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Protein

RNA polymerase sigma factor RpoD

Gene

rpoD

Organism
Buchnera aphidicola subsp. Acyrthosiphon pisum (strain APS) (Acyrthosiphon pisum symbiotic bacterium)
Status
Reviewed-Annotation score: Annotation score: 2 out of 5-Protein inferred from homologyi

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

GO - Biological processi

Complete GO annotation...

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 Componenti: Chromosome

Subcellular locationi

  • Cytoplasm UniRule annotation

GO - Cellular componenti

Complete GO annotation...

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

Protein-protein interaction databases

STRINGi107806.BU055.

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.
OMAiEMPEDKV.
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

« Hide

        10         20         30         40         50
MDQNPQSQLK LLVTHGKEQG YLTYSEVNDH LPEDIIDSEQ IDDIIQMIND
60 70 80 90 100
MGIPVVEEAP DADDLILNEI NTDTDEDAVE AATQVLSSVE SELGRTTDPV
110 120 130 140 150
RMYMREMGTV ELLTREGEID IAKRIEEGIN QVQCSVSEYP EAITYLLEQY
160 170 180 190 200
DRVKTGQIRL SDIITGFVDP NAEEIFPPTA IHIGSELLDE QQNNEEDEEN
210 220 230 240 250
NQEDHEDDHS IDPELANEKF SELRIQYNNT NNTIKNKNRT HKDSLLEIYN
260 270 280 290 300
LSEVFKQFRL VPKQFDHLVN NMRHMMERVR KQERIIIKLC VEICKMPKKN
310 320 330 340 350
FIKIFPIKKI NYLWFIREQN TNQPWSENLK KVKEDVFISV KKLIKIEEET
360 370 380 390 400
GLTIEQVKDI NKRMSIGEAK ARRAKKEMVE ANLRLVISIA KKYTNRGLQF
410 420 430 440 450
LDLIQEGNIG LMKAVDKFEY RRGYKFSTYA TWWIRQAITR SIADQARTIR
460 470 480 490 500
IPVHMIETIN KLNRISRQML QEIGREPTPE ELSEKMLIPE DKIRKVLKIA
510 520 530 540 550
KEPISMETPI GDDDDSHLGD FIEDTTLELP LDSATSESLR SATHDVLSGL
560 570 580 590 600
TAREAKVLRM RFGIDMNTDH TLEEVGKQFD VTRERIRQIE AKALRKLRHP
610
SRSEVLRSFL DD
Length:612
Mass (Da):71,050
Last modified:December 1, 2000 - v1
Checksum:i6BDD03CC2E1D112A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000003 Genomic DNA. Translation: BAB12778.1.
RefSeqiNP_239892.1. NC_002528.1.
WP_009874012.1. NC_002528.1.

Genome annotation databases

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

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BA000003 Genomic DNA. Translation: BAB12778.1.
RefSeqiNP_239892.1. NC_002528.1.
WP_009874012.1. NC_002528.1.

3D structure databases

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

Protein-protein interaction databases

STRINGi107806.BU055.

Proteomic databases

PRIDEiP57163.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

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

Phylogenomic databases

eggNOGiCOG0568.
HOGENOMiHOG000270272.
KOiK03086.
OMAiEMPEDKV.
OrthoDBiEOG6XHC70.

Enzyme and pathway databases

BioCyciBAPH107806:GBZJ-55-MONOMER.

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]
ProtoNetiSearch...

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: June 24, 2015
This is version 94 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

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.