adrA:Gene Product(s): Difference between revisions

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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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!{{table heading style}} |Standard name
!align=left {{table heading style}} |Standard name
|
||
YaiC product
YaiC  
|-
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!{{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
|
||
predicted diguanylate cyclase product<ref name='LIB:Riley_2006'/>, AdrA product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YaiC product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, B0385 product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''predicted diguanylate cyclase<ref name='LIB:Riley_2006'/>, AdrA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YaiC<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, B0385<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK0380, JW0376, yaiC, b0385''
|-
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!{{table heading style}} |Product description
!align=left {{table heading style}} |Product description
|
||
predicted diguanylate cyclase<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>
predicted diguanylate cyclase<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>


Cellulose, biofilm, motility regulator, diguanylate cyclase; CsgD-regulated; membrane protein<ref name='LIB:EcoGene'/>
|-
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!{{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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<protect>
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<big>'''Gene Ontology'''</big><br />{{Product_GO_help}}<!--box uid=421aa90e079fa326b6494f812ad13e79.20390.P46aa2c4182676-->
<big>'''Gene Ontology'''</big><br /><!--box uid=421aa90e079fa326b6494f812ad13e79.20390.P46aa2c4182676-->
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|- {{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
|-  
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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: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
|-
|
 
|
GO:0016020
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|
membrane
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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|
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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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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
|-
|
 
|
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  
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
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
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membrane
membrane
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From EcoCyc<ref name='LIB:EcoCyc11.1'/>   
From EcoCyc<ref name='LIB:EcoCyc11.1'/>  
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Inner Membrane
|
 
|
PMID:10760159, PMID:12673057, PMID:16585767
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[http://www.york.ac.uk/res/thomas/Echolocation.cfm?EB_SubLocID=EB1237 EchoLocation:adrA]
|
   
 
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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=EG11257-MONOMER at EcoCyc]  
[http://biocyc.org/ECOLI/sequence-aa?object=EG11257-MONOMER at EcoCyc]  
<pre>MFPKIMNDEN FFKKAAAHGE EPPLTPQNEH QRSGLRFARR VRLPRAVGLA GMFLPIASTL
<pre>MFPKIMNDEN FFKKAAAHGE EPPLTPQNEH QRSGLRFARR VRLPRAVGLA GMFLPIASTL
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KAGRNRTEVA A</pre>  
KAGRNRTEVA A</pre>  
|-
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!{{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Length
|
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41.54 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
371
|-
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!{{table heading style}} |pI
!align=left {{table heading style}} |Mol. Wt
|
||
41.537 kDa
|-
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!{{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |pI
|
||
80440 - 80815 (calc based on 6 Y, 13 W, and 3 C residues)  
9.9 (calculated)
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!align=left {{table heading style}} |Extinction coefficient
||
80,440 - 80,815 (calc based on 6 Y, 13 W, and 3 C residues)
 
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<big>'''Domains/Motifs/Modification Sites'''</big>
 
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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=421aa90e079fa326b6494f812ad13e79.20390.V46aa2c446e27b-->
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|- {{table heading style}}
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!Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
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Domain
|
210..366
|
[http://pfam.janelia.org/family/PF00990 PF00990  GGDEF domain]
|
 
|
PMID:19920124
|-
|
Domain
|
39..129
|
[http://pfam.janelia.org/family/PF05230 PF05230  MASE2 domain]
|
 
|
PMID:19920124
 
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<td>
<!-- motifs column 2-->
<motif_map/>
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<span id="Structure"></span><big>'''Structure'''</big>
<table><tr valign='top'><td>
<span id='Structure'></span><big>'''Structure'''</big><br />
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!Structure Type!!Organism!!Accession!!Residues covered!!Notes
|-
|-class='sortbottom'
!align=left {{table heading style}} |Structures
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.20390.Y46a7bd926f067&page=20390&pagename={{FULLPAGENAMEE}} edit table] || || || ||
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<beststructure>
gene=adrA
taxon=562,83333
</beststructure>
|-
!align=left {{table heading style}} |Models
||
View models at:
* [http://www.proteinmodelportal.org/query/uniprot/P0AAP1 Protein Model Portal]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P0AAP1 PSI-PRED (P0AAP1)]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P0AAP1 Genomes TO Protein (P0AAP1)] (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/16128370 GI:16128370]
|
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_414919.1 GeneID:945037]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0001336
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P0AAP1 UniProtKB/Swiss-Prot:P0AAP1]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
EcoCyc:EG11257
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11257-MONOMER EcoCyc:EG11257-MONOMER] 
EcoGene:EG11257
|
|
''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:P0AAP1|UniProt:P0AAP1]] 
[http://www.ncbi.nlm.nih.gov/gene?term=945037 GeneID:945037]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://pfam.sanger.ac.uk/family?acc=PF05230 PFAM:PF05230] 
RegulonDB:ECK120001232
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[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_414919 RefSeq:NP_414919] 
EchoBASE:EB1237
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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:Location:membrane]]
[[Category:Location:membrane]]
[[Category:Proteins]]
[[Category:Pfam:PF00990_!_GGDEF domain]]
[[Category:Pfam:PF05230_!_MASE2 domain]]

Latest revision as of 20:24, 17 February 2015

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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

YaiC

Synonyms

predicted diguanylate cyclase[1], AdrA[2][1], YaiC[2][1], B0385[2][1] , ECK0380, JW0376, yaiC, b0385

Product description

predicted diguanylate cyclase[2][3]

Cellulose, biofilm, motility regulator, diguanylate cyclase; CsgD-regulated; membrane 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-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: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

membrane

From EcoCyc[3]

Inner Membrane

PMID:10760159[5], PMID:12673057[6], PMID:16585767[7]

EchoLocation:adrA


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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 

MFPKIMNDEN FFKKAAAHGE EPPLTPQNEH QRSGLRFARR VRLPRAVGLA GMFLPIASTL
VSHPPPGWWW LVLVGWAFVW PHLAWQIASR AVDPLSREIY NLKTDAVLAG MWVGVMGVNV
LPSTAMLMIM CLNLMGAGGP RLFVAGLVLM VVSCLVTLEL TGITVSFNSA PLEWWLSLPI
IVIYPLLFGW VSYQTATKLA EHKRRLQVMS TRDGMTGVYN RRHWETMLRN EFDNCRRHNR
DATLLIIDID HFKSINDTWG HDVGDEAIVA LTRQLQITLR GSDVIGRFGG DEFAVIMSGT
PAESAITAML RVHEGLNTLR LPNTPQVTLR ISVGVAPLNP QMSHYREWLK SADLALYKAK
KAGRNRTEVA A
Length

371

Mol. Wt

41.537 kDa

pI

9.9 (calculated)

Extinction coefficient

80,440 - 80,815 (calc based on 6 Y, 13 W, and 3 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

210..366

PF00990 GGDEF domain

PMID:19920124[8]

Domain

39..129

PF05230 MASE2 domain

PMID:19920124[8]

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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=adrA 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:16128370

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945037

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001336

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AAP1

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11257

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11257

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945037

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001232

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1237

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. ↑ Römling, U et al. (2000) AgfD, the checkpoint of multicellular and aggregative behaviour in Salmonella typhimurium regulates at least two independent pathways. Mol. Microbiol. 36 10-23 PubMed
  6. ↑ Nikolskaya, AN et al. (2003) MASE1 and MASE2: two novel integral membrane sensory domains. J. Mol. Microbiol. Biotechnol. 5 11-6 PubMed
  7. ↑ Da Re, S & Ghigo, JM (2006) A CsgD-independent pathway for cellulose production and biofilm formation in Escherichia coli. J. Bacteriol. 188 3073-87 PubMed
  8. ↑ 8.0 8.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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