agaB:On One Page - EcoliWiki
EcoliHub logo

E. coli is indeed the coolest thing on the planet - Carl Zimmer

agaB:On One Page

From EcoliWiki

Jump to: navigation, search
Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

Quickview

[back to top]



Gene Name

agaB (synonyms: ECK3126, b3138, JW3107, yraD)[1]

Product(s)

AgaB product[1]: N-acetylgalactosamine-specific enzyme IIB component of PTS product, B3138 product, YraD product

Description

AgaB[2][3]

Component of EIIAga[2]

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): agaSYBCDI[2], agaSkbaYagaBCDI

Regulation/Activity
edit table

See Help:Quickview for help with entering information in the Quickview table.

Notes

[back to top]



Gene

[back to top]


Nomenclature

[back to top]


Standard name

agaB

Mnemonic
Synonyms

ECK3126, b3138, JW3107, yraD[1]

edit table

See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Notes

Location(s) and DNA Sequence

[back to top]


StrainMap locationGenome coordinatesGenome browsersSequence links

MG1655

70.74 minutes 

MG1655: 3282192..3282668
gbrowse_img.php?coord=3281192..3283668&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 3284025..3284501
gbrowse_img.php?coord=3283025..3285501&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

edit table

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

Notes

Sequence Features

[back to top]


Feature typeLocationDescription
edit table

See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Notes

Alleles and Phenotypes

[back to top]


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

ΔagaB (Keio:JW3107)

deletion

deletion

PMID:16738554[4]

Shigen
CGSC10366[5]

ΔagaB752::kan

PMID:16738554[4]

CGSC:99936


edit table

See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Notes

Genetic Resources

[back to top]


ResourceResource TypeSourceNotes/Reference

JW3107

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCACCAGTCCAAATATTCTCTT

Primer 2:CCGTCAGGGATTTGTTCTTTTTG

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: 10% [7]

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

edit table

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

Notes

Accessions in Other Databases

[back to top]


DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG12769

EchoBASE (EcoliWiki Page)

EchoBASE:EB2622

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3138

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3895

EcoGene (EcoliWiki Page)

EcoGene:EG12769

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:AGAB

ASAP (EcoliWikiPage)

ASAP:ABE-0010310


edit table

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

Notes

Links

[back to top]


NameURLComments
edit table

See Help:Links_table for how to enter or edit information in this section of EcoliWiki.


Categories

Product(s)

[back to top]



Nomenclature

Standard name

AgaB

Synonyms

N-acetylgalactosamine-specific enzyme IIB component of PTS[1], B3138[2][1], YraD[2][1], AgaB[2][1]

Product description

AgaB[2][3];

Component of ; EIIAga[2][3]

EC number (for enzymes)
edit table

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

Notes

Function

[back to top]


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 12.5 [8]

complete

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: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 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: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 12.5 [8]

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 12.5 [8]

complete

edit table

Interactions

Partner TypePartnerNotesReferences

Protein

Subunits of EIIAga

could be indirect


edit table

See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Notes

Localization

CompartmentDescriptionEvidenceNotes

plasma membrane

From EcoCyc[3]

edit table

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

Notes

Structure and Physical Properties

[back to top]


Physical Properties

Sequence

at EcoCyc 

MTSPNILLTR IDNRLVHGQV GVTWTSTIGA NLLVVVDDVV ANDDIQQKLM GITAETYGFG
IRFFTIEKTI NVIGKAAPHQ KIFLICRTPQ TVRKLVEGGI DLKDVNVGNM HFSEGKKQIS
SKVYVDDQDL TDLRFIKQRG VNVFIQDVPG DQKEQIPD
Mol. Wt

17.62 kDa (calc) [2]

pI
Extinction coefficient

8480 - 8605 (calc based on 2 Y, 1 W, and 1 C residues)

edit table

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

Domains/Motifs/Modification Sites

TypeResiduesDescriptionNotes

Domain

1 - 158

PTS EIIB type-4

UniProt:P42909

edit table

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

Structure

Structures
  • Representative homolog:
    1BLE|A (Bacillus subtilis)
    3-152 of 158 residues (E-value: 1.5e-17) (Percent Identity: 29.03)
  • View all other structures.
Models

View models at:

edit table

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

Notes

Gene Product Resources

[back to top]


Resource typeSourceNotes/Reference
edit table

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

Notes

Accessions in Other Databases

[back to top]


DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:AGAB-MONOMER

UniProt (EcoliWiki Page)

UniProt:P42909

PFAM (EcoliWiki Page)

PFAM:PF03830

RefSeq (EcoliWiki Page)

RefSeq:NP_417607

ModBase (EcoliWiki Page)

ModBase:P42909


edit table

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

Notes

Links

[back to top]


NameURLComments
edit table

See Help:Links_table for how to enter or edit information in this section of EcoliWiki.



Categories

[back to top]


Expression

[back to top]



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

[back to top]


Transcription unit(s)

agaSYBCDI

edit table
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

[back to top]


gbrowse_img.php?coord=3282172..3282212&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

[back to top]


Mutations Affecting Expression

Allele NameMutationPhenotypeReference
edit table

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

Expression Studies

TypeReferenceNotes

microarray

GenExpDB:b3138 (EcoliWiki Page)

Summary of data for agaB from multiple microarray studies

microarray

GEO Profiles:b3138 (EcoliWiki Page)

NCBI GEO profiles for agaB

edit table

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

Expression Resources

Resource NameResource TypeDescriptionSourceNotes
edit table

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

Notes

Accessions Related to agaB Expression

[back to top]


DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG12769

EchoBASE (EcoliWiki Page)

EchoBASE:EB2622

EcoliGenExpDB (EcoliWiki Page)

GenExpDB:b3138

EcoGene (EcoliWiki Page)

EcoGene:EG12769

edit table

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

Notes

Links

[back to top]


NameURLComments
edit table

See Help:Links_table for how to enter or edit information in this section of EcoliWiki.

Categories

[back to top]


Evolution

[back to top]



Homologs in Other Organisms

[back to top]


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

Do-It-Yourself Web Tools

Notes

Families

[back to top]


DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF03830

edit table

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

Notes

Links

[back to top]


NameURLComments
edit table

See Help:Links_table for how to enter or edit information in this section of EcoliWiki.

References

[back to top]


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 1.7 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 3.3 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 8.3 8.4 8.5 8.6 EcoCyc (release 12.5; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7

Categories

[back to top]


Retrieved from "http://ecoliwiki.net/colipedia/index.php/agaB:On_One_Page"
Personal tools