RegulonDB RegulonDB 10.8: Gene Form
   

ybaQ gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

copA ybaP ybaQ chiX TSS_651 TSS_651 TSS_650 TSS_650 ybaPp6 ybaPp6 ybaPp4 ybaPp4 ybaPp3 ybaPp3 ybaQp ybaQp ybaQp3 ybaQp3 TSS_649 TSS_649

Gene      
Name: ybaQ    Texpresso search in the literature
Synonym(s): ECK0477, G6259, b0483
Genome position(nucleotides): 508218 --> 508559 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
44.74
External database links:  
ASAP:
ABE-0001677
ECHOBASE:
EB3034
OU-MICROARRAY:
b0483
PortEco:
ybaQ
STRING:
511145.b0483
COLOMBOS: ybaQ


Product      
Name: DNA-binding transcriptional regulator YbaQ
Synonym(s): YbaQ
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 13.171
Isoelectric point: 5.792
Motif(s):
 
Type Positions Sequence
16 -> 70 LYEYLEPLDLKINELAELLHVHRNSVSALINNNRKLTTEMAFRLAKVFDTTVDFW
27 -> 46 INELAELLHVHRNSVSALIN

 

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
biological_process GO:0006351 - transcription, DNA-templated
Note(s): Note(s): ...[more].
Evidence: [AIFS] Automated inference of function from sequence
[IPI] Inferred from physical interaction
Reference(s): [1] Gao Y., et al., 2018
[2] Perez-Rueda E., et al., 2000
[3] Perez-Rueda E., et al., 2004
External database links:  
ECOCYC:
G6259-MONOMER
ECOLIWIKI:
b0483
INTERPRO:
IPR001387
INTERPRO:
IPR013430
INTERPRO:
IPR010982
PANTHER:
PTHR36924
PDB:
2EBY
PFAM:
PF01381
PRIDE:
P0A9T6
PROSITE:
PS50943
REFSEQ:
NP_415016
SMART:
SM00530
SMR:
P0A9T6
UNIPROT:
P0A9T6


Operon      
Name: ybaQ         
Operon arrangement:
Transcription unit        Promoter
ybaQ


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_649 508097 reverse nd [RS-EPT-CBR] [4]
  promoter ybaQp3 508174 forward Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter ybaPp3 508262 reverse Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter ybaPp4 508264 reverse Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter ybaPp6 508284 reverse Similarity to the consensus
Read more >
[ICWHO] [5]
  promoter TSS_650 511367 reverse nd [RS-EPT-CBR] [4]
  promoter TSS_651 511370 reverse nd [RS-EPT-CBR] [4]


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] 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., 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


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