{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Standard Name	dapF
Gene Synonym(s)	ECK3804, b3809, JW5592^[1], JW5592
Product Desc.	Diaminopimelate epimerase^[2]
Product Synonyms(s)	diaminopimelate epimerase^[1], B3809^[3]^[1], DapF^[3]^[1] , ECK3804, JW5592, b3809
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yifL^[3]
Regulation/Activity
Quick Links
edit table

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]

Gene

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]

See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	dapF
Mnemonic	DiAminoPimelate
Synonyms	ECK3804, b3809, JW5592^[1], JW5592
edit table

</protect>

Notes

Location(s) and DNA Sequence

[back to top]

<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	86.06 minutes, 86.06 minutes	MG1655: 3992785..3993609 <gbrowseImage> name=NC_000913:3992785..3993609 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3956599..3957423 <gbrowseImage> name=NC_012967:3956599..3957423 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3882454..3883278 <gbrowseImage> name=NC_012759:3882454..3883278 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3641919..3641095 <gbrowseImage> name=NC_007779:3641095..3641919 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4091705..4092529 <gbrowseImage> name=NC_010473:4091705..4092529 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
edit table

</protect>

Notes

Sequence Features

[back to top]

See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
edit table

Notes

Alleles and Phenotypes

[back to top]

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
ΔdapF (Keio:JW5592)	deletion	deletion			PMID:16738554	Shigen CGSC11481^[4]
ΔdapF755::kan					PMID:16738554	CGSC:100530
dapF	deletion		Sensitivity to	increases sensitivity to bicyclomycin	PMID:21357484		fig 2
edit table

Notes

Genetic Interactions

[back to top]

Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
edit table

</protect>

Notes

Genetic Resources

[back to top]

See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW5592	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCAGTTCTCGAAAATGCATGG Primer 2:CCTAGATGAATAAATCCGTCGTA
12G1	Kohara Phage	Genobase	PMID:3038334
ilvD500::Tn10	Linked marker	CAG18431 = CGSC7462^[4]	est. P1 cotransduction: 19% ^[5] Synonyms:ilv500::Tn10
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.
edit table

Notes

Accessions in Other Databases

[back to top]

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10209	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10209	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000203	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948364	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0205	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012442	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Product(s)

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name	DapF
Synonyms	diaminopimelate epimerase^[1], B3809^[3]^[1], DapF^[3]^[1] , ECK3804, JW5592, b3809
Product description	Diaminopimelate epimerase^[2]
EC number (for enzymes)	5.1.1.7^[1]
edit table

Notes

Function

[back to top]

<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	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00197	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001653	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018510	C	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:0008652	cellular amino acid biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0028	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008837	diaminopimelate epimerase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00197	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008837	diaminopimelate epimerase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001653	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008837	diaminopimelate epimerase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018510	F	Seeded from EcoCyc (v14.0)	complete
	GO:0008837	diaminopimelate epimerase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:5.1.1.7	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009085	lysine biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0457	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009089	lysine biosynthetic process via diaminopimelate	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00197	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009089	lysine biosynthetic process via diaminopimelate	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001653	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009089	lysine biosynthetic process via diaminopimelate	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018510	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016853	isomerase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0413	F	Seeded from EcoCyc (v14.0)	complete
edit table

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
edit table

</protect>

Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source	Notes
edit table

Notes

Structure and Physical Properties

[back to top]

<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 MMQFSKMHGL GNDFMVVDAV TQNVFFSPEL IRRLADRHLG VGFDQLLVVE PPYDPELDFH YRIFNADGSE VAQCGNGARC FARFVRLKGL TNKRDIRVST ANGRMVLTVT DDDLVRVNMG EPNFEPSAVP FRANKAEKTY IMRAAEQTIL CGVVSMGNPH CVIQVDDVDT AAVETLGPVL ESHERFPERA NIGFMQVVKR EHIRLRVYER GAGETQACGS GACAAVAVGI QQGLLAEEVR VELPGGRLDI AWKGPGHPLY MTGPAVHVYD GFIHL
Length	275
Mol. Wt	30.338 kDa
pI	6.2 (calculated)
Extinction coefficient	14,440 - 15,190 (calc based on 6 Y, 1 W, and 6 C residues)
edit table

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	3..124	PF01678 Diaminopimelate epimerase	PMID:19920124
Domain	151..267	PF01678 Diaminopimelate epimerase	PMID:19920124
edit table

<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=dapF taxon=562,83333 </beststructure>

Models

View models at:

edit table

</protect>

Structure figures

</protect>

Notes

Gene Product Resources

[back to top]

See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
edit table

Notes

Accessions in Other Databases

[back to top]

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

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:90111650	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948364	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012442	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A6K1	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10209	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10209	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948364	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000203	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0205	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Expression

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

[back to top]

See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Notes	Reference(s)
Protein	Ecoli K-12	34.124+/-0.476	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.098300971	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	756	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	294	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	736	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
edit table

Notes

Transcription and Transcriptional Regulation

[back to top]

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
yifL
edit table

Figure courtesy of RegulonDB

</protect>

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

[back to top]

<protect><gbrowseImage> name=NC_000913:3992765..3992805 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

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

</protect>

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

[back to top]

<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
edit table

Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b3809 (EcoliWiki Page)	NCBI GEO profiles for dapF
microarray	GenExpDB:b3809 (EcoliWiki Page)	Summary of data for dapF from multiple microarray studies
edit table

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 (3991875..3992386) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ01; Well:B4^[6]
edit table

Notes

Accessions Related to dapF Expression

[back to top]

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10209	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0205	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3809
EcoGene	EcoGene:EG10209	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000203	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012442	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Evolution

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]

See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Anopheles gambiae	ENSANGP00000001955 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT3G53580 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0220128 (score: 1.000; bootstrap: 85%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000047127 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Shigella flexneri	DAPF	From SHIGELLACYC
E. coli O157	DAPF	From ECOO157CYC
edit table

Do-It-Yourself Web Tools

Notes

Families

[back to top]

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

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF01678 Diaminopimelate epimerase
Pfam (EcoliWiki Page)	PF01678 Diaminopimelate epimerase
Superfamily (EcoliWiki Page)	SUPERFAMILY:54506
EcoCyc	EcoCyc:EG10209	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10209	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000203	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0205	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012442	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

References

[back to top]

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 ^1.8 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

dapF: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 dapF Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

Categories

Navigation menu

Search