qseB: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

qseB

Gene Synonym(s)

ECK3016, b3025, JW2993, ygiX[1], preA, ygiX

Product Desc.

QseB transcriptional activator[2][3]

Quorum sensing two-component response regulator cognate to QseC sensor kinase; regulates flagella synthesis and motilty by activating transcription of flhDC[4]

Product Synonyms(s)

DNA-binding response regulator in two-component regulatory system with QseC[1], B3025[2][1], YgiX[2][1] , ECK3016, JW2993, preA, ygiX, b3025

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): qseBC[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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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

qseB

Mnemonic

Quorum sensing E. coli

Synonyms

ECK3016, b3025, JW2993, ygiX[1], preA, ygiX

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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

68.28 minutes 

MG1655: 3167850..3168509
<gbrowseImage> name=NC_000913:3167850..3168509 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3104000..3104659
<gbrowseImage> name=NC_012967:3104000..3104659 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3054998..3055657
<gbrowseImage> name=NC_012759:3054998..3055657 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3168484..3169143
<gbrowseImage> name=NC_007779:3168484..3169143 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3265595..3266254
<gbrowseImage> name=NC_010473:3265595..3266254 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

ΔqseB (Keio:JW2993)

deletion

deletion

PMID:16738554

Shigen
CGSC10294[5]

ΔqseB723::kan

PMID:16738554

CGSC:102582


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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

JW2993

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCGAATTTTACTGATAGAAGA

Primer 2:CCTTTCTCACCTAATGTGTAACC

17B2

Kohara Phage

Genobase

PMID:3038334

metC162::Tn10

Linked marker

CAG18475 = CGSC7435[5]

est. P1 cotransduction: 53% [6]

tolC210::Tn10

Linked marker

CAG12184 = CGSC7437[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:G7575

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13026

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004133

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945369

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2844

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009936

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

QseB

Synonyms

DNA-binding response regulator in two-component regulatory system with QseC[1], B3025[2][1], YgiX[2][1] , ECK3016, JW2993, preA, ygiX, b3025

Product description

QseB transcriptional activator[2][3]

Quorum sensing two-component response regulator cognate to QseC sensor kinase; regulates flagella synthesis and motilty by activating transcription of flhDC[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: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

deoR

PMID:16606699

Experiment(s):EBI-1144574

Protein

hdhA

PMID:16606699

Experiment(s):EBI-1144574

Protein

fabI

PMID:16606699

Experiment(s):EBI-1144574
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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 

MRILLIEDDM LIGDGIKTGL SKMGFSVDWF TQGRQGKEAL YSAPYDAVIL DLTLPGMDGR
DILREWREKG QREPVLILTA RDALAERVEG LRLGADDYLC KPFALIEVAA RLEALMRRTN
GQASNELRHG NVMLDPGKRI ATLAGEPLTL KPKEFALLEL LMRNAGRVLS RKLIEEKLYT
WDEEVTSNAV EVHVHHLRRK LGSDFIRTVH GIGYTLGEK
Length

219

Mol. Wt

24.678 kDa

pI

7.0 (calculated)

Extinction coefficient

23,950 - 24,075 (calc based on 5 Y, 3 W, and 1 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

145..216

PF00486 Transcriptional regulatory protein, C terminal

PMID:19920124

Domain

3..113

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=qseB 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:16130921

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945369

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009936

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P52076

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7575

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13026

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945369

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004133

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2844

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 MG1655

138

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

74

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

150

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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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)

qseBC

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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_000913:3167830..3167870 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:b3025 (EcoliWiki Page)

NCBI GEO profiles for qseB

microarray

GenExpDB:b3025 (EcoliWiki Page)

Summary of data for qseB 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 (3167613..3167887) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ08; Well:G3[7]

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Notes

Accessions Related to qseB Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G7575

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2844

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3025

EcoGene

EcoGene:EG13026

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004133

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009936

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

Shigella flexneri

YGIX

From SHIGELLACYC

E. coli O157

YGIX

From ECOO157CYC

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

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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)

PF00486 Transcriptional regulatory protein, C terminal

Pfam (EcoliWiki Page)

PF00072 Response regulator receiver 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 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 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 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

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