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m (Text replacement - "* <aureodatabase>protein Genbank</aureodatabase> " to "")
m (Text replacement - "gene Genbank" to "gene RefSeq")
 
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__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>


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==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>


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==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>


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==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>


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==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>


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==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>


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==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>


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==Operon==
==Operon==


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


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==Regulation==
==Regulation==


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


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==Transcription pattern==
==Transcription pattern==


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


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==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 09:34, 11 March 2016

NCBI: 02-MAR-2017

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus USA300_FPR3757
  • locus tag: SAUSA300_RS12700 [old locus tag: SAUSA300_2299 ]
  • pan locus tag?: SAUPAN005853000
  • symbol: SAUSA300_RS12700
  • pan gene symbol?: —
  • synonym:
  • product: HlyD family secretion protein

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SAUSA300_RS12700 [old locus tag: SAUSA300_2299 ]
  • symbol: SAUSA300_RS12700
  • product: HlyD family secretion protein
  • replicon: chromosome
  • strand: -
  • coordinates: 2471697..2472344
  • length: 648
  • 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
    ATGAAAAAGATGATATTAATTAATGTCATTACGGTTGTTGTACTGTTAGCAATTGGGATT
    GCTGGCTTTTATTTTTGGAATAAAACAACAAGCTATGTAACAACTGATAATGCAAAAGTA
    AATGGCGATCAAATTAAAATAGCAAGTCCTGCATCTGGACAAATTAAATCACTTAATGTT
    AAACAAGGTGACAAACTCGATAAAGGTGACAAAGTAGCAATTGTTACTGTACAAGGTCAA
    GATGGCGAAACGAAAGATATGGATCTTAAAATGCCTCAAAAAGGTACAATTGCCAAATTA
    GATGGTATGGAAGGTTCAATGGTGCAAGCTGGTAACCCAATCGCTTATGCATACAATTTA
    GATGATTTATATGTAACAGCAAATATTGACGAAAAAGATATTAAAGATGTTGAAGTAGGT
    AAAGATGTTGATGTGACTATTGACGGTCAAAAAGCTTCTATTAAAGGTAAAGTTGATAGT
    ATTGGAAAAGCAACTGCTGCAAGCTTTTCATTAATGCCATCATCAAATAGTGATGGTAAC
    TACACTAAAGTTTCTCAAGTAATACCTGTTAAAATCACTCTAGAATCAGAACCGTCTAAA
    CAAGTTGTTCCTGGAATGAACGCTGAAGTAAAAATCCATAAAAATTAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    648

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SAUSA300_RS12700 [old locus tag: SAUSA300_2299 ]
  • symbol: SAUSA300_RS12700
  • description: HlyD family secretion protein
  • length: 215
  • theoretical pI: 7.49286
  • theoretical MW: 23024.3
  • GRAVY: -0.206977

⊟Function[edit | edit source]

  • TIGRFAM:
    Metabolism Transport and binding proteins Other efflux pump membrane protein (TIGR00998; HMM-score: 126.2)
    and 12 more
    Metabolism Transport and binding proteins Unknown substrate efflux transporter, RND family, MFP subunit (TIGR01730; HMM-score: 45.5)
    ABC exporter membrane fusion protein, DevB family (TIGR02971; HMM-score: 44.2)
    Genetic information processing Protein fate Protein and peptide secretion and trafficking type I secretion membrane fusion protein, HlyD family (TIGR01843; HMM-score: 39.3)
    Metabolism Transport and binding proteins Other membrane fusion protein cluster 2 protein (TIGR00999; HMM-score: 31.5)
    Metabolism Central intermediary metabolism Nitrogen metabolism urea carboxylase (TIGR02712; EC 6.3.4.6; HMM-score: 24.2)
    Cellular processes Cellular processes Biosynthesis of natural products NHLM bacteriocin system secretion protein (TIGR03794; HMM-score: 24.1)
    Metabolism Transport and binding proteins Amino acids, peptides and amines NHLM bacteriocin system secretion protein (TIGR03794; HMM-score: 24.1)
    Metabolism Energy metabolism Glycolysis/gluconeogenesis pyruvate carboxylase (TIGR01235; EC 6.4.1.1; HMM-score: 17.8)
    Metabolism Energy metabolism Pyruvate dehydrogenase dihydrolipoyllysine-residue acetyltransferase (TIGR01348; EC 2.3.1.12; HMM-score: 17.4)
    Metabolism Transport and binding proteins Cations and iron carrying compounds oxaloacetate decarboxylase alpha subunit (TIGR01108; EC 4.1.1.3; HMM-score: 14.6)
    Metabolism Energy metabolism Other oxaloacetate decarboxylase alpha subunit (TIGR01108; EC 4.1.1.3; HMM-score: 14.6)
    Metabolism Energy metabolism TCA cycle dihydrolipoyllysine-residue succinyltransferase, E2 component of oxoglutarate dehydrogenase (succinyl-transferring) complex (TIGR01347; EC 2.3.1.61; HMM-score: 14)
  • TheSEED: see SAUSA300_2299
  • PFAM:
    Hybrid (CL0105) HlyD_3; HlyD family secretion protein (PF13437; HMM-score: 61.3)
    HlyD_D23; Barrel-sandwich domain of CusB or HlyD membrane-fusion (PF16576; HMM-score: 54.6)
    and 8 more
    Biotin_lipoyl_2; Biotin-lipoyl like (PF13533; HMM-score: 37.5)
    Biotin_lipoyl; Biotin-requiring enzyme (PF00364; HMM-score: 36.5)
    HlyD; HlyD membrane-fusion protein of T1SS (PF00529; HMM-score: 16.7)
    DUF2118; Uncharacterized protein conserved in archaea (DUF2118) (PF09891; HMM-score: 15.3)
    no clan defined PASTA; PASTA domain (PF03793; HMM-score: 14.1)
    Hybrid (CL0105) Peptidase_M23; Peptidase family M23 (PF01551; HMM-score: 13.1)
    LysM (CL0187) OapA; Opacity-associated protein A LysM-like domain (PF04225; HMM-score: 11.6)
    DRMIP-like (CL0538) DUF4448; Protein of unknown function (DUF4448) (PF14610; HMM-score: 9.7)

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

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

⊟Localization[edit | edit source]

  • PSORTb: Cytoplasmic Membrane
    • Cytoplasmic Score: 0.17
    • Cytoplasmic Membrane Score: 9.51
    • Cellwall Score: 0.16
    • Extracellular Score: 0.15
    • Internal Helix: 1
  • LocateP:
  • SignalP: no predicted signal peptide
    • SP(Sec/SPI): 0.367511
    • TAT(Tat/SPI): 0.000603
    • LIPO(Sec/SPII): 0.070569
  • predicted transmembrane helices (TMHMM): 1

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MKKMILINVITVVVLLAIGIAGFYFWNKTTSYVTTDNAKVNGDQIKIASPASGQIKSLNVKQGDKLDKGDKVAIVTVQGQDGETKDMDLKMPQKGTIAKLDGMEGSMVQAGNPIAYAYNLDDLYVTANIDEKDIKDVEVGKDVDVTIDGQKASIKGKVDSIGKATAASFSLMPSSNSDGNYTKVSQVIPVKITLESEPSKQVVPGMNAEVKIHKN

⊟Experimental data[edit | edit source]

  • experimentally validated: data available for COL, NCTC8325
  • 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]

⊟Relevant publications[edit | edit source]

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