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NCBI: 10-JUN-2013

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus COL
  • locus tag: SACOL2488 [new locus tag: SACOL_RS13040 ]
  • pan locus tag?: SAUPAN006056000
  • symbol: SACOL2488
  • pan gene symbol?: —
  • synonym:
  • product: short chain dehydrogenase/reductase oxidoreductase

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SACOL2488 [new locus tag: SACOL_RS13040 ]
  • symbol: SACOL2488
  • product: short chain dehydrogenase/reductase oxidoreductase
  • replicon: chromosome
  • strand: -
  • coordinates: 2543619..2544314
  • length: 696
  • 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
    ATGACAGTATTAACAGATAAAGTAGCAGTAGTTACAGGTGCAGGTAGTGGTATTGGAGAA
    GCAATTGCAACATTACTACATGAAGAAGGGGCAAAAGTTGTCTTAGCAGGTAGAAATAAA
    GAAAAATTACAAAACGTAGCGAATCAATTGTCACAAGATAGTGTGAAGGTAGTGCCAACA
    GATGTAACGAATAAAGAAGAAGTCGATGAATTGATAAAAATTGCACAACAAACATTCGGT
    GGTTTGGATATTGTTATCAATAGTGCGGGGCAAATGTTGTCGTCTAAGATTACTGATTAT
    CAAGTAGATGAGTGGGATAGTATGATTGATGTGAATATCAAAGGCACTTTATATACGGCA
    CAGGCTGCATTACCAACTATGTTAGAACAATCAAGTGGCCATCTTATTAACATTGCATCT
    ATTTCTGGCTTTGAAGTAACGAAAAGTAGTACGATTTATAGTGCGACGAAAGCAGCAGTT
    CACACTATTACTCAAGGATTAGAAAAAGAGTTGGCAAAGACAGGCGTTAAAGTAACAAGC
    ATTTCTCCAGGAATGGTAGATACAGCCATAACTGCCGCATACAATCCAACAGATCGTAAA
    AAACTTGAACCACAAGATATTGCAGAAGCAGTATTATATGCATTAACACAACCAAAGCAC
    GTTAACGTGAATGAAATTACAGTGCGTCCTGTATAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    696

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SACOL2488 [new locus tag: SACOL_RS13040 ]
  • symbol: SACOL2488
  • description: short chain dehydrogenase/reductase oxidoreductase
  • length: 231
  • theoretical pI: 4.91397
  • theoretical MW: 24603.9
  • GRAVY: -0.0290043

⊟Function[edit | edit source]

  • reaction:
    EC 1.-.-.-?  ExPASy
  • ⊞TIGRFAM:
    3-hydroxybutyrate dehydrogenase (TIGR01963; HMM-score: 155.3)
    Metabolism Energy metabolism Fermentation acetoin reductases (TIGR02415; EC 1.1.1.-; HMM-score: 149.3)
    Metabolism Fatty acid and phospholipid metabolism Biosynthesis 3-oxoacyl-[acyl-carrier-protein] reductase (TIGR01830; EC 1.1.1.100; HMM-score: 147.8)
    acetoacetyl-CoA reductase (TIGR01829; EC 1.1.1.36; HMM-score: 126.4)
    Unknown function Enzymes of unknown specificity SDR family mycofactocin-dependent oxidoreductase (TIGR03971; EC 1.1.99.-; HMM-score: 125.5)
    rhamnulose-1-phosphate aldolase/alcohol dehydrogenase (TIGR02632; EC 1.1.1.1,4.1.2.19; HMM-score: 124.7)
    and 18 more
    2,3-dihydro-2,3-dihydroxybenzoate dehydrogenase (TIGR04316; EC 1.3.1.28; HMM-score: 123.5)
    2-hydroxycyclohexanecarboxyl-CoA dehydrogenase (TIGR03206; EC 1.1.1.-; HMM-score: 119.2)
    Metabolism Energy metabolism Biosynthesis and degradation of polysaccharides 2-deoxy-D-gluconate 3-dehydrogenase (TIGR01832; EC 1.1.1.125; HMM-score: 117)
    Unknown function Enzymes of unknown specificity SDR family mycofactocin-dependent oxidoreductase (TIGR04504; EC 1.1.99.-; HMM-score: 114.8)
    cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase (TIGR03325; EC 1.3.1.56; HMM-score: 83.7)
    Metabolism Fatty acid and phospholipid metabolism Biosynthesis putative 3-oxoacyl-(acyl-carrier-protein) reductase (TIGR01831; HMM-score: 80)
    sepiapterin reductase (TIGR01500; EC 1.1.1.153; HMM-score: 58.3)
    pteridine reductase (TIGR02685; EC 1.5.1.33; HMM-score: 46.3)
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Chlorophyll and bacteriochlorphyll light-dependent protochlorophyllide reductase (TIGR01289; EC 1.3.1.33; HMM-score: 34.9)
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Heme, porphyrin, and cobalamin glutamyl-tRNA reductase (TIGR01035; EC 1.2.1.70; HMM-score: 21)
    Hypothetical proteins Conserved TIGR01777 family protein (TIGR01777; HMM-score: 20)
    Metabolism Amino acid biosynthesis Aromatic amino acid family shikimate dehydrogenase (TIGR00507; EC 1.1.1.25; HMM-score: 19.9)
    hopanoid-associated sugar epimerase (TIGR03466; HMM-score: 17.1)
    Genetic information processing Mobile and extrachromosomal element functions Plasmid functions integrating conjugative element protein PilL, PFGI-1 class (TIGR03748; HMM-score: 16.4)
    Unknown function Enzymes of unknown specificity putative NAD(P)H quinone oxidoreductase, PIG3 family (TIGR02824; HMM-score: 15.8)
    Cell structure Cell envelope Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides dTDP-glucose 4,6-dehydratase (TIGR01181; EC 4.2.1.46; HMM-score: 11.3)
    Genetic information processing Protein synthesis Ribosomal proteins: synthesis and modification ribosomal protein uS11 (TIGR03632; HMM-score: 11.1)
    Metabolism Fatty acid and phospholipid metabolism Biosynthesis hopanoid C-3 methylase HpnR (TIGR04367; HMM-score: 10.8)
  • TheSEED  :
    • Oxidoreductase, short-chain dehydrogenase/reductase family
  • ⊞PFAM:
    NADP_Rossmann (CL0063) adh_short; short chain dehydrogenase (PF00106; HMM-score: 196.2)
    adh_short_C2; Enoyl-(Acyl carrier protein) reductase (PF13561; HMM-score: 159.8)
    and 25 more
    KR; KR domain (PF08659; HMM-score: 62.7)
    NAD_binding_10; NAD(P)H-binding (PF13460; HMM-score: 41.6)
    Sacchrp_dh_NADP; Saccharopine dehydrogenase NADP binding domain (PF03435; HMM-score: 38.1)
    Epimerase; NAD dependent epimerase/dehydratase family (PF01370; HMM-score: 35.1)
    Shikimate_DH; Shikimate / quinate 5-dehydrogenase (PF01488; HMM-score: 26.4)
    3HCDH_N; 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain (PF02737; HMM-score: 24.6)
    Polysacc_synt_2; Polysaccharide biosynthesis protein (PF02719; HMM-score: 24)
    SDR; SDR-like rossmann domain (PF23441; HMM-score: 23.4)
    F420_oxidored; NADP oxidoreductase coenzyme F420-dependent (PF03807; HMM-score: 21.4)
    GDP_Man_Dehyd; GDP-mannose 4,6 dehydratase (PF16363; HMM-score: 19.7)
    ApbA; Ketopantoate reductase PanE/ApbA (PF02558; HMM-score: 19.5)
    NAD_Gly3P_dh_N; NAD-dependent glycerol-3-phosphate dehydrogenase N-terminus (PF01210; HMM-score: 18.8)
    NmrA; NmrA-like family (PF05368; HMM-score: 17.8)
    S11_L18p (CL0267) Ribosomal_S11; Ribosomal protein S11 (PF00411; HMM-score: 17.4)
    no clan defined Arg_tRNA_synt_N; Arginyl tRNA synthetase N terminal domain (PF03485; HMM-score: 16.5)
    NADP_Rossmann (CL0063) ADH_zinc_N; Zinc-binding dehydrogenase (PF00107; HMM-score: 15.8)
    no clan defined Asp23; Asp23 family, cell envelope-related function (PF03780; HMM-score: 15)
    NADP_Rossmann (CL0063) THF_DHG_CYH_C; Tetrahydrofolate dehydrogenase/cyclohydrolase, NAD(P)-binding domain (PF02882; HMM-score: 14.8)
    TrkA_N; TrkA-N domain (PF02254; HMM-score: 14.1)
    RNase_H (CL0219) DDE_Tnp_1_3; Transposase DDE domain (PF13612; HMM-score: 13.9)
    NADP_Rossmann (CL0063) KARI_N; Acetohydroxy acid isomeroreductase, NADPH-binding domain (PF07991; HMM-score: 12.9)
    DUF1776; Fungal family of unknown function (DUF1776) (PF08643; HMM-score: 12.9)
    P-loop_NTPase (CL0023) Helicase_RecD; Helicase (PF05127; HMM-score: 12.7)
    NADP_Rossmann (CL0063) YjeF_N; YjeF-related protein N-terminus (PF03853; HMM-score: 11.7)
    no clan defined Nitro_FeMo-Co; Dinitrogenase iron-molybdenum cofactor (PF02579; HMM-score: 11.5)

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

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

⊟Localization[edit | edit source]

  • ⊞PSORTb: Cytoplasmic
    • Cytoplasmic Score: 9.67
    • Cytoplasmic Membrane Score: 0.01
    • Cellwall Score: 0.15
    • Extracellular Score: 0.17
    • Internal Helices: 0
  • ⊞DeepLocPro: Cytoplasmic
    • Cytoplasmic Score: 0.9289
    • Cytoplasmic Membrane Score: 0.0423
    • Cell wall & surface Score: 0.0053
    • Extracellular Score: 0.0235
  • ⊞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): 0.009386
    • TAT(Tat/SPI): 0.001928
    • LIPO(Sec/SPII): 0.00181
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MTVLTDKVAVVTGAGSGIGEAIATLLHEEGAKVVLAGRNKEKLQNVANQLSQDSVKVVPTDVTNKEEVDELIKIAQQTFGGLDIVINSAGQMLSSKITDYQVDEWDSMIDVNIKGTLYTAQAALPTMLEQSSGHLINIASISGFEVTKSSTIYSATKAAVHTITQGLEKELAKTGVKVTSISPGMVDTAITAAYNPTDRKKLEPQDIAEAVLYALTQPKHVNVNEITVRPV

⊟Experimental data[edit | edit source]

  • experimentally validated: PeptideAtlas
  • protein localization: Cytoplasmic [1] [2] [3]
  • quantitative data / protein copy number per cell: 932 [4]
  • 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: 32.05 h [5]

⊞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. ↑ Dörte Becher, Kristina Hempel, Susanne Sievers, Daniela Zühlke, Jan Pané-Farré, Andreas Otto, Stephan Fuchs, Dirk Albrecht, Jörg Bernhardt, Susanne Engelmann, Uwe Völker, Jan Maarten van Dijl, Michael Hecker
    A proteomic view of an important human pathogen--towards the quantification of the entire Staphylococcus aureus proteome.
    PLoS One: 2009, 4(12);e8176
    [PubMed:19997597] [WorldCat.org] [DOI] (I e)
  2. ↑ Kristina Hempel, Florian-Alexander Herbst, Martin Moche, Michael Hecker, Dörte Becher
    Quantitative proteomic view on secreted, cell surface-associated, and cytoplasmic proteins of the methicillin-resistant human pathogen Staphylococcus aureus under iron-limited conditions.
    J Proteome Res: 2011, 10(4);1657-66
    [PubMed:21323324] [WorldCat.org] [DOI] (I p)
  3. ↑ Andreas Otto, Jan Maarten van Dijl, Michael Hecker, Dörte Becher
    The Staphylococcus aureus proteome.
    Int J Med Microbiol: 2014, 304(2);110-20
    [PubMed:24439828] [WorldCat.org] [DOI] (I p)
  4. ↑ Daniela Zühlke, Kirsten Dörries, Jörg Bernhardt, Sandra Maaß, Jan Muntel, Volkmar Liebscher, Jan Pané-Farré, Katharina Riedel, Michael Lalk, Uwe Völker, Susanne Engelmann, Dörte Becher, Stephan Fuchs, Michael Hecker
    Costs of life - Dynamics of the protein inventory of Staphylococcus aureus during anaerobiosis.
    Sci Rep: 2016, 6;28172
    [PubMed:27344979] [WorldCat.org] [DOI] (I e)
  5. ↑ Stephan Michalik, Jörg Bernhardt, Andreas Otto, Martin Moche, Dörte Becher, Hanna Meyer, Michael Lalk, Claudia Schurmann, Rabea Schlüter, Holger Kock, Ulf Gerth, Michael Hecker
    Life and death of proteins: a case study of glucose-starved Staphylococcus aureus.
    Mol Cell Proteomics: 2012, 11(9);558-70
    [PubMed:22556279] [WorldCat.org] [DOI] (I p)

⊟Relevant publications[edit | edit source]

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