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Expression|

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Standard Name	cdaR
Gene Synonym(s)	ECK0161, b0162, JW5013, yaeG, sdaR^[1], sdaR
Product Desc.	CdaR transcriptional activator^[2]^[3] Transcriptional regulator for gar and gud operons^[4]
Product Synonyms(s)	DNA-binding transcriptional activator^[1], B0162^[2]^[1], SdaR^[2]^[1], CdaR^[2]^[1], YaeG^[2]^[1] , ECK0161, JW5013, sdaR, yaeG, b0162
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): cdaR^[2], sdaR
Regulation/Activity
Quick Links
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Notes

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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	cdaR
Mnemonic	Carbohydrate diacid regulator
Synonyms	ECK0161, b0162, JW5013, yaeG, sdaR^[1], sdaR
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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	3.93 minutes	MG1655: 182463..183620 <gbrowseImage> name=NC_000913:182463..183620 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 185305..186462 <gbrowseImage> name=NC_012967:185305..186462 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 182462..183619 <gbrowseImage> name=NC_012759:182462..183619 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 182463..183620 <gbrowseImage> name=NC_007779:182463..183620 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 156567..157724 <gbrowseImage> name=NC_010473:156567..157724 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
cdaRP292S		P292S		(in strain: JA176; unable to grow on galactarate, glucarate and glycerate)			Strain variation; seeded from UniProt:P37047
cdaR(del) (Keio:JW5013)	deletion	deletion			PMID:16738554	Shigen CGSC11128^[5]
yaeG::Tn5KAN-I-SceI (FB20029)	Insertion at nt 188 in Minus orientation				PMID:15262929	E. coli Genome Project:FB20029	does not contain pKD46
yaeG::Tn5KAN-I-SceI (FB20030)	Insertion at nt 188 in Minus orientation				PMID:15262929	E. coli Genome Project:FB20030	contains pKD46
yaeG(del)::kan	deletion		Biolog:respiration	unable to respire Acetate	PMID:16095938
cdaR776(del)::kan					PMID:16738554	CGSC:100268
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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
JW5013	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCTGGCTGGCATCTTGATAC Primer 2:CCaCGCTCTTCATCCAGTTGTAA
9H2	Kohara Phage	Genobase	PMID:3038334
4E4	Kohara Phage	Genobase	PMID:3038334
21C8	Kohara Phage	Genobase	PMID:3038334
zad-220::Tn10	Linked marker	CAG12025 = CGSC7326^[5]	est. P1 cotransduction: 25% ^[6]
yafC502::Tn10	Linked marker	CAG18436 = CGSC7328^[5]	est. P1 cotransduction: 10% ^[6] Synonyms:zae-502::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:EG12335	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12335	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002210	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:944860	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2239	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000554	Escherichia coli str. K-12 substr. MG1655
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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	CdaR
Synonyms	DNA-binding transcriptional activator^[1], B0162^[2]^[1], SdaR^[2]^[1], CdaR^[2]^[1], YaeG^[2]^[1] , ECK0161, JW5013, sdaR, yaeG, b0162
Product description	CdaR transcriptional activator^[2]^[3] Transcriptional regulator for gar and gud operons^[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:0003700	transcription factor activity	PMID:10762278	IMP: Inferred from Mutant Phenotype		F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	PMID:10762278	ISS: Inferred from Sequence or Structural Similarity	Swiss-Prot:P0ACI3	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016563	transcription activator activity	PMID:10762278	IMP: Inferred from Mutant Phenotype		F	Seeded from EcoCyc (v14.0)	complete
	GO:0016563	transcription activator activity	PMID:10762278	ISS: Inferred from Sequence or Structural Similarity	Swiss-Prot:P0ACI3	F	Seeded from EcoCyc (v14.0)	complete
	GO:0043193	positive regulation of gene-specific transcription	PMID:10762278	IMP: Inferred from Mutant Phenotype		P	Seeded from EcoCyc (v14.0)	complete
	GO:0043193	positive regulation of gene-specific transcription	PMID:10762278	ISS: Inferred from Sequence or Structural Similarity	Swiss-Prot:P0ACI3	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
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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 MHNGGLMAGW HLDTKMAQDI VARTMRIIDT NINVMDARGR IIGSGDRERI GELHEGALLV LSQGRVVDID DAVARHLHGV RQGINLPLRL EGEIVGVIGL TGEPENLRKY GELVCMTAEM MLEQSRLMHL LAQDSRLREE LVMNLIQAEE NTPALTEWAQ RLGIDLNQPR VVAIVEVDSG QLGVDSAMAE LQQLQNALTT PERNNLVAIV SLTEMVVLKP ALNSFGRWDA EDHRKRVEQL ITRMKEYGQL RFRVSLGNYF TGPGSIARSY RTAKTTMVVG KQRMPESRCY FYQDLMLPVL LDSLRGDWQA NELARPLARL KTMDNNGLLR RTLAAWFRHN VQPLATSKAL FIHRNTLEYR LNRISELTGL DLGNFDDRLL LYVALQLDEE R
Length	391
Mol. Wt	44.297 kDa
pI	6.8 (calculated)
Extinction coefficient	39,420 - 39,670 (calc based on 8 Y, 5 W, and 2 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	6..140	PF05651 Putative sugar diacid recognition		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=cdaR 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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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:90111093	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944860	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000554	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P37047	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12335	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12335	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944860	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002210	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2239	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	0.642+/-0.101	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
Protein	E. coli K-12 MG1655	9^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	7	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)
cdaR
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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_000913:182443..182483 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:b0162 (EcoliWiki Page)	NCBI GEO profiles for cdaR
microarray	GenExpDB:b0162 (EcoliWiki Page)	Summary of data for cdaR 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 (182232..182466) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ11; Well:G4^[7]
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Notes

Accessions Related to cdaR Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12335	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2239	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0162
EcoGene	EcoGene:EG12335	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002210	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000554	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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<protect> See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
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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)	PF05651 Putative sugar diacid recognition
EcoCyc	EcoCyc:EG12335	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12335	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002210	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2239	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000554	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.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 ^1.11 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 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 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

cdaR:On One Page

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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 cdaR Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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