RegulonDB RegulonDB 10.8: Gene Form
   

ydeE gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

ydeE eamA mgtS PhoP mgtSp mgtSp TSS_1843 TSS_1843 ydeEp1 ydeEp1 TSS_1842 TSS_1842 ydeEp4 ydeEp4 TSS_1841 TSS_1841

Gene      
Name: ydeE    Texpresso search in the literature
Synonym(s): ECK1527, EG11640, b1534, ydeF
Genome position(nucleotides): 1621332 --> 1622519 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
49.83
External database links:  
ASAP:
ABE-0005121
ECHOBASE:
EB1595
OU-MICROARRAY:
b1534
PortEco:
ydeE
STRING:
511145.b1534
COLOMBOS: ydeE


Product      
Name: dipeptide exporter
Synonym(s): YdeE, YdeF
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 42.659
Isoelectric point: 9.619
Motif(s):
 
Type Positions Sequence
12 -> 34 LLASSLLLTIGRGATLPFMTIYL
208 -> 230 LLWFTCSGFLASFVSGAFASCIS
245 -> 264 VVAVVLPVNAAMVVTLQYSV
75 -> 94 YMLLAITAFASGFIAITLVN
298 -> 320 LLLWGMSAAVFTVGEIIYAPGEY

 

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:0016021 - integral component of membrane
molecular_function GO:0022857 - transmembrane transporter activity
GO:0071916 - dipeptide transmembrane transporter activity
biological_process GO:0015031 - protein transport
GO:0015833 - peptide transport
GO:0055085 - transmembrane transport
GO:0035442 - dipeptide transmembrane transport
Note(s): Note(s): ...[more].
Reference(s): [1] Jindal S., et al., 2019
[2] Pao SS., et al., 1998
External database links:  
ECOCYC:
YDEF-MONOMER
ECOLIWIKI:
b1534
INTERPRO:
IPR011701
INTERPRO:
IPR036259
INTERPRO:
IPR020846
MODBASE:
P31126
PFAM:
PF07690
PRIDE:
P31126
PROSITE:
PS50850
REFSEQ:
NP_416051
SMR:
P31126
UNIPROT:
P31126


Operon      
Name: ydeE         
Operon arrangement:
Transcription unit        Promoter
ydeE


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_1841 1621167 reverse nd [RS-EPT-CBR] [3]
  promoter ydeEp4 1621264 forward Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter TSS_1842 1621290 forward nd [RS-EPT-CBR] [3]
  promoter ydeEp1 1621304 forward Similarity to the consensus
Read more >
[ICWHO] [4]
  promoter TSS_1843 1622587 forward nd [RS-EPT-CBR] [3]


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] Jindal S., Yang L., Day PJ., Kell DB., 2019, Involvement of multiple influx and efflux transporters in the accumulation of cationic fluorescent dyes by Escherichia coli., BMC Microbiol 19(1):195

 [2] Pao SS., Paulsen IT., Saier MH., 1998, Major facilitator superfamily., Microbiol Mol Biol Rev 62(1):1-34

 [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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