ygeX:Gene Product(s): Difference between revisions

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)	4.3.1.15^[1]
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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: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
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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	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)
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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	39..377	PF00291 Pyridoxal-phosphate dependent enzyme		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=ygeX 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: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
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^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)
↑ ^2.0 ^2.1 ^2.2 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^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
↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

ygeX:Gene Product(s): Difference between revisions

Latest revision as of 20:56, 17 February 2015

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

References

Categories

Navigation menu

@@ Line 35: / Line 35: @@
 *
 ****************************************************************************************** -->{{Product_nomenclature_help}}
-{|  id="M46aac3bfbe32c"  class=" tableEdit Product_nomenclature_table"
+{|   id="M46aac3bfbe32c"  class=" tableEdit Product_nomenclature_table"
 |-
@@ Line 44: / Line 44: @@
 !align=left {{table heading style}} |Synonyms
 ||
-,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''
 |-
 !align=left {{table heading style}} |Product description
@@ Line 77: / Line 77: @@
 *
 ****************************************************************************************** -->{{Product_GO_help}}
-{|   id="L46aac3c136356"  class=" tableEdit GO_table_product dataTable"
+{| 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}}
-!|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:0016829
+GO:0005737
+|
+cytoplasm
+|
 |
-lyase activity
 |
-GO_REF:0000004
+|
+C
+|
+Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.
+|
+Missing: evidence, reference
+|-
+|
+|
+GO:0003824
+|
+catalytic activity
+|
+GOA:interpro<br />GO_REF:0000002
 |
 IEA: Inferred from Electronic Annotation
 |
-SP_KW:KW-0456
+InterPro:IPR001926
 |
 F
 |
-Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 103: / Line 122: @@
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-GO:0030170
+GO:0008152
 |
-pyridoxal phosphate binding
+metabolic process
 |
-GO_REF:0000002
+GOA:interpro<br />GO_REF:0000002
 |
 IEA: Inferred from Electronic Annotation
@@ Line 113: / Line 132: @@
 InterPro:IPR001926
 |
-F
+P
 |
-Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 126: / Line 145: @@
 diaminopropionate ammonia-lyase activity
 |
-GO_REF:0000003
+GOA:interpro<br />GO_REF:0000002
 |
 IEA: Inferred from Electronic Annotation
 |
-EC:4.3.1.15
+InterPro:IPR010081
 |
 F
 |
-Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 141: / Line 160: @@
 |
-GO:0008152
+GO:0008838
 |
-metabolic process
+diaminopropionate ammonia-lyase activity
 |
-GO_REF:0000002
+GOA:spec<br />GO_REF:0000003
 |
 IEA: Inferred from Electronic Annotation
 |
-InterPro:IPR001926
+EC:4.3.1.15
 |
-P
+F
 |
-Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 160: / Line 179: @@
 |
-GO:0003824
+GO:0030170
 |
-catalytic activity
+pyridoxal phosphate binding
 |
-GO_REF:0000002
+GOA:interpro<br />GO_REF:0000002
 |
 IEA: Inferred from Electronic Annotation
@@ Line 172: / Line 191: @@
 F
 |
-Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
 |-
 |
 |
-GO:0005737
+GO:0030170
 |
-cytoplasm
+pyridoxal phosphate binding
 |
+GOA:interpro<br />GO_REF:0000002
 |
+IEA: Inferred from Electronic Annotation
 |
+InterPro:IPR010081
 |
-C
+F
 |
-Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.
+Seeded from [[EcoCyc]] (v14.0)
 |
-required fields missing
+complete
 |-
 |
@@ Line 248: / Line 267: @@
 *
 ****************************************************************************************** -->{{Product_interactions_help}}
-{|   id="A46aac3c709aa8"  class=" tableEdit Product_interactions_table dataTable"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="A46aac3c709aa8"  class=" tableEdit Product_interactions_table dataTable"
 |- {{table heading style}}
 !|Partner Type!!Partner!!Notes!!References!!Evidence
@@ Line 280: / Line 299: @@
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 ****************************************************************************************** -->{{Product_localization_help}}
-{|   id="F46a859b21ddb0"  class=" tableEdit Product_localization_table"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="F46a859b21ddb0"  class=" tableEdit Product_localization_table"
 |- {{table heading style}}
-!|Compartment!!Description!!Evidence!!Source!!Notes
+!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
 |- class="tableEdit_footer"
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 ****************************************************************************************** -->{{Product_physical_properties_help}}
-{|  id="X46aac3c96b824"  class=" tableEdit Product_phys_prop_table"
+{|   id="X46aac3c96b824"  class=" tableEdit Product_phys_prop_table"
+|-
+!align=left {{table heading style}} |Name
+||
 |-
@@ Line 350: / Line 373: @@
 *
 ****************************************************************************************** -->{{Product_domains_motifs_help}}
-{|   id="O46aac3c9db8ee"  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="O46aac3c9db8ee"  class=" tableEdit Product_motif_table dataTable"
 |- {{table heading style}}
 !|Type!!Residues!!Description!!Notes!!References
+|-
+|
+Domain
+|
+..377
+|
+[http://pfam.janelia.org/family/PF00291 PF00291  Pyridoxal-phosphate dependent enzyme]
+|
+|
+PMID:19920124
 |- class="tableEdit_footer"
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 ****************************************************************************************** -->{{Product_structure_help}}
-{|  id="Z46a859b3b1ae1"  class=" tableEdit Product_structure_table"
+{|   id="Z46a859b3b1ae1"  class=" tableEdit Product_structure_table"
 |-
@@ Line 388: / Line 422: @@
 ||
 View models at:
-* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=recA 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=recA&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)
 |- class="tableEdit_footer"
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 *
 ****************************************************************************************** -->{{Product_resources_help}}
-{|   id="O46aac3caa6521"  class=" tableEdit Product_resource_table"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O46aac3caa6521"  class=" tableEdit Product_resource_table"
 |- {{table_heading_style}}
 !|Resource type!!Source!!Notes/Reference
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 ****************************************************************************************** -->{{Gene_accessions_help}}
-{|   id="S46aac3cb11345"  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="S46aac3cb11345"  class=" tableEdit Gene_accessions_table"
 |- {{table_heading_style}}
 !|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/16130773 GI:16130773]
+|
+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_417347.1 GeneID:947012]
+|
+Escherichia coli str. K-12 substr. MG1655
+|-
+|
+[[ASAP]]
 |
-[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7490-MONOMER EcoCyc:G7490-MONOMER]
+ASAP:ABE-0009428
 |
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
+|-
+|
+[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
+|
+[http://www.uniprot.org/uniprot/P66899 UniProtKB/Swiss-Prot:P66899]
+|
+Escherichia coli str. K-12 substr. MG1655
+|-
+|
+[[EcoCyc]]
+|
+EcoCyc:G7490
+|
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
+|-
+|
+[[EcoGene]]
+|
+EcoGene:EG13054
+|
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
 |-
 |
-[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
+[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
 |
-[[uniprot:P66899|UniProt:P66899]]
+[http://www.ncbi.nlm.nih.gov/gene?term=947012 GeneID:947012]
 |
+Escherichia coli str. K-12 substr. MG1655
 |-
 |
-[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
+[[RegulonDB]]
 |
-[http://pfam.sanger.ac.uk/family?acc=PF00291 PFAM:PF00291]
+RegulonDB:ECK120004053
 |
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
 |-
 |
-[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
+[[EchoBASE]]
 |
-[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_417347 RefSeq:NP_417347]
+EchoBASE:EB2866
 |
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
 |- class="tableEdit_footer"
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 *
 ****************************************************************************************** -->
-{|   id="E46a859b735198"  class=" tableEdit Links_table"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="E46a859b735198"  class=" tableEdit Links_table"
 |- {{table_heading_style}}
 !|Name!!URL!!Comments
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 {{BacktoTop}}
 [[Category:Proteins]]
-[[Category:GO:0005737_!_cytoplasm]][[Category:GO:0008152_!_metabolic process]][[Category:Complex:2,3-diaminopropionate ammonia-lyase]]
 [[Category:RefGenome_Annotated_Gene]]

ygeX:Gene Product(s): Difference between revisions

Latest revision as of 20:56, 17 February 2015

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

References

Categories

Navigation menu

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