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araD:On One Page

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Quickview | Gene | Product(s) | Expression| Evolution | References |

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See Help:Quickview for help with entering information in the Quickview table.

Standard Name

araD

Gene Synonym(s)

ECK0062, b0061, JW0060[1]

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]

Function from GO

Molecular Function

Biological Process

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): araBAD[2], OP00302, ara

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(araD)    Textpresso(araD)

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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]

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Notes

Location(s) and DNA Sequence

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

1.42 minutes 

MG1655: 66550..65855
gbrowse_img.php?coord=65855..66550&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 69354..68659
gbrowse_img.php?coord=68659..69354&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 66550..65855
gbrowse_img.php?coord=65855..66550&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

BW2952

NC_012759: 65855..66549
gbrowse_img.php?coord=65855..66549&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

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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 typeLocationDescription
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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.

AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments

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 Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

ResourceResource TypeSourceNotes/Reference

JW0060

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTTAGAAGATCTCAAACGCCA

Primer 2:CCCTGCCCGTAATATGCCTTCGC

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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10055

EchoBASE (EcoliWiki Page)

EchoBASE:EB0053

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0061

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0073

EcoGene (EcoliWiki Page)

EcoGene:EG10055

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:ARAD

CGSC (EcoliWiki Page)

CGSC:1025

ASAP (EcoliWikiPage)

ASAP:ABE-0000209


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Notes

Links

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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]

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)
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Notes

Function

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Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus

GO:0046872

metal ion binding

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR001303
SP_KW:KW-0479

F

Seeded from EcoCyc [7]

complete

GO:0008742

L-ribulose-phosphate 4-epimerase activity

GO_REF:0000002
GO_REF:0000003

IEA: Inferred from Electronic Annotation

InterPro:IPR004661
EC:5.1.3.4

F

Seeded from EcoCyc 12.5 [8]

complete

GO:0008270

zinc ion binding

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR004661
SP_KW:KW-0862

F

Seeded from EcoCyc [7]

complete

GO:0008742

L-ribulose-phosphate 4-epimerase activity

PMID:9548961

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc 12.5 [8]

complete

GO:0019324

L-lyxose metabolic process

PMID:10913097

IMP: Inferred from Mutant Phenotype

P

Seeded from EcoCyc [7]

complete

GO:0019569

L-arabinose catabolic process to xylulose 5-phosphate

PMID:7768852

IEP: Inferred from Expression Pattern

P

Seeded from EcoCyc [7]

complete

GO:0005737

cytoplasm

C

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0005975

carbohydrate metabolic process

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0119

P

Seeded from EcoCyc [7]

complete

GO:0016853

isomerase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0413

F

Seeded from EcoCyc [7]

complete

GO:0019568

arabinose catabolic process

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0054

P

Seeded from EcoCyc [7]

complete

GO:0019572

L-arabinose catabolic process

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004661

P

Seeded from EcoCyc [7]

complete

GO:0016052

carbohydrate catabolic process

P

Seeded from EcoCyc 11.1[3].

required fields missing

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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 TypePartnerNotesReferencesEvidence

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.

CompartmentDescriptionEvidenceSourceNotes
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Notes

Structure and Physical Properties

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Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

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.

TypeResiduesDescriptionNotesReferences
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Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures
Models

View models at:

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Structure figures

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 typeSourceNotes/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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:RIBULPEPIM-MONOMER

UniProt (EcoliWiki Page)

UniProt:P08203

PFAM (EcoliWiki Page)

PFAM:PF00596

RefSeq (EcoliWiki Page)

RefSeq:NP_414603


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Notes

Links

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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

MoleculeOrganism or StrainCellular levelUnitsMediumTemperature °COther (e.g. anaerobic)Growth rateAssay usedNotesReference(s)
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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

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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gbrowse_img.php?coord=66530..66570&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein+flip&width=400&figure=Nterm&.png
This picture shows the sequence around the N-terminus.

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

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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Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele NameMutationPhenotypeReference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

TypeReferenceNotes

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 NameResource TypeDescriptionSourceNotes

GFP Fusion

Intergenic region (66473..66870) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ20; Well:E4[9]

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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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10055

EchoBASE (EcoliWiki Page)

EchoBASE:EB0053

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0061

EcoGene (EcoliWiki Page)

EcoGene:EG10055


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Notes

Links

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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.

OrganismHomologs (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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DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF00596


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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 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. ↑ 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. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 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. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  6. ↑ 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).
  7. ↑ 7.0 7.1 7.2 7.3 7.4 7.5 7.6 7.7 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  8. ↑ 8.0 8.1 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  9. ↑ Zaslaver A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3: 623-8 PubMed EcoliWiki page

Categories

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