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FunGene: 08-OCT-2024

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus JSNZ
  • locus tag: JSNZ_001936
  • pan locus tag?: SAUPAN004933000
  • symbol: ligA
  • pan gene symbol?: ligA
  • synonym:
  • product: NAD-dependent DNA ligase LigA

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: JSNZ_001936
  • symbol: ligA
  • product: NAD-dependent DNA ligase LigA
  • replicon: chromosome
  • strand: -
  • coordinates: 1950234..1952237
  • length: 2004
  • essential: unknown other strains

⊟Accession numbers[edit | edit source]

  • Gene ID:
  • RefSeq:
  • BioCyc:
  • MicrobesOnline:

⊟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
    AGTTTAGGGAATGCATTTAATGAAGATGATTTGAGAAAATTCGACCAACGCATACGTGAA
    CAAATTGGCAACGTTGAATATATGTGCGAATTAAAAATTGATGGCTTAGCAGTATCATTG
    AAATATGTTGATGGATACTTCGTTCAAGGTTTAACACGTGGTGATGGAACAACAGGTGAA
    GATATTACCGAAAATTTAAAAACAATTCATGCGATACCTTTGAAAATGAAAGAACCATTA
    AATGTAGAAGTTCGTGGTGAAGCATATATGCCGAGACGTTCATTTTTACGATTAAATGAA
    GAAAAAGAAAAAAATGATGAGCAGTTATTTGCAAATCCAAGAAACGCTGCTGCGGGATCA
    TTAAGACAGTTAGATTCTAAATTAACGGCAAAACGAAAGCTAAGCGTATTTATATATAGT
    GTCAATGATTTCACTGATTTCAATGCGCGTTCGCAAAGTGAAGCATTAGATGAGTTAGAT
    AAATTAGGTTTTACAACGAATAAAAATAGAGCGCGTGTAAATAATATCGATGGTGTTTTA
    GAGTATATTGAAAAATGGACAAGCCAAAGAGAGTCATTACCTTATGATATTGATGGGATT
    GTTATTAAGGTTAATGATTTAGATCAACAGGATGAGATGGGATTCACACAAAAATCTCCT
    AGATGGGCCATTGCTTATAAATTTCCAGCTGAGGAAGTAGTAACTAAATTATTAGATATT
    GAATTAAGTATTGGACGAACAGGTGTAGTCACACCTACTGCTATTTTAGAACCAGTAAAA
    GTAGCTGGTACAACTGTATCAAGAGCATCTTTGCACAATGAGGATTTAATTCATGACAGA
    GATATTCGAATTGGTGATAGTGTTGTAGTGAAAAAAGCAGGTGACATCATACCTGAAGTT
    GTACGTAGTATTCCAGAACGTAGACCTGAGGATGCTGTCACATATCATATGCCAACCCAT
    TGTCCAAGTTGTGGACATGAATTAGTACGTATTGAAGGCGAAGTAGCACTTCGTTGCATT
    AATCCAAAATGCCAAGCACAACTTGTTGAAGGATTAATTCACTTTGTATCAAGACAAGCC
    ATGAATATTGATGGTTTAGGCACTAAAATTATTCAACAGCTTTATCAAAGCGAATTAATT
    AAAGATGTTGCTGATATTTTCTATTTAACAGAAGAAGATTTATTACCTTTAGATAGAATG
    GGGCAGAAAAAAGTTGATAATTTATTAGCTGCCATTCAACAAGCTAAGGACAACTCTTTA
    GAAAATTTATTATTTGGTCTAGGTATTAGGCATTTAGGTGTTAAAGCGAGCCAAGTGTTA
    ACAGAAAAATATGAAACGATAGATCGATTACTAACGGTAACTGAAGCGGAATTAGTAGGA
    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: JSNZ_001936
  • symbol: LigA
  • description: NAD-dependent DNA ligase LigA
  • length: 667
  • theoretical pI: 4.94135
  • theoretical MW: 75038.4
  • GRAVY: -0.425187

⊟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: 878.5)
    and 1 more
    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: data available for COL, N315, NCTC8325, Newman, USA300_FPR3757
  • PFAM:
    ATP-grasp (CL0179) DNA_ligase_aden; NAD-dependent DNA ligase adenylation domain (PF01653; HMM-score: 344.4)
    and 13 more
    OB (CL0021) DNA_ligase_OB; NAD-dependent DNA ligase OB-fold domain (PF03120; HMM-score: 116.9)
    HHH (CL0198) HHH_2; Helix-hairpin-helix motif (PF12826; HMM-score: 70.7)
    BRCT-like (CL0459) BRCT; BRCA1 C Terminus (BRCT) domain (PF00533; HMM-score: 61.8)
    no clan defined DNA_ligase_ZBD; NAD-dependent DNA ligase C4 zinc finger domain (PF03119; HMM-score: 47.6)
    HHH (CL0198) HHH_5; Helix-hairpin-helix domain (PF14520; HMM-score: 34.4)
    no clan defined Nlig-Ia; DNA ligase-like, N-terminal NAD+-binding domain (PF22745; HMM-score: 26.5)
    BRCT-like (CL0459) PTCB-BRCT; twin BRCT domain (PF12738; HMM-score: 21.9)
    Zn_Beta_Ribbon (CL0167) Zn_ribbon_NUD; NADH pyrophosphatase zinc ribbon domain (PF09297; HMM-score: 21.6)
    HHH (CL0198) RNA_pol_A_CTD; Bacterial RNA polymerase, alpha chain C terminal domain (PF03118; HMM-score: 20.2)
    ATP-grasp (CL0179) RNA_ligase; RNA ligase (PF09414; HMM-score: 14.7)
    no clan defined zf-IS66; zinc-finger binding domain of transposase IS66 (PF13005; HMM-score: 14.2)
    HHH (CL0198) HHH; Helix-hairpin-helix motif (PF00633; HMM-score: 14.1)
    Zn_Beta_Ribbon (CL0167) DUF7575; Domain of unknown function (DUF7575) (PF24460; HMM-score: 11.1)

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

  • domains:
  • modifications:
  • cofactors:
  • 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
  • DeepLocPro: Cytoplasmic
    • Cytoplasmic Score: 0.999
    • Cytoplasmic Membrane Score: 0.0003
    • Cell wall & surface Score: 0.0001
    • Extracellular Score: 0.0006
  • LocateP:
  • 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]

  • GI:
  • RefSeq:
  • UniProt:

⊟Protein sequence[edit | edit source]

  • MADLSSRVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYKTVDSPTVRVGGEAQASFNKVNHDTPMLSLGNAFNEDDLRKFDQRIREQIGNVEYMCELKIDGLAVSLKYVDGYFVQGLTRGDGTTGEDITENLKTIHAIPLKMKEPLNVEVRGEAYMPRRSFLRLNEEKEKNDEQLFANPRNAAAGSLRQLDSKLTAKRKLSVFIYSVNDFTDFNARSQSEALDELDKLGFTTNKNRARVNNIDGVLEYIEKWTSQRESLPYDIDGIVIKVNDLDQQDEMGFTQKSPRWAIAYKFPAEEVVTKLLDIELSIGRTGVVTPTAILEPVKVAGTTVSRASLHNEDLIHDRDIRIGDSVVVKKAGDIIPEVVRSIPERRPEDAVTYHMPTHCPSCGHELVRIEGEVALRCINPKCQAQLVEGLIHFVSRQAMNIDGLGTKIIQQLYQSELIKDVADIFYLTEEDLLPLDRMGQKKVDNLLAAIQQAKDNSLENLLFGLGIRHLGVKASQVLTEKYETIDRLLTVTEAELVGIHDIGDKVAQSVVTYLENEDIRALIQKLKDKHVNMIYKGIKTSDIEGHPEFSGKTIVLTGKLHQMTRNEASKWLASQGAKVTSSVTKNTDVVIAGEDAGSKLTKAQSLGIEIWTEQQFVDKQNELNS

⊟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: data available for COL
  • 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 can add further information about the gene and protein here. [edit]

⊟Literature[edit | edit source]

⊟References[edit | edit source]

  1. ↑ Blanca Taboada, Karel Estrada, Ricardo Ciria, Enrique Merino
    Operon-mapper: a web server for precise operon identification in bacterial and archaeal genomes.
    Bioinformatics: 2018, 34(23);4118-4120
    [PubMed:29931111] [WorldCat.org] [DOI] (I p)

⊟Relevant publications[edit | edit source]

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