ygeX:Gene Product(s): Difference between revisions

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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
2,3-diaminopropionate ammonia-lyase<ref name='LIB:Riley_2006'/>, B2871<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YgeX<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''2,3-diaminopropionate ammonia-lyase<ref name='LIB:Riley_2006'/>, B2871<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YgeX<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK2867, JW2839, b2871''
|-
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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Component of [[:Category:Complex:2,3-diaminopropionate ammonia-lyase|2,3-diaminopropionate ammonia-lyase]]<ref name='LIB:EcoCyc11.1'/>
Component of [[:Category:Complex:2,3-diaminopropionate ammonia-lyase|2,3-diaminopropionate ammonia-lyase]]<ref name='LIB:EcoCyc11.1'/>


2,3-diaminopropionate ammonia lyase<ref name='LIB:EcoGene'/>
|-
|-
!align=left {{table heading style}} |EC number (for enzymes)
!align=left {{table heading style}} |EC number (for enzymes)
||
||
** [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.15 4.3.1.15]<ref name='LIB:Riley_2006'/>
* [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.3.1.15 4.3.1.15]<ref name='LIB:Riley_2006'/>


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===Notes===
===Notes===
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{{BacktoTop}}
{{BacktoTop}}
<protect>
<protect>
<big>'''Gene Ontology'''</big><br />{{Product_GO_help}}<!--box uid=421aa90e079fa326b6494f812ad13e79.26102.L46aac3c136356-->
<big>'''Gene Ontology'''</big><br /><!--box uid=421aa90e079fa326b6494f812ad13e79.26102.L46aac3c136356-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="L46aac3c136356"  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:0016829_!_lyase_activity]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0016829_!_lyase_activity GO:0016829]
GO:0005737
|
|
lyase activity
cytoplasm
|
|
[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000004 GO_REF:0000004]
 
|
 
|
 
|
C
|
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.  
|
Missing: evidence, reference
|-  
|
 
|
GO:0003824
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catalytic activity
|
GOA:interpro<br />GO_REF:0000002
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|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.uniprot.org/keywords/KW-0456 SP_KW:KW-0456]
InterPro:IPR001926
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
[[Category:GO:0030170_!_pyridoxal_phosphate_binding]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0030170_!_pyridoxal_phosphate_binding GO:0030170]
GO:0008152
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|
pyridoxal phosphate binding
metabolic process
|
GOA:interpro<br />GO_REF:0000002
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IEA: Inferred from Electronic Annotation
|
InterPro:IPR001926
|
P
|
Seeded from [[EcoCyc]] (v14.0)
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complete
|-
|
 
|
GO:0008838
|
diaminopropionate ammonia-lyase activity
|
|
[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000002 GO_REF:0000002]
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR001926 InterPro:IPR001926]
InterPro:IPR010081
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
[[Category:GO:0008838_!_diaminopropionate_ammonia-lyase_activity]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0008838_!_diaminopropionate_ammonia-lyase_activity GO:0008838]
GO:0008838
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|
diaminopropionate ammonia-lyase activity
diaminopropionate ammonia-lyase activity
|
|
[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000003 GO_REF:0000003]
GOA:spec<br />GO_REF:0000003
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.expasy.org/cgi-bin/nicezyme.pl?4.3.1.15 EC:4.3.1.15]
EC:4.3.1.15
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
[[Category:GO:0008152_!_metabolic_process]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0008152_!_metabolic_process GO:0008152]
GO:0030170
|
|
metabolic process
pyridoxal phosphate binding
|
|
[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000002 GO_REF:0000002]
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR001926 InterPro:IPR001926]
InterPro:IPR001926
|
|
P
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
[[Category:GO:0003824_!_catalytic_activity]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0003824_!_catalytic_activity GO:0003824]
GO:0030170
|
|
catalytic activity
pyridoxal phosphate binding
|
|
[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000002 GO_REF:0000002]
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR001926 InterPro:IPR001926]
InterPro:IPR010081
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
|-  
|-  
|
|
 
|
GO:0008838
|
diaminopropionate ammonia-lyase activity
|
PMID:12596860
|
IDA: Inferred from Direct Assay
|
 
|
F
|
 
|
complete
|-
|
|
[[Category:GO:0005737_!_cytoplasm]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0005737_!_cytoplasm GO:0005737]
 
|
|
cytoplasm
GO:0009063
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|
cellular amino acid catabolic process
|
|
PMID:12596860
|
|
ISA: Inferred from Sequence Alignment
|
|
C
UniProtKB:P40817
 
 
|
|
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.
P
|
|
required fields missing 


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complete
 
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!|Partner Type!!Partner!!Notes!!References
!|Partner Type!!Partner!!Notes!!References!!Evidence
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could be indirect  
could be indirect  
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===Notes===
===Notes===
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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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ILRNCATQFI SCQDSVAALG MRVLGNPYGN DPRIISGESG AVGLGVLAAV HYHPQRQSLM
ILRNCATQFI SCQDSVAALG MRVLGNPYGN DPRIISGESG AVGLGVLAAV HYHPQRQSLM
EKLALNKDAV VLVISTEGDT DVKHYREVVW EGKHAVAP</pre>  
EKLALNKDAV VLVISTEGDT DVKHYREVVW EGKHAVAP</pre>  
|-
!align=left {{table heading style}} |Length
||
398
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
43.33 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
43.327 kDa
|-
|-
!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
5.8 (calculated)
|-
|-
!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
52370 - 53245 (calc based on 13 Y, 6 W, and 7 C residues)  
52,370 - 53,245 (calc based on 13 Y, 6 W, and 7 C residues)


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<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span>
 
<!--box uid=421aa90e079fa326b6494f812ad13e79.26102.O46aac3c9db8ee-->
<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span><table>
<tr align="left" valign="top">
<td><!--box uid=421aa90e079fa326b6494f812ad13e79.26102.O46aac3c9db8ee-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O46aac3c9db8ee"  class=" tableEdit Product_motif_table dataTable"   
|- {{table heading style}}
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!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-
|
Domain
|
39..377
|
[http://pfam.janelia.org/family/PF00291 PF00291  Pyridoxal-phosphate dependent enzyme]
|


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PMID:19920124
 
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<td>
<!-- motifs column 2-->
<motif_map/>
</td>
</tr>
</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>ygeX
<beststructure>
562</beststructure>
gene=ygeX
 
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=ygeX&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P66899 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=ygeX&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P66899 PSI-PRED (P66899)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P66899 Genomes TO Protein (P66899)] (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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[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/16130773 GI:16130773]
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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_417347.1 GeneID:947012]
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Escherichia coli str. K-12 substr. MG1655
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[[ASAP]]
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ASAP:ABE-0009428
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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/P66899 UniProtKB/Swiss-Prot:P66899]
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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=G7490-MONOMER EcoCyc:G7490-MONOMER]
EcoCyc:G7490
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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]])
[[EcoGene]]
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[[uniprot:P66899|UniProt:P66899]]
EcoGene:EG13054
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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=PF00291 PFAM:PF00291]
[http://www.ncbi.nlm.nih.gov/gene?term=947012 GeneID:947012]
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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_417347 RefSeq:NP_417347]
RegulonDB:ECK120004053
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://modbase.compbio.ucsf.edu ModBase] ([[ModBase|EcoliWiki Page]])
[[EchoBASE]]
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[http://salilab.org/modbase/searchbyid?databaseID=P66899 ModBase:P66899]
EchoBASE:EB2866
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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===Notes===
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===Categories===
===Categories===
{{BacktoTop}}
{{BacktoTop}}
[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0005737_!_cytoplasm]][[Category:GO:0008152_!_metabolic process]][[Category:Complex:2,3-diaminopropionate ammonia-lyase]]
[[Category:RefGenome_Annotated_Gene]]

Latest revision as of 20:56, 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

YgeX

Synonyms

2,3-diaminopropionate ammonia-lyase[1], B2871[2][1], YgeX[2][1] , ECK2867, JW2839, b2871

Product description

2,3-diaminopropionate ammonia-lyase[2][3];

Component of 2,3-diaminopropionate ammonia-lyase[3]

2,3-diaminopropionate ammonia lyase[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:0005737

cytoplasm

C

Seeded from Riley et al 2006 [1].

Missing: evidence, reference

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001926

F

Seeded from EcoCyc (v14.0)

complete

GO:0008152

metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001926

P

Seeded from EcoCyc (v14.0)

complete

GO:0008838

diaminopropionate ammonia-lyase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010081

F

Seeded from EcoCyc (v14.0)

complete

GO:0008838

diaminopropionate ammonia-lyase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:4.3.1.15

F

Seeded from EcoCyc (v14.0)

complete

GO:0030170

pyridoxal phosphate binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001926

F

Seeded from EcoCyc (v14.0)

complete

GO:0030170

pyridoxal phosphate binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR010081

F

Seeded from EcoCyc (v14.0)

complete

GO:0008838

diaminopropionate ammonia-lyase activity

PMID:12596860[5]

IDA: Inferred from Direct Assay

F

complete

GO:0009063

cellular amino acid catabolic process

PMID:12596860[5]

ISA: Inferred from Sequence Alignment

UniProtKB:P40817


P

complete

edit table

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

Subunits of 2,3-diaminopropionate ammonia-lyase

could be indirect


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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 

MSVFSLKIDI ADNKFFNGET SPLFSQSQAK LARQFHQKIA GYRPTPLCAL DDLANLFGVK
KILVKDESKR FGLNAFKMLG GAYAIAQLLC EKYHLDIETL SFEHLKNAIG EKMTFATTTD
GNHGRGVAWA AQQLGQNAVI YMPKGSAQER VDAILNLGAE CIVTDMNYDD TVRLTMQHAQ
QHGWEVVQDT AWEGYTKIPT WIMQGYATLA DEAVEQMREM GVTPTHVLLQ AGVGAMAGGV
LGYLVDVYSP QNLHSIIVEP DKADCIYRSG VKGDIVNVGG DMATIMAGLA CGEPNPLGWE
ILRNCATQFI SCQDSVAALG MRVLGNPYGN DPRIISGESG AVGLGVLAAV HYHPQRQSLM
EKLALNKDAV VLVISTEGDT DVKHYREVVW EGKHAVAP
Length

398

Mol. Wt

43.327 kDa

pI

5.8 (calculated)

Extinction coefficient

52,370 - 53,245 (calc based on 13 Y, 6 W, and 7 C residues)

edit table


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

39..377

PF00291 Pyridoxal-phosphate dependent enzyme

PMID:19920124[6]

edit table

<motif_map/>

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

Structures

<beststructure> gene=ygeX taxon=562,83333 </beststructure>

Models

View models at:

edit table

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:16130773

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947012

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009428

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P66899

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G7490

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13054

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947012

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004053

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2866

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 1.4 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 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 Uo, T et al. (2002) Gene cloning, purification, and characterization of 2,3-diaminopropionate ammonia-lyase from Escherichia coli. Biosci. Biotechnol. Biochem. 66 2639-44 PubMed
  6. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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