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Standard Name	yifE
Gene Synonym(s)	ECK3757, b3764, JW3737^[1], JW3737
Product Desc.	conserved protein^[2]^[3] Function unknown, expressed protein^[4]
Product Synonyms(s)	conserved protein^[1], B3764^[2]^[1], YifE^[2]^[1] , ECK3757, JW3737, b3764
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yifE^[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	yifE
Mnemonic	Systematic nomenclature
Synonyms	ECK3757, b3764, JW3737^[1], JW3737
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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	85.05 minutes, 85.05 minutes	MG1655: 3946109..3946447 <gbrowseImage> name=NC_000913:3946109..3946447 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3909886..3910224 <gbrowseImage> name=NC_012967:3909886..3910224 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3835778..3836116 <gbrowseImage> name=NC_012759:3835778..3836116 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3688595..3688257 <gbrowseImage> name=NC_007779:3688257..3688595 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4045029..4045367 <gbrowseImage> name=NC_010473:4045029..4045367 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	3946112	Edman degradation	PMID:9298646
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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
yifE(del) (Keio:JW3737)	deletion	deletion			PMID:16738554	Shigen CGSC10727^[5]
yifE786(del)::kan					PMID:16738554	CGSC:105370
yifE782(del)::FRT	deletion		Mutagenesis Rate	Decrease in Stress Induced mutagenesis (SIM).	PMID:23224554	Parent Strain: SMR4562 Experimental Strain: SMR12238	The mutation caused a strong decrease in SIM with mutant frequency being reduced by over 90 percent. See table S3 for complete results.
yifE782(del)::FRT	deletion		Sensitivity to	UV Sensitivity	PMID:23224554	Parent Strain: SMR4562 Experimental Strain: SMR12238	The mutation conferred an increase in UV sensitivity. See tables S7 and S1 for summarized experimental data.
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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
JW3737	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCGGAAAGCTTTACGACGAC Primer 2:CCATCGTCAGAATCGGTGTAGTC
2E6	Kohara Phage	Genobase	PMID:3038334
15D10	Kohara Phage	Genobase	PMID:3038334
rbsD296::Tn10	Linked marker	CAG18501 = CGSC7460^[5]	est. P1 cotransduction: 56% ^[6] Synonyms:zie-296::Tn10
ilvD500::Tn10	Linked marker	CAG18431 = CGSC7462^[5]	est. P1 cotransduction: 79% ^[6] Synonyms:ilv500::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:EG11450	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11450	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001413	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948274	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1419	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012298	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	YifE
Synonyms	conserved protein^[1], B3764^[2]^[1], YifE^[2]^[1] , ECK3757, JW3737, b3764
Product description	conserved protein^[2]^[3] Function unknown, expressed protein^[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
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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	dnaN	PMID:19402753	LCMS(ID Probability):99.6
Protein	ypeA	PMID:19402753	LCMS(ID Probability):99.6
Protein	rpoB	PMID:19402753	LCMS(ID Probability):99.6
Protein	rpoA	PMID:19402753	LCMS(ID Probability):99.6
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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
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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 MAESFTTTNR YFDNKHYPRG FSRHGDFTIK EAQLLERHGY AFNELDLGKR EPVTEEEKLF VAVCRGEREP VTEAERVWSK YMTRIKRPKR FHTLSGGKPQ VEGAEDYTDS DD
Length	112
Mol. Wt	13.133 kDa
pI	6.5 (calculated)
Extinction coefficient	12,950 - 13,075 (calc based on 5 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
Initiator Methionine	1	Removed	UniProt:P0ADN2
Domain	10..102	PF04219 Protein of unknown function, DUF		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=yifE 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:16131624	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948274	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012298	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0ADN2	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11450	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11450	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948274	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001413	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1419	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 MC4100	1.28E+04	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI		PMID:18304323
Protein	E. coli K-12 EMG2	340	molecules/cell	Medium: MOPS glucose minimal Temperature (°C): 37 Doubling time (min): Growth phase: Exponential OD: OD600 = 0.2 to 0.25 other: aerated	Quantitative protein sequencing	Spot ID: Ml47-l	PMID: 9298646
Protein	E. coli K-12 MG1655	43279	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	7863	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	21614	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)
yifE
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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_000913:3946089..3946129 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:b3764 (EcoliWiki Page)	NCBI GEO profiles for yifE
microarray	GenExpDB:b3764 (EcoliWiki Page)	Summary of data for yifE 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 (3945513..3945788) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ08; Well:H5^[7]
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Notes

Accessions Related to yifE Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11450	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1419	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3764
EcoGene	EcoGene:EG11450	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001413	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012298	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	YIFE	From SHIGELLACYC
E. coli O157	YIFE	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)	PF04219 Protein of unknown function, DUF
EcoCyc	EcoCyc:EG11450	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11450	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001413	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1419	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012298	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 ^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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

yifE:On One Page

Quickview

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 yifE Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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