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Quickview | Gene | Product(s) | Expression| Evolution | References |

Quickview

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Gene Name

agaA (synonyms: ECK3123, b3135, JW5527, yraA)[1]

Product(s)

AgaA product[1]: predicted truncated N-acetylgalactosamine-6-phosphate deacetylase product, B3135 product, YraA product

Description

predicted truncated N-acetylgalactosamine-6-phosphate deacetylase[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

agaA

Mnemonic
Synonyms

ECK3123, b3135, JW5527, yraA[1]

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Notes

Location(s) and DNA Sequence

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StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

70.68 minutes 

MG1655: 3279144..3279647
gbrowse_img.php?coord=3278144..3280647&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 3280977..3281480
gbrowse_img.php?coord=3279977..3282480&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

ΔagaA (Keio:JW5527)

deletion

deletion

PMID:16738554[4]

Shigen
CGSC11444[5]

ΔagaA749::kan

PMID:16738554[4]

CGSC:99934


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Notes

Genetic Resources

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ResourceResource TypeSourceNotes/Reference

JW5527

Plasmid clone

Shigen

PMID:16769691[6]

Status:cloned as old JW

Primer 1:GCCCATTGCTATAACGGGATGAC

Primer 2:CCAAACGAAGCTAATTGACCCTG

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:EG12766

EchoBASE (EcoliWiki Page)

EchoBASE:EB2619

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3135

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3892

EcoGene (EcoliWiki Page)

EcoGene:EG12766

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:Z4489

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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

AgaA

Synonyms

predicted truncated N-acetylgalactosamine-6-phosphate deacetylase[1], B3135[2][1], YraA[2][1], AgaA[2][1]

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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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:0005975

carbohydrate metabolic process

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0119

P

Seeded from EcoCyc 12.5 [8]

complete

GO:0016787

hydrolase activity

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR006680
SP_KW:KW-0378

F

Seeded from EcoCyc 12.5 [8]

complete

GO:0009401

phosphoenolpyruvate-dependent sugar phosphotransferase system

P

Seeded from EcoCyc 11.1[3].

required fields missing

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Interactions

Partner TypePartnerNotesReferences
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Notes

Localization

CompartmentDescriptionEvidenceNotes
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Notes

Structure and Physical Properties

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Physical Properties

Sequence

at EcoCyc 

MHCYNGMTGL HHREPGMVGA GLTDKRAWLE LIADGHHVHP AAMSLCCCCA KERIVLITDA
MQAAGMPDGR YTLCGEEVQM HGGVVRTASG GLAGSTLSVD AAVRNMVELT GVTPAEAIHM
ASLHPARMLG VDGVLGSLKP GKRASVVALD SGLHVQQIWI QGQLASF
Mol. Wt

17.52 kDa (calc) [2]

pI
Extinction coefficient

13980 - 14730 (calc based on 2 Y, 2 W, and 6 C residues)

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Domains/Motifs/Modification Sites

TypeResiduesDescriptionNotes
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Structure

Structures
  • Representative homolog:
    1O12|A (Thermotoga maritima)
    209-371 of 167 residues (E-value: 1.1e-21) (Percent Identity: 39.63)
  • View all other structures.
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

EcoCyc (EcoliWiki Page)

EcoCyc:AGAA-MONOMER

SwissModel (EcoliWiki Page)

SwissModel:P42906

UniProt (EcoliWiki Page)

UniProt:P42906

PFAM (EcoliWiki Page)

PFAM:PF01979

RefSeq (EcoliWiki Page)

RefSeq:YP_026206

ModBase (EcoliWiki Page)

ModBase:P42906

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:Z4489-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=3279124..3279164&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:b3135 (EcoliWiki Page)

Summary of data for agaA from multiple microarray studies

microarray

GEO Profiles:b3135 (EcoliWiki Page)

NCBI GEO profiles for agaA

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Expression Resources

Resource NameResource TypeDescriptionSourceNotes
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Notes

Accessions Related to agaA Expression

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DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG12766

EchoBASE (EcoliWiki Page)

EchoBASE:EB2619

EcoliGenExpDB (EcoliWiki Page)

GenExpDB:b3135

EcoGene (EcoliWiki Page)

EcoGene:EG12766

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

Do-It-Yourself Web Tools

Notes

Families

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DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF01979

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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 1.2 1.3 1.4 1.5 1.6 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 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. ↑ 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. ↑ 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 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7

Categories

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