From AureoWiki
Jump to navigation Jump to search
VisualWikitext
m (Text replacement - "* <aureodatabase>protein Genbank</aureodatabase> " to "")
m (Text replacement - "gene Genbank" to "gene RefSeq")
 
Line 1: Line 1:
__TOC__
<protect>
<protect>
<aureodatabase>NCBI date</aureodatabase>
<aureodatabase>annotation</aureodatabase>


=Summary=
=Summary=


* <aureodatabase>organism</aureodatabase>
*<aureodatabase>organism</aureodatabase>
* <aureodatabase>locus</aureodatabase>
*<aureodatabase>locus</aureodatabase>
* <aureodatabase>pan locus</aureodatabase>
*<aureodatabase>pan locus</aureodatabase>
* <aureodatabase>gene symbol</aureodatabase>
*<aureodatabase>gene symbol</aureodatabase>
* <aureodatabase>pan gene symbol</aureodatabase>
*<aureodatabase>pan gene symbol</aureodatabase>
* <aureodatabase>gene synonyms</aureodatabase>
*<aureodatabase>gene synonyms</aureodatabase>
* <aureodatabase>product</aureodatabase>
*<aureodatabase>product</aureodatabase>
</protect>
</protect>


Line 24: Line 25:
==General==
==General==


* <aureodatabase>gene type</aureodatabase>
*<aureodatabase>gene type</aureodatabase>
* <aureodatabase>locus</aureodatabase>
*<aureodatabase>locus</aureodatabase>
* <aureodatabase>gene symbol</aureodatabase>
*<aureodatabase>gene symbol</aureodatabase>
* <aureodatabase>product</aureodatabase>
*<aureodatabase>product</aureodatabase>
* <aureodatabase>gene replicon</aureodatabase>
*<aureodatabase>gene replicon</aureodatabase>
* <aureodatabase>strand</aureodatabase>
*<aureodatabase>strand</aureodatabase>
* <aureodatabase>gene coordinates</aureodatabase>
*<aureodatabase>gene coordinates</aureodatabase>
* <aureodatabase>gene length</aureodatabase>
*<aureodatabase>gene length</aureodatabase>
* <aureodatabase>essential</aureodatabase>
*<aureodatabase>essential</aureodatabase>
*<aureodatabase>gene comment</aureodatabase>
</protect>
</protect>


Line 38: Line 40:
==Accession numbers==
==Accession numbers==


* <aureodatabase>gene GI</aureodatabase>
*<aureodatabase>gene GI</aureodatabase>
* <aureodatabase>gene Genbank</aureodatabase>
*<aureodatabase>gene RefSeq</aureodatabase>
*<aureodatabase>gene BioCyc</aureodatabase>
*<aureodatabase>gene MicrobesOnline</aureodatabase>
</protect>
</protect>
   
   
<protect>  
<protect>
==Phenotype==
==Phenotype==
</protect>
</protect>
* Share your knowledge and add information here. [<span class="plainlinks">[http://www.protecs.uni-greifswald.de/aureowiki/index.php?title={{PAGENAMEE}}&action=edit&section=6 edit]</span>]
Share your knowledge and add information here. [<span class="plainlinks">[//aureowiki.med.uni-greifswald.de/index.php?title={{PAGENAMEE}}&veaction=edit&section=6 edit]</span>]


<protect>
<protect>
==DNA sequence==
==DNA sequence==


* <aureodatabase>gene sequence</aureodatabase>
*<aureodatabase>gene sequence</aureodatabase>
</protect>
</protect>


<protect>
<protect>
<aureodatabase>RNA regulated operons</aureodatabase>
</protect>


<protect>
=Protein=
=Protein=
<aureodatabase>protein 3D view</aureodatabase>
<aureodatabase>protein 3D view</aureodatabase>
==General==
==General==


* <aureodatabase>locus</aureodatabase>
*<aureodatabase>locus</aureodatabase>
* <aureodatabase>protein symbol</aureodatabase>
*<aureodatabase>protein symbol</aureodatabase>
* <aureodatabase>protein description</aureodatabase>
*<aureodatabase>protein description</aureodatabase>
* <aureodatabase>protein length</aureodatabase>
*<aureodatabase>protein length</aureodatabase>
* <aureodatabase>theoretical pI</aureodatabase>
*<aureodatabase>theoretical pI</aureodatabase>
* <aureodatabase>theoretical MW</aureodatabase>
*<aureodatabase>theoretical MW</aureodatabase>
* <aureodatabase>GRAVY</aureodatabase>
*<aureodatabase>GRAVY</aureodatabase>
</protect>
</protect>


Line 71: Line 78:
==Function==
==Function==


* <aureodatabase>protein reaction</aureodatabase>
*<aureodatabase>protein reaction</aureodatabase>
* <aureodatabase>protein TIGRFAM</aureodatabase>
*<aureodatabase>protein TIGRFAM</aureodatabase>
* <aureodatabase>protein TheSeed</aureodatabase>
*<aureodatabase>protein TheSeed</aureodatabase>
* <aureodatabase>protein PFAM</aureodatabase>
*<aureodatabase>protein PFAM</aureodatabase>
</protect>
</protect>


<protect>
<protect>
==Structure, modifications & interactions==
==Structure, modifications & cofactors==


* <aureodatabase>protein domains</aureodatabase>
*<aureodatabase>protein domains</aureodatabase>
* <aureodatabase>protein modifications</aureodatabase>
*<aureodatabase>protein modifications</aureodatabase>
* <aureodatabase>protein cofactors</aureodatabase>
*<aureodatabase>protein cofactors</aureodatabase>
* <aureodatabase>protein effectors</aureodatabase>
*<aureodatabase>protein effectors</aureodatabase>
* <aureodatabase>protein partners</aureodatabase>
*<aureodatabase>protein regulated operons</aureodatabase>
</protect>
</protect>


Line 90: Line 97:
==Localization==
==Localization==


* <aureodatabase>protein Psortb</aureodatabase>
*<aureodatabase>protein Psortb</aureodatabase>
* <aureodatabase>protein LocateP</aureodatabase>
*<aureodatabase>protein LocateP</aureodatabase>
* <aureodatabase>protein SignalP</aureodatabase>
*<aureodatabase>protein SignalP</aureodatabase>
* <aureodatabase>protein TMHMM</aureodatabase>
*<aureodatabase>protein TMHMM</aureodatabase>
</protect>
</protect>


Line 99: Line 106:
==Accession numbers==
==Accession numbers==


* <aureodatabase>protein GI</aureodatabase>
*<aureodatabase>protein GI</aureodatabase>
* <aureodatabase>protein UniProt</aureodatabase>
*<aureodatabase>protein RefSeq</aureodatabase>
* <aureodatabase>protein RefSeq</aureodatabase>
*<aureodatabase>protein UniProt</aureodatabase>
</protect>
</protect>


Line 107: Line 114:
==Protein sequence==
==Protein sequence==


* <aureodatabase>protein sequence</aureodatabase>
*<aureodatabase>protein sequence</aureodatabase>
</protect>
</protect>


<protect>
<protect>
==Peptides==
==Experimental data==


* <aureodatabase>protein validated peptides</aureodatabase>
*<aureodatabase>protein validated peptides</aureodatabase>
*<aureodatabase>protein validated localization</aureodatabase>
*<aureodatabase>protein validated quantitative data</aureodatabase>
*<aureodatabase>protein partners</aureodatabase>
</protect>
</protect>


Line 124: Line 134:
==Operon==
==Operon==


* <aureodatabase>operons</aureodatabase>
*<aureodatabase>operons</aureodatabase>
</protect>
</protect>


Line 130: Line 140:
==Regulation==
==Regulation==


* <aureodatabase>sigma factors</aureodatabase>
*<aureodatabase>regulators</aureodatabase>
* <aureodatabase>regulators</aureodatabase>
</protect>
</protect>


Line 137: Line 146:
==Transcription pattern==
==Transcription pattern==


* <aureodatabase>expression browser</aureodatabase>
*<aureodatabase>expression browser</aureodatabase>
</protect>
</protect>


Line 143: Line 152:
==Protein synthesis (provided by Aureolib)==
==Protein synthesis (provided by Aureolib)==


* <aureodatabase>protein synthesis Aureolib</aureodatabase>
*<aureodatabase>protein synthesis Aureolib</aureodatabase>
</protect>
</protect>


<protect>
<protect>
==Stability==
==Protein stability==


* <aureodatabase>protein half-life</aureodatabase>
*<aureodatabase>protein half-life</aureodatabase>
</protect>
</protect>


Latest revision as of 12:21, 11 March 2016

NCBI: 10-JUN-2013

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL1622 [new locus tag: SACOL_RS08270 ]
  • pan locus tag?: SAUPAN004146000
  • symbol: glyS
  • pan gene symbol?: glyS
  • synonym:
  • product: glycyl-tRNA synthetase

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SACOL1622 [new locus tag: SACOL_RS08270 ]
  • symbol: glyS
  • product: glycyl-tRNA synthetase
  • replicon: chromosome
  • strand: +
  • coordinates: 1653436..1654827
  • length: 1392
  • 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
    1141
    1201
    1261
    1321
    1381
    ATGGCAAAAGATATGGATACAATTGTTTCATTAGCAAAACACAGAGGTTTTGTGTTCCCT
    GGTAGTGATATTTACGGTGGTTTATCAAACACATGGGATTATGGTCCTTTAGGTGTTGAA
    TTAAAGAATAATGTTAAAAAAGCTTGGTGGCAAAAATTCATTACACAATCACCGTTTAAC
    GTTGGTATCGATGCTGCAATCTTAATGAATCCAAAAGTATGGGAAGCTTCAGGACACTTA
    AACAACTTCAACGACCCAATGATTGATAATAAAGATAGTAAAATTCGATATCGCGCTGAT
    AAATTAATTGAAGATTATATGCAAGATGTTAAAGGTGATGAAAACTTCATTGCCGATGGT
    TTAAGTTTTGAACAAATGAAAAAAATTATTGACGATGAAGGTATTGTTTGTCCTGTAAGT
    AAAACTGCTAACTGGACTGAAATTCGCCAATTCAATTTAATGTTTAAAACATTCCAAGGT
    GTAACTGAAGATTCTACAAATGAAATTTTCTTACGTCCTGAAACAGCACAAGGTATTTTT
    GTAAACTATAAAAACGTGCAACGTTCAATGCGTAAAAAATTACCATTTGGTATCGGTCAA
    ATTGGTAAATCATTCCGTAATGAAATCACTCCAGGTAACTTCATTTTCAGAACAAGAGAA
    TTTGAACAAATGGAACTTGAATTCTTCTGTAAACCTGGAGAAGAAATCGAATGGCAAAAT
    TATTGGAAAACTTTTGCAAGTGACTGGTTAACAAGCTTAAATATGAGCAGTGAAAATATG
    CGTTTACGTGATCATGATGAAGATGAATTATCTCATTACTCAAATGCAACAACTGATATT
    GAATATAAATTCCCATTTGGTTGGGGTGAGTTATGGGGTATCGCAAGTCGTACAGACTTC
    GACTTACGTAAACATGCTGAACACTCTGGTGAAGATTTCAGATACCATGATCCAGAAACG
    AACGAAAAATATATTCCATATTGTATCGAGCCATCACTTGGTGCAGATCGTGTAACATTA
    GCTTTCTTATGTGATGCATATGATGAAGAAGGCGTTGAAGGTAGTAAAGATGCACGTACA
    GTTTTACACTTCCATCCTGCATTAGCACCATATAAAGCAGCGATTTTACCTTTAAGTAAG
    AAATTATCTGGCGAAGCGATTAAGATTTTTGAGCAATTAAGTTCTAAATTCTCAATCGAT
    TTCGATGAATCACAATCTATCGGTAAAAGATACCGTCGTCAAGATGAAATCGGTACACCT
    TATTGTGTAACATTCGACTTTGATTCATTAGAAGATAATCAAGTTACAGTACGTGACAGA
    GATTCAATGGAACAAGTTCGTATGCCAATCTCAGAGTTAGAAGCTTTCTTAACTGAAAAA
    ACAAAATTCTAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    1020
    1080
    1140
    1200
    1260
    1320
    1380
    1392

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SACOL1622 [new locus tag: SACOL_RS08270 ]
  • symbol: GlyS
  • description: glycyl-tRNA synthetase
  • length: 463
  • theoretical pI: 4.7417
  • theoretical MW: 53619.9
  • GRAVY: -0.588769

⊟Function[edit | edit source]

  • reaction:
    EC 6.1.1.14?  ExPASy
    Glycine--tRNA ligase ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly)
  • TIGRFAM:
    Genetic information processing Protein synthesis tRNA aminoacylation glycine--tRNA ligase (TIGR00389; EC 6.1.1.14; HMM-score: 525.6)
    and 5 more
    Genetic information processing Protein synthesis tRNA aminoacylation threonine--tRNA ligase (TIGR00418; EC 6.1.1.3; HMM-score: 54.8)
    Genetic information processing Protein synthesis tRNA aminoacylation proline--tRNA ligase (TIGR00409; EC 6.1.1.15; HMM-score: 38.8)
    Genetic information processing Protein synthesis tRNA aminoacylation histidine--tRNA ligase (TIGR00442; EC 6.1.1.21; HMM-score: 37.7)
    Genetic information processing Protein synthesis tRNA aminoacylation proline--tRNA ligase (TIGR00408; EC 6.1.1.15; HMM-score: 28.5)
    Genetic information processing Protein synthesis tRNA aminoacylation serine--tRNA ligase (TIGR00414; EC 6.1.1.11; HMM-score: 15.9)
  • TheSEED  :
    • Glycyl-tRNA synthetase (EC 6.1.1.14)
    tRNA synthetase relationships  Glycyl-tRNA synthetase (EC 6.1.1.14)
  • PFAM:
    IIaaRS-ABD (CL0458) HGTP_anticodon; Anticodon binding domain (PF03129; HMM-score: 84.1)
    and 2 more
    tRNA_synt_II (CL0040) tRNA-synt_2b; tRNA synthetase class II core domain (G, H, P, S and T) (PF00587; HMM-score: 37.9)
    no clan defined PHF12_MRG_bd; PHD finger protein 12 MRG binding domain (PF16737; HMM-score: 12.2)

⊟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
  • 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): 0.012542
    • TAT(Tat/SPI): 0.000444
    • LIPO(Sec/SPII): 0.001066
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MAKDMDTIVSLAKHRGFVFPGSDIYGGLSNTWDYGPLGVELKNNVKKAWWQKFITQSPFNVGIDAAILMNPKVWEASGHLNNFNDPMIDNKDSKIRYRADKLIEDYMQDVKGDENFIADGLSFEQMKKIIDDEGIVCPVSKTANWTEIRQFNLMFKTFQGVTEDSTNEIFLRPETAQGIFVNYKNVQRSMRKKLPFGIGQIGKSFRNEITPGNFIFRTREFEQMELEFFCKPGEEIEWQNYWKTFASDWLTSLNMSSENMRLRDHDEDELSHYSNATTDIEYKFPFGWGELWGIASRTDFDLRKHAEHSGEDFRYHDPETNEKYIPYCIEPSLGADRVTLAFLCDAYDEEGVEGSKDARTVLHFHPALAPYKAAILPLSKKLSGEAIKIFEQLSSKFSIDFDESQSIGKRYRRQDEIGTPYCVTFDFDSLEDNQVTVRDRDSMEQVRMPISELEAFLTEKTKF

⊟Experimental data[edit | edit source]

  • experimentally validated: PeptideAtlas
  • protein localization: Cytoplasmic [1] [2] [3] [4]
  • quantitative data / protein copy number per cell: 5176 [5]
  • interaction partners:
    SACOL2233(rpsC)30S ribosomal protein S3  [6] (data from MRSA252)
    SACOL0731LysR family transcriptional regulator  [6] (data from MRSA252)

⊟Expression & Regulation[edit | edit source]

⊟Operon[edit | edit source]

⊟Regulation[edit | edit source]

  • regulator: T-box(Gly) (transcription antitermination) regulon
    T-box(Gly)(RNA)important in Amino acid metabolism; regulatory site identified based on RegPrecise data for N315 RegPrecise 

⊟Transcription pattern[edit | edit source]

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

⊟Protein stability[edit | edit source]

  • half-life: 29.02 h [7]

⊟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, 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. ↑ 6.0 6.1 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)
  7. ↑ 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=SACOL1622&oldid=99046"