yafC:Gene Product(s): Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older edit
Data loaded by TableEdit_Loader.
touch table
 
(45 intermediate revisions by 2 users not shown)
Line 35: Line 35:
*  
*  
****************************************************************************************** -->{{Product_nomenclature_help}}
****************************************************************************************** -->{{Product_nomenclature_help}}
{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  
{|   id="A46aa237d9ebb3" class=" tableEdit Product_nomenclature_table"


|-
|-
Line 44: Line 44:
!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
predicted DNA-binding transcriptional regulator<ref name='LIB:Riley_2006'/>, B0208<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YafC<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''predicted DNA-binding transcriptional regulator<ref name='LIB:Riley_2006'/>, B0208<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YafC<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK0208, JW0198, b0208''
|-
|-
!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
Line 56: Line 56:




|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.20005.A46aa237d9ebb3&page=20005&pagename={{FULLPAGENAMEE}}&type=1&template=Product_nomenclature_table edit table] ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.20005.A46aa237d9ebb3&page=20005&pagename={{FULLPAGENAMEE}}&type=1&template=Product_nomenclature_table edit table]</span> ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.20005.A46aa237d9ebb3-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.20005.A46aa237d9ebb3-->
Line 75: Line 75:
*  
*  
****************************************************************************************** -->{{Product_GO_help}}
****************************************************************************************** -->{{Product_GO_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="R46aa237e9345b"  class=" tableEdit GO_table_product dataTable"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|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
|-  
|-  
|
|


|
|
GO:0006355
GO:0003677
|
DNA binding
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0238
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0003700
|
|
regulation of transcription, DNA-dependent
transcription factor activity
|
|
GO_REF:0000002<br />GO_REF:0000004
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR000847<br />SP_KW:KW-0805
InterPro:IPR000847
|
|
P
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 105: Line 124:
transcription
transcription
|
|
GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
Line 113: Line 132:
P
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 120: Line 139:


|
|
GO:0003700
GO:0006350
|
|
transcription factor activity
transcription
|
|
GO_REF:0000002
PMID:15556475
|
|
IEA: Inferred from Electronic Annotation
ISS: Inferred from Sequence or Structural Similarity
|
|
InterPro:IPR000847
Swiss-Prot:P03030
|
|
F
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 139: Line 158:


|
|
GO:0003677
GO:0006355
|
|
DNA binding
regulation of transcription, DNA-dependent
|
|
GO_REF:0000004
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0238
InterPro:IPR000847
|
|
F
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 158: Line 177:


|
|
GO:0005515
GO:0016563
|
|
protein binding
transcription activator activity
|
|
PMID:16606699
PMID:15556475
|
|
IPI: Inferred from Physical Interaction
ISS: Inferred from Sequence or Structural Similarity
|
|
UniProtKB:P0A7B1
Swiss-Prot:P03030
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 177: Line 196:


|
|
GO:0003677
GO:0016564
|
|
DNA binding
transcription repressor activity
|
|
GO_REF:0000004
PMID:15556475
|
|
IEA: Inferred from Electronic Annotation
ISS: Inferred from Sequence or Structural Similarity
|
|
SP_KW:KW-0238
Swiss-Prot:P03030
|
|
F
F
|
|
Seeded from EcoCyc
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.20005.R46aa237e9345b&page=20005&pagename={{FULLPAGENAMEE}}&type=&template=GO_table_product edit table]</span> || || || || || || || ||
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.20005.R46aa237e9345b-->
<span id="Interactions"></span><big>'''Interactions'''</big>
<!--box uid=421aa90e079fa326b6494f812ad13e79.20005.D46aa23869dd78-->
<!--
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
****************************************************************************************** -->{{Product_interactions_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="D46aa23869dd78"  class=" tableEdit Product_interactions_table dataTable" 
|- {{table heading style}}
!|Partner Type!!Partner!!Notes!!References!!Evidence
|-  
|-  
|
|
Protein
|
ppk<br />
|
|
GO:0016564
 
|
|
transcription repressor activity
PMID:16606699
|
|
Experiment(s):EBI-1135942<br />
|-
|
|
Protein
|
|
hns
|
|
F
 
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
PMID:19402753
|
|
required fields missing 
LCMS(ID Probability):99.6
|-  
|-  
|
|
Protein
|
fis
|
|
GO:0016563
 
|
|
transcription activator activity
PMID:19402753
|
|
LCMS(ID Probability):99.6
|-
|
|
Protein
|
|
rpmB
|
|
F
 
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
PMID:19402753
|
|
required fields missing 
LCMS(ID Probability):99.6
|-  
|-  
|
Protein
|
dnaJ
|
|


|
|
GO:0003700
PMID:19402753
|
|
transcription factor activity
LCMS(ID Probability):99.6
|-
|
|
GO_REF:0000002
Protein
|
|
IEA: Inferred from Electronic Annotation
ulaR
|
|
InterPro:IPR000847
 
|
|
F
PMID:19402753
|
|
Seeded from EcoCyc
LCMS(ID Probability):99.6
|
complete
 
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.20005.R46aa237e9345b&page=20005&pagename={{FULLPAGENAMEE}}&type=&template=GO_table_product edit table] || || || || || || || ||
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.20005.R46aa237e9345b-->
 
<span id="Interactions"></span><big>'''Interactions'''</big>
<!--box uid=421aa90e079fa326b6494f812ad13e79.20005.D46aa23869dd78-->
<!--
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
****************************************************************************************** -->{{Product_interactions_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" 
|- {{table heading style}}
!|Partner Type!!Partner!!Notes!!References!!Evidence
|-  
|-  
|
|
Protein
Protein
|
|
ppk<br />
yfhH
|
|


|
|
PMID:16606699
PMID:19402753
|
|
Experiment(s):EBI-1135942<br />
LCMS(ID Probability):99.6


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.20005.D46aa23869dd78&page=20005&pagename={{FULLPAGENAMEE}}&type=&template=Product_interactions_table edit table] || || || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.20005.D46aa23869dd78&page=20005&pagename={{FULLPAGENAMEE}}&type=&template=Product_interactions_table edit table]</span> || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.20005.D46aa23869dd78-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.20005.D46aa23869dd78-->
Line 295: Line 323:
*  
*  
****************************************************************************************** -->{{Product_localization_help}}
****************************************************************************************** -->{{Product_localization_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="G46a7b4baa7754"  class=" tableEdit Product_localization_table"   
|- {{table heading style}}
|- {{table heading style}}
!|Compartment!!Description!!Evidence!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.20005.G46a7b4baa7754&page=20005&pagename={{FULLPAGENAMEE}}&type=&template=Product_localization_table edit table] || || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.20005.G46a7b4baa7754&page=20005&pagename={{FULLPAGENAMEE}}&type=&template=Product_localization_table edit table]</span> || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.20005.G46a7b4baa7754-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.20005.G46a7b4baa7754-->
Line 320: Line 348:
*  
*  
****************************************************************************************** -->{{Product_physical_properties_help}}
****************************************************************************************** -->{{Product_physical_properties_help}}
{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"
{|   id="K46aa23885e1b4" class=" tableEdit Product_phys_prop_table"
 
|-
!align=left {{table heading style}} |Name
||


|-
|-
Line 338: Line 370:
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
33.78 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
33.776 kDa
|-
|-
!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
7.7 (calculated)
|-
|-
!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
18910 - 19285 (calc based on 9 Y, 1 W, and 3 C residues)  
18,910 - 19,285 (calc based on 9 Y, 1 W, and 3 C residues)


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.20005.K46aa23885e1b4&page=20005&pagename={{FULLPAGENAMEE}}&type=1&template=Product_phys_prop_table edit table] ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.20005.K46aa23885e1b4&page=20005&pagename={{FULLPAGENAMEE}}&type=1&template=Product_phys_prop_table edit table]</span> ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.20005.K46aa23885e1b4-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.20005.K46aa23885e1b4-->
Line 363: Line 395:
*  
*  
****************************************************************************************** -->{{Product_domains_motifs_help}}
****************************************************************************************** -->{{Product_domains_motifs_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="V46aa2388b8602"  class=" tableEdit Product_motif_table dataTable"   
|- {{table heading style}}
|- {{table heading style}}
!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-  
|-  
|
|
Domain
Domain
|
|
1 - 60
88..294
|
|
[[interpro:IPR000847|HTH lysR-type]]
[http://pfam.janelia.org/family/PF03466 PF03466  LysR substrate binding domain]
|
 
|
PMID:19920124
|-
|
Domain
|
5..64
|
[http://pfam.janelia.org/family/PF00126 PF00126  Bacterial regulatory helix-turn-helix protein, lysR family]
|
 
|
|
[http://www.uniprot.org/uniprot/P30864#section_features UniProt:P30864]
PMID:19920124


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.20005.V46aa2388b8602&page=20005&pagename={{FULLPAGENAMEE}}&type=&template=Product_motif_table edit table] || || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.20005.V46aa2388b8602&page=20005&pagename={{FULLPAGENAMEE}}&type=&template=Product_motif_table edit table]</span> || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.20005.V46aa2388b8602--></td>
<!--box uid=421aa90e079fa326b6494f812ad13e79.20005.V46aa2388b8602--></td>
Line 388: Line 433:
</table>
</table>


<span id="Structure"></span><big>'''Structure'''</big>
<table><tr valign='top'><td>
<span id='Structure'></span><big>'''Structure'''</big><br />
<!--box uid=421aa90e079fa326b6494f812ad13e79.20005.F46a7b4bc47c9d-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.20005.F46a7b4bc47c9d-->
<!--
<!--
Line 396: Line 442:
*  
*  
****************************************************************************************** -->{{Product_structure_help}}
****************************************************************************************** -->{{Product_structure_help}}
{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  
{|   id="F46a7b4bc47c9d" class=" tableEdit Product_structure_table"


|-
|-
!align=left {{table heading style}} |Structures
!align=left {{table heading style}} |Structures
||
||
<beststructure>yafC
<beststructure>
562</beststructure>
gene=yafC
 
taxon=562,83333
</beststructure>
|-
|-
!align=left {{table heading style}} |Models
!align=left {{table heading style}} |Models
||
||
View models at:
View models at:
* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=yafC&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P30864 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=yafC&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P30864 PSI-PRED (P30864)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P30864 Genomes TO Protein (P30864)] (GTOP)
* [http://www.ebi.ac.uk/msd-srv/pqs/ Protein Quaternary Structure] (PQS)
* [http://spock.genes.nig.ac.jp/~genome/search.html Genomes TO Protein] (GTOP)


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.20005.F46a7b4bc47c9d&page=20005&pagename={{FULLPAGENAMEE}}&type=1&template=Product_structure_table edit table] ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.20005.F46a7b4bc47c9d&page=20005&pagename={{FULLPAGENAMEE}}&type=1&template=Product_structure_table edit table]</span> ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.20005.F46a7b4bc47c9d-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.20005.F46a7b4bc47c9d-->


<!--Structure_notes--></protect>
</td><td></protect>
==== Structure figures ====
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
<protect><!--          ***** PLEASE DO NOT EDIT BELOW THIS LINE *****        -->
</td><tr><table><!--Structure_notes--></protect>
===Notes===
===Notes===


Line 433: Line 498:
*  
*  
****************************************************************************************** -->{{Product_resources_help}}
****************************************************************************************** -->{{Product_resources_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="K46aa23895784f"  class=" tableEdit Product_resource_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Resource type!!Source!!Notes/Reference
!|Resource type!!Source!!Notes/Reference


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.20005.K46aa23895784f&page=20005&pagename={{FULLPAGENAMEE}}&type=&template=Product_resource_table edit table] || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.20005.K46aa23895784f&page=20005&pagename={{FULLPAGENAMEE}}&type=&template=Product_resource_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.20005.K46aa23895784f-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.20005.K46aa23895784f-->
Line 455: Line 520:
*  
*  
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="F46aa2389a0f3b"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/16128195 GI:16128195]
|
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_414744.1 GeneID:947507]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11649-MONOMER EcoCyc:EG11649-MONOMER]
Escherichia coli str. K-12 substr. MG1655
|-  
|
|
[[ASAP]]
|
ASAP:ABE-0000694
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P30864 UniProtKB/Swiss-Prot:P30864]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
EcoCyc:EG11649
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
[[EcoGene]]
|
|
[[uniprot:P30864|UniProt:P30864]]
EcoGene:EG11649
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
|
[http://pfam.sanger.ac.uk/family?acc=PF00126 PFAM:PF00126]
[http://www.ncbi.nlm.nih.gov/gene?term=947507 GeneID:947507]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_414744 RefSeq:NP_414744]
RegulonDB:ECK120001593
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://modbase.compbio.ucsf.edu ModBase] ([[ModBase|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://salilab.org/modbase/searchbyid?databaseID=P30864 ModBase:P30864]
EchoBASE:EB1602
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.20005.F46aa2389a0f3b&page=20005&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table] || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.20005.F46aa2389a0f3b&page=20005&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.20005.F46aa2389a0f3b-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.20005.F46aa2389a0f3b-->
Line 512: Line 605:
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Q46a7b4bfca36e"  class=" tableEdit Links_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Name!!URL!!Comments
!|Name!!URL!!Comments


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.20005.Q46a7b4bfca36e&page=20005&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table] || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.20005.Q46a7b4bfca36e&page=20005&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.20005.Q46a7b4bfca36e-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.20005.Q46a7b4bfca36e-->
Line 527: Line 620:
==References==
==References==
{{BacktoTop}}
{{BacktoTop}}
 
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</noinclude>
===Categories===
===Categories===
{{BacktoTop}}
{{BacktoTop}}
[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0006350_!_transcription]][[Category:GO:0016564_!_transcription repressor activity]][[Category:GO:0016563_!_transcription activator activity]]

Latest revision as of 20:22, 17 February 2015

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

YafC

Synonyms

predicted DNA-binding transcriptional regulator[1], B0208[2][1], YafC[2][1] , ECK0208, JW0198, b0208

Product description

predicted DNA-binding transcriptional regulator LYSR-type[2][3]

Putative LysR-family transcriptional regulator, function unknown[4]

EC number (for enzymes)


edit table


Notes

Function

[back to top]


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:0003677

DNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0238

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000847

F

Seeded from EcoCyc (v14.0)

complete

GO:0006350

transcription

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0804

P

Seeded from EcoCyc (v14.0)

complete

GO:0006350

transcription

PMID:15556475[5]

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P03030

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000847

P

Seeded from EcoCyc (v14.0)

complete

GO:0016563

transcription activator activity

PMID:15556475[5]

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P03030

F

Seeded from EcoCyc (v14.0)

complete

GO:0016564

transcription repressor activity

PMID:15556475[5]

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P03030

F

Seeded from EcoCyc (v14.0)

complete

edit table

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

ppk

PMID:16606699[6]

Experiment(s):EBI-1135942

Protein

hns

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

fis

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

rpmB

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

dnaJ

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

ulaR

PMID:19402753[7]

LCMS(ID Probability):99.6

Protein

yfhH

PMID:19402753[7]

LCMS(ID Probability):99.6

edit table


Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
edit table


Notes

Structure and Physical Properties

[back to top]


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 

MKATSEELAI FVSVVESGSF SRAAEQLGQA NSAVSRAVKK LEMKLGVSLL NRTTRQLSLT
EEGERYFRRV QSILQEMAAA ESEIMETRNT PRGLLRIDAA TPVVLHFLMP LIKPFRERYP
EVTLSLVSSE TIINLIERKV DVAIRAGTLT DSSLRARPLF NSYRKIIASP DYISRYGKPE
TIDDLKQHIC LGFTEPASLN TWPIARSDGQ LHEVKYGLSS NSGETLKQLC LSGNGIACLS
DYMIDKEIAR GELVELMADK VLPVEMPFSA VYYSDRAVST RIRAFIDFLS EHVKTAPGGA VREA
Length

304

Mol. Wt

33.776 kDa

pI

7.7 (calculated)

Extinction coefficient

18,910 - 19,285 (calc based on 9 Y, 1 W, and 3 C residues)

edit table


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

88..294

PF03466 LysR substrate binding domain

PMID:19920124[8]

Domain

5..64

PF00126 Bacterial regulatory helix-turn-helix protein, lysR family

PMID:19920124[8]

edit table

<motif_map/>

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

Structures

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

Models

View models at:

edit table

Structure figures

Notes

Gene Product Resources

[back to top]


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

Resource type Source Notes/Reference
edit table


Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16128195

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947507

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000694

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P30864

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11649

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11649

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947507

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001593

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1602

Escherichia coli str. K-12 substr. MG1655

edit table


Notes

Links

[back to top]




References

[back to top]


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 5.2 Pérez-Rueda, E et al. (2004) Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea. Comput Biol Chem 28 341-50 PubMed
  6. ↑ Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  7. ↑ 7.0 7.1 7.2 7.3 7.4 7.5 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  8. ↑ 8.0 8.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

[back to top]


Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=yafC:Gene_Product(s)&oldid=1492247"