RegulonDB RegulonDB 10.8: Gene Form
   

ybdR gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ybdR uspG yldA unknown terminator TSS_747 TSS_747 TSS_746 TSS_746 ybdRp6 ybdRp6 uspGp uspGp

Gene      
Name: ybdR    Texpresso search in the literature
Synonym(s): ECK0602, G6335, b0608
Genome position(nucleotides): 642088 --> 643326 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
50.12
External database links:  
ASAP:
ABE-0002099
ECHOBASE:
EB3307
OU-MICROARRAY:
b0608
PortEco:
ybdR
STRING:
511145.b0608
COLOMBOS: ybdR


Product      
Name: putative Zn2+-dependent alcohol dehydrogenase YbdR
Synonym(s): YbdR
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 44.176
Isoelectric point: 6.561
Motif(s):
 
Type Positions Sequence
197 -> 280 PVGLLTIACARLLGAEQIFVVDHHPYRLHFAADRYGAIPINFDEDSDPAQSIIEQTAGHRGVDAVIDAVGFEAKGSTTETVLTN
26 -> 151 DDIILRITATAICGSDLHLYRGKIPQVKHGDIFGHEFMGEVVETGKDVKNLQKGDRVVIPFVIACGDCFFCRLQQYAACENTNAGKGAALNKKQIPAPAALFGYSHLYGGVPGGQAEYVRVPKGNV
1 -> 23 MKALTYHGPHHVQVENVPDPGVE

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0046872 - metal ion binding
GO:0016491 - oxidoreductase activity
GO:0008270 - zinc ion binding
biological_process GO:0055114 - oxidation-reduction process
Note(s): Note(s): ...[more].
External database links:  
DIP:
DIP-11355N
ECOCYC:
G6335-MONOMER
ECOLIWIKI:
b0608
INTERPRO:
IPR036291
INTERPRO:
IPR027399
INTERPRO:
IPR013154
INTERPRO:
IPR013149
INTERPRO:
IPR002328
INTERPRO:
IPR011032
MODBASE:
P77316
PANTHER:
PTHR11695
PFAM:
PF00107
PFAM:
PF13823
PFAM:
PF08240
PRIDE:
P77316
PROSITE:
PS00059
REFSEQ:
NP_415141
SMR:
P77316
UNIPROT:
P77316


Operon      
Name: ybdR         
Operon arrangement:
Transcription unit        Promoter
 


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 ybdRp6 641922 forward Similarity to the consensus
Read more >
[ICWHO] [1]
  promoter TSS_746 642181 forward nd [RS-EPT-CBR] [2]
  promoter TSS_747 643027 forward nd [RS-EPT-CBR] [2]


Evidence    

 [ICWHO] Inferred computationally without human oversight

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



Reference(s)    

 [1] 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

 [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.


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