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m (Text replacement - "* <aureodatabase>protein Genbank</aureodatabase> " to "")
m (Text replacement - "gene Genbank" to "gene RefSeq")
 
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__TOC__
<protect>
<protect>
<aureodatabase>NCBI date</aureodatabase>
<aureodatabase>annotation</aureodatabase>


=Summary=
=Summary=


* <aureodatabase>organism</aureodatabase>
*<aureodatabase>organism</aureodatabase>
* <aureodatabase>locus</aureodatabase>
*<aureodatabase>locus</aureodatabase>
* <aureodatabase>pan locus</aureodatabase>
*<aureodatabase>pan locus</aureodatabase>
* <aureodatabase>gene symbol</aureodatabase>
*<aureodatabase>gene symbol</aureodatabase>
* <aureodatabase>pan gene symbol</aureodatabase>
*<aureodatabase>pan gene symbol</aureodatabase>
* <aureodatabase>gene synonyms</aureodatabase>
*<aureodatabase>gene synonyms</aureodatabase>
* <aureodatabase>product</aureodatabase>
*<aureodatabase>product</aureodatabase>
</protect>
</protect>


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==General==
==General==


* <aureodatabase>gene type</aureodatabase>
*<aureodatabase>gene type</aureodatabase>
* <aureodatabase>locus</aureodatabase>
*<aureodatabase>locus</aureodatabase>
* <aureodatabase>gene symbol</aureodatabase>
*<aureodatabase>gene symbol</aureodatabase>
* <aureodatabase>product</aureodatabase>
*<aureodatabase>product</aureodatabase>
* <aureodatabase>gene replicon</aureodatabase>
*<aureodatabase>gene replicon</aureodatabase>
* <aureodatabase>strand</aureodatabase>
*<aureodatabase>strand</aureodatabase>
* <aureodatabase>gene coordinates</aureodatabase>
*<aureodatabase>gene coordinates</aureodatabase>
* <aureodatabase>gene length</aureodatabase>
*<aureodatabase>gene length</aureodatabase>
* <aureodatabase>essential</aureodatabase>
*<aureodatabase>essential</aureodatabase>
*<aureodatabase>gene comment</aureodatabase>
</protect>
</protect>


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==Accession numbers==
==Accession numbers==


* <aureodatabase>gene GI</aureodatabase>
*<aureodatabase>gene GI</aureodatabase>
* <aureodatabase>gene Genbank</aureodatabase>
*<aureodatabase>gene RefSeq</aureodatabase>
*<aureodatabase>gene BioCyc</aureodatabase>
*<aureodatabase>gene MicrobesOnline</aureodatabase>
</protect>
</protect>
   
   
<protect>  
<protect>
==Phenotype==
==Phenotype==
</protect>
</protect>
* Share your knowledge and add information here. [<span class="plainlinks">[http://www.protecs.uni-greifswald.de/aureowiki/index.php?title={{PAGENAMEE}}&action=edit&section=6 edit]</span>]
Share your knowledge and add information here. [<span class="plainlinks">[//aureowiki.med.uni-greifswald.de/index.php?title={{PAGENAMEE}}&veaction=edit&section=6 edit]</span>]


<protect>
<protect>
==DNA sequence==
==DNA sequence==


* <aureodatabase>gene sequence</aureodatabase>
*<aureodatabase>gene sequence</aureodatabase>
</protect>
</protect>


<protect>
<protect>
<aureodatabase>RNA regulated operons</aureodatabase>
</protect>


<protect>
=Protein=
=Protein=
<aureodatabase>protein 3D view</aureodatabase>
<aureodatabase>protein 3D view</aureodatabase>
==General==
==General==


* <aureodatabase>locus</aureodatabase>
*<aureodatabase>locus</aureodatabase>
* <aureodatabase>protein symbol</aureodatabase>
*<aureodatabase>protein symbol</aureodatabase>
* <aureodatabase>protein description</aureodatabase>
*<aureodatabase>protein description</aureodatabase>
* <aureodatabase>protein length</aureodatabase>
*<aureodatabase>protein length</aureodatabase>
* <aureodatabase>theoretical pI</aureodatabase>
*<aureodatabase>theoretical pI</aureodatabase>
* <aureodatabase>theoretical MW</aureodatabase>
*<aureodatabase>theoretical MW</aureodatabase>
* <aureodatabase>GRAVY</aureodatabase>
*<aureodatabase>GRAVY</aureodatabase>
</protect>
</protect>


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==Function==
==Function==


* <aureodatabase>protein reaction</aureodatabase>
*<aureodatabase>protein reaction</aureodatabase>
* <aureodatabase>protein TIGRFAM</aureodatabase>
*<aureodatabase>protein TIGRFAM</aureodatabase>
* <aureodatabase>protein TheSeed</aureodatabase>
*<aureodatabase>protein TheSeed</aureodatabase>
* <aureodatabase>protein PFAM</aureodatabase>
*<aureodatabase>protein PFAM</aureodatabase>
</protect>
</protect>


<protect>
<protect>
==Structure, modifications & interactions==
==Structure, modifications & cofactors==


* <aureodatabase>protein domains</aureodatabase>
*<aureodatabase>protein domains</aureodatabase>
* <aureodatabase>protein modifications</aureodatabase>
*<aureodatabase>protein modifications</aureodatabase>
* <aureodatabase>protein cofactors</aureodatabase>
*<aureodatabase>protein cofactors</aureodatabase>
* <aureodatabase>protein effectors</aureodatabase>
*<aureodatabase>protein effectors</aureodatabase>
* <aureodatabase>protein partners</aureodatabase>
*<aureodatabase>protein regulated operons</aureodatabase>
</protect>
</protect>


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==Localization==
==Localization==


* <aureodatabase>protein Psortb</aureodatabase>
*<aureodatabase>protein Psortb</aureodatabase>
* <aureodatabase>protein LocateP</aureodatabase>
*<aureodatabase>protein LocateP</aureodatabase>
* <aureodatabase>protein SignalP</aureodatabase>
*<aureodatabase>protein SignalP</aureodatabase>
* <aureodatabase>protein TMHMM</aureodatabase>
*<aureodatabase>protein TMHMM</aureodatabase>
</protect>
</protect>


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==Accession numbers==
==Accession numbers==


* <aureodatabase>protein GI</aureodatabase>
*<aureodatabase>protein GI</aureodatabase>
* <aureodatabase>protein UniProt</aureodatabase>
*<aureodatabase>protein RefSeq</aureodatabase>
* <aureodatabase>protein RefSeq</aureodatabase>
*<aureodatabase>protein UniProt</aureodatabase>
</protect>
</protect>


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==Protein sequence==
==Protein sequence==


* <aureodatabase>protein sequence</aureodatabase>
*<aureodatabase>protein sequence</aureodatabase>
</protect>
</protect>


<protect>
<protect>
==Peptides==
==Experimental data==


* <aureodatabase>protein validated peptides</aureodatabase>
*<aureodatabase>protein validated peptides</aureodatabase>
*<aureodatabase>protein validated localization</aureodatabase>
*<aureodatabase>protein validated quantitative data</aureodatabase>
*<aureodatabase>protein partners</aureodatabase>
</protect>
</protect>


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==Operon==
==Operon==


* <aureodatabase>operons</aureodatabase>
*<aureodatabase>operons</aureodatabase>
</protect>
</protect>


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==Regulation==
==Regulation==


* <aureodatabase>sigma factors</aureodatabase>
*<aureodatabase>regulators</aureodatabase>
* <aureodatabase>regulators</aureodatabase>
</protect>
</protect>


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==Transcription pattern==
==Transcription pattern==


* <aureodatabase>expression browser</aureodatabase>
*<aureodatabase>expression browser</aureodatabase>
</protect>
</protect>


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==Protein synthesis (provided by Aureolib)==
==Protein synthesis (provided by Aureolib)==


* <aureodatabase>protein synthesis Aureolib</aureodatabase>
*<aureodatabase>protein synthesis Aureolib</aureodatabase>
</protect>
</protect>


<protect>
<protect>
==Stability==
==Protein stability==


* <aureodatabase>protein half-life</aureodatabase>
*<aureodatabase>protein half-life</aureodatabase>
</protect>
</protect>


Latest revision as of 16:13, 10 March 2016

NCBI: 06-JUL-2013

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus Newman
  • locus tag: NWMN_1195 [new locus tag: NWMN_RS06730 ]
  • pan locus tag?: SAUPAN003588000
  • symbol: NWMN_1195
  • 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: NWMN_1195 [new locus tag: NWMN_RS06730 ]
  • symbol: NWMN_1195
  • product: phosphodiesterase
  • replicon: chromosome
  • strand: +
  • coordinates: 1317576..1319135
  • length: 1560
  • 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
    GTGAATTTATTAAGCCTCCTACTCATTTTGCTGGGGATCATTCTAGGAGTTGTTGGAGGG
    TATGTTGTTGCCCGAAATTTGTTGCTTCAAAAGCAATCACAAGCTAGACAAACTGCCGAA
    GATATTGTAAATCAAGCACATAAAGAAGCTGACAATATCAAAAAAGAGAAATTACTTGAG
    GCAAAAGAAGAAAACCAAATCCTAAGAGAACAAACTGAAGCAGAACTACGAGAAAGACGT
    AGCGAACTTCAAAGACAAGAAACCCGACTTCTTCAAAAAGAAGAAAACTTAGAGCGCAAA
    TCTGATCTATTAGATAAAAAAGATGAGATTTTAGAGCAAAAAGAATCAAAAATTGAAGAA
    AAACAACAACAAGTAGATGCAAAAGAGAGTAGTGTTCAAACGTTAATAATGAAGCATGAA
    CAAGAATTAGAACGCATCTCCGGTCTCACTCAAGAAGAAGCTATTAATGAGCAACTTCAA
    AGAGTAGAGGAAGAACTGTCACAAGATATTGCAGTACTTGTTAAAGAAAAAGAAAAAGAA
    GCTAAAGAAAAAGTTGATAAAACAGCAAAAGAATTATTAGCTACAGCAGTACAAAGATTA
    GCAGCAGATCACACAAGTGAATCAACGGTATCAGTAGTTAACTTACCTAATGATGAGATG
    AAAGGTCGAATCATTGGACGAGAAGGACGAAACATCCGCACACTTGAAACTTTAACTGGC
    ATTGATTTAATTATTGATGACACACCAGAAGCGGTTATATTATCTGGTTTTGATCCAATA
    AGAAGAGAAATTGCTAGAACAGCACTTGTTAACTTAGTATCTGATGGACGTATTCATCCA
    GGTAGAATTGAAGATATGGTCGAAAAAGCTAGAAAAGAAGTAGACGATATTATTAGAGAA
    GCAGGTGAACAAGCTACATTTGAAGTGAACGCACATAATATGCATCCTGACTTAGTAAAA
    ATTGTAGGGCGTTTAAACTATCGTACGAGTTACGGTCAAAATGTACTTAAACATTCAATT
    GAAGTTGCGCATCTTGCTAGTATGTTAGCTGCTGAGCTAGGCGAAGATGAGACATTAGCG
    AAACGAGCTGGACTTTTACATGATGTTGGTAAAGCAATTGATCATGAAGTAGAAGGTAGT
    CATGTTGAAATCGGTGTAGAATTAGCGAAAAAATATGGTGAAAATGAAACAGTTATTAAT
    GCAATCCATTCTCATCATGGTGATGTTGAACCTACATCTATTATATCTATCCTTGTTGCT
    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: NWMN_1195 [new locus tag: NWMN_RS06730 ]
  • symbol: NWMN_1195
  • 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: data available for COL, N315, NCTC8325, USA300_FPR3757
  • PFAM:
    no clan defined DUF3552; Domain of unknown function (DUF3552) (PF12072; HMM-score: 212.2)
    and 6 more
    HD_PDEase (CL0237) HD; HD domain (PF01966; HMM-score: 69.3)
    HDOD; HDOD domain (PF08668; HMM-score: 29.9)
    KH (CL0007) KH_1; KH domain (PF00013; HMM-score: 29.3)
    KH_4; KH domain (PF13083; HMM-score: 21.8)
    KH_2; KH domain (PF07650; HMM-score: 14.4)
    no clan defined UPF0242; Uncharacterised protein family (UPF0242) (PF06785; HMM-score: 8.1)

⊟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
  • 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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