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Standard Name

caiC

Gene Synonym(s)

ECK0038, b0037, JW0036, yaaM[1]

Product Desc.

CAIC[2][3]

Crotonobetain/carnitine-CoA ligase[4]

Product Synonyms(s)

predicted crotonobetaine CoA ligase:carnitine CoA ligase[1], B0037[2][1], YaaM[2][1], CaiC[2][1]

Function from GO

Molecular Function

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): caiTABCDE[2]

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(caiC)    Textpresso(caiC)

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Notes

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Simliarity comparisons with Salmonella, Desulfotomaculum, Shewanella and Proteus CaiC homologs indicate that the second ATG is the likely start site, which also has a good predicted RBS of GGAG (Personal communication, G. Plunkett, 6/07).[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

caiC

Mnemonic

Carnitine inducible

Synonyms

ECK0038, b0037, JW0036, yaaM[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

0.78 minutes 

MG1655: 37839..36271
gbrowse_img.php?coord=36271..37839&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 42033..40465
gbrowse_img.php?coord=40465..42033&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 37839..36271
gbrowse_img.php?coord=36271..37839&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 37839..36271
gbrowse_img.php?coord=36271..37839&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 36271..37839
gbrowse_img.php?coord=36271..37839&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

caiCL503LDL

L503LDL

(in strain: O44:K74)

Strain variation; seeded from UniProt:P31552

caiCR359C

R359C

(in strain: B)

Strain variation; seeded from UniProt:P31552

caiCI374V

I374V

(in strain: O44:K74 and B)

Strain variation; seeded from UniProt:P31552

caiCA396V

A396V

(in strain: O44:K74)

Strain variation; seeded from UniProt:P31552

caiCR408C

R408C

(in strain: O44:K74)

Strain variation; seeded from UniProt:P31552

caiCD412G

D412G

(in strain: O44:K74 and B)

Strain variation; seeded from UniProt:P31552

caiCA442T

A442T

(in strain: O44:K74 and B)

Strain variation; seeded from UniProt:P31552

caiCQ388K

Q388K

(in strain: O44:K74 and B)

Strain variation; seeded from UniProt:P31552

caiCI328S

I328S

(in strain: O44:K74)

Strain variation; seeded from UniProt:P31552

caiCV345A

V345A

(in strain: O44:K74 and B)

Strain variation; seeded from UniProt:P31552

caiCC98R

C98R

(in strain: O44:K74)

Strain variation; seeded from UniProt:P31552

caiCRA252PR

RA252PR

(in strain: O44:K74)

Strain variation; seeded from UniProt:P31552

caiCQ286R

Q286R

(in strain: O44:K74 and B)

Strain variation; seeded from UniProt:P31552

ΔcaiC (Keio:JW0036)

deletion

deletion

PMID:16738554

Shigen
CGSC8352[5]

ΔcaiC750::kan

PMID:16738554

CGSC:100230


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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

JW0036

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGATAGAGGTGCAATGGATAT

Primer 2:CCTTTCAGATTCTTTCTAATTAT

carB96::Tn10

Linked marker

CAG12093 = CGSC7322[5]

est. P1 cotransduction: 88% [6]
Synonyms:car-96::Tn10

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[5]

est. P1 cotransduction: 12% [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:EG11558

EchoBASE (EcoliWiki Page)

EchoBASE:EB1519

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0037

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0046

EcoGene (EcoliWiki Page)

EcoGene:EG11558

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:CAIC

CGSC (EcoliWiki Page)

CGSC:36828

ASAP (EcoliWikiPage)

ASAP:ABE-0000133


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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

CaiC

Synonyms

predicted crotonobetaine CoA ligase:carnitine CoA ligase[1], B0037[2][1], YaaM[2][1], CaiC[2][1]

Product description

CAIC[2][3]

Crotonobetain/carnitine-CoA ligase[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:0003824

catalytic activity

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000873

F

Seeded from EcoCyc [7]

complete

GO:0008152

metabolic process

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000873

P

Seeded from EcoCyc [7]

complete

GO:0016405

CoA-ligase activity

GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01524

F

Seeded from EcoCyc [7]

complete

GO:0016874

ligase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0436

F

Seeded from EcoCyc [7]

complete

GO:0051108

carnitine-CoA ligase activity

PMID:18266698

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc [7]

complete

GO:0051109

crotonobetaine-CoA ligase activity

PMID:18266698

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc [7]

complete

GO:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

required fields missing

GO:0009310

amine catabolic process

P

Seeded from EcoCyc 11.1[3].

required fields missing

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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

dnaK

PMID:16606699

Experiment(s):EBI-1135392

Protein

uvrD

PMID:16606699

Experiment(s):EBI-1135392

Protein

araF

PMID:16606699

Experiment(s):EBI-1135392

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Notes

Localization

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

CompartmentDescriptionEvidenceSourceNotes

plasma membrane

From EcoCyc[3]


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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 

MDRGAMDIIG GQHLRQMWDD LADVYGHKTA LICESSGGVV NRYSYLELNQ EINRTANLFY
TLGIRKGDKV ALHLDNCPEF IFCWFGLAKI GAIMVPINAR LLCEESAWIL QNSQACLLVT
SAQFYPMYQQ IQQEDATQLR HICLTDVALP ADDGVSSFTQ LKNQQPATLC YAPPLSTDDT
AEILFTSGTT SRPKGVVITH YNLRFAGYYS AWQCALRDDD VYLTVMPAFH IDCQCTAAMA
AFSAGATFVL VEKYSARAFW GQVQKYRATV TECIPMMIRT LMVQPPSAND QQHRLREVMF
YLNLSEQEKD AFCERFGVRL LTSYGMTETI VGIIGDRPGD KRRWPSIGRV GFCYEAEIRD
DHNRPLPAGE IGEICIKGIP GKTIFKEYFL NPQATAKVLE ADGWLHTGDT GYRDEEDFFY
FVDRRCNMIK RGGENVSCVE LENIIAAHPK IQDIVVVGIK DSIRDEAIKA FVVLNEGETL
SEEEFFRFCE QNMAKFKVPS YLEIRKDLPR NCSGKIIRKN LK
Length

522

Mol. Wt

59.09 kDa

pI

5.8 (calculated)

Extinction coefficient

68,300 - 70,550 (calc based on 20 Y, 7 W, and 18 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:CAIC-MONOMER

UniProt (EcoliWiki Page)

UniProt:P31552

PFAM (EcoliWiki Page)

PFAM:PF00501

RefSeq (EcoliWiki Page)

RefSeq:NP_414579


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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)

caiTABCDE

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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=37819..37859&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein+flip&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:b0037 (EcoliWiki Page)

NCBI GEO profiles for caiC

microarray

GenExpDB:b0037 (EcoliWiki Page)

Summary of data for caiC 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

GFP Fusion

Intergenic region (37768..37914) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ02; Well:C7[8]

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Notes

Accessions Related to caiC Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11558

EchoBASE (EcoliWiki Page)

EchoBASE:EB1519

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0037

EcoGene (EcoliWiki Page)

EcoGene:EG11558


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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

Caenorhabditis briggsae

  • WBGene00023673 (score: 1.000; bootstrap: 62%)
  • WBGene00026207 (score: 0.399)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00009218 (score: 1.000; bootstrap: 67%)
  • WBGene00017012 (score: 0.416)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000025707 (score: 1.000; bootstrap: 56%)
  • ENSCAFP00000001025 (score: 0.393)
  • ENSCAFP00000022190 (score: 0.358)
  • ENSCAFP00000003428 (score: 0.342)
  • ENSCAFP00000022577 (score: 0.244)
  • ENSCAFP00000029725 (score: 0.237)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-050706-104 (score: 1.000; bootstrap: 97%)
  • ZDB-CDNA-050706-41 (score: 1.000; bootstrap: 97%)
  • ZDB-CDNA-041212-76 (score: 0.512)
  • ZDB-GENE-041212-67 (score: 0.512)
  • ZDB-CDNA-050417-249 (score: 0.262)
  • ZDB-GENE-050417-248 (score: 0.262)
  • ZDB-CDNA-050320-112 (score: 0.246)
  • ZDB-GENE-050320-112 (score: 0.246)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0205849 (score: 1.000; bootstrap: 89%)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000000239 (score: 1.000; bootstrap: 56%)
  • ENSGALP00000022652 (score: 0.263)
  • ENSGALP00000007948 (score: 0.245)
  • ENSGALP00000021686 (score: 0.209)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000004721 (score: 1.000; bootstrap: 65%)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YBR222C (score: 1.000; bootstrap: 89%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000137549 (score: 1.000; bootstrap: 77%)
  • NEWSINFRUP00000130941 (score: 0.563)
  • NEWSINFRUP00000161913 (score: 0.547)
  • NEWSINFRUP00000157971 (score: 0.359)
  • NEWSINFRUP00000181817 (score: 0.303)
  • NEWSINFRUP00000151747 (score: 0.262)
  • NEWSINFRUP00000176592 (score: 0.145)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00018048001 (score: 1.000; bootstrap: 67%)
  • GSTENP00018016001 (score: 0.512)
  • GSTENP00025601001 (score: 0.366)
  • GSTENP00004594001 (score: 0.333)
  • GSTENP00025600001 (score: 0.332)
  • GSTENP00005731001 (score: 0.311)
  • GSTENP00024733001 (score: 0.163)
  • GSTENP00034356001 (score: 0.129)

From Inparanoid:20070104

Shigella flexneri

CAIC

From SHIGELLACYC

E. coli O157

CAIC

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.

DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF00501


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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. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 1.11 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 3.2 3.3 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 7.4 7.5 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  8. ↑ Zaslaver A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3: 623-8 PubMed EcoliWiki page

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