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Gene |

Product(s) |

Expression|

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Standard Name	bfr
Gene Synonym(s)	ECK3323, b3336, JW3298^[1], JW3298
Product Desc.	bacterioferritin^[2]^[3]; Component of bacterioferritin^[3] Bacterioferritin; negatively regulated by ryhB RNA as part of indirect positive regulation by Fur; 24-mer^[4]
Product Synonyms(s)	bacterioferritin, iron storage and detoxification protein^[1], B3336^[2]^[1], Bfr^[2]^[1], bacterioferritin^[2]^[1], cytochrome b1^[2]^[1], cytochrome b557^[2]^[1] , ECK3323, JW3298, b3336
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): bfr^[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	bfr
Mnemonic	Bacterioferritin
Synonyms	ECK3323, b3336, JW3298^[1], JW3298
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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	74.67 minutes, 74.67 minutes	MG1655: 3464747..3464271 <gbrowseImage> name=NC_000913:3464271..3464747 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3394630..3394154 <gbrowseImage> name=NC_012967:3394154..3394630 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3351428..3351904 <gbrowseImage> name=NC_012759:3351428..3351904 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4173691..4174167 <gbrowseImage> name=NC_007779:4173691..4174167 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3562492..3562016 <gbrowseImage> name=NC_010473:3562016..3562492 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	3464271	Edman degradation	PMID:2644932
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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: Description	Reference	Availability	Comments
bfrN78G		N78G	(in strain: ECOR 30)			Strain variation; seeded from UniProt:P0ABD3
bfrR57K		R57K	(in strain: ECOR 30)			Strain variation; seeded from UniProt:P0ABD3
bfrL68I		L68I	(in strain: ECOR 30)			Strain variation; seeded from UniProt:P0ABD3
bfrAQIREEG152SQIKVKD		AQIREEG152SQIKVKD	(in strain: ECOR 30)			Strain variation; seeded from UniProt:P0ABD3
bfrR88Q		R88Q	(in strain: ECOR 30)			Strain variation; seeded from UniProt:P0ABD3
bfrA92R		A92R	(in strain: ECOR 30)			Strain variation; seeded from UniProt:P0ABD3
bfrD96E		D96E	(in strain: ECOR 30)			Strain variation; seeded from UniProt:P0ABD3
bfrG106A		G106A	(in strain: ECOR 30)			Strain variation; seeded from UniProt:P0ABD3
bfrR125A		R125A	(in strain: ECOR 30)			Strain variation; seeded from UniProt:P0ABD3
bfrN100D		N100D	(in strain: ECOR 30)			Strain variation; seeded from UniProt:P0ABD3
bfrTKV5VKI		TKV5VKI	(in strain: ECOR 30)			Strain variation; seeded from UniProt:P0ABD3
bfrK38M		K38M	(in strain: ECOR 30)			Strain variation; seeded from UniProt:P0ABD3
Δbfr (Keio:JW3298)	deletion	deletion		PMID:16738554	Shigen CGSC10467^[5]
bfrQKM142GKI		QKM142GKI	(in strain: ECOR 30)			Strain variation; seeded from UniProt:P0ABD3
bfr::Tn5KAN-I-SceI (FB21118)	Insertion at nt 178 in Minus orientation			PMID:15262929	E. coli Genome Project:FB21118	contains pKD46
bfr::Tn5KAN-I-SceI (FB21119)	Insertion at nt 178 in Minus orientation			PMID:15262929	E. coli Genome Project:FB21119	does not contain pKD46
Δbfr-746::kan				PMID:16738554	CGSC:100182
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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
JW3298	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAAGGTGATACTAAAGTTAT Primer 2:CCACCTTCTTCGCGGATCTGTGC
9H3	Kohara Phage	Genobase	PMID:3038334
smg-3082::Tn10	Linked marker	CAG12071 = CGSC7444^[5]	est. P1 cotransduction: 23% ^[6] Synonyms:zhb-3082::Tn10, zhd-3082::Tn10
zhf-3084::Tn10	Linked marker	CAG18456 = CGSC7576^[5]	est. P1 cotransduction: 20% ^[6] Synonyms:zhe-3084::Tn10nnnCAG18456 also carries cysG0 (CGSC).
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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:EG10113	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10113	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000109	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947839	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0111	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010903	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	Bfr
Synonyms	bacterioferritin, iron storage and detoxification protein^[1], B3336^[2]^[1], Bfr^[2]^[1], bacterioferritin^[2]^[1], cytochrome b1^[2]^[1], cytochrome b557^[2]^[1] , ECK3323, JW3298, b3336
Product description	bacterioferritin^[2]^[3]; Component of bacterioferritin^[3] Bacterioferritin; negatively regulated by ryhB RNA as part of indirect positive regulation by Fur; 24-mer^[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: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:0005829	cytosol	PMID:16858726	IDA: Inferred from Direct Assay		C	Seeded from EcoCyc (v14.0)	complete
	GO:0006826	iron ion transport	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002024	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006879	cellular iron ion homeostasis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002024	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006879	cellular iron ion homeostasis	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR008331	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006879	cellular iron ion homeostasis	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0409	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008199	ferric iron binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002024	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008199	ferric iron binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR008331	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	PMID:16858726	IDA: Inferred from Direct Assay		C	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR009078	F	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:0046914	transition metal ion binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR009078	F	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR009078	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	PMID:8477705	NAS: Non-traceable Author Statement		F		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
Protein	Subunits of bacterioferritin	could be indirect
Protein	mlc		PMID:16606699	Experiment(s):EBI-1145589
Protein	murB		PMID:16606699	Experiment(s):EBI-1145589
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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^[3]
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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 MKGDTKVINY LNKLLGNELV AINQYFLHAR MFKNWGLKRL NDVEYHESID EMKHADRYIE RILFLEGLPN LQDLGKLNIG EDVEEMLRSD LALELDGAKN LREAIGYADS VHDYVSRDMM IEILRDEEGH IDWLETELDL IQKMGLQNYL QAQIREEG
Length	158
Mol. Wt	18.495 kDa
pI	4.6 (calculated)
Extinction coefficient	21,430 (calc based on 7 Y, 2 W, and 0 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
Domain	8..144	PF00210 Ferritin-like 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=bfr 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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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:16131215	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947839	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010903	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0ABD3	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10113	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10113	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947839	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000109	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0111	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	2.89E+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	192	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	4062	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	107	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)
bfr
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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_000913:3464727..3464767 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:b3336 (EcoliWiki Page)	NCBI GEO profiles for bfr
microarray	GenExpDB:b3336 (EcoliWiki Page)	Summary of data for bfr 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 bfr Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10113	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0111	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3336
EcoGene	EcoGene:EG10113	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000109	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010903	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
Xenopus tropicalis	ENSXETP00000024194 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Shigella flexneri	BFR	From SHIGELLACYC
E. coli O157	Z4695	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)	PF00210 Ferritin-like domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:47240
EcoCyc	EcoCyc:EG10113	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10113	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000109	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0111	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010903	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 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 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).

bfr: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 bfr Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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