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adiY:On One Page

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Gene Name	adiY (synonyms: ECK4109, b4116, JW4077)^[1]
Product(s)	AdiY product^[1]: DNA-binding transcriptional activator product, B4116 product
Description	AdiY transcriptional activator^[2]^[3]
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): adiY^[2]
Regulation/Activity
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Notes

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Gene

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Nomenclature

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Standard name	adiY
Mnemonic
Synonyms	ECK4109, b4116, JW4077^[1]
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Notes

Location(s) and DNA Sequence

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Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	93.44 minutes, 93.44 minutes	MG1655: 4335952..4335191	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
W3110		W3110: 4342607..4341846	GBrowse(W3110)	FASTA Dump
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Strain

Map location

Genome coordinates

Genome browsers

Sequence links

MG1655

93.44 minutes, 93.44 minutes

MG1655: 4335952..4335191
gbrowse_img.php?coord=4334191..4336952&genome=ecoli&name=MG1655&trackset=0&width=300&.png

EcoCyc

GBrowse(MG1655)

W3110

W3110: 4342607..4341846
gbrowse_img.php?coord=4340846..4343607&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

GBrowse(W3110)

FASTA Dump

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Notes

Sequence Features

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Feature type	Location	Description
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Notes

Alleles and Phenotypes

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Allele	Nt change(s)	AA change(s)	Reference	Availability
ΔadiY (Keio:JW4077)	deletion	deletion	PMID:16738554^[4]	Shigen CGSC10934^[5]
ΔadiY742::kan			PMID:16738554^[4]	CGSC:99922
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Notes

Genetic Resources

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Resource	Resource Type	Source	Notes/Reference
JW4077	Plasmid clone	Shigen	PMID:16769691^[6] Status:Clone OK Primer 1:GCCAGGATTTGCAGCGACCAACC Primer 2:CCGGCGACAGTGCGTTCTCTGTG
zje-2241::Tn10	Linked marker	CAG18427 = CGSC7481^[5]	est. P1 cotransduction: 32% ^[7]
cadB2231::Tn10	Linked marker	CAG18488 = CGSC7479^[5]	est. P1 cotransduction: 45% ^[7] Synonyms:zjd-2231::Tn10
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Notes

Accessions in Other Databases

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:EG11966
EchoBASE (EcoliWiki Page)	EchoBASE:EB1909
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4116
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C5121
EcoGene (EcoliWiki Page)	EcoGene:EG11966
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:ADIY
CGSC (EcoliWiki Page)	CGSC:35597
ASAP (EcoliWikiPage)	ASAP:ABE-0013479
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Links

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Name	URL	Comments
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Product(s)

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Nomenclature

Standard name	AdiY product
Synonyms	DNA-binding transcriptional activator product^[1], B4116 product^[2]^[1], AdiY product^[2]^[1]
Product description	AdiY transcriptional activator^[2]^[3]
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(s)	Evidence Code	with/from	Aspect	Notes	Status
	GO:0043565	sequence-specific DNA binding	GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000005	F	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0003677	DNA binding	GO_REF:0000002 GO_REF:0000004	IEA: Inferred from Electronic Annotation	InterPro:IPR012287 SP_KW:KW-0238	F	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0003700	transcription factor activity	GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000005	F	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0005622	intracellular	GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000005	C	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0006350	transcription	GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0804	P	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0006355	regulation of transcription, DNA-dependent	GO_REF:0000002 GO_REF:0000004	IEA: Inferred from Electronic Annotation	InterPro:IPR000005 SP_KW:KW-0805	P	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0045449	regulation of transcription	GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012287	P	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0005515	protein binding	PMID:16606699^[9]	IPI: Inferred from Physical Interaction	UniProtKB:P0A6F5	F	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0006350	transcription	PMID:8704970^[10]	IEP: Inferred from Expression Pattern		P	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0016563	transcription activator activity	PMID:8704970^[10]	IEP: Inferred from Expression Pattern		F	Seeded from EcoCyc 12.5 ^[8]	complete
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Interactions

Partner Type	Partner	Notes	References
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Notes

Localization

Compartment	Description	Evidence	Notes
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Notes

Structure and Physical Properties

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Physical Properties

Sequence	at EcoCyc MRICSDQPCI VLLTEKDVWI RVNGKEPISL KANHMALLNC ENNIIDVSSL NNTLVAHISH DIIKDYLRFL NKDLSQIPVW QRSATPILTL PCLTPDVFRV AAQHSMMPAE TESEKERTRA LLFTVLSRFL DSKKFVSLMM YMLRNCVSDS VYQIIESDIH KDWNLSMVAS CLCLSPSLLK KKLKSENTSY SQIITTCRMR YAVNELMMDG KNISQVSQSC GYNSTSYFIS VFKDFYGMTP LHYVSQHRER TVA
Mol. Wt	29.01 kDa (calc) ^[2]
pI
Extinction coefficient	29910 - 31035 (calc based on 9 Y, 3 W, and 9 C residues)
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Domains/Motifs/Modification Sites

Type	Residues	Description	Notes
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Structure

Structures	No results found.
Models	View models at: EcoliPredict ModBase PSI-PRED Protein Quaternary Structure (PQS) Genomes TO Protein (GTOP)
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Structures

No results found.

Models

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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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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:EG11966-MONOMER
UniProt (EcoliWiki Page)	UniProt:P33234
PFAM (EcoliWiki Page)	PFAM:PF00165
RefSeq (EcoliWiki Page)	RefSeq:NP_418540
ModBase (EcoliWiki Page)	ModBase:P33234
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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.

Transcription and Transcriptional Regulation

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Transcription unit(s)
adiY
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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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gbrowse_img.php?coord=4335932..4335972&genome=ecoli&name=MG1655&trackset=Genes_unlabeled+DNA_unlabeled+flip&width=400&.png
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

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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

Allele Name	Mutation	Phenotype	Reference
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Expression Studies

Type	Reference	Notes
microarray	GenExpDB:b4116 (EcoliWiki Page)	Summary of data for adiY from multiple microarray studies
microarray	GEO Profiles:b4116 (EcoliWiki Page)	NCBI GEO profiles for adiY
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Expression Resources

Resource Name	Resource Type	Description	Source	Notes
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Notes

Accessions Related to adiY Expression

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:EG11966
EchoBASE (EcoliWiki Page)	EchoBASE:EB1909
EcoliGenExpDB (EcoliWiki Page)	GenExpDB:b4116
EcoGene (EcoliWiki Page)	EcoGene:EG11966
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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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Organism	Homologs (Statistics)	Comments
Shigella flexneri	ADIY	From SHIGELLACYC
E. coli O157	ADIY	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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Database	Accession	Notes
PFAM (EcoliWiki Page)	PFAM:PF00165
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Links

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Name	URL	Comments
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References

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↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 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 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 Baba T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2: 2006.0008 PubMed EcoliWiki page
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ Kitagawa M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (A Complete Set of E. coli K-12 ORF Archive): Unique Resources for Biological Research. DNA Res 12: 291-9 PubMed EcoliWiki page
↑ ^7.0 ^7.1 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).
↑ ^8.0 ^8.1 ^8.2 ^8.3 ^8.4 ^8.5 ^8.6 ^8.7 ^8.8 ^8.9 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ Arifuzzaman M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res 16: 686-91 PubMed EcoliWiki page
↑ ^10.0 ^10.1 Stim-Herndon KP et al. (1996) Molecular characterization of adiY, a regulatory gene which affects expression of the biodegradative acid-induced arginine decarboxylase gene (adiA) of Escherichia coli. Microbiology 142 ( Pt 5): 1311-20 PubMed EcoliWiki page

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Retrieved from "http://ecoliwiki.net/colipedia/index.php/adiY:On_One_Page"

adiY:On One Page

From EcoliWiki

Quickview

Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Categories

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Categories

Expression

Overview

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to adiY Expression

Notes

Links

Categories

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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