RegulonDB RegulonDB 10.6.3: Gene Form
   

cydB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

cydA cydB cydX ybgEp4 ybgEp4 TSS_888 TSS_888 TSS_887 TSS_887 TSS_886 TSS_886 TSS_885 TSS_885 TSS_884 (cluster) TSS_884 (cluster) TSS_883 TSS_883 TSS_882 TSS_882 TSS_881 TSS_881 TSS_880 TSS_880 TSS_879 TSS_879 TSS_878 TSS_878 TSS_877 TSS_877 TSS_876 TSS_876 TSS_875 TSS_875 TSS_874 TSS_874 TSS_873 TSS_873 TSS_872 TSS_872 TSS_871 TSS_871 TSS_870 TSS_870 TSS_869 TSS_869 TSS_868 TSS_868

Gene      
Name: cydB    Texpresso search in the literature
Synonym(s): ECK0722, EG10174, b0734, cyd-2
Genome position(nucleotides): 773042 --> 774181 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
53.86
External database links:  
ASAP:
ABE-0002501
CGSC:
9469
ECHOBASE:
EB0171
ECOCYC:
EG10174
ECOLIHUB:
cydB
OU-MICROARRAY:
b0734
REGULONDB:
b0734
STRING:
511145.b0734
M3D: cydB
COLOMBOS: cydB
PortEco: b0734


Product      
Name: cytochrome bd-I ubiquinol oxidase subunit II
Synonym(s): Cyd-2, CydB
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 42.453
Isoelectric point: 7.497
Motif(s):
 
Type Positions Sequence
197 -> 197 H
263 -> 282 PILWAIPALGVVLPLLTILT
7 -> 362 LRFIWWLLVGVLLIGFAVTDGFDMGVGMLTRFLGRNDTERRIMINSIAPHWDGNQVWLITAGGALFAAWPMVYAAAFSGFYVAMILVLASLFFRPVGFDYRSKIEETRWRNMWDWGIFIGSFVPPLVIGVAFGNLLQGVPFNVDEYLRLYYTGNFFQLLNPFGLLAGVVSVGMIITQGATYLQMRTVGELHLRTRATAQVAALVTLVCFALAGVWVMYGIDGYVVKSTMDHYAASNPLNKEVVREAGAWLVNFNNTPILWAIPALGVVLPLLTILTARMDKAAWAFVFSSLTLACIILTAGIAMFPFVMPSSTMMNASLTMWDATSSQLTLNVMTWVAVVLVPIILLYTAWCYWKM
80 -> 99 AAAFSGFYVAMILVLASLFF
165 -> 184 LNPFGLLAGVVSVGMIITQG

 

Classification:
Multifun Terms (GenProtEC)  
  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:0070069 - cytochrome complex
molecular_function GO:0005515 - protein binding
GO:0009055 - electron transfer activity
GO:0046872 - metal ion binding
GO:0016682 - oxidoreductase activity, acting on diphenols and related substances as donors, oxygen as acceptor
GO:0020037 - heme binding
biological_process GO:0006119 - oxidative phosphorylation
GO:0019646 - aerobic electron transport chain
GO:0055114 - oxidation-reduction process
Note(s): Note(s): ...[more].
Reference(s): [1] Lobritz MA., et al., 2015
External database links:  
ECOCYC:
CYDB-MONOMER
ECOLIWIKI:
b0734
ECOO157CYC:
CYDB-MONOMER
INTERPRO:
IPR003317
MINT:
P0ABK2
PANTHER:
PTHR43141
PFAM:
PF02322
PRIDE:
P0ABK2
PRODB:
PRO_000022362
PROTEINMODELPORTAL:
P0ABK2
REFSEQ:
NP_415262
UNIPROT:
P0ABK2


Operon      
Name: cydAB         
Operon arrangement:
Transcription unit        Promoter
cydAB
cydAB
cydAB
cydAB
cydAB


Transcriptional Regulation      
Display Regulation             
Activated by: FNR, Cra, ArcA, HypT
Repressed by: FNR, H-NS


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_868 771778 forward nd [RS-EPT-CBR] [2]
  promoter TSS_869 771784 forward nd [RS-EPT-CBR] [2]
  promoter TSS_870 771797 forward nd [RS-EPT-CBR] [2]
  promoter TSS_871 771799 forward nd [RS-EPT-CBR] [2]
  promoter TSS_872 771802 forward nd [RS-EPT-CBR] [2]
  promoter TSS_873 771808 forward nd [RS-EPT-CBR] [2]
  promoter TSS_874 772115 forward nd [RS-EPT-CBR] [2]
  promoter TSS_875 772368 forward nd [RS-EPT-CBR] [2]
  promoter TSS_876 772487 forward nd [RS-EPT-CBR] [2]
  promoter TSS_877 773190 forward nd [RS-EPT-CBR] [2]
  promoter TSS_878 773198 forward nd [RS-EPT-CBR] [2]
  promoter TSS_879 773312 forward nd [RS-EPT-CBR] [2]
  promoter TSS_880 773782 forward nd [RS-EPT-CBR] [2]
  promoter TSS_881 773787 forward nd [RS-EPT-CBR] [2]
  promoter TSS_882 773945 forward nd [RS-EPT-CBR] [2]
  promoter TSS_883 773948 forward nd [RS-EPT-CBR] [2]
  promoter TSS_884 (cluster) 773972 forward For this promoter, there
Read more >
[RS-EPT-CBR] [2]
  promoter TSS_885 774006 forward nd [RS-EPT-CBR] [2]
  promoter TSS_886 774011 forward nd [RS-EPT-CBR] [2]
  promoter TSS_887 774017 forward nd [RS-EPT-CBR] [2]
  promoter TSS_888 774033 forward nd [RS-EPT-CBR] [2]
  promoter ybgEp4 774150 forward Similarity to the consensus
Read more >
[ICWHO] [3]


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] Lobritz MA., Belenky P., Porter CB., Gutierrez A., Yang JH., Schwarz EG., Dwyer DJ., Khalil AS., Collins JJ., 2015, Antibiotic efficacy is linked to bacterial cellular respiration., Proc Natl Acad Sci U S A 112(27):8173-80

 [2] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Mu¿¿iz-Rascado L, Garc¿¿a-Sotelo JS, Weiss V, Solano-Lira H, Mart¿¿nez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hern¿¿ndez S, Alquicira-Hern¿¿ndez K, L¿¿pez-Fuentes A, Porr¿¿n-Sotelo L, Huerta AM, Bonavides-Mart¿¿nez C, Balderas-Mart¿¿nez YI, Pannier L, Olvera M, Labastida A, Jim¿¿nez-Jacinto V, Vega-Alvarado L, Del Moral-Ch¿¿vez V, Hern¿¿ndez-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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