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agaD:On One Page

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Gene Name	agaD (synonyms: ECK3128, b3140, JW3109, yraF)^[1]
Product(s)	AgaD product^[1]: N-acetylgalactosamine-specific enzyme IID component of PTS product, B3140 product, YraF product
Description	AGAD-MONOMER^[2]^[3] Component of EIIAga^[2]
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): agaSYBCDI^[2], agaSkbaYagaBCDI
Regulation/Activity
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Notes

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Gene

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Nomenclature

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Standard name	agaD
Mnemonic
Synonyms	ECK3128, b3140, JW3109, yraF^[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	70.77 minutes	MG1655: 3283500..3284291	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
W3110		W3110: 3285333..3286124	GBrowse(W3110)	FASTA Dump
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Strain

Map location

Genome coordinates

Genome browsers

Sequence links

MG1655

70.77 minutes

MG1655: 3283500..3284291
gbrowse_img.php?coord=3282500..3285291&genome=ecoli&name=MG1655&trackset=0&width=300&.png

EcoCyc

GBrowse(MG1655)

W3110

W3110: 3285333..3286124
gbrowse_img.php?coord=3284333..3287124&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
ΔagaD (Keio:JW3109)	deletion	deletion	PMID:16738554^[4]	Shigen CGSC10368^[5]
ΔagaD754::kan			PMID:16738554^[4]	CGSC:99940
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Notes

Genetic Resources

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Resource	Resource Type	Source	Notes/Reference
JW3109	Plasmid clone	Shigen	PMID:16769691^[6] Status:Clone OK Primer 1:GCCGGATCTGAAATCAGTAAAAA Primer 2:CCtAAAATGCCGAATGCGGAACA
aer-3075::Tn10	Linked marker	CAG12152 = CGSC7438^[5]	est. P1 cotransduction: 2% ^[7] Synonyms:zgh-3075::Tn10, zgj-3075::Tn10
sfsB203::Tn10	Linked marker	CAG12072 = CGSC7440^[5]	est. P1 cotransduction: 11% ^[7] Synonyms:zgj-203::Tn10, zha-203::Tn10
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Notes

Accessions in Other Databases

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:G7635
EchoBASE (EcoliWiki Page)	EchoBASE:EB2624
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3140
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C3897
EcoGene (EcoliWiki Page)	EcoGene:EG12771
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:AGAD
ASAP (EcoliWikiPage)	ASAP:ABE-0010314
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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	AgaD
Synonyms	N-acetylgalactosamine-specific enzyme IID component of PTS^[1], B3140^[2]^[1], YraF^[2]^[1], AgaD^[2]^[1]
Product description	AGAD^[2]^[3]; Component of ; EIIAga^[2]^[3]
EC number (for enzymes)	2.7.1.69^[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:0005351	sugar:hydrogen symporter activity	GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0762	F	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0006810	transport	GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0813	P	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0008643	carbohydrate transport	GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0762	P	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0009401	phosphoenolpyruvate-dependent sugar phosphotransferase system	GO_REF:0000002 GO_REF:0000004	IEA: Inferred from Electronic Annotation	InterPro:IPR004704 SP_KW:KW-0598	P	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0016020	membrane	GO_REF:0000004 GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0397 SP_KW:KW-0472	C	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0016021	integral to membrane	GO_REF:0000002 GO_REF:0000004	IEA: Inferred from Electronic Annotation	InterPro:IPR004704 SP_KW:KW-0812	C	Seeded from EcoCyc 12.5 ^[8]	complete
	GO:0046349	amino sugar biosynthetic process				P	Seeded from EcoCyc 11.1^[3].	required fields missing
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Interactions

Partner Type	Partner	Notes	References
Protein	Subunits of EIIAga	could be indirect
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Notes

Localization

Compartment	Description	Evidence	Notes
plasma membrane	C-terminus localized to the periplasm with 5 predicted transmembrane domains	Daley et al. (2005) ^[9]/>
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Notes

Structure and Physical Properties

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Physical Properties

Sequence	at EcoCyc MGSEISKKDI TRLGFRSSLL QASFNYERMQ AGGFTWAMLP ILKKIYKDDK PGLSAAMKDN LEFINTHPNL VGFLMGLLIS MEEKGENRDT IKGLKVALFG PIAGIGDAIF WFTLLPIMAG ICSSFASQGN LLGPILFFAV YLLIFFLRVG WTHVGYSVGV KAIDKVRENS QMIARSATIL GITVIGGLIA SYVHINVVTS FAIDNTHSVA LQQDFFDKVF PNILPMAYTL LMYYFLRVKK AHPVLLIGVT FVLSIVCSAF GIL
Mol. Wt	29 kDa (calc) ^[2]
pI
Extinction coefficient	28420 - 28670 (calc based on 8 Y, 3 W, and 2 C residues)
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Domains/Motifs/Modification Sites

Type	Residues	Description	Notes
Domain	3 - 263	PTS EIID	UniProt:P42911
Domain	98 - 120	Predicted membrane-spanning helix.	TMD predicted by TMHMM^[10]' />
Domain	135 - 157	Predicted membrane-spanning helix.	TMD predicted by TMHMM^[10]' />
Domain	177 - 199	Predicted membrane-spanning helix.	TMD predicted by TMHMM^[10]' />
Domain	219 - 236	Predicted membrane-spanning helix.	TMD predicted by TMHMM^[10]' />
Domain	243 - 262	Predicted membrane-spanning helix.	TMD predicted by TMHMM^[10]' />
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Click the image to view raw output from TMHMM.

Structure

Structures	No results found.
Models	View models at: EcoliPredict ModBase PSI-PRED Protein Quaternary Structure (PQS) Genomes TO Protein (GTOP)
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Structures

No results found.

Models

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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:AGAD-MONOMER
UniProt (EcoliWiki Page)	UniProt:P42911
PFAM (EcoliWiki Page)	PFAM:PF03613
RefSeq (EcoliWiki Page)	RefSeq:NP_417609
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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)
agaSYBCDI
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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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gbrowse_img.php?coord=3283480..3283520&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

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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Mutations Affecting Expression

Allele Name	Mutation	Phenotype	Reference
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Expression Studies

Type	Reference	Notes
microarray	GenExpDB:b3140 (EcoliWiki Page)	Summary of data for agaD from multiple microarray studies
microarray	GEO Profiles:b3140 (EcoliWiki Page)	NCBI GEO profiles for agaD
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Expression Resources

Resource Name	Resource Type	Description	Source	Notes
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Notes

Accessions Related to agaD Expression

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Database	Accession	Notes
EcoCyc (EcoliWiki Page)	EcoCyc:G7635
EchoBASE (EcoliWiki Page)	EchoBASE:EB2624
EcoliGenExpDB (EcoliWiki Page)	GenExpDB:b3140
EcoGene (EcoliWiki Page)	EcoGene:EG12771
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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
Shigella flexneri	AGAD	From SHIGELLACYC
E. coli O157	AGAD	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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Database	Accession	Notes
PFAM (EcoliWiki Page)	PFAM:PF03613
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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 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 ^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 ^8.5 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ Daley DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308: 1321-3 PubMed EcoliWiki page
↑ ^10.0 ^10.1 ^10.2 ^10.3 ^10.4 Krogh A et al. (2001) Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol 305: 567-80 PubMed EcoliWiki page

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

agaD:On One Page

From EcoliWiki

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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 agaD Expression

Notes

Links

Categories

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

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References

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