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On One Page

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Expression|

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Standard Name	agaA
Gene Synonym(s)	ECK3123, b3135, JW5527, yraA^[1], yraA
Product Desc.	predicted truncated N-acetylgalactosamine-6-phosphate deacetylase^[2]^[3]
Product Synonyms(s)	predicted truncated N-acetylgalactosamine-6-phosphate deacetylase^[1], B3135^[2]^[1], YraA^[2]^[1], AgaA^[2]^[1] , ECK3123, JW5527, yraA, b3135
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): kbaZ-agaVWA^[2], kbaZagaVWEFA, agaZVWA
Regulation/Activity
Quick Links
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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	agaA
Mnemonic
Synonyms	ECK3123, b3135, JW5527, yraA^[1], yraA
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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	70.68 minutes	MG1655: 3279144..3279647 <gbrowseImage> name=NC_000913:3279144..3279647 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3215725..3216858 <gbrowseImage> name=NC_012967:3215725..3216858 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
W3110		W3110: 3280977..3281480 <gbrowseImage> name=NC_007779:3280977..3281480 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3376889..3377392 <gbrowseImage> name=NC_010473:3376889..3377392 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)	Reference	Availability	Comments
ΔagaA (Keio:JW5527)	deletion	deletion	PMID:16738554	Shigen CGSC11444^[4]
agaA::Tn5KAN-I-SceI (FB21035)	Insertion at nt 166 in Minus orientation		PMID:15262929	E. coli Genome Project:FB21035	contains pKD46
agaA::Tn5KAN-I-SceI (FB21036)	Insertion at nt 251 in Plus orientation		PMID:15262929	E. coli Genome Project:FB21036	contains pKD46
ΔagaA749::kan			PMID:16738554	CGSC:99934
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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
JW5527	Plasmid clone	Shigen	PMID:16769691 Status:cloned as old JW Primer 1:GCCCATTGCTATAACGGGATGAC Primer 2:CCAAACGAAGCTAATTGACCCTG
20F4	Kohara Phage	Genobase	PMID:3038334
16C4	Kohara Phage	Genobase	PMID:3038334
aer-3075::Tn10	Linked marker	CAG12152 = CGSC7438^[4]	est. P1 cotransduction: 3% ^[5] Synonyms:zgh-3075::Tn10, zgj-3075::Tn10
sfsB203::Tn10	Linked marker	CAG12072 = CGSC7440^[4]	est. P1 cotransduction: 8% ^[5] Synonyms:zgj-203::Tn10, zha-203::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:EG12766	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12766	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002380	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947646	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2619	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010302	Escherichia coli str. K-12 substr. MG1655
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Notes

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	AgaA
Synonyms	predicted truncated N-acetylgalactosamine-6-phosphate deacetylase^[1], B3135^[2]^[1], YraA^[2]^[1], AgaA^[2]^[1] , ECK3123, JW5527, yraA, b3135
Product description	predicted truncated N-acetylgalactosamine-6-phosphate deacetylase^[2]^[3]
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:0005975	carbohydrate metabolic process	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0119	P	Seeded from EcoCyc (v14.0)	complete
	GO:0016787	hydrolase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR006680	F	Seeded from EcoCyc (v14.0)	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
	GO:0003674	molecular function	PMID:8932697, PMID:12234664	ISS: Inferred from Sequence or Structural Similarity	UniProtKB:P0AF18	F	Non-functional protein As per discussion of PMID:8932697: "Because the N-terminal truncation eliminates much of the region that is conserved in the NagA protein of E. coli and the putative NagA protein of Caen. elegans, it cannot be concluded that AgaA is functional for catalysis." PMID:12234664 Table 1, line 16 notes agaA is likely pseudogene.	complete
	GO:0008150	biological process	PMID:8932697, PMID:12234664	ISS: Inferred from Sequence or Structural Similarity	UniProtKB:P0AF18	P	Non-functional protein As per discussion of PMID:8932697: "Because the N-terminal truncation eliminates much of the region that is conserved in the NagA protein of E. coli and the putative NagA protein of Caen. elegans, it cannot be concluded that AgaA is functional for catalysis." PMID:12234664 Table 1, line 16 notes agaA is likely pseudogene.	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
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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 MHCYNGMTGL HHREPGMVGA GLTDKRAWLE LIADGHHVHP AAMSLCCCCA KERIVLITDA MQAAGMPDGR YTLCGEEVQM HGGVVRTASG GLAGSTLSVD AAVRNMVELT GVTPAEAIHM ASLHPARMLG VDGVLGSLKP GKRASVVALD SGLHVQQIWI QGQLASF
Length	167
Mol. Wt	17.518 kDa
pI	7.0 (calculated)
Extinction coefficient	13,980 - 14,730 (calc based on 2 Y, 2 W, and 6 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	9..150	PF01979 Amidohydrolase family		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=agaA 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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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
ASAP	ASAP:ABE-0010302	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947646	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P42906	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12766	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12766	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947646	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002380	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2619	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)
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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)
kbaZ-agaVWA
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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_000913:3279124..3279164 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
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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:b3135 (EcoliWiki Page)	NCBI GEO profiles for agaA
microarray	GenExpDB:b3135 (EcoliWiki Page)	Summary of data for agaA 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 agaA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12766	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2619	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3135
EcoGene	EcoGene:EG12766	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002380	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010302	Escherichia coli str. K-12 substr. MG1655
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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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<protect> See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
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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)	PF01979 Amidohydrolase family
Panther (EcoliWiki Page)	PTHR11113:SF0
EcoCyc	EcoCyc:EG12766	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12766	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002380	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2619	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010302	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.

↑ ^1.0 ^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 ^4.2 CGSC: The Coli Genetics Stock Center
↑ ^5.0 ^5.1 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).

agaA:On One Page

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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 agaA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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