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

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Standard Name

araB

Gene Synonym(s)

ECK0064, b0063, JW0062[1]

Product Desc.

L-ribulokinase[2][3];

Component of L-ribulokinase[2][3]

Ribulokinase[4]

Product Synonyms(s)

L-ribulokinase[1], B0063[2][1], AraB[2][1], ribulokinase[2][1], ATP:L-ribulose 5-phosphotransferase[2][1]

Function from GO

Molecular Function

Biological Process

Cellular Component

Knock-Out Phenotype
Regulation/Expression

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

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(araB)    Textpresso(araB)

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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

araB

Mnemonic

Arabinose

Synonyms

ECK0064, b0063, JW0062[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

1.47 minutes 

MG1655: 70048..68348
gbrowse_img.php?coord=68348..70048&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 72852..71152
gbrowse_img.php?coord=71152..72852&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 70048..68348
gbrowse_img.php?coord=68348..70048&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

BW2952

NC_012759: 68347..70047
gbrowse_img.php?coord=68347..70047&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

araB16(TempR)

PMID:5340694

CGSC:13808

araB6

CGSC:6923

araB201

CGSC:14401

araB857(polar)

CGSC:14573

araB82

CGSC:18980

araB206

CGSC:27483

araB208

CGSC:27485

araB215

CGSC:27488

araB216

CGSC:27489

araB223

CGSC:27491

araB224

CGSC:27492

araB9999

CGSC:27513


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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

JW0062

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGCGATTGCAATTGGCCTCGA

Primer 2:CCTAGAGTCGCAACGGCCTGGG

carB96::Tn10

Linked marker

CAG12093 = CGSC7322[5]

est. P1 cotransduction: 23% [6]
Synonyms:car-96::Tn10

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[5]

est. P1 cotransduction: 59% [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:EG10053

EchoBASE (EcoliWiki Page)

EchoBASE:EB0051

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0063

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0075

EcoGene (EcoliWiki Page)

EcoGene:EG10053

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:ARAB

CGSC (EcoliWiki Page)

CGSC:1027

ASAP (EcoliWikiPage)

ASAP:ABE-0000223


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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

AraB

Synonyms

L-ribulokinase[1], B0063[2][1], AraB[2][1], ribulokinase[2][1], ATP:L-ribulose 5-phosphotransferase[2][1]

Product description

L-ribulokinase[2][3];

Component of L-ribulokinase[2][3]

Ribulokinase[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:0008741

ribulokinase activity

GO_REF:0000002
GO_REF:0000003
GO_REF:0000020

IEA: Inferred from Electronic Annotation

InterPro:IPR005929
EC:2.7.1.16
HAMAP:MF_00520

F

Seeded from EcoCyc 12.5 [7]

complete

GO:0005515

protein binding

PMID:16606699

IPI: Inferred from Physical Interaction

UniProtKB:P18843

F

Seeded from EcoCyc [8]

complete

GO:0008741

ribulokinase activity

PMID:11747300

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc 12.5 [7]

complete

GO:0019569

L-arabinose catabolic process to xylulose 5-phosphate

PMID:7768852

IEP: Inferred from Expression Pattern

P

Seeded from EcoCyc [8]

complete

GO:0005737

cytoplasm

C

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0005975

carbohydrate metabolic process

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR000577
SP_KW:KW-0119

P

Seeded from EcoCyc [8]

complete

GO:0016301

kinase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0418

F

Seeded from EcoCyc [8]

complete

GO:0016740

transferase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0808

F

Seeded from EcoCyc [8]

complete

GO:0016773

phosphotransferase activity, alcohol group as acceptor

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000577

F

Seeded from EcoCyc [8]

complete

GO:0019572

L-arabinose catabolic process

GO_REF:0000020
GO_REF:0000002

IEA: Inferred from Electronic Annotation

HAMAP:MF_00520
InterPro:IPR005929

P

Seeded from EcoCyc [8]

complete

GO:0016052

carbohydrate catabolic process

P

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0019568

arabinose catabolic process

PMID:13829634

IMP: Inferred from Mutant Phenotype

P

complete

GO:0008741

ribulokinase activity

PMID:13829634

IMP: Inferred from Mutant Phenotype

F

complete

GO:0019569

L-arabinose catabolic process to xylulose 5-phosphate

ISA: Inferred from Sequence Alignment

P

E. coli AraB is xx% identical,

required field missing

GO:0008741

ribulokinase activity

PMID:5336963

IDA: Inferred from Direct Assay

F

complete

GO:0005737

cytoplasm

PMID:5336963

IDA: Inferred from Direct Assay

C

complete

GO:0005515

protein binding

PMID:5336963

IDA: Inferred from Direct Assay

F

complete

GO:0016773

phosphotransferase activity, alcohol group as acceptor

PMID:5336963

IDA: Inferred from Direct Assay

F

complete

GO:0019572

L-arabinose catabolic process

PMID:5336963

IDA: Inferred from Direct Assay

P

complete

GO:0019568

arabinose catabolic process

PMID:5336963

IDA: Inferred from Direct Assay

P

complete

GO:0016052

carbohydrate catabolic process

PMID:5336963

IDA: Inferred from Direct Assay

P

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 TypePartnerNotesReferencesEvidence

Protein

Subunits of L-ribulokinase

could be indirect

Protein

nadE

PMID:16606699

Experiment(s):EBI-1135476

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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 

MAIAIGLDFG SDSVRALAVD CATGEEIATS VEWYPRWQKG QFCDAPNNQF RHHPRDYIES
MEAALKTVLA ELSVEQRAAV VGIGVDSTGS TPAPIDADGN VLALRPEFAE NPNAMFVLWK
DHTAVEEAEE ITRLCHAPGN VDYSRYIGGI YSSEWFWAKI LHVTRQDSAV AQSAASWIEL
CDWVPALLSG TTRPQDIRRG RCSAGHKSLW HESWGGLPPA SFFDELDPIL NRHLPSPLFT
DTWTADIPVG TLCPEWAQRL GLPESVVISG GAFDCHMGAV GAGAQPNALV KVIGTSTCDI
LIADKQSVGE RAVKGICGQV DGSVVPGFIG LEAGQSAFGD IYAWFGRVLG WPLEQLAAQH
PELKTQINAS QKQLLPALTE AWAKNPSLDH LPVVLDWFNG RRTPNANQRL KGVITDLNLA
TDAPLLFGGL IAATAFGARA IMECFTDQGI AVNNVMALGG IARKNQVIMQ ACCDVLNRPL
QIVASDQCCA LGAAIFAAVA AKVHADIPSA QQKMASAVEK TLQPCSEQAQ RFEQLYRRYQ
QWAMSAEQHY LPTSAPAQAA QAVATL
Length

566

Mol. Wt

61.088 kDa

pI

5.2 (calculated)

Extinction coefficient

101,410 - 103,285 (calc based on 9 Y, 16 W, and 15 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

Initiator Methionine

1

Removed

UniProt:P08204


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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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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:RIBULOKIN-MONOMER

UniProt (EcoliWiki Page)

UniProt:P08204

PFAM (EcoliWiki Page)

PFAM:PF00370

RefSeq (EcoliWiki Page)

RefSeq:NP_414605


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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=70028..70068&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:b0063 (EcoliWiki Page)

NCBI GEO profiles for araB

microarray

GenExpDB:b0063 (EcoliWiki Page)

Summary of data for araB 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 (69973..70452) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ20; Well:E1[9]

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Notes

Accessions Related to araB Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10053

EchoBASE (EcoliWiki Page)

EchoBASE:EB0051

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0063

EcoGene (EcoliWiki Page)

EcoGene:EG10053


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Notes

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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

Anopheles gambiae

  • ENSANGP00000010773 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT4G30310 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000027864 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000015220 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-040426-2461 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-040425-3408 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0035484 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA11088-PA (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000017662 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000326322 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000003201 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Mus musculus

  • MGI:1922828 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q6ETN0 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000001369 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000011767 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YDR109C (score: 1.000; bootstrap: 100%)
  • YNL249C (score: 0.088)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000166169 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00015029001 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000019511 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

ARAB

From SHIGELLACYC

E. coli O157

ARAB

From ECOO157CYC

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Do-It-Yourself Web Tools

Notes

Families

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DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF00370


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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. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 1.12 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 2.11 2.12 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 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 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  8. ↑ 8.0 8.1 8.2 8.3 8.4 8.5 8.6 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  9. ↑ Zaslaver A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3: 623-8 PubMed EcoliWiki page

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