icd:Gene Product(s): Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older edit
/Volumes/r3/t3/ul/phpwikibots/trunk/touch_all_product_tables.php
touch table
 
(6 intermediate revisions by 2 users not shown)
Line 44: Line 44:
!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
e14 prophage; isocitrate dehydrogenase, specific for NADP+<ref name='LIB:Riley_2006'/>, B1136<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Icd<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, IcdE<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, IcdA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''e14 prophage; isocitrate dehydrogenase, specific for NADP+<ref name='LIB:Riley_2006'/>, B1136<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Icd<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, IcdE<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, IcdA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK1122, icdA, icdE, JW1122, b1136''
|-
|-
!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
Line 77: Line 77:
*  
*  
****************************************************************************************** -->{{Product_GO_help}}
****************************************************************************************** -->{{Product_GO_help}}
{| {{Prettytable}} id="Z46aa58e4767b5"  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="Z46aa58e4767b5"  class=" tableEdit GO_table_product dataTable"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Qualifier!!GO ID!!GO term name!!Reference!!Evidence Code!!with/from!!Aspect!!Notes!!Status
!|Qualifier!!GO ID!!GO term name!!Reference!!Evidence Code!!with/from!!Aspect!!Notes!!Status
Line 479: Line 479:


|
|
complete
Missing: reference
|-  
|-  
|
|
Line 551: Line 551:
*  
*  
****************************************************************************************** -->{{Product_interactions_help}}
****************************************************************************************** -->{{Product_interactions_help}}
{|   id="M46aa58f31fc83"  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="M46aa58f31fc83"  class=" tableEdit Product_interactions_table dataTable"   
|- {{table heading style}}
|- {{table heading style}}
!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
Line 627: Line 627:
*  
*  
****************************************************************************************** -->{{Product_localization_help}}
****************************************************************************************** -->{{Product_localization_help}}
{|   id="E46a7ebe18453c"  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="E46a7ebe18453c"  class=" tableEdit Product_localization_table"   
|- {{table heading style}}
|- {{table heading style}}
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
Line 701: Line 701:
*  
*  
****************************************************************************************** -->{{Product_domains_motifs_help}}
****************************************************************************************** -->{{Product_domains_motifs_help}}
{|   id="T46aa58f59edb0"  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="T46aa58f59edb0"  class=" tableEdit Product_motif_table dataTable"   
|- {{table heading style}}
|- {{table heading style}}
!|Type!!Residues!!Description!!Notes!!References
!|Type!!Residues!!Description!!Notes!!References
Line 762: Line 762:
View models at:
View models at:
* [http://www.proteinmodelportal.org/query/uniprot/P08200 Protein Model Portal]
* [http://www.proteinmodelportal.org/query/uniprot/P08200 Protein Model Portal]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P08200 PSI-PRED (P08200)]
* [http://spock.genes.nig.ac.jp/~genome/search.html Genomes TO Protein] (GTOP)
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P08200 Genomes TO Protein (P08200)] (GTOP)


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 804: Line 804:
*  
*  
****************************************************************************************** -->{{Product_resources_help}}
****************************************************************************************** -->{{Product_resources_help}}
{|   id="P46aa590ed0838"  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="P46aa590ed0838"  class=" tableEdit Product_resource_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Resource type!!Source!!Notes/Reference
!|Resource type!!Source!!Notes/Reference
Line 826: Line 826:
*  
*  
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|   id="A46aa590f2996e"  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="A46aa590f2996e"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|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/16129099 GI:16129099]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=ISOCITDEH-SUBUNIT EcoCyc:ISOCITDEH-SUBUNIT]
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
|
[http://www.ncbi.nlm.nih.gov/protein/NP_415654.1 GeneID:945702]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0003823
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P08200 UniProtKB/Swiss-Prot:P08200]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
EcoCyc:EG10489
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EcoGene]]
|
EcoGene:EG10489
|
''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]])
|
|
[http://www.uniprot.org/uniprot/P08200 UniProt:P08200]
[http://www.ncbi.nlm.nih.gov/gene?term=945702 GeneID:945702]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://pfam.janelia.org/protein/P08200 Pfam:P08200]
RegulonDB:ECK120000482
|
|
''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_415654 RefSeq:NP_415654]
EchoBASE:EB0484
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 876: Line 911:
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|   id="Y46a7ec0601cf4"  class=" tableEdit Links_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Y46a7ec0601cf4"  class=" tableEdit Links_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:35, 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

Icd

Synonyms

e14 prophage; isocitrate dehydrogenase, specific for NADP+[1], B1136[2][1], Icd[2][1], IcdE[2][1], IcdA[2][1] , ECK1122, icdA, icdE, JW1122, b1136

Product description

Icd[2][3];

Component of isocitrate dehydrogenase[2][3]

Isocitrate dehydrogenase, NADP+-specific; e14 attachment site[4]

EC number (for enzymes)
edit table


Notes

Function

[back to top]


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:0000287

magnesium ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001804

F

Seeded from EcoCyc (v14.0)

complete

GO:0000287

magnesium ion binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019818

F

Seeded from EcoCyc (v14.0)

complete

GO:0000287

magnesium ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0460

F

Seeded from EcoCyc (v14.0)

complete

GO:0004450

isocitrate dehydrogenase (NADP+) activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004439

F

Seeded from EcoCyc (v14.0)

complete

GO:0004450

isocitrate dehydrogenase (NADP+) activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:1.1.1.42

F

Seeded from EcoCyc (v14.0)

complete

GO:0006099

tricarboxylic acid cycle

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004439

P

Seeded from EcoCyc (v14.0)

complete

GO:0006099

tricarboxylic acid cycle

PMID:4932752[5]

IDA: Inferred from Direct Assay

P

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:0016616

oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001804

F

Seeded from EcoCyc (v14.0)

complete

GO:0016616

oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019818

F

Seeded from EcoCyc (v14.0)

complete

GO:0022900

electron transport chain

PMID:776950[6] PMID:15221231[7]

IMP: Inferred from Mutant Phenotype

P

complete

GO:0030145

manganese ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0464

F

Seeded from EcoCyc (v14.0)

complete

GO:0046872

metal ion binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0479

F

Seeded from EcoCyc (v14.0)

complete

GO:0051287

NAD or NADH binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001804

F

Seeded from EcoCyc (v14.0)

complete

GO:0051287

NAD or NADH binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019818

F

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001804

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004439

P

Seeded from EcoCyc (v14.0)

complete

GO:0055114

oxidation reduction

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR019818

P

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

GO:0004450

isocitrate dehydrogenase (NADP+) activity

PMID 3112144

IDA: Inferred from Direct Assay

F

Missing: reference

GO:0005737

cytoplasm

PMID:34215[8]

IDA: Inferred from Direct Assay

C

complete

GO:0006097

glyoxylate cycle

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0329

P

Seeded from EcoCyc (v14.0)

complete

GO:0006099

tricarboxylic acid cycle

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0816

P

Seeded from EcoCyc (v14.0)

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 isocitrate dehydrogenase

could be indirect

Protein

yneG

PMID:16606699[9]

Experiment(s):EBI-1138992

Protein

yibL

PMID:16606699[9]

Experiment(s):EBI-1138992

Protein

yfdS

PMID:16606699[9]

Experiment(s):EBI-1138992

Protein

nadE

PMID:16606699[9]

Experiment(s):EBI-1138992
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

[back to top]


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 

MESKVVVPAQ GKKITLQNGK LNVPENPIIP YIEGDGIGVD VTPAMLKVVD AAVEKAYKGE
RKISWMEIYT GEKSTQVYGQ DVWLPAETLD LIREYRVAIK GPLTTPVGGG IRSLNVALRQ
ELDLYICLRP VRYYQGTPSP VKHPELTDMV IFRENSEDIY AGIEWKADSA DAEKVIKFLR
EEMGVKKIRF PEHCGIGIKP CSEEGTKRLV RAAIEYAIAN DRDSVTLVHK GNIMKFTEGA
FKDWGYQLAR EEFGGELIDG GPWLKVKNPN TGKEIVIKDV IADAFLQQIL LRPAEYDVIA
CMNLNGDYIS DALAAQVGGI GIAPGANIGD ECALFEATHG TAPKYAGQDK VNPGSIILSA
EMMLRHMGWT EAADLIVKGM EGAINAKTVT YDFERLMDGA KLLKCSEFGD AIIENM
Length

416

Mol. Wt

45.757 kDa

pI

5.0 (calculated)

Extinction coefficient

55,350 - 56,100 (calc based on 15 Y, 6 W, and 6 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

Modification Site

113

phosphorylation site at S113

probability greater than 75%

PMID:17938405[10]

Domain

28..412

PF00180 Isocitrate/isopropylmalate dehydrogenase

PMID:19920124[11]

edit table

<motif_map/>

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

Structures

<beststructure> gene=icd 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:16129099

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945702

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003823

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P08200

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10489

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10489

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945702

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000482

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0484

Escherichia coli str. K-12 substr. MG1655

edit table


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 1.4 1.5 1.6 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 2.4 2.5 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. ↑ Holms, WH & Bennett, PM (1971) Regulation of isocitrate dehydrogenase activity in Escherichia coli on adaptation to acetate. J. Gen. Microbiol. 65 57-68 PubMed
  6. ↑ Lakshmi, TM & Helling, RB (1976) Selection for citrate synthase deficiency in icd mutants of Escherichia coli. J. Bacteriol. 127 76-83 PubMed
  7. ↑ Kabir, MM & Shimizu, K (2004) Metabolic regulation analysis of icd-gene knockout Escherichia coli based on 2D electrophoresis with MALDI-TOF mass spectrometry and enzyme activity measurements. Appl. Microbiol. Biotechnol. 65 84-96 PubMed
  8. ↑ Garnak, M & Reeves, HC (1979) Phosphorylation of Isocitrate dehydrogenase of Escherichia coli. Science 203 1111-2 PubMed
  9. ↑ 9.0 9.1 9.2 9.3 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  10. ↑ Macek, B et al. (2008) Phosphoproteome analysis of E. coli reveals evolutionary conservation of bacterial Ser/Thr/Tyr phosphorylation. Mol. Cell Proteomics 7 299-307 PubMed
  11. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

[back to top]


Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=icd:Gene_Product(s)&oldid=1493101"