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PangenomeCOLN315NCTC8325NewmanUSA300_FPR375704-0298108BA0217611819-97685071193ECT-R 2ED133ED98HO 5096 0412JH1JH9JKD6008JKD6159JSNZLGA251M013MRSA252MSHR1132MSSA476MW2Mu3Mu50RF122ST398T0131TCH60TW20USA300_TCH1516VC40

NCBI: 03-AUG-2016

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⊟Summary[edit | edit source]

Contents

  • 1 Summary
  • 2 Genome View
  • 3 Gene
    • 3.1 General
    • 3.2 Accession numbers
    • 3.3 Phenotype
    • 3.4 DNA sequence
  • 4 Protein
    • 4.1 General
    • 4.2 Function
    • 4.3 Structure, modifications & cofactors
    • 4.4 Localization
    • 4.5 Accession numbers
    • 4.6 Protein sequence
    • 4.7 Experimental data
  • 5 Expression & Regulation
    • 5.1 Operon
    • 5.2 Regulation
    • 5.3 Transcription pattern
    • 5.4 Protein synthesis (provided by Aureolib)
    • 5.5 Protein stability
  • 6 Biological Material
    • 6.1 Mutants
    • 6.2 Expression vector
    • 6.3 lacZ fusion
    • 6.4 GFP fusion
    • 6.5 two-hybrid system
    • 6.6 FLAG-tag construct
    • 6.7 Antibody
  • 7 Other Information
  • 8 Literature
    • 8.1 References
    • 8.2 Relevant publications
  • organism: Staphylococcus aureus NCTC8325
  • locus tag: SAOUHSC_02359
  • pan locus tag?: SAUPAN005409000
  • symbol: prfA
  • pan gene symbol?: prfA
  • synonym:
  • product: peptide chain release factor 1

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SAOUHSC_02359
  • symbol: prfA
  • product: peptide chain release factor 1
  • replicon: chromosome
  • strand: -
  • coordinates: 2180579..2181655
  • length: 1077
  • essential: yes [1] DEG other strains

⊟Accession numbers[edit | edit source]

  • Gene ID: 3919402 NCBI
  • RefSeq: YP_500835 NCBI
  • BioCyc: G1I0R-2228 BioCyc
  • MicrobesOnline: 1290796 MicrobesOnline

⊟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
    GTGTTTGATCAATTAGATATTGTAGAAGAAAGATACGAACAGTTAAATGAACTGTTAAGT
    GACCCAGATGTTGTAAATGATTCAGATAAATTACGTAAATATTCTAAAGAGCAAGCTGAT
    TTACAAAAAACTGTAGATGTTTATCGTAACTATAAAGCTAAAAAAGAAGAATTAGCTGAT
    ATTGAAGAAATGTTAAGTGAGACTGATGATAAAGAAGAAGTAGAAATGTTAAAAGAGGAG
    AGTAATGGTATTAAAGCTGAACTTCCAAATCTTGAAGAAGAGCTTAAAATATTATTGATT
    CCTAAAGATCCTAATGATGACAAAGACGTTATTGTAGAAATAAGAGCAGCAGCAGGTGGT
    GATGAGGCTGCGATTTTTGCTGGTGATTTAATGCGTATGTATTCAAAGTATGCTGAATCA
    CAAGGATTCAAAACTGAAATAGTAGAAGCGTCTGAAAGTGACCATGGTGGTTACAAAGAA
    ATTAGTTTCTCAGTTTCTGGTAATGGCGCGTATAGTAAATTGAAATTTGAAAATGGTGCG
    CACCGCGTTCAACGTGTGCCTGAAACAGAATCAGGTGGACGTATTCATACTTCAACAGCT
    ACAGTGGCAGTTTTACCAGAAGTTGAAGATGTAGAAATTGAAATTAGAAATGAAGATTTA
    AAAATCGACACGTATCGTTCAAGTGGTGCAGGTGGTCAGCACGTAAACACAACTGACTCT
    GCAGTACGTATTACCCATTTACCAACTGGTGTCATTGCAACATCTTCTGAGAAGTCTCAA
    ATTCAAAACCGTGAAAAAGCAATGAAAGTGTTAAAAGCACGTTTATACGATATGAAAGTT
    CAAGAAGAACAACAAAAGTATGCGTCACAACGTAAATCAGCAGTCGGTACTGGTGATCGT
    TCAGAACGTATTCGAACTTATAATTATCCACAAAGCCGTGTAACAGACCATCGTATAGGT
    CTAACGCTTCAAAAATTAGGGCAAATTATGGAAGGCCATTTAGAAGAAATTATAGATGCA
    CTGACTTTATCAGAGCAGACAGATAAATTGAAAGAACTTAATAATGGTGAATTATAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    1020
    1077

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SAOUHSC_02359
  • symbol: PrfA
  • description: peptide chain release factor 1
  • length: 358
  • theoretical pI: 4.5415
  • theoretical MW: 40349.6
  • GRAVY: -0.760056

⊟Function[edit | edit source]

  • ⊞TIGRFAM:
    Genetic information processing Protein synthesis Translation factors peptide chain release factor 1 (TIGR00019; HMM-score: 529.5)
    and 2 more
    Genetic information processing Protein synthesis Translation factors peptide chain release factor 2 (TIGR00020; HMM-score: 300.8)
    Genetic information processing Protein synthesis Translation factors putative peptide chain release factor H (TIGR03072; HMM-score: 89.2)
  • ⊞TheSEED  :
    • Peptide chain release factor 1
    Protein Metabolism Protein biosynthesis Translation termination factors bacterial  Peptide chain release factor 1
    and 1 more
    Stress Response Oxidative stress Glutaredoxins  Peptide chain release factor 1
  • ⊞PFAM:
    no clan defined PCRF; PCRF domain (PF03462; HMM-score: 259.2)
    and 7 more
    RF (CL0337) RF-1; RF-1 domain (PF00472; HMM-score: 144.9)
    no clan defined ABC_tran_CTD; ABC transporter C-terminal domain (PF16326; HMM-score: 22.1)
    Trefoil (CL0066) MIR; MIR domain (PF02815; HMM-score: 13.4)
    Spectrin (CL0743) Spectrin_SYNE1; Nesprin-1, spectrin repeats (PF25034; HMM-score: 13.2)
    Glutaminase_I (CL0014) Peptidase_S66; LD-carboxypeptidase N-terminal domain (PF02016; HMM-score: 11.5)
    C_Lectin (CL0056) Ly49; Ly49-like protein, N-terminal region (PF08391; HMM-score: 9.1)
    no clan defined DUF6779; Domain of unknown function (DUF6779) (PF20570; HMM-score: 8)

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

  • domains:
  • modifications:
  • cofactors:
  • effectors:

⊟Localization[edit | edit source]

  • ⊞PSORTb: Cytoplasmic
    • Cytoplasmic Score: 10
    • Cytoplasmic Membrane Score: 0
    • Cellwall Score: 0
    • Extracellular Score: 0
    • Internal Helices: 0
  • ⊞DeepLocPro: Cytoplasmic
    • Cytoplasmic Score: 0.9943
    • Cytoplasmic Membrane Score: 0.0002
    • Cell wall & surface Score: 0
    • Extracellular Score: 0.0056
  • ⊞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): 0.002146
    • TAT(Tat/SPI): 0.000487
    • LIPO(Sec/SPII): 0.000597
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

  • GI: 88196022 NCBI
  • RefSeq: YP_500835 NCBI
  • UniProt: Q2FWE0 UniProt
  • STRING: 93061.SAOUHSC_02359 STRING

⊟Protein sequence[edit | edit source]

  • MFDQLDIVEERYEQLNELLSDPDVVNDSDKLRKYSKEQADLQKTVDVYRNYKAKKEELADIEEMLSETDDKEEVEMLKEESNGIKAELPNLEEELKILLIPKDPNDDKDVIVEIRAAAGGDEAAIFAGDLMRMYSKYAESQGFKTEIVEASESDHGGYKEISFSVSGNGAYSKLKFENGAHRVQRVPETESGGRIHTSTATVAVLPEVEDVEIEIRNEDLKIDTYRSSGAGGQHVNTTDSAVRITHLPTGVIATSSEKSQIQNREKAMKVLKARLYDMKVQEEQQKYASQRKSAVGTGDRSERIRTYNYPQSRVTDHRIGLTLQKLGQIMEGHLEEIIDALTLSEQTDKLKELNNGEL

⊟Experimental data[edit | edit source]

  • experimentally validated: PeptideAtlas [2] [3]
  • protein localization: data available for COL
  • quantitative data / protein copy number per cell: data available for COL
  • ⊟interaction partners:
    SAOUHSC_02490(adk)adenylate kinase  [4] (data from MRSA252)
    SAOUHSC_00799(eno)phosphopyruvate hydratase  [4] (data from MRSA252)
    SAOUHSC_02117(gatA)aspartyl/glutamyl-tRNA amidotransferase subunit A  [4] (data from MRSA252)
    SAOUHSC_00796(pgk)phosphoglycerate kinase  [4] (data from MRSA252)
    SAOUHSC_00519(rplA)50S ribosomal protein L1  [4] (data from MRSA252)
    SAOUHSC_02509(rplB)50S ribosomal protein L2  [4] (data from MRSA252)
    SAOUHSC_02511(rplD)50S ribosomal protein L4  [4] (data from MRSA252)
    SAOUHSC_02500(rplE)50S ribosomal protein L5  [4] (data from MRSA252)
    SAOUHSC_02496(rplF)50S ribosomal protein L6  [4] (data from MRSA252)
    SAOUHSC_00520(rplJ)50S ribosomal protein L10  [4] (data from MRSA252)
    SAOUHSC_00521(rplL)50S ribosomal protein L7/L12  [4] (data from MRSA252)
    SAOUHSC_02492(rplO)50S ribosomal protein L15  [4] (data from MRSA252)
    SAOUHSC_02484(rplQ)50S ribosomal protein L17  [4] (data from MRSA252)
    SAOUHSC_01757(rplU)50S ribosomal protein L21  [4] (data from MRSA252)
    SAOUHSC_02510(rplW)50S ribosomal protein L23  [4] (data from MRSA252)
    SAOUHSC_01755(rpmA)50S ribosomal protein L27  [4] (data from MRSA252)
    SAOUHSC_01232(rpsB)30S ribosomal protein S2  [4] (data from MRSA252)
    SAOUHSC_02494(rpsE)30S ribosomal protein S5  [4] (data from MRSA252)
    SAOUHSC_00348(rpsF)30S ribosomal protein S6  [4] (data from MRSA252)
    SAOUHSC_02477(rpsI)30S ribosomal protein S9  [4] (data from MRSA252)
    SAOUHSC_01208(rpsP)30S ribosomal protein S16  [4] (data from MRSA252)
    SAOUHSC_02503(rpsQ)30S ribosomal protein S17  [4] (data from MRSA252)
    SAOUHSC_02508(rpsS)30S ribosomal protein S19  [4] (data from MRSA252)
    SAOUHSC_01689(rpsT)30S ribosomal protein S20  [4] (data from MRSA252)
    SAOUHSC_01779(tig)trigger factor  [4] (data from MRSA252)
    SAOUHSC_00797(tpiA)triosephosphate isomerase  [4] (data from MRSA252)
    SAOUHSC_01234(tsf)elongation factor Ts  [4] (data from MRSA252)
    SAOUHSC_02353(upp)uracil phosphoribosyltransferase  [4] (data from MRSA252)
    SAOUHSC_00187formate acetyltransferase  [4] (data from MRSA252)
    SAOUHSC_00365alkyl hydroperoxide reductase subunit C  [4] (data from MRSA252)
    SAOUHSC_00426ABC transporter substrate-binding protein  [4] (data from MRSA252)
    SAOUHSC_0047450S ribosomal protein L25/general stress protein Ctc  [4] (data from MRSA252)
    SAOUHSC_00488hypothetical protein  [4] (data from MRSA252)
    SAOUHSC_00499pyridoxal biosynthesis lyase PdxS  [4] (data from MRSA252)
    SAOUHSC_0052830S ribosomal protein S7  [4] (data from MRSA252)
    SAOUHSC_00608alcohol dehydrogenase  [4] (data from MRSA252)
    SAOUHSC_00795glyceraldehyde-3-phosphate dehydrogenase  [4] (data from MRSA252)
    SAOUHSC_00878hypothetical protein  [4] (data from MRSA252)
    SAOUHSC_01028phosphocarrier protein HPr  [4] (data from MRSA252)
    SAOUHSC_01040pyruvate dehydrogenase complex, E1 component subunit alpha  [4] (data from MRSA252)
    SAOUHSC_01041pyruvate dehydrogenase complex, E1 component subunit beta  [4] (data from MRSA252)
    SAOUHSC_01100thioredoxin  [4] (data from MRSA252)
    SAOUHSC_01150cell division protein FtsZ  [4] (data from MRSA252)
    SAOUHSC_01218succinyl-CoA synthetase subunit alpha  [4] (data from MRSA252)
    SAOUHSC_01287glutamine synthetase  [4] (data from MRSA252)
    SAOUHSC_01416dihydrolipoamide succinyltransferase  [4] (data from MRSA252)
    SAOUHSC_01490DNA-binding protein HU  [4] (data from MRSA252)
    SAOUHSC_016056-phosphogluconate dehydrogenase  [4] (data from MRSA252)
    SAOUHSC_01814hypothetical protein  [4] (data from MRSA252)
    SAOUHSC_01845formate--tetrahydrofolate ligase  [4] (data from MRSA252)
    SAOUHSC_01901putative translaldolase  [4] (data from MRSA252)
    SAOUHSC_02441alkaline shock protein 23  [4] (data from MRSA252)
    SAOUHSC_02926fructose-1,6-bisphosphate aldolase  [4] (data from MRSA252)
    SAOUHSC_02927malate:quinone oxidoreductase  [4] (data from MRSA252)

⊟Expression & Regulation[edit | edit source]

⊟Operon[edit | edit source]

  • MicrobesOnline: SAOUHSC_02356 < SAOUHSC_02357 < SAOUHSC_02358 < prfA < SAOUHSC_02360
    predicted SigA promoter [5] : atpC < SAOUHSC_02341 < SAOUHSC_02343 < SAOUHSC_02345 < SAOUHSC_02346 < SAOUHSC_02347 < S904 < SAOUHSC_02349 < SAOUHSC_02350 < SAOUHSC_02351 < SAOUHSC_02352 < upp < glyA < SAOUHSC_02355 < S905 < SAOUHSC_02356 < SAOUHSC_02357 < SAOUHSC_02358 < S906 < prfA < SAOUHSC_02360

⊟Regulation[edit | edit source]

  • regulator:

⊟Transcription pattern[edit | edit source]

  • S.aureus Expression Data Browser:  [5] 
    Expression Data Browser
    ⊟Multi-gene expression profiles



    Click on any data point to display a description of the corresponding condition!

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

  • Aureolib: data available for COL

⊟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. ↑ 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. ↑ 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);3648-61
    [PubMed:26224020] [WorldCat.org] [DOI] (I p)
  3. ↑ Stephan Michalik, Maren Depke, Annette Murr, Manuela Gesell Salazar, Ulrike Kusebauch, Zhi Sun, Tanja C Meyer, Kristin Surmann, Henrike Pförtner, Petra Hildebrandt, Stefan Weiss, Laura Marcela Palma Medina, Melanie Gutjahr, Elke Hammer, Dörte Becher, Thomas Pribyl, Sven Hammerschmidt, Eric W Deutsch, Samuel L Bader, Michael Hecker, Robert L Moritz, Ulrike Mäder, Uwe Völker, Frank Schmidt
    A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host-pathogen interactions.
    Sci Rep: 2017, 7(1);9718
    [PubMed:28887440] [WorldCat.org] [DOI] (I e)
  4. ↑ Jump up to: 4.00 4.01 4.02 4.03 4.04 4.05 4.06 4.07 4.08 4.09 4.10 4.11 4.12 4.13 4.14 4.15 4.16 4.17 4.18 4.19 4.20 4.21 4.22 4.23 4.24 4.25 4.26 4.27 4.28 4.29 4.30 4.31 4.32 4.33 4.34 4.35 4.36 4.37 4.38 4.39 4.40 4.41 4.42 4.43 4.44 4.45 4.46 4.47 4.48 4.49 4.50 4.51 4.52 4.53 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)
  5. ↑ Jump up to: 5.0 5.1 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 | edit source]

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  • This page was last edited on 11 March 2016, at 04:19.
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