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NCBI: 03-AUG-2016

Summary[edit source | edit]

  • organism: Staphylococcus aureus NCTC8325
  • locus tag: SAOUHSC_01662
  • pan locus tag?: SAUPAN004142000
  • symbol: SAOUHSC_01662
  • pan gene symbol?: sigA
  • synonym:
  • product: RNA polymerase sigma factor RpoD

Genome View[edit source | edit]

Gene[edit source | edit]

General[edit source | edit]

  • type: CDS
  • locus tag: SAOUHSC_01662
  • symbol: SAOUHSC_01662
  • product: RNA polymerase sigma factor RpoD
  • replicon: chromosome
  • strand: -
  • coordinates: 1574498..1575604
  • length: 1107
  • essential: yes [1] DEG other strains

Accession numbers[edit source | edit]

Phenotype[edit source | edit]

  • Share your knowledge and add information here. [edit]

DNA sequence[edit source | edit]

  • 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 source | edit]

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

General[edit source | edit]

  • locus tag: SAOUHSC_01662
  • symbol: SAOUHSC_01662
  • description: RNA polymerase sigma factor RpoD
  • length: 368
  • theoretical pI: 4.72503
  • theoretical MW: 42170.5
  • GRAVY: -0.629891

Function[edit source | edit]

  • reaction:
  • TIGRFAM:
    Genetic information processingTranscriptionTranscription factorsRNA polymerase sigma factor RpoD (TIGR02393; HMM-score: 410.6)
    RNA polymerase sigma factor, cyanobacterial RpoD-like family (TIGR02997; HMM-score: 354)
    Cellular processesCellular processesAdaptations to atypical conditionsRNA polymerase sigma factor RpoS (TIGR02394; HMM-score: 323.7)
    Genetic information processingTranscriptionTranscription factorsRNA polymerase sigma factor RpoS (TIGR02394; HMM-score: 323.7)
    Cellular processesCellular processesAdaptations to atypical conditionsalternative sigma factor RpoH (TIGR02392; HMM-score: 162.9)
    Genetic information processingTranscriptionTranscription factorsalternative 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 processesCellular processesSporulation and germinationRNA polymerase sigma-G factor (TIGR02850; HMM-score: 127)
    Genetic information processingTranscriptionTranscription factorsRNA polymerase sigma-G factor (TIGR02850; HMM-score: 127)
    RNA polymerase sigma factor, FliA/WhiG family (TIGR02479; HMM-score: 121.2)
    Cellular processesCellular processesSporulation and germinationRNA polymerase sigma-F factor (TIGR02885; HMM-score: 120.8)
    Genetic information processingTranscriptionTranscription factorsRNA polymerase sigma-F factor (TIGR02885; HMM-score: 120.8)
    Cellular processesCellular processesSporulation and germinationRNA polymerase sigma-K factor (TIGR02846; HMM-score: 114.8)
    Genetic information processingTranscriptionTranscription factorsRNA polymerase sigma-K factor (TIGR02846; HMM-score: 114.8)
    Cellular processesCellular processesSporulation and germinationRNA polymerase sigma-E factor (TIGR02835; HMM-score: 103.7)
    Genetic information processingTranscriptionTranscription factorsRNA polymerase sigma-E factor (TIGR02835; HMM-score: 103.7)
    RNA polymerase sigma-B factor (TIGR02941; HMM-score: 75.2)
    Cellular processesCellular processesSporulation and germinationRNA polymerase sigma-H factor (TIGR02859; HMM-score: 40.4)
    Genetic information processingTranscriptionTranscription factorsRNA 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 processingDNA metabolismDegradation of DNAexodeoxyribonuclease VII, large subunit (TIGR00237; EC 3.1.11.6; HMM-score: 13.8)
    RNA polymerase sigma factor RpoE (TIGR02939; HMM-score: 12.8)
    Cellular processesCellular processesSporulation and germinationRNA polymerase sigma-I factor (TIGR02895; HMM-score: 12.5)
    Genetic information processingTranscriptionTranscription factorsRNA polymerase sigma-I factor (TIGR02895; HMM-score: 12.5)
    RNA polymerase sigma-70 factor, sigma-E family (TIGR02983; HMM-score: 12.5)
    Signal transductionRegulatory functionsDNA interactionsDNA-binding protein, Tfx family (TIGR00721; HMM-score: 12.4)
    RNA polymerase sigma-70 factor, TIGR02954 family (TIGR02954; HMM-score: 11.7)
    MetabolismBiosynthesis of cofactors, prosthetic groups, and carriersChlorophyll and bacteriochlorphylllight-independent protochlorophyllide reductase, N subunit (TIGR01279; EC 1.3.7.7; HMM-score: 11.2)
  • TheSEED:  
    RNA MetabolismTranscriptionTranscription initiation, bacterial sigma factors RNA polymerase sigma factor RpoD 
  • PFAM:
    HTH (CL0123) Sigma70_r3; Sigma-70 region 3 (PF04539; HMM-score: 106.7)
    Sigma70_r4; Sigma-70, region 4 (PF04545; HMM-score: 83.7)
    Sigma70_r2; Sigma-70 region 2 (PF04542; HMM-score: 77.9)
    no clan definedSigma70_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 definedPolyA_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 & interactions[edit source | edit]

Localization[edit source | edit]

  • 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
    • Ymax: 0.127
    • Ymax_pos: 31
    • Cmax: 0.105
    • Cmax_pos: 35
    • Smax: 0.209
    • Smax_pos: 24
    • Smean: 0.125
    • D: 0.126
  • predicted transmembrane helices (TMHMM): 0

Accession numbers[edit source | edit]

Protein sequence[edit source | edit]

  • MSDNTVKIKKQTIDPTLTLEDVKKQLIEKGKKEGHLSHEEIAEKLQNFDIDSDQMDDFFDQLNDNDISLVNEKDSSDTDEKLNPSDLSAPPGVKINDPVRMYLKEIGRVNLLSAQEEIELAKRIEQGDEVAKSRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLIKAVEKFDFNKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLIRVQRQLLQDLGRDPAPEEIGEEMDLPAEKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDQEAQSPSDHAAYELLKEQLEDVLDTLTDREENVLRLRFGLDDGRTRTLEEVGKVFGVTRERIRQIEAKALRKLRHPSRSKRLKDFMD

Experimental data[edit source | edit]

Expression & Regulation[edit source | edit]

Operon[edit source | edit]

Regulation[edit source | edit]

  • sigma factor:
  • regulator:

Transcription pattern[edit source | edit]

Protein synthesis (provided by Aureolib)[edit source | edit]

Protein stability[edit source | edit]

  • half-life: no data available

Biological Material[edit source | edit]

Mutants[edit source | edit]

Expression vector[edit source | edit]

lacZ fusion[edit source | edit]

GFP fusion[edit source | edit]

two-hybrid system[edit source | edit]

FLAG-tag construct[edit source | edit]

Antibody[edit source | edit]

Other Information[edit source | edit]

You are kindly invited to share additional interesting facts.

Literature[edit source | edit]

References[edit source | edit]

  1. Roy R Chaudhuri, Andrew G Allen, Paul J Owen, Gil Shalom, Karl Stone, Marcus Harrison, Timothy A Burgis, Michael Lockyer, Jorge Garcia-Lara, Simon J Foster, Stephen J Pleasance, Sarah E Peters, Duncan J Maskell, Ian G Charles
    Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH).
    BMC Genomics: 2009, 10;291
    [PubMed:19570206] [WorldCat.org] [DOI] (I e)
  2. 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 2.9 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)
  3. Maren Depke, Stephan Michalik, Alexander Rabe, Kristin Surmann, Lars Brinkmann, Nico Jehmlich, Jörg Bernhardt, Michael Hecker, Bernd Wollscheid, Zhi Sun, Robert L Moritz, Uwe Völker, Frank Schmidt
    A peptide resource for the analysis of Staphylococcus aureus in host-pathogen interaction studies.
    Proteomics: 2015, 15(21);3648-3661
    [PubMed:26224020] [WorldCat.org] [DOI] (I p)
  4. Ulrike Mäder, Pierre Nicolas, Maren Depke, Jan Pané-Farré, Michel Debarbouille, Magdalena M van der Kooi-Pol, Cyprien Guérin, Sandra Dérozier, Aurelia Hiron, Hanne Jarmer, Aurélie Leduc, Stephan Michalik, Ewoud Reilman, Marc Schaffer, Frank Schmidt, Philippe Bessières, Philippe Noirot, Michael Hecker, Tarek Msadek, Uwe Völker, Jan Maarten van Dijl
    Staphylococcus aureus Transcriptome Architecture: From Laboratory to Infection-Mimicking Conditions.
    PLoS Genet.: 2016, 12(4);e1005962
    [PubMed:27035918] [WorldCat.org] [DOI] (I e)

Relevant publications[edit source | edit]

R Basheer, S Iordanescu
The Staphylococcus aureus chromosomal gene plaC, identified by mutations amplifying plasmid pT181, encodes a sigma factor.
Nucleic Acids Res.: 1991, 19(18);4921-4
[PubMed:1923759] [WorldCat.org] (P p)
Joseph Osmundson, Cristina Montero-Diez, Lars F Westblade, Ann Hochschild, Seth A Darst
Promoter-specific transcription inhibition in Staphylococcus aureus by a phage protein.
Cell: 2012, 151(5);1005-16
[PubMed:23178120] [WorldCat.org] [DOI] (I p)