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NCBI: 10-JUN-2013

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL0563 [new locus tag: SACOL_RS02925 ]
  • pan locus tag?: SAUPAN002282000
  • symbol: SACOL0563
  • pan gene symbol?: pdxR
  • synonym:
  • product: GntR family transcriptional regulator

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SACOL0563 [new locus tag: SACOL_RS02925 ]
  • symbol: SACOL0563
  • product: GntR family transcriptional regulator
  • replicon: chromosome
  • strand: -
  • coordinates: 583479..584861
  • length: 1383
  • 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
    TTGAAAAACACTTTATACCATCAACTTTATGAAAAATTAAAAAAACAAATAATTGAAGGT
    CAATTTAAAGAAGGCGATAAATTTTATTCTAAAAGACAATTAAGCAAACATTTATCTATT
    AGCCAAACAACCGTAGAGCATGCATATCAACTTCTATTAGACGAAGGTTACATTTATTCA
    AGACCTCGCTCTGGATATTTTGTGTCCGAAATTGAATCTTTAACAATTTTAAACAATCAA
    CCTATCCCCTCTCTTTTTGATGATGATTCATATAAACCAAAAGCGAGTGATGAAGCTTAT
    GATTATGCTTTTAATTTGGATGAAATAGATACGAAACATTTCCCTATAGAACTTTTCAGA
    AAGTATTCCAAAGATCTTTATGATACAAATCATTTAAATCAATTACGTAGAGGACATTTT
    CAAGGAGAATTACATTTGCGGTTTCAACTGGCATTTTATTTATTTACTAATCGTGGCGTA
    ATTTGTGATCCTAATCAAATTATAATTGGCTCATCTACCGAACAATTAGTAAATCAATTA
    GTCGATTTACTTTATACTTCAACATTTATTATCGAAAAACCTAGTTATCCACCAATCAAA
    AATATTTTAGATAAAAAACAAGTTGAATATGAACAAATTGAAGTTGAAGATAATGGAATA
    AACGTAGATGAAGTTATTAAATCACAAAAAAATATAGTATATATAACGCCTTCCCATCAA
    TTTCCAACTGGATATGTGATGGACTTAAAAAAACGAACTCAATTAATACAATGGGCTCAA
    GAAAAAGAAGAACGATTTATTATAGAAGATGATTATGATTCCGAGTTTAGATATTTCGGC
    AAACCCATTCCAGCAATTCAAGGTCTATATTCAAGAGGAGAAAAAGTGATTTATATCAGT
    ACATTTTCAAAGTCTATTTTTCCTAGCTGTCGAGTTGCATATATGGTGTTACCCTATTCT
    ATAATGAAAAAATATCATTCTCAAAATCACATTGAAGGCAACACTGTACCTGTTCATATG
    CAAAACCTTATTGCAACGTTTATATCTTCCGGTGGTTTTGAAAGGCATTTAAATAAAATG
    AGACGAATTTATCGTAGAAAACTAACCTATATTTTAAAAAGATTGAAACCTTACAAAGAG
    CAGCTTGATATTCAAGGTGCTGAAACGGGTATGCATTTTACAATTACAGTAAAAAATGGA
    TTAACATTACAAGAGTGTCTTGATAGAGCAAACAAAGTAAAGTTAAAATTACAAGTTTAT
    AATTTTGATGATGATCAAGACTATAAGAAAACCCCTAAATTTATATTAGGCTTTGGCGGT
    ATAGACGATGATGCTTTAAAACCGCATGTAGACGCTCTAATAAAATCATTAATTATAAAG
    TAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    1020
    1080
    1140
    1200
    1260
    1320
    1380
    1383

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SACOL0563 [new locus tag: SACOL_RS02925 ]
  • symbol: SACOL0563
  • description: GntR family transcriptional regulator
  • length: 460
  • theoretical pI: 8.55168
  • theoretical MW: 53954.4
  • GRAVY: -0.510217

⊟Function[edit | edit source]

  • ⊞TIGRFAM:
    enduracididine biosynthesis enzyme MppQ (TIGR04461; EC 2.-.-.-; HMM-score: 87.9)
    and 12 more
    succinyldiaminopimelate transaminase (TIGR03538; EC 2.6.1.17; HMM-score: 33.8)
    Signal transduction Regulatory functions DNA interactions phosphonate utilization transcriptional regulator PhnR (TIGR03337; HMM-score: 32.5)
    Signal transduction Regulatory functions DNA interactions trehalose operon repressor (TIGR02404; HMM-score: 31.9)
    Metabolism Energy metabolism Amino acids and amines histidine utilization repressor (TIGR02018; HMM-score: 29.9)
    Signal transduction Regulatory functions DNA interactions histidine utilization repressor (TIGR02018; HMM-score: 29.9)
    Metabolism Transport and binding proteins Anions phosphonate metabolism transcriptional regulator PhnF (TIGR02325; HMM-score: 24.4)
    Signal transduction Regulatory functions DNA interactions phosphonate metabolism transcriptional regulator PhnF (TIGR02325; HMM-score: 24.4)
    LL-diaminopimelate aminotransferase (TIGR03542; EC 2.6.1.83; HMM-score: 18.1)
    Signal transduction Regulatory functions DNA interactions biotin operon repressor (TIGR00122; HMM-score: 16.6)
    succinyldiaminopimelate transaminase (TIGR03539; EC 2.6.1.17; HMM-score: 16.1)
    beta-methylarginine biosynthesis bifunctional aminotransferase (TIGR04544; EC 2.6.-.-; HMM-score: 15.5)
    glutaredoxin-like protein, YruB-family (TIGR02196; HMM-score: 13.7)
  • TheSEED  :
    • Pyridoxamine phosphate aminotransferase (EC 2.6.1.54)
    • Pyridoxine biosynthesis transcriptional regulator PdxR, MocR family
    Cofactors, Vitamins, Prosthetic Groups, Pigments Pyridoxine Pyridoxin (Vitamin B6) Biosynthesis  Predicted transcriptional regulator of pyridoxine metabolism
  • ⊞PFAM:
    PLP_aminotran (CL0061) Aminotran_1_2; Aminotransferase class I and II (PF00155; HMM-score: 50.9)
    HTH (CL0123) GntR; Bacterial regulatory proteins, gntR family (PF00392; HMM-score: 43.8)
    and 7 more
    HTH_54; ParA helix turn helix domain (PF18607; HMM-score: 22.1)
    HTH_11; HTH domain (PF08279; HMM-score: 18.5)
    HTH_24; Winged helix-turn-helix DNA-binding (PF13412; HMM-score: 15.7)
    HTH_41; Helix-turn-helix domain (PF14502; HMM-score: 15.3)
    RPA_C; Replication protein A C terminal (PF08784; HMM-score: 14.6)
    DnaD_N; DnaD N-terminal domain (PF21984; HMM-score: 14.3)
    NUMOD1; NUMOD1 domain (PF07453; HMM-score: 14)

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

  • domains:
  • modifications:
  • cofactors:
  • effectors:
  • genes regulated by PdxR*, TF important in Pyridoxine biosynthesis: in JSNZ, N315

⊟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
  • ⊞DeepLocPro: Cytoplasmic
    • Cytoplasmic Score: 0.9026
    • Cytoplasmic Membrane Score: 0.0593
    • Cell wall & surface Score: 0.0021
    • Extracellular Score: 0.036
  • ⊞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): 0.00453
    • TAT(Tat/SPI): 0.000382
    • LIPO(Sec/SPII): 0.000587
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MKNTLYHQLYEKLKKQIIEGQFKEGDKFYSKRQLSKHLSISQTTVEHAYQLLLDEGYIYSRPRSGYFVSEIESLTILNNQPIPSLFDDDSYKPKASDEAYDYAFNLDEIDTKHFPIELFRKYSKDLYDTNHLNQLRRGHFQGELHLRFQLAFYLFTNRGVICDPNQIIIGSSTEQLVNQLVDLLYTSTFIIEKPSYPPIKNILDKKQVEYEQIEVEDNGINVDEVIKSQKNIVYITPSHQFPTGYVMDLKKRTQLIQWAQEKEERFIIEDDYDSEFRYFGKPIPAIQGLYSRGEKVIYISTFSKSIFPSCRVAYMVLPYSIMKKYHSQNHIEGNTVPVHMQNLIATFISSGGFERHLNKMRRIYRRKLTYILKRLKPYKEQLDIQGAETGMHFTITVKNGLTLQECLDRANKVKLKLQVYNFDDDQDYKKTPKFILGFGGIDDDALKPHVDALIKSLIIK

⊟Experimental data[edit | edit source]

  • experimentally validated: PeptideAtlas
  • protein localization: Cytoplasmic [1] [2]
  • 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]

  1. ↑ Dörte Becher, Kristina Hempel, Susanne Sievers, Daniela Zühlke, Jan Pané-Farré, Andreas Otto, Stephan Fuchs, Dirk Albrecht, Jörg Bernhardt, Susanne Engelmann, Uwe Völker, Jan Maarten van Dijl, Michael Hecker
    A proteomic view of an important human pathogen--towards the quantification of the entire Staphylococcus aureus proteome.
    PLoS One: 2009, 4(12);e8176
    [PubMed:19997597] [WorldCat.org] [DOI] (I e)
  2. ↑ Andreas Otto, Jan Maarten van Dijl, Michael Hecker, Dörte Becher
    The Staphylococcus aureus proteome.
    Int J Med Microbiol: 2014, 304(2);110-20
    [PubMed:24439828] [WorldCat.org] [DOI] (I p)

⊟Relevant publications[edit | edit source]

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