RegulonDB RegulonDB 11.1: Gene Form
   

yebK gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

zwf pykA yebK Rob MarA SoxS Cra Qin prophage; DicF TSS_2208 TSS_2208 TSS_2207 TSS_2207 TSS_2206 TSS_2206 TSS_2205 TSS_2205 TSS_2204 TSS_2204 TSS_2203 TSS_2203 pykAp1 pykAp1 pykAp pykAp TSS_2201 TSS_2201 pykAp3 pykAp3 pykAp2 pykAp2 TSS_2199 TSS_2199 yebKp2 yebKp2 zwfp zwfp TSS_2197 TSS_2197 TSS_2196 TSS_2196

Gene      
Name: yebK    Texpresso search in the literature
Synonym(s): ECK1854, EG12860, b1853, hexR(P.a.)
Genome position(nucleotides): 1936652 --> 1937521
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 48.97
External database links:  
ASAP:
 ABE-0006179
ECHOBASE:
 EB2702
ECOLIHUB:
 yebK
OU-MICROARRAY:
 b1853
STRING:
 511145.b1853
COLOMBOS: yebK


Product      
Name: DNA-binding transcriptional repressor YebK
Synonym(s): YebK
Sequence: Get amino acid sequence Fasta Format
Regulator Family: RpiR
Cellular location: cytosol
Molecular weight: 31.976
Isoelectric point: 6.634
Motif(s):
 
Type Positions Sequence Comment
1 -> 76 MNMLEKIQSQLEHLSKSERKVAEVILASPDNAIHSSIAAMALEANVSEPTVNRFCRSMDTRGFPDFKLHLAQSLAN
37 -> 56 IAAMALEANVSEPTVNRFCR UniProt: H-T-H motif.
82 -> 82 N UniProt: In Ref. 5; AAA68942..
121 -> 260 AVDLLTQAKKIAFFGLGSSAAVAHDAMNKFFRFNVPVVYSDDIVLQRMSCMNCSDGDVVVLISHTGRTKNLVELAQLARENDAMVIALTSAGTPLAREATLAITLDVPEDTDIYMPMVSRLAQLTVIDVLATGFTLRRGA UniProt: SIS.
124 -> 252 LLTQAKKIAFFGLGSSAAVAHDAMNKFFRFNVPVVYSDDIVLQRMSCMNCSDGDVVVLISHTGRTKNLVELAQLARENDAMVIALTSAGTPLAREATLAITLDVPEDTDIYMPMVSRLAQLTVIDVLAT

 
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
Gene Ontology Terms (GO)  
cellular_component GO:0005829 - cytosol
molecular_function GO:0003677 - DNA binding
GO:0003700 - DNA-binding transcription factor activity
GO:0097367 - carbohydrate derivative binding
biological_process GO:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
GO:0006974 - cellular response to DNA damage stimulus
GO:1901135 - carbohydrate derivative metabolic process
Note(s): Note(s): ...[more].
Evidence: [COMP-AINF-FN-FROM-SEQ] Automated inference of function from sequence
[COMP-AINF-SEQ-ORTHOLOGY] Automated inference of function by sequence orthology
[COMP-HINF-FN-FROM-SEQ] Human inference of function from sequence
[IDA-PURIFIED-PROTEIN-NH] Assay of protein purified to homogeneity from its native host
Reference(s): [1] Leyn SA., et al., 2011
[2] Parisutham V., et al., 2015
[3] Perez-Rueda E., et al., 2000
[4] Perez-Rueda E., et al., 2004
External database links:  
ALPHAFOLD:
 P46118
DIP:
 DIP-9891N
ECOCYC:
 EG12860-MONOMER
ECOLIWIKI:
 b1853
INTERPRO:
 IPR035472
INTERPRO:
 IPR036388
INTERPRO:
 IPR009057
INTERPRO:
 IPR001347
INTERPRO:
 IPR000281
MODBASE:
 P46118
PFAM:
 PF01418
PFAM:
 PF01380
PRIDE:
 P46118
PRODB:
 PRO_000022881
PROSITE:
 PS51464
PROSITE:
 PS51071
REFSEQ:
 NP_416367
SMR:
 P46118
UNIPROT:
 P46118


Operon      
Name: yebK         
Operon arrangement:
Transcription unit        Promoter
yebK


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_2196 1935229 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_2197 1935719 reverse nd [RS-EPT-CBR] [5]
  promoter yebKp2 1936590 forward nd [COMP-AINF], [RS-EPT-CBR] [5], [6]
  promoter TSS_2199 1936593 forward nd [RS-EPT-CBR] [5]
  promoter TSS_2201 1937542 forward nd [RS-EPT-CBR] [5]
  promoter TSS_2203 1937547 forward nd [RS-EPT-CBR] [5]
  promoter TSS_2204 1937561 reverse nd [RS-EPT-CBR] [5]
  promoter TSS_2205 1937670 forward nd [RS-EPT-CBR] [5]
  promoter TSS_2206 1937972 forward nd [RS-EPT-CBR] [5]
  promoter TSS_2207 1938121 forward nd [RS-EPT-CBR] [5]
  promoter TSS_2208 1938452 forward nd [RS-EPT-CBR] [5]


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] Leyn SA., Li X., Zheng Q., Novichkov PS., Reed S., Romine MF., Fredrickson JK., Yang C., Osterman AL., Rodionov DA., 2011, Control of proteobacterial central carbon metabolism by the HexR transcriptional regulator: a case study in Shewanella oneidensis., J Biol Chem 286(41):35782-94

 [2] Parisutham V., Lee SK., 2015, Novel Functions and Regulation of Cryptic Cellobiose Operons in Escherichia coli., PLoS One 10(6):e0131928

 [3] 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

 [4] 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

 [5] 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.

 [6] 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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