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{{Tab|Quickview|yfaU}}{{Tab|Gene|yfaU}}{{Tab On|Gene Product(s)|yfaU}}{{Tab|Expression|yfaU}}{{Tab|Evolution|yfaU}}{{Tab|On One Page|yfaU}}{{TabsBottom}}
{|
|-
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Function |Function]]
|{{Sub}}[[#Interactions |Interactions]]
|{{Sub}}[[#Localization |Localization]]
|{{Sub}}[[#Sequence|Sequence]]
|{{Sub}}[[#Structure|Structure]]
|{{Sub}}[[#Gene Product Resources|Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Links |Links]]
|{{Sub}}[[#References| References]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
</noinclude>
==Nomenclature==


{|{{Prettytable}}
|-
!{{table heading style}} |Standard name
|
YfaU product
|-
!{{table heading style}} |Synonyms
|
predicted 2,4-dihydroxyhept-2-ene-1,7-dioic acid aldolase product<ref name='LIB:Riley_2006'/>, B2245 product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YfaU product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>
|-
!{{table heading style}} |Product description
|
predicted aldolase<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>

|-
!{{table heading style}} |EC number (for enzymes)
|
*
|-
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===Notes===

==Function==
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<protect>
<big>'''Gene Ontology'''</big> {{Product_GO_help}}

{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"
|- {{table_heading_style}}
!|Qualifier!!GO ID!!GO term name!!Reference(s)!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-
|

|
[[Category:GO:0003824_!_catalytic_activity]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0003824_!_catalytic_activity GO:0003824]
|
catalytic_activity
|
[http://www.geneontology.org/cgi-bin/references.cgi/#GO_REF:0000002 GO_REF:0000002] 
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR015813
|
F
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
|

|-
|

|
[[Category:GO:0006725_!_cellular_aromatic_compound_metabolic_process]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0006725_!_cellular_aromatic_compound_metabolic_process GO:0006725]
|
aromatic_compound_metabolism
|
[http://www.geneontology.org/cgi-bin/references.cgi/#GO_REF:0000002 GO_REF:0000002] 
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR005000
|
P
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
|

|-
|

|
[[Category:GO:0016829_!_lyase_activity]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0016829_!_lyase_activity GO:0016829]
|
lyase_activity
|
[http://www.geneontology.org/cgi-bin/references.cgi/#GO_REF:0000004 GO_REF:0000004] 
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0456
|
F
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
|

|-
|

|
[[Category:GO:0008152_!_metabolic_process]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0008152_!_metabolic_process GO:0008152]
|
metabolic process
|

|

|

|
P
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
|
required fields missing
|-
|

|
[[Category:GO:0016830_!_carbon-carbon_lyase_activity]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0016830_!_carbon-carbon_lyase_activity GO:0016830]
|
carbon-carbon_lyase_activity
|
[http://www.geneontology.org/cgi-bin/references.cgi/#GO_REF:0000002 GO_REF:0000002] 
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR005000
|
F
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
|

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<big>'''Interactions'''</big>


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!Partner Type!!Partner!!Notes
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===Notes===

==Localization==


{|class = 'sortable' {{Prettytable}} id='113831'
|- {{table heading style}}
!Compartment!!Description!!Evidence!!Notes
|-class='sortbottom'
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===Notes===

==Structure and Physical Properties==
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<protect>
<big>'''Physical Properties'''</big>


{|{{Prettytable}}
|-
!{{table heading style}} |Sequence
|
[http://biocyc.org/ECOLI/sequence-aa?object=G7158-MONOMER at EcoCyc]
<pre>MNALLSNPFK ERLRKGEVQI GLWLSSTTAY MAEIAATSGY DWLLIDGEHA PNTIQDLYHQ
LQAVAPYASQ PVIRPVEGSK PLIKQVLDIG AQTLLIPMVD TAEQARQVVS ATRYPPYGER
GVGASVARAA RWGRIENYMA QVNDSLCLLV QVESKTALDN LDEILDVEGI DGVFIGPADL
SASLGYPDNA GHPEVQRIIE TSIRRIRAAG KAAGFLAVAP DMAQQCLAWG ANFVAVGVDT
MLYSDALDQR LAMFKSGKNG PRIKGSY</pre>
|-
!{{table heading style}} |Mol. Wt
|
28.92 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
|-
!{{table heading style}} |pI
|

|-
!{{table heading style}} |Extinction coefficient
|
36900 - 37150 (calc based on 10 Y, 4 W, and 2 C residues)
|-
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{{Product_physical_properties_help}}

<big>'''Domains/Motifs/Modification Sites'''</big>


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!Type!!Residues!!Description!!Notes
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{{Product_domains_motifs_help}}

<big>'''Structure'''</big>


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|- {{table heading style}}
!|Structures!!Models
|-
|
1.39 A structure of apo-YfaU and the Mg2+-pyruvate product complex
<ref name='PMID:18754683'/>
|

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</protect>
===Notes===

==Gene Product Resources==
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!Resource type!!Source!!Notes/Reference
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.24677.I46aa9b9b8cd87&page=24677&pagename={{FULLPAGENAMEE}} edit table] || ||
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===Notes===

==Accessions in Other Databases==
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{|class = 'sortable' {{Prettytable}} id='167961'
|- {{table_heading_style}}
!Database!!Accession!!Notes
|-
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7158-MONOMER EcoCyc:G7158-MONOMER]
|

|-
|
[http://swissmodel.expasy.org/repository/ SwissModel] ([[SwissModel|EcoliWiki Page]])
|
[http://swissmodel.expasy.org/repository/smr.php?job=2&sptr_ac=P76469 SwissModel:P76469]
|

|-
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[[uniprot:P76469|UniProt:P76469]]
|

|-
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
|
[http://pfam.sanger.ac.uk/family?acc=PF03328 PFAM:PF03328]
|

|-
|
[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_416748 RefSeq:NP_416748]
|

|-
|
[http://modbase.compbio.ucsf.edu ModBase] ([[ModBase|EcoliWiki Page]])
|
[http://salilab.org/modbase/searchbyid?databaseID=P76469 ModBase:P76469]
|

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{{Product_accessions_help}}
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===Notes===

==Links==
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{|class = 'sortable' {{Prettytable}} id='113836'
|- {{table_heading_style}}
!Name!!URL!!Comments
|-class='sortbottom'
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|}

{{Links_help}}

<noinclude>
==References==
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{{RefHelp}}
<references/>
__NOTOC__
</noinclude>
===Categories===
{{BacktoTop}}
[[Category:Proteins]]
[[Category:GO:0008152_!_metabolic process]]

Letter to Science about wikifying genome information

2008-04-07T21:05:35Z

Gribskov: /* signatures */

The March 21, 2008 issue of ''Science'' included a [http://www.sciencemag.org/cgi/content/full/319/5870/1598 News piece]<ref name='PMID:18356493'/> stimulated by an open letter from a large group of fungal researchers about using wiki models for improving GenBank. We thought we should send a letter to Science in response.

Please help us edit the text and add your signature if you want to go on record with us. Limit is 300 words. Plan is to submit by April 11, 2008
==draft==
We noted with interest the recent correspondence<ref name='PMID:18356505'/> and accompanying news article <ref name='PMID:18356493'/> regarding a proposal to "wikify" GenBank. While David Lipman’s fears that "It would be chaos." are widely shared, the expertise of GenBank's single staff mycologist is unlikely to be superior to the collective, albeit intermittently applied, expertise of the scientists who might participate in wiki curation, including the 250 signers of the Bidartondo et al. letter. Nevertheless, we understand that changing the GenBank model should not be done lightly. There are now well-established expectations, both good and bad, about GenBank and RefSeq, and wikifying them could be quite disruptive.

We have been working on wiki-based systems for gene annotation, including EcoliWiki (http://ecoliwiki.net), the community annotation component of the EcoliHub project (http://ecolihub.org) and GONUTS (http://gowiki.tamu.edu), a wiki-based browser and annotation engine for the Gene Ontology. We regard these, and other wiki-based efforts <ref name='PMID:18259167'/><ref name='PMID:17090585'/> as experiments to determine whether wiki-based community curation will work. So far, the biggest problem is not chaos, it's lack of participation. Thus, we are also experimenting with literature-based curation by undergraduates under the supervision of a more experienced scientist. Incorporating wiki-based annotation as part of genomics undergraduate education leverages how we teach critical thinking about the literature, accelerates the pace of curation, and provides institutional incentives for established scientists to participate.

While these experiments are in progress, perhaps GenBank could support an arms length relationship to wikis via the LinkOut service. We look forward to the ongoing discussion of the future of how community curation could be added to GenBank. In the meantime, we encourage the signers of the Bidartondo et al. letter to help us build wiki-based fungal curation of gene function via GO at GONUTS.

===signatures===
*James C. Hu, Texas A&M Univ.
*Michael Gribskov, Purdue University
<references/>

----

Letter to Science about wikifying genome information

2008-04-07T21:04:54Z

Gribskov: /* draft */

The March 21, 2008 issue of ''Science'' included a [http://www.sciencemag.org/cgi/content/full/319/5870/1598 News piece]<ref name='PMID:18356493'/> stimulated by an open letter from a large group of fungal researchers about using wiki models for improving GenBank. We thought we should send a letter to Science in response.

Please help us edit the text and add your signature if you want to go on record with us. Limit is 300 words. Plan is to submit by April 11, 2008
==draft==
We noted with interest the recent correspondence<ref name='PMID:18356505'/> and accompanying news article <ref name='PMID:18356493'/> regarding a proposal to "wikify" GenBank. While David Lipman’s fears that "It would be chaos." are widely shared, the expertise of GenBank's single staff mycologist is unlikely to be superior to the collective, albeit intermittently applied, expertise of the scientists who might participate in wiki curation, including the 250 signers of the Bidartondo et al. letter. Nevertheless, we understand that changing the GenBank model should not be done lightly. There are now well-established expectations, both good and bad, about GenBank and RefSeq, and wikifying them could be quite disruptive.

We have been working on wiki-based systems for gene annotation, including EcoliWiki (http://ecoliwiki.net), the community annotation component of the EcoliHub project (http://ecolihub.org) and GONUTS (http://gowiki.tamu.edu), a wiki-based browser and annotation engine for the Gene Ontology. We regard these, and other wiki-based efforts <ref name='PMID:18259167'/><ref name='PMID:17090585'/> as experiments to determine whether wiki-based community curation will work. So far, the biggest problem is not chaos, it's lack of participation. Thus, we are also experimenting with literature-based curation by undergraduates under the supervision of a more experienced scientist. Incorporating wiki-based annotation as part of genomics undergraduate education leverages how we teach critical thinking about the literature, accelerates the pace of curation, and provides institutional incentives for established scientists to participate.

While these experiments are in progress, perhaps GenBank could support an arms length relationship to wikis via the LinkOut service. We look forward to the ongoing discussion of the future of how community curation could be added to GenBank. In the meantime, we encourage the signers of the Bidartondo et al. letter to help us build wiki-based fungal curation of gene function via GO at GONUTS.

===signatures===
James C. Hu, Texas A&M Univ.
Michael Gribskov, Purdue University
<references/>

----