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On One Page

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Gene |

Product(s) |

Expression|

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Standard Name	gatR
Gene Synonym(s)	Note that this is a pseudogene in K12 strains., ECK2083, JW2074, JW5340, b4498
Product Desc.	Note that this is a pseudogene in K12 strains. negative DNA-binding transcriptional regulator of galactitol metabolism^[1]^[2]; GatR_2^[1]^[2]; Component of GatR transcriptional repressor^[1]^[2]
Product Synonyms(s)	B2087^[1], GatR_1^[1], GatR^[1], split galactitol utilization operon repressor, fragment 1^[1], B2090^[1], split galactitol utilization operon repressor, fragment 2^[1] , ECK2083, JW2074, JW5340, b4498
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): gatR_1^[1]
Regulation/Activity
Quick Links
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Notes

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This is a pseudogene in K12 strains.

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	gatR
Mnemonic
Synonyms	Note that this is a pseudogene in K12 strains., ECK2083, JW2074, JW5340, b4498
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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	46.72 minutes, 46.72 minutes	MG1655: 2168163..2167717 <gbrowseImage> name=NC_000913:2167717..2168163 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
W3110		W3110: 2172276..2171830 <gbrowseImage> name=NC_007779:2171830..2172276 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
MG1655	46.76 minutes	MG1655: 2169757..2169419 <gbrowseImage> name=NC_000913:2169419..2169757 source=ecoli preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse (MG1655)	FASTA Dump
W3110		W3110: 2173870..2173532 <gbrowseImage> name=NC_007779:2173532..2173870 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse (W3110)	FASTA Dump
MG1655		MG1655: 2169757..2167717 <gbrowseImage> name=NC_000913:2167717..2169757 source=ecoli preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse (MG1655)	FASTA Dump
W3110		W3110: 2173870..2171830 <gbrowseImage> name=NC_007779:2171830..2173870 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse (W3110)	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)	Reference	Availability	Comments
gatR_1::Tn5KAN-2 (FB20608)	Insertion at nt 230 in Plus orientation	PMID:15262929	E. coli Genome Project:FB20607	contains pKD46
gatR_1::Tn5KAN-2 (FB20608)	Insertion at nt 230 in Plus orientation	PMID:15262929	E. coli Genome Project:FB20608	does not contain pKD46
ΔgatR785::kan		PMID:16738554	CGSC:101108
ΔgatR784::kan		PMID:16738554	CGSC:101110
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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
	Plasmid clone	Shigen	PMID:16769691 Status: Primer 1: Primer 2:
1H4	Kohara Phage	Genobase	PMID:3038334
10H4	Kohara Phage	Genobase	PMID:3038334
zef-3129::Tn10	Linked marker	CAG12099 = CGSC7397^[3]	est. P1 cotransduction: % ^[4] Synonyms:zee-3129::Tn10
zbd-3104::Tn10	Linked marker	CAG12021 = CGSC7344^[3]	est. P1 cotransduction: 80% ^[4] Synonyms:zbc-3105::Tn10, zbd-3105::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:EG12162	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2090
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C2615
EcoGene	EcoGene:EG12162	Escherichia coli str. K-12 substr. MG1655
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:GATR
CGSC (EcoliWiki Page)	CGSC:32562
ASAP	ASAP:ABE-0006921	Escherichia coli str. K-12 substr. MG1655
ASAP (EcoliWikiPage)	ASAP:ABE-0006921
NCBI (EcoliWiki Page)	GeneID:2847672	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002058	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	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	GatR
Synonyms	B2087^[1], GatR_1^[1], GatR^[1], split galactitol utilization operon repressor, fragment 1^[1], B2090^[1], split galactitol utilization operon repressor, fragment 2^[1] , ECK2083, JW2074, JW5340, b4498
Product description	Note that this is a pseudogene in K12 strains. negative DNA-binding transcriptional regulator of galactitol metabolism^[1]^[2]; GatR_2^[1]^[2]; Component of GatR transcriptional repressor^[1]^[2]
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: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:IPR001034	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018356	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005622	intracellular	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001034	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005622	intracellular	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018356	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:IPR001034	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:IPR018356	P	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	Subunits of GatR transcriptional repressor	could be indirect
Protein	ptrA		PMID:16606699	Experiment(s):EBI-1141888
Protein	dnaK		PMID:16606699	Experiment(s):EBI-1141888
Protein	nadE		PMID:16606699	Experiment(s):EBI-1141888
Protein	groL		PMID:16606699	Experiment(s):EBI-1141888
Protein	lacZ		PMID:16606699	Experiment(s):EBI-1141888
Protein	fabZ		PMID:16606699	Experiment(s):EBI-1141888
Protein	tatE		PMID:16606699	Experiment(s):EBI-1141888
Protein	tktB		PMID:16606699	Experiment(s):EBI-1141888
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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	E. coli B strain REL606 GatR GenBank record ACT39674.1
Sequence	MNSFERRNKIIQLVNEQGTVLVQDLAGVFAASEATIRADLRFLEQKGVVTRFHGGAAKIMSGNSETETQE VGFKERFQLASAPKNRIAQAAVKMIHEGMTVILDSGSTTMLIAEGLMTAKNITVITNSLPAAFALSENKD ITLVVCGGTVRHKTRSMHGSIAERSLQDINADLMFVGADGIDAVNGITTFNEGYSISGAMVTAANKVIAV LDSSKFNRRGFNQVLPIEKIDIIITDDAVSEVDKLALQKTRVKLITV
Length	257
Mol. Wt	27.726 kDa
pI	7.5 (calculated)
Extinction coefficient	1,490 - 1,615 (calc based on 1 Y, 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	References
Domain	83..238	PF00455 Bacterial regulatory proteins, deoR family	PMID:19920124
Domain	8..63	PF08220 DeoR-like helix-turn-helix 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=gatR_2 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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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

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
ASAP	ASAP:ABE-0006921	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:2847672	Escherichia coli str. K-12 substr. MG1655
ASAP (EcoliWiki Page)	ASAP:ABE-0006921	Escherichia coli str. K-12 substr. MG1655
ASAP (EcoliWiki Page)	ASAP:ABE-0285099	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P36930	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12162	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:2847672	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12162	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002058	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	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)
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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)
gatR_1
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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_000913:2168143..2168183 source=MG1655 flip=1 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:b2090 (EcoliWiki Page)	NCBI GEO profiles for gatR_2
microarray	GenExpDB:b2090 (EcoliWiki Page)	Summary of data for gatR_2 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 (2168094..314545) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ03; Well:E1^[5]
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Notes

Accessions Related to gatR Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12162	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2090
EcoGene	EcoGene:EG12162	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002058	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006921	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	GATR	From SHIGELLACYC
E. coli O157	GATR	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)	PF08220 DeoR-like helix-turn-helix domain
Pfam (EcoliWiki Page)	PF00455 Bacterial regulatory proteins, deoR 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 ^1.14 ^1.15 ^1.16 ^1.17 ^1.18 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 CGSC: The Coli Genetics Stock Center
↑ ^4.0 ^4.1 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

gatR: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 gatR Expression

Notes

Links

Evolution

Homologs in Other Organisms

Notes

Families

Notes

Links

References

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