sucA:Gene Product(s): Difference between revisions

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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
2-oxoglutarate decarboxylase, thiamin-requiring<ref name='LIB:Riley_2006'/>  
''2-oxoglutarate decarboxylase, thiamin-requiring<ref name='LIB:Riley_2006'/> , ECK0714, JW0715, lys, b0726''
|-
|-
!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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* [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.4.2 1.2.4.2]<ref name='LIB:Riley_2006'/>
* [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=1.2.4.2 1.2.4.2]<ref name='LIB:Riley_2006'/>


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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Q46aa3fb870112"  class=" tableEdit GO_table_product dataTable" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!|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:0030976
GO:0005737
|
cytoplasm
|
 
|
 
|
 
|
C
|
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.
|
Missing: evidence, reference
|-
|
 
|
GO:0006099
|
tricarboxylic acid cycle
|
 
|
 
|
 
|
P
|
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.
|
Missing: evidence, reference
|-
|
 
|
GO:0004591
|
|
thiamin pyrophosphate binding
oxoglutarate dehydrogenase (succinyl-transferring) activity
|
|
GO_REF:0000002
GOA:interpro<br />GO_REF:0000002
|
|
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)
|
|
complete  
complete  
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|
|
GO:0016624
GO:0004591
|
|
oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
oxoglutarate dehydrogenase (succinyl-transferring) activity
|
|
GO_REF:0000002
GOA:spec<br />GO_REF:0000003
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR001017
EC:1.2.4.2
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
GO:0016491
GO:0005829
|
|
oxidoreductase activity
cytosol
|
|
GO_REF:0000004
PMID:16858726
|
|
IEA: Inferred from Electronic Annotation
IDA: Inferred from Direct Assay
|
|
SP_KW:KW-0560
 
|
|
F
C
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
GO:0008152
GO:0006096
|
|
metabolic process
glycolysis
|
|
GO_REF:0000002
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR001017
InterPro:IPR011603
|
|
P
P
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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glycolysis
glycolysis
|
|
GO_REF:0000002<br />GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR011603<br />SP_KW:KW-0324
SP_KW:KW-0324
|
|
P
P
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
|-  
|-  
|
|
 
|
|
GO:0005737
GO:0008152
|
|
cytoplasm
metabolic process
|
|
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR001017
|
|
C
P
|
|
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
|-  
|-  
|
|


|
|
GO:0006099
GO:0016491
|
oxidoreductase activity
|
GOA:spkw<br />SP_KW:GO_REF:0000004
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IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0560
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
|
tricarboxylic acid cycle
complete
|-
|
|


|
GO:0016624
|
oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR001017
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
|


|
|
 
GO:0030976
|
thiamin pyrophosphate binding
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR011603
|
|
P
F
|
|
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required field missing
complete
|-  
|-  
|
|


|
|
GO:0004591
GO:0055114
|
|
oxoglutarate dehydrogenase (succinyl-transferring) activity
oxidation reduction
|
|
GO_REF:0000002<br />GO_REF:0000003
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR011603<br />EC:1.2.4.2
SP_KW:KW-0560
|
|
F
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  


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!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
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|
|
Experiment(s):EBI-886788<br />  
Experiment(s):EBI-886788<br />  
|-
|
Protein
|
lipA
|
|
PMID:19402753
|
MALDI(Z-score):25.667279
|-
|
Protein
|
sucB
|
|
PMID:19402753
|
LCMS(ID Probability):99.6 MALDI(Z-score):33.552055
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!|Compartment!!Description!!Evidence!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes


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!align=left {{table heading style}} |Name
||


|-
|-
!align=left {{table heading style}} |Sequence
!align=left {{table heading style}} |Sequence
||
||
[http://biocyc.org/ECOLI/sequence-aa?object= at EcoCyc]
<pre>MRITIILVAP ARAENIGAAA RAMKTMGFSD LRIVDSQAHL EPATRWVAHG SGDIIDNIKV
<pre></pre>  
FPTLAESLHD VDFTVATTAR SRAKYHYYAT PVELVPLLEE KSSWMSHAAL VFGREDSGLT
NEELALADVL TGVPMVADYP SLNLGQAVMV YCYQLATLIQ QPAKSDATAD QHQLQALRER
AMTLLTTLAV ADDIKLVDWL QQRLGLLEQR DTAMLHRLLH DIEKNITK</pre>
|-
!align=left {{table heading style}} |Length
||
228
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
25.259 kDa
|-
|-
!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
5.9 (calculated)
|-
|-
!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
25,440 - 25,565 (calc based on 6 Y, 3 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><table>
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|- {{table heading style}}
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!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-
|
Domain
|
589..785
|
[http://pfam.janelia.org/family/PF02779 PF02779  Transketolase, pyrimidine binding domain]
|
 
|
PMID:19920124
|-
|
Domain
|
207..516
|
[http://pfam.janelia.org/family/PF00676 PF00676  Dehydrogenase E1 component]
|


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PMID:19920124
 
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<td>
<!-- motifs column 2-->
<motif_map/>
</td>
</tr>
</table>


 
<table><tr valign='top'><td>
<span id="Structure"></span><big>'''Structure'''</big>
<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>sucA
<beststructure>
562</beststructure>
gene=sucA
 
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=sucA&sub=keywordSearc EcoliPredict]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P0AFG3 PSI-PRED (P0AFG3)]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=sucA&organism=562&organismtext= ModBase]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P0AFG3 Genomes TO Protein (P0AFG3)] (GTOP)
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [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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</td><tr><table><!--Structure_notes--></protect>
===Notes===
===Notes===


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!|Resource type!!Source!!Notes/Reference
!|Resource type!!Source!!Notes/Reference


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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/16128701 GI:16128701]
|
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_415254.1 GeneID:945303]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0002478
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P0AFG3 UniProtKB/Swiss-Prot:P0AFG3]
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Escherichia coli str. K-12 substr. MG1655
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[[EcoCyc]]
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EcoCyc:EG10979
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EcoGene]]
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EcoGene:EG10979
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
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[http://www.ncbi.nlm.nih.gov/gene?term=945303 GeneID:945303]
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Escherichia coli str. K-12 substr. MG1655
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[[RegulonDB]]
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RegulonDB:ECK120000968
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EchoBASE]]
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EchoBASE:EB0972
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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==References==
==References==
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{{BacktoTop}}
 
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
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===Categories===
===Categories===
{{BacktoTop}}
{{BacktoTop}}
[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0005737_!_cytoplasm]][[Category:GO:0006099_!_tricarboxylic acid cycle]]

Latest revision as of 20:29, 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

SucA

Synonyms

2-oxoglutarate decarboxylase, thiamin-requiring[1] , ECK0714, JW0715, lys, b0726

Product description


2-oxoglutarate dehydrogenase, E1 component; yields succinyl-CoA and CO(2)[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:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0006099

tricarboxylic acid cycle

P

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0004591

oxoglutarate dehydrogenase (succinyl-transferring) activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011603

F

Seeded from EcoCyc (v14.0)

complete

GO:0004591

oxoglutarate dehydrogenase (succinyl-transferring) activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:1.2.4.2

F

Seeded from EcoCyc (v14.0)

complete

GO:0005829

cytosol

PMID:16858726[3]

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

GO:0006096

glycolysis

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011603

P

Seeded from EcoCyc (v14.0)

complete

GO:0006096

glycolysis

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0324

P

Seeded from EcoCyc (v14.0)

complete

GO:0008152

metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001017

P

Seeded from EcoCyc (v14.0)

complete

GO:0016491

oxidoreductase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

F

Seeded from EcoCyc (v14.0)

complete

GO:0016624

oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001017

F

Seeded from EcoCyc (v14.0)

complete

GO:0030976

thiamin pyrophosphate binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011603

F

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0560

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

Protein

hflK

PMID:15690043[4]

Experiment(s):EBI-880717

Protein

lipA

PMID:15690043[4]

Experiment(s):EBI-880717

Protein

lpdA

PMID:15690043[4]

Experiment(s):EBI-880717, EBI-886788

Protein

sucB

PMID:15690043[4]

Experiment(s):EBI-880717, EBI-880739, EBI-886788

Protein

groL

PMID:16606699[5]

Experiment(s):EBI-1137802

Protein

dnaE

PMID:16606699[5]

Experiment(s):EBI-1137802

Protein

oxc

PMID:16606699[5]

Experiment(s):EBI-1137802

Protein

rplC

PMID:15690043[4]

Experiment(s):EBI-886788

Protein

lipA

PMID:19402753[6]

MALDI(Z-score):25.667279

Protein

sucB

PMID:19402753[6]

LCMS(ID Probability):99.6 MALDI(Z-score):33.552055

Small Molecule

TTTPP

selectively inhibits pyruvate or 2-oxoglutarate dehydrogenase (El).


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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
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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 
MRITIILVAP ARAENIGAAA RAMKTMGFSD LRIVDSQAHL EPATRWVAHG SGDIIDNIKV
FPTLAESLHD VDFTVATTAR SRAKYHYYAT PVELVPLLEE KSSWMSHAAL VFGREDSGLT
NEELALADVL TGVPMVADYP SLNLGQAVMV YCYQLATLIQ QPAKSDATAD QHQLQALRER
AMTLLTTLAV ADDIKLVDWL QQRLGLLEQR DTAMLHRLLH DIEKNITK
Length

228

Mol. Wt

25.259 kDa

pI

5.9 (calculated)

Extinction coefficient

25,440 - 25,565 (calc based on 6 Y, 3 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

589..785

PF02779 Transketolase, pyrimidine binding domain

PMID:19920124[7]

Domain

207..516

PF00676 Dehydrogenase E1 component

PMID:19920124[7]

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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=sucA 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:16128701

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945303

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002478

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AFG3

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10979

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10979

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945303

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000968

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0972

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. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  3. ↑ Lasserre, JP et al. (2006) A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis. Electrophoresis 27 3306-21 PubMed
  4. ↑ 4.0 4.1 4.2 4.3 4.4 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  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. ↑ 6.0 6.1 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  7. ↑ 7.0 7.1 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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