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NCBI: 03-AUG-2016

⊟Summary[edit | edit source]

  • organism: Staphylococcus aureus NCTC8325
  • locus tag: SAOUHSC_02354
  • pan locus tag?: SAUPAN005404000
  • symbol: glyA
  • pan gene symbol?: glyA
  • synonym:
  • product: serine hydroxymethyltransferase

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SAOUHSC_02354
  • symbol: glyA
  • product: serine hydroxymethyltransferase
  • replicon: chromosome
  • strand: -
  • coordinates: 2176314..2177552
  • length: 1239
  • essential: no [1] DEG 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
    ATGTCTTATATCACCAAGCAAGATAAAGTTATCGCAGAAGCAATCGAGAGAGAATTTCAG
    AGACAAAATAGCAACATAGAGTTAATCGCATCGGAAAATTTTGTATCGGAAGCGGTTATG
    GAAGCACAAGGTTCAGTGTTGACTAATAAGTATGCTGAAGGCTATCCAGGACGCCGATAT
    TATGGTGGCTGTGAGTTTGTAGATGTTACTGAAAGCATCGCAATTGATCGTGCTAAAGCA
    TTGTTTGGAGCTGAACATGTCAATGTTCAACCACATTCAGGTTCACAAGCGAACATGGCT
    GTTTACTTAGTTGCATTAGAAATGGGCGACACAGTTTTAGGTATGAATTTGAGTCATGGT
    GGTCACTTGACACATGGAGCGCCTGTTAATTTTAGTGGTAAATTCTACAATTTCGTTGAA
    TATGGAGTAGATAAAGACACAGAACGAATCAATTATGATGAAGTTCGTAAATTAGCGTTA
    GAGCATAAGCCTAAGCTTATTGTGGCAGGAGCATCAGCATATTCAAGAACAATTGACTTC
    AAAAAGTTTAAAGAAATCGCAGATGAAGTAAACGCTAAGTTAATGGTAGACATGGCACAT
    ATTGCAGGATTAGTAGCGGCAGGTTTACATCCAAATCCAGTAGAATATGCTGATTTTGTA
    ACAACTACAACACACAAAACATTACGCGGACCACGTGGTGGTATGATTTTATGTAAGGAA
    GAATATAAAAAAGACATAGATAAAACAATTTTCCCTGGTATTCAAGGTGGACCTCTTGAG
    CATGTTATTGCAGCAAAAGCAGTTGCTTTTGGAGAAGCGTTAGAAAATAATTTCAAAACG
    TATCAACAACAAGTGGTTAAAAACGCAAAAGTTCTTGCAGAAGCATTAATTAATGAAGGA
    TTTAGAATTGTTTCTGGCGGTACAGATAATCACTTAGTAGCTGTTGATGTAAAAGGGTCT
    ATAGGACTTACTGGTAAAGAAGCTGAAGAGACTTTAGATTCAGTTGGTATCACATGTAAC
    AAAAATACCATTCCGTTCGATCAAGAAAAACCTTTTGTAACGAGTGGTATACGTTTAGGT
    ACACCTGCTGCAACAACGCGTGGATTTGATGAAAAAGCTTTTGAGGAAGTTGCAAAAATC
    ATCAGTTTAGCATTGAAAAATAGTAAAGATGAAGAAAAATTACAACAAGCTAAAGAACGC
    GTTGCGAAATTAACAGCTGAATATCCTCTATATCAATAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    1020
    1080
    1140
    1200
    1239

⊟Protein[edit | edit source]

Protein Data Bank: 3PGY

⊟General[edit | edit source]

  • locus tag: SAOUHSC_02354
  • symbol: GlyA
  • description: serine hydroxymethyltransferase
  • length: 412
  • theoretical pI: 5.99288
  • theoretical MW: 45172
  • GRAVY: -0.269417

⊟Function[edit | edit source]

  • reaction:
    EC 2.1.2.1?  ExPASy
    Glycine hydroxymethyltransferase 5,10-methylenetetrahydrofolate + glycine + H2O = tetrahydrofolate + L-serine
  • TIGRFAM:
    Cellular processes Cellular processes Biosynthesis of natural products fluorothreonine transaldolase (TIGR04506; EC 2.2.1.8; HMM-score: 114.6)
    and 7 more
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Biotin 8-amino-7-oxononanoate synthase (TIGR00858; EC 2.3.1.47; HMM-score: 26.8)
    Unknown function Enzymes of unknown specificity cysteine desulfurase family protein (TIGR01977; HMM-score: 22.3)
    Unknown function Enzymes of unknown specificity pyridoxal phosphate enzyme, MJ0158 family (TIGR03576; HMM-score: 20)
    Metabolism Energy metabolism Amino acids and amines glycine C-acetyltransferase (TIGR01822; EC 2.3.1.29; HMM-score: 18.8)
    UDP-4-amino-4,6-dideoxy-N-acetyl-beta-L-altrosamine transaminase (TIGR03588; EC 2.6.1.92; HMM-score: 16.6)
    dTDP-4-dehydro-6-deoxyglucose aminotransferase (TIGR04427; EC 2.-.-.-; HMM-score: 14.1)
    putative methanogenesis marker protein 8 (TIGR03275; HMM-score: 12.8)
  • TheSEED  :
    • Serine hydroxymethyltransferase (EC 2.1.2.1)
    Amino Acids and Derivatives Alanine, serine, and glycine Glycine and Serine Utilization  Serine hydroxymethyltransferase (EC 2.1.2.1)
    and 6 more
    Amino Acids and Derivatives Alanine, serine, and glycine Glycine Biosynthesis  Serine hydroxymethyltransferase (EC 2.1.2.1)
    Amino Acids and Derivatives Alanine, serine, and glycine Glycine cleavage system  Serine hydroxymethyltransferase (EC 2.1.2.1)
    Amino Acids and Derivatives Alanine, serine, and glycine Serine Biosynthesis  Serine hydroxymethyltransferase (EC 2.1.2.1)
    Carbohydrates One-carbon Metabolism Serine-glyoxylate cycle  Serine hydroxymethyltransferase (EC 2.1.2.1)
    Cofactors, Vitamins, Prosthetic Groups, Pigments Folate and pterines Folate Biosynthesis  Serine hydroxymethyltransferase (EC 2.1.2.1)
    Stress Response Stress Response - no subcategory Flavohaemoglobin  Serine hydroxymethyltransferase (EC 2.1.2.1)
  • PFAM:
    PLP_aminotran (CL0061) SHMT; Serine hydroxymethyltransferase (PF00464; HMM-score: 589.1)
    and 5 more
    Beta_elim_lyase; Beta-eliminating lyase (PF01212; HMM-score: 29.9)
    Aminotran_1_2; Aminotransferase class I and II (PF00155; HMM-score: 28)
    DegT_DnrJ_EryC1; DegT/DnrJ/EryC1/StrS aminotransferase family (PF01041; HMM-score: 13.4)
    Aminotran_5; Aminotransferase class-V (PF00266; HMM-score: 13.1)
    Cys_Met_Meta_PP; Cys/Met metabolism PLP-dependent enzyme (PF01053; HMM-score: 11.5)

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

  • domains:
  • modifications:
  • cofactors: pyridoxal 5'-phosphate
  • effectors:

⊟Localization[edit | edit source]

  • PSORTb: Cytoplasmic
    • Cytoplasmic Score: 9.97
    • Cytoplasmic Membrane Score: 0
    • Cellwall Score: 0.01
    • Extracellular Score: 0.02
    • Internal Helices: 0
  • DeepLocPro: Cytoplasmic
    • Cytoplasmic Score: 0.8918
    • Cytoplasmic Membrane Score: 0.0012
    • Cell wall & surface Score: 0.0001
    • Extracellular Score: 0.1069
  • 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): 0.005746
    • TAT(Tat/SPI): 0.001573
    • LIPO(Sec/SPII): 0.000815
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MSYITKQDKVIAEAIEREFQRQNSNIELIASENFVSEAVMEAQGSVLTNKYAEGYPGRRYYGGCEFVDVTESIAIDRAKALFGAEHVNVQPHSGSQANMAVYLVALEMGDTVLGMNLSHGGHLTHGAPVNFSGKFYNFVEYGVDKDTERINYDEVRKLALEHKPKLIVAGASAYSRTIDFKKFKEIADEVNAKLMVDMAHIAGLVAAGLHPNPVEYADFVTTTTHKTLRGPRGGMILCKEEYKKDIDKTIFPGIQGGPLEHVIAAKAVAFGEALENNFKTYQQQVVKNAKVLAEALINEGFRIVSGGTDNHLVAVDVKGSIGLTGKEAEETLDSVGITCNKNTIPFDQEKPFVTSGIRLGTPAATTRGFDEKAFEEVAKIISLALKNSKDEEKLQQAKERVAKLTAEYPLYQ

⊟Experimental data[edit | edit source]

  • experimentally validated: PeptideAtlas [2] [3]
  • protein localization: data available for COL
  • quantitative data / protein copy number per cell: data available for COL
  • interaction partners:
    SAOUHSC_02500(rplE)50S ribosomal protein L5  [4] (data from MRSA252)
    SAOUHSC_02494(rpsE)30S ribosomal protein S5  [4] (data from MRSA252)
    SAOUHSC_02353(upp)uracil phosphoribosyltransferase  [4] (data from MRSA252)
    SAOUHSC_00195acetyl-CoA acetyltransferase  [4] (data from MRSA252)
    SAOUHSC_00530elongation factor Tu  [4] (data from MRSA252)
    SAOUHSC_01040pyruvate dehydrogenase complex, E1 component subunit alpha  [4] (data from MRSA252)

⊟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. ↑ Roy R Chaudhuri, Andrew G Allen, Paul J Owen, Gil Shalom, Karl Stone, Marcus Harrison, Timothy A Burgis, Michael Lockyer, Jorge Garcia-Lara, Simon J Foster, Stephen J Pleasance, Sarah E Peters, Duncan J Maskell, Ian G Charles
    Comprehensive identification of essential Staphylococcus aureus genes using Transposon-Mediated Differential Hybridisation (TMDH).
    BMC Genomics: 2009, 10;291
    [PubMed:19570206] [WorldCat.org] [DOI] (I e)
  2. ↑ Maren Depke, Stephan Michalik, Alexander Rabe, Kristin Surmann, Lars Brinkmann, Nico Jehmlich, Jörg Bernhardt, Michael Hecker, Bernd Wollscheid, Zhi Sun, Robert L Moritz, Uwe Völker, Frank Schmidt
    A peptide resource for the analysis of Staphylococcus aureus in host-pathogen interaction studies.
    Proteomics: 2015, 15(21);3648-61
    [PubMed:26224020] [WorldCat.org] [DOI] (I p)
  3. ↑ Stephan Michalik, Maren Depke, Annette Murr, Manuela Gesell Salazar, Ulrike Kusebauch, Zhi Sun, Tanja C Meyer, Kristin Surmann, Henrike Pförtner, Petra Hildebrandt, Stefan Weiss, Laura Marcela Palma Medina, Melanie Gutjahr, Elke Hammer, Dörte Becher, Thomas Pribyl, Sven Hammerschmidt, Eric W Deutsch, Samuel L Bader, Michael Hecker, Robert L Moritz, Ulrike Mäder, Uwe Völker, Frank Schmidt
    A global Staphylococcus aureus proteome resource applied to the in vivo characterization of host-pathogen interactions.
    Sci Rep: 2017, 7(1);9718
    [PubMed:28887440] [WorldCat.org] [DOI] (I e)
  4. ↑ 4.0 4.1 4.2 4.3 4.4 4.5 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)
  5. ↑ 5.0 5.1 5.2 Ulrike Mäder, Pierre Nicolas, Maren Depke, Jan Pané-Farré, Michel Debarbouille, Magdalena M van der Kooi-Pol, Cyprien Guérin, Sandra Dérozier, Aurelia Hiron, Hanne Jarmer, Aurélie Leduc, Stephan Michalik, Ewoud Reilman, Marc Schaffer, Frank Schmidt, Philippe Bessières, Philippe Noirot, Michael Hecker, Tarek Msadek, Uwe Völker, Jan Maarten van Dijl
    Staphylococcus aureus Transcriptome Architecture: From Laboratory to Infection-Mimicking Conditions.
    PLoS Genet: 2016, 12(4);e1005962
    [PubMed:27035918] [WorldCat.org] [DOI] (I e)

⊟Relevant publications[edit | edit source]

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