prkB: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
|
||
PrkB product
PrkB  
|-
|-
!{{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
|
||
predicted phosphoribulokinase product<ref name='LIB:Riley_2006'/>, B3355 product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YhfF product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, PrkB product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''predicted phosphoribulokinase<ref name='LIB:Riley_2006'/>, B3355<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YhfF<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, PrkB<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK3343, JW3318, prk?, yhfF, b3355''
|-
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!{{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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predicted phosphoribulokinase<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>
predicted phosphoribulokinase<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>


Putative phosphoribulokinase<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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<protect>
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<big>'''Gene Ontology'''</big>
<big>'''Gene Ontology'''</big><br /><!--box uid=421aa90e079fa326b6494f812ad13e79.27185.W46aae3fbcd011-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="W46aae3fbcd011"  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
|-  
|-  
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|
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[[Category:GO:0000166_!_nucleotide_binding]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0000166_!_nucleotide_binding GO:0000166]
GO:0000166
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|
nucleotide binding
nucleotide binding
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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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F
F
|
|
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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[[Category:GO:0006006_!_glucose_metabolic_process]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0006006_!_glucose_metabolic_process GO:0006006]
GO:0005524
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|
glucose metabolic process
ATP binding
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|
GOA:interpro<br />GO_REF:0000002
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|
IEA: Inferred from Electronic Annotation
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InterPro:IPR006082
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|
P
F
|
|
Seeded from EcoCyc 10.6<ref name='LIB:EcoCyc10.6'/>.  
Seeded from [[EcoCyc]] (v14.0)
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required fields missing 
complete
|-  
|-  
|
|
 
|
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[[Category:GO:0008974_!_phosphoribulokinase_activity]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0008974_!_phosphoribulokinase_activity GO:0008974]
GO:0005524
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phosphoribulokinase activity
ATP binding
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|
GOA:interpro<br />GO_REF:0000002
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HINF
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR006083
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|
F  
F
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
|-  
|-  
|
|


|
|
[[Category:GO:0005524_!_ATP_binding]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0005524_!_ATP_binding GO:0005524]
GO:0005524
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|
ATP binding
ATP binding
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|
GO_REF:0000002
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0067
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F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0005975
|
carbohydrate metabolic process
|
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR006082
InterPro:IPR006082
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
|
GO:0008152
|
metabolic process
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR006083
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
|
GO:0008974
|
phosphoribulokinase activity
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR006082
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
|
GO:0008974
|
phosphoribulokinase activity
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GOA:spec<br />GO_REF:0000003
|
IEA: Inferred from Electronic Annotation
|
EC:2.7.1.19
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
|
GO:0016301
|
kinase activity
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR006083
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
|-
|


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GO:0016301
|
kinase activity
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0418
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0016740
|
transferase activity
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0808
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
 
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<span id="Interactions"></span><big>'''Interactions'''</big>
<span id="Interactions"></span><big>'''Interactions'''</big>
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!Partner Type!!Partner!!Notes
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Protein
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dapB<br />
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PMID:16606699
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Experiment(s):EBI-1145680<br />
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Protein
|
purC<br />
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PMID:16606699
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Experiment(s):EBI-1145680<br />
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Protein
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groL<br />
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PMID:16606699
|
Experiment(s):EBI-1145680<br />
 
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===Notes===
===Notes===
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!Compartment!!Description!!Evidence!!Notes
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!align=left {{table heading style}} |Name
||
 
|-
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!{{table heading style}} |Sequence
!align=left {{table heading style}} |Sequence
|
||
[http://biocyc.org/ECOLI/sequence-aa?object=EG12365-MONOMER at EcoCyc]  
[http://biocyc.org/ECOLI/sequence-aa?object=EG12365-MONOMER at EcoCyc]  
<pre>MSAKHPVIAV TGSSGAGTTT TSLAFRKIFA QLNLHAAEVE GDSFHRYTRP EMDMAIRKAR
<pre>MSAKHPVIAV TGSSGAGTTT TSLAFRKIFA QLNLHAAEVE GDSFHRYTRP EMDMAIRKAR
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DFPWLLAMLQ GSFISHINTL VVPGGKMGLA MELIMLPLVQ RLMEGKKIE</pre>  
DFPWLLAMLQ GSFISHINTL VVPGGKMGLA MELIMLPLVQ RLMEGKKIE</pre>  
|-
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!{{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Length
|
||
32.34 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
289
|-
|-
!{{table heading style}} |pI
!align=left {{table heading style}} |Mol. Wt
|
||
32.343 kDa
|-
|-
!{{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |pI
|
||
33920 (calc based on 8 Y, 4 W, and 0 C residues)  
6.7 (calculated)
|-
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!align=left {{table heading style}} |Extinction coefficient
||
33,920 (calc based on 8 Y, 4 W, and 0 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=421aa90e079fa326b6494f812ad13e79.27185.J46aae402480d4-->
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!Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
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Domain
|
7..214
|
[http://pfam.janelia.org/family/PF00485 PF00485  Phosphoribulokinase / Uridine kinase family]
|
 
|
PMID:19920124
 
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<td>
<!-- motifs column 2-->
<motif_map/>
</td>
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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
|-
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!align=left {{table heading style}} |Structures
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<beststructure>
gene=prkB
taxon=562,83333
</beststructure>
|-
!align=left {{table heading style}} |Models
||
View models at:
* [http://www.proteinmodelportal.org/query/uniprot/P0AEX5 Protein Model Portal]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P0AEX5 PSI-PRED (P0AEX5)]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P0AEX5 Genomes TO Protein (P0AEX5)] (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
|-
|-
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[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/16131234 GI:16131234]
|
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_417814.1 GeneID:947862]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0010962
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12365-MONOMER EcoCyc:EG12365-MONOMER]
[http://www.uniprot.org/uniprot/P0AEX5 UniProtKB/Swiss-Prot:P0AEX5]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://swissmodel.expasy.org/repository/ SwissModel] ([[SwissModel|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://swissmodel.expasy.org/repository/smr.php?job=2&sptr_ac=P0AEX5 SwissModel:P0AEX5] 
EcoCyc:EG12365
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
[[EcoGene]]
|
|
[[uniprot:P0AEX5|UniProt:P0AEX5]] 
EcoGene:EG12365
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
|
[http://pfam.sanger.ac.uk/family?acc=PF00485 PFAM:PF00485]
[http://www.ncbi.nlm.nih.gov/gene?term=947862 GeneID:947862]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_417814 RefSeq:NP_417814] 
RegulonDB:ECK120002233
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://modbase.compbio.ucsf.edu ModBase] ([[ModBase|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://salilab.org/modbase/searchbyid?databaseID=P0AEX5 ModBase:P0AEX5] 
EchoBASE:EB2268
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
===Notes===
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__NOTOC__
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===Categories===
===Categories===
{{BacktoTop}}
{{BacktoTop}}
[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0006006_!_glucose metabolic process]][[Category:GO:0008974_!_phosphoribulokinase activity]]

Latest revision as of 21:02, 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

PrkB

Synonyms

predicted phosphoribulokinase[1], B3355[2][1], YhfF[2][1], PrkB[2][1] , ECK3343, JW3318, prk?, yhfF, b3355

Product description

predicted phosphoribulokinase[2][3]

Putative phosphoribulokinase[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:0000166

nucleotide binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0547

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006082

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006083

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0067

F

Seeded from EcoCyc (v14.0)

complete

GO:0005975

carbohydrate metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006082

P

Seeded from EcoCyc (v14.0)

complete

GO:0008152

metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006083

P

Seeded from EcoCyc (v14.0)

complete

GO:0008974

phosphoribulokinase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006082

F

Seeded from EcoCyc (v14.0)

complete

GO:0008974

phosphoribulokinase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.7.1.19

F

Seeded from EcoCyc (v14.0)

complete

GO:0016301

kinase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR006083

F

Seeded from EcoCyc (v14.0)

complete

GO:0016301

kinase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0418

F

Seeded from EcoCyc (v14.0)

complete

GO:0016740

transferase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0808

F

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

Protein

dapB

PMID:16606699[5]

Experiment(s):EBI-1145680

Protein

purC

PMID:16606699[5]

Experiment(s):EBI-1145680

Protein

groL

PMID:16606699[5]

Experiment(s):EBI-1145680
edit table


Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
edit table


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 

MSAKHPVIAV TGSSGAGTTT TSLAFRKIFA QLNLHAAEVE GDSFHRYTRP EMDMAIRKAR
DAGRHISYFG PEANDFGLLE QTFIEYGQSG KGKSRKYLHT YDEAVPWNQV PGTFTPWQPL
PEPTDVLFYE GLHGGVVTPQ HNVAQHVDLL VGVVPIVNLE WIQKLIRDTS ERGHSREAVM
DSVVRSMEDY INYITPQFSR THLNFQRVPT VDTSNPFAAK GIPSLDESFV VIHFRNLEGI
DFPWLLAMLQ GSFISHINTL VVPGGKMGLA MELIMLPLVQ RLMEGKKIE
Length

289

Mol. Wt

32.343 kDa

pI

6.7 (calculated)

Extinction coefficient

33,920 (calc based on 8 Y, 4 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

Domain

7..214

PF00485 Phosphoribulokinase / Uridine kinase family

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=prkB taxon=562,83333 </beststructure>

Models

View models at:

edit table

Structure figures

Notes

Gene Product Resources

[back to top]


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

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16131234

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947862

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010962

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AEX5

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG12365

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12365

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947862

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002233

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2268

Escherichia coli str. K-12 substr. MG1655

edit table


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. ↑ 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 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  6. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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