{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Standard Name	alr
Gene Synonym(s)	ECK4045, b4053, JW4013, alr5^[1]
Product Desc.	Alr^[2]; alanine racemase 1, PLP-binding, biosynthetic^[3]; Component of alanine racemase, minor^[2] Alanine racemase^[4]
Product Synonyms(s)	alanine racemase 1, PLP-binding, biosynthetic^[1], B4053^[2]^[1], Alr^[2]^[1] , ECK4045, JW4013, b4053
Function from GO	<GO_nr />
Knock-Out Phenotype	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): alr^[2]
Regulation/Activity	low level constitutive
Quick Links
edit table

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]

Gene

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]

See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	alr
Mnemonic	Alanine racemase
Synonyms	ECK4045, b4053, JW4013, alr5^[1]
edit table

</protect>

Notes

Location(s) and DNA Sequence

[back to top]

<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	91.9 minutes	MG1655: 4263805..4264884 <gbrowseImage> name=NC_000913:4263805..4264884 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4244714..4245793 <gbrowseImage> name=NC_012967:4244714..4245793 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4202650..4203729 <gbrowseImage> name=NC_012759:4202650..4203729 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4269372..4270451 <gbrowseImage> name=NC_007779:4269372..4270451 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4363501..4364580 <gbrowseImage> name=NC_010473:4363501..4364580 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
edit table

</protect>

Notes

Sequence Features

[back to top]

See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
edit table

Notes

Alleles and Phenotypes

[back to top]

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
Δalr (Keio:JW4013)	deletion	deletion	No phenotype to Δalr except in a ΔdadX background. Double mutant requires D-alanine for growth.	PMID:16738554	Shigen
alr-1(ts)			temperature sensitive		CGSC:5683
Δalr-746::kan				PMID:16738554	CGSC:99980
edit table

Notes

Genetic Interactions

[back to top]

Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
edit table

</protect>

Notes

Genetic Resources

[back to top]

See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW4013	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCAAGCGGCAACTGTTGTGAT Primer 2:CCATCCACGTATTTCATCGCGAC
1E4	Kohara Phage	Genobase	PMID:3038334
12D1	Kohara Phage	Genobase	PMID:3038334
malF3089::Tn10	Linked marker	CAG12164 = CGSC7476^[5]	est. P1 cotransduction: 42% ^[6]
zje-2241::Tn10	Linked marker	CAG18427 = CGSC7481^[5]	est. P1 cotransduction: 17% ^[6]
edit table

Notes

Accessions in Other Databases

[back to top]

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10001	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10001	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000001	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948564	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0001	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013272	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Product(s)

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

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

Standard name	Alr
Synonyms	alanine racemase 1, PLP-binding, biosynthetic^[1], B4053^[2]^[1], Alr^[2]^[1] , ECK4045, JW4013, b4053
Product description	Alr^[2]; alanine racemase 1, PLP-binding, biosynthetic^[3]; Component of alanine racemase, minor^[2] Alanine racemase^[4]
EC number (for enzymes)	5.1.1.1^[1]
edit table

Notes

Function

[back to top]

<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:0007047	cellular cell wall organization	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0961	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008360	regulation of cell shape	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0133	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:0009252	peptidoglycan biosynthetic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0573	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
edit table

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, minor	could be indirect
edit table

</protect>

Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source	Notes
edit table

Notes

Structure and Physical Properties

[back to top]

<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 MQAATVVINR RALRHNLQRL RELAPASKMV AVVKANAYGH GLLETARTLP DADAFGVARL EEALRLRAGG ITKPVLLLEG FFDARDLPTI SAQHFHTAVH NEEQLAALEE ASLDEPVTVW MKLDTGMHRL GVRPEQAEAF YHRLTQCKNV RQPVNIVSHF ARADEPKCGA TEKQLAIFNT FCEGKPGQRS IAASGGILLW PQSHFDWVRP GIILYGVSPL EDRSTGADFG CQPVMSLTSS LIAVREHKAG EPVGYGGTWV SERDTRLGVV AMGYGDGYPR AAPSGTPVLV NGREVPIVGR VAMDMICVDL GPQAQDKAGD PVILWGEGLP VERIAEMTKV SAYELITRLT SRVAMKYVD
Length	359
Mol. Wt	39.152 kDa
pI	7.0 (calculated)
Extinction coefficient	39,420 - 40,045 (calc based on 8 Y, 5 W, and 5 C residues)
edit table

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	234..358	PF00842 Alanine racemase, C-terminal domain	PMID:19920124
Domain	8..219	PF01168 Alanine racemase, N-terminal domain	PMID:19920124
edit table

<motif_map/>

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

Structures

<beststructure> gene=alr taxon=562,83333 </beststructure>

Models

View models at:

edit table

</protect>

Structure figures

</protect>

Notes

Gene Product Resources

[back to top]

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

Resource type	Source	Notes/Reference
edit table

Notes

Accessions in Other Databases

[back to top]

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

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16131879	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948564	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013272	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A6B4	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10001	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10001	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948564	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000001	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0001	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Expression

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

[back to top]

See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Notes	Reference(s)
Protein	Ecoli K-12	8.011+/-0.093	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.032900834	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	586	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	158	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	349	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
edit table

Notes

Transcription and Transcriptional Regulation

[back to top]

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

Transcription unit(s)
alr
edit table

Figure courtesy of RegulonDB

</protect>

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

[back to top]

<protect><gbrowseImage> name=NC_000913:4263785..4263825 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

[back to top]

<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
edit table

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

Type	Reference	Notes
microarray	GEO Profiles:b4053 (EcoliWiki Page)	NCBI GEO profiles for alr
microarray	GenExpDB:b4053 (EcoliWiki Page)	Summary of data for alr from multiple microarray studies
edit table

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

Resource Name	Resource Type	Description	Source	Notes
edit table

Notes

Accessions Related to alr Expression

[back to top]

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10001	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0001	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4053
EcoGene	EcoGene:EG10001	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000001	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013272	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Evolution

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]

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

Organism	Homologs (Statistics)	Comments
Anopheles gambiae	ENSANGP00000026308 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPCC9658c (score: 1.000; bootstrap: 100%) SPBC3592 (score: 0.445)	From Inparanoid:20070104
Shigella flexneri	ALR	From SHIGELLACYC
E. coli O157	ALR	From ECOO157CYC
edit table

Do-It-Yourself Web Tools

Notes

Families

[back to top]

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:EG10001	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10001	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000001	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0001	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013272	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

References

[back to top]

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 ^1.8 ^1.9 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 ^2.7 ^2.8 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
↑ ^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 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).

alr:On One Page

Quickview

Notes

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 alr Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

Categories

Navigation menu

Search