From AureoWiki
Jump to navigation Jump to search

NCBI: 10-JUN-2013

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL1618 [new locus tag: SACOL_RS08250 ]
  • 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: SACOL1618 [new locus tag: SACOL_RS08250 ]
  • symbol: rpoD
  • product: RNA polymerase sigma factor RpoD
  • replicon: chromosome
  • strand: -
  • coordinates: 1648459..1649565
  • 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

⊟General[edit | edit source]

  • locus tag: SACOL1618 [new locus tag: SACOL_RS08250 ]
  • 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: 104.8)
    Sigma70_r2; Sigma-70 region 2 (PF04542; HMM-score: 85.1)
    and 7 more
    Sigma70_r4; Sigma-70, region 4 (PF04545; HMM-score: 80.7)
    no clan defined Sigma70_r1_2; Sigma-70 factor, region 1.2 (PF00140; HMM-score: 67.5)
    Sigma70_r1_1; Sigma-70 factor, region 1.1 (PF03979; HMM-score: 62.6)
    Exonuc_VII_L; Exonuclease VII, large subunit (PF02601; HMM-score: 15.9)
    HTH (CL0123) HTH_10; HTH DNA binding domain (PF04967; HMM-score: 13.3)
    Sigma70_r4_2; Sigma-70, region 4 (PF08281; HMM-score: 11)
    DBD_HTH; Putative DNA-binding domain (PF18430; HMM-score: 8.6)

⊟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
  • ⊞DeepLocPro: Cytoplasmic
    • Cytoplasmic Score: 0.987
    • Cytoplasmic Membrane Score: 0.0064
    • Cell wall & surface Score: 0
    • Extracellular Score: 0.0066
  • ⊞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: PeptideAtlas
  • protein localization: Cytoplasmic [1] [2] [3]
  • quantitative data / protein copy number per cell: 1067 [4]
  • ⊟interaction partners:
    SACOL1513(hup)DNA-binding protein HU  [5] (data from MRSA252)
    SACOL2213(rpoA)DNA-directed RNA polymerase subunit alpha  [5] (data from MRSA252)
    SACOL0588(rpoB)DNA-directed RNA polymerase subunit beta  [5] (data from MRSA252)
    SACOL0589(rpoC)DNA-directed RNA polymerase subunit beta'  [5] (data from MRSA252)
    SACOL2120(rpoE)DNA-directed RNA polymerase subunit delta  [5] (data from MRSA252)
    SACOL2287(sarR)accessory regulator R  [5] (data from MRSA252)
    SACOL0096(sarS)accessory regulator S  [5] (data from MRSA252)
    SACOL1002(spxA)transcriptional regulator Spx  [5] (data from MRSA252)
    SACOL1099hypothetical protein  [5] (data from MRSA252)
    SACOL1904transcriptional regulator  [5] (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: 14.6 h [6]

⊞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. ↑ Kristina Hempel, Florian-Alexander Herbst, Martin Moche, Michael Hecker, Dörte Becher
    Quantitative proteomic view on secreted, cell surface-associated, and cytoplasmic proteins of the methicillin-resistant human pathogen Staphylococcus aureus under iron-limited conditions.
    J Proteome Res: 2011, 10(4);1657-66
    [PubMed:21323324] [WorldCat.org] [DOI] (I p)
  3. ↑ 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)
  4. ↑ Daniela Zühlke, Kirsten Dörries, Jörg Bernhardt, Sandra Maaß, Jan Muntel, Volkmar Liebscher, Jan Pané-Farré, Katharina Riedel, Michael Lalk, Uwe Völker, Susanne Engelmann, Dörte Becher, Stephan Fuchs, Michael Hecker
    Costs of life - Dynamics of the protein inventory of Staphylococcus aureus during anaerobiosis.
    Sci Rep: 2016, 6;28172
    [PubMed:27344979] [WorldCat.org] [DOI] (I e)
  5. ↑ Jump up to: 5.0 5.1 5.2 5.3 5.4 5.5 5.6 5.7 5.8 5.9 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)
  6. ↑ Stephan Michalik, Jörg Bernhardt, Andreas Otto, Martin Moche, Dörte Becher, Hanna Meyer, Michael Lalk, Claudia Schurmann, Rabea Schlüter, Holger Kock, Ulf Gerth, Michael Hecker
    Life and death of proteins: a case study of glucose-starved Staphylococcus aureus.
    Mol Cell Proteomics: 2012, 11(9);558-70
    [PubMed:22556279] [WorldCat.org] [DOI] (I p)

⊟Relevant publications[edit | edit source]

Retrieved from "http://fungenwikiserver.biologie.uni-greifswald.de/aureowiki/index.php?title=SACOL1618&oldid=60445"