PangenomeCOLN315NCTC8325NewmanUSA300_FPR375704-0298108BA0217611819-97685071193ECT-R 2ED133ED98HO 5096 0412JH1JH9JKD6008JKD6159JSNZLGA251M013MRSA252MSHR1132MSSA476MW2Mu3Mu50RF122ST398T0131TCH60TW20USA300_TCH1516VC40

NCBI: 10-JUN-2013

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⊟Summary

• organism: Staphylococcus aureus COL
locus tag: SACOL2397 [new locus tag: SACOL_RS12575 ]
pan locus tag^?: SAUPAN005931000
symbol: nirD
pan gene symbol^?: nasE
• synonym:
• product: nitrite reductase [NAD(P)H], small subunit

⊟Genome View

⊟Gene

⊟General

• type: CDS
• locus tag: SACOL2397 [new locus tag: SACOL_RS12575 ]
• symbol: nirD
• product: nitrite reductase [NAD(P)H], small subunit
• replicon: chromosome
• strand: -
• coordinates: 2458192..2458506
• length: 315
• essential: unknown other strains

⊟Accession numbers

• Gene ID: 3236579 NCBI
• RefSeq: YP_187200 NCBI
• BioCyc: see SACOL_RS12575
• MicrobesOnline: 913877 MicrobesOnline

⊟Phenotype

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⊟DNA sequence

• 1
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  301
  
  ATGGAAACAAAAGAAAAAATTAAAGTGACAACTATAGATGAATTAACACCCCTAATTGGA
  AAAAAGGTTATTGTCAAAGGCAAAGAGGTAGGGTTGTTTTTAACAGAAAGTGGCAAAATT
  CATGCGATTCACAATATCTGTCCACACAAACAAGGACCATTGTCTGAAGGGACAGTGAGT
  GGGGAATATGTATTTTGCCCGCTCCACGATCAAAAAATTGATTTAAATACAGGTATTGTT
  CAAGAACCTGATGAAGGTTGTGTAGATGTTTATGAGGTAGAAGTTACAGACGGGAACGTA
  TATATATGTCTGTAG
  60
  120
  180
  240
  300
  315
  

⊟Protein

⊟General

• locus tag: SACOL2397 [new locus tag: SACOL_RS12575 ]
• symbol: NirD
• description: nitrite reductase [NAD(P)H], small subunit
• length: 104
• theoretical pI: 4.70663
• theoretical MW: 11437.1
• GRAVY: -0.106731

⊟Function

• ⊞reaction:
  EC 1.7.1.4?  ExPASy
  Nitrite reductase (NAD(P)H) Ammonia + 3 NAD(P)⁺ + 2 H₂O = nitrite + 3 NAD(P)H
• ⊞TIGRFAM:
  Metabolism Central intermediary metabolism Nitrogen metabolism nitrite reductase [NAD(P)H], small subunit (TIGR02378; EC 1.7.1.4; HMM-score: 82.3)
  and 1 more
  Rieske [2Fe-2S] domain protein, MocE subfamily (TIGR02377; HMM-score: 35.7)
• TheSEED  :
  • Nitrite reductase [NAD(P)H] small subunit (EC 1.7.1.4)
  Nitrogen Metabolism Nitrogen Metabolism - no subcategory Nitrate and nitrite ammonification  Nitrite reductase [NAD(P)H] small subunit (EC 1.7.1.4)
• ⊞PFAM:
  ISP-domain (CL0516) Rieske_2; Rieske-like [2Fe-2S] domain (PF13806; HMM-score: 64.4)
  Rieske; Rieske [2Fe-2S] domain (PF00355; HMM-score: 55.8)
  and 1 more
  Rieske_4; Soluble Rieske-type ferredoxin (PF22543; HMM-score: 21.6)

⊟Structure, modifications & cofactors

• domains:
• modifications:
• cofactors:
• effectors:

⊟Localization

• ⊞PSORTb: Cytoplasmic
  • Cytoplasmic Score: 7.5
  • Cytoplasmic Membrane Score: 1.15
  • Cellwall Score: 0.62
  • Extracellular Score: 0.73
  • Internal Helices: 0
• ⊞DeepLocPro: Cytoplasmic
  • Cytoplasmic Score: 0.997
  • Cytoplasmic Membrane Score: 0.0009
  • Cell wall & surface Score: 0
  • Extracellular Score: 0.002
• ⊞LocateP: Intracellular
  • Prediction by SwissProt Classification: Cytoplasmic
  • Pathway Prediction: No pathway
  • Intracellular possibility: 1
  • Signal peptide possibility: -1
  • N-terminally Anchored Score: 1
  • Predicted Cleavage Site: No CleavageSite
• ⊞SignalP: no predicted signal peptide
  • SP(Sec/SPI): 0.011677
  • TAT(Tat/SPI): 0.000435
  • LIPO(Sec/SPII): 0.000882
• predicted transmembrane helices (TMHMM): 0

⊟Accession numbers

• GI: 57650942 NCBI
• RefSeq: YP_187200 NCBI
• UniProt: A0A0H2WX65 UniProt

⊟Protein sequence

• METKEKIKVTTIDELTPLIGKKVIVKGKEVGLFLTESGKIHAIHNICPHKQGPLSEGTVSGEYVFCPLHDQKIDLNTGIVQEPDEGCVDVYEVEVTDGNVYICL

⊟Experimental data

• experimentally validated: data available for NCTC8325
• protein localization:
• quantitative data / protein copy number per cell:
• interaction partners:

⊟Expression & Regulation

⊟Operon

• MicrobesOnline: SACOL2396 < nirD < nirB < nirR

⊟Regulation

• ⊞regulators: Rex* (repression) regulon, NreC* (activation) regulon

  Rex*	(TF)	important in Energy metabolism; RegPrecise    transcription unit transferred from N315 data RegPrecise
  NreC*	(TF)	important in Nitrate and nitrite respiration; RegPrecise    transcription unit transferred from N315 data RegPrecise

⊟Transcription pattern

• S.aureus Expression Data Browser: data available for NCTC8325

⊟Protein synthesis (provided by Aureolib)

• Aureolib: no data available

⊟Protein stability

• half-life: no data available

⊞Biological Material

⊟Mutants

⊟Expression vector

⊟lacZ fusion

⊟GFP fusion

⊟two-hybrid system

⊟FLAG-tag construct

⊟Antibody

⊞Other Information

You are kindly invited to share additional interesting facts.

⊟Literature

⊟References

⊟Relevant publications