ybeH: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

ybeH

Gene Synonym(s)

ECK0618, b0625, JW0620[1]

Product Desc.

predicted protein[2][3]

Product Synonyms(s)

predicted protein[1], B0625[2][1], YbeH[2][1]

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ybeH[2]

Regulation/Activity
Quick Links

porteco.png

dnadisplay.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

ybeH

Mnemonic
Synonyms

ECK0618, b0625, JW0620[1]

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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

14.17 minutes 

MG1655: 657254..657481
<gbrowseImage> name=NC_000913:657254..657481 source=MG1655 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 658453..658680
<gbrowseImage> name=NC_007779:658453..658680 source=W3110 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

ΔybeH (Keio:JW0620)

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

JW0620

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCCTGGTTGCCGCAGGACAGTT

Primer 2:CCTGTTACGTTTACTTTCTCGCC

1G6

Kohara Phage

Genobase

PMID:3038334

crcA280::Tn10

Linked marker

CAG12077 = CGSC7347[4]

est. P1 cotransduction: 90% [5]
Synonyms:zbe-280::Tn10

asnB3057::Tn10

Linked marker

CAG18433 = CGSC7349[4]

est. P1 cotransduction: 15% [5]
Synonyms:zbf-3057::Tn10 nnnThe Tn10 in CAG18433 is inserted in the asnB regulatory region, 4 bp before the start of the asnB ORF.

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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:

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:

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

YbeH

Synonyms

predicted protein[1], B0625[2][1], YbeH[2][1]

Product description

predicted protein[2][3]

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
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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 

 




Length






Mol. Wt






pI






Extinction coefficient












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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





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<motif_map/>










Structure

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








Structures



<beststructure>
gene=ybeH
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






EcoCyc





EcoCyc:





Escherichia coli str. K-12 substr. MG1655 








EcoGene





EcoGene:





Escherichia coli str. K-12 substr. MG1655 








RegulonDB





RegulonDB:





Escherichia coli str. K-12 substr. MG1655 








EchoBASE





EchoBASE:





Escherichia coli str. K-12 substr. MG1655 








ASAP





ASAP:





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)





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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)






ybeH 







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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_000913:657234..657274
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





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







Type
Reference
Notes






microarray





GEO Profiles:b0625 (EcoliWiki Page)





NCBI GEO profiles for ybeH 








microarray





GenExpDB:b0625 (EcoliWiki Page) 





Summary of data for ybeH from multiple microarray studies  







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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 ybeH Expression


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







Database
Accession
Notes






EcoliGenExpDB (EcoliWiki Page) 





EcoliGenExpDB:b0625










RegulonDB





RegulonDB:





Escherichia coli str. K-12 substr. MG1655 








ASAP





ASAP:





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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<protect>
See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.







Organism
Homologs (Statistics)
Comments





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Do-It-Yourself Web Tools



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Notes


Families


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Database
Accession
Notes






PFAM (EcoliWiki Page) 





PFAM:PF02537  








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Notes


Families


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<protect>
See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.







Database
Accession
Notes





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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. ↑ 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. ↑ 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7  

    4. 

  4. ↑ 4.0 4.1 CGSC: The Coli Genetics Stock Center  

    5. 

  5. ↑ 5.0 5.1 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).  

    6. 



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