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aaeR:On One Page

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Gene Name	aaeR (synonyms: ECK3232, b3243, JW3212, yhcS, qseA)^[1]^[2]
Product(s)	AaeR product^[1]: predicted DNA-binding transcriptional regulator, efflux system product, B3243 product, YhcS product, QseA product
Description	quorum sensing transcriptional regulator of LYSR-type^[2]^[3]
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): aaeR^[2]
Regulation/Activity
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Gene

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Nomenclature

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Standard name	aaeR
Mnemonic
Synonyms	ECK3232, b3243, JW3212, yhcS, qseA^[1]^[2]
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Notes

Location(s) and DNA Sequence

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Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	73.01 minutes	MG1655: 3387542..3388471	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
W3110		W3110: 3389375..3390304	GBrowse(W3110)	FASTA Dump
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Strain

Map location

Genome coordinates

Genome browsers

Sequence links

MG1655

73.01 minutes

MG1655: 3387542..3388471
gbrowse_img.php?coord=3386542..3389471&genome=ecoli&name=MG1655&trackset=0&width=300&.png

EcoCyc

GBrowse(MG1655)

W3110

W3110: 3389375..3390304
gbrowse_img.php?coord=3388375..3391304&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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Alleles and Phenotypes

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Allele	Nt change(s)	AA change(s)	Reference	Availability
ΔaaeR (Keio:JW3212)	deletion	deletion	PMID:16738554^[4]	Shigen CGSC10435^[5]
ΔaaeR768::kan			PMID:16738554^[4]	CGSC:99870
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Notes

Genetic Resources

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Resource	Resource Type	Source	Notes/Reference
JW3212	Plasmid clone	Shigen	PMID:16769691^[6] Status:Clone OK Primer 1:GCCGAACGACTAAAACGCATGTC Primer 2:CCtTTCTCTTTCCCGCGCCCGTG
zhc-6::Tn10	Linked marker	CAG12153 = CGSC7442^[5]	est. P1 cotransduction: 41% ^[7] Synonyms:zha-6::Tn10
acrF3083::Tn10	Linked marker	CAG12075 = CGSC7447^[5]	est. P1 cotransduction: 35% ^[7] Synonyms:zhd-3083::Tn10, zhe-3083::Tn10
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Notes

Accessions in Other Databases

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:G7688
EchoBASE (EcoliWiki Page)	EchoBASE:EB2676
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3243
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C3998
EcoGene (EcoliWiki Page)	EcoGene:EG12825
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:YHCS
ASAP (EcoliWikiPage)	ASAP:ABE-0010639
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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	AaeR
Synonyms	predicted DNA-binding transcriptional regulator, efflux system^[1], B3243^[2]^[1], YhcS^[2]^[1], AaeR^[2]^[1], QseA^[2]^[1]
Product description	quorum sensing transcriptional regulator of LYSR-type^[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:0003677	DNA binding	GO_REF:0000004	IEA: Inferred from Electronic Annotation	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:IPR000847	F	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:IPR000847 SP_KW:KW-0805	P	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0006350	transcription	PMID:12011002^[9]	NR		P	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0006350	transcription	PMID:12011002^[9]	RCA: inferred from Reviewed Computational Analysis		P	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0006350	transcription	PMID:15489430^[10]	IMP: Inferred from Mutant Phenotype		P	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0016563	transcription activator activity	PMID:12011002^[9]	NR		F	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0016563	transcription activator activity	PMID:12011002^[9]	RCA: inferred from Reviewed Computational Analysis		F	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0016563	transcription activator activity	PMID:15489430^[10]	IMP: Inferred from Mutant Phenotype		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 MERLKRMSVF AKVVEFGSFT AAARQLQMSV SSISQTVSKL EDELQVKLLN RSTRSIGLTE AGRIYYQGCR RMLHEVQDVH EQLYAFNNTP IGTLRIGCSS TMAQNVLAGL TAKMLKEYPG LSVNLVTGIP APDLIADGLD VVIRVGALQD SSLFSRRLGA MPMVVCAAKS YLTQYGIPEK PADLSSHSWL EYSVRPDNEF ELIAPEGIST RLIPQGRFVT NDPMTLVRWL TAGAGIAYVP LMWVINEINR GELEILLPRY QSDPRPVYAL YTEKDKLPLK VQVVINSLTD YFVEVGKLFQ EMHGRGKEK
Mol. Wt	34.52 kDa (calc) ^[2]
pI
Extinction coefficient	34380 - 34755 (calc based on 12 Y, 3 W, and 3 C residues)
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Domains/Motifs/Modification Sites

Type	Residues	Description	Notes
Domain	1 - 59	HTH lysR-type	UniProt:P67662
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Structure

Structures	Representative homolog: 1IZ1\|A (Cupriavidus necator) 1-243 of 309 residues (E-value: 1.2e-07) (Percent Identity: 27.02) View all other structures.
Models	View models at: EcoliPredict ModBase PSI-PRED Protein Quaternary Structure (PQS) Genomes TO Protein (GTOP)
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Structures

Representative homolog:
1IZ1|A (Cupriavidus necator)
1-243 of 309 residues (E-value: 1.2e-07) (Percent Identity: 27.02)
View all other structures.

Models

View models at:

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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:G7688-MONOMER
UniProt (EcoliWiki Page)	UniProt:P67662
PFAM (EcoliWiki Page)	PFAM:PF00126
RefSeq (EcoliWiki Page)	RefSeq:NP_417710
ModBase (EcoliWiki Page)	ModBase:P67662
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:YHCS-MONOMER
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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)
aaeR
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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=3387522..3387562&genome=ecoli&name=MG1655&trackset=Genes_unlabeled+DNA_unlabeled&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

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

Allele Name	Mutation	Phenotype	Reference
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Expression Studies

Type	Reference	Notes
microarray	GenExpDB:b3243 (EcoliWiki Page)	Summary of data for aaeR from multiple microarray studies
microarray	GEO Profiles:b3243 (EcoliWiki Page)	NCBI GEO profiles for aaeR
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Expression Resources

Resource Name	Resource Type	Description	Source	Notes
	GFP Fusion	Intergenic region (3386941..3387237) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ07; Well:H6^[11]
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Notes

Accessions Related to aaeR Expression

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:G7688
EchoBASE (EcoliWiki Page)	EchoBASE:EB2676
EcoliGenExpDB (EcoliWiki Page)	GenExpDB:b3243
EcoGene (EcoliWiki Page)	EcoGene:EG12825
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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	YHCS	From SHIGELLACYC
E. coli O157	YHCS	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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Database	Accession	Notes
PFAM (EcoliWiki Page)	PFAM:PF00126
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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 ^1.6 ^1.7 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 ^2.9 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
↑ ^9.0 ^9.1 ^9.2 ^9.3 Sperandio V et al. (2002) Quorum-sensing Escherichia coli regulator A: a regulator of the LysR family involved in the regulation of the locus of enterocyte effacement pathogenicity island in enterohemorrhagic E. coli. Infect Immun 70: 3085-93 PubMed EcoliWiki page
↑ ^10.0 ^10.1 Van Dyk TK et al. (2004) Characterization of the Escherichia coli AaeAB efflux pump: a metabolic relief valve? J Bacteriol 186: 7196-204 PubMed EcoliWiki page
↑ Zaslaver A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3: 623-8 PubMed EcoliWiki page

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

aaeR:On One Page

From EcoliWiki

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Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

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Alleles and Phenotypes

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Genetic Resources

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Accessions in Other Databases

Notes

Links

Categories

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

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Gene Product Resources

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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 aaeR Expression

Notes

Links

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Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

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