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PangenomeTIGR4
serotype 4
D39
serotype 2
D39V
serotype 2
Hungary19A-6
serotype 19A
EF3030
serotype 19F
670-6B
serotype 6B
6A-10
serotype 6A
70585
serotype 5
A026
serotype 19F
A66
serotype 3
AP200
serotype 11A
ASP0581
serotype 12F
ATCC 49619
serotype 19F
ATCC 700669
serotype 23F
BVJ1JL
serotype 1
CGSP14
serotype 14
G54
serotype 19F
HU-OH
serotype 3
Hu15
serotype 19A
Hu17
serotype 19A
INV104
serotype 1
INV200
serotype 14
JJA
serotype 14
MDRSPN001
serotype 19F
NCTC7466
serotype 2
NU83127
serotype 4
OXC141
serotype 3
P1031
serotype 1
R6
serotype 2
SP49
serotype 19A
SPN032672
serotype 1
SPN034156
serotype 3
SPN034183
serotype 3
SPN994038
serotype 3
SPN994039
serotype 3
SPNA45
serotype 3
ST556
serotype 19F
TCH8431/19A
serotype 19A
Taiwan19F-14
serotype 19F
Xen35
serotype 4
gamPNI0373
serotype 1

NCBI: 02-MAY-2018

⊟Summary[edit | edit source]

  • organism: Streptococcus pneumoniae D39
  • locus tag: SPD_1309 [new locus tag: SPD_RS06975 ]
  • pan locus tag?: PNEUPAN002806000
  • symbol: pgdA
  • pan gene symbol?: pgdA
  • synonym:
  • product: peptidoglycan GlcNAc deacetylase

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SPD_1309 [new locus tag: SPD_RS06975 ]
  • symbol: pgdA
  • product: peptidoglycan GlcNAc deacetylase
  • replicon: chromosome
  • strand: -
  • coordinates: 1327262..1328704
  • length: 1443
  • essential: unknown

⊟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
    TTGCCAAATTGTATCATTGAAATTATTGCTCAAATTTGTTATGATATAAATATGAATAAA
    AGTAGACTAGGACGTGGCAGACACGGGAAAACGAGACATGTATTATTGGCTTTGATTGGT
    ATTTTAGCAATTTCTATTTGCCTATTAGGCGGATTTATTGCTTTTAAGATCTACCAGCAA
    AAAAGTTTTGAGCAAAAGATTGAATCGCTCAAAAAAGAGAAAGATGATCAATTGAGTGAG
    GGAAATCAGAAGGAGCATTTTCGTCAGGGGCAAGCCGAAGTGATTGCCTATTATCCTCTC
    CAAGGGGAGAAAGTGATTTCCTCTGTTAGGGAGCTGATAAATCAAGATGTTAAGGACAAG
    CTAGAAAGTAAGGACAATCTTGTTTTCTACTATACAGAGCAAGAAGAGTCAGGTTTAAAG
    GGAGTCGTTAATCGTAATGTGACCAAACAAATCTATGATTTAGTTGCTTTTAAGATTGAA
    GAGACTGAAAAGACCAGTCTAGGAAAGGTTCACTTAACAGAAGATGGGCAACCTTTTACA
    CTTGACCAACTGTTTTCAGATGCTAGTAAGGCTAAGGAACAGCTGATAAAAGAGTTGACC
    TCCTTCATAGAGGATAAAAAAATAGAGCAAGACCAGAGTGAGCAGATTGTAAAAAACTTC
    TCTGACCAAGACTTGTCTGCATGGAATTTTGATTACAAGGATAGTCAGATTATCCTTTAT
    CCAAGTCCTGTGGTTGAAAATTTAGAAGAGATAGCCTTGCCAGTATCTGCTTTCTTTGAT
    GTTATCCAATCTTCGTACTTACTCGAAAAAGATGCGGCCTTGTACCAATCTTACTTTGAT
    AAGAAACATCAAAAAGTTGTCGCTCTAACCTTTGATGATGGTCCAAATCCAGCAACGACC
    CCGCAGGTATTAGAGACCCTAGCTAAATATGATATTAAAGCGACTTTCTTTGTGCTTGGG
    AAAAATGTTTCTGGGAATGAGGACTTGGTGAAGAGGATAAAATCTGAAGGTCATGTTGTT
    GGAAACCATAGCTGGAGCCATCCGATTCTCTCGCAACTCTCTCTTGATGAAGCTAAAAAG
    CAGATTACTGATACTGAGGATGTGCTAACTAAAGTGCTGGGTTCTAGTTCTAAACTCATG
    CGTCCACCTTATGGTGCTATTACAGATGATATTCGCAATAGCTTGGATTTGAGCTTTATC
    ATGTGGGATGTGGATAGTCTGGACTGGAAGAGTAAAAATGAAGCATCTATTTTGACAGAA
    ATTCAGCATCAAGTAGCTAATGGCTCTATCGTTTTGATGCATGATATTCACAGTCCGACA
    GTCAATGCCTTGCCAAGGGTCATTGAGTATTTGAAAAATCAAGGTTATACCTTTGTGACC
    ATACCAGAGATGCTCAATACTCGCCTAAAAGCTCATGAGCTGTACTATAGTCGTGATGAA
    TAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    1020
    1080
    1140
    1200
    1260
    1320
    1380
    1440
    1443

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SPD_1309 [new locus tag: SPD_RS06975 ]
  • symbol: PgdA
  • description: peptidoglycan GlcNAc deacetylase
  • length: 480
  • theoretical pI: 5.18107
  • theoretical MW: 54622.7
  • GRAVY: -0.373333

⊟Function[edit | edit source]

  • reaction:
    EC 3.5.1.-?  ExPASy
  • TIGRFAM:
    Cellular processes Cellular processes Sporulation and germination polysaccharide deacetylase family sporulation protein PdaB (TIGR02764; HMM-score: 174.6)
    Cell structure Cell envelope Biosynthesis and degradation of murein sacculus and peptidoglycan delta-lactam-biosynthetic de-N-acetylase (TIGR02884; EC 3.5.-.-; HMM-score: 140.3)
    Cellular processes Cellular processes Sporulation and germination delta-lactam-biosynthetic de-N-acetylase (TIGR02884; EC 3.5.-.-; HMM-score: 140.3)
    and 4 more
    chitooligosaccharide deacetylase NodB (TIGR04243; EC 3.5.1.-; HMM-score: 139.2)
    Cellular processes Cellular processes Sporulation and germination probable sporulation protein, polysaccharide deacetylase family (TIGR02873; HMM-score: 134.8)
    Metabolism Energy metabolism Biosynthesis and degradation of polysaccharides probable sporulation protein, polysaccharide deacetylase family (TIGR02873; HMM-score: 134.8)
    Cell structure Cell envelope Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides polysaccharide deacetylase family protein, PEP-CTERM locus subfamily (TIGR03006; HMM-score: 43.9)
  • TheSEED  :
    • Peptidoglycan N-acetylglucosamine deacetylase (EC 3.5.1.-)
    Cell Wall and Capsule Capsular and extracellular polysacchrides Polysaccharide deacetylases  Peptidoglycan N-acetylglucosamine deacetylase (EC 3.5.1.-)
  • PFAM:
    no clan defined PgdA_N; Peptidoglycan GlcNAc deacetylase N-terminal domain (PF18627; HMM-score: 284.6)
    and 7 more
    GH_CE (CL0158) Polysacc_deac_1; Polysaccharide deacetylase (PF01522; HMM-score: 123.2)
    Glyco_hydro_57; Glycosyl hydrolase family 57 (PF03065; HMM-score: 16.1)
    Polysacc_deac_2; Divergent polysaccharide deacetylase (PF04748; HMM-score: 14.4)
    no clan defined PAP_PilO; Pilin accessory protein (PilO) (PF06864; HMM-score: 13.9)
    FAM165; FAM165 family (PF14981; HMM-score: 13.9)
    DUF2681; Protein of unknown function (DUF2681) (PF10883; HMM-score: 13.1)
    GutM; Glucitol operon activator protein (GutM) (PF06923; HMM-score: 12.7)

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

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

⊟Localization[edit | edit source]

  • PSORTb: Extracellular
    • Cytoplasmic Score: 0.1
    • Cytoplasmic Membrane Score: 0.14
    • Cellwall Score: 0.15
    • Extracellular Score: 9.6
    • Internal Helix: 1
  • SignalP: no predicted signal peptide
    • SP(Sec/SPI): 0.003772
    • TAT(Tat/SPI): 0.000241
    • LIPO(Sec/SPII): 0.005039
  • predicted transmembrane helices (TMHMM): 1

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MPNCIIEIIAQICYDINMNKSRLGRGRHGKTRHVLLALIGILAISICLLGGFIAFKIYQQKSFEQKIESLKKEKDDQLSEGNQKEHFRQGQAEVIAYYPLQGEKVISSVRELINQDVKDKLESKDNLVFYYTEQEESGLKGVVNRNVTKQIYDLVAFKIEETEKTSLGKVHLTEDGQPFTLDQLFSDASKAKEQLIKELTSFIEDKKIEQDQSEQIVKNFSDQDLSAWNFDYKDSQIILYPSPVVENLEEIALPVSAFFDVIQSSYLLEKDAALYQSYFDKKHQKVVALTFDDGPNPATTPQVLETLAKYDIKATFFVLGKNVSGNEDLVKRIKSEGHVVGNHSWSHPILSQLSLDEAKKQITDTEDVLTKVLGSSSKLMRPPYGAITDDIRNSLDLSFIMWDVDSLDWKSKNEASILTEIQHQVANGSIVLMHDIHSPTVNALPRVIEYLKNQGYTFVTIPEMLNTRLKAHELYYSRDE

⊟Experimental data[edit | edit source]

  • protein localization:
  • interaction partners:

⊟Expression & Regulation[edit | edit source]

⊟Operon[edit | edit source]

⊟Regulation[edit | edit source]

  • regulator: ComX1 regulon
    ComX1(sigma factor)controls the expression of late competence genes [1]   other strains

⊟Expression data[edit | edit source]

⊟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. ↑ Jelle Slager, Rieza Aprianto, Jan-Willem Veening
    Refining the Pneumococcal Competence Regulon by RNA Sequencing.
    J Bacteriol: 2019, 201(13);
    [PubMed:30885934] [WorldCat.org] [DOI] (I e)

⊟Relevant publications[edit | edit source]

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