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Product(s) |

Expression|

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Standard Name	yfbR
Gene Synonym(s)	ECK2285, b2291, JW2288^[1], JW2288
Product Desc.	deoxyribonucleoside 5'-monophosphate phosphatase^[2]^[3] Nucleotidase, 5'-monophosphates; only canonical deoxyribonucleoside used as substrates^[4]
Product Synonyms(s)	deoxyribonucleoside 5'-monophosphatase^[1], B2291^[2]^[1], YfbR^[2]^[1] , ECK2285, JW2288, b2291
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yfbR^[2]
Regulation/Activity
Quick Links
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Notes

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Divalent metal required for catalytic activity. YfbR inhibited by both ribo- and deoxyribonucleoside di- and triphosphates, along with sensitivity to ATP, dATP and ADP.^[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	yfbR
Mnemonic	Systematic nomenclature
Synonyms	ECK2285, b2291, JW2288^[1], JW2288
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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	51.88 minutes, 51.88 minutes	MG1655: 2406884..2407483 <gbrowseImage> name=NC_000913:2406884..2407483 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 2352453..2353052 <gbrowseImage> name=NC_012967:2352453..2353052 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 2292689..2293288 <gbrowseImage> name=NC_012759:2292689..2293288 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 2414308..2414907 <gbrowseImage> name=NC_007779:2414308..2414907 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2498649..2499248 <gbrowseImage> name=NC_010473:2498649..2499248 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)	Reference	Availability
ΔyfbR (Keio:JW2288)	deletion	deletion	PMID:16738554	Shigen CGSC9840^[5]
ΔyfbR773::kan			PMID:16738554	CGSC:104660
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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
JW2288	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAACAGAGCCATTTTTTTGC Primer 2:CCaAGCGGTGAATCCTGGCTAAT
9C2	Kohara Phage	Genobase	PMID:3038334
E9C9	Kohara Phage	Genobase	PMID:3038334
zfb-223::Tn10	Linked marker	CAG18484 = CGSC7406^[5]	est. P1 cotransduction: 54% ^[6] Synonyms:zej-223::Tn10
zfd-1::Tn10	Linked marker	CAG18467 = CGSC7408^[5]	est. P1 cotransduction: % ^[6] Synonyms:zfb-1::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:G7185	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14102	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003760	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946771	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3855	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007563	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	YfbR	YfbR
Synonyms	deoxyribonucleoside 5'-monophosphatase^[1], B2291^[2]^[1], YfbR^[2]^[1] , ECK2285, JW2288, b2291	deoxyribonucleoside 5'-monophosphatase^[1], B2291^[2]^[1], YfbR^[2]^[1]
Product description	deoxyribonucleoside 5'-monophosphate phosphatase^[2]^[3] Nucleotidase, 5'-monophosphates; only canonical deoxyribonucleoside used as substrates^[4]	deoxyribonucleoside 5'-monophosphate phosphatase^[2]^[3]
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:0000166	nucleotide binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0547	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005507	copper ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0186	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	Seeded from EcoCyc (v14.0)	complete
	GO:0008253	5'-nucleotidase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:3.1.3.5	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030145	manganese ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0464	F	Seeded from EcoCyc (v14.0)	complete
	GO:0050897	cobalt ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0170	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	References	Evidence
Protein	yphF	PMID:16606699	Experiment(s):EBI-1142459
Protein	fliG	PMID:16606699	Experiment(s):EBI-1142459
Protein	rpsP	PMID:19402753	LCMS(ID Probability):99.6
Protein	ymfD	PMID:19402753	LCMS(ID Probability):99.6
Protein	rpsN	PMID:19402753	LCMS(ID Probability):99.6
Protein	slyD	PMID:19402753	LCMS(ID Probability):99.6
Protein	rplS	PMID:19402753	LCMS(ID Probability):99.6
Protein	rpsT	PMID:19402753	LCMS(ID Probability):99.6
Protein	hupA	PMID:19402753	LCMS(ID Probability):99.6
Protein	rplM	PMID:19402753	LCMS(ID Probability):99.6
Protein	yeiT	PMID:19402753	LCMS(ID Probability):99.6
Protein	yfaY	PMID:19402753	LCMS(ID Probability):99.6
Protein	ydjL	PMID:19402753	LCMS(ID Probability):99.6
Protein	gatD	PMID:19402753	LCMS(ID Probability):99.6
Protein	ycbV	PMID:19402753	LCMS(ID Probability):99.4
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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 MKQSHFFAHL SRLKLINRWP LMRNVRTENV SEHSLQVAMV AHALAAIKNR KFGGNVNAER IALLAMYHDA SEVLTGDLPT PVKYFNSQIA QEYKAIEKIA QQKLVDMVPE ELRDIFAPLI DEHAYSDEEK SLVKQADALC AYLKCLEELA AGNNEFLLAK TRLEATLEAR RSQEMDYFME IFVPSFHLSL DEISQDSPL	at EcoCyc MKQSHFFAHL SRLKLINRWP LMRNVRTENV SEHSLQVAMV AHALAAIKNR KFGGNVNAER IALLAMYHDA SEVLTGDLPT PVKYFNSQIA QEYKAIEKIA QQKLVDMVPE ELRDIFAPLI DEHAYSDEEK SLVKQADALC AYLKCLEELA AGNNEFLLAK TRLEATLEAR RSQEMDYFME IFVPSFHLSL DEISQDSPL
Length	199	199
Mol. Wt	22.708 kDa	22.708 kDa
pI	5.5 (calculated)	5.5 (calculated)
Extinction coefficient	14,440 - 14,690 (calc based on 6 Y, 1 W, and 2 C residues)	14,440 - 14,690 (calc based on 6 Y, 1 W, and 2 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	30..179	PF01966 HD 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=yfbR 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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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:16130226	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946771	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007563	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P76491	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7185	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14102	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946771	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003760	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3855	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 MG1655	616	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	252	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	538	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)
yfbR
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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_000913:2406864..2406904 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:b2291 (EcoliWiki Page)	NCBI GEO profiles for yfbR
microarray	GenExpDB:b2291 (EcoliWiki Page)	Summary of data for yfbR 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 (2406709..2406956) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ05; Well:C5^[7]
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Notes

Accessions Related to yfbR Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7185	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3855	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2291
EcoGene	EcoGene:EG14102	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003760	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007563	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	S2502	From SHIGELLACYC
E. coli O157	Z3552	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)	PF01966 HD domain
Panther (EcoliWiki Page)	PTHR11845:SF4
Superfamily (EcoliWiki Page)	SUPERFAMILY:109604
EcoCyc	EcoCyc:G7185	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG14102	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003760	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3855	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0007563	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 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 ^2.7 ^2.8 ^2.9 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 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 ^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

yfbR: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 yfbR Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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