yhdY:On One Page

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

Quickview

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Standard Name

yhdY

Gene Synonym(s)

ECK3257, b3270, JW5545[1], JW5545

Product Desc.

YhdY[2][3];

Component of YhdW/YhdX/YhdY/YhdZ ABC transporter[2][3]

Putative ABC transporter permease protein; function unknown[4]

Product Synonyms(s)

predicted amino-acid transporter subunit[1], membrane component of ABC superfamily[1], B3270[2][1], YhdY[2][1] , ECK3257, JW5545, b3270

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): yhdWXYZ[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

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Notes

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Putative ABC transporter YhdWXYZ has an unknown substrate and yhdW' is an apparent pseudogene.[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

yhdY

Mnemonic

Systematic nomenclature

Synonyms

ECK3257, b3270, JW5545[1], JW5545

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Notes

Location(s) and DNA Sequence

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

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

73.7 minutes 

MG1655: 3419347..3420450
<gbrowseImage> name=NC_000913:3419347..3420450 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3349217..3350320
<gbrowseImage> name=NC_012967:3349217..3350320 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3306495..3307598
<gbrowseImage> name=NC_012759:3306495..3307598 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3421180..3422283
<gbrowseImage> name=NC_007779:3421180..3422283 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3517092..3518195
<gbrowseImage> name=NC_010473:3517092..3518195 source=DH10B preset=GeneLocation </gbrowseImage>

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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 Type Strain Genomic Location Evidence Reference Notes

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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.

Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

ΔyhdY (Keio:JW5545)

deletion

deletion

PMID:16738554

Shigen
CGSC11456[5]

ΔyhdY788::kan

PMID:16738554

CGSC:105166


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Notes

Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes

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Notes

Genetic Resources

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

Resource Resource Type Source Notes/Reference

JW5545

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCACAAAAGTATTGCTGTCTCA

Primer 2:CCATGCGGTGTACGCCCGGTGTT

6G9

Kohara Phage

Genobase

PMID:3038334

acrF3083::Tn10

Linked marker

CAG12075 = CGSC7447[5]

est. P1 cotransduction: 86% [6]
Synonyms:zhd-3083::Tn10, zhe-3083::Tn10

smg-3082::Tn10

Linked marker

CAG12071 = CGSC7444[5]

est. P1 cotransduction: 73% [6]
Synonyms:zhb-3082::Tn10, zhd-3082::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.

Database Accession Notes

EcoCyc

EcoCyc:EG12836

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12836

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002393

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947764

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2685

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010736

Escherichia coli str. K-12 substr. MG1655

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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

YhdY

Synonyms

predicted amino-acid transporter subunit[1], membrane component of ABC superfamily[1], B3270[2][1], YhdY[2][1] , ECK3257, JW5545, b3270

Product description

YhdY[2][3];

Component of YhdW/YhdX/YhdY/YhdZ ABC transporter[2][3]

Putative ABC transporter permease protein; function unknown[4]

EC number (for enzymes)


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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status

GO:0005215

transporter activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000515

F

Seeded from EcoCyc (v14.0)

complete

GO:0005215

transporter activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010065

F

Seeded from EcoCyc (v14.0)

complete

GO:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0997

C

Seeded from EcoCyc (v14.0)

complete

GO:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-1003

C

Seeded from EcoCyc (v14.0)

complete

GO:0006810

transport

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000515

P

Seeded from EcoCyc (v14.0)

complete

GO:0006810

transport

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010065

P

Seeded from EcoCyc (v14.0)

complete

GO:0006810

transport

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0813

P

Seeded from EcoCyc (v14.0)

complete

GO:0006865

amino acid transport

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0029

P

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000515

C

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0472

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010065

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0812

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-9909

C

Seeded from EcoCyc (v14.0)

complete

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

Partner Type Partner Notes References Evidence

Protein

Subunits of YhdW/YhdX/YhdY/YhdZ ABC transporter

could be indirect


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Notes

Localization

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

Compartment Description Evidence Reference/Source Notes

plasma membrane

C-terminus localized in the cytoplasm with 8 predicted transmembrane domains

Daley et al. (2005) [7]

plasma membrane

From EcoCyc[3]


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Notes

Structure and Physical Properties

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

Name
Sequence

at EcoCyc

MMTKVLLSHP PRPASHNSSR AMVWVRKNLF SSWSNSLLTI GCIWLMWELI PPLLNWAFLQ
ANWVGSTRAD CTKAGACWVF IHERFGQFMY GLYPHDQRWR INLALLIGLV SIAPMFWKIL
PHRGRYIAAW AVIYPLIVWW LMYGGFFALE RVETRQWGGL TLTLIIASVG IAGALPWGIL
LALGRRSHMP IVRILSVIFI EFWRGVPLIT VLFMSSVMLP LFMAEGTSID KLIRALVGVI
LFQSAYVAEV VRGGLQALPK GQYEAAESLA LGYWKTQGLV ILPQALKLVI PGLVNTIIAL
FKDTSLVIII GLFDLFSSVQ QATVDPAWLG MSTEGYVFAA LIYWIFCFSM SRYSQYLEKR
FNTGRTPH
Length

368

Mol. Wt

41.616 kDa

pI

10.2 (calculated)

Extinction coefficient

116,880 - 117,380 (calc based on 12 Y, 18 W, and 4 C residues)


Domains/Motifs/Modification Sites

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

Type Residues Description Notes References

Domain

173..362

PF00528 Binding-protein-dependent transport system inner membrane component

PMID:19920124

<motif_map/>

tmhmm.php?gene=yhdY&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

<beststructure> gene=yhdY taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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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 type Source Notes/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.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:90111567

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947764

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010736

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P45768

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12836

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12836

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947764

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002393

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2685

Escherichia coli str. K-12 substr. MG1655

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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

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MG1655

0a

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

Low confidence in the sequencing data set.

PMID: 24766808

Protein

E. coli K-12 MG1655

1a

molecules/cell/generation

  • Medium: MOPS Minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

Low confidence in the sequencing data set.

PMID: 24766808

Protein

E. coli K-12 MG1655

0a

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

Low confidence in the sequencing data set.

PMID: 24766808

Notes

Transcription and Transcriptional Regulation

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<protect>

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

Transcription unit(s)

yhdWXYZ

Figure courtesy of RegulonDB

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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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<protect><gbrowseImage> name=NC_000913:3419327..3419367 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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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

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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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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference


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

Type Reference Notes

microarray

GEO Profiles:b3270 (EcoliWiki Page)

NCBI GEO profiles for yhdY

microarray

GenExpDB:b3270 (EcoliWiki Page)

Summary of data for yhdY from multiple microarray studies


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

Resource Name Resource Type Description Source Notes

GFP Fusion

Intergenic region (3418781..3418995) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ14; Well:E5[8]

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Notes

Accessions Related to yhdY Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG12836

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2685

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3270

EcoGene

EcoGene:EG12836

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002393

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010736

Escherichia coli str. K-12 substr. MG1655

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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.

Organism Homologs (Statistics) Comments

Shigella flexneri

YHDY

From SHIGELLACYC

E. coli O157

YHDY

From ECOO157CYC


Do-It-Yourself Web Tools

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Notes

Families

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

Database Accession Notes

Pfam (EcoliWiki Page)

PF00528 Binding-protein-dependent transport system inner membrane component

EcoCyc

EcoCyc:EG12836

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12836

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002393

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2685

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010736

Escherichia coli str. K-12 substr. MG1655

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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. Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed
  8. Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

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