dadX:On One Page

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

Quickview

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Standard Name

dadX

Gene Synonym(s)

ECK1178, b1190, JW1179, alnA, alnB, dadB, msuA?[1][2], msuA?

Product Desc.

ALARACECAT[2][3];

Component of alanine racemase 2, PLP-binding[3]

Alanine racemase; homodimeric[4]

Product Synonyms(s)

alanine racemase 2, PLP-binding[1], B1190[2][1], DadB[2][1], AlnB[2][1], AlnA[2][1], DadX[2][1], alanine racemase[2][1] , alnB, dadB, ECK1178, JW1179, msuA?, b1190

Function from GO

<GO_nr />

Knock-Out Phenotype

ΔdadX fails to grow on L-alanine as sole carbon source. No D-alanine auxotrophy except in the double ΔalrΔdadX mutant. Either Alr or DadX supplies sufficient D-alanine for cell wall biosynthesis.

Regulation/Expression

transcription unit(s): dadAX[2], dad

Regulation/Activity

Induced by L-alanine. Converts L- to D-alanine for catabolism.

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

dadX

Mnemonic

D-Amino acid dehydrogenase

Synonyms

ECK1178, b1190, JW1179, alnA, alnB, dadB, msuA?[1][2], msuA?

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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

26.69 minutes 

MG1655: 1238102..1239172
<gbrowseImage> name=NC_000913:1238102..1239172 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1239029..1240099
<gbrowseImage> name=NC_012967:1239029..1240099 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1126823..1127893
<gbrowseImage> name=NC_012759:1126823..1127893 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1240456..1241526
<gbrowseImage> name=NC_007779:1240456..1241526 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1278343..1279413
<gbrowseImage> name=NC_010473:1278343..1279413 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

ΔdadX (Keio:JW1179)

deletion

deletion

PMID:16738554

Shigen
CGSC9085[5]

dadX::Tn5KAN-2 (FB20266)

Insertion at nt 307 in Plus orientation

PMID:15262929

E. coli Genome Project:FB20266

does not contain pKD46

dadB3

PMID:4571807

CGSC:6496

dadX20

PMID:4594607 PMID:6298185

CGSC:79525

dadB21(ts)

temperature sensitive

CGSC:79526

ΔdadX779::kan

PMID:16738554

CGSC:100526


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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

JW1179

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCACCCGTCCGATACAGGCCAG

Primer 2:CCaACCGTCACAACCGGGACGCG

11G8

Kohara Phage

Genobase

PMID:3038334

7C10

Kohara Phage

Genobase

PMID:3038334

fadR13::Tn10

Linked marker

CAG18497 = CGSC7365[5]

est. P1 cotransduction: 88% [6]

oppC506::Tn10

Linked marker

CAG12169 = CGSC7369[5]

est. P1 cotransduction: 3% [6]
Synonyms:zch-506::Tn10, zci-506::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:EG11408

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11408

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001374

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945754

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1380

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003997

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

DadX

Synonyms

alanine racemase 2, PLP-binding[1], B1190[2][1], DadB[2][1], AlnB[2][1], AlnA[2][1], DadX[2][1], alanine racemase[2][1] , alnB, dadB, ECK1178, JW1179, msuA?, b1190

Product description

ALARACECAT[2][3];

Component of alanine racemase 2, PLP-binding[3]

Alanine racemase; homodimeric[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:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR009006

F

Seeded from EcoCyc (v14.0)

complete

GO:0006522

alanine metabolic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01201

P

Seeded from EcoCyc (v14.0)

complete

GO:0006522

alanine metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000821

P

Seeded from EcoCyc (v14.0)

complete

GO:0006522

alanine metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011079

P

Seeded from EcoCyc (v14.0)

complete

GO:0006522

alanine metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020622

P

Seeded from EcoCyc (v14.0)

complete

GO:0008784

alanine racemase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01201

F

Seeded from EcoCyc (v14.0)

complete

GO:0008784

alanine racemase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000821

F

Seeded from EcoCyc (v14.0)

complete

GO:0008784

alanine racemase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011079

F

Seeded from EcoCyc (v14.0)

complete

GO:0008784

alanine racemase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020622

F

Seeded from EcoCyc (v14.0)

complete

GO:0008784

alanine racemase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:5.1.1.1

F

Seeded from EcoCyc (v14.0)

complete

GO:0009252

peptidoglycan biosynthetic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01201

P

Seeded from EcoCyc (v14.0)

complete

GO:0016853

isomerase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0413

F

Seeded from EcoCyc (v14.0)

complete

GO:0030170

pyridoxal phosphate binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01201

F

Seeded from EcoCyc (v14.0)

complete

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

Subunits of alanine racemase 2, PLP-binding

could be indirect

Protein

groL

PMID:16606699

Experiment(s):EBI-1139129

Protein

rplB

PMID:16606699

Experiment(s):EBI-1139129

Protein

gatA

PMID:19402753

LCMS(ID Probability):99.6

Protein

ycfD

PMID:19402753

LCMS(ID Probability):99.6

Protein

groS

PMID:19402753

LCMS(ID Probability):99.6 MALDI(Z-score):19.151211

Protein

dapB

PMID:19402753

LCMS(ID Probability):99.6

Protein

gabD

PMID:19402753

LCMS(ID Probability):99.6

Protein

gcvP

PMID:19402753

LCMS(ID Probability):99.6

Protein

deoA

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

MTRPIQASLD LQALKQNLSI VRQAATHARV WSVVKANAYG HGIERIWSAI GATDGFALLN
LEEAITLRER GWKGPILMLE GFFHAQDLEI YDQHRLTTCV HSNWQLKALQ NARLKAPLDI
YLKVNSGMNR LGFQPDRVLT VWQQLRAMAN VGEMTLMSHF AEAEHPDGIS GAMARIEQAA
EGLECRRSLS NSAATLWHPE AHFDWVRPGI ILYGASPSGQ WRDIANTGLR PVMTLSSEII
GVQTLKAGER VGYGGRYTAR DEQRIGIVAA GYADGYPRHA PTGTPVLVDG VRTMTVGTVS
MDMLAVDLTP CPQAGIGTPV ELWGKEIKID DVAAAAGTVG YELMCALALR VPVVTV
Length

356

Mol. Wt

38.844 kDa

pI

7.1 (calculated)

Extinction coefficient

62,910 - 63,410 (calc based on 9 Y, 9 W, and 4 C residues)


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

232..356

PF00842 Alanine racemase, C-terminal domain

PMID:19920124

Domain

9..217

PF01168 Alanine racemase, N-terminal domain

PMID:19920124

<motif_map/>

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

Structures

<beststructure> gene=dadX 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:16129153

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945754

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003997

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P29012

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11408

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11408

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945754

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001374

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1380

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

10.883+/-0.189

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182

mRNA

Ecoli K-12

0.08317757

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

744

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

54

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

664

molecules/cell/generation

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

Ribosome Profiling

PMID: 24766808

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)

dadAX

Figure courtesy of RegulonDB

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Notes

Expression induced by L-alanine.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:1238082..1238122 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


Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b1190 (EcoliWiki Page)

NCBI GEO profiles for dadX

microarray

GenExpDB:b1190 (EcoliWiki Page)

Summary of data for dadX from multiple microarray studies


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 dadX Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11408

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1380

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1190

EcoGene

EcoGene:EG11408

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001374

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003997

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

Shigella flexneri

DADX

From SHIGELLACYC

E. coli O157

DADX

From ECOO157CYC


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)

PF01168 Alanine racemase, N-terminal domain

Pfam (EcoliWiki Page)

PF00842 Alanine racemase, C-terminal domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:50621

Superfamily (EcoliWiki Page)

SUPERFAMILY:51419

EcoCyc

EcoCyc:EG11408

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11408

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001374

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1380

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003997

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 1.11 1.12 1.13 1.14 1.15 1.16 1.17 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. 2.00 2.01 2.02 2.03 2.04 2.05 2.06 2.07 2.08 2.09 2.10 2.11 2.12 2.13 2.14 2.15 2.16 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 3.3 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).

Categories

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