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Gene |

Product(s) |

Expression|

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Standard Name	fre
Gene Synonym(s)	ECK3836, b3844, JW3820, fsrC, flrd, luxG, G2019, lux^[1]^[2], fadI, flrD
Product Desc.	NAD(P)H-flavin oxidoreductase; ferrisiderophore reductase C^[3]
Product Synonyms(s)	flavin reductase^[1], B3844^[2]^[1], Lux^[2]^[1], FsrC^[2]^[1], FlRd^[2]^[1], FadI^[2]^[1], Fre^[2]^[1] , ECK3836, fadI, flrD, fsrC, JW3820, b3844
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): fre^[2]
Regulation/Activity
Quick Links
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</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

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The fre gene was mistakenly thought to be ubiB.^[3]

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	fre
Mnemonic	Flavin reductase
Synonyms	ECK3836, b3844, JW3820, fsrC, flrd, luxG, G2019, lux^[1]^[2], fadI, flrD
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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	86.74 minutes	MG1655: 4024550..4025251 <gbrowseImage> name=NC_000913:4024550..4025251 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4004998..4005699 <gbrowseImage> name=NC_012967:4004998..4005699 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3914219..3914920 <gbrowseImage> name=NC_012759:3914219..3914920 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3610154..3609453 <gbrowseImage> name=NC_007779:3609453..3610154 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4123470..4124171 <gbrowseImage> name=NC_010473:4123470..4124171 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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</protect>

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	4024553	Edman degradation	PMID:2050627
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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
fre(del) (Keio:JW3820)	deletion	deletion			PMID:16738554	Shigen CGSC10763^[4]
fre-352						CGSC:5420
fre-784(del)::kan					PMID:16738554	CGSC:101000
fre784(del)::FRTKanFRT			Mutagenesis rate	Decreased stress-induced mutagenesis (SIM) phenotype.	PMID:23224554	Parental Strain: SMR4562 Experimental Strain: SMR12007	Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.
SMR4562 yiaG-yfp FRTcatFRT fre784(del)::FRTKanFRT	Deletion & Insertion		Sigma ^S activity	Decrease in Sigma ^S activity	PMID:23224554	Parental Strain: SMR10582 Experimental Strain: SMR14267	See table S8 for full experimental results.
CAG45114 fre784(del)::FRTKanFRT	deletion		Sigma^E activity	Decrease in sigma^E activity	PMID:23224554	Parental Strain: CAG45114 Experimental Strain: SMR15362	See table S11 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
JW3820	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACAACCTTAAGCTGTAAAGT Primer 2:CCGATAAATGCAAACGCATCGCC
16G1	Kohara Phage	Genobase	PMID:3038334
metEo-3079::Tn10	Linked marker	CAG18491 = CGSC7464^[4]	est. P1 cotransduction: 57% ^[5] Synonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.
fad-751::Tn10	Linked marker	CAG18496 = CGSC7465^[4]	est. P1 cotransduction: 92% ^[5] Synonyms:fadAB101::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:EG10334	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10334	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000328	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948325	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0330	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012559	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	Fre
Synonyms	flavin reductase^[1], B3844^[2]^[1], Lux^[2]^[1], FsrC^[2]^[1], FlRd^[2]^[1], FadI^[2]^[1], Fre^[2]^[1] , ECK3836, fadI, flrD, fsrC, JW3820, b3844
Product description	NAD(P)H-flavin oxidoreductase; ferrisiderophore reductase C^[3]
EC number (for enzymes)	1.5.1.29^[1]
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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:0005737	cytoplasm				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	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:0006810	transport	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0813	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006811	ion transport	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0406	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006826	iron ion transport	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0410	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008752	FMN reductase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.5.1.29	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001433	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR008333	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017927	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0560	F	Seeded from EcoCyc (v14.0)	complete
	GO:0047138	aquacobalamin reductase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:1.16.1.3	F	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001221	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001433	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR008333	P	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017927	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
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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	nadE	PMID:16606699	Experiment(s):EBI-1146778
Protein	intS	PMID:16606699	Experiment(s):EBI-1146778
Protein	rplF	PMID:16606699	Experiment(s):EBI-1146778
Protein	rho	PMID:16606699	Experiment(s):EBI-1146778
Protein	puuB	PMID:16606699	Experiment(s):EBI-1146778
Protein	atpD	PMID:16606699	Experiment(s):EBI-1146778
Protein	ahpC	PMID:16606699	Experiment(s):EBI-1146778
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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
cytoplasm			From EcoCyc^[6]
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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 MTTLSCKVTS VEAITDTVYR VRIVPDAAFS FRAGQYLMVV MDERDKRPFS MASTPDEKGF IELHIGASEI NLYAKAVMDR ILKDHQIVVD IPHGEAWLRD DEERPMILIA GGTGFSYARS ILLTALARNP NRDITIYWGG REEQHLYDLC ELEALSLKHP GLQVVPVVEQ PEAGWRGRTG TVLTAVLQDH GTLAEHDIYI AGRFEMAKIA RDLFCSERNA REDRLFGDAF AFI
Length	233
Mol. Wt	26.242 kDa
pI	5.3 (calculated)
Extinction coefficient	26,930 - 27,305 (calc based on 7 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	Notes	References
Initiator Methionine	1	Removed	UniProt:P0AEN1
Domain	5..97	PF00970 Oxidoreductase FAD-binding domain		PMID:19920124
Domain	108..212	PF00175 Oxidoreductase NAD-binding domain		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=fre taxon=12017 </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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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:16131690	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948325	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012559	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AEN1	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10334	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10334	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948325	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000328	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0330	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 MC4100	2.78E+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	E. coli K-12 MG1655	2512	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	759	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	993	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)
fre
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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_000913:4024530..4024570 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:b3844 (EcoliWiki Page)	NCBI GEO profiles for fre
microarray	GenExpDB:b3844 (EcoliWiki Page)	Summary of data for fre 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 fre Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10334	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0330	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3844
EcoGene	EcoGene:EG10334	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000328	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012559	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
Arabidopsis thaliana	AT1G15140 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0218707 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	UBIB	From SHIGELLACYC
E. coli O157	UBIB	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)	PF00175 Oxidoreductase NAD-binding domain
Pfam (EcoliWiki Page)	PF00970 Oxidoreductase FAD-binding domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:52343
Panther (EcoliWiki Page)	PTHR19370:SF39
Superfamily (EcoliWiki Page)	SUPERFAMILY:63380
EcoCyc	EcoCyc:EG10334	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10334	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000328	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0330	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012559	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.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 ^1.11 ^1.12 ^1.13 ^1.14 ^1.15 ^1.16 ^1.17 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 ^2.11 ^2.12 ^2.13 ^2.14 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^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).
↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7

fre: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 fre Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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