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

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>

Standard Name	rhaR
Gene Synonym(s)	ECK3899, b3906, JW3877, rhaC, rhaC1^[1], rhaC1
Product Desc.	RhaR transcriptional activator^[2]^[3] Transcriptional activator for rhaSR, AraC family^[4]
Product Synonyms(s)	DNA-binding transcriptional activator, L-rhamnose-binding^[1], B3906^[2]^[1], RhaR^[2]^[1], positive regulator for rhaRS operon^[2]^[1] , ECK3899, JW3877, rhaC1, b3906
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): rhaSR^[2], OP00087, rha
Regulation/Activity
Quick Links
edit table

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

Notes

[back to top]

A GTG start codon 31 codons internal to the previously annotated start codon is predicted based on conservation with Salmonella, eliminating the overlap with rhaS, and having a better RBS (E. Pradel, personal communication, July, 2007).^[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	rhaR
Mnemonic	Rhamnose
Synonyms	ECK3899, b3906, JW3877, rhaC, rhaC1^[1], rhaC1
edit table

</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	88.29 minutes	MG1655: 4096579..4097517 <gbrowseImage> name=NC_000913:4096579..4097517 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4078038..4078976 <gbrowseImage> name=NC_012967:4078038..4078976 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3986338..3987186 <gbrowseImage> name=NC_012759:3986338..3987186 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3538125..3537187 <gbrowseImage> name=NC_007779:3537187..3538125 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4196276..4197214 <gbrowseImage> name=NC_010473:4196276..4197214 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
edit table

</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
edit table

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)	Reference	Availability
ΔrhaR (Keio:JW3877)	deletion	deletion	PMID:16738554	Shigen CGSC10796^[5]
ΔrhaR766::kan			PMID:16738554	CGSC:102686
edit table

Notes

Genetic Interactions

[back to top]

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

</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
JW3877	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCTTTCTGCAATAACGCGAA Primer 2:CCATCTTTCTGCGAATTGAGATG
4B6	Kohara Phage	Genobase	PMID:3038334
7G8	Kohara Phage	Genobase	PMID:3038334
zih-35::Tn10	Linked marker	CAG18495 = CGSC7467^[5]	est. P1 cotransduction: 28% ^[6]
pflD501::Tn10	Linked marker	CAG18477 = CGSC7470^[5]	est. P1 cotransduction: 12% ^[6] Synonyms:zij-501::Tn10 nnnCAG18477 also carries metF79(Am) (CGSC).
edit table

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:EG10842	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10842	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000833	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948396	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0835	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012747	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

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	RhaR
Synonyms	DNA-binding transcriptional activator, L-rhamnose-binding^[1], B3906^[2]^[1], RhaR^[2]^[1], positive regulator for rhaRS operon^[2]^[1] , ECK3899, JW3877, rhaC1, b3906
Product description	RhaR transcriptional activator^[2]^[3] Transcriptional activator for rhaSR, AraC family^[4]
EC number (for enzymes)
edit table

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: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:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01533	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000005	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020449	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005622	intracellular	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000005	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005622	intracellular	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020449	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01533	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	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:IPR000005	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:IPR003313	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:IPR020449	P	Seeded from EcoCyc (v14.0)	complete
	GO:0019299	rhamnose metabolic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01533	P	Seeded from EcoCyc (v14.0)	complete
	GO:0019299	rhamnose metabolic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0684	P	Seeded from EcoCyc (v14.0)	complete
	GO:0043565	sequence-specific DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000005	F	Seeded from EcoCyc (v14.0)	complete
	GO:0043565	sequence-specific DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020449	F	Seeded from EcoCyc (v14.0)	complete
	GO:0045893	positive regulation of transcription, DNA-dependent	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01533	P	Seeded from EcoCyc (v14.0)	complete
edit table

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

Partner Type	Partner	References	Evidence
Protein	iscS	PMID:16606699	Experiment(s):EBI-1146979
Protein	ttcA	PMID:16606699	Experiment(s):EBI-1146979
Protein	htrB	PMID:16606699	Experiment(s):EBI-1146979
Protein	groL	PMID:16606699	Experiment(s):EBI-1146979
Protein	fdhD	PMID:16606699	Experiment(s):EBI-1146979
edit table

</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
edit table

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 MAFCNNANLL NVFVRHIANN QLRSLAEVAT VAHQLKLLKD DFFASDQQAV AVADRYPQDV FAEHTHDFCE LVIVWRGNGL HVLNDRPYRI TRGDLFYIHA DDKHSYASVN DLVLQNIIYC PERLKLNLDW QGAIPGFNAS AGQPHWRLGS MGMAQARQVI GQLEHESSQH VPFANEMAEL LFGQLVMLLN RHRYTSDSLP PTSSETLLDK LITRLAASLK SPFALDKFCD EASCSERVLR QQFRQQTGMT INQYLRQVRV CHAQYLLQHS RLLISDISTE CGFEDSNYFS VVFTRETGMT PSQWRHLNSQ KD
Length	312
Mol. Wt	35.667 kDa
pI	6.9 (calculated)
Extinction coefficient	35,410 - 36,285 (calc based on 9 Y, 4 W, and 7 C residues)
edit table

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	19..156	PF02311 AraC-like ligand binding domain	PMID:19920124
Domain	185..226	PF00165 Bacterial regulatory helix-turn-helix proteins, AraC family	PMID:19920124
Domain	237..276	PF00165 Bacterial regulatory helix-turn-helix proteins, AraC family	PMID:19920124
edit table

<motif_map/>

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

Structures

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

Models

View models at:

edit table

</protect>

Structure figures

</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
edit table

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:171701684	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948396	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012747	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P09378	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10842	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10842	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948396	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000833	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0835	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

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	2^a	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	1^a	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	0^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
edit table

Notes

Transcription and Transcriptional Regulation

[back to top]

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

Transcription unit(s)
rhaSR
edit table

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_000913:4096559..4096599 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
edit table

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

Type	Reference	Notes
microarray	GEO Profiles:b3906 (EcoliWiki Page)	NCBI GEO profiles for rhaR
microarray	GenExpDB:b3906 (EcoliWiki Page)	Summary of data for rhaR from multiple microarray studies
edit table

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

Resource Name	Resource Type	Description	Source	Notes
edit table

Notes

Accessions Related to rhaR Expression

[back to top]

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10842	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0835	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3906
EcoGene	EcoGene:EG10842	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000833	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012747	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

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
Xenopus tropicalis	ENSXETP00000020771 (score: 1.000; bootstrap: 100%) ENSXETP00000051238 (score: 0.204)	From Inparanoid:20070104
Shigella flexneri	RHAR	From SHIGELLACYC
E. coli O157	RHAR	From ECOO157CYC
edit table

Notes

Families

[back to top]

<protect> See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF02311 AraC-like ligand binding domain
Pfam (EcoliWiki Page)	PF00165 Bacterial regulatory helix-turn-helix proteins, AraC family
Pfam (EcoliWiki Page)	PF00165 Bacterial regulatory helix-turn-helix proteins, AraC family
edit table

</protect> <protect></protect>

Notes

Links

[back to top]

Name	URL	Comments
edit table

References

[back to top]

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 ^5.2 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).

rhaR:On One Page

Quickview

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 rhaR Expression

Notes

Links

Evolution

Homologs in Other Organisms

Notes

Families

Notes

Links

References

Categories

Navigation menu

Search