RegulonDB RegulonDB 10.8: Gene Form
   

ycaK gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ycaN pflA ycaK TSS_1102 TSS_1102 TSS_1101 TSS_1101 TSS_1100 TSS_1100 TSS_1099 TSS_1099 ycaKp5 ycaKp5 ycaKp4 ycaKp4 ycaKp3 ycaKp3

Gene      
Name: ycaK    Texpresso search in the literature
Synonym(s): ECK0892, EG12702, b0901
Genome position(nucleotides): 949668 --> 950258 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
42.81
External database links:  
ASAP:
ABE-0003065
ECHOBASE:
EB2564
OU-MICROARRAY:
b0901
PortEco:
ycaK
STRING:
511145.b0901
COLOMBOS: ycaK


Product      
Name: putative NAD(P)H-dependent oxidoreductase YcaK
Synonym(s): YcaK
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 23.036
Isoelectric point: 5.067
Motif(s):
 
Type Positions Sequence
5 -> 181 RIYLVWAHPRHDSLTAHIADAIHQRAMERKIQVTELDLYRRNFNPVMTPEDEPDWKNMDKRYSPEVHQLYSELLEHDTLVVVFPLWWYSFPAMLKGYIDRVWNNGLAYGDGHKLPFNKVRWVALVGGDKESFVQMGWEKNISDYLKNMCSYLGIEDADVTFLCNTVVFDGEELHASY

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0016491 - oxidoreductase activity
GO:0003955 - NAD(P)H dehydrogenase (quinone) activity
GO:0010181 - FMN binding
biological_process GO:0055114 - oxidation-reduction process
Note(s): Note(s): ...[more].
Evidence: [HIFS] Human inference of function from sequence
Reference(s): [1] Paradis-Bleau C., et al., 2014
[2] Reed JL., et al., 2003
External database links:  
ECOCYC:
EG12702-MONOMER
ECOLIWIKI:
b0901
INTERPRO:
IPR003680
INTERPRO:
IPR029039
MODBASE:
P43340
PFAM:
PF02525
PRIDE:
P43340
REFSEQ:
NP_415421
SMR:
P43340
UNIPROT:
P43340


Operon      
Name: ycaK         
Operon arrangement:
Transcription unit        Promoter
ycaK


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 ycaKp3 949547 forward Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter ycaKp4 949574 forward Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter ycaKp5 949643 forward Similarity to the consensus
Read more >
[ICWHO] [3]
  promoter TSS_1099 950823 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_1100 950832 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_1101 950837 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_1102 950916 reverse nd [RS-EPT-CBR] [4]


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] Paradis-Bleau C., Kritikos G., Orlova K., Typas A., Bernhardt TG., 2014, A genome-wide screen for bacterial envelope biogenesis mutants identifies a novel factor involved in cell wall precursor metabolism., PLoS Genet 10(1):e1004056

 [2] Reed JL., Vo TD., Schilling CH., Palsson BO., 2003, An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR)., Genome Biol 4(9):R54

 [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.


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