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agaV:On One Page

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Standard Name

agaV

Gene Synonym(s)

ECK3121, b3133, JW3102, yhaY[1]

Product Desc.

PTS system, cytoplasmic, N-acetylgalactosamine-specific IIB component 2 (EIIB-AGA)[2][3]

Enzyme IIB Nag, PTS system; N-acetylgalactosamine-specific enzyme IIB; EIIB-Nag[4]

Product Synonyms(s)

N-acetylgalactosamine-specific enzyme IIB component of PTS[1], B3133[2][1], YhaY[2][1], AgaV[2][1]

Function from GO
Knock-Out Phenotype
Regulation/Expression

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

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(agaV)    Textpresso(agaV)

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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

agaV

Mnemonic

Acetylgalactosamine

Synonyms

ECK3121, b3133, JW3102, yhaY[1]

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Notes

Location(s) and DNA Sequence

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

70.66 minutes 

MG1655: 3278239..3278712
gbrowse_img.php?coord=3278239..3278712&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 3213145..3213618
gbrowse_img.php?coord=3213145..3213618&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 3280072..3280545
gbrowse_img.php?coord=3280072..3280545&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 3375984..3376457
gbrowse_img.php?coord=3375984..3376457&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 3165387..3165860
gbrowse_img.php?coord=3165387..3165860&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

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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 typeLocationDescription
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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.

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

ΔagaV (Keio:JW3102)

deletion

deletion

PMID:16738554

Shigen
CGSC10363[5]

agaV::Tn5KAN

PMID:12519969

ASAP

At position 288 in Minus orientation, contains plasmid pKD46.
ASAP strain name: FB21034

ΔagaV747::kan

PMID:16738554

CGSC:99948


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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

ResourceResource TypeSourceNotes/Reference

JW3102

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCCAAATATTGTTTTAAGCCG

Primer 2:CCAAGTAATTTAAAGAGGTCCAC

aer-3075::Tn10

Linked marker

CAG12152 = CGSC7438[5]

est. P1 cotransduction: 3% [6]
Synonyms:zgh-3075::Tn10, zgj-3075::Tn10

sfsB203::Tn10

Linked marker

CAG12072 = CGSC7440[5]

est. P1 cotransduction: 8% [6]
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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:G7632

EchoBASE (EcoliWiki Page)

EchoBASE:EB2617

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3133

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3888

EcoGene (EcoliWiki Page)

EcoGene:EG12764

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:AGAV

ASAP (EcoliWikiPage)

ASAP:ABE-0010297


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Notes

Links

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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

AgaV

Synonyms

N-acetylgalactosamine-specific enzyme IIB component of PTS[1], B3133[2][1], YhaY[2][1], AgaV[2][1]

Product description

PTS system, cytoplasmic, N-acetylgalactosamine-specific IIB component 2 (EIIB-AGA)[2][3]

Enzyme IIB Nag, PTS system; N-acetylgalactosamine-specific enzyme IIB; EIIB-Nag[4]

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:0016740

transferase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0808

F

Seeded from EcoCyc [7]

complete

GO:0009401

phosphoenolpyruvate-dependent sugar phosphotransferase system

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR004720
SP_KW:KW-0598

P

Seeded from EcoCyc [7]

complete

GO:0005351

sugar:hydrogen symporter activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0762

F

Seeded from EcoCyc [7]

complete

GO:0005737

cytoplasm

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR004720
SP_KW:KW-0963

C

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 [7]

complete

GO:0008643

carbohydrate transport

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0762

P

Seeded from EcoCyc [7]

complete

GO:0008982

protein-N(PI)-phosphohistidine-sugar phosphotransferase activity

GO_REF:0000002
GO_REF:0000003

IEA: Inferred from Electronic Annotation

InterPro:IPR004720
EC:2.7.1.69

F

Seeded from EcoCyc [7]

complete

GO:0016301

kinase activity

GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0418

F

Seeded from EcoCyc [7]

complete

GO:0046349

amino sugar biosynthetic process

P

Seeded from EcoCyc 11.1[3].

required fields missing

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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 TypePartnerNotesReferencesEvidence

Protein

sucB

PMID:16606699

Experiment(s):EBI-1144876

Protein

umuC

PMID:16606699

Experiment(s):EBI-1144876

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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

CompartmentDescriptionEvidenceSourceNotes
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Notes

Structure and Physical Properties

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Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Sequence

at EcoCyc 

MKANKQNKEE HAMPNIVLSR IDERLIHGQV GVQWVGFAGA NLVLVANDEV AEDPVQQNLM
EMVLAEGIAV RFWTLQKVID NIHRAADRQK ILLVCKTPAD FLTLVKGGVP VNRINVGNMH
YANGKQQIAK TVSVDAGDIA AFNDLKTAGV ECFVQGVPTE PAVDLFKLL
Length

169

Mol. Wt

18.494 kDa

pI

6.5 (calculated)

Extinction coefficient

12,490 - 12,740 (calc based on 1 Y, 2 W, and 2 C residues)

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Domains/Motifs/Modification Sites

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TypeResiduesDescriptionNotesReferences
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Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures
Models

View models at:

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Structure figures

Notes

Gene Product Resources

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Resource typeSourceNotes/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.

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:G7632-MONOMER

UniProt (EcoliWiki Page)

UniProt:P42904

PFAM (EcoliWiki Page)

PFAM:PF03830

RefSeq (EcoliWiki Page)

RefSeq:NP_417602


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Notes

Links

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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

MoleculeOrganism or StrainCellular levelUnitsMediumTemperature °COther (e.g. anaerobic)Growth rateAssay usedNotesReference(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

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=3278219..3278259&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein&width=400&figure=Nterm&.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 See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele NameMutationPhenotypeReference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

TypeReferenceNotes

microarray

GEO Profiles:b3133 (EcoliWiki Page)

NCBI GEO profiles for agaV

microarray

GenExpDB:b3133 (EcoliWiki Page)

Summary of data for agaV 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 NameResource TypeDescriptionSourceNotes
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Notes

Accessions Related to agaV Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:G7632

EchoBASE (EcoliWiki Page)

EchoBASE:EB2617

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3133

EcoGene (EcoliWiki Page)

EcoGene:EG12764


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Notes

Links

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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.

OrganismHomologs (Statistics)Comments

Shigella flexneri

AGAV

From SHIGELLACYC

E. coli O157

AGAV

From ECOO157CYC

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Do-It-Yourself Web Tools

Notes

Families

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DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF03830


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Notes

Links

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References

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  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 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 2.8 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 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 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).
  7. ↑ 7.0 7.1 7.2 7.3 7.4 7.5 7.6 EcoCyc (release 13.0; 2009) Keseler, IM et al. (2009) Nucleic Acids Res. 37(Database issue):D464-70
  8. ↑ EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7

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