RegulonDB RegulonDB 11.1: Gene Form
   

nikD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

Gene      
Name: nikD    Texpresso search in the literature
Synonym(s): ECK3463, EG12078, b3479, hydC, hydD
Genome position(nucleotides): 3617015 --> 3617779
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 59.22
External database links:  
ASAP:
 ABE-0011360
CGSC:
 33186
ECHOBASE:
 EB2003
ECOLIHUB:
 nikD
OU-MICROARRAY:
 b3479
STRING:
 511145.b3479
COLOMBOS: nikD


Product      
Name: Ni(2+) ABC transporter ATP binding subunit NikD
Synonym(s): HydC, HydD, NikD
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 26.82
Isoelectric point: 6.389
Motif(s):
 
Type Positions Sequence Comment
2 -> 241 PQQIELRNIALQAAQPLVHGVSLTLQRGRVLALVGGSGSGKSLTCAATLGILPAGVRQTAGEILADGKPVSPCALRGIKIATIMQNPRSAFNPLHTMHTHARETCLALGKPADDATLTAAIEAVGLENAARVLKLYPFEMSGGMLQRMMIAMAVLCESPFIIADEPTTDLDVVAQARILDLLESIMQKQAPGMLLVTHDMGVVARLADDVAVMSDGKIVEQGDVETLFNAPKHTVTRSLV UniProt: ABC transporter.
20 -> 168 HGVSLTLQRGRVLALVGGSGSGKSLTCAATLGILPAGVRQTAGEILADGKPVSPCALRGIKIATIMQNPRSAFNPLHTMHTHARETCLALGKPADDATLTAAIEAVGLENAARVLKLYPFEMSGGMLQRMMIAMAVLCESPFIIADEPT
36 -> 43 GGSGSGKS UniProt: ATP.
141 -> 144 MSGG
165 -> 172 DEPTTDLD

 
Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.3 - energy metabolism, carbon --> 1.3.6 - aerobic respiration
  1 - metabolism --> 1.3 - energy metabolism, carbon --> 1.3.7 - anaerobic respiration
  4 - transport --> 4.3 - Primary Active Transporters --> 4.3.A - Pyrophosphate Bond (ATP; GTP; P2) Hydrolysis-driven Active Transporters --> 4.3.A.1 - The ATP-binding Cassette (ABC) Superfamily + ABC-type Uptake Permeases --> 4.3.A.1.a - ABC superfamily ATP binding cytoplasmic component
Gene Ontology Terms (GO)  
cellular_component GO:0016020 - membrane
GO:0005886 - plasma membrane
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing
molecular_function GO:0000166 - nucleotide binding
GO:0005524 - ATP binding
GO:0016151 - nickel cation binding
GO:0015413 - ABC-type nickel transporter activity
GO:0022857 - transmembrane transporter activity
biological_process GO:0098716 - nickel cation import across plasma membrane
GO:0006811 - ion transport
GO:0015675 - nickel cation transport
GO:0055085 - transmembrane transport
GO:0035444 - nickel cation transmembrane transport
GO:0035672 - oligopeptide transmembrane transport
Note(s): Note(s): ...[more].
Reference(s): [1] Jindal S., et al., 2019
External database links:  
ALPHAFOLD:
 P33593
DIP:
 DIP-10343N
ECOCYC:
 NIKD-MONOMER
ECOLIWIKI:
 b3479
INTERPRO:
 IPR027417
INTERPRO:
 IPR017871
INTERPRO:
 IPR015857
INTERPRO:
 IPR014138
INTERPRO:
 IPR003439
INTERPRO:
 IPR003593
MODBASE:
 P33593
PFAM:
 PF00005
PRIDE:
 P33593
PRODB:
 PRO_000023387
PROSITE:
 PS00211
PROSITE:
 PS51247
PROSITE:
 PS50893
REFSEQ:
 NP_417936
SMART:
 SM00382
SMR:
 P33593
UNIPROT:
 P33593


Operon      
Name: nikABCDER         
Operon arrangement:
Transcription unit        Promoter
nikABCDER
nikABCDER
nikR


Transcriptional Regulation      
Display Regulation             
Activated by: FNR
Repressed by: NarL, NikR


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_4081 3616046 forward nd [RS-EPT-CBR] [2]
  promoter TSS_4082 3616409 forward nd [RS-EPT-CBR] [2]
  promoter TSS_4083 (cluster) 3616882 forward nd [RS-EPT-CBR] [2]
  promoter TSS_4084 3616908 forward nd [RS-EPT-CBR] [2]
  promoter TSS_4085 3617570 forward nd [RS-EPT-CBR] [2]
  promoter TSS_4086 3617581 forward nd [RS-EPT-CBR] [2]


Evidence    

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


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] 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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