yajR:Gene Product(s): Difference between revisions

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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
predicted transporter<ref name='LIB:Riley_2006'/>, B0427<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YajR<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''predicted transporter<ref name='LIB:Riley_2006'/>, B0427<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YajR<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK0421, JW5059, b0427''
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="C46aa2eee718ae"  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
|-  
|-  
|
|


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GO:0016021
GO:0005886
|
|
integral to membrane
plasma membrane
|
|
GO_REF:0000002<br />GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR007114<br />SP_KW:KW-0812
SP_KW:KW-0997
|
|
C
C
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
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GO:0016020
GO:0005886
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membrane
plasma membrane
|
|
GO_REF:0000004<br />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
|
|
SP_KW:KW-0397<br />SP_KW:KW-0472
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)
|
|
complete  
complete  
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transport
transport
|
|
GO_REF:0000002<br />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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InterPro:IPR007114<br />SP_KW:KW-0813
SP_KW:KW-0813
|
|
P
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
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GO:0005215
GO:0016020
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transporter activity
membrane
|
|
GO_REF:0000002
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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InterPro:IPR007114
SP_KW:KW-0472
|
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F
C
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
|-  
|-  
|
|
 
|
|
GO:0042493
GO:0016021
|
|
response to drug
integral to membrane
|
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0812
|
|
P
C
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
|-  
|-  
|
|


|
|
GO:0005886
GO:0016021
|
|
plasma membrane
integral to membrane
|
|
GO_REF:0000004<br />GO_REF:0000004<br />GO_REF:0000023
GO_REF:0000023
|
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IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
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SP_KW:KW-0997<br />SP_KW:KW-1003<br />SP_SL:SL-0037
SP_SL:SL-9909
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C
C
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
|-  
|-  
|
|
 
|
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GO:0015292
GO:0055085
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uniporter activity
transmembrane transport
|
|
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR011701
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|
F
P
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete


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!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence


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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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GWINGMFDGQ GVFLAGAMLA AVWLTVASTM KEPPYVSSLR IEIPANIAAN EALKVRLLET
GWINGMFDGQ GVFLAGAMLA AVWLTVASTM KEPPYVSSLR IEIPANIAAN EALKVRLLET
EGIKEVLIAE EEHSAYVKID SKVTNRFEIE QAIRQA</pre>  
EGIKEVLIAE EEHSAYVKID SKVTNRFEIE QAIRQA</pre>  
|-
!align=left {{table heading style}} |Length
||
456
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
48.81 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
49.041 kDa
|-
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!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
9.4 (calculated)
|-
|-
!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
62910 - 63160 (calc based on 9 Y, 9 W, and 2 C residues)  
62,910 - 63,160 (calc based on 9 Y, 9 W, and 2 C residues)


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!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-  
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Domain
Domain
|
|
52 - 74
17..354
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|
Predicted membrane-spanning helix.
[http://pfam.janelia.org/family/PF07690 PF07690  Major Facilitator Superfamily]
|
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
 
|-
|
Domain
|
81 - 100
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
104 - 126
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
139 - 161
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
166 - 188
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
219 - 241
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
256 - 275
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
282 - 304
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
308 - 330
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
343 - 365
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
370 - 387
|
|
Predicted membrane-spanning helix.
PMID:19920124
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
20 - 42
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />


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</td>
</td>
<td>
<td>
<!-- motifs column 2-->
<motif_map/>
{{TMHMM Picture|yajR}}
{{TMHMM Picture|yajR}}
</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>yajR
<beststructure>
562</beststructure>
gene=yajR
 
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=yajR&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P77726 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=yajR&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P77726 PSI-PRED (P77726)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P77726 Genomes TO Protein (P77726)] (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 ====
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
<protect><!--          ***** PLEASE DO NOT EDIT BELOW THIS LINE *****        -->
</td><tr><table><!--Structure_notes--></protect>
===Notes===
===Notes===


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


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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="L46aa2ef7bf5a1"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
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|
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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://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=B0427-MONOMER EcoCyc:B0427-MONOMER]
[http://www.ncbi.nlm.nih.gov/protein/90111133 GI:90111133]
|
|
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_414961.4 GeneID:945058]
|
Escherichia coli str. K-12 substr. MG1655
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[[ASAP]]
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ASAP:ABE-0001481
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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/P77726 UniProtKB/Swiss-Prot:P77726]
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Escherichia coli str. K-12 substr. MG1655
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[[EcoCyc]]
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EcoCyc:G6241
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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|-  
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[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
[[EcoGene]]
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[[uniprot:P77726|UniProt:P77726]]
EcoGene:EG13614
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
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[http://pfam.sanger.ac.uk/family?acc=PF07690 PFAM:PF07690]
[http://www.ncbi.nlm.nih.gov/gene?term=945058 GeneID:945058]
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Escherichia coli str. K-12 substr. MG1655
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|-  
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[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
[[RegulonDB]]
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[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_414961 RefSeq:NP_414961]
RegulonDB:ECK120002852
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://modbase.compbio.ucsf.edu ModBase] ([[ModBase|EcoliWiki Page]])
[[EchoBASE]]
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[http://salilab.org/modbase/searchbyid?databaseID=P77726 ModBase:P77726]
EchoBASE:EB3380
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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==References==
==References==
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{{BacktoTop}}
 
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<references/>
<references />
__NOTOC__
__NOTOC__
</noinclude>
===Categories===
===Categories===
{{BacktoTop}}
{{BacktoTop}}
[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0042493_!_response to drug]][[Category:GO:0015292_!_uniporter activity]]

Latest revision as of 20:25, 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

YajR

Synonyms

predicted transporter[1], B0427[2][1], YajR[2][1] , ECK0421, JW5059, b0427

Product description

YajR MFS transporter[2][3]

Putative transporter, function unknown; no overexpression resistances found[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:0006810

transport

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0813

P

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: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

GO:0055085

transmembrane transport

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011701

P

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 12 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 

MVMNDYKMTP GERRATWGLG TVFSLRMLGM FMVLPVLTTY GMALQGASEA LIGIAIGIYG
LTQAVFQIPF GLLSDRIGRK PLIVGGLAVF AAGSVIAALS DSIWGIILGR ALQGSGAIAA
AVMALLSDLT REQNRTKAMA FIGVSFGITF AIAMVLGPII THKLGLHALF WMIAILATTG
IALTIWVVPN SSTHVLNRES GMVKGSFSKV LAEPRLLKLN FGIMCLHILL MSTFVALPGQ
LADAGFPAAE HWKVYLATML IAFGSVVPFI IYAEVKRKMK QVFVFCVGLI VVAEIVLWNA
QTQFWQLVVG VQLFFVAFNL MEALLPSLIS KESPAGYKGT AMGVYSTSQF LGVAIGGSLG
GWINGMFDGQ GVFLAGAMLA AVWLTVASTM KEPPYVSSLR IEIPANIAAN EALKVRLLET
EGIKEVLIAE EEHSAYVKID SKVTNRFEIE QAIRQA
Length

456

Mol. Wt

49.041 kDa

pI

9.4 (calculated)

Extinction coefficient

62,910 - 63,160 (calc based on 9 Y, 9 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

17..354

PF07690 Major Facilitator Superfamily

PMID:19920124[6]

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<motif_map/>

tmhmm.php?gene=yajR&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=yajR 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:90111133

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945058

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001481

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P77726

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6241

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13614

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945058

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002852

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3380

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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