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FunGene: 08-OCT-2024

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus JSNZ
  • locus tag: JSNZ_001760
  • pan locus tag?: SAUPAN004458000
  • symbol: ribD
  • pan gene symbol?: ribD
  • synonym:
  • product: bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase RibD

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: JSNZ_001760
  • symbol: ribD
  • product: bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase RibD
  • replicon: chromosome
  • strand: -
  • coordinates: 1812858..1813901
  • length: 1044
  • essential: unknown other strains

⊟Accession numbers[edit | edit source]

  • Gene ID:
  • RefSeq:
  • BioCyc:
  • MicrobesOnline:

⊟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
    CCCTGTGTTAACAAAATTATTGATTGTAAGATAACTAAAGTAGTTTACGCAACAAAAGAC
    AATTCGTTAGATACACATGGTGATGAGACATTACGGGCTCAAGGTATTGAGGTTGAATGC
    GTTGATGATGAACGGGCATTACAATTATATCAAGACTTTTTTAAAGCAAAAGCAAAGCAA
    CTGCCACAAATTACAGTGAAAGTATCTGCAAGTTTAGATGGTAAACAAGCGAATGATAAT
    GGACAAAGTCAATGGATTACTAACAAAGAGGTTAAACAAGATGTCTATAAGTTAAGACAT
    CGACACGACGCAGTGTTAACTGGAAGACGTACAGTTGAATTAGATGATCCACAATATACT
    ACACGTATTCAAGATGGAAAAAACCCTATAAAAGTAATATTGTCTAAGTCTGGGAATATT
    CATTTTAATCAGCAAATTTATCAAGATGAATCAACACCAATTTGGATATATACTGAAAAT
    CCAAATTTAACAACCAATCAAACACATATTGAAATTATTTACTTGAAGTCTTGTGAATTA
    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: JSNZ_001760
  • symbol: RibD
  • description: bifunctional diaminohydroxyphosphoribosylaminopyrimidine deaminase/5-amino-6-(5-phosphoribosylamino)uracil reductase RibD
  • length: 347
  • theoretical pI: 6.34974
  • theoretical MW: 39013.9
  • GRAVY: -0.431412

⊟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
    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: 303.7)
    and 3 more
    riboflavin-specific deaminase C-terminal domain (TIGR00227; EC 3.5.4.-; HMM-score: 149.7)
    diaminohydroxyphosphoribosylaminopyrimidine reductase (TIGR01508; EC 1.1.1.-; HMM-score: 97)
    ComE operon protein 2 (TIGR02571; HMM-score: 17.2)
  • TheSEED: data available for COL, N315, NCTC8325, Newman, USA300_FPR3757
  • PFAM:
    DHFred (CL0387) RibD_C; RibD C-terminal domain (PF01872; HMM-score: 145.9)
    and 5 more
    CDA (CL0109) dCMP_cyt_deam_1; Cytidine and deoxycytidylate deaminase zinc-binding region (PF00383; HMM-score: 64.6)
    MafB19-deam; MafB19-like deaminase (PF14437; HMM-score: 43.8)
    Inv-AAD; Invertebrate-AID/APOBEC-deaminase (PF18785; HMM-score: 20.2)
    P53-like (CL0073) Calmodulin_bind; Calmodulin binding protein-like N-terminal domain (PF07887; HMM-score: 13.1)
    no clan defined HUTI_composite_bact; Imidazolonepropionase-like composite domain, bacteria (PF22039; HMM-score: 7.6)

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

  • domains:
  • modifications:
  • cofactors:
  • 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
  • DeepLocPro: Cytoplasmic
    • Cytoplasmic Score: 0.9966
    • Cytoplasmic Membrane Score: 0.0005
    • Cell wall & surface Score: 0.001
    • Extracellular Score: 0.0018
  • LocateP:
  • 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]

  • GI:
  • RefSeq:
  • UniProt:

⊟Protein sequence[edit | edit source]

  • MSQFMDYAIQLANMVQGQTGVNPPVGAVVVKEGRIVGIGAHLRKGDKHAEVQALDMAQQNAEGATIYITLEPCSHFGSTPPCVNKIIDCKITKVVYATKDNSLDTHGDETLRAQGIEVECVDDERALQLYQDFFKAKAKQLPQITVKVSASLDGKQANDNGQSQWITNKEVKQDVYKLRHRHDAVLTGRRTVELDDPQYTTRIQDGKNPIKVILSKSGNIHFNQQIYQDESTPIWIYTENPNLTTNQTHIEIIYLKSCELTTILHNLYKRGVGTLLVEAGPTTTSEFLQSNYIDEFILYYAPKLIGGSGNYQFYQTNDVIEIPDANQFEIVHSELLNQNVKLTLRKK

⊟Experimental data[edit | edit source]

  • experimentally validated: data available for COL, NCTC8325
  • 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]

⊟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 can add further information about the gene and protein here. [edit]

⊟Literature[edit | edit source]

⊟References[edit | edit source]

  1. ↑ Blanca Taboada, Karel Estrada, Ricardo Ciria, Enrique Merino
    Operon-mapper: a web server for precise operon identification in bacterial and archaeal genomes.
    Bioinformatics: 2018, 34(23);4118-4120
    [PubMed:29931111] [WorldCat.org] [DOI] (I p)

⊟Relevant publications[edit | edit source]

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