yeaI: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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{|{{Prettytable}}
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|-
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!{{table heading style}} |Standard name
!align=left {{table heading style}} |Standard name
|
||
YeaI product
YeaI  
|-
|-
!{{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
|
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predicted diguanylate cyclase product<ref name='LIB:Riley_2006'/>, YeaI product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, B1785 product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''predicted diguanylate cyclase<ref name='LIB:Riley_2006'/>, YeaI<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, B1785<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK1783, JW1774, b1785''
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!{{table heading style}} |Product description
!align=left {{table heading style}} |Product description
|
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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'/>


Probable diguanylate cyclase, function unknown<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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<big>'''Gene Ontology'''</big><br />{{Product_GO_help}}<!--box uid=421aa90e079fa326b6494f812ad13e79.23659.O46aa7de7207be-->
<big>'''Gene Ontology'''</big><br /><!--box uid=421aa90e079fa326b6494f812ad13e79.23659.O46aa7de7207be-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O46aa7de7207be"  class=" tableEdit GO_table_product dataTable"   
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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
|
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
|-  
|-  
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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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|
membrane
plasma membrane
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[http://www.geneontology.org/cgi-bin/references.cgi/#GO_REF:0000004 GO_REF:0000004]<br />
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-0397
SP_KW:KW-1003
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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
|-  
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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 />
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
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
|-  
|-  
|
|


|
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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:0000004 GO_REF:0000004]<br />
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
|
SP_SL:SL-9909
|
C
|
Seeded from [[EcoCyc]] (v14.0)
|
complete


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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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!{{table heading style}} |Sequence
!align=left {{table heading style}} |Sequence
|
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[http://biocyc.org/ECOLI/sequence-aa?object=G6971-MONOMER at EcoCyc]  
[http://biocyc.org/ECOLI/sequence-aa?object=G6971-MONOMER at EcoCyc]  
<pre>MIQSTRISMG LFFKYFLSLT KIDPGQNYIS LPSIKSSTHI ALLFMVSMGT QKLKAQSFFI
<pre>MIQSTRISMG LFFKYFLSLT KIDPGQNYIS LPSIKSSTHI ALLFMVSMGT QKLKAQSFFI
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EGGNKVIIHH I</pre>  
EGGNKVIIHH I</pre>  
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!{{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Length
|
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56.1 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
491
|-
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!{{table heading style}} |pI
!align=left {{table heading style}} |Mol. Wt
|
||
56.104 kDa
|-
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!{{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |pI
|
||
57300 - 58425 (calc based on 20 Y, 5 W, and 9 C residues)  
8.9 (calculated)
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!align=left {{table heading style}} |Extinction coefficient
||
57,300 - 58,425 (calc based on 20 Y, 5 W, and 9 C residues)
 
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<big>'''Domains/Motifs/Modification Sites'''</big>
 
<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span>
<table>
<table>
<tr align="left" valign="top">
<tr align="left" valign="top">
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|- {{table heading style}}
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!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-  
|-  
|
|
Domain
Domain
|
|
121 - 143
328..485
|
|
Predicted membrane-spanning helix.
[http://pfam.janelia.org/family/PF00990 PF00990  GGDEF domain]
|
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
 
|-
|
Domain
|
163 - 182
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
195 - 214
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
|
234 - 256
PMID:19920124
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
263 - 285
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
58 - 77
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
87 - 109
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
295 - 317
|
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|yeaI}}
{{TMHMM Picture|yeaI}}
</td>
</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>yeaI
<beststructure>
562</beststructure>
gene=yeaI
 
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=yeaI&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P76236 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=yeaI&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P76236 PSI-PRED (P76236)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P76236 Genomes TO Protein (P76236)] (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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===Notes===
===Notes===
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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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/16129739 GI:16129739]
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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_416299.1 GeneID:946366]
|
Escherichia coli str. K-12 substr. MG1655
|-
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[[ASAP]]
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ASAP:ABE-0005941
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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]])
|
[http://www.uniprot.org/uniprot/P76236 UniProtKB/Swiss-Prot:P76236]
|
Escherichia coli str. K-12 substr. MG1655
|-
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[[EcoCyc]]
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EcoCyc:G6971
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoGene]]
|
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6971-MONOMER EcoCyc:G6971-MONOMER] 
EcoGene:EG13495
|
|
''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:P76236|UniProt:P76236]] 
[http://www.ncbi.nlm.nih.gov/gene?term=946366 GeneID:946366]
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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=PF00990 PFAM:PF00990] 
RegulonDB:ECK120003558
|
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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]]
|
|
[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_416299 RefSeq:NP_416299] 
EchoBASE:EB3268
|
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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===
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[[Category:Proteins]]
[[Category:Pfam:PF00990_!_GGDEF domain]]

Latest revision as of 20:42, 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

YeaI

Synonyms

predicted diguanylate cyclase[1], YeaI[2][1], B1785[2][1] , ECK1783, JW1774, b1785

Product description

predicted diguanylate cyclase[2][3]

Probable diguanylate cyclase, function unknown[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: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 8 predicted transmembrane domains

Daley et al. (2005) [5]


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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 

MIQSTRISMG LFFKYFLSLT KIDPGQNYIS LPSIKSSTHI ALLFMVSMGT QKLKAQSFFI
FSLLLTLILF CITTLYNENT NVKLIPQMNY LMVVVALFFL NAVIFLFMLM KYFTNKQILP
TLILSLAFLS GLIYLVETIV IIHKPINGST LIQTKSNDVS IFYIFRQLSF ICLTSLALFC
YGKDNILDNN KKKTGILLLA LIPFLVFPLL AHNLSSYNAD YSLYVVDYCP DNHTATWGIN
YTKILVCLWA FLLFFIIMRT RLASELWPLI ALLCLASLCC NLLLLTLDEY NYTIWYISRG
IEVSSKLFVV SFLIYNIFQE LQLSSKLAVH DVLTNIYNRR YFFNSVESLL SRPVVKDFCV
MLVDINQFKR INAQWGHRVG DKVLVSIVDI IQQSIRPDDI LARLEGEVFG LLFTELNSAQ
AKIIAERMRK NVELLTGFSN RYDVPEQMTI SIGTVFSTGD TRNISLVMTE ADKALREAKS
EGGNKVIIHH I
Length

491

Mol. Wt

56.104 kDa

pI

8.9 (calculated)

Extinction coefficient

57,300 - 58,425 (calc based on 20 Y, 5 W, and 9 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

328..485

PF00990 GGDEF domain

PMID:19920124[6]

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<motif_map/>

tmhmm.php?gene=yeaI&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=yeaI 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:16129739

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946366

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005941

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P76236

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6971

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13495

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946366

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003558

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3268

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 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 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. ↑ 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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