From AureoWiki
Revision as of 08:01, 11 March 2016 by AureoSysAdmin (talk | contribs) (Text replacement - "* <aureodatabase>protein Genbank</aureodatabase> " to "")
(diff) ← Older revision | Latest revision (diff) | Newer revision → (diff)
Jump to navigation Jump to search

NCBI: 10-JUN-2013

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL1769 [new locus tag: SACOL_RS09045 ]
  • pan locus tag?: SAUPAN004372000
  • symbol: rpsD
  • pan gene symbol?: rpsD
  • synonym:
  • product: 30S ribosomal protein S4

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SACOL1769 [new locus tag: SACOL_RS09045 ]
  • symbol: rpsD
  • product: 30S ribosomal protein S4
  • replicon: chromosome
  • strand: +
  • coordinates: 1808536..1809138
  • length: 603
  • 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
    ATGGCTCGATTCAGAGGTTCAAACTGGAAAAAATCTCGTCGTTTAGGTATCTCTTTAAGC
    GGTACTGGTAAAGAATTAGAAAAACGTCCTTACGCACCAGGACAACATGGTCCAAACCAA
    CGTAAAAAATTATCAGAATATGGTTTACAATTACGTGAAAAACAAAAATTACGTTACTTA
    TATGGAATGACTGAAAGACAATTCCGTAACACATTTGACATCGCTGGTAAAAAATTCGGT
    GTACACGGTGAAAACTTCATGATCTTATTAGCAAGTCGTTTAGACGCTGTTGTTTATTCA
    TTAGGTTTAGCTCGTACTCGTCGTCAAGCACGTCAATTAGTTAACCACGGTCATATCTTA
    GTAGATGGTAAACGTGTTGATATTCCATCTTATTCTGTTAAACCTGGTCAAACAATTTCA
    GTTCGTGAAAAATCTCAAAAATTAAACATCATCGTTGAATCAGTTGAAATCAACAATTTC
    GTACCTGAGTACTTAAACTTTGATGCTGACAGCTTAACTGGTACTTTCGTACGTTTACCA
    GAACGTAGCGAATTACCTGCTGAAATTAACGAACAATTAATCGTTGAGTACTACTCAAGA
    TAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    603

⊟Protein[edit | edit source]

Protein Data Bank: 5LI0
Protein Data Bank: 5ND8
Protein Data Bank: 5ND9
Protein Data Bank: 5TCU

⊟General[edit | edit source]

  • locus tag: SACOL1769 [new locus tag: SACOL_RS09045 ]
  • symbol: RpsD
  • description: 30S ribosomal protein S4
  • length: 200
  • theoretical pI: 10.559
  • theoretical MW: 23013.2
  • GRAVY: -0.607

⊟Function[edit | edit source]

  • TIGRFAM:
    Genetic information processing Protein synthesis Ribosomal proteins: synthesis and modification ribosomal protein uS4 (TIGR01017; HMM-score: 271.5)
    and 4 more
    Genetic information processing Protein synthesis Ribosomal proteins: synthesis and modification ribosomal protein uS4 (TIGR01018; HMM-score: 52.7)
    Unknown function General TlyA family rRNA methyltransferase/putative hemolysin (TIGR00478; HMM-score: 28)
    Genetic information processing Protein synthesis tRNA and rRNA base modification pseudouridine synthase, RluA family (TIGR00005; EC 5.4.99.-; HMM-score: 14.8)
    Metabolism Energy metabolism Photosynthesis photosystem II S4 domain protein (TIGR03069; HMM-score: 14.8)
  • TheSEED  :
    • SSU ribosomal protein S4p (S9e)
    • SSU ribosomal protein S4p (S9e), zinc-independent
    Protein Metabolism Protein biosynthesis Ribosome SSU bacterial  SSU ribosomal protein S4p (S9e)
  • PFAM:
    S4 (CL0492) Ribosomal_S4; Ribosomal protein S4/S9 N-terminal domain (PF00163; HMM-score: 91.5)
    and 1 more
    S4; S4 domain (PF01479; HMM-score: 73)

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

  • domains:
  • modifications:
  • cofactors:
  • 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): 0.016333
    • TAT(Tat/SPI): 0.011778
    • LIPO(Sec/SPII): 0.010986
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MARFRGSNWKKSRRLGISLSGTGKELEKRPYAPGQHGPNQRKKLSEYGLQLREKQKLRYLYGMTERQFRNTFDIAGKKFGVHGENFMILLASRLDAVVYSLGLARTRRQARQLVNHGHILVDGKRVDIPSYSVKPGQTISVREKSQKLNIIVESVEINNFVPEYLNFDADSLTGTFVRLPERSELPAEINEQLIVEYYSR

⊟Experimental data[edit | edit source]

  • experimentally validated: PeptideAtlas
  • protein localization: Cytoplasmic [1] [2] [3]
  • quantitative data / protein copy number per cell: 3371 [4]
  • interaction partners:
    SACOL1272(codY)transcriptional repressor CodY  [5] (data from MRSA252)
    SACOL2130(deoD)purine nucleoside phosphorylase  [5] (data from MRSA252)
    SACOL1637(dnaK)molecular chaperone DnaK  [5] (data from MRSA252)
    SACOL0842(eno)phosphopyruvate hydratase  [5] (data from MRSA252)
    SACOL1245(fabG1)3-oxoacyl-ACP reductase  [5] (data from MRSA252)
    SACOL2117(fbaA)fructose-bisphosphate aldolase  [5] (data from MRSA252)
    SACOL1329(femC)glutamine synthetase  [5] (data from MRSA252)
    SACOL2253(femX)femX protein  [5] (data from MRSA252)
    SACOL0838(gapA1)glyceraldehyde 3-phosphate dehydrogenase  [5] (data from MRSA252)
    SACOL2145(glmS)glucosamine--fructose-6-phosphate aminotransferase  [5] (data from MRSA252)
    SACOL0961(gluD)glutamate dehydrogenase  [5] (data from MRSA252)
    SACOL1513(hup)DNA-binding protein HU  [5] (data from MRSA252)
    SACOL1741(icd)isocitrate dehydrogenase  [5] (data from MRSA252)
    SACOL1727(infC)translation initiation factor IF-3  [5] (data from MRSA252)
    SACOL0222(ldh1)L-lactate dehydrogenase  [5] (data from MRSA252)
    SACOL0033(mecA)penicillin-binding protein 2'  [5] (data from MRSA252)
    SACOL2623(mqo2)malate:quinone oxidoreductase  [5] (data from MRSA252)
    SACOL0792(nrdE)ribonucleotide-diphosphate reductase subunit alpha  [5] (data from MRSA252)
    SACOL1102(pdhA)pyruvate dehydrogenase complex E1 component subunit alpha  [5] (data from MRSA252)
    SACOL2128(pdp)pyrimidine-nucleoside phosphorylase  [5] (data from MRSA252)
    SACOL0204(pflB)formate acetyltransferase  [5] (data from MRSA252)
    SACOL0966(pgi)glucose-6-phosphate isomerase  [5] (data from MRSA252)
    SACOL0841(pgm)phosphoglyceromutase  [5] (data from MRSA252)
    SACOL1982(ppaC)manganese-dependent inorganic pyrophosphatase  [5] (data from MRSA252)
    SACOL0584(rplA)50S ribosomal protein L1  [5] (data from MRSA252)
    SACOL2236(rplB)50S ribosomal protein L2  [5] (data from MRSA252)
    SACOL2239(rplC)50S ribosomal protein L3  [5] (data from MRSA252)
    SACOL2238(rplD)50S ribosomal protein L4  [5] (data from MRSA252)
    SACOL0015(rplI)50S ribosomal protein L9  [5] (data from MRSA252)
    SACOL0585(rplJ)50S ribosomal protein L10  [5] (data from MRSA252)
    SACOL0583(rplK)50S ribosomal protein L11  [5] (data from MRSA252)
    SACOL0586(rplL)50S ribosomal protein L7/L12  [5] (data from MRSA252)
    SACOL2220(rplO)50S ribosomal protein L15  [5] (data from MRSA252)
    SACOL2232(rplP)50S ribosomal protein L16  [5] (data from MRSA252)
    SACOL2212(rplQ)50S ribosomal protein L17  [5] (data from MRSA252)
    SACOL1257(rplS)50S ribosomal protein L19  [5] (data from MRSA252)
    SACOL1725(rplT)50S ribosomal protein L20  [5] (data from MRSA252)
    SACOL1702(rplU)50S ribosomal protein L21  [5] (data from MRSA252)
    SACOL2234(rplV)50S ribosomal protein L22  [5] (data from MRSA252)
    SACOL2237(rplW)50S ribosomal protein L23  [5] (data from MRSA252)
    SACOL2228(rplX)50S ribosomal protein L24  [5] (data from MRSA252)
    SACOL0545(rplY)50S ribosomal protein L25/general stress protein Ctc  [5] (data from MRSA252)
    SACOL1700(rpmA)50S ribosomal protein L27  [5] (data from MRSA252)
    SACOL2231(rpmC)50S ribosomal protein L29  [5] (data from MRSA252)
    SACOL2112(rpmE2)50S ribosomal protein L31  [5] (data from MRSA252)
    SACOL1726(rpmI)50S ribosomal protein L35  [5] (data from MRSA252)
    SACOL0588(rpoB)DNA-directed RNA polymerase subunit beta  [5] (data from MRSA252)
    SACOL2120(rpoE)DNA-directed RNA polymerase subunit delta  [5] (data from MRSA252)
    SACOL2233(rpsC)30S ribosomal protein S3  [5] (data from MRSA252)
    SACOL0437(rpsF)30S ribosomal protein S6  [5] (data from MRSA252)
    SACOL0592(rpsG)30S ribosomal protein S7  [5] (data from MRSA252)
    SACOL2225(rpsH)30S ribosomal protein S8  [5] (data from MRSA252)
    SACOL2206(rpsI)30S ribosomal protein S9  [5] (data from MRSA252)
    SACOL2214(rpsK)30S ribosomal protein S11  [5] (data from MRSA252)
    SACOL0591(rpsL)30S ribosomal protein S12  [5] (data from MRSA252)
    SACOL2215(rpsM)30S ribosomal protein S13  [5] (data from MRSA252)
    SACOL1292(rpsO)30S ribosomal protein S15  [5] (data from MRSA252)
    SACOL2230(rpsQ)30S ribosomal protein S17  [5] (data from MRSA252)
    SACOL2235(rpsS)30S ribosomal protein S19  [5] (data from MRSA252)
    SACOL1377(tkt)transketolase  [5] (data from MRSA252)
    SACOL03035'-nucleotidase  [5] (data from MRSA252)
    SACOL0521hypothetical protein  [5] (data from MRSA252)
    SACOL0731LysR family transcriptional regulator  [5] (data from MRSA252)
    SACOL0742hypothetical protein  [5] (data from MRSA252)
    SACOL0815ribosomal subunit interface protein  [5] (data from MRSA252)
    SACOL0876hypothetical protein  [5] (data from MRSA252)
    SACOL0944NADH dehydrogenase  [5] (data from MRSA252)
    SACOL1098hypothetical protein  [5] (data from MRSA252)
    SACOL1426hypothetical protein  [5] (data from MRSA252)
    SACOL1588proline dipeptidase  [5] (data from MRSA252)
    SACOL1651hypothetical protein  [5] (data from MRSA252)
    SACOL1753universal stress protein  [5] (data from MRSA252)
    SACOL1777serine protease HtrA  [5] (data from MRSA252)
    SACOL1788hypothetical protein  [5] (data from MRSA252)
    SACOL2072DEAD/DEAH box helicase  [5] (data from MRSA252)
    SACOL2173alkaline shock protein 23  [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: 9.67 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. ↑ 5.00 5.01 5.02 5.03 5.04 5.05 5.06 5.07 5.08 5.09 5.10 5.11 5.12 5.13 5.14 5.15 5.16 5.17 5.18 5.19 5.20 5.21 5.22 5.23 5.24 5.25 5.26 5.27 5.28 5.29 5.30 5.31 5.32 5.33 5.34 5.35 5.36 5.37 5.38 5.39 5.40 5.41 5.42 5.43 5.44 5.45 5.46 5.47 5.48 5.49 5.50 5.51 5.52 5.53 5.54 5.55 5.56 5.57 5.58 5.59 5.60 5.61 5.62 5.63 5.64 5.65 5.66 5.67 5.68 5.69 5.70 5.71 5.72 5.73 5.74 5.75 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=SACOL1769&oldid=90638"