alx:Gene Product(s): Difference between revisions

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|-
|-
!align=left {{table heading style}} |Standard name
!align=left {{table heading style}} |Standard name
||
||
Alx product
Alx  
|-
|-
!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
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predicted inner membrane protein, part of terminus product<ref name='LIB:Riley_2006'/>, B3088 product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Alx product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YgjT product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''predicted inner membrane protein, part of terminus<ref name='LIB:Riley_2006'/>, B3088<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Alx<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YgjT<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK3079, JW5515, ygjT, b3088''
|-
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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putative membrane-bound redox modulator that is induced by high pH<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>
putative membrane-bound redox modulator that is induced by high pH<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>


Function unknown; induced by alkali; putative membrane transport or efflux protein<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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<protect><!--Nomenclature_notes--></protect>
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===Notes===
===Notes===
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{{BacktoTop}}
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<protect>
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<big>'''Gene Ontology'''</big><br />{{Product_GO_help}}<!--box uid=421aa90e079fa326b6494f812ad13e79.26603.K46aad103e5283-->
<big>'''Gene Ontology'''</big><br /><!--box uid=421aa90e079fa326b6494f812ad13e79.26603.K46aad103e5283-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="K46aad103e5283"  class=" tableEdit GO_table_product dataTable"   
|- {{table_heading_style}}
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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
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plasma membrane
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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
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Seeded from [[EcoCyc]] (v14.0)
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complete
|-
|
 
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GO:0005886
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plasma membrane
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GOA:spkw<br />SP_KW:GO_REF:0000004
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IEA: Inferred from Electronic Annotation
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SP_KW:KW-1003
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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: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 />[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000004 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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[http://www.uniprot.org/keywords/KW-0397 SP_KW:KW-0397]<br />[http://www.uniprot.org/keywords/KW-0472 SP_KW:KW-0472]
SP_KW:KW-0472
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C
C
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|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
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complete  
complete  
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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:0000002 GO_REF:0000002]<br />[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000004 GO_REF:0000004]
GOA:interpro<br />GO_REF:0000002
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IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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[http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR005496 InterPro:IPR005496]<br />[http://www.uniprot.org/keywords/KW-0812 SP_KW:KW-0812]
InterPro:IPR005496
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C
C
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|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
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complete  
complete  
|-
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GO:0016021
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integral to membrane
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GOA:spkw<br />SP_KW:GO_REF:0000004
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IEA: Inferred from Electronic Annotation
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SP_KW:KW-0812
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C
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Seeded from [[EcoCyc]] (v14.0)
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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
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SP_SL:SL-9909
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C
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Seeded from [[EcoCyc]] (v14.0)
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complete
 
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!|Partner Type!!Partner!!Notes!!References
!|Partner Type!!Partner!!Notes!!References!!Evidence


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<!--Function_notes--></protect>
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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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From EcoCyc<ref name='LIB:EcoCyc11.1'/>   
From EcoCyc<ref name='LIB:EcoCyc11.1'/>  
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!align=left {{table heading style}} |Name
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NLFAILGLRA MYFLLAGVAE RFSMLKYGLA VILVFIGIKM LIVDFYHIPI AVSLGVVFGI
NLFAILGLRA MYFLLAGVAE RFSMLKYGLA VILVFIGIKM LIVDFYHIPI AVSLGVVFGI
LVMTFIINAW VNYRHDKQRG G</pre>  
LVMTFIINAW VNYRHDKQRG G</pre>  
|-
!align=left {{table heading style}} |Length
||
321
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
35.91 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
35.909 kDa
|-
|-
!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
||
||
69900 (calc based on 10 Y, 10 W, and 0 C residues)  
69,900 (calc based on 10 Y, 10 W, and 0 C residues)


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<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span>
<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span>
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!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-  
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Domain
Domain
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|
264 - 286
80..284
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|
Predicted membrane-spanning helix.
[http://pfam.janelia.org/family/PF03741 PF03741  Integral membrane protein TerC family]
|
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
 
|-
|
Domain
|
290 - 312
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
10 - 29
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
42 - 64
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
88 - 110
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
115 - 137
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
142 - 161
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
198 - 220
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
|
Domain
PMID:19920124
|
235 - 257
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />


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</td>
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<td>
<td>
<!-- motifs column 2-->
<motif_map/>
{{TMHMM Picture|alx}}
{{TMHMM Picture|alx}}
</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>alx
<beststructure>
562</beststructure>
gene=alx
 
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=alx&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P42601 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=alx&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P42601 PSI-PRED (P42601)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P42601 Genomes TO Protein (P42601)] (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>
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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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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7607-MONOMER EcoCyc:G7607-MONOMER]
[http://www.ncbi.nlm.nih.gov/protein/49176311 GI:49176311]
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Escherichia coli str. K-12 substr. MG1655
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[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
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[http://www.ncbi.nlm.nih.gov/protein/YP_026201.1 GeneID:947607]
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Escherichia coli str. K-12 substr. MG1655
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[[ASAP]]
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ASAP:ABE-0010151
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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/P42601 UniProtKB/Swiss-Prot:P42601]
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Escherichia coli str. K-12 substr. MG1655
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[[EcoCyc]]
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EcoCyc:G7607
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EcoGene]]
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EcoGene:EG12731
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
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[[uniprot:P42601|UniProt:P42601]]
[http://www.ncbi.nlm.nih.gov/gene?term=947607 GeneID:947607]
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Escherichia coli str. K-12 substr. MG1655
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[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[RegulonDB]]
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[http://pfam.sanger.ac.uk/family?acc=PF03741 PFAM:PF03741]
RegulonDB:ECK120004160
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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=YP_026201 RefSeq:YP_026201]
EchoBASE:EB2589
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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__NOTOC__
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</noinclude>
===Categories===
===Categories===
{{BacktoTop}}
{{BacktoTop}}
[[Category:Proteins]]
[[Category:Proteins]]
[[Category:Location:membrane]]
[[Category:Location:membrane]]
[[Category:Pfam:PF03741_!_Integral membrane protein TerC family]]

Latest revision as of 20:59, 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

Alx

Synonyms

predicted inner membrane protein, part of terminus[1], B3088[2][1], Alx[2][1], YgjT[2][1] , ECK3079, JW5515, ygjT, b3088

Product description

putative membrane-bound redox modulator that is induced by high pH[2][3]

Function unknown; induced by alkali; putative membrane transport or efflux protein[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:IPR005496

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 9 predicted transmembrane domains

Daley et al. (2005) [5]

membrane

From EcoCyc[3]


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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 

MNTVGTPLLW GGFAVVVAIM LAIDLLLQGR RGAHAMTMKQ AAAWSLVWVT LSLLFNAAFW
WYLVQTEGRA VADPQALAFL TGYLIEKSLA VDNVFVWLML FSYFSVPAAL QRRVLVYGVL
GAIVLRTIMI FTGSWLISQF DWILYIFGAF LLFTGVKMAL AHEDESGIGD KPLVRWLRGH
LRMTDTIDNE HFFVRKNGLL YATPLMLVLI LVELSDVIFA VDSIPAIFAV TTDPFIVLTS
NLFAILGLRA MYFLLAGVAE RFSMLKYGLA VILVFIGIKM LIVDFYHIPI AVSLGVVFGI
LVMTFIINAW VNYRHDKQRG G
Length

321

Mol. Wt

35.909 kDa

pI

9.4 (calculated)

Extinction coefficient

69,900 (calc based on 10 Y, 10 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

80..284

PF03741 Integral membrane protein TerC family

PMID:19920124[6]

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<motif_map/>

tmhmm.php?gene=alx&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=alx taxon=562,83333 </beststructure>

Models

View models at:

edit table

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:49176311

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947607

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010151

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P42601

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7607

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12731

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947607

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004160

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2589

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 1.3 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 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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