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caiF:On One Page

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Quickview | Gene | Product(s) | Expression| Evolution | References |

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See Help:Quickview for help with entering information in the Quickview table.

Standard Name

caiF

Gene Synonym(s)

ECK0035, b0034, JW0033[1]

Product Desc.

CaiF transcriptional activator[2][3]

Transcriptional activator of cai operon[4]

Product Synonyms(s)

DNA-binding transcriptional activator[1], B0034[2][1], CaiF[2][1]

Function from GO

Biological Process

Molecular Function

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): caiF[2]

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(caiF)    Textpresso(caiF)

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Notes

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A 59 aa ORF yaaV (EG12706) was previously annotated upstream of caiF. yaaV has also been reported as a pseudogene, but the allelic variation, lack of homologs, rare codons, map position and poor RBS indicate it is not a gene and it has been removed.[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

caiF

Mnemonic

Carnitine inducible

Synonyms

ECK0035, b0034, JW0033[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

0.74 minutes 

MG1655: 34300..34695
gbrowse_img.php?coord=34300..34695&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 38371..38766
gbrowse_img.php?coord=38371..38766&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 34300..34695
gbrowse_img.php?coord=34300..34695&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 34300..34695
gbrowse_img.php?coord=34300..34695&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 34300..34695
gbrowse_img.php?coord=34300..34695&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

ΔcaiF (Keio:JW0033)

deletion

deletion

PMID:16738554

Shigen
CGSC8350[5]

ΔcaiF747::kan

PMID:16738554

CGSC:100236


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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

JW0033

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTGTGAAGGATATGTTGAAAA

Primer 2:CCACGACGCATACTCTTTGACAA

carB96::Tn10

Linked marker

CAG12093 = CGSC7322[5]

est. P1 cotransduction: 94% [6]
Synonyms:car-96::Tn10

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[5]

est. P1 cotransduction: 10% [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:G6088

EchoBASE (EcoliWiki Page)

EchoBASE:EB3224

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0034

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0043

EcoGene (EcoliWiki Page)

EcoGene:EG13451

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:Z0040

ASAP (EcoliWikiPage)

ASAP:ABE-0000125


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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

CaiF

Synonyms

DNA-binding transcriptional activator[1], B0034[2][1], CaiF[2][1]

Product description

CaiF transcriptional activator[2][3]

Transcriptional activator of cai operon[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:0006350

transcription

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0804

P

Seeded from EcoCyc 12.5 [7]

complete

GO:0006355

regulation of transcription, DNA-dependent

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0805

P

Seeded from EcoCyc [8]

complete

GO:0006350

transcription

PMID:10564497

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc 12.5 [7]

complete

GO:0006350

transcription

PMID:8631699

IEP: Inferred from Expression Pattern

P

Seeded from EcoCyc 12.5 [7]

complete

GO:0006350

transcription

PMID:9573142

IEP: Inferred from Expression Pattern

P

Seeded from EcoCyc 12.5 [7]

complete

GO:0005737

cytoplasm

C

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0016563

transcription activator activity

F

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0009310

amine catabolic process

P

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0016563

transcription activator activity

PMID:8631699

EXP: Inferred from Experiment

F

Seeded from EcoCyc 11.1[3].

complete

GO:0009437

carnitine metabolic process

PMID:8631699

EXP: Inferred from Experiment

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

sdhA

PMID:16606699

Experiment(s):EBI-1135382

Protein

tatE

PMID:16606699

Experiment(s):EBI-1135382

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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 

MKLHTIDIST ILIWPCLIAS KRVIARLLIC ETGVRMCEGY VEKPLYLLIA EWMMAENRWV
IAREISIHFD IEHSKAVNTL TYILSEVTEI SCEVKMIPNK LEGRGCQCQR LVKVVDIDEQ
IYARLRNNSR EKLVGVRKTP RIPAVPLTEL NREQKWQMML SKSMRR
Length

166

Mol. Wt

19.396 kDa

pI

9.2 (calculated)

Extinction coefficient

27,960 - 28,710 (calc based on 4 Y, 4 W, and 6 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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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

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:G6088-MONOMER

UniProt (EcoliWiki Page)

UniProt:P0AE58

RefSeq (EcoliWiki Page)

RefSeq:NP_414576


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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)

caiF

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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=34280..34320&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:b0034 (EcoliWiki Page)

NCBI GEO profiles for caiF

microarray

GenExpDB:b0034 (EcoliWiki Page)

Summary of data for caiF 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 caiF Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:G6088

EchoBASE (EcoliWiki Page)

EchoBASE:EB3224

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0034

EcoGene (EcoliWiki Page)

EcoGene:EG13451


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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

Shigella flexneri

CAIF

From SHIGELLACYC

E. coli O157

Z0040

From ECOO157CYC

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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 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 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. ↑ 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 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  8. ↑ EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70

Categories

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