From AureoWiki
Jump to navigation Jump to search

NCBI: 10-JUN-2013

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL1255 [new locus tag: SACOL_RS06410 ]
  • pan locus tag?: SAUPAN003528000
  • symbol: rimM
  • pan gene symbol?: rimM
  • synonym:
  • product: 16S rRNA-processing protein RimM

⊟Additional information (user-provided)[edit | edit source]

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SACOL1255 [new locus tag: SACOL_RS06410 ]
  • symbol: rimM
  • product: 16S rRNA-processing protein RimM
  • replicon: chromosome
  • strand: +
  • coordinates: 1263964..1264467
  • length: 504
  • essential: unknown other strains

⊟Accession numbers[edit | edit source]

⊟Phenotype[edit | edit source]

⊟Additional information (user-provided)[edit | edit source]

⊟DNA sequence[edit | edit source]

  • 1
    61
    121
    181
    241
    301
    361
    421
    481
    ATGAGAGTTGAAGTTGGTCAAATTGTTAACACACATGGTATTAAAGGTGAAATTAAAGTA
    AAATCCAATTCAGACTTTACAGACGTTCGTTTTCAACCCGGTCAAGTGCTGACAGTTGTG
    CATAACAATAACGACCTTGAATATACTGTTAAGTCACATAGAGTGCATAAAGGGCTTCAT
    ATGCTTACATTTGAAGGTATTAATAATATTAATGATATTGAGCATTTAAAAGGGAGTTCT
    ATTTATCAAGAGCGTGATCATGAAGATATCGTACTTGAGGAAAATGAATTTTATTATTCA
    GATATTATAGGATGTACAGTTTTTGATGATCAAGAAACACCAATAGGTCGTGTAATTAAT
    ATATTTGAAACAGGTGCGAATGATGTGTGGGTGATTAAAGGATCTAAAGAATATTTGATT
    CCTTATATTGCTGATGTTGTAAAAGAAGTGGATGTTGAAAATAAAAAAATTATCATCACG
    CCAATGGAAGGATTGTTGGATTAA
    60
    120
    180
    240
    300
    360
    420
    480
    504


⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SACOL1255 [new locus tag: SACOL_RS06410 ]
  • symbol: RimM
  • description: 16S rRNA-processing protein RimM
  • length: 167
  • theoretical pI: 4.60086
  • theoretical MW: 19072.4
  • GRAVY: -0.314371

⊟Function[edit | edit source]

  • TIGRFAM:
    Genetic information processing Transcription RNA processing 16S rRNA processing protein RimM (TIGR02273; HMM-score: 162.5)
  • TheSEED  :
    • 16S rRNA processing protein RimM
    Protein Metabolism Protein biosynthesis Ribosome biogenesis bacterial  16S rRNA processing protein RimM
  • PFAM:
    Hybrid (CL0105) RimM; RimM N-terminal domain (PF01782; HMM-score: 89.3)
    and 3 more
    PRC-barrel (CL0350) PRC_RimM; RimM PRC barrel domain (PF24986; HMM-score: 62.7)
    PRC; PRC-barrel domain (PF05239; HMM-score: 58.7)
    SH3 (CL0010) DUF4772; Domain of unknown function (DUF4772) (PF15997; HMM-score: 13.8)

⊟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
  • DeepLocPro: Cytoplasmic
    • Cytoplasmic Score: 0.9994
    • Cytoplasmic Membrane Score: 0.0002
    • Cell wall & surface Score: 0
    • Extracellular Score: 0.0003
  • 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): 0.009289
    • TAT(Tat/SPI): 0.000262
    • LIPO(Sec/SPII): 0.001629
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Additional information (user-provided)[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MRVEVGQIVNTHGIKGEIKVKSNSDFTDVRFQPGQVLTVVHNNNDLEYTVKSHRVHKGLHMLTFEGINNINDIEHLKGSSIYQERDHEDIVLEENEFYYSDIIGCTVFDDQETPIGRVINIFETGANDVWVIKGSKEYLIPYIADVVKEVDVENKKIIITPMEGLLD

⊟Experimental data[edit | edit source]

  • experimentally validated: PeptideAtlas
  • protein localization: Cytoplasmic [1] [2] [3] [4]
  • quantitative data / protein copy number per cell: 145 [5]
  • interaction partners:

⊟Expression & Regulation[edit | edit source]

⊟Operon[edit | edit source]

⊟Regulation[edit | edit source]

  • regulator:

⊟Additional information (user-provided)[edit | edit source]

⊟Transcription pattern[edit | edit source]

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

⊟Protein stability[edit | edit source]

  • half-life: 6.11 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]

⊟Additional information (user-provided)[edit | edit source]

⊟Other information (user-provided)[edit | edit source]

You can add further information about the gene and protein here. [edit]

⊟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, Jan Pané-Farré, Andreas Otto, Susanne Sievers, Michael Hecker, Dörte Becher
    Quantitative cell surface proteome profiling for SigB-dependent protein expression in the human pathogen Staphylococcus aureus via biotinylation approach.
    J Proteome Res: 2010, 9(3);1579-90
    [PubMed:20108986] [WorldCat.org] [DOI] (I p)
  3. ↑ 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)
  4. ↑ 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)
  5. ↑ 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)
  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=SACOL1255&oldid=129983"