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Standard Name

garP

Gene Synonym(s)

ECK3115, b3127, JW3096, yhaU[1]

Product Desc.

YhaU MFS transporter[2][3]

Probable D-galactarate transporter, membrane protein[4]

Product Synonyms(s)

predicted (D)-galactarate transporter[1], B3127[2][1], GarP[2][1], YhaU[2][1]

Function from GO
Knock-Out Phenotype
Regulation/Expression

transcription unit(s): garPLRK-rnpB[2], yhaUFED-rnpB

Regulation/Activity
Quick Links

DNA display    Protein display    Pubmed(garP)    Textpresso(garP)

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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

garP

Mnemonic

Galactarate

Synonyms

ECK3115, b3127, JW3096, yhaU[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

70.51 minutes 

MG1655: 3272929..3271595
gbrowse_img.php?coord=3271595..3272929&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 3207836..3206502
gbrowse_img.php?coord=3206502..3207836&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 3274762..3273428
gbrowse_img.php?coord=3273428..3274762&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 3370674..3369340
gbrowse_img.php?coord=3369340..3370674&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

BW2952

NC_012759: 3158743..3160077
gbrowse_img.php?coord=3158743..3160077&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

ΔgarP (Keio:JW3096)

deletion

deletion

PMID:16738554

Shigen
CGSC10358[5]

ΔgarP741::kan

PMID:16738554

CGSC:101100


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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

JW3096

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCATTCTGGACACCGTTGACGA

Primer 2:CCTTTCTGCAATTCCATACGTTT

aer-3075::Tn10

Linked marker

CAG12152 = CGSC7438[5]

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

sfsB203::Tn10

Linked marker

CAG12072 = CGSC7440[5]

est. P1 cotransduction: 5% [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:EG12760

EchoBASE (EcoliWiki Page)

EchoBASE:EB2613

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3127

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3882

EcoGene (EcoliWiki Page)

EcoGene:EG12760

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YHAU

ASAP (EcoliWikiPage)

ASAP:ABE-0010279


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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

GarP

Synonyms

predicted (D)-galactarate transporter[1], B3127[2][1], GarP[2][1], YhaU[2][1]

Product description

YhaU MFS transporter[2][3]

Probable D-galactarate transporter, membrane protein[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:IPR004744
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:0006810

transport

GO_REF:0000002
GO_REF:0000002
GO_REF:0000004

IEA: Inferred from Electronic Annotation

InterPro:IPR004744
InterPro:IPR007114
SP_KW:KW-0813

P

Seeded from EcoCyc [7]

complete

GO:0005215

transporter activity

GO_REF:0000002
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004744
InterPro:IPR007114

F

Seeded from EcoCyc [7]

complete

GO:0015292

uniporter activity

F

Seeded from EcoCyc 11.1[3].

required fields missing

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

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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 11 predicted transmembrane domains

Daley et al. (2005) [9]

plasma membrane

From EcoCyc[3]


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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 

MILDTVDEKK KGVHTRYLIL LIIFIVTAVN YADRATLSIA GTEVAKELQL SAVSMGYIFS
AFGWAYLLMQ IPGGWLLDKF GSKKVYTYSL FFWSLFTFLQ GFVDMFPLAW AGISMFFMRF
MLGFSEAPSF PANARIVAAW FPTKERGTAS AIFNSAQYFS LALFSPLLGW LTFAWGWEHV
FTVMGVIGFV LTALWIKLIH NPTDHPRMSA EELKFISENG AVVDMDHKKP GSAAASGPKL
HYIKQLLSNR MMLGVFFGQY FINTITWFFL TWFPIYLVQE KGMSILKVGL VASIPALCGF
AGGVLGGVFS DYLIKRGLSL TLARKLPIVL GMLLASTIIL CNYTNNTTLV VMLMALAFFG
KGFGALGWPV ISDTAPKEIV GLCGGVFNVF GNVASIVTPL VIGYLVSELH SFNAALVFVG
CSALMAMVCY LFVVGDIKRM ELQK
Length

444

Mol. Wt

49.01 kDa

pI

9.3 (calculated)

Extinction coefficient

86,860 - 87,485 (calc based on 14 Y, 12 W, and 5 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=garP&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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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:YHAU-MONOMER

UniProt (EcoliWiki Page)

UniProt:P0AA80

PFAM (EcoliWiki Page)

PFAM:PF00083

RefSeq (EcoliWiki Page)

RefSeq:NP_417596


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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)

garPLRK-rnpB

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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=3272909..3272949&genome=ecoli&name=MG1655&trackset=Gene+DNA_+Protein+flip&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:b3127 (EcoliWiki Page)

NCBI GEO profiles for garP

microarray

GenExpDB:b3127 (EcoliWiki Page)

Summary of data for garP 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 garP Expression

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

DatabaseAccessionNotes

EcoCyc (EcoliWiki Page)

EcoCyc:EG12760

EchoBASE (EcoliWiki Page)

EchoBASE:EB2613

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3127

EcoGene (EcoliWiki Page)

EcoGene:EG12760


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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

Anopheles gambiae

  • ENSANGP00000010934 (score: 1.000; bootstrap: 93%)
  • ENSANGP00000022197 (score: 1.000; bootstrap: 84%)
  • ENSANGP00000011442 (score: 0.700)
  • ENSANGP00000009081 (score: 0.301)
  • ENSANGP00000022236 (score: 0.264)
  • ENSANGP00000021422 (score: 0.226)
  • ENSANGP00000011785 (score: 0.216)
  • ENSANGP00000010456 (score: 0.196)
  • ENSANGP00000016038 (score: 0.169)
  • ENSANGP00000019885 (score: 0.125)
  • ENSANGP00000029280 (score: 0.110)
  • ENSANGP00000013021 (score: 0.092)

From Inparanoid:20070104

Apis mellifera

  • ENSAPMP00000010652 (score: 1.000; bootstrap: 92%)
  • ENSAPMP00000029890 (score: 1.000; bootstrap: 63%)
  • ENSAPMP00000003545 (score: 0.250)
  • ENSAPMP00000015840 (score: 0.243)
  • ENSAPMP00000032854 (score: 0.178)
  • ENSAPMP00000034543 (score: 0.148)
  • ENSAPMP00000003525 (score: 0.144)
  • ENSAPMP00000018328 (score: 0.144)
  • ENSAPMP00000008626 (score: 0.086)

From Inparanoid:20070104

Arabidopsis thaliana

  • AT4G00370 (score: 1.000; bootstrap: 100%)
  • AT2G38060 (score: 1.000; bootstrap: 100%)
  • AT3G46980 (score: 1.000; bootstrap: 100%)
  • AT2G29650 (score: 0.594)
  • AT5G44370 (score: 0.109)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000009255 (score: 1.000; bootstrap: 94%)
  • ENSBTAP00000007935 (score: 0.750)
  • ENSBTAP00000001445 (score: 0.647)
  • ENSBTAP00000014654 (score: 0.213)
  • ENSBTAP00000003426 (score: 0.112)
  • ENSBTAP00000035519 (score: 0.103)
  • ENSBTAP00000026833 (score: 0.095)
  • ENSBTAP00000008247 (score: 0.082)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00025040 (score: 1.000; bootstrap: 79%)
  • WBGene00029008 (score: 0.179)
  • WBGene00031579 (score: 0.171)
  • WBGene00042684 (score: 0.120)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00022647 (score: 1.000; bootstrap: 84%)
  • WBGene00008000 (score: 0.174)
  • WBGene00001135 (score: 0.168)
  • WBGene00011556 (score: 0.110)
  • WBGene00010755 (score: 0.110)

From Inparanoid:20070104

Canis familiaris

  • ENSCAFP00000005458 (score: 1.000; bootstrap: 79%)
  • ENSCAFP00000015622 (score: 1.000; bootstrap: 55%)
  • ENSCAFP00000014842 (score: 0.685)
  • ENSCAFP00000010148 (score: 0.638)
  • ENSCAFP00000015668 (score: 0.379)
  • ENSCAFP00000015578 (score: 0.259)
  • ENSCAFP00000003868 (score: 0.209)

From Inparanoid:20070104

Ciona intestinalis

  • ENSCINP00000011106 (score: 1.000; bootstrap: -1%)
  • ENSCINP00000014430 (score: 1.000; bootstrap: 91%)
  • ENSCINP00000002822 (score: 0.250)
  • ENSCINP00000020110 (score: 0.248)
  • ENSCINP00000016071 (score: 0.205)
  • ENSCINP00000018354 (score: 0.196)
  • ENSCINP00000001647 (score: 0.168)
  • ENSCINP00000015291 (score: 0.156)

From Inparanoid:20070104

Danio rerio

  • ZDB-GENE-050105-4 (score: 1.000; bootstrap: 91%)
  • ZDB-GENE-030616-554 (score: 0.840)
  • ZDB-GENE-050105-5 (score: 0.128)

From Inparanoid:20070104

Dictyostelium discoideum

  • DDB0204713 (score: 1.000; bootstrap: 100%)
  • DDB0205875 (score: 0.300)

From Inparanoid:20070104

Drosophila melanogaster

  • FBgn0030452 (score: 1.000; bootstrap: 94%)
  • FBgn0034392 (score: 1.000; bootstrap: 94%)
  • FBgn0038799 (score: 1.000; bootstrap: 89%)
  • FBgn0034394 (score: 0.422)
  • FBgn0010651 (score: 0.370)
  • FBgn0033234 (score: 0.290)
  • FBgn0034784 (score: 0.287)
  • FBgn0034783 (score: 0.278)
  • FBgn0050272 (score: 0.270)
  • FBgn0050265 (score: 0.267)
  • FBgn0034782 (score: 0.262)
  • FBgn0033048 (score: 0.244)
  • FBgn0024315 (score: 0.241)
  • FBgn0039886 (score: 0.238)
  • FBgn0031424 (score: 0.225)
  • FBgn0034785 (score: 0.224)
  • FBgn0010497 (score: 0.204)
  • FBgn0029727 (score: 0.198)
  • FBgn0031645 (score: 0.195)
  • FBgn0031307 (score: 0.165)
  • FBgn0028513 (score: 0.164)
  • FBgn0034490 (score: 0.144)
  • FBgn0016684 (score: 0.140)
  • FBgn0058263 (score: 0.073)
  • FBgn0025684 (score: 0.053)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA18114-PA (score: 1.000; bootstrap: 93%)
  • GA18084-PA (score: 1.000; bootstrap: 87%)
  • GA13487-PA (score: 1.000; bootstrap: 87%)
  • GA13486-PA (score: 0.396)
  • GA21326-PA (score: 0.356)
  • GA15741-PA (score: 0.320)
  • GA22061-PA (score: 0.319)
  • GA15735-PA (score: 0.288)
  • GA20823-PA (score: 0.274)
  • GA15178-PA (score: 0.250)
  • GA15786-PA (score: 0.238)
  • GA17586-PA (score: 0.236)
  • GA18795-PA (score: 0.227)
  • GA20000-PA (score: 0.223)
  • GA18388-PA (score: 0.203)
  • GA22101-PA (score: 0.187)
  • GA22082-PA (score: 0.169)
  • GA10155-PA (score: 0.163)
  • GA13728-PA (score: 0.057)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000018888 (score: 1.000; bootstrap: 92%)
  • ENSGALP00000005839 (score: 0.713)
  • ENSGALP00000025604 (score: 0.213)

From Inparanoid:20070104

Homo sapiens

  • ENSP00000221485 (score: 1.000; bootstrap: 95%)
  • ENSP00000351776 (score: 0.751)
  • ENSP00000316909 (score: 0.701)
  • ENSP00000311506 (score: 0.217)
  • ENSP00000274755 (score: 0.113)
  • ENSP00000265425 (score: 0.110)
  • ENSP00000244527 (score: 0.098)

From Inparanoid:20070104

Macaca mulatta

  • ENSMMUP00000023220 (score: 1.000; bootstrap: 94%)
  • ENSMMUP00000026804 (score: 0.610)
  • ENSMMUP00000019427 (score: 0.499)
  • ENSMMUP00000003481 (score: 0.123)
  • ENSMMUP00000003471 (score: 0.121)
  • ENSMMUP00000003473 (score: 0.077)
  • ENSMMUP00000010648 (score: 0.070)

From Inparanoid:20070104

Monodelphis domestica

  • ENSMODP00000011627 (score: 1.000; bootstrap: 94%)
  • ENSMODP00000006178 (score: 0.601)
  • ENSMODP00000023095 (score: 0.202)
  • ENSMODP00000017634 (score: 0.135)
  • ENSMODP00000005059 (score: 0.129)
  • ENSMODP00000013332 (score: 0.127)
  • ENSMODP00000016033 (score: 0.111)

From Inparanoid:20070104

Mus musculus

  • MGI:2156052 (score: 1.000; bootstrap: 92%)
  • MGI:3039629 (score: 0.698)
  • MGI:1920211 (score: 0.500)
  • MGI:1924105 (score: 0.221)
  • MGI:2443098 (score: 0.121)
  • MGI:2442850 (score: 0.110)
  • MGI:103209 (score: 0.099)
  • MGI:2389216 (score: 0.099)

From Inparanoid:20070104

Oryza gramene

  • Q652N5 (score: 1.000; bootstrap: 100%)
  • Q53WP9 (score: 1.000; bootstrap: 100%)
  • Q9SDI4 (score: 0.535)
  • Q8W0H5 (score: 0.365)
  • Q5N7A9 (score: 0.257)
  • Q53P54 (score: 0.130)

From Inparanoid:20070104

Pan troglodytes

  • ENSPTRP00000045307 (score: 1.000; bootstrap: 94%)
  • ENSPTRP00000009086 (score: 0.466)
  • ENSPTRP00000019388 (score: 0.245)
  • ENSPTRP00000031355 (score: 0.222)
  • ENSPTRP00000030375 (score: 0.121)
  • ENSPTRP00000030376 (score: 0.097)

From Inparanoid:20070104

Rattus norvegicus

  • ENSRNOP00000022383 (score: 1.000; bootstrap: 95%)
  • ENSRNOP00000028064 (score: 0.723)
  • ENSRNOP00000010207 (score: 0.712)
  • ENSRNOP00000012474 (score: 0.221)
  • ENSRNOP00000023241 (score: 0.085)
  • ENSRNOP00000029152 (score: 0.063)

From Inparanoid:20070104

Saccharomyces cerevisiae

  • YLR004C (score: 1.000; bootstrap: 100%)
  • YJR152W (score: 0.190)
  • YLL055W (score: 0.140)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000141633 (score: 1.000; bootstrap: 74%)
  • NEWSINFRUP00000158609 (score: 0.877)
  • NEWSINFRUP00000143039 (score: 0.742)
  • NEWSINFRUP00000171314 (score: 0.740)
  • NEWSINFRUP00000132367 (score: 0.595)
  • NEWSINFRUP00000131655 (score: 0.260)
  • NEWSINFRUP00000148094 (score: 0.057)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00022797001 (score: 1.000; bootstrap: 77%)
  • GSTENP00024087001 (score: 0.656)
  • GSTENP00035063001 (score: 0.592)
  • GSTENP00017860001 (score: 0.585)
  • GSTENP00025579001 (score: 0.509)
  • GSTENP00018669001 (score: 0.217)
  • GSTENP00010472001 (score: 0.096)

From Inparanoid:20070104

Xenopus tropicalis

  • ENSXETP00000005429 (score: 1.000; bootstrap: 90%)
  • ENSXETP00000018393 (score: 0.674)
  • ENSXETP00000007371 (score: 0.478)
  • ENSXETP00000048895 (score: 0.223)

From Inparanoid:20070104

Shigella flexneri

YHAU

From SHIGELLACYC

E. coli O157

YHAU

From ECOO157CYC

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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:PF00083


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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 3.3 3.4 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 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
  9. ↑ Daley DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308: 1321-3 PubMed EcoliWiki page

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