ykfG:Gene Product(s): Difference between revisions

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|{{Sub}}[[#Localization |Localization]]
|{{Sub}}[[#Localization |Localization]]
|{{Sub}}[[#Sequence|Sequence]]
|{{Sub}}[[#Sequence|Sequence]]
|{{Sub}}[[#Domains/Motifs/Modification Sites|Domains]]
|{{Sub}}[[#Structure|Structure]]
|{{Sub}}[[#Structure|Structure]]
|{{Sub}}[[#Gene Product Resources|Resources]]
|{{Sub}}[[#Gene Product Resources|Resources]]
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!{{table heading style}} |Standard name
!align=left {{table heading style}} |Standard name
|
||
YkfG product
YkfG  
|-
|-
!{{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
|
||
CP4-6 prophage; predicted DNA repair protein product<ref name='LIB:Riley_2006'/>, B0247 product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YkfG product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''CP4-6 prophage; predicted DNA repair protein<ref name='LIB:Riley_2006'/>, B0247<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YkfG<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK0249, JW0236, b0247''
|-
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!{{table heading style}} |Product description
!align=left {{table heading style}} |Product description
|
||
putative DNA repair protein<ref name='LIB:EcoCyc10.6'/>; CP4-6 prophage; predicted DNA repair protein<ref name='LIB:EcoCyc11.1'/>
putative DNA repair protein<ref name='LIB:EcoCyc10.6'/>; CP4-6 prophage; predicted DNA repair protein<ref name='LIB:EcoCyc11.1'/>


Function unknown, CP4-6 putative prophage remnant<ref name='LIB:EcoGene'/>
|-
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!{{table heading style}} |EC number (for enzymes)
!align=left {{table heading style}} |EC number (for enzymes)
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*
 
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===Notes===
===Notes===
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<protect>
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<big>'''Gene Ontology'''</big>
<big>'''Gene Ontology'''</big><br /><!--box uid=421aa90e079fa326b6494f812ad13e79.20102.R46aa25a79370b-->
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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
|-
|
 
|
[[Category:GO:0005515_!_protein_binding]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0005515_!_protein_binding GO:0005515]
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protein_binding
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[[PMID:16606699]]<ref name=PMID:16606699/><br />
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IPI: Inferred from Physical Interaction
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UniProtKB:P0AE60
|
F
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
|


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<span id="Interactions"></span><big>'''Interactions'''</big>
<span id="Interactions"></span><big>'''Interactions'''</big>
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!Partner Type!!Partner!!Notes
!|Partner Type!!Partner!!Notes!!References!!Evidence
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Protein
|
cedA<br />
|
 
|
PMID:16606699
|
Experiment(s):EBI-1136014<br />
 
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===Notes===
===Notes===
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!Compartment!!Description!!Evidence!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
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!align=left {{table heading style}} |Name
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|-
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!{{table heading style}} |Sequence
!align=left {{table heading style}} |Sequence
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[http://biocyc.org/ECOLI/sequence-aa?object=G6122-MONOMER at EcoCyc]  
[http://biocyc.org/ECOLI/sequence-aa?object=G6122-MONOMER at EcoCyc]  
<pre>MKQLSFLPGE MTPQDRRLIQ RALRALDRHL HEPGVAFTST HAVREWLRLH MAALEREEFR
<pre>MKQLSFLPGE MTPQDRRLIQ RALRALDRHL HEPGVAFTST HAVREWLRLH MAALEREEFR
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KTLTQRLVQV LQLVDIRVPD HLIVGGRQIY SFAEHGLL</pre>  
KTLTQRLVQV LQLVDIRVPD HLIVGGRQIY SFAEHGLL</pre>  
|-
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!{{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Length
|
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18.1 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
158
|-
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!{{table heading style}} |pI
!align=left {{table heading style}} |Mol. Wt
|
||
18.098 kDa
|-
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!{{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |pI
|
||
8480 (calc based on 2 Y, 1 W, and 0 C residues)  
8.9 (calculated)
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!align=left {{table heading style}} |Extinction coefficient
||
8,480 (calc based on 2 Y, 1 W, and 0 C residues)
 
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<big>'''Domains/Motifs/Modification Sites'''</big>
 
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<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span><table>
<tr align="left" valign="top">
<td><!--box uid=421aa90e079fa326b6494f812ad13e79.20102.G46aa25aa26f27-->
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!Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
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Domain
|
36..158
|
[http://pfam.janelia.org/family/PF04002 PF04002  Protein of unknown function (DUF2466)]
|
 
|
PMID:19920124
 
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<td>
<!-- motifs column 2-->
<motif_map/>
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<span id="Structure"></span><big>'''Structure'''</big>
<table><tr valign='top'><td>
<span id='Structure'></span><big>'''Structure'''</big><br />
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!Structure Type!!Organism!!Accession!!Residues covered!!Notes
|-
|-class='sortbottom'
!align=left {{table heading style}} |Structures
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.20102.D46a7b6e47fe98&page=20102&pagename={{FULLPAGENAMEE}} edit table] || || || ||
||
<beststructure>
gene=ykfG
taxon=562,83333
</beststructure>
|-
!align=left {{table heading style}} |Models
||
View models at:
* [http://www.proteinmodelportal.org/query/uniprot/Q47685 Protein Model Portal]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=Q47685 PSI-PRED (Q47685)]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=Q47685 Genomes TO Protein (Q47685)] (GTOP)
 
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<!--Structure_notes--></protect>
</td><td></protect>
==== Structure figures ====
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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===Notes===
===Notes===


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===Notes===
===Notes===
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-
|
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/16128232 GI:16128232]
|
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_414781.1 GeneID:944930]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0000841
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/Q47685 UniProtKB/Swiss-Prot:Q47685]
|
Escherichia coli str. K-12 substr. MG1655
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6122-MONOMER EcoCyc:G6122-MONOMER] 
EcoCyc:G6122
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
[[EcoGene]]
|
|
[[uniprot:Q47685|UniProt:Q47685]] 
EcoGene:EG14331
|
|
''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=PF04002 PFAM:PF04002]
[http://www.ncbi.nlm.nih.gov/gene?term=944930 GeneID:944930]
|
|
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_414781 RefSeq:NP_414781] 
RegulonDB:ECK120002742
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=Z1657-MONOMER ECOO157CYC:Z1657-MONOMER] 
EchoBASE:EB4077
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
===Notes===
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[[Category:Proteins]]
[[Category:Pfam:PF04002_!_Protein of unknown function (DUF2466)]]

Latest revision as of 20:23, 17 February 2015

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

Nomenclature

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

Standard name

YkfG

Synonyms

CP4-6 prophage; predicted DNA repair protein[1], B0247[2][1], YkfG[2][1] , ECK0249, JW0236, b0247

Product description

putative DNA repair protein[2]; CP4-6 prophage; predicted DNA repair protein[3]

Function unknown, CP4-6 putative prophage remnant[4]

EC number (for enzymes)


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Notes

Function

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Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

cedA

PMID:16606699[5]

Experiment(s):EBI-1136014
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Notes

Localization

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

Compartment Description Evidence Reference/Source Notes
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Notes

Structure and Physical Properties

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

Name
Sequence

at EcoCyc 

MKQLSFLPGE MTPQDRRLIQ RALRALDRHL HEPGVAFTST HAVREWLRLH MAALEREEFR
VLYLDNQNQL IAHETLFTGT INRTEVHPRE VVKRALHFNA AAVILAHNHP SGETTPSQAD
KTLTQRLVQV LQLVDIRVPD HLIVGGRQIY SFAEHGLL
Length

158

Mol. Wt

18.098 kDa

pI

8.9 (calculated)

Extinction coefficient

8,480 (calc based on 2 Y, 1 W, and 0 C residues)

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Domains/Motifs/Modification Sites

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

Type Residues Description Notes References

Domain

36..158

PF04002 Protein of unknown function (DUF2466)

PMID:19920124[6]

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<motif_map/>

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

Structures

<beststructure> gene=ykfG 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:16128232

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:944930

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000841

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:Q47685

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6122

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14331

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:944930

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002742

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4077

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. ↑ Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  6. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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