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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
BM6001
serotype 19F
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
NCTC7465
serotype 1
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: 24-APR-2025

⊟Summary[edit | edit source]

  • organism: Streptococcus pneumoniae 6A-10
  • locus tag: HKM25_RS01870 [old locus tag: HKM25_377 ]
  • pan locus tag?: PNEUPAN000104000
  • symbol: rfbB
  • pan gene symbol?: cps2N
  • synonym:
  • product: dTDP-glucose 4,6-dehydratase

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: HKM25_RS01870 [old locus tag: HKM25_377 ]
  • symbol: rfbB
  • product: dTDP-glucose 4,6-dehydratase
  • replicon: chromosome
  • strand: +
  • coordinates: 347452..348501
  • length: 1050
  • essential: unknown

⊟Accession numbers[edit | edit source]

  • Location: NZ_CP053210 (347452..348501) NCBI
  • BioCyc:
  • MicrobesOnline:
  • PneumoBrowse for strain D39V: SPV_0330 PneumoBrowse

⊟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
    ATGACTGAATACAAAAATATTATCGTGACAGGTGGAGCTGGCTTTATCGGTTCTAACTTT
    GTCCATTATGTTTACGAGAACTTTCCAGATGTTCATGTGACAGTCCTAGATAAGTTGACT
    TATGCTGGAAACCGCGCGAATATTGAGGAAATTTTAGGTAATCGTGTTGAGTTAGTTGTT
    GGTGACATTGCTGATGCGGAGTTGGTAGACAAGTTGGCTGCTCAAGCAGATGCTATCGTT
    CATTATGCAGCGGAAAGCCACAATGATAATTCGCTCAATGATCCATCGCCATTTATTCAT
    ACTAACTTCATCGGAACCTATACTCTTTTAGAAGCTGCTCGTAAGTATGATATTCGCTTC
    CACCATGTATCGACAGATGAAGTTTATGGGGATCTCCCTTTACGCGAAGATTTGCCAGGT
    CATGGTGAAGGACCAGGTGAGAAATTTACTGCTGAAACAAAATACAACCCAAGCTCTCCG
    TACTCATCAACCAAGGCAGCCTCAGATTTGATTGTCAAAGCCTGGGTGCGTTCTTTTGGA
    GTCAAGGCAACGATTTCCAACTGTTCAAATAACTACGGTCCTTATCAACATATCGAAAAA
    TTCATCCCACGTCAGATTACTAACATCCTAAGTGGAATTAAGCCAAAACTTTACGGTGAA
    GGTAAGAATGTTCGTGACTGGATTCATACCAATGACCATTCTTCAGGAGTTTGGACAATC
    TTGACAAAAGGGCAAATCGATGAAACCTACTTGATTGGGGCTGATGGTGAGAAGAACAAT
    AAGGAAGTTTTGGAACTTATCCTTAAGGAAATGGGACAAGCTGTGGATGCCTATGATCAT
    GTGACTGACCGTGCAGGACATGACCTTCGCTATGCGATTGATGCCAGCAAGCTCCGTGAG
    GAGTTGGGGTGGAAACCTGAATTTACCAACTTTGAAGCTGGGCTCAAGGCAACAATCAAG
    TGGTATACAGATAACCAAGAATGGTGGAAAGCAGAAAAAGAAGCTGTTGAAGCCAATTAT
    GCTAAGACTCAGGAGATTATTACAGTATAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    1020
    1050

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: HKM25_RS01870 [old locus tag: HKM25_377 ]
  • symbol: RfbB
  • description: dTDP-glucose 4,6-dehydratase
  • length: 349
  • theoretical pI: 5.05328
  • theoretical MW: 39143.4
  • GRAVY: -0.462178

⊟Function[edit | edit source]

  • reaction:
    EC 4.2.1.46?  ExPASy
    dTDP-glucose 4,6-dehydratase dTDP-alpha-D-glucose = dTDP-4-dehydro-6-deoxy-alpha-D-glucose + H2O
  • TIGRFAM:
    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: 444)
    and 13 more
    NAD dependent epimerase/dehydratase, LLPSF_EDH_00030 family (TIGR04180; HMM-score: 122.9)
    Metabolism Energy metabolism Sugars UDP-glucose 4-epimerase GalE (TIGR01179; EC 5.1.3.2; HMM-score: 101.5)
    Cell structure Cell envelope Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides CDP-glucose 4,6-dehydratase (TIGR02622; EC 4.2.1.45; HMM-score: 74.8)
    Cell structure Cell envelope Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides ADP-glyceromanno-heptose 6-epimerase (TIGR02197; EC 5.1.3.20; HMM-score: 69.9)
    Cell structure Cell envelope Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides GDP-mannose 4,6-dehydratase (TIGR01472; EC 4.2.1.47; HMM-score: 67.2)
    hopanoid-associated sugar epimerase (TIGR03466; HMM-score: 65.1)
    thioester reductase domain (TIGR01746; HMM-score: 42.7)
    UDP-N-acetylglucosamine 4,6-dehydratase (inverting) (TIGR03589; EC 4.2.1.115; HMM-score: 42.5)
    Cell structure Cell envelope Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides dTDP-4-dehydrorhamnose reductase (TIGR01214; EC 1.1.1.133; HMM-score: 36.3)
    Hypothetical proteins Conserved TIGR01777 family protein (TIGR01777; HMM-score: 21.9)
    UDP-N-acetylglucosamine 4,6-dehydratase/5-epimerase (TIGR04130; EC 4.2.1.-,5.1.3.-; HMM-score: 17.2)
    Genetic information processing Protein synthesis Translation factors mRNA surveillance protein pelota (TIGR00111; HMM-score: 13.6)
    2-hydroxycyclohexanecarboxyl-CoA dehydrogenase (TIGR03206; EC 1.1.1.-; HMM-score: 12.2)
  • TheSEED: data available for D39, Hungary19A-6
  • PFAM:
    NADP_Rossmann (CL0063) GDP_Man_Dehyd; GDP-mannose 4,6 dehydratase (PF16363; HMM-score: 246.5)
    Epimerase; NAD dependent epimerase/dehydratase family (PF01370; HMM-score: 207)
    and 9 more
    NAD_binding_4; Male sterility protein (PF07993; HMM-score: 59)
    3Beta_HSD; 3-beta hydroxysteroid dehydrogenase/isomerase family (PF01073; HMM-score: 48.1)
    Polysacc_synt_2; Polysaccharide biosynthesis protein (PF02719; HMM-score: 43.6)
    RmlD_sub_bind; RmlD substrate binding domain (PF04321; HMM-score: 41.9)
    NAD_binding_10; NAD(P)H-binding (PF13460; HMM-score: 21.8)
    NmrA; NmrA-like family (PF05368; HMM-score: 21)
    adh_short; short chain dehydrogenase (PF00106; HMM-score: 20.9)
    Sacchrp_dh_NADP; Saccharopine dehydrogenase NADP binding domain (PF03435; HMM-score: 19.6)
    KR; KR domain (PF08659; HMM-score: 14.6)

⊟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: 0.9257
    • Cytoplasmic Membrane Score: 0.0184
    • Cell wall & surface Score: 0.0006
    • Extracellular Score: 0.0553
  • SignalP: no predicted signal peptide
    • SP(Sec/SPI): 0.006266
    • TAT(Tat/SPI): 0.000194
    • LIPO(Sec/SPII): 0.000758
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

  • GI:
  • RefSeq: WP_170835794 NCBI
  • UniProt:

⊟Protein sequence[edit | edit source]

  • MTEYKNIIVTGGAGFIGSNFVHYVYENFPDVHVTVLDKLTYAGNRANIEEILGNRVELVVGDIADAELVDKLAAQADAIVHYAAESHNDNSLNDPSPFIHTNFIGTYTLLEAARKYDIRFHHVSTDEVYGDLPLREDLPGHGEGPGEKFTAETKYNPSSPYSSTKAASDLIVKAWVRSFGVKATISNCSNNYGPYQHIEKFIPRQITNILSGIKPKLYGEGKNVRDWIHTNDHSSGVWTILTKGQIDETYLIGADGEKNNKEVLELILKEMGQAVDAYDHVTDRAGHDLRYAIDASKLREELGWKPEFTNFEAGLKATIKWYTDNQEWWKAEKEAVEANYAKTQEIITV

⊟Experimental data[edit | edit source]

  • protein localization:
  • interaction partners:

⊟Expression & Regulation[edit | edit source]

⊟Operon[edit | edit source]

⊟Regulation[edit | edit source]

  • regulator:

⊟Transcription[edit | edit source]

  • transcription start site:

⊟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 can add further information about the gene and protein here. [edit]

⊟Literature[edit | edit source]

⊟References[edit | edit source]

⊟Relevant publications[edit | edit source]

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