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NCBI: 10-JUN-2013

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL0124 [new locus tag: SACOL_RS00625 ]
  • pan locus tag?: SAUPAN000951000
  • symbol: deoB
  • pan gene symbol?: deoB
  • synonym:
  • product: phosphopentomutase

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SACOL0124 [new locus tag: SACOL_RS00625 ]
  • symbol: deoB
  • product: phosphopentomutase
  • replicon: chromosome
  • strand: +
  • coordinates: 139111..140289
  • length: 1179
  • 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
    841
    901
    961
    1021
    1081
    1141
    ATGACAAGACCATTTAATCGTGTACATTTAATCGTAATGGATTCAGTAGGTATTGGTGAA
    GCGCCAGACGCAGCTGATTTTAAAGATGAAGGTTCACATACTTTAAGACATACCTTAGAA
    GGTTTCGATCAAACTTTACCAAACCTTGAAAAGTTAGGTCTAGGGAACATCGATAAATTA
    CCAGTAGTAAATGCAGTTGAACAACCAGAAGCATACTATACTAAATTGAGTGAAGCTTCA
    GTTGGTAAAGATACAATGACTGGTCACTGGGAAATTATGGGATTAAATATTATGCAACCT
    TTTAAAGTATACCCTAATGGATTCCCTGAAGAGTTAATTCAACAAATTGAAGAAATGACA
    GGTCGTAAAGTTGTTGCTAACAAACCGGCATCGGGTACGCAAATTATCGATGAGTGGGGC
    GAGCACCAAATGAAAACTGGTGACTTAATTGTTTATACAAGTGCAGACCCAGTATTGCAA
    ATTGCTGCACATGAAGACATTATCCCATTAGAAGAGTTATATGATATTTGTGAAAAGGTT
    CGTGAGTTGACAAAAGACCCTAAATATTTAATTGGTCGTATTATCGCACGTCCATATGTT
    GGTGAACCAGGAAACTTTACACGTACATCTAATCGACATGACTATGCGTTAAAACCTTTT
    GGTAAAACTGTCTTAGATCATTTGAAAGACGGTGGTTATGATGTTATTGCCATCGGTAAA
    ATTAATGACATTTATGATGGTGAAGGTGTAACAGAAGCGGTTCGTACGAAGAGTAACATG
    GACGGTATGGATCAATTGATGAAAATTGTTAAGAAAGATTTCACAGGTATTAGCTTCTTA
    AACTTAGTAGACTTTGATGCATTATACGGTCATCGTCGTGATAAACCAGGTTATGCACAA
    GCAATTAAAGATTTCGATGATCGCTTGCCAGAACTGTTTAGCAACTTAAAAGAAGACGAT
    TTAGTAATTATTACAGCAGACCATGGTAATGACCCGACAGCGCCAGGTACGGACCATACG
    AGAGAATATATCCCAGTAATTATGTACAGTCCGAAATTTAAAGGTGGTCATGCACTAGAA
    AGTGATACTACATTCAGTTCTATCGGTGCAACTATAGCAGATAATTTCAACGTAACATTA
    CCAGAGTTCGGTAAAAGTTATTTAAAGGAATTGAAATAG
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    1020
    1080
    1140
    1179

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SACOL0124 [new locus tag: SACOL_RS00625 ]
  • symbol: DeoB
  • description: phosphopentomutase
  • length: 392
  • theoretical pI: 4.76649
  • theoretical MW: 43795.3
  • GRAVY: -0.406122

⊟Function[edit | edit source]

  • reaction:
    EC 5.4.2.7?  ExPASy
    Phosphopentomutase Alpha-D-ribose 1-phosphate = D-ribose 5-phosphate 2-deoxy-alpha-D-ribose 1-phosphate = 2-deoxy-alpha-D-ribose 5-phosphate?
  • TIGRFAM:
    Metabolism Purines, pyrimidines, nucleosides, and nucleotides Other phosphopentomutase (TIGR01696; EC 5.4.2.7; HMM-score: 743.7)
    and 2 more
    Metabolism Energy metabolism Glycolysis/gluconeogenesis phosphoglycerate mutase (2,3-diphosphoglycerate-independent) (TIGR01307; EC 5.4.2.12; HMM-score: 22.3)
    Metabolism Energy metabolism Glycolysis/gluconeogenesis phosphoglycerate mutase (2,3-diphosphoglycerate-independent), archaeal form (TIGR00306; EC 5.4.2.12; HMM-score: 21.9)
  • TheSEED  :
    • Phosphopentomutase (EC 5.4.2.7)
    Carbohydrates Monosaccharides Deoxyribose and Deoxynucleoside Catabolism  Phosphopentomutase (EC 5.4.2.7)
  • PFAM:
    Alk_phosphatase (CL0088) Metalloenzyme; Metalloenzyme superfamily (PF01676; HMM-score: 133.8)
    and 3 more
    Phosphodiest; Type I phosphodiesterase / nucleotide pyrophosphatase (PF01663; HMM-score: 19.6)
    no clan defined GFRP; GTP cyclohydrolase I feedback regulatory protein (GFRP) (PF06399; HMM-score: 12.9)
    Alk_phosphatase (CL0088) Sulfatase; Sulfatase (PF00884; HMM-score: 12.3)

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

  • domains:
  • modifications:
  • cofactors: Mn2+
  • effectors:

⊟Localization[edit | edit source]

  • PSORTb: Cytoplasmic
    • Cytoplasmic Score: 9.97
    • Cytoplasmic Membrane Score: 0
    • Cellwall Score: 0.01
    • Extracellular Score: 0.02
    • 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): 0.01247
    • TAT(Tat/SPI): 0.001408
    • LIPO(Sec/SPII): 0.001664
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MTRPFNRVHLIVMDSVGIGEAPDAADFKDEGSHTLRHTLEGFDQTLPNLEKLGLGNIDKLPVVNAVEQPEAYYTKLSEASVGKDTMTGHWEIMGLNIMQPFKVYPNGFPEELIQQIEEMTGRKVVANKPASGTQIIDEWGEHQMKTGDLIVYTSADPVLQIAAHEDIIPLEELYDICEKVRELTKDPKYLIGRIIARPYVGEPGNFTRTSNRHDYALKPFGKTVLDHLKDGGYDVIAIGKINDIYDGEGVTEAVRTKSNMDGMDQLMKIVKKDFTGISFLNLVDFDALYGHRRDKPGYAQAIKDFDDRLPELFSNLKEDDLVIITADHGNDPTAPGTDHTREYIPVIMYSPKFKGGHALESDTTFSSIGATIADNFNVTLPEFGKSYLKELK

⊟Experimental data[edit | edit source]

  • experimentally validated: PeptideAtlas
  • protein localization: Cytoplasmic [1] [2] [3]
  • quantitative data / protein copy number per cell: 1202 [4]
  • 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: 43.19 h [5]

⊟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, 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)
  4. ↑ 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)
  5. ↑ 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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