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m (Text replacement - "gene Genbank" to "gene RefSeq")
m (Text replacement - "* <aureodatabase>protein Genbank</aureodatabase> " to "")
 
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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 RefSeq</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 Genbank</aureodatabase>
*<aureodatabase>protein UniProt</aureodatabase>
* <aureodatabase>protein RefSeq</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 19:26, 10 March 2016

NCBI: 06-JUL-2013

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus Newman
  • locus tag: NWMN_1960 [new locus tag: NWMN_RS11310 ]
  • pan locus tag?: SAUPAN005303000
  • symbol: ilvD
  • pan gene symbol?: ilvD
  • synonym:
  • product: dihydroxy-acid dehydratase

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: NWMN_1960 [new locus tag: NWMN_RS11310 ]
  • symbol: ilvD
  • product: dihydroxy-acid dehydratase
  • replicon: chromosome
  • strand: +
  • coordinates: 2169452..2171140
  • length: 1689
  • 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
    1561
    1621
    1681
    ATGCGAAGCGACATGATCAAAAAAGGAGATCACCAAGCACCAGCAAGAAGTCTTTTACAT
    GCCACGGGCGCGCTAAAAAGTCCAACTGATATGAACAAACCATTTGTAGCTATTTGTAAC
    TCTTATATTGATATTGTTCCTGGACATGTTCACTTGAGAGAGCTTGCAGATATAGCTAAA
    GAAGCAATTAGAGAAGCCGGTGCCATTCCATTTGAATTCAATACAATTGGTGTTGATGAT
    GGAATAGCTATGGGACATATCGGAATGCGATATTCTCTACCATCACGTGAAATTATTGCA
    GATGCAGCTGAAACTGTAATTAACGCTCATTGGTTTGACGGCGTATTTTACATTCCTAAT
    TGTGACAAGATTACACCCGGTATGATTTTAGCAGCCATGAGGACAAACGTACCAGCTATC
    TTTTGCTCTGGTGGACCAATGAAAGCTGGCTTATCTGCACATGGAAAAGCATTAACACTT
    TCATCAATGTTTGAAGCAGTCGGCGCATTTAAAGAAGGATCGATTTCTAAAGAAGAATTT
    TTAGATATGGAACAAAATGCCTGCCCTACTTGTGGTTCATGTGCTGGGATGTTTACTGCA
    AATTCAATGAACTGTTTGATGGAAGTTTTAGGTCTAGCATTACCATACAACGGTACTGCA
    CTTGCAGTCAGTGATCAGCGACGAGAAATGATTCGCCAAGCAGCTTTTAAATTAGTTGAA
    AATATTAAAAATGATTTAAAACCACGTGATATCGTTACTCGCGAAGCAATTGATGATGCA
    TTTGCACTTGATATGGCTATGGGTGGTTCAACAAACACGGTACTGCATACGTTAGCCATT
    GCCAATGAAGCTGGTATTGATTATGACTTAGAGCGCATTAATGCTATTGCCAAACGCACG
    CCATATTTATCAAAAATAGCACCTAGTTCATCGTATTCAATGCATGATGTGCATGAAGCT
    GGTGGCGTCCCAGCAATTATTAATGAATTGATGAAGAAAGATGGCACGTTACACCCAGAT
    AGAATCACAGTTACTGGCAAAACGTTACGTGAAAATAACGAAGGCAAAGAAATTAAGAAC
    TTTGATGTCATTCACCCTCTTGATGCACCATATGATGCACAAGGCGGTTTATCTATCTTA
    TTTGGTAATATCGCCCCTAAAGGCGCAGTTATTAAAGTTGGCGGCGTTGATCCATCTATC
    AAAACATTTACTAGGAAAGCAATTTGTTTCAATTCGCATGATGAAGCTGTTGAAGCAATA
    GACAATCGTACCGTTCGTGCAGGCCACGTCGTTGTCATTAGATATGAAGGACCTAAAGGT
    GGACCAGGTATGCCTGAAATGTTAGCACCTACTTCCTCTATTGTTGGTCGCGGCTTAGGT
    AAAGATGTTGCATTAATTACTGATGGGCGTTTTTCCGGTGCCACAAGAGGTATTGCAGTT
    GGTCATATTTCCCCTGAAGCTGCATCTGGTGGACCAATTGCCTTAATTGAAGATGGTGAT
    GAGATTACTATTGATTTAACAAATCGTACATTAAACGTAAACCAGCCTGAAGATGTTCTA
    GCGCGTCGCCGAGAATCTTTAACACCATTTAAAGCGAAAGTAAAAACAGGTTATCTAGCT
    CGTTATACTGCCCTAGTAACTAGCGCAAATACAGGTGGCGTCATGCAAGTCCCTGAGAAT
    TTAATTTAA
    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
    1620
    1680
    1689

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: NWMN_1960 [new locus tag: NWMN_RS11310 ]
  • symbol: IlvD
  • description: dihydroxy-acid dehydratase
  • length: 562
  • theoretical pI: 6.35197
  • theoretical MW: 60120.6
  • GRAVY: -0.0613879

⊟Function[edit | edit source]

  • reaction:
    EC 4.2.1.9?  ExPASy
    Dihydroxy-acid dehydratase 2,3-dihydroxy-3-methylbutanoate = 3-methyl-2-oxobutanoate + H2O
  • TIGRFAM:
    Metabolism Amino acid biosynthesis Pyruvate family dihydroxy-acid dehydratase (TIGR00110; EC 4.2.1.9; HMM-score: 779.7)
    and 2 more
    Metabolism Energy metabolism Entner-Doudoroff phosphogluconate dehydratase (TIGR01196; EC 4.2.1.12; HMM-score: 285.2)
    Unknown function Enzymes of unknown specificity putative dehydratase, YjhG/YagF family (TIGR03432; HMM-score: 220.3)
  • TheSEED: data available for COL, N315, NCTC8325, USA300_FPR3757
  • PFAM:
    no clan defined ILVD_EDD; Dehydratase family (PF00920; HMM-score: 731.9)
    and 1 more
    NADP_Rossmann (CL0063) adh_short_C2; Enoyl-(Acyl carrier protein) reductase (PF13561; HMM-score: 12.5)

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

  • domains:
  • modifications:
  • cofactors: [4Fe-4S] cluster
  • 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
  • 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): 0.013615
    • TAT(Tat/SPI): 0.0042
    • LIPO(Sec/SPII): 0.004851
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MRSDMIKKGDHQAPARSLLHATGALKSPTDMNKPFVAICNSYIDIVPGHVHLRELADIAKEAIREAGAIPFEFNTIGVDDGIAMGHIGMRYSLPSREIIADAAETVINAHWFDGVFYIPNCDKITPGMILAAMRTNVPAIFCSGGPMKAGLSAHGKALTLSSMFEAVGAFKEGSISKEEFLDMEQNACPTCGSCAGMFTANSMNCLMEVLGLALPYNGTALAVSDQRREMIRQAAFKLVENIKNDLKPRDIVTREAIDDAFALDMAMGGSTNTVLHTLAIANEAGIDYDLERINAIAKRTPYLSKIAPSSSYSMHDVHEAGGVPAIINELMKKDGTLHPDRITVTGKTLRENNEGKEIKNFDVIHPLDAPYDAQGGLSILFGNIAPKGAVIKVGGVDPSIKTFTRKAICFNSHDEAVEAIDNRTVRAGHVVVIRYEGPKGGPGMPEMLAPTSSIVGRGLGKDVALITDGRFSGATRGIAVGHISPEAASGGPIALIEDGDEITIDLTNRTLNVNQPEDVLARRRESLTPFKAKVKTGYLARYTALVTSANTGGVMQVPENLI

⊟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:

⊟Expression & Regulation[edit | edit source]

⊟Operon[edit | edit source]

⊟Regulation[edit | edit source]

  • regulator: CodY (repression) regulon
    CodY(TF)important in Amino acid metabolism; RegPrecise 

⊟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. ↑ Charlotte D Majerczyk, Paul M Dunman, Thanh T Luong, Chia Y Lee, Marat R Sadykov, Greg A Somerville, Kip Bodi, Abraham L Sonenshein
    Direct targets of CodY in Staphylococcus aureus.
    J Bacteriol: 2010, 192(11);2861-77
    [PubMed:20363936] [WorldCat.org] [DOI] (I p)

⊟Relevant publications[edit | edit source]

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