RegulonDB RegulonDB 10.8: Gene Form
   

ynfB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

speG ynfB ynfA GadX TSS_1871 TSS_1871 TSS_1870 TSS_1870 ynfBp ynfBp ynfAp4 ynfAp4 ynfAp5 ynfAp5 ynfAp7 ynfAp7

Gene      
Name: ynfB    Texpresso search in the literature
Synonym(s): ECK1578, G6841, b1583
Genome position(nucleotides): 1655808 --> 1656149 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
51.17
External database links:  
ASAP:
ABE-0005284
ECHOBASE:
EB3601
OU-MICROARRAY:
b1583
PortEco:
ynfB
STRING:
511145.b1583
COLOMBOS: ynfB


Product      
Name: DUF1283 domain-containing protein YnfB
Synonym(s): YnfB
Sequence: Get amino acid sequence Fasta Format
Cellular location: outer membrane
Molecular weight: 12.909
Isoelectric point: 9.385
Motif(s):
 
Type Positions Sequence
32 -> 113 KLVIESGDSAQSRQHAAMEKEQWNDTRNLRQKVNKRTEKEWDKADAAFDNRDKCEQSANINAYWEPNTLRCLDRRTGRVITP
1 -> 28 MKITLSKRIGLLAILLPCALALSTTVHA
29 -> 113 ETNKLVIESGDSAQSRQHAAMEKEQWNDTRNLRQKVNKRTEKEWDKADAAFDNRDKCEQSANINAYWEPNTLRCLDRRTGRVITP

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
cellular_component GO:0009279 - cell outer membrane
molecular_function GO:0005515 - protein binding
Note(s): Note(s): ...[more].
Reference(s): [1] Paradis-Bleau C., et al., 2014
External database links:  
DIP:
DIP-12762N
ECOCYC:
G6841-MONOMER
ECOLIWIKI:
b1583
INTERPRO:
IPR009700
PFAM:
PF06932
PRIDE:
P76170
PRODOM:
PD073251
REFSEQ:
NP_416100
UNIPROT:
P76170


Operon      
Name: ynfB-speG         
Operon arrangement:
Transcription unit        Promoter
ynfB-speG


Transcriptional Regulation      
Display Regulation             
Repressed by: GadX


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 ynfAp7 1655679 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter ynfAp5 1655690 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter ynfAp4 1655699 reverse Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_1870 1656041 forward nd [RS-EPT-CBR] [3]
  promoter TSS_1871 1656100 forward nd [RS-EPT-CBR] [3]


Evidence    

 [ICWHO] Inferred computationally without human oversight

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



Reference(s)    

 [1] 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

 [2] 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

 [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.


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