aidB: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

aidB

Gene Synonym(s)

ECK4183, b4187, JW5867[1], JW5867

Product Desc.

EG11811- Flavin-containing, DNA binding protein; low level isovaleryl CoA dehydrogenase activity; Ada-regulated adaptive response to DNA methylation damage[2]

Product Synonyms(s)

isovaleryl CoA dehydrogenase[1], B4187[3][1], AidB[3][1] , ECK4183, JW5867, b4187

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): aidB[3], OP00135

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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Induced by anaerobiosis and acetate. Overexpression reduces nitrosoguanidine-induced mutagenesis.[2]



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

aidB

Mnemonic

Alkylating agent induced

Synonyms

ECK4183, b4187, JW5867[1], JW5867

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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

95.1 minutes 

MG1655: 4412298..4413923
<gbrowseImage> name=NC_000913:4412298..4413923 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4392430..4394055
<gbrowseImage> name=NC_012967:4392430..4394055 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4351033..4352658
<gbrowseImage> name=NC_012759:4351033..4352658 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4418955..4420580
<gbrowseImage> name=NC_007779:4418955..4420580 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4512660..4514285
<gbrowseImage> name=NC_010473:4512660..4514285 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

ΔaidB (Keio:JW5867)

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

JW5867

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCACTGGCAAACTCACACCGT

Primer 2:CCaACACACACTCCCCCCGTCGC

6G4

Kohara Phage

Genobase

PMID:3038334

1G10

Kohara Phage

Genobase

PMID:3038334

cadB2231::Tn10

Linked marker

CAG18488 = CGSC7479[4]

est. P1 cotransduction: 6% [5]
Synonyms:zjd-2231::Tn10

cycA30::Tn10

Linked marker

CAG12073 = CGSC7482[4]

est. P1 cotransduction: 61% [5]

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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:EG11811

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11811

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001745

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948710

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1759

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013701

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

AidB

Synonyms

isovaleryl CoA dehydrogenase[1], B4187[3][1], AidB[3][1] , ECK4183, JW5867, b4187

Product description

EG11811- Flavin-containing, DNA binding protein; low level isovaleryl CoA dehydrogenase activity; Ada-regulated adaptive response to DNA methylation damage[2]

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:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006089

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006090

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006091

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR009075

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR009100

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR013764

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

GO:0005515

protein binding

PMID:18829440

IPI: Inferred from Physical Interaction

EcoliWiki:aidB


F

AidB is a homotetramer (Figure 2).

complete

GO:0003677

DNA binding

PMID:18829440

IPI: Inferred from Physical Interaction

F

Missing: with/from

GO:0050660

FAD binding

PMID:18829440

IPI: Inferred from Physical Interaction

F

Missing: with/from

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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

aceF

PMID:15690043

Experiment(s):EBI-881555, EBI-888995

Protein

dnaK

PMID:15690043

Experiment(s):EBI-881555, EBI-888995

Protein

groL

PMID:15690043

Experiment(s):EBI-881555, EBI-888995

Protein

hldD

PMID:15690043

Experiment(s):EBI-881555

Protein

rplC

PMID:15690043

Experiment(s):EBI-881555, EBI-888995

Protein

rpsD

PMID:15690043

Experiment(s):EBI-881555

Protein

rplA

PMID:15690043

Experiment(s):EBI-888995

Protein

rplM

PMID:15690043

Experiment(s):EBI-888995

Protein

rplS

PMID:15690043

Experiment(s):EBI-888995

Protein

rplU

PMID:15690043

Experiment(s):EBI-888995

Protein

rplV

PMID:15690043

Experiment(s):EBI-888995

Protein

rpmB

PMID:15690043

Experiment(s):EBI-888995

Protein

rpsB

PMID:15690043

Experiment(s):EBI-888995

Protein

rpsE

PMID:15690043

Experiment(s):EBI-888995

Protein

rpsF

PMID:15690043

Experiment(s):EBI-888995

Protein

rpsG

PMID:15690043

Experiment(s):EBI-888995

Protein

rpsL

PMID:15690043

Experiment(s):EBI-888995

Protein

rpsN

PMID:15690043

Experiment(s):EBI-888995

Protein

rpsS

PMID:15690043

Experiment(s):EBI-888995

Protein

rpsT

PMID:15690043

Experiment(s):EBI-888995

Protein

yhbY

PMID:15690043

Experiment(s):EBI-888995

Protein

yjgD

PMID:15690043

Experiment(s):EBI-888995

Protein

groL

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):17.053160

Protein

rpsL

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsS

PMID:19402753

LCMS(ID Probability):99.6

Protein

rraB

PMID:19402753

LCMS(ID Probability):99.6

Protein

groS

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):27.610802

Protein

rfaD

PMID:19402753

MALDI(Z-score):38.923930

Protein

rplU

PMID:19402753

LCMS(ID Probability):99.4

Protein

rpsT

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsN

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplA

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):5.981968

Protein

rpsF

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpmB

PMID:19402753

LCMS(ID Probability):99.6

Protein

rplS

PMID:19402753

LCMS(ID Probability):99.6

Protein

rpsD

PMID:19402753

MALDI(Z-score):18.402235

Protein

rplM

PMID:19402753

LCMS(ID Probability):99.6

Protein

yhbY

PMID:19402753

LCMS(ID Probability):99.6

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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
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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 

MEGDTVHWQT HTVFNQPIPL NNSNLYLSDG ALCEAVTREG AGWDSDFLAS IGQQLGTAES
LELGRLANVN PPELLRYDAQ GRRLDDVRFH PAWHLLMQAL CTNRVHNLAW EEDARSGAFV
ARAARFMLHA QVEAGSLCPI TMTFAATPLL LQMLPAPFQD WTTPLLSDRY DSHLLPGGQK
RGLLIGMGMT EKQGGSDVMS NTTRAERLED GSYRLVGHKW FFSVPQSDAH LVLAQTAGGL
SCFFVPRFLP DGQRNAIRLE RLKDKLGNRS NASCEVEFQD AIGWLLGLEG EGIRLILKMG
GMTRFDCALG SHAMMRRAFS LAIYHAHQRH VFGNPLIQQP LMRHVLSRMA LQLEGQTALL
FRLARAWDRR ADAKEALWAR LFTPAAKFVI CKRGMPFVAE AMEVLGGIGY CEESELPRLY
REMPVNSIWE GSGNIMCLDV LRVLNKQAGV YDLLSEAFVE VKGQDRYFDR AVRRLQQQLR
KPAEELGREI THQLFLLGCG AQMLKYASPP MAQAWCQVML DTRGGVRLSE QIQNDLLLRA
TGGVCV
Length

546

Mol. Wt

61.092 kDa

pI

7.5 (calculated)

Extinction coefficient

75,400 - 76,900 (calc based on 10 Y, 11 W, and 12 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

285..440

PF00441 Acyl-CoA dehydrogenase, C-terminal domain

PMID:19920124

Domain

181..233

PF02770 Acyl-CoA dehydrogenase, middle domain

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=aidB 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:162135915

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948710

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013701

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P33224

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11811

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11811

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948710

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001745

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1759

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

Ecoli K-12

26.165+/-0.13

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.048923077

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by RNA_Seq

PMID:20671182

Protein

E. coli K-12 MG1655

19

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

150

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

12a

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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<protect>

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

Transcription unit(s)

aidB

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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_000913:4412278..4412318 source=MG1655 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:b4187 (EcoliWiki Page)

NCBI GEO profiles for aidB

microarray

GenExpDB:b4187 (EcoliWiki Page)

Summary of data for aidB 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 (4411677..4411859) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ12; Well:H6[6]

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Notes

Accessions Related to aidB Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11811

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1759

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4187

EcoGene

EcoGene:EG11811

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001745

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013701

Escherichia coli str. K-12 substr. MG1655

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Notes

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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

  • WBGene00037799 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00012860 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000019331 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0190990 (score: 1.000; bootstrap: 100%)
  • DDB0190988 (score: 0.348)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000013032 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000011477 (score: 1.000; bootstrap: 99%)
  • ENSMODP00000011343 (score: 0.443)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000155002 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00029554001 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000001166 (score: 1.000; bootstrap: 99%)

From Inparanoid:20070104

E. coli O157

AIDB

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)

PF00441 Acyl-CoA dehydrogenase, C-terminal domain

Pfam (EcoliWiki Page)

PF02770 Acyl-CoA dehydrogenase, middle domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:47203

Panther (EcoliWiki Page)

PTHR10909:SF177

Superfamily (EcoliWiki Page)

SUPERFAMILY:56645

EcoCyc

EcoCyc:EG11811

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11811

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001745

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1759

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013701

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. ↑ 1.0 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 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  3. ↑ 3.0 3.1 3.2 3.3 3.4 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 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).
  6. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

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