yhdZ: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

yhdZ

Gene Synonym(s)

ECK3258, b3271, JW3239[1], JW3239

Product Desc.

YhdZ[2][3];

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

Putative ABC transporter ATP-binding protein; function unknown[4]

Product Synonyms(s)

predicted amino-acid transporter subunit[1], ATP-binding component of ABC superfamily[1], B3271[2][1], YhdZ[2][1] , ECK3258, JW3239, b3271

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  

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

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

yhdZ

Mnemonic

Systematic nomenclature

Synonyms

ECK3258, b3271, JW3239[1], JW3239

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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

73.72 minutes 

MG1655: 3420458..3421216
<gbrowseImage> name=NC_000913:3420458..3421216 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3350328..3351086
<gbrowseImage> name=NC_012967:3350328..3351086 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3307606..3308364
<gbrowseImage> name=NC_012759:3307606..3308364 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3422291..3423049
<gbrowseImage> name=NC_007779:3422291..3423049 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3518203..3518961
<gbrowseImage> name=NC_010473:3518203..3518961 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

ΔyhdZ (Keio:JW3239)

deletion

deletion

PMID:16738554

Shigen


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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

JW3239

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCAGCCAAATTTTACTGCAACC

Primer 2:CCATGGATTACCTGCGATAAAAA

6G9

Kohara Phage

Genobase

PMID:3038334

acrF3083::Tn10

Linked marker

CAG12075 = CGSC7447[5]

est. P1 cotransduction: 83% [6]
Synonyms:zhd-3083::Tn10, zhe-3083::Tn10

smg-3082::Tn10

Linked marker

CAG12071 = CGSC7444[5]

est. P1 cotransduction: 76% [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:EG12837

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12837

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002394

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947763

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2686

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010738

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

YhdZ

Synonyms

predicted amino-acid transporter subunit[1], ATP-binding component of ABC superfamily[1], B3271[2][1], YhdZ[2][1] , ECK3258, JW3239, b3271

Product description

YhdZ[2][3];

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

Putative ABC transporter ATP-binding 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:0000166

nucleotide binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

Seeded from EcoCyc (v14.0)

complete

GO:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003439

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017871

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

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: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:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0472

C

Seeded from EcoCyc (v14.0)

complete

GO:0016887

ATPase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003439

F

Seeded from EcoCyc (v14.0)

complete

GO:0016887

ATPase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017871

F

Seeded from EcoCyc (v14.0)

complete

GO:0017111

nucleoside-triphosphatase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003593

F

Seeded from EcoCyc (v14.0)

complete

GO:0019898

extrinsic to membrane

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-9903

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

Protein

groL

PMID:16606699

Experiment(s):EBI-1145342

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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

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

MSQILLQPAN AMITLENVNK WYGQFHVLKN INLTVQPGER IVLCGPSGSG KSTTIRCINH
LEEHQQGRIV VDGIELNEDI RNIERVRQEV GMVFQHFNLF PHLTVLQNCT LAPIWVRKMP
KKEAEDLAVH YLERVRIAEH AHKFPGQISG GQQQRVAIAR SLCMKPKIML FDEPTSALDP
EMVKEVLDTM IGLAQSGMTM LCVTHEMGFA RTVADRVIFM DRGEIVEQAA PDEFFAHPKS
ERTRAFLSQV IH
Length

252

Mol. Wt

28.573 kDa

pI

7.1 (calculated)

Extinction coefficient

13,980 - 14,605 (calc based on 2 Y, 2 W, and 5 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

52..176

PF00005 ABC transporter

PMID:19920124

<motif_map/>

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

Structures

<beststructure> gene=yhdZ 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:16131159

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947763

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010738

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P45769

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12837

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12837

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947763

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002394

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2686

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

29

molecules/cell/generation

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

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

21

molecules/cell/generation

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

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

27a

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_000913:3420438..3420478 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:b3271 (EcoliWiki Page)

NCBI GEO profiles for yhdZ

microarray

GenExpDB:b3271 (EcoliWiki Page)

Summary of data for yhdZ 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

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Notes

Accessions Related to yhdZ Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG12837

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2686

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3271

EcoGene

EcoGene:EG12837

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002394

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010738

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

Oryza gramene

  • Q5Z8H2 (score: 1.000; bootstrap: 87%)

From Inparanoid:20070104

Takifugu rubripes

  • NEWSINFRUP00000130824 (score: 1.000; bootstrap: 57%)
  • NEWSINFRUP00000130826 (score: 0.180)
  • NEWSINFRUP00000167567 (score: 0.137)
  • NEWSINFRUP00000182359 (score: 0.125)
  • NEWSINFRUP00000177047 (score: 0.125)
  • NEWSINFRUP00000168237 (score: 0.097)
  • NEWSINFRUP00000171182 (score: 0.092)

From Inparanoid:20070104

Tetraodon nigroviridis

  • GSTENP00014344001 (score: 1.000; bootstrap: 57%)
  • GSTENP00014343001 (score: 0.105)
  • GSTENP00020877001 (score: 0.101)
  • GSTENP00038511001 (score: 0.091)
  • GSTENP00014937001 (score: 0.051)

From Inparanoid:20070104

Shigella flexneri

YHDZ

From SHIGELLACYC

E. coli O157

YHDZ

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)

PF00005 ABC transporter

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

PFAM (EcoliWiki Page)

PFAM:PF00005

EcoCyc

EcoCyc:EG12837

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12837

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002394

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2686

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010738

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 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).

Categories

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