oxc:Gene Product(s): Difference between revisions

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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
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predicted oxalyl-CoA decarboxylase<ref name='LIB:Riley_2006'/>, B2373<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YfdU<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Oxc<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''predicted oxalyl-CoA decarboxylase<ref name='LIB:Riley_2006'/>, B2373<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YfdU<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Oxc<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK2369, JW2370, yfdU, b2373''
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="X46aaa426e7bc4"  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
|-  
|-  
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Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
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complete
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Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
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complete
|-  
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Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
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complete
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Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
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complete
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Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
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complete
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Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
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complete
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Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
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complete
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Seeded from [[EcoCyc]] (v14.0)
Seeded from [[EcoCyc]] (v14.0)
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complete
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Seeded from [[EcoCyc]] (v14.0)
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complete
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Seeded from [[EcoCyc]] (v14.0)
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complete
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complete
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Seeded from [[EcoCyc]] (v14.0)
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complete


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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="D46aaa427779f2"  class=" tableEdit Product_interactions_table dataTable"   
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!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
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Experiment(s):EBI-1142672<br />  
Experiment(s):EBI-1142672<br />  
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Protein
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hupA
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PMID:19402753
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LCMS(ID Probability):99.6
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Protein
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ybgI
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PMID:19402753
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LCMS(ID Probability):99.6
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Protein
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phnI
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PMID:19402753
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LCMS(ID Probability):99.6


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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="D46a83ba3690d5"  class=" tableEdit Product_localization_table"   
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!|Compartment!!Description!!Evidence!!Source!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes


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!align=left {{table heading style}} |Name
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{|   id="Z46aaa429ce876"  class=" tableEdit Product_motif_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46aaa429ce876"  class=" tableEdit Product_motif_table dataTable"   
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!|Type!!Residues!!Description!!Notes!!References
!|Type!!Residues!!Description!!Notes!!References
|-
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Domain
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201..329
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[http://pfam.janelia.org/family/PF00205 PF00205  Thiamine pyrophosphate enzyme, central domain]
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PMID:19920124
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Domain
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394..540
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[http://pfam.janelia.org/family/PF02775 PF02775  Thiamine pyrophosphate enzyme, C-terminal TPP binding domain]
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PMID:19920124
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Domain
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8..179
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[http://pfam.janelia.org/family/PF02776 PF02776  Thiamine pyrophosphate enzyme, N-terminal TPP binding domain]
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PMID:19920124


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View models at:
View models at:
* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=recA EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P0AFI0 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=recA&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P0AFI0 PSI-PRED (P0AFI0)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P0AFI0 Genomes TO Protein (P0AFI0)] (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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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N46aaa42a96454"  class=" tableEdit Product_resource_table"   
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!|Resource type!!Source!!Notes/Reference
!|Resource type!!Source!!Notes/Reference
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{|   id="X46aaa42af3c45"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="X46aaa42af3c45"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
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[http://www.ncbi.nlm.nih.gov/protein/16130305 GI:16130305]
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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_416874.1 GeneID:946845]
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Escherichia coli str. K-12 substr. MG1655
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[[ASAP]]
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ASAP:ABE-0007826
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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]])
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[http://www.uniprot.org/uniprot/P0AFI0 UniProtKB/Swiss-Prot:P0AFI0]
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Escherichia coli str. K-12 substr. MG1655
|-
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[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7236-MONOMER EcoCyc:G7236-MONOMER]
EcoCyc:G7236
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[http://swissmodel.expasy.org/repository/ SwissModel] ([[SwissModel|EcoliWiki Page]])
[[EcoGene]]
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[http://swissmodel.expasy.org/repository/smr.php?job=2&sptr_ac=P0AFI0 SwissModel:P0AFI0]
EcoGene:EG14143
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''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]])
|
|
[[uniprot:P0AFI0|UniProt:P0AFI0]]
[http://www.ncbi.nlm.nih.gov/gene?term=946845 GeneID:946845]
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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=PF02776 PFAM:PF02776]
RegulonDB:ECK120003811
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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]]
|
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[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_416874 RefSeq:NP_416874]
EchoBASE:EB3895
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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{{BacktoTop}}
{{BacktoTop}}
[[Category:Proteins]]
[[Category:Proteins]]
[[Category:Pfam:PF00205_!_Thiamine pyrophosphate enzyme, central domain]]
[[Category:Pfam:PF02775_!_Thiamine pyrophosphate enzyme, C-terminal TPP binding domain]]
[[Category:Pfam:PF02776_!_Thiamine pyrophosphate enzyme, N-terminal TPP binding domain]]

Latest revision as of 20:50, 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

Oxc

Synonyms

predicted oxalyl-CoA decarboxylase[1], B2373[2][1], YfdU[2][1], Oxc[2][1] , ECK2369, JW2370, yfdU, b2373

Product description

predicted oxalyl-CoA decarboxylase[2][3]

Probable oxalyl-CoA decarboxylase, oxalate catabolism[4]

EC number (for enzymes)


edit table


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:0000287

magnesium ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012000

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011766

F

Seeded from EcoCyc (v14.0)

complete

GO:0008949

oxalyl-CoA decarboxylase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017660

F

Seeded from EcoCyc (v14.0)

complete

GO:0008949

oxalyl-CoA decarboxylase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:4.1.1.8

F

Seeded from EcoCyc (v14.0)

complete

GO:0016829

lyase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0456

F

Seeded from EcoCyc (v14.0)

complete

GO:0016831

carboxy-lyase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0210

F

Seeded from EcoCyc (v14.0)

complete

GO:0030976

thiamin pyrophosphate binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011766

F

Seeded from EcoCyc (v14.0)

complete

GO:0030976

thiamin pyrophosphate binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012000

F

Seeded from EcoCyc (v14.0)

complete

GO:0030976

thiamin pyrophosphate binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR012001

F

Seeded from EcoCyc (v14.0)

complete

GO:0030976

thiamin pyrophosphate binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017660

F

Seeded from EcoCyc (v14.0)

complete

GO:0033611

oxalate catabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017660

P

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017660

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

rrmA

PMID:16606699[5]

Experiment(s):EBI-1142672

Protein

uvrY

PMID:16606699[5]

Experiment(s):EBI-1142672

Protein

hchA

PMID:16606699[5]

Experiment(s):EBI-1142672

Protein

nadE

PMID:16606699[5]

Experiment(s):EBI-1142672

Protein

hupA

PMID:19402753[6]

LCMS(ID Probability):99.6

Protein

ybgI

PMID:19402753[6]

LCMS(ID Probability):99.6

Protein

phnI

PMID:19402753[6]

LCMS(ID Probability):99.6

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 

MSDQLQMTDG MHIIVEALKQ NNIDTIYGVV GIPVTDMARH AQAEGIRYIG FRHEQSAGYA
AAASGFLTQK PGICLTVSAP GFLNGLTALA NATVNGFPMI MISGSSDRAI VDLQQGDYEE
LDQMNAAKPY AKAAFRVNQP QDLGIALARA IRVSVSGRPG GVYLDLPANV LAATMEKDEA
LTTIVKVENP SPALLPCPKS VTSAISLLAK AERPLIILGK GAAYSQADEQ LREFIESAQI
PFLPMSMAKG ILEDTHPLSA AAARSFALAN ADVVMLVGAR LNWLLAHGKK GWAADTQFIQ
LDIEPQEIDS NRPIAVPVVG DIASSMQGML AELKQNTFTT PLVWRDILNI HKQQNAQKMH
EKLSTDTQPL NYFNALSAVR DVLRENQDIY LVNEGANTLD NARNIIDMYK PRRRLDCGTW
GVMGIGMGYA IGASVTSGSP VVAIEGDSAF GFSGMEIETI CRYNLPVTIV IFNNGGIYRG
DGVDLSGAGA PSPTDLLHHA RYDKLMDAFR GVGYNVTTTD ELRHALTTGI QSRKPTIINV
VIDPAAGTES GHITKLNPKQ VAGN
Length

564

Mol. Wt

60.582 kDa

pI

5.8 (calculated)

Extinction coefficient

44,350 - 44,850 (calc based on 15 Y, 4 W, and 4 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

201..329

PF00205 Thiamine pyrophosphate enzyme, central domain

PMID:19920124[7]

Domain

394..540

PF02775 Thiamine pyrophosphate enzyme, C-terminal TPP binding domain

PMID:19920124[7]

Domain

8..179

PF02776 Thiamine pyrophosphate enzyme, N-terminal TPP binding domain

PMID:19920124[7]

edit table

<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=oxc 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
edit table


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:16130305

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946845

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007826

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0AFI0

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7236

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14143

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946845

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003811

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3895

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

[back to top]




References

[back to top]


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 5.3 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 6.2 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 7.2 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=oxc:Gene_Product(s)&oldid=1494254"