RegulonDB RegulonDB 11.1: Gene Form
   

nikB gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

nikA nikB nikC nikD acpT nikE NikR FNR terminator anti-terminator anti-anti-terminator TSS_4086 TSS_4086 TSS_4085 TSS_4085 TSS_4084 TSS_4084 TSS_4083 (cluster) TSS_4083 (cluster) TSS_4082 TSS_4082 TSS_4081 TSS_4081 TSS_4080 (cluster) TSS_4080 (cluster) TSS_4079 TSS_4079 nikAp1 nikAp1 nikAp2 nikAp2

Gene      
Name: nikB    Texpresso search in the literature
Synonym(s): ECK3461, EG12076, b3477, hydC, hydD
Genome position(nucleotides): 3615241 --> 3616185
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
 58.41
External database links:  
ASAP:
 ABE-0011356
CGSC:
 33180
ECHOBASE:
 EB2001
ECOLIHUB:
 nikB
OU-MICROARRAY:
 b3477
STRING:
 511145.b3477
COLOMBOS: nikB


Product      
Name: Ni(2+) ABC transporter membrane subunit NikB
Synonym(s): HydC, HydD, NikB
Sequence: Get amino acid sequence Fasta Format
Cellular location: inner membrane
Molecular weight: 35.248
Isoelectric point: 10.043
Motif(s):
 
Type Positions Sequence Comment
1 -> 105 MLRYVLRRFLLLIPMVLAASVIIFLMLRLGTGDPALDYLRLSNLPPTPEMLASTRTMLGLDQPLYVQYGTWLWKALHLDFGISFASQRPVLDDMLNFLPATLELA
9 -> 29 FLLLIPMVLAASVIIFLMLRL UniProt: Helical.
26 -> 27 ML UniProt: In Ref. 1; CAA51660..
98 -> 295 LPATLELAGAALVLILLTSVPLGIWAARHRDRLPDFAVRFIAFLGVSMPNFWLAFLLVMAFSVYLQWLPAMGYGGWQHIILPAVSIAFMSLAINARLLRASMLDVAGQRHVTWARLRGLNDKQTERRHILRNASLPMITAVGMHIGELIGGTMIIENIFAWPGVGRYAVSAIFNRDYPVIQCFTLMMVVVFVVCNLIV UniProt: ABC transmembrane type-1.
104 -> 124 LAGAALVLILLTSVPLGIWAA UniProt: Helical.

 
Classification:
Multifun Terms (GenProtEC)  
  6 - cell structure --> 6.1 - membrane
  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.m - ABC superfamily, membrane component
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
GO:0055052 - ATP-binding cassette (ABC) transporter complex, substrate-binding subunit-containing
molecular_function GO:0016151 - nickel cation binding
GO:0015099 - nickel cation transmembrane transporter activity
GO:0015413 - ABC-type nickel transporter activity
GO:0071916 - dipeptide 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:0035442 - dipeptide transmembrane transport
Note(s): Note(s): ...[more].
External database links:  
ALPHAFOLD:
 P33591
DIP:
 DIP-10341N
ECOCYC:
 NIKB-MONOMER
ECOLIWIKI:
 b3477
INTERPRO:
 IPR014156
INTERPRO:
 IPR035906
INTERPRO:
 IPR000515
PFAM:
 PF19300
PFAM:
 PF00528
PRIDE:
 P33591
PRODB:
 PRO_000023385
PROSITE:
 PS50928
REFSEQ:
 NP_417934
SMR:
 P33591
UNIPROT:
 P33591


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_4079 3615136 forward nd [RS-EPT-CBR] [1]
  promoter TSS_4080 (cluster) 3615142 forward nd [RS-EPT-CBR] [1]
  promoter TSS_4081 3616046 forward nd [RS-EPT-CBR] [1]
  promoter TSS_4082 3616409 forward nd [RS-EPT-CBR] [1]
  promoter TSS_4083 (cluster) 3616882 forward nd [RS-EPT-CBR] [1]
  promoter TSS_4084 3616908 forward nd [RS-EPT-CBR] [1]
  promoter TSS_4085 3617570 forward nd [RS-EPT-CBR] [1]
  promoter TSS_4086 3617581 forward nd [RS-EPT-CBR] [1]


Evidence    

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


Reference(s)    

 [1] 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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