agaW:Gene Product(s): Difference between revisions

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|-
|-
!align=left {{table heading style}} |Standard name
!align=left {{table heading style}} |Standard name
||
||
AgaW product
AgaW  
|-
|-
!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
B3134 product<ref name='LIB:EcoCyc10.6'/>, YhaZ product<ref name='LIB:EcoCyc10.6'/>, AgaW product<ref name='LIB:EcoCyc10.6'/>  
''B3134<ref name='LIB:EcoCyc10.6'/>, YhaZ<ref name='LIB:EcoCyc10.6'/>, AgaW<ref name='LIB:EcoCyc10.6'/> , ECK3122, JW3103, yhaZ, b3134''
|-
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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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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<protect>
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<big>'''Gene Ontology'''</big><br />{{Product_GO_help}}<!--box uid=421aa90e079fa326b6494f812ad13e79.26692.Q46aad39f09d0f-->
<big>'''Gene Ontology'''</big><br /><!--box uid=421aa90e079fa326b6494f812ad13e79.26692.Q46aad39f09d0f-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Q46aad39f09d0f"  class=" tableEdit GO_table_product dataTable"   
|- {{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
|-
|
 
|
GO:0005886
|
plasma membrane
|
GOA:spkw<br />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<br />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<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0813
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0008643
|
carbohydrate transport
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0762
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0009401
|
phosphoenolpyruvate-dependent sugar phosphotransferase system
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR004700
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0009401
|
phosphoenolpyruvate-dependent sugar phosphotransferase system
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0598
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-  
|-  
|
|
 
|
GO:0016020
|
membrane
|
GOA:spkw<br />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:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR004700
|
C
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
|
[[Category:GO:0046349_!_amino_sugar_biosynthetic_process]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0046349_!_amino_sugar_biosynthetic_process GO:0046349]
GO:0016021
|
|
amino sugar biosynthetic process
integral to membrane
|
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0812
|
|
P
C
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
|-  
|-  
|
|


|
|
[[Category:GO:0005351_!_sugar:hydrogen_symporter_activity]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0005351_!_sugar:hydrogen_symporter_activity GO:0005351]
GO:0016021
|
|
sugar:hydrogen symporter activity
integral to membrane
|
|
[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000004 GO_REF:0000004]
GO_REF:0000023
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.uniprot.org/keywords/KW-0762 SP_KW:KW-0762]
SP_SL:SL-9909
|
|
F
C
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
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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Daley et al. (2005) <ref name=PMID:15919996/>
Daley et al. (2005) <ref name=PMID:15919996/>
|
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|
   
   


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!align=left {{table heading style}} |Name
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MGLAPLAGAQ PPNVIIGTIV GTAFAITTGV KPDVAVGVAV PFAVAVQMGI TFLFSVMSGV
MGLAPLAGAQ PPNVIIGTIV GTAFAITTGV KPDVAVGVAV PFAVAVQMGI TFLFSVMSGV
MSRCDLATNP RRI</pre>  
MSRCDLATNP RRI</pre>  
|-
!align=left {{table heading style}} |Length
||
133
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
13.72 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
13.721 kDa
|-
|-
!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
6.7 (calculated)
|-
|-
!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
5500 - 5625 (calc based on 0 Y, 1 W, and 1 C residues)  
5,500 - 5,625 (calc based on 0 Y, 1 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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|
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Domain
Domain
|
|
1 - 133
1..132
|
|
PTS EIIC type-4
[http://pfam.janelia.org/family/PF03609 PF03609  PTS system sorbose-specific iic component]
|
|
[http://www.uniprot.org/uniprot/P42905#section_features UniProt:P42905]
 
|-
|
Domain
|
|
5 - 27
PMID:19920124
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
34 - 56
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />
|-
|
Domain
|
94 - 116
|
Predicted membrane-spanning helix.
|
TMD predicted by [http://www.cbs.dtu.dk/services/TMHMM TMHMM]<ref name='PMID:11152613' />


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</td>
</td>
<td>
<td>
<!-- motifs column 2-->
<motif_map/>
{{TMHMM Picture|agaW}}
{{TMHMM Picture|agaW}}
</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>agaW
<beststructure>
562</beststructure>
gene=agaW
 
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=agaW&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P42905 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=agaW&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P42905 PSI-PRED (P42905)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P42905 Genomes TO Protein (P42905)] (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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===Notes===
===Notes===
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])  
[[ASAP]]
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ASAP:ABE-0010299
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|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/ GeneID:947647]
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Escherichia coli str. K-12 substr. MG1655
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[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
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[http://www.uniprot.org/uniprot/P42905 UniProtKB/Swiss-Prot:P42905]
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Escherichia coli str. K-12 substr. MG1655
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[[EcoCyc]]
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EcoCyc:G7633
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EcoGene]]
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[[uniprot:P42905|UniProt:P42905]]
EcoGene:EG12765
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
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[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
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[http://pfam.sanger.ac.uk/family?acc=PF03609 PFAM:PF03609]
[http://www.ncbi.nlm.nih.gov/gene?term=947647 GeneID:947647]
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Escherichia coli str. K-12 substr. MG1655
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[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
[[RegulonDB]]
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[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_417603 RefSeq:NP_417603]
RegulonDB:ECK120004183
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
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[http://BioCyc.org/ECOO157/new-image?object=Z4486-MONOMER ECOO157CYC:Z4486-MONOMER]
EchoBASE:EB2618
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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===Categories===
===Categories===
{{BacktoTop}}
{{BacktoTop}}
[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0046349_!_amino sugar biosynthetic process]]

Latest revision as of 21:00, 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

AgaW

Synonyms

B3134[1], YhaZ[1], AgaW[1] , ECK3122, JW3103, yhaZ, b3134

Product description

PTS system N-acetylgalactosameine-specific IIC component 2[1][2]

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: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: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:0009401

phosphoenolpyruvate-dependent sugar phosphotransferase system

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004700

P

Seeded from EcoCyc (v14.0)

complete

GO:0009401

phosphoenolpyruvate-dependent sugar phosphotransferase system

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0598

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:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004700

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 3 predicted transmembrane domains

Daley et al. (2005) [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 

MEISLLQAFA LGIIAFIAGL DMFNGLTHMH RPVVLGPLVG LVLGDLHTGI LTGGTLELVW
MGLAPLAGAQ PPNVIIGTIV GTAFAITTGV KPDVAVGVAV PFAVAVQMGI TFLFSVMSGV
MSRCDLATNP RRI
Length

133

Mol. Wt

13.721 kDa

pI

6.7 (calculated)

Extinction coefficient

5,500 - 5,625 (calc based on 0 Y, 1 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

1..132

PF03609 PTS system sorbose-specific iic component

PMID:19920124[4]

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<motif_map/>

tmhmm.php?gene=agaW&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=agaW 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

ASAP

ASAP:ABE-0010299

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947647

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P42905

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7633

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12765

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947647

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004183

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2618

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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  2. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ Daley, DO et al. (2005) Global topology analysis of the Escherichia coli inner membrane proteome. Science 308 1321-3 PubMed
  4. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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