allA:Gene Product(s): Difference between revisions

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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
ureidoglycolate hydrolase<ref name='LIB:Riley_2006'/>, B0505<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YbbT<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, AllA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''ureidoglycolate hydrolase<ref name='LIB:Riley_2006'/>, B0505<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YbbT<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, AllA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK0498, glxA2, JW0493, ybbT, b0505''
|-
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!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=3.5.3.19 3.5.3.19]<ref name='LIB:Riley_2006'/>
* [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=3.5.3.19 3.5.3.19]<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="A46aa339a71c82"  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:0005737
|
cytoplasm
|
 
|
 
|
 
|
C
|
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.
|
Missing: evidence, reference
|-  
|-  
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|
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allantoin catabolic process
allantoin catabolic process
|
|
GO_REF:0000002
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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P
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
GO:0006144
GO:0004848
|
|
purine base metabolic process
ureidoglycolate hydrolase activity
|
|
GO_REF:0000004
GOA:hamap<br />GO_REF:0000020
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0659
HAMAP:MF_00616
|
|
P
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
GO:0006145
GO:0004848
|
|
purine base catabolic process
ureidoglycolate hydrolase activity
|
|
GO_REF:0000020
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
HAMAP:MF_00616
InterPro:IPR007247
|
|
P
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
GO:0016787
GO:0004848
|
|
hydrolase activity
ureidoglycolate hydrolase activity
|
|
GO_REF:0000004
GOA:spec<br />GO_REF:0000003
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0378
EC:3.5.3.19
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
GO:0050385
GO:0006144
|
|
ureidoglycolate lyase activity
purine base metabolic process
|
|
PMID:10601204
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IDA: Inferred from Direct Assay
IEA: Inferred from Electronic Annotation
|
|
 
SP_KW:KW-0659
|
|
F
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
|-  
|-  
|
|
 
|
|
GO:0005737
GO:0006145
|
|
cytoplasm
purine base catabolic process
|
|
GOA:hamap<br />GO_REF:0000020
|
|
IEA: Inferred from Electronic Annotation
|
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HAMAP:MF_00616
|
|
C
P
|
|
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
|-  
|-  
|
|


|
|
GO:0004848
GO:0016787
|
|
ureidoglycolate hydrolase activity
hydrolase activity
|
|
GO_REF:0000020<br />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
|
|
HAMAP:MF_00616<br />InterPro:IPR007247<br />EC:3.5.3.19
SP_KW:KW-0378
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
|-  
|-  
|
|
 
|
|
GO:0006807
GO:0050385
|
|
nitrogen compound metabolic process
ureidoglycolate lyase activity
|
|
PMID:10601204
|
|
IDA: Inferred from Direct Assay
|
|
 
|
|
P
F
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
|-  
|-  
|
|
 
|
|
GO:0009442
GO:0050385
|
|
allantoin assimilation pathway
ureidoglycolate lyase activity
|
|
PMID:19935661
|
|
IDA: Inferred from Direct Assay
|
|
 
|
|
P
F
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete


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!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
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Experiment(s):EBI-1136944<br />  
Experiment(s):EBI-1136944<br />  


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!|Compartment!!Description!!Evidence!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes


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


|-
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PANLPLTIHE LERHPLGTQA FIPMKGEVFV VVVALGDDKP DLSTLRAFIT NGEQGVNYHR
PANLPLTIHE LERHPLGTQA FIPMKGEVFV VVVALGDDKP DLSTLRAFIT NGEQGVNYHR
NVWHHPLFAW QRVTDFLTID RGGSDNCDVE SIPEQELCFA</pre>  
NVWHHPLFAW QRVTDFLTID RGGSDNCDVE SIPEQELCFA</pre>  
|-
!align=left {{table heading style}} |Length
||
160
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
18.17 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
18.169 kDa
|-
|-
!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
4.7 (calculated)
|-
|-
!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
15470 - 15845 (calc based on 3 Y, 2 W, and 3 C residues)  
15,470 - 15,845 (calc based on 3 Y, 2 W, and 3 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
|
1..159
|
[http://pfam.janelia.org/family/PF04115 PF04115  Ureidoglycolate hydrolase ]
|
 
|
PMID:19920124


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<td>
<!-- motifs column 2-->
<motif_map/>
</td>
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</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>allA
<beststructure>
562</beststructure>
gene=allA
 
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=allA&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P77731 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=allA&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P77731 PSI-PRED (P77731)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P77731 Genomes TO Protein (P77731)] (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 ====
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
<protect><!--          ***** PLEASE DO NOT EDIT BELOW THIS LINE *****        -->
</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://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/16128489 GI:16128489]
|
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_415038.1 GeneID:945141]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0001747
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P77731 UniProtKB/Swiss-Prot:P77731]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6275-MONOMER EcoCyc:G6275-MONOMER]
EcoCyc:G6275
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
[[EcoGene]]
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[[uniprot:P77731|UniProt:P77731]]
EcoGene:EG13615
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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=PF04115 PFAM:PF04115]
[http://www.ncbi.nlm.nih.gov/gene?term=945141 GeneID:945141]
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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_415038 RefSeq:NP_415038]
RegulonDB:ECK120002883
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.rcsb.org/pdb PDB] ([[PDB|EcoliWiki Page]])
[[EchoBASE]]
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[http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1XSQ PDB:1XSQ]
EchoBASE:EB3381
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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}}
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[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0005737_!_cytoplasm]][[Category:GO:0006807_!_nitrogen compound metabolic process]][[Category:GO:0009442_!_allantoin assimilation pathway]][[Category:Products with structures in PDB]]

Latest revision as of 20:26, 17 February 2015

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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

AllA

Synonyms

ureidoglycolate hydrolase[1], B0505[2][1], YbbT[2][1], AllA[2][1] , ECK0498, glxA2, JW0493, ybbT, b0505

Product description

G6275[2][3]

Ureidoglycolate hydrolase: allantoin for anaerobic nitrogen[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:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0000256

allantoin catabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007247

P

Seeded from EcoCyc (v14.0)

complete

GO:0004848

ureidoglycolate hydrolase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00616

F

Seeded from EcoCyc (v14.0)

complete

GO:0004848

ureidoglycolate hydrolase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR007247

F

Seeded from EcoCyc (v14.0)

complete

GO:0004848

ureidoglycolate hydrolase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.5.3.19

F

Seeded from EcoCyc (v14.0)

complete

GO:0006144

purine base metabolic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0659

P

Seeded from EcoCyc (v14.0)

complete

GO:0006145

purine base catabolic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00616

P

Seeded from EcoCyc (v14.0)

complete

GO:0016787

hydrolase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0378

F

Seeded from EcoCyc (v14.0)

complete

GO:0050385

ureidoglycolate lyase activity

PMID:10601204[5]

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0050385

ureidoglycolate lyase activity

PMID:19935661[6]

IDA: Inferred from Direct Assay

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

clpB

PMID:16606699[7]

Experiment(s):EBI-1136944

Protein

sdhA

PMID:16606699[7]

Experiment(s):EBI-1136944

Protein

lacZ

PMID:16606699[7]

Experiment(s):EBI-1136944

Protein

rimJ

PMID:16606699[7]

Experiment(s):EBI-1136944
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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

at EcoCyc 

MKLQVLPLSQ EAFSAYGDVI ETQQRDFFHI NNGLVERYHD LALVEILEQD CTLISINRAQ
PANLPLTIHE LERHPLGTQA FIPMKGEVFV VVVALGDDKP DLSTLRAFIT NGEQGVNYHR
NVWHHPLFAW QRVTDFLTID RGGSDNCDVE SIPEQELCFA
Length

160

Mol. Wt

18.169 kDa

pI

4.7 (calculated)

Extinction coefficient

15,470 - 15,845 (calc based on 3 Y, 2 W, and 3 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..159

PF04115 Ureidoglycolate hydrolase

PMID:19920124[8]

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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=allA 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:16128489

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945141

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001747

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P77731

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6275

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13615

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945141

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002883

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3381

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 1.4 1.5 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. ↑ Cusa, E et al. (1999) Genetic analysis of a chromosomal region containing genes required for assimilation of allantoin nitrogen and linked glyoxylate metabolism in Escherichia coli. J. Bacteriol. 181 7479-84 PubMed
  6. ↑ Werner, AK et al. (2010) Ureide catabolism in Arabidopsis thaliana and Escherichia coli. Nat. Chem. Biol. 6 19-21 PubMed
  7. ↑ 7.0 7.1 7.2 7.3 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  8. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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