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NCBI: 10-JUN-2013

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL0626 [new locus tag: SACOL_RS03235 ]
  • pan locus tag?: SAUPAN002357000
  • symbol: thiD1
  • pan gene symbol?: pdxK
  • synonym:
  • product: phosphomethylpyrimidine kinase

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SACOL0626 [new locus tag: SACOL_RS03235 ]
  • symbol: thiD1
  • product: phosphomethylpyrimidine kinase
  • replicon: chromosome
  • strand: -
  • coordinates: 658750..659580
  • length: 831
  • 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
    ATGGCTTTAAAGAAAGTTTTAACAATTGCCGGTTCTGACACAAGTGCTGGCGCAGGTATG
    CAAGCAGATTTGAAAACGTTCCAAGAATTAGATACGTATGGCATGGTCGCTTTAACTGCC
    ATCGTTACTATGGATAAAGATACATGGTCACACGATGTTACACCATTACCAATGGATGTA
    TTTGAAAAACAACTTGAAACGGCTTTATCAATCGGACCTGATGCTATTAAAACAGGTATG
    TTAGGTACTGAGGAGATAATCAAACGTGCTGGAGAAGTATATGAGGCATCTAATGCACAA
    TATTTTGTAGTAGATCCTGTCATGGTTTGTAAAGGCGAAGATGAAGTGCTTAATCCTGGA
    AATACTGAGGCGATGATTAAATATTTACTACCTAAAGCAACGGTAGTGACACCAAACTTA
    TTTGAAGCGGGTCAATTATCAGGATTAGGTAAATTAAATTCAATTGAAGATATGAAAAAG
    GCTGCAACAATTATCTTTGATAAAGGCGCACAGCATGTCATCATTAAAGGTGGCAAAGCT
    TTAGATCAAGATAAATCGTATGACTTATACTATGATGGTCAAACATTTTATCAACTAACA
    ACAGACATGTTCCAACAAAGTTATAACCATGGTGCTGGTTGTACATTTGCTGCGGCAACA
    ACTGCATATTTAGCTAACGGTAAGTCACCGAAAGAAGCTGTGATTAGCGCGAAAGCTTTC
    GTCGCTTCTGCTATTAAAAACGGTTGGAAAATGAATGATTTTGTTGGTCCTGTGGATCAC
    GGTGCATACAACCGTATTGAACATATCGATGTTGAAGTAACAGAGGTTTAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    831

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SACOL0626 [new locus tag: SACOL_RS03235 ]
  • symbol: ThiD1
  • description: phosphomethylpyrimidine kinase
  • length: 276
  • theoretical pI: 4.61494
  • theoretical MW: 29856.8
  • GRAVY: -0.105435

⊟Function[edit | edit source]

  • reaction:
    EC 2.7.4.7?  ExPASy
    Phosphooxymethylpyrimidine kinase ATP + 4-amino-2-methyl-5-(phosphooxymethyl)pyrimidine = ADP + 4-amino-2-methyl-5-(diphosphooxymethyl)pyrimidine
    EC 2.7.1.35?  ExPASy
    Pyridoxal kinase ATP + pyridoxal = ADP + pyridoxal 5'-phosphate
  • TIGRFAM:
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Thiamine hydroxymethylpyrimidine kinase/phosphomethylpyrimidine kinase (TIGR00097; EC 2.7.1.49,2.7.4.7; HMM-score: 235.7)
    and 7 more
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Pyridoxine pyridoxal kinase (TIGR00687; EC 2.7.1.35; HMM-score: 54.9)
    Metabolism Energy metabolism Sugars ribokinase (TIGR02152; EC 2.7.1.15; HMM-score: 38.4)
    hexose kinase, 1-phosphofructokinase family (TIGR03168; EC 2.7.1.-; HMM-score: 27.2)
    1-phosphofructokinase (TIGR03828; EC 2.7.1.56; HMM-score: 24.1)
    Cell structure Cell envelope Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides bifunctional protein RfaE, domain I (TIGR02198; EC 2.7.1.-; HMM-score: 20.5)
    Metabolism Energy metabolism Sugars 5-dehydro-2-deoxygluconokinase (TIGR04382; EC 2.7.1.92; HMM-score: 17.6)
    Metabolism Energy metabolism Biosynthesis and degradation of polysaccharides tagatose-6-phosphate kinase (TIGR01231; EC 2.7.1.144; HMM-score: 13.4)
  • TheSEED  :
    • Novel pyridoxal kinase, ThiD family (EC 2.7.1.35)
  • PFAM:
    Ribokinase (CL0118) Phos_pyr_kin; Phosphomethylpyrimidine kinase (PF08543; HMM-score: 260.5)
    and 1 more
    PfkB; pfkB family carbohydrate kinase (PF00294; HMM-score: 39.4)

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

  • domains:
  • modifications:
  • cofactors:
  • effectors:

⊟Localization[edit | edit source]

  • PSORTb: unknown (no significant prediction)
    • Cytoplasmic Score: 2.5
    • Cytoplasmic Membrane Score: 2.5
    • Cellwall Score: 2.5
    • Extracellular Score: 2.5
    • 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): 0.031077
    • TAT(Tat/SPI): 0.001203
    • LIPO(Sec/SPII): 0.007461
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MALKKVLTIAGSDTSAGAGMQADLKTFQELDTYGMVALTAIVTMDKDTWSHDVTPLPMDVFEKQLETALSIGPDAIKTGMLGTEEIIKRAGEVYEASNAQYFVVDPVMVCKGEDEVLNPGNTEAMIKYLLPKATVVTPNLFEAGQLSGLGKLNSIEDMKKAATIIFDKGAQHVIIKGGKALDQDKSYDLYYDGQTFYQLTTDMFQQSYNHGAGCTFAAATTAYLANGKSPKEAVISAKAFVASAIKNGWKMNDFVGPVDHGAYNRIEHIDVEVTEV

⊟Experimental data[edit | edit source]

  • experimentally validated: PeptideAtlas
  • protein localization: Cytoplasmic [1] [2] [3] [4]
  • quantitative data / protein copy number per cell: 766 [5]
  • 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: 49.32 h [6]

⊟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, Jan Pané-Farré, Andreas Otto, Susanne Sievers, Michael Hecker, Dörte Becher
    Quantitative cell surface proteome profiling for SigB-dependent protein expression in the human pathogen Staphylococcus aureus via biotinylation approach.
    J Proteome Res: 2010, 9(3);1579-90
    [PubMed:20108986] [WorldCat.org] [DOI] (I p)
  3. ↑ 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)
  4. ↑ 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)
  5. ↑ Daniela Zühlke, Kirsten Dörries, Jörg Bernhardt, Sandra Maaß, Jan Muntel, Volkmar Liebscher, Jan Pané-Farré, Katharina Riedel, Michael Lalk, Uwe Völker, Susanne Engelmann, Dörte Becher, Stephan Fuchs, Michael Hecker
    Costs of life - Dynamics of the protein inventory of Staphylococcus aureus during anaerobiosis.
    Sci Rep: 2016, 6;28172
    [PubMed:27344979] [WorldCat.org] [DOI] (I e)
  6. ↑ Stephan Michalik, Jörg Bernhardt, Andreas Otto, Martin Moche, Dörte Becher, Hanna Meyer, Michael Lalk, Claudia Schurmann, Rabea Schlüter, Holger Kock, Ulf Gerth, Michael Hecker
    Life and death of proteins: a case study of glucose-starved Staphylococcus aureus.
    Mol Cell Proteomics: 2012, 11(9);558-70
    [PubMed:22556279] [WorldCat.org] [DOI] (I p)

⊟Relevant publications[edit | edit source]

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