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serotype 4
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D39V
serotype 2
Hungary19A-6
serotype 19A
EF3030
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670-6B
serotype 6B
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70585
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A66
serotype 3
AP200
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Hu15
serotype 19A
Hu17
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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
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TCH8431/19A
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Taiwan19F-14
serotype 19F
Xen35
serotype 4
gamPNI0373
serotype 1

NCBI: 25-NOV-2024

⊟Summary[edit | edit source]

  • organism: Streptococcus pneumoniae R6
  • locus tag: SPR_RS04905 [old locus tag: spr0979 ]
  • pan locus tag?: PNEUPAN002211000
  • symbol: rpoD
  • pan gene symbol?: rpoD
  • synonym:
  • product: RNA polymerase sigma factor RpoD

⊟Genome View[edit | edit source]

⊟Gene[edit | edit source]

⊟General[edit | edit source]

  • type: CDS
  • locus tag: SPR_RS04905 [old locus tag: spr0979 ]
  • symbol: rpoD
  • product: RNA polymerase sigma factor RpoD
  • replicon: chromosome
  • strand: +
  • coordinates: 965281..966390
  • length: 1110
  • essential: yes [1] DEG other strains

⊟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
    ATGGCAACAAAACAAAAAGAAGTAACAACATTTGACGTACAGGTAGCAGAATTTATCCGT
    AATCATAAGCAAAAAGGGACAGCAACAGATGATGAAATCAATGCAAGTCTGGTTATTCCT
    TTTACCTTGGACGCTGATGGGATTGAAGATCTCTTGCAACGGATTCAGGATGCAGGGATT
    TCTATCACAGATAACGAAGGAAATCCAAGTGCGCGTGTTCTTAGCAATGAAGAAGAACCA
    GAACTCAGCGATGAGGACTTGATTGGGTCAACTTCTGCTAAGGTCAATGACCCTGTCCGT
    ATGTACTTGAAAGAAATAGGGGTCGTTCCTCTCTTGACCAATGAAGAGGAGAAAGAGTTG
    GCACTGGCTGTTGAAGCTGGTGATATCGAAGCCAAACAACGTCTTGCGGAAGCCAATCTT
    CGTTTGGTTGTTTCCATTGCCAAACGCTATGTCGGTCGTGGTATGCAGTTCCTTGACTTG
    ATTCAAGAAGGAAATATGGGCTTGATGAAGGCGGTTGACAAGTTTGACTATTCTAAAGGG
    TTCAAGTTTTCAACTTATGCAACTTGGTGGATTCGTCAGGCTATCACTCGTGCTATTGCG
    GACCAAGCTCGTACCATCCGTATCCCAGTTCACATGGTTGAAACTATCAATAAATTGGTT
    CGTGAACAGCGGAATCTCCTTCAAGAATTGGGGCAAGATCCGACACCAGAACAGATTGCT
    GAACGAATGGATATGACACCTGATAAGGTTCGTGAAATCTTGAAGATTGCCCAAGAACCA
    GTATCTCTTGAAACTCCTATCGGTGAAGAGGACGATAGCCACCTTGGAGACTTTATCGAA
    GATGAAGTGATTGAAAATCCAGTGGATTATACGACTCGTATCGTCTTGCGTGAGCAATTG
    GATGAAATCTTAGATACTCTTACAGACCGTGAAGAAAATGTTCTGCGTCTACGTTTTGGA
    CTAGATGATGGAAAAATGCGCACACTTGAAGATGTGGGGAAAGTCTTTAACGTAACTCGT
    GAGCGTATCCGTCAGATTGAAGCAAAGGCTTTGAGAAAACTACGCCAACCAAGTCGTAGC
    AAACCGCTTCGTGATTTTATTGAAGACTAA
    60
    120
    180
    240
    300
    360
    420
    480
    540
    600
    660
    720
    780
    840
    900
    960
    1020
    1080
    1110

⊟Protein[edit | edit source]

⊟General[edit | edit source]

  • locus tag: SPR_RS04905 [old locus tag: spr0979 ]
  • symbol: RpoD
  • description: RNA polymerase sigma factor RpoD
  • length: 369
  • theoretical pI: 4.46493
  • theoretical MW: 42030.3
  • GRAVY: -0.492683

⊟Function[edit | edit source]

  • TIGRFAM:
    Genetic information processing Transcription Transcription factors RNA polymerase sigma factor RpoD (TIGR02393; HMM-score: 411.8)
    RNA polymerase sigma factor, cyanobacterial RpoD-like family (TIGR02997; HMM-score: 345.4)
    and 25 more
    Cellular processes Cellular processes Adaptations to atypical conditions RNA polymerase sigma factor RpoS (TIGR02394; HMM-score: 328.1)
    Genetic information processing Transcription Transcription factors RNA polymerase sigma factor RpoS (TIGR02394; HMM-score: 328.1)
    Cellular processes Cellular processes Adaptations to atypical conditions alternative sigma factor RpoH (TIGR02392; HMM-score: 162.9)
    Genetic information processing Transcription Transcription factors alternative sigma factor RpoH (TIGR02392; HMM-score: 162.9)
    RNA polymerase sigma factor, sigma-70 family (TIGR02937; HMM-score: 132.4)
    RNA polymerase sigma-70 factor, sigma-B/F/G subfamily (TIGR02980; HMM-score: 132.4)
    Cellular processes Cellular processes Sporulation and germination RNA polymerase sigma-G factor (TIGR02850; HMM-score: 128.5)
    Genetic information processing Transcription Transcription factors RNA polymerase sigma-G factor (TIGR02850; HMM-score: 128.5)
    Cellular processes Cellular processes Sporulation and germination RNA polymerase sigma-F factor (TIGR02885; HMM-score: 122.4)
    Genetic information processing Transcription Transcription factors RNA polymerase sigma-F factor (TIGR02885; HMM-score: 122.4)
    RNA polymerase sigma factor, FliA/WhiG family (TIGR02479; HMM-score: 118.9)
    Cellular processes Cellular processes Sporulation and germination RNA polymerase sigma-K factor (TIGR02846; HMM-score: 107.1)
    Genetic information processing Transcription Transcription factors RNA polymerase sigma-K factor (TIGR02846; HMM-score: 107.1)
    Cellular processes Cellular processes Sporulation and germination RNA polymerase sigma-E factor (TIGR02835; HMM-score: 97.7)
    Genetic information processing Transcription Transcription factors RNA polymerase sigma-E factor (TIGR02835; HMM-score: 97.7)
    RNA polymerase sigma-B factor (TIGR02941; HMM-score: 76)
    Cellular processes Cellular processes Sporulation and germination RNA polymerase sigma-H factor (TIGR02859; HMM-score: 39.1)
    Genetic information processing Transcription Transcription factors RNA polymerase sigma-H factor (TIGR02859; HMM-score: 39.1)
    RNA polymerase sigma-70 factor, TIGR02952 family (TIGR02952; HMM-score: 26.7)
    RNA polymerase sigma-70 factor, Bacteroides expansion family 1 (TIGR02985; HMM-score: 20)
    RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family (TIGR02989; HMM-score: 15.7)
    Cellular processes Cellular processes Sporulation and germination RNA polymerase sigma-I factor (TIGR02895; HMM-score: 12.9)
    Genetic information processing Transcription Transcription factors RNA polymerase sigma-I factor (TIGR02895; HMM-score: 12.9)
    RNA polymerase sigma-W factor (TIGR02948; HMM-score: 12.3)
    RNA polymerase sigma-70 factor, sigma-E family (TIGR02983; HMM-score: 12.1)
  • TheSEED: see spr0979
  • PFAM:
    HTH (CL0123) Sigma70_r3; Sigma-70 region 3 (PF04539; HMM-score: 109.6)
    and 9 more
    Sigma70_r2; Sigma-70 region 2 (PF04542; HMM-score: 82.2)
    Sigma70_r4; Sigma-70, region 4 (PF04545; HMM-score: 73.5)
    no clan defined Sigma70_r1_2; Sigma-70 factor, region 1.2 (PF00140; HMM-score: 52.4)
    Sigma70_r1_1; Sigma-70 factor, region 1.1 (PF03979; HMM-score: 37.8)
    HTH (CL0123) DUF2316; Uncharacterized protein conserved in bacteria (DUF2316) (PF10078; HMM-score: 15.1)
    HTH_29; Winged helix-turn helix (PF13551; HMM-score: 14.4)
    DBD_HTH; Putative DNA-binding domain (PF18430; HMM-score: 13.6)
    no clan defined DUF4279; Domain of unknown function (DUF4279) (PF14106; HMM-score: 11.5)
    Met_repress (CL0057) RHH_1; Ribbon-helix-helix protein, copG family (PF01402; HMM-score: 11)

⊟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
  • DeepLocPro: Cytoplasmic
    • Cytoplasmic Score: 0.9884
    • Cytoplasmic Membrane Score: 0.0064
    • Cell wall & surface Score: 0
    • Extracellular Score: 0.0052
  • SignalP: no predicted signal peptide
    • SP(Sec/SPI): 0.004266
    • TAT(Tat/SPI): 0.000602
    • LIPO(Sec/SPII): 0.000553
  • predicted transmembrane helices (TMHMM): 0

⊟Accession numbers[edit | edit source]

⊟Protein sequence[edit | edit source]

  • MATKQKEVTTFDVQVAEFIRNHKQKGTATDDEINASLVIPFTLDADGIEDLLQRIQDAGISITDNEGNPSARVLSNEEEPELSDEDLIGSTSAKVNDPVRMYLKEIGVVPLLTNEEEKELALAVEAGDIEAKQRLAEANLRLVVSIAKRYVGRGMQFLDLIQEGNMGLMKAVDKFDYSKGFKFSTYATWWIRQAITRAIADQARTIRIPVHMVETINKLVREQRNLLQELGQDPTPEQIAERMDMTPDKVREILKIAQEPVSLETPIGEEDDSHLGDFIEDEVIENPVDYTTRIVLREQLDEILDTLTDREENVLRLRFGLDDGKMRTLEDVGKVFNVTRERIRQIEAKALRKLRQPSRSKPLRDFIED

⊟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]

  1. ↑ Jane A Thanassi, Sandra L Hartman-Neumann, Thomas J Dougherty, Brian A Dougherty, Michael J Pucci
    Identification of 113 conserved essential genes using a high-throughput gene disruption system in Streptococcus pneumoniae.
    Nucleic Acids Res: 2002, 30(14);3152-62
    [PubMed:12136097] [WorldCat.org] [DOI] (I p)

⊟Relevant publications[edit | edit source]

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