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Protein

RNA polymerase sigma factor RpoD

Gene

rpoD

Organism
Alicycliphilus denitrificans (strain DSM 14773 / CIP 107495 / K601)
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.UniRule annotation
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 bindingi761 – 78020H-T-H motifUniRule annotationAdd
BLAST

GO - Molecular functioni

  1. DNA binding Source: UniProtKB-HAMAP
  2. sequence-specific DNA binding transcription factor activity Source: InterPro
  3. sigma factor activity Source: UniProtKB-HAMAP

GO - Biological processi

  1. transcription initiation from bacterial-type RNA polymerase promoter Source: UniProtKB-HAMAP
Complete GO annotation...

Keywords - Molecular functioni

Sigma factorUniRule annotation

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-bindingUniRule annotation

Enzyme and pathway databases

BioCyciADEN596154:GHU6-3645-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:Alide2_3600Imported
OrganismiAlicycliphilus denitrificans (strain DSM 14773 / CIP 107495 / K601)Imported
Taxonomic identifieri596154 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaBetaproteobacteriaBurkholderialesComamonadaceaeAlicycliphilus
ProteomesiUP000007938 Componenti: Chromosome

Subcellular locationi

  1. Cytoplasm UniRule annotationSAAS annotation

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
Complete GO annotation...

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotation

Interactioni

Subunit structurei

Interacts transiently with the RNA polymerase catalytic core.UniRule annotation

Family & Domainsi

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni567 – 63771Sigma-70 factor domain-2UniRule annotationAdd
BLAST
Regioni646 – 72277Sigma-70 factor domain-3UniRule annotationAdd
BLAST
Regioni735 – 78854Sigma-70 factor domain-4UniRule annotationAdd
BLAST

Motif

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Motifi591 – 5944Interaction with polymerase core subunit RpoCUniRule annotation

Sequence similaritiesi

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

Phylogenomic databases

KOiK03086.

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.

F4GCJ4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MPVQKSAKSP KPASGTAAKA ASKAATPVKT AAKAPAKAAT AKAADAALQA
60 70 80 90 100
ATKVKTVPTP KTTAELTKAA DELLKKKPAR APKAAAAQAE ASEDAPKKKP
110 120 130 140 150
GRPAKAAGSA TAAAKAPAKR GRKPKAKEEG LEDDADLSDI EAELEGEPEA
160 170 180 190 200
PEAEAEAATA EKAKPLRMKI SKAKERALMK EFGLDETVLS EEDMAKRRSQ
210 220 230 240 250
LKKLITLGKT RGYLTQVEIS DHLPDKLVDA ETMEVVVAML GDMGVAVYEQ
260 270 280 290 300
TPDAETLFQN NVAPTATTVE EAEEEAEAAL STVDSEFGRT TDPVRMYMRE
310 320 330 340 350
MGTVELLTRE GEIEIAKRIE GGLMDMMEAI SASPATIAEI LNMGEEIREG
360 370 380 390 400
KVVISTVVDG FSNPEEADDY VAEEDFDEYD EEDDDDGKGG SKAMTRLLEK
410 420 430 440 450
LKTEALDRFD ELRSLFEKMH KIYDKEGYGS PAYMKVQHEI SAKLMTIRFT
460 470 480 490 500
AKTIEKLCDM VRAQVDDVRK KERELRRIIV DKCGMPQETF IKEFPPNLLN
510 520 530 540 550
LQWVEKQAAA GKPWSAVMQR NIPPIQELQQ HLIDLQSRVV VPLAELKAIN
560 570 580 590 600
KRMNQGEANS RDAKKEMIEA NLRLVISIAK KYTNRGLQFL DLIQEGNIGL
610 620 630 640 650
MKAVDKFEYR RGYKFSTYAT WWIRQAITRS IADQARTIRI PVHMIETINK
660 670 680 690 700
MNRISRQHLQ EFGFEPDASI LAAKMEIPED KIRKIMKIAK EPISMETPIG
710 720 730 740 750
DDDDSHLGDF IEDSNNTAPI DAAMQAGLRD VVKDILDGLT PREAKVLRMR
760 770 780 790 800
FGIEMSTDHT LEEVGKQFDV TRERIRQIEA KALRKLKHPS RSDKLRSFID

SL
Length:802
Mass (Da):89,003
Last modified:June 28, 2011 - v1
Checksum:iE02C9C576CE608A3
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002657 Genomic DNA. Translation: AEB85926.1.
RefSeqiWP_013722798.1. NC_015422.1.
YP_004389442.1. NC_015422.1.

Genome annotation databases

EnsemblBacteriaiAEB85926; AEB85926; Alide2_3600.
KEGGiadk:Alide2_3600.
PATRICi54529923. VBIAliDen79014_3623.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CP002657 Genomic DNA. Translation: AEB85926.1.
RefSeqiWP_013722798.1. NC_015422.1.
YP_004389442.1. NC_015422.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAEB85926; AEB85926; Alide2_3600.
KEGGiadk:Alide2_3600.
PATRICi54529923. VBIAliDen79014_3623.

Phylogenomic databases

KOiK03086.

Enzyme and pathway databases

BioCyciADEN596154:GHU6-3645-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. "Complete sequence of chromosome of Alicycliphilus denitrificans K601."
    US DOE Joint Genome Institute
    Lucas S., Han J., Lapidus A., Cheng J.-F., Goodwin L., Pitluck S., Peters L., Zeytun A., Detter J.C., Han C., Tapia R., Land M., Hauser L., Kyrpides N., Ivanova N., Mikhailova N., Pagani I., Oosterkamp M.
    , Pieper D., van Berkel W., Langenhoff A., Smidt H., Stams A., Woyke T.
    Submitted (APR-2011) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: DSM 14773 / CIP 107495 / K601Imported.

Entry informationi

Entry nameiF4GCJ4_ALIDK
AccessioniPrimary (citable) accession number: F4GCJ4
Entry historyi
Integrated into UniProtKB/TrEMBL: June 28, 2011
Last sequence update: June 28, 2011
Last modified: April 29, 2015
This is version 35 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteomeImported

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.