appY: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

appY

Gene Synonym(s)

ECK0556, b0564, JW0553[1], JW0553

Product Desc.

AppY transcriptional activator[2][3]

Global transcription regulator, AraC family, DLP12 prophage[4]

Product Synonyms(s)

DLP12 prophage; DNA-binding transcriptional activator[1], B0564[2][1], AppY[2][1], regulatory protein affecting appA and other genes[2][1] , ECK0556, JW0553, b0564

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): appY[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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appY expression is induced by PO4 starvation and stationary phase. AppY activates appABC as growth slows and either activates or repressses other genes during exponential or stationary phase.[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

appY

Mnemonic

Acid (poly)phosphatase

Synonyms

ECK0556, b0564, JW0553[1], JW0553

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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

12.56 minutes 

MG1655: 582904..583653
<gbrowseImage> name=NC_000913:582904..583653 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 559033..559782
<gbrowseImage> name=NC_012967:559033..559782 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 485664..486413
<gbrowseImage> name=NC_012759:485664..486413 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 582904..583653
<gbrowseImage> name=NC_007779:582904..583653 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 522236..522985
<gbrowseImage> name=NC_010473:522236..522985 source=DH10B preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 635496..636245
<gbrowseImage> name=NC_010473:635496..636245 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

ΔappY (Keio:JW0553)

deletion

deletion

PMID:16738554

Shigen
CGSC8679[5]

ΔappY773::kan

PMID:16738554

CGSC:100022


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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

JW0553

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGATTATGTTTGCTCCGTAGT

Primer 2:CCGTCAATTGTTTTGTTTATTCC

23E10

Kohara Phage

Genobase

PMID:3038334

12A1

Kohara Phage

Genobase

PMID:3038334

purK79::Tn10

Linked marker

CAG12171 = CGSC7342[5]

est. P1 cotransduction: 30% [6]
Synonyms:purE79::Tn10

dsbG601::Tn10

Linked marker

CAG12149 = CGSC7346[5]

est. P1 cotransduction: 8% [6]
Synonyms:zbd-601::Tn10, zbe-601::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:EG10050

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10050

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000046

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948797

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0048

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001929

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

AppY

Synonyms

DLP12 prophage; DNA-binding transcriptional activator[1], B0564[2][1], AppY[2][1], regulatory protein affecting appA and other genes[2][1] , ECK0556, JW0553, b0564

Product description

AppY transcriptional activator[2][3]

Global transcription regulator, AraC family, DLP12 prophage[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

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000005

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020449

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

PMID:15225322

IMP: Inferred from Mutant Phenotype

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

PMID:8451183

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P27029
Swiss-Prot:P16114
Swiss-Prot:P22539
Swiss-Prot:P28816
Swiss-Prot:P13225
Swiss-Prot:P07859
Swiss-Prot:P10411
Swiss-Prot:P28809
Swiss-Prot:P09378
Swiss-Prot:P09377
Swiss-Prot:P28808
Swiss-Prot:P23774
Swiss-Prot:P26993
Swiss-Prot:P10805
Swiss-Prot:P192193
Swiss-Prot:P11765
Swiss-Prot:P03021
Swiss-Prot:P07642
Swiss-Prot:P03022
Swiss-Prot:P17410
Swiss-Prot:P25393

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

PMID:8626281

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

PMID:9079897

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000005

C

Seeded from EcoCyc (v14.0)

complete

GO:0005622

intracellular

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020449

C

Seeded from EcoCyc (v14.0)

complete

GO:0016036

cellular response to phosphate starvation

PMID:8626281

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc (v14.0)

complete

GO:0016036

cellular response to phosphate starvation

PMID:9079899

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc (v14.0)

complete

GO:0016563

transcription activator activity

PMID:15225322

IMP: Inferred from Mutant Phenotype

F

Seeded from EcoCyc (v14.0)

complete

GO:0016563

transcription activator activity

PMID:8451183

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P27029
Swiss-Prot:P16114
Swiss-Prot:P22539
Swiss-Prot:P28816
Swiss-Prot:P13225
Swiss-Prot:P07859
Swiss-Prot:P10411
Swiss-Prot:P28809
Swiss-Prot:P09378
Swiss-Prot:P09377
Swiss-Prot:P28808
Swiss-Prot:P23774
Swiss-Prot:P26993
Swiss-Prot:P10805
Swiss-Prot:P192193
Swiss-Prot:P11765
Swiss-Prot:P03021
Swiss-Prot:P07642
Swiss-Prot:P03022
Swiss-Prot:P17410
Swiss-Prot:P25393

F

Seeded from EcoCyc (v14.0)

complete

GO:0016563

transcription activator activity

PMID:8626281

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0016563

transcription activator activity

PMID:9079897

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0043193

positive regulation of gene-specific transcription

PMID:15225322

IMP: Inferred from Mutant Phenotype

P

Seeded from EcoCyc (v14.0)

complete

GO:0043193

positive regulation of gene-specific transcription

PMID:8451183

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P27029
Swiss-Prot:P16114
Swiss-Prot:P22539
Swiss-Prot:P28816
Swiss-Prot:P13225
Swiss-Prot:P07859
Swiss-Prot:P10411
Swiss-Prot:P28809
Swiss-Prot:P09378
Swiss-Prot:P09377
Swiss-Prot:P28808
Swiss-Prot:P23774
Swiss-Prot:P26993
Swiss-Prot:P10805
Swiss-Prot:P192193
Swiss-Prot:P11765
Swiss-Prot:P03021
Swiss-Prot:P07642
Swiss-Prot:P03022
Swiss-Prot:P17410
Swiss-Prot:P25393

P

Seeded from EcoCyc (v14.0)

complete

GO:0043193

positive regulation of gene-specific transcription

PMID:8626281

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc (v14.0)

complete

GO:0043193

positive regulation of gene-specific transcription

PMID:9079897

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc (v14.0)

complete

GO:0043565

sequence-specific DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000005

F

Seeded from EcoCyc (v14.0)

complete

GO:0043565

sequence-specific DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020449

F

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

glnD

PMID:16606699

Experiment(s):EBI-1137163

Protein

relE

PMID:16606699

Experiment(s):EBI-1137163

Protein

nadE

PMID:16606699

Experiment(s):EBI-1137163

Protein

fdhE

PMID:16606699

Experiment(s):EBI-1137163

Protein

rpsI

PMID:16606699

Experiment(s):EBI-1137163

Protein

iscS

PMID:16606699

Experiment(s):EBI-1137163

Protein

rplD

PMID:16606699

Experiment(s):EBI-1137163

Protein

ddpC

PMID:16606699

Experiment(s):EBI-1137163

Protein

hyaB

PMID:16606699

Experiment(s):EBI-1137163

Protein

yciH

PMID:16606699

Experiment(s):EBI-1137163

Protein

caiB

PMID:16606699

Experiment(s):EBI-1137163

Protein

ahpF

PMID:16606699

Experiment(s):EBI-1137163

Protein

rplB

PMID:16606699

Experiment(s):EBI-1137163

Protein

glpC

PMID:16606699

Experiment(s):EBI-1137163

Protein

rtcB

PMID:16606699

Experiment(s):EBI-1137163
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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 

MDYVCSVVFI CQSFDLIINR RVISFKKNSL FIVSDKIRRE LPVCPSKLRI VDIDKKTCLS
FFIDVNNELP GKFTLDKNGY IAEEEPPLSL VFSLFEGIKI ADSHSLWLKE RLCISLLAMF
KKRESVNSFI LTNINTFTCK ITGIISFNIE RQWHLKDIAE LIYTSESLIK KRLRDEGTSF
TEILRDTRMR YAKKLITSNS YSINVVAQKC GYNSTSYFIC AFKDYYGVTP SHYFEKIIGV
TDGINKTID
Length

249

Mol. Wt

28.764 kDa

pI

8.9 (calculated)

Extinction coefficient

25,900 - 26,900 (calc based on 10 Y, 2 W, and 8 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..185

PF00165 Bacterial regulatory helix-turn-helix proteins, AraC family

PMID:19920124

Domain

195..235

PF00165 Bacterial regulatory helix-turn-helix proteins, AraC family

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=appY 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:16128547

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948797

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001929

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P05052

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10050

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10050

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948797

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000046

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0048

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

86

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

72

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

35a

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)

appY

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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_000913:582884..582924 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:b0564 (EcoliWiki Page)

NCBI GEO profiles for appY

microarray

GenExpDB:b0564 (EcoliWiki Page)

Summary of data for appY 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 appY Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10050

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0048

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0564

EcoGene

EcoGene:EG10050

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000046

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001929

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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<protect> See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism Homologs (Statistics) Comments
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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)

PF00165 Bacterial regulatory helix-turn-helix proteins, AraC family

Pfam (EcoliWiki Page)

PF00165 Bacterial regulatory helix-turn-helix proteins, AraC family

Superfamily (EcoliWiki Page)

SUPERFAMILY:46689

EcoCyc

EcoCyc:EG10050

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10050

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000046

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0048

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001929

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 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).

Categories

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