RegulonDB RegulonDB 11.1: Gene Form
   

ybdO gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ybdN ybdO dsbG ybdM FNR CysB FNR ArcA TSS_729 TSS_729 ybdNp ybdNp ybdMp2 ybdMp2

Gene      
Name: ybdO    Texpresso search in the literature
Synonym(s): ECK0597, G6332, b0603
Genome position(nucleotides): 636716 <-- 637618
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 38.65
External database links:  
ASAP:
 ABE-0002077
ECHOBASE:
 EB3305
ECOLIHUB:
 ybdO
OU-MICROARRAY:
 b0603
STRING:
 511145.b0603
COLOMBOS: ybdO


Product      
Name: putative LysR family DNA-binding transcriptional regulator YbdO
Synonym(s): YbdO
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 34.397
Isoelectric point: 7.556
Motif(s):
 
Type Positions Sequence Comment
10 -> 67 FDLNLLVIFECIYQHLSISKAAESLYITPSAVSQSLQRLRAQFNDPLFIRSGKGIAPT UniProt: HTH lysR-type.
12 -> 70 LNLLVIFECIYQHLSISKAAESLYITPSAVSQSLQRLRAQFNDPLFIRSGKGIAPTTTG
27 -> 46 ISKAAESLYITPSAVSQSLQ UniProt: H-T-H motif.
134 -> 299 LMSAENAEELLVHRKADLVITQMPVISRSVICMPLHTIRNTLICSNRHPRITDNSTYEQIMAEEFTQLISKSAGVDDIQMEIDERFMNRKISFRGSSLLTIINSIAVTDLLGIVPYELYNSYRDFLNLKEIKLEHPLPSIKLYISYNKSSLNNLVFSRFIDRLNES

 
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
biological_process GO:0006355 - regulation of transcription, DNA-templated
Note(s): Note(s): ...[more].
Evidence: [COMP-AINF-FN-FROM-SEQ] Automated inference of function from sequence
Reference(s): [1] Higashi K., et al., 2016
[2] Perez-Rueda E., et al., 2004
External database links:  
ALPHAFOLD:
 P77746
ECOCYC:
 G6332-MONOMER
ECOLIWIKI:
 b0603
INTERPRO:
 IPR036388
INTERPRO:
 IPR036390
INTERPRO:
 IPR005119
INTERPRO:
 IPR000847
MODBASE:
 P77746
PFAM:
 PF03466
PFAM:
 PF00126
PRIDE:
 P77746
PRINTS:
 PR00039
PROSITE:
 PS50931
REFSEQ:
 NP_415136
SMR:
 P77746
UNIPROT:
 P77746


Operon      
Name: ybdO         
Operon arrangement:
Transcription unit        Promoter
ybdO


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 ybdMp2 635555 reverse nd [COMP-AINF] [3]
  promoter TSS_729 637288 forward nd [RS-EPT-CBR] [4]


Evidence    

 [COMP-AINF] Inferred computationally without human oversight

 [RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates


Reference(s)    

 [1] Higashi K., Tobe T., Kanai A., Uyar E., Ishikawa S., Suzuki Y., Ogasawara N., Kurokawa K., Oshima T., 2016, H-NS Facilitates Sequence Diversification of Horizontally Transferred DNAs during Their Integration in Host Chromosomes., PLoS Genet 12(1):e1005796

 [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] 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

 [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.

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