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alkA:On One Page

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Gene Name	alkA (synonyms: ECK2062, b2068, JW2053, aidA)^[1]
Product(s)	AlkA product^[1]: 3-methyl-adenine DNA glycosylase II product, B2068 product, AidA product
Description	3-methyl-adenine DNA glycosylase II, inducible^[2]^[3]
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): alkA^[2], OP00002
Regulation/Activity
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Notes

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Gene

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Nomenclature

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Standard name	alkA
Mnemonic
Synonyms	ECK2062, b2068, JW2053, aidA^[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	46.23 minutes, 46.23 minutes	MG1655: 2145564..2144716	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
W3110		W3110: 2149677..2148829	GBrowse(W3110)	FASTA Dump
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Strain

Map location

Genome coordinates

Genome browsers

Sequence links

MG1655

46.23 minutes, 46.23 minutes

MG1655: 2145564..2144716
gbrowse_img.php?coord=2143716..2146564&genome=ecoli&name=MG1655&trackset=0&width=300&.png

EcoCyc

GBrowse(MG1655)

W3110

W3110: 2149677..2148829
gbrowse_img.php?coord=2147829..2150677&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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Alleles and Phenotypes

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Allele	Nt change(s)	AA change(s)	Reference	Availability
ΔalkA (Keio:JW2053)	deletion	deletion	PMID:16738554^[4]	Shigen CGSC9686^[5]
ΔalkA766::kan			PMID:16738554^[4]	CGSC:99966
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Notes

Genetic Resources

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Resource	Resource Type	Source	Notes/Reference
JW2053	Plasmid clone	Shigen	PMID:16769691^[6] Status:Clone OK Primer 1:GCCTATACCCTGAACTGGCAGCC Primer 2:CCTGCTTCGTCTGGTTGCCAGCC
zef-3129::Tn10	Linked marker	CAG12099 = CGSC7397^[5]	est. P1 cotransduction: 4% ^[7] Synonyms:zee-3129::Tn10
zbd-3104::Tn10	Linked marker	CAG12021 = CGSC7344^[5]	est. P1 cotransduction: 29% ^[7] Synonyms:zbc-3105::Tn10, zbd-3105::Tn10
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Notes

Accessions in Other Databases

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:EG11222
EchoBASE (EcoliWiki Page)	EchoBASE:EB1204
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b2068
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C2595
EcoGene (EcoliWiki Page)	EcoGene:EG11222
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:ALKA
CGSC (EcoliWiki Page)	CGSC:1035
ASAP (EcoliWikiPage)	ASAP:ABE-0006848
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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	AlkA
Synonyms	3-methyl-adenine DNA glycosylase II^[1], B2068^[2]^[1], AidA^[2]^[1], AlkA^[2]^[1]
Product description	3-methyl-adenine DNA glycosylase II, inducible^[2]^[3]
EC number (for enzymes)	3.2.2.21^[1]
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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:0006281	DNA repair	GO_REF:0000002 GO_REF:0000002 GO_REF:0000004	IEA: Inferred from Electronic Annotation	InterPro:IPR000035 InterPro:IPR011257 SP_KW:KW-0234	P	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0003824	catalytic activity	GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011257	F	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0003905	alkylbase DNA N-glycosylase activity	GO_REF:0000002 GO_REF:0000003	IEA: Inferred from Electronic Annotation	InterPro:IPR000035 EC:3.2.2.21	F	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0003677	DNA binding	GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR012294	F	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0006284	base-excision repair	GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003265	P	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0006974	response to DNA damage stimulus	GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0227	P	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0016787	hydrolase activity	GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0378	F	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0005515	protein binding	PMID:15690043^[9]	IPI: Inferred from Physical Interaction	UniProtKB:P06959	F	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0005737	cytoplasm				C	Seeded from EcoCyc 11.1^[3].	required fields missing
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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 MYTLNWQPPY DWSWMLGFLA ARAVSSVETV ADSYYARSLA VGEYRGVVTA IPDIARHTLH INLSAGLEPV AAECLAKMSR LFDLQCNPQI VNGALGRLGA ARPGLRLPGC VDAFEQGVRA ILGQLVSVAM AAKLTARVAQ LYGERLDDFP EYICFPTPQR LAAADPQALK ALGMPLKRAE ALIHLANAAL EGTLPMTIPG DVEQAMKTLQ TFPGIGRWTA NYFALRGWQA KDVFLPDDYL IKQRFPGMTP AQIRRYAERW KPWRSYALLH IWYTEGWQPD EA
Mol. Wt	31.39 kDa (calc) ^[2]
pI
Extinction coefficient	67380 - 67880 (calc based on 12 Y, 9 W, and 4 C residues)
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Domains/Motifs/Modification Sites

Type	Residues	Description	Notes
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Structure

Structures	Representative Escherichia coli structure: 1MPG\|A 1-282 of 282 residues (E-value: 2.9e-154) (Percent Identity: 100.00) Representative homolog: 2H56\|A (Bacillus halodurans) 43-219 of 282 residues (E-value: 1.2e-06) (Percent Identity: 23.66) 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:
1MPG|A
1-282 of 282 residues (E-value: 2.9e-154) (Percent Identity: 100.00)
Representative homolog:
2H56|A (Bacillus halodurans)
43-219 of 282 residues (E-value: 1.2e-06) (Percent Identity: 23.66)
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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:EG11222-MONOMER
UniProt (EcoliWiki Page)	UniProt:P04395
PFAM (EcoliWiki Page)	PFAM:PF06029
RefSeq (EcoliWiki Page)	RefSeq:NP_416572
ModBase (EcoliWiki Page)	ModBase:P04395
PDB (EcoliWiki Page)	PDB:1MPG
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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)
alkA
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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=2145544..2145584&genome=ecoli&name=MG1655&trackset=Genes_unlabeled+DNA_unlabeled+flip&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:b2068 (EcoliWiki Page)	Summary of data for alkA from multiple microarray studies
microarray	GEO Profiles:b2068 (EcoliWiki Page)	NCBI GEO profiles for alkA
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Expression Resources

Resource Name	Resource Type	Description	Source	Notes
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Notes

Accessions Related to alkA Expression

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:EG11222
EchoBASE (EcoliWiki Page)	EchoBASE:EB1204
EcoliGenExpDB (EcoliWiki Page)	GenExpDB:b2068
EcoGene (EcoliWiki Page)	EcoGene:EG11222
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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
Anopheles gambiae	ENSANGP00000002170 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q688W2 (score: 1.000; bootstrap: 100%) Q9XHW2 (score: 0.423) Q688U5 (score: 0.423) Q656W2 (score: 0.164)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAPB24D34c (score: 1.000; bootstrap: 100%) SPBC23G71 (score: 0.287)	From Inparanoid:20070104
Shigella flexneri	ALKA	From SHIGELLACYC
E. coli O157	ALKA	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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Database	Accession	Notes
PFAM (EcoliWiki Page)	PFAM:PF06029
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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 ^1.6 ^1.7 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 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 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
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ 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
↑ ^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 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ Butland G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433: 531-7 PubMed EcoliWiki page

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Retrieved from "http://ecoliwiki.net/colipedia/index.php/alkA:On_One_Page"

alkA:On One Page

From EcoliWiki

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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 alkA Expression

Notes

Links

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Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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