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aidB:On One Page

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Gene Name	aidB (synonyms: ECK4183, b4187, JW5867)^[1]
Product(s)	AidB product^[1]: isovaleryl CoA dehydrogenase product, B4187 product
Description	EG11811-MONOMER^[2]^[3]
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): aidB^[2], OP00135
Regulation/Activity
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Gene

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Nomenclature

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Standard name	aidB
Mnemonic
Synonyms	ECK4183, b4187, JW5867^[1]
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Notes

Location(s) and DNA Sequence

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Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	95.1 minutes	MG1655: 4412298..4413923	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
W3110		W3110: 4418955..4420580	GBrowse(W3110)	FASTA Dump
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Strain

Map location

Genome coordinates

Genome browsers

Sequence links

MG1655

95.1 minutes

MG1655: 4412298..4413923
gbrowse_img.php?coord=4411298..4414923&genome=ecoli&name=MG1655&trackset=0&width=300&.png

EcoCyc

GBrowse(MG1655)

W3110

W3110: 4418955..4420580
gbrowse_img.php?coord=4417955..4421580&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

GBrowse(W3110)

FASTA Dump

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Notes

Sequence Features

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Feature type	Location	Description
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Notes

Alleles and Phenotypes

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Allele	Nt change(s)	AA change(s)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
ΔaidB (Keio:JW5867)	deletion	deletion			PMID:16738554^[4]	Shigen
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Notes

Genetic Resources

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Resource	Resource Type	Source	Notes/Reference
JW5867	Plasmid clone	Shigen	PMID:16769691^[5] Status:Clone OK Primer 1:GCCCACTGGCAAACTCACACCGT Primer 2:CCaACACACACTCCCCCCGTCGC
cadB2231::Tn10	Linked marker	CAG18488 = CGSC7479^[6]	est. P1 cotransduction: 6% ^[7] Synonyms:zjd-2231::Tn10
cycA30::Tn10	Linked marker	CAG12073 = CGSC7482^[6]	est. P1 cotransduction: 61% ^[7]
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Notes

Accessions in Other Databases

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:EG11811
EchoBASE (EcoliWiki Page)	EchoBASE:EB1759
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4187
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C5275
EcoGene (EcoliWiki Page)	EcoGene:EG11811
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:AIDB
CGSC (EcoliWiki Page)	CGSC:18553
ASAP (EcoliWikiPage)	ASAP:ABE-0013701
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Links

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Name	URL	Comments
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Product(s)

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Nomenclature

Standard name	AidB product
Synonyms	isovaleryl CoA dehydrogenase product^[1], B4187 product^[2]^[1], AidB product^[2]^[1]
Product description	EG11811-MONOMER^[2]^[3]
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.

Qualifier	GO ID	GO term name	Reference(s)	Evidence Code	with/from	Aspect	Notes	Status
	GO:0016627	oxidoreductase activity, acting on the CH-CH group of donors	GO_REF:0000002 GO_REF:0000002 GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006090 InterPro:IPR009075 InterPro:IPR009100	F	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0016491	oxidoreductase activity	GO_REF:0000002 GO_REF:0000004	IEA: Inferred from Electronic Annotation	InterPro:IPR013764 SP_KW:KW-0560	F	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0008152	metabolic process	GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR009100	P	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0003995	acyl-CoA dehydrogenase activity	GO_REF:0000002 GO_REF:0000002 GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006089 InterPro:IPR006091 InterPro:IPR006092	F	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0003677	DNA binding	PMID:16352838^[9]	IPI: Inferred from Physical Interaction		F	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0006281	DNA repair	PMID:16352838^[9]	NR		P	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0006307	DNA dealkylation	PMID:16352838^[9]	NR		P	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0006950	response to stress	PMID:6330740^[10]	IEP: Inferred from Expression Pattern		P	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0008470	isovaleryl-CoA dehydrogenase activity	PMID:16352838^[9]	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc 12.5 ^[8]	complete
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Interactions

Partner Type	Partner	Notes	References
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Notes

Localization

Compartment	Description	Evidence	Notes
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Notes

Structure and Physical Properties

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Physical Properties

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
Mol. Wt	60.59 kDa (calc) ^[2]
pI
Extinction coefficient	75400 - 76900 (calc based on 10 Y, 11 W, and 12 C residues)
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Domains/Motifs/Modification Sites

Type	Residues	Description	Notes
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Structure

Structures	Representative Escherichia coli structure: 3DJL\|A 1-541 of 546 residues (E-value: 1.1e-296) (Percent Identity: 99.82) Representative homolog: 2EBA\|A (Thermus thermophilus) 122-373 of 546 residues (E-value: 1.1e-08) (Percent Identity: 27.55) View all other structures.
Models	View models at: EcoliPredict ModBase PSI-PRED Protein Quaternary Structure (PQS) Genomes TO Protein (GTOP)
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Structures

Representative Escherichia coli structure:
3DJL|A
1-541 of 546 residues (E-value: 1.1e-296) (Percent Identity: 99.82)
Representative homolog:
2EBA|A (Thermus thermophilus)
122-373 of 546 residues (E-value: 1.1e-08) (Percent Identity: 27.55)
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Models

View models at:

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Notes

Gene Product Resources

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Resource type	Source	Notes/Reference
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Notes

Accessions in Other Databases

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:EG11811-MONOMER
UniProt (EcoliWiki Page)	UniProt:P33224
PFAM (EcoliWiki Page)	PFAM:PF02771
RefSeq (EcoliWiki Page)	RefSeq:NP_418608
ModBase (EcoliWiki Page)	ModBase:P33224
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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.

Transcription and Transcriptional Regulation

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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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gbrowse_img.php?coord=4412278..4412318&genome=ecoli&name=MG1655&trackset=Genes_unlabeled+DNA_unlabeled&width=400&.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

Allele Name	Mutation	Phenotype	Reference
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Expression Studies

Type	Reference	Notes
microarray	GenExpDB:b4187 (EcoliWiki Page)	Summary of data for aidB from multiple microarray studies
microarray	GEO Profiles:b4187 (EcoliWiki Page)	NCBI GEO profiles for aidB
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Expression Resources

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^[11]
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Notes

Accessions Related to aidB Expression

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:EG11811
EchoBASE (EcoliWiki Page)	EchoBASE:EB1759
EcoliGenExpDB (EcoliWiki Page)	GenExpDB:b4187
EcoGene (EcoliWiki Page)	EcoGene:EG11811
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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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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

Notes

Families

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Database	Accession	Notes
PFAM (EcoliWiki Page)	PFAM:PF02771
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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.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ Baba T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol Syst Biol 2: 2006.0008 PubMed EcoliWiki page
↑ Kitagawa M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (A Complete Set of E. coli K-12 ORF Archive): Unique Resources for Biological Research. DNA Res 12: 291-9 PubMed EcoliWiki page
↑ ^6.0 ^6.1 CGSC: The Coli Genetics Stock Center
↑ ^7.0 ^7.1 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).
↑ ^8.0 ^8.1 ^8.2 ^8.3 ^8.4 ^8.5 ^8.6 ^8.7 ^8.8 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^9.0 ^9.1 ^9.2 ^9.3 Rohankhedkar MS et al. (2006) The AidB component of the Escherichia coli adaptive response to alkylating agents is a flavin-containing, DNA-binding protein. J Bacteriol 188: 223-30 PubMed EcoliWiki page
↑ Volkert MR & Nguyen DC (1984) Induction of specific Escherichia coli genes by sublethal treatments with alkylating agents. Proc Natl Acad Sci U S A 81: 4110-4 PubMed EcoliWiki page
↑ 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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Retrieved from "http://ecoliwiki.net/colipedia/index.php/aidB:On_One_Page"

aidB:On One Page

From EcoliWiki

Quickview

Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Categories

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Categories

Expression

Overview

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to aidB Expression

Notes

Links

Categories

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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