ydiK: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

ydiK

Gene Synonym(s)

ECK1685, b1688, JW1678[1], JW1678

Product Desc.

hypothetical protein; transcription may be purine regulated[2]; predicted inner membrane protein[3]

Putative membrane permease, 9 TM helices; has predicted PurR box[4]

Product Synonyms(s)

predicted inner membrane protein[1], B1688[2][1], YdiK[2][1] , ECK1685, JW1678, b1688

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ydiK[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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Probable false positive lipoprotein prediction, Cys not conserved, 9 CM TMs predicted.[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

ydiK

Mnemonic

Systematic nomenclature

Synonyms

ECK1685, b1688, JW1678[1], JW1678

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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

38.09 minutes 

MG1655: 1767098..1768210
<gbrowseImage> name=NC_000913:1767098..1768210 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1746341..1747453
<gbrowseImage> name=NC_012967:1746341..1747453 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1659157..1660269
<gbrowseImage> name=NC_012759:1659157..1660269 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1770788..1771900
<gbrowseImage> name=NC_007779:1770788..1771900 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1857669..1858781
<gbrowseImage> name=NC_010473:1857669..1858781 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

ΔydiK (Keio:JW1678)

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

Plasmid clone

Shigen

PMID:16769691

Status:

Primer 1:

Primer 2:

15G10

Kohara Phage

Genobase

PMID:3038334

8G8

Kohara Phage

Genobase

PMID:3038334

zdd-235::Tn10

Linked marker

CAG18461 = CGSC7378[5]

est. P1 cotransduction: % [6]
Synonyms:zdc-235::Tn10

zdi-925::Tn10

Linked marker

CAG12151 = CGSC7385[5]

est. P1 cotransduction: 71% [6]
Synonyms:zdh-925::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:G6914

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13970

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003502

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946183

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3727

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005637

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

YdiK

Synonyms

predicted inner membrane protein[1], B1688[2][1], YdiK[2][1] , ECK1685, JW1678, b1688

Product description

hypothetical protein; transcription may be purine regulated[2]; predicted inner membrane protein[3]

Putative membrane permease, 9 TM helices; has predicted PurR box[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: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: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: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

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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]


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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

MVNVRQPRDV AQILLSVLFL AIMIVACLWI VQPFILGFAW AGTVVIATWP VLLRLQKIMF
GRRSLAVLVM TLLLVMVFII PIALLVNSIV DGSGPLIKAI SSGDMTLPDL AWLNTIPVIG
AKLYAGWHNL LDMGGTAIMA KVRPYIGTTT TWFVGQAAHI GRFMVHCALM LLFSALLYWR
GEQVAQGIRH FATRLAGVRG DAAVLLAAQA IRAVALGVVV TALVQAVLGG IGLAVSGVPY
ATLLTVLMIL SCLVQLGPLP VLIPAIIWLY WTGDTTWGTV LLVWSGVVGT LDNVIRPMLI
RMGADLPLIL ILSGVIGGLI AFGMIGLFIG PVLLAVSWRL FAAWVEEVPP PTDQPEEILE
ELGEIEKPNK
Length

370

Mol. Wt

39.841 kDa

pI

8.5 (calculated)

Extinction coefficient

78,950 - 79,325 (calc based on 5 Y, 13 W, and 3 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

14..345

PF01594 Domain of unknown function DUF20

PMID:19920124

<motif_map/>

tmhmm.php?gene=ydiK&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=ydiK 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:16129644

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946183

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005637

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AFS7

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6914

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13970

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946183

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003502

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3727

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

789

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

137

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

210

molecules/cell/generation

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

Ribosome Profiling

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)

ydiK

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_000913:1767078..1767118 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:b1688 (EcoliWiki Page)

NCBI GEO profiles for ydiK

microarray

GenExpDB:b1688 (EcoliWiki Page)

Summary of data for ydiK 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 ydiK Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G6914

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3727

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1688

EcoGene

EcoGene:EG13970

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003502

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005637

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

S1850

From SHIGELLACYC

E. coli O157

Z2716

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)

PF01594 Domain of unknown function DUF20

EcoCyc

EcoCyc:G6914

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13970

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003502

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3727

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005637

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 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. 3.0 3.1 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).
  7. Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed

Categories

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