RegulonDB RegulonDB 11.1: Gene Form
   

yobA gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yebZ yobA holE TSS_2185 TSS_2185 yobBp8 yobBp8 TSS_2184 TSS_2184 holEp6 holEp6 holEp4 holEp4 holEp5 holEp5

Gene      
Name: yobA    Texpresso search in the literature
Synonym(s): ECK1842, G7014, b1841
Genome position(nucleotides): 1924595 <-- 1924969
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 49.87
External database links:  
ASAP:
 ABE-0006123
ECHOBASE:
 EB3783
ECOLIHUB:
 yobA
OU-MICROARRAY:
 b1841
STRING:
 511145.b1841
COLOMBOS: yobA


Product      
Name: copper-binding protein
Synonym(s): YobA
Sequence: Get amino acid sequence Fasta Format
Cellular location: periplasmic space
Molecular weight: 13.41
Isoelectric point: 9.999
Motif(s):
 
Type Positions Sequence Comment
1 -> 26 MASTARSLRYALAILTTSLVTPSVWA
27 -> 124 HAHLTHQYPAANAQVTAAPQAITLNFSEGVETGFSGAKITGPKNENIKTLPAKRNEQDQKQLIVPLADSLKPGTYTVDWHVVSVDGHKTKGHYTFSVK UniProt: Protein YobA.

 
Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0030288 - outer membrane-bounded periplasmic space
GO:0042597 - periplasmic space
molecular_function GO:0005507 - copper ion binding
GO:0046872 - metal ion binding
biological_process GO:0046688 - response to copper ion
GO:0006825 - copper ion transport
GO:0055070 - copper ion homeostasis
Note(s): Note(s): ...[more].
Evidence: [EXP-IDA] Inferred from direct assay
Reference(s): [1] Hadley RC., et al., 2021
[2] Myers KS., et al., 2013
External database links:  
ALPHAFOLD:
 P0AA57
ECOCYC:
 G7014-MONOMER
ECOLIWIKI:
 b1841
INTERPRO:
 IPR032694
INTERPRO:
 IPR014756
INTERPRO:
 IPR007348
MODBASE:
 P0AA57
PANTHER:
 PTHR34820
PFAM:
 PF04234
PRIDE:
 P0AA57
REFSEQ:
 NP_416355
SMR:
 P0AA57
SWISSMODEL:
 P0AA57
UNIPROT:
 P0AA57


Operon      
Name: yobA-yebZY         
Operon arrangement:
Transcription unit        Promoter
yobA-yebZY


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 holEp5 1925020 forward nd [COMP-AINF] [3]
  promoter holEp4 1925029 forward nd [COMP-AINF] [3]
  promoter holEp6 1925086 forward nd [COMP-AINF] [3]
  promoter TSS_2184 1925088 forward nd [RS-EPT-CBR] [4]
  promoter yobBp8 1925209 forward nd [COMP-AINF] [3]
  promoter TSS_2185 1925307 reverse nd [RS-EPT-CBR] [4]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

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


Reference(s)    

 [1] Hadley RC., Zhitnitsky D., Livnat-Levanon N., Masrati G., Vigonsky E., Rose J., Ben-Tal N., Rosenzweig AC., Lewinson O., 2021, The copper-linked Escherichia coli AZY operon: Structure, metal binding, and a possible physiological role in copper delivery., J Biol Chem 298(1):101445

 [2] Myers KS., Yan H., Ong IM., Chung D., Liang K., Tran F., Keles S., Landick R., Kiley PJ., 2013, Genome-scale analysis of escherichia coli FNR reveals complex features of transcription factor binding., PLoS Genet 9(6):e1003565

 [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

 [4] 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.

RegulonDB