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FunGene: 08-OCT-2024

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus JSNZ
  • locus tag: JSNZ_001780
  • pan locus tag?: SAUPAN004508000
  • symbol: ytkD
  • pan gene symbol?: rppH
  • synonym:
  • product: RNA deprotection pyrophosphohydrolase

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: JSNZ_001780
  • symbol: ytkD
  • product: RNA deprotection pyrophosphohydrolase
  • replicon: chromosome
  • strand: -
  • coordinates: 1833311..1833784
  • length: 474
  • 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
    GTGAAGTTTAGGGATAAAGATAATCGTCAAGTTAATTTGACATTTAAAGAGGATAATGAG
    ATAGCAGATGGCAATCATGTGCTAGCTATTCCAACGTTTAAAAATCAATTGCTTTTTACC
    AAACATAATTTACGGGGTATTGAATTTCCTGGTGGTAAAAGGGAACGCGGGGAAAGTAGT
    GCTGAAGCAGTTACCCGTGAATTATATGAAGAAACAGGCGCCAAAGTTAAAAATATTCAT
    TACATAGCACAATATACCATTGAAACACATGATCAAACTGATTTTGTAAAAGATGTATAT
    TTTATCGAAGTTGAATCATTGGTAAGCAAGAACGATTATTTAGAAACAGCAGGGCCAGTG
    TTGTTTAACTGTATCAATGATATTGAACTCGCCCAACGGAGTTTCTTACTGCAAGATAGT
    ACTATTTTAAAATGCGTAGAGAGGGTGCAATCACTTGGATTTTATCAAACGTAA
    60
    120
    180
    240
    300
    360
    420
    474

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: JSNZ_001780
  • symbol: YtkD
  • description: RNA deprotection pyrophosphohydrolase
  • length: 157
  • theoretical pI: 5.06443
  • theoretical MW: 18112.2
  • GRAVY: -0.494268

⊟Function[edit | edit source]

  • TIGRFAM:
    Genetic information processing DNA metabolism DNA replication, recombination, and repair nucleoside triphosphatase YtkD (TIGR02705; EC 3.6.1.-; HMM-score: 228.6)
    and 2 more
    Genetic information processing DNA metabolism DNA replication, recombination, and repair mutator mutT protein (TIGR00586; EC 3.6.1.-; HMM-score: 32.4)
    Unknown function Enzymes of unknown specificity nudix-type nucleoside diphosphatase, YffH/AdpP family (TIGR00052; EC 3.6.1.-; HMM-score: 13.4)
  • TheSEED: data available for COL, N315, NCTC8325, Newman, USA300_FPR3757
  • PFAM:
    NUDIX (CL0261) NUDIX; NUDIX domain (PF00293; HMM-score: 44.4)
    and 6 more
    Nudt16-like; U8 snoRNA-decapping enzyme-like (PF22327; HMM-score: 17)
    NUDIX_4; NUDIX domain (PF14815; HMM-score: 14.6)
    PBP_GOBP (CL0803) Sol_i_2; Ant venom allergen Sol i 2 family (PF22750; HMM-score: 14.5)
    PDDEXK (CL0236) DUF1064; Protein of unknown function (DUF1064) (PF06356; HMM-score: 13.9)
    no clan defined LED_rpt; LED repeat (PF20854; HMM-score: 12.2)
    RepB_primase; RepB DNA-primase N-terminal domain (PF16793; HMM-score: 12)

⊟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: 0.918
    • Cytoplasmic Membrane Score: 0.0386
    • Cell wall & surface Score: 0.0008
    • Extracellular Score: 0.0427
  • LocateP:
  • SignalP: no predicted signal peptide
    • SP(Sec/SPI): 0.004352
    • TAT(Tat/SPI): 0.000446
    • LIPO(Sec/SPII): 0.000498
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

  • GI:
  • RefSeq:
  • UniProt:

⊟Protein sequence[edit | edit source]

  • MKFRDKDNRQVNLTFKEDNEIADGNHVLAIPTFKNQLLFTKHNLRGIEFPGGKRERGESSAEAVTRELYEETGAKVKNIHYIAQYTIETHDQTDFVKDVYFIEVESLVSKNDYLETAGPVLFNCINDIELAQRSFLLQDSTILKCVERVQSLGFYQT

⊟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]

  • regulator:

⊟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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