From AureoWiki
Jump to navigation Jump to search
VisualWikitext
m (Text replacement - "gene Genbank" to "gene RefSeq")
m (Text replacement - "* <aureodatabase>protein Genbank</aureodatabase> " to "")
 
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 location</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 77:
==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 96:
==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 105:
==Accession numbers==
==Accession numbers==


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


Line 108: Line 113:
==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 125: Line 133:
==Operon==
==Operon==


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


Line 131: Line 139:
==Regulation==
==Regulation==


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


Line 138: Line 145:
==Transcription pattern==
==Transcription pattern==


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


Line 144: Line 151:
==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 11:48, 11 March 2016

NCBI: 02-MAR-2017

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL_RS08355 [old locus tag: SACOL1639 ]
  • pan locus tag?: SAUPAN004165000
  • symbol: SACOL_RS08355
  • pan gene symbol?: hrcA
  • synonym:
  • product: HrcA family transcriptional regulator

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SACOL_RS08355 [old locus tag: SACOL1639 ]
  • symbol: SACOL_RS08355
  • product: HrcA family transcriptional regulator
  • replicon: chromosome
  • strand: -
  • coordinates: 1669133..1670110
  • length: 978
  • essential: unknown other strains

⊟Accession numbers[edit | edit source]

  • Location: NC_002951 (1669133..1670110) NCBI
  • BioCyc: G1G4B-1752 BioCyc
  • MicrobesOnline: see SACOL1639

⊟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
    ATGATTACAGATAGGCAATTGAGTATATTAAACGCAATTGTTGAGGATTATGTTGATTTT
    GGACAACCCGTTGGTTCTAAAACACTAATTGAGCGACATAACTTGAATGTTAGTCCTGCT
    ACAATTAGAAATGAGATGAAACAGCTTGAAGATTTAAACTATATCGAGAAGACACATAGT
    TCTTCAGGGCGTTCGCCATCACAATTAGGTTTTAGGTATTATGTCAATCGTTTACTTGAA
    CAAACATCTCATCAAAAAACAAATAAATTAAGACGATTAAATCAATTGTTAGTTGAGAAT
    CAATATGATGTATCATCAGCATTGACATATTTTGCAGATGAATTATCAAATATATCTCAA
    TATACAACTTTAGTTGTTCATCCTAATCATAAACAAGATATTATCAATAATGTACACTTG
    ATTCGTGCTAATCCTAATTTAGTTATAATGGTTATCGTATTTTCATCAGGTCATGTTGAG
    CATGTACATCTTGCTTCAGACATACCGTTTAATAATGACAAACTAAATACAATATCAAAT
    TTTGTTACAAACAAACTAACTGAGTTTAATCAGAATTTACAAGATGATATTGTCTCTTTT
    GTTCAATCAGAGCAGGAAGAAATTTTTATCAATAAATTGTTAAATACGATGAATAATCAT
    ATTTCTAATCAAAGTAATAGCATTTATATGGGTGGAAAGGTTAAACTTATTGATGCATTG
    AATGAAAGTAATGTATCTTCAATTCAGCCCATTCTACAATATATAGAATCAAATAGAATT
    GCAGAATTATTACAAGATATATCTTCACCAAATATTAATGTAAAAATTGGTAATGAAATT
    GATGACAGCTTAAGTGATATTTCAATTGTAACAAGTCAATATCATTTTGATGAAACGTTA
    AAAGGTCAAATCGCTGTGATTGGACCTACAGCTATGCATTATCAAAATGTCATTCAATTA
    TTAAATAGAATTTGGTAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    978

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SACOL_RS08355 [old locus tag: SACOL1639 ]
  • symbol: SACOL_RS08355
  • description: HrcA family transcriptional regulator
  • length: 325
  • theoretical pI: 5.71442
  • theoretical MW: 37015.4
  • GRAVY: -0.301231

⊟Function[edit | edit source]

  • TIGRFAM:
    Signal transduction Regulatory functions DNA interactions heat-inducible transcription repressor HrcA (TIGR00331; HMM-score: 345.7)
  • TheSEED: see SACOL1639
  • PFAM:
    GAF (CL0161) HrcA; HrcA protein C terminal domain (PF01628; HMM-score: 138.5)
    and 8 more
    HTH (CL0123) HrcA_DNA-bdg; Winged helix-turn-helix transcription repressor, HrcA DNA-binding (PF03444; HMM-score: 18.7)
    HTH_DeoR; DeoR-like helix-turn-helix domain (PF08220; HMM-score: 18.2)
    HTH_11; HTH domain (PF08279; HMM-score: 16.7)
    no clan defined FOXO_KIX_bdg; KIX-binding domain of forkhead box O, CR2 (PF16675; HMM-score: 13.3)
    HTH (CL0123) HTH_34; Winged helix DNA-binding domain (PF13601; HMM-score: 12.5)
    LexA_DNA_bind; LexA DNA binding domain (PF01726; HMM-score: 12.4)
    Tubulin_C (CL0442) FtsZ_C; FtsZ family, C-terminal domain (PF12327; HMM-score: 12.3)
    HTH (CL0123) Ribosomal_S19e; Ribosomal protein S19e (PF01090; HMM-score: 12.1)

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

  • domains:
  • modifications:
  • cofactors:
  • effectors:
  • genes regulated by HrcA, TF important in Heat shock response: see SACOL1639

⊟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:
  • SignalP: no predicted signal peptide
    • SP(Sec/SPI): 0.004618
    • TAT(Tat/SPI): 0.002068
    • LIPO(Sec/SPII): 0.000521
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MITDRQLSILNAIVEDYVDFGQPVGSKTLIERHNLNVSPATIRNEMKQLEDLNYIEKTHSSSGRSPSQLGFRYYVNRLLEQTSHQKTNKLRRLNQLLVENQYDVSSALTYFADELSNISQYTTLVVHPNHKQDIINNVHLIRANPNLVIMVIVFSSGHVEHVHLASDIPFNNDKLNTISNFVTNKLTEFNQNLQDDIVSFVQSEQEEIFINKLLNTMNNHISNQSNSIYMGGKVKLIDALNESNVSSIQPILQYIESNRIAELLQDISSPNINVKIGNEIDDSLSDISIVTSQYHFDETLKGQIAVIGPTAMHYQNVIQLLNRIW

⊟Experimental data[edit | edit source]

  • experimentally validated: data available for NCTC8325
  • protein localization: see SACOL1639
  • quantitative data / protein copy number per cell:
  • interaction partners:

⊟Expression & Regulation[edit | edit source]

⊟Operon[edit | edit source]

⊟Regulation[edit | edit source]

⊟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]

⊟Relevant publications[edit | edit source]

Retrieved from "http://fungenwikiserver.biologie.uni-greifswald.de/aureowiki/index.php?title=SACOL_RS08355&oldid=97883"