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Protein

RNA polymerase sigma factor RpoD

Gene

rpoD

Organism
Shewanella violacea (strain JCM 10179 / CIP 106290 / LMG 19151 / DSS12)
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 bindingi574 – 59320H-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

BioCyciSVIO637905:GCRO-905-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:SVI_0878
OrganismiShewanella violacea (strain JCM 10179 / CIP 106290 / LMG 19151 / DSS12)
Taxonomic identifieri637905 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaAlteromonadalesShewanellaceaeShewanella
Proteomesi
  • UP000002350 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 – 614614RNA polymerase sigma factor RpoDPRO_0000093912Add
BLAST

Proteomic databases

PRIDEiO24744.

Interactioni

Subunit structurei

Interacts transiently with the RNA polymerase catalytic core.UniRule annotation

Protein-protein interaction databases

STRINGi637905.SVI_0878.

Structurei

3D structure databases

ProteinModelPortaliO24744.
SMRiO24744. Positions 114-613.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni380 – 45071Sigma-70 factor domain-2UniRule annotationAdd
BLAST
Regioni459 – 53577Sigma-70 factor domain-3UniRule annotationAdd
BLAST
Regioni548 – 60154Sigma-70 factor domain-4UniRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi404 – 4074Interaction 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.
OMAiRDAKKEM.
OrthoDBiPOG091H0012.

Family and domain databases

Gene3Di1.10.10.10. 2 hits.
HAMAPiMF_00963. Sigma70_RpoD_SigA. 1 hit.
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.

O24744-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MEHTPQSQLK LLLAKGKEQG YLTYAEVNDH LPADMVDADQ IEDIVQMIND
60 70 80 90 100
MGIRVYEQAP DADEIMMTED STDDDAAEEA AAALATVEAE LGRTTDPVRM
110 120 130 140 150
YMREMGTVEL LTREGEIVIA KRIEEGIYTV QASVAEYPPA IASILDQFDR
160 170 180 190 200
YEAEEVRLSD IISGFIDPNA ADIAPTATHI GSDLSQSERD KDDSKDDSKD
210 220 230 240 250
DDEDEEEEGP KGPDPEESKE RFTQLREVHE NTLKIIADKG RGHPEATVAL
260 270 280 290 300
FEIGELFKEF RLMPKQFDRL VKNMRATMDK VRVQERLIMK LCVEQAKMPK
310 320 330 340 350
KNFVKGYTAD ESSIAWFDTE LASKKPYAEG LKMIEPDVRR CRFKLDIIEK
360 370 380 390 400
ETGLAIASIK DINRRMSIGE AKARRAKKEM VEANLRLVIS IAKKYTNRGL
410 420 430 440 450
QFLDLIQEGN IGLMKAVDKF EYRRGYKFST YATWWIRQAI TRSIADQART
460 470 480 490 500
IRIPVHMIET INKLNRISRQ MLQEMGREPT PEELAERMLM PEDKIRKVLK
510 520 530 540 550
IAKEPISMET PIGDDEDSHL GDFIEDTTLE LPLDSATGES LRNATHEVLA
560 570 580 590 600
GLTAREAKVL RMRFGIDMNT DHTLEEVGKQ FDVTRERIRQ IEAKALRKLR
610
HPSRSEILKS FLDE
Length:614
Mass (Da):70,031
Last modified:January 1, 1998 - v1
Checksum:i652634FE5131AB39
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB002098 Genomic DNA. Translation: BAA19475.1.
AP011177 Genomic DNA. Translation: BAJ00849.1.
PIRiJC7652.

Genome annotation databases

EnsemblBacteriaiBAJ00849; BAJ00849; SVI_0878.
KEGGisvo:SVI_0878.
PATRICi35457961. VBISheVio92117_0852.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AB002098 Genomic DNA. Translation: BAA19475.1.
AP011177 Genomic DNA. Translation: BAJ00849.1.
PIRiJC7652.

3D structure databases

ProteinModelPortaliO24744.
SMRiO24744. Positions 114-613.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi637905.SVI_0878.

Proteomic databases

PRIDEiO24744.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiBAJ00849; BAJ00849; SVI_0878.
KEGGisvo:SVI_0878.
PATRICi35457961. VBISheVio92117_0852.

Phylogenomic databases

eggNOGiENOG4105DG1. Bacteria.
COG0568. LUCA.
HOGENOMiHOG000270272.
KOiK03086.
OMAiRDAKKEM.
OrthoDBiPOG091H0012.

Enzyme and pathway databases

BioCyciSVIO637905:GCRO-905-MONOMER.

Family and domain databases

Gene3Di1.10.10.10. 2 hits.
HAMAPiMF_00963. Sigma70_RpoD_SigA. 1 hit.
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...

Entry informationi

Entry nameiRPOD_SHEVD
AccessioniPrimary (citable) accession number: O24744
Secondary accession number(s): D4ZGQ0
Entry historyi
Integrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: January 1, 1998
Last modified: September 7, 2016
This is version 99 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.