Skip Header

You are using a version of Internet Explorer that may not display all features of this website. Please upgrade to a modern browser.
Contribute Send feedback
Read comments (?) or add your own

F4GCJ4 (F4GCJ4_ALIDK) Unreviewed, UniProtKB/TrEMBL

Last modified June 11, 2014. Version 26. Feed History...

Clusters with 100%, 90%, 50% identity | Third-party data text xml rdf/xml gff fasta
to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry infoCustomize order

Names and origin

Protein namesRecommended name:
RNA polymerase sigma factor RpoD HAMAP-Rule MF_00963
Alternative name(s):
Sigma-70 HAMAP-Rule MF_00963
Gene names
Name:rpoD HAMAP-Rule MF_00963
Ordered Locus Names:Alide2_3600 EMBL AEB85926.1
OrganismAlicycliphilus denitrificans (strain DSM 14773 / CIP 107495 / K601) [Complete proteome] [HAMAP] EMBL AEB85926.1
Taxonomic identifier596154 [NCBI]
Taxonomic lineageBacteriaProteobacteriaBetaproteobacteriaBurkholderialesComamonadaceaeAlicycliphilus

Protein attributes

Sequence length802 AA.
Sequence statusComplete.
Protein existenceInferred from homology

General annotation (Comments)

Function

Sigma factors are initiation factors that promote the attachment of RNA polymerase to specific initiation sites and are then released By similarity. RuleBase RU000715

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. HAMAP-Rule MF_00963

Subunit structure

Interacts transiently with the RNA polymerase catalytic core By similarity. HAMAP-Rule MF_00963

Subcellular location

Cytoplasm By similarity HAMAP-Rule MF_00963 SAAS SAAS000943.

Sequence similarities

Belongs to the sigma-70 factor family. RuleBase RU000715

Belongs to the sigma-70 factor family. RpoD/SigA subfamily. HAMAP-Rule MF_00963

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Regions

DNA binding761 – 78020H-T-H motif By similarity HAMAP-Rule MF_00963
Region567 – 63771Sigma-70 factor domain-2 By similarity HAMAP-Rule MF_00963
Region646 – 72277Sigma-70 factor domain-3 By similarity HAMAP-Rule MF_00963
Region735 – 78854Sigma-70 factor domain-4 By similarity HAMAP-Rule MF_00963
Motif591 – 5944Interaction with polymerase core subunit RpoC By similarity HAMAP-Rule MF_00963

Sequences

Sequence LengthMass (Da)Tools
F4GCJ4 [UniParc].

Last modified June 28, 2011. Version 1.
Checksum: E02C9C576CE608A3

FASTA80289,003
        10         20         30         40         50         60 
MPVQKSAKSP KPASGTAAKA ASKAATPVKT AAKAPAKAAT AKAADAALQA ATKVKTVPTP 

        70         80         90        100        110        120 
KTTAELTKAA DELLKKKPAR APKAAAAQAE ASEDAPKKKP GRPAKAAGSA TAAAKAPAKR 

       130        140        150        160        170        180 
GRKPKAKEEG LEDDADLSDI EAELEGEPEA PEAEAEAATA EKAKPLRMKI SKAKERALMK 

       190        200        210        220        230        240 
EFGLDETVLS EEDMAKRRSQ LKKLITLGKT RGYLTQVEIS DHLPDKLVDA ETMEVVVAML 

       250        260        270        280        290        300 
GDMGVAVYEQ TPDAETLFQN NVAPTATTVE EAEEEAEAAL STVDSEFGRT TDPVRMYMRE 

       310        320        330        340        350        360 
MGTVELLTRE GEIEIAKRIE GGLMDMMEAI SASPATIAEI LNMGEEIREG KVVISTVVDG 

       370        380        390        400        410        420 
FSNPEEADDY VAEEDFDEYD EEDDDDGKGG SKAMTRLLEK LKTEALDRFD ELRSLFEKMH 

       430        440        450        460        470        480 
KIYDKEGYGS PAYMKVQHEI SAKLMTIRFT AKTIEKLCDM VRAQVDDVRK KERELRRIIV 

       490        500        510        520        530        540 
DKCGMPQETF IKEFPPNLLN LQWVEKQAAA GKPWSAVMQR NIPPIQELQQ HLIDLQSRVV 

       550        560        570        580        590        600 
VPLAELKAIN KRMNQGEANS RDAKKEMIEA NLRLVISIAK KYTNRGLQFL DLIQEGNIGL 

       610        620        630        640        650        660 
MKAVDKFEYR RGYKFSTYAT WWIRQAITRS IADQARTIRI PVHMIETINK MNRISRQHLQ 

       670        680        690        700        710        720 
EFGFEPDASI LAAKMEIPED KIRKIMKIAK EPISMETPIG DDDDSHLGDF IEDSNNTAPI 

       730        740        750        760        770        780 
DAAMQAGLRD VVKDILDGLT PREAKVLRMR FGIEMSTDHT LEEVGKQFDV TRERIRQIEA 

       790        800 
KALRKLKHPS RSDKLRSFID SL 

« Hide

References

[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. expand/collapse author list , 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.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ
CP002657 Genomic DNA. Translation: AEB85926.1.
RefSeqYP_004389442.1. NC_015422.1.

3D structure databases

ModBaseSearch...
MobiDBSearch...

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaAEB85926; AEB85926; Alide2_3600.
GeneID10484660.
KEGGadk:Alide2_3600.
PATRIC54529923. VBIAliDen79014_3623.

Organism-specific databases

CMRSearch...

Phylogenomic databases

KOK03086.

Enzyme and pathway databases

BioCycADEN596154:GHU6-3645-MONOMER.

Family and domain databases

Gene3D1.10.10.10. 2 hits.
HAMAPMF_00963. Sigma70_RpoD_SigA.
InterProIPR014284. 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]
PfamPF04546. 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]
PRINTSPR00046. SIGMA70FCT.
SUPFAMSSF88659. SSF88659. 2 hits.
SSF88946. SSF88946. 1 hit.
TIGRFAMsTIGR02393. RpoD_Cterm. 1 hit.
TIGR02937. sigma70-ECF. 1 hit.
PROSITEPS00715. SIGMA70_1. 1 hit.
PS00716. SIGMA70_2. 1 hit.
[Graphical view]
ProtoNetSearch...

Entry information

Entry nameF4GCJ4_ALIDK
AccessionPrimary (citable) accession number: F4GCJ4
Entry history
Integrated into UniProtKB/TrEMBL: June 28, 2011
Last sequence update: June 28, 2011
Last modified: June 11, 2014
This is version 26 of the entry and version 1 of the sequence. [Complete history]
Entry statusUnreviewed (UniProtKB/TrEMBL)