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Gene |

Product(s) |

Expression|

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Standard Name	garD
Gene Synonym(s)	ECK3116, b3128, JW3097, yhaG^[1], yhaG
Product Desc.	D-galactarate dehydratase; uxaA paralog; contains conserved CxxS redox motif^[2]
Product Synonyms(s)	(D)-galactarate dehydrogenase^[1], B3128^[3]^[1], YhaG^[3]^[1], GarD^[3]^[1] , ECK3116, JW3097, yhaG, b3128
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): garD^[3]
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	garD
Mnemonic	Galactarate
Synonyms	ECK3116, b3128, JW3097, yhaG^[1], yhaG
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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	70.55 minutes	MG1655: 3273304..3274875 <gbrowseImage> name=NC_000913:3273304..3274875 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3208211..3209782 <gbrowseImage> name=NC_012967:3208211..3209782 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3160452..3162023 <gbrowseImage> name=NC_012759:3160452..3162023 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3275137..3276708 <gbrowseImage> name=NC_007779:3275137..3276708 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3371049..3372620 <gbrowseImage> name=NC_010473:3371049..3372620 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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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
ΔgarD (Keio:JW3097)	deletion	deletion	PMID:16738554	Shigen CGSC10359^[4]
ΔgarD742::kan			PMID:16738554	CGSC:101094
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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
JW3097	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCCAACATCGAAATCAGACA Primer 2:CCGGTCACCGGTGCCGGGTTAAA
8F8	Kohara Phage	Genobase	PMID:3038334
20F4	Kohara Phage	Genobase	PMID:3038334
aer-3075::Tn10	Linked marker	CAG12152 = CGSC7438^[4]	est. P1 cotransduction: 5% ^[5] Synonyms:zgh-3075::Tn10, zgj-3075::Tn10
sfsB203::Tn10	Linked marker	CAG12072 = CGSC7440^[4]	est. P1 cotransduction: 5% ^[5] Synonyms:zgj-203::Tn10, zha-203::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:EG12522	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12522	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002315	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947641	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2413	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010284	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	GarD
Synonyms	(D)-galactarate dehydrogenase^[1], B3128^[3]^[1], YhaG^[3]^[1], GarD^[3]^[1] , ECK3116, JW3097, yhaG, b3128
Product description	D-galactarate dehydratase; uxaA paralog; contains conserved CxxS redox motif^[2]
EC number (for enzymes)	4.2.1.42^[1]
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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:0005737	cytoplasm				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0008867	galactarate dehydratase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:4.2.1.42	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	References	Evidence
Protein	tatE	PMID:16606699	Experiment(s):EBI-1144856
Protein	rpsM	PMID:16606699	Experiment(s):EBI-1144856
Protein	rplW	PMID:16606699	Experiment(s):EBI-1144856
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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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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 MANIEIRQET PTAFYIKVHD TDNVAIIVND NGLKAGTRFP DGLELIEHIP QGHKVALLDI PANGEIIRYG EVIGYAVRAI PRGSWIDESM VVLPEAPPLH TLPLATKVPE PLPPLEGYTF EGYRNADGSV GTKNLLGITT SVHCVAGVVD YVVKIIERDL LPKYPNVDGV VGLNHLYGCG VAINAPAAVV PIRTIHNISL NPNFGGEVMV IGLGCEKLQP ERLLTGTDDV QAIPVESASI VSLQDEKHVG FQSMVEDILQ IAERHLQKLN QRQRETCPAS ELVVGMQCGG SDAFSGVTAN PAVGYASDLL VRCGATVMFS EVTEVRDAIH LLTPRAVNEE VGKRLLEEME WYDNYLNMGK TDRSANPSPG NKKGGLANVV EKALGSIAKS GKSAIVEVLS PGQRPTKRGL IYAATPASDF VCGTQQVASG ITVQVFTTGR GTPYGLMAVP VIKMATRTEL ANRWFDLMDI NAGTIATGEE TIEEVGWKLF HFILDVASGK KKTFSDQWGL HNQLAVFNPA PVT
Length	523
Mol. Wt	56.4 kDa
pI	5.4 (calculated)
Extinction coefficient	46,870 - 47,745 (calc based on 13 Y, 5 W, and 7 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	116..523	PF04295 D-galactarate dehydratase / Altronate hydrolase, C terminus	PMID:19920124
Domain	22..92	PF08666 SAF 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=garD 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:16131020	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947641	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010284	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P39829	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12522	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12522	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947641	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002315	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2413	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	E. coli K-12 MG1655	29	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	15	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	8^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)
garD
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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_000913:3273284..3273324 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:b3128 (EcoliWiki Page)	NCBI GEO profiles for garD
microarray	GenExpDB:b3128 (EcoliWiki Page)	Summary of data for garD 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 garD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12522	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2413	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3128
EcoGene	EcoGene:EG12522	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002315	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010284	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	YHAG	From SHIGELLACYC
E. coli O157	YHAG	From ECOO157CYC
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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)	PF04295 D-galactarate dehydratase / Altronate hydrolase, C terminus
Pfam (EcoliWiki Page)	PF08666 SAF domain
EcoCyc	EcoCyc:EG12522	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12522	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002315	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2413	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010284	Escherichia coli str. K-12 substr. MG1655
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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)
↑ ^2.0 ^2.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 ^3.5 ^3.6 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 CGSC: The Coli Genetics Stock Center
↑ ^5.0 ^5.1 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).

garD: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 garD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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