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NCBI: 03-AUG-2016

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus NCTC8325
  • locus tag: SAOUHSC_01222
  • pan locus tag?: SAUPAN003548000
  • symbol: SAOUHSC_01222
  • pan gene symbol?: topA
  • synonym:
  • product: DNA topoisomerase I

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SAOUHSC_01222
  • symbol: SAOUHSC_01222
  • product: DNA topoisomerase I
  • replicon: chromosome
  • strand: +
  • coordinates: 1172818..1174893
  • length: 2076
  • essential: yes [1] DEG 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
    ATGACATTGGCAGATAATTTAGTCATTGTTGAATCGCCTGCAAAAGCAAAAACCATTGAA
    AAGTATTTAGGTAAGAAATATAAAGTTATAGCTTCAATGGGACACGTCAGAGACTTACCA
    AGAAGTCAAATGGGTGTCGACACTGAAGATAATTACGAACCAAAATATATAACAATACGC
    GGAAAAGGTCCTGTTGTAAAAGAATTGAAAAAACATGCAAAAAAAGCGAAAAACGTCTTT
    CTCGCAAGTGACCCCGACCGTGAAGGTGAAGCAATTGCTTGGCATTTATCAAAAATTTTA
    GAGCTTGAAGATTCTAAAGAAAATCGCGTTGTTTTCAACGAAATAACTAAAGACGCTGTT
    AAAGAAAGTTTTAAAAATCCTAGAGAAATTGAAATGAACTTAGTCGATGCACAACAAGCG
    CGTCGAATATTAGATAGATTAGTTGGCTATAACATCTCGCCAGTTCTTTGGAAAAAAGTA
    AAAAAAGGGTTGTCAGCGGGTCGAGTTCAATCTGTTGCACTTCGTTTAGTCATTGACCGT
    GAAAATGAAATTCGAAACTTTAAACCAGAAGAATATTGGACTATTGAAGGAGAATTTAGA
    TACAAAAAATCAAAATTCAATGCTAAATTCCTTCATTATAAAAATAAACCTTTTAAACTA
    AAAACGAAAAAAGATGTTGAGAAAATTACAGCTGCATTAGATGGAGATCAATTCGAAATT
    ACAAACGTGACTAAAAAAGAAAAAACGCGTAATCCAGCAAACCCATTTACAACTTCTACA
    TTACAACAAGAGGCGGCACGTAAATTAAACTTTAAAGCAAGAAAAACAATGATGGTCGCA
    CAACAATTATATGAAGGTATAGATTTGAAAAAACAAGGTACGATTGGTTTAATAACATAT
    ATGAGAACCGATTCTACACGTATTTCAGATACTGCCAAAGTTGAAGCAAAACAGTATATA
    ACTGATAAATACGGTGAATCTTACACTTCTAAACGTAAAGCATCAGGGAAACAAGGTGAC
    CAAGATGCCCATGAGGCTATTAGACCTTCAAGTACTATGCGTACGCCAGATGATATGAAG
    TCATTTTTGACGAAAGACCAATACCGATTATACAAATTAATTTGGGAACGATTTGTTGCT
    AGTCAAATGGCTCCAGCAATACTTGATACAGTCTCATTAGACATAACACAAGGTGACATT
    AAATTTAGAGCGAATGGTCAAACAATCAAGTTTAAAGGATTTATGACACTTTATGTAGAA
    ACTAAAGATGATAGTGATAGCGAAAAGGAAAATAAACTGCCTAAATTAGAGCAAGGTGAT
    AAAGTCACAGCAACTCAAATTGAACCAGCTCAACACTATACACAACCACCTCCAAGATAT
    ACTGAGGCGAGATTAGTAAAAACACTAGAAGAATTGAAAATTGGGCGACCATCAACTTAT
    GCACCGACAATAGATACGATTCAAAAGCGTAACTATGTCAAATTAGAAAGTAAGCGTTTT
    GTTCCTACTGAGTTGGGAGAAATAGTTCATGAACAAGTGAAAGAATACTTCCCAGAGATT
    ATTGATGTGGAATTCACAGTGAATATGGAAACGTTACTTGATAAGATTGCAGAAGGCGAC
    ATTACATGGAGGAAAGTAATCGACGGTTTCTTTAGTAGCTTTAAACAAGATGTTGAACGT
    GCTGAAGAAGAGATGGAAAAGATTGAAATCAAAGATGAGCCAGCCGGTGAAGACTGTGAA
    ATTTGTGGTTCTCCTATGGTTATAAAAATGGGACGCTATGGTAAGTTCATGGCTTGCTCA
    AACTTCCCGGATTGTCGTAATACAAAAGCGATAGTTAAGTCTATTGGTGTTAAATGTCCA
    AAATGTAATGATGGTGACGTCGTAGAAAGAAAATCTAAAAAGAATCGTGTCTTTTATGGA
    TGTTCGAAATATCCTGAATGCGACTTTATCTCTTGGGATAAGCCGATTGGAAGAGATTGT
    CCAAAATGTAACCAATATCTTGTTGAAAATAAAAAAGGCAAGACAACACAAGTAATATGT
    TCAAATTGCGATTATAAAGAGGCAGCGCAGAAATAA
    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
    2076

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SAOUHSC_01222
  • symbol: SAOUHSC_01222
  • description: DNA topoisomerase I
  • length: 691
  • theoretical pI: 9.4884
  • theoretical MW: 79326.5
  • GRAVY: -0.719247

⊟Function[edit | edit source]

  • reaction:
    EC 5.99.1.2?  ExPASy
    DNA topoisomerase ATP-independent breakage of single-stranded DNA, followed by passage and rejoining
  • TIGRFAM:
    Genetic information processing DNA metabolism DNA replication, recombination, and repair DNA topoisomerase I (TIGR01051; EC 5.99.1.2; HMM-score: 859.4)
    and 6 more
    Genetic information processing DNA metabolism DNA replication, recombination, and repair DNA topoisomerase I (TIGR01057; EC 5.99.1.2; HMM-score: 311.8)
    Genetic information processing DNA metabolism DNA replication, recombination, and repair reverse gyrase (TIGR01054; EC 3.6.4.12,5.99.1.3; HMM-score: 309.9)
    Genetic information processing DNA metabolism DNA replication, recombination, and repair DNA topoisomerase III (TIGR01056; EC 5.99.1.2; HMM-score: 211.2)
    Genetic information processing Transcription RNA processing ribonuclease M5 (TIGR00334; EC 3.1.26.8; HMM-score: 15.2)
    conserved hypothetical protein (TIGR02443; HMM-score: 5.8)
    Metabolism Energy metabolism Methanogenesis methyl coenzyme M reductase system, component A2 (TIGR03269; HMM-score: 5.6)
  • TheSEED  :
    • DNA topoisomerase I (EC 5.99.1.2)
    Conserved gene cluster associated with Met-tRNA formyltransferase  DNA topoisomerase I (EC 5.99.1.2)
  • PFAM:
    no clan defined Topoisom_bac; DNA topoisomerase (PF01131; HMM-score: 446.1)
    and 10 more
    Zn_Beta_Ribbon (CL0167) zf-C4_Topoisom; Topoisomerase DNA binding C4 zinc finger (PF01396; HMM-score: 108.3)
    Toprim-like (CL0413) Toprim; Toprim domain (PF01751; HMM-score: 106.4)
    Toprim_4; Toprim domain (PF13662; HMM-score: 18.5)
    Toprim_2; Toprim-like (PF13155; HMM-score: 15.5)
    Zn_Beta_Ribbon (CL0167) RNA_POL_M_15KD; RNA polymerases M/15 Kd subunit (PF02150; HMM-score: 14.8)
    Auto_anti-p27; Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27) (PF06677; HMM-score: 12.1)
    IHF-likeDNA-bdg (CL0548) Bac_DNA_binding; Bacterial DNA-binding protein (PF00216; HMM-score: 11.8)
    no clan defined HypA; Hydrogenase/urease nickel incorporation, metallochaperone, hypA (PF01155; HMM-score: 10)
    Zn_Beta_Ribbon (CL0167) zf-TFIIB; Transcription factor zinc-finger (PF13453; HMM-score: 9.5)
    RING (CL0229) IBR; IBR domain, a half RING-finger domain (PF01485; HMM-score: 7.1)

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

  • domains:
  • modifications:
  • cofactors: Mg2+
  • 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): 0.009849
    • TAT(Tat/SPI): 0.000672
    • LIPO(Sec/SPII): 0.001226
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MTLADNLVIVESPAKAKTIEKYLGKKYKVIASMGHVRDLPRSQMGVDTEDNYEPKYITIRGKGPVVKELKKHAKKAKNVFLASDPDREGEAIAWHLSKILELEDSKENRVVFNEITKDAVKESFKNPREIEMNLVDAQQARRILDRLVGYNISPVLWKKVKKGLSAGRVQSVALRLVIDRENEIRNFKPEEYWTIEGEFRYKKSKFNAKFLHYKNKPFKLKTKKDVEKITAALDGDQFEITNVTKKEKTRNPANPFTTSTLQQEAARKLNFKARKTMMVAQQLYEGIDLKKQGTIGLITYMRTDSTRISDTAKVEAKQYITDKYGESYTSKRKASGKQGDQDAHEAIRPSSTMRTPDDMKSFLTKDQYRLYKLIWERFVASQMAPAILDTVSLDITQGDIKFRANGQTIKFKGFMTLYVETKDDSDSEKENKLPKLEQGDKVTATQIEPAQHYTQPPPRYTEARLVKTLEELKIGRPSTYAPTIDTIQKRNYVKLESKRFVPTELGEIVHEQVKEYFPEIIDVEFTVNMETLLDKIAEGDITWRKVIDGFFSSFKQDVERAEEEMEKIEIKDEPAGEDCEICGSPMVIKMGRYGKFMACSNFPDCRNTKAIVKSIGVKCPKCNDGDVVERKSKKNRVFYGCSKYPECDFISWDKPIGRDCPKCNQYLVENKKGKTTQVICSNCDYKEAAQK

⊟Experimental data[edit | edit source]

  • experimentally validated: PeptideAtlas [2] [3]
  • protein localization: data available for COL
  • quantitative data / protein copy number per cell: data available for COL
  • 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 are kindly invited to share additional interesting facts.

⊟Literature[edit | edit source]

⊟References[edit | edit source]

  1. ↑ Roy R Chaudhuri, Andrew G Allen, Paul J Owen, Gil Shalom, Karl Stone, Marcus Harrison, Timothy A Burgis, Michael Lockyer, Jorge Garcia-Lara, Simon J Foster, Stephen J Pleasance, Sarah E Peters, Duncan J Maskell, Ian G Charles
    Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH).
    BMC Genomics: 2009, 10;291
    [PubMed:19570206] [WorldCat.org] [DOI] (I e)
  2. ↑ Maren Depke, Stephan Michalik, Alexander Rabe, Kristin Surmann, Lars Brinkmann, Nico Jehmlich, Jörg Bernhardt, Michael Hecker, Bernd Wollscheid, Zhi Sun, Robert L Moritz, Uwe Völker, Frank Schmidt
    A peptide resource for the analysis of Staphylococcus aureus in host-pathogen interaction studies.
    Proteomics: 2015, 15(21);3648-61
    [PubMed:26224020] [WorldCat.org] [DOI] (I p)
  3. ↑ Stephan Michalik, Maren Depke, Annette Murr, Manuela Gesell Salazar, Ulrike Kusebauch, Zhi Sun, Tanja C Meyer, Kristin Surmann, Henrike Pförtner, Petra Hildebrandt, Stefan Weiss, Laura Marcela Palma Medina, Melanie Gutjahr, Elke Hammer, Dörte Becher, Thomas Pribyl, Sven Hammerschmidt, Eric W Deutsch, Samuel L Bader, Michael Hecker, Robert L Moritz, Ulrike Mäder, Uwe Völker, Frank Schmidt
    A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host-pathogen interactions.
    Sci Rep: 2017, 7(1);9718
    [PubMed:28887440] [WorldCat.org] [DOI] (I e)
  4. ↑ 4.0 4.1 4.2 Ulrike Mäder, Pierre Nicolas, Maren Depke, Jan Pané-Farré, Michel Debarbouille, Magdalena M van der Kooi-Pol, Cyprien Guérin, Sandra Dérozier, Aurelia Hiron, Hanne Jarmer, Aurélie Leduc, Stephan Michalik, Ewoud Reilman, Marc Schaffer, Frank Schmidt, Philippe Bessières, Philippe Noirot, Michael Hecker, Tarek Msadek, Uwe Völker, Jan Maarten van Dijl
    Staphylococcus aureus Transcriptome Architecture: From Laboratory to Infection-Mimicking Conditions.
    PLoS Genet: 2016, 12(4);e1005962
    [PubMed:27035918] [WorldCat.org] [DOI] (I e)

⊟Relevant publications[edit | edit source]

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