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FunGene: 08-OCT-2024

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus JSNZ
  • locus tag: JSNZ_000520
  • pan locus tag?: SAUPAN002336000
  • symbol: sdrD
  • pan gene symbol?: sdrD
  • synonym:
  • product: MSCRAMM family adhesin SdrD

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: JSNZ_000520
  • symbol: sdrD
  • product: MSCRAMM family adhesin SdrD
  • replicon: chromosome
  • strand: +
  • coordinates: 556500..560717
  • length: 4218
  • 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
    2041
    2101
    2161
    2221
    2281
    2341
    2401
    2461
    2521
    2581
    2641
    2701
    2761
    2821
    2881
    2941
    3001
    3061
    3121
    3181
    3241
    3301
    3361
    3421
    3481
    3541
    3601
    3661
    3721
    3781
    3841
    3901
    3961
    4021
    4081
    4141
    4201
    ATGCTAAACAGAGAAAATAAAACGGCAATAACAAGAAAAGGCATGGTATCCAATCGATTA
    AATAAATTTTCGATTAGAAAGTACACAGTGGGAACAGCATCAATTTTAGTAGGTACAACA
    TTAATTTTTGGTCTGGGGAACCAAGAAGCAAAGGCTGCAGAAAGTACTAATAAAGAATTG
    AACGAAGCGACAACTTCAGCAAGTGATAATCAATCGAGTGATAAAGTTGATATGCAGCAA
    CTAAATCAAGAAGACAATACTAAAAATGATAATCAAAAAGAAATGGTATCATCTCAAGGT
    AATGAAACGACTTCAAATGGGAATAAATTAATAGAAAAAGAAAGTGTACAATCTACCACT
    GGAAATAAAGTTGAAGTTTCAACTGCCAAATCAGATGAGCAAGCTTCACCAAAATCTACG
    AATGAAGATTTAAACACTAAACAAACTATAAGTAATCAAGAAGCGTTACAACCTGATTTG
    CAAGAGAATAAATCAGTGGTAAATGTTCAACCAACTAATGAGGAAAACAAAAAGGTAGAT
    GCGAAAACTGAATCAACTACATTAAATGTTAAAAGTGATGCTATCAAGAGTAATGCTGAA
    AATCTTGTTGATAACAATAGTAACTCAAATAATGAAAATAATGCAGATATCATTTTGCCA
    AAAAGTACAGCACCTAAACGTTTGAATACAAGAATGCGTATGGCAGCAATACAACCAAAC
    TCAACAGATTCTAAAAATGTTAATAATTTAATTACTTCAACTACAACTTTAACTGTAGTC
    GATGCAGATAAAAACAATAAAATCGTACCAGCACAAGATTATCTAACATTAAAATCACAA
    ATTAAAGTTGATGACAAAGTTAAATCAGGTGATTATTTCACAATAAAATACTCAGATACA
    GTACAAGTATATGGATTGAATCCGGAAGATATTAAAAATATTGGAGATATTAAAGATCCA
    AATAATGGTGAAACAATTGCGACTGCAAAACATGATACTGCAAATAATTTAATTACATAT
    ACATTTACAGATTATGTAGATAGATTTAATTCTGTACAAATGGGAATTAATTATTCAATT
    TATATGGATGCTGATACAATTCCTGTTAGTAAAAACGATGTTGAGTTTAATGTTACGATA
    GGTAATACTACAACAAAAACAACTGCTAACATTCAATATCCAGATTATGTTTCTAGAGAT
    AATAATTCTATAGGTTCAGCATTTACTGAAACTGTTTCACATGCAGGTAATGCAGAAGAC
    CCGGGTTACTATATACAGACTGTTTATGTAAATCCATCGGAAAAAACTTTAACAAATGCT
    AAATTAAAAGTTGAAGCTTATCATAAGGATTATCCTGACAATGTAGGTCAAATAAATAAA
    AATGTAACTAAAATTAAAATTTATCAAGCACCAAAAGACTATGTTTTAAACAAAGGTTAT
    GATGTTAATACAAATCAACTTATAGATGTGACTGAACAATTTAAAGATAAGATTACATAC
    GGAACTAATGACAGTGTAAATGTTGATTTTGGTAGCATTAACAATTCTTATGTAGTTATG
    GTGGATACAAAATTTGAATTTACAACTAGTGAAAGTCCAACACTTGTTCAAATGGCAACT
    TTGACTTCTGATGGAAACAGATCCGTTTCTACTGGCAATGCTTTAGGATTTACTAATAAC
    CAAAGTGGCGGAGCTGGTCAAGAAGTATATAAAATTGGTAACTACGTATGGGAAGATACT
    AATAAAAACGGTGTTCAAGAATTAGGAGAAAAAGGCGTTGGCAATGTAACTGTAACTGTA
    TTTGATAATAATACAAATACAAAAGTAGGAGAAGCAGTTACTAAAGAAGATGGGTCATAC
    TTGATTCCAAACTTACCTAATGGAGATTACCGTGTAGAATTTTCAAACTTACCAAAAGGT
    TATGAAGTAACCCCTTCAAAACAAGGTAATAACGAAGAATTAGATTCAAACGGCTTATCT
    TCAGTTATTACAGTTAATGGCAAAGATAACTTATCTGCAGACTTAGGTATTTACAAACCT
    AAATACAACTTAGGTGACTATGTCTGGGAAGATACAAATAAAAATGGTATCCAAGACCAA
    GATGAAAAAGGTATATCTGGCGTAACGGTAACATTAAAAGATGAAAACGGTAACGTGTTA
    AAAACAGTTACAACAGACGCAGATGGCAAATATAAATTTACTGATTTAGATAATGGTAAT
    TATAAAGTTGAATTTACTACACCAGAAGGCTATACACCGACTACAGTAACATCTGGTAGC
    GACATTGAAAAAGACTCTAATGGTTTAACAACAACAGGTGTTATTAATGGTGCTGATAAC
    ATGACATTAGATAGTGGATTCTACAAAACACCAAAATATAATTTAGGTAATTATGTATGG
    GAAGATACAAATAAAGATGGTAAGCAGGATTCAACTGAAAAAGGTATTTCAGGCGTAACA
    GTTACATTGAAAAATGAAAACGGTGAAGTTTTACAAACAACTAAAACAGATAAAGATGGT
    AAATATCAATTTACTGGATTAGAAAATGGAACTTATAAAGTTGAATTCGAAACACCATCA
    GGTTACACACCAACACAAGTAGGTTCAGGAACTGATGAAGGTATAGATTCAAATGGTACA
    TCAACAACAGGTGTCATTAAAGATAAAGATAACGATACTATTGACTCTGGTTTCTACAAA
    CCGACTTACAACTTAGGTGACTATGTATGGGAAGATACAAATAAAAACGGTGTTCAAGAT
    AAAGATGAAAAGGGTATTTCAGGTGTAACAGTTACGTTAAAAGATGAAAACGACAAAGTT
    TTAAAAACAGTTACAACAGATGAAAATGGTAAATATCAATTCACTGATTTAAACAATGGA
    ACTTATAAAGTTGAATTCGAGACACCATCAGGTTATACACCAACTTCAGTAACTTCTGGA
    AATGATACTGAAAAAGATTCTAATGGTTTAACAACAACAGGTGTCATTAAAGATGCAGAT
    AACATGACATTAGACAGTGGTTTCTATAAAACACCAAAATATAGTTTAGGTGATTATGTT
    TGGTACGACAGTAATAAAGACGGCAAACAAGATTCAACTGAAAAAGGTATCAAAGATGTT
    AAAGTTACTTTATTAAATGAAAAAGGCGAAGTAATTGGAACAACTAAAACAGATGAAAAT
    GGTAAATATCGTTTCGATAATTTAGATAGCGGTAAATACAAAGTTATTTTTGAAAAGCCT
    GCTGGCTTAACACAAACAGGTACAAATACAACTGAAGATGATAAAGATGCAGATGGTGGC
    GAAGTTGACGTAACAATTACGGATCATGATGATTTCACACTTGATAACGGATACTTCGAA
    GAAGATACATCAGATAGCGACTCAGATTCAGATAGCGATTCAGATTCAGATAGCGACTCA
    GACTCAGACAGCGACTCAGATTCAGACAGCGACTCAGACTCGGATAGCGATTCAGATTCA
    GACAGTGATTCAGATTCAGACAGCGATTCGGATTCAGACAGCGACTCAGACTCGGATAGC
    GACTCAGACTCAGATAGCGACTCAGATTCGGATAGCGACTCAGACTCAGACAGCGACTCA
    GATTCAGACAGCGACTCAGACACAGATAGCGACTCAGACTCAGACAGCGACTCAGACAGT
    GATTCAGACTCAGATAGCGACTCAGACTCAGACAGCGACTCAGACTCAGATAGTGACTCA
    GATTCAGATAGTGACTCAGACTCAGACAGTGATTCAGACTCAGACAGTGATTCAGACTCA
    GATAGCGACTCAGACTCAGACAGCGACTCAGACTCAGATAGTGACTCAGATTCAGATAGC
    GATTCGGACTCAGACAGTGATTCAGATTCGGACAGCGACTCAGACTCAGACAGTGATTCA
    GATTCAGATAGCGACTCAGACTCAGATAGCGACTCAGATTCAGACAGCGATTCAGACTCA
    GATAGTGACTCAGATTCGGACAGCGATTCAGACTCAGATAGCGACTCAGATTCAGACAGT
    GATTCAGACTCAGATGCAGGTAAGCACACACCTGTTAAACCAATGAGTACTACTAAAGAC
    CATCACAATAAAGCAAAAGCATTACCAGAAACAGGTAATGAAAATAGCGGCTCAAATAAC
    GCAACGTTATTTGGCGGATTATTCGCAGCATTAGGATCATTATTGTTATTCGGTCGTCGT
    AAAAAACAAAATAAATAA
    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
    2040
    2100
    2160
    2220
    2280
    2340
    2400
    2460
    2520
    2580
    2640
    2700
    2760
    2820
    2880
    2940
    3000
    3060
    3120
    3180
    3240
    3300
    3360
    3420
    3480
    3540
    3600
    3660
    3720
    3780
    3840
    3900
    3960
    4020
    4080
    4140
    4200
    4218

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: JSNZ_000520
  • symbol: SdrD
  • description: MSCRAMM family adhesin SdrD
  • length: 1405
  • theoretical pI: 3.87841
  • theoretical MW: 151943
  • GRAVY: -1.06256

⊟Function[edit | edit source]

  • TIGRFAM:
    gram-positive signal peptide, YSIRK family (TIGR01168; HMM-score: 48.9)
    and 3 more
    Cell structure Cell envelope Other LPXTG cell wall anchor domain (TIGR01167; HMM-score: 18.6)
    Metabolism Energy metabolism Other protocatechuate 3,4-dioxygenase, beta subunit (TIGR02422; EC 1.13.11.3; HMM-score: 18.5)
    Por secretion system C-terminal sorting domain (TIGR04183; HMM-score: 10.4)
  • TheSEED: data available for COL, N315, NCTC8325, Newman, USA300_FPR3757
  • PFAM:
    Transthyretin (CL0287) SdrD_B; SdrD B-like domain (PF17210; HMM-score: 495)
    and 28 more
    CarboxypepD_reg; Carboxypeptidase regulatory-like domain (PF13620; HMM-score: 177.9)
    SpaA; Prealbumin-like fold domain (PF17802; HMM-score: 110.5)
    Adhesin (CL0204) SdrG_C_C; C-terminus of bacterial fibrinogen-binding adhesin (PF10425; HMM-score: 102.6)
    E-set (CL0159) bMG3; Bacterial alpha-2-macroglobulin MG3 domain (PF11974; HMM-score: 87.2)
    Big_8; Bacterial Ig domain (PF17961; HMM-score: 87.2)
    Transthyretin (CL0287) CarbopepD_reg_2; CarboxypepD_reg-like domain (PF13715; HMM-score: 68.8)
    Ig_DR_A0283-like; DR_A0283-like, Ig-like domain (PF24025; HMM-score: 61.8)
    EMC7_beta-sandw; ER membrane protein complex subunit 7, beta-sandwich domain (PF09430; HMM-score: 60.4)
    MetallophosN; N terminal of Calcineurin-like phosphoesterase (PF16371; HMM-score: 54.8)
    NOMO1-like_9th; BOS complex subunit NOMO1-like, beta sandwich domain (PF22902; HMM-score: 53)
    no clan defined YSIRK_signal; YSIRK type signal peptide (PF04650; HMM-score: 46)
    Transthyretin (CL0287) NOMO1-like_1st; BOS complex subunit NOMO1-like, first beta sandwich domain (PF22898; HMM-score: 39.2)
    no clan defined Gram_pos_anchor; LPXTG cell wall anchor motif (PF00746; HMM-score: 37.2)
    E-set (CL0159) Ig_J; Tip attachment protein J, Ig-like domain (PF24421; HMM-score: 37.1)
    Transthyretin (CL0287) DUF1416; Protein of unknown function (DUF1416) (PF07210; HMM-score: 35.5)
    E-set (CL0159) Big_6; Bacterial Ig domain (PF17936; HMM-score: 34.4)
    Transthyretin (CL0287) TTR-52; Transthyretin-like family (PF01060; HMM-score: 30.6)
    GOLD-like (CL0521) EMP24_GP25L; emp24/gp25L/p24 family/GOLD (PF01105; HMM-score: 29.8)
    Transthyretin (CL0287) NOMO_3rd; NOMO third transthyretin-like domain (PF23193; HMM-score: 25.6)
    Dioxygenase_C; Dioxygenase (PF00775; HMM-score: 25.3)
    NOMO1-like_2nd; BOS complex subunit NOMO1-like, second beta sandwich domain (PF22904; HMM-score: 24.3)
    E-set (CL0159) MG4; Macroglobulin domain MG4 (PF17789; HMM-score: 20.5)
    Transthyretin (CL0287) NOMO_5th; NOMO fifth transthyretin-like domain (PF23194; HMM-score: 19.9)
    fn3_3; Polysaccharide lyase family 4, domain II (PF14686; HMM-score: 18.5)
    SH3 (CL0010) DUF4926; Domain of unknown function (DUF4926) (PF16277; HMM-score: 16.5)
    E-set (CL0159) Y_Y_Y; Y_Y_Y domain (PF07495; HMM-score: 16.2)
    no clan defined ArgL-like; ArgL-like (PF22864; HMM-score: 14.5)
    bBprotInhib (CL0354) Inh; Protease inhibitor Inh (PF02974; HMM-score: 12.4)

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

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

⊟Localization[edit | edit source]

  • PSORTb: Cellwall
    • Cytoplasmic Score: 0
    • Cytoplasmic Membrane Score: 0
    • Cellwall Score: 10
    • Extracellular Score: 0
    • Internal Helix: 1
  • DeepLocPro: Cell wall & surface
    • Cytoplasmic Score: 0
    • Cytoplasmic Membrane Score: 0.0006
    • Cell wall & surface Score: 0.905
    • Extracellular Score: 0.0944
  • LocateP:
  • SignalP: Signal peptide SP(Sec/SPI) length 52 aa
    • SP(Sec/SPI): 0.812615
    • TAT(Tat/SPI): 0.093189
    • LIPO(Sec/SPII): 0.002787
    • Cleavage Site: CS pos: 52-53. AKA-AE. Pr: 0.8678
  • predicted transmembrane helices (TMHMM): 1

⊟Accession numbers[edit | edit source]

  • GI:
  • RefSeq:
  • UniProt:

⊟Protein sequence[edit | edit source]

  • MLNRENKTAITRKGMVSNRLNKFSIRKYTVGTASILVGTTLIFGLGNQEAKAAESTNKELNEATTSASDNQSSDKVDMQQLNQEDNTKNDNQKEMVSSQGNETTSNGNKLIEKESVQSTTGNKVEVSTAKSDEQASPKSTNEDLNTKQTISNQEALQPDLQENKSVVNVQPTNEENKKVDAKTESTTLNVKSDAIKSNAENLVDNNSNSNNENNADIILPKSTAPKRLNTRMRMAAIQPNSTDSKNVNNLITSTTTLTVVDADKNNKIVPAQDYLTLKSQIKVDDKVKSGDYFTIKYSDTVQVYGLNPEDIKNIGDIKDPNNGETIATAKHDTANNLITYTFTDYVDRFNSVQMGINYSIYMDADTIPVSKNDVEFNVTIGNTTTKTTANIQYPDYVSRDNNSIGSAFTETVSHAGNAEDPGYYIQTVYVNPSEKTLTNAKLKVEAYHKDYPDNVGQINKNVTKIKIYQAPKDYVLNKGYDVNTNQLIDVTEQFKDKITYGTNDSVNVDFGSINNSYVVMVDTKFEFTTSESPTLVQMATLTSDGNRSVSTGNALGFTNNQSGGAGQEVYKIGNYVWEDTNKNGVQELGEKGVGNVTVTVFDNNTNTKVGEAVTKEDGSYLIPNLPNGDYRVEFSNLPKGYEVTPSKQGNNEELDSNGLSSVITVNGKDNLSADLGIYKPKYNLGDYVWEDTNKNGIQDQDEKGISGVTVTLKDENGNVLKTVTTDADGKYKFTDLDNGNYKVEFTTPEGYTPTTVTSGSDIEKDSNGLTTTGVINGADNMTLDSGFYKTPKYNLGNYVWEDTNKDGKQDSTEKGISGVTVTLKNENGEVLQTTKTDKDGKYQFTGLENGTYKVEFETPSGYTPTQVGSGTDEGIDSNGTSTTGVIKDKDNDTIDSGFYKPTYNLGDYVWEDTNKNGVQDKDEKGISGVTVTLKDENDKVLKTVTTDENGKYQFTDLNNGTYKVEFETPSGYTPTSVTSGNDTEKDSNGLTTTGVIKDADNMTLDSGFYKTPKYSLGDYVWYDSNKDGKQDSTEKGIKDVKVTLLNEKGEVIGTTKTDENGKYRFDNLDSGKYKVIFEKPAGLTQTGTNTTEDDKDADGGEVDVTITDHDDFTLDNGYFEEDTSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDTDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDSDAGKHTPVKPMSTTKDHHNKAKALPETGNENSGSNNATLFGGLFAALGSLLLFGRRKKQNK

⊟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 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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