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Protein

RNA polymerase sigma factor RpoD

Gene

sigA

Organism
Bradyrhizobium japonicum
Status
Unreviewed-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.SAAS annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi679 – 69820H-T-H motifUniRule annotationAdd
BLAST

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Sigma factorUniRule annotationSAAS annotation

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-bindingUniRule annotationSAAS annotation

Names & Taxonomyi

Protein namesi
Recommended name:
RNA polymerase sigma factor RpoDUniRule annotation
Alternative name(s):
Sigma-70UniRule annotation
Gene namesi
Name:sigAImported
Synonyms:rpoDUniRule annotation
ORF Names:AF336_39140Imported
OrganismiBradyrhizobium japonicumImported
Taxonomic identifieri375 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesBradyrhizobiaceaeBradyrhizobium
Proteomesi
  • UP000037708 Componenti: Unassembled WGS sequence

Subcellular locationi

  • Cytoplasm UniRule annotationSAAS annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotation

Interactioni

Subunit structurei

Interacts transiently with the RNA polymerase catalytic core.UniRule annotationSAAS annotation

Protein-protein interaction databases

STRINGi1037409.BJ6T_19620.

Structurei

3D structure databases

ProteinModelPortaliP94321.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini509 – 52214RNA_pol_sigma70InterPro annotationAdd
BLAST
Domaini678 – 70427RNA_pol_sigma70InterPro annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni485 – 55571Sigma-70 factor domain-2UniRule annotationAdd
BLAST
Regioni564 – 64077Sigma-70 factor domain-3UniRule annotationAdd
BLAST
Regioni653 – 70654Sigma-70 factor domain-4UniRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi509 – 5124Interaction with polymerase core subunit RpoCUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105DG1. Bacteria.
COG0568. LUCA.
HOGENOMiHOG000270272.

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. 2 hits.
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.

P94321-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MATKAKTLQA KDKEKDDKAA DAPEKDSQDA PSPLLDLSDA AVKKMIKQAK
60 70 80 90 100
KRGFVTFDQL NEVLPSDQTS PEQIEDIMSM LSDMGINVTE ADDSEGEEDK
110 120 130 140 150
DEGGEDETDN ELVEVTQKAV TEVKKSEPGE RTDDPVRMYL REMGTVELLS
160 170 180 190 200
REGEIAIAKR IEAGREAMIA GLCESPLSFQ AIIIWRDELN EGKIFLRDII
210 220 230 240 250
DLEATYAGPE AKGGMNTAMI GGPTGENGEA TAEGGEAVAV TGAAPAHVAP
260 270 280 290 300
PAAPPAPTPF RAAPAAGNGA EAEKDPGEAA AEADMDEDDE FENQMSLAAI
310 320 330 340 350
EAELKPKVVE IFDKIAESYK KLRKLQEQDI QNQLESTSHG PSLSPHQERK
360 370 380 390 400
YRKLKDEIIV EVKSLRLNQA RIDSLVEQLY DINKRLVSHE GRLMRLADSH
410 420 430 440 450
GVAREDFLRN YTGSELDPRW LNRVSKLSAK GWKNFVHHEK DRIKDLRHEV
460 470 480 490 500
HQLAALTGLE IVEFRKIVHS VQKGEREARQ AKKEMVEANL RLVISIAKKY
510 520 530 540 550
TNRGLQFLDL IQEGNIGLMK AVDKFEYRRG YKFSTYATWW IRQAITRSIA
560 570 580 590 600
DQARTIRIPV HMIETINKIV RTSRQMLNEI GREPTPEELA EKLGMPLEKV
610 620 630 640 650
RKVLKIAKEP LSLETPVGDE EDSHLGDFIE DKNAILPIDA AIQSNLRETT
660 670 680 690 700
TRVLASLTPR EERVLRMRFG IGMNTDHTLE EVGQQFSVTR ERIRQIEAKA
710
LRKLKHPSRS RKLRSFLDN
Length:719
Mass (Da):80,652
Last modified:May 1, 1997 - v1
Checksum:i4B0A6B87F8D43162
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X99588 Genomic DNA. Translation: CAA67902.1.
LGUJ01000044 Genomic DNA. Translation: KOY04978.1.
RefSeqiWP_011090084.1. NZ_LGUJ01000044.1.

Genome annotation databases

EnsemblBacteriaiKOY04978; KOY04978; AF336_39140.
PATRICi21198639. VBIBraJap65052_7551.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
X99588 Genomic DNA. Translation: CAA67902.1.
LGUJ01000044 Genomic DNA. Translation: KOY04978.1.
RefSeqiWP_011090084.1. NZ_LGUJ01000044.1.

3D structure databases

ProteinModelPortaliP94321.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi1037409.BJ6T_19620.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiKOY04978; KOY04978; AF336_39140.
PATRICi21198639. VBIBraJap65052_7551.

Phylogenomic databases

eggNOGiENOG4105DG1. Bacteria.
COG0568. LUCA.
HOGENOMiHOG000270272.

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. 2 hits.
TIGRFAMsiTIGR02393. RpoD_Cterm. 1 hit.
TIGR02937. sigma70-ECF. 1 hit.
PROSITEiPS00715. SIGMA70_1. 1 hit.
PS00716. SIGMA70_2. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Dissection of the transcription machinery for housekeeping genes of Bradyrhizobium japonicum."
    Beck C., Marty R., Klausli S., Hennecke H., Gottfert M.
    J. Bacteriol. 179:364-369(1997) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE.
    Strain: 110spc4Imported.
  2. Noorani M.
    Submitted (JUL-2015) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Is-1Imported.
  3. "Draft genome of Bradyrhizobium japonicum Is-1, which is incompatible with Rj2-genotype soybeans."
    Sakata T.
    Submitted (SEP-2015) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: Is-1Imported.

Entry informationi

Entry nameiP94321_BRAJP
AccessioniPrimary (citable) accession number: P94321
Secondary accession number(s): D4AFB0, E7FHX8, Q79U39
Entry historyi
Integrated into UniProtKB/TrEMBL: May 1, 1997
Last sequence update: May 1, 1997
Last modified: July 6, 2016
This is version 117 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteomeImported

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 one 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.