alkA: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

alkA

Gene Synonym(s)

ECK2062, b2068, JW2053, aidA[1], aidA

Product Desc.

3-methyl-adenine DNA glycosylase II, inducible[2][3]

3-methyl-adenine DNA glycosylase II, inducible; repairs by single-and double-strand excision of 3-methyl adenine[4]

Product Synonyms(s)

3-methyl-adenine DNA glycosylase II[1], B2068[2][1], AidA[2][1], AlkA[2][1] , aidA, ECK2062, JW2053, b2068

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): alkA[2], OP00002

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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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

alkA

Mnemonic

Alkylation

Synonyms

ECK2062, b2068, JW2053, aidA[1], aidA

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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

46.23 minutes, 46.23 minutes 

MG1655: 2145564..2144716
<gbrowseImage> name=NC_000913:2144716..2145564 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2080726..2079878
<gbrowseImage> name=NC_012967:2079878..2080726 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2037199..2038047
<gbrowseImage> name=NC_012759:2037199..2038047 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2149677..2148829
<gbrowseImage> name=NC_007779:2148829..2149677 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2236572..2235724
<gbrowseImage> name=NC_010473:2235724..2236572 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

2144716

Edman degradation

PMID:6094528


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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

alkAD238N

D238N

No catalytic activity, methylmethane sulfonate-sensitive

seeded from UniProt:P04395

alkAD237N

D237N

More than 30% catalytic activity, methylmethane sulfonate-resistant

seeded from UniProt:P04395

alkAQ124A

Q124A

Methylmethane sulfonate-resistant

seeded from UniProt:P04395

alkAW218A

W218A

No catalytic activity, methylmethane sulfonate-sensitive

seeded from UniProt:P04395

ΔalkA (Keio:JW2053)

deletion

deletion

PMID:16738554

Shigen
CGSC9686[5]

ΔalkA766::kan

PMID:16738554

CGSC:99966


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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

JW2053

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTATACCCTGAACTGGCAGCC

Primer 2:CCTGCTTCGTCTGGTTGCCAGCC

2E1

Kohara Phage

Genobase

PMID:3038334

3G4

Kohara Phage

Genobase

PMID:3038334

zef-3129::Tn10

Linked marker

CAG12099 = CGSC7397[5]

est. P1 cotransduction: 4% [6]
Synonyms:zee-3129::Tn10

zbd-3104::Tn10

Linked marker

CAG12021 = CGSC7344[5]

est. P1 cotransduction: 29% [6]
Synonyms:zbc-3105::Tn10, zbd-3105::Tn10

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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:EG11222

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11222

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001200

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947371

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1204

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006848

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

AlkA

Synonyms

3-methyl-adenine DNA glycosylase II[1], B2068[2][1], AidA[2][1], AlkA[2][1] , aidA, ECK2062, JW2053, b2068

Product description

3-methyl-adenine DNA glycosylase II, inducible[2][3]

3-methyl-adenine DNA glycosylase II, inducible; repairs by single-and double-strand excision of 3-methyl adenine[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:0003677

DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012294

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011257

F

Seeded from EcoCyc (v14.0)

complete

GO:0003905

alkylbase DNA N-glycosylase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000035

F

Seeded from EcoCyc (v14.0)

complete

GO:0006284

base-excision repair

PMID:7982966

IDA: Inferred from Direct Assay

P

complete

GO:0003905

alkylbase DNA N-glycosylase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.2.2.21

F

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

PMID:7982966

IDA: Inferred from Direct Assay

P

complete

GO:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000035

P

Seeded from EcoCyc (v14.0)

complete

GO:0003905

alkylbase DNA N-glycosylase activity

PMID:3536857

IDA: Inferred from Direct Assay

F

complete

GO:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011257

P

Seeded from EcoCyc (v14.0)

complete

GO:0006974

response to DNA damage stimulus

PMID:3536857

IMP: Inferred from Mutant Phenotype

P

complete

GO:0006281

DNA repair

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0234

P

Seeded from EcoCyc (v14.0)

complete

GO:0006307

DNA dealkylation involved in DNA repair

PMID:3536857

IMP: Inferred from Mutant Phenotype

P

complete

GO:0006284

base-excision repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003265

P

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

PMID:7982966

IDA: Inferred from Direct Assay

C

complete

GO:0006974

response to DNA damage stimulus

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0227

P

Seeded from EcoCyc (v14.0)

complete

GO:0003905

alkylbase DNA N-glycosylase activity

PMID:7982966

IDA: Inferred from Direct Assay

F

complete

GO:0016787

hydrolase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0378

F

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

aceF

PMID:15690043

Experiment(s):EBI-882436

Protein

xthA

PMID:16606699

Experiment(s):EBI-1141837

Protein

rplE

PMID:16606699

Experiment(s):EBI-1141837

Protein

rpsI

PMID:16606699

Experiment(s):EBI-1141837

Protein

rplD

PMID:16606699

Experiment(s):EBI-1141837

Protein

rpsD

PMID:16606699

Experiment(s):EBI-1141837

Protein

rplA

PMID:16606699

Experiment(s):EBI-1141837

Protein

yhaJ

PMID:16606699

Experiment(s):EBI-1141837

Protein

betI

PMID:16606699

Experiment(s):EBI-1141837

Protein

matC

PMID:16606699

Experiment(s):EBI-1141837

Protein

slyD

PMID:16606699

Experiment(s):EBI-1141837

Protein

rplF

PMID:16606699

Experiment(s):EBI-1141837

Protein

udk

PMID:16606699

Experiment(s):EBI-1141837

Protein

rpsC

PMID:16606699

Experiment(s):EBI-1141837

Protein

rplQ

PMID:16606699

Experiment(s):EBI-1141837

Protein

phnN

PMID:16606699

Experiment(s):EBI-1141837

Protein

nadE

PMID:16606699

Experiment(s):EBI-1141837

Protein

adiA

PMID:19402753

MALDI(Z-score):28.892711

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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 

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
Length

282

Mol. Wt

31.393 kDa

pI

8.3 (calculated)

Extinction coefficient

67,380 - 67,880 (calc based on 12 Y, 9 W, and 4 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

118..263

PF00730 HhH-GPD superfamily base excision DNA repair protein

PMID:19920124

Domain

1..112

PF06029 AlkA N-terminal 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=alkA 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:16130008

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947371

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006848

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P04395

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11222

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11222

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947371

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001200

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1204

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

2.002+/-0.062

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.01120283

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

32

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

37

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

14a

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)

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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<protect><gbrowseImage> name=NC_000913:2145544..2145584 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:b2068 (EcoliWiki Page)

NCBI GEO profiles for alkA

microarray

GenExpDB:b2068 (EcoliWiki Page)

Summary of data for alkA 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 alkA Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11222

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1204

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2068

EcoGene

EcoGene:EG11222

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001200

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006848

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

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

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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)

PF00730 HhH-GPD superfamily base excision DNA repair protein

Superfamily (EcoliWiki Page)

SUPERFAMILY:48150

Superfamily (EcoliWiki Page)

SUPERFAMILY:55945

Pfam (EcoliWiki Page)

PF06029 AlkA N-terminal domain

EcoCyc

EcoCyc:EG11222

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11222

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001200

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1204

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006848

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 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 2.7 2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 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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