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Protein

RNA polymerase sigma factor RpoD

Gene

rpoD

Organism
Pseudomonas putida (Arthrobacter siderocapsulatus)
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. This sigma factor is the primary sigma factor during exponential growth.SAAS annotation

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
DNA bindingi576 – 595H-T-H motifUniRule annotationAdd BLAST20

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Sigma factorUniRule annotationSAAS annotation

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-bindingUniRule annotationSAAS annotation

Names & Taxonomyi

Protein namesi
Recommended name:
RNA polymerase sigma factor RpoDUniRule annotation
Alternative name(s):
Sigma-70UniRule annotation
Gene namesi
Name:rpoDUniRule annotationImported
ORF Names:AYO08_05815Imported
OrganismiPseudomonas putida (Arthrobacter siderocapsulatus)Imported
Taxonomic identifieri303 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaGammaproteobacteriaPseudomonadalesPseudomonadaceaePseudomonas
Proteomesi
  • UP000078222 Componenti: Unassembled WGS sequence

Subcellular locationi

  • Cytoplasm UniRule annotationSAAS annotation

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

CytoplasmUniRule annotationSAAS annotation, DNA-directed RNA polymeraseImported

Interactioni

Subunit structurei

Interacts transiently with the RNA polymerase catalytic core.UniRule annotationSAAS annotation

Protein-protein interaction databases

STRINGi160488.PP_0387.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini406 – 419RNA_pol_sigma70InterPro annotationAdd BLAST14
Domaini575 – 601RNA_pol_sigma70InterPro annotationAdd BLAST27

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Regioni382 – 452Sigma-70 factor domain-2UniRule annotationAdd BLAST71
Regioni461 – 537Sigma-70 factor domain-3UniRule annotationAdd BLAST77
Regioni550 – 603Sigma-70 factor domain-4UniRule annotationAdd BLAST54

Motif

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Motifi406 – 409Interaction with polymerase core subunit RpoCUniRule annotation4

Sequence similaritiesi

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

Phylogenomic databases

eggNOGiENOG4105DG1. Bacteria.
COG0568. LUCA.

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.

O54540-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MSGKAQQQSR IKELITRGRE QGYLTYAEVN DHLPEDISDP EQVEDIIRMI
60 70 80 90 100
NDMGINVFES APDADALLLA EADTDEAAAE EAAAALAAVE TDIGRTTDPV
110 120 130 140 150
RMYMREMGTV ELLTREGEIE IAKRIEEGIR EVMGAIAHFP GTVDYILGEY
160 170 180 190 200
DRVTTEGGRL SDVLSGYIDP DDNIAAPTEE VPIPGAKAAA AKEESDDDEE
210 220 230 240 250
ESESGDDEEE AESGPDPVVA AQRFGAVSDQ LQATSKVLKK NGRNHKESIE
260 270 280 290 300
ALQALADLFM PIKLVPKQFE VLVERVRDAL NRLRQQERAI MQLCVRDARM
310 320 330 340 350
PRADFLRMFP SNETDQTWSG DLAKRNTKWA AALGEKNAAI VACQQKLIDL
360 370 380 390 400
ETETGLTVAE IKEINRRMSI GEAKARRAKK EMVEANLRLV ISIAKKYTNR
410 420 430 440 450
GLQFLDLIQE GNIGLMKAVD KFEYRRGYKF STYATWWIRQ AITRSIADQA
460 470 480 490 500
RTIRIPVHMI ETINKLNRIS RQMLQEMGRE PTPEELGERM EMPEDKIRKV
510 520 530 540 550
LKIAKEPISM ETPIGDDEDS HLGDFIEDST MQSPIDVATV ESLKEATRDV
560 570 580 590 600
LSGLTAREAK VLRMRFGIDM NTDHTLEEVG KQFDVTRERI RQIEAKALRK
610
LRHPTRSEHL RSFLDE
Length:616
Mass (Da):69,397
Last modified:June 1, 1998 - v1
Checksum:i74F98D281EEFC6D6
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U93292 Genomic DNA. Translation: AAB87749.1.
AF014397 Genomic DNA. Translation: AAC38073.1.
LSUZ01000113 Genomic DNA. Translation: OAS13096.1.
RefSeqiWP_003255578.1. NZ_LSUZ01000113.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U93292 Genomic DNA. Translation: AAB87749.1.
AF014397 Genomic DNA. Translation: AAC38073.1.
LSUZ01000113 Genomic DNA. Translation: OAS13096.1.
RefSeqiWP_003255578.1. NZ_LSUZ01000113.1.

3D structure databases

ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi160488.PP_0387.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4105DG1. Bacteria.
COG0568. LUCA.

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 nameiO54540_PSEPU
AccessioniPrimary (citable) accession number: O54540
Entry historyi
Integrated into UniProtKB/TrEMBL: June 1, 1998
Last sequence update: June 1, 1998
Last modified: November 2, 2016
This is version 98 of the entry and version 1 of the sequence. [Complete history]
Entry statusiUnreviewed (UniProtKB/TrEMBL)

Miscellaneousi

Keywords - Technical termi

Complete proteomeImported

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.