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NCBI: 10-JUN-2013

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL1820 [new locus tag: SACOL_RS09330 ]
  • pan locus tag?: SAUPAN004458000
  • symbol: ribD
  • pan gene symbol?: ribD
  • synonym:
  • product: riboflavin biosynthesis protein RibD

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SACOL1820 [new locus tag: SACOL_RS09330 ]
  • symbol: ribD
  • product: riboflavin biosynthesis protein RibD
  • replicon: chromosome
  • strand: -
  • coordinates: 1874917..1875960
  • length: 1044
  • essential: unknown other strains

⊟Accession numbers[edit | edit source]

⊟Phenotype[edit | edit source]

Share your knowledge and add information here. [edit]

⊟DNA sequence[edit | edit source]

  • 1
    61
    121
    181
    241
    301
    361
    421
    481
    541
    601
    661
    721
    781
    841
    901
    961
    1021
    TTGAGTCAATTTATGGATTATGCGATTCAACTTGCAAATATGGTACAAGGTCAAACAGGT
    GTTAATCCACCCGTTGGCGCTGTTGTAGTTAAAGAAGGTAGGATTGTTGGTATTGGTGCA
    CACTTGAGAAAAGGTGACAAGCATGCGGAGGTTCAAGCACTTGATATGGCACAACAAAAT
    GCTGAAGGTGCGACGATTTATATTACGTTAGAGCCATGTAGTCATTTTGGTTCAACACCA
    CCCTGTGTTAACAAAATAATTGATTGTAAGATAGCAAAAGTAGTATACGCAACAAAAGAC
    AATTCGTTAGACACACATGGTGATGAGACGTTACGGGCTCACGGTATTGAGGTTGAATGC
    GTTGATGATGAACGGGCATCACAATTATACCAAGACTTTTTTAAAGCAAAAGCAAAGCAA
    CTGCCACAAATTACAGTGAAAGTATCTGCAAGTTTAGATGGTAAACAAGCGAATGATAAT
    GGACAAAGTCAATGGATTACTAACAAAGAGGTTAAACAAGATGTCTATAAGTTAAGACAT
    CGACACGACGCAGTGTTAACTGGAAGACGTACAGTTGAATTAGATGATCCACAATATACT
    ACACGTATTCAAGATGGAAAAAACCCTATAAAAGTAATATTGTCTAAGTCTGGGAATATT
    CATTTTAATCAGCAAATTTATCAAGATGAATCAACACCAATTTGGATATATACTGAAAAT
    CCAAATTTAACAACCAATCAAACACATATTGAAATTATTTACTTGAAGTCTTGCGATTTA
    ACAACAATTCTTCACAATTTATATAAAAGAGGAGTTGGAACTTTGCTAGTCGAGGCAGGT
    CCAACCACTACTTCAGAATTTCTCCAATCTAATTATATAGATGAATTTATTCTCTATTAT
    GCCCCGAAATTAATTGGCGGATCTGGAAATTATCAATTTTATCAAACAAATGATGTGATT
    GAGATACCAGATGCGAACCAATTTGAAATTGTTCATTCCGAGTTATTAAATCAAAATGTT
    AAATTAACTTTACGAAAGAAGTGA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    1020
    1044

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SACOL1820 [new locus tag: SACOL_RS09330 ]
  • symbol: RibD
  • description: riboflavin biosynthesis protein RibD
  • length: 347
  • theoretical pI: 6.43647
  • theoretical MW: 38952.8
  • GRAVY: -0.436599

⊟Function[edit | edit source]

  • 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
  • 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: 302.7)
    and 3 more
    riboflavin-specific deaminase C-terminal domain (TIGR00227; EC 3.5.4.-; HMM-score: 150.6)
    diaminohydroxyphosphoribosylaminopyrimidine reductase (TIGR01508; EC 1.1.1.-; HMM-score: 96.5)
    ComE operon protein 2 (TIGR02571; HMM-score: 16.2)
  • 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: 141.7)
    and 3 more
    CDA (CL0109) dCMP_cyt_deam_1; Cytidine and deoxycytidylate deaminase zinc-binding region (PF00383; HMM-score: 67.1)
    MafB19-deam; MafB19-like deaminase (PF14437; HMM-score: 44.1)
    APOBEC_N; APOBEC-like N-terminal domain (PF08210; HMM-score: 13.6)

⊟Structure, modifications & cofactors[edit | edit source]

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

⊟Localization[edit | edit source]

  • 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): 0.012615
    • TAT(Tat/SPI): 0.00165
    • LIPO(Sec/SPII): 0.002115
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MSQFMDYAIQLANMVQGQTGVNPPVGAVVVKEGRIVGIGAHLRKGDKHAEVQALDMAQQNAEGATIYITLEPCSHFGSTPPCVNKIIDCKIAKVVYATKDNSLDTHGDETLRAHGIEVECVDDERASQLYQDFFKAKAKQLPQITVKVSASLDGKQANDNGQSQWITNKEVKQDVYKLRHRHDAVLTGRRTVELDDPQYTTRIQDGKNPIKVILSKSGNIHFNQQIYQDESTPIWIYTENPNLTTNQTHIEIIYLKSCDLTTILHNLYKRGVGTLLVEAGPTTTSEFLQSNYIDEFILYYAPKLIGGSGNYQFYQTNDVIEIPDANQFEIVHSELLNQNVKLTLRKK

⊟Experimental data[edit | edit source]

  • experimentally validated: PeptideAtlas
  • protein localization: Cytoplasmic [1] [2] [3]
  • quantitative data / protein copy number per cell:
  • interaction partners:

⊟Expression & Regulation[edit | edit source]

⊟Operon[edit | edit source]

⊟Regulation[edit | edit source]

  • 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[edit | edit source]

⊟Protein synthesis (provided by Aureolib)[edit | edit source]

⊟Protein stability[edit | edit source]

  • half-life: no data available

⊟Biological Material[edit | edit source]

⊟Mutants[edit | edit source]

⊟Expression vector[edit | edit source]

⊟lacZ fusion[edit | edit source]

⊟GFP fusion[edit | edit source]

⊟two-hybrid system[edit | edit source]

⊟FLAG-tag construct[edit | edit source]

⊟Antibody[edit | edit source]

⊟Other Information[edit | edit source]

You are kindly invited to share additional interesting facts.

⊟Literature[edit | edit source]

⊟References[edit | edit source]

  1. ↑ Dörte Becher, Kristina Hempel, Susanne Sievers, Daniela Zühlke, Jan Pané-Farré, Andreas Otto, Stephan Fuchs, Dirk Albrecht, Jörg Bernhardt, Susanne Engelmann, Uwe Völker, Jan Maarten van Dijl, Michael Hecker
    A proteomic view of an important human pathogen--towards the quantification of the entire Staphylococcus aureus proteome.
    PLoS One: 2009, 4(12);e8176
    [PubMed:19997597] [WorldCat.org] [DOI] (I e)
  2. ↑ Kristina Hempel, Florian-Alexander Herbst, Martin Moche, Michael Hecker, Dörte Becher
    Quantitative proteomic view on secreted, cell surface-associated, and cytoplasmic proteins of the methicillin-resistant human pathogen Staphylococcus aureus under iron-limited conditions.
    J Proteome Res: 2011, 10(4);1657-66
    [PubMed:21323324] [WorldCat.org] [DOI] (I p)
  3. ↑ Andreas Otto, Jan Maarten van Dijl, Michael Hecker, Dörte Becher
    The Staphylococcus aureus proteome.
    Int J Med Microbiol: 2014, 304(2);110-20
    [PubMed:24439828] [WorldCat.org] [DOI] (I p)

⊟Relevant publications[edit | edit source]

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