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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_0862 [new locus tag: SPD_RS04640 ]
  • pan locus tag?: PNEUPAN002002000
  • symbol: rnr
  • pan gene symbol?: rnr
  • synonym:
  • product: ribonuclease R

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SPD_0862 [new locus tag: SPD_RS04640 ]
  • symbol: rnr
  • product: ribonuclease R
  • replicon: chromosome
  • strand: +
  • coordinates: 875465..877819
  • length: 2355
  • 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
    1501
    1561
    1621
    1681
    1741
    1801
    1861
    1921
    1981
    2041
    2101
    2161
    2221
    2281
    2341
    ATGAAAGATAGAATAAAAGAATATTTACAAGACAAGGGAAAGGTGACTGTTAATGATTTG
    GCTCAGGCTTTGGGAAAAGACAGTTCCAAGGATTTTCGTGAGTTGATTAAAACCTTGTCC
    TTAATGGAAAGAAAGCACCAGATTCGCTTTGAAGAAGATGGCAGTCTGACCTTGGAAGCC
    AAGAAAAAACATGAGATTACCCTCAAGGGGATTTTTCATGCCCATAAAAATGGTTTTGGT
    TTTGTCAGCCTAGAAGGGGAAGAGGACGACCTTTTTGTAGGGAAAAATGATGTCAACTAT
    GCTATTGATGGTGATACCGTCGAGGTAGTGATTAAGAAAGTCGCTGACCGCAATAAGGGA
    ACAGCAGCAGAAGCCAAAATTATTGATATCCTAGAACACAGTTTGACAACAGTTGTCGGG
    CAAATCGTTCTGGATCAGGAAAAGCCTAAGTATGCTGGCTATATTCGTTCAAAAAATCAG
    AAAATCAGTCAACCGATTTATGTTAAGAAATCAGCCCTAAAGTTAGAAGGAACAGAAGTT
    CTCAAGGTCTTTATCGATAAATACCCAAGCAAGAAACATGATTTCTTTGTCGCGAGTGTT
    CTCGATGTAGTGGGACACTCAACGGATGTCGGAATTGATGTTCTTGAGGTCTTGGAATCA
    ATGGACATTGTATCCGAGTTTCCAGAAGCTGTTGTTAAGGAAGCAGAAAGTGTGCCTGAT
    GCTCCGTCTCAAAAGGATATGGAAGGTCGTCTGGATCTAAGAGATGAAATTACCTTTACC
    ATTGACGGTGCGGATGCCAAGGACTTGGACGATGCAGTGCATATCAAGGCTCTGAAAAAT
    GGCAATCTGGAGCTTGGGGTTCACATCGCAGATGTTTCTTATTATGTGACCGAGGGGTCT
    GCCCTTGACAAGGAAGCCCTTAACCGTGCGACTTCTGTTTACGTGACAGACCGAGTGGTG
    CCAATGCTTCCAGAACGACTATCAAATGGCATCTGCTCTCTCAATCCCCAAGTTGACCGC
    CTGACCCAGTCTGCTATTATGGAGATTGATAAACATGGTCGTGTGGTCAACTATACCATT
    ACACAAACAGTTATCAAGACCAGTTTTCGTATGACCTATAGCGATGTCAATGATATCCTA
    GCTGGCGATGAAGAAAAGAGAAAAGAATATCATAAAATTGTATCAAGTATCGAACTCATG
    GCCAAGCTTCATGAAACTTTAGAAAACATGCGTGTGAAACGTGGAGCTCTCAATTTTGAT
    ACCAATGAAGCGAAGATTTTAGTGGATAAACAAGGTAAGCCTGTTGATATCGTTCTTCGG
    CAGCGTGGTATTGCCGAGCGGATGATTGAGTCTTTTATGTTGATGGCTAATGAAACAGTT
    GCCGAACATTTCAGCAAGTTGGATTTGCCTTTTATCTATCGAATTCACGAGGAGCCTAAG
    GCTGAAAAGGTTCAGAAGTTTATTGATTATGCTTCGAGTTTTGGCTTGCGCATTTATGGG
    ACTGCCAGTGAGATTAGTCAGGAGGCACTTCAAGACATCATGCGTGCTGTTGAGGGAGAA
    CCTTATGCAGATGTATTGTCCATGATGCTTCTTCGCTCTATGCAGCAGGCTCGTTATTCG
    GAGCACAATCACGGCCACTATGGACTAGCTGCTGACTATTATACTCACTTTACCAGTCCA
    ATTCGTCGTTATCCAGACCTTCTTGTTCACCGTATGATTCGGGATTACGGCCGTTCTAAG
    GAAATAGCAGAGCATTTTGAACAAGTGATTCCAGAGATTGCGACCCAGTCTTCCAACCGT
    GAACGTCGTGCCATAGAAGCTGAGCGTGAAGTTGAAGCCATGAAAAAGGCTGAGTATATG
    GAAGAATACGTGGGTGAAGAGTATGATGCAGTTGTATCAAGTATTGTCAAATTCGGTCTC
    TTTGTCGAATTGCCAAACACAGTTGAAGGCTTGATTCACATCACTAATCTACCTGAATTT
    TATCATTTCAATGAGCGTGATTTGACTCTTCGTGGAGAAAAATCAGGTATCACTTTCCGA
    GTGGGTCAGCAGATCCGTATCCGTGTTGAAAGAGCGGATAAAATGACTGGAGAGATTGAT
    TTTTCATTCGTACCTAGTGAGTTTGATGTGATTGAAAAAGGCTTGAAACAGTCTAGTCGT
    AGTGGCAGAGGGCGTGGTTCAAATCGTCGTTCGGATAAGAAGGAAGACAAGAGAAAATCA
    GGACGCTCAAATGATAAGCGTAAGCATTCACAAAAAGACAAGAAGAAAAAAGGAAAGAAA
    CCTTTTTACAAGGAAGTAGCTAAGAAAGGAGCCAAGCATGGCAAAGGGCGAGGGAAAGGT
    CGTCGCACAAAATAA
    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
    1680
    1740
    1800
    1860
    1920
    1980
    2040
    2100
    2160
    2220
    2280
    2340
    2355

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SPD_0862 [new locus tag: SPD_RS04640 ]
  • symbol: Rnr
  • description: ribonuclease R
  • length: 784
  • theoretical pI: 7.70848
  • theoretical MW: 89136.9
  • GRAVY: -0.575765

⊟Function[edit | edit source]

  • reaction:
    EC 3.1.-.-?  ExPASy
  • TIGRFAM:
    Genetic information processing Transcription Degradation of RNA ribonuclease R (TIGR02063; EC 3.1.-.-; HMM-score: 810.1)
    and 7 more
    Genetic information processing Transcription Degradation of RNA VacB and RNase II family 3'-5' exoribonucleases (TIGR00358; EC 3.1.13.1; HMM-score: 603.6)
    Genetic information processing Transcription Degradation of RNA exoribonuclease II (TIGR02062; EC 3.1.13.1; HMM-score: 190.9)
    Genetic information processing Protein synthesis Ribosomal proteins: synthesis and modification ribosomal protein bS1 (TIGR00717; HMM-score: 24.4)
    Genetic information processing Transcription Degradation of RNA polyribonucleotide nucleotidyltransferase (TIGR03591; EC 2.7.7.8; HMM-score: 23.2)
    Genetic information processing Transcription DNA-dependent RNA polymerase DNA-directed RNA polymerase (TIGR00448; EC 2.7.7.6; HMM-score: 21.8)
    Cellular processes Cellular processes Adaptations to atypical conditions cold shock domain protein CspD (TIGR02381; HMM-score: 14.6)
    Genetic information processing DNA metabolism DNA replication, recombination, and repair cold shock domain protein CspD (TIGR02381; HMM-score: 14.6)
  • TheSEED  :
    • 3'-to-5' exoribonuclease RNase R
    RNA Metabolism RNA processing and modification RNA processing and degradation, bacterial  3'-to-5' exoribonuclease RNase R
  • PFAM:
    no clan defined RNB; RNB domain (PF00773; HMM-score: 371.3)
    and 6 more
    OB (CL0021) OB_RNB; Ribonuclease B OB domain (PF08206; HMM-score: 64.2)
    S1; S1 RNA binding domain (PF00575; HMM-score: 56.4)
    CSD2; Cold shock domain (PF17876; HMM-score: 51.4)
    no clan defined ASL_C; Adenylosuccinate lyase C-terminal (PF08328; HMM-score: 14.1)
    OB (CL0021) CSD; 'Cold-shock' DNA-binding domain (PF00313; HMM-score: 13.9)
    RNase_II_C_S1; RNase II-type exonuclease C-terminal S1 domain (PF18614; HMM-score: 13.4)

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

  • domains:
  • modifications:
  • cofactors:
  • 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
  • SignalP: no predicted signal peptide
    • SP(Sec/SPI): 0.003457
    • TAT(Tat/SPI): 0.000473
    • LIPO(Sec/SPII): 0.00069
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MKDRIKEYLQDKGKVTVNDLAQALGKDSSKDFRELIKTLSLMERKHQIRFEEDGSLTLEAKKKHEITLKGIFHAHKNGFGFVSLEGEEDDLFVGKNDVNYAIDGDTVEVVIKKVADRNKGTAAEAKIIDILEHSLTTVVGQIVLDQEKPKYAGYIRSKNQKISQPIYVKKSALKLEGTEVLKVFIDKYPSKKHDFFVASVLDVVGHSTDVGIDVLEVLESMDIVSEFPEAVVKEAESVPDAPSQKDMEGRLDLRDEITFTIDGADAKDLDDAVHIKALKNGNLELGVHIADVSYYVTEGSALDKEALNRATSVYVTDRVVPMLPERLSNGICSLNPQVDRLTQSAIMEIDKHGRVVNYTITQTVIKTSFRMTYSDVNDILAGDEEKRKEYHKIVSSIELMAKLHETLENMRVKRGALNFDTNEAKILVDKQGKPVDIVLRQRGIAERMIESFMLMANETVAEHFSKLDLPFIYRIHEEPKAEKVQKFIDYASSFGLRIYGTASEISQEALQDIMRAVEGEPYADVLSMMLLRSMQQARYSEHNHGHYGLAADYYTHFTSPIRRYPDLLVHRMIRDYGRSKEIAEHFEQVIPEIATQSSNRERRAIEAEREVEAMKKAEYMEEYVGEEYDAVVSSIVKFGLFVELPNTVEGLIHITNLPEFYHFNERDLTLRGEKSGITFRVGQQIRIRVERADKMTGEIDFSFVPSEFDVIEKGLKQSSRSGRGRGSNRRSDKKEDKRKSGRSNDKRKHSQKDKKKKGKKPFYKEVAKKGAKHGKGRGKGRRTK

⊟Experimental data[edit | edit source]

  • protein localization:
  • interaction partners:

⊟Expression & Regulation[edit | edit source]

⊟Operon[edit | edit source]

⊟Regulation[edit | edit source]

  • regulator:

⊟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]

⊟Relevant publications[edit | edit source]

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