caiD:Gene Product(s): Difference between revisions

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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
crotonobetainyl CoA hydratase<ref name='LIB:Riley_2006'/>, B0036<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YaaL<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, CaiD<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''crotonobetainyl CoA hydratase<ref name='LIB:Riley_2006'/>, B0036<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YaaL<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, CaiD<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK0037, JW0035, yaaL, b0036''
|-
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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=4.2.1.- 4.2.1.-]<ref name='LIB:Riley_2006'/>
* [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=4.2.1.- 4.2.1.-]<ref name='LIB:Riley_2006'/>


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|- {{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:0008152
GO:0005737
|
|
metabolic process
cytoplasm
|
|
GO_REF:0000002
 
|
|
IEA: Inferred from Electronic Annotation
 
|
|
InterPro:IPR001753
 
|
|
P
C
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.
|
|
complete
Missing: evidence, reference
|-  
|-  
|
|


|
|
GO:0003824
GO:0009310
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|
catalytic activity
amine catabolic process
|
|
GO_REF:0000002
 
|
|
IEA: Inferred from Electronic Annotation
 
|
|
InterPro:IPR001753
 
|
|
F
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.
|
|
complete
Missing: evidence, reference
|-  
|-  
|
|


|
|
GO:0016829
GO:0003824
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|
lyase activity
catalytic activity
|
|
GO_REF:0000004
GOA:interpro<br />GO_REF:0000002
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|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0456
InterPro:IPR001753
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
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GO:0016836
GO:0003824
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|
hydro-lyase activity
catalytic activity
|
|
GO_REF:0000020
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
HAMAP:MF_01051
InterPro:IPR018376
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
|-
|
|
GO:0005737
|
cytoplasm
|
|
|
|
C
|
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.
|
required fields missing 
|-  
|-  
|
|


|
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GO:0003824
GO:0008152
|
|
catalytic activity
metabolic process
|
|
GO_REF:0000002
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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InterPro:IPR001753
InterPro:IPR001753
|
|
F
P
|
|
Seeded from EcoCyc
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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metabolic process
metabolic process
|
|
GO_REF:0000002
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR001753
InterPro:IPR018376
|
|
P
P
|
|
Seeded from EcoCyc
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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lyase activity
lyase activity
|
|
GO_REF:0000004
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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F
F
|
|
Seeded from EcoCyc
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
|-  
|-  
|
|
 
|
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GO:0009310
GO:0016836
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amine catabolic process
hydro-lyase activity
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|
GOA:hamap<br />GO_REF:0000020
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IEA: Inferred from Electronic Annotation
|
|
HAMAP:MF_01051
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|
P
F
|
|
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
|-  
|-  
|
|
 
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GO:0042413
GO:0008809
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carnitine catabolic process
carnitine racemase activity
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PMID:7815937
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EXP: Inferred from Experiment
|
|
 
|
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P
F
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
 
|
|
required fields missing 
complete
|-  
|-  
|
|


|
|
GO:0016836
GO:0042413
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|
hydro-lyase activity
carnitine catabolic process
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|
GO_REF:0000020<br />PMID:11551212
PMID:7815937
|
|
ISS: Inferred from Sequence or Structural Similarity
EXP: Inferred from Experiment
|
|
HAMAP:MF_01051<br />
 
|
|
F
P
|
|
Seeded from EcoCyc
 
|
|
complete  
complete  


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!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
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Experiment(s):EBI-1135386<br />  
Experiment(s):EBI-1135386<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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!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
32.31 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
32.311 kDa
|-
|-
!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
6.2 (calculated)
|-
|-
!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
30940 - 31065 (calc based on 6 Y, 4 W, and 1 C residues)  
30,940 - 31,065 (calc based on 6 Y, 4 W, and 1 C residues)


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|- {{table heading style}}
|- {{table heading style}}
!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-
|
Initiator Methionine
|
1
|
Removed
|
[http://www.uniprot.org/uniprot/P31551#section_features UniProt:P31551]
|
|-
|
Domain
|
14..181
|
[http://pfam.janelia.org/family/PF00378 PF00378  Enoyl-CoA hydratase/isomerase family]
|


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PMID:19920124
 
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</table>
</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>caiD
<beststructure>
562</beststructure>
gene=caiD
 
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=caiD&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P31551 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=caiD&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P31551 PSI-PRED (P31551)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P31551 Genomes TO Protein (P31551)] (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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</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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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Y46aa170338fc8"  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/221800779 GI:221800779]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0000130
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P31551 UniProtKB/Swiss-Prot:P31551]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
EcoCyc:EG11557
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EcoGene]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=CARNRACE-MONOMER EcoCyc:CARNRACE-MONOMER]
EcoGene:EG11557
|
|
''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:P31551|UniProt:P31551]]
[http://www.ncbi.nlm.nih.gov/gene?term=948995 GeneID:948995]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://pfam.sanger.ac.uk/family?acc=PF00378 PFAM:PF00378]
RegulonDB:ECK120001510
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|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/entrez/viewer.fcgi?db=nucleotide&val=NP_414578 RefSeq:NP_414578]
[http://www.ncbi.nlm.nig.gov/protein/Array GeneID:948995]
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Escherichia coli str. K-12 substr. 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=P31551 ModBase:P31551]
EchoBASE:EB1518
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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==References==
==References==
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===Categories===
===Categories===
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[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0005737_!_cytoplasm]][[Category:GO:0009310_!_amine catabolic process]][[Category:GO:0042413_!_carnitine catabolic process]]

Latest revision as of 20:19, 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

CaiD

Synonyms

crotonobetainyl CoA hydratase[1], B0036[2][1], YaaL[2][1], CaiD[2][1] , ECK0037, JW0035, yaaL, b0036

Product description

Carnitine racemase[3]

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:0009310

amine catabolic process

P

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:IPR001753

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018376

F

Seeded from EcoCyc (v14.0)

complete

GO:0008152

metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001753

P

Seeded from EcoCyc (v14.0)

complete

GO:0008152

metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR018376

P

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:0016836

hydro-lyase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01051

F

Seeded from EcoCyc (v14.0)

complete

GO:0008809

carnitine racemase activity

PMID:7815937[4]

EXP: Inferred from Experiment

F

complete

GO:0042413

carnitine catabolic process

PMID:7815937[4]

EXP: Inferred from Experiment

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

truA

PMID:16606699[5]

Experiment(s):EBI-1135386

Protein

sdhA

PMID:16606699[5]

Experiment(s):EBI-1135386

Protein

groL

PMID:16606699[5]

Experiment(s):EBI-1135386

Protein

dnaK

PMID:16606699[5]

Experiment(s):EBI-1135386
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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 

MKQQGTTLPA NNHTLKQYAF FAGMLSSLKK QKWRKGMSES LHLTRNGSIL EITLDRPKAN
AIDAKTSFEM GEVFLNFRDD PQLRVAIITG AGEKFFSAGW DLKAAAEGEA PDADFGPGGF
AGLTEIFNLD KPVIAAVNGY AFGGGFELAL AADFIVCADN ASFALPEAKL GIVPDSGGVL
RLPKILPPAI VNEMVMTGRR MGAEEALRWG IVNRVVSQAE LMDNARELAQ QLVNSAPLAI
AALKEIYRTT SEMPVEEAYR YIRSGVLKHY PSVLHSEDAI EGPLAFAEKR DPVWKGR
Length

297

Mol. Wt

32.311 kDa

pI

6.2 (calculated)

Extinction coefficient

30,940 - 31,065 (calc based on 6 Y, 4 W, and 1 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

Initiator Methionine

1

Removed

UniProt:P31551

Domain

14..181

PF00378 Enoyl-CoA hydratase/isomerase family

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=caiD 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:221800779

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000130

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P31551

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11557

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11557

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:948995

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001510

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:948995

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1518

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 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 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  4. ↑ 4.0 4.1 Eichler, K et al. (1994) Molecular characterization of the cai operon necessary for carnitine metabolism in Escherichia coli. Mol. Microbiol. 13 775-86 PubMed
  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. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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