PangenomeCOLN315NCTC8325NewmanUSA300_FPR375704-0298108BA0217611819-97685071193ECT-R 2ED133ED98HO 5096 0412JH1JH9JKD6008JKD6159LGA251M013MRSA252MSHR1132MSSA476MW2Mu3Mu50RF122ST398T0131TCH60TW20USA300_TCH1516VC40

NCBI: 10-JUN-2013

⊟Summary

• organism: Staphylococcus aureus USA300_FPR3757
• locus tag: SAUSA300_1715 [new locus tag: SAUSA300_RS09370 ]
• pan locus tag^?: SAUPAN004458000
• symbol: ribD
• pan gene symbol^?: ribD
• synonym:
• product: riboflavin biosynthesis protein

⊟Genome View

⊟Gene

⊟General

• type: CDS
• locus tag: SAUSA300_1715 [new locus tag: SAUSA300_RS09370 ]
• symbol: ribD
• product: riboflavin biosynthesis protein
• replicon: chromosome
• strand: -
• coordinates: 1897228..1898232
• length: 1005
• essential: unknown other strains

⊟Accession numbers

• Gene ID: 3913191 NCBI
• RefSeq: YP_494408 NCBI
• BioCyc: GH3C-1706 BioCyc
• MicrobesOnline: 1293230 MicrobesOnline

⊟Phenotype

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⊟DNA sequence

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  ATGGTACAAGGTCAAACAGGTGTTAATCCACCCGTTGGCGCTGTTGTAGTTAAAGAAGGT
  AGGATTGTTGGTATTGGTGCACACTTGAGAAAAGGTGACAAGCATGCGGAGGTTCAAGCA
  CTTGATATGGCACAACAAAATGCTGAAGGTGCGACGATTTATATTACGTTAGAGCCATGT
  AGTCATTTTGGTTCAACACCACCCTGTGTTAACAAAATAATTGATTGTAAGATAGCAAAA
  GTAGTATACGCAACAAAAGACAATTCGTTAGACACACATGGTGATGAGACGTTACGGGCT
  CACGGTATTGAGGTTGAATGCGTTGATGATGAACGGGCATCACAATTATACCAAGACTTT
  TTTAAAGCAAAAGCAAAGCAACTGCCACAAATTACAGTGAAAGTATCTGCAAGTTTAGAT
  GGTAAACAAGCGAATGATAATGGACAAAGTCAATGGATTACTAACAAAGAGGTTAAACAA
  GATGTCTATAAGTTAAGACATCGACACGACGCAGTGTTAACTGGAAGACGTACAGTTGAA
  TTAGATGATCCACAATATACTACACGTATTCAAGATGGAAAAAACCCTATAAAAGTAATA
  TTGTCTAAGTCTGGGAATATTCATTTTAATCAGCAAATTTATCAAGATGAATCAACACCA
  ATTTGGATATATACTGAAAATCCAAATTTAACAACCAATCAAACACATATTGAAATTATT
  TACTTGAAGTCTTGCGATTTAACAACAATTCTTCACAATTTATATAAAAGAGGAGTTGGA
  ACTTTGCTAGTTGAGGCAGGTCCAACCACTACTTCAGAATTTCTCCAATCTAATTATATA
  GATGAATTTATTCTCTATTATGCCCCGAAATTAATTGGCGGATCTGGAAATTATCAATTT
  TATCAAACAAATGATGTGATTGAGATACCAGATGCGAACCAATTTGAAATTGTTCATTCC
  GAGTTATTAAATCAAAATGTTAAATTAACTTTACGAAAGAAGTGA
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⊟Protein

⊟General

• locus tag: SAUSA300_1715 [new locus tag: SAUSA300_RS09370 ]
• symbol: RibD
• description: riboflavin biosynthesis protein
• length: 334
• theoretical pI: 6.58415
• theoretical MW: 37439
• GRAVY: -0.460778

⊟Function

• reaction:
  EC 3.5.4.26?  ExPASy
  Diaminohydroxyphosphoribosylaminopyrimidine deaminase 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + H₂O = 5-amino-6-(5-phosphoribosylamino)uracil + NH₃
  EC 1.1.1.193?  ExPASy
  5-amino-6-(5-phosphoribosylamino)uracil reductase 5-amino-6-(5-phospho-D-ribitylamino)uracil + NADP⁺ = 5-amino-6-(5-phospho-D-ribosylamino)uracil + NADPH
• TIGRFAM:
  Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Riboflavin, FMN, and FAD riboflavin biosynthesis protein RibD (TIGR00326; EC 1.1.1.193,3.5.4.26; HMM-score: 293.9)
  and 3 more
  riboflavin-specific deaminase C-terminal domain (TIGR00227; EC 3.5.4.-; HMM-score: 150.8)
  diaminohydroxyphosphoribosylaminopyrimidine reductase (TIGR01508; EC 1.1.1.-; HMM-score: 96.7)
  ComE operon protein 2 (TIGR02571; HMM-score: 15.4)
• TheSEED  :
  • 5-amino-6-(5-phosphoribosylamino)uracil reductase (EC 1.1.1.193)
  • Diaminohydroxyphosphoribosylaminopyrimidine deaminase (EC 3.5.4.26)
• PFAM:
  DHFred (CL0387) RibD_C; RibD C-terminal domain (PF01872; HMM-score: 141.8)
  and 3 more
  CDA (CL0109) dCMP_cyt_deam_1; Cytidine and deoxycytidylate deaminase zinc-binding region (PF00383; HMM-score: 60.7)
  MafB19-deam; MafB19-like deaminase (PF14437; HMM-score: 43.4)
  APOBEC_N; APOBEC-like N-terminal domain (PF08210; HMM-score: 13.7)

⊟Structure, modifications & cofactors

• domains:
• modifications:
• cofactors: Zn²⁺
• effectors:

⊟Localization

• PSORTb: Cytoplasmic
  • Cytoplasmic Score: 7.5
  • Cytoplasmic Membrane Score: 1.15
  • Cellwall Score: 0.62
  • Extracellular Score: 0.73
  • Internal Helices: 0
• 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): 0.018645
  • TAT(Tat/SPI): 0.002
  • LIPO(Sec/SPII): 0.002366
• predicted transmembrane helices (TMHMM): 0

⊟Accession numbers

• GI: 87161517 NCBI
• RefSeq: YP_494408 NCBI
• UniProt: A0A0H2XHA4 UniProt

⊟Protein sequence

• MVQGQTGVNPPVGAVVVKEGRIVGIGAHLRKGDKHAEVQALDMAQQNAEGATIYITLEPCSHFGSTPPCVNKIIDCKIAKVVYATKDNSLDTHGDETLRAHGIEVECVDDERASQLYQDFFKAKAKQLPQITVKVSASLDGKQANDNGQSQWITNKEVKQDVYKLRHRHDAVLTGRRTVELDDPQYTTRIQDGKNPIKVILSKSGNIHFNQQIYQDESTPIWIYTENPNLTTNQTHIEIIYLKSCDLTTILHNLYKRGVGTLLVEAGPTTTSEFLQSNYIDEFILYYAPKLIGGSGNYQFYQTNDVIEIPDANQFEIVHSELLNQNVKLTLRKK

⊟Experimental data

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

⊟Expression & Regulation

⊟Operon

• MicrobesOnline: ribH < ribBA < ribE < ribD

⊟Regulation

• regulator: FMN-box (transcription termination) regulon

  FMN-box

  (RNA)

  important in Riboflavin biosynthesis; regulatory site identified based on RegPrecise data for N315 RegPrecise

⊟Transcription pattern

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

⊟Protein synthesis (provided by Aureolib)

• Aureolib: data available for COL

⊟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