rpoD:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

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Standard Name

rpoD

Gene Synonym(s)

ECK3057, b3067, JW3039, alt[1], alt

Product Desc.

sigma70 factor[2]; RNA polymerase, sigma 70 (sigma D) factor[3];

Component of RNA polymerase sigma70[2]; RNA polymerase sigma 70[3]

RNA polymerase subunit, sigma 70, initiates transcription; housekeeping sigma[4]

Product Synonyms(s)

RNA polymerase, sigma 70 (sigma D) factor[1], B3067[2][1], Alt[2][1], RpoD[2][1], sigmaD factor[2][1], sigma D factor[3][1], sigma 70 factor[3][1] , alt, ECK3057, JW3039, b3067

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): rpoD[2], rpsU-dnaG-rpoD[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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Notes

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Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

rpoD

Mnemonic

RNA polymerase

Synonyms

ECK3057, b3067, JW3039, alt[1], alt

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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

69.21 minutes 

MG1655: 3211069..3212910
<gbrowseImage> name=NC_000913:3211069..3212910 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3145864..3147705
<gbrowseImage> name=NC_012967:3145864..3147705 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3098217..3100058
<gbrowseImage> name=NC_012759:3098217..3100058 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3211703..3213544
<gbrowseImage> name=NC_007779:3211703..3213544 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3308814..3310655
<gbrowseImage> name=NC_010473:3308814..3310655 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type Strain Genomic Location Evidence Reference Notes

Coding Start (SO:0000323)

MG1655

3211069

Edman degradation

PMID:1095419


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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

rpoD800

Growth Phenotype

Temperature-sensitive for growth at 42°C.

rpoD2 (alt)

R596H

Suppresses Ara(-) phenotype of crp and cya mutants

PMID:3889551 PMID:351406

rpoD40

Growth Phenotype

Nonsense mutation

PMID:7007812

rpoD(P504L)

P504L

Suppresses multiple amino acid auxotrophy of relA spoT double mutant

PMID:7563072

rpoD(S506F)

S506F

Suppresses multiple amino acid auxotrophy of relA spoT double mutant

PMID:7563072

rpoD800(ts)

deletion 329-342

temperature sensitive

CGSC:7186

rpoD285(ts)

deletion 329-342

temperature sensitive

PMID:2841288 PMID:3052291 PMID:366614 PMID:6355770

CGSC:7191

rpoD899(ts)

temperature sensitive

CGSC:9407

rpoD(K99E)

K99E

defective in abortive initiation

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Notes

The Keio collection[5] lists a deletion of rpoD, which is an essential gene. The insertion in this strain is a duplication of the rpoD region.[6]


Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW3039

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGAGCAAAACCCGCAGTCACA

Primer 2:CCATCGTCCAGGAAGCTACGCAG

19F2

Kohara Phage

Genobase

PMID:3038334

17E4

Kohara Phage

Genobase

PMID:3038334

tolC210::Tn10

Linked marker

CAG12184 = CGSC7437[7]

est. P1 cotransduction: 27% [8]

aer-3075::Tn10

Linked marker

CAG12152 = CGSC7438[7]

est. P1 cotransduction: 87% [8]

Synonyms:zgh-3075::Tn10, zgj-3075::Tn10

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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG10896

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10896

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000887

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947567

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0889

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010070

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

RpoD

Synonyms

RNA polymerase, sigma 70 (sigma D) factor[1], B3067[2][1], Alt[2][1], RpoD[2][1], sigmaD factor[2][1], sigma D factor[3][1], sigma 70 factor[3][1] , alt, ECK3057, JW3039, b3067

Product description

sigma70 factor[2]; RNA polymerase, sigma 70 (sigma D) factor[3];

Component of RNA polymerase sigma70[2]; RNA polymerase sigma 70[3]

RNA polymerase subunit, sigma 70, initiates transcription; housekeeping sigma[4]

EC number (for enzymes)


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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status

GO:0016987

sigma factor activity

PMID:4882047

IDA: Inferred from Direct Assay

F

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000943

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007127

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007624

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007627

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007630

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007631

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR009042

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012760

F

Seeded from EcoCyc (v14.0)

complete

GO:0009408

response to heat

PMID:8349564

IEP: Inferred from Expression Pattern

P

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013324

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013325

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR014284

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0238

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000943

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007624

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007627

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007630

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007631

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR009042

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013324

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013325

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR014284

F

Seeded from EcoCyc (v14.0)

complete

GO:0005515

protein binding

PMID:10764785

IPI: Inferred from Physical Interaction

UniProtKB:P0A8T7

F

Seeded from EcoCyc (v14.0)

complete

GO:0006350

transcription

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0804

P

Seeded from EcoCyc (v14.0)

complete

GO:0006352

transcription initiation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000943

P

Seeded from EcoCyc (v14.0)

complete

GO:0006352

transcription initiation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007624

P

Seeded from EcoCyc (v14.0)

complete

GO:0006352

transcription initiation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007627

P

Seeded from EcoCyc (v14.0)

complete

GO:0006352

transcription initiation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007630

P

Seeded from EcoCyc (v14.0)

complete

GO:0006352

transcription initiation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007631

P

Seeded from EcoCyc (v14.0)

complete

GO:0006352

transcription initiation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR009042

P

Seeded from EcoCyc (v14.0)

complete

GO:0006352

transcription initiation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012760

P

Seeded from EcoCyc (v14.0)

complete

GO:0006352

transcription initiation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013324

P

Seeded from EcoCyc (v14.0)

complete

GO:0006352

transcription initiation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013325

P

Seeded from EcoCyc (v14.0)

complete

GO:0006352

transcription initiation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR014284

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000943

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007624

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007627

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007630

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007631

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR009042

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012760

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013324

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013325

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR014284

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0731

P

Seeded from EcoCyc (v14.0)

complete

GO:0016987

sigma factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000943

F

Seeded from EcoCyc (v14.0)

complete

GO:0016987

sigma factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007624

F

Seeded from EcoCyc (v14.0)

complete

GO:0016987

sigma factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007627

F

Seeded from EcoCyc (v14.0)

complete

GO:0016987

sigma factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007630

F

Seeded from EcoCyc (v14.0)

complete

GO:0016987

sigma factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007631

F

Seeded from EcoCyc (v14.0)

complete

GO:0016987

sigma factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR009042

F

Seeded from EcoCyc (v14.0)

complete

GO:0016987

sigma factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012760

F

Seeded from EcoCyc (v14.0)

complete

GO:0016987

sigma factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013324

F

Seeded from EcoCyc (v14.0)

complete

GO:0016987

sigma factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013325

F

Seeded from EcoCyc (v14.0)

complete

GO:0016987

sigma factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR014284

F

Seeded from EcoCyc (v14.0)

complete

GO:0016987

sigma factor activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0731

F

Seeded from EcoCyc (v14.0)

complete

GO:0030528

transcription regulator activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007127

F

Seeded from EcoCyc (v14.0)

complete

GO:0045449

regulation of transcription

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007127

P

Seeded from EcoCyc (v14.0)

complete

GO:0045449

regulation of transcription

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0805

P

Seeded from EcoCyc (v14.0)

complete

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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

Subunits of RNA polymerase sigma70

could be indirect

Protein

rpoC

PMID:15690043

Experiment(s):EBI-886257, EBI-879261, EBI-883046, EBI-892741

Protein

rpoZ

PMID:15690043

Experiment(s):EBI-886257, EBI-879161, EBI-882858, EBI-892741

Protein

rpsB

PMID:15690043

Experiment(s):EBI-886257

Protein

rpsC

PMID:15690043

Experiment(s):EBI-886257

Protein

rpsD

PMID:15690043

Experiment(s):EBI-886257

Protein

rpsE

PMID:15690043

Experiment(s):EBI-886257

Protein

rpsG

PMID:15690043

Experiment(s):EBI-886257, EBI-892741

Protein

accA

PMID:15690043

Experiment(s):EBI-886257

Protein

infB

PMID:15690043

Experiment(s):EBI-886257, EBI-892741

Protein

nusA

PMID:15690043

Experiment(s):EBI-886257, EBI-892741, EBI-893117

Protein

rplA

PMID:15690043

Experiment(s):EBI-886257, EBI-892741

Protein

rplB

PMID:15690043

Experiment(s):EBI-886257

Protein

rplD

PMID:15690043

Experiment(s):EBI-886257, EBI-892741

Protein

rplO

PMID:15690043

Experiment(s):EBI-886257

Protein

rplV

PMID:15690043

Experiment(s):EBI-886257

Protein

rpoA

PMID:15690043

Experiment(s):EBI-886257, EBI-879354, EBI-883271, EBI-892741

Protein

rpoB

PMID:15690043

Experiment(s):EBI-886257, EBI-879304, EBI-883170, EBI-892741

Protein

pepB

PMID:15690043

Experiment(s):EBI-892741

Protein

rho

PMID:15690043

Experiment(s):EBI-892741

Protein

rplL

PMID:15690043

Experiment(s):EBI-892741

Protein

rplS

PMID:15690043

Experiment(s):EBI-892741

Protein

rplU

PMID:15690043

Experiment(s):EBI-892741

Protein

rpmB

PMID:15690043

Experiment(s):EBI-892741

Protein

rpsA

PMID:15690043

Experiment(s):EBI-892741

Protein

rpsF

PMID:15690043

Experiment(s):EBI-892741

Protein

tufA

PMID:15690043

Experiment(s):EBI-892741

Protein

yeeX

PMID:15690043

Experiment(s):EBI-892741

Protein

rho

PMID:16606699

Experiment(s):EBI-1144702

Protein

rpoB

PMID:16606699

Experiment(s):EBI-1144702

Protein

dnaG

PMID:16606699

Experiment(s):EBI-1144702

Protein

nadE

PMID:16606699

Experiment(s):EBI-1144702

Protein

rplE

PMID:16606699

Experiment(s):EBI-1144702

Protein

matC

PMID:16606699

Experiment(s):EBI-1144702

Protein

potD

PMID:16606699

Experiment(s):EBI-1144702

Protein

rpsB

PMID:16606699

Experiment(s):EBI-1144702

Protein

rpoC

PMID:16606699

Experiment(s):EBI-1144702

Protein

mfd

PMID:16606699

Experiment(s):EBI-1144702

Protein

yfaS

PMID:16606699

Experiment(s):EBI-1144702

Protein

yniC

PMID:16606699

Experiment(s):EBI-1144702

Protein

gadX

PMID:16606699

Experiment(s):EBI-1144702

Protein

rplD

PMID:16606699

Experiment(s):EBI-1144702

Protein

gmhB

PMID:16606699

Experiment(s):EBI-1144702

Protein

blc

PMID:16606699

Experiment(s):EBI-1144702

Protein

pepB

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpmB

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplU

PMID:19402753

LCMS(ID Probability):99.6

Protein

infB

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):10.756318

Protein

rpsF

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):6.241428

Protein

rho

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplS

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):29.174139

Protein

rplD

PMID:19402753

LCMS(ID Probability):99.4 MALDI(Z-score):17.053160

Protein

rpoZ

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):27.779532

Protein

nusA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):23.202327

Protein

rpoB

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):26.899873

Protein

rpoC

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):14.555460

Protein

yeeX

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplL

PMID:19402753

LCMS(ID Probability):99.6

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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

MEQNPQSQLK LLVTRGKEQG YLTYAEVNDH LPEDIVDSDQ IEDIIQMIND MGIQVMEEAP
DADDLMLAEN TADEDAAEAA AQVLSSVESE IGRTTDPVRM YMREMGTVEL LTREGEIDIA
KRIEDGINQV QCSVAEYPEA ITYLLEQYDR VEAEEARLSD LITGFVDPNA EEDLAPTATH
VGSELSQEDL DDDEDEDEED GDDDSADDDN SIDPELAREK FAELRAQYVV TRDTIKAKGR
SHATAQEEIL KLSEVFKQFR LVPKQFDYLV NSMRVMMDRV RTQERLIMKL CVEQCKMPKK
NFITLFTGNE TSDTWFNAAI AMNKPWSEKL HDVSEEVHRA LQKLQQIEEE TGLTIEQVKD
INRRMSIGEA KARRAKKEMV EANLRLVISI AKKYTNRGLQ FLDLIQEGNI GLMKAVDKFE
YRRGYKFSTY ATWWIRQAIT RSIADQARTI RIPVHMIETI NKLNRISRQM LQEMGREPTP
EELAERMLMP EDKIRKVLKI AKEPISMETP IGDDEDSHLG DFIEDTTLEL PLDSATTESL
RAATHDVLAG LTAREAKVLR MRFGIDMNTD YTLEEVGKQF DVTRERIRQI EAKALRKLRH
PSRSEVLRSF LDD
Length

613

Mol. Wt

70.264 kDa

pI

4.5 (calculated)

Extinction coefficient

41,370 - 41,745 (calc based on 13 Y, 4 W, and 3 C residues)

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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Domain

379..449

PF04542 Sigma-70 region 2

PMID:19920124

Domain

547..600

PF04545 Sigma-70, region 4

PMID:19920124

Domain

137..348

PF04546 Sigma-70, non-essential region

PMID:19920124

Domain

1..81

PF03979 Sigma-70 factor, region 1.1

PMID:19920124

Domain

95..130

PF00140 Sigma-70 factor, region 1.2

PMID:19920124

Domain

458..535

PF04539 Sigma-70 region 3

PMID:19920124

92-132

Region 1.2

377-447

Region 2.1-2.4

457-515

Region 3.0-3.1

525-535

Region 3.2

545-595

Region 4.1-4.2

-35 recognition


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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=rpoD taxon=562,83333 </beststructure>

Models

View models at:

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</protect>

Structure figures

<protect>

</protect>

Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16130963

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947567

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010070

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P00579

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10896

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10896

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947567

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000887

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0889

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Expression

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{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.


Cellular Levels

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See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MC4100

1.32E+03

molecules/cell

  • Medium: median data from rich and minimal media
  • Temperature (°C): 37
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

emPAI

PMID:18304323

Protein

E. coli K-12 MG1655

11809

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

2284

molecules/cell/generation

  • Medium: MOPS Minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

5289

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

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Notes

Transcription and Transcriptional Regulation

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<protect>

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

rpoD

rpsU-dnaG-rpoD

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Figure courtesy of RegulonDB

</protect>

Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:3211049..3211089 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

</protect>

Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b3067 (EcoliWiki Page)

NCBI GEO profiles for rpoD

microarray

GenExpDB:b3067 (EcoliWiki Page)

Summary of data for rpoD from multiple microarray studies

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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes

GFP Fusion

Intergenic region (3210420..3210769) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ20; Well:D8[9]

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Notes

Accessions Related to rpoD Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG10896

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0889

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3067

EcoGene

EcoGene:EG10896

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000887

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010070

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Evolution

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{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism Homologs (Statistics) Comments

Arabidopsis thaliana

  • AT5G13730 (score: 1.000; bootstrap: 69%)

From Inparanoid:20070104

Oryza gramene

  • Q7EY07 (score: 1.000; bootstrap: 53%)
  • O48655 (score: 1.000; bootstrap: 52%)
  • Q7EY08 (score: 1.000; bootstrap: 53%)
  • Q9ZP70 (score: 0.867)
  • O24348 (score: 0.861)
  • Q9ZTI2 (score: 0.845)
  • Q9ZTI3 (score: 0.839)

From Inparanoid:20070104

Shigella flexneri

RPOD

From SHIGELLACYC

E. coli O157

RPOD

From ECOO157CYC

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Do-It-Yourself Web Tools

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Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

Pfam (EcoliWiki Page)

PF04542 Sigma-70 region 2

Pfam (EcoliWiki Page)

PF04545 Sigma-70, region 4

Superfamily (EcoliWiki Page)

SUPERFAMILY:88659

Superfamily (EcoliWiki Page)

SUPERFAMILY:88659

Superfamily (EcoliWiki Page)

SUPERFAMILY:88946

Pfam (EcoliWiki Page)

PF04546 Sigma-70, non-essential region

Pfam (EcoliWiki Page)

PF03979 Sigma-70 factor, region 1.1

Pfam (EcoliWiki Page)

PF00140 Sigma-70 factor, region 1.2

Pfam (EcoliWiki Page)

PF04539 Sigma-70 region 3

EcoCyc

EcoCyc:EG10896

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10896

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000887

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0889

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010070

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 1.13 1.14 1.15 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 2.11 2.12 2.13 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 3.6 3.7 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed
  6. ↑ Yamamoto, N et al. (2009) Update on the Keio collection of Escherichia coli single-gene deletion mutants. Mol. Syst. Biol. 5 335 PubMed
  7. ↑ 7.0 7.1 CGSC: The Coli Genetics Stock Center
  8. ↑ 8.0 8.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
  9. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

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