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Gene Name

agaW (synonyms: ECK3122, b3134, JW3103, yhaZ)[1]

Product(s)

AgaW product[2]: B3134 product, YhaZ product

Description

PTS system N-acetylgalactosameine-specific IIC component 2[2][3]

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): kbaZ-agaVWA[2], kbaZagaVWEFA, agaZVWA

Regulation/Activity
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Notes

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Gene

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Nomenclature

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Standard name

agaW

Mnemonic
Synonyms

ECK3122, b3134, JW3103, yhaZ[1]

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Notes

Location(s) and DNA Sequence

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StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

70.67 minutes 

MG1655: 3278723..3279124
gbrowse_img.php?coord=3277723..3280124&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 3280556..3280957
gbrowse_img.php?coord=3279556..3281957&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

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Notes

Sequence Features

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Feature typeLocationDescription
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Notes

Alleles and Phenotypes

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AlleleNt change(s)AA change(s)Phenotype: TypePhenotype: DescriptionReferenceAvailabilityComments

ΔagaW (Keio:JW3103)

deletion

deletion

PMID:16738554[4]

Shigen
CGSC10364[5]

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Notes

Genetic Resources

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ResourceResource TypeSourceNotes/Reference

JW3103

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCGAAATCAGCCTGTTGCAGGC

Primer 2:CCAATGCGGCGCGGGTTTGTTGC

aer-3075::Tn10

Linked marker

CAG12152 = CGSC7438[5]

est. P1 cotransduction: 3% [7]

Synonyms:zgh-3075::Tn10, zgj-3075::Tn10

sfsB203::Tn10

Linked marker

CAG12072 = CGSC7440[5]

est. P1 cotransduction: 8% [7]

Synonyms:zgj-203::Tn10, zha-203::Tn10

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Notes

Accessions in Other Databases

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DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:G7633

EchoBASE (EcoliWiki Page)

EchoBASE:EB2618

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3134

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3889

EcoGene (EcoliWiki Page)

EcoGene:EG12765

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:Z4486

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Notes

Links

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NameURLComments
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Categories

Product(s)

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Nomenclature

Standard name

AgaW

Synonyms

B3134[2], YhaZ[2], AgaW[2]

Product description

PTS system N-acetylgalactosameine-specific IIC component 2[2][3]

EC number (for enzymes)
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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.

QualifierGO IDGO term nameReference(s)Evidence Codewith/fromAspectNotesStatus
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:IPR004700
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:IPR004700
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 TypePartnerNotesReferences
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Notes

Localization

CompartmentDescriptionEvidenceNotes

plasma membrane

C-terminus localized in the cytoplasm with 3 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 

MEISLLQAFA LGIIAFIAGL DMFNGLTHMH RPVVLGPLVG LVLGDLHTGI LTGGTLELVW
MGLAPLAGAQ PPNVIIGTIV GTAFAITTGV KPDVAVGVAV PFAVAVQMGI TFLFSVMSGV
MSRCDLATNP RRI
Mol. Wt

13.72 kDa (calc) [2]

pI
Extinction coefficient

5500 - 5625 (calc based on 0 Y, 1 W, and 1 C residues)

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Domains/Motifs/Modification Sites

TypeResiduesDescriptionNotes

Domain

1 - 133

PTS EIIC type-4

UniProt:P42905

Domain

5 - 27

Predicted membrane-spanning helix.

TMD predicted by TMHMM[10]' />

Domain

34 - 56

Predicted membrane-spanning helix.

TMD predicted by TMHMM[10]' />

Domain

94 - 116

Predicted membrane-spanning helix.

TMD predicted by TMHMM[10]' />

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tmhmm.php?gene=agaW&show=pic&.jpg
Click the image to view raw output from TMHMM.

Structure

Structures
  • No results found.
Models

View models at:

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Notes

Gene Product Resources

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Resource typeSourceNotes/Reference
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Notes

Accessions in Other Databases

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DatabaseAccessionNotes

UniProt (EcoliWiki Page)

UniProt:P42905

PFAM (EcoliWiki Page)

PFAM:PF03609

RefSeq (EcoliWiki Page)

RefSeq:NP_417603

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:Z4486-MONOMER


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Notes

Links

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NameURLComments
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Categories

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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)

kbaZ-agaVWA

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Figure courtesy of RegulonDB
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=3278703..3278743&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 NameMutationPhenotypeReference
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Expression Studies

TypeReferenceNotes

microarray

GenExpDB:b3134 (EcoliWiki Page)

Summary of data for agaW from multiple microarray studies

microarray

GEO Profiles:b3134 (EcoliWiki Page)

NCBI GEO profiles for agaW

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Expression Resources

Resource NameResource TypeDescriptionSourceNotes
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Notes

Accessions Related to agaW Expression

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DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:G7633

EchoBASE (EcoliWiki Page)

EchoBASE:EB2618

EcoliGenExpDB (EcoliWiki Page)

GenExpDB:b3134

EcoGene (EcoliWiki Page)

EcoGene:EG12765

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Notes

Links

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NameURLComments
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Categories

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Evolution

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Homologs in Other Organisms

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OrganismHomologs (Statistics)Comments

Shigella flexneri

AGAW

From SHIGELLACYC

E. coli O157

Z4486

From ECOO157CYC

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Do-It-Yourself Web Tools

Notes

Families

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DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF03609

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Notes

Links

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NameURLComments
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References

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

  1. ↑ 1.0 1.1 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 2.7 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 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. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 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. ↑ 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. ↑ 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
  9. ↑ Daley DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308: 1321-3 PubMed EcoliWiki page
  10. ↑ 10.0 10.1 10.2 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

Categories

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