RegulonDB RegulonDB 10.9: 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
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
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:
IPR037112
INTERPRO:
IPR017896
INTERPRO:
IPR017900
INTERPRO:
IPR019456
INTERPRO:
IPR019752
INTERPRO:
IPR029061
INTERPRO:
IPR033412
INTERPRO:
IPR009014
INTERPRO:
IPR002880
INTERPRO:
IPR002869
INTERPRO:
IPR011895
MODBASE:
P52647
PFAM:
PF01855
PFAM:
PF17147
PFAM:
PF13484
PFAM:
PF10371
PFAM:
PF02775
PFAM:
PF01558
PRIDE:
P52647
PROSITE:
PS00198
PROSITE:
PS51379
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 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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