atoS: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

atoS

Gene Synonym(s)

ECK2212, b2219, JW2213[1], JW2213

Product Desc.

sensor histidine protein kinase regulator of the atoDAEB operon[2] Transcriptional histidine protein kinase regulator of atoDAEB; membrane sensor; AtoC is the two-component cognate response regulator; induced by acetoacetate[3]

Product Synonyms(s)

B2219[4], ECK2212, JW2213, b2219

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): atoS[4]

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

atoS

Mnemonic

Acetoacetate

Synonyms

ECK2212, b2219, JW2213[1], JW2213

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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

49.96 minutes 

MG1655: 2318065..2319891
<gbrowseImage> name=NC_000913:2318065..2319891 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2266743..2268569
<gbrowseImage> name=NC_012967:2266743..2268569 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2203870..2205696
<gbrowseImage> name=NC_012759:2203870..2205696 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2324713..2326539
<gbrowseImage> name=NC_007779:2324713..2326539 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2409053..2410879
<gbrowseImage> name=NC_010473:2409053..2410879 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

ΔatoS (Keio:JW2213)

deletion

deletion

PMID:16738554

Shigen
CGSC9784[5]

atoS::Tn5KAN-2 (FB20716)

Insertion at nt 923 in Minus orientation

PMID:15262929

E. coli Genome Project:FB20716

contains pKD46

atoS::Tn5KAN-2 (FB20717)

Insertion at nt 923 in Minus orientation

PMID:15262929

E. coli Genome Project:FB20717

does not contain pKD46

ΔatoS::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938

ΔatoS::kan

deletion

Biolog:respiration

unable to respire a-Ketobutyrate

PMID:16095938

atoS298::Tn10

Insertion at 2,318,296 bp in MG1655 (NC_000913)

adapted from Nichols et al.[6]

CAG12177 gyrA = CGSC7525[5]

Synonyms: zeh-298::Tn10, zej-298::Tn10 nnnThe original CAG12177 was NalR. This is a NalS derivative constructed by S. McAteer (CGSC).

atoS298::Tn10

PMID:2540407 PMID:9829956

CGSC:8751

atoS3142::Tn10kan

PMID:2540407 PMID:9829956

CGSC:40008

ΔatoS773::kan

PMID:16738554

CGSC:100132


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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

JW2213

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCATTATATGAAGTGGATTTA

Primer 2:CCTACAGTCTGATTTCCCTGCGG

5A1

Kohara Phage

Genobase

PMID:3038334

4F12

Kohara Phage

Genobase

PMID:3038334

napA722::Tn10

Linked marker

CAG12098 = CGSC7400[5]

est. P1 cotransduction: 55% [6]
Synonyms:zeg-722, zei-722::Tn10

zfa-723::Tn10

Linked marker

CAG12178 gyrA+ = CGSC7526[5]

est. P1 cotransduction: 39% [6]
Synonyms:zei-723::Tn10, zfa-723::Tn10 nnnThe original CAG12178 was NalR. This is a NalS derivative constructed by S. McAteer (CGSC).

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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:EG11667

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11667

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001610

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:949011

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1618

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007341

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

AtoS

Synonyms

B2219[4], ECK2212, JW2213, b2219

Product description

sensor histidine protein kinase regulator of the atoDAEB operon[2] Transcriptional histidine protein kinase regulator of atoDAEB; membrane sensor; AtoC is the two-component cognate response regulator; induced by acetoacetate[3]

EC number (for enzymes)


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Notes

AtoS is a membrane sensor; AtoC is the two-component cognate response regulator; induced by acetoacetate[2]

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:0000155

two-component sensor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000700

F

Seeded from EcoCyc (v14.0)

complete

GO:0000155

two-component sensor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003661

F

Seeded from EcoCyc (v14.0)

complete

GO:0000155

two-component sensor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005467

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:IPR000700

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: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:0004673

protein histidine kinase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005467

F

Seeded from EcoCyc (v14.0)

complete

GO:0004673

protein histidine kinase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.7.13.3

F

Seeded from EcoCyc (v14.0)

complete

GO:0004871

signal transducer activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000014

F

Seeded from EcoCyc (v14.0)

complete

GO:0004871

signal transducer activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003660

F

Seeded from EcoCyc (v14.0)

complete

GO:0004871

signal transducer activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR009082

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003594

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:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0997

C

Seeded from EcoCyc (v14.0)

complete

GO:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-1003

C

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013767

P

Seeded from EcoCyc (v14.0)

complete

GO:0007165

signal transduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000014

P

Seeded from EcoCyc (v14.0)

complete

GO:0007165

signal transduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003660

P

Seeded from EcoCyc (v14.0)

complete

GO:0007165

signal transduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003661

P

Seeded from EcoCyc (v14.0)

complete

GO:0007165

signal transduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005467

P

Seeded from EcoCyc (v14.0)

complete

GO:0007165

signal transduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR009082

P

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003661

C

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0472

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003660

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0812

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-9909

C

Seeded from EcoCyc (v14.0)

complete

GO:0016301

kinase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0418

F

Seeded from EcoCyc (v14.0)

complete

GO:0016310

phosphorylation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004358

P

Seeded from EcoCyc (v14.0)

complete

GO:0016740

transferase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0808

F

Seeded from EcoCyc (v14.0)

complete

GO:0016772

transferase activity, transferring phosphorus-containing groups

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004358

F

Seeded from EcoCyc (v14.0)

complete

GO:0018106

peptidyl-histidine phosphorylation

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005467

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
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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

plasma membrane

C-terminus localized in the cytoplasm with 2 predicted transmembrane domains

Daley et al. (2005) [7]

plasma membrane

From EcoCyc[8]


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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 

MHYMKWIYPR RLRNQMILMA ILMVIVPTLT IGYIVETEGR SAVLSEKEKK LSAVVNLLNQ
ALGDRYDLYI DLPREERIRA LNAELAPITE NITHAFPGIG AGYYNKMLDA IITYAPSALY
QNNVGVTIAA DHPGREVMRT NTPLVYSGRQ VRGDILNSML PIERNGEILG YIWANELTED
IRRQAWKMDV RIIIVLTAGL LISLLLIVLF SRRLSANIDI ITDGLSTLAQ NIPTRLPQLP
GEMGQISQSV NNLAQALRET RTLNDLIIEN AADGVIAIDR QGDVTTMNPA AEVITGYQRH
ELVGQPYSML FDNTQFYSPV LDTLEHGTEH VALEISFPGR DRTIELSVTT SRIHNTHGEM
IGALVIFSDL TARKETQRRM AQAERLATLG ELMAGVAHEV RNPLTAIRGY VQILRQQTSD
PIHQEYLSVV LKEIDSINKV IQQLLEFSRP RHSQWQQVSL NALVEETLVL VQTAGVQARV
DFISELDNEL SPINADRELL KQVLLNILIN AVQAISARGK IRIQTWQYSD SQQAISIEDN
GCGIDLSLQK KIFDPFFTTK ASGTGLGLAL SQRIINAHQG DIRVASLPGY GATFTLILPI
NPQGNQTV
Length

608

Mol. Wt

67.791 kDa

pI

6.1 (calculated)

Extinction coefficient

54,320 - 54,445 (calc based on 18 Y, 5 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

192..259

PF00672 HAMP domain

PMID:19920124

Domain

495..601

PF02518 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase

PMID:19920124

Domain

388..453

PF00512 His Kinase A (phosphoacceptor) domain

PMID:19920124

Domain

262..370

PF00989 PAS fold

PMID:19920124

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<motif_map/>

tmhmm.php?gene=atoS&show=pic&.jpg
Click the image to view raw output from TMHMM.

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

Structures

<beststructure> gene=atoS 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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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:16130156

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:949011

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007341

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:Q06067

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11667

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11667

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:949011

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001610

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1618

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

5a

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

3

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

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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)

atoS

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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_000913:2318045..2318085 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:b2219 (EcoliWiki Page)

NCBI GEO profiles for atoS

microarray

GenExpDB:b2219 (EcoliWiki Page)

Summary of data for atoS 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 (2317751..2318083) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ18; Well:D12[9]

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Notes

Accessions Related to atoS Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11667

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1618

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2219

EcoGene

EcoGene:EG11667

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001610

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007341

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

  • AT4G18130 (score: 1.000; bootstrap: 100%)
  • AT2G18790 (score: 0.549)
  • AT4G16250 (score: 0.524)
  • AT1G09570 (score: 0.438)
  • AT5G35840 (score: 0.432)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0191389 (score: 1.000; bootstrap: 100%)
  • DDB0214934 (score: 0.093)
  • DDB0185038 (score: 0.077)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000008930 (score: 1.000; bootstrap: 59%)

From Inparanoid:20070104

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Do-It-Yourself Web Tools

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Notes

Families

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Database Accession Notes

Pfam (EcoliWiki Page)

PF00512 His Kinase A (phosphoacceptor) domain

Pfam (EcoliWiki Page)

PF02518 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase

Pfam (EcoliWiki Page)

PF00672 HAMP domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:47384

Panther (EcoliWiki Page)

PTHR24423:SF372

Superfamily (EcoliWiki Page)

SUPERFAMILY:55785

Superfamily (EcoliWiki Page)

SUPERFAMILY:55874

Pfam (EcoliWiki Page)

PF00989 PAS fold

EcoCyc

EcoCyc:EG11667

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11667

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001610

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1618

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007341

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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2
  3. ↑ 3.0 3.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  4. ↑ 4.0 4.1 4.2 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  5. ↑ 5.0 5.1 5.2 5.3 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 6.2 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. ↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed
  8. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  9. ↑ 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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