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FunGene: 08-OCT-2024

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus JSNZ
  • locus tag: JSNZ_002252
  • pan locus tag?: SAUPAN005749000
  • symbol: JSNZ_002252
  • pan gene symbol?: ydbM
  • synonym:
  • product: acyl-CoA dehydrogenase family protein

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: JSNZ_002252
  • symbol: JSNZ_002252
  • product: acyl-CoA dehydrogenase family protein
  • replicon: chromosome
  • strand: -
  • coordinates: 2249445..2250599
  • length: 1155
  • essential: unknown other strains

⊟Accession numbers[edit | edit source]

  • Gene ID:
  • RefSeq:
  • BioCyc:
  • MicrobesOnline:

⊟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
    ATGAATGATATGGATAATTCCTTTTTAATAACAACGGAAATTCAAAGAAAATGGATTGAA
    AAATTCAAAGTAATTAGAGATACATTTAAGGCTAAAGCTGAATATAATGATCAACATAGC
    CAATTTCCATATAAAAATATTGAATGGTTAATTAAAGAAGGTTATGGAAAATTAACGTTA
    CCAAAAGCATATGGTGGTGAAGGTGCGACCATAGAAGACATGGTTATTTTGCAATCATTT
    TTAGGCGAACTTGATGGTGCCACAGCATTATCTATTGGTTGGCATGTGAGTGTCGTAGGA
    CAAATTTATGAACAGAAATTATGGTCTCAAGATATGTTGGAGCAATTTGCTGTTGAAATT
    AATAATGGTGCATTAGTTAATAGAGCAGTTAGTGAAGCTGAAATGGGTAGTCCAACAAGA
    GGGGGAAGACCAAGTACACATGCTGTTAAAGCTGATGATGGGTATATTTTAAATGGTGTG
    AAGACATATACATCAATGAGTAAAGCACTAACACATATTATTGTTGCTGCTTATATAGAA
    GAATTAGAAAGTGTTGGTTTTTTCTTAGTGGACAGGAATTTGCCTGGTGTTGAAATTGCC
    GATAATTGGGACGTATTAGGTATGCGAGCGACAGAAAGTCATGATTTAATATTAAATGAT
    GTAAAAGTACCATTAAAACATTTAGTGGAAACAGAGAAAAGTAAAGCGCCAAATGGTTGG
    ATATTGCATATACCAAGCTGTTATTTAGGTATAGCACAAGCTGCTAGAAATTATGCTGTA
    GACTTTGCAATCCAACATAGCCCTAATAGTATTGAAGGAACGATTGCAACATTGCCAACT
    GTGCAACAAAATTTAGGGAAAATGGAAACGCTATTGTTATGTGCGAGACAATTTTTATGG
    AGTACAGCAAAAGGGTATCAACAATATAAAGATGACAGTCAGATAAGAAATCCAACAAGT
    GCGAGTAAAGTGATGGTAATGAATCAAGGGCTTGAAGTGATTGATTTAGCGATGAGAATA
    GTTGGTGCTAAAAGCTTAGAAATGAATCGACCATTACAACGTTACTATCGTGACATGCGT
    GCAGGATTACACAATCCACCTATGGAAGATGCAGCATATACAAATATTGCTAAGAGTATT
    ACAGATACATTTTAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    1020
    1080
    1140
    1155

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: JSNZ_002252
  • symbol: JSNZ_002252
  • description: acyl-CoA dehydrogenase family protein
  • length: 384
  • theoretical pI: 5.85467
  • theoretical MW: 42999.8
  • GRAVY: -0.246354

⊟Function[edit | edit source]

  • reaction:
    EC 1.-.-.-?  ExPASy
  • TIGRFAM:
    Metabolism Central intermediary metabolism Sulfur metabolism sulfur acquisition oxidoreductase, SfnB family (TIGR04022; EC 1.-.-.-; HMM-score: 104.2)
    and 2 more
    pimeloyl-CoA dehydrogenase, large subunit (TIGR03204; EC 1.3.1.62; HMM-score: 34.3)
    cyclohexanecarboxyl-CoA dehydrogenase (TIGR03207; EC 1.1.1.-; HMM-score: 32.9)
  • TheSEED: data available for COL, N315, NCTC8325, Newman, USA300_FPR3757
  • PFAM:
    no clan defined Acyl-CoA_dh_M; Acyl-CoA dehydrogenase, middle domain (PF02770; HMM-score: 55.6)
    Acyl-CoA_dh (CL0087) Acyl-CoA_dh_2; Acyl-CoA dehydrogenase, C-terminal domain (PF08028; HMM-score: 49.8)
    Acyl-CoA_dh_1; Acyl-CoA dehydrogenase, C-terminal domain (PF00441; HMM-score: 45.4)
    and 1 more
    AcylCoA_ox_dh_N (CL0544) Acyl-CoA_dh_N; Acyl-CoA dehydrogenase, N-terminal domain (PF02771; HMM-score: 29.4)

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

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

⊟Localization[edit | edit source]

  • PSORTb: Cytoplasmic
    • Cytoplasmic Score: 7.5
    • Cytoplasmic Membrane Score: 1.15
    • Cellwall Score: 0.62
    • Extracellular Score: 0.73
    • Internal Helices: 0
  • DeepLocPro: Cytoplasmic
    • Cytoplasmic Score: 0.968
    • Cytoplasmic Membrane Score: 0.0273
    • Cell wall & surface Score: 0.0005
    • Extracellular Score: 0.0042
  • LocateP:
  • SignalP: no predicted signal peptide
    • SP(Sec/SPI): 0.0164
    • TAT(Tat/SPI): 0.001229
    • LIPO(Sec/SPII): 0.002022
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

  • GI:
  • RefSeq:
  • UniProt:

⊟Protein sequence[edit | edit source]

  • MNDMDNSFLITTEIQRKWIEKFKVIRDTFKAKAEYNDQHSQFPYKNIEWLIKEGYGKLTLPKAYGGEGATIEDMVILQSFLGELDGATALSIGWHVSVVGQIYEQKLWSQDMLEQFAVEINNGALVNRAVSEAEMGSPTRGGRPSTHAVKADDGYILNGVKTYTSMSKALTHIIVAAYIEELESVGFFLVDRNLPGVEIADNWDVLGMRATESHDLILNDVKVPLKHLVETEKSKAPNGWILHIPSCYLGIAQAARNYAVDFAIQHSPNSIEGTIATLPTVQQNLGKMETLLLCARQFLWSTAKGYQQYKDDSQIRNPTSASKVMVMNQGLEVIDLAMRIVGAKSLEMNRPLQRYYRDMRAGLHNPPMEDAAYTNIAKSITDTF

⊟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: CymR* (repression) regulon, SigB (activation) regulon
    CymR*(TF)important in Cysteine metabolism;  regulation predicted or transferred from N315 and NCTC 8325  [1]
    SigB(sigma factor)controlling a large regulon involved in stress/starvation response and adaptation;  regulation predicted or transferred from N315 and NCTC 8325  [2] [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. ↑ Hannes Wolfgramm, Larissa Milena Busch, Jöran Tebben, Henry Mehlan, Lisa Hagenau, Thomas Sura, Tilly Hoffmüller, Elisa Bludau, Manuela Gesell Salazar, Alexander Reder, Stephan Michalik, Leif Steil, Kristin Surmann, Ulrike Mäder, Silva Holtfreter, Uwe Völker
    Integrated genomic and proteomic analysis of the mouse-adapted Staphylococcus aureus strain JSNZ.
    Curr Res Microb Sci: 2025, 9;100489
    [PubMed:41146725] [WorldCat.org] [DOI] (I e)
  2. ↑ 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)
  3. ↑ Jan Pané-Farré, Beate Jonas, Konrad Förstner, Susanne Engelmann, Michael Hecker
    The sigmaB regulon in Staphylococcus aureus and its regulation.
    Int J Med Microbiol: 2006, 296(4-5);237-58
    [PubMed:16644280] [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]

Olga Soutourina, Sarah Dubrac, Olivier Poupel, Tarek Msadek, Isabelle Martin-Verstraete
The pleiotropic CymR regulator of Staphylococcus aureus plays an important role in virulence and stress response.
PLoS Pathog: 2010, 6(5);e1000894
[PubMed:20485570] [WorldCat.org] [DOI] (I e)

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