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agaR:On One Page

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Gene Name	agaR (synonyms: ECK3119, b3131, JW3100, yhaW)^[1]
Product(s)	AgaR product^[1]: DNA-binding transcriptional dual regulator product, B3131 product, YhaW product
Description	AgaR transcriptional regulator^[2] AgaR transcriptional repressor^[3]
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): agaR^[2]
Regulation/Activity
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Notes

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Gene

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Nomenclature

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Standard name	agaR
Mnemonic
Synonyms	ECK3119, b3131, JW3100, yhaW^[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	70.61 minutes	MG1655: 3276687..3275878	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
W3110		W3110: 3278520..3277711	GBrowse(W3110)	FASTA Dump
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Strain

Map location

Genome coordinates

Genome browsers

Sequence links

MG1655

70.61 minutes

MG1655: 3276687..3275878
gbrowse_img.php?coord=3274878..3277687&genome=ecoli&name=MG1655&trackset=0&width=300&.png

EcoCyc

GBrowse(MG1655)

W3110

W3110: 3278520..3277711
gbrowse_img.php?coord=3276711..3279520&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
ΔagaR (Keio:JW3100)	deletion	deletion	PMID:16738554^[4]	Shigen CGSC10362^[5]
ΔagaR745::kan			PMID:16738554^[4]	CGSC:99944
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Notes

Genetic Resources

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Resource	Resource Type	Source	Notes/Reference
JW3100	Plasmid clone	Shigen	PMID:16769691^[6] Status:Clone OK Primer 1:GCCAGTAATACCGACGCTTCAGG Primer 2:CCtTCCCCGACCAGAATCACTTC
aer-3075::Tn10	Linked marker	CAG12152 = CGSC7438^[5]	est. P1 cotransduction: 4% ^[7] Synonyms:zgh-3075::Tn10, zgj-3075::Tn10
sfsB203::Tn10	Linked marker	CAG12072 = CGSC7440^[5]	est. P1 cotransduction: 7% ^[7] Synonyms:zgj-203::Tn10, zha-203::Tn10
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Notes

Accessions in Other Databases

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:G7630
EchoBASE (EcoliWiki Page)	EchoBASE:EB2615
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3131
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C3886
EcoGene (EcoliWiki Page)	EcoGene:EG12762
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:AGAR
ASAP (EcoliWikiPage)	ASAP:ABE-0010291
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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	AgaR
Synonyms	DNA-binding transcriptional dual regulator^[1], B3131^[2]^[1], YhaW^[2]^[1], AgaR^[2]^[1]
Product description	AgaR transcriptional regulator^[2]; AgaR transcriptional repressor^[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:IPR001034	F	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0005622	intracellular	GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001034	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:IPR001034 SP_KW:KW-0805	P	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0016564	transcription repressor activity				F	Seeded from EcoCyc 11.1^[3].	required fields missing
	GO:0046349	amino sugar biosynthetic process				P	Seeded from EcoCyc 11.1^[3].	required fields missing
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Interactions

Partner Type	Partner	Notes	References
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Notes

Localization

Compartment	Description	Evidence	Notes
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Structure and Physical Properties

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Physical Properties

Sequence	at EcoCyc MSNTDASGEK RVTGTSERRE QIIQRLRQQG SVQVNDLSAL YGVSTVTIRN DLAFLEKQGI AVRAYGGALI CDSTTPSVEP SVEDKSALNT AMKRSVAKAA VELIQPGHRV ILDSGTTTFE IARLMRKHTD VIAMTNGMNV ANALLEAEGV ELLMTGGHLR RQSQSFYGDQ AEQSLQNYHF DMLFLGVDAI DLERGVSTHN EDEARLNRRM CEVAERIIVV TDSSKFNRSS LHKIIDTQRI DMIIVDEGIP ADSLEGLRKA GVEVILVGE
Mol. Wt	29.57 kDa (calc) ^[2]
pI
Extinction coefficient	5960 - 6210 (calc based on 4 Y, 0 W, and 2 C residues)
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Domains/Motifs/Modification Sites

Type	Residues	Description	Notes
Domain	15 - 70	HTH deoR-type	UniProt:P0ACK2
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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:G7630-MONOMER
UniProt (EcoliWiki Page)	UniProt:P0ACK2
PFAM (EcoliWiki Page)	PFAM:PF00455
RefSeq (EcoliWiki Page)	RefSeq:NP_417600
ModBase (EcoliWiki Page)	ModBase:P0ACK2
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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)
agaR
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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=3276667..3276707&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

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:b3131 (EcoliWiki Page)	Summary of data for agaR from multiple microarray studies
microarray	GEO Profiles:b3131 (EcoliWiki Page)	NCBI GEO profiles for agaR
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Expression Resources

Resource Name	Resource Type	Description	Source	Notes
	GFP Fusion	Intergenic region (3276212..3276638) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ08; Well:E5^[9]
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Notes

Accessions Related to agaR Expression

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:G7630
EchoBASE (EcoliWiki Page)	EchoBASE:EB2615
EcoliGenExpDB (EcoliWiki Page)	GenExpDB:b3131
EcoGene (EcoliWiki Page)	EcoGene:EG12762
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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
Apis mellifera	ENSAPMP00000020045 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000019507 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	AGAR	From SHIGELLACYC
E. coli O157	AGAR	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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Database	Accession	Notes
PFAM (EcoliWiki Page)	PFAM:PF00455
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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 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 ^3.3 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 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ 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/agaR:On_One_Page"

agaR: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 agaR Expression

Notes

Links

Categories

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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