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NCBI: 26-AUG-2013

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus N315
  • locus tag: SA1129 [new locus tag: SA_RS06380 ]
  • pan locus tag?: SAUPAN003588000
  • symbol: SA1129
  • pan gene symbol?: rny
  • synonym: cvfA
  • product: phosphodiesterase

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SA1129 [new locus tag: SA_RS06380 ]
  • symbol: SA1129
  • product: phosphodiesterase
  • replicon: chromosome
  • strand: +
  • coordinates: 1281967..1283526
  • length: 1560
  • essential: no 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
    GTGAATTTATTAAGCCTCCTACTCATTTTGCTGGGGATCATTCTAGGAGTTGTTGGAGGG
    TATGTTGTTGCCCGAAATTTGTTGCTTCAAAAGCAATCACAAGCTAGACAAACTGCCGAA
    GATATTGTAAATCAAGCACATAAAGAAGCTGACAATATCAAAAAAGAGAAATTACTTGAG
    GCAAAAGAAGAAAACCAAATCCTAAGAGAACAAACTGAAGCAGAACTACGAGAAAGACGT
    AGCGAACTTCAAAGACAAGAAACCCGACTTCTTCAAAAAGAAGAAAACTTAGAGCGCAAA
    TCTGATCTATTAGATAAAAAAGATGAGATTTTAGAGCAAAAAGAATCAAAAATTGAAGAA
    AAACAACAACAAGTAGATGCAAAAGAGAGTAGTGTTCAAACGTTAATAATGAAGCATGAA
    CAAGAATTAGAACGCATCTCCGGTCTCACTCAAGAAGAAGCTATTAATGAGCAACTTCAA
    AGAGTAGAGGAAGAACTGTCACAAGATATTGCAGTACTTGTTAAAGAAAAAGAAAAAGAA
    GCTAAAGAAAAAGTTGATAAAACAGCAAAAGAATTATTAGCTACAGCAGTACAAAGATTA
    GCAGCAGATCACACAAGTGAATCAACGGTATCAGTAGTTAACTTACCTAATGATGAGATG
    AAAGGTCGAATCATTGGACGAGAAGGACGAAACATCCGCACACTTGAAACTTTAACTGGC
    ATTGATTTAATTATTGATGACACACCAGAAGCGGTTATATTATCTGGTTTTGATCCAATA
    AGAAGAGAAATTGCTAGAACAGCACTTGTTAACTTAGTATCTGATGGACGTATTCATCCA
    GGTAGAATTGAAGATATGGTCGAAAAAGCTAGAAAAGAAGTAGACGATATTATTAGAGAA
    GCAGGTGAACAAGCTACATTTGAAGTGAACGCACATAATATGCATCCTGACTTAGTAAAA
    ATTGTAGGGCGTTTAAACTATCGTACGAGTTACGGTCAAAATGTACTTAAACATTCAATT
    GAAGTTGCGCATCTTGCTAGTATGTTAGCTGCTGAGCTAGGCGAAGATGAGACATTAGCG
    AAACGAGCTGGACTTTTACATGATGTTGGTAAAGCAATTGATCATGAAGTAGAAGGTAGT
    CATGTTGAAATCGGTGTAGAATTAGCGAAAAAATATGGTGAAAATGAAACAGTTATTAAT
    GCAATCCATTCTCACCATGGTGATGTTGAACCTACATCTATTATATCTATCCTTGTTGCT
    GCTGCAGATGCATTGTCTGCGGCTCGTCCAGGTGCAAGAAAAGAAACATTAGAGAATTAT
    ATTCGTCGATTAGAACGTTTAGAAACGTTATCAGAAAGTTATGATGGTGTAGAAAAAGCA
    TTTGCGATTCAGGCAGGTAGAGAAATCCGAGTGATTGTATCTCCTGAAGAAATTGATGAT
    TTAAAATCTTATCGATTGGCTAGAGATATTAAAAATCAGATTGAAGATGAATTACAATAT
    CCTGGTCATATCAAGGTGACAGTTGTTCGAGAGACTAGAGCAGTAGAATATGCGAAATAA
    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

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SA1129 [new locus tag: SA_RS06380 ]
  • symbol: SA1129
  • description: phosphodiesterase
  • length: 519
  • theoretical pI: 4.9413
  • theoretical MW: 58511.8
  • GRAVY: -0.519268

⊟Function[edit | edit source]

  • reaction:
    EC 3.1.-.-?  ExPASy
  • ⊞TIGRFAM:
    Genetic information processing Transcription Degradation of RNA ribonuclease Y (TIGR03319; EC 3.1.-.-; HMM-score: 795.6)
    and 6 more
    HDIG domain (TIGR00277; HMM-score: 86.3)
    arCOG04150 universal archaeal KH domain protein (TIGR03665; HMM-score: 27.1)
    Unknown function Enzymes of unknown specificity putative HD superfamily hydrolase (TIGR00488; HMM-score: 26.4)
    NusA family KH domain protein, archaeal (TIGR01952; HMM-score: 18.2)
    CRISPR-associated endonuclease Cas3-HD (TIGR01596; EC 3.1.-.-; HMM-score: 17.9)
    Metabolism Transport and binding proteins Cations and iron carrying compounds potassium uptake protein, Trk family (TIGR00934; HMM-score: 3.3)
  • ⊞TheSEED  :
    • Ribonuclease Y
    CBSS-257314.1.peg.676  FIG002344: Hydrolase (HAD superfamily)
    and 1 more
    Competence or DNA damage-inducible protein CinA and related protein families  FIG002344: Hydrolase (HAD superfamily)
  • ⊞PFAM:
    no clan defined RNase_Y_N; RNase Y N-terminal region (PF12072; HMM-score: 219.4)
    and 9 more
    HD_PDEase (CL0237) HD; HD domain (PF01966; HMM-score: 74.8)
    KH (CL0007) KH_1; KH domain (PF00013; HMM-score: 29.4)
    HD_PDEase (CL0237) HDOD; HDOD domain (PF08668; HMM-score: 27.7)
    KH (CL0007) KH_KhpA-B; KhpA/KhpB, KH domain (PF13083; HMM-score: 21.3)
    no clan defined VNG_1110C; VNG_1110C-like (PF24397; HMM-score: 17.2)
    PIGBOS1; PIGBOS1-like (PF23670; HMM-score: 16.1)
    KH (CL0007) KH_2; KH domain (PF07650; HMM-score: 13.3)
    HTH (CL0123) DUF7669; Domain of unknown function (DUF7669) (PF24706; HMM-score: 13.2)
    no clan defined GAGA_bind; GAGA binding protein-like family (PF06217; HMM-score: 8.6)

⊟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 Helix: 1
  • ⊞DeepLocPro: Cytoplasmic Membrane
    • Cytoplasmic Score: 0.0135
    • Cytoplasmic Membrane Score: 0.9585
    • Cell wall & surface Score: 0.0007
    • Extracellular Score: 0.0273
  • ⊞LocateP: N-terminally anchored (with CS)
    • Prediction by SwissProt Classification: Membrane
    • Pathway Prediction: Sec-(SPI)
    • Intracellular possibility: 0.17
    • Signal peptide possibility: 0.5
    • N-terminally Anchored Score: 1
    • Predicted Cleavage Site: GYVVARNL
  • ⊞SignalP: no predicted signal peptide
    • SP(Sec/SPI): 0.328428
    • TAT(Tat/SPI): 0.004027
    • LIPO(Sec/SPII): 0.063802
  • predicted transmembrane helices (TMHMM): 1

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MNLLSLLLILLGIILGVVGGYVVARNLLLQKQSQARQTAEDIVNQAHKEADNIKKEKLLEAKEENQILREQTEAELRERRSELQRQETRLLQKEENLERKSDLLDKKDEILEQKESKIEEKQQQVDAKESSVQTLIMKHEQELERISGLTQEEAINEQLQRVEEELSQDIAVLVKEKEKEAKEKVDKTAKELLATAVQRLAADHTSESTVSVVNLPNDEMKGRIIGREGRNIRTLETLTGIDLIIDDTPEAVILSGFDPIRREIARTALVNLVSDGRIHPGRIEDMVEKARKEVDDIIREAGEQATFEVNAHNMHPDLVKIVGRLNYRTSYGQNVLKHSIEVAHLASMLAAELGEDETLAKRAGLLHDVGKAIDHEVEGSHVEIGVELAKKYGENETVINAIHSHHGDVEPTSIISILVAAADALSAARPGARKETLENYIRRLERLETLSESYDGVEKAFAIQAGREIRVIVSPEEIDDLKSYRLARDIKNQIEDELQYPGHIKVTVVRETRAVEYAK

⊟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]

  • 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]

⊟Relevant publications[edit | edit source]

Gabriella Marincola, Tina Schäfer, Juliane Behler, Jörg Bernhardt, Knut Ohlsen, Christiane Goerke, Christiane Wolz
RNase Y of Staphylococcus aureus and its role in the activation of virulence genes.
Mol Microbiol: 2012, 85(5);817-32
[PubMed:22780584] [WorldCat.org] [DOI] (I p)

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