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fixB:On One Page

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Standard Name

fixB

Gene Synonym(s)

ECK0043, b0042, JW0041, yaaR[1]

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, NAD/FAD-binding domain and ETFP adenine nucleotide-binding domain-like[1], B0042[2][1], YaaR[2][1], FixB[2][1]

Function from GO

Biological Process

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): fixABCX[2]

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(fixB)    Textpresso(fixB)

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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

fixB

Mnemonic

Fixation

Synonyms

ECK0043, b0042, JW0041, yaaR[1]

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Notes

Location(s) and DNA Sequence

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

0.93 minutes 

MG1655: 43188..44129
gbrowse_img.php?coord=43188..44129&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 47383..48324
gbrowse_img.php?coord=47383..48324&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 43188..44129
gbrowse_img.php?coord=43188..44129&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 43188..44129
gbrowse_img.php?coord=43188..44129&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 43188..44129
gbrowse_img.php?coord=43188..44129&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

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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 typeLocationDescription
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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.

AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments

ΔfixB (Keio:JW0041)

deletion

deletion

PMID:16738554

Shigen
CGSC8354[5]

ΔfixB755::kan

PMID:16738554

CGSC:100884


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Notes

Genetic Resources

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

ResourceResource TypeSourceNotes/Reference

JW0041

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAACACGTTTTCTCAAGTCTG

Primer 2:CCACGCGCTAAAGCTGCGGTCAG

carB96::Tn10

Linked marker

CAG12093 = CGSC7322[5]

est. P1 cotransduction: 69% [6]
Synonyms:car-96::Tn10

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[5]

est. P1 cotransduction: 18% [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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11563

EchoBASE (EcoliWiki Page)

EchoBASE:EB1524

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0042

EcoGene (EcoliWiki Page)

EcoGene:EG11563

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:FIXB

ASAP (EcoliWikiPage)

ASAP:ABE-0000147


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Notes

Links

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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

FixB

Synonyms

predicted electron transfer flavoprotein, NAD/FAD-binding domain and ETFP adenine nucleotide-binding domain-like[1], B0042[2][1], YaaR[2][1], FixB[2][1]

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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Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus

GO:0050660

FAD binding

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001308

F

Seeded from EcoCyc [7]

complete

GO:0009437

carnitine metabolic process

GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01056

P

Seeded from EcoCyc [7]

complete

GO:0009055

electron carrier activity

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001308

F

Seeded from EcoCyc [7]

complete

GO:0006810

transport

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0813

P

Seeded from EcoCyc [7]

complete

GO:0022900

electron transport chain

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0249

P

Seeded from EcoCyc [7]

complete

GO:0055114

oxidation reduction

GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01056

P

Seeded from EcoCyc [7]

complete

GO:0009437

carnitine metabolic process

PMID:12081978

IMP: Inferred from Mutant Phenotype

P

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 TypePartnerNotesReferencesEvidence

Protein

groL

PMID:16606699

Experiment(s):EBI-1135416

Protein

pta

PMID:16606699

Experiment(s):EBI-1135416

Protein

fhlA

PMID:16606699

Experiment(s):EBI-1135416

Protein

dnaK

PMID:16606699

Experiment(s):EBI-1135416

Protein

rplJ

PMID:16606699

Experiment(s):EBI-1135416

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Notes

Localization

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

CompartmentDescriptionEvidenceSourceNotes
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Notes

Structure and Physical Properties

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Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Sequence

at EcoCyc 

MNTFSQVWVF SDTPSRLPEL MNGAQALANQ INTFVLNDAD GAQAIQLGAN HVWKLNGKPD
DRMIEDYAGV MADTIRQHGA DGLVLLPNTR RGKLLAAKLG YRLKAAVSND ASTVSVQDGK
ATVKHMVYGG LAIGEERIAT PYAVLTISSG TFDAAQPDAS RTGETHTVEW QAPAVAITRT
ATQARQSNSV DLDKARLVVS VGRGIGSKEN IALAEQLCKA IGAELACSRP VAENEKWMEH
ERYVGISNLM LKPELYLAVG ISGQIQHMVG ANASQTIFAI NKDKNAPIFQ YADYGIVGDA
VKILPALTAA LAR
Length

313

Mol. Wt

33.513 kDa

pI

7.2 (calculated)

Extinction coefficient

33,920 - 34,170 (calc based on 8 Y, 4 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.

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

Structures
Models

View models at:

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Structure figures

Notes

Gene Product Resources

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Resource typeSourceNotes/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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11563-MONOMER

UniProt (EcoliWiki Page)

UniProt:P31574

PFAM (EcoliWiki Page)

PFAM:PF00766

RefSeq (EcoliWiki Page)

RefSeq:NP_414584


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Notes

Links

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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

MoleculeOrganism or StrainCellular levelUnitsMediumTemperature °COther (e.g. anaerobic)Growth rateAssay usedNotesReference(s)
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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

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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gbrowse_img.php?coord=43168..43208&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein&width=400&figure=Nterm&.png
This picture shows the sequence around the N-terminus.

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

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

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

TypeReferenceNotes

microarray

GEO Profiles:b0042 (EcoliWiki Page)

NCBI GEO profiles for fixB

microarray

GenExpDB:b0042 (EcoliWiki Page)

Summary of data for fixB 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 NameResource TypeDescriptionSourceNotes
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Notes

Accessions Related to fixB Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11563

EchoBASE (EcoliWiki Page)

EchoBASE:EB1524

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0042

EcoGene (EcoliWiki Page)

EcoGene:EG11563


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Notes

Links

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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.

OrganismHomologs (Statistics)Comments

Anopheles gambiae

  • ENSANGP00000014287 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000035078 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT1G50940 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00023711 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00009187 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000026809 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000013153 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Danio rerio

  • ZDB-CDNA-040425-287 (score: 1.000; bootstrap: 100%)
  • ZDB-GENE-030131-4449 (score: 1.000; bootstrap: 100%)
  • ZDB-CDNA-040625-227 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0189158 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0010516 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA21463-PA (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000004621 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000267950 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000014462 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000014996 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Mus musculus

  • MGI:106092 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q75LJ3 (score: 1.000; bootstrap: 100%)
  • Q75LJ2 (score: 0.509)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000012506 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000020544 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YPR004C (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPAC27D76 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000138121 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00015947001 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000019967 (score: 1.000; bootstrap: 100%)
  • ENSXETP00000009481 (score: 0.618)
  • ENSXETP00000033499 (score: 0.380)

From Inparanoid:20070104

E. coli O157

FIXB

From ECOO157CYC

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Do-It-Yourself Web Tools

Notes

Families

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DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF00766


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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 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. ↑ 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. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 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. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 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).
  7. ↑ 7.0 7.1 7.2 7.3 7.4 7.5 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70

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