{{#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	glrR
Gene Synonym(s)	ECK2551, b2554, JW2538, yfhA, qseF^[1], JW2538, qseF
Product Desc.	predicted DNA-binding response regulator in two-component system^[2]^[3] Putative response regulator, function unknown^[4]
Product Synonyms(s)	predicted DNA-binding response regulator in two-component system^[1], B2554^[2]^[1], YfhA^[2]^[1] , ECK2551, JW2538, qseF, yfhA, b2554
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s):
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]

YfhKA may be a cognate two-component system sensor-regulator pair. AFMB Structural Genomics target No. 7 (http://afmb.cnrs-mrs.fr/article171.html)^[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	glrR
Mnemonic
Synonyms	ECK2551, b2554, JW2538, yfhA, qseF^[1], JW2538, qseF
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	57.88 minutes	MG1655: 2686825..2685491 <gbrowseImage> name=NC_000913:2685491..2686825 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2608168..2609502 <gbrowseImage> name=NC_012967:2608168..2609502 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2571296..2572630 <gbrowseImage> name=NC_012759:2571296..2572630 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2687459..2686125 <gbrowseImage> name=NC_007779:2686125..2687459 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2778590..2777256 <gbrowseImage> name=NC_010473:2777256..2778590 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)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
ΔyfhA (Keio:JW2538)	deletion	deletion			PMID:16738554	Shigen CGSC10021^[5]
yfhA::Tn5KAN-I-SceI (FB20282)	Insertion at nt 539 in Minus orientation				PMID:15262929	E. coli Genome Project:FB20851	contains pKD46
yfhA::Tn5KAN-I-SceI (FB20282)	Insertion at nt 539 in Minus orientation				PMID:15262929	E. coli Genome Project:FB20852	does not contain pKD46
ΔyfhA::kan	deletion		Biolog:respiration	unable to respire Acetate	PMID:16095938
ΔyfhA::kan	deletion		Biolog:respiration	unable to respire a-Ketobutyrate	PMID:16095938
ΔyfhA1326					PMID:12897016	CGSC:84708
ΔyfhA728::kan					PMID:16738554	CGSC:104774
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
JW2538	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAGCCATAAACCTGCGCATTT Primer 2:CCTTCCTTGAAATCGTTTGCATC
8E12	Kohara Phage	Genobase	PMID:3038334
6H2	Kohara Phage	Genobase	PMID:3038334
zfh-208::Tn10	Linked marker	CAG18481 = CGSC7417^[5]	est. P1 cotransduction: 44% ^[6] Synonyms:zff-208::Tn10
nadB51::Tn10	Linked marker	CAG18480 = CGSC7419^[5]	est. P1 cotransduction: 41% ^[6]
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
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2554
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C3077
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:YFHA
EcoCyc (EcoliWiki Page)	ECOCYC:EG11285	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947042	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	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	GlrR
Synonyms	predicted DNA-binding response regulator in two-component system^[1], B2554^[2]^[1], YfhA^[2]^[1] , ECK2551, JW2538, qseF, yfhA, b2554
Product description	predicted DNA-binding response regulator in two-component system^[2]^[3] Putative response regulator, function unknown^[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:0000156	two-component response regulator activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001789	F	Seeded from EcoCyc (v14.0)	complete
	GO:0000156	two-component response regulator activity	PMID:19843219	IMP: Inferred from Mutant Phenotype		F	Seeded from EcoCyc (v14.0)	complete
	GO:0000160	two-component signal transduction system (phosphorelay)	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001789	P	Seeded from EcoCyc (v14.0)	complete
	GO:0000160	two-component signal transduction system (phosphorelay)	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0902	P	Seeded from EcoCyc (v14.0)	complete
	GO:0000160	two-component signal transduction system (phosphorelay)	PMID:19843219	IMP: Inferred from Mutant Phenotype		P	Seeded from EcoCyc (v14.0)	complete
	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:0003700	transcription factor activity	PMID:19843219	IEP: Inferred from Expression Pattern		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:0006350	transcription	PMID:15522865	IDA: Inferred from Direct Assay		P	Seeded from EcoCyc (v14.0)	complete
	GO:0006350	transcription	PMID:15556475	ISS: Inferred from Sequence or Structural Similarity	Swiss-Prot:P0AFB8 Swiss-Prot:P37344 Swiss-Prot:P19323	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:IPR001789	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	PMID:19843219	IEP: Inferred from Expression Pattern		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:0016563	transcription activator activity	PMID:15522865	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0016563	transcription activator activity	PMID:15556475	ISS: Inferred from Sequence or Structural Similarity	Swiss-Prot:P0AFB8 Swiss-Prot:P37344 Swiss-Prot:P19323	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016563	transcription activator activity	PMID:19843219	IEP: Inferred from Expression Pattern		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
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	rimJ	PMID:16606699	Experiment(s):EBI-1143243
Protein	rplJ	PMID:16606699	Experiment(s):EBI-1143243
Protein	nadE	PMID:16606699	Experiment(s):EBI-1143243
Protein	rplD	PMID:16606699	Experiment(s):EBI-1143243
Protein	tmk	PMID:16606699	Experiment(s):EBI-1143243
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 MSHKPAHLLL VDDDPGLLKL LGLRLTSEGY SVVTAESGAE GLRVLNREKV DLVISDLRMD EMDGMQLFAE IQKVQPGMPV IILTAHGSIP DAVAATQQGV FSFLTKPVDK DALYQAIDDA LEQSAPATDE RWREAIVTRS PLMLRLLEQA RLVAQSDVSV LINGQSGTGK EIFAQAIHNA SPRNSKPFIA INCGALPEQL LESELFGHAR GAFTGAVSNR EGLFQAAEGG TLFLDEIGDM PAPLQVKLLR VLQERKVRPL GSNRDIDINV RIISATHRDL PKAMARGEFR EDLYYRLNVV SLKIPALAER TEDIPLLANH LLRQAAERHK PFVRAFSTDA MKRLMTASWP GNVRQLVNVI EQCVALTSSP VISDALVEQA LEGENTALPT FVEARNQFEL NYLRKLLQIT KGNVTHAARM AGRNRTEFYK LLSRHELDAN DFKE
Length
Mol. Wt
pI
Extinction coefficient
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	8..118	PF00072 Response regulator receiver domain	PMID:19920124
Domain	136..303	PF00158 Sigma-54 interaction domain	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=yfhA 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:16130479	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947042	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AFU4	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947042	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	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	Ecoli K-12	9.277+/-0.058	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.022113943	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	118	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	60	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	66	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		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)
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_000913:2686805..2686845 source=MG1655 flip=1 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:b2554 (EcoliWiki Page)	NCBI GEO profiles for yfhA
microarray	GenExpDB:b2554 (EcoliWiki Page)	Summary of data for yfhA 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 glrR Expression

[back to top]

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

Database	Accession	Notes
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2554
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	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
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
Xenopus tropicalis	ENSXETP00000041194 (score: 1.000; bootstrap: 78%)	From Inparanoid:20070104
Shigella flexneri	YFHA	From SHIGELLACYC
E. coli O157	YFHA	From ECOO157CYC
edit table

Do-It-Yourself Web Tools

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)	PFAM:PF00072
Superfamily (EcoliWiki Page)	SUPERFAMILY:52172
Panther (EcoliWiki Page)	PTHR24423:SF207
Superfamily (EcoliWiki Page)	SUPERFAMILY:52540
Pfam (EcoliWiki Page)	PF00072 Response regulator receiver domain
Pfam (EcoliWiki Page)	PF00158 Sigma-54 interaction domain
EcoCyc	EcoCyc:	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	Escherichia coli str. K-12 substr. MG1655
edit table

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 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 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).

glrR: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 glrR Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

Categories

Navigation menu

Search