betA:On One Page

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

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Standard Name

betA

Gene Synonym(s)

ECK0309, b0311, JW0303[1], JW0303

Product Desc.

CHD[2][3]

Choline dehydrogenase, oxygen-dependent; bet genes confer protection against osmotic stress by making the osmoprotectant glycine betaine from choline[4]

Product Synonyms(s)

choline dehydrogenase, a flavoprotein[1], B0311[2][1], BetA[2][1] , ECK0309, JW0303, b0311

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): betIBA[2], OP00155

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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The bet genes are induced by choline, oxygen, and osmotic stress. ArcA regulon.[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

betA

Mnemonic

Betaine

Synonyms

ECK0309, b0311, JW0303[1], JW0303

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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

7 minutes 

MG1655: 326471..324801
<gbrowseImage> name=NC_000913:324801..326471 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 299896..298226
<gbrowseImage> name=NC_012967:298226..299896 source=REL606 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 326471..324801
<gbrowseImage> name=NC_007779:324801..326471 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 302021..300351
<gbrowseImage> name=NC_010473:300351..302021 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
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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

betA(del) (Keio:JW0303)

deletion

deletion

PMID:16738554

Shigen

CGSC8503[5]

betA753(del)::kan

PMID:16738554

CGSC:100174


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Notes

Genetic Interactions

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<protect>

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

JW0303

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCAATTTGACTACATCATTAT

Primer 2:CCTTTTTTCGCTCTCACCGGCAT

9G4

Kohara Phage

Genobase

PMID:3038334

6E6

Kohara Phage

Genobase

PMID:3038334

proA81::Tn10

Linked marker

CAG18447 = CGSC7330[5]

est. P1 cotransduction: 3% [6]

lacI3042::Tn10

Linked marker

CAG18439 = CGSC7334[5]

est. P1 cotransduction: 17% [6]
Synonyms:lacI42::Tn10 nnnCAG18439 also carries lacZ118(0c) (CGSC).

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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:EG10109

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10109

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000105

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945716

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0107

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001070

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

BetA

Synonyms

choline dehydrogenase, a flavoprotein[1], B0311[2][1], BetA[2][1] , ECK0309, JW0303, b0311

Product description

CHD[2][3]

Choline dehydrogenase, oxygen-dependent; bet genes confer protection against osmotic stress by making the osmoprotectant glycine betaine from choline[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:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-1003

C

Seeded from EcoCyc (v14.0)

complete

GO:0006066

alcohol metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012132

P

Seeded from EcoCyc (v14.0)

complete

GO:0006950

response to stress

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0346

P

Seeded from EcoCyc (v14.0)

complete

GO:0008812

choline dehydrogenase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00750

F

Seeded from EcoCyc (v14.0)

complete

GO:0008812

choline dehydrogenase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011533

F

Seeded from EcoCyc (v14.0)

complete

GO:0008812

choline dehydrogenase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:1.1.99.1

F

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0472

C

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

F

Seeded from EcoCyc (v14.0)

complete

GO:0016614

oxidoreductase activity, acting on CH-OH group of donors

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000172

F

Seeded from EcoCyc (v14.0)

complete

GO:0016614

oxidoreductase activity, acting on CH-OH group of donors

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007867

F

Seeded from EcoCyc (v14.0)

complete

GO:0016614

oxidoreductase activity, acting on CH-OH group of donors

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012132

F

Seeded from EcoCyc (v14.0)

complete

GO:0019285

glycine betaine biosynthetic process from choline

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00750

P

Seeded from EcoCyc (v14.0)

complete

GO:0019285

glycine betaine biosynthetic process from choline

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011533

P

Seeded from EcoCyc (v14.0)

complete

GO:0019898

extrinsic to membrane

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-9903

C

Seeded from EcoCyc (v14.0)

complete

GO:0050660

FAD binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000172

F

Seeded from EcoCyc (v14.0)

complete

GO:0050660

FAD binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012132

F

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011533

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

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 Notes References Evidence

Protein

phnN

PMID:16606699

Experiment(s):EBI-1136170

Protein

rimJ

PMID:16606699

Experiment(s):EBI-1136170

Protein

dnaK

PMID:16606699

Experiment(s):EBI-1136170

Protein

hemG

PMID:16606699

Experiment(s):EBI-1136170

Protein

groL

PMID:16606699

Experiment(s):EBI-1136170

Protein

surE

PMID:16606699

Experiment(s):EBI-1143801
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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 

MQFDYIIIGA GSAGNVLATR LTEDPNTSVL LLEAGGPDYR FDFRTQMPAA LAFPLQGKRY
NWAYETEPEP FMNNRRMECG RGKGLGGSSL INGMCYIRGN ALDLDNWAQE PGLENWSYLD
CLPYYRKAET RDMGENDYHG GDGPVSVTTS KPGVNPLFEA MIEAGVQAGY PRTDDLNGYQ
QEGFGPMDRT VTPQGRRAST ARGYLDQAKS RPNLTIRTHA MTDHIIFDGK RAVGVEWLEG
DSTIPTRATA NKEVLLCAGA IASPQILQRS GVGNAELLAE FDIPLVHELP GVGENLQDHL
EMYLQYECKE PVSLYPALQW WNQPKIGAEW LFGGTGVGAS NHFEAGGFIR SREEFAWPNI
QYHFLPVAIN YNGSNAVKEH GFQCHVGSMR SPSRGHVRIK SRDPHQHPAI LFNYMSHEQD
WQEFRDAIRI TREIMHQPAL DQYRGREISP GVECQTDEQL DEFVRNHAET AFHPCGTCKM
GYDEMSVVDG EGRVHGLEGL RVVDASIMPQ IITGNLNATT IMIGEKIADM IRGQEALPRS
TAGYFVANGM PVRAKK
Length

556

Mol. Wt

61.877 kDa

pI

5.6 (calculated)

Extinction coefficient

80,790 - 81,915 (calc based on 21 Y, 9 W, and 9 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

391..527

PF05199 GMC oxidoreductase

PMID:19920124

Domain

3..301

PF00732 GMC oxidoreductase

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=betA 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:16128296

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945716

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001070

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P17444

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10109

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10109

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945716

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000105

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0107

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

131

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

67

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

91

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

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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)

betIBA

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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_000913:326451..326491 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:b0311 (EcoliWiki Page)

NCBI GEO profiles for betA

microarray

GenExpDB:b0311 (EcoliWiki Page)

Summary of data for betA 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
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Notes

Accessions Related to betA Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG10109

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0107

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0311

EcoGene

EcoGene:EG10109

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000105

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001070

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

Anopheles gambiae

  • ENSANGP00000024305 (score: 1.000; bootstrap: 98%)
  • ENSANGP00000015190 (score: 0.448)
  • ENSANGP00000012795 (score: 0.221)
  • ENSANGP00000022822 (score: 0.219)
  • ENSANGP00000015865 (score: 0.206)
  • ENSANGP00000002989 (score: 0.205)
  • ENSANGP00000025265 (score: 0.204)
  • ENSANGP00000005507 (score: 0.178)
  • ENSANGP00000012169 (score: 0.150)
  • ENSANGP00000005577 (score: 0.133)
  • ENSANGP00000015052 (score: 0.132)
  • ENSANGP00000027087 (score: 0.127)
  • ENSANGP00000016488 (score: 0.101)
  • ENSANGP00000005557 (score: 0.091)
  • ENSANGP00000005452 (score: 0.086)
  • ENSANGP00000026044 (score: 0.083)
  • ENSANGP00000002145 (score: 0.083)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000013035 (score: 1.000; bootstrap: 98%)
  • ENSAPMP00000002616 (score: 0.375)
  • ENSAPMP00000012876 (score: 0.121)
  • ENSAPMP00000012972 (score: 0.095)
  • ENSAPMP00000012902 (score: 0.093)
  • ENSAPMP00000029877 (score: 0.080)
  • ENSAPMP00000006409 (score: 0.078)
  • ENSAPMP00000032879 (score: 0.072)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT1G12570 (score: 1.000; bootstrap: 100%)
  • AT5G51950 (score: 0.480)
  • AT3G56060 (score: 0.468)
  • AT1G72970 (score: 0.417)
  • AT5G51930 (score: 0.411)
  • AT1G73050 (score: 0.343)
  • AT1G14185 (score: 0.240)
  • AT1G14190 (score: 0.237)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000013227 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00032297 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00007917 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000012205 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000007524 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0187375 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0030592 (score: 1.000; bootstrap: 99%)
  • FBgn0030598 (score: 0.334)
  • FBgn0030590 (score: 0.327)
  • FBgn0030591 (score: 0.278)
  • FBgn0039415 (score: 0.183)
  • FBgn0030596 (score: 0.154)
  • FBgn0001112 (score: 0.153)
  • FBgn0030588 (score: 0.149)
  • FBgn0030589 (score: 0.131)
  • FBgn0030587 (score: 0.108)
  • FBgn0030586 (score: 0.099)
  • FBgn0030594 (score: 0.061)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA21838-PA (score: 1.000; bootstrap: 97%)
  • GA21849-PA (score: 0.494)
  • GA21847-PA (score: 0.396)
  • GA19386-PA (score: 0.256)
  • GA11607-PA (score: 0.208)
  • GA11047-PA (score: 0.198)
  • GA21852-PA (score: 0.174)
  • GA21850-PA (score: 0.162)
  • GA11686-PA (score: 0.160)
  • GA21853-PA (score: 0.136)
  • GA21846-PA (score: 0.079)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000008595 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000319851 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000025315 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000015674 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Mus musculus

  • MGI:1860776 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Oryza gramene

  • Q6EPQ2 (score: 1.000; bootstrap: 79%)
  • Q6K4D7 (score: 1.000; bootstrap: 80%)
  • Q6Z290 (score: 0.731)
  • Q7XTZ0 (score: 0.636)
  • Q8H094 (score: 0.507)
  • Q8H052 (score: 0.504)
  • Q9M4V5 (score: 0.494)
  • Q67W87 (score: 0.263)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000025961 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000021407 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000172206 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00022584001 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000001316 (score: 1.000; bootstrap: 50%)

From Inparanoid:20070104

E. coli O157

BETA

From ECOO157CYC

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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)

PF05199 GMC oxidoreductase

Pfam (EcoliWiki Page)

PF00732 GMC oxidoreductase

Superfamily (EcoliWiki Page)

SUPERFAMILY:51905

Panther (EcoliWiki Page)

PTHR11552:SF26

Superfamily (EcoliWiki Page)

SUPERFAMILY:54373

EcoCyc

EcoCyc:EG10109

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10109

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000105

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0107

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001070

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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  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 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 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).

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