RegulonDB RegulonDB 10.10: Gene Form
   

cyoD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

cyoB cyoE cyoC cyoD anti-anti-terminator anti-terminator TSS_553 TSS_553 TSS_552 TSS_552 TSS_551 TSS_551 TSS_550 (cluster) TSS_550 (cluster) TSS_549 TSS_549 TSS_548 (cluster) TSS_548 (cluster) TSS_547 TSS_547 cyoEp3 cyoEp3 TSS_546 TSS_546

Gene      
Name: cyoD    Texpresso search in the literature
Synonym(s): ECK0423, EG10181, b0429
Genome position(nucleotides): 447717 <-- 448046 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 49.7
External database links:  
ASAP:
 ABE-0001487
CGSC:
 31008
ECHOBASE:
 EB0178
ECOLIHUB:
 cyoD
OU-MICROARRAY:
 b0429
STRING:
 511145.b0429
COLOMBOS: cyoD


Product      
Name: cytochrome bo3 ubiquinol oxidase subunit 4
Synonym(s): CyoD, cytochrome bo3 terminal oxidase subunit IV, cytochrome bo3 ubiquinol oxidase subunit IV, cytochrome o ubiquinol oxidase subunit IV
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 12.029
Isoelectric point: 7.161
Motif(s):
 
Type Positions Sequence
1 -> 33 MSHSTDHSGASHGSVKTYMTGFILSIILTVIPF
42 -> 68 SPAVILGTILAMAVVQVLVHLVCFLHM
46 -> 64 ILGTILAMAVVQVLVHLVC
72 -> 106 SDEGWNMTAFVFTVLIIAILVVGSIWIMWNLNYNM
18 -> 36 YMTGFILSIILTVIPFWMV

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.3 - energy metabolism, carbon --> 1.3.6 - aerobic respiration
  1 - metabolism --> 1.4 - energy production/transport --> 1.4.2 - electron acceptors
  6 - cell structure --> 6.1 - membrane
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0005887 - integral component of plasma membrane
GO:0016021 - integral component of membrane
GO:0009319 - cytochrome o ubiquinol oxidase complex
molecular_function GO:0005515 - protein binding
GO:0009055 - electron transfer activity
GO:0015453 - oxidoreduction-driven active transmembrane transporter activity
GO:0016491 - oxidoreductase activity
GO:0015078 - proton transmembrane transporter activity
GO:0009486 - cytochrome bo3 ubiquinol oxidase activity
biological_process GO:0009060 - aerobic respiration
GO:0015990 - electron transport coupled proton transport
GO:0019646 - aerobic electron transport chain
Note(s): Note(s): ...[more].
External database links:  
DIP:
 DIP-48238N
ECOCYC:
 CYOD-MONOMER
ECOLIWIKI:
 b0429
INTERPRO:
 IPR005171
INTERPRO:
 IPR014210
PDB:
 1FFT
PFAM:
 PF03626
PRIDE:
 P0ABJ6
PRODB:
 PRO_000022371
REFSEQ:
 NP_414963
SMR:
 P0ABJ6
UNIPROT:
 P0ABJ6


Operon      
Name: cyoABCDE         
Operon arrangement:
Transcription unit        Promoter
cyoABCDE


Transcriptional Regulation      
Display Regulation             
Activated by: CRP, GadE, CusR, Fis
Repressed by: FNR, Fur, HprR, Cra, ArcA, PdhR


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_546 447668 reverse nd [RS-EPT-CBR] [1]
  promoter cyoEp3 447770 reverse nd [ICWHO] [2]
  promoter TSS_547 448138 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_548 (cluster) 448146 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_549 448244 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_550 (cluster) 448247 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_551 448549 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_552 448681 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_553 449899 reverse nd [RS-EPT-CBR] [1]


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] 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.

 [2] 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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