⊟Summary[edit | edit source]

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: 10-NOV-2021

⊟Summary

• organism: Streptococcus pneumoniae G54
locus tag: SPG_RS09060 [old locus tag: SPG_1810 ]
pan locus tag^?: PNEUPAN003434000
symbol: rlmD
pan gene symbol^?: rumA-2
• synonym:
• product: 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD

⊟Genome View

⊟Gene

⊟General

• type: CDS
• locus tag: SPG_RS09060 [old locus tag: SPG_1810 ]
• symbol: rlmD
• product: 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD
• replicon: chromosome
• strand: -
• coordinates: 1732106..1733461
• length: 1356
• essential: unknown

⊟Accession numbers

• Location: NC_011072 (1732106..1733461) NCBI
• BioCyc: SPG_RS09060 BioCyc
• MicrobesOnline: see SPG_1810
• PneumoBrowse for strain D39V: SPV_1704 PneumoBrowse

⊟Phenotype

Share your knowledge and add information here. [edit]

⊟DNA sequence

• 1
  61
  121
  181
  241
  301
  361
  421
  481
  541
  601
  661
  721
  781
  841
  901
  961
  1021
  1081
  1141
  1201
  1261
  1321
  
  ATGAATCTGAAAGTGAAACAAAAAATACCATTAAAAATCAAGCGCATGGGAATTAACGGT
  GAGGGAATCGGCTTTTACCAAAAAACATTAGTCTTTGTACCAGGAGCTCTCAAAGGCGAA
  GATATCTATTGTCAGATTACTTCTATTAGACGCAACTTTGTTGAAGCAAAATTACTGAAG
  GTCAACAAGAAGTCTAAATTTCGAATTGTGCCATCTTGTACTATTTATAATGAATGCGGA
  GGCTGCCAAATCATGCACCTGCATTATGATAAGCAGCTGGAGTTCAAGACGGACTTACTT
  CATCAAGCGCTGAAAAAATTTGCTCCTGCAGGATATGAAAATTATGAAATTCGTCCAACT
  ATTGGAATGCAGGAACCAAAATATTACAGAGCTAAGTTACAATTTCAGACCCGAAAATTT
  AAAAATCAGGTCAAGGCGGGCTTATATGCACAAAACTCTCACTATTTAGTAGAGTTGAAA
  GACTGCCTGGTACAAGATAAGGAAACCCAAGTGATTGCTAATCGCTTAGCAGAATTACTT
  ACTTATCACCAGATTCCAATCACGGATGAGAGAAAAGTTCTAGGTGTCCGTACTATTATG
  GTCCGACGCGCGAGAAAGACCGGACAGGTTCAGATTATTATTGTTACAAACCGCCAGCTT
  AATTTAACTCAATTGGTAAAAGAGTTGGTTAAAGATTTCCCAGAAGTTGTGACAGTAGCT
  GTTAATACAAATACAGCTAAAACCAGTGAGATATATGGTGAAAAGACAGAGATTATCTGG
  GGGCAAGAGAGTATTCAAGAAGGTGTACTCAATTATGAATTTTCACTATCCCCTCGAGCT
  TTTTATCAACTAAATCCTGAACAAACAGAAGTCCTTTATAGCGAGGCAGTAAAAGCGCTG
  GATGTTAGTAAAGAAGACCATTTGATTGACGCTTATTGTGGAGTTGGAACAATTGGTTTT
  GCCTTTGCAAAGAAAGTAAAAACACTCAGAGGTATGGATATTATTCCAGAAGCTATTGAA
  GATGCCAAGCGAAATGCTAAAAGAATGGGATTTGACAATACTCATTATGAAGCTGGAACG
  GCAGAAGAGATTATTCCTCGTTGGTACAAGGAAGGCTACCGAGCAGATGCTTTGATTGTT
  GACCCACCACGTACAGGTCTGGATGATAAGTTATTAGATACTATTCTTACTTATGTACCA
  GAAAAAATGGTTTATATTTCTTGTAATGTTTCGACCTTGGCTCGTGATTTGGTACGCTTA
  GTAGAAGTCTATGATCTTCATTATATTCAGTCGGTCGATATGTTCCCACATACAGCTCGA
  ACTGAAGCTGTTGTAAAATTAATAAAAAAAGTTTAA
  60
  120
  180
  240
  300
  360
  420
  480
  540
  600
  660
  720
  780
  840
  900
  960
  1020
  1080
  1140
  1200
  1260
  1320
  1356
  

⊟Protein

⊟General

• locus tag: SPG_RS09060 [old locus tag: SPG_1810 ]
• symbol: RlmD
• description: 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD
• length: 451
• theoretical pI: 9.35833
• theoretical MW: 51713.7
• GRAVY: -0.286031

⊟Function

• ⊞⊞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: 433.5)
  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: 143.8)
  Genetic information processing Protein synthesis tRNA and rRNA base modification tRNA (uracil(54)-C(5))-methyltransferase (TIGR02143; EC 2.1.1.35; HMM-score: 74.8)
  Genetic information processing Protein fate Protein modification and repair protein-(glutamine-N5) methyltransferase, release factor-specific (TIGR03534; EC 2.1.1.-; HMM-score: 33.4)
  Genetic information processing Protein fate Protein modification and repair methyltransferase, HemK family (TIGR00536; HMM-score: 25.2)
  Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Chlorophyll and bacteriochlorphyll magnesium protoporphyrin O-methyltransferase (TIGR02021; EC 2.1.1.11; HMM-score: 23.4)
  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: 22.9)
  Genetic information processing Protein synthesis Ribosomal proteins: synthesis and modification putative protein-(glutamine-N5) methyltransferase, unknown substrate-specific (TIGR03704; EC 2.1.1.-; HMM-score: 21.7)
  Unknown function Enzymes of unknown specificity putative methylase (TIGR00537; HMM-score: 20.8)
  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: 20.5)
  Genetic information processing Protein synthesis Ribosomal proteins: synthesis and modification ribosomal protein L11 methyltransferase (TIGR00406; EC 2.1.1.-; HMM-score: 19.5)
  Metabolism Biosynthesis of cofactors, prosthetic groups, and carriers Menaquinone and ubiquinone ubiquinone/menaquinone biosynthesis methyltransferase (TIGR01934; EC 2.1.1.-; HMM-score: 18.4)
• TheSEED: see SPG_1810
• ⊞⊞PFAM:
  NADP_Rossmann (CL0063) tRNA_U5-meth_tr; tRNA (Uracil-5-)-methyltransferase (PF05958; HMM-score: 74.1)
  and 12 more
  Methyltransf_31; Methyltransferase domain (PF13847; HMM-score: 39.8)
  MTS; Methyltransferase small domain (PF05175; HMM-score: 27.3)
  OB (CL0021) TRAM; TRAM domain (PF01938; HMM-score: 26.4)
  NADP_Rossmann (CL0063) Methyltransf_25; Methyltransferase domain (PF13649; HMM-score: 23.5)
  Cons_hypoth95; Conserved hypothetical protein 95 (PF03602; HMM-score: 18.5)
  Methyltransf_15; RNA cap guanine-N2 methyltransferase (PF09445; HMM-score: 17.5)
  UPF0020; Putative RNA methylase family UPF0020 (PF01170; HMM-score: 17.3)
  Methyltransf_11; Methyltransferase domain (PF08241; HMM-score: 15.2)
  Methyltransf_12; Methyltransferase domain (PF08242; HMM-score: 14.9)
  Ubie_methyltran; ubiE/COQ5 methyltransferase family (PF01209; HMM-score: 13.6)
  no clan defined PriA_C; Primosomal protein N C-terminal domain (PF18074; HMM-score: 13.4)
  Stomagen; Stomagen (PF16851; HMM-score: 12.5)

⊟Structure, modifications & cofactors

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

⊟Localization

• ⊞⊞PSORTb: Cytoplasmic
  • Cytoplasmic Score: 7.5
  • Cytoplasmic Membrane Score: 1.15
  • Cellwall Score: 0.62
  • Extracellular Score: 0.73
  • Internal Helices: 0
• ⊞⊞SignalP: no predicted signal peptide
  • SP(Sec/SPI): 0.007588
  • TAT(Tat/SPI): 0.000307
  • LIPO(Sec/SPII): 0.001027
• predicted transmembrane helices (TMHMM): 0

⊟Accession numbers

• GI:
• RefSeq: WP_001050312 NCBI
• UniProt:

⊟Protein sequence

• MNLKVKQKIPLKIKRMGINGEGIGFYQKTLVFVPGALKGEDIYCQITSIRRNFVEAKLLKVNKKSKFRIVPSCTIYNECGGCQIMHLHYDKQLEFKTDLLHQALKKFAPAGYENYEIRPTIGMQEPKYYRAKLQFQTRKFKNQVKAGLYAQNSHYLVELKDCLVQDKETQVIANRLAELLTYHQIPITDERKVLGVRTIMVRRARKTGQVQIIIVTNRQLNLTQLVKELVKDFPEVVTVAVNTNTAKTSEIYGEKTEIIWGQESIQEGVLNYEFSLSPRAFYQLNPEQTEVLYSEAVKALDVSKEDHLIDAYCGVGTIGFAFAKKVKTLRGMDIIPEAIEDAKRNAKRMGFDNTHYEAGTAEEIIPRWYKEGYRADALIVDPPRTGLDDKLLDTILTYVPEKMVYISCNVSTLARDLVRLVEVYDLHYIQSVDMFPHTARTEAVVKLIKKV

⊟Experimental data

• protein localization:
• interaction partners:

⊟Expression & Regulation

⊟Operon

• MicrobesOnline: SPG_RS09055 < rlmD

⊟Regulation

• regulator:

⊟Expression data

• PneumoExpress for strain D39V: SPV_1704 PneumoExpress

⊞Biological Material

⊟Mutants

⊟Expression vector

⊟lacZ fusion

⊟GFP fusion

⊟two-hybrid system

⊟FLAG-tag construct

⊟Antibody

⊞Other Information

You are kindly invited to share additional interesting facts.

⊟Literature

⊟References

⊟Relevant publications