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Expression|

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Standard Name	fadK
Gene Synonym(s)	ydiD, ECK1699, b1701, JW5910^[1]^[2], JW5910
Product Desc.	FadK^[2]^[3]; Component of short chain acyl-CoA synthetase^[3] Acyl-CoA synthase, anaerobic^[4]
Product Synonyms(s)	short chain acyl-CoA synthetase, anaerobic^[1], B1701^[2]^[1], FadK^[2]^[1], YdiD^[2]^[1] , ECK1699, JW5910, ydiD, b1701
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ydiQRST-fadK^[2], ydiQRSTD
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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AFMB Structural Genomics target No. 54 (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	fadK
Mnemonic	Fatty acid degradation
Synonyms	ydiD, ECK1699, b1701, JW5910^[1]^[2], JW5910
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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	38.39 minutes	MG1655: 1781001..1782701 <gbrowseImage> name=NC_000913:1781001..1782701 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1760245..1761945 <gbrowseImage> name=NC_012967:1760245..1761945 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1673114..1674760 <gbrowseImage> name=NC_012759:1673114..1674760 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1784691..1786391 <gbrowseImage> name=NC_007779:1784691..1786391 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	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)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
ΔydiD::kan	deletion		Biolog:respiration	unable to respire Acetate	PMID:16095938
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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
	Plasmid clone	Shigen	PMID:16769691 Status: Primer 1: Primer 2:
8G8	Kohara Phage	Genobase	PMID:3038334
20F5	Kohara Phage	Genobase	PMID:3038334
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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:EG12357	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12357	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002225	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946213	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2260	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005676	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	YdiD
Synonyms	short chain acyl-CoA synthetase, anaerobic^[1], B1701^[2]^[1], FadK^[2]^[1], YdiD^[2]^[1] , ECK1699, JW5910, ydiD, b1701
Product description	FadK^[2]^[3]; Component of short chain acyl-CoA synthetase^[3] Acyl-CoA synthase, anaerobic^[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: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:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000873	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0067	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006629	lipid metabolic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0443	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006631	fatty acid metabolic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0276	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000873	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016020	membrane	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0472	C	Seeded from EcoCyc (v14.0)	complete
	GO:0016874	ligase activity	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0436	F	Seeded from EcoCyc (v14.0)	complete
	GO:0019898	extrinsic to membrane	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-9903	C	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	Notes	References	Evidence
Protein	Subunits of short chain acyl-CoA synthetase	could be indirect
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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 MHPTGPHLGP DVLFRESNMK VTLTFNEQRR AAYRQQGLWG DASLADYWQQ TARAMPDKIA VVDNHGASYT YSALDHAASC LANWMLAKGI ESGDRIAFQL PGWCEFTVIY LACLKIGAVS VPLLPSWREA ELVWVLNKCQ AKMFFAPTLF KQTRPVDLIL PLQNQLPQLQ QIVGVDKLAP ATSSLSLSQI IADNTSLTTA ITTHGDELAA VLFTSGTEGL PKGVMLTHNN ILASERAYCA RLNLTWQDVF MMPAPLGHAT GFLHGVTAPF LIGARSVLLD IFTPDACLAL LEQQRCTCML GATPFVYDLL NVLEKQPADL SALRFFLCGG TTIPKKVARE CQQRGIKLLS VYGSTESSPH AVVNLDDPLS RFMHTDGYAA AGVEIKVVDD ARKTLPPGCE GEEASRGPNV FMGYFDEPEL TARALDEEGW YYSGDLCRMD EAGYIKITGR KKDIIVRGGE NISSREVEDI LLQHPKIHDA CVVAMSDERL GERSCAYVVL KAPHHSLSLE EVVAFFSRKR VAKYKYPEHI VVIEKLPRTT SGKIQKFLLR KDIMRRLTQD VCEEIE
Length	566
Mol. Wt	62.759 kDa
pI	6.8 (calculated)
Extinction coefficient	67,840 - 69,715 (calc based on 16 Y, 8 W, and 15 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	52..464	PF00501 AMP-binding enzyme		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=fadK 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:145698273	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946213	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005676	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P38135	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12357	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12357	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946213	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002225	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2260	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	3^a	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	4	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	0^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)
ydiQRST-fadK
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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

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<protect><gbrowseImage> name=NC_000913:1780981..1781021 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:b1701 (EcoliWiki Page)	NCBI GEO profiles for fadK
microarray	GenExpDB:b1701 (EcoliWiki Page)	Summary of data for fadK 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 fadK Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12357	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2260	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1701
EcoGene	EcoGene:EG12357	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002225	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005676	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
Anopheles gambiae	ENSANGP00000020797 (score: 1.000; bootstrap: 87%) ENSANGP00000016291 (score: 0.989)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000023787 (score: 1.000; bootstrap: 87%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00037984 (score: 1.000; bootstrap: 74%) WBGene00038255 (score: 0.383)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00009221 (score: 1.000; bootstrap: 81%) WBGene00018488 (score: 0.380)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0031703 (score: 1.000; bootstrap: 96%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000011082 (score: 1.000; bootstrap: 95%)	From Inparanoid:20070104
Homo sapiens	ENSP00000300441 (score: 1.000; bootstrap: 93%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000022670 (score: 1.000; bootstrap: 98%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000026134 (score: 1.000; bootstrap: 95%)	From Inparanoid:20070104
Mus musculus	MGI:2388287 (score: 1.000; bootstrap: 96%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000015964 (score: 1.000; bootstrap: 79%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPCC18273c (score: 1.000; bootstrap: 92%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000160542 (score: 1.000; bootstrap: 89%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00007139001 (score: 1.000; bootstrap: 90%) GSTENP00019733001 (score: 0.574) GSTENP00022277001 (score: 0.138)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000014935 (score: 1.000; bootstrap: 75%)	From Inparanoid:20070104
Shigella flexneri	YDID	From SHIGELLACYC
E. coli O157	YDID	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)	PF00501 AMP-binding enzyme
Panther (EcoliWiki Page)	PTHR24095:SF44
Superfamily (EcoliWiki Page)	SUPERFAMILY:56801
EcoCyc	EcoCyc:EG12357	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12357	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002225	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2260	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0005676	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 ^1.8 ^1.9 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 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 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.

fadK: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 fadK Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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