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Expression|

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Standard Name	fixA
Gene Synonym(s)	ECK0042, b0041, JW0040, yaaQ^[1], yaaQ
Product Desc.	probable flavoprotein subunit required for anaerobic carnitine metabolism^[2]^[3] Required for anaerobic carnitine reduction; similar to Rhizobium fix gene^[4]
Product Synonyms(s)	predicted electron transfer flavoprotein subunit, ETFP adenine nucleotide-binding domain^[1], B0041^[2]^[1], YaaQ^[2]^[1], FixA^[2]^[1] , ECK0042, JW0040, yaaQ, b0041
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): fixABCX^[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	fixA
Mnemonic	Fixation
Synonyms	ECK0042, b0041, JW0040, yaaQ^[1], yaaQ
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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	0.91 minutes	MG1655: 42403..43173 <gbrowseImage> name=NC_000913:42403..43173 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 46598..47368 <gbrowseImage> name=NC_012967:46598..47368 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 42403..43173 <gbrowseImage> name=NC_012759:42403..43173 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 42403..43173 <gbrowseImage> name=NC_007779:42403..43173 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 42403..43173 <gbrowseImage> name=NC_010473:42403..43173 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)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
fixA(del) (Keio:JW0040)	deletion	deletion			PMID:16738554	Shigen
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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
JW0040	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAGATTATTACTTGCTATAA Primer 2:CCAATGACTTTGCGAAGATTTTC
2F7	Kohara Phage	Genobase	PMID:3038334
4A3	Kohara Phage	Genobase	PMID:3038334
carB96::Tn10	Linked marker	CAG12093 = CGSC7322^[5]	est. P1 cotransduction: 71% ^[6] Synonyms:car-96::Tn10
leuO3051::Tn10	Linked marker	CAG12095 = CGSC7324^[5]	est. P1 cotransduction: 17% ^[6] Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).
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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:EG11562	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11562	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001515	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947316	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1523	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000145	Escherichia coli str. K-12 substr. MG1655
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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	FixA
Synonyms	predicted electron transfer flavoprotein subunit, ETFP adenine nucleotide-binding domain^[1], B0041^[2]^[1], YaaQ^[2]^[1], FixA^[2]^[1] , ECK0042, JW0040, yaaQ, b0041
Product description	probable flavoprotein subunit required for anaerobic carnitine metabolism^[2]^[3] Required for anaerobic carnitine reduction; similar to Rhizobium fix gene^[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: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:IPR000049	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009055	electron carrier activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012255	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009437	carnitine metabolic process	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01055	P	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:0009437	carnitine metabolic process	PMID:12081978	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0055114	oxidation reduction	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01055	P	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	dnaK	PMID:16606699	Experiment(s):EBI-1135409
Protein	ulaF	PMID:16606699	Experiment(s):EBI-1135409
Protein	nadE	PMID:16606699	Experiment(s):EBI-1135409
Protein	ttdA	PMID:16606699	Experiment(s):EBI-1135409
Protein	rpsC	PMID:16606699	Experiment(s):EBI-1135409
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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 MNDVSFMISG DAMKIITCYK CVPDEQDIAV NNADGSLDFS KADAKISQYD LNAIEAACQL KQQAAEAQVT ALSVGGKALT NAKGRKDVLS RGPDELIVVI DDQFEQALPQ QTASALAAAA QKAGFDLILC GDGSSDLYAQ QVGLLVGEIL NIPAVNGVSK IISLTADTLT VERELEDETE TLSIPLPAVV AVSTDINSPQ IPSMKAILGA AKKPVQVWSA ADIGFNAEAA WSEQQVAAPK QRERQRIVIE GDGEEQIAAF AENLRKVI
Length	268
Mol. Wt	28.412 kDa
pI	4.2 (calculated)
Extinction coefficient	15,470 - 15,970 (calc based on 3 Y, 2 W, and 4 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	24..187	PF01012 Electron transfer flavoprotein 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=fixA 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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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:90111081	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000145	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P60566	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11562	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11562	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947316	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001515	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947316	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1523	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	15^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^a	molecules/cell/generation	Medium: MOPS Minimal 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	1^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)
fixABCX
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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_000913:42383..42423 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:b0041 (EcoliWiki Page)	NCBI GEO profiles for fixA
microarray	GenExpDB:b0041 (EcoliWiki Page)	Summary of data for fixA 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 fixA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11562	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1523	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0041
EcoGene	EcoGene:EG11562	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001515	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000145	Escherichia coli str. K-12 substr. MG1655
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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	ENSANGP00000016103 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000009688 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT5G43430 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000027250 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00026736 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00017734 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000004217 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000015668 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-040426-1931 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040425-2878 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0204353 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0039697 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA20618-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000311930 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000030973 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000026039 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:106098 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q7F9U3 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000019549 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000024083 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YGR207C (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC18052c (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000155202 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000048085 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	FIXA	From SHIGELLACYC
E. coli O157	FIXA	From ECOO157CYC
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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)	PF01012 Electron transfer flavoprotein domain
Superfamily (EcoliWiki Page)	SUPERFAMILY:52402
Panther (EcoliWiki Page)	PTHR21294:SF0
EcoCyc	EcoCyc:EG11562	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11562	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001515	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1523	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000145	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)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 ^2.7 ^2.8 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 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 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).

fixA:On One Page

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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 fixA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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