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NCBI: 06-JUL-2013

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus Newman
  • locus tag: NWMN_0098 [new locus tag: NWMN_RS00550 ]
  • pan locus tag?: SAUPAN000977000
  • symbol: capD
  • pan gene symbol?: capD
  • synonym:
  • product: polysaccharide biosynthesis protein CapD

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: NWMN_0098 [new locus tag: NWMN_RS00550 ]
  • symbol: capD
  • product: polysaccharide biosynthesis protein CapD
  • replicon: chromosome
  • strand: +
  • coordinates: 121614..123449
  • length: 1836
  • 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
    1201
    1261
    1321
    1381
    1441
    1501
    1561
    1621
    1681
    1741
    1801
    ATGAGGGGTTTTATGGCACATTTATCTGTGAAATTGCGGCTTTTAATACTAGCATTAATC
    GATTCACTGATAGTGACATTTTCAGTATTCGTAAGTTATTACATTTTAGAACCGTATTTC
    AAAACATATTCTGTCAAATTATTAATATTGGCAGCTATATCACTATTCATATCGCATCAT
    ATTTCAGCATTTATTTTTAATATGTATCATCGAGCGTGGGAATATGCCAGTGTGAGTGAA
    TTGATTTTAATTGTTAAAGCTGTGACGACATCTATCGTTATTACGATGGTGGTCGTGACA
    ATTGTTACAGGCAATAGACCGTTTTTTAGATTGTATTTAATTACTTGGATGATGCACTTG
    ATTTTAATAGGTGGCTCAAGGTTATTTTGGCGTATTTATCGGAAATACCTTGGAGGTAAG
    TCATTTAATAAGAAGCCAACTTTAGTTGTTGGTGCTGGTCAAGCAGGTTCAATGCTGATT
    AGACAAATGTTGAAAAGTGACGAAATGAAACTTGAACCGGTATTAGCAGTCGATGATGAC
    GAACATAAACGCAATATCACAATTACTGAGGGTGTAAAAGTCCAAGGTAAAATTGCGGAT
    ATTCCAGAACTAGTGAGGAAATATAAGATTAAAAAAATCATCATTGCAATTCCAACTATT
    GGTCAAGAGCGTTTGAAAGAAATTAATAATATTTGCCATATGGATGGCGTTGAGTTATTG
    AAAATGCCAAATATAGAAGACGTCATGTCTGGTGAGTTAGAAGTGAACCAACTTAAAAAA
    GTTGAAGTAGAAGATTTACTAGGCAGAGATCCTGTTGAATTAGATATGGATATGATATCA
    AATGAATTGACGAATAAAACTATTTTAGTTACGGGTGCAGGTGGTTCAATAGGATCAGAA
    ATTTGTAGACAAGTTTGTAATTTCTATCCAGAACGTATTATTCTACTTGGCCATGGTGAA
    AACAGTATTTATTTAATCAATCGTGAATTGCGAAATCGCTTCGGAAAAAATGTTGATATC
    GTTCCTATTATAGCGGATGTGCAAAATAGAGCGCGTATGTTTGAAATTATGGAAACGTAT
    AAACCATACGCAGTTTATCATGCAGCAGCACACAAGCACGTGCCGTTAATGGAAGACAAC
    CCTGAAGAAGCAGTACGTAATAATATTTTAGGTACGAAAAATACTGCTGAAGCTGCTAAA
    AATGCAGAGGTAAAGAAATTCGTTATGATTTCTACGGATAAAGCCGTTAATCCGCCTAAT
    GTCATGGGAGCTTCAAAGCGAATTGCAGAAATGATTATTCAAAGTTTAAATGATGAAACG
    CATCGAACAAATTTTGTTGCAGTGAGATTTGGTAATGTACTTGGATCGAGAGGATCTGTG
    ATTCCACTTTTCAAAAGTCAAATTGAAGAAGGTGGGCCAGTTACTGTGACACATCCTGAA
    ATGACACGTTACTTTATGACAATTCCTGAAGCTTCTAGACTAGTTTTGCAGGCAGGGGCA
    TTAGCAGAAGGTGGCGAAGTATTTGTGCTAGATATGGGAGAACCAGTGAAAATTGTAGAT
    TTGGCACGTAATTTAATTAAGCTAAGTGGTAAAAAAGAAGACGACATACGCATTACTTAT
    ACAGGGATTAGACCCGGCGAAAAAATGTTTGAAGAGCTTATGAATAAAGATGAGGTTCAT
    CCTGAACAAGTATTTGAAAAAATTTATCGTGGCAAAGTACAACATATGAAATGTAATGAA
    GTTGAAGCGATTATTCAAGACATCGTCAATGACTTTAGTAAAGAAAAAATTATTAACTAT
    GCCAATGGCAAAAAGGGAGATAATTATGTTCGATGA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    1020
    1080
    1140
    1200
    1260
    1320
    1380
    1440
    1500
    1560
    1620
    1680
    1740
    1800
    1836

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: NWMN_0098 [new locus tag: NWMN_RS00550 ]
  • symbol: CapD
  • description: polysaccharide biosynthesis protein CapD
  • length: 611
  • theoretical pI: 8.69271
  • theoretical MW: 69131.5
  • GRAVY: -0.00180033

⊟Function[edit | edit source]

  • TIGRFAM:
    UDP-N-acetylglucosamine 4,6-dehydratase (inverting) (TIGR03589; EC 4.2.1.115; HMM-score: 204.3)
    UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase (TIGR04130; EC 4.2.1.-,5.1.3.-; HMM-score: 164.9)
    and 15 more
    exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase (TIGR03025; HMM-score: 98.1)
    undecaprenyl-phosphate glucose phosphotransferase (TIGR03023; EC 2.7.8.-; HMM-score: 87.3)
    Metabolism Energy metabolism Sugars UDP-glucose 4-epimerase GalE (TIGR01179; EC 5.1.3.2; HMM-score: 63.2)
    Cell structure Cell envelope Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides dTDP-glucose 4,6-dehydratase (TIGR01181; EC 4.2.1.46; HMM-score: 54.9)
    undecaprenyl-phosphate galactose phosphotransferase WbaP (TIGR03022; EC 2.7.8.6; HMM-score: 52.3)
    Cell structure Cell envelope Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides dTDP-4-dehydrorhamnose reductase (TIGR01214; EC 1.1.1.133; HMM-score: 45.1)
    NAD dependent epimerase/dehydratase, LLPSF_EDH_00030 family (TIGR04180; HMM-score: 42.3)
    Cell structure Cell envelope Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides CDP-glucose 4,6-dehydratase (TIGR02622; EC 4.2.1.45; HMM-score: 39.2)
    hopanoid-associated sugar epimerase (TIGR03466; HMM-score: 33.6)
    sugar transferase, PEP-CTERM system associated (TIGR03013; HMM-score: 29.9)
    Cell structure Cell envelope Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides ADP-glyceromanno-heptose 6-epimerase (TIGR02197; EC 5.1.3.20; HMM-score: 24.4)
    rhamnulose-1-phosphate aldolase/alcohol dehydrogenase (TIGR02632; EC 1.1.1.1,4.1.2.19; HMM-score: 15.7)
    thioester reductase domain (TIGR01746; HMM-score: 15.1)
    Cell structure Cell envelope Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides GDP-mannose 4,6-dehydratase (TIGR01472; EC 4.2.1.47; HMM-score: 14.5)
    2-hydroxycyclohexanecarboxyl-CoA dehydrogenase (TIGR03206; EC 1.1.1.-; HMM-score: 12.7)
  • TheSEED  :
    • Capsular polysaccharide synthesis enzyme Cap8D
  • PFAM:
    NADP_Rossmann (CL0063) Polysacc_synt_2; Polysaccharide biosynthesis protein (PF02719; HMM-score: 427.1)
    and 18 more
    Epimerase; NAD dependent epimerase/dehydratase family (PF01370; HMM-score: 88.2)
    CoA_binding_3; CoA-binding domain (PF13727; HMM-score: 64.9)
    GDP_Man_Dehyd; GDP-mannose 4,6 dehydratase (PF16363; HMM-score: 57.2)
    RmlD_sub_bind; RmlD substrate binding domain (PF04321; HMM-score: 50.9)
    3Beta_HSD; 3-beta hydroxysteroid dehydrogenase/isomerase family (PF01073; HMM-score: 43.9)
    NAD_binding_10; NAD(P)H-binding (PF13460; HMM-score: 30)
    KR; KR domain (PF08659; HMM-score: 25.2)
    NAD_binding_4; Male sterility protein (PF07993; HMM-score: 22.2)
    adh_short; short chain dehydrogenase (PF00106; HMM-score: 20.5)
    GFO_IDH_MocA; Oxidoreductase family, NAD-binding Rossmann fold (PF01408; HMM-score: 17.4)
    TrkA_N; TrkA-N domain (PF02254; HMM-score: 16.6)
    NmrA; NmrA-like family (PF05368; HMM-score: 15.6)
    Shikimate_DH; Shikimate / quinate 5-dehydrogenase (PF01488; HMM-score: 14.3)
    no clan defined Tmemb_170; Putative transmembrane protein 170 (PF10190; HMM-score: 14.1)
    DUF3842; Domain of unknown function (DUF3842) (PF12953; HMM-score: 13.9)
    HTH (CL0123) wHTH_TTC3; TTC3-like, winged helix turn helix domain (PF24812; HMM-score: 13.3)
    NADP_Rossmann (CL0063) DapB_N; Dihydrodipicolinate reductase, N-terminus (PF01113; HMM-score: 13)
    DXP_reductoisom; 1-deoxy-D-xylulose 5-phosphate reductoisomerase (PF02670; HMM-score: 11)

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

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

⊟Localization[edit | edit source]

  • PSORTb: Cytoplasmic Membrane
    • Cytoplasmic Score: 0
    • Cytoplasmic Membrane Score: 10
    • Cellwall Score: 0
    • Extracellular Score: 0
    • Internal Helices: 4
  • DeepLocPro: Cytoplasmic Membrane
    • Cytoplasmic Score: 0.0005
    • Cytoplasmic Membrane Score: 0.9981
    • Cell wall & surface Score: 0
    • Extracellular Score: 0.0014
  • LocateP: Multi-transmembrane
    • Prediction by SwissProt Classification: Membrane
    • Pathway Prediction: Sec-(SPI)
    • Intracellular possibility: 0.17
    • Signal peptide possibility: 0
    • N-terminally Anchored Score: 1
    • Predicted Cleavage Site: No CleavageSite
  • SignalP: no predicted signal peptide
    • SP(Sec/SPI): 0.00152
    • TAT(Tat/SPI): 0.000088
    • LIPO(Sec/SPII): 0.012636
  • predicted transmembrane helices (TMHMM): 4

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MRGFMAHLSVKLRLLILALIDSLIVTFSVFVSYYILEPYFKTYSVKLLILAAISLFISHHISAFIFNMYHRAWEYASVSELILIVKAVTTSIVITMVVVTIVTGNRPFFRLYLITWMMHLILIGGSRLFWRIYRKYLGGKSFNKKPTLVVGAGQAGSMLIRQMLKSDEMKLEPVLAVDDDEHKRNITITEGVKVQGKIADIPELVRKYKIKKIIIAIPTIGQERLKEINNICHMDGVELLKMPNIEDVMSGELEVNQLKKVEVEDLLGRDPVELDMDMISNELTNKTILVTGAGGSIGSEICRQVCNFYPERIILLGHGENSIYLINRELRNRFGKNVDIVPIIADVQNRARMFEIMETYKPYAVYHAAAHKHVPLMEDNPEEAVRNNILGTKNTAEAAKNAEVKKFVMISTDKAVNPPNVMGASKRIAEMIIQSLNDETHRTNFVAVRFGNVLGSRGSVIPLFKSQIEEGGPVTVTHPEMTRYFMTIPEASRLVLQAGALAEGGEVFVLDMGEPVKIVDLARNLIKLSGKKEDDIRITYTGIRPGEKMFEELMNKDEVHPEQVFEKIYRGKVQHMKCNEVEAIIQDIVNDFSKEKIINYANGKKGDNYVR

⊟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]

  • regulators: CodY (repression) regulon, SigB (activation) regulon
    CodY(TF)important in Amino acid metabolism; RegPrecise    transcription unit transferred from N315 data RegPrecise 
    SigB(sigma factor)controlling a large regulon involved in stress/starvation response and adaptation;  [3] [4]   other strains

⊟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. ↑ Daniela Keinhörster, Shilpa Elizabeth George, Christopher Weidenmaier, Christiane Wolz
    Function and regulation of Staphylococcus aureus wall teichoic acids and capsular polysaccharides.
    Int J Med Microbiol: 2019, 309(6);151333
    [PubMed:31362856] [WorldCat.org] [DOI] (I p)
  2. ↑ S Sau, J Sun, C Y Lee
    Molecular characterization and transcriptional analysis of type 8 capsule genes in Staphylococcus aureus.
    J Bacteriol: 1997, 179(5);1614-21
    [PubMed:9045821] [WorldCat.org] [DOI] (P p)
  3. ↑ Markus Bischoff, Paul Dunman, Jan Kormanec, Daphne Macapagal, Ellen Murphy, William Mounts, Brigitte Berger-Bächi, Steven Projan
    Microarray-based analysis of the Staphylococcus aureus sigmaB regulon.
    J Bacteriol: 2004, 186(13);4085-99
    [PubMed:15205410] [WorldCat.org] [DOI] (P p)
  4. ↑ Bettina Schulthess, Dominik A Bloes, Patrice François, Myriam Girard, Jacques Schrenzel, Markus Bischoff, Brigitte Berger-Bächi
    The σB-dependent yabJ-spoVG operon is involved in the regulation of extracellular nuclease, lipase, and protease expression in Staphylococcus aureus.
    J Bacteriol: 2011, 193(18);4954-62
    [PubMed:21725011] [WorldCat.org] [DOI] (I p)

⊟Relevant publications[edit | edit source]

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