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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: -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)DescriptionActionsGraphical viewLength
DNA bindingi574 – 593H-T-H motifUniRule annotationAdd BLAST20

GO - Molecular functioni

GO - Biological processi

Keywordsi

Molecular functionDNA-binding, Sigma factor
Biological processTranscription, Transcription regulation

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

Keywords - Cellular componenti

Cytoplasm

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000939121 – 614RNA polymerase sigma factor RpoDAdd BLAST614

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
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni380 – 450Sigma-70 factor domain-2UniRule annotationAdd BLAST71
Regioni459 – 535Sigma-70 factor domain-3UniRule annotationAdd BLAST77
Regioni548 – 601Sigma-70 factor domain-4UniRule annotationAdd BLAST54

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi404 – 407Interaction with polymerase core subunit RpoC4

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105DG1 Bacteria
COG0568 LUCA
HOGENOMiHOG000270272
KOiK03086
OMAiYKLPLFN
OrthoDBiPOG091H0012

Family and domain databases

Gene3Di1.10.10.10, 2 hits
HAMAPiMF_00963 Sigma70_RpoD_SigA, 1 hit
InterProiView protein in InterPro
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-like
IPR012760 RNA_pol_sigma_RpoD_C
IPR028630 Sigma70_RpoD
IPR036388 WH-like_DNA-bd_sf
PfamiView protein in Pfam
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
PRINTSiPR00046 SIGMA70FCT
SUPFAMiSSF88659 SSF88659, 2 hits
SSF88946 SSF88946, 1 hit
TIGRFAMsiTIGR02393 RpoD_Cterm, 1 hit
TIGR02937 sigma70-ECF, 1 hit
PROSITEiView protein in PROSITE
PS00715 SIGMA70_1, 1 hit
PS00716 SIGMA70_2, 1 hit

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

Similar proteinsi

Entry informationi

Entry nameiRPOD_SHEVD
AccessioniPrimary (citable) accession number: O24744
Secondary accession number(s): D4ZGQ0
Entry historyiIntegrated into UniProtKB/Swiss-Prot: May 30, 2000
Last sequence update: January 1, 1998
Last modified: April 25, 2018
This is version 108 of the entry and version 1 of the sequence. See complete history.
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

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