ybhK: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

ybhK

Gene Synonym(s)

ECK0769, b0780, JW0763[1], JW0763

Product Desc.

predicted transferase with NAD(P)-binding Rossmann-fold domain[2][3]

Complements B. subtilis yvcK mutant, function unknown; Yvck, and perhaps YbhK, has a role in carbon metabolism[4]

Product Synonyms(s)

predicted transferase with NAD(P)-binding Rossmann-fold domain[1], B0780[2][1], YbhK[2][1] , ECK0769, JW0763, b0780

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ybhK[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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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

ybhK

Mnemonic

Systematic nomenclature

Synonyms

ECK0769, b0780, JW0763[1], JW0763

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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

17.57 minutes 

MG1655: 815870..814962
<gbrowseImage> name=NC_000913:814962..815870 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 809273..808365
<gbrowseImage> name=NC_012967:808365..809273 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 717930..718838
<gbrowseImage> name=NC_012759:717930..718838 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 817069..816161
<gbrowseImage> name=NC_007779:816161..817069 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 869798..868890
<gbrowseImage> name=NC_010473:868890..869798 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

ΔybhK (Keio:JW0763)

deletion

deletion

PMID:16738554

Shigen
CGSC8820[5]

ΔybhK752::kan

PMID:16738554

CGSC:103814

ybhK+

Growth Phenotype

In multicopy, complements the growth defect of a B. subtilis yvcK(del) mutant on DSM medium supplemented with 1 mM IPTG.

PMID:16272399


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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

JW0763

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCGCAATCGTACGCTGGCTGA

Primer 2:CCACCTAAAGCCTGTAACGCCTT

4H7

Kohara Phage

Genobase

PMID:3038334

3D4

Kohara Phage

Genobase

PMID:3038334

24F9

Kohara Phage

Genobase

PMID:3038334

nadA57::Tn10

Linked marker

CAG12147 = CGSC7351[5]

est. P1 cotransduction: 24% [6]

zbh-29::Tn10

Linked marker

CAG18493 = CGSC7353[5]

est. P1 cotransduction: 81% [6]
Synonyms:zbi-29::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:G6402

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13667

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003002

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945390

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3431

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002661

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

YbhK

Synonyms

predicted transferase with NAD(P)-binding Rossmann-fold domain[1], B0780[2][1], YbhK[2][1] , ECK0769, JW0763, b0780

Product description

predicted transferase with NAD(P)-binding Rossmann-fold domain[2][3]

Complements B. subtilis yvcK mutant, function unknown; Yvck, and perhaps YbhK, has a role in carbon metabolism[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

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

lpdA

PMID:15690043

Experiment(s):EBI-886623, EBI-892986

Protein

rpoB

PMID:15690043

Experiment(s):EBI-886623

Protein

nadE

PMID:16606699

Experiment(s):EBI-1137943

Protein

hemG

PMID:16606699

Experiment(s):EBI-1137943

Protein

htpG

PMID:16606699

Experiment(s):EBI-1137943

Protein

groL

PMID:16606699

Experiment(s):EBI-1137943

Protein

glgB

PMID:16606699

Experiment(s):EBI-1137943

Protein

yiiQ

PMID:16606699

Experiment(s):EBI-1137943

Protein

rpsD

PMID:16606699

Experiment(s):EBI-1137943

Protein

aceE

PMID:15690043

Experiment(s):EBI-892986

Protein

yfaW

PMID:15690043

Experiment(s):EBI-892986

Protein

basS

PMID:15690043

Experiment(s):EBI-892986

Protein

ccmH

PMID:15690043

Experiment(s):EBI-892986

Protein

ftsK

PMID:15690043

Experiment(s):EBI-892986

Protein

glgC

PMID:15690043

Experiment(s):EBI-892986

Protein

gsk

PMID:15690043

Experiment(s):EBI-892986

Protein

idnT

PMID:15690043

Experiment(s):EBI-892986

Protein

narI

PMID:15690043

Experiment(s):EBI-892986

Protein

rplC

PMID:15690043

Experiment(s):EBI-892986

Protein

rplD

PMID:15690043

Experiment(s):EBI-892986

Protein

rplM

PMID:15690043

Experiment(s):EBI-892986

Protein

rplU

PMID:15690043

Experiment(s):EBI-892986

Protein

rplV

PMID:15690043

Experiment(s):EBI-892986

Protein

rplW

PMID:15690043

Experiment(s):EBI-892986

Protein

rpsB

PMID:15690043

Experiment(s):EBI-892986

Protein

rpsE

PMID:15690043

Experiment(s):EBI-892986

Protein

rpsF

PMID:15690043

Experiment(s):EBI-892986

Protein

rpsG

PMID:15690043

Experiment(s):EBI-892986

Protein

secA

PMID:15690043

Experiment(s):EBI-892986

Protein

valS

PMID:15690043

Experiment(s):EBI-892986

Protein

ybhF

PMID:15690043

Experiment(s):EBI-892986

Protein

yfdE

PMID:15690043

Experiment(s):EBI-892986

Protein

ftsK

PMID:19402753

LCMS(ID Probability):99.0

Protein

ccmH

PMID:19402753

LCMS(ID Probability):99.0

Protein

ybhF

PMID:19402753

LCMS(ID Probability):99.0

Protein

valS

PMID:19402753

LCMS(ID Probability):99.0

Protein

basS

PMID:19402753

LCMS(ID Probability):99.0

Protein

rhmD

PMID:19402753

LCMS(ID Probability):99.0

Protein

gsk

PMID:19402753

LCMS(ID Probability):99.0

Protein

narI

PMID:19402753

LCMS(ID Probability):99.0

Protein

yfdE

PMID:19402753

LCMS(ID Probability):99.0

Protein

glgC

PMID:19402753

LCMS(ID Probability):99.0

Protein

idnT

PMID:19402753

LCMS(ID Probability):99.0

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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

MRNRTLADLD RVVALGGGHG LGRVLSSLSS LGSRLTGIVT TTDNGGSTGR IRRSEGGIAW
GDMRNCLNQL ITEPSVASAM FEYRFGGNGE LSGHNLGNLM LKALDHLSVR PLEAINLIRN
LLKVDTHLIP MSEHPVDLMA IDDQGHEVYG EVNIDQLTTP IQELLLTPNV PATREAVHAI
NEADLIIIGP GSFYTSLMPI LLLKEIAQAL RRTPAPMVYI GNLGRELSLP AANLKLESKL
AIMEQYVGKK VIDAVIVGPK VDVSAVKERI VIQEVLEASD IPYRHDRQLL HNALEKALQA LG
Length

302

Mol. Wt

32.788 kDa

pI

6.4 (calculated)

Extinction coefficient

14,440 - 14,565 (calc based on 6 Y, 1 W, and 1 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

12..301

PF01933 Uncharacterised protein family UPF0052

PMID:19920124

<motif_map/>

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

Structures

<beststructure> gene=ybhK 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:16128748

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945390

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002661

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P75767

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6402

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13667

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945390

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003002

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3431

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

166

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

67

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

135

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)

ybhK

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_000913:815850..815890 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:b0780 (EcoliWiki Page)

NCBI GEO profiles for ybhK

microarray

GenExpDB:b0780 (EcoliWiki Page)

Summary of data for ybhK 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 (815792..816315) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ07; Well:G10[7]

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Notes

Accessions Related to ybhK Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G6402

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3431

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0780

EcoGene

EcoGene:EG13667

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003002

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002661

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

Anopheles gambiae

  • ENSANGP00000001370 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Shigella flexneri

YBHK

From SHIGELLACYC

E. coli O157

YBHK

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

Superfamily (EcoliWiki Page)

SUPERFAMILY:142338

Pfam (EcoliWiki Page)

PF01933 Uncharacterised protein family UPF0052

EcoCyc

EcoCyc:G6402

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13667

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003002

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3431

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002661

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 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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