RegulonDB RegulonDB 10.7: Gene Form
   

ynfD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ynfE ynfC ynfD NarL NarL FNR ynfEp ynfEp ynfCp9 ynfCp9 TSS_1873 TSS_1873 TSS_1872 TSS_1872 ynfDp6 ynfDp6

Gene      
Name: ynfD    Texpresso search in the literature
Synonym(s): ECK1581, G6844, b1586
Genome position(nucleotides): 1657565 --> 1657870 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
56.21
External database links:  
ASAP:
ABE-0005297
ECHOBASE:
EB3603
OU-MICROARRAY:
b1586
PORTECO:
ynfD
REGULONDB:
b1586
STRING:
511145.b1586
M3D: ynfD
COLOMBOS: ynfD
PortEco: b1586


Product      
Name: DUF1161 domain-containing protein YnfD
Synonym(s): YnfD
Sequence: Get amino acid sequence Fasta Format
Molecular weight: 10.477
Isoelectric point: 4.546
Motif(s):
 
Type Positions Sequence
26 -> 79 CERIQSDISQRIINNGVPESSFTLSIVPNDQVDQPDSQVVGHCANDTHKILYTR
22 -> 101 APGSCERIQSDISQRIINNGVPESSFTLSIVPNDQVDQPDSQVVGHCANDTHKILYTRTTSGNVSAPAQSSQDGAPAEPQ
1 -> 21 MKLSTCCAALLLALASPAVLA

 

Classification:
Multifun Terms (GenProtEC)  
Gene Ontology Terms (GO)  
Note(s): Note(s): ...[more].
Reference(s): [1] Paradis-Bleau C., et al., 2014
External database links:  
DIP:
DIP-12764N
ECOCYC:
G6844-MONOMER
ECOLIWIKI:
b1586
INTERPRO:
IPR010595
PFAM:
PF06649
PRIDE:
P76172
PRODOM:
PD336997
PROTEINMODELPORTAL:
P76172
REFSEQ:
NP_416103
UNIPROT:
P76172


Operon      
Name: ynfD         
Operon arrangement:
Transcription unit        Promoter
 


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 ynfDp6 1657414 forward Similarity to the consensus
Read more >
[ICWHO] [2]
  promoter TSS_1872 1657482 reverse nd [RS-EPT-CBR] [3]
  promoter TSS_1873 1657539 forward nd [RS-EPT-CBR] [3]
  promoter ynfCp9 1657547 reverse Similarity to the consensus
Read more >
[ICWHO] [2]


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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