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NCBI: 10-JUN-2013

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL0979 [new locus tag: SACOL_RS05010 ]
  • pan locus tag?: SAUPAN003113000
  • symbol: clpB
  • pan gene symbol?: clpB
  • synonym:
  • product: ATP-dependent Clp protease, ATP-binding subunit ClpB

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SACOL0979 [new locus tag: SACOL_RS05010 ]
  • symbol: clpB
  • product: ATP-dependent Clp protease, ATP-binding subunit ClpB
  • replicon: chromosome
  • strand: +
  • coordinates: 986247..988856
  • length: 2610
  • 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
    1861
    1921
    1981
    2041
    2101
    2161
    2221
    2281
    2341
    2401
    2461
    2521
    2581
    ATGGATATAAATAAAATGACATATGCTGTTCAAAGTGCTTTACAACAAGCAGTTGAACTG
    AGTCAGCAACATAAATTACAAAATATAGAAATTGAGGCAATTTTAAGCGCTGCCTTAAAT
    GAAAGTGAAAGCTTATATAAAAGTATTTTAGAACGAGCAAATATTGAGGTAGATCAATTA
    AACAAAGCTTATGAAGACAAACTAAACACGTATGCATCTGTAGAAGGTGACAATATACAA
    TATGGTCAATATATTAGCCAACAAGCAAACCAATTGATAACTAAGGCTGAATCATACATG
    AAAGAATATGAAGATGAATATATTTCAATGGAGCATATTTTACGTTCGGCAATGGACATT
    GATCAAACAACAAAACATTATATAAATAATAAAGTAGAAGTTATCAAAGAAATTATTAAA
    AAAGTAAGAGGGGGAAATCACGTGACATCACAAAATCCAGAAGTTAATTACGAAGCATTA
    GCTAAATATGGCCGCGACTTAGTAGAAGAAGTTAGACAAGGTAAAATGGATCCTGTTATA
    GGAAGAGATGAAGAAATTCGAAATACGATTCGTATTTTAAGTCGTAAAACTAAAAACAAC
    CCTGTGCTCATTGGTGAACCAGGTGTTGGTAAAACTGCAATTGTTGAAGGATTAGCGCAA
    CGTATAGTTAAGAAAGATGTGCCAGAATCATTATTAGATAAAACTGTTTTTGAGTTAGAT
    TTAAGCGCATTAGTAGCGGGCGCTAAATATCGTGGTGAATTTGAAGAGAGATTAAAAGCA
    GTCCTAAAAGAAGTTAAAGAGTCTGATGGTAGAATTATATTATTTATTGATGAAATCCAT
    ATGCTTGTAGGTGCTGGTAAAACAGATGGTGCCATGGATGCAGGCAACATGCTAAAACCA
    ATGTTAGCACGAGGAGAGTTACATTGTATTGGTGCAACAACTTTAAATGAATATCGAGAA
    TATATTGAAAAAGATTCGGCATTAGAGCGTCGTTTCCAAAAAGTAGCAGTTAGTGAGCCT
    GATGTTGAAGATACAATTTCAATTTTACGTGGTTTAAAAGAACGATATGAAGTGTATCAT
    GGTGTGCGTATTCAAGATAGAGCCTTAGTTGCTGCCGCTGAATTGTCTGATCGTTACATC
    ACTGATCGTTTTTTACCAGATAAAGCGATTGATTTAGTTGACCAAGCATGTGCAACAATT
    CGTACGGAAATGGGATCAAATCCAACTGAATTGGATCAAGTTAATAGACGTGTCATGCAA
    TTAGAAATTGAAGAAAGCGCACTTAAAAATGAATCTGACAATGCGAGCAAACAGAGATTA
    CAAGAACTACAAGAAGAGCTTGCCAATGAAAAAGAGAAACAAGCAGCACTTCAATCTCGT
    GTAGAATCAGAAAAAGAAAAAATAGCAAATTTACAAGAAAAACGTGCGCAACTAGATGAA
    AGTAGACAAGCGTTGGAAGATGCACAAACAAATAACAATTTAGAAAAAGCTGCTGAACTA
    CAATATGGAACAATTCCTCAATTGGAAAAAGAACTTAGAGAATTAGAGGATAATTTCCAA
    GATGAGCAAGGTGAAGATACAGATCGAATGATTCGTGAAGTTGTAACAGACGAAGAAATT
    GGCGATATTGTCAGCCAATGGACAGGCATACCAGTTTCAAAATTAGTTGAAACAGAACGT
    GAAAAATTACTTCACTTAAGTGACATCTTGCATAAACGTGTTGTAGGTCAAGATAAAGCG
    GTTGACCTGGTTTCAGATGCAGTAGTTAGAGCAAGAGCAGGTATTAAAGATCCAAACAGA
    CCTATTGGTAGTTTCTTATTCCTAGGTCCAACTGGAGTAGGTAAAACTGAATTAGCTAAA
    TCATTAGCTGCATCATTATTTGATTCTGAAAAACATATGATTCGTATTGATATGAGTGAA
    TATATGGAAAAACATGCAGTATCAAGATTGATAGGGGCACCTCCAGGATATATTGGACAT
    GATGAAGGGGGTCAATTAACTGAAGCGGTTCGTCGTAATCCATACTCAGTTATTTTATTA
    GATGAGGTTGAAAAAGCGCATACTGACGTCTTTAATGTATTATTGCAAATTTTAGATGAA
    GGCCGTTTAACTGATTCTAAAGGACGTAGCGTTGATTTTAAAAATACTATTATTATTATG
    ACAAGTAATATTGGATCTCAAGTTTTATTAGAAAACGTAAAAGAGACTGGTGAAATTACA
    GAATCAACAGAAAAAGCTGTTATGACAAGTTTAAATGCATATTTCAAACCAGAAATTTTG
    AATCGTATGGATGATATCGTATTATTTAAACCATTATCTATTGATGACATGAGTATGATT
    GTAGATAAAATCTTAACGCAATTAAATATAAGATTATTAGAACAACGAATCTCAATTGAA
    GTTTCTGATGATGCTAAAGCTTGGCTAGGTCAAGAAGCTTATGAACCTCAATACGGTGCA
    AGACCATTAAAACGTTTTGTACAACGCCAAATTGAAACACCATTAGCACGTATGATGATT
    AAAGAGGGATTCCCAGAAGGTACAACGATTAAAGTTAATTTAAATTCAGACAATAACTTA
    ACGTTTAATGTTGAAAAAATTCATGAATAA
    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
    1860
    1920
    1980
    2040
    2100
    2160
    2220
    2280
    2340
    2400
    2460
    2520
    2580
    2610

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SACOL0979 [new locus tag: SACOL_RS05010 ]
  • symbol: ClpB
  • description: ATP-dependent Clp protease, ATP-binding subunit ClpB
  • length: 869
  • theoretical pI: 4.68338
  • theoretical MW: 98302.8
  • GRAVY: -0.488493

⊟Function[edit | edit source]

  • TIGRFAM:
    Genetic information processing Protein fate Protein folding and stabilization ATP-dependent chaperone protein ClpB (TIGR03346; HMM-score: 1277)
    and 16 more
    Cellular processes Cellular processes Pathogenesis type VI secretion ATPase, ClpV1 family (TIGR03345; HMM-score: 802.1)
    Genetic information processing Protein fate Protein and peptide secretion and trafficking type VI secretion ATPase, ClpV1 family (TIGR03345; HMM-score: 802.1)
    Genetic information processing Protein fate Degradation of proteins, peptides, and glycopeptides ATP-dependent Clp protease ATP-binding subunit ClpA (TIGR02639; HMM-score: 778.7)
    Genetic information processing DNA metabolism DNA replication, recombination, and repair Holliday junction DNA helicase RuvB (TIGR00635; EC 3.6.4.12; HMM-score: 23.8)
    Genetic information processing DNA metabolism DNA replication, recombination, and repair DnaA regulatory inactivator Hda (TIGR03420; HMM-score: 21.4)
    Cellular processes Cellular processes Cell division chromosome segregation protein SMC (TIGR02169; HMM-score: 20.4)
    Genetic information processing DNA metabolism Chromosome-associated proteins chromosome segregation protein SMC (TIGR02169; HMM-score: 20.4)
    Genetic information processing DNA metabolism DNA replication, recombination, and repair DNA polymerase III, delta' subunit (TIGR00678; EC 2.7.7.7; HMM-score: 20.3)
    Cellular processes Cellular processes Other gas vesicle protein GvpN (TIGR02640; HMM-score: 19.3)
    Cellular processes Cellular processes Sporulation and germination ATP-dependent protease LonB (TIGR02902; EC 3.4.21.-; HMM-score: 17.7)
    Genetic information processing Protein fate Degradation of proteins, peptides, and glycopeptides ATP-dependent protease LonB (TIGR02902; EC 3.4.21.-; HMM-score: 17.7)
    Cellular processes Cellular processes Cell division chromosome segregation protein SMC (TIGR02168; HMM-score: 17.5)
    Genetic information processing DNA metabolism Chromosome-associated proteins chromosome segregation protein SMC (TIGR02168; HMM-score: 17.5)
    Genetic information processing DNA metabolism DNA replication, recombination, and repair DNA polymerase III, subunit gamma and tau (TIGR02397; EC 2.7.7.7; HMM-score: 16.5)
    Cellular processes Cellular processes Chemotaxis and motility flagellar biosynthesis protein FlhF (TIGR03499; HMM-score: 16.1)
    Metabolism Purines, pyrimidines, nucleosides, and nucleotides Purine ribonucleotide biosynthesis adenylosuccinate synthase (TIGR00184; EC 6.3.4.4; HMM-score: 9.5)
  • TheSEED  :
    • ClpB protein
    Protein Metabolism Protein degradation Proteolysis in bacteria, ATP-dependent  ClpB protein
    and 1 more
    Protein Metabolism Protein folding Protein chaperones  ClpB protein
  • PFAM:
    P-loop_NTPase (CL0023) AAA_2; AAA domain (Cdc48 subfamily) (PF07724; HMM-score: 242.5)
    and 43 more
    AAA_lid (CL0671) AAA_lid_9; AAA lid domain (PF17871; HMM-score: 121.2)
    P-loop_NTPase (CL0023) AAA; ATPase family associated with various cellular activities (AAA) (PF00004; HMM-score: 93.3)
    AAA_lid (CL0671) ClpB_D2-small; C-terminal, D2-small domain, of ClpB protein (PF10431; HMM-score: 87.5)
    P-loop_NTPase (CL0023) AAA_5; AAA domain (dynein-related subfamily) (PF07728; HMM-score: 77.4)
    no clan defined Clp_N; Clp amino terminal domain, pathogenicity island component (PF02861; HMM-score: 52.8)
    P-loop_NTPase (CL0023) AAA_22; AAA domain (PF13401; HMM-score: 44.4)
    AAA_16; AAA ATPase domain (PF13191; HMM-score: 44.2)
    Sigma54_activat; Sigma-54 interaction domain (PF00158; HMM-score: 41.8)
    AAA_7; P-loop containing dynein motor region (PF12775; HMM-score: 33.8)
    AAA_14; AAA domain (PF13173; HMM-score: 33.5)
    bpMoxR; MoxR domain in the MoxR-vWA-beta-propeller ternary systems (PF20030; HMM-score: 31)
    DUF815; Protein of unknown function (DUF815) (PF05673; HMM-score: 27.3)
    ATPase_2; ATPase domain predominantly from Archaea (PF01637; HMM-score: 26.2)
    TniB; Bacterial TniB protein (PF05621; HMM-score: 25.4)
    AAA_18; AAA domain (PF13238; HMM-score: 25)
    IstB_IS21; IstB-like ATP binding protein (PF01695; HMM-score: 24.6)
    Mg_chelatase; Magnesium chelatase, subunit ChlI (PF01078; HMM-score: 24.5)
    RNA_helicase; RNA helicase (PF00910; HMM-score: 23.6)
    DNA_pol3_delta2; DNA polymerase III, delta subunit (PF13177; HMM-score: 23.5)
    RuvB_N; Holliday junction DNA helicase RuvB P-loop domain (PF05496; HMM-score: 23.4)
    nSTAND3; Novel STAND NTPase 3 (PF20720; HMM-score: 23.2)
    NACHT; NACHT domain (PF05729; HMM-score: 22.5)
    Roc; Ras of Complex, Roc, domain of DAPkinase (PF08477; HMM-score: 21.9)
    AAA_24; AAA domain (PF13479; HMM-score: 20.4)
    AAA_25; AAA domain (PF13481; HMM-score: 20.2)
    AAA_28; AAA domain (PF13521; HMM-score: 20.1)
    Zeta_toxin; Zeta toxin (PF06414; HMM-score: 19.9)
    TsaE; Threonylcarbamoyl adenosine biosynthesis protein TsaE (PF02367; HMM-score: 19.6)
    AAA_3; ATPase family associated with various cellular activities (AAA) (PF07726; HMM-score: 19.4)
    RsgA_GTPase; RsgA GTPase (PF03193; HMM-score: 18.7)
    AAA_33; AAA domain (PF13671; HMM-score: 17.6)
    NTPase_1; NTPase (PF03266; HMM-score: 16.3)
    ABC_tran; ABC transporter (PF00005; HMM-score: 15.7)
    CbiA; CobQ/CobB/MinD/ParA nucleotide binding domain (PF01656; HMM-score: 14.9)
    SRP54; SRP54-type protein, GTPase domain (PF00448; HMM-score: 14.6)
    AAA_19; AAA domain (PF13245; HMM-score: 14.6)
    NBD_SMAX1; SMAX1 nucleotide binding domain (PF23569; HMM-score: 14.4)
    Ras; Ras family (PF00071; HMM-score: 13.6)
    AAA_29; P-loop containing region of AAA domain (PF13555; HMM-score: 12.7)
    DUF87; Helicase HerA, central domain (PF01935; HMM-score: 11.9)
    ResIII; Type III restriction enzyme, res subunit (PF04851; HMM-score: 11.1)
    AAA_31; AAA domain (PF13614; HMM-score: 9.8)
    no clan defined Mis12; Mis12 protein (PF05859; HMM-score: 8.3)

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

  • domains:
  • modifications:
  • cofactors:
  • 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
  • DeepLocPro: Cytoplasmic
    • Cytoplasmic Score: 0.9507
    • Cytoplasmic Membrane Score: 0.0204
    • Cell wall & surface Score: 0.0017
    • Extracellular Score: 0.0271
  • 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): 0.003381
    • TAT(Tat/SPI): 0.000314
    • LIPO(Sec/SPII): 0.000432
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MDINKMTYAVQSALQQAVELSQQHKLQNIEIEAILSAALNESESLYKSILERANIEVDQLNKAYEDKLNTYASVEGDNIQYGQYISQQANQLITKAESYMKEYEDEYISMEHILRSAMDIDQTTKHYINNKVEVIKEIIKKVRGGNHVTSQNPEVNYEALAKYGRDLVEEVRQGKMDPVIGRDEEIRNTIRILSRKTKNNPVLIGEPGVGKTAIVEGLAQRIVKKDVPESLLDKTVFELDLSALVAGAKYRGEFEERLKAVLKEVKESDGRIILFIDEIHMLVGAGKTDGAMDAGNMLKPMLARGELHCIGATTLNEYREYIEKDSALERRFQKVAVSEPDVEDTISILRGLKERYEVYHGVRIQDRALVAAAELSDRYITDRFLPDKAIDLVDQACATIRTEMGSNPTELDQVNRRVMQLEIEESALKNESDNASKQRLQELQEELANEKEKQAALQSRVESEKEKIANLQEKRAQLDESRQALEDAQTNNNLEKAAELQYGTIPQLEKELRELEDNFQDEQGEDTDRMIREVVTDEEIGDIVSQWTGIPVSKLVETEREKLLHLSDILHKRVVGQDKAVDLVSDAVVRARAGIKDPNRPIGSFLFLGPTGVGKTELAKSLAASLFDSEKHMIRIDMSEYMEKHAVSRLIGAPPGYIGHDEGGQLTEAVRRNPYSVILLDEVEKAHTDVFNVLLQILDEGRLTDSKGRSVDFKNTIIIMTSNIGSQVLLENVKETGEITESTEKAVMTSLNAYFKPEILNRMDDIVLFKPLSIDDMSMIVDKILTQLNIRLLEQRISIEVSDDAKAWLGQEAYEPQYGARPLKRFVQRQIETPLARMMIKEGFPEGTTIKVNLNSDNNLTFNVEKIHE

⊟Experimental data[edit | edit source]

  • experimentally validated: PeptideAtlas
  • protein localization: Cytoplasmic [1] [2] [3] [4]
  • quantitative data / protein copy number per cell: 204 [5]
  • interaction partners:
    SACOL2525ABC transporter ATP-binding protein  [6] (data from MRSA252)

⊟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. ↑ 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. ↑ Artem Cherkasov, Michael Hsing, Roya Zoraghi, Leonard J Foster, Raymond H See, Nikolay Stoynov, Jihong Jiang, Sukhbir Kaur, Tian Lian, Linda Jackson, Huansheng Gong, Rick Swayze, Emily Amandoron, Farhad Hormozdiari, Phuong Dao, Cenk Sahinalp, Osvaldo Santos-Filho, Peter Axerio-Cilies, Kendall Byler, William R McMaster, Robert C Brunham, B Brett Finlay, Neil E Reiner
    Mapping the protein interaction network in methicillin-resistant Staphylococcus aureus.
    J Proteome Res: 2011, 10(3);1139-50
    [PubMed:21166474] [WorldCat.org] [DOI] (I p)

⊟Relevant publications[edit | edit source]

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