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Standard Name	kdgR
Gene Synonym(s)	ECK1826, b1827, JW1816, yebP^[1], yebP
Product Desc.	KdgR transcriptional repressor^[2]^[3] Regulator of kdgK, kdgT, eda; possibly regulates several other genes, e.g. yjgK^[4]
Product Synonyms(s)	predicted DNA-binding transcriptional regulator^[1], B1827^[2]^[1], YebP^[2]^[1], KdgR^[2]^[1] , ECK1826, JW1816, yebP, b1827
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): kdgR^[2]
Regulation/Activity
Quick Links
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Notes

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A kdgRyebQ clone conferred hypersensitivity to trimethoprim, but a yebQ-alone expression clone did not, leading the authors to conclude that overexpression of the transcriptional regulator YnfL was responsible for the Acr-S phenoptype.^[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	kdgR
Mnemonic	Ketodeoxygluconate
Synonyms	ECK1826, b1827, JW1816, yebP^[1], yebP
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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	41.11 minutes	MG1655: 1908123..1907332 <gbrowseImage> name=NC_000913:1907332..1908123 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1888676..1887885 <gbrowseImage> name=NC_012967:1887885..1888676 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1799391..1800182 <gbrowseImage> name=NC_012759:1799391..1800182 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1911813..1911022 <gbrowseImage> name=NC_007779:1911022..1911813 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1998694..1997903 <gbrowseImage> name=NC_010473:1997903..1998694 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)	Reference	Availability
ΔkdgR (Keio:JW1816)	deletion	deletion	PMID:16738554	Shigen CGSC9518^[5]
kdgR10				CGSC:6785
kdgR50				CGSC:12976
ΔkdgR752::kan			PMID:16738554	CGSC:101604
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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
JW1816	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCTAACGCAGATCTGGATAA Primer 2:CCGAACGGATAGTCGTGATAACC
15D5	Kohara Phage	Genobase	PMID:3038334
zea-225::Tn10	Linked marker	CAG18465 = CGSC7388^[5]	est. P1 cotransduction: 21% ^[6] Synonyms:zdj-225::Tn10
eda-51::Tn10	Linked marker	CAG18486 = CGSC7392^[5]	est. P1 cotransduction: 43% ^[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:G7003	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14018	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003590	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946129	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3772	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006081	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	KdgR
Synonyms	predicted DNA-binding transcriptional regulator^[1], B1827^[2]^[1], YebP^[2]^[1], KdgR^[2]^[1] , ECK1826, JW1816, yebP, b1827
Product description	KdgR transcriptional repressor^[2]^[3] Regulator of kdgK, kdgT, eda; possibly regulates several other genes, e.g. yjgK^[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	Aspect	Notes	Status
	GO:0003700	transcription factor activity	PMID:15659677	IDA: Inferred from Direct Assay	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	PMID:4359651	IDA: Inferred from Direct Assay	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	PMID:4359651	IMP: Inferred from Mutant Phenotype	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016566	specific transcriptional repressor activity	PMID:15659677	IDA: Inferred from Direct Assay	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016566	specific transcriptional repressor activity	PMID:4359651	IDA: Inferred from Direct Assay	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016566	specific transcriptional repressor activity	PMID:4359651	IMP: Inferred from Mutant Phenotype	F	Seeded from EcoCyc (v14.0)	complete
	GO:0032582	negative regulation of gene-specific transcription	PMID:15659677	IDA: Inferred from Direct Assay	P	Seeded from EcoCyc (v14.0)	complete
	GO:0032582	negative regulation of gene-specific transcription	PMID:4359651	IDA: Inferred from Direct Assay	P	Seeded from EcoCyc (v14.0)	complete
	GO:0032582	negative regulation of gene-specific transcription	PMID:4359651	IMP: Inferred from Mutant Phenotype	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	References	Evidence
Protein	ihfA	PMID:19402753	LCMS(ID Probability):99.6
Protein	slyD	PMID:19402753	LCMS(ID Probability):99.6
Protein	lipA	PMID:19402753	LCMS(ID Probability):99.6
Protein	rpoD	PMID:19402753	LCMS(ID Probability):99.5
Protein	ymfD	PMID:19402753	LCMS(ID Probability):99.6
Protein	malP	PMID:19402753	LCMS(ID Probability):99.6
Protein	hns	PMID:19402753	LCMS(ID Probability):99.6
Protein	topA	PMID:19402753	LCMS(ID Probability):99.6
Protein	rdgC	PMID:19402753	LCMS(ID Probability):99.6
Protein	fis	PMID:19402753	LCMS(ID Probability):99.6
Protein	polA	PMID:19402753	LCMS(ID Probability):99.6
Protein	rpoB	PMID:19402753	LCMS(ID Probability):99.6
Protein	xseB	PMID:19402753	LCMS(ID Probability):99.6
Protein	uvrA	PMID:19402753	LCMS(ID Probability):99.6
Protein	hupA	PMID:19402753	LCMS(ID Probability):99.6
Protein	manX	PMID:19402753	LCMS(ID Probability):99.6
Protein	rpoA	PMID:19402753	LCMS(ID Probability):99.6
Protein	rpoC	PMID:19402753	LCMS(ID Probability):99.6
Protein	ynjE	PMID:19402753	LCMS(ID Probability):99.6
Protein	rpoH	PMID:19402753	LCMS(ID Probability):99.6
Protein	yciT	PMID:19402753	LCMS(ID Probability):99.6
Protein	purR	PMID:19402753	LCMS(ID Probability):99.6
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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 MANADLDKQP DSVSSVLKVF GILQALGEER EIGITELSQR VMMSKSTVYR FLQTMKTLGY VAQEGESEKY SLTLKLFELG ARALQNVDLI RSADIQMREL SRLTKETIHL GALDEDSIVY IHKIDSMYNL RMYSRIGRRN PLYSTAIGKV LLAWRDRDEV KQILEGVEYK RSTERTITST EALLPVLDQV REQGYGEDNE EQEEGLRCIA VPVFDRFGVV IAGLSISFPT LRFSEERLQE YVAMLHTAAR KISAQMGYHD YPF
Length	263
Mol. Wt	30.029 kDa
pI	5.4 (calculated)
Extinction coefficient	23,380 - 23,505 (calc based on 12 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
Modification Site	12	phosphorylation site at S12	probability less than 75%	PMID:17938405
Modification Site	14	phosphorylation site at S14	probability less than 75%	PMID:17938405
Modification Site	15	phosphorylation site at S15	probability less than 75%	PMID:17938405
Domain	128..255	PF01614 Bacterial transcriptional regulator		PMID:19920124
Domain	15..65	PF09339 IclR 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=kdgR 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
NCBI (Protein) (EcoliWiki Page)	GI:16129781	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946129	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006081	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P76268	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7003	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14018	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946129	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003590	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3772	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 MC4100	1.04E+03	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI	PMID:18304323
Protein	E. coli K-12 MG1655	2240	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	649	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	1174	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)
kdgR
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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_000913:1908103..1908143 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:b1827 (EcoliWiki Page)	NCBI GEO profiles for kdgR
microarray	GenExpDB:b1827 (EcoliWiki Page)	Summary of data for kdgR 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 (1908037..1908196) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ16; Well:D5^[7]
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Notes

Accessions Related to kdgR Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7003	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3772	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1827
EcoGene	EcoGene:EG14018	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003590	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006081	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
Xenopus tropicalis	ENSXETP00000011286 (score: 1.000; bootstrap: 80%)	From Inparanoid:20070104
Shigella flexneri	S1514	From SHIGELLACYC
E. coli O157	Z2874	From ECOO157CYC
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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)	PF01614 Bacterial transcriptional regulator
Superfamily (EcoliWiki Page)	SUPERFAMILY:46785
Superfamily (EcoliWiki Page)	SUPERFAMILY:55781
Pfam (EcoliWiki Page)	PF09339 IclR helix-turn-helix domain
EcoCyc	EcoCyc:G7003	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14018	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003590	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3772	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006081	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 ^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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

kdgR: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 kdgR Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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