RegulonDB RegulonDB 10.10: Gene Form
   

fliA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

fliA fliZ fliC3\' NsrR IHF IHF FlhDC FlhDC CsgD NsrR anti-anti-terminator anti-terminator terminator fliAp1 fliAp1 fliAp2 fliAp2 TSS_2259 TSS_2259 TSS_2258 TSS_2258

Gene      
Name: fliA    Texpresso search in the literature
Synonym(s): ECK1921, EG11355, b1922, flaD, rpoF
Genome position(nucleotides): 2001070 <-- 2001789 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 54.17
External database links:  
ASAP:
 ABE-0006396
CGSC:
 771
ECHOBASE:
 EB1330
ECOLIHUB:
 fliA
OU-MICROARRAY:
 b1922
STRING:
 511145.b1922
COLOMBOS: fliA


Shine dalgarno      
Sequence: tcatataacgCAGGGCtgtttatCGT


Product      
Name: RNA polymerase, sigma 28 (sigma F) factor
Synonym(s): sigma;28, FlaD, FliA, RpoF, sigma 28 factor, sigma F factor
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 27.521
Isoelectric point: 4.965
Motif(s):
 
Type Positions Sequence
43 -> 46 DLLQ
73 -> 73 Q
96 -> 96 N
185 -> 233 AIETLPEREKLVLTLYYQEELNLKEIGAVLEVGESRVSQLHSQAIKRLR
16 -> 88 LWQRYVPLVRHEALRLQVRLPASVELDDLLQAGGIGLLNAVERYDALQGTAFTTYAVQRIRGAMLDELRSRDW

 
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 --> 3.1.2.1 - sigma factors, anti-sigmafactors
  3 - regulation --> 3.3 - genetic unit regulated --> 3.3.3 - stimulon
  5 - cell processes --> 5.3 - motility, chemotaxis, energytaxis (aerotaxis, redoxtaxis etc)
  6 - cell structure --> 6.4 - flagella
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0005515 - protein binding
GO:0016987 - sigma factor activity
GO:0003700 - DNA-binding transcription factor activity
GO:0003899 - DNA-directed 5'-3' RNA polymerase activity
biological_process GO:0006355 - regulation of transcription, DNA-templated
GO:0006352 - DNA-templated transcription, initiation
GO:0010468 - regulation of gene expression
GO:2000142 - regulation of DNA-templated transcription, initiation
GO:0001123 - transcription initiation from bacterial-type RNA polymerase promoter
Note(s): Note(s): ...[more].
External database links:  
DIP:
 DIP-47959N
ECOCYC:
 EG11355-MONOMER
ECOLIWIKI:
 b1922
INTERPRO:
 IPR007624
INTERPRO:
 IPR007627
INTERPRO:
 IPR007630
INTERPRO:
 IPR012845
INTERPRO:
 IPR013324
INTERPRO:
 IPR013325
INTERPRO:
 IPR014284
INTERPRO:
 IPR028617
INTERPRO:
 IPR000943
MODBASE:
 P0AEM6
PDB:
 6PMI
PDB:
 6PMJ
PFAM:
 PF04539
PFAM:
 PF04542
PFAM:
 PF04545
PRIDE:
 P0AEM6
PRINTS:
 PR00046
PRODB:
 PRO_000022654
PROSITE:
 PS00716
PROSITE:
 PS00715
REFSEQ:
 NP_416432
SMR:
 P0AEM6
UNIPROT:
 P0AEM6


Operon      
Name: fliAZ-tcyJ         
Operon arrangement:
Transcription unit        Promoter
tcyJ
fliAZY
fliAZY


Transcriptional Regulation      
Display Regulation             
Activated by: H-NS, FlhDC
Repressed by: NsrR, SutR, IHF, MatA, CsgD


RNA cis-regulatory element    
Attenuation: Transcriptional


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_2258 2001544 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_2259 2001807 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_2261 2002392 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_2262 2002401 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_2263 2003300 reverse nd [RS-EPT-CBR] [1]


Evidence    

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


Reference(s)    

 [1] 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.

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