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Standard Name	hemY
Gene Synonym(s)	ECK3796, b3802, JW3774^[1], JW3774
Product Desc.	conserved protein^[2]^[3] Member of uro (hemC) operon^[4]
Product Synonyms(s)	predicted protoheme IX synthesis protein^[1], B3802^[2]^[1], HemY^[2]^[1] , ECK3796, JW3774, b3802
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): hemCDXY^[2]
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	hemY
Mnemonic	Hemin
Synonyms	ECK3796, b3802, JW3774^[1], JW3774
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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	85.88 minutes, 85.88 minutes	MG1655: 3985905..3984709 <gbrowseImage> name=NC_000913:3984709..3985905 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3949688..3948492 <gbrowseImage> name=NC_012967:3948492..3949688 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3874378..3875574 <gbrowseImage> name=NC_012759:3874378..3875574 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3648799..3649995 <gbrowseImage> name=NC_007779:3648799..3649995 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4084825..4083629 <gbrowseImage> name=NC_010473:4083629..4084825 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
ΔhemY (Keio:JW3774)	deletion	deletion	PMID:16738554	Shigen
hemY::Tn5KAN-I-SceI (FB21461)	Insertion at nt 884 in Plus orientation		PMID:15262929	E. coli Genome Project:FB21461	contains pKD46
hemY::Tn5KAN-I-SceI (FB21462)	Insertion at nt 884 in Plus orientation		PMID:15262929	E. coli Genome Project:FB21462	does not contain pKD46
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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
JW3774	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCTAAAAGTGTTATTGCTCTT Primer 2:CCtTGTGGCGGGTTATTCTGCAA
12G1	Kohara Phage	Genobase	PMID:3038334
10F4	Kohara Phage	Genobase	PMID:3038334
ilvD500::Tn10	Linked marker	CAG18431 = CGSC7462^[5]	est. P1 cotransduction: 29% ^[6] Synonyms:ilv500::Tn10
metEo-3079::Tn10	Linked marker	CAG18491 = CGSC7464^[5]	est. P1 cotransduction: 41% ^[6] Synonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.
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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:EG10434	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10434	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000427	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948311	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0429	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012417	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	HemY
Synonyms	predicted protoheme IX synthesis protein^[1], B3802^[2]^[1], HemY^[2]^[1] , ECK3796, JW3774, b3802
Product description	conserved protein^[2]^[3] Member of uro (hemC) operon^[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:0005488	binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011990	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0997	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-1003	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006779	porphyrin biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0627	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005254	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0472	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0812	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016021	integral to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9909	C	Seeded from EcoCyc (v14.0)	complete
	GO:0042168	heme metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR005254	P	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	References	Evidence
Protein	phnI	PMID:19402753	MALDI(Z-score):39.959765
Protein	rbsA	PMID:19402753	MALDI(Z-score):26.761112
Protein	phnJ	PMID:19402753	MALDI(Z-score):28.600064
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Notes

Panek and O'Brian^[7] state that hemY in E. coli is dissimilar to hemY in other organisms and is probably not a protoporphyrin oxidase.

Localization

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

Compartment	Description	Evidence	Reference/Source	Notes
plasma membrane	C-terminus localized in the cytoplasm with 2 predicted transmembrane domains	Daley et al. (2005) ^[8]
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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 MLKVLLLFVL LIAGIVVGPM IAGHQGYVLI QTDNYNIETS VTGLAIILIL AMVVLFAIEW LLRRIFRTGA HTRGWFVGRK RRRARKQTEQ ALLKLAEGDY QQVEKLMAKN ADHAEQPVVN YLLAAEAAQQ RGDEARANQH LERAAELAGN DTIPVEITRV RLQLARNENH AARHGVDKLL EVTPRHPEVL RLAEQAYIRT GAWSSLLDII PSMAKAHVGD EEHRAMLEQQ AWIGLMDQAR ADNGSEGLRN WWKNQSRKTR HQVALQVAMA EHLIECDDHD TAQQIIIDGL KRQYDDRLLL PIPRLKTNNP EQLEKVLRQQ IKNVGDRPLL WSTLGQSLMK HGEWQEASLA FRAALKQRPD AYDYAWLADA LDRLHKPEEA AAMRRDGLML TLQNNPPQ
Length	398
Mol. Wt	45.245 kDa
pI	8.8 (calculated)
Extinction coefficient	61,420 - 61,545 (calc based on 8 Y, 9 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	References
Domain	1..133	PF07219 HemY protein N-terminus	PMID:19920124
Domain	328..361	PF07719 Tetratricopeptide repeat	PMID:19920124
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<motif_map/>

Click the image to view raw output from TMHMM.

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=hemY 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:16131654	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948311	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012417	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0ACB7	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10434	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10434	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948311	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000427	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0429	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	1.869+/-0.049	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.073160535	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	798	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	305	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	393	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)
hemCDXY
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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_000913:3985885..3985925 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:b3802 (EcoliWiki Page)	NCBI GEO profiles for hemY
microarray	GenExpDB:b3802 (EcoliWiki Page)	Summary of data for hemY 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 hemY Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10434	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0429	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3802
EcoGene	EcoGene:EG10434	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000427	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012417	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
Shigella flexneri	HEMY	From SHIGELLACYC
E. coli O157	HEMY	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:48452
Pfam (EcoliWiki Page)	PF07219 HemY protein N-terminus
Pfam (EcoliWiki Page)	PF07719 Tetratricopeptide repeat
EcoCyc	EcoCyc:EG10434	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10434	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000427	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0429	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012417	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 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 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 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).
↑ Panek, H & O'Brian, MR (2002) A whole genome view of prokaryotic haem biosynthesis. Microbiology (Reading, Engl.) 148 2273-82 PubMed
↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed

hemY: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 hemY Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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