yafO:Gene Product(s): Difference between revisions

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|{{Sub}}[[#Localization |Localization]]
|{{Sub}}[[#Localization |Localization]]
|{{Sub}}[[#Sequence|Sequence]]
|{{Sub}}[[#Sequence|Sequence]]
|{{Sub}}[[#Domains/Motifs/Modification Sites|Domains]]
|{{Sub}}[[#Structure|Structure]]
|{{Sub}}[[#Structure|Structure]]
|{{Sub}}[[#Gene Product Resources|Resources]]
|{{Sub}}[[#Gene Product Resources|Resources]]
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!{{table heading style}} |Standard name
!align=left {{table heading style}} |Standard name
|
||
YafO product
YafO  
|-
|-
!{{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
|
||
predicted toxin of the YafO-YafN toxin-antitoxin system product<ref name='LIB:Riley_2006'/>, B0233 product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YafO product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''predicted toxin of the YafO-YafN toxin-antitoxin system<ref name='LIB:Riley_2006'/>, B0233<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YafO<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK0234, JW0223, b0233''
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!{{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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conserved protein with a possible role in spontaneous mutagenesis;  toxin of a putative toxin-antitoxin pair<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>
conserved protein with a possible role in spontaneous mutagenesis;  toxin of a putative toxin-antitoxin pair<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>


Possible toxin, function unknown<ref name='LIB:EcoGene'/>
|-
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!{{table heading style}} |EC number (for enzymes)
!align=left {{table heading style}} |EC number (for enzymes)
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*
 
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===Notes===
===Notes===
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<big>'''Gene Ontology'''</big><br />{{Product_GO_help}}<!--box uid=421aa90e079fa326b6494f812ad13e79.20064.Z46aa24eb7eb6f-->
<big>'''Gene Ontology'''</big><br /><!--box uid=421aa90e079fa326b6494f812ad13e79.20064.Z46aa24eb7eb6f-->
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!Qualifier!!GO ID!!GO term name!!Reference(s)!!Evidence Code!!with/from!!Aspect!!Notes!!Status
!|Qualifier!!GO ID!!GO term name!!Reference!!Evidence Code!!with/from!!Aspect!!Notes!!Status
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GO:0017148
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negative regulation of translation
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PMID:19617347
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IDA: Inferred from Direct Assay
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P
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Seeded from [[EcoCyc]] (v14.0)
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complete
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GO:0043023
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ribosomal large subunit binding
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PMID:19617347
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IDA: Inferred from Direct Assay
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F
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Seeded from [[EcoCyc]] (v14.0)
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complete
 
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!Partner Type!!Partner!!Notes
!|Partner Type!!Partner!!Notes!!References!!Evidence
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===Notes===
===Notes===
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!Compartment!!Description!!Evidence!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
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!align=left {{table heading style}} |Name
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!{{table heading style}} |Sequence
!align=left {{table heading style}} |Sequence
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[http://biocyc.org/ECOLI/sequence-aa?object=G6117-MONOMER at EcoCyc]  
[http://biocyc.org/ECOLI/sequence-aa?object=G6117-MONOMER at EcoCyc]  
<pre>MRVFKTKLIR LQLTAEELDA LTADFISYKR DGVLPDIFGR DALYDDSFTW PLIKFERVAH
<pre>MRVFKTKLIR LQLTAEELDA LTADFISYKR DGVLPDIFGR DALYDDSFTW PLIKFERVAH
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IGKMAEAFRM RF</pre>  
IGKMAEAFRM RF</pre>  
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!{{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Length
|
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15.49 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
132
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!{{table heading style}} |pI
!align=left {{table heading style}} |Mol. Wt
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15.488 kDa
|-
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!{{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |pI
|
||
15470 - 15595 (calc based on 3 Y, 2 W, and 1 C residues)  
7.6 (calculated)
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!align=left {{table heading style}} |Extinction coefficient
||
15,470 - 15,595 (calc based on 3 Y, 2 W, and 1 C residues)
 
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<big>'''Domains/Motifs/Modification Sites'''</big>
 
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<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span><table>
<tr align="left" valign="top">
<td><!--box uid=421aa90e079fa326b6494f812ad13e79.20064.X46aa24ee11115-->
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!Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
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<td>
<!-- motifs column 2-->
<motif_map/>
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<span id="Structure"></span><big>'''Structure'''</big>
<table><tr valign='top'><td>
<span id='Structure'></span><big>'''Structure'''</big><br />
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!Structure Type!!Organism!!Accession!!Residues covered!!Notes
|-
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!align=left {{table heading style}} |Structures
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||
<beststructure>
gene=yafO
taxon=562,83333
</beststructure>
|-
!align=left {{table heading style}} |Models
||
View models at:
* [http://www.proteinmodelportal.org/query/uniprot/Q47157 Protein Model Portal]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=Q47157 PSI-PRED (Q47157)]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=Q47157 Genomes TO Protein (Q47157)] (GTOP)
 
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<!--Structure_notes--></protect>
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==== Structure figures ====
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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===Notes===
===Notes===


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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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|-
|
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/16128219 GI:16128219]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/NP_414768.1 GeneID:944916]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0000795
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/Q47157 UniProtKB/Swiss-Prot:Q47157]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
EcoCyc:G6117
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EcoGene]]
|
EcoGene:EG13152
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6117-MONOMER EcoCyc:G6117-MONOMER]
[http://www.ncbi.nlm.nih.gov/gene?term=944916 GeneID:944916]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
[[RegulonDB]]
|
|
[[uniprot:Q47157|UniProt:Q47157]] 
RegulonDB:ECK120002737
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_414768 RefSeq:NP_414768] 
EchoBASE:EB2946
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[Category:Proteins]]

Latest revision as of 20:23, 17 February 2015

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Function Interactions Localization Sequence Domains Structure Resources Accessions Links References Suggestions

Nomenclature

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

Standard name

YafO

Synonyms

predicted toxin of the YafO-YafN toxin-antitoxin system[1], B0233[2][1], YafO[2][1] , ECK0234, JW0223, b0233

Product description

conserved protein with a possible role in spontaneous mutagenesis; toxin of a putative toxin-antitoxin pair[2][3]

Possible toxin, function unknown[4]

EC number (for enzymes)


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Notes

Function

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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:0017148

negative regulation of translation

PMID:19617347[5]

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc (v14.0)

complete

GO:0043023

ribosomal large subunit binding

PMID:19617347[5]

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

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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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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 

MRVFKTKLIR LQLTAEELDA LTADFISYKR DGVLPDIFGR DALYDDSFTW PLIKFERVAH
IHLANENNPF PPQLRQFSRT NDEAHLVYCQ GAFDEQAWLL IAILKPEPHK LARDNNQMHK
IGKMAEAFRM RF
Length

132

Mol. Wt

15.488 kDa

pI

7.6 (calculated)

Extinction coefficient

15,470 - 15,595 (calc based on 3 Y, 2 W, and 1 C residues)

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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
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Structures

<beststructure> gene=yafO taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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:16128219

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:944916

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000795

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:Q47157

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6117

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13152

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:944916

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002737

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2946

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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 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 Zhang, Y et al. (2009) Characterization of YafO, an Escherichia coli toxin. J. Biol. Chem. 284 25522-31 PubMed

Categories

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