RegulonDB RegulonDB 11.1: Gene Form
   

yafC gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

yafC dkgB yafD aspU NsrR NsrR terminator anti-terminator anti-anti-terminator TSS_428 TSS_428 TSS_427 TSS_427 TSS_426 TSS_426 TSS_425 TSS_425 yafCp6 yafCp6 yafDp yafDp TSS_424 TSS_424 TSS_423 TSS_423 TSS_422 TSS_422 dkgBp dkgBp TSS_421 TSS_421

Gene      
Name: yafC    Texpresso search in the literature
Synonym(s): ECK0208, EG11649, b0208
Genome position(nucleotides): 229967 <-- 230881
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 49.62
External database links:  
ASAP:
 ABE-0000694
ECHOBASE:
 EB1602
ECOLIHUB:
 yafC
OU-MICROARRAY:
 b0208
STRING:
 511145.b0208
COLOMBOS: yafC


Product      
Name: DNA-binding transcriptional regulator YafC
Synonym(s): YafC, predicted DNA-binding transcriptional regulator LYSR-type
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 33.776
Isoelectric point: 7.497
Motif(s):
 
Type Positions Sequence Comment
1 -> 60 MKATSEELAIFVSVVESGSFSRAAEQLGQANSAVSRAVKKLEMKLGVSLLNRTTRQLSLT UniProt: HTH lysR-type.
7 -> 64 ELAIFVSVVESGSFSRAAEQLGQANSAVSRAVKKLEMKLGVSLLNRTTRQLSLTEEGE
20 -> 39 FSRAAEQLGQANSAVSRAVK UniProt: H-T-H motif.
89 -> 293 NTPRGLLRIDAATPVVLHFLMPLIKPFRERYPEVTLSLVSSETIINLIERKVDVAIRAGTLTDSSLRARPLFNSYRKIIASPDYISRYGKPETIDDLKQHICLGFTEPASLNTWPIARSDGQLHEVKYGLSSNSGETLKQLCLSGNGIACLSDYMIDKEIARGELVELMADKVLPVEMPFSAVYYSDRAVSTRIRAFIDFLSEHV

 
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
  3 - regulation --> 3.1 - type of regulation --> 3.1.2 - transcriptional level --> 3.1.2.3 - repressor
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
GO:0000976 - transcription cis-regulatory region binding
biological_process GO:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
GO:0010212 - response to ionizing radiation
Note(s): Note(s): ...[more].
Evidence: [COMP-HINF-FN-FROM-SEQ] Human inference of function from sequence
[EXP-IPI] Inferred from physical interaction
Reference(s): [1] Gao Y., et al., 2018
[2] Perez-Rueda E., et al., 2004
External database links:  
ALPHAFOLD:
 P30864
DIP:
 DIP-11210N
ECOCYC:
 EG11649-MONOMER
ECOLIWIKI:
 b0208
INTERPRO:
 IPR036388
INTERPRO:
 IPR036390
INTERPRO:
 IPR005119
INTERPRO:
 IPR000847
MODBASE:
 P30864
PFAM:
 PF03466
PFAM:
 PF00126
PRIDE:
 P30864
PRINTS:
 PR00039
PROSITE:
 PS50931
REFSEQ:
 NP_414744
SMR:
 P30864
UNIPROT:
 P30864


Operon      
Name: yafC         
Operon arrangement:
Transcription unit        Promoter
yafC


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_421 228928 forward nd [RS-EPT-CBR] [3]
  promoter TSS_422 230910 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_423 230912 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_424 230918 reverse nd [RS-EPT-CBR] [3]
  promoter yafCp6 231083 reverse nd [COMP-AINF] [4]
  promoter TSS_425 231274 forward nd [RS-EPT-CBR] [3]
  promoter TSS_426 231276 forward nd [RS-EPT-CBR] [3]
  promoter TSS_427 231280 forward nd [RS-EPT-CBR] [3]
  promoter TSS_428 231299 forward nd [RS-EPT-CBR] [3]


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] Gao Y., Yurkovich JT., Seo SW., Kabimoldayev I., Drager A., Chen K., Sastry AV., Fang X., Mih N., Yang L., Eichner J., Cho BK., Kim D., Palsson BO., 2018, Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655., Nucleic Acids Res 46(20):10682-10696

 [2] 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

 [3] 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.

 [4] 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