oxc:Gene Product(s): Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older edit
imported>Wikientrybot
No edit summary
touch table
 
(61 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="J46aaa425d8767" class=" tableEdit Product_nomenclature_table"


|-
|-
Line 44: Line 44:
!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
predicted oxalyl-CoA decarboxylase<ref name='LIB:Riley_2006'/>, B2373<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YfdU<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Oxc<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''predicted oxalyl-CoA decarboxylase<ref name='LIB:Riley_2006'/>, B2373<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YfdU<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Oxc<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK2369, JW2370, yfdU, b2373''
|-
|-
!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
Line 50: Line 50:
predicted oxalyl-CoA decarboxylase<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>
predicted oxalyl-CoA decarboxylase<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>


Probable oxalyl-CoA decarboxylase, oxalate catabolism<ref name='LIB:EcoGene'/>
|-
|-
!align=left {{table heading style}} |EC number (for enzymes)
!align=left {{table heading style}} |EC number (for enzymes)
||
||
*


|-class='sortbottom'
 
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24972.J46aaa425d8767&page=24972&pagename={{FULLPAGENAMEE}}&type=1&template=Product_nomenclature_table edit table] ||
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24972.J46aaa425d8767&page=24972&pagename={{FULLPAGENAMEE}}&type=1&template=Product_nomenclature_table edit table]</span> ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.24972.J46aaa425d8767-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.24972.J46aaa425d8767-->
{{Product_nomenclature_help}}
 
<protect><!--Nomenclature_notes--></protect>
<protect><!--Nomenclature_notes--></protect>
===Notes===
===Notes===
Line 67: Line 68:
{{BacktoTop}}
{{BacktoTop}}
<protect>
<protect>
<big>'''Gene Ontology'''</big><br />{{Product_GO_help}}<!--box uid=421aa90e079fa326b6494f812ad13e79.24972.X46aaa426e7bc4-->
<big>'''Gene Ontology'''</big><br /><!--box uid=421aa90e079fa326b6494f812ad13e79.24972.X46aaa426e7bc4-->
<!--
<!--
******************************************************************************************
******************************************************************************************
Line 74: 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="X46aaa426e7bc4"  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
|-  
|-  
|
|


|
|
[[Category:GO:0000287_!_magnesium_ion_binding]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0000287_!_magnesium_ion_binding GO:0000287]
GO:0000287
|
|
magnesium ion binding
magnesium ion binding
|
|
[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000002 GO_REF:0000002]
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR012000 InterPro:IPR012000]
InterPro:IPR012000
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 100: Line 101:


|
|
[[Category:GO:0003824_!_catalytic_activity]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0003824_!_catalytic_activity GO:0003824]
GO:0003824
|
|
catalytic activity
catalytic activity
|
|
[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000002 GO_REF:0000002]
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR011766 InterPro:IPR011766]
InterPro:IPR011766
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 119: Line 120:


|
|
[[Category:GO:0008949_!_oxalyl-CoA_decarboxylase_activity]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0008949_!_oxalyl-CoA_decarboxylase_activity GO:0008949]
GO:0008949
|
|
oxalyl-CoA decarboxylase activity
oxalyl-CoA decarboxylase activity
|
|
[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000003 GO_REF:0000003]
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.expasy.org/cgi-bin/nicezyme.pl?4.1.1.8 EC:4.1.1.8]
InterPro:IPR017660
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 138: Line 139:


|
|
[[Category:GO:0016829_!_lyase_activity]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0016829_!_lyase_activity GO:0016829]
GO:0008949
|
oxalyl-CoA decarboxylase activity
|
GOA:spec<br />GO_REF:0000003
|
IEA: Inferred from Electronic Annotation
|
EC:4.1.1.8
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0016829
|
|
lyase activity
lyase activity
|
|
[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000004 GO_REF:0000004]
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.uniprot.org/keywords/KW-0456 SP_KW:KW-0456]
SP_KW:KW-0456
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 157: Line 177:


|
|
[[Category:GO:0016831_!_carboxy-lyase_activity]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0016831_!_carboxy-lyase_activity GO:0016831]
GO:0016831
|
|
carboxy-lyase activity
carboxy-lyase activity
|
|
[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000004 GO_REF:0000004]
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0210
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0030976
|
thiamin pyrophosphate binding
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR011766
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-  
|
 
|
GO:0030976
|
thiamin pyrophosphate binding
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR012000
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0030976
|
thiamin pyrophosphate binding
|
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.uniprot.org/keywords/KW-0210 SP_KW:KW-0210]
InterPro:IPR012001
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 176: Line 253:


|
|
[[Category:GO:0030976_!_thiamin_pyrophosphate_binding]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0030976_!_thiamin_pyrophosphate_binding GO:0030976]
GO:0030976
|
|
thiamin pyrophosphate binding
thiamin pyrophosphate binding
|
|
[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000002 GO_REF:0000002]<br />[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000002 GO_REF:0000002]<br />[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000002 GO_REF:0000002]
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR011766 InterPro:IPR011766]<br />[http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR012000 InterPro:IPR012000]<br />[http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR012001 InterPro:IPR012001]
InterPro:IPR017660
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
|-
|


|-class='sortbottom'
|
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24972.X46aaa426e7bc4&page=24972&pagename={{FULLPAGENAMEE}}&type=&template=GO_table_product edit table] || || || || || || || ||
GO:0033611
|
oxalate catabolic process
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR017660
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0046872
|
metal ion binding
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR017660
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24972.X46aaa426e7bc4&page=24972&pagename={{FULLPAGENAMEE}}&type=&template=GO_table_product edit table]</span> || || || || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.24972.X46aaa426e7bc4-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.24972.X46aaa426e7bc4-->
Line 205: Line 320:
*  
*  
****************************************************************************************** -->{{Product_interactions_help}}
****************************************************************************************** -->{{Product_interactions_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="D46aaa427779f2"  class=" tableEdit Product_interactions_table dataTable"   
|- {{table heading style}}
|- {{table heading style}}
!|Partner Type!!Partner!!Notes!!References
!|Partner Type!!Partner!!Notes!!References!!Evidence
|-
|
Protein
|
rrmA<br />
|


|-class='sortbottom'
|
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24972.D46aaa427779f2&page=24972&pagename={{FULLPAGENAMEE}}&type=&template=Product_interactions_table edit table] || || ||
PMID:16606699
|
Experiment(s):EBI-1142672<br />
|-
|
Protein
|
uvrY<br />
|
 
|
PMID:16606699
|
Experiment(s):EBI-1142672<br />
|-
|
Protein
|
hchA<br />
|
 
|
PMID:16606699
|
Experiment(s):EBI-1142672<br />
|-
|
Protein
|
nadE<br />
|
 
|
PMID:16606699
|
Experiment(s):EBI-1142672<br />
|-
|
Protein
|
hupA
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
ybgI
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
|
Protein
|
phnI
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.6
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24972.D46aaa427779f2&page=24972&pagename={{FULLPAGENAMEE}}&type=&template=Product_interactions_table edit table]</span> || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.24972.D46aaa427779f2-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.24972.D46aaa427779f2-->
{{Product_interactions_help}}
 
<!--Function_notes--></protect>
<!--Function_notes--></protect>
===Notes===
===Notes===
Line 226: Line 418:
*  
*  
****************************************************************************************** -->{{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="D46a83ba3690d5"  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=421aa90e079fa326b6494f812ad13e79.24972.D46a83ba3690d5&page=24972&pagename={{FULLPAGENAMEE}}&type=&template=Product_localization_table edit table] || || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24972.D46a83ba3690d5&page=24972&pagename={{FULLPAGENAMEE}}&type=&template=Product_localization_table edit table]</span> || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.24972.D46a83ba3690d5-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.24972.D46a83ba3690d5-->
{{Product_localization_help}}
 
<protect><!--Localization_notes--></protect>
<protect><!--Localization_notes--></protect>


Line 251: Line 443:
*  
*  
****************************************************************************************** -->{{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="U46aaa4295ffc5" class=" tableEdit Product_phys_prop_table"
 
|-
!align=left {{table heading style}} |Name
||


|-
|-
Line 267: Line 463:
DGVDLSGAGA PSPTDLLHHA RYDKLMDAFR GVGYNVTTTD ELRHALTTGI QSRKPTIINV
DGVDLSGAGA PSPTDLLHHA RYDKLMDAFR GVGYNVTTTD ELRHALTTGI QSRKPTIINV
VIDPAAGTES GHITKLNPKQ VAGN</pre>  
VIDPAAGTES GHITKLNPKQ VAGN</pre>  
|-
!align=left {{table heading style}} |Length
||
564
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
60.58 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
60.582 kDa
|-
|-
!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
5.8 (calculated)
|-
|-
!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
44350 - 44850 (calc based on 15 Y, 4 W, and 4 C residues)  
44,350 - 44,850 (calc based on 15 Y, 4 W, and 4 C residues)


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24972.U46aaa4295ffc5&page=24972&pagename={{FULLPAGENAMEE}}&type=1&template=Product_phys_prop_table edit table] ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24972.U46aaa4295ffc5&page=24972&pagename={{FULLPAGENAMEE}}&type=1&template=Product_phys_prop_table edit table]</span> ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.24972.U46aaa4295ffc5-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.24972.U46aaa4295ffc5-->
{{Product_physical_properties_help}}


<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span>
 
<!--box uid=421aa90e079fa326b6494f812ad13e79.24972.Z46aaa429ce876-->
<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span><table>
<tr align="left" valign="top">
<td><!--box uid=421aa90e079fa326b6494f812ad13e79.24972.Z46aaa429ce876-->
<!--
<!--
******************************************************************************************
******************************************************************************************
Line 294: Line 495:
*  
*  
****************************************************************************************** -->{{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="Z46aaa429ce876"  class=" tableEdit Product_motif_table dataTable"   
|- {{table heading style}}
|- {{table heading style}}
!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-
|
Domain
|
201..329
|
[http://pfam.janelia.org/family/PF00205 PF00205  Thiamine pyrophosphate enzyme, central domain]
|


|-class='sortbottom'
|
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24972.Z46aaa429ce876&page=24972&pagename={{FULLPAGENAMEE}}&type=&template=Product_motif_table edit table] || || ||
PMID:19920124
|-
|
Domain
|
394..540
|
[http://pfam.janelia.org/family/PF02775 PF02775  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain]
|
 
|
PMID:19920124
|-
|
Domain
|
8..179
|
[http://pfam.janelia.org/family/PF02776 PF02776  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain]
|
 
|
PMID:19920124
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24972.Z46aaa429ce876&page=24972&pagename={{FULLPAGENAMEE}}&type=&template=Product_motif_table edit table]</span> || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.24972.Z46aaa429ce876-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.24972.Z46aaa429ce876--></td>
{{Product_domains_motifs_help}}
<td>
<!-- motifs column 2-->
<motif_map/>
</td>
</tr>
</table>


<span id="Structure"></span><big>'''Structure'''</big>
<table><tr valign='top'><td>
<span id='Structure'></span><big>'''Structure'''</big><br />
<!--box uid=421aa90e079fa326b6494f812ad13e79.24972.Y46a83ba5beaa2-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.24972.Y46a83ba5beaa2-->
<!--
<!--
Line 312: Line 553:
*  
*  
****************************************************************************************** -->{{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="Y46a83ba5beaa2" class=" tableEdit Product_structure_table"


|-
|-
!align=left {{table heading style}} |Structures
!align=left {{table heading style}} |Structures
||
||
<beststructure>oxc
<beststructure>
562</beststructure>
gene=oxc
 
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=oxc&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P0AFI0 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=oxc&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P0AFI0 PSI-PRED (P0AFI0)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P0AFI0 Genomes TO Protein (P0AFI0)] (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=421aa90e079fa326b6494f812ad13e79.24972.Y46a83ba5beaa2&page=24972&pagename={{FULLPAGENAMEE}}&type=1&template=Product_structure_table edit table] ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24972.Y46a83ba5beaa2&page=24972&pagename={{FULLPAGENAMEE}}&type=1&template=Product_structure_table edit table]</span> ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.24972.Y46a83ba5beaa2-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.24972.Y46a83ba5beaa2-->
{{Product_structure_help}}
 
<!--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 349: Line 609:
*  
*  
****************************************************************************************** -->{{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="N46aaa42a96454"  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=421aa90e079fa326b6494f812ad13e79.24972.N46aaa42a96454&page=24972&pagename={{FULLPAGENAMEE}}&type=&template=Product_resource_table edit table] || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24972.N46aaa42a96454&page=24972&pagename={{FULLPAGENAMEE}}&type=&template=Product_resource_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.24972.N46aaa42a96454-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.24972.N46aaa42a96454-->
{{Product_resources_help}}
 
<protect><!--Resources_notes--></protect>
<protect><!--Resources_notes--></protect>
===Notes===
===Notes===
Line 371: Line 631:
*  
*  
****************************************************************************************** -->{{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="X46aaa42af3c45"  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/16130305 GI:16130305]
|
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_416874.1 GeneID:946845]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0007826
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7236-MONOMER EcoCyc:G7236-MONOMER]
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
|
[http://www.uniprot.org/uniprot/P0AFI0 UniProtKB/Swiss-Prot:P0AFI0]
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://swissmodel.expasy.org/repository/ SwissModel] ([[SwissModel|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://swissmodel.expasy.org/repository/smr.php?job=2&sptr_ac=P0AFI0 SwissModel:P0AFI0]
EcoCyc:G7236
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
[[EcoGene]]
|
|
[[uniprot:P0AFI0|UniProt:P0AFI0]]
EcoGene:EG14143
|
|
''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=PF02776 PFAM:PF02776]
[http://www.ncbi.nlm.nih.gov/gene?term=946845 GeneID:946845]
|
|
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_416874 RefSeq:NP_416874]
RegulonDB:ECK120003811
|
|
''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=P0AFI0 ModBase:P0AFI0]
EchoBASE:EB3895
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24972.X46aaa42af3c45&page=24972&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table] || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24972.X46aaa42af3c45&page=24972&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.24972.X46aaa42af3c45-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.24972.X46aaa42af3c45-->
{{Product_accessions_help}}
 
<protect><!--Accessions_notes--></protect>
<protect><!--Accessions_notes--></protect>
===Notes===
===Notes===
Line 435: Line 716:
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|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="J46a83bab7929c"  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=421aa90e079fa326b6494f812ad13e79.24972.J46a83bab7929c&page=24972&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table] || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24972.J46a83bab7929c&page=24972&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.24972.J46a83bab7929c-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.24972.J46a83bab7929c-->
{{Links_help}}
 




Line 451: Line 732:
{{BacktoTop}}
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</noinclude>
===Categories===
===Categories===
{{BacktoTop}}
{{BacktoTop}}
[[Category:Proteins]]
[[Category:Proteins]]
[[Category:Pfam:PF00205_!_Thiamine pyrophosphate enzyme, central domain]]
[[Category:Pfam:PF02775_!_Thiamine pyrophosphate enzyme, C-terminal TPP binding domain]]
[[Category:Pfam:PF02776_!_Thiamine pyrophosphate enzyme, N-terminal TPP binding domain]]

Latest revision as of 20:50, 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

Oxc

Synonyms

predicted oxalyl-CoA decarboxylase[1], B2373[2][1], YfdU[2][1], Oxc[2][1] , ECK2369, JW2370, yfdU, b2373

Product description

predicted oxalyl-CoA decarboxylase[2][3]

Probable oxalyl-CoA decarboxylase, oxalate catabolism[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:0000287

magnesium ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012000

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011766

F

Seeded from EcoCyc (v14.0)

complete

GO:0008949

oxalyl-CoA decarboxylase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017660

F

Seeded from EcoCyc (v14.0)

complete

GO:0008949

oxalyl-CoA decarboxylase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:4.1.1.8

F

Seeded from EcoCyc (v14.0)

complete

GO:0016829

lyase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0456

F

Seeded from EcoCyc (v14.0)

complete

GO:0016831

carboxy-lyase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0210

F

Seeded from EcoCyc (v14.0)

complete

GO:0030976

thiamin pyrophosphate binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011766

F

Seeded from EcoCyc (v14.0)

complete

GO:0030976

thiamin pyrophosphate binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012000

F

Seeded from EcoCyc (v14.0)

complete

GO:0030976

thiamin pyrophosphate binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012001

F

Seeded from EcoCyc (v14.0)

complete

GO:0030976

thiamin pyrophosphate binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017660

F

Seeded from EcoCyc (v14.0)

complete

GO:0033611

oxalate catabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017660

P

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017660

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

rrmA

PMID:16606699[5]

Experiment(s):EBI-1142672

Protein

uvrY

PMID:16606699[5]

Experiment(s):EBI-1142672

Protein

hchA

PMID:16606699[5]

Experiment(s):EBI-1142672

Protein

nadE

PMID:16606699[5]

Experiment(s):EBI-1142672

Protein

hupA

PMID:19402753[6]

LCMS(ID Probability):99.6

Protein

ybgI

PMID:19402753[6]

LCMS(ID Probability):99.6

Protein

phnI

PMID:19402753[6]

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 

MSDQLQMTDG MHIIVEALKQ NNIDTIYGVV GIPVTDMARH AQAEGIRYIG FRHEQSAGYA
AAASGFLTQK PGICLTVSAP GFLNGLTALA NATVNGFPMI MISGSSDRAI VDLQQGDYEE
LDQMNAAKPY AKAAFRVNQP QDLGIALARA IRVSVSGRPG GVYLDLPANV LAATMEKDEA
LTTIVKVENP SPALLPCPKS VTSAISLLAK AERPLIILGK GAAYSQADEQ LREFIESAQI
PFLPMSMAKG ILEDTHPLSA AAARSFALAN ADVVMLVGAR LNWLLAHGKK GWAADTQFIQ
LDIEPQEIDS NRPIAVPVVG DIASSMQGML AELKQNTFTT PLVWRDILNI HKQQNAQKMH
EKLSTDTQPL NYFNALSAVR DVLRENQDIY LVNEGANTLD NARNIIDMYK PRRRLDCGTW
GVMGIGMGYA IGASVTSGSP VVAIEGDSAF GFSGMEIETI CRYNLPVTIV IFNNGGIYRG
DGVDLSGAGA PSPTDLLHHA RYDKLMDAFR GVGYNVTTTD ELRHALTTGI QSRKPTIINV
VIDPAAGTES GHITKLNPKQ VAGN
Length

564

Mol. Wt

60.582 kDa

pI

5.8 (calculated)

Extinction coefficient

44,350 - 44,850 (calc based on 15 Y, 4 W, and 4 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

201..329

PF00205 Thiamine pyrophosphate enzyme, central domain

PMID:19920124[7]

Domain

394..540

PF02775 Thiamine pyrophosphate enzyme, C-terminal TPP binding domain

PMID:19920124[7]

Domain

8..179

PF02776 Thiamine pyrophosphate enzyme, N-terminal TPP binding domain

PMID:19920124[7]

edit table

<motif_map/>

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

Structures

<beststructure> gene=oxc 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:16130305

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946845

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007826

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AFI0

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7236

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14143

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946845

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003811

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3895

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 1.3 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 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 5.3 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  6. ↑ 6.0 6.1 6.2 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  7. ↑ 7.0 7.1 7.2 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=oxc:Gene_Product(s)&oldid=1494254"