caiB:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

Quickview

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Standard Name

caiB

Gene Synonym(s)

ECK0039, b0038, JW0037, yaaN[1], yaaN

Product Desc.

CaiB[2][3];

Component of γ-butyrobetainyl-CoA:carnitine CoA transferase[2][3]

Carnitine dehydratase; crotonobetaine reductase, CI component[4]

Product Synonyms(s)

crotonobetainyl CoA:carnitine CoA transferase[1], B0038[2][1], YaaN[2][1], CaiB[2][1] , ECK0039, JW0037, yaaN, b0038

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): caiTABCDE[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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Notes

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Uses gamma-butyrobetainyl-CoA as co-factor.[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

caiB

Mnemonic

Carnitine inducible

Synonyms

ECK0039, b0038, JW0037, yaaN[1], yaaN

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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

0.82 minutes 

MG1655: 39115..37898
<gbrowseImage> name=NC_000913:37898..39115 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 37898..39115
<gbrowseImage> name=NC_012759:37898..39115 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 39115..37898
<gbrowseImage> name=NC_007779:37898..39115 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 39115..37898
<gbrowseImage> name=NC_010473:37898..39115 source=DH10B preset=GeneLocation </gbrowseImage>

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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

Coding Start (SO:0000323)

MG1655

37898

Edman degradation

PMID:8188598
PMID:10209289


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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

caiBT302A

T302A

(in strain: O44:K74)

Strain variation; seeded from UniProt:P31572

caiBV187A

V187A

(in strain: O44:K74)

Strain variation; seeded from UniProt:P31572

caiB(del) (Keio:JW0037)

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

JW0037

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCGATCATCTACCCATGCCGAA

Primer 2:CCGTCCTCAACTTTGGCCAGACC

22B12

Kohara Phage

Genobase

PMID:3038334

2F7

Kohara Phage

Genobase

PMID:3038334

4A3

Kohara Phage

Genobase

PMID:3038334

carB96::Tn10

Linked marker

CAG12093 = CGSC7322[5]

est. P1 cotransduction: 83% [6]
Synonyms:car-96::Tn10

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[5]

est. P1 cotransduction: 13% [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:EG11559

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11559

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001512

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948997

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1520

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000136

Escherichia coli str. K-12 substr. MG1655

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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

CaiB

Synonyms

crotonobetainyl CoA:carnitine CoA transferase[1], B0038[2][1], YaaN[2][1], CaiB[2][1] , ECK0039, JW0037, yaaN, b0038

Product description

CaiB[2][3];

Component of γ-butyrobetainyl-CoA:carnitine CoA transferase[2][3]

Carnitine dehydratase; crotonobetaine reductase, CI component[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:0009310

amine catabolic process

P

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003673

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01050

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

Seeded from EcoCyc (v14.0)

complete

GO:0008152

metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003673

P

Seeded from EcoCyc (v14.0)

complete

GO:0008410

CoA-transferase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01050

F

Seeded from EcoCyc (v14.0)

complete

GO:0016740

transferase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0808

F

Seeded from EcoCyc (v14.0)

complete

GO:0008735

carnitine dehydratase activity

PMID:8188598

EXP: Inferred from Experiment

F

complete

GO:0042413

carnitine catabolic process

PMID:8188598

EXP: Inferred from Experiment

P

complete

GO:0008735

carnitine dehydratase activity

PMID:7815937

EXP: Inferred from Experiment

F

complete

Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

Subunits of γ-butyrobetainyl-CoA:carnitine CoA transferase

could be indirect

Protein

dld

PMID:16606699

Experiment(s):EBI-1135397

Protein

rhsD

PMID:16606699

Experiment(s):EBI-1135397

Protein

sdhA

PMID:16606699

Experiment(s):EBI-1135397

Protein

rhsA

PMID:16606699

Experiment(s):EBI-1135397

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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

cytoplasm

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

MDHLPMPKFG PLAGLRVVFS GIEIAGPFAG QMFAEWGAEV IWIENVAWAD TIRVQPNYPQ
LSRRNLHALS LNIFKDEGRE AFLKLMETTD IFIEASKGPA FARRGITDEV LWQHNPKLVI
AHLSGFGQYG TEEYTNLPAY NTIAQAFSGY LIQNGDVDQP MPAFPYTADY FSGLTATTAA
LAALHKVRET GKGESIDIAM YEVMLRMGQY FMMDYFNGGE MCPRMSKGKD PYYAGCGLYK
CADGYIVMEL VGITQIEECF KDIGLAHLLG TPEIPEGTQL IHRIECPYGP LVEEKLDAWL
ATHTIAEVKE RFAELNIACA KVLTVPELES NPQYVARESI TQWQTMDGRT CKGPNIMPKF
KNNPGQIWRG MPSHGMDTAA ILKNIGYSEN DIQELVSKGL AKVED
Length

405

Mol. Wt

45.127 kDa

pI

4.9 (calculated)

Extinction coefficient

63,830 - 64,705 (calc based on 17 Y, 7 W, and 7 C residues)


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

69..258

PF02515 CoA-transferase family III

PMID:19920124

<motif_map/>

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

Structures

<beststructure> gene=caiB 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:16128032

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000136

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P31572

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11559

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11559

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948997

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001512

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948997

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1520

Escherichia coli str. K-12 substr. MG1655

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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

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MG1655

29

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

11

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

6a

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

Notes

Transcription and Transcriptional Regulation

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<protect>

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

caiTABCDE

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_000913:39095..39135 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


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

Type Reference Notes

microarray

GEO Profiles:b0038 (EcoliWiki Page)

NCBI GEO profiles for caiB

microarray

GenExpDB:b0038 (EcoliWiki Page)

Summary of data for caiB from multiple microarray studies


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 caiB Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11559

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1520

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0038

EcoGene

EcoGene:EG11559

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001512

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000136

Escherichia coli str. K-12 substr. MG1655

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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.

Organism Homologs (Statistics) Comments

Caenorhabditis elegans

  • WBGene00014128 (score: 1.000; bootstrap: 100%)
  • WBGene00016034 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000017701 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

CAIB

From SHIGELLACYC

E. coli O157

CAIB

From ECOO157CYC


Do-It-Yourself Web Tools

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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)

PF02515 CoA-transferase family III

Superfamily (EcoliWiki Page)

SUPERFAMILY:89796

EcoCyc

EcoCyc:EG11559

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11559

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001512

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1520

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000136

Escherichia coli str. K-12 substr. MG1655

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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. 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 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 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 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).

Categories

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