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Expression|

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Standard Name	efeB
Gene Synonym(s)	ECK1009, b1019, JW1004, ycdB^[1], JW1004, ycdB
Product Desc.	conserved protein^[2]; heme-containing peroxidase^[3]
Product Synonyms(s)	conserved protein^[1], B1019^[2]^[1], YcdB^[2]^[1] , ECK1009, JW1004, ycdB, b1019
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression
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	efeB
Mnemonic	Systematic nomenclature
Synonyms	ECK1009, b1019, JW1004, ycdB^[1], JW1004, ycdB
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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	23.33 minutes	MG1655: 1082599..1083870 <gbrowseImage> name=NC_000913:1082599..1083870 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1099661..1100932 <gbrowseImage> name=NC_012967:1099661..1100932 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 985567..986838 <gbrowseImage> name=NC_012759:985567..986838 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1083798..1085069 <gbrowseImage> name=NC_007779:1083798..1085069 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1136527..1137798 <gbrowseImage> name=NC_010473:1136527..1137798 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)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
ΔycdB (Keio:JW1004)	deletion	deletion			PMID:16738554	Shigen CGSC8985^[4]
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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
JW1004	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCAGTATAAAGATGAAAACGG Primer 2:CCAACCCGCAATAACGCGCTTCC
zcc-282::Tn10	Linked marker	CAG18466 = CGSC7359^[4]	est. P1 cotransduction: 48% ^[5]
zce-726::Tn10	Linked marker	CAG12078 = CGSC7361^[4]	est. P1 cotransduction: 1% ^[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:EG11735	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11735	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001674	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946500	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1686	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003451	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	YcdB
Synonyms	conserved protein^[1], B1019^[2]^[1], YcdB^[2]^[1] , ECK1009, JW1004, ycdB, b1019
Product description	conserved protein^[2]; heme-containing peroxidase^[3]
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. 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:0004601	peroxidase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0575	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005506	iron ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006313	F	Seeded from EcoCyc (v14.0)	complete
	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:0016684	oxidoreductase activity, acting on peroxide as acceptor	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006313	F	Seeded from EcoCyc (v14.0)	complete
	GO:0042597	periplasmic space	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0574	C	Seeded from EcoCyc (v14.0)	complete
	GO:0042597	periplasmic space	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0200	C	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
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006313	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:0006974	response to DNA damage stimulus	PMID:11967071	IEP: Inferred from Expression Pattern		P		complete
	GO:0020037	heme binding	PMID:16551627	IDA: Inferred from Direct Assay		F	Figure 3b. Mass spectrometry indicates heme is bound noncovalently.	complete
	GO:0004601	peroxidase activity	PMID:16551627	IDA: Inferred from Direct Assay		F	Figure 5. Peroxidase activity highest at pH 4.0.	complete
	GO:0042597	periplasmic space	PMID:16551627	IDA: Inferred from Direct Assay		C	Fig. 1	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	groL	PMID:16606699	Experiment(s):EBI-1138657
Protein	dnaK	PMID:16606699	Experiment(s):EBI-1138657
Protein	fdhF	PMID:16606699	Experiment(s):EBI-1138657
Protein	uspG	PMID:16606699	Experiment(s):EBI-1138657
Protein	rplB	PMID:16606699	Experiment(s):EBI-1138657
Protein	uxaA	PMID:16606699	Experiment(s):EBI-1138657
Protein	phoB	PMID:16606699	Experiment(s):EBI-1138657
Protein	dinG	PMID:16606699	Experiment(s):EBI-1138657
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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
periplasm
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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 MQYKDENGVN EPSRRRLLKV IGALALAGSC PVAHAQKTQS APGTLSPDAR NEKQPFYGEH QAGILTPQQA AMMLVAFDVL ASDKADLERL FRLLTQRFAF LTQGGAAPET PNPRLPPLDS GILGGYIAPD NLTITLSVGH SLFDERFGLA PQMPKKLQKM TRFPNDSLDA ALCHGDVLLQ ICANTQDTVI HALRDIIKHT PDLLSVRWKR EGFISDHAAR SKGKETPINL LGFKDGTANP DSQNDKLMQK VVWVTADQQE PAWTIGGSYQ AVRLIQFRVE FWDRTPLKEQ QTIFGRDKQT GAPLGMQHEH DVPDYASDPE GKVIALDSHI RLANPRTAES ESSLMLRRGY SYSLGVTNSG QLDMGLLFVC YQHDLEKGFL TVQKRLNGEA LEEYVKPIGG GYFFALPGVK DANDYFGSAL LRV
Length	423
Mol. Wt	46.755 kDa
pI	6.9 (calculated)
Extinction coefficient	38,390 - 38,890 (calc based on 11 Y, 4 W, and 4 C residues)
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See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

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
motif	1-35	UniProt Manual:Signal Peptides	UniProt:P31545
Domain	61..411	PF04261 Dyp-type peroxidase family		PMID:19920124
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See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

<motif_map/>

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

Structures

<beststructure> gene=efeB taxon=562,83333 </beststructure>

Models

View models at:

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

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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:16128983	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946500	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003451	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P31545	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11735	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11735	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946500	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001674	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1686	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 MG1655	135	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	67	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	72	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)
ycdO
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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_000913:1082579..1082619 source=MG1655 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:b1019 (EcoliWiki Page)	NCBI GEO profiles for ycdB
microarray	GenExpDB:b1019 (EcoliWiki Page)	Summary of data for ycdB 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 efeB Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11735	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1686	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1019
EcoGene	EcoGene:EG11735	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001674	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003451	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	YCDB	From SHIGELLACYC
E. coli O157	YCDB	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)	PF04261 Dyp-type peroxidase family
Superfamily (EcoliWiki Page)	SUPERFAMILY:54909
EcoCyc	EcoCyc:EG11735	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11735	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001674	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1686	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003451	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 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 ^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).

efeB: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 efeB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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