selU:Gene Product(s): Difference between revisions

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{{Tab|Quickview|ybbB}}{{Tab|Gene|ybbB}}{{Tab On|Gene Product(s)|ybbB}}{{Tab|Expression|ybbB}}{{Tab|Evolution|ybbB}}{{Tab|On One Page|ybbB}}{{TabsBottom}}
{{Tab|Quickview|selU}}{{Tab|Gene|selU}}{{Tab On|Gene Product(s)|selU}}{{Tab|Expression|selU}}{{Tab|Evolution|selU}}{{Tab|On One Page|selU}}{{TabsBottom}}
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|-
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!align=left {{table heading style}} |Standard name
!align=left {{table heading style}} |Standard name
||
||
YbbB
SelU
|-
|-
!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
tRNA 2-selenouridine synthase, selenophosphate-dependent<ref name='LIB:Riley_2006'/>, B0503<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YbbB<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''tRNA 2-selenouridine synthase, selenophosphate-dependent<ref name='LIB:Riley_2006'/>, B0503<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YbbB<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK0496, JW0491, selE, ybbB, b0503''
|-
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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{|   id="E46aa337ecd7d4" class=" tableEdit GO_table_product dataTable"   
|- {{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:0016785
GO:0001887
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|
transferase activity, transferring selenium-containing groups
selenium metabolic process
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|
GO_REF:0000020
GOA:hamap<br />GO_REF:0000020
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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HAMAP:MF_01622
HAMAP:MF_01622
|
|
F
P
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
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|
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GO:0016740
GO:0001887
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|
transferase activity
selenium metabolic process
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GO_REF:0000004
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0808
InterPro:IPR017582
|
|
F
P
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
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complete  
complete  
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selenium binding
selenium binding
|
|
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-0711
InterPro:IPR017582
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
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complete  
complete  
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|
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GO:0001887
GO:0008430
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selenium metabolic process
selenium binding
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GO_REF:0000020
GOA:spkw<br />SP_KW:GO_REF:0000004
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IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
HAMAP:MF_01622
SP_KW:KW-0711
|
|
P
F
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
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complete
|-
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GO:0006399
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tRNA metabolic process
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|
|
|
P
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
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required fields missing 
|-
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GO:0002098
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tRNA wobble uridine modification
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PMID:14594807
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IMP: Inferred from Mutant Phenotype
|
 
|
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
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complete  
complete  
|-
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GO:0009451
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RNA modification
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|
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|
P
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
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required fields missing 


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!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence


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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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VVEDPFEIRL ERLNEEYFLR MHHDFTHAYG DEQGWQEYCE YLHHGLSAIK RRLGLQRYNE
VVEDPFEIRL ERLNEEYFLR MHHDFTHAYG DEQGWQEYCE YLHHGLSAIK RRLGLQRYNE
LAARLDAALT TQLTTGSTDG HLAWLVPLLE EYYDPMYRYQ LEKKAEKVVF RGEWAEVAEW VKAR</pre>  
LAARLDAALT TQLTTGSTDG HLAWLVPLLE EYYDPMYRYQ LEKKAEKVVF RGEWAEVAEW VKAR</pre>  
|-
!align=left {{table heading style}} |Length
||
364
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
41.11 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
41.11 kDa
|-
|-
!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
6.3 (calculated)
|-
|-
!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
57870 - 58745 (calc based on 13 Y, 7 W, and 7 C residues)  
57,870 - 58,745 (calc based on 13 Y, 7 W, and 7 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}}
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!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-
|
Domain
|
6..131
|
[http://pfam.janelia.org/family/PF00581 PF00581  Rhodanese-like domain]
|
 
|
PMID:19920124


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<td>
<!-- motifs column 2-->
<motif_map/>
</td>
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<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>ybbB
<beststructure>
562</beststructure>
gene=ybbB
 
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=ybbB&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P33667 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=ybbB&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P33667 PSI-PRED (P33667)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P33667 Genomes TO Protein (P33667)] (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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!|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/16128487 GI:16128487]
|
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_415036.1 GeneID:947063]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0001740
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P33667 UniProtKB/Swiss-Prot:P33667]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
EcoCyc:EG11768
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11768-MONOMER EcoCyc:EG11768-MONOMER]
[[EcoGene]]
|
|
EcoGene:EG11768
|
''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:P33667|UniProt:P33667]]
[http://www.ncbi.nlm.nih.gov/gene?term=947063 GeneID:947063]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_415036 RefSeq:NP_415036]
RegulonDB:ECK120001704
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://modbase.compbio.ucsf.edu ModBase] ([[ModBase|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://salilab.org/modbase/searchbyid?databaseID=P33667 ModBase:P33667]
EchoBASE:EB1718
|
|
''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:0006399_!_tRNA metabolic process]][[Category:GO:0009451_!_RNA modification]]

Latest revision as of 16:26, 5 October 2013

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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

SelU

Synonyms

tRNA 2-selenouridine synthase, selenophosphate-dependent[1], B0503[2][1], YbbB[2][1] , ECK0496, JW0491, selE, ybbB, b0503

Product description

EG11768[2][3]

tRNA 2-selenouridine synthase, selenophosphate-dependent; replaces a sulfur atom in 2-thiouridine in tRNA with selenium; required for 5-methylaminomethyl-2-selenouridine synthesis[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:0001887

selenium metabolic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01622

P

Seeded from EcoCyc (v14.0)

complete

GO:0001887

selenium metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017582

P

Seeded from EcoCyc (v14.0)

complete

GO:0008430

selenium binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR017582

F

Seeded from EcoCyc (v14.0)

complete

GO:0008430

selenium binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0711

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
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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 

MQERHTEQDY RALLIADTPI IDVRAPIEFE HGAMPAAINL PLMNNDERAA VGTCYKQQGS
DAALALGHKL VAGEIRQQRM DAWRAACLQN PQGILCCARG GQRSHIVQSW LHAAGIDYPL
VEGGYKALRQ TAIQATIELA QKPIVLIGGC TGSGKTLLVQ QQPNGVDLEG LARHRGSAFG
RTLQPQLSQA SFENLLAAEM LKTDARQNLR LWVLEDESRM IGSNHLPECL RERMTQAAIA
VVEDPFEIRL ERLNEEYFLR MHHDFTHAYG DEQGWQEYCE YLHHGLSAIK RRLGLQRYNE
LAARLDAALT TQLTTGSTDG HLAWLVPLLE EYYDPMYRYQ LEKKAEKVVF RGEWAEVAEW VKAR
Length

364

Mol. Wt

41.11 kDa

pI

6.3 (calculated)

Extinction coefficient

57,870 - 58,745 (calc based on 13 Y, 7 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

6..131

PF00581 Rhodanese-like domain

PMID:19920124[5]

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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=ybbB 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:16128487

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:947063

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001740

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P33667

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11768

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11768

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:947063

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001704

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1718

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 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. ↑ 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. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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