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Standard Name	ykgF
Gene Synonym(s)	ECK0306, b0307, JW0300^[1], JW0300
Product Desc.	predicted amino acid dehydrogenase with NAD(P)-binding domain and ferridoxin-like domain^[2]^[3] Function unknown^[4]
Product Synonyms(s)	predicted amino acid dehydrogenase with NAD(P)-binding domain and ferridoxin-like domain^[1], YkgF^[2]^[1], B0307^[2]^[1] , ECK0306, JW0300, b0307
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ykgE^[2]
Regulation/Activity
Quick Links
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Notes

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AFMB Structural Genomics target No. (http://afmb.cnrs-mrs.fr/article171.html).^[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	ykgF
Mnemonic	Systematic nomenclature
Synonyms	ECK0306, b0307, JW0300^[1], JW0300
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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	6.93 minutes	MG1655: 321562..322989 <gbrowseImage> name=NC_000913:321562..322989 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 294987..296414 <gbrowseImage> name=NC_012967:294987..296414 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
W3110		W3110: 321562..322989 <gbrowseImage> name=NC_007779:321562..322989 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 297112..298539 <gbrowseImage> name=NC_010473:297112..298539 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	Comments
ykgF(del) (Keio:JW0300)	deletion	deletion	PMID:16738554	Shigen CGSC8501^[5]
ykgF::Tn5KAN-I-SceI (FB20135)	Insertion at nt 529 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20135	does not contain pKD46
ykgF::Tn5KAN-I-SceI (FB20136)	Insertion at nt 529 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20136	contains pKD46
ykgF750(del)::kan			PMID:16738554	CGSC:105670
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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
JW0300	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTCGATCAAAACCAGTAATAC Primer 2:CCTCCATTCTTTTTCTCCTGCGC
9G4	Kohara Phage	Genobase	PMID:3038334
6E6	Kohara Phage	Genobase	PMID:3038334
proA81::Tn10	Linked marker	CAG18447 = CGSC7330^[5]	est. P1 cotransduction: 4% ^[6]
lacI3042::Tn10	Linked marker	CAG18439 = CGSC7334^[5]	est. P1 cotransduction: 14% ^[6] Synonyms:lacI42::Tn10 nnnCAG18439 also carries lacZ118(0c) (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:G6177	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13583	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002796	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:944980	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3353	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001060	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	YkgF
Synonyms	predicted amino acid dehydrogenase with NAD(P)-binding domain and ferridoxin-like domain^[1], YkgF^[2]^[1], B0307^[2]^[1] , ECK0306, JW0300, b0307
Product description	predicted amino acid dehydrogenase with NAD(P)-binding domain and ferridoxin-like domain^[2]^[3] Function unknown^[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: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:0009055	electron carrier activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017900	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR009051	F	Seeded from EcoCyc (v14.0)	complete
	GO:0016491	oxidoreductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012285	F	Seeded from EcoCyc (v14.0)	complete
	GO:0022900	electron transport chain	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0249	P	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:0051536	iron-sulfur cluster binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR009051	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051536	iron-sulfur cluster binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012285	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051536	iron-sulfur cluster binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR017900	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051536	iron-sulfur cluster binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0411	F	Seeded from EcoCyc (v14.0)	complete
	GO:0051539	4 iron, 4 sulfur cluster binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0004	F	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR009051	P	Seeded from EcoCyc (v14.0)	complete
	GO:0003674	molecular function	n/a	ND: No biological Data available		F		Missing: reference
	GO:0005575	cellular component	n/a	ND: No biological Data available		C		Missing: reference
	GO:0008150	biological process	n/a	ND: No biological Data available		P		Missing: reference
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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	groL	PMID:16606699	Experiment(s):EBI-1136162
Protein	clpB	PMID:16606699	Experiment(s):EBI-1136162
Protein	ttdA	PMID:16606699	Experiment(s):EBI-1136162
Protein	rtcB	PMID:16606699	Experiment(s):EBI-1136162
Protein	hisJ	PMID:16606699	Experiment(s):EBI-1136162
Protein	rspA	PMID:16606699	Experiment(s):EBI-1136162
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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 MSIKTSNTDF KTRIRQQIED PIMRKAVANA QQRIGANRQK MVDELGHWEE WRDRAAQIRD HVLSNLDAYL YQLSEKVTQN GGHVYFARTK EDATRYILQV AQRKNARKVV KSKSMVTEEI GVNHVLQDAG IQVIETDLGE YILQLDQDPP SHVVVPAIHK DRHQIRRVLH ERLGYEGPET PEAMTLFIRQ KIREDFLSAE IGITGCNFAV AETGSVCLVT NEGNARMCTT LPKTHIAVMG MERIAPTFAE VDVLITMLAR SAVGARLTGY NTWLTGPREA GHVDGPEEFH LVIVDNGRSE VLASEFRDVL RCIRCGACMN TCPAYRHIGG HGYGSIYPGP IGAVISPLLG GYKDFKDLPY ACSLCTACDN VCPVRIPLSK LILRHRRVMA EKGITAKAEQ RAIKMFAYAN SHPGLWKVGM MAGAHAASWF INGGKTPLKF GAISDWMEAR DLPEADGESF RSWFKKHQAQ EKKNG
Length	475
Mol. Wt	53.051 kDa
pI	8.6 (calculated)
Extinction coefficient	57,870 - 59,245 (calc based on 13 Y, 7 W, and 11 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	194..294	PF02589 Uncharacterised ACR, YkgG family COG1556	PMID:19920124
Domain	379..471	PF11870 Domain of unknown function (DUF3390)	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=ykgF 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:16128292	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944980	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001060	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P77536	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6177	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13583	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944980	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002796	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3353	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 MG1655	37	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	34	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	21^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	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)
ykgE
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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_000913:321542..321582 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:b0307 (EcoliWiki Page)	NCBI GEO profiles for ykgF
microarray	GenExpDB:b0307 (EcoliWiki Page)	Summary of data for ykgF 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 (321480..321615) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ11; Well:E8^[7]
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Notes

Accessions Related to ykgF Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6177	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3353	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0307
EcoGene	EcoGene:EG13583	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002796	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001060	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	YKGF	From SHIGELLACYC
E. coli O157	YKGF	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)	PF02589 Uncharacterised ACR, YkgG family COG1556
Superfamily (EcoliWiki Page)	SUPERFAMILY:46548
Superfamily (EcoliWiki Page)	SUPERFAMILY:100950
Pfam (EcoliWiki Page)	PF11870 Domain of unknown function (DUF3390)
EcoCyc	EcoCyc:G6177	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13583	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002796	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3353	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001060	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 ^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

ykgF: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 ykgF Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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