yaiY: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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|-
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!{{table heading style}} |Standard name
!align=left {{table heading style}} |Standard name
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YaiY product
YaiY  
|-
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!{{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
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predicted inner membrane protein product<ref name='LIB:Riley_2006'/>, YaiY product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, B0379 product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''predicted inner membrane protein<ref name='LIB:Riley_2006'/>, YaiY<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, B0379<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK0374, JW0370, b0379''
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!{{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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inner membrane protein<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>
inner membrane protein<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>


Function unknown<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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<big>'''Gene Ontology'''</big><br />{{Product_GO_help}}<!--box uid=421aa90e079fa326b6494f812ad13e79.20375.N46aa2bd29ec9f-->
<big>'''Gene Ontology'''</big><br /><!--box uid=421aa90e079fa326b6494f812ad13e79.20375.N46aa2bd29ec9f-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N46aa2bd29ec9f"  class=" tableEdit GO_table_product dataTable"   
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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
|-
|
 
|
GO:0005886
|
plasma membrane
|
GOA:spkw<br />SP_KW:GO_REF:0000004
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IEA: Inferred from Electronic Annotation
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SP_KW:KW-0997
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C
|
Seeded from [[EcoCyc]] (v14.0)
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complete
|-  
|-  
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|


|
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[[Category:GO:0016020_!_membrane]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0016020_!_membrane GO:0016020]
GO:0005886
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membrane
plasma membrane
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[http://www.geneontology.org/cgi-bin/references.cgi/#GO_REF:0000004 GO_REF:0000004]<br />
GOA:spkw<br />SP_KW:GO_REF:0000004
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|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0397
SP_KW:KW-1003
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|
C
C
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
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complete
|-  
|-  
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|
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[[Category:GO:0016020_!_membrane]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0016020_!_membrane GO:0016020]
GO:0016020
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membrane
membrane
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[http://www.geneontology.org/cgi-bin/references.cgi/#GO_REF:0000004 GO_REF:0000004]<br />
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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C
C
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0016021
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integral to membrane
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GOA:interpro<br />GO_REF:0000002
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IEA: Inferred from Electronic Annotation
|
InterPro:IPR020513
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C
|
Seeded from [[EcoCyc]] (v14.0)
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complete
|-  
|-  
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|


|
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[[Category:GO:0016021_!_integral_to_membrane]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0016021_!_integral_to_membrane GO:0016021]
GO:0016021
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integral_to_membrane
integral to membrane
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[http://www.geneontology.org/cgi-bin/references.cgi/#GO_REF:0000004 GO_REF:0000004]<br />
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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C
C
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0016021
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integral to membrane
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GO_REF:0000023
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IEA: Inferred from Electronic Annotation
|
SP_SL:SL-9909
|
C
|
Seeded from [[EcoCyc]] (v14.0)
|
|
complete


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===Notes===
===Notes===
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!|Compartment!!Description!!Evidence!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
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Daley et al. (2005) <ref name=PMID:15919996/>
Daley et al. (2005) <ref name=PMID:15919996/>
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!align=left {{table heading style}} |Name
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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=G6228-MONOMER at EcoCyc]  
[http://biocyc.org/ECOLI/sequence-aa?object=G6228-MONOMER at EcoCyc]  
<pre>MADFTLSKSL FSGKYRNASS TPGNIAYALF VLFCFWAGAQ LLNLLVHAPG VYERLMQVQE
<pre>MADFTLSKSL FSGKYRNASS TPGNIAYALF VLFCFWAGAQ LLNLLVHAPG VYERLMQVQE
TGRPRVEIGL GVGTIFGLIP FLVGCLIFAV VALWLHWRHR RQ</pre>  
TGRPRVEIGL GVGTIFGLIP FLVGCLIFAV VALWLHWRHR RQ</pre>  
|-
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!{{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Length
|
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11.42 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
102
|-
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!{{table heading style}} |pI
!align=left {{table heading style}} |Mol. Wt
|
||
11.424 kDa
|-
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!{{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |pI
|
||
20970 - 21220 (calc based on 3 Y, 3 W, and 2 C residues)  
10.3 (calculated)
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!align=left {{table heading style}} |Extinction coefficient
||
20,970 - 21,220 (calc based on 3 Y, 3 W, and 2 C residues)
 
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<big>'''Domains/Motifs/Modification Sites'''</big>
 
<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span>
<table>
<table>
<tr align="left" valign="top">
<tr align="left" valign="top">
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!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-  
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Domain
Domain
|
|
25 - 47
1..101
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Predicted membrane-spanning helix.
[http://pfam.janelia.org/family/PF10954 PF10954  Protein of unknown function (DUF2755)]
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TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
 
|-
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Domain
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68 - 90
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Predicted membrane-spanning helix.
|
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
PMID:19920124


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</td>
</td>
<td>
<td>
<!-- motifs column 2-->
<motif_map/>
{{TMHMM Picture|yaiY}}
{{TMHMM Picture|yaiY}}
</td>
</td>
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</table>
</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>yaiY
<beststructure>
562</beststructure>
gene=yaiY
 
taxon=562,83333
</beststructure>
|-
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!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=yaiY&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P0AAP7 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=yaiY&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P0AAP7 PSI-PRED (P0AAP7)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P0AAP7 Genomes TO Protein (P0AAP7)] (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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===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/16128364 GI:16128364]
|
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_414913.1 GeneID:945223]
|
Escherichia coli str. K-12 substr. MG1655
|-
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[[ASAP]]
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ASAP:ABE-0001302
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
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[http://www.uniprot.org/uniprot/P0AAP7 UniProtKB/Swiss-Prot:P0AAP7]
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Escherichia coli str. K-12 substr. MG1655
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[[EcoCyc]]
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EcoCyc:G6228
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EcoGene]]
|
EcoGene:EG14279
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6228-MONOMER EcoCyc:G6228-MONOMER]
[http://www.ncbi.nlm.nih.gov/gene?term=945223 GeneID:945223]
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Escherichia coli str. K-12 substr. MG1655
|-
|-  
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[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
[[RegulonDB]]
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[[uniprot:P0AAP7|UniProt:P0AAP7]] 
RegulonDB:ECK120002841
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''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]]
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[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_414913 RefSeq:NP_414913] 
EchoBASE:EB4027
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
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===Categories===
===Categories===
{{BacktoTop}}
{{BacktoTop}}
[[Category:Proteins]]
[[Category:Pfam:PF10954_!_Protein of unknown function (DUF2755)]]

Latest revision as of 20:24, 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

YaiY

Synonyms

predicted inner membrane protein[1], YaiY[2][1], B0379[2][1] , ECK0374, JW0370, b0379

Product description

inner membrane protein[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
GO:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0997

C

Seeded from EcoCyc (v14.0)

complete

GO:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-1003

C

Seeded from EcoCyc (v14.0)

complete

GO:0016020

membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0472

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020513

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0812

C

Seeded from EcoCyc (v14.0)

complete

GO:0016021

integral to membrane

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-9909

C

Seeded from EcoCyc (v14.0)

complete

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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
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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

plasma membrane

C-terminus localized in the cytoplasm with 2 predicted transmembrane domains

Daley et al. (2005) [5]


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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 

MADFTLSKSL FSGKYRNASS TPGNIAYALF VLFCFWAGAQ LLNLLVHAPG VYERLMQVQE
TGRPRVEIGL GVGTIFGLIP FLVGCLIFAV VALWLHWRHR RQ
Length

102

Mol. Wt

11.424 kDa

pI

10.3 (calculated)

Extinction coefficient

20,970 - 21,220 (calc based on 3 Y, 3 W, and 2 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

1..101

PF10954 Protein of unknown function (DUF2755)

PMID:19920124[6]

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<motif_map/>

tmhmm.php?gene=yaiY&show=pic&.jpg
Click the image to view raw output from TMHMM.

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

Structures

<beststructure> gene=yaiY 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:16128364

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945223

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001302

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AAP7

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6228

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14279

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945223

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002841

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4027

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. ↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed
  6. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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