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>
*<aureodatabase>protein STRING</aureodatabase>
</protect>
</protect>


Line 107: Line 115:
==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 135:
==Operon==
==Operon==


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


Line 130: Line 141:
==Regulation==
==Regulation==


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


Line 137: Line 147:
==Transcription pattern==
==Transcription pattern==


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


Line 143: Line 153:
==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 06:54, 11 March 2016

NCBI: 03-AUG-2016

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus NCTC8325
  • locus tag: SAOUHSC_00673
  • pan locus tag?: SAUPAN002547000
  • symbol: SAOUHSC_00673
  • pan gene symbol?: rbf
  • synonym:
  • product: hypothetical protein

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SAOUHSC_00673
  • symbol: SAOUHSC_00673
  • product: hypothetical protein
  • replicon: chromosome
  • strand: +
  • coordinates: 662031..664181
  • length: 2151
  • essential: no DEG 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
    1441
    1501
    1561
    1621
    1681
    1741
    1801
    1861
    1921
    1981
    2041
    2101
    ATGGCAAAATCATGCTTGCATATACTTACTAATAATGAATATGCGACAACGCGTTGCCAA
    GATGGCATAGTCTTATTTTGGCCAATTGACGGGGAAATCGAACTACAAAAATTTCGTAAA
    AGTAAAATAATTGAAGATGATATATATATTATTAATCATCTGGATGTATTTAGTATTAAG
    AATAATAAAAAAACGATCATGTTGTATTTGAGTAGCGATTGGTTTGCGGAATTAGGCTTT
    ACTTTCTTTAATTACCACTATACAGCAAAGTTGATTAAATCATCCTATAATTTGAAATGT
    CTACTATTAAAATTGACATATCGATACCTTGATAATCAGCCTCTTAATGACGCTGATATT
    AGAAAATTACAGGATATTATTAAAATCATTGCAAAAGAAGCAAGTATGGATAAAAAGATT
    GCACAAAATCAATATCGATATGCGTATTATGGTGATTTGCGTGATGAGCTCGAATATATT
    TATCAAAATGTAAATCAACGATTGACATTAAAAAGTGTCGCTGATAAATTATTTGTCTCA
    AAGTCAAATTTGTCATCACAATTCCACTTACTTATGGGCATGGGTTTTAAAAAATATATT
    GATACTTTGAAAATTGGTAAATCGATTGAAATTCTACTTACTACTGATAGTACTATTAGC
    AACATAAGTGAACATTTAGGTTTTAGTAGTAGCTCCACTTACTCTAAAATGTTTAAAAGT
    TATATGGATATAACACCGAATGAATATCGTAATTTATCAAAATATAATAAATGTTTAATG
    CTAAAGCCAGAACCACTAGTAGGCAAAATGGTGCAAGAAGTAAAAGAAATCATATTGAAT
    TATATTGAACATTATAAAAACCACCTAACTGATGTTATACATATTGATGAAGACAAATTT
    GAAACACCTAAATTGTTTCAAACGGTTATTCAAATAAATACTTATACAGAAATGAAATTA
    GTTTTCTTAGAAGGAATCTTTAAAACCTTATTGAATAAGAACAGTCAAGTTGTCTTTTTC
    ATCATGCCATCGATTCTAAAAAGTAAAAATACCATGTCCGAAGAAGAAAAATTCACAATC
    ATTAAAACAATAATTGAAAGTGATCTAAAGATAGCATTTAATATAAATAATATTGAAACA
    ACTTATTTTGTTGAAGAAGCTTTTATGAGTGTTTTCAGACAAATATCTCCAAACGAATTA
    AGTAATCATAATAATTACGAAGTGCATTTTGTTTTTGATTTATCATTGATGGAAATTAGA
    ACAATTTATCGAATGATATTAAAATTACATAACATCATGTTGAATGTGAAATTAGGATTG
    AACATTACCTGTTTATTTGAAAAACCTTCAGTTTTTAAATCACTAGTATCACAAATAAAG
    CGACTTAAATTCGATTCGTTAATAATAGATAATGCAAATTTAAGTAGCCCTTATTTGATG
    GGGGAAAGTGATGAGTTACTATTGAAAAATATTTTGCATTTTAAAAATTTAAAACAAGTA
    ATTAATGAATTGGATATTGAACAAGAAAAGCTGATTTTTCTAAATGTTGAAAATCATAAA
    CTGCTTAATAATAAAGAACGAGATCTAAGTAATAGTGCTCCATTAATTTATAAGACATTA
    AGTGCGCTGTATCACAACTTTGATGGCTTTGGATTAAACATTTTTGACAATCATCAAGCA
    TTTAATGCGATGCATCTATATGACAAAAATGGATTTAAAACAACACTAGGTCTTATATTA
    GAAAAGTTTATCGAATATGTCTCGAAACCAAAATACGAAAACAGTTATTATTCTATTTTT
    GATATAGAGAATTATTATTGTCTTGTTATTTATGATTGGCGAGTGATAGAGAGCGAGACA
    ATTATGAGTAATTTTGAGGATAGTCAAGTTTATATAAATTTTAAAAACAATGTTTTAAAC
    GATAAATATCTAATTGTAATAGAAACATTGGACGAAAATAGTGGCAACATTAATCATTTG
    ATTTCTAAAGAATTAAGAGATAAATATGAATGGAACCCTAGTTTACTATCTAAAATTGAC
    AACTACCTTAAACCAGCAATAGAGATTAAAGAGCATAATTTTAGTGATAATTCCTTGAAT
    ATTAACGTTACTTTTAATGCGTTATACATAATTAAAATAGGAAAAAAATAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    1020
    1080
    1140
    1200
    1260
    1320
    1380
    1440
    1500
    1560
    1620
    1680
    1740
    1800
    1860
    1920
    1980
    2040
    2100
    2151

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SAOUHSC_00673
  • symbol: SAOUHSC_00673
  • description: hypothetical protein
  • length: 716
  • theoretical pI: 7.02006
  • theoretical MW: 84116.6
  • GRAVY: -0.215922

⊟Function[edit | edit source]

  • TIGRFAM:
    YSIRK-targeted surface antigen transcriptional regulator (TIGR04094; HMM-score: 62)
    and 1 more
    4-hydroxyphenylacetate catabolism regulatory protein HpaA (TIGR02297; HMM-score: 27.8)
  • TheSEED  :
    • Transcriptional regulator of biofilm formation (AraC/XylS family)
    Regulation and Cell signaling Quorum sensing and biofilm formation Biofilm formation in Staphylococcus  Transcriptional regulator of biofilm formation (AraC/XylS family)
  • PFAM:
    HTH (CL0123) HTH_AraC; Bacterial regulatory helix-turn-helix proteins, AraC family (PF00165; HMM-score: 60.2)
    HTH_18; Helix-turn-helix domain (PF12833; HMM-score: 51.9)

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

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

⊟Localization[edit | edit source]

  • PSORTb: Cytoplasmic Membrane
    • Cytoplasmic Score: 1.78
    • Cytoplasmic Membrane Score: 8.16
    • Cellwall Score: 0.06
    • Extracellular Score: 0.01
    • 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): 0.003011
    • TAT(Tat/SPI): 0.000108
    • LIPO(Sec/SPII): 0.000899
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MAKSCLHILTNNEYATTRCQDGIVLFWPIDGEIELQKFRKSKIIEDDIYIINHLDVFSIKNNKKTIMLYLSSDWFAELGFTFFNYHYTAKLIKSSYNLKCLLLKLTYRYLDNQPLNDADIRKLQDIIKIIAKEASMDKKIAQNQYRYAYYGDLRDELEYIYQNVNQRLTLKSVADKLFVSKSNLSSQFHLLMGMGFKKYIDTLKIGKSIEILLTTDSTISNISEHLGFSSSSTYSKMFKSYMDITPNEYRNLSKYNKCLMLKPEPLVGKMVQEVKEIILNYIEHYKNHLTDVIHIDEDKFETPKLFQTVIQINTYTEMKLVFLEGIFKTLLNKNSQVVFFIMPSILKSKNTMSEEEKFTIIKTIIESDLKIAFNINNIETTYFVEEAFMSVFRQISPNELSNHNNYEVHFVFDLSLMEIRTIYRMILKLHNIMLNVKLGLNITCLFEKPSVFKSLVSQIKRLKFDSLIIDNANLSSPYLMGESDELLLKNILHFKNLKQVINELDIEQEKLIFLNVENHKLLNNKERDLSNSAPLIYKTLSALYHNFDGFGLNIFDNHQAFNAMHLYDKNGFKTTLGLILEKFIEYVSKPKYENSYYSIFDIENYYCLVIYDWRVIESETIMSNFEDSQVYINFKNNVLNDKYLIVIETLDENSGNINHLISKELRDKYEWNPSLLSKIDNYLKPAIEIKEHNFSDNSLNINVTFNALYIIKIGKK

⊟Experimental data[edit | edit source]

  • experimentally validated: PeptideAtlas [1] [2]
  • protein localization: data available for COL
  • quantitative data / protein copy number per cell:
  • interaction partners:

⊟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: 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. ↑ 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)
  2. ↑ 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)
  3. ↑ 3.0 3.1 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]

Retrieved from "http://fungenwikiserver.biologie.uni-greifswald.de/aureowiki/index.php?title=SAOUHSC_00673&oldid=88502"