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Product(s) |

Expression|

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Standard Name	ccmE
Gene Synonym(s)	ECK2189, b2197, JW2185, yejS^[1], yejS
Product Desc.	CcmE^[2]^[3]; Component of [[:Category:Complex:CcmABCDEFGH cytochrome c biogenesis system\|CcmABCDEFGH cytochrome c biogenesis system]]^[3] Heme chaperone, membrane-anchored, periplasmic^[4]
Product Synonyms(s)	periplasmic heme chaperone^[1], B2197^[2]^[1], YejS^[2]^[1], CcmE^[2]^[1] , ECK2189, JW2185, yejS, b2197
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ccmABCDEFGH^[2], napFDAGHBC-ccmABCDEFGH^[2], aeg-46.5
Regulation/Activity
Quick Links
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Notes

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CcmE makes a transient covalent linkage to heme at His-130 and then transfers heme to apocytochrome C in the presence of CcmFGH. Overexpression causes abnormal biofilm architecture.^[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	ccmE
Mnemonic	Cytochrome c maturation
Synonyms	ECK2189, b2197, JW2185, yejS^[1], yejS
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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	49.42 minutes	MG1655: 2293402..2292923 <gbrowseImage> name=NC_000913:2292923..2293402 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2245369..2244890 <gbrowseImage> name=NC_012967:2244890..2245369 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2178728..2179207 <gbrowseImage> name=NC_012759:2178728..2179207 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2298714..2298235 <gbrowseImage> name=NC_007779:2298235..2298714 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2384390..2383911 <gbrowseImage> name=NC_010473:2383911..2384390 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
Coding Start (SO:0000323)	MG1655	2292923	Edman degradation	PMID:9770295
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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)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
ccmEH130A		H130A		Abolishes heme binding			seeded from UniProt:P69490
ccmEH130C		H130C		Can still form a covalent bond with heme, but blocks heme release transfer to cytochrome c			seeded from UniProt:P69490
ccmE(del) (Keio:JW2185)	deletion	deletion			PMID:16738554	Shigen CGSC9767^[5]
ccmE750(del)::kan					PMID:16738554	CGSC:100260
ccmABCDEFG(del)	deletion		Protien Accumulation	loss of heme-containing proteins	PMID:7635817		See figure 3 for experimental results.
ccmABCDEFG(del)	deletion		cytochrome accumulation	loss of cytochrome _c550	PMID:7635817		See Figure 4 for experimental results.
ccmABCDEFG(del)	deletion		cytochrome biogenesis	Deficient cytochrome biogenesis	PMID:7635817		See Figure 5 for experimental results.
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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
JW2185	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAATATTCGCCGTAAAAACCG Primer 2:CCTGATGCTGGGTCCTTATAAAC
20F6	Kohara Phage	Genobase	PMID:3038334
19D1	Kohara Phage	Genobase	PMID:3038334
zbd-3104::Tn10	Linked marker	CAG12021 = CGSC7344^[5]	est. P1 cotransduction: % ^[6] Synonyms:zbc-3105::Tn10, zbd-3105::Tn10
napA722::Tn10	Linked marker	CAG12098 = CGSC7400^[5]	est. P1 cotransduction: 75% ^[6] Synonyms:zeg-722, zei-722::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:EG12055	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12055	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001968	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946697	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1986	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007271	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	CcmE
Synonyms	periplasmic heme chaperone^[1], B2197^[2]^[1], YejS^[2]^[1], CcmE^[2]^[1] , ECK2189, JW2185, yejS, b2197
Product description	CcmE^[2]^[3]; Component of [[:Category:Complex:CcmABCDEFGH cytochrome c biogenesis system\|CcmABCDEFGH cytochrome c biogenesis system]]^[3] Heme chaperone, membrane-anchored, periplasmic^[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:0005506	iron ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0408	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005515	protein binding	PMID:11744735	IPI: Inferred from Physical Interaction	UniProtKB:P0ABM1	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005515	protein binding	PMID:11744735	IPI: Inferred from Physical Interaction	UniProtKB:P33927	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01959	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005886	plasma membrane	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004329	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-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: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:0017003	protein-heme linkage	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01959	P	Seeded from EcoCyc (v14.0)	complete
	GO:0017003	protein-heme linkage	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004329	P	Seeded from EcoCyc (v14.0)	complete
	GO:0017004	cytochrome complex assembly	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004329	P	Seeded from EcoCyc (v14.0)	complete
	GO:0017004	cytochrome complex assembly	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0201	P	Seeded from EcoCyc (v14.0)	complete
	GO:0046872	metal ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0479	F	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	Notes	References	Evidence
Protein	Subunits of [[:Category:Complex:CcmABCDEFGH cytochrome c biogenesis system\|CcmABCDEFGH cytochrome c biogenesis system]]	could be indirect
Protein	rplB		PMID:16606699	Experiment(s):EBI-1142153
Protein	ycgE		PMID:16606699	Experiment(s):EBI-1142153
Protein	ompL		PMID:16606699	Experiment(s):EBI-1142153
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Notes

Localization

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

Compartment	Evidence	Reference/Source
periplasm		From EcoCyc^[3]
Inner Membrane	PMID:9770295	EchoLocation:ccmE
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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 MNIRRKNRLW IACAVLAGLA LTIGLVLYAL RSNIDLFYTP GEILYGKRET QQMPEVGQRL RVGGMVMPGS VQRDPNSLKV TFTIYDAEGS VDVSYEGILP DLFREGQGVV VQGELEKGNH ILAKEVLAKH DENYTPPEVE KAMEANHRRP ASVYKDPAS
Length	159
Mol. Wt	17.697 kDa
pI	6.9 (calculated)
Extinction coefficient	15,930 - 16,055 (calc based on 7 Y, 1 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	Notes	References
Domain	2..138	PF03100 CcmE		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=ccmE taxon=562,83333 </beststructure>

Models

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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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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:16130134	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946697	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007271	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P69490	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12055	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12055	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946697	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001968	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1986	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	E. coli K-12 MG1655	159	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	58	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	63^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	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)
ccmABCDEFGH
napFDAGHBC-ccmABCDEFGH
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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_000913:2293382..2293422 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:b2197 (EcoliWiki Page)	NCBI GEO profiles for ccmE
microarray	GenExpDB:b2197 (EcoliWiki Page)	Summary of data for ccmE 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 ccmE Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12055	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1986	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2197
EcoGene	EcoGene:EG12055	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001968	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007271	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	ENSANGP00000024206 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT3G51790 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	CCME	From SHIGELLACYC
E. coli O157	CCME	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)	PF03100 CcmE
Superfamily (EcoliWiki Page)	SUPERFAMILY:82093
EcoCyc	EcoCyc:EG12055	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12055	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001968	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1986	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007271	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 ^1.8 ^1.9 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 ^3.4 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).

ccmE: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 ccmE Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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