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Gene |

Product(s) |

Expression|

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Standard Name	araC
Gene Synonym(s)	ECK0065, b0064, JW0063^[1], JW0063
Product Desc.	AraC^[2]^[3]; Component of AraC transcriptional dual regulator^[2]^[3] Transcriptional activator for the ara regulon; autorepressor in the absence of arabinose co-activator^[4]
Product Synonyms(s)	DNA-binding transcriptional dual regulator^[1], B0064^[2]^[1], AraC^[2]^[1], transcriptional regulator for ara operon^[2]^[1] , ECK0065, JW0063, b0064
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): araC^[2], OP00004
Regulation/Activity
Quick Links
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Notes

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AraC activates transcrption for araE and the araBAD and araFGH operons; AraC transcriptional activator family prototype.^[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	araC
Mnemonic	Arabinose
Synonyms	ECK0065, b0064, JW0063^[1], JW0063
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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	1.52 minutes	MG1655: 70387..71265 <gbrowseImage> name=NC_000913:70387..71265 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 73191..74069 <gbrowseImage> name=NC_012967:73191..74069 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 70386..71264 <gbrowseImage> name=NC_012759:70386..71264 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 70387..71265 <gbrowseImage> name=NC_007779:70387..71265 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	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
Coding Start (SO:0000323)	MG1655	70390	Edman degradation	PMID:7019009
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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: Description	Reference	Availability
araC(del) (Keio:JW0063)	deletion	deletion		PMID:16738554	Shigen
araC14					CGSC:4493
araC2022(Const)			constitutive		CGSC:6926
araC859					CGSC:8508
araC766(del)					CGSC:10895
araC17					CGSC:13810
araC203					CGSC:14408
araC510					CGSC:14414
araC219					CGSC:27427
araC205					CGSC:27482
araC212					CGSC:27486
araC221					CGSC:27490
araC501					CGSC:27494
araC502					CGSC:27495
araC505					CGSC:27496
araC506					CGSC:27497
araC60					CGSC:27516
araC64					CGSC:27517
araC67					CGSC:27518
araC70					CGSC:27519
araC605(FucR, Const)			"D-fucose resistant, constitutive"		CGSC:27569
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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
JW0063	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCTGAAGCGCAAAATGATCC Primer 2:CCTGACAACTTGACGGCTACAT
5H5	Kohara Phage	Genobase	PMID:3038334
8H11	Kohara Phage	Genobase	PMID:3038334
carB96::Tn10	Linked marker	CAG12093 = CGSC7322^[5]	est. P1 cotransduction: 21% ^[6] Synonyms:car-96::Tn10
leuO3051::Tn10	Linked marker	CAG12095 = CGSC7324^[5]	est. P1 cotransduction: 63% ^[6] Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).
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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:EG10054	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10054	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000050	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:944780	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0052	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000236	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	AraC
Synonyms	DNA-binding transcriptional dual regulator^[1], B0064^[2]^[1], AraC^[2]^[1], transcriptional regulator for ara operon^[2]^[1] , ECK0065, JW0063, b0064
Product description	AraC^[2]^[3]; Component of AraC transcriptional dual regulator^[2]^[3] Transcriptional activator for the ara regulon; autorepressor in the absence of arabinose co-activator^[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:0003677	DNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012287	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003677	DNA binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0238	F	Seeded from EcoCyc (v14.0)	complete
	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:0019568	arabinose catabolic process	PMID:13829634	IMP: Inferred from Mutant Phenotype		P		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: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:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006350	transcription	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0804	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006355	regulation of transcription, DNA-dependent	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000005	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006355	regulation of transcription, DNA-dependent	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003313	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006355	regulation of transcription, DNA-dependent	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020449	P	Seeded from EcoCyc (v14.0)	complete
	GO:0019568	arabinose catabolic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0054	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
	GO:0045449	regulation of transcription	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012287	P	Seeded from EcoCyc (v14.0)	complete
	GO:0045449	regulation of transcription	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0805	P	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	Subunits of AraC transcriptional dual regulator	homodimer
Protein	gabT		PMID:16606699	Experiment(s):EBI-1135479
Protein	groL		PMID:16606699	Experiment(s):EBI-1135479
Small Molecule	arabinose	inducer
Small Molecule	fucose	anti-inducer
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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 MAEAQNDPLL PGYSFNAHLV AGLTPIEANG YLDFFIDRPL GMKGYILNLT IRGQGVVKNQ GREFVCRPGD ILLFPPGEIH HYGRHPEARE WYHQWVYFRP RAYWHEWLNW PSIFANTGFF RPDEAHQPHF SDLFGQIINA GQGEGRYSEL LAINLLEQLL LRRMEAINES LHPPMDNRVR EACQYISDHL ADSNFDIASV AQHVCLSPSR LSHLFRQQLG ISVLSWREDQ RISQAKLLLS TTRMPIATVG RNVGFDDQLY FSRVFKKCTG ASPSEFRAGC EEKVNDVAVK LS
Length	292
Mol. Wt	33.384 kDa
pI	7.0 (calculated)
Extinction coefficient	47,900 - 48,525 (calc based on 10 Y, 6 W, and 5 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	20..160	PF02311 AraC-like ligand binding domain	PMID:19920124
Domain	186..228	PF00165 Bacterial regulatory helix-turn-helix proteins, AraC family	PMID:19920124
Domain	239..278	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=araC 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:16128058	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944780	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000236	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A9E0	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10054	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10054	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944780	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000050	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0052	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	Reference(s)
Protein	E. coli K-12 MC4100	2.29E+02	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI	PMID:18304323
Protein	E. coli K-12 MG1655	105	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	115	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	69	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	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)
araC
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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_000913:70367..70407 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	GenExpDB:b0064 (EcoliWiki Page)	Summary of data for araC from multiple microarray studies
microarray	GEO Profiles:b0064 (EcoliWiki Page)	NCBI GEO profiles for araC
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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
	GFP Fusion	Intergenic region (69973..70452) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ20; Well:F6^[7]
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Notes

Accessions Related to araC Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10054	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0052	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0064
EcoGene	EcoGene:EG10054	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000050	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000236	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
Shigella flexneri	ARAC	From SHIGELLACYC
E. coli O157	ARAC	From ECOO157CYC
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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)	PF02311 AraC-like ligand binding domain
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
Superfamily (EcoliWiki Page)	SUPERFAMILY:46689
Superfamily (EcoliWiki Page)	SUPERFAMILY:51215
Panther (EcoliWiki Page)	PTHR11019:SF25
EcoCyc	EcoCyc:EG10054	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10054	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000050	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0052	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000236	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.

↑ ^1.0 ^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)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 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 ^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 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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

araC:On One Page

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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 araC Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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