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acrF:On One Page

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Gene Name	acrF (synonyms: ECK3253, b3266, JW3234, envD)^[1]
Product(s)	AcrF product^[1]: multidrug efflux system protein product, B3266 product, EnvD product
Description	AcrF^[2]^[3] Component of AcrEF-TolC Multidrug Efflux Transport System^[3]
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): acrEF^[2]
Regulation/Activity
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Notes

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Gene

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Nomenclature

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Standard name	acrF
Mnemonic
Synonyms	ECK3253, b3266, JW3234, envD^[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	73.56 minutes	MG1655: 3413055..3416159	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
W3110		W3110: 3414888..3417992	GBrowse(W3110)	FASTA Dump
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Strain

Map location

Genome coordinates

Genome browsers

Sequence links

MG1655

73.56 minutes

MG1655: 3413055..3416159
gbrowse_img.php?coord=3412055..3417159&genome=ecoli&name=MG1655&trackset=0&width=300&.png

EcoCyc

GBrowse(MG1655)

W3110

W3110: 3414888..3417992
gbrowse_img.php?coord=3413888..3418992&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	Comments
ΔacrF (Keio:JW3234)	deletion	deletion	PMID:16738554^[4]	Shigen CGSC10446^[5]
acrF3083::Tn10	Insertion at 3,413,219 bp in MG1655 (NC_000913)		adapted from Nichols et al.^[6]	CAG12075 = CGSC7447^[5]	Synonyms: zhd-3083::Tn10, zhe-3083::Tn10
acrF3083::Tn10			PMID:2540407^[7] PMID:9829956^[8]	CGSC:40245
acrF3171::Tn10kan			PMID:2540407^[7]	CGSC:40249
ΔacrF784::kan			PMID:16738554^[4]	CGSC:99902
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Notes

Genetic Resources

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Resource	Resource Type	Source	Notes/Reference
JW3234	Plasmid clone	Shigen	PMID:16769691^[9] Status:Clone OK Primer 1:GCCGCAAACTTTTTTATTCGACG Primer 2:CCTCCTTTAAAGCAACGGCGGAT
zhc-6::Tn10	Linked marker	CAG12153 = CGSC7442^[5]	est. P1 cotransduction: 10% ^[6] Synonyms:zha-6::Tn10
smg-3082::Tn10	Linked marker	CAG12071 = CGSC7444^[5]	est. P1 cotransduction: 57% ^[6] Synonyms:zhb-3082::Tn10, zhd-3082::Tn10
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Notes

Accessions in Other Databases

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:EG10267
EchoBASE (EcoliWiki Page)	EchoBASE:EB0263
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3266
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C4032
EcoGene (EcoliWiki Page)	EcoGene:EG10267
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:ACRF_2
CGSC (EcoliWiki Page)	CGSC:33608
ASAP (EcoliWikiPage)	ASAP:ABE-0010724
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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	AcrF
Synonyms	multidrug efflux system protein^[1], B3266^[2]^[1], EnvD^[2]^[1], AcrF^[2]^[1]
Product description	AcrF^[2]^[3]; Component of ; AcrEF-TolC Multidrug Efflux Transport System^[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:0005215	transporter activity	GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004764	F	Seeded from EcoCyc 12.5 ^[10]	complete
	GO:0006810	transport	GO_REF:0000002 GO_REF:0000004	IEA: Inferred from Electronic Annotation	InterPro:IPR004764 SP_KW:KW-0813	P	Seeded from EcoCyc 12.5 ^[10]	complete
	GO:0007049	cell cycle	GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0131	P	Seeded from EcoCyc 12.5 ^[10]	complete
	GO:0016020	membrane	GO_REF:0000004 GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0397 SP_KW:KW-0472	C	Seeded from EcoCyc 12.5 ^[10]	complete
	GO:0016021	integral to membrane	GO_REF:0000002 GO_REF:0000004	IEA: Inferred from Electronic Annotation	InterPro:IPR004764 SP_KW:KW-0812	C	Seeded from EcoCyc 12.5 ^[10]	complete
	GO:0051301	cell division	GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0132	P	Seeded from EcoCyc 12.5 ^[10]	complete
	GO:0042493	response to drug				P	Seeded from EcoCyc 11.1^[3].	required fields missing
	GO:0015292	uniporter activity				F	Seeded from EcoCyc 11.1^[3].	required fields missing
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Interactions

Partner Type	Partner	Notes	References
Protein	Subunits of AcrEF-TolC Multidrug Efflux Transport System	could be indirect
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Notes

Localization

Compartment	Description	Evidence	Notes
plasma membrane	C-terminus localized in the cytoplasm with 12 predicted transmembrane domains	Daley et al. (2005) ^[11]/>
plasma membrane			From EcoCyc^[3]
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Notes

Structure and Physical Properties

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Physical Properties

Sequence	at EcoCyc MANFFIRRPI FAWVLAIILM MAGALAILQL PVAQYPTIAP PAVSVSANYP GADAQTVQDT VTQVIEQNMN GIDNLMYMSS TSDSAGSVTI TLTFQSGTDP DIAQVQVQNK LQLATPLLPQ EVQQQGISVE KSSSSYLMVA GFVSDNPGTT QDDISDYVAS NVKDTLSRLN GVGDVQLFGA QYAMRIWLDA DLLNKYKLTP VDVINQLKVQ NDQIAAGQLG GTPALPGQQL NASIIAQTRF KNPEEFGKVT LRVNSDGSVV RLKDVARVEL GGENYNVIAR INGKPAAGLG IKLATGANAL DTAKAIKAKL AELQPFFPQG MKVLYPYDTT PFVQLSIHEV VKTLFEAIML VFLVMYLFLQ NMRATLIPTI AVPVVLLGTF AILAAFGYSI NTLTMFGMVL AIGLLVDDAI VVVENVERVM MEDKLPPKEA TEKSMSQIQG ALVGIAMVLS AVFIPMAFFG GSTGAIYRQF SITIVSAMAL SVLVALILTP ALCATLLKPV SAEHHENKGG FFGWFNTTFD HSVNHYTNSV GKILGSTGRY LLIYALIVAG MVVLFLRLPS SFLPEEDQGV FLTMIQLPAG ATQERTQKVL DQVTDYYLKN EKANVESVFT VNGFSFSGQA QNAGMAFVSL KPWEERNGDE NSAEAVIHRA KMELGKIRDG FVIPFNMPAI VELGTATGFD FELIDQAGLG HDALTQARNQ LLGMAAQHPA SLVSVRPNGL EDTAQFKLEV DQEKAQALGV SLSDINQTIS TALGGTYVND FIDRGRVKKL YVQADAKFRM LPEDVDKLYV RSANGEMVPF SAFTTSHWVY GSPRLERYNG LPSMEIQGEA APGTSSGDAM ALMENLASKL PAGIGYDWTG MSYQERLSGN QAPALVAISF VVVFLCLAAL YESWSIPVSV MLVVPLGIVG VLLAATLFNQ KNDVYFMVGL LTTIGLSAKN AILIVEFAKD LMEKEGKGVV EATLMAVRMR LRPILMTSLA FILGVLPLAI SNGAGSGAQN AVGIGVMGGM VSATLLAIFF VPVFFVVIRR CFKG
Mol. Wt	111.45 kDa (calc) ^[2]
pI
Extinction coefficient	78730 - 79105 (calc based on 27 Y, 7 W, and 3 C residues)
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Domains/Motifs/Modification Sites

Type	Residues	Description	Notes
Domain	11 - 33	Predicted membrane-spanning helix.	TMD predicted by TMHMM^[12]' />
Domain	337 - 359	Predicted membrane-spanning helix.	TMD predicted by TMHMM^[12]' />
Domain	366 - 388	Predicted membrane-spanning helix.	TMD predicted by TMHMM^[12]' />
Domain	392 - 414	Predicted membrane-spanning helix.	TMD predicted by TMHMM^[12]' />
Domain	438 - 460	Predicted membrane-spanning helix.	TMD predicted by TMHMM^[12]' />
Domain	470 - 492	Predicted membrane-spanning helix.	TMD predicted by TMHMM^[12]' />
Domain	540 - 562	Predicted membrane-spanning helix.	TMD predicted by TMHMM^[12]' />
Domain	869 - 891	Predicted membrane-spanning helix.	TMD predicted by TMHMM^[12]' />
Domain	896 - 918	Predicted membrane-spanning helix.	TMD predicted by TMHMM^[12]' />
Domain	923 - 945	Predicted membrane-spanning helix.	TMD predicted by TMHMM^[12]' />
Domain	974 - 996	Predicted membrane-spanning helix.	TMD predicted by TMHMM^[12]' />
Domain	1006 - 1028	Predicted membrane-spanning helix.	TMD predicted by TMHMM^[12]' />
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Click the image to view raw output from TMHMM.

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

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:ACRF-MONOMER
SwissModel (EcoliWiki Page)	SwissModel:P24181
UniProt (EcoliWiki Page)	UniProt:P24181
PFAM (EcoliWiki Page)	PFAM:PF00873
RefSeq (EcoliWiki Page)	RefSeq:NP_417732
ModBase (EcoliWiki Page)	ModBase:P24181
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:ACRF_2-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)
acrEF
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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=3413035..3413075&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:b3266 (EcoliWiki Page)	Summary of data for acrF from multiple microarray studies
microarray	GEO Profiles:b3266 (EcoliWiki Page)	NCBI GEO profiles for acrF
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Expression Resources

Resource Name	Resource Type	Description	Source	Notes
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Notes

Accessions Related to acrF Expression

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:EG10267
EchoBASE (EcoliWiki Page)	EchoBASE:EB0263
EcoliGenExpDB (EcoliWiki Page)	GenExpDB:b3266
EcoGene (EcoliWiki Page)	EcoGene:EG10267
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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
Anopheles gambiae	ENSANGP00000029650 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000006739 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
E. coli O157	ACRF_2	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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Database	Accession	Notes
PFAM (EcoliWiki Page)	PFAM:PF00873
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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 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 ^3.4 ^3.5 ^3.6 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 ^5.3 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 ^6.2 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).
↑ ^7.0 ^7.1 Singer M et al. (1989) A collection of strains containing genetically linked alternating antibiotic resistance elements for genetic mapping of Escherichia coli. Microbiol Rev 53: 1-24 PubMed EcoliWiki page
↑ Nichols BP et al. (1998) Sequence analysis of Tn10 insertion sites in a collection of Escherichia coli strains used for genetic mapping and strain construction. J Bacteriol 180: 6408-11 PubMed EcoliWiki page
↑ 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
↑ ^10.0 ^10.1 ^10.2 ^10.3 ^10.4 ^10.5 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ Daley DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308: 1321-3 PubMed EcoliWiki page
↑ ^12.00 ^12.01 ^12.02 ^12.03 ^12.04 ^12.05 ^12.06 ^12.07 ^12.08 ^12.09 ^12.10 ^12.11 Krogh A et al. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305: 567-80 PubMed EcoliWiki page

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

acrF:On One Page

From EcoliWiki

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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 acrF Expression

Notes

Links

Categories

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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