RegulonDB RegulonDB 11.1: Gene Form
   

ygbI gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ygbJ ygbI pphB ygbK ygbKp ygbKp ygbIp5 ygbIp5 ygbIp6 ygbIp6 TSS_3025 TSS_3025

Gene      
Name: ygbI    Texpresso search in the literature
Synonym(s): ECK2730, G7416, b2735
Genome position(nucleotides): 2860467 <-- 2861234
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 51.56
External database links:  
ASAP:
 ABE-0008982
ECHOBASE:
 EB2906
ECOLIHUB:
 ygbI
OU-MICROARRAY:
 b2735
STRING:
 511145.b2735
COLOMBOS: ygbI


Product      
Name: DNA-binding transcriptional repressor YgbI
Synonym(s): YgbI
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 27.435
Isoelectric point: 6.781
Motif(s):
 
Type Positions Sequence Comment
3 -> 58 PVERRQIILEMVAEKGIVSIAELTDRMNVSHMTIRRDLQKLEQQGAVVLVSGGVQS UniProt: HTH deoR-type.
6 -> 59 RRQIILEMVAEKGIVSIAELTDRMNVSHMTIRRDLQKLEQQGAVVLVSGGVQSP
20 -> 39 VSIAELTDRMNVSHMTIRRD UniProt: H-T-H motif.
76 -> 231 MTQKAAIGKLAASLVQPGSCIYLDAGTTTLAIAQHLIHMESLTVVTNDFVIADYLLDNSNCTIIHTGGAVCRENRSCVGEAAATMLRSLMIDQAFISASSWSVRGISTPAEDKVTVKRAIASASRQRVLVCDATKYGQVATWLALPLSEFDQIITD

 
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
biological_process GO:0006351 - transcription, DNA-templated
GO:0006355 - regulation of transcription, DNA-templated
Note(s): Note(s): ...[more].
Evidence: [COMP-HINF-FN-FROM-SEQ] Human inference of function from sequence
Reference(s): [1] Perez-Rueda E., et al., 2000
[2] Perez-Rueda E., et al., 2004
External database links:  
ALPHAFOLD:
 P52598
DIP:
 DIP-12110N
ECOCYC:
 G7416-MONOMER
ECOLIWIKI:
 b2735
INTERPRO:
 IPR036390
INTERPRO:
 IPR037171
INTERPRO:
 IPR036388
INTERPRO:
 IPR018356
INTERPRO:
 IPR014036
INTERPRO:
 IPR001034
MODBASE:
 P52598
PFAM:
 PF08220
PFAM:
 PF00455
PRIDE:
 P52598
PRINTS:
 PR00037
PROSITE:
 PS51000
PROSITE:
 PS00894
REFSEQ:
 NP_417215
SMART:
 SM00420
UNIPROT:
 P52598


Operon      
Name: ygbI         
Operon arrangement:
Transcription unit        Promoter
ygbI


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_3025 2861256 reverse nd [RS-EPT-CBR] [3]
  promoter ygbIp6 2861362 reverse nd [COMP-AINF] [4]
  promoter ygbIp5 2861441 reverse nd [COMP-AINF] [4]


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] 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

 [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

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