ynfK: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

ynfK

Gene Synonym(s)

ECK1588, b1593, JW5264[1], JW5264

Product Desc.

hypothetical protein[2][3]

Putative dethiobiotin synthase, function unknown[4]

Product Synonyms(s)

predicted dethiobiotin synthetase[1], B1593[2][1], YnfK[2][1] , ECK1588, JW5264, b1593

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ynfK[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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YnfK is 50% identical to paralog BioD.[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

ynfK

Mnemonic

Systematic nomenclature

Synonyms

ECK1588, b1593, JW5264[1], JW5264

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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

35.88 minutes 

MG1655: 1665243..1664548
<gbrowseImage> name=NC_000913:1664548..1665243 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1644414..1643719
<gbrowseImage> name=NC_012967:1643719..1644414 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1556607..1557302
<gbrowseImage> name=NC_012759:1556607..1557302 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1668933..1668238
<gbrowseImage> name=NC_007779:1668238..1668933 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1756204..1755509
<gbrowseImage> name=NC_010473:1755509..1756204 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

ΔynfK (Keio:JW5264)

deletion

deletion

PMID:16738554

Shigen
CGSC11279[5]

ΔynfK741::kan

PMID:16738554

CGSC:105820


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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

JW5264

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCTGAAGCGTTTCTTTATTAC

Primer 2:CCaACCGTGACTCTATCTACCGC

6F6

Kohara Phage

Genobase

PMID:3038334

E3F2

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: % [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:G6851

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13849

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003440

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944927

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3610

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005319

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

YnfK

Synonyms

predicted dethiobiotin synthetase[1], B1593[2][1], YnfK[2][1] , ECK1588, JW5264, b1593

Product description

hypothetical protein[2][3]

Putative dethiobiotin synthase, 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:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0000287

magnesium ion binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00336

F

Seeded from EcoCyc (v14.0)

complete

GO:0000287

magnesium ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004472

F

Seeded from EcoCyc (v14.0)

complete

GO:0000287

magnesium ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0460

F

Seeded from EcoCyc (v14.0)

complete

GO:0004141

dethiobiotin synthase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00336

F

Seeded from EcoCyc (v14.0)

complete

GO:0004141

dethiobiotin synthase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004472

F

Seeded from EcoCyc (v14.0)

complete

GO:0004141

dethiobiotin synthase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:6.3.3.3

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00336

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004472

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:0009102

biotin biosynthetic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00336

P

Seeded from EcoCyc (v14.0)

complete

GO:0009102

biotin biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004472

P

Seeded from EcoCyc (v14.0)

complete

GO:0009102

biotin biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0093

P

Seeded from EcoCyc (v14.0)

complete

GO:0009236

cobalamin biosynthetic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002586

P

Seeded from EcoCyc (v14.0)

complete

GO:0016874

ligase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0436

F

Seeded from EcoCyc (v14.0)

complete

GO:0042242

cobyrinic acid a,c-diamide synthase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR002586

F

Seeded from EcoCyc (v14.0)

complete

GO:0003674

molecular function

n/a

ND: No biological Data available

F

Missing: reference

GO:0005575

cellular component

n/a

ND: No biological Data available

C

Missing: reference

GO:0008150

biological process

n/a

ND: No biological Data available

P

Missing: reference

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

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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

MELVMLKRFF ITGTDTSVGK TVVSRALLQA LASQGKTVAG YKPVAKGSKE TPEGLRNKDA
LVLQSVSTIE LPYEAVNPIA LSEEESSVAH SCPINYTLIS NGLANLTEKV DHVVVEGTGG
WRSLMNDLRP LSEWVVQEQL PVLMVVGIQE GCINHALLTA QAIANDGLPL IGWVANRINP
GLAHYAEIID VLGKKLPAPL IGELPYLPRA EQRELGQYIR LAMLRSVLAV DRVTV
Length

235

Mol. Wt

25.453 kDa

pI

6.2 (calculated)

Extinction coefficient

25,440 - 25,690 (calc based on 6 Y, 3 W, and 2 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

5..212

PF01656 CobQ/CobB/MinD/ParA nucleotide binding domain

PMID:19920124

<motif_map/>

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

Structures

<beststructure> gene=ynfK 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:90111304

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:944927

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005319

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A6E9

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6851

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13849

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:944927

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003440

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3610

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

42

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

30

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

65a

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)

ynfK

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_000913:1665223..1665263 source=MG1655 flip=1 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:b1593 (EcoliWiki Page)

NCBI GEO profiles for ynfK

microarray

GenExpDB:b1593 (EcoliWiki Page)

Summary of data for ynfK 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 (1665155..1665436) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ07; Well:A7[7]

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Notes

Accessions Related to ynfK Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G6851

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3610

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1593

EcoGene

EcoGene:EG13849

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003440

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005319

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

S1746

From SHIGELLACYC

E. coli O157

Z2585

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)

PF01656 CobQ/CobB/MinD/ParA nucleotide binding domain

Superfamily (EcoliWiki Page)

SUPERFAMILY:52540

Panther (EcoliWiki Page)

PTHR21343:SF0

EcoCyc

EcoCyc:G6851

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13849

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003440

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3610

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005319

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 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. 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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