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allA:On One Page

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Gene Name	allA (synonyms: ECK0498, b0505, JW0493, glxA2, ybbT)^[1]
Product(s)	AllA product^[1]: ureidoglycolate hydrolase product, B0505 product, YbbT product
Description	G6275-MONOMER^[2]^[3]
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): allA^[2]
Regulation/Activity
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Gene

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Nomenclature

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Standard name	allA
Mnemonic
Synonyms	ECK0498, b0505, JW0493, glxA2, ybbT^[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	11.46 minutes	MG1655: 531675..532157	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
W3110		W3110: 531675..532157	GBrowse(W3110)	FASTA Dump
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Strain

Map location

Genome coordinates

Genome browsers

Sequence links

MG1655

11.46 minutes

MG1655: 531675..532157
gbrowse_img.php?coord=530675..533157&genome=ecoli&name=MG1655&trackset=0&width=300&.png

EcoCyc

GBrowse(MG1655)

W3110

W3110: 531675..532157
gbrowse_img.php?coord=530675..533157&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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Notes

Alleles and Phenotypes

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Allele	Nt change(s)	AA change(s)	Reference	Availability
ΔallA (Keio:JW0493)	deletion	deletion	PMID:16738554^[4]	Shigen CGSC8638^[5]
ΔallA788::kan			PMID:16738554^[4]	CGSC:99970
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Notes

Genetic Resources

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Resource	Resource Type	Source	Notes/Reference
JW0493	Plasmid clone	Shigen	PMID:16769691^[6] Status:Clone OK Primer 1:GCCAAACTTCAGGTATTACCGTT Primer 2:CCCGCAAAACAGAGTTCCTGTTC
gsk-3055::Tn10	Linked marker	CAG12154 = CGSC7341^[5]	est. P1 cotransduction: 30% ^[7] Synonyms:zbb-30-55::TnlO, zba-3055::Tn10
purK79::Tn10	Linked marker	CAG12171 = CGSC7342^[5]	est. P1 cotransduction: 47% ^[7] Synonyms:purE79::Tn10
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Notes

Accessions in Other Databases

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:G6275
EchoBASE (EcoliWiki Page)	EchoBASE:EB3381
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0505
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C0620
EcoGene (EcoliWiki Page)	EcoGene:EG13615
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:YBBT
ASAP (EcoliWikiPage)	ASAP:ABE-0001747
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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	AllA
Synonyms	ureidoglycolate hydrolase^[1], B0505^[2]^[1], YbbT^[2]^[1], AllA^[2]^[1]
Product description	G6275^[2]^[3]
EC number (for enzymes)	3.5.3.19^[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:0000256	allantoin catabolic process	GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR007247	P	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0006144	purine base metabolic process	GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0659	P	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0006145	purine base catabolic process	GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00616	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:0050385	ureidoglycolate lyase activity	PMID:10601204^[9]	IDA: Inferred from Direct Assay		F	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0005737	cytoplasm				C	Seeded from Riley et al 2006 ^[1].	required fields missing
	GO:0006807	nitrogen compound metabolic process				P	Seeded from EcoCyc 11.1^[3].	required fields missing
	GO:0009442	allantoin assimilation pathway				P	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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Structure and Physical Properties

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Physical Properties

Sequence	at EcoCyc MKLQVLPLSQ EAFSAYGDVI ETQQRDFFHI NNGLVERYHD LALVEILEQD CTLISINRAQ PANLPLTIHE LERHPLGTQA FIPMKGEVFV VVVALGDDKP DLSTLRAFIT NGEQGVNYHR NVWHHPLFAW QRVTDFLTID RGGSDNCDVE SIPEQELCFA
Mol. Wt	18.17 kDa (calc) ^[2]
pI
Extinction coefficient	15470 - 15845 (calc based on 3 Y, 2 W, and 3 C residues)
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Domains/Motifs/Modification Sites

Type	Residues	Description	Notes
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Structure

Structures	Representative Escherichia coli structure: 1XSQ\|A 2-160 of 160 residues (E-value: 2.0e-84) (Percent Identity: 99.37) Representative homolog: 1XSR\|A (Shigella flexneri) 2-160 of 160 residues (E-value: 3.7e-83) (Percent Identity: 98.74) 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:
1XSQ|A
2-160 of 160 residues (E-value: 2.0e-84) (Percent Identity: 99.37)
Representative homolog:
1XSR|A (Shigella flexneri)
2-160 of 160 residues (E-value: 3.7e-83) (Percent Identity: 98.74)
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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:G6275-MONOMER
UniProt (EcoliWiki Page)	UniProt:P77731
PFAM (EcoliWiki Page)	PFAM:PF04115
RefSeq (EcoliWiki Page)	RefSeq:NP_415038
PDB (EcoliWiki Page)	PDB:1XSQ
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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)
allA
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Figure courtesy of RegulonDB

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

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=531655..531695&genome=ecoli&name=MG1655&trackset=Genes_unlabeled+DNA_unlabeled&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

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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:b0505 (EcoliWiki Page)	Summary of data for allA from multiple microarray studies
microarray	GEO Profiles:b0505 (EcoliWiki Page)	NCBI GEO profiles for allA
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Expression Resources

Resource Name	Resource Type	Description	Source	Notes
	GFP Fusion	Intergenic region (531370..531723) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ13; Well:D8^[10]
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Notes

Accessions Related to allA Expression

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:G6275
EchoBASE (EcoliWiki Page)	EchoBASE:EB3381
EcoliGenExpDB (EcoliWiki Page)	GenExpDB:b0505
EcoGene (EcoliWiki Page)	EcoGene:EG13615
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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
Schizosaccharomyces pombe	SPAC19G124 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YBBT	From SHIGELLACYC
E. coli O157	YBBT	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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Database	Accession	Notes
PFAM (EcoliWiki Page)	PFAM:PF04115
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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 ^1.8 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 ^3.3 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 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ Cusa E et al. (1999) Genetic analysis of a chromosomal region containing genes required for assimilation of allantoin nitrogen and linked glyoxylate metabolism in Escherichia coli. J Bacteriol 181: 7479-84 PubMed EcoliWiki page
↑ Zaslaver A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3: 623-8 PubMed EcoliWiki page

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

allA:On One Page

From EcoliWiki

Quickview

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 allA Expression

Notes

Links

Categories

Evolution

Homologs in Other Organisms

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Notes

Families

Notes

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References

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