dhaR:On One Page

From EcoliWiki
Jump to: navigation, search

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

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

Quickview

[back to top]


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

<protect>

Standard Name

dhaR

Gene Synonym(s)

ECK1189, b1201, JW5188, ptsD, ycgU[1], ycgU

Product Desc.

DhaR transcriptional dual regulator[2][3]

Transcription activator of the dhaKLM operon[4]

Product Synonyms(s)

predicted DNA-binding transcriptional regulator, dihydroxyacetone[1], B1201[2][1], YcgU[2][1], DhaR[2][1] , ECK1189, JW5188, ptsD, ycgU, b1201

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): dhaR[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

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

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]


DhaR is an auto-repressor of dhaR transcription. DhaL and DhaK are co-activator and co-repressor, respectively, of DhaR. AAA(+) family.[4]



Gene

[back to top]


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

Nomenclature

[back to top]


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

Standard name

dhaR

Mnemonic

Dihydroxyacetone

Synonyms

ECK1189, b1201, JW5188, ptsD, ycgU[1], ycgU

</protect>

Notes

Location(s) and DNA Sequence

[back to top]


<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

26.95 minutes 

MG1655: 1250289..1252208
<gbrowseImage> name=NC_000913:1250289..1252208 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1251216..1253135
<gbrowseImage> name=NC_012967:1251216..1253135 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1139010..1140929
<gbrowseImage> name=NC_012759:1139010..1140929 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1252643..1254562
<gbrowseImage> name=NC_007779:1252643..1254562 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1290530..1292449
<gbrowseImage> name=NC_010473:1290530..1292449 source=DH10B preset=GeneLocation </gbrowseImage>

</protect>

Notes

Sequence Features

[back to top]


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

Feature Type Strain Genomic Location Evidence Reference Notes

<protect></protect>

Notes

Alleles and Phenotypes

[back to top]


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

ΔdhaR (Keio:JW5188)

deletion

deletion

PMID:16738554

Shigen


<protect></protect>

Notes

Genetic Interactions

[back to top]


<protect>

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

</protect>

Notes

Genetic Resources

[back to top]


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

Resource Resource Type Source Notes/Reference

JW5188

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAGTGGCGCTTTTAACAACGA

Primer 2:CCTACCCGGCGCTTAAACTGCCC

7C10

Kohara Phage

Genobase

PMID:3038334

12A3

Kohara Phage

Genobase

PMID:3038334

fadR13::Tn10

Linked marker

CAG18497 = CGSC7365[5]

est. P1 cotransduction: 56% [6]

oppC506::Tn10

Linked marker

CAG12169 = CGSC7369[5]

est. P1 cotransduction: 8% [6]
Synonyms:zch-506::Tn10, zci-506::Tn10

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:G6628

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13902

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003223

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945743

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3661

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004033

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]



Product(s)

[back to top]


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

Nomenclature

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

Standard name

DhaR

Synonyms

predicted DNA-binding transcriptional regulator, dihydroxyacetone[1], B1201[2][1], YcgU[2][1], DhaR[2][1] , ECK1189, JW5188, ptsD, ycgU, b1201

Product description

DhaR transcriptional dual regulator[2][3]

Transcription activator of the dhaKLM operon[4]

EC number (for enzymes)


<protect></protect>

Notes

Function

[back to top]


<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:0000166

nucleotide binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

Seeded from EcoCyc (v14.0)

complete

GO:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

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:IPR002197

F

Seeded from EcoCyc (v14.0)

complete

GO:0004871

signal transducer activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000014

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002078

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

F

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002078

C

Seeded from EcoCyc (v14.0)

complete

GO:0006071

glycerol metabolic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0319

P

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:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002078

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:IPR002197

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:IPR013767

P

Seeded from EcoCyc (v14.0)

complete

GO:0007165

signal transduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000014

P

Seeded from EcoCyc (v14.0)

complete

GO:0008134

transcription factor binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002078

F

Seeded from EcoCyc (v14.0)

complete

GO:0017111

nucleoside-triphosphatase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

Seeded from EcoCyc (v14.0)

complete

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

</protect>

Notes

Localization

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

Compartment Description Evidence Reference/Source Notes

<protect></protect>

Notes

Structure and Physical Properties

[back to top]


<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

MRDMSGAFNN DGRGISPLIA TSWERCNKLM KRETWNVPHQ AQGVTFASIY RRKKAMLTLG
QAALEDAWEY MAPRECALFI LDETACILSR NGDPQTLQQL SALGFNDGTY CAEGIIGTCA
LSLAAISGQA VKTMADQHFK QVLWNWAFCA TPLFDSKGRL TGTIALACPV EQTTAADLPL
TLAIAREVGN LLLTDSLLAE TNRHLNQLNA LLESMDDGVI SWDEQGNLQF INAQAARVLR
LDATASQGRA ITELLTLPAV LQQAIKQAHP LKHVEATFES QHQFIDAVIT LKPIIETQGT
SFILLLHPVE QMRQLMTSQL GKVSHTFAHM PQDDPQTRRL IHFGRQAARS SFPVLLCGEE
GVGKALLSQA IHNESERAAG PYIAVNCELY GDAALAEEFI GGDRTDNENG RLSRLELAHG
GTLFLEKIEY LAVELQSALL QVIKQGVITR LDARRLIPID VKVIATTTAD LAMLVEQNRF
SRQLYYALHA FEITIPPLRM RRGSIPALVN NKLRSLEKRF STRLKIDDDA LARLVSCAWP
GNDFELYSVI ENLALSSDNG RIRVSDLPEH LFTEQATDDV SATRLSTSLS FAEVEKEAII
NAAQVTGGRI QEMSALLGIG RTTLWRKMKQ HGIDAGQFKR RV
Length

642

Mol. Wt

70.966 kDa

pI

6.6 (calculated)

Extinction coefficient

57,410 - 58,660 (calc based on 9 Y, 8 W, and 10 C residues)


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

53..189

PF01590 GAF domain

PMID:19920124

Domain

587..628

PF02954 Bacterial regulatory protein, Fis family

PMID:19920124

Domain

203..306

PF00989 PAS fold

PMID:19920124

Domain

327..491

PF00158 Sigma-54 interaction domain

PMID:19920124

<motif_map/>

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

Structures

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

Models

View models at:

</protect>

Structure figures

<protect>

</protect>

Notes

Gene Product Resources

[back to top]


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

Resource type Source Notes/Reference

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:90111234

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945743

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004033

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P76016

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6628

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13902

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945743

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003223

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3661

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]




Expression

[back to top]


{{#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

[back to top]


See Help:Cellular levels

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

Protein

E. coli K-12 MG1655

39

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

24

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

48

molecules/cell/generation

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

Ribosome Profiling

PMID: 24766808

Notes

Transcription and Transcriptional Regulation

[back to top]


<protect>

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

Transcription unit(s)

dhaR

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

[back to top]


<protect><gbrowseImage> name=NC_000913:1250269..1250309 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

[back to top]


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

Allele Name Mutation Phenotype Reference


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

Type Reference Notes

microarray

GEO Profiles:b1201 (EcoliWiki Page)

NCBI GEO profiles for dhaR

microarray

GenExpDB:b1201 (EcoliWiki Page)

Summary of data for dhaR from multiple microarray studies


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 (1250003..1250314) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ03; Well:D6[7]

<protect></protect>

Notes

Accessions Related to dhaR Expression

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:G6628

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3661

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1201

EcoGene

EcoGene:EG13902

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003223

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004033

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]



Evolution

[back to top]


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

Homologs in Other Organisms

[back to top]


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

Organism Homologs (Statistics) Comments

Arabidopsis thaliana

  • AT1G19050 (score: 1.000; bootstrap: 100%)
  • AT1G74890 (score: 0.581)
  • AT5G24470 (score: 0.061)
  • AT5G02810 (score: 0.052)

From Inparanoid:20070104

Oryza gramene

  • Q4GZL0 (score: 1.000; bootstrap: 100%)
  • Q9FRY8 (score: 0.455)
  • Q6YVX7 (score: 0.448)
  • Q4GZK9 (score: 0.448)
  • Q7XRI1 (score: 0.361)
  • Q6H468 (score: 0.164)
  • Q9FRZ0 (score: 0.159)
  • Q9FXQ7 (score: 0.157)
  • Q7XKF6 (score: 0.157)
  • Q4GZK6 (score: 0.152)
  • Q942A1 (score: 0.152)
  • Q4GZK7 (score: 0.152)
  • Q9FRZ1 (score: 0.147)
  • Q6K9T0 (score: 0.144)
  • Q4GZK8 (score: 0.144)
  • Q4GZK2 (score: 0.137)
  • Q9FRY9 (score: 0.134)
  • Q9S7U8 (score: 0.134)
  • Q7XQA6 (score: 0.134)
  • Q4JF20 (score: 0.134)
  • Q4GZK5 (score: 0.134)
  • Q8H5N4 (score: 0.122)
  • Q4GZK4 (score: 0.122)
  • Q9ZQW0 (score: 0.117)
  • Q8GVV6 (score: 0.092)
  • Q4GZK3 (score: 0.092)
  • Q8GVV1 (score: 0.055)
  • Q6YZK8 (score: 0.055)

From Inparanoid:20070104

Shigella flexneri

S1288

From SHIGELLACYC


Do-It-Yourself Web Tools

<protect></protect>

Notes

Families

[back to top]


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

Database Accession Notes

Pfam (EcoliWiki Page)

PF02954 Bacterial regulatory protein, Fis family

Pfam (EcoliWiki Page)

PF01590 GAF domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:46689

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

Superfamily (EcoliWiki Page)

SUPERFAMILY:55785

Pfam (EcoliWiki Page)

PF00989 PAS fold

Pfam (EcoliWiki Page)

PF00158 Sigma-54 interaction domain

EcoCyc

EcoCyc:G6628

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13902

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003223

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3661

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004033

Escherichia coli str. K-12 substr. MG1655

<protect></protect>

Notes

Links

[back to top]



References

[back to top]


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

  1. 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 1.8 1.9 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. 4.0 4.1 4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. 5.0 5.1 CGSC: The Coli Genetics Stock Center
  6. 6.0 6.1 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).
  7. Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

[back to top]