RegulonDB RegulonDB 11.1: Gene Form
   

cybB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

aldA gapC cybB rydC rydCp rydCp cybBp6 cybBp6 cybBp7 cybBp7 cybBp5 cybBp5 TSS_1804 (cluster) TSS_1804 (cluster) TSS_1803 (cluster) TSS_1803 (cluster)

Gene      
Name: cybB    Texpresso search in the literature
Synonym(s): ECK1410, EG10172, b1418
Genome position(nucleotides): 1490902 --> 1491432
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 47.65
External database links:  
ASAP:
 ABE-0004733
CGSC:
 17728
ECHOBASE:
 EB0169
ECOLIHUB:
 cybB
OU-MICROARRAY:
 b1418
STRING:
 511145.b1418
COLOMBOS: cybB


Product      
Name: superoxide oxidase
Synonym(s): CybB, superoxide:ubiquinone oxidoreductase
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 20.286
Isoelectric point: 10.35
Motif(s):
 
Type Positions Sequence Comment
1 -> 28 MENKYSRLQISIHWLVFLLVIAAYCAME UniProt: In Ref. 1; CAA30454 and 2; no nucleotide entry..
4 -> 172 KYSRLQISIHWLVFLLVIAAYCAMEFRGFFPRSDRPLINMIHVSCGISILVLMVVRLLLRLKYPTPPIIPKPKPMMTGLAHLGHLVIYLLFIALPVIGLVMMYNRGNPWFAFGLTMPYASEANFERVDSLKSWHETLANLGYFVIGLHAAAALAHHYFWKDNTLLRMMP
9 -> 29 QISIHWLVFLLVIAAYCAMEF UniProt: Helical.
41 -> 61 INMIHVSCGISILVLMVVRLL UniProt: Helical.
85 -> 105 LGHLVIYLLFIALPVIGLVMM UniProt: Helical.

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.4 - energy production/transport --> 1.4.3 - electron carriers
  1 - metabolism --> 1.6 - biosynthesis of macromolecules (cellular constituents) --> 1.6.15 - large molecule carriers --> 1.6.15.1 - cytochromes
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
molecular_function GO:0009055 - electron transfer activity
GO:0046872 - metal ion binding
GO:0020037 - heme binding
biological_process GO:0019430 - removal of superoxide radicals
GO:0022904 - respiratory electron transport chain
Note(s): Note(s): ...[more].
Reference(s): [1] Nakamura H., et al., 1988
External database links:  
ALPHAFOLD:
 P0ABE5
ECOCYC:
 CYTOCHROME-B561-MONOMER
ECOLIWIKI:
 b1418
INTERPRO:
 IPR011577
INTERPRO:
 IPR016174
PDB:
 5OC0
PFAM:
 PF01292
PRIDE:
 P0ABE5
REFSEQ:
 NP_415935
SMR:
 P0ABE5
UNIPROT:
 P0ABE5


Operon      
Name: cybB         
Operon arrangement:
Transcription unit        Promoter
cybB


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_1803 (cluster) 1490746 reverse nd [RS-EPT-CBR] [2]
  promoter TSS_1804 (cluster) 1490754 reverse nd [RS-EPT-CBR] [2]
  promoter cybBp5 1490761 forward nd [COMP-AINF] [3]
  promoter cybBp7 1490766 forward nd [COMP-AINF] [3]
  promoter cybBp6 1490887 forward nd [COMP-AINF] [3]


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] Nakamura H., Murakami H., Yamato I., Anraku Y., 1988, Nucleotide sequence of the cybB gene encoding cytochrome b561 in Escherichia coli K12., Mol Gen Genet 212(1):1-5

 [2] 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.

 [3] 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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