RegulonDB RegulonDB 11.1: Gene Form
   

ydbK gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ydbK ydbJ micC hslJ SoxS SoxS anti-anti-terminator anti-terminator terminator ydbJp ydbJp TSS_1788 (cluster) TSS_1788 (cluster) ydbJp1 ydbJp1 ydbKp4 ydbKp4 TSS_1787 TSS_1787 ydbKp ydbKp TSS_1786 TSS_1786 TSS_1785 TSS_1785 TSS_1784 TSS_1784 micCp micCp

Gene      
Name: ydbK    Texpresso search in the literature
Synonym(s): ECK1374, G6701, b1378, pfo
Genome position(nucleotides): 1437260 <-- 1440784
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 53.25
External database links:  
ASAP:
 ABE-0004613
ECHOBASE:
 EB2975
ECOLIHUB:
 ydbK
OU-MICROARRAY:
 b1378
STRING:
 511145.b1378
COLOMBOS: ydbK


Product      
Name: putative pyruvate-flavodoxin oxidoreductase
Synonym(s): Pfo, YdbK
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 128.824
Isoelectric point: 5.563
Motif(s):
 
Type Positions Sequence Comment
13 -> 243 VAFRTSEVIAIYPITPSSTMAEQADAWAGNGLKNVWGDTPRVVEMQSEAGAIATVHGALQTGALSTSFTSSQGLLLMIPTLYKLAGELTPFVLHVAARTVATHALSIFGDHSDVMAVRQTGCAMLCAANVQEAQDFALISQIATLKSRVPFIHFFDGFRTSHEINKIVPLADDTILDLMPQVEIDAHRARALNPEHPVIRGTSANPDTYFQSREATNPWYNAVYDHVEQAM
40 -> 40 A UniProt: In Ref. 4..
51 -> 51 T UniProt: In Ref. 4..
265 -> 347 AERVIILMGSAIGTCEEVVDELLTRGEKVGVLKVRLYRPFSAKHLLQALPGSVRSVAVLDRTKEPGAQAEPLYLDVMTALAEA
426 -> 610 GSDGSVSATKNNIKIIGNSTPWYAQGYFVYDSKKAGGLTVSHLRVSEQPIRSAYLISQADFVGCHQLQFIDKYQMAERLKPGGIFLLNTPYSADEVWSRLPQEVQAVLNQKKARFYVINAAKIARECGLAARINTVMQMAFFHLTQILPGDSALAELQGAIAKSYSSKGQDLVERNWQALALARE

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism
Gene Ontology Terms (GO)  
cellular_component GO:0005886 - plasma membrane
molecular_function GO:0003824 - catalytic activity
GO:0046872 - metal ion binding
GO:0016491 - oxidoreductase activity
GO:0051536 - iron-sulfur cluster binding
GO:0051539 - 4 iron, 4 sulfur cluster binding
GO:0016903 - oxidoreductase activity, acting on the aldehyde or oxo group of donors
GO:0005506 - iron ion binding
GO:0030976 - thiamine pyrophosphate binding
GO:0043873 - pyruvate-flavodoxin oxidoreductase activity
biological_process GO:0006979 - response to oxidative stress
GO:0022900 - electron transport chain
Note(s): Note(s): ...[more].
External database links:  
ALPHAFOLD:
 P52647
DIP:
 DIP-11636N
ECOCYC:
 G6701-MONOMER
ECOLIWIKI:
 b1378
INTERPRO:
 IPR037112
INTERPRO:
 IPR033412
INTERPRO:
 IPR029061
INTERPRO:
 IPR019752
INTERPRO:
 IPR019456
INTERPRO:
 IPR011766
INTERPRO:
 IPR002869
INTERPRO:
 IPR011895
INTERPRO:
 IPR009014
INTERPRO:
 IPR002880
INTERPRO:
 IPR017900
INTERPRO:
 IPR017896
MODBASE:
 P52647
PFAM:
 PF17147
PFAM:
 PF13484
PFAM:
 PF10371
PFAM:
 PF02775
PFAM:
 PF01558
PFAM:
 PF01855
PRIDE:
 P52647
PROSITE:
 PS51379
PROSITE:
 PS00198
REFSEQ:
 NP_415896
SMART:
 SM00890
SMR:
 P52647
SWISSMODEL:
 P52647
UNIPROT:
 P52647


Operon      
Name: ydbK-ompN         
Operon arrangement:
Transcription unit        Promoter
ompN
ydbK
ydbK-ompN
ydbK-ompN


Transcriptional Regulation      
Display Regulation             
Activated by: SoxS


RNA cis-regulatory element    
Attenuation: Transcriptional


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_1784 1438596 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1785 1438744 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1786 1438759 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_1787 1440845 reverse nd [RS-EPT-CBR] [1]
  promoter ydbJp1 1440856 forward nd [COMP-AINF] [2]
  promoter TSS_1788 (cluster) 1441022 forward nd [RS-EPT-CBR] [1]


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] 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.

 [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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