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Gene |

Product(s) |

Expression|

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Standard Name	caiC
Gene Synonym(s)	ECK0038, b0037, JW0036, yaaM^[1], yaaM
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] , ECK0038, JW0036, yaaM, b0037
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): caiTABCDE^[2]
Regulation/Activity
Quick Links
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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], yaaM
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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	0.78 minutes	MG1655: 37839..36271 <gbrowseImage> name=NC_000913:36271..37839 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 42033..40465 <gbrowseImage> name=NC_012967:40465..42033 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 36271..37839 <gbrowseImage> name=NC_012759:36271..37839 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 37839..36271 <gbrowseImage> name=NC_007779:36271..37839 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 37839..36271 <gbrowseImage> name=NC_010473:36271..37839 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: Description	Reference	Availability	Comments
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
caiC(del) (Keio:JW0036)	deletion	deletion		PMID:16738554	Shigen CGSC8352^[5]
caiC750(del)::kan				PMID:16738554	CGSC:100230
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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
JW0036	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGATAGAGGTGCAATGGATAT Primer 2:CCTTTCAGATTCTTTCTAATTAT
22B12	Kohara Phage	Genobase	PMID:3038334
2F7	Kohara Phage	Genobase	PMID:3038334
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.

Database	Accession	Notes
EcoCyc	EcoCyc:EG11558	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11558	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001511	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:944886	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1519	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000133	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	CaiC
Synonyms	predicted crotonobetaine CoA ligase:carnitine CoA ligase^[1], B0037^[2]^[1], YaaM^[2]^[1], CaiC^[2]^[1] , ECK0038, JW0036, yaaM, b0037
Product description	CAIC^[2]^[3] Crotonobetain/carnitine-CoA ligase^[4]
EC number (for enzymes)	6.3.2.-^[1]
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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:0005737	cytoplasm				C	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0008152	metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000873	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-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.

Compartment	Description	Evidence	Reference/Source	Notes
plasma membrane			From EcoCyc^[3]
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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 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.

Type	Residues	Description	Notes	References
Domain	39..451	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=caiC 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:221800780	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000133	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P31552	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11558	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11558	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:944886	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001511	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:944886	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1519	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	35	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
Protein	E. coli K-12 MG1655	8	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	14^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)
caiTABCDE
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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_000913:37819..37859 source=MG1655 flip=1 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: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 Name	Resource Type	Description	Source	Notes
	GFP Fusion	Intergenic region (37768..37914) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ02; Well:C7^[7]
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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.

Database	Accession	Notes
EcoCyc	EcoCyc:EG11558	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1519	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0037
EcoGene	EcoGene:EG11558	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001511	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000133	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
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.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF00501 AMP-binding enzyme
Panther (EcoliWiki Page)	PTHR24096:SF39
Superfamily (EcoliWiki Page)	SUPERFAMILY:56801
EcoCyc	EcoCyc:EG11558	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11558	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001511	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1519	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0000133	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.

↑ ^1.00 ^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)
↑ ^2.0 ^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 ^3.2 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.
↑ ^5.0 ^5.1 ^5.2 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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

caiC:On One Page

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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 caiC Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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