lptD:Gene Product(s): Difference between revisions

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{{Tab|Quickview|imp}}{{Tab|Gene|imp}}{{Tab On|Gene Product(s)|imp}}{{Tab|Expression|imp}}{{Tab|Evolution|imp}}{{Tab|On One Page|imp}}{{TabsBottom}}
{{Tab|Quickview|lptD}}{{Tab|Gene|lptD}}{{Tab On|Gene Product(s)|lptD}}{{Tab|Expression|lptD}}{{Tab|Evolution|lptD}}{{Tab|On One Page|lptD}}{{TabsBottom}}
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|{{Sub}}[[#Localization |Localization]]
|{{Sub}}[[#Localization |Localization]]
|{{Sub}}[[#Sequence|Sequence]]
|{{Sub}}[[#Sequence|Sequence]]
|{{Sub}}[[#Domains/Motifs/Modification Sites|Domains]]
|{{Sub}}[[#Structure|Structure]]
|{{Sub}}[[#Structure|Structure]]
|{{Sub}}[[#Gene Product Resources|Resources]]
|{{Sub}}[[#Gene Product Resources|Resources]]
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|-
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!{{table heading style}} |Standard name
!align=left {{table heading style}} |Standard name
|
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Imp product
LptD
|-
|-
!{{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
|
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exported protein required for envelope biosynthesis and integrity product<ref name='LIB:Riley_2006'/>, B0054 product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YabG product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, OstA product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Imp product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''exported protein required for envelope biosynthesis and integrity<ref name='LIB:Riley_2006'/>, B0054<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YabG<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, OstA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Imp<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK0055, imp, JW0053, ostA, yabG, b0054''
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!{{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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exported protein required for envelope biosynthesis and integrity<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>
exported protein required for envelope biosynthesis and integrity<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>


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!{{table heading style}} |EC number (for enzymes)
!align=left {{table heading style}} |EC number (for enzymes)
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===Notes===
===Notes===
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<big>'''Gene Ontology'''</big><br />{{Product_GO_help}}<!--box uid=421aa90e079fa326b6494f812ad13e79.19558.H46aa186aed1c2-->
<big>'''Gene Ontology'''</big><br /><!--box uid=421aa90e079fa326b6494f812ad13e79.19558.H46aa186aed1c2-->
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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:0005515
|
protein binding
|
PMID:16861298
|
IPI: Inferred from Physical Interaction
|
EcoliWiki:rlpB
 
 
|
F
|
 
|
complete
|-
|
 
|
GO:0005515
|
protein binding
|
PMID:16861298
|
IPI: Inferred from Physical Interaction
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UniProtKB:P0ADC1
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F
|
Seeded from [[EcoCyc]] (v14.0)
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complete
|-
|
 
|
GO:0043165
|
Gram-negative-bacterium-type cell outer membrane assembly
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PMID:16861298
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IGI: Inferred from Genetic Interaction
|
EcoliWiki:rlpB
 
 
|
P
|
 
|
complete
|-
|
 
|
GO:0015920
|
lipopolysaccharide transport
|
PMID:16861298
|
IMP: Inferred from Mutant Phenotype
|
 
|
P
|
 
|
complete
|-
|
 
|
GO:0009279
|
cell outer membrane
|
PMID:12207697
|
IDA: Inferred from Direct Assay
|
 
|
C
|
Fig. 2
|
complete
|-
|
 
|
GO:0010033
|
response to organic substance
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR007543
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0010033
|
response to organic substance
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR020889
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-  
|
|
 
|
|
GO:0006979
GO:0043165
|
|
response to oxidative stress
Gram-negative-bacterium-type cell outer membrane assembly
|
|
GOA:hamap<br />GO_REF:0000020
|
|
IEA: Inferred from Electronic Annotation
|
|
HAMAP:MF_01411
|
|
P  
P
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
|-
|-  
|
|
 
|
|
GO:0009279
GO:0043165
|
|
cell outer membrane  
Gram-negative-bacterium-type cell outer membrane assembly
|
|
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR020889
|
|
C
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
!|Partner Type!!Partner!!Notes!!References!!Evidence
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===Notes===
===Notes===
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!Compartment!!Description!!Evidence!!Notes
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outer membrane
outer membrane
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Outer Membrane
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|PMID:9298646
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[http://www.york.ac.uk/res/thomas/Echolocation.cfm?EB_SubLocID=EB1529 EchoLocation:imp]
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!align=left {{table heading style}} |Name
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!{{table heading style}} |Sequence
!align=left {{table heading style}} |Sequence
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[http://biocyc.org/ECOLI/sequence-aa?object=EG11569-MONOMER at EcoCyc]  
[http://biocyc.org/ECOLI/sequence-aa?object=EG11569-MONOMER at EcoCyc]  
<pre>MKKRIPTLLA TMIATALYSQ QGLAADLASQ CMLGVPSYDR PLVQGDTNDL PVTINADHAK
<pre>MKKRIPTLLA TMIATALYSQ QGLAADLASQ CMLGVPSYDR PLVQGDTNDL PVTINADHAK
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YSSCCYAIRV GYERKLNGWD NDKQHAVYDN AIGFNIELRG LSSNYGLGTQ EMLRSNILPY QNTL</pre>  
YSSCCYAIRV GYERKLNGWD NDKQHAVYDN AIGFNIELRG LSSNYGLGTQ EMLRSNILPY QNTL</pre>  
|-
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!{{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Length
|
||
89.67 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
 
|-
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!{{table heading style}} |pI
!align=left {{table heading style}} |Mol. Wt
|
||
 
|-
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!{{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |pI
|
||
185420 - 185920 (calc based on 58 Y, 18 W, and 4 C residues)
 
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!align=left {{table heading style}} |Extinction coefficient
||
 
 
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==Domains/Motifs/Modification Sites==
 
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<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span><table>
<tr align="left" valign="top">
<td><!--box uid=421aa90e079fa326b6494f812ad13e79.19558.J46aa18728e2d9-->
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!Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
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motif
|
1-24
|
[[uniprotmanual:signal|UniProt Manual:Signal Peptides]]
|
[http://www.uniprot.org/uniprot/P31554#section_features UniProt:P31554]
|
|-
|
Domain
|
6..195
|
[http://pfam.janelia.org/family/PF03968 PF03968  OstA-like protein]
|
 
|
PMID:19920124
|-
|
Domain
|
308..697
|
[http://pfam.janelia.org/family/PF04453 PF04453  Organic solvent tolerance protein]
|
 
|
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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|-
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!align=left {{table heading style}} |Structures
!align=left {{table heading style}} |Structures
||
||
<beststructure>imp
<beststructure>
562</beststructure>
gene=lptD
 
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=imp&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P31554 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=imp&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P31554 PSI-PRED (P31554)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P31554 Genomes TO Protein (P31554)] (GTOP)
* [http://www.ebi.ac.uk/msd-srv/pqs/ Protein Quaternary Structure] (PQS)
* [http://spock.genes.nig.ac.jp/~genome/search.html Genomes TO Protein] (GTOP)


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<!--Structure_notes--></protect>
</td><td></protect>
==== Structure figures ====
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
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===Notes===
===Notes===


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===Notes===
===Notes===
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-
|
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/16128048 GI:16128048]
|
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_414596.1 GeneID:945011]
|
Escherichia coli str. K-12 substr. MG1655
|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11569-MONOMER EcoCyc:EG11569-MONOMER]
[http://www.uniprot.org/uniprot/P31554 UniProtKB/Swiss-Prot:P31554]
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Escherichia coli str. K-12 substr. 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:P31554|UniProt:P31554]] 
[http://www.ncbi.nlm.nih.gov/gene?term=945011 GeneID:945011]
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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=PF04453 PFAM:PF04453] 
RegulonDB:
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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_414596 RefSeq:NP_414596] 
EchoBASE:
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
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===Categories===
===Categories===
{{BacktoTop}}
{{BacktoTop}}
[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0006979_!_response to oxidative stress]][[Category:GO:0009279_!_cell outer membrane]][[Category:Location:outer membrane]]

Latest revision as of 22:52, 20 May 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

LptD

Synonyms

exported protein required for envelope biosynthesis and integrity[1], B0054[2][1], YabG[2][1], OstA[2][1], Imp[2][1] , ECK0055, imp, JW0053, ostA, yabG, b0054

Product description

exported protein required for envelope biosynthesis and integrity[2][3]

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:0005515

protein binding

PMID:16861298[4]

IPI: Inferred from Physical Interaction

EcoliWiki:rlpB


F

complete

GO:0005515

protein binding

PMID:16861298[4]

IPI: Inferred from Physical Interaction

UniProtKB:P0ADC1

F

Seeded from EcoCyc (v14.0)

complete

GO:0043165

Gram-negative-bacterium-type cell outer membrane assembly

PMID:16861298[4]

IGI: Inferred from Genetic Interaction

EcoliWiki:rlpB


P

complete

GO:0015920

lipopolysaccharide transport

PMID:16861298[4]

IMP: Inferred from Mutant Phenotype

P

complete

GO:0009279

cell outer membrane

PMID:12207697[5]

IDA: Inferred from Direct Assay

C

Fig. 2

complete

GO:0010033

response to organic substance

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007543

P

Seeded from EcoCyc (v14.0)

complete

GO:0010033

response to organic substance

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020889

P

Seeded from EcoCyc (v14.0)

complete

GO:0043165

Gram-negative-bacterium-type cell outer membrane assembly

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01411

P

Seeded from EcoCyc (v14.0)

complete

GO:0043165

Gram-negative-bacterium-type cell outer membrane assembly

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020889

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

outer membrane

Outer Membrane

PMID:9298646

EchoLocation:imp


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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 

MKKRIPTLLA TMIATALYSQ QGLAADLASQ CMLGVPSYDR PLVQGDTNDL PVTINADHAK
GDYPDDAVFT GSVDIMQGNS RLQADEVQLH QKEAPGQPEP VRTVDALGNV HYDDNQVILK
GPKGWANLNT KDTNVWEGDY QMVGRQGRGK ADLMKQRGEN RYTILDNGSF TSCLPGSDTW
SVVGSEIIHD REEQVAEIWN ARFKVGPVPI FYSPYLQLPV GDKRRSGFLI PNAKYTTTNY
FEFYLPYYWN IAPNMDATIT PHYMHRRGNI MWENEFRYLS QAGAGLMELD YLPSDKVYED
EHPNDDSSRR WLFYWNHSGV MDQVWRFNVD YTKVSDPSYF NDFDNKYGSS TDGYATQKFS
VGYAVQNFNA TVSTKQFQVF SEQNTSSYSA EPQLDVNYYQ NDVGPFDTRI YGQAVHFVNT
RDDMPEATRV HLEPTINLPL SNNWGSINTE AKLLATHYQQ TNLDWYNSRN TTKLDESVNR
VMPQFKVDGK MVFERDMEML APGYTQTLEP RAQYLYVPYR DQSDIYNYDS SLLQSDYSGL
FRDRTYGGLD RIASANQVTT GVTSRIYDDA AVERFNISVG QIYYFTESRT GDDNITWEND
DKTGSLVWAG DTYWRISERW GLRGGIQYDT RLDNVATSNS SIEYRRDEDR LVQLNYRYAS
PEYIQATLPK YYSTAEQYKN GISQVGAVAS WPIADRWSIV GAYYYDTNAN KQADSMLGVQ
YSSCCYAIRV GYERKLNGWD NDKQHAVYDN AIGFNIELRG LSSNYGLGTQ EMLRSNILPY QNTL
Length
Mol. Wt
pI
Extinction coefficient


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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

1-24

UniProt Manual:Signal Peptides

UniProt:P31554

Domain

6..195

PF03968 OstA-like protein

PMID:19920124[6]

Domain

308..697

PF04453 Organic solvent tolerance protein

PMID:19920124[6]

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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=lptD 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:16128048

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945011

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P31554

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945011

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:

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 1.4 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 2.4 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 Wu, T et al. (2006) Identification of a protein complex that assembles lipopolysaccharide in the outer membrane of Escherichia coli. Proc. Natl. Acad. Sci. U.S.A. 103 11754-9 PubMed
  5. ↑ Braun, M & Silhavy, TJ (2002) Imp/OstA is required for cell envelope biogenesis in Escherichia coli. Mol. Microbiol. 45 1289-302 PubMed
  6. ↑ 6.0 6.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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