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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 13:38, 11 March 2016

NCBI: 10-JUN-2013

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus USA300_FPR3757
  • locus tag: SAUSA300_1521 [new locus tag: SAUSA300_RS08300 ]
  • pan locus tag?: SAUPAN004142000
  • symbol: rpoD
  • pan gene symbol?: sigA
  • synonym:
  • product: RNA polymerase sigma factor RpoD

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SAUSA300_1521 [new locus tag: SAUSA300_RS08300 ]
  • symbol: rpoD
  • product: RNA polymerase sigma factor RpoD
  • replicon: chromosome
  • strand: -
  • coordinates: 1671296..1672402
  • length: 1107
  • 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
    ATGTCTGATAACACAGTTAAAATTAAAAAACAAACAATTGATCCGACATTAACATTAGAA
    GATGTTAAGAAGCAATTAATTGAAAAAGGTAAAAAAGAGGGTCATTTAAGTCATGAAGAA
    ATTGCTGAAAAACTTCAGAATTTTGATATCGACTCTGATCAAATGGATGATTTCTTTGAT
    CAATTAAATGATAATGATATTTCACTAGTTAATGAAAAAGATAGTTCAGATACTGACGAG
    AAACTGAATCCAAGTGATCTTAGTGCCCCTCCAGGTGTTAAAATAAATGACCCAGTTCGT
    ATGTACCTTAAAGAAATTGGGCGTGTTAACTTATTAAGTGCACAAGAAGAAATCGAATTA
    GCCAAACGTATTGAACAAGGTGATGAAGTAGCAAAATCAAGACTTGCAGAAGCGAACTTA
    CGTTTAGTTGTAAGTATTGCTAAAAGATACGTAGGTCGTGGTATGTTATTCCTTGATTTA
    ATCCAAGAAGGTAATATGGGTCTTATTAAAGCTGTTGAAAAATTTGACTTTAACAAAGGA
    TTTAAGTTTTCAACATATGCAACATGGTGGATTAGACAAGCAATCACTCGTGCAATTGCT
    GACCAAGCACGTACGATTCGTATCCCTGTGCATATGGTAGAAACAATTAATAAATTAATT
    CGTGTTCAACGTCAATTATTACAGGACTTAGGTCGAGATCCAGCACCAGAAGAAATTGGT
    GAAGAAATGGATTTACCAGCAGAAAAAGTTCGTGAAATTTTAAAAATTGCGCAAGAACCT
    GTTTCATTAGAAACACCAATTGGTGAAGAAGATGATAGTCATTTAGGAGACTTTATTGAG
    GATCAGGAAGCACAAAGTCCTTCAGATCATGCTGCTTATGAATTATTAAAAGAGCAATTA
    GAAGATGTGCTTGATACATTAACTGATAGAGAAGAAAATGTATTACGATTAAGATTTGGT
    CTTGATGACGGCAGAACAAGAACACTTGAAGAAGTTGGTAAAGTTTTCGGTGTTACACGT
    GAACGTATTCGACAAATTGAAGCAAAAGCACTTAGAAAATTAAGACATCCAAGTCGTAGT
    AAACGTTTGAAAGACTTTATGGATTAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    1020
    1080
    1107

⊟Protein[edit | edit source]

Protein Data Bank: 4G6D
Protein Data Bank: 4G8X
Protein Data Bank: 4G94

⊟General[edit | edit source]

  • locus tag: SAUSA300_1521 [new locus tag: SAUSA300_RS08300 ]
  • symbol: RpoD
  • description: RNA polymerase sigma factor RpoD
  • length: 368
  • theoretical pI: 4.72503
  • theoretical MW: 42170.5
  • GRAVY: -0.629891

⊟Function[edit | edit source]

  • TIGRFAM:
    Genetic information processing Transcription Transcription factors RNA polymerase sigma factor RpoD (TIGR02393; HMM-score: 410.6)
    RNA polymerase sigma factor, cyanobacterial RpoD-like family (TIGR02997; HMM-score: 354)
    and 28 more
    Cellular processes Cellular processes Adaptations to atypical conditions RNA polymerase sigma factor RpoS (TIGR02394; HMM-score: 323.7)
    Genetic information processing Transcription Transcription factors RNA polymerase sigma factor RpoS (TIGR02394; HMM-score: 323.7)
    Cellular processes Cellular processes Adaptations to atypical conditions alternative sigma factor RpoH (TIGR02392; HMM-score: 162.9)
    Genetic information processing Transcription Transcription factors alternative sigma factor RpoH (TIGR02392; HMM-score: 162.9)
    RNA polymerase sigma-70 factor, sigma-B/F/G subfamily (TIGR02980; HMM-score: 131.8)
    RNA polymerase sigma factor, sigma-70 family (TIGR02937; HMM-score: 131.6)
    Cellular processes Cellular processes Sporulation and germination RNA polymerase sigma-G factor (TIGR02850; HMM-score: 127)
    Genetic information processing Transcription Transcription factors RNA polymerase sigma-G factor (TIGR02850; HMM-score: 127)
    RNA polymerase sigma factor, FliA/WhiG family (TIGR02479; HMM-score: 121.2)
    Cellular processes Cellular processes Sporulation and germination RNA polymerase sigma-F factor (TIGR02885; HMM-score: 120.8)
    Genetic information processing Transcription Transcription factors RNA polymerase sigma-F factor (TIGR02885; HMM-score: 120.8)
    Cellular processes Cellular processes Sporulation and germination RNA polymerase sigma-K factor (TIGR02846; HMM-score: 114.8)
    Genetic information processing Transcription Transcription factors RNA polymerase sigma-K factor (TIGR02846; HMM-score: 114.8)
    Cellular processes Cellular processes Sporulation and germination RNA polymerase sigma-E factor (TIGR02835; HMM-score: 103.7)
    Genetic information processing Transcription Transcription factors RNA polymerase sigma-E factor (TIGR02835; HMM-score: 103.7)
    RNA polymerase sigma-B factor (TIGR02941; HMM-score: 75.2)
    Cellular processes Cellular processes Sporulation and germination RNA polymerase sigma-H factor (TIGR02859; HMM-score: 40.4)
    Genetic information processing Transcription Transcription factors RNA polymerase sigma-H factor (TIGR02859; HMM-score: 40.4)
    RNA polymerase sigma-70 factor, TIGR02952 family (TIGR02952; HMM-score: 31.2)
    RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1 (TIGR02984; HMM-score: 19.6)
    Genetic information processing DNA metabolism Degradation of DNA exodeoxyribonuclease VII, large subunit (TIGR00237; EC 3.1.11.6; HMM-score: 13.8)
    RNA polymerase sigma factor RpoE (TIGR02939; HMM-score: 12.8)
    Cellular processes Cellular processes Sporulation and germination RNA polymerase sigma-I factor (TIGR02895; HMM-score: 12.5)
    Genetic information processing Transcription Transcription factors RNA polymerase sigma-I factor (TIGR02895; HMM-score: 12.5)
    RNA polymerase sigma-70 factor, sigma-E family (TIGR02983; HMM-score: 12.5)
    Signal transduction Regulatory functions DNA interactions DNA-binding protein, Tfx family (TIGR00721; HMM-score: 12.4)
    RNA polymerase sigma-70 factor, TIGR02954 family (TIGR02954; HMM-score: 11.7)
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Chlorophyll and bacteriochlorphyll light-independent protochlorophyllide reductase, N subunit (TIGR01279; EC 1.3.7.7; HMM-score: 11.2)
  • TheSEED  :
    • RNA polymerase sigma factor RpoD
    RNA Metabolism Transcription Transcription initiation, bacterial sigma factors  RNA polymerase sigma factor RpoD
  • PFAM:
    HTH (CL0123) Sigma70_r3; Sigma-70 region 3 (PF04539; HMM-score: 106.7)
    and 8 more
    Sigma70_r4; Sigma-70, region 4 (PF04545; HMM-score: 83.7)
    Sigma70_r2; Sigma-70 region 2 (PF04542; HMM-score: 77.9)
    no clan defined Sigma70_r1_2; Sigma-70 factor, region 1.2 (PF00140; HMM-score: 67.7)
    Sigma70_r1_1; Sigma-70 factor, region 1.1 (PF03979; HMM-score: 61.1)
    Exonuc_VII_L; Exonuclease VII, large subunit (PF02601; HMM-score: 16.5)
    HTH (CL0123) HTH_10; HTH DNA binding domain (PF04967; HMM-score: 13.3)
    no clan defined PolyA_pol_arg_C; Polymerase A arginine-rich C-terminus (PF12626; HMM-score: 12.5)
    DUF4107; Protein of unknown function (DUF4107) (PF13389; HMM-score: 10.9)

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

  • domains:
  • modifications:
  • cofactors:
  • 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): 0.003774
    • TAT(Tat/SPI): 0.00031
    • LIPO(Sec/SPII): 0.000504
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MSDNTVKIKKQTIDPTLTLEDVKKQLIEKGKKEGHLSHEEIAEKLQNFDIDSDQMDDFFDQLNDNDISLVNEKDSSDTDEKLNPSDLSAPPGVKINDPVRMYLKEIGRVNLLSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD

⊟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: data available for COL
  • interaction partners:
    SAUSA300_1362(hup)DNA-binding protein HU  [1] (data from MRSA252)
    SAUSA300_2178(rpoA)DNA-directed RNA polymerase subunit alpha  [1] (data from MRSA252)
    SAUSA300_0527(rpoB)DNA-directed RNA polymerase subunit beta  [1] (data from MRSA252)
    SAUSA300_0528(rpoC)DNA-directed RNA polymerase subunit beta'  [1] (data from MRSA252)
    SAUSA300_2082(rpoE)DNA-directed RNA polymerase subunit delta  [1] (data from MRSA252)
    SAUSA300_0898(spxA)transcriptional regulator Spx  [1] (data from MRSA252)
    SAUSA300_0114accessory regulator  [1] (data from MRSA252)
    SAUSA300_0990hypothetical protein  [1] (data from MRSA252)
    SAUSA300_1797hypothetical protein  [1] (data from MRSA252)
    SAUSA300_2245accessory regulator R  [1] (data from MRSA252)

⊟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. ↑ 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 Artem Cherkasov, Michael Hsing, Roya Zoraghi, Leonard J Foster, Raymond H See, Nikolay Stoynov, Jihong Jiang, Sukhbir Kaur, Tian Lian, Linda Jackson, Huansheng Gong, Rick Swayze, Emily Amandoron, Farhad Hormozdiari, Phuong Dao, Cenk Sahinalp, Osvaldo Santos-Filho, Peter Axerio-Cilies, Kendall Byler, William R McMaster, Robert C Brunham, B Brett Finlay, Neil E Reiner
    Mapping the protein interaction network in methicillin-resistant Staphylococcus aureus.
    J Proteome Res: 2011, 10(3);1139-50
    [PubMed:21166474] [WorldCat.org] [DOI] (I p)

⊟Relevant publications[edit | edit source]

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