baeR: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

baeR

Gene Synonym(s)

ECK2075, b2079, JW2064[1], JW2064

Product Desc.

DNA-binding response regulator in two-component regulatory system with BaeS[1]

Response regulator for mdtABCD, acrD and spy[2]

Product Synonyms(s)

B2079, ECK2075, JW2064, b2079

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): mdtABCD-baeSR[3], baeSR[3]

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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Confers novobiocin and deoxycholate resistance via activation of mdtABCD and acrD transcription. BaeRS multicopy suppresses envZ and phoR/creC mutations. Spy is induced by envelope stress, dependent on both CpxR and BaeSR.[2]



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

baeR

Mnemonic

Bacterial Adaptive rEsponse

Synonyms

ECK2075, b2079, JW2064[1], JW2064

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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

46.6 minutes, 46.6 minutes 

MG1655: 2162300..2163022
<gbrowseImage> name=NC_000913:2162300..2163022 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2097384..2098106
<gbrowseImage> name=NC_012967:2097384..2098106 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2054783..2055505
<gbrowseImage> name=NC_012759:2054783..2055505 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2166413..2167135
<gbrowseImage> name=NC_007779:2166413..2167135 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2253308..2254030
<gbrowseImage> name=NC_010473:2253308..2254030 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

ΔbaeR (Keio:JW2064)

deletion

deletion

PMID:16738554

Shigen


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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

JW2064

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCACCGAGTTACCAATCGACGA

Primer 2:CCAACGATGCGGCAGGCGTCGGC

1H4

Kohara Phage

Genobase

PMID:3038334

10H4

Kohara Phage

Genobase

PMID:3038334

zef-3129::Tn10

Linked marker

CAG12099 = CGSC7397[4]

est. P1 cotransduction: % [5]
Synonyms:zee-3129::Tn10

zbd-3104::Tn10

Linked marker

CAG12021 = CGSC7344[4]

est. P1 cotransduction: 62% [5]
Synonyms:zbc-3105::Tn10, zbd-3105::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:EG11618

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11618

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001566

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946605

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1575

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006884

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

BaeR

Synonyms

B2079, ECK2075, JW2064, b2079

Product description

DNA-binding response regulator in two-component regulatory system with BaeS[1]

Response regulator for mdtABCD, acrD and spy[2]

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:0000156

two-component response regulator activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001789

F

Seeded from EcoCyc (v14.0)

complete

GO:0000156

two-component response regulator activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001867

F

Seeded from EcoCyc (v14.0)

complete

GO:0000160

two-component signal transduction system (phosphorelay)

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001789

P

Seeded from EcoCyc (v14.0)

complete

GO:0000160

two-component signal transduction system (phosphorelay)

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001867

P

Seeded from EcoCyc (v14.0)

complete

GO:0000160

two-component signal transduction system (phosphorelay)

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0902

P

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001867

F

Seeded from EcoCyc (v14.0)

complete

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: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:IPR001789

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:IPR001867

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

udk

PMID:16606699

Experiment(s):EBI-1141871

Protein

iscS

PMID:16606699

Experiment(s):EBI-1141871

Protein

nadE

PMID:16606699

Experiment(s):EBI-1141871
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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

cytoplasm

From EcoCyc[6]


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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 

MTELPIDENT PRILIVEDEP KLGQLLIDYL RAASYAPTLI SHGDQVLPYV RQTPPDLILL
DLMLPGTDGL TLCREIRRFS DIPIVMVTAK IEEIDRLLGL EIGADDYICK PYSPREVVAR
VKTILRRCKP QRELQQQDAE SPLIIDEGRF QASWRGKMLD LTPAEFRLLK TLSHEPGKVF
SREQLLNHLY DDYRVVTDRT IDSHIKNLRR KLESLDAEQS FIRAVYGVGY RWEADACRIV
Length

240

Mol. Wt

27.656 kDa

pI

5.5 (calculated)

Extinction coefficient

24,410 - 24,910 (calc based on 9 Y, 2 W, and 4 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

156..232

PF00486 Transcriptional regulatory protein, C terminal

PMID:19920124

Domain

13..122

PF00072 Response regulator receiver domain

PMID:19920124

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

Structures

<beststructure> gene=baeR 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:16130019

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946605

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006884

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P69228

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11618

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11618

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946605

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001566

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1575

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

1.67E+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

12.299+/-0.073

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.017313019

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

555

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

226

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

323

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)

mdtABCD-baeSR

baeSR

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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_000913:2162280..2162320 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:b2079 (EcoliWiki Page)

NCBI GEO profiles for baeR

microarray

GenExpDB:b2079 (EcoliWiki Page)

Summary of data for baeR 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
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Notes

Accessions Related to baeR Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11618

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1575

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2079

EcoGene

EcoGene:EG11618

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001566

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006884

Escherichia coli str. K-12 substr. MG1655

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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

Arabidopsis thaliana

  • AT4G31920 (score: 1.000; bootstrap: 100%)
  • AT2G01760 (score: 1.000; bootstrap: 100%)
  • AT2G25180 (score: 0.521)
  • AT3G16857 (score: 0.312)
  • AT4G16110 (score: 0.186)
  • AT5G49240 (score: 0.157)
  • AT1G49190 (score: 0.149)
  • AT3G62670 (score: 0.115)
  • AT4G18020 (score: 0.115)
  • AT5G07210 (score: 0.102)
  • AT2G27070 (score: 0.098)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0183884 (score: 1.000; bootstrap: 71%)
  • DDB0191388 (score: 1.000; bootstrap: 62%)
  • DDB0220512 (score: 0.106)
  • DDB0231984 (score: 0.080)
  • DDB0185194 (score: 0.077)
  • DDB0187191 (score: 0.076)
  • DDB0191306 (score: 0.075)
  • DDB0204819 (score: 0.075)
  • DDB0218392 (score: 0.066)
  • DDB0218263 (score: 0.065)
  • DDB0187593 (score: 0.065)
  • DDB0185325 (score: 0.061)
  • DDB0217795 (score: 0.060)
  • DDB0220485 (score: 0.058)
  • DDB0191407 (score: 0.058)
  • DDB0188118 (score: 0.058)
  • DDB0216671 (score: 0.056)
  • DDB0206390 (score: 0.052)

From Inparanoid:20070104

Oryza gramene

  • Q6H805 (score: 1.000; bootstrap: 63%)
  • Q94LW1 (score: 0.703)
  • Q5SML5 (score: 0.284)
  • Q6K8X6 (score: 0.277)
  • Q67W50 (score: 0.231)
  • Q948L2 (score: 0.203)
  • Q7Y0W5 (score: 0.111)
  • Q7Y0W3 (score: 0.111)
  • Q7Y0W2 (score: 0.111)
  • Q7Y0W4 (score: 0.108)
  • Q6AU68 (score: 0.069)
  • Q8H908 (score: 0.057)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YHR206W (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPAC8C94 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

BAER

From SHIGELLACYC

E. coli O157

BAER

From ECOO157CYC

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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)

PF00486 Transcriptional regulatory protein, C terminal

Superfamily (EcoliWiki Page)

SUPERFAMILY:46894

Superfamily (EcoliWiki Page)

SUPERFAMILY:52172

Pfam (EcoliWiki Page)

PF00072 Response regulator receiver domain

EcoCyc

EcoCyc:EG11618

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11618

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001566

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1575

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006884

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. ↑ 1.0 1.1 1.2 1.3 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  3. ↑ 3.0 3.1 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 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).
  6. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7

Categories

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