RegulonDB RegulonDB 11.1: Gene Form
   

ydcO gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

insQ ydcO sutR SutR SutR anti-terminator anti-anti-terminator anti-anti-terminator anti-terminator terminator terminator ydcNp5 ydcNp5 sutRp sutRp TSS_1812 TSS_1812

Gene      
Name: ydcO    Texpresso search in the literature
Synonym(s): ECK1427, G6744, b1433
Genome position(nucleotides): 1504905 <-- 1506080
Strand: reverse
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 52.98
External database links:  
ASAP:
 ABE-0004780
ECHOBASE:
 EB3521
ECOLIHUB:
 ydcO
OU-MICROARRAY:
 b1433
STRING:
 511145.b1433
COLOMBOS: ydcO


Product      
Name: putative transport protein YdcO
Synonym(s): YdcO
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 40.583
Isoelectric point: 8.595
Motif(s):
 
Type Positions Sequence Comment
6 -> 381 IPPPTLLAGFLAVLIGYASSAAIIWQAAIVAGATTAQISGWMTALGLAMGVSTLTLTLWYRVPVLTAWSTPGAALLVTGLQGLTLNEAIGVFIVTNALIVLCGITGLFARLMRIIPHSLAAAMLAGILLRFGLQAFASLDGQFTLCGSMLLVWLATKAVAPRYAVIAAMIIGIVIVIAQGDVVTTDVVFKPVLPTYITPDFSFAHSLSVALPLFLVTMASQNAPGIAAMKAAGYSAPVSPLIVFTGLLALVFSPFGVYSVGIAAITAAICQSPEAHPDKDQRWLAAAVAGIFYLLAGLFGSAITGMMAALPVSWIQMLAGLALLSTIGGSLYQALHNERERDAAVVAFLVTASGLTLVGIGSAFWGLIAGGVCYVV
10 -> 30 TLLAGFLAVLIGYASSAAIIW UniProt: Helical.
43 -> 63 ISGWMTALGLAMGVSTLTLTL UniProt: Helical.
94 -> 114 IGVFIVTNALIVLCGITGLFA UniProt: Helical.
124 -> 144 LAAAMLAGILLRFGLQAFASL UniProt: Helical.

 
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:0042925 - benzoate transmembrane transporter activity
biological_process GO:0042919 - benzoate transport
Note(s): Note(s): ...[more].
Reference(s): [1] Jindal S., et al., 2019
[2] Pao SS., et al., 1998
External database links:  
ALPHAFOLD:
 P76103
ECOCYC:
 B1433-MONOMER
ECOLIWIKI:
 b1433
INTERPRO:
 IPR004711
PANTHER:
 PTHR30199
PFAM:
 PF03594
PRIDE:
 P76103
PROSITE:
 PS00041
REFSEQ:
 NP_415950
UNIPROT:
 P76103


Operon      
Name: ydcO         
Operon arrangement:
Transcription unit        Promoter
ydcO


RNA cis-regulatory element    
Attenuation: Transcriptional


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_1812 1503657 forward nd [RS-EPT-CBR] [3]
  promoter ydcNp5 1506154 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] 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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