speE:Gene Product(s): Difference between revisions

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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
spermidine synthase (putrescine aminopropyltransferase)<ref name='LIB:Riley_2006'/>, B0121<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, SpeE<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''spermidine synthase (putrescine aminopropyltransferase)<ref name='LIB:Riley_2006'/>, B0121<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, SpeE<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK0120, JW0117, b0121''
|-
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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=2.5.1.16 2.5.1.16]<ref name='LIB:Riley_2006'/>
* [http://www.brenda-enzymes.info/php/result_flat.php4?ecno=2.5.1.16 2.5.1.16]<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:0016740
GO:0005737
|
|
transferase activity
cytoplasm
|
|
GO_REF:0000004
 
|
|
IEA: Inferred from Electronic Annotation
 
|
|
SP_KW:KW-0808
 
|
|
F
C
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.
|
|
complete
Missing: evidence, reference
|-  
|-  
|
|


|
|
GO:0008295
GO:0003824
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|
spermidine biosynthetic process
catalytic activity
|
|
GO_REF:0000004<br />GO_REF:0000020
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0745<br />HAMAP:MF_00198
InterPro:IPR001045
|
|
P
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
GO:0006596
GO:0004766
|
|
polyamine biosynthetic process
spermidine synthase activity
|
|
GO_REF:0000004
GOA:hamap<br />GO_REF:0000020
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0620
HAMAP:MF_00198
|
|
P
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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spermidine synthase activity
spermidine synthase activity
|
|
GO_REF:0000003<br />GO_REF:0000020
GOA:spec<br />GO_REF:0000003
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
EC:2.5.1.16<br />HAMAP:MF_00198
EC:2.5.1.16
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0005829
|
cytosol
|
PMID:16858726
|
IDA: Inferred from Direct Assay
|
 
|
C
|
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
|
GO:0003824
GO:0006596
|
|
catalytic activity
polyamine biosynthetic process
|
|
GO_REF:0000002
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR001045
SP_KW:KW-0620
|
|
F
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
|-  
|-  
|
|
 
|
|
GO:0005737
GO:0008295
|
|
cytoplasm
spermidine biosynthetic process
|
|
GOA:hamap<br />GO_REF:0000020
|
|
IEA: Inferred from Electronic Annotation
|
|
HAMAP:MF_00198
|
|
C
P
|
|
Seeded from Riley et  al 2006 <ref name='LIB:Riley_2006'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
|-  
|-  
|
|


|
|
GO:0005829
GO:0008295
|
spermidine biosynthetic process
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GOA:spkw<br />SP_KW:GO_REF:0000004
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IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0745
|
|
cytosol
P
|
|
PMID:16858726
Seeded from [[EcoCyc]] (v14.0)
|
|
IDA: Inferred from Direct Assay
complete
|-
|
|


|
|
C
GO:0016740
|
transferase activity
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0808
|
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
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-1135645<br />  
Experiment(s):EBI-1135645<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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CLNPGGIFVA QNGVCFLQQE EAIDSHRKLS HYFSDVGFYQ AAIPTYYGGI MTFAWATDND
CLNPGGIFVA QNGVCFLQQE EAIDSHRKLS HYFSDVGFYQ AAIPTYYGGI MTFAWATDND
ALRHLSTEII QARFLASGLK CRYYNPAIHT AAFALPQYLQ DALASQPS</pre>  
ALRHLSTEII QARFLASGLK CRYYNPAIHT AAFALPQYLQ DALASQPS</pre>  
|-
!align=left {{table heading style}} |Length
||
288
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
32.32 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
32.32 kDa
|-
|-
!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
5.65<ref name='LIB:EcoCyc10.6'/>
5.5 (calculated)
|-
|-
!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
30370 - 31120 (calc based on 13 Y, 2 W, and 6 C residues)  
30,370 - 31,120 (calc based on 13 Y, 2 W, and 6 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}}
|- {{table heading style}}
!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-
|
Initiator Methionine
|
1
|
Removed
|
[http://www.uniprot.org/uniprot/P09158#section_features UniProt:P09158]
|
|-
|
Domain
|
3..247
|
[http://pfam.janelia.org/family/PF01564 PF01564  Spermine/spermidine synthase]
|


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PMID:19920124
 
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<td>
<!-- motifs column 2-->
<motif_map/>
</td>
</tr>
</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>speE
<beststructure>
562</beststructure>
gene=speE
 
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=speE&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P09158 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=speE&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P09158 PSI-PRED (P09158)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P09158 Genomes TO Protein (P09158)] (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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|- {{table_heading_style}}
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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/16128114 GI:16128114]
|
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_414663.1 GeneID:947726]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0000418
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=SPERMIDINESYN-MONOMER EcoCyc:SPERMIDINESYN-MONOMER]
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P09158 UniProtKB/Swiss-Prot:P09158]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
EcoCyc:EG10963
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
[[EcoGene]]
|
|
[[uniprot:P09158|UniProt:P09158]]
EcoGene:EG10963
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[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=PF01564 PFAM:PF01564]
[http://www.ncbi.nlm.nih.gov/gene?term=947726 GeneID:947726]
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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_414663 RefSeq:NP_414663]
RegulonDB:ECK120000952
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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=P09158 ModBase:P09158]
EchoBASE:EB0956
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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==References==
==References==
{{BacktoTop}}
{{BacktoTop}}
 
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</noinclude>
===Categories===
===Categories===
{{BacktoTop}}
{{BacktoTop}}
[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0005737_!_cytoplasm]][[Category:GO:0006596_!_polyamine biosynthetic process]][[Category:Complex:spermidine synthase]]

Latest revision as of 20:21, 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

SpeE

Synonyms

spermidine synthase (putrescine aminopropyltransferase)[1], B0121[2][1], SpeE[2][1] , ECK0120, JW0117, b0121

Product description

SpeE[2][3];

Component of spermidine synthase[2][3]

Spermidine synthase[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:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001045

F

Seeded from EcoCyc (v14.0)

complete

GO:0004766

spermidine synthase activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00198

F

Seeded from EcoCyc (v14.0)

complete

GO:0004766

spermidine synthase activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:2.5.1.16

F

Seeded from EcoCyc (v14.0)

complete

GO:0005829

cytosol

PMID:16858726[5]

IDA: Inferred from Direct Assay

C

Seeded from EcoCyc (v14.0)

complete

GO:0006596

polyamine biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0620

P

Seeded from EcoCyc (v14.0)

complete

GO:0008295

spermidine biosynthetic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_00198

P

Seeded from EcoCyc (v14.0)

complete

GO:0008295

spermidine biosynthetic process

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0745

P

Seeded from EcoCyc (v14.0)

complete

GO:0016740

transferase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0808

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

Subunits of spermidine synthase

could be indirect

Protein

argS

PMID:16606699[6]

Experiment(s):EBI-1135645

Protein

rpsL

PMID:16606699[6]

Experiment(s):EBI-1135645

Protein

yacL

PMID:16606699[6]

Experiment(s):EBI-1135645

Protein

evgA

PMID:16606699[6]

Experiment(s):EBI-1135645

Protein

nrdI

PMID:16606699[6]

Experiment(s):EBI-1135645

Protein

groL

PMID:16606699[6]

Experiment(s):EBI-1135645

Protein

yedD

PMID:16606699[6]

Experiment(s):EBI-1135645

Protein

cueO

PMID:16606699[6]

Experiment(s):EBI-1135645

Protein

uspG

PMID:16606699[6]

Experiment(s):EBI-1135645

Protein

rplN

PMID:16606699[6]

Experiment(s):EBI-1135645
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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 

MAEKKQWHET LHDQFGQYFA VDNVLYHEKT DHQDLIIFEN AAFGRVMALD GVVQTTERDE
FIYHEMMTHV PLLAHGHAKH VLIIGGGDGA MLREVTRHKN VESITMVEID AGVVSFCRQY
LPNHNAGSYD DPRFKLVIDD GVNFVNQTSQ TFDVIISDCT DPIGPGESLF TSAFYEGCKR
CLNPGGIFVA QNGVCFLQQE EAIDSHRKLS HYFSDVGFYQ AAIPTYYGGI MTFAWATDND
ALRHLSTEII QARFLASGLK CRYYNPAIHT AAFALPQYLQ DALASQPS
Length

288

Mol. Wt

32.32 kDa

pI

5.5 (calculated)

Extinction coefficient

30,370 - 31,120 (calc based on 13 Y, 2 W, and 6 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:P09158

Domain

3..247

PF01564 Spermine/spermidine synthase

PMID:19920124[7]

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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=speE 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:16128114

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947726

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000418

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P09158

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG10963

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10963

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947726

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000952

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0956

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 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. ↑ 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. ↑ Lasserre, JP et al. (2006) A complexomic study of Escherichia coli using two-dimensional blue native/SDS polyacrylamide gel electrophoresis. Electrophoresis 27 3306-21 PubMed
  6. ↑ 6.00 6.01 6.02 6.03 6.04 6.05 6.06 6.07 6.08 6.09 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  7. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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