RegulonDB RegulonDB 11.1: Gene Form
   

yodB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

zinT yodB serU terminator yodBp13 yodBp13 yodBp16 yodBp16 yodBp14 yodBp14 yodBp15 yodBp15

Gene      
Name: yodB    Texpresso search in the literature
Synonym(s): ECK1970, G7062, b1974
Genome position(nucleotides): 2042368 --> 2042898
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 42.18
External database links:  
ASAP:
 ABE-0006552
ECHOBASE:
 EB3803
ECOLIHUB:
 yodB
OU-MICROARRAY:
 b1974
STRING:
 511145.b1974
COLOMBOS: yodB


Product      
Name: putative cytochrome b561 YodB
Synonym(s): YodB
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 20.337
Isoelectric point: 10.555
Motif(s):
 
Type Positions Sequence Comment
3 -> 173 RFSKTQIYLHWITLLFVAITYAAMELRGWFPKGSSTYLLMRETHYNAGIFVWVLMFSRLIIKHRYSDPSIVPPPPAWQMKAASLMHIMLYITFLALPLLGIALMAYSGKSWSFLGFNVSPFVTPNSEIKALIKNIHETWANIGYFLIAAHAGAALFHHYIQKDNTLLRMMP
8 -> 28 QIYLHWITLLFVAITYAAMEL UniProt: Helical.
86 -> 106 LMHIMLYITFLALPLLGIALM UniProt: Helical.
142 -> 162 ANIGYFLIAAHAGAALFHHYI UniProt: Helical.

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - 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:0022904 - respiratory electron transport chain
Note(s): Note(s): ...[more].
Reference(s): [1] Paradis-Bleau C., et al., 2014
External database links:  
ALPHAFOLD:
 P76345
ECOCYC:
 G7062-MONOMER
ECOLIWIKI:
 b1974
INTERPRO:
 IPR011577
INTERPRO:
 IPR016174
PFAM:
 PF01292
PRIDE:
 P76345
REFSEQ:
 NP_416483
SMR:
 P76345
UNIPROT:
 P76345


Operon      
Name: yodB         
Operon arrangement:
Transcription unit        Promoter
yodB


RNA cis-regulatory element    
Attenuation: Translational


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 yodBp15 2042176 forward nd [COMP-AINF] [2]
  promoter yodBp14 2042261 forward nd [COMP-AINF] [2]
  promoter yodBp16 2042294 forward nd [COMP-AINF] [2]
  promoter yodBp13 2042308 forward nd [COMP-AINF] [2]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight


Reference(s)    

 [1] Paradis-Bleau C., Kritikos G., Orlova K., Typas A., Bernhardt TG., 2014, A genome-wide screen for bacterial envelope biogenesis mutants identifies a novel factor involved in cell wall precursor metabolism., PLoS Genet 10(1):e1004056

 [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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