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P57163

- RPOD_BUCAI

UniProt

P57163 - RPOD_BUCAI

Protein

RNA polymerase sigma factor RpoD

Gene

rpoD

Organism
Buchnera aphidicola subsp. Acyrthosiphon pisum (strain APS) (Acyrthosiphon pisum symbiotic bacterium)
Status
Reviewed - Annotation score: 2 out of 5- Protein inferred from homologyi
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    • History
      Entry version 90 (01 Oct 2014)
      Sequence version 1 (01 Dec 2000)
      Previous versions | rss
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    Functioni

    Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released. This sigma factor is the primary sigma factor during exponential growth.UniRule annotation

    Regions

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    DNA bindingi572 – 59120H-T-H motifUniRule annotationAdd
    BLAST

    GO - Molecular functioni

    1. DNA binding Source: UniProtKB-HAMAP
    2. sequence-specific DNA binding transcription factor activity Source: InterPro
    3. sigma factor activity Source: UniProtKB-HAMAP

    GO - Biological processi

    1. transcription initiation from bacterial-type RNA polymerase promoter Source: UniProtKB-HAMAP

    Keywords - Molecular functioni

    Sigma factor

    Keywords - Biological processi

    Transcription, Transcription regulation

    Keywords - Ligandi

    DNA-binding

    Enzyme and pathway databases

    BioCyciBAPH107806:GBZJ-55-MONOMER.

    Names & Taxonomyi

    Protein namesi
    Recommended name:
    RNA polymerase sigma factor RpoDUniRule annotation
    Alternative name(s):
    Sigma-70UniRule annotation
    Gene namesi
    Name:rpoDUniRule annotation
    Ordered Locus Names:BU055
    OrganismiBuchnera aphidicola subsp. Acyrthosiphon pisum (strain APS) (Acyrthosiphon pisum symbiotic bacterium)
    Taxonomic identifieri107806 [NCBI]
    Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaEnterobacterialesEnterobacteriaceaeBuchnera
    ProteomesiUP000001806: Chromosome

    Subcellular locationi

    Cytoplasm UniRule annotation

    GO - Cellular componenti

    1. cytoplasm Source: UniProtKB-SubCell

    Keywords - Cellular componenti

    Cytoplasm

    PTM / Processingi

    Molecule processing

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Chaini1 – 612612RNA polymerase sigma factor RpoDPRO_0000093877Add
    BLAST

    Proteomic databases

    PRIDEiP57163.

    Interactioni

    Subunit structurei

    Interacts transiently with the RNA polymerase catalytic core.UniRule annotation

    Structurei

    3D structure databases

    ProteinModelPortaliP57163.
    SMRiP57163. Positions 116-445, 545-612.
    ModBaseiSearch...
    MobiDBiSearch...

    Family & Domainsi

    Region

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Regioni378 – 44871Sigma-70 factor domain-2UniRule annotationAdd
    BLAST
    Regioni457 – 53377Sigma-70 factor domain-3UniRule annotationAdd
    BLAST
    Regioni546 – 59954Sigma-70 factor domain-4UniRule annotationAdd
    BLAST

    Motif

    Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
    Motifi402 – 4054Interaction with polymerase core subunit RpoC

    Sequence similaritiesi

    Belongs to the sigma-70 factor family. RpoD/SigA subfamily.UniRule annotation

    Phylogenomic databases

    eggNOGiCOG0568.
    HOGENOMiHOG000270272.
    KOiK03086.
    OMAiFDFLVNS.
    OrthoDBiEOG6XHC70.

    Family and domain databases

    Gene3Di1.10.10.10. 2 hits.
    HAMAPiMF_00963. Sigma70_RpoD_SigA.
    InterProiIPR014284. RNA_pol_sigma-70_dom.
    IPR000943. RNA_pol_sigma70.
    IPR009042. RNA_pol_sigma70_r1_2.
    IPR007627. RNA_pol_sigma70_r2.
    IPR007624. RNA_pol_sigma70_r3.
    IPR007630. RNA_pol_sigma70_r4.
    IPR007631. RNA_pol_sigma_70_non-ess.
    IPR007127. RNA_pol_sigma_70_r1_1.
    IPR013325. RNA_pol_sigma_r2.
    IPR013324. RNA_pol_sigma_r3_r4.
    IPR012760. RNA_pol_sigma_RpoD_C.
    IPR028630. Sigma70_RpoD.
    IPR011991. WHTH_DNA-bd_dom.
    [Graphical view]
    PfamiPF04546. Sigma70_ner. 1 hit.
    PF03979. Sigma70_r1_1. 1 hit.
    PF00140. Sigma70_r1_2. 1 hit.
    PF04542. Sigma70_r2. 1 hit.
    PF04539. Sigma70_r3. 1 hit.
    PF04545. Sigma70_r4. 1 hit.
    [Graphical view]
    PRINTSiPR00046. SIGMA70FCT.
    SUPFAMiSSF88659. SSF88659. 2 hits.
    SSF88946. SSF88946. 1 hit.
    TIGRFAMsiTIGR02393. RpoD_Cterm. 1 hit.
    TIGR02937. sigma70-ECF. 1 hit.
    PROSITEiPS00715. SIGMA70_1. 1 hit.
    PS00716. SIGMA70_2. 1 hit.
    [Graphical view]

    Sequencei

    Sequence statusi: Complete.

    P57163-1 [UniParc]FASTAAdd to Basket

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    MDQNPQSQLK LLVTHGKEQG YLTYSEVNDH LPEDIIDSEQ IDDIIQMIND    50
    MGIPVVEEAP DADDLILNEI NTDTDEDAVE AATQVLSSVE SELGRTTDPV 100
    RMYMREMGTV ELLTREGEID IAKRIEEGIN QVQCSVSEYP EAITYLLEQY 150
    DRVKTGQIRL SDIITGFVDP NAEEIFPPTA IHIGSELLDE QQNNEEDEEN 200
    NQEDHEDDHS IDPELANEKF SELRIQYNNT NNTIKNKNRT HKDSLLEIYN 250
    LSEVFKQFRL VPKQFDHLVN NMRHMMERVR KQERIIIKLC VEICKMPKKN 300
    FIKIFPIKKI NYLWFIREQN TNQPWSENLK KVKEDVFISV KKLIKIEEET 350
    GLTIEQVKDI NKRMSIGEAK ARRAKKEMVE ANLRLVISIA KKYTNRGLQF 400
    LDLIQEGNIG LMKAVDKFEY RRGYKFSTYA TWWIRQAITR SIADQARTIR 450
    IPVHMIETIN KLNRISRQML QEIGREPTPE ELSEKMLIPE DKIRKVLKIA 500
    KEPISMETPI GDDDDSHLGD FIEDTTLELP LDSATSESLR SATHDVLSGL 550
    TAREAKVLRM RFGIDMNTDH TLEEVGKQFD VTRERIRQIE AKALRKLRHP 600
    SRSEVLRSFL DD 612
    Length:612
    Mass (Da):71,050
    Last modified:December 1, 2000 - v1
    Checksum:i6BDD03CC2E1D112A
    GO

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BA000003 Genomic DNA. Translation: BAB12778.1.
    RefSeqiNP_239892.1. NC_002528.1.

    Genome annotation databases

    EnsemblBacteriaiBAB12778; BAB12778; BAB12778.
    GeneIDi1109462.
    KEGGibuc:BU055.
    PATRICi21243616. VBIBucAph127364_0064.

    Cross-referencesi

    Sequence databases

    Select the link destinations:
    EMBL
    GenBank
    DDBJ
    Links Updated
    BA000003 Genomic DNA. Translation: BAB12778.1 .
    RefSeqi NP_239892.1. NC_002528.1.

    3D structure databases

    ProteinModelPortali P57163.
    SMRi P57163. Positions 116-445, 545-612.
    ModBasei Search...
    MobiDBi Search...

    Proteomic databases

    PRIDEi P57163.

    Protocols and materials databases

    Structural Biology Knowledgebase Search...

    Genome annotation databases

    EnsemblBacteriai BAB12778 ; BAB12778 ; BAB12778 .
    GeneIDi 1109462.
    KEGGi buc:BU055.
    PATRICi 21243616. VBIBucAph127364_0064.

    Phylogenomic databases

    eggNOGi COG0568.
    HOGENOMi HOG000270272.
    KOi K03086.
    OMAi FDFLVNS.
    OrthoDBi EOG6XHC70.

    Enzyme and pathway databases

    BioCyci BAPH107806:GBZJ-55-MONOMER.

    Family and domain databases

    Gene3Di 1.10.10.10. 2 hits.
    HAMAPi MF_00963. Sigma70_RpoD_SigA.
    InterProi IPR014284. RNA_pol_sigma-70_dom.
    IPR000943. RNA_pol_sigma70.
    IPR009042. RNA_pol_sigma70_r1_2.
    IPR007627. RNA_pol_sigma70_r2.
    IPR007624. RNA_pol_sigma70_r3.
    IPR007630. RNA_pol_sigma70_r4.
    IPR007631. RNA_pol_sigma_70_non-ess.
    IPR007127. RNA_pol_sigma_70_r1_1.
    IPR013325. RNA_pol_sigma_r2.
    IPR013324. RNA_pol_sigma_r3_r4.
    IPR012760. RNA_pol_sigma_RpoD_C.
    IPR028630. Sigma70_RpoD.
    IPR011991. WHTH_DNA-bd_dom.
    [Graphical view ]
    Pfami PF04546. Sigma70_ner. 1 hit.
    PF03979. Sigma70_r1_1. 1 hit.
    PF00140. Sigma70_r1_2. 1 hit.
    PF04542. Sigma70_r2. 1 hit.
    PF04539. Sigma70_r3. 1 hit.
    PF04545. Sigma70_r4. 1 hit.
    [Graphical view ]
    PRINTSi PR00046. SIGMA70FCT.
    SUPFAMi SSF88659. SSF88659. 2 hits.
    SSF88946. SSF88946. 1 hit.
    TIGRFAMsi TIGR02393. RpoD_Cterm. 1 hit.
    TIGR02937. sigma70-ECF. 1 hit.
    PROSITEi PS00715. SIGMA70_1. 1 hit.
    PS00716. SIGMA70_2. 1 hit.
    [Graphical view ]
    ProtoNeti Search...

    Publicationsi

    1. "Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp. APS."
      Shigenobu S., Watanabe H., Hattori M., Sakaki Y., Ishikawa H.
      Nature 407:81-86(2000) [PubMed] [Europe PMC] [Abstract]
      Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
      Strain: APS.

    Entry informationi

    Entry nameiRPOD_BUCAI
    AccessioniPrimary (citable) accession number: P57163
    Entry historyi
    Integrated into UniProtKB/Swiss-Prot: December 1, 2000
    Last sequence update: December 1, 2000
    Last modified: October 1, 2014
    This is version 90 of the entry and version 1 of the sequence. [Complete history]
    Entry statusiReviewed (UniProtKB/Swiss-Prot)
    Annotation programProkaryotic Protein Annotation Program

    Miscellaneousi

    Keywords - Technical termi

    Complete proteome, Reference proteome

    Documents

    1. Buchnera aphidicola (subsp. Acyrthosiphon pisum)
      Buchnera aphidicola (subsp. Acyrthosiphon pisum): entries and gene names
    2. SIMILARITY comments
      Index of protein domains and families

    External Data

    Dasty 3