RegulonDB RegulonDB 10.7: 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 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
53.25
External database links:  
ASAP:
ABE-0004613
ECHOBASE:
EB2975
OU-MICROARRAY:
b1378
PORTECO:
ydbK
REGULONDB:
b1378
STRING:
511145.b1378
M3D: ydbK
COLOMBOS: ydbK
PortEco: b1378


Product      
Name: putative pyruvate-flavodoxin oxidoreductase
Synonym(s): Pfo, YdbK
Sequence: Get amino acid sequence Fasta Format
Molecular weight: 128.824
Isoelectric point: 5.563
Motif(s):
 
Type Positions Sequence
954 -> 1066 EKSIWLIGGDGWAYDIGFGGLDHVLSLTENVNILVLDTQCYSNTGGQASKATPLGAVTKFGEHGKRKARKDLGVSMMMYGHVYVAQISLGAQLNQTVKAIQEAEAYPGPSLII
40 -> 40 A
426 -> 610 GSDGSVSATKNNIKIIGNSTPWYAQGYFVYDSKKAGGLTVSHLRVSEQPIRSAYLISQADFVGCHQLQFIDKYQMAERLKPGGIFLLNTPYSADEVWSRLPQEVQAVLNQKKARFYVINAAKIARECGLAARINTVMQMAFFHLTQILPGDSALAELQGAIAKSYSSKGQDLVERNWQALALARE
626 -> 678 NRPPVVSDAAPDFVKTVTAAMLAGLGDALPVSALPPDGTWPMGTTRWEKRNIA
13 -> 243 VAFRTSEVIAIYPITPSSTMAEQADAWAGNGLKNVWGDTPRVVEMQSEAGAIATVHGALQTGALSTSFTSSQGLLLMIPTLYKLAGELTPFVLHVAARTVATHALSIFGDHSDVMAVRQTGCAMLCAANVQEAQDFALISQIATLKSRVPFIHFFDGFRTSHEINKIVPLADDTILDLMPQVEIDAHRARALNPEHPVIRGTSANPDTYFQSREATNPWYNAVYDHVEQAM

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism
Gene Ontology Terms (GO)  
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
GO:0055114 - oxidation-reduction process
Note(s): Note(s): ...[more].
External database links:  
DIP:
DIP-11636N
ECOCYC:
G6701-MONOMER
ECOLIWIKI:
b1378
INTERPRO:
IPR011766
INTERPRO:
IPR002869
INTERPRO:
IPR002880
INTERPRO:
IPR009014
INTERPRO:
IPR037112
INTERPRO:
IPR011895
INTERPRO:
IPR017896
INTERPRO:
IPR017900
INTERPRO:
IPR019456
INTERPRO:
IPR019752
INTERPRO:
IPR029061
INTERPRO:
IPR033412
MINT:
MINT-1299276
MODBASE:
P52647
PFAM:
PF01855
PFAM:
PF17147
PFAM:
PF10371
PFAM:
PF02775
PFAM:
PF01558
PRIDE:
P52647
PROSITE:
PS51379
PROSITE:
PS00198
PROTEINMODELPORTAL:
P52647
REFSEQ:
NP_415896
SMART:
SM00890
SMR:
P52647
SWISSMODEL:
P52647
UNIPROT:
P52647


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


Transcriptional Regulation      
Display Regulation             
Activated by: SoxS


RNA cis-regulatory element    
Attenuation: Transcriptional


Regulation by small RNA    
  Display Regulation
small RNA ryhB


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 Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_1788 (cluster) 1441022 forward For this promoter, there
Read more >
[RS-EPT-CBR] [1]


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] 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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