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F4GCJ4

- F4GCJ4_ALIDK

UniProt

F4GCJ4 - F4GCJ4_ALIDK

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Protein
RNA polymerase sigma factor RpoD
Gene
rpoD, Alide2_3600
Organism
Alicycliphilus denitrificans (strain DSM 14773 / CIP 107495 / K601)
Status
Unreviewed - 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 By similarity.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 By similarity.UniRule annotation

Regions

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
DNA bindingi761 – 78020H-T-H motif By similarityUniRule annotation
Add
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
Complete GO annotation...

GO - Biological processi

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

Keywords - Molecular functioni

Sigma factorUniRule annotationSAAS annotations

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-bindingUniRule annotationSAAS annotations

Enzyme and pathway databases

BioCyciADEN596154:GHU6-3645-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
RNA polymerase sigma factor RpoDUniRule annotation
Alternative name(s):
Sigma-70
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: Chromosome

Subcellular locationi

Cytoplasm By similarity UniRule annotationSAAS annotations

GO - Cellular componenti

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

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotations

Interactioni

Subunit structurei

Interacts transiently with the RNA polymerase catalytic core By similarity.UniRule annotation

Family & Domainsi

Region

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

Motif

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

Sequence similaritiesi

Belongs to the sigma-70 factor family.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

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MPVQKSAKSP KPASGTAAKA ASKAATPVKT AAKAPAKAAT AKAADAALQA    50
ATKVKTVPTP KTTAELTKAA DELLKKKPAR APKAAAAQAE ASEDAPKKKP 100
GRPAKAAGSA TAAAKAPAKR GRKPKAKEEG LEDDADLSDI EAELEGEPEA 150
PEAEAEAATA EKAKPLRMKI SKAKERALMK EFGLDETVLS EEDMAKRRSQ 200
LKKLITLGKT RGYLTQVEIS DHLPDKLVDA ETMEVVVAML GDMGVAVYEQ 250
TPDAETLFQN NVAPTATTVE EAEEEAEAAL STVDSEFGRT TDPVRMYMRE 300
MGTVELLTRE GEIEIAKRIE GGLMDMMEAI SASPATIAEI LNMGEEIREG 350
KVVISTVVDG FSNPEEADDY VAEEDFDEYD EEDDDDGKGG SKAMTRLLEK 400
LKTEALDRFD ELRSLFEKMH KIYDKEGYGS PAYMKVQHEI SAKLMTIRFT 450
AKTIEKLCDM VRAQVDDVRK KERELRRIIV DKCGMPQETF IKEFPPNLLN 500
LQWVEKQAAA GKPWSAVMQR NIPPIQELQQ HLIDLQSRVV VPLAELKAIN 550
KRMNQGEANS RDAKKEMIEA NLRLVISIAK KYTNRGLQFL DLIQEGNIGL 600
MKAVDKFEYR RGYKFSTYAT WWIRQAITRS IADQARTIRI PVHMIETINK 650
MNRISRQHLQ EFGFEPDASI LAAKMEIPED KIRKIMKIAK EPISMETPIG 700
DDDDSHLGDF IEDSNNTAPI DAAMQAGLRD VVKDILDGLT PREAKVLRMR 750
FGIEMSTDHT LEEVGKQFDV TRERIRQIEA KALRKLKHPS RSDKLRSFID 800
SL 802
Length:802
Mass (Da):89,003
Last modified:June 28, 2011 - v1
Checksum:iE02C9C576CE608A3
GO

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
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.
GeneIDi10484660.
KEGGiadk:Alide2_3600.
PATRICi54529923. VBIAliDen79014_3623.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBL
GenBank
DDBJ
Links Updated
CP002657 Genomic DNA. Translation: AEB85926.1 .
RefSeqi WP_013722798.1. NC_015422.1.
YP_004389442.1. NC_015422.1.

3D structure databases

ModBasei Search...

Protocols and materials databases

Structural Biology Knowledgebase Search...

Genome annotation databases

EnsemblBacteriai AEB85926 ; AEB85926 ; Alide2_3600 .
GeneIDi 10484660.
KEGGi adk:Alide2_3600.
PATRICi 54529923. VBIAliDen79014_3623.

Phylogenomic databases

KOi K03086.

Enzyme and pathway databases

BioCyci ADEN596154:GHU6-3645-MONOMER.

Family and domain databases

Gene3Di 1.10.10.10. 2 hits.
HAMAPi MF_00963. Sigma70_RpoD_SigA.
InterProi 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.
IPR012760. RNA_pol_sigma_RpoD_C.
IPR028630. Sigma70_RpoD.
IPR011991. WHTH_DNA-bd_dom.
[Graphical view ]
Pfami 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.
[Graphical view ]
PRINTSi PR00046. SIGMA70FCT.
SUPFAMi SSF88659. SSF88659. 2 hits.
SSF88946. SSF88946. 1 hit.
TIGRFAMsi TIGR02393. RpoD_Cterm. 1 hit.
TIGR02937. sigma70-ECF. 1 hit.
PROSITEi PS00715. SIGMA70_1. 1 hit.
PS00716. SIGMA70_2. 1 hit.
[Graphical view ]
ProtoNeti Search...

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 / K601.

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: September 3, 2014
This is version 27 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteome

External Data

Dasty 3

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