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Protein

RNA polymerase sigma factor RpoD

Gene

rpoD

Organism
Rhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)
Status
Reviewed-Annotation score: Annotation score: 3 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 bindingi644 – 66320H-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

BioCyciSMEL266834:GJF6-2369-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
RNA polymerase sigma factor RpoDUniRule annotation
Short name:
Sigma-A
Alternative name(s):
Major vegetative sigma factor
Gene namesi
Name:rpoDUniRule annotation
Synonyms:sigA
Ordered Locus Names:R02314
ORF Names:SMc01563
OrganismiRhizobium meliloti (strain 1021) (Ensifer meliloti) (Sinorhizobium meliloti)
Taxonomic identifieri266834 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhizobialesRhizobiaceaeSinorhizobium/Ensifer groupSinorhizobium
Proteomesi
  • UP000001976 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 – 684684RNA polymerase sigma factor RpoDPRO_0000093908Add
BLAST

Interactioni

Subunit structurei

Interacts transiently with the RNA polymerase catalytic core.UniRule annotation

Protein-protein interaction databases

STRINGi266834.SMc01563.

Structurei

3D structure databases

ProteinModelPortaliQ59753.
SMRiQ59753. Positions 618-683.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni450 – 52071Sigma-70 factor domain-2UniRule annotationAdd
BLAST
Regioni529 – 60577Sigma-70 factor domain-3UniRule annotationAdd
BLAST
Regioni618 – 67154Sigma-70 factor domain-4UniRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi474 – 4774Interaction with polymerase core subunit RpoC

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105DG1. Bacteria.
COG0568. LUCA.
HOGENOMiHOG000270272.
KOiK03086.
OMAiQIEDTMA.
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. 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.

Q59753-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MATKVKENEE ADVEREGAPD GPLLDLSDDA VKKMIKAAKK RGYVTMDELN
60 70 80 90 100
SVLPSEEVTS EQIEDTMSML SDMGINVIED EEAEEAAASD DDDGADEGES
110 120 130 140 150
EGGELAPASG TALAASKKKE PTDRTDDPVR MYLREMGSVE LLSREGEIAI
160 170 180 190 200
AKRIEAGRET MIAGLCESPL TFQALIIWRD ELNEGQTLLR EIIDLETTYS
210 220 230 240 250
GPEAKAAPQF QSPEKIEADR KAAEEKEKVR RTRTAANDDD ITNVGGEGQA
260 270 280 290 300
PEEEEEDDDE SNLSLAAMEA ELRPQVMETL DVIAETYKKL RKLQDQQVEA
310 320 330 340 350
RLAATGTLSP AQERRYKELK DELIKAVKSL SLNQNRIDAL VEQLYDISKR
360 370 380 390 400
LTQNEGRLLR LAESYGVKRE AFLEQYSGAE LDPNWMKSIS NLAGKGWKEF
410 420 430 440 450
ARAENQTIRD IRQEIQNLAT ETGISIAEFR RIVSMVQKGE REARIAKKEM
460 470 480 490 500
VEANLRLVIS IAKKYTNRGL QFLDLIQEGN IGLMKAVDKF EYRRGYKFST
510 520 530 540 550
YATWWIRQAI TRSIADQART IRIPVHMIET INKIVRTSRQ MLHEIGREPT
560 570 580 590 600
PEELAEKLAM PLEKVRKVLK IAKEPISLET PVGDEEDSHL GDFIEDKNAL
610 620 630 640 650
LPIDAAIQAN LRETTTRVLA SLTPREERVL RMRFGIGMNT DHTLEEVGQQ
660 670 680
FSVTRERIRQ IEAKALRKLK HPSRSRKLRS FLDS
Length:684
Mass (Da):77,174
Last modified:November 1, 1996 - v1
Checksum:i297E53CCD9FF4EF5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L47288 Genomic DNA. Translation: AAA88524.1.
AL591688 Genomic DNA. Translation: CAC46893.1.
RefSeqiNP_386420.1. NC_003047.1.
WP_003532953.1. NC_003047.1.

Genome annotation databases

EnsemblBacteriaiCAC46893; CAC46893; SMc01563.
GeneIDi1233981.
KEGGisme:SMc01563.
PATRICi23634109. VBISinMel96828_3792.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L47288 Genomic DNA. Translation: AAA88524.1.
AL591688 Genomic DNA. Translation: CAC46893.1.
RefSeqiNP_386420.1. NC_003047.1.
WP_003532953.1. NC_003047.1.

3D structure databases

ProteinModelPortaliQ59753.
SMRiQ59753. Positions 618-683.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi266834.SMc01563.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiCAC46893; CAC46893; SMc01563.
GeneIDi1233981.
KEGGisme:SMc01563.
PATRICi23634109. VBISinMel96828_3792.

Phylogenomic databases

eggNOGiENOG4105DG1. Bacteria.
COG0568. LUCA.
HOGENOMiHOG000270272.
KOiK03086.
OMAiQIEDTMA.
OrthoDBiEOG6XHC70.

Enzyme and pathway databases

BioCyciSMEL266834:GJF6-2369-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. 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. "Cloning and characterization of the sigA gene encoding the major sigma subunit of Rhizobium meliloti."
    Rushing B.G., Long S.R.
    J. Bacteriol. 177:6952-6957(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
    Strain: 1021.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 1021.
  3. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: 1021.

Entry informationi

Entry nameiRPOD_RHIME
AccessioniPrimary (citable) accession number: Q59753
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: November 1, 1996
Last modified: November 11, 2015
This is version 108 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. SIMILARITY comments
    Index of protein domains and families

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.