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NCBI: 03-AUG-2016

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus NCTC8325
  • locus tag: SAOUHSC_01889
  • pan locus tag?: SAUPAN004458000
  • symbol: SAOUHSC_01889
  • 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: SAOUHSC_01889
  • symbol: SAOUHSC_01889
  • product: riboflavin biosynthesis protein RibD
  • replicon: chromosome
  • strand: -
  • coordinates: 1800919..1801923
  • length: 1005
  • essential: no DEG 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
    ATGGTACAAGGTCAAACAGGTGTTAATCCACCCGTTGGCGCTGTTGTAGTTAAAGAAGGT
    AGGATTGTTGGTATTGGTGCACACTTGAGAAAAGGTGACAAGCATGCGGAGGTTCAAGCA
    CTTGATATGGCACAACAAAATGCTGAAGGTGCGACGATTTATATTACGTTAGAGCCATGT
    AGTCATTTTGGTTCAACACCACCCTGTGTTAACAAAATAATTGATTGTAAGATAGCAAAA
    GTAGTATACGCAACAAAAGACAATTCGTTAGACACACATGGTGATGAGACGTTACGGGCT
    CACGGTATTGAGGTTGAATGCGTTGATGATGAACGGGCATCACAATTATACCAAGACTTT
    TTTAAAGCAAAAGCAAAGCAACTGCCACAAATTACAGTGAAAGTATCTGCAAGTTTAGAT
    GGTAAACAAGCGAATGATAATGGACAAAGTCAATGGATTACTAACAAAGAGGTTAAACAA
    GATGTCTATAAGTTAAGACATCGACACGACGCAGTGTTAACTGGAAGACGTACAGTTGAA
    TTAGATGATCCACAATATACTACACGTATTCAAGATGGAAAAAACCCTATAAAAGTAATA
    TTGTCTAAGTCTGGGAATATTCATTTTAATCAGCAAATTTATCAAGATGAATCAACACCA
    ATTTGGATATATACTGAAAATCCAAATTTAACAACCAATCAAACACATATTGAAATTATT
    TACTTGAAGTCTTGCGATTTAACAACAATTCTTCACAATTTATATAAAAGAGGAGTTGGA
    ACTTTGCTAGTCGAGGCAGGTCCAACCACTACTTCAGAATTTCTCCAATCTAATTATATA
    GATGAATTTATTCTCTATTATGCCCCGAAATTAATTGGCGGATCTGGAAATTATCAATTT
    TATCAAACAAATGATGTGATTGAGATACCAGATGCGAACCAATTTGAAATTGTTCATTCC
    GAGTTATTAAATCAAAATGTTAAATTAACTTTACGAAAGAAGTGA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    1005

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SAOUHSC_01889
  • symbol: SAOUHSC_01889
  • description: riboflavin biosynthesis protein RibD
  • length: 334
  • theoretical pI: 6.58415
  • theoretical MW: 37439
  • GRAVY: -0.460778

⊟Function[edit | edit source]

  • 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)
    Cofactors, Vitamins, Prosthetic Groups, Pigments Riboflavin, FMN, FAD Riboflavin, FMN and FAD metabolism Extended  5-amino-6-(5-phosphoribosylamino)uracil reductase (EC 1.1.1.193)
    and 1 more
    Cofactors, Vitamins, Prosthetic Groups, Pigments Riboflavin, FMN, FAD Riboflavin, FMN and FAD metabolism Extended  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[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): 0.018645
    • TAT(Tat/SPI): 0.002
    • LIPO(Sec/SPII): 0.002366
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MVQGQTGVNPPVGAVVVKEGRIVGIGAHLRKGDKHAEVQALDMAQQNAEGATIYITLEPCSHFGSTPPCVNKIIDCKIAKVVYATKDNSLDTHGDETLRAHGIEVECVDDERASQLYQDFFKAKAKQLPQITVKVSASLDGKQANDNGQSQWITNKEVKQDVYKLRHRHDAVLTGRRTVELDDPQYTTRIQDGKNPIKVILSKSGNIHFNQQIYQDESTPIWIYTENPNLTTNQTHIEIIYLKSCDLTTILHNLYKRGVGTLLVEAGPTTTSEFLQSNYIDEFILYYAPKLIGGSGNYQFYQTNDVIEIPDANQFEIVHSELLNQNVKLTLRKK

⊟Experimental data[edit | edit source]

  • experimentally validated: PeptideAtlas [1] [2]
  • protein localization: data available for COL
  • 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(5' cis-acting region)important in Riboflavin biosynthesis; compare RegPrecise for N315 

⊟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. ↑ Maren Depke, Stephan Michalik, Alexander Rabe, Kristin Surmann, Lars Brinkmann, Nico Jehmlich, Jörg Bernhardt, Michael Hecker, Bernd Wollscheid, Zhi Sun, Robert L Moritz, Uwe Völker, Frank Schmidt
    A peptide resource for the analysis of Staphylococcus aureus in host-pathogen interaction studies.
    Proteomics: 2015, 15(21);3648-61
    [PubMed:26224020] [WorldCat.org] [DOI] (I p)
  2. ↑ Stephan Michalik, Maren Depke, Annette Murr, Manuela Gesell Salazar, Ulrike Kusebauch, Zhi Sun, Tanja C Meyer, Kristin Surmann, Henrike Pförtner, Petra Hildebrandt, Stefan Weiss, Laura Marcela Palma Medina, Melanie Gutjahr, Elke Hammer, Dörte Becher, Thomas Pribyl, Sven Hammerschmidt, Eric W Deutsch, Samuel L Bader, Michael Hecker, Robert L Moritz, Ulrike Mäder, Uwe Völker, Frank Schmidt
    A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host-pathogen interactions.
    Sci Rep: 2017, 7(1);9718
    [PubMed:28887440] [WorldCat.org] [DOI] (I e)
  3. ↑ 3.0 3.1 Ulrike Mäder, Pierre Nicolas, Maren Depke, Jan Pané-Farré, Michel Debarbouille, Magdalena M van der Kooi-Pol, Cyprien Guérin, Sandra Dérozier, Aurelia Hiron, Hanne Jarmer, Aurélie Leduc, Stephan Michalik, Ewoud Reilman, Marc Schaffer, Frank Schmidt, Philippe Bessières, Philippe Noirot, Michael Hecker, Tarek Msadek, Uwe Völker, Jan Maarten van Dijl
    Staphylococcus aureus Transcriptome Architecture: From Laboratory to Infection-Mimicking Conditions.
    PLoS Genet: 2016, 12(4);e1005962
    [PubMed:27035918] [WorldCat.org] [DOI] (I e)

⊟Relevant publications[edit | edit source]

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