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Gene |

Product(s) |

Expression|

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Standard Name	araF
Gene Synonym(s)	ECK1899, b1901, JW1889^[1], JW1889
Product Desc.	AraF^[2]^[3]; Component of arabinose ABC transporter^[2]^[3] L-Arabinose-binding protein^[4]
Product Synonyms(s)	L-arabinose transporter subunit^[1], periplasmic-binding component of ABC superfamily^[1], B1901^[2]^[1], AraF^[2]^[1] , ECK1899, JW1889, b1901
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): araFGH^[2], OP00138, araFG-w1867-araH
Regulation/Activity
Quick Links
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Notes

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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	araF
Mnemonic	Arabinose
Synonyms	ECK1899, b1901, JW1889^[1], JW1889
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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	42.74 minutes	MG1655: 1984152..1983163 <gbrowseImage> name=NC_000913:1983163..1984152 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1964122..1963133 <gbrowseImage> name=NC_012967:1963133..1964122 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1875646..1876635 <gbrowseImage> name=NC_012759:1875646..1876635 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1988265..1987276 <gbrowseImage> name=NC_007779:1987276..1988265 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2075160..2074171 <gbrowseImage> name=NC_010473:2074171..2075160 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
Coding Start (SO:0000323)	MG1655	1983166	Edman degradation	PMID:326784 PMID:9298646
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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	Comments
araFP277G		P277G	Improves binding to galactose			seeded from UniProt:P02924
ΔaraF (Keio:JW1889)	deletion	deletion		PMID:16738554	Shigen CGSC9571^[5]
araF::Tn5KAN-2 (FB20510)	Insertion at nt 512 in Minus orientation			PMID:15262929	E. coli Genome Project:FB20510	contains pKD46
araF::Tn5KAN-2 (FB20511)	Insertion at nt 512 in Minus orientation			PMID:15262929	E. coli Genome Project:FB20511	does not contain pKD46
araF432					CGSC:80485
araF434					CGSC:80488
ΔaraF751::kan				PMID:16738554	CGSC:100026
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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
JW1889	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCACAAATTTACTAAAGCCCT Primer 2:CCtTTACCGCCTAAACCTTTTTT
7F11	Kohara Phage	Genobase	PMID:3038334
18A9	Kohara Phage	Genobase	PMID:3038334
16B12	Kohara Phage	Genobase	PMID:3038334
eda-51::Tn10	Linked marker	CAG18486 = CGSC7392^[5]	est. P1 cotransduction: 8% ^[6]
uvrC279::Tn10	Linked marker	CAG12156 = CGSC7394^[5]	est. P1 cotransduction: 78% ^[6]
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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:EG10057	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10057	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000053	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946409	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0055	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006330	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	AraF
Synonyms	L-arabinose transporter subunit^[1], periplasmic-binding component of ABC superfamily^[1], B1901^[2]^[1], AraF^[2]^[1] , ECK1899, JW1889, b1901
Product description	AraF^[2]^[3]; Component of arabinose ABC transporter^[2]^[3] L-Arabinose-binding protein^[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:0006810	transport	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0813	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008643	carbohydrate transport	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0762	P	Seeded from EcoCyc (v14.0)	complete
	GO:0042597	periplasmic space	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0574	C	Seeded from EcoCyc (v14.0)	complete
	GO:0042597	periplasmic space	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0200	C	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 arabinose ABC transporter	could be indirect
Protein	dnaK		PMID:16606699	Experiment(s):EBI-1141251
Protein	nadE		PMID:16606699	Experiment(s):EBI-1141251
Protein	rpmB		PMID:16606699	Experiment(s):EBI-1141251
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Evidence	Reference/Source
periplasm		From EcoCyc^[3]
Periplasm	PMID:9298646	EchoLocation:araF
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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 MHKFTKALAA IGLAAVMSQS AMAENLKLGF LVKQPEEPWF QTEWKFADKA GKDLGFEVIK IAVPDGEKTL NAIDSLAASG AKGFVICTPD PKLGSAIVAK ARGYDMKVIA VDDQFVNAKG KPMDTVPLVM MAATKIGERQ GQELYKEMQK RGWDVKESAV MAITANELDT ARRRTTGSMD ALKAAGFPEK QIYQVPTKSN DIPGAFDAAN SMLVQHPEVK HWLIVGMNDS TVLGGVRATE GQGFKAADII GIGINGVDAV SELSKAQATG FYGSLLPSPD VHGYKSSEML YNWVAKDVEP PKFTEVTDVV LITRDNFKEE LEKKGLGGK
Length	329
Mol. Wt	35.541 kDa
pI	6.3 (calculated)
Extinction coefficient	36,440 - 36,565 (calc based on 6 Y, 5 W, and 1 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	Notes	References
motif	1-23	UniProt Manual:Signal Peptides	UniProt:P02924
Domain	25..320	PF00532 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=araF 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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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:16129851	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946409	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006330	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P02924	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10057	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10057	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946409	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000053	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0055	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 MC4100	1.37E+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	4^a	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	9	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	0^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)
araFGH
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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_000913:1984132..1984172 source=MG1655 flip=1 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	GEO Profiles:b1901 (EcoliWiki Page)	NCBI GEO profiles for araF
microarray	GenExpDB:b1901 (EcoliWiki Page)	Summary of data for araF 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 araF Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10057	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0055	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1901
EcoGene	EcoGene:EG10057	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000053	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006330	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
Anopheles gambiae	ENSANGP00000001793 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
E. coli O157	ARAF	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
Superfamily (EcoliWiki Page)	SUPERFAMILY:53822
Pfam (EcoliWiki Page)	PF00532 family
EcoCyc	EcoCyc:EG10057	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10057	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000053	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0055	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006330	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)
↑ ^2.0 ^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 ^3.2 ^3.3 ^3.4 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 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).

araF: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 araF Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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