ydfZ:Gene Product(s): Difference between revisions

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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
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conserved protein<ref name='LIB:Riley_2006'/>, YdfZ<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, B1541<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''conserved protein<ref name='LIB:Riley_2006'/>, YdfZ<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, B1541<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK1534, JW1534, b1541''
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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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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selenium binding
selenium binding
|
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GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
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IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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F
F
|
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Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
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complete  
complete  


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!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
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Experiment(s):EBI-1140096<br />  
Experiment(s):EBI-1140096<br />  


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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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<pre>MTTYDRNRNA ITTGSRVMVS GTGHTGKILS IDTEGLTAEQ IRRGKTVVVE GCEEKLAPLD
<pre>MTTYDRNRNA ITTGSRVMVS GTGHTGKILS IDTEGLTAEQ IRRGKTVVVE GCEEKLAPLD
LIRLGMN</pre>  
LIRLGMN</pre>  
|-
!align=left {{table heading style}} |Length
||
67
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
7.28 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
7.275 kDa
|-
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!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
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8.1 (calculated)
|-
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!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
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1490 - 1615 (calc based on 1 Y, 0 W, and 1 C residues)  
1,490 - 1,615 (calc based on 1 Y, 0 W, and 1 C residues)


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<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span>
<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span><table>
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|- {{table heading style}}
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!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-
|
Modification Site
|
52
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S-selanylcysteine (Potential)
|
[http://www.uniprot.org/uniprot/P64463#section_features UniProt:P64463]


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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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!align=left {{table heading style}} |Structures
!align=left {{table heading style}} |Structures
||
||
<beststructure>ydfZ
<beststructure>
562</beststructure>
gene=ydfZ
 
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=ydfZ&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P64463 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=ydfZ&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P64463 PSI-PRED (P64463)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P64463 Genomes TO Protein (P64463)] (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)


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<!--Structure_notes--></protect>
</td><td></protect>
==== Structure figures ====
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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===Notes===
===Notes===


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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
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[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/16129500 GI:16129500]
|
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_416059.1 GeneID:948796]
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Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0005147
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P64463 UniProtKB/Swiss-Prot:P64463]
|
Escherichia coli str. K-12 substr. MG1655
|-
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[[EcoCyc]]
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EcoCyc:G6815
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[[EcoGene]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6815-MONOMER EcoCyc:G6815-MONOMER]
EcoGene:EG13838
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/gene?term=948796 GeneID:948796]
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
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[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
[[RegulonDB]]
|
|
[[uniprot:P64463|UniProt:P64463]]
RegulonDB:ECK120003404
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[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_416059 RefSeq:NP_416059]
EchoBASE:EB3599
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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==References==
==References==
{{BacktoTop}}
{{BacktoTop}}
 
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</noinclude>
===Categories===
===Categories===
{{BacktoTop}}
{{BacktoTop}}
[[Category:Proteins]]
[[Category:Proteins]]

Latest revision as of 20:39, 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

YdfZ

Synonyms

conserved protein[1], YdfZ[2][1], B1541[2][1] , ECK1534, JW1534, b1541

Product description

conserved protein[2][3]

Binds selenium, 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:0008430

selenium binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0711

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

nadE

PMID:16606699[5]

Experiment(s):EBI-1140096

Protein

mngB

PMID:16606699[5]

Experiment(s):EBI-1140096

Protein

ybdD

PMID:16606699[5]

Experiment(s):EBI-1140096

Protein

pepD

PMID:16606699[5]

Experiment(s):EBI-1140096

Protein

ykgF

PMID:16606699[5]

Experiment(s):EBI-1140096

Protein

pflB

PMID:16606699[5]

Experiment(s):EBI-1140096

Protein

lacZ

PMID:16606699[5]

Experiment(s):EBI-1140096

Protein

pqqL

PMID:16606699[5]

Experiment(s):EBI-1140096

Protein

napC

PMID:16606699[5]

Experiment(s):EBI-1140096
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Notes

Localization

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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 

MTTYDRNRNA ITTGSRVMVS GTGHTGKILS IDTEGLTAEQ IRRGKTVVVE GCEEKLAPLD
LIRLGMN
Length

67

Mol. Wt

7.275 kDa

pI

8.1 (calculated)

Extinction coefficient

1,490 - 1,615 (calc based on 1 Y, 0 W, and 1 C residues)

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Domains/Motifs/Modification Sites

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Type Residues Description Notes References
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<motif_map/>

Structure
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Structures

<beststructure> gene=ydfZ 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:16129500

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948796

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005147

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P64463

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6815

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13838

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948796

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003404

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3599

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 5.2 5.3 5.4 5.5 5.6 5.7 5.8 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed

Categories

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