ulaR: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

ulaR

Gene Synonym(s)

ECK4187, b4191, JW4149, yjfQ[1], yjfQ

Product Desc.

UlaR transcriptional repressor[2][3]

Repressor for the L-ascorbate utilization (ula) divergon[4]

Product Synonyms(s)

DNA-binding transcriptional dual regulator[1], UlaR[2][1], B4191[2][1], YjfQ[2][1] , ECK4187, JW4149, yjfQ, b4191

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ulaR[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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The ula divergon is comprised of the two divergent ulaGR and ulaABCDEF operons.[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

ulaR

Mnemonic

Utilization of L-ascorbate

Synonyms

ECK4187, b4191, JW4149, yjfQ[1], yjfQ

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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

95.17 minutes 

MG1655: 4416476..4415721
<gbrowseImage> name=NC_000913:4415721..4416476 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4395853..4396608
<gbrowseImage> name=NC_012967:4395853..4396608 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4354456..4355211
<gbrowseImage> name=NC_012759:4354456..4355211 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4423133..4422378
<gbrowseImage> name=NC_007779:4422378..4423133 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4516838..4516083
<gbrowseImage> name=NC_010473:4516083..4516838 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

ΔulaR (Keio:JW4149)

deletion

deletion

PMID:16738554

Shigen
CGSC10988[5]

ΔulaR741::kan

PMID:16738554

CGSC:103318


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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

JW4149

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCACTGAAGCACAAAGACATCA

Primer 2:CCAACACGCAGAATGCTGACCCC

6G4

Kohara Phage

Genobase

PMID:3038334

1G10

Kohara Phage

Genobase

PMID:3038334

cadB2231::Tn10

Linked marker

CAG18488 = CGSC7479[5]

est. P1 cotransduction: 5% [6]
Synonyms:zjd-2231::Tn10

cycA30::Tn10

Linked marker

CAG12073 = CGSC7482[5]

est. P1 cotransduction: 70% [6]

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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:G7854

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12491

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004350

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948706

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2384

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013713

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

UlaR

Synonyms

DNA-binding transcriptional dual regulator[1], UlaR[2][1], B4191[2][1], YjfQ[2][1] , ECK4187, JW4149, yjfQ, b4191

Product description

UlaR transcriptional repressor[2][3]

Repressor for the L-ascorbate utilization (ula) divergon[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:0003677

DNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0238

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001034

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018356

F

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001034

C

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018356

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01563

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

Seeded from EcoCyc (v14.0)

complete

GO:0006350

transcription

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0804

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001034

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018356

P

Seeded from EcoCyc (v14.0)

complete

GO:0016564

transcription repressor activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01563

F

Seeded from EcoCyc (v14.0)

complete

GO:0045892

negative regulation of transcription, DNA-dependent

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01563

P

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

aceF

PMID:15690043

Experiment(s):EBI-889746

Protein

ynbC

PMID:15690043

Experiment(s):EBI-889746

Protein

groL

PMID:15690043

Experiment(s):EBI-889746, EBI-894652

Protein

rplA

PMID:15690043

Experiment(s):EBI-889746

Protein

rplC

PMID:15690043

Experiment(s):EBI-889746, EBI-894652

Protein

rpsA

PMID:15690043

Experiment(s):EBI-889746

Protein

rpsD

PMID:15690043

Experiment(s):EBI-889746, EBI-894652

Protein

rpsE

PMID:15690043

Experiment(s):EBI-889746, EBI-894652

Protein

rpsM

PMID:15690043

Experiment(s):EBI-889746, EBI-894652

Protein

tufA

PMID:15690043

Experiment(s):EBI-889746, EBI-894652

Protein

dnaK

PMID:15690043

Experiment(s):EBI-889746

Protein

yfgC

PMID:15690043

Experiment(s):EBI-894652

Protein

yfhM

PMID:15690043

Experiment(s):EBI-894652

Protein

dnaJ

PMID:15690043

Experiment(s):EBI-894652

Protein

hupB

PMID:15690043

Experiment(s):EBI-894652

Protein

lpdA

PMID:15690043

Experiment(s):EBI-894652

Protein

lysR

PMID:15690043

Experiment(s):EBI-894652

Protein

rplD

PMID:15690043

Experiment(s):EBI-894652

Protein

rplL

PMID:15690043

Experiment(s):EBI-894652

Protein

rplM

PMID:15690043

Experiment(s):EBI-894652

Protein

rplN

PMID:15690043

Experiment(s):EBI-894652

Protein

rplS

PMID:15690043

Experiment(s):EBI-894652

Protein

rplU

PMID:15690043

Experiment(s):EBI-894652

Protein

rplV

PMID:15690043

Experiment(s):EBI-894652

Protein

rpmB

PMID:15690043

Experiment(s):EBI-894652

Protein

rpsB

PMID:15690043

Experiment(s):EBI-894652

Protein

rpsC

PMID:15690043

Experiment(s):EBI-894652

Protein

rpsG

PMID:15690043

Experiment(s):EBI-894652

Protein

rpsH

PMID:15690043

Experiment(s):EBI-894652

Protein

rpsI

PMID:15690043

Experiment(s):EBI-894652

Protein

rpsJ

PMID:15690043

Experiment(s):EBI-894652

Protein

rpsL

PMID:15690043

Experiment(s):EBI-894652

Protein

rpsN

PMID:15690043

Experiment(s):EBI-894652

Protein

rpsS

PMID:15690043

Experiment(s):EBI-894652

Protein

rpsT

PMID:15690043

Experiment(s):EBI-894652

Protein

yagX

PMID:15690043

Experiment(s):EBI-894652

Protein

ybgH

PMID:15690043

Experiment(s):EBI-894652

Protein

yhaJ

PMID:15690043

Experiment(s):EBI-894652

Protein

groL

PMID:16606699

Experiment(s):EBI-1147646

Protein

rplU

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsL

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplS

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):2.332434

Protein

rpsS

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsT

PMID:19402753

LCMS(ID Probability):99.6

Protein

groS

PMID:19402753

LCMS(ID Probability):99.4 MALDI(Z-score):16.486861

Protein

rpsD

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):26.547926

Protein

groL

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):17.053160

Protein

rplM

PMID:19402753

LCMS(ID Probability):99.6

Protein

hupB

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsN

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplA

PMID:19402753

LCMS(ID Probability):97.9 MALDI(Z-score):16.571227

Protein

rpsC

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):7.542789

Protein

tufB

PMID:19402753

MALDI(Z-score):20.349012

Protein

rpsM

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):17.053160

Protein

rpmB

PMID:19402753

LCMS(ID Probability):99.6

Protein

dnaJ

PMID:19402753

LCMS(ID Probability):99.6

Protein

yfhM

PMID:19402753

LCMS(ID Probability):99.0

Protein

yagX

PMID:19402753

LCMS(ID Probability):99.0

Protein

yfgC

PMID:19402753

LCMS(ID Probability):99.0

Protein

yhaJ

PMID:19402753

LCMS(ID Probability):99.0

Protein

lysR

PMID:19402753

LCMS(ID Probability):99.0

Protein

dtpD

PMID:19402753

LCMS(ID Probability):99.0

Protein

rplL

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 

MTEAQRHQIL LEMLAQLGFV TVEKVVERLG ISPATARRDI NKLDESGKLK KVRNGAEAIT
QQRPRWTPMN LHQAQNHDEK VRIAKAASQL VNPGESVVIN CGSTAFLLGR EMCGKPVQII
TNYLPLANYL IDQEHDSVII MGGQYNKSQS ITLSPQGSEN SLYAGHWMFT SGKGLTAEGL
YKTDMLTAMA EQKMLSVVGK LVVLVDSSKI GERAGMLFSR ADQIDMLITG KNANPEILQQ
LEAQGVSILR V
Length

251

Mol. Wt

27.601 kDa

pI

8.6 (calculated)

Extinction coefficient

18,450 - 18,700 (calc based on 5 Y, 2 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

77..230

PF00455 Bacterial regulatory proteins, deoR family

PMID:19920124

Domain

6..62

PF08220 DeoR-like 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=ulaR 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:16132013

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948706

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013713

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A9W0

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7854

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12491

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948706

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004350

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2384

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

Ecoli K-12

10.504+/-0.131

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

Protein

E. coli K-12 MG1655

411

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

121

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

328

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)

ulaR

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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_000913:4416456..4416496 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:b4191 (EcoliWiki Page)

NCBI GEO profiles for ulaR

microarray

GenExpDB:b4191 (EcoliWiki Page)

Summary of data for ulaR 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 (4415940..4338875) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ03; Well:H2[7]

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Notes

Accessions Related to ulaR Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G7854

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2384

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4191

EcoGene

EcoGene:EG12491

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004350

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013713

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

Shigella flexneri

YJFQ

From SHIGELLACYC

E. coli O157

YJFQ

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)

PF08220 DeoR-like helix-turn-helix domain

Pfam (EcoliWiki Page)

PF00455 Bacterial regulatory proteins, deoR family


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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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