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Standard Name	araD
Gene Synonym(s)	ECK0062, b0061, JW0060^[1], JW0060
Product Desc.	L-ribulose-phosphate 4-epimerase^[2]^[3]; Component of L-ribulose-phosphate 4-epimerase^[2]^[3] L-ribulose-5-phosphate 4-epimerase^[4]
Product Synonyms(s)	L-ribulose-5-phosphate 4-epimerase^[1], B0061^[2]^[1], AraD^[2]^[1] , ECK0062, JW0060, b0061
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): araBAD^[2], OP00302, ara
Regulation/Activity
Quick Links
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</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

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AraD is a masked class II aldolase.^[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	araD
Mnemonic	Arabinose
Synonyms	ECK0062, b0061, JW0060^[1], JW0060
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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	1.42 minutes	MG1655: 66550..65855 <gbrowseImage> name=NC_000913:65855..66550 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 69354..68659 <gbrowseImage> name=NC_012967:68659..69354 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 65855..66549 <gbrowseImage> name=NC_012759:65855..66549 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 66550..65855 <gbrowseImage> name=NC_007779:65855..66550 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
Coding Start (SO:0000323)	MG1655	65855	Edman degradation	PMID:8520491
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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	AA change(s)	Phenotype: Description	Availability	Comments
araDV50I	V50I			Strain variation; seeded from UniProt:P08203
araDT70A	T70A			Strain variation; seeded from UniProt:P08203
araDD216N	D216N			Strain variation; seeded from UniProt:P08203
araD53			CGSC:14410
[araD139]		arabinose sensitive	CGSC:7064	null allele
araD591			CGSC:18969
araD54			CGSC:27568
araD138			CGSC:74738
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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
JW0060	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTTAGAAGATCTCAAACGCCA Primer 2:CCCTGCCCGTAATATGCCTTCGC
5H5	Kohara Phage	Genobase	PMID:3038334
carB96::Tn10	Linked marker	CAG12093 = CGSC7322^[5]	est. P1 cotransduction: 26% ^[6] Synonyms:car-96::Tn10
leuO3051::Tn10	Linked marker	CAG12095 = CGSC7324^[5]	est. P1 cotransduction: 53% ^[6] Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).
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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:EG10055	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10055	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000051	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945294	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0053	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000209	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	AraD
Synonyms	L-ribulose-5-phosphate 4-epimerase^[1], B0061^[2]^[1], AraD^[2]^[1] , ECK0062, JW0060, b0061
Product description	L-ribulose-phosphate 4-epimerase^[2]^[3]; Component of L-ribulose-phosphate 4-epimerase^[2]^[3] L-ribulose-5-phosphate 4-epimerase^[4]
EC number (for enzymes)	5.1.3.4^[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:0008270	zinc ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004661	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008270	zinc ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0862	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008742	L-ribulose-phosphate 4-epimerase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004661	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008742	L-ribulose-phosphate 4-epimerase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:5.1.3.4	F	Seeded from EcoCyc (v14.0)	complete
	GO:0046872	metal ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001303	F	Seeded from EcoCyc (v14.0)	complete
	GO:0046872	metal ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0479	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	Notes	References	Evidence
Protein	Subunits of L-ribulose-phosphate 4-epimerase	could be indirect
Protein	rhsE		PMID:16606699	Experiment(s):EBI-1135466
Protein	aceB		PMID:16606699	Experiment(s):EBI-1135466
Protein	parE		PMID:16606699	Experiment(s):EBI-1135466
Protein	yjiR		PMID:16606699	Experiment(s):EBI-1135466
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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 MLEDLKRQVL EANLALPKHN LVTLTWGNVS AVDRERGVFV IKPSGVDYSV MTADDMVVVS IETGEVVEGT KKPSSDTPTH RLLYQAFPSI GGIVHTHSRH ATIWAQAGQS IPATGTTHAD YFYGTIPCTR KMTDAEINGE YEWETGNVIV ETFEKQGIDA AQMPGVLVHS HGPFAWGKNA EDAVHNAIVL EEVAYMGIFC RQLAPQLPDM QQTLLDKHYL RKHGAKAYYG Q
Length	231
Mol. Wt	25.517 kDa
pI	6.6 (calculated)
Extinction coefficient	35,410 - 35,660 (calc based on 9 Y, 4 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	7..198	PF00596 Class II Aldolase and Adducin N-terminal 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=araD 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:16128055	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945294	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000209	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P08203	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10055	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10055	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945294	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000051	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0053	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 MC4100	2.50E+02	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	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	4^a	molecules/cell/generation	Medium: MOPS Minimal 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	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)
araBAD
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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_000913:66530..66570 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:b0061 (EcoliWiki Page)	NCBI GEO profiles for araD
microarray	GenExpDB:b0061 (EcoliWiki Page)	Summary of data for araD 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 (66473..66870) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ20; Well:E4^[7]
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Notes

Accessions Related to araD Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10055	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0053	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0061
EcoGene	EcoGene:EG10055	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000051	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000209	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
Apis mellifera	ENSAPMP00000012633 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YJR024C (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00024942001 (score: 1.000; bootstrap: 100%) GSTENP00031118001 (score: 1.000; bootstrap: 100%) GSTENP00020027001 (score: 0.494) GSTENP00014406001 (score: 0.320)	From Inparanoid:20070104
Shigella flexneri	ARAD	From SHIGELLACYC
E. coli O157	ARAD	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)	PF00596 Class II Aldolase and Adducin N-terminal domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:53639
EcoCyc	EcoCyc:EG10055	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10055	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000051	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0053	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000209	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 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 ^3.2 ^3.3 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 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

araD: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 araD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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