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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

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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
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Notes

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

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	dhaR
Mnemonic	Dihydroxyacetone
Synonyms	ECK1189, b1201, JW5188, ptsD, ycgU^[1], ycgU
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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	26.95 minutes	MG1655: 1250289..1252208 <gbrowseImage> name=NC_000913:1250289..1252208 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1251216..1253135 <gbrowseImage> name=NC_012967:1251216..1253135 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1139010..1140929 <gbrowseImage> name=NC_012759:1139010..1140929 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1252643..1254562 <gbrowseImage> name=NC_007779:1252643..1254562 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1290530..1292449 <gbrowseImage> name=NC_010473:1290530..1292449 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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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
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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
ΔdhaR (Keio:JW5188)	deletion	deletion			PMID:16738554	Shigen
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Notes

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
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
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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: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
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Notes

Links

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Name	URL	Comments
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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	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)
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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: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
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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
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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 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)
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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	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
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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=dhaR taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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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: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
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Notes

Links

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Name	URL	Comments
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Expression

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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	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
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Notes

Transcription and Transcriptional Regulation

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

Transcription unit(s)
dhaR
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Figure courtesy of RegulonDB

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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_000913:1250269..1250309 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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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

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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:b1201 (EcoliWiki Page)	NCBI GEO profiles for dhaR
microarray	GenExpDB:b1201 (EcoliWiki Page)	Summary of data for dhaR 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 (1250003..1250314) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ03; Well:D6^[7]
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Notes

Accessions Related to dhaR Expression

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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
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Notes

Links

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Name	URL	Comments
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Evolution

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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	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
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Do-It-Yourself Web Tools

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)	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
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Notes

Links

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Name	URL	Comments
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References

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

↑ ^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)
↑ ^2.0 ^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
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^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.
↑ ^5.0 ^5.1 CGSC: The Coli Genetics Stock Center
↑ ^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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

dhaR:On One Page

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to dhaR Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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