araB:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

Quickview

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Standard Name

araB

Gene Synonym(s)

ECK0064, b0063, JW0062[1], JW0062

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] , ECK0064, JW0062, b0063

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

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

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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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], JW0062

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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

1.47 minutes 

MG1655: 70048..68348
<gbrowseImage> name=NC_000913:68348..70048 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 72852..71152
<gbrowseImage> name=NC_012967:71152..72852 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 68347..70047
<gbrowseImage> name=NC_012759:68347..70047 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 70048..68348
<gbrowseImage> name=NC_007779:68348..70048 source=W3110 preset=GeneLocation </gbrowseImage>

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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

68351

Edman degradation

PMID:189315


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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

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 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

JW0062

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGCGATTGCAATTGGCCTCGA

Primer 2:CCTAGAGTCGCAACGGCCTGGG

5H5

Kohara Phage

Genobase

PMID:3038334

8H11

Kohara Phage

Genobase

PMID:3038334

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.

Database Accession Notes

EcoCyc

EcoCyc:EG10053

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10053

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000049

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946017

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0051

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000223

Escherichia coli str. K-12 substr. MG1655

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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] , ECK0064, JW0062, b0063

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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<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: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,

Missing: with/from, reference

GO:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

F

Seeded from EcoCyc (v14.0)

complete

GO:0008741

ribulokinase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00520

F

Seeded from EcoCyc (v14.0)

complete

GO:0008741

ribulokinase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005929

F

Seeded from EcoCyc (v14.0)

complete

GO:0008741

ribulokinase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.7.1.16

F

Seeded from EcoCyc (v14.0)

complete

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

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-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.

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

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)


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

Initiator Methionine

1

Removed

UniProt:P08204

Domain

3..193

PF00370 FGGY family of carbohydrate kinases, N-terminal domain

PMID:19920124

Domain

289..501

PF02782 FGGY family of carbohydrate kinases, C-terminal domain

PMID:19920124

<motif_map/>

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

Structures

<beststructure> gene=araB 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:16128057

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946017

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000223

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P08204

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10053

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10053

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946017

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000049

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0051

Escherichia coli str. K-12 substr. MG1655

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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

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MC4100

8.77E+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

Ecoli K-12

1.594+/-0.146

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by RNA_Seq

PMID:20671182

Protein

E. coli K-12 MG1655

2a

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

5

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

0a

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

Notes

Transcription and Transcriptional Regulation

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<protect>

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

araBAD

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_000913:70028..70068 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


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

Type Reference Notes

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


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 (69973..70452) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ20; Well:E1[7]

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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.

Database Accession Notes

EcoCyc

EcoCyc:EG10053

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0051

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0063

EcoGene

EcoGene:EG10053

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000049

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000223

Escherichia coli str. K-12 substr. MG1655

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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.

Organism Homologs (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


Do-It-Yourself Web Tools

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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)

PF02782 FGGY family of carbohydrate kinases, C-terminal domain

Pfam (EcoliWiki Page)

PF00370 FGGY family of carbohydrate kinases, N-terminal domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:53067

Superfamily (EcoliWiki Page)

SUPERFAMILY:53067

Panther (EcoliWiki Page)

PTHR10196:SF8

EcoCyc

EcoCyc:EG10053

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10053

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000049

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0051

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000223

Escherichia coli str. K-12 substr. MG1655

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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 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. Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

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