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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 13:04, 11 March 2016

NCBI: 10-JUN-2013

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus USA300_FPR3757
  • locus tag: SAUSA300_1289 [new locus tag: SAUSA300_RS07005 ]
  • pan locus tag?: SAUPAN003809000
  • symbol: dapB
  • pan gene symbol?: dapB
  • synonym:
  • product: dihydrodipicolinate reductase

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SAUSA300_1289 [new locus tag: SAUSA300_RS07005 ]
  • symbol: dapB
  • product: dihydrodipicolinate reductase
  • replicon: chromosome
  • strand: +
  • coordinates: 1419948..1420670
  • length: 723
  • 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
    GTGAAAATATTACTAATTGGCTATGGCGCAATGAATCAACGCGTTGCTAGATTAGCAGAA
    GAAAAAGGACATGAAATCGTTGGGGTCATTGAAAATACACCGAAAGCAACAACGCCATAT
    CAACAATATCAACATATTGCAGATGTTAAAGGTGCCGATGTTGCAATAGATTTTTCAAAT
    CCAAATCTGCTTTTCCCTTTATTAGATGAAGATTTTCATTTGCCATTAGTTGTGGCAACA
    ACTGGCGAGAAAGAAAAACTACTTAATAAGTTAGATGAATTGAGTCAAAATATGCCTGTG
    TTTTTCAGCGCGAACATGAGTTATGGCGTTCATGCATTGACTAAAATTTTAGCAGCTGCT
    GTTCCCCTACTTGATGATTTCGACATCGAATTGACTGAGGCACATCATAATAAAAAAGTA
    GATGCACCAAGTGGTACGTTAGAAAAATTGTATGATGTGATCGTATCTTTGAAAGAAAAT
    GTAACACCTGTGTATGATAGACATGAATTAAATGAAAAACGCCAGCCACAAGATATTGGT
    ATACATTCTATTCGTGGAGGTACGATTGTCGGTGAACATGAAGTTCTATTTGCTGGCACT
    GATGAAACGATTCAAATCACGCATCGTGCACAATCAAAAGATATTTTTGCGAATGGTGCA
    ATACAAGCAGCAGAACGCTTAGTTAATAAACCAAACGGCTTTTATACGTTTGACAACTTA
    TAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    723

⊟Protein[edit | edit source]

Protein Data Bank: 3QY9

⊟General[edit | edit source]

  • locus tag: SAUSA300_1289 [new locus tag: SAUSA300_RS07005 ]
  • symbol: DapB
  • description: dihydrodipicolinate reductase
  • length: 240
  • theoretical pI: 5.13738
  • theoretical MW: 26654.1
  • GRAVY: -0.2225

⊟Function[edit | edit source]

  • reaction:
    EC 1.17.1.8?  ExPASy
    4-hydroxy-tetrahydrodipicolinate reductase (S)-2,3,4,5-tetrahydropyridine-2,6-dicarboxylate + NAD(P)+ + H2O = (2S,4S)-4-hydroxy-2,3,4,5-tetrahydrodipicolinate + NAD(P)H
    EC 1.3.1.26?  ExPASy
    Transferred entry: 1.17.1.8
  • TIGRFAM:
    Metabolism Amino acid biosynthesis Aspartate family 4-hydroxy-tetrahydrodipicolinate reductase (TIGR00036; EC 1.17.1.8; HMM-score: 165.6)
    and 2 more
    Metabolism Amino acid biosynthesis Aspartate family dihydrodipicolinate reductase (TIGR02130; EC 1.17.1.8; HMM-score: 24.2)
    Metabolism Energy metabolism Pentose phosphate pathway 6-phosphogluconate dehydrogenase (decarboxylating) (TIGR00872; EC 1.1.1.44; HMM-score: 14.8)
  • TheSEED  :
    • 4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8)
    Amino Acids and Derivatives Lysine, threonine, methionine, and cysteine Lysine Biosynthesis DAP Pathway  4-hydroxy-tetrahydrodipicolinate reductase (EC 1.17.1.8)
  • PFAM:
    NADP_Rossmann (CL0063) DapB_C; Dihydrodipicolinate reductase, C-terminus (PF05173; HMM-score: 130.2)
    and 3 more
    DapB_N; Dihydrodipicolinate reductase, N-terminus (PF01113; HMM-score: 56.2)
    F420_oxidored; NADP oxidoreductase coenzyme F420-dependent (PF03807; HMM-score: 12.9)
    TPR (CL0020) Cse1; Cse1 (PF08506; HMM-score: 12.4)

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

  • domains:
  • modifications:
  • cofactors:
  • effectors:

⊟Localization[edit | edit source]

  • PSORTb: Cytoplasmic
    • Cytoplasmic Score: 9.67
    • Cytoplasmic Membrane Score: 0.01
    • Cellwall Score: 0.15
    • Extracellular Score: 0.17
    • 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): 0.018788
    • TAT(Tat/SPI): 0.000318
    • LIPO(Sec/SPII): 0.002442
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MKILLIGYGAMNQRVARLAEEKGHEIVGVIENTPKATTPYQQYQHIADVKGADVAIDFSNPNLLFPLLDEDFHLPLVVATTGEKEKLLNKLDELSQNMPVFFSANMSYGVHALTKILAAAVPLLDDFDIELTEAHHNKKVDAPSGTLEKLYDVIVSLKENVTPVYDRHELNEKRQPQDIGIHSIRGGTIVGEHEVLFAGTDETIQITHRAQSKDIFANGAIQAAERLVNKPNGFYTFDNL

⊟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]

  • regulators: L-box (transcription termination) regulon, CodY (repression) regulon
    L-box(RNA)important in Lysine biosynthesis; transcription unit transferred from N315 data RegPrecise 
    CodY(TF)important in Amino acid metabolism; RegPrecise    transcription unit transferred from N315 data 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]

⊟Relevant publications[edit | edit source]

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