RegulonDB RegulonDB 10.8: Gene Form
   

ycjW gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ycjX ycjW ompG ycjF ycjXp ycjXp ycjWp2 ycjWp2 TSS_1745 TSS_1745

Gene      
Name: ycjW    Texpresso search in the literature
Synonym(s): ECK1316, G6658, b1320
Genome position(nucleotides): 1382963 <-- 1383961 Genome Browser
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 45.45
External database links:  
ASAP:
 ABE-0004428
ECHOBASE:
 EB3679
OU-MICROARRAY:
 b1320
PortEco:
 ycjW
STRING:
 511145.b1320
COLOMBOS: ycjW


Product      
Name: DNA-binding transcriptional repressor YcjW
Synonym(s): YcjW, putative LacI-type DNA-binding transcriptional regulator YcjW
Sequence: Get amino acid sequence Fasta Format
Regulator Family: GalR/LacI
Cellular location: cytosol
Molecular weight: 36.134
Isoelectric point: 6.046
Motif(s):
 
Type Positions Sequence
77 -> 321 NPFFSEVLHAITAKAEEEGFDVILQTSHNPAEDLQKCESKIKQKMIKGIIMLSSPADESFFAQLDKYDIPVVVIGKVEGQYAHVYSVDTDNFGDSIALTDALIESGHQNIACLHAPLDVHVSVDRVNGYKQSLAAHNIAVRDEWIVDGGYTHETALKAARQLLSQSPLPEAVFATDSLKLMSIYRAAAEKNIAIPQQLAVVGYSNETLSFILTPAPGGIDVPTQELGQQSCELLFRLISGKPSPQ
4 -> 49 TIYDIARVAGVSKSTVSRVLNKQTNISPEAREKVLRAIEELQYQPN
5 -> 24 IYDIARVAGVSKSTVSRVLN
1 -> 57 MSPTIYDIARVAGVSKSTVSRVLNKQTNISPEAREKVLRAIEELQYQPNKLARALTS

 
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 --> 3.1.2.3 - 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 regulatory region sequence-specific DNA binding
GO:0000984 - bacterial-type RNA polymerase regulatory region sequence-specific DNA binding
biological_process GO:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
GO:0006974 - cellular response to DNA damage stimulus
GO:0045892 - negative regulation of transcription, DNA-templated
Note(s): Note(s): ...[more].
Evidence: [HIFS] Human inference of function from sequence
[IDA] Inferred from direct assay
[IMP] Inferred from mutant phenotype
Reference(s): [1] Luhachack L., et al., 2019
[2] Paradis-Bleau C., et al., 2014
[3] Perez-Rueda E., et al., 2000
[4] Perez-Rueda E., et al., 2004
External database links:  
DIP:
 DIP-11614N
ECOCYC:
 G6658-MONOMER
ECOLIWIKI:
 b1320
INTERPRO:
 IPR000843
INTERPRO:
 IPR028082
INTERPRO:
 IPR010982
INTERPRO:
 IPR001761
MODBASE:
 P77615
PANTHER:
 PTHR30146:SF7
PFAM:
 PF00356
PFAM:
 PF00532
PRIDE:
 P77615
PRINTS:
 PR00036
PROSITE:
 PS50932
PROSITE:
 PS00356
REFSEQ:
 NP_415836
SMART:
 SM00354
SMR:
 P77615
UNIPROT:
 P77615


Operon      
Name: ycjW         
Operon arrangement:
Transcription unit        Promoter
ycjW


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_1745 1383989 reverse nd [RS-EPT-CBR] [5]
  promoter ycjWp2 1383991 reverse Similarity to the consensus
Read more > 		[ICWHO] [6]


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] Luhachack L., Rasouly A., Shamovsky I., Nudler E., 2019, Transcription factor YcjW controls the emergency H2 S production in E. coli., Nat Commun 10(1):2868

 [2] 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

 [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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