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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	ahpF
Gene Synonym(s)	ECK0600, b0606, JW0599^[1], JW0599
Product Desc.	AhpF component^[2]^[3]; Component of alkylhydroperoxide reductase^[3] Alkyl hydroperoxide reductase, subunit F; NAD(P)H:peroxiredoxin oxidoreductase, reduces AhpC; contains one FAD/monomer^[4]
Product Synonyms(s)	alkyl hydroperoxide reductase, F52a subunit, FAD/NAD(P)-binding^[1], B0606^[2]^[1], AhpF^[2]^[1], alkyl hydroperoxide reductase, F52a subunit^[2]^[1] , ECK0600, JW0599, b0606
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ahpF^[2], ahpCF^[2], OP00101, ahpC
Regulation/Activity
Quick Links
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Notes

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The native AhpF from Salmonella has been N-terminally sequenced (Jacobson et al, 1989), supporting the choice of this alternate initiation codon in E. coli by inference.^[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	ahpF
Mnemonic	Alkyl hydroperoxide
Synonyms	ECK0600, b0606, JW0599^[1], JW0599
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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	13.77 minutes	MG1655: 638976..640541 <gbrowseImage> name=NC_000913:638976..640541 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 621804..623369 <gbrowseImage> name=NC_012967:621804..623369 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 541736..543301 <gbrowseImage> name=NC_012759:541736..543301 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 638976..640541 <gbrowseImage> name=NC_007779:638976..640541 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 578308..579873 <gbrowseImage> name=NC_010473:578308..579873 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
DH10B		DH10B: 691568..693133 <gbrowseImage> name=NC_010473:691568..693133 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
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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)	Reference	Availability	Comments
ΔahpF (Keio:JW0599)	deletion	deletion	PMID:16738554	Shigen CGSC8714^[5]
ahpF::Tn5KAN-2 (FB20212)	Insertion at nt 743 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20212	does not contain pKD46
ΔahpF745::kan			PMID:16738554	CGSC:99956
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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
JW0599	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCTCGACACAAATATGAAAAC Primer 2:CCTGCAGTTTTGGTGCGAATCAG
4A5	Kohara Phage	Genobase	PMID:3038334
3G5	Kohara Phage	Genobase	PMID:3038334
dsbG601::Tn10	Linked marker	CAG12149 = CGSC7346^[5]	est. P1 cotransduction: 90% ^[6] Synonyms:zbd-601::Tn10, zbe-601::Tn10
crcA280::Tn10	Linked marker	CAG12077 = CGSC7347^[5]	est. P1 cotransduction: 58% ^[6] Synonyms:zbe-280::Tn10
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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:EG11385	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11385	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001352	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947540	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1358	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002093	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	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] , ECK0600, JW0599, b0606
Product description	AhpF component^[2]^[3]; Component of alkylhydroperoxide reductase^[3] Alkyl hydroperoxide reductase, subunit F; NAD(P)H:peroxiredoxin oxidoreductase, reduces AhpC; contains one FAD/monomer^[4]
EC number (for enzymes)	1.6.4.-^[1]
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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:0005737	cytoplasm				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0005829	cytosol	PMID:16858726	IDA: Inferred from Direct Assay		C	Seeded from EcoCyc (v14.0)	complete
	GO:0009055	electron carrier activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002109	F	Seeded from EcoCyc (v14.0)	complete
	GO:0015035	protein disulfide oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002109	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000103	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001327	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR008255	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016651	oxidoreductase activity, acting on NADH or NADPH	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012081	F	Seeded from EcoCyc (v14.0)	complete
	GO:0045454	cell redox homeostasis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002109	P	Seeded from EcoCyc (v14.0)	complete
	GO:0050660	FAD binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001327	F	Seeded from EcoCyc (v14.0)	complete
	GO:0050660	FAD binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012081	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051287	NAD or NADH binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012081	F	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000103	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001327	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR008255	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012081	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	P	Seeded from EcoCyc (v14.0)	complete
	GO:0005625	soluble fraction	PMID:10666639	IDA: Inferred from Direct Assay		C		complete
	GO:0050660	flavin adenine dinucleotide binding	PMID:11243797	ISM: Inferred from Sequence Model	UniProtKB:Q39243	F		complete
	GO:0070402	NADPH binding	PMID:11243797	ISM: Inferred from Sequence Model	UniProtKB:Q39243	F		complete
	GO:0008785	alkyl hydroperoxide reductase activity	PMID:11717276	IGI: Inferred from Genetic Interaction	EcoliWiki:ahpC EcoliWiki:katE EcoliWiki:katG	F		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 alkylhydroperoxide reductase	could be indirect
Protein	Q79BD2		PMID:16606699	Experiment(s):EBI-1137379
Protein	ydfT		PMID:16606699	Experiment(s):EBI-1137379
Protein	yfeS		PMID:16606699	Experiment(s):EBI-1137379
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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 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
Length	531
Mol. Wt	57.402 kDa
pI	5.5 (calculated)
Extinction coefficient	34,380 - 35,130 (calc based on 12 Y, 3 W, and 6 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	357..437	PF00070 Pyridine nucleotide-disulphide oxidoreductase	PMID:19920124
Domain	214..494	PF07992 Pyridine nucleotide-disulphide oxidoreductase	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=ahpF taxon=562,83333 </beststructure>

Models

View models at:

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</protect>

Structure figures

</protect>

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:90111152	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947540	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002093	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P35340	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11385	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11385	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947540	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001352	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1358	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	1.25E+03	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	5698	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	1554	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	4883	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)
ahpF
ahpCF
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Figure courtesy of RegulonDB

</protect>

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_000913:638956..638996 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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:b0606 (EcoliWiki Page)	NCBI GEO profiles for ahpF
microarray	GenExpDB:b0606 (EcoliWiki Page)	Summary of data for ahpF 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
	GFP Fusion	Intergenic region (638655..638960) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ13; Well:F8^[7]
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Notes

Accessions Related to ahpF Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11385	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1358	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0606
EcoGene	EcoGene:EG11385	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001352	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002093	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	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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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF00070 Pyridine nucleotide-disulphide oxidoreductase
Superfamily (EcoliWiki Page)	SUPERFAMILY:51905
Panther (EcoliWiki Page)	PTHR22912:SF54
Superfamily (EcoliWiki Page)	SUPERFAMILY:52833
Superfamily (EcoliWiki Page)	SUPERFAMILY:52833
Pfam (EcoliWiki Page)	PF07992 Pyridine nucleotide-disulphide oxidoreductase
EcoCyc	EcoCyc:EG11385	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11385	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001352	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1358	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002093	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.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 ^1.11 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 ^2.9 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 ^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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

ahpF: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 ahpF Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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