tqsA:Gene Product(s): Difference between revisions

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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
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predicted inner membrane protein<ref name='LIB:Riley_2006'/>, B1601<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YdgG<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, TqsA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''predicted inner membrane protein<ref name='LIB:Riley_2006'/>, B1601<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YdgG<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, TqsA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK1596, JW1593, ydgG, b1601''
|-
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
||
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transporter of quorum signal AI-2<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>
transporter of quorum signal AI-2<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/><ref name='PMID:16385049'/>


Pheromone AI-2 transporter; mutants have increased intracellular AI-2 and decreased extracellular AI-2; controls biofilm formation<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=421aa90e079fa326b6494f812ad13e79.23223.R46aa7120cf377-->
<big>'''Gene Ontology'''</big><br /><!--box uid=421aa90e079fa326b6494f812ad13e79.23223.R46aa7120cf377-->
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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
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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
|
Seeded from [[EcoCyc]] (v14.0)
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complete
|-
|
 
|
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)
|
complete
|-
|
 
|
GO:0006810
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transport
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GOA:spkw<br />SP_KW:GO_REF:0000004
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IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0813
|
P
|
Seeded from [[EcoCyc]] (v14.0)
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complete
|-
|
 
|
GO:0009372
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quorum sensing
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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-0673
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P
|
Seeded from [[EcoCyc]] (v14.0)
|
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:0016020
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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-0472
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C
|
Seeded from [[EcoCyc]] (v14.0)
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complete
|-
|
 
|
GO:0016021
|
|
integral to membrane
integral to membrane
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[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-0812 SP_KW:KW-0812]
SP_KW:KW-0812
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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  
complete  
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[[Category:GO:0016020_!_membrane]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0016020_!_membrane GO:0016020]
GO:0016021
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membrane
integral to 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]
GO_REF:0000023
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|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.uniprot.org/keywords/KW-0397 SP_KW:KW-0397]<br />[http://www.uniprot.org/keywords/KW-0472 SP_KW:KW-0472]
SP_SL:SL-9909
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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  
complete  
|-  
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|
|
 
|
GO:0042710
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biofilm formation
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PMID:16385049
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IMP: Inferred from Mutant Phenotype
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|
P
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ydgG(del) results in increased biofilm formation
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complete
|-
|
 
|
GO:0006810
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transport
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PMID:16385049
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IMP: Inferred from Mutant Phenotype
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|
P
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ydg(del) results in decreased extracellular AI-2 and increased intracelular AI-2
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complete
|-
|
 
|
|
[[Category:GO:0006810_!_transport]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0006810_!_transport GO:0006810]
GO:0005887
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|
transport
integral component of plasma membrane
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PMID:16385049
|
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ISM: Inferred from Sequence Model
|
|
 
|
|
P
C
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Fig. 4 shows predicted topology in plasma membrane, using the prediction programs MEMSTAT-2, TMHMM, and PHDhtm
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required fields missing 
Missing: with/from


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


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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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|-
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SVLAAIPPIA QVLVFNGFYE ALLVLAGYLL INLVFGNILE PRIMGRGLGL STLVVFLSLI
SVLAAIPPIA QVLVFNGFYE ALLVLAGYLL INLVFGNILE PRIMGRGLGL STLVVFLSLI
FWGWLLGPVG MLLSVPLTII VKIALEQTAG GQSIAVLLSD LNKE</pre>  
FWGWLLGPVG MLLSVPLTII VKIALEQTAG GQSIAVLLSD LNKE</pre>  
|-
!align=left {{table heading style}} |Length
||
344
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
37.54 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
37.544 kDa
|-
|-
!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
9.3 (calculated)
|-
|-
!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
37930 - 38055 (calc based on 7 Y, 5 W, and 1 C residues)  
37,930 - 38,055 (calc based on 7 Y, 5 W, and 1 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
|
|
62 - 84
13..329
|
|
Predicted membrane-spanning helix.
[http://pfam.janelia.org/family/PF01594 PF01594  Domain of unknown function DUF20]
|
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
 
|-
|
Domain
|
|
144 - 166
PMID:19920124
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
196 - 218
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
222 - 244
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
257 - 279
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
299 - 321
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
7 - 29
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
33 - 55
|
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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<!-- motifs column 2-->
<motif_map/>
{{TMHMM Picture|tqsA}}
{{TMHMM Picture|tqsA}}
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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>tqsA
<beststructure>
562</beststructure>
gene=tqsA
 
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=tqsA&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P0AFS5 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=tqsA&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P0AFS5 PSI-PRED (P0AFS5)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P0AFS5 Genomes TO Protein (P0AFS5)] (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


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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://www.ncbi.nlm.nih.gov/protein/16129559 GI:16129559]
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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/NP_416118.1 GeneID:946142]
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Escherichia coli str. K-12 substr. MG1655
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[[ASAP]]
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ASAP:ABE-0005350
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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/P0AFS5 UniProtKB/Swiss-Prot:P0AFS5]
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Escherichia coli str. K-12 substr. MG1655
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[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6859-MONOMER EcoCyc:G6859-MONOMER]
EcoCyc:G6859
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EcoGene]]
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EcoGene:EG13928
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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:P0AFS5|UniProt:P0AFS5]]
[http://www.ncbi.nlm.nih.gov/gene?term=946142 GeneID:946142]
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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=PF01594 PFAM:PF01594]
RegulonDB:ECK120003448
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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_416118 RefSeq:NP_416118]
EchoBASE:EB3687
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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===Categories===
===Categories===
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[[Category:GO:0006810_!_transport]]
[[Category:Proteins]]

Latest revision as of 18:38, 8 June 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

YdgG

Synonyms

predicted inner membrane protein[1], B1601[2][1], YdgG[2][1], TqsA[2][1] , ECK1596, JW1593, ydgG, b1601

Product description

transporter of quorum signal AI-2[2][3][4]

Pheromone AI-2 transporter; mutants have increased intracellular AI-2 and decreased extracellular AI-2; controls biofilm formation[5]

EC number (for enzymes)


edit table


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:0009372

quorum sensing

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0673

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:0042710

biofilm formation

PMID:16385049[4]

IMP: Inferred from Mutant Phenotype

P

ydgG(del) results in increased biofilm formation

complete

GO:0006810

transport

PMID:16385049[4]

IMP: Inferred from Mutant Phenotype

P

ydg(del) results in decreased extracellular AI-2 and increased intracelular AI-2

complete

GO:0005887

integral component of plasma membrane

PMID:16385049[4]

ISM: Inferred from Sequence Model

C

Fig. 4 shows predicted topology in plasma membrane, using the prediction programs MEMSTAT-2, TMHMM, and PHDhtm

Missing: with/from

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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 8 predicted transmembrane domains

Daley et al. (2005) [6]


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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 

MAKPIITLNG LKIVIMLGML VIILCGIRFA AEIIVPFILA LFIAVILNPL VQHMVRWRVP
RVLAVSILMT IIVMAMVLLL AYLGSALNEL TRTLPQYRNS IMTPLQALEP LLQRVGIDVS
VDQLAHYIDP NAAMTLLTNL LTQLSNAMSS IFLLLLTVLF MLLEVPQLPG KFQQMMARPV
EGMAAIQRAI DSVSHYLVLK TAISIITGLV AWAMLAALDV RFAFVWGLLA FALNYIPNIG
SVLAAIPPIA QVLVFNGFYE ALLVLAGYLL INLVFGNILE PRIMGRGLGL STLVVFLSLI
FWGWLLGPVG MLLSVPLTII VKIALEQTAG GQSIAVLLSD LNKE
Length

344

Mol. Wt

37.544 kDa

pI

9.3 (calculated)

Extinction coefficient

37,930 - 38,055 (calc based on 7 Y, 5 W, and 1 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

13..329

PF01594 Domain of unknown function DUF20

PMID:19920124[7]

edit table

<motif_map/>

tmhmm.php?gene=tqsA&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=tqsA 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:16129559

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946142

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005350

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AFS5

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6859

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13928

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946142

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003448

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3687

Escherichia coli str. K-12 substr. MG1655

edit table


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. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 4.2 4.3 Herzberg, M et al. (2006) YdgG (TqsA) controls biofilm formation in Escherichia coli K-12 through autoinducer 2 transport. J. Bacteriol. 188 587-98 PubMed
  5. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  6. ↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed
  7. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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