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Standard Name	fumD
Gene Synonym(s)	ydhZ, ECK1671, b1675, JW1665^[1], JW1665
Product Desc.	In vitro catalyzes the addition of water to fumarate, forming malate. Cannot catalyze the reverse reaction. ^[2]
Product Synonyms(s)	FumD, B1675^[3]^[1], YdhZ^[3]^[1] , ECK1671, JW1665
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ydhZ^[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	fumD
Mnemonic	fumarate
Synonyms	ydhZ, ECK1671, b1675, JW1665^[1], JW1665
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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	37.78 minutes	MG1655: 1753165..1752956 <gbrowseImage> name=NC_000913:1752956..1753165 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1732408..1732199 <gbrowseImage> name=NC_012967:1732199..1732408 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1645015..1645224 <gbrowseImage> name=NC_012759:1645015..1645224 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1756855..1756646 <gbrowseImage> name=NC_007779:1756646..1756855 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1843736..1843527 <gbrowseImage> name=NC_010473:1843527..1843736 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
ΔydhZ (Keio:JW1665)	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
JW1665	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGGAAATCGGACAAAAGAGGA Primer 2:CCTTTTACCAGTGCGTTAATGAC
13H4	Kohara Phage	Genobase	PMID:3038334
zdd-235::Tn10	Linked marker	CAG18461 = CGSC7378^[4]	est. P1 cotransduction: % ^[5] Synonyms:zdc-235::Tn10
zdi-925::Tn10	Linked marker	CAG12151 = CGSC7385^[4]	est. P1 cotransduction: 41% ^[5] Synonyms:zdh-925::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:G6903	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13960	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003492	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946180	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3718	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005591	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	FumD
Synonyms	FumD, B1675^[3]^[1], YdhZ^[3]^[1] , ECK1671, JW1665
Product description	In vitro catalyzes the addition of water to fumarate, forming malate. Cannot catalyze the reverse reaction. ^[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:0004333

fumarate hydratase activity

PMID:27914785

IDA: Inferred from Direct Assay

F

Fig. 3e, assayed with purified protein

complete

GO:0005829

cytosol

PMID:19054114

IEA: Inferred from Electronic Annotation

PMID:19054114

C

from EcoCyc ver. 21.0

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	udk	PMID:16606699	Experiment(s):EBI-1140446
Protein	arcA	PMID:16606699	Experiment(s):EBI-1140446
Protein	nadE	PMID:16606699	Experiment(s):EBI-1140446
Protein	htpG	PMID:16606699	Experiment(s):EBI-1140446
Protein	rplO	PMID:16606699	Experiment(s):EBI-1140446
Protein	rplE	PMID:16606699	Experiment(s):EBI-1140446
Protein	rpsI	PMID:16606699	Experiment(s):EBI-1140446
Protein	rplF	PMID:16606699	Experiment(s):EBI-1140446
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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 MGNRTKEDEL YREMCRVVGK VVLEMRDLGQ EPKHIVIAGV LRTALANKRI QRSELEKQAM ETVINALVK
Length	69
Mol. Wt	7.906 kDa
pI	9.7 (calculated)
Extinction coefficient	1,490 - 1,615 (calc based on 1 Y, 0 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	1..69	PF10965 Protein of unknown function (DUF2767)		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=ydhZ 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:16129631	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946180	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005591	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0ACX5	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6903	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13960	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946180	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003492	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3718	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 MG1655	1033	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	413	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	690	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)
ydhZ
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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_000913:1753145..1753185 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:b1675 (EcoliWiki Page)	NCBI GEO profiles for ydhZ
microarray	GenExpDB:b1675 (EcoliWiki Page)	Summary of data for ydhZ 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 (1753070..1753745) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ02; Well:C2^[6]
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Notes

Accessions Related to ydhZ Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6903	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3718	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1675
EcoGene	EcoGene:EG13960	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003492	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005591	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	S1835	From SHIGELLACYC
E. coli O157	Z2703	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)	PF10965 Protein of unknown function (DUF2767)
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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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 Sévin, DC et al. (2017) Nontargeted in vitro metabolomics for high-throughput identification of novel enzymes in Escherichia coli. Nat. Methods 14 187-194 PubMed
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

ydhZ: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 ydhZ Expression

Notes

Links

Evolution

Homologs in Other Organisms

Notes

Families

Notes

Links

References

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