RegulonDB RegulonDB 10.6.3: Gene Form
   

nirD gene in Escherichia coli K-12 genome


Gene local context to scale (view description)

nirB tsgA nirC nirD Fis Cra FNR CRP NarP NarL NarP NarL IHF Fis IHF Fis CRP terminator anti-terminator anti-anti-terminator cysGp2 cysGp2 cysGp1 cysGp1 TSS_3976 TSS_3976 TSS_3975 TSS_3975 TSS_3974 TSS_3974 TSS_3973 TSS_3973 TSS_3972 TSS_3972 TSS_3971 TSS_3971 TSS_3970 TSS_3970 TSS_3969 TSS_3969 TSS_3968 (cluster) TSS_3968 (cluster) TSS_3967 TSS_3967 nirBp nirBp

Gene      
Name: nirD    Texpresso search in the literature
Synonym(s): ECK3354, EG10655, b3366
Genome position(nucleotides): 3496551 --> 3496877 Genome Browser
Strand: forward
Sequence: Get nucleotide sequence FastaFormat
GC content %:  
55.96
External database links:  
ASAP:
ABE-0011005
CGSC:
35425
ECHOBASE:
EB0649
ECOCYC:
EG10655
ECOLIHUB:
nirD
OU-MICROARRAY:
b3366
REGULONDB:
b3366
STRING:
511145.b3366
M3D: nirD
COLOMBOS: nirD
PortEco: b3366


Product      
Name: nitrite reductase subunit NirD
Synonym(s): NirD, nitrite reductase small subunit
Sequence: Get amino acid sequence Fasta Format
Cellular location: cytosol
Molecular weight: 12.284
Isoelectric point: 4.876
Motif(s):
 
Type Positions Sequence
102 -> 102 G
3 -> 106 QWKDICKIDDILPETGVCALLGDEQVAIFRPYHSDQVFAISNIDPFFESSVLSRGLIAEHQGELWVASPLKKQRFRLSDGLCMEDEQFSVKHYEARVKDGVVQL

 

Classification:
Multifun Terms (GenProtEC)  
  1 - metabolism --> 1.3 - energy metabolism, carbon --> 1.3.7 - anaerobic respiration
Gene Ontology Terms (GO)  
cellular_component GO:0005737 - cytoplasm
GO:0005829 - cytosol
GO:0009344 - nitrite reductase complex [NAD(P)H]
molecular_function GO:0016491 - oxidoreductase activity
GO:0051537 - 2 iron, 2 sulfur cluster binding
GO:0008942 - nitrite reductase [NAD(P)H] activity
biological_process GO:0009061 - anaerobic respiration
GO:0042128 - nitrate assimilation
GO:0055114 - oxidation-reduction process
Note(s): Note(s): ...[more].
External database links:  
ECOCYC:
NIRD-MONOMER
ECOLIWIKI:
b3366
INTERPRO:
IPR036922
INTERPRO:
IPR017881
INTERPRO:
IPR012748
MODBASE:
P0A9I8
PANTHER:
PTHR40562
PDB:
2JO6
PFAM:
PF13806
PRIDE:
P0A9I8
PRODB:
PRO_000023391
PROSITE:
PS51300
PROTEINMODELPORTAL:
P0A9I8
REFSEQ:
NP_417825
SMR:
P0A9I8
UNIPROT:
P0A9I8


Operon      
Name: nirBDC-cysG         
Operon arrangement:
Transcription unit        Promoter
nirBDC-cysG
cysG
cysG


Transcriptional Regulation      
Display Regulation             
Activated by: FNR, IHF, NarL, NarP
Repressed by: CRP, H-NS, IHF, Cra, Fis


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_3967 3493998 forward nd [RS-EPT-CBR] [1]
  promoter TSS_3968 (cluster) 3494032 forward For this promoter, there
Read more >
[RS-EPT-CBR] [1]
  promoter TSS_3969 3494035 forward nd [RS-EPT-CBR] [1]
  promoter TSS_3970 3494404 forward nd [RS-EPT-CBR] [1]
  promoter TSS_3971 3494422 forward nd [RS-EPT-CBR] [1]
  promoter TSS_3972 3494535 forward nd [RS-EPT-CBR] [1]
  promoter TSS_3973 3494981 forward nd [RS-EPT-CBR] [1]
  promoter TSS_3974 3495073 forward nd [RS-EPT-CBR] [1]
  promoter TSS_3975 3495419 reverse nd [RS-EPT-CBR] [1]
  promoter TSS_3976 3496522 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, Mu¿¿iz-Rascado L, Garc¿¿a-Sotelo JS, Weiss V, Solano-Lira H, Mart¿¿nez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hern¿¿ndez S, Alquicira-Hern¿¿ndez K, L¿¿pez-Fuentes A, Porr¿¿n-Sotelo L, Huerta AM, Bonavides-Mart¿¿nez C, Balderas-Mart¿¿nez YI, Pannier L, Olvera M, Labastida A, Jim¿¿nez-Jacinto V, Vega-Alvarado L, Del Moral-Ch¿¿vez V, Hern¿¿ndez-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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