Latest revision as of 05:20, 29 July 2007

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On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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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
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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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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>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 559033..559782 <gbrowseImage> name=NC_012967:559033..559782 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 485664..486413 <gbrowseImage> name=NC_012759:485664..486413 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 582904..583653 <gbrowseImage> name=NC_007779:582904..583653 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 522236..522985 <gbrowseImage> name=NC_010473:522236..522985 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
DH10B		DH10B: 635496..636245 <gbrowseImage> name=NC_010473:635496..636245 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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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)	Reference	Availability
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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Name	URL	Comments
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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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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^[7]	IMP: Inferred from Mutant Phenotype		F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	PMID:8451183^[8]	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^[9]	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	PMID:9079897^[10]	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^[9]	IDA: Inferred from Direct Assay		P	Seeded from EcoCyc (v14.0)	complete
	GO:0016036	cellular response to phosphate starvation	PMID:9079899^[11]	IDA: Inferred from Direct Assay		P	Seeded from EcoCyc (v14.0)	complete
	GO:0016563	transcription activator activity	PMID:15225322^[7]	IMP: Inferred from Mutant Phenotype		F	Seeded from EcoCyc (v14.0)	complete
	GO:0016563	transcription activator activity	PMID:8451183^[8]	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^[9]	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0016563	transcription activator activity	PMID:9079897^[10]	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc (v14.0)	complete
	GO:0043193	positive regulation of gene-specific transcription	PMID:15225322^[7]	IMP: Inferred from Mutant Phenotype		P	Seeded from EcoCyc (v14.0)	complete
	GO:0043193	positive regulation of gene-specific transcription	PMID:8451183^[8]	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^[9]	IDA: Inferred from Direct Assay		P	Seeded from EcoCyc (v14.0)	complete
	GO:0043193	positive regulation of gene-specific transcription	PMID:9079897^[10]	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	References	Evidence
Protein	glnD	PMID:16606699^[12]	Experiment(s):EBI-1137163
Protein	relE	PMID:16606699^[12]	Experiment(s):EBI-1137163
Protein	nadE	PMID:16606699^[12]	Experiment(s):EBI-1137163
Protein	fdhE	PMID:16606699^[12]	Experiment(s):EBI-1137163
Protein	rpsI	PMID:16606699^[12]	Experiment(s):EBI-1137163
Protein	iscS	PMID:16606699^[12]	Experiment(s):EBI-1137163
Protein	rplD	PMID:16606699^[12]	Experiment(s):EBI-1137163
Protein	ddpC	PMID:16606699^[12]	Experiment(s):EBI-1137163
Protein	hyaB	PMID:16606699^[12]	Experiment(s):EBI-1137163
Protein	yciH	PMID:16606699^[12]	Experiment(s):EBI-1137163
Protein	caiB	PMID:16606699^[12]	Experiment(s):EBI-1137163
Protein	ahpF	PMID:16606699^[12]	Experiment(s):EBI-1137163
Protein	rplB	PMID:16606699^[12]	Experiment(s):EBI-1137163
Protein	glpC	PMID:16606699^[12]	Experiment(s):EBI-1137163
Protein	rtcB	PMID:16606699^[12]	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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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	References
Domain	145..185	PF00165 Bacterial regulatory helix-turn-helix proteins, AraC family	PMID:19920124^[13]
Domain	195..235	PF00165 Bacterial regulatory helix-turn-helix proteins, AraC family	PMID:19920124^[13]
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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

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: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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Name	URL	Comments
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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	35^a	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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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
appY
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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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<gbrowseImage> name=NC_000913:582884..582924 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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

</protect>

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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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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Name	URL	Comments
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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
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Do-It-Yourself Web Tools

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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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^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
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^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.
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ ^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).
↑ ^7.0 ^7.1 ^7.2 Yang, H et al. (2004) Identification of mutator genes and mutational pathways in Escherichia coli using a multicopy cloning approach. Mol. Microbiol. 53 283-95 PubMed
↑ ^8.0 ^8.1 ^8.2 Gallegos, MT et al. (1993) The XylS/AraC family of regulators. Nucleic Acids Res. 21 807-10 PubMed
↑ ^9.0 ^9.1 ^9.2 ^9.3 Brøndsted, L & Atlung, T (1996) Effect of growth conditions on expression of the acid phosphatase (cyx-appA) operon and the appY gene, which encodes a transcriptional activator of Escherichia coli. J. Bacteriol. 178 1556-64 PubMed
↑ ^10.0 ^10.1 ^10.2 Atlung, T et al. (1997) Effects of sigmaS and the transcriptional activator AppY on induction of the Escherichia coli hya and cbdAB-appA operons in response to carbon and phosphate starvation. J. Bacteriol. 179 2141-6 PubMed
↑ Moukadiri, I et al. (1997) Identification of a mannoprotein present in the inner layer of the cell wall of Saccharomyces cerevisiae. J. Bacteriol. 179 2154-62 PubMed
↑ ^12.00 ^12.01 ^12.02 ^12.03 ^12.04 ^12.05 ^12.06 ^12.07 ^12.08 ^12.09 ^12.10 ^12.11 ^12.12 ^12.13 ^12.14 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
↑ ^13.0 ^13.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

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+-->{{#css:Suppresslinks.css}}<css>{{:Suppresslinks.css}}</css><noinclude>{{TabsTop}}
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+|[[#References | References]] |
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 __NOTOC__

appY:On One Page: Difference between revisions

Latest revision as of 05:20, 29 July 2007

Quickview

Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to appY Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

Categories

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