From AureoWiki
Jump to navigation Jump to search
VisualWikitext
(Created page with "<protect> <aureodatabase>NCBI date</aureodatabase> =Summary= * <aureodatabase>organism</aureodatabase> * <aureodatabase>locus</aureodatabase> * <aureodatabase>pan locus</aur...")
 
m (Text replacement - "gene Genbank" to "gene RefSeq")
 
(One intermediate revision by the same user not shown)
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 Genbank</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 02:35, 11 March 2016

NCBI: 02-MAR-2017

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL_RS05925 [old locus tag: SACOL1160 ]
  • pan locus tag?: SAUPAN003389000
  • symbol: SACOL_RS05925
  • pan gene symbol?: sdhB
  • synonym:
  • product: succinate dehydrogenase iron-sulfur subunit

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SACOL_RS05925 [old locus tag: SACOL1160 ]
  • symbol: SACOL_RS05925
  • product: succinate dehydrogenase iron-sulfur subunit
  • replicon: chromosome
  • strand: +
  • coordinates: 1170763..1171578
  • length: 816
  • essential: unknown other strains

⊟Accession numbers[edit | edit source]

  • Location: NC_002951 (1170763..1171578) NCBI
  • BioCyc: SACOL_RS05925 BioCyc
  • MicrobesOnline: see SACOL1160

⊟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
    ATGACTGAACAATCAGTGAAAAACACTCCACAACATGAAACACAATCTAAACCGAAACAA
    AAAACAGTAAAATTAATTATTAAACGACAAGATACAAGTGATTCTAAGCCTTATGAAGAA
    ACATTTGAAATTCCATATCGTGAAAATTTAAACGTCATTGCTTGTTTAATGGAAATTAGA
    CGTAACCCAGTTAATATTAAAGGTGAAAAAACAACACCTGTTGTCTGGGATATGAACTGC
    TTAGAAGAAGTATGTGGAGCATGTTCTATGGTTATCAATGGTCGTGCAAGACAATCTTGT
    TCTGCGATTGTTGATCAATTAGAACAACCTATTCGTTTAGAGCCAATGAATACTTTCCCA
    GTTATCCGTGACTTACAAGTTGATCGTTCTAGAATGTTCGATAACTTAAAACGTATGAAA
    GCATGGATCCCAATTGATGGAACGTATGATTTAGGTCCGGGACCACGTATGCCAGAGAAA
    AAACGTCAAACAGCTTATGAATTATCTAAATGTATGACATGTGGTGTATGTTTAGAGGTT
    TGTCCTAATGTTACTGAAAATAATAAATTCGTTGGTGCACAAGCAATCTCGCAAGTTCGT
    TTGTTTAATTTGCACCCAACAGGATCTATGACTAAAGATGAACGTTTAAATGCATTAATG
    GGTACTGGTGGCTTACAGCAGTGTGGTAATTCACAAAACTGTGTTAATGCTTGCCCTAAA
    GGTATTCCATTAACAACATCCATTGCAGCAATGAACAGAGAAACAACATTCCACATGTTT
    AAATCATTCTTTGGTTCAGACCATGAAGTAGAATAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    816

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SACOL_RS05925 [old locus tag: SACOL1160 ]
  • symbol: SACOL_RS05925
  • description: succinate dehydrogenase iron-sulfur subunit
  • length: 271
  • theoretical pI: 7.99685
  • theoretical MW: 30583.1
  • GRAVY: -0.501845

⊟Function[edit | edit source]

  • reaction:
    EC 1.3.99.1?  ExPASy
    Deleted entry
  • TIGRFAM:
    Metabolism Energy metabolism TCA cycle succinate dehydrogenase and fumarate reductase iron-sulfur protein (TIGR00384; HMM-score: 137.1)
    Metabolism Energy metabolism Anaerobic succinate dehydrogenase and fumarate reductase iron-sulfur protein (TIGR00384; HMM-score: 137.1)
    Metabolism Energy metabolism Aerobic succinate dehydrogenase and fumarate reductase iron-sulfur protein (TIGR00384; HMM-score: 137.1)
    and 25 more
    Metabolism Energy metabolism Electron transport NADH-quinone oxidoreductase, chain I (TIGR01971; HMM-score: 19)
    Unknown function General archaeoflavoprotein, MJ0208 family (TIGR02700; HMM-score: 18.7)
    cytochrome c oxidase accessory protein CcoG (TIGR02745; HMM-score: 18)
    CoB--CoM heterodisulfide reductase, subunit C (TIGR03290; EC 1.8.98.1; HMM-score: 15.4)
    4-hydroxybenzoyl-CoA reductase, gamma subunit (TIGR03193; EC 1.3.7.9; HMM-score: 15.1)
    Metabolism Purines, pyrimidines, nucleosides, and nucleotides Other selenium-dependent xanthine dehydrogenase (TIGR03311; EC 1.17.1.4; HMM-score: 15.1)
    pyruvate:ferredoxin (flavodoxin) oxidoreductase (TIGR02176; EC 1.2.7.1; HMM-score: 14.1)
    Metabolism Energy metabolism Amino acids and amines choline TMA-lyase-activating enzyme (TIGR04395; EC 1.97.-.-; HMM-score: 13.8)
    Metabolism Energy metabolism Anaerobic glycerol-3-phosphate dehydrogenase, anaerobic, C subunit (TIGR03379; EC 1.1.5.3; HMM-score: 13.5)
    2-oxoacid:acceptor oxidoreductase, delta subunit, pyruvate/2-ketoisovalerate family (TIGR02179; HMM-score: 13.2)
    Metabolism Energy metabolism Electron transport NADH-plastoquinone oxidoreductase, I subunit (TIGR00403; EC 1.6.5.3; HMM-score: 13.1)
    Metabolism Energy metabolism Electron transport iron-sulfur cluster-binding protein (TIGR00273; HMM-score: 12)
    Metabolism Energy metabolism Methanogenesis putative methanogenesis marker 16 metalloprotein (TIGR03287; HMM-score: 11.9)
    Genetic information processing Protein synthesis tRNA and rRNA base modification epoxyqueuosine reductase (TIGR00276; EC 1.-.-.-; HMM-score: 11.8)
    Metabolism Energy metabolism Electron transport cytochrome c nitrite reductase, Fe-S protein (TIGR03149; EC 1.7.2.2; HMM-score: 11.5)
    Metabolism Energy metabolism Electron transport ferredoxin-type protein NapF (TIGR00402; HMM-score: 10.3)
    [FeFe] hydrogenase, group A (TIGR02512; EC 1.12.-.-; HMM-score: 9.9)
    Metabolism Energy metabolism Chemoautotrophy CO dehydrogenase/acetyl-CoA synthase complex, epsilon subunit (TIGR00314; EC 1.2.99.2; HMM-score: 9.4)
    methylamine methyltransferase corrinoid protein reductive activase (TIGR04270; HMM-score: 9.4)
    Metabolism Central intermediary metabolism Nitrogen fixation ferredoxin III, nif-specific (TIGR02936; HMM-score: 8.2)
    Metabolism Energy metabolism Electron transport electron transport complex, RnfABCDGE type, C subunit (TIGR01945; HMM-score: 7.7)
    glycyl-radical enzyme activating protein (TIGR02494; EC 1.97.1.-; HMM-score: 6.8)
    Genetic information processing Protein fate Protein modification and repair glycine radical enzyme activase, YjjW family (TIGR04041; EC 1.97.1.-; HMM-score: 6.6)
    ferredoxin-type protein, NapH/MauN family (TIGR02163; HMM-score: 6.5)
    Metabolism Central intermediary metabolism Sulfur metabolism sulfite reductase, dissimilatory-type beta subunit (TIGR02066; EC 1.8.99.3; HMM-score: 5.3)
  • TheSEED: see SACOL1160
  • PFAM:
    Fer2 (CL0486) Fer2_3; 2Fe-2S iron-sulfur cluster binding domain (PF13085; HMM-score: 97.9)
    and 15 more
    4Fe-4S (CL0344) Fer4_8; 4Fe-4S dicluster domain (PF13183; HMM-score: 35.6)
    Fer4_7; 4Fe-4S dicluster domain (PF12838; HMM-score: 33.9)
    Fer4_9; 4Fe-4S dicluster domain (PF13187; HMM-score: 30.5)
    Fer4_10; 4Fe-4S dicluster domain (PF13237; HMM-score: 28.2)
    Fer4_17; 4Fe-4S dicluster domain (PF13534; HMM-score: 25.6)
    Fer4_16; 4Fe-4S double cluster binding domain (PF13484; HMM-score: 19.5)
    Fer4_2; 4Fe-4S binding domain (PF12797; HMM-score: 19.3)
    Fer4; 4Fe-4S binding domain (PF00037; HMM-score: 17.8)
    Fer4_15; 4Fe-4S single cluster domain (PF13459; HMM-score: 17.2)
    Fer4_13; 4Fe-4S single cluster domain of Ferredoxin I (PF13370; HMM-score: 16.8)
    Fer4_21; 4Fe-4S dicluster domain (PF14697; HMM-score: 14.7)
    Fer4_6; 4Fe-4S binding domain (PF12837; HMM-score: 13.8)
    Fer4_4; 4Fe-4S binding domain (PF12800; HMM-score: 12.9)
    Fer4_18; 4Fe-4S dicluster domain (PF13746; HMM-score: 11.5)
    Fer4_3; 4Fe-4S binding domain (PF12798; HMM-score: 9.8)

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

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

⊟Localization[edit | edit source]

  • PSORTb: Cytoplasmic
    • Cytoplasmic Score: 9.89
    • Cytoplasmic Membrane Score: 0.09
    • Cellwall Score: 0.01
    • Extracellular Score: 0.02
    • Internal Helices: 0
  • LocateP:
  • SignalP: no predicted signal peptide
    • SP(Sec/SPI): 0.004685
    • TAT(Tat/SPI): 0.00098
    • LIPO(Sec/SPII): 0.000969
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MTEQSVKNTPQHETQSKPKQKTVKLIIKRQDTSDSKPYEETFEIPYRENLNVIACLMEIRRNPVNIKGEKTTPVVWDMNCLEEVCGACSMVINGRARQSCSAIVDQLEQPIRLEPMNTFPVIRDLQVDRSRMFDNLKRMKAWIPIDGTYDLGPGPRMPEKKRQTAYELSKCMTCGVCLEVCPNVTENNKFVGAQAISQVRLFNLHPTGSMTKDERLNALMGTGGLQQCGNSQNCVNACPKGIPLTTSIAAMNRETTFHMFKSFFGSDHEVE

⊟Experimental data[edit | edit source]

  • experimentally validated: see SACOL1160
  • protein localization: see SACOL1160
  • 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_RS05925&oldid=81299"