yaeR:Gene Product(s): Difference between revisions

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!align=left {{table heading style}} |Standard name
!align=left {{table heading style}} |Standard name
||
||
YaeR product
YaeR  
|-
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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
predicted lyase product<ref name='LIB:Riley_2006'/>, B0187 product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YaeR product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''predicted lyase<ref name='LIB:Riley_2006'/>, B0187<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YaeR<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK0186, JW0182, b0187''
|-
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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predicted lyase<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>
predicted lyase<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>


Function unknown<ref name='LIB:EcoGene'/>
|-
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!align=left {{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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{{BacktoTop}}
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<big>'''Gene Ontology'''</big><br />{{Product_GO_help}}<!--box uid=421aa90e079fa326b6494f812ad13e79.19950.W46aa22468b0f1-->
<big>'''Gene Ontology'''</big><br /><!--box uid=421aa90e079fa326b6494f812ad13e79.19950.W46aa22468b0f1-->
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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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|- {{table heading style}}
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!|Partner Type!!Partner!!Notes!!References
!|Partner Type!!Partner!!Notes!!References!!Evidence
|-
|
Protein
|
groL<br />
|
 
|
PMID:16606699
|
Experiment(s):EBI-1135867<br />
|-
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Protein
|
zwf<br />
|
 
|
PMID:16606699
|
Experiment(s):EBI-1135867<br />
|-
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Protein
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wcaI
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
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Protein
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yegV
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.0
|-
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Protein
|
rraB
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
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Protein
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rfaD
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
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Protein
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ycfD
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
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Protein
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yaeH
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.6
|-
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Protein
|
oppF
|
 
|
PMID:19402753
|
LCMS(ID Probability):97.8


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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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GQYVIELFSF PFPPERPSRP EACGLRHLAF SVDDIDAAVA HLESHNVKCE TIRVDPYTQK
GQYVIELFSF PFPPERPSRP EACGLRHLAF SVDDIDAAVA HLESHNVKCE TIRVDPYTQK
RFTFFNDPDG LPLELYEQ</pre>  
RFTFFNDPDG LPLELYEQ</pre>  
|-
!align=left {{table heading style}} |Length
||
138
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
14.74 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
15.708 kDa
|-
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!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
5.1 (calculated)
|-
|-
!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
14440 - 14815 (calc based on 6 Y, 1 W, and 3 C residues)  
14,440 - 14,815 (calc based on 6 Y, 1 W, and 3 C residues)


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<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span>
 
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<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span><table>
<tr align="left" valign="top">
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!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-
|
Domain
|
6..126
|
[http://pfam.janelia.org/family/PF00903 PF00903  Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily]
|
 
|
PMID:19920124


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<td>
<!-- motifs column 2-->
<motif_map/>
</td>
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</table>


<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>yaeR
<beststructure>
562</beststructure>
gene=yaeR
 
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=yaeR&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P76543 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=yaeR&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P52096 PSI-PRED (P52096)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P52096 Genomes TO Protein (P52096)] (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 figures ====
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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===Notes===
===Notes===


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!|Resource type!!Source!!Notes/Reference
!|Resource type!!Source!!Notes/Reference


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===Notes===
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!|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/90111096 GI:90111096]
|
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_414729.4 GeneID:944875]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6095-MONOMER EcoCyc:G6095-MONOMER]
ASAP:ABE-0000635
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P52096 UniProtKB/Swiss-Prot:P52096]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
EcoCyc:G6095
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
[[EcoGene]]
|
|
[[uniprot:P52096|UniProt:P52096]]
EcoGene:EG13224
|
|
''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=PF00903 PFAM:PF00903]
[http://www.ncbi.nlm.nih.gov/gene?term=944875 GeneID:944875]
|
|
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_414729 RefSeq:NP_414729]
RegulonDB:ECK120002715
|
|
''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=P52096 ModBase:P52096]
EchoBASE:EB3015
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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===Categories===
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[[Category:Proteins]]
[[Category:Proteins]]
[[Category:Pfam:PF00903_!_Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily]]

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

YaeR

Synonyms

predicted lyase[1], B0187[2][1], YaeR[2][1] , ECK0186, JW0182, b0187

Product description

predicted lyase[2][3]

Function unknown[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

groL

PMID:16606699[5]

Experiment(s):EBI-1135867

Protein

zwf

PMID:16606699[5]

Experiment(s):EBI-1135867

Protein

wcaI

PMID:19402753[6]

LCMS(ID Probability):99.6

Protein

yegV

PMID:19402753[6]

LCMS(ID Probability):99.0

Protein

rraB

PMID:19402753[6]

LCMS(ID Probability):99.6

Protein

rfaD

PMID:19402753[6]

LCMS(ID Probability):99.6

Protein

ycfD

PMID:19402753[6]

LCMS(ID Probability):99.6

Protein

yaeH

PMID:19402753[6]

LCMS(ID Probability):99.6

Protein

oppF

PMID:19402753[6]

LCMS(ID Probability):97.8

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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 

MLLTNKGDVM LGLKQVHHIA IIATDYAVSK AFYCDILGFT LQSEVYREAR DSWKGDLALN
GQYVIELFSF PFPPERPSRP EACGLRHLAF SVDDIDAAVA HLESHNVKCE TIRVDPYTQK
RFTFFNDPDG LPLELYEQ
Length

138

Mol. Wt

15.708 kDa

pI

5.1 (calculated)

Extinction coefficient

14,440 - 14,815 (calc based on 6 Y, 1 W, and 3 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

6..126

PF00903 Glyoxalase/Bleomycin resistance protein/Dioxygenase superfamily

PMID:19920124[7]

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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=yaeR 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:90111096

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:944875

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000635

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P52096

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6095

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13224

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:944875

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002715

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3015

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 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 6.3 6.4 6.5 6.6 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  7. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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