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Standard Name	efeO
Gene Synonym(s)	ECK1008, b1018, JW1003, ycdO^[1], JW1003, ycdO
Product Desc.	conserved protein^[2]^[3]
Product Synonyms(s)	conserved protein^[1], B1018^[2]^[1], YcdO^[2]^[1] , ECK1008, JW1003, ycdO, b1018
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	efeO
Mnemonic	Systematic nomenclature
Synonyms	ECK1008, b1018, JW1003, ycdO^[1], JW1003, ycdO
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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	23.31 minutes	MG1655: 1081466..1082593 <gbrowseImage> name=NC_000913:1081466..1082593 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 984434..985561 <gbrowseImage> name=NC_012759:984434..985561 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1082665..1083792 <gbrowseImage> name=NC_007779:1082665..1083792 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1135394..1136521 <gbrowseImage> name=NC_010473:1135394..1136521 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
ΔycdO (Keio:JW1003)	deletion	deletion			PMID:16738554	Shigen CGSC8984^[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
JW1003	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACCATTAACTTCCGCCGTAA Primer 2:CCATCCAGTCCCAGCACACCGCG
zcc-282::Tn10	Linked marker	CAG18466 = CGSC7359^[4]	est. P1 cotransduction: 50% ^[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:G6527	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13861	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003125	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945603	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3621	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003448	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	YcdO
Synonyms	conserved protein^[1], B1018^[2]^[1], YcdO^[2]^[1] , ECK1008, JW1003, ycdO, b1018
Product description	conserved protein^[2]^[3]
EC number (for enzymes)
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See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki. <protect></protect>

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: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
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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	yciN	PMID:16606699	Experiment(s):EBI-1138650
Protein	htpG	PMID:16606699	Experiment(s):EBI-1138650
Protein	uspG	PMID:16606699	Experiment(s):EBI-1138650
Protein	nadE	PMID:16606699	Experiment(s):EBI-1138650
Protein	dnaK	PMID:16606699	Experiment(s):EBI-1138650
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See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki. </protect>

Notes

Localization

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

Compartment	Evidence	Reference/Source
periplasm
Periplasm	PMID:12107143	EchoLocation:ycdO
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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 MTINFRRNAL QLSVAALFSS AFMANAADVP QVKVTVTDKQ CEPMTITVNA GKTQFIIQNH SQKALEWEIL KGVMVVEERE NIAPGFSQKM TANLQPGEYD MTCGLLTNPK GKLIVKGEAT ADAAQSDALL SLGGAITAYK AYVMAETTQL VTDTKAFTDA IKAGDIEKAK ALYAPTRQHY ERIEPIAELF SDLDGSIDAR EDDYEQKAAD PKFTGFHRLE KALFGDNTTK GMDQYAEQLY TDVVDLQKRI SELAFPPSKV VGGAAGLIEE VAASKISGEE DRYSHTDLWD FQANVEGSQK IVDLLRPQLQ KANPELLAKV DANFKKVDTI LAKYRTKDGF ETYDKLTDAD RNALKGPITA LAEDLAQLRG VLGLD
Length	375
Mol. Wt	41.138 kDa
pI	4.8 (calculated)
Extinction coefficient	27,390 - 27,640 (calc based on 11 Y, 2 W, and 2 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	1-26	UniProt Manual:Signal Peptides	UniProt:P0AB24
Domain	135..368	PF09375 Imelysin		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=efeO 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:16128982	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945603	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003448	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AB24	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6527	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13861	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945603	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003125	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3621	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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See Help:Links_table for how to enter or edit information in this section of EcoliWiki.

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	895	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	566	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	456	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

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 MC4100	3.28E+02	molecules/cell	Medium: combined data from rich and minimal media	37
Protein	E. coli K-12 MC4100	3.28E+02	molecules/cell	Medium: combined data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI		PMID:18304323
Protein	Ecoli K-12	5.872+/-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	0.043478261	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	895	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	566	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	456	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_000913:1081446..1081486 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:b1018 (EcoliWiki Page)	NCBI GEO profiles for ycdO
microarray	GenExpDB:b1018 (EcoliWiki Page)	Summary of data for ycdO 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 (1081316..1081491) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ14; Well:D12^[6]
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Notes

Accessions Related to efeO Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6527	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3621	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1018
EcoGene	EcoGene:EG13861	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003125	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003448	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	YCDO	From SHIGELLACYC
E. coli O157	YCDO	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)	PF09375 Imelysin
EcoCyc	EcoCyc:G6527	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13861	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003125	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3621	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003448	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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

efeO: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

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 efeO Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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