RegulonDB RegulonDB 10.10: Gene Form
   

yqhC gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yqhD yqhC yghB YqhC YqhC anti-anti-terminator anti-terminator terminator yqhCp1 yqhCp1 TSS_3318 TSS_3318 yqhDp yqhDp TSS_3317 TSS_3317

Gene      
Name: yqhC    Texpresso search in the literature
Synonym(s): ECK3002, G7563, b3010
Genome position(nucleotides): 3154262 <-- 3155218 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 50.47
External database links:  
ASAP:
 ABE-0009884
ECHOBASE:
 EB2833
ECOLIHUB:
 yqhC
OU-MICROARRAY:
 b3010
STRING:
 511145.b3010
COLOMBOS: yqhC


Product      
Name: DNA-binding transcriptional activator YqhC
Synonym(s): YqhC
Sequence: Get amino acid sequence Fasta Format
Regulator Family: AraC/XylS
Cellular location: cytosol
Molecular weight: 35.957
Isoelectric point: 8.346
Motif(s):
 
Type Positions Sequence
230 -> 251 EQLAAEANMSVSAFHHNFKSVT
47 -> 197 LPDVRLLYGETPFARTPVMYEPGIIILFSGHKIGYINERVFRYDANEYLLLTVPLPFECETYATSEVPLAGLRLNVDILQLQELLMDIGEDEHFQPSMAASGINSATLSEEILCAAERLLDVMERPLDARILGKQIIREILYYVLTGPCGG
213 -> 311 SRVLKRIENKYTENLSVEQLAAEANMSVSAFHHNFKSVTSTSPLQYLKNYRLHKARMMIIHDGMKASAAAMRVGYESASQFSREFKRYFGVTPGEDAAR
232 -> 307 LAAEANMSVSAFHHNFKSVTSTSPLQYLKNYRLHKARMMIIHDGMKASAAAMRVGYESASQFSREFKRYFGVTPGE
278 -> 301 ASAAAMRVGYESASQFSREFKRYF

 
Classification:
Multifun Terms (GenProtEC)  
  2 - information transfer --> 2.2 - RNA related --> 2.2.2 - Transcription related
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.2 - activator
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
GO:0043565 - sequence-specific DNA binding
GO:0000986 - bacterial-type cis-regulatory region sequence-specific DNA binding
GO:0001216 - DNA-binding transcription activator activity
biological_process GO:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
GO:0045893 - positive regulation of transcription, DNA-templated
Note(s): Note(s): ...[more].
Evidence: [APPHINH] Assay of protein purified to homogeneity from its native host
[HIFS] Human inference of function from sequence
[IEP] Inferred from expression pattern
Reference(s): [1] Lee C., et al., 2010
[2] Perez-Rueda E., et al., 2000
[3] Perez-Rueda E., et al., 2004
External database links:  
ECOCYC:
 G7563-MONOMER
ECOLIWIKI:
 b3010
INTERPRO:
 IPR018060
INTERPRO:
 IPR009594
INTERPRO:
 IPR009057
MODBASE:
 Q46855
PFAM:
 PF12833
PFAM:
 PF06719
PRIDE:
 Q46855
PROSITE:
 PS01124
REFSEQ:
 NP_417483
SMART:
 SM00342
SMR:
 Q46855
UNIPROT:
 Q46855


Operon      
Name: yqhC         
Operon arrangement:
Transcription unit        Promoter
yqhC


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_3317 3153632 forward nd [RS-EPT-CBR] [4]
  promoter TSS_3318 3155303 forward nd [RS-EPT-CBR] [4]
  promoter yqhCp1 3155384 reverse nd [ICWHO] [5]


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] Lee C., Kim I., Lee J., Lee KL., Min B., Park C., 2010, Transcriptional activation of the aldehyde reductase YqhD by YqhC and its implication in glyoxal metabolism of Escherichia coli K-12., J Bacteriol 192(16):4205-14

 [2] Perez-Rueda E., Collado-Vides J., 2000, The repertoire of DNA-binding transcriptional regulators in Escherichia coli K-12., Nucleic Acids Res 28(8):1838-47

 [3] Perez-Rueda E., Collado-Vides J., Segovia L., 2004, Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea., Comput Biol Chem 28(5-6):341-50

 [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.

 [5] 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

RegulonDB