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ahpF:On One Page

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Gene Name	ahpF (synonyms: ECK0600, b0606, JW0599)^[1]
Product(s)	AhpF product^[1]: alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)-binding product, B0606 product, alkyl hydroperoxide reductase, F52a subunit product
Description	AhpF component^[2]^[3] Component of alkylhydroperoxide reductase^[3]
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ahpF^[2], ahpCF^[2], OP00101, ahpC
Regulation/Activity
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Notes

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Gene

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Nomenclature

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Standard name	ahpF
Mnemonic
Synonyms	ECK0600, b0606, JW0599^[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	13.77 minutes	MG1655: 638976..640541	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
W3110		W3110: 638976..640541	GBrowse(W3110)	FASTA Dump
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Strain

Map location

Genome coordinates

Genome browsers

Sequence links

MG1655

13.77 minutes

MG1655: 638976..640541
gbrowse_img.php?coord=637976..641541&genome=ecoli&name=MG1655&trackset=0&width=300&.png

EcoCyc

GBrowse(MG1655)

W3110

W3110: 638976..640541
gbrowse_img.php?coord=637976..641541&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
ΔahpF (Keio:JW0599)	deletion	deletion	PMID:16738554^[4]	Shigen CGSC8714^[5]
ΔahpF745::kan			PMID:16738554^[4]	CGSC:99956
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Notes

Genetic Resources

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Resource	Resource Type	Source	Notes/Reference
JW0599	Plasmid clone	Shigen	PMID:16769691^[6] Status:Clone OK Primer 1:GCCCTCGACACAAATATGAAAAC Primer 2:CCTGCAGTTTTGGTGCGAATCAG
dsbG601::Tn10	Linked marker	CAG12149 = CGSC7346^[5]	est. P1 cotransduction: 90% ^[7] Synonyms:zbd-601::Tn10, zbe-601::Tn10
crcA280::Tn10	Linked marker	CAG12077 = CGSC7347^[5]	est. P1 cotransduction: 58% ^[7] Synonyms:zbe-280::Tn10
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Notes

Accessions in Other Databases

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:EG11385
EchoBASE (EcoliWiki Page)	EchoBASE:EB1358
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0606
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C0695
EcoGene (EcoliWiki Page)	EcoGene:EG11385
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:AHPF
CGSC (EcoliWiki Page)	CGSC:31194
ASAP (EcoliWikiPage)	ASAP:ABE-0002093
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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	AhpF
Synonyms	alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)-binding^[1], B0606^[2]^[1], AhpF^[2]^[1], alkyl hydroperoxide reductase, F52a subunit^[2]^[1]
Product description	AhpF component^[2]^[3]; Component of ; alkylhydroperoxide reductase^[3]
EC number (for enzymes)	1.6.4.-^[1]
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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:0016491	oxidoreductase activity	GO_REF:0000002 GO_REF:0000002 GO_REF:0000002 GO_REF:0000002 GO_REF:0000004	IEA: Inferred from Electronic Annotation	InterPro:IPR000103 InterPro:IPR001327 InterPro:IPR003042 InterPro:IPR008255 SP_KW:KW-0560	F	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0016651	oxidoreductase activity, acting on NADH or NADPH	GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012081	F	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0050660	FAD binding	GO_REF:0000002 GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001327 InterPro:IPR012081	F	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0051287	NAD binding	GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012081	F	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0005515	protein binding	PMID:16606699^[9]	IPI: Inferred from Physical Interaction	UniProtKB:P07604	F	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0005515	protein binding	PMID:16606699^[9]	IPI: Inferred from Physical Interaction	UniProtKB:P32719	F	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0005737	cytoplasm				C	Seeded from Riley et al 2006 ^[1].	required fields missing
	GO:0006805	xenobiotic metabolic process				P	Seeded from EcoCyc 11.1^[3].	required fields missing
	GO:0009398	FMN biosynthetic process				P	Seeded from EcoCyc 11.1^[3].	required fields missing
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Interactions

Partner Type	Partner	Notes	References
Protein	Subunits of alkylhydroperoxide reductase	could be indirect
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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 MMMFKAQEIN MLDTNMKTQL KAYLEKLTKP VELIATLDDS AKSAEIKELL AEIAELSDKV TFKEDNSLPV RKPSFLITNP GSNQGPRFAG SPLGHEFTSL VLALLWTGGH PSKEAQSLLE QIRHIDGDFE FETYYSLSCH NCPDVVQALN LMSVLNPRIK HTAIDGGTFQ NEITDRNVMG VPAVFVNGKE FGQGRMTLTE IVAKIDTGAE KRAAEELNKR DAYDVLIVGS GPAGAAAAIY SARKGIRTGL MGERFGGQIL DTVDIENYIS VPKTEGQKLA GALKVHVDEY DVDVIDSQSA SKLIPAAVEG GLHQIETASG AVLKARSIIV ATGAKWRNMN VPGEDQYRTK GVTYCPHCDG PLFKGKRVAV IGGGNSGVEA AIDLAGIVEH VTLLEFAPEM KADQVLQDKL RSLKNVDIIL NAQTTEVKGD GSKVVGLEYR DRVSGDIHNI ELAGIFVQIG LLPNTNWLEG AVERNRMGEI IIDAKCETNV KGVFAAGDCT TVPYKQIIIA TGEGAKASLS AFDYLIRTKT A
Mol. Wt	56.18 kDa (calc) ^[2]
pI
Extinction coefficient	34380 - 35130 (calc based on 12 Y, 3 W, and 6 C residues)
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Domains/Motifs/Modification Sites

Type	Residues	Description	Notes
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Structure

Structures	Representative Escherichia coli structure: 1FL2\|A 1-310 of 531 residues (E-value: 1.6e-162) (Percent Identity: 100.00) Representative homolog: 1EBD\|A (Geobacillus stearothermophilus) 68-172 of 531 residues (E-value: 1.0e-07) (Percent Identity: 28.97) 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 Escherichia coli structure:
1FL2|A
1-310 of 531 residues (E-value: 1.6e-162) (Percent Identity: 100.00)
Representative homolog:
1EBD|A (Geobacillus stearothermophilus)
68-172 of 531 residues (E-value: 1.0e-07) (Percent Identity: 28.97)
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:EG11385-MONOMER
SwissModel (EcoliWiki Page)	SwissModel:P35340
UniProt (EcoliWiki Page)	UniProt:P35340
PFAM (EcoliWiki Page)	PFAM:PF00070
RefSeq (EcoliWiki Page)	RefSeq:NP_415139
ModBase (EcoliWiki Page)	ModBase:P35340
PDB (EcoliWiki Page)	PDB:1FL2
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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)
ahpF
ahpCF
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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=638956..638996&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:b0606 (EcoliWiki Page)	Summary of data for ahpF from multiple microarray studies
microarray	GEO Profiles:b0606 (EcoliWiki Page)	NCBI GEO profiles for ahpF
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Expression Resources

Resource Name	Resource Type	Description	Source	Notes
	GFP Fusion	Intergenic region (638655..638960) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ13; Well:F8^[10]
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Notes

Accessions Related to ahpF Expression

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:EG11385
EchoBASE (EcoliWiki Page)	EchoBASE:EB1358
EcoliGenExpDB (EcoliWiki Page)	GenExpDB:b0606
EcoGene (EcoliWiki Page)	EcoGene:EG11385
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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	ENSANGP00000016322 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000024198 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	AHPF	From SHIGELLACYC
E. coli O157	AHPF	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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Database	Accession	Notes
PFAM (EcoliWiki Page)	PFAM:PF00070
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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 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 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 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 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^9.0 ^9.1 Arifuzzaman M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res 16: 686-91 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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ahpF: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 ahpF Expression

Notes

Links

Categories

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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