allR:On One Page

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

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Standard Name

allR

Gene Synonym(s)

ECK0499, b0506, JW0494, gclR, glxA3, ybbU[1], ybbU

Product Desc.

AllR transcriptional regulator[2]; AllR transcriptional repressor[3]

Repressor for all (allantoin) and gcl (glyoxylate) operons; glyoxylate-induced[4]

Product Synonyms(s)

DNA-binding transcriptional repressor[1], B0506[2][1], YbbU[2][1], AllR[2][1] , ECK0499, glxA3, JW0494, ybbU, b0506

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): allR[2]

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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IclR family.[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

allR

Mnemonic

Allantoin

Synonyms

ECK0499, b0506, JW0494, gclR, glxA3, ybbU[1], ybbU

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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

11.47 minutes 

MG1655: 532235..533050
<gbrowseImage> name=NC_000913:532235..533050 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 505177..505992
<gbrowseImage> name=NC_012967:505177..505992 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 434994..435809
<gbrowseImage> name=NC_012759:434994..435809 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 532235..533050
<gbrowseImage> name=NC_007779:532235..533050 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 471566..472381
<gbrowseImage> name=NC_010473:471566..472381 source=DH10B 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
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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

allRM141A

M141A

No effect on repressor activity. Loss of glyoxylate-triggered dissociation from DNA

seeded from UniProt:P0ACN4

allRC142W

C142W

Strongly reduced repressor activity. Reduces DNA binding. Prevents assembly into functionally active tetramers

seeded from UniProt:P0ACN4

allRCKSMVRMC135APA

CKSMVRMC135APA

Loss of repressor activity. Loss of DNA binding. Reduces assembly into functionally active tetramers

seeded from UniProt:P0ACN4

allRS236A,M

S236A,M

Slightly reduced repressor activity. Loss of glyoxylate-triggered dissociation from DNA

seeded from UniProt:P0ACN4

allRC217A,S

C217A,S

Slightly reduced repressor activity. Loss of glyoxylate-triggered dissociation from DNA

seeded from UniProt:P0ACN4

allRL215A

L215A

Reduced repressor activity. Loss of glyoxylate-triggered dissociation from DNA

seeded from UniProt:P0ACN4

allRS234A,N

S234A,N

Reduced repressor activity. Loss of glyoxylate-triggered dissociation from DNA

seeded from UniProt:P0ACN4

ΔallR (Keio:JW0494)

deletion

deletion

PMID:16738554

Shigen
CGSC8639[5]

ΔallR789::kan

PMID:16738554

CGSC:99978


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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

JW0494

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCACGGAAGTTAGACGGCGCGG

Primer 2:CCTGGATGTGCTTTCAGTCCCAA

8E4

Kohara Phage

Genobase

PMID:3038334

9E5

Kohara Phage

Genobase

PMID:3038334

gsk-3055::Tn10

Linked marker

CAG12154 = CGSC7341[5]

est. P1 cotransduction: 29% [6]
Synonyms:zbb-30-55::TnlO, zba-3055::Tn10

purK79::Tn10

Linked marker

CAG12171 = CGSC7342[5]

est. P1 cotransduction: 49% [6]
Synonyms:purE79::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:G6276

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13616

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002884

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945333

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3382

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001750

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

AllR

Synonyms

DNA-binding transcriptional repressor[1], B0506[2][1], YbbU[2][1], AllR[2][1] , ECK0499, glxA3, JW0494, ybbU, b0506

Product description

AllR transcriptional regulator[2]; AllR transcriptional repressor[3]

Repressor for all (allantoin) and gcl (glyoxylate) operons; glyoxylate-induced[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:0003700

transcription factor activity

PMID:10601204

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

PMID:10601204

ISS: Inferred from Sequence or Structural Similarity

NCBI_gi:1786468
NCBI_gi:1736468
NCBI_gi:1790449
NCBI_gi:1789999
NCBI_gi:1790752
NCBI_gi:1799601
1786541
NCBI_gi:3172124
NCBI_gi:3264839

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

PMID:16546208

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

PMID:16546208

ISS: Inferred from Sequence or Structural Similarity

NCBI_gi:1786468
NCBI_gi:1736468
NCBI_gi:1790449
NCBI_gi:1789999
NCBI_gi:1790752
NCBI_gi:1799601
1786541
NCBI_gi:3172124
NCBI_gi:3264839

F

Seeded from EcoCyc (v14.0)

complete

GO:0016566

specific transcriptional repressor activity

PMID:10601204

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0016566

specific transcriptional repressor activity

PMID:10601204

ISS: Inferred from Sequence or Structural Similarity

NCBI_gi:1786468
NCBI_gi:1736468
NCBI_gi:1790449
NCBI_gi:1789999
NCBI_gi:1790752
NCBI_gi:1799601
1786541
NCBI_gi:3172124
NCBI_gi:3264839

F

Seeded from EcoCyc (v14.0)

complete

GO:0016566

specific transcriptional repressor activity

PMID:16546208

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0016566

specific transcriptional repressor activity

PMID:16546208

ISS: Inferred from Sequence or Structural Similarity

NCBI_gi:1786468
NCBI_gi:1736468
NCBI_gi:1790449
NCBI_gi:1789999
NCBI_gi:1790752
NCBI_gi:1799601
1786541
NCBI_gi:3172124
NCBI_gi:3264839

F

Seeded from EcoCyc (v14.0)

complete

GO:0032582

negative regulation of gene-specific transcription

PMID:10601204

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc (v14.0)

complete

GO:0032582

negative regulation of gene-specific transcription

PMID:10601204

ISS: Inferred from Sequence or Structural Similarity

NCBI_gi:1786468
NCBI_gi:1736468
NCBI_gi:1790449
NCBI_gi:1789999
NCBI_gi:1790752
NCBI_gi:1799601
1786541
NCBI_gi:3172124
NCBI_gi:3264839

P

Seeded from EcoCyc (v14.0)

complete

GO:0032582

negative regulation of gene-specific transcription

PMID:16546208

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc (v14.0)

complete

GO:0032582

negative regulation of gene-specific transcription

PMID:16546208

ISS: Inferred from Sequence or Structural Similarity

NCBI_gi:1786468
NCBI_gi:1736468
NCBI_gi:1790449
NCBI_gi:1789999
NCBI_gi:1790752
NCBI_gi:1799601
1786541
NCBI_gi:3172124
NCBI_gi:3264839

P

Seeded from EcoCyc (v14.0)

complete

GO:0006974

response to DNA damage stimulus

PMID:11967071

IEP: Inferred from Expression Pattern

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 Type Partner Notes References Evidence

Protein

hupA

PMID:15690043

Experiment(s):EBI-889682

Protein

rplA

PMID:15690043

Experiment(s):EBI-889682

Protein

rplB

PMID:15690043

Experiment(s):EBI-889682

Protein

rplR

PMID:15690043

Experiment(s):EBI-889682

Protein

rplS

PMID:15690043

Experiment(s):EBI-889682

Protein

rplU

PMID:15690043

Experiment(s):EBI-889682

Protein

rplX

PMID:15690043

Experiment(s):EBI-889682

Protein

rpsE

PMID:15690043

Experiment(s):EBI-889682

Protein

rpsF

PMID:15690043

Experiment(s):EBI-889682

Protein

rpsG

PMID:15690043

Experiment(s):EBI-889682

Protein

rpsL

PMID:15690043

Experiment(s):EBI-889682

Protein

rpsM

PMID:15690043

Experiment(s):EBI-889682

Protein

rpsN

PMID:15690043

Experiment(s):EBI-889682

Protein

rpsO

PMID:15690043

Experiment(s):EBI-889682

Protein

rmuC

PMID:16606699

Experiment(s):EBI-1136950

Protein

tatE

PMID:16606699

Experiment(s):EBI-1136950

Protein

glpK

PMID:16606699

Experiment(s):EBI-1136950

Protein

sdhA

PMID:16606699

Experiment(s):EBI-1136950

Protein

rplU

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplS

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplR

PMID:19402753

LCMS(ID Probability):99.5

Protein

rpsF

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsM

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsL

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsO

PMID:19402753

LCMS(ID Probability):99.6

Protein

hupA

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsN

PMID:19402753

LCMS(ID Probability):99.6

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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 

MTEVRRRGRP GQAEPVAQKG AQALERGIAI LQYLEKSGGS SSVSDISLNL DLPLSTTFRL
LKVLQAADFV YQDSQLGWWH IGLGVFNVGA AYIHNRDVLS VAGPFMRRLM LLSGETVNVA
IRNGNEAVLI GQLECKSMVR MCAPLGSRLP LHASGAGKAL LYPLAEEELM SIILQTGLQQ
FTPTTLVDMP TLLKDLEQAR ELGYTVDKEE HVVGLNCIAS AIYDDVGSVV AAISISGPSS
RLTEDRFVSQ GELVRDTARD ISTALGLKAH P
Length

271

Mol. Wt

29.269 kDa

pI

6.0 (calculated)

Extinction coefficient

19,940 - 20,315 (calc based on 6 Y, 2 W, and 3 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

139..264

PF01614 Bacterial transcriptional regulator

PMID:19920124

Domain

23..74

PF09339 IclR helix-turn-helix 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=allR 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:16128490

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945333

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001750

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0ACN4

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6276

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13616

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945333

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002884

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3382

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

5.82E+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

1771

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

857

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

1332

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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<protect>

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

Transcription unit(s)

allR

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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_000913:532215..532255 source=MG1655 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:b0506 (EcoliWiki Page)

NCBI GEO profiles for allR

microarray

GenExpDB:b0506 (EcoliWiki Page)

Summary of data for allR 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 (532066..532301) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ07; Well:D6[7]

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Notes

Accessions Related to allR Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G6276

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3382

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0506

EcoGene

EcoGene:EG13616

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002884

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001750

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

Xenopus tropicalis

  • ENSXETP00000047490 (score: 1.000; bootstrap: 84%)
  • ENSXETP00000050568 (score: 0.064)

From Inparanoid:20070104

Shigella flexneri

YBBU

From SHIGELLACYC

E. coli O157

YBBU

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)

PF01614 Bacterial transcriptional regulator

Pfam (EcoliWiki Page)

PF09339 IclR helix-turn-helix domain


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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 1.9 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 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 5.2 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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