RegulonDB RegulonDB 11.1: Gene Form
   

ydfJ gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ydfI ydfJ ynfT anti-anti-terminator anti-terminator terminator terminator ydfKp5 ydfKp5 TSS_1860 TSS_1860 TSS_1859 TSS_1859 TSS_1858 TSS_1858 TSS_1857 TSS_1857 TSS_1856 TSS_1856 TSS_1855 TSS_1855 TSS_1854 TSS_1854 ynfTp ynfTp TSS_1853 TSS_1853 TSS_1852 TSS_1852

Gene      
Name: ydfJ    Texpresso search in the literature
Synonym(s): ECK1536, G6817, b1543, ydfJ_2
Genome position(nucleotides): 1631002 <-- 1632285
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 46.96
External database links:  
ASAP:
 ABE-0005152
ASAP:
 ABE-0285155
ECHOBASE:
 EB3583
ECOLIHUB:
 ydfJ
OU-MICROARRAY:
 b1543
COLOMBOS: ydfJ


Product      
Name: putative transporter YdfJ
Synonym(s): YdfJ
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 46.267
Isoelectric point: 9.458
Motif(s):
 
Type Positions Sequence Comment
8 -> 28 LGAALVFHEIFFPESSTAMAL UniProt: Helical; Name=1.
29 -> 49 ILAMGTYGAGYVARIVGAFIF UniProt: Helical; Name=2.
30 -> 191 LAMGTYGAGYVARIVGAFIFGKMGDRIGRKKVLFITITMMGICTTLIGVLPTYAQIGVFAPILLVTLRIIQGLGAGAEISGAGTMLAEYAPKGKRGIISSFVAMGTNCGTLSATAIWAFMFFILSKEELLAWGWRIPFLASVVVMVFAIWLRMNLKESPVFE
75 -> 95 LIGVLPTYAQIGVFAPILLVT UniProt: Helical; Name=3.
98 -> 118 IIQGLGAGAEISGAGTMLAEY UniProt: Helical; Name=4.

 
Classification:
Multifun Terms (GenProtEC)  
  4 - transport --> 4.2 - Electrochemical potential driven transporters --> 4.2.A - Porters (Uni-, Sym- and Antiporters)
  6 - cell structure --> 6.1 - membrane
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0005887 - integral component of plasma membrane
GO:0016021 - integral component of membrane
molecular_function GO:0015293 - symporter activity
GO:0022857 - transmembrane transporter activity
GO:0005267 - potassium channel activity
biological_process GO:0055085 - transmembrane transport
GO:0071805 - potassium ion transmembrane transport
Note(s): Note(s): ...[more].
Evidence: [COMP-HINF-FN-FROM-SEQ] Human inference of function from sequence
[EXP-IDA-UNPURIFIED-PROTEIN-HH] Assay of unpurified protein expressed in a heterologous host
Reference(s): [1] Pao SS., et al., 1998
[2] Tang G., et al., 2011
External database links:  
ALPHAFOLD:
 P77228
DIP:
 DIP-11699N
ECOCYC:
 B1543-MONOMER
ECOLIWIKI:
 b1543
INTERPRO:
 IPR020846
INTERPRO:
 IPR036259
INTERPRO:
 IPR011701
INTERPRO:
 IPR005828
INTERPRO:
 IPR004736
MODBASE:
 P77228
PFAM:
 PF00083
PFAM:
 PF07690
PRIDE:
 P77228
PROSITE:
 PS50850
REFSEQ:
 NP_416061
UNIPROT:
 P77228


Operon      
Name: ydfJ         
Operon arrangement:
Transcription unit        Promoter
ydfJ


RNA cis-regulatory element    
Attenuation: Translational


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_1852 1632714 forward nd [RS-EPT-CBR] [3]
  promoter TSS_1853 1632716 forward nd [RS-EPT-CBR] [3]
  promoter TSS_1854 1632860 forward nd [RS-EPT-CBR] [3]
  promoter TSS_1855 1632862 forward nd [RS-EPT-CBR] [3]
  promoter TSS_1856 1632864 forward nd [RS-EPT-CBR] [3]
  promoter TSS_1857 1632866 forward nd [RS-EPT-CBR] [3]
  promoter TSS_1858 1632868 forward nd [RS-EPT-CBR] [3]
  promoter TSS_1859 1632871 forward nd [RS-EPT-CBR] [3]
  promoter TSS_1860 1632878 forward nd [RS-EPT-CBR] [3]
  promoter ydfKp5 1632985 forward 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] Pao SS., Paulsen IT., Saier MH., 1998, Major facilitator superfamily., Microbiol Mol Biol Rev 62(1):1-34

 [2] Tang G., Jiang B., Huang Y., Fu M., Wu L., Wang R., 2011, Identification of a novel bacterial k(+) channel., J Membr Biol 242(3):153-64

 [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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