dsdC:Gene Product(s): Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older editNewer edit →
Edited by wikibot
imported>Wikientrybot
Collapsing IEA rows.
Line 31: Line 31:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|{{Prettytable}}
{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"
 
|-
|-
!{{table heading style}} |Standard name
!align=left {{table heading style}} |Standard name
|
||
DsdC product  
DsdC product  
|-
|-
!{{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
|
||
DNA-binding transcriptional dual regulator product<ref name='LIB:Riley_2006'/>, B2364 product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, DsdC product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, D-serine dehydratase (deaminase) transcriptional activator product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
DNA-binding transcriptional dual regulator product<ref name='LIB:Riley_2006'/>, B2364 product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, DsdC product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, D-serine dehydratase (deaminase) transcriptional activator product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
|-
|-
!{{table heading style}} |Product description
!align=left {{table heading style}} |Product description
|
||
DsdC transcriptional dual regulator<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>
DsdC transcriptional dual regulator<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>


|-
|-
!{{table heading style}} |EC number (for enzymes)
!align=left {{table heading style}} |EC number (for enzymes)
|
||
*
*
|-
 
|colspan='2'|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24953.N46aaa37a0d98b&page=24953&pagename={{FULLPAGENAMEE}} edit table]
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24953.N46aaa37a0d98b&page=24953&pagename={{FULLPAGENAMEE}}&type=1&template=Product_nomenclature_table edit table] ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.24953.N46aaa37a0d98b-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.24953.N46aaa37a0d98b-->
Line 75: Line 77:
|- {{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(s)!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-
|
|
[[Category:GO:0003677_!_DNA_binding]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0003677_!_DNA_binding GO:0003677]
|
DNA binding
|
GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0238
|
F
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
|
complete
|-
|
|
[[Category:GO:0003700_!_transcription_factor_activity]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0003700_!_transcription_factor_activity GO:0003700]
|
transcription factor activity
|
GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR000847
|
F
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
|
complete
|-
|
|
[[Category:GO:0006350_!_transcription]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0006350_!_transcription GO:0006350]
|
transcription
|
GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0804
|
P
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
|
complete
|-
|
|
[[Category:GO:0006355_!_regulation_of_transcription,_DNA-dependent]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0006355_!_regulation_of_transcription,_DNA-dependent GO:0006355]
|
regulation of transcription, DNA-dependent
|
GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR000847
|
P
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
|
complete
|-  
|-  
|
|
Line 208: Line 134:
|
|
required fields missing   
required fields missing   
|-
|
|
[[Category:GO:0006355_!_regulation_of_transcription,_DNA-dependent]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0006355_!_regulation_of_transcription,_DNA-dependent GO:0006355]
|
regulation of transcription, DNA-dependent
|
GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0805
|
P
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
|
complete


|-class='sortbottom'
|-class='sortbottom'
Line 237: Line 144:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|class = 'sortable' {{Prettytable}} id='168846'
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" 
|- {{table heading style}}
|- {{table heading style}}
!Partner Type!!Partner!!Notes
!|Partner Type!!Partner!!Notes
 
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24953.E46aaa38c2adf1&page=24953&pagename={{FULLPAGENAMEE}} edit table] || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24953.E46aaa38c2adf1&page=24953&pagename={{FULLPAGENAMEE}}&type=&template=Product_interactions_table edit table] || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.24953.E46aaa38c2adf1-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.24953.E46aaa38c2adf1-->
Line 257: Line 165:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|class = 'sortable' {{Prettytable}} id='114497'
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" 
|- {{table heading style}}
|- {{table heading style}}
!Compartment!!Description!!Evidence!!Notes
!|Compartment!!Description!!Evidence!!Notes
 
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24953.X46a83ac3bb61f&page=24953&pagename={{FULLPAGENAMEE}} edit table] || || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24953.X46a83ac3bb61f&page=24953&pagename={{FULLPAGENAMEE}}&type=&template=Product_localization_table edit table] || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.24953.X46a83ac3bb61f-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.24953.X46a83ac3bb61f-->
Line 281: Line 190:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|{{Prettytable}}
{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"
 
|-
|-
!{{table heading style}} |Sequence
!align=left {{table heading style}} |Sequence
|
||
[http://biocyc.org/ECOLI/sequence-aa?object=PD00297 at EcoCyc]  
[http://biocyc.org/ECOLI/sequence-aa?object=PD00297 at EcoCyc]  
<pre>MEPLREIRNR LLNGWQLSKM HTFEVAARHQ SFALAAEELS LSPSAVSHRI NQLEEELGIQ
<pre>MEPLREIRNR LLNGWQLSKM HTFEVAARHQ SFALAAEELS LSPSAVSHRI NQLEEELGIQ
Line 297: Line 207:
IWLREQVKTT S</pre>  
IWLREQVKTT S</pre>  
|-
|-
!{{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
|
||
35.33 kDa (calc) <ref name='LIB:EcoCyc10.6'/>  
35.33 kDa (calc) <ref name='LIB:EcoCyc10.6'/>  
|-
|-
!{{table heading style}} |pI
!align=left {{table heading style}} |pI
|
||
6.88<ref name='LIB:EcoCyc10.6'/>  
6.88<ref name='LIB:EcoCyc10.6'/>  
|-
|-
!{{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
|
||
55920 - 56545 (calc based on 8 Y, 8 W, and 5 C residues)  
55920 - 56545 (calc based on 8 Y, 8 W, and 5 C residues)  
|-
 
|colspan='2'|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24953.G46aaa38e1212c&page=24953&pagename={{FULLPAGENAMEE}} edit table]
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24953.G46aaa38e1212c&page=24953&pagename={{FULLPAGENAMEE}}&type=1&template=Product_phys_prop_table edit table] ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.24953.G46aaa38e1212c-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.24953.G46aaa38e1212c-->
Line 382: Line 293:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|class = 'sortable' {{Prettytable}} id='168849'
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Resource type!!Source!!Notes/Reference
!|Resource type!!Source!!Notes/Reference
 
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24953.X46aaa38f47912&page=24953&pagename={{FULLPAGENAMEE}} edit table] || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24953.X46aaa38f47912&page=24953&pagename={{FULLPAGENAMEE}}&type=&template=Product_resource_table edit table] || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.24953.X46aaa38f47912-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.24953.X46aaa38f47912-->
Line 403: Line 315:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|class = 'sortable' {{Prettytable}} id='168850'
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=PD00297 EcoCyc:PD00297]
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=PD00297 EcoCyc:PD00297]
|
|
   
   
|-
|-  
|
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])  
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])  
|
|
[[uniprot:P46068|UniProt:P46068]]
[[uniprot:P46068|UniProt:P46068]]
|
|
   
   
|-
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])  
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])  
|
|
[http://pfam.sanger.ac.uk/family?acc=PF00126 PFAM:PF00126]
[http://pfam.sanger.ac.uk/family?acc=PF00126 PFAM:PF00126]
|
|
   
   
|-
|-  
|
|
[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])  
|
|
[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_416865 RefSeq:NP_416865]
[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_416865 RefSeq:NP_416865]
|
|
   
   
|-
|-  
|
|
[http://modbase.compbio.ucsf.edu ModBase] ([[ModBase|EcoliWiki Page]])  
[http://modbase.compbio.ucsf.edu ModBase] ([[ModBase|EcoliWiki Page]])  
|
|
[http://salilab.org/modbase/searchbyid?databaseID=P46068 ModBase:P46068]
[http://salilab.org/modbase/searchbyid?databaseID=P46068 ModBase:P46068]
|
|
   
   
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
|
|
[http://BioCyc.org/ECOO157/new-image?object=Z0885-MONOMER ECOO157CYC:Z0885-MONOMER]
[http://BioCyc.org/ECOO157/new-image?object=Z0885-MONOMER ECOO157CYC:Z0885-MONOMER]
|
|
   
   
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24953.P46aaa38fa502c&page=24953&pagename={{FULLPAGENAMEE}} edit table] || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24953.P46aaa38fa502c&page=24953&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table] || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.24953.P46aaa38fa502c-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.24953.P46aaa38fa502c-->
Line 466: Line 379:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|class = 'sortable' {{Prettytable}} id='114499'
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Name!!URL!!Comments
!|Name!!URL!!Comments
 
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24953.L46a83acb61361&page=24953&pagename={{FULLPAGENAMEE}} edit table] || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24953.L46a83acb61361&page=24953&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table] || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.24953.L46a83acb61361-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.24953.L46a83acb61361-->

Revision as of 01:39, 15 November 2008

{{#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

Standard name

DsdC product

Synonyms

DNA-binding transcriptional dual regulator product[1], B2364 product[2][1], DsdC product[2][1], D-serine dehydratase (deaminase) transcriptional activator product[2][1]

Product description

DsdC transcriptional dual regulator[2][3]

EC number (for enzymes)
edit table

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

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(s) Evidence Code with/from Aspect Notes Status
GO:0009063

amino acid catabolic process

P

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0005737

cytoplasm

C

Seeded from EcoCyc 11.1[3].

required fields missing

GO:0016563

transcription activator activity

F

Seeded from EcoCyc 11.1[3].

required fields missing

edit table

Interactions

Partner Type Partner Notes
edit table

See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Notes

Localization

Compartment Description Evidence Notes
edit table

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


Notes

Structure and Physical Properties

[back to top]


Physical Properties

Sequence

at EcoCyc 

MEPLREIRNR LLNGWQLSKM HTFEVAARHQ SFALAAEELS LSPSAVSHRI NQLEEELGIQ
LFVRSHRKVE LTHEGKRVYW ALKSSLDTLN QEILDIKNQE LSGTLTLYSR PSIAQCWLVP
ALGDFTRRYP SISLTVLTGN DNVNLQRAGI DLAIYFDDAP SAQLTHHFLM DEEILPVCSP
EYAQRHALTN TVINLCHCTL LHDRQAWSND SGTDEWHSWA QHYAVNLPTS SGIGFDRSDL
AVIAAMNHIG VAMGRKRLVQ KRLASGELVA PFGDMTVKCH QHYYITTLPG RQWPKIEAFI
IWLREQVKTT S
Mol. Wt

35.33 kDa (calc) [2]

pI

6.88[2]

Extinction coefficient

55920 - 56545 (calc based on 8 Y, 8 W, and 5 C residues)

edit table

See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Domains/Motifs/Modification Sites

Type Residues Description Notes

Domain

15 - 72

HTH lysR-type

UniProt:P46068

edit table

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

Structure

Structures

<beststructure>dsdC 562</beststructure>

Models

View models at:

edit table

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

Notes

Gene Product Resources

[back to top]


Resource type Source Notes/Reference
edit table

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

Notes

Accessions in Other Databases

[back to top]


Database Accession Notes

EcoCyc (EcoliWiki Page)

EcoCyc:PD00297

UniProt (EcoliWiki Page)

UniProt:P46068

PFAM (EcoliWiki Page)

PFAM:PF00126

RefSeq (EcoliWiki Page)

RefSeq:NP_416865

ModBase (EcoliWiki Page)

ModBase:P46068

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:Z0885-MONOMER


edit table

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

Notes

Links

[back to top]


Name URL Comments
edit table

See Help:Links_table for how to enter or edit information in this section of EcoliWiki.



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 2.4 2.5 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 3.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7


Categories

[back to top]


Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=dsdC:Gene_Product(s)&oldid=580224"