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Gene |

Product(s) |

Expression|

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Standard Name	gadE
Gene Synonym(s)	ECK3496, b3512, JW3480, yhiE, yhiT^[1], yhiT
Product Desc.	GadE transcriptional activator^[2]^[3] Transcriptional regulator of the gadABC operon^[4]
Product Synonyms(s)	DNA-binding transcriptional activator^[1], B3512^[2]^[1], YhiT^[2]^[1], YhiE^[2]^[1], GadE^[2]^[1], acid-responsive regulator of gadA and gadBC^[2]^[1] , ECK3496, JW3480, yhiE, yhiT, b3512
Function from GO	<GO_nr />
Knock-Out Phenotype	Sensitive to pH below pH 2.5
Regulation/Expression	transcription unit(s): gadE^[2]
Regulation/Activity	Activated by EvgA, YdeO, GadX, GadW, GadE, MnmE(indirect?)
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Notes

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GadE overexpression confers acid resistance. GadE is induced by YdeO overexpression. GadE is in the EvgAS regulon. GadE is a LuxR family regulator. GadE is possibly involved in the regulation of type III secretion systems in enterohemorrhagic E. coli O157:H7. Required for stationary phase-induced, pH 5.5 growth medium-induced, and EvgA-induced acid resistance^[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	gadE
Mnemonic	Glutamic acid decarboxylase
Synonyms	ECK3496, b3512, JW3480, yhiE, yhiT^[1], yhiT
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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	78.81 minutes, 78.81 minutes	MG1655: 3656389..3656916 <gbrowseImage> name=NC_000913:3656389..3656916 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 3544883..3545410 <gbrowseImage> name=NC_012759:3544883..3545410 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3982049..3981522 <gbrowseImage> name=NC_007779:3981522..3982049 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3754134..3754661 <gbrowseImage> name=NC_010473:3754134..3754661 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
ΔgadE (Keio:JW3480)	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
JW3480	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCATTTTTCTCATGACGAAAGA Primer 2:CCAAAATAAGATGTGATACCCAG
9G3	Kohara Phage	Genobase	PMID:3038334
4D9	Kohara Phage	Genobase	PMID:3038334
zhg-50::Tn10	Linked marker	CAG18450 = CGSC7450^[5]	est. P1 cotransduction: 3% ^[6] Synonyms:zhf-50::Tn10, zhf-5::Tn10
zic-4901::Tn10	Linked marker	CAG18492 = CGSC7457^[5]	est. P1 cotransduction: % ^[6]
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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:EG11544	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11544	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001498	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948023	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1506	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011475	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	GadE
Synonyms	DNA-binding transcriptional activator^[1], B3512^[2]^[1], YhiT^[2]^[1], YhiE^[2]^[1], GadE^[2]^[1], acid-responsive regulator of gadA and gadBC^[2]^[1] , ECK3496, JW3480, yhiE, yhiT, b3512
Product description	GadE transcriptional activator^[2]^[3] Transcriptional regulator of the gadABC 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:0000156	two-component response regulator activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016032	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:IPR016032	P	Seeded from EcoCyc (v14.0)	complete
	GO:0003677	DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016032	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:IPR000792	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005622	intracellular	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000792	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005622	intracellular	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR016032	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:IPR000792	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:IPR016032	P	Seeded from EcoCyc (v14.0)	complete
	GO:0043565	sequence-specific DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000792	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
Protein	rplF		PMID:16606699	Experiment(s):EBI-1146050
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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 MIFLMTKDSF LLQGFWQLKD NHEMIKINSL SEIKKVGNKP FKVIIDTYHN HILDEEAIKF LEKLDAERII VLAPYHISKL KAKAPIYFVS RKESIKNLLE ITYGKHLPHK NSQLCFSHNQ FKIMQLILKN KNESNITSTL NISQQTLKIQ KFNIMYKLKL RRMSDIVTLG ITSYF
Length	175
Mol. Wt	20.6 kDa
pI	10.1 (calculated)
Extinction coefficient	14,440 - 14,565 (calc based on 6 Y, 1 W, and 1 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	115..169	PF00196 Bacterial regulatory proteins, luxR family		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=gadE taxon=562,83333 </beststructure>

Models

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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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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:16131384	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948023	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011475	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P63204	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11544	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11544	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948023	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001498	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1506	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	Notes	Reference(s)
Protein	Ecoli K-12	133.248+/-1.165	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.42501+/-0.0588	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by FISH	PMID:20671182
mRNA	Ecoli K-12	0.243833017	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	5^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	552	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	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
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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)
gadE
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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_000913:3656369..3656409 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:b3512 (EcoliWiki Page)	NCBI GEO profiles for gadE
microarray	GenExpDB:b3512 (EcoliWiki Page)	Summary of data for gadE 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
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Notes

Accessions Related to gadE Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11544	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1506	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3512
EcoGene	EcoGene:EG11544	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001498	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0011475	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
Shigella flexneri	YHIE	From SHIGELLACYC
E. coli O157	YHIE	From ECOO157CYC
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Notes

Families

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

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF00196 Bacterial regulatory proteins, luxR family
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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.

↑ ^1.00 ^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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^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 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).

gadE: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 gadE Expression

Notes

Links

Evolution

Homologs in Other Organisms

Notes

Families

Notes

Links

References

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