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NCBI: 10-JUN-2013

Summary[edit source | edit]

  • 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 source | edit]

Gene[edit source | edit]

General[edit source | edit]

  • 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 source | edit]

Phenotype[edit source | edit]

  • Share your knowledge and add information here. [edit]

DNA sequence[edit source | edit]

  • 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 source | edit]

General[edit source | edit]

  • 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 source | edit]

  • reaction:
    EC 3.5.4.26?  ExPASy
    Diaminohydroxyphosphoribosylaminopyrimidine deaminase2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine + H2O = 5-amino-6-(5-phosphoribosylamino)uracil + NH3
  • TIGRFAM:
    MetabolismBiosynthesis of cofactors, prosthetic groups, and carriersRiboflavin, FMN, and FADriboflavin biosynthesis protein RibD (TIGR00326; EC 1.1.1.193,3.5.4.26; HMM-score: 302.7)
    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:  
    Diaminohydroxyphosphoribosylaminopyrimidine deaminase (EC 3.5.4.26) / 5-amino-6-(5-phosphoribosylamino)uracil reductase (EC 1.1.1.193) 
  • PFAM:
    DHFred (CL0387) RibD_C; RibD C-terminal domain (PF01872; HMM-score: 141.7)
    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 & interactions[edit source | edit]

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

Localization[edit source | edit]

  • 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
    • Ymax: 0.172
    • Ymax_pos: 18
    • Cmax: 0.192
    • Cmax_pos: 18
    • Smax: 0.284
    • Smax_pos: 17
    • Smean: 0.139
    • D: 0.159
  • predicted transmembrane helices (TMHMM): 0

Accession numbers[edit source | edit]

Protein sequence[edit source | edit]

  • MSQFMDYAIQLANMVQGQTGVNPPVGAVVVKEGRIVGIGAHLRKGDKHAEVQALDMAQQNAEGATIYITLEPCSHFGSTPPCVNKIIDCKIAKVVYATKDNSLDTHGDETLRAHGIEVECVDDERASQLYQDFFKAKAKQLPQITVKVSASLDGKQANDNGQSQWITNKEVKQDVYKLRHRHDAVLTGRRTVELDDPQYTTRIQDGKNPIKVILSKSGNIHFNQQIYQDESTPIWIYTENPNLTTNQTHIEIIYLKSCDLTTILHNLYKRGVGTLLVEAGPTTTSEFLQSNYIDEFILYYAPKLIGGSGNYQFYQTNDVIEIPDANQFEIVHSELLNQNVKLTLRKK

Experimental data[edit source | edit]

Expression & Regulation[edit source | edit]

Operon[edit source | edit]

Regulation[edit source | edit]

  • sigma factor:
  • regulator:

Transcription pattern[edit source | edit]

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

Protein stability[edit source | edit]

  • half-life: no data available

Biological Material[edit source | edit]

Mutants[edit source | edit]

Expression vector[edit source | edit]

lacZ fusion[edit source | edit]

GFP fusion[edit source | edit]

two-hybrid system[edit source | edit]

FLAG-tag construct[edit source | edit]

Antibody[edit source | edit]

Other Information[edit source | edit]

You are kindly invited to share additional interesting facts.

Literature[edit source | edit]

References[edit source | edit]

  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 source | edit]