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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: 25-OCT-2024

⊟Summary[edit | edit source]

  • organism: Streptococcus pneumoniae TCH8431/19A
  • locus tag: HMPREF0837_RS06940 [old locus tag: HMPREF0837_11450 ]
  • pan locus tag?: PNEUPAN002051000
  • symbol: rlmD
  • pan gene symbol?: rlmCD
  • synonym:
  • product: 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: HMPREF0837_RS06940 [old locus tag: HMPREF0837_11450 ]
  • symbol: rlmD
  • product: 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD
  • replicon: chromosome
  • strand: -
  • coordinates: 1338855..1340486
  • length: 1632
  • essential: unknown

⊟Accession numbers[edit | edit source]

  • Location: NC_014251 (1338855..1340486) NCBI
  • BioCyc: HMPREF0837_RS06940 BioCyc
  • MicrobesOnline:
  • PneumoBrowse for strain D39V: SPV_0914 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
    1081
    1141
    1201
    1261
    1321
    1381
    1441
    1501
    1561
    1621
    ATGTTAAAGAAAAATGATATTGTAGAAGTTGAAATTGTTGACTTGACCCATGAAGGGGCA
    GGAGTTGCCAAGGTAGATGGTTTGGTCTTTTTTGTAGAGAATGCTTTACCGAGTGAAAAA
    ATTCTCATGCGTGTCCTCAAGGTCAATAAAAAGATTGGCTTTGGAAAAGTTGAAAAATAC
    CTTGTCCAGTCACCACACCGTAATCAAGATCTAGATTTGGCTTACCTGCGTTCAGGAATC
    GCGGATTTAGGACACCTTTCTTATCCAGAACAGCTCAAGTTTAAAACCAAGCAAGTCAAG
    GACAGTCTCTACAAGATTGCTGGAATTGCAGATGTAGAAGTTGCTGAAACGCTTGGTATG
    GAACATCCAGTCAAGTATCGCAATAAGGCGCAGGTGCCCGTTCGTCGAGTGAATGGTGTC
    TTGGAAACAGGATTTTTCCGTAAGAATTCGCACGACCTCATGCCCCTTGAAGATTTCTTT
    ATCCAGGATCCTGTCATTGACCAAGTCGTAGTAGCTCTTCGAGACCTGCTCCGTCGTTTT
    GATTTAAAACCTTATGACGAAAAGGAACAGTCTGGATTGATTCGGAATCTTGTGGTGCGT
    CGTGGTCACTATTCAGGACAAATCATGGTCGTTTTGGTGACAACTCGTCCAAAAGTTTTT
    CGTGTTGACCAATTGATTGAACAAGTTATCAAGCAGTTCCCAGAGATTGTGTCTGTCATG
    CAAAATATCAACGACCAGAATACCAATGCGATTTTTGGTAAGGAGTGGCGCACTCTTTAT
    GGTCAAGACTATATTACGGACCAGATGTTGGGAAATGACTTCCAAATCGCTGGCCCAGCC
    TTTTACCAAGTCAATACTGAAATGGCGGAGAAACTCTATCAAACAGCCATTGACTTTGCA
    GAGTTAAAAAAAGATGACGTGGTTATTGATGCTTATTCTGGTATTGGAACCATTGGTTTA
    TCAGTCGCCAAGCATGTCAAAGAAGTCTACGGTGTTGAACTGATTCCAGAAGCGGTTGAG
    AATAGTAAAAAAAATGCTCAGCTGAACAATATTTCAAACGCCCACTATGTCTGTGACACA
    GCTGAAAATGCTATGAAGAATTGGCTTAAAGATGGGATTCAACCAACCGTTATCTTGGTT
    GATCCTCCACGCAAGGGCTTGACAGAAAGCTTTATCAAAGCAAGCGCCCAAACAGGAGCC
    GATCGCATCGCCTATATCTCCTGCAATGTCGCAACCATGGCGCGTGATATCAAACTCTAC
    CAAGAATTGGGATATGAATTGAAGAAAGTCCAGCCGGTGGATCTATTTCCTCAAACGCAT
    CACGTCGAGACGGTAGCACTTTTGTCCAAACTCGATGTCGATAAGCACATAAGTGTTGAA
    ATTGAGCTGGATGAGATGAATTTGACAAGTGCGGAGAGCAAAGCAACATATGCTCAAATC
    AAAGAATATGTTTGGAATAAATTTGAATTAAAAGTTTCGACATTATATATTGCACAGATA
    AAAAAGAAATGTGGAATAGAATTACGAGAACATTACAACAAGTCTAAAAAGGATAAACAA
    ATTATTCCACAGTGTACACCTGAAAAAGAAGAAGCCATCATGGATGCTTTGAGACACTTC
    AAAATGATTTAA
    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
    1632

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: HMPREF0837_RS06940 [old locus tag: HMPREF0837_11450 ]
  • symbol: RlmD
  • description: 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD
  • length: 543
  • theoretical pI: 7.00493
  • theoretical MW: 61788.9
  • GRAVY: -0.276059

⊟Function[edit | edit source]

  • reaction:
    EC 2.1.1.190?  ExPASy
    23S rRNA (uracil1939-C5)-methyltransferase S-adenosyl-L-methionine + uracil1939 in 23S rRNA = S-adenosyl-L-homocysteine + 5-methyluracil1939 in 23S rRNA
  • TIGRFAM:
    Genetic information processing Protein synthesis tRNA and rRNA base modification 23S rRNA (uracil-5-)-methyltransferase RumA (TIGR00479; EC 2.1.1.-; HMM-score: 414.3)
    and 11 more
    Genetic information processing Protein synthesis tRNA and rRNA base modification 23S rRNA (uracil-5-)-methyltransferase RumB (TIGR02085; EC 2.1.1.189; HMM-score: 141.1)
    Genetic information processing Protein synthesis tRNA and rRNA base modification tRNA (uracil(54)-C(5))-methyltransferase (TIGR02143; EC 2.1.1.35; HMM-score: 81.5)
    Genetic information processing Protein fate Protein modification and repair protein-(glutamine-N5) methyltransferase, release factor-specific (TIGR03534; EC 2.1.1.-; HMM-score: 28.2)
    Genetic information processing Protein synthesis Ribosomal proteins: synthesis and modification ribosomal protein L11 methyltransferase (TIGR00406; EC 2.1.1.-; HMM-score: 27.1)
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Heme, porphyrin, and cobalamin precorrin-6Y C5,15-methyltransferase (decarboxylating), CbiT subunit (TIGR02469; EC 2.1.1.132; HMM-score: 26.2)
    Genetic information processing Protein synthesis tRNA and rRNA base modification N2,N2-dimethylguanosine tRNA methyltransferase (TIGR00308; EC 2.1.1.-; HMM-score: 24.6)
    Unknown function Enzymes of unknown specificity putative methylase (TIGR00537; HMM-score: 23.9)
    Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Menaquinone and ubiquinone 3-demethylubiquinone-9 3-O-methyltransferase (TIGR01983; EC 2.1.1.64; HMM-score: 19.9)
    Genetic information processing Protein fate Protein modification and repair methyltransferase, HemK family (TIGR00536; HMM-score: 17.7)
    Genetic information processing Protein synthesis tRNA and rRNA base modification ribosomal RNA small subunit methyltransferase A (TIGR00755; EC 2.1.1.182; HMM-score: 15.2)
    Genetic information processing Protein synthesis tRNA and rRNA base modification 16S rRNA (guanine(966)-N(2))-methyltransferase RsmD (TIGR00095; EC 2.1.1.171; HMM-score: 15.1)
  • TheSEED: see HMPREF0837_11450
  • PFAM:
    NADP_Rossmann (CL0063) tRNA_U5-meth_tr; tRNA (Uracil-5-)-methyltransferase (PF05958; HMM-score: 79.1)
    and 13 more
    Met_10; Met-10+ like-protein (PF02475; HMM-score: 39.6)
    Cons_hypoth95; Conserved hypothetical protein 95 (PF03602; HMM-score: 24.7)
    N6_N4_Mtase; DNA methylase (PF01555; HMM-score: 23.8)
    MTS; Methyltransferase small domain (PF05175; HMM-score: 23.5)
    Methyltransf_31; Methyltransferase domain (PF13847; HMM-score: 21.4)
    RrnaAD; Ribosomal RNA adenine dimethylase (PF00398; HMM-score: 21.3)
    DOT1; Histone methylation protein DOT1 (PF08123; HMM-score: 20.1)
    Methyltransf_15; RNA cap guanine-N2 methyltransferase (PF09445; HMM-score: 20.1)
    TRM; N2,N2-dimethylguanosine tRNA methyltransferase (PF02005; HMM-score: 19.8)
    PrmA; Ribosomal protein L11 methyltransferase (PrmA) (PF06325; HMM-score: 19.2)
    Methyltransf_25; Methyltransferase domain (PF13649; HMM-score: 18.1)
    PCMT; Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT) (PF01135; HMM-score: 14.9)
    Methyltransf_11; Methyltransferase domain (PF08241; HMM-score: 13.8)

⊟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: 0.9975
    • Cytoplasmic Membrane Score: 0.0003
    • Cell wall & surface Score: 0.0014
    • Extracellular Score: 0.0008
  • SignalP: no predicted signal peptide
    • SP(Sec/SPI): 0.002023
    • TAT(Tat/SPI): 0.00028
    • LIPO(Sec/SPII): 0.000377
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

  • GI:
  • RefSeq: WP_000914573 NCBI
  • UniProt:

⊟Protein sequence[edit | edit source]

  • MLKKNDIVEVEIVDLTHEGAGVAKVDGLVFFVENALPSEKILMRVLKVNKKIGFGKVEKYLVQSPHRNQDLDLAYLRSGIADLGHLSYPEQLKFKTKQVKDSLYKIAGIADVEVAETLGMEHPVKYRNKAQVPVRRVNGVLETGFFRKNSHDLMPLEDFFIQDPVIDQVVVALRDLLRRFDLKPYDEKEQSGLIRNLVVRRGHYSGQIMVVLVTTRPKVFRVDQLIEQVIKQFPEIVSVMQNINDQNTNAIFGKEWRTLYGQDYITDQMLGNDFQIAGPAFYQVNTEMAEKLYQTAIDFAELKKDDVVIDAYSGIGTIGLSVAKHVKEVYGVELIPEAVENSKKNAQLNNISNAHYVCDTAENAMKNWLKDGIQPTVILVDPPRKGLTESFIKASAQTGADRIAYISCNVATMARDIKLYQELGYELKKVQPVDLFPQTHHVETVALLSKLDVDKHISVEIELDEMNLTSAESKATYAQIKEYVWNKFELKVSTLYIAQIKKKCGIELREHYNKSKKDKQIIPQCTPEKEEAIMDALRHFKMI

⊟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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