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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 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>


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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 20:19, 10 March 2016

NCBI: 10-JUN-2013

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus USA300_FPR3757
  • locus tag: SAUSA300_1885 [new locus tag: SAUSA300_RS10315 ]
  • pan locus tag?: SAUPAN004933000
  • symbol: ligA
  • pan gene symbol?: ligA
  • synonym:
  • product: DNA ligase

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SAUSA300_1885 [new locus tag: SAUSA300_RS10315 ]
  • symbol: ligA
  • product: DNA ligase
  • replicon: chromosome
  • strand: -
  • coordinates: 2047455..2049458
  • length: 2004
  • 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
    1441
    1501
    1561
    1621
    1681
    1741
    1801
    1861
    1921
    1981
    ATGGCTGATTTATCGTCTCGTGTGAACGAGTTACATGATTTATTAAATCAATACAGTTAT
    GAATACTATGTAGAGGATAATCCATCTGTACCAGATAGTGAATATGACAAATTACTTCAT
    GAACTGATTAAAATAGAAGAGGAGCATCCTGAGTATAAGACTGTAGATTCTCCAACAGTT
    AGAGTTGGCGGTGAAGCCCAAGCCTCTTTCAATAAAGTCAACCATGACACGCCAATGTTA
    AGTTTAGGGAATGCATTTAATGAGGATGATTTGAGAAAATTCGACCAACGCATACGTGAA
    CAAATTGGCAACGTTGAATATATGTGCGAATTAAAAATTGATGGCTTAGCAGTATCATTG
    AAATATGTTGATGGATACTTCGTTCAAGGTTTAACACGTGGTGATGGAACAACAGGTGAA
    GATATTACCGAAAATTTAAAAACAATTCATGCGATACCTTTGAAAATGAAAGAACCATTA
    AATGTAGAAGTTCGTGGTGAAGCATATATGCCGAGACGTTCATTTTTACGATTAAATGAA
    GAAAAAGAAAAAAATGATGAGCAGTTATTTGCAAATCCAAGAAACGCTGCTGCGGGATCA
    TTAAGACAGTTAGATTCTAAATTAACGGCAAAACGAAAGCTAAGCGTATTTATATATAGT
    GTCAATGATTTCACTGATTTCAATGCGCGTTCGCAAAGTGAAGCATTAGATGAGTTAGAT
    AAATTAGGTTTTACAACGAATAAAAATAGAGCGCGTGTAAATAATATCGATGGTGTTTTA
    GAGTATATTGAAAAATGGACAAGCCAAAGAGAGTCATTACCTTATGATATTGATGGGATT
    GTTATTAAGGTTAATGATTTAGATCAACAGGATGAGATGGGATTCACACAAAAATCTCCT
    AGATGGGCCATTGCTTATAAATTTCCAGCTGAGGAAGTAGTAACTAAATTATTAGATATT
    GAATTAAGTATTGGACGAACAGGTGTAGTCACACCTACTGCTATTTTAGAACCAGTAAAA
    GTAGCTGGTACAACTGTATCAAGAGCATCTTTGCACAATGAGGATTTAATTCATGACAGA
    GATATTCGAATTGGTGATAGTGTTGTAGTGAAAAAAGCAGGTGACATCATACCTGAAGTT
    GTACGTAGTATTCCAGAACGTAGACCTGAGGATGCTGTCACATATCATATGCCAACCCAT
    TGTCCAAGTTGTGGACATGAATTAGTACGTATTGAAGGCGAAGTAGCACTTCGTTGCATT
    AATCCAAAATGCCAAGCACAACTTGTTGAAGGATTGATTCACTTTGTATCAAGACAAGCC
    ATGAATATTGATGGTTTAGGCACTAAAATTATTCAACAGCTTTATCAAAGCGAATTAATT
    AAAGATGTTGCTGATATTTTCTATTTAACAGAAGAAGATTTATTACCTTTAGACAGAATG
    GGGCAGAAAAAAGTTGATAATTTATTAGCTGCCATTCAACAAGCTAAGGACAACTCTTTA
    GAAAATTTATTATTTGGTCTAGGTATTAGGCATTTAGGTGTTAAAGCGAGCCAAGTGTTA
    GCAGAAAAATATGAAACGATAGATCGATTACTAACGGTAACTGAAGCGGAATTAGTAGAA
    ATTCATGATATAGGTGATAAAGTAGCACAATCTGTAGTTACTTATTTAGAAAATGAAGAT
    ATTCGTGCTTTAATTCAAAAATTAAAAGATAAACATGTTAATATGATTTATAAAGGTATC
    AAAACATCAGATATTGAAGGACATCCTGAATTTAGTGGTAAAACGATAGTACTGACTGGT
    AAGCTACATCAAATGACACGCAATGAAGCATCTAAATGGCTTGCATCACAAGGTGCTAAA
    GTTACAAGTAGCGTTACTAAAAATACAGATGTCGTTATTGCTGGTGAAGATGCAGGTTCA
    AAATTAACAAAAGCACAAAGTTTAGGTATTGAAATTTGGACAGAGCAACAATTTGTAGAT
    AAGCAAAATGAATTAAATAGTTAG
    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
    2004

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SAUSA300_1885 [new locus tag: SAUSA300_RS10315 ]
  • symbol: LigA
  • description: DNA ligase
  • length: 667
  • theoretical pI: 4.90683
  • theoretical MW: 75080.5
  • GRAVY: -0.426087

⊟Function[edit | edit source]

  • reaction:
    EC 6.5.1.2?  ExPASy
    DNA ligase (NAD+) NAD+ + (deoxyribonucleotide)(n)-3'-hydroxyl + 5'-phospho-(deoxyribonucleotide)(m) = (deoxyribonucleotide)(n+m) + AMP + beta-nicotinamide D-nucleotide
  • TIGRFAM:
    Genetic information processing DNA metabolism DNA replication, recombination, and repair DNA ligase, NAD-dependent (TIGR00575; EC 6.5.1.2; HMM-score: 880.9)
    and 2 more
    Genetic information processing Transcription DNA-dependent RNA polymerase DNA-directed RNA polymerase, alpha subunit (TIGR02027; EC 2.7.7.6; HMM-score: 13.7)
    Genetic information processing Protein fate Degradation of proteins, peptides, and glycopeptides zinc-dependent metalloproteinase lipoprotein, BF0631 family (TIGR03952; EC 3.4.24.-; HMM-score: 12.2)
  • TheSEED  :
    • DNA ligase (EC 6.5.1.2)
    DNA Metabolism DNA repair DNA Repair Base Excision  DNA ligase (EC 6.5.1.2)
  • PFAM:
    DNA_ligase (CL0078) DNA_ligase_aden; NAD-dependent DNA ligase adenylation domain (PF01653; HMM-score: 438.3)
    and 12 more
    OB (CL0021) DNA_ligase_OB; NAD-dependent DNA ligase OB-fold domain (PF03120; HMM-score: 115)
    HHH (CL0198) HHH_2; Helix-hairpin-helix motif (PF12826; HMM-score: 74.4)
    BRCT-like (CL0459) BRCT; BRCA1 C Terminus (BRCT) domain (PF00533; HMM-score: 50.9)
    no clan defined DNA_ligase_ZBD; NAD-dependent DNA ligase C4 zinc finger domain (PF03119; HMM-score: 42.8)
    HHH (CL0198) HHH_5; Helix-hairpin-helix domain (PF14520; HMM-score: 42.6)
    RNA_pol_A_CTD; Bacterial RNA polymerase, alpha chain C terminal domain (PF03118; HMM-score: 22)
    BRCT-like (CL0459) PTCB-BRCT; twin BRCT domain (PF12738; HMM-score: 21.5)
    Zn_Beta_Ribbon (CL0167) zf-NADH-PPase; NADH pyrophosphatase zinc ribbon domain (PF09297; HMM-score: 21.3)
    HHH (CL0198) HHH; Helix-hairpin-helix motif (PF00633; HMM-score: 14.7)
    Glyoxalase (CL0104) Glyoxalase_2; Glyoxalase-like domain (PF12681; HMM-score: 14)
    no clan defined zf-IS66; zinc-finger binding domain of transposase IS66 (PF13005; HMM-score: 12.9)
    zf-tcix; Putative treble-clef, zinc-finger, Zn-binding (PF14952; HMM-score: 11.4)

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

  • domains:
  • modifications:
  • cofactors: Mg2+, Mn2+
  • effectors:

⊟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: 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): 0.003115
    • TAT(Tat/SPI): 0.000545
    • LIPO(Sec/SPII): 0.000491
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MADLSSRVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYKTVDSPTVRVGGEAQASFNKVNHDTPMLSLGNAFNEDDLRKFDQRIREQIGNVEYMCELKIDGLAVSLKYVDGYFVQGLTRGDGTTGEDITENLKTIHAIPLKMKEPLNVEVRGEAYMPRRSFLRLNEEKEKNDEQLFANPRNAAAGSLRQLDSKLTAKRKLSVFIYSVNDFTDFNARSQSEALDELDKLGFTTNKNRARVNNIDGVLEYIEKWTSQRESLPYDIDGIVIKVNDLDQQDEMGFTQKSPRWAIAYKFPAEEVVTKLLDIELSIGRTGVVTPTAILEPVKVAGTTVSRASLHNEDLIHDRDIRIGDSVVVKKAGDIIPEVVRSIPERRPEDAVTYHMPTHCPSCGHELVRIEGEVALRCINPKCQAQLVEGLIHFVSRQAMNIDGLGTKIIQQLYQSELIKDVADIFYLTEEDLLPLDRMGQKKVDNLLAAIQQAKDNSLENLLFGLGIRHLGVKASQVLAEKYETIDRLLTVTEAELVEIHDIGDKVAQSVVTYLENEDIRALIQKLKDKHVNMIYKGIKTSDIEGHPEFSGKTIVLTGKLHQMTRNEASKWLASQGAKVTSSVTKNTDVVIAGEDAGSKLTKAQSLGIEIWTEQQFVDKQNELNS

⊟Experimental data[edit | edit source]

⊟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. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 1.15 1.16 1.17 1.18 1.19 1.20 1.21 1.22 1.23 1.24 1.25 1.26 1.27 1.28 1.29 1.30 1.31 1.32 1.33 1.34 1.35 1.36 1.37 1.38 1.39 1.40 1.41 1.42 1.43 1.44 1.45 1.46 1.47 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)

⊟Relevant publications[edit | edit source]

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