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Product(s) |

Expression|

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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.
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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>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1239029..1240099 <gbrowseImage> name=NC_012967:1239029..1240099 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1126823..1127893 <gbrowseImage> name=NC_012759:1126823..1127893 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1240456..1241526 <gbrowseImage> name=NC_007779:1240456..1241526 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1278343..1279413 <gbrowseImage> name=NC_010473:1278343..1279413 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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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: 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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Links

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Name	URL	Comments
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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)	5.1.1.1^[1]
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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
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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	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)
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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	References
Domain	232..356	PF00842 Alanine racemase, C-terminal domain	PMID:19920124
Domain	9..217	PF01168 Alanine racemase, 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=dadX taxon=562,83333 </beststructure>

Models

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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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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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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.

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
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Notes

Transcription and Transcriptional Regulation

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

Transcription unit(s)
dadAX
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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.

</protect>

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

</protect>

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:b1190 (EcoliWiki Page)	NCBI GEO profiles for dadX
microarray	GenExpDB:b1190 (EcoliWiki Page)	Summary of data for dadX 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 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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Name	URL	Comments
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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
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Do-It-Yourself Web Tools

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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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^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)
↑ ^2.00 ^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
↑ ^3.0 ^3.1 ^3.2 ^3.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 ^5.2 CGSC: The Coli Genetics Stock Center
↑ ^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).

dadX:On One Page

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Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to dadX Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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