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Gene |

Product(s) |

Expression|

Evolution |

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Standard Name	yfeR
Gene Synonym(s)	ECK2403, b2409, JW2400^[1], JW2400, osmT
Product Desc.	predicted DNA-binding transcriptional regulator, LYSR-type^[2]^[3] Required for swarming phenotype, function unknown; predicted transcriptional regulator^[4]
Product Synonyms(s)	predicted DNA-binding transcriptional regulator^[1], B2409^[2]^[1], YfeR^[2]^[1] , ECK2403, JW2400, osmT, b2409
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yfeR^[2]
Regulation/Activity
Quick Links
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Notes

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LysR family. The Salmonella ortholog has been named osmT in Genbank CAC44465.^[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	yfeR
Mnemonic	Systematic nomenclature
Synonyms	ECK2403, b2409, JW2400^[1], JW2400, osmT
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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	54.4 minutes	MG1655: 2524878..2523952 <gbrowseImage> name=NC_000913:2523952..2524878 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2455582..2454656 <gbrowseImage> name=NC_012967:2454656..2455582 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2409757..2410683 <gbrowseImage> name=NC_012759:2409757..2410683 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2532302..2531376 <gbrowseImage> name=NC_007779:2531376..2532302 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2616643..2615717 <gbrowseImage> name=NC_010473:2615717..2616643 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
ΔyfeR (Keio:JW2400)	deletion	deletion			PMID:16738554	Shigen
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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
JW2400	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAATTATTCTTTAAAACAATT Primer 2:CCTATCTGATACAACGGATCCCC
3E7	Kohara Phage	Genobase	PMID:3038334
nupC510::Tn10	Linked marker	CAG18468 = CGSC7410^[5]	est. P1 cotransduction: 61% ^[6]
purC80::Tn10	Linked marker	CAG18470 = CGSC7413^[5]	est. P1 cotransduction: 2% ^[6]
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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:G7257	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14159	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003831	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946873	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3911	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007932	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	YfeR
Synonyms	predicted DNA-binding transcriptional regulator^[1], B2409^[2]^[1], YfeR^[2]^[1] , ECK2403, JW2400, osmT, b2409
Product description	predicted DNA-binding transcriptional regulator, LYSR-type^[2]^[3] Required for swarming phenotype, function unknown; predicted transcriptional regulator^[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:0003677	DNA binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0238	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003700	transcription factor activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000847	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006350	transcription	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0804	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006350	transcription	PMID:15556475	ISS: Inferred from Sequence or Structural Similarity	Swiss-Prot:P03030	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006355	regulation of transcription, DNA-dependent	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000847	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016563	transcription activator activity	PMID:15556475	ISS: Inferred from Sequence or Structural Similarity	Swiss-Prot:P03030	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016564	transcription repressor activity	PMID:15556475	ISS: Inferred from Sequence or Structural Similarity	Swiss-Prot:P03030	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
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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 MNYSLKQLKV FVTVAQEKSF SRAGERIGLS QSAVSHSVKE LENHTGVRLL DRTTREVVLT DAGQQLALRL ERLLDELNST LRDTGRMGQQ LSGKVRVAAS QTISAHLIPQ CIAESHRRYP DIQFVLHDRP QQWVMESIRQ GDVDFGIVID PGPVGDLQCE AILSEPFFLL CHRDSALAVE DYVPWQALQG AKLVLQDYAS GSRPLIDAAL ARNGIQANIV QEIGHPATLF PMVAAGIGIS ILPALALPLP EGSPLVVKRI TPVVERQLML VRRKNRSLST AAEALWDVVR DQGNALMAGR EGDPLYQI
Length	308
Mol. Wt	33.902 kDa
pI	6.8 (calculated)
Extinction coefficient	23,950 - 24,325 (calc based on 5 Y, 3 W, and 3 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	88..294	PF03466 LysR substrate binding domain	PMID:19920124
Domain	5..64	PF00126 Bacterial regulatory helix-turn-helix protein, lysR family	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=yfeR 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:16130335	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946873	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007932	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0ACR7	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7257	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14159	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946873	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003831	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3911	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	1.76E+02	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	Ecoli K-12	2.465+/-0.03	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.004319654	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	95	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	28	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	74	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)
yfeR
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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_000913:2524858..2524898 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:b2409 (EcoliWiki Page)	NCBI GEO profiles for yfeR
microarray	GenExpDB:b2409 (EcoliWiki Page)	Summary of data for yfeR 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 yfeR Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7257	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3911	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2409
EcoGene	EcoGene:EG14159	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003831	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007932	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	ENSANGP00000000050 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000027355 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000018362 (score: 1.000; bootstrap: 98%)	From Inparanoid:20070104
Shigella flexneri	YFER	From SHIGELLACYC
E. coli O157	YFER_1	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)	PF03466 LysR substrate binding domain
Pfam (EcoliWiki Page)	PF00126 Bacterial regulatory helix-turn-helix protein, lysR family
Superfamily (EcoliWiki Page)	SUPERFAMILY:46785
Superfamily (EcoliWiki Page)	SUPERFAMILY:53850
EcoCyc	EcoCyc:G7257	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14159	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003831	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3911	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007932	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 ^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 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).

yfeR: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 yfeR Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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