0001836
ECHOBASE:
 EB1095
ECOLIHUB:
 fimZ
OU-MICROARRAY:
 b0535
STRING:
 511145.b0535
COLOMBOS: fimZ


Product      
Name: putative LuxR family transcriptional regulator FimZ
Synonym(s): FimZ, YbcA
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 23.664
Isoelectric point: 9.033
Motif(s):
 
Type Positions Sequence Comment
5 -> 121 SVIIMDTHPIIRMSIEVLLQKNSELQIVLKTDDYRITIDYLRTRPVDLIIMDIDLPGTDGFTFLKRIKQIQSTVKVLFLSSKSECFYAGRAIQAGANGFVSKCNDQNDIFHAVQMIL UniProt: Response regulatory.
6 -> 117 VIIMDTHPIIRMSIEVLLQKNSELQIVLKTDDYRITIDYLRTRPVDLIIMDIDLPGTDGFTFLKRIKQIQSTVKVLFLSSKSECFYAGRAIQAGANGFVSKCNDQNDIFHAV
143 -> 208 NSSTVTVLSNREVTILRYLVSGLSNKEIADKLLLSNKTVSAHKSNIYGKLGLHSIVELIDYAKLYE UniProt: HTH luxR-type.
149 -> 204 VLSNREVTILRYLVSGLSNKEIADKLLLSNKTVSAHKSNIYGKLGLHSIVELIDYA
167 -> 186 NKEIADKLLLSNKTVSAHKS UniProt: H-T-H motif.

 
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 --> 3.3 - genetic unit regulated --> 3.3.1 - operon
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0000160 - phosphorelay signal transduction system
Note(s): Note(s): ...[more].
Evidence: [EXP-IEP] Inferred from expression pattern
[EXP-IMP] Inferred from mutant phenotype
Reference(s): [1] Domka J., et al., 2007
[2] Hirakawa H., et al., 2003
External database links:  
ALPHAFOLD:
 P0AEL8
DIP:
 DIP-48119N
ECOCYC:
 EG11103-MONOMER
ECOLIWIKI:
 b0535
INTERPRO:
 IPR000792
INTERPRO:
 IPR001789
INTERPRO:
 IPR036388
INTERPRO:
 IPR016032
INTERPRO:
 IPR011006
MODBASE:
 P0AEL8
PFAM:
 PF00072
PFAM:
 PF00196
PRIDE:
 P0AEL8
PRINTS:
 PR00038
PRODB:
 PRO_000022625
PROSITE:
 PS50110
PROSITE:
 PS50043
PROSITE:
 PS00622
REFSEQ:
 NP_415068
SMART:
 SM00448
SMART:
 SM00421
SMR:
 P0AEL8
UNIPROT:
 P0AEL8


Operon      
Name: fimZ         
Operon arrangement:
Transcription unit        Promoter
fimZ


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_681 564377 forward nd [RS-EPT-CBR] [3]
  promoter fimZp3 564607 reverse nd [COMP-AINF] [4]


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] Domka J., Lee J., Bansal T., Wood TK., 2007, Temporal gene-expression in Escherichia coli K-12 biofilms., Environ Microbiol 9(2):332-46

 [2] Hirakawa H., Nishino K., Hirata T., Yamaguchi A., 2003, Comprehensive studies of drug resistance mediated by overexpression of response regulators of two-component signal transduction systems in Escherichia coli., J Bacteriol 185(6):1851-6

 [3] 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.

 [4] 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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