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Gene Name

agaS (synonyms: ECK3124, b3136, JW3105, yraB)[1]

Product(s)

AgaS product[1]: tagatose-6-phosphate ketose/aldose isomerase product, B3136 product, YraB product

Description

putative tagatose-6-phosphate aldose/ketose isomerase[2][3]

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

agaS

Mnemonic
Synonyms

ECK3124, b3136, JW3105, yraB[1]

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Notes

Location(s) and DNA Sequence

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StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

70.69 minutes 

MG1655: 3279998..3281152
gbrowse_img.php?coord=3278998..3282152&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 3281831..3282985
gbrowse_img.php?coord=3280831..3283985&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

ΔagaS (Keio:JW3105)

deletion

deletion

PMID:16738554[4]

Shigen
CGSC10365[5]

ΔagaS750::kan

PMID:16738554[4]

CGSC:99946


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Notes

Genetic Resources

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ResourceResource TypeSourceNotes/Reference

JW3105

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCCCAGAAAATTACACCCCTGC

Primer 2:CCTGCCTGCCACGGATGAATGAT

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: 9% [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:G7634

EchoBASE (EcoliWiki Page)

EchoBASE:EB2620

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3136

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3893

EcoGene (EcoliWiki Page)

EcoGene:EG12767

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:AGAS

ASAP (EcoliWikiPage)

ASAP:ABE-0010305


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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

AgaS

Synonyms

tagatose-6-phosphate ketose/aldose isomerase[1], B3136[2][1], YraB[2][1], AgaS[2][1]

Product description

putative tagatose-6-phosphate aldose/ketose isomerase[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:0005529

sugar binding

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001347

F

Seeded from EcoCyc 12.5 [8]

complete

GO:0005975

carbohydrate metabolic process

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001347

P

Seeded from EcoCyc 12.5 [8]

complete

GO:0016853

isomerase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0413

F

Seeded from EcoCyc 12.5 [8]

complete

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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 

MPENYTPAAA ATGTWTEEEI RHQPRAWIRS LTNIDALRSA LNNFLEPLLR KENLRIILTG
AGTSAFIGDI IAPWLASHTG KNFSAVPTTD LVTNPMDYLN PAHPLLLISF GRSGNSPESV
AAVELANQFV PECYHLPITC NEAGALYQNA INSDNAFALL MPAETHDRGF AMTSSITTMM
ASCLAVFAPE TINSQTFRDV ADRCQAILTS LGDFSEGVFG YAPWKRIVYL GSGGLQGAAR
ESALKVLELT AGKLAAFYDS PTGFRHGPKS LVDDETLVVV FVSSHPYTRQ YDLDLLAELR
RDNQAMRVIA IAAESSDIVA AGPHIILPPS RHFIDVEQAF CFLMYAQTFA LMQSLHMGNT
PDTPSASGTV NRVVQGVIIH PWQA
Mol. Wt

41.78 kDa (calc) [2]

pI
Extinction coefficient

42400 - 43025 (calc based on 10 Y, 5 W, and 5 C residues)

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Domains/Motifs/Modification Sites

TypeResiduesDescriptionNotes
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Structure

Structures
  • Representative homolog:
    3C3J|A (Escherichia coli K12)
    2-384 of 384 residues (E-value: 1.8e-200) (Percent Identity: 97.65)
  • 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:G7634-MONOMER

UniProt (EcoliWiki Page)

UniProt:P42907

PFAM (EcoliWiki Page)

PFAM:PF01380

RefSeq (EcoliWiki Page)

RefSeq:NP_417605

ModBase (EcoliWiki Page)

ModBase:P42907


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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)

agaSYBCDI

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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=3279978..3280018&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:b3136 (EcoliWiki Page)

Summary of data for agaS from multiple microarray studies

microarray

GEO Profiles:b3136 (EcoliWiki Page)

NCBI GEO profiles for agaS

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Expression Resources

Resource NameResource TypeDescriptionSourceNotes

GFP Fusion

Intergenic region (3279195..3279646) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ11; Well:D9[9]

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Notes

Accessions Related to agaS Expression

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DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:G7634

EchoBASE (EcoliWiki Page)

EchoBASE:EB2620

EcoliGenExpDB (EcoliWiki Page)

GenExpDB:b3136

EcoGene (EcoliWiki Page)

EcoGene:EG12767

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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:PF01380

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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 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 8.2 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  9. ↑ Zaslaver A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3: 623-8 PubMed EcoliWiki page

Categories

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