ompL: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 outer membrane porin L<ref name='LIB:Riley_2006'/>, B3875<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YshA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, OmpL<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''predicted outer membrane porin L<ref name='LIB:Riley_2006'/>, B3875<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YshA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, OmpL<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK3868, JW3846, yshA, b3875''
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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predicted outer membrane porin L<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>
predicted outer membrane porin L<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>


Outer membrane porin L<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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!|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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NOT
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GO:0005351
GO:0005886
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|
sugar:hydrogen symporter activity
plasma membrane
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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-0762
 
|
|
F
C
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete
Missing: with/from
|-  
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transport
transport
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|
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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P
P
|
|
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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ion transport
ion transport
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|
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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P
P
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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carbohydrate transport
carbohydrate transport
|
|
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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P
P
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
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complete
|-
|
 
|
GO:0009279
|
cell outer 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-0998
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C
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Seeded from [[EcoCyc]] (v14.0)
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complete
|-
|
 
|
GO:0009279
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cell outer membrane
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GO_REF:0000023
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IEA: Inferred from Electronic Annotation
|
SP_SL:SL-0040
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C
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Seeded from [[EcoCyc]] (v14.0)
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|
complete  
complete  
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membrane
membrane
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|
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
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SP_KW:KW-0472<br />SP_KW:KW-0626
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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integral to membrane
integral to membrane
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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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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:0019867
GO:0046930
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outer membrane
pore complex
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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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SP_KW:KW-0557
SP_KW:KW-0626
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C
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Seeded from [[EcoCyc]] (v14.0)
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complete
|-
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|
GO:0009279
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cell outer membrane
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PMID:11080145
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IDA: Inferred from Direct Assay
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|
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C
C
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|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
 
|
complete
|-
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|
GO:0046323
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glucose import
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PMID:11080145
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IDA: Inferred from Direct Assay
|
 
|
P
|
 
|
|
complete  
complete  
|-
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GO:0015757
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galactose transport
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PMID:11080145
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IDA: Inferred from Direct Assay
|
 
|
P
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complete
|-
|
 
|
GO:0015751
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arabinose transport
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PMID:11080145
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IDA: Inferred from Direct Assay
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|
P
|
 
|
complete
 
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!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
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Experiment(s):EBI-1146860<br />  
Experiment(s):EBI-1146860<br />  


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!|Compartment!!Description!!Evidence!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
|-
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Outer Membrane
|
|PMID:11080145
|
[http://www.york.ac.uk/res/thomas/Echolocation.cfm?EB_SubLocID=EB3156 EchoLocation:ompL]
|
 
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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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TVRNRYNHNN YSSTDLSGEL DNNDTYEIGT YWNFKITDKF SYTFEPHYFM RVNDFNSSNG
TVRNRYNHNN YSSTDLSGEL DNNDTYEIGT YWNFKITDKF SYTFEPHYFM RVNDFNSSNG
KDHHWEITNT FRYRINEHWL PYFELRWLDR NVEPYHREQN QIRIGTKYFF</pre>  
KDHHWEITNT FRYRINEHWL PYFELRWLDR NVEPYHREQN QIRIGTKYFF</pre>  
|-
!align=left {{table heading style}} |Length
||
230
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
27.2 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
27.2 kDa
|-
|-
!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
6.2 (calculated)
|-
|-
!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
59820 (calc based on 18 Y, 6 W, and 0 C residues)  
59,820 (calc based on 18 Y, 6 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><table>
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<tr align="left" valign="top">
<td><!--box uid=421aa90e079fa326b6494f812ad13e79.28369.G46ab0a14caf9a-->
<!--
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|- {{table heading style}}
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!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-  
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[[uniprotmanual:signal|UniProt Manual:Signal Peptides]]
[[uniprotmanual:signal|UniProt Manual:Signal Peptides]]
|
|
[http://www.uniprot.org/uniprot/P76773#section_features UniProt:P76773]  
[http://www.uniprot.org/uniprot/P76773#section_features UniProt:P76773]
|
|-
|
Domain
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14..230
|
[http://pfam.janelia.org/family/PF06178 PF06178  Oligogalacturonate-specific porin protein (KdgM)]
|


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PMID:19920124
 
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<td>
<!-- motifs column 2-->
<motif_map/>
</td>
</tr>
</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>ompL
<beststructure>
562</beststructure>
gene=ompL
 
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=ompL&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P76773 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=ompL&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P76773 PSI-PRED (P76773)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P76773 Genomes TO Protein (P76773)] (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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!|Resource type!!Source!!Notes/Reference
!|Resource type!!Source!!Notes/Reference


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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/16131715 GI:16131715]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7814-MONOMER EcoCyc:G7814-MONOMER]
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_418311.1 GeneID:948366]
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Escherichia coli str. K-12 substr. MG1655
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[[ASAP]]
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ASAP:ABE-0012659
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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/P76773 UniProtKB/Swiss-Prot:P76773]
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Escherichia coli str. K-12 substr. MG1655
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[[EcoCyc]]
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EcoCyc:G7814
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EcoGene]]
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EcoGene:EG13374
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
|
[[uniprot:P76773|UniProt:P76773]]
[http://www.ncbi.nlm.nih.gov/gene?term=948366 GeneID:948366]
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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=PF06178 PFAM:PF06178]
RegulonDB:ECK120004316
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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|-  
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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_418311 RefSeq:NP_418311]
EchoBASE:EB3156
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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==References==
==References==
{{BacktoTop}}
{{BacktoTop}}
 
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</noinclude>
===Categories===
===Categories===
{{BacktoTop}}
{{BacktoTop}}
[[Category:Proteins]]
[[Category:Proteins]]
[[Category:Location:outer membrane]]
[[Category:Location:outer membrane]]
[[Category:Pfam:PF06178_!_Oligogalacturonate-specific porin protein (KdgM)]]

Latest revision as of 21:09, 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

OmpL

Synonyms

predicted outer membrane porin L[1], B3875[2][1], YshA[2][1], OmpL[2][1] , ECK3868, JW3846, yshA, b3875

Product description

predicted outer membrane porin L[2][3]

Outer membrane porin L[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

NOT

GO:0005886

plasma membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

C

Seeded from EcoCyc (v14.0)

Missing: with/from

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:0006811

ion transport

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0406

P

Seeded from EcoCyc (v14.0)

complete

GO:0008643

carbohydrate transport

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0762

P

Seeded from EcoCyc (v14.0)

complete

GO:0009279

cell outer membrane

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0998

C

Seeded from EcoCyc (v14.0)

complete

GO:0009279

cell outer membrane

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0040

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:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0812

C

Seeded from EcoCyc (v14.0)

complete

GO:0046930

pore complex

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0626

C

Seeded from EcoCyc (v14.0)

complete

GO:0009279

cell outer membrane

PMID:11080145[5]

IDA: Inferred from Direct Assay

C

complete

GO:0046323

glucose import

PMID:11080145[5]

IDA: Inferred from Direct Assay

P

complete

GO:0015757

galactose transport

PMID:11080145[5]

IDA: Inferred from Direct Assay

P

complete

GO:0015751

arabinose transport

PMID:11080145[5]

IDA: Inferred from Direct Assay

P

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

Protein

ybaK

PMID:16606699[6]

Experiment(s):EBI-1146860

Protein

yhdZ

PMID:16606699[6]

Experiment(s):EBI-1146860

Protein

groL

PMID:16606699[6]

Experiment(s):EBI-1146860

Protein

tsf

PMID:16606699[6]

Experiment(s):EBI-1146860

Protein

wecG

PMID:16606699[6]

Experiment(s):EBI-1146860
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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

Outer Membrane

PMID:11080145

EchoLocation:ompL

outer 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 

MKKINAIILL SSLTSASVFA GAYVENREAY NLASDQGEVM LRVGYNFDMG AGIMLTNTYN
FQREDELKHG YNEIEGWYPL FKPTDKLTIQ PGGLINDKSI GSGGAVYLDV NYKFVPWFNL
TVRNRYNHNN YSSTDLSGEL DNNDTYEIGT YWNFKITDKF SYTFEPHYFM RVNDFNSSNG
KDHHWEITNT FRYRINEHWL PYFELRWLDR NVEPYHREQN QIRIGTKYFF
Length

230

Mol. Wt

27.2 kDa

pI

6.2 (calculated)

Extinction coefficient

59,820 (calc based on 18 Y, 6 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

motif

1-20

UniProt Manual:Signal Peptides

UniProt:P76773

Domain

14..230

PF06178 Oligogalacturonate-specific porin protein (KdgM)

PMID:19920124[7]

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<motif_map/>

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

Structures

<beststructure> gene=ompL 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:16131715

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948366

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012659

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P76773

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7814

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13374

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948366

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004316

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3156

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. ↑ 5.0 5.1 5.2 5.3 Dartigalongue, C et al. (2000) Protein folding in the periplasm in the absence of primary oxidant DsbA: modulation of redox potential in periplasmic space via OmpL porin. EMBO J. 19 5980-8 PubMed
  6. ↑ 6.0 6.1 6.2 6.3 6.4 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  7. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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