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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	hemF
Gene Synonym(s)	ECK2431, b2436, JW2429, popB, sec^[1], sec
Product Desc.	Coproporphyrinogen III oxidase, oxygen-dependent; stimulated by manganese; dimeric^[2]
Product Synonyms(s)	coproporphyrinogen III oxidase^[1], B2436^[3]^[1], Sec^[3]^[1], PopB^[3]^[1], HemF^[3]^[1] , ECK2431, JW2429, popB, sec, b2436
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): hemF^[3], amiA-hemF^[3]
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	hemF
Mnemonic	Hemin
Synonyms	ECK2431, b2436, JW2429, popB, sec^[1], sec
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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	54.99 minutes	MG1655: 2551247..2552146 <gbrowseImage> name=NC_000913:2551247..2552146 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2480744..2481643 <gbrowseImage> name=NC_012967:2480744..2481643 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2437052..2437951 <gbrowseImage> name=NC_012759:2437052..2437951 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2558671..2559570 <gbrowseImage> name=NC_007779:2558671..2559570 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2643012..2643911 <gbrowseImage> name=NC_010473:2643012..2643911 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
ΔhemF (Keio:JW2429)	deletion	deletion	PMID:16738554	Shigen CGSC9935^[4]
hemF::Tn5KAN-2 (FB20799)	Insertion at nt 304 in Minus orientation		PMID:15262929	E. coli Genome Project:FB20799	contains pKD46
ΔhemF765::kan			PMID:16738554	CGSC:101340
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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
JW2429	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAACCCGACGCACACCAGGT Primer 2:CCaACCCAATCCCTGACCTTAAT
E8E3	Kohara Phage	Genobase	PMID:3038334
4E10	Kohara Phage	Genobase	PMID:3038334
nupC510::Tn10	Linked marker	CAG18468 = CGSC7410^[4]	est. P1 cotransduction: 17% ^[5]
purC80::Tn10	Linked marker	CAG18470 = CGSC7413^[4]	est. P1 cotransduction: 16% ^[5]
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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:EG12189	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12189	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002078	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946908	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2106	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008034	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	HemF
Synonyms	coproporphyrinogen III oxidase^[1], B2436^[3]^[1], Sec^[3]^[1], PopB^[3]^[1], HemF^[3]^[1] , ECK2431, JW2429, popB, sec, b2436
Product description	Coproporphyrinogen III oxidase, oxygen-dependent; stimulated by manganese; dimeric^[2]
EC number (for enzymes)	1.3.3.3^[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:0004109	coproporphyrinogen oxidase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00333	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004109	coproporphyrinogen oxidase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001260	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004109	coproporphyrinogen oxidase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018375	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004109	coproporphyrinogen oxidase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.3.3.3	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00333	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:0030145	manganese ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0464	F	Seeded from EcoCyc (v14.0)	complete
	GO:0042803	protein homodimerization activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00333	F	Seeded from EcoCyc (v14.0)	complete
	GO:0042803	protein homodimerization activity	GO_REF:0000024	ISS: Inferred from Sequence or Structural Similarity	UniProtKB:P36551	F	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001260	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018375	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:0005737	cytoplasm	PMID:12975365	IDA: Inferred from Direct Assay		C		complete
	GO:0030145	manganese ion binding	PMID:12975365	IDA: Inferred from Direct Assay		F		complete
	GO:0046906	tetrapyrrole binding	PMID:12975365	IMP: Inferred from Mutant Phenotype		F		complete
	GO:0004109	coproporphyrinogen oxidase activity	PMID:12975365	IMP: Inferred from Mutant Phenotype		F		complete
	GO:0006783	heme biosynthetic process	PMID:8300522	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0005515	protein binding	PMID:12975365	IDA: Inferred from Direct Assay		F	HemF is homodimeric.	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	nadE		PMID:16606699	Experiment(s):EBI-1142825
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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
cytoplasm			From EcoCyc^[6]
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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 MKPDAHQVKQ FLLNLQDTIC QQLTAVDGAE FVEDSWQREA GGGGRSRVLR NGGVFEQAGV NFSHVHGEAM PASATAHRPE LAGRSFEAMG VSLVVHPHNP YVPTSHANVR FFIAEKPGAD PVWWFGGGFD LTPFYGFEED AIHWHRTARD LCLPFGEDVY PRYKKWCDEY FYLKHRNEQR GIGGLFFDDL NTPDFDRCFA FMQAVGKGYT DAYLPIVERR KAMAYGERER NFQLYRRGRY VEFNLVWDRG TLFGLQTGGR TESILMSMPP LVRWEYDYQP KDGSPEAALS EFIKVRDWV
Length	299
Mol. Wt	34.322 kDa
pI	6.4 (calculated)
Extinction coefficient	63,370 - 63,870 (calc based on 13 Y, 8 W, and 4 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
Domain	6..299	PF01218 Coproporphyrinogen III oxidase		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=hemF taxon=562,83333 </beststructure>

Models

View models at:

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</protect>

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:16130361	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946908	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008034	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P36553	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12189	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12189	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946908	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002078	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2106	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	Ecoli K-12	12.758+/-0.103	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.0189099	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	221	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	85	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	112	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)
hemF
amiA-hemF
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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_000913:2551227..2551267 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

</protect>

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:b2436 (EcoliWiki Page)	NCBI GEO profiles for hemF
microarray	GenExpDB:b2436 (EcoliWiki Page)	Summary of data for hemF 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 hemF Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12189	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2106	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2436
EcoGene	EcoGene:EG12189	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002078	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008034	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	ENSANGP00000010734 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000007412 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT1G03475 (score: 1.000; bootstrap: 100%) AT4G03205 (score: 0.244)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000005398 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000013507 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000010961 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0231414 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0021944 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA17449-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000024546 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000264193 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000014197 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000021292 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:104841 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q42840 (score: 1.000; bootstrap: 100%) Q7XPL2 (score: 0.720) Q84VE2 (score: 0.591)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000026149 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000002257 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YDR044W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC2221 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000133100 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00028915001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000051825 (score: 1.000; bootstrap: 98%)	From Inparanoid:20070104
E. coli O157	HEMF	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)	PF01218 Coproporphyrinogen III oxidase
Panther (EcoliWiki Page)	PTHR10755:SF0
Superfamily (EcoliWiki Page)	SUPERFAMILY:102886
EcoCyc	EcoCyc:EG12189	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12189	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002078	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2106	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0008034	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 ^1.12 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 ^3.5 ^3.6 ^3.7 ^3.8 ^3.9 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 CGSC: The Coli Genetics Stock Center
↑ ^5.0 ^5.1 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).
↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7

hemF: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 hemF Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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