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

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Standard Name

setA

Gene Synonym(s)

ECK0072, b0070, JW0069, yabM[1]

Product Desc.

YabM MFS transporter[2][3]

Broad specificity sugar efflux transporter[4]

Product Synonyms(s)

broad specificity sugar efflux system[1], B0070[2][1], SetA[2][1], YabM[2][1]

Function from GO

Biological Process

Molecular Function

Cellular Component

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): sgrS[2]

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(setA)    Textpresso(setA)

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Notes

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Major Facilitator Superfamily (MFS).[4]



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

setA

Mnemonic

Sugar efflux transporter

Synonyms

ECK0072, b0070, JW0069, yabM[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

1.67 minutes 

MG1655: 77621..78799
gbrowse_img.php?coord=77621..78799&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 80425..81603
gbrowse_img.php?coord=80425..81603&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 77621..78799
gbrowse_img.php?coord=77621..78799&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

BW2952

NC_012759: 77620..78798
gbrowse_img.php?coord=77620..78798&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

ΔsetA (Keio:JW0069)

deletion

deletion

PMID:16738554

Shigen
CGSC8370[5]

ΔsetA777::kan

PMID:16738554

CGSC:102920


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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

JW0069

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCATCTGGATAATGACGATGGC

Primer 2:CCAACGTCTTTAACCTTTGCGGT

carB96::Tn10

Linked marker

CAG12093 = CGSC7322[5]

est. P1 cotransduction: 14% [6]
Synonyms:car-96::Tn10

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[5]

est. P1 cotransduction: 82% [6]
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).

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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:EG11754

EchoBASE (EcoliWiki Page)

EchoBASE:EB1704

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0070

EcoGene (EcoliWiki Page)

EcoGene:EG11754

ASAP (EcoliWikiPage)

ASAP:ABE-0000257


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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

SetA

Synonyms

broad specificity sugar efflux system[1], B0070[2][1], SetA[2][1], YabM[2][1]

Product description

YabM MFS transporter[2][3]

Broad specificity sugar efflux transporter[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:0016021

integral to membrane

GO_REF:0000002
GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR004750
InterPro:IPR007114
SP_KW:KW-0812

C

Seeded from EcoCyc [7]

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:0015542

sugar efflux transmembrane transporter activity

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004750

F

Seeded from EcoCyc 12.5 [8]

complete

GO:0008643

carbohydrate transport

GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR004750
SP_KW:KW-0762

P

Seeded from EcoCyc [7]

complete

GO:0015767

lactose transport

PMID:10438463

IDA: Inferred from Direct Assay

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:0005215

transporter activity

GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007114

F

Seeded from EcoCyc [7]

complete

GO:0015758

glucose transport

PMID:10438463

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc [7]

complete

GO:0005886

plasma membrane

GO_REF:0000004
GO_REF:0000004
GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_KW:KW-0997
SP_KW:KW-1003
SP_SL:SL-0037

C

Seeded from EcoCyc [7]

complete

GO:0016052

carbohydrate catabolic process

P

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0015767

lactose transport

PMID:10438463

IDA: Inferred from Direct Assay

P

complete

GO:0015542

sugar efflux transmembrane transporter activity

PMID:10438463

IDA: Inferred from Direct Assay

F

complete

GO:0015758

glucose transport

PMID:10438463

IDA: Inferred from Direct Assay

P

complete

GO:0016020

membrane

PMID:10438463

IDA: Inferred from Direct Assay

C

complete

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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
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Notes

Localization

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

CompartmentDescriptionEvidenceSourceNotes

plasma membrane

C-terminus localized in the cytoplasm with 12 predicted transmembrane domains

Daley et al. (2005) [9]


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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 

MIWIMTMARR MNGVYAAFML VAFMMGVAGA LQAPTLSLFL SREVGAQPFW IGLFYTVNAI
AGIGVSLWLA KRSDSQGDRR KLIIFCCLMA IGNALLFAFN RHYLTLITCG VLLASLANTA
MPQLFALARE YADNSAREVV MFSSVMRAQL SLAWVIGPPL AFMLALNYGF TVMFSIAAGI
FTLSLVLIAF MLPSVARVEL PSENALSMQG GWQDSNVRML FVASTLMWTC NTMYIIDMPL
WISSELGLPD KLAGFLMGTA AGLEIPAMIL AGYYVKRYGK RRMMVIAVAA GVLFYTGLIF
FNSRMALMTL QLFNAVFIGI VAGIGMLWFQ DLMPGRAGAA TTLFTNSIST GVILAGVIQG
AIAQSWGHFA VYWVIAVISV VALFLTAKVK DV
Length

392

Mol. Wt

42.714 kDa

pI

9.9 (calculated)

Extinction coefficient

71,390 - 71,890 (calc based on 11 Y, 10 W, and 4 C residues)

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Domains/Motifs/Modification Sites

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

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

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

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:B0070-MONOMER

UniProt (EcoliWiki Page)

UniProt:P31675

PFAM (EcoliWiki Page)

PFAM:PF07690

RefSeq (EcoliWiki Page)

RefSeq:YP_025293


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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)

sgrS

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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=77601..77641&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:b0070 (EcoliWiki Page)

NCBI GEO profiles for setA

microarray

GenExpDB:b0070 (EcoliWiki Page)

Summary of data for setA 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

GFP Fusion

Intergenic region (77211..77657) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ15; Well:H6[10]

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Notes

Accessions Related to setA Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG11754

EchoBASE (EcoliWiki Page)

EchoBASE:EB1704

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0070

EcoGene (EcoliWiki Page)

EcoGene:EG11754


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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

YABM

From SHIGELLACYC

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Do-It-Yourself Web Tools

Notes

Families

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

DatabaseAccessionNotes

PFAM (EcoliWiki Page)

PFAM:PF07690


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Notes

Links

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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 1.7 1.8 1.9 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 4.2 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. ↑ 8.0 8.1 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. ↑ Zaslaver A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat Methods 3: 623-8 PubMed EcoliWiki page

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