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NCBI: 03-AUG-2016

Summary[edit source | edit]

  • organism: Staphylococcus aureus NCTC8325
  • locus tag: SAOUHSC_01973
  • pan locus tag?: SAUPAN004772000
  • symbol: SAOUHSC_01973
  • pan gene symbol?: cbf1
  • synonym:
  • product: 3'-5' exoribonuclease YhaM

Genome View[edit source | edit]

Gene[edit source | edit]

General[edit source | edit]

  • type: CDS
  • locus tag: SAOUHSC_01973
  • symbol: SAOUHSC_01973
  • product: 3'-5' exoribonuclease YhaM
  • replicon: chromosome
  • strand: -
  • coordinates: 1876332..1877273
  • length: 942
  • essential: no DEG other strains

Accession numbers[edit source | edit]

Phenotype[edit source | edit]

  • Share your knowledge and add information here. [edit]

DNA sequence[edit source | edit]

  • 1
    61
    121
    181
    241
    301
    361
    421
    481
    541
    601
    661
    721
    781
    841
    901
    ATGAGAAATATAGAGAATCTAAATCCCGGAGATTCAGTTGATCACTTTTTCTTAGTGCAT
    AAAGCTACACAGGGTGTAACAGCACAAGGTAAAGATTATATGACATTACATTTGCAAGAT
    AAAAGTGGTGAAATTGAAGCGAAATTTTGGACGGCTACAAAAAATGATATGGCAACAATC
    AAGCCTGAAGAAATTGTACATGTTAAAGGTGACATCATAAACTATCGCGGAAATAAACAG
    ATGAAAGTCAACCAAATTAGACTAGCGACAACTGAAGATCAATTAAAAACAGAACAATTT
    GTAGATGGTGCACCTTTATCACCGGCAGAAATACAAGAAGAGATTTCTCATTATTTGCTA
    GATATTGAAAATGCTAATTTACAACGTATCACACGTCATTTATTGAAAAAATATCAAGAA
    CGATTTTACACATATCCAGCTGCTAGTTCTCATCATCATAACTTTGCGAGTGGCTTAAGC
    TATCATGTATTAACGATGTTACGTATTGCAAAATCAATTTGTGACATTTATCCATTGTTA
    AACAAAAGTTTGTTATATAGTGGTATTATTTTGCATGATATTGGTAAAGTTAGAGAATTG
    AGTGGTCCTGTTGCGACGTCGTATACAGTCGAAGGTAACTTATTAGGACACATCTCGATT
    GCGAGTGATGAAGTAGTTGAAGCAGCTCGTGAATTGAACATTGAAGGAGAAGAAATCATG
    TTGTTAAGACATATGATTTTATCTCATCATGGTAAGTTAGAGTATGGTTCTCCAAAACTG
    CCATACTTAAAAGAAGCAGAAATTTTATGCTATATCGATAATATCGATGCTAGAATGAAT
    ATGTTTGAAAAGGCATATAAAAAAACTGACAAGGGTCAGTTTACAGATAAAATATTTGGT
    CTTGAAAATCGTAGATTCTACAATCCTGAATCACTCGATTAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    942

Protein[edit source | edit]

General[edit source | edit]

  • locus tag: SAOUHSC_01973
  • symbol: SAOUHSC_01973
  • description: 3'-5' exoribonuclease YhaM
  • length: 313
  • theoretical pI: 6.56818
  • theoretical MW: 35778.6
  • GRAVY: -0.417891

Function[edit source | edit]

  • reaction:
  • TIGRFAM:
    CRISPR-associated endonuclease Cas3-HD (TIGR01596; EC 3.1.-.-; HMM-score: 23.3)
    HDIG domain (TIGR00277; HMM-score: 20.9)
    integrating conjugative element relaxase, PFGI-1 class (TIGR03760; HMM-score: 13.9)
  • TheSEED:  
    3'->5' exoribonuclease Bsu YhaM 
  • PFAM:
    HD_PDEase (CL0237) HD; HD domain (PF01966; HMM-score: 41.2)
    OB (CL0021) tRNA_anti-codon; OB-fold nucleic acid binding domain (PF01336; HMM-score: 34.9)
    HD_PDEase (CL0237) TraI_2; Putative helicase (PF07514; HMM-score: 18.5)

Structure, modifications & interactions[edit source | edit]

  • domains:
  • modifications:
  • cofactors:
  • effectors:
  • protein partners:

Localization[edit source | edit]

  • PSORTb: Cytoplasmic
    • Cytoplasmic Score: 7.5
    • Cytoplasmic Membrane Score: 1.15
    • Cellwall Score: 0.62
    • Extracellular Score: 0.73
    • 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
    • Ymax: 0.162
    • Ymax_pos: 31
    • Cmax: 0.212
    • Cmax_pos: 31
    • Smax: 0.176
    • Smax_pos: 27
    • Smean: 0.117
    • D: 0.145
  • predicted transmembrane helices (TMHMM): 0

Accession numbers[edit source | edit]

Protein sequence[edit source | edit]

  • MRNIENLNPGDSVDHFFLVHKATQGVTAQGKDYMTLHLQDKSGEIEAKFWTATKNDMATIKPEEIVHVKGDIINYRGNKQMKVNQIRLATTEDQLKTEQFVDGAPLSPAEIQEEISHYLLDIENANLQRITRHLLKKYQERFYTYPAASSHHHNFASGLSYHVLTMLRIAKSICDIYPLLNKSLLYSGIILHDIGKVRELSGPVATSYTVEGNLLGHISIASDEVVEAARELNIEGEEIMLLRHMILSHHGKLEYGSPKLPYLKEAEILCYIDNIDARMNMFEKAYKKTDKGQFTDKIFGLENRRFYNPESLD

Experimental data[edit source | edit]

Expression & Regulation[edit source | edit]

Operon[edit source | edit]

Regulation[edit source | edit]

  • sigma factor:
  • regulator:

Transcription pattern[edit source | edit]

Protein synthesis (provided by Aureolib)[edit source | edit]

Protein stability[edit source | edit]

  • half-life: no data available

Biological Material[edit source | edit]

Mutants[edit source | edit]

Expression vector[edit source | edit]

lacZ fusion[edit source | edit]

GFP fusion[edit source | edit]

two-hybrid system[edit source | edit]

FLAG-tag construct[edit source | edit]

Antibody[edit source | edit]

Other Information[edit source | edit]

You are kindly invited to share additional interesting facts.

Literature[edit source | edit]

References[edit source | edit]

  1. 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)
  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);3648-3661
    [PubMed:26224020] [WorldCat.org] [DOI] (I p)
  3. 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 source | edit]

Q Zhang, S Soares de Oliveira, R Colangeli, M L Gennaro
Binding of a novel host factor to the pT181 plasmid replication enhancer.
J. Bacteriol.: 1997, 179(3);684-8
[PubMed:9006021] [WorldCat.org] (P p)