yagF:Gene Product(s): Difference between revisions

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Adding "length" to the physical properties table.
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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
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CP4-6 prophage; predicted dehydratase<ref name='LIB:Riley_2006'/>, B0269<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YagF<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''CP4-6 prophage; predicted dehydratase<ref name='LIB:Riley_2006'/>, B0269<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YagF<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK0270, JW0262, b0269''
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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!|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:0003824
|
catalytic activity
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GOA:interpro<br />GO_REF:0000002
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IEA: Inferred from Electronic Annotation
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InterPro:IPR000581
|
F
|
Seeded from [[EcoCyc]] (v14.0)
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complete
|-
|
 
|
GO:0003824
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|
lyase activity
catalytic activity
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GO_REF:0000004
GOA:interpro<br />GO_REF:0000002
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IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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SP_KW:KW-0456
InterPro:IPR020558
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|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
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complete  
complete  
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metabolic process
metabolic process
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GO_REF:0000002
GOA:interpro<br />GO_REF:0000002
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IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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P
P
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
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complete  
complete  
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|
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GO:0003824
GO:0008152
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metabolic process
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GOA:interpro<br />GO_REF:0000002
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IEA: Inferred from Electronic Annotation
|
InterPro:IPR020558
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P
|
Seeded from [[EcoCyc]] (v14.0)
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complete
|-
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|
GO:0016829
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catalytic activity
lyase activity
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GO_REF:0000002
GOA:spkw<br />SP_KW:GO_REF:0000004
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IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
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InterPro:IPR000581
SP_KW:KW-0456
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
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complete  
complete  


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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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!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
69.4 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
69.399 kDa
|-
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!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
6.4 (calculated)
|-
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!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
59930 - 61180 (calc based on 7 Y, 9 W, and 10 C residues)  
59,930 - 61,180 (calc based on 7 Y, 9 W, and 10 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
|-
|
Domain
|
63..635
|
[http://pfam.janelia.org/family/PF00920 PF00920  Dehydratase family]
|
 
|
PMID:19920124


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<td>
<!-- motifs column 2-->
<motif_map/>
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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>yagF
<beststructure>
562</beststructure>
gene=yagF
 
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=yagF&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P77596 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=yagF&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P77596 PSI-PRED (P77596)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P77596 Genomes TO Protein (P77596)] (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://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6141-MONOMER EcoCyc:G6141-MONOMER]
[http://www.ncbi.nlm.nih.gov/protein/16128254 GI:16128254]
|
|
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_414803.1 GeneID:944928]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0000923
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P77596 UniProtKB/Swiss-Prot:P77596]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
EcoCyc:G6141
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EcoGene]]
|
EcoGene:EG13345
|
''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:P77596|UniProt:P77596]]
[http://www.ncbi.nlm.nih.gov/gene?term=944928 GeneID:944928]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://pfam.sanger.ac.uk/family?acc=PF00920 PFAM:PF00920]
RegulonDB:ECK120002761
|
|
''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_414803 RefSeq:NP_414803]
EchoBASE:EB3129
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments


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==References==
==References==
{{BacktoTop}}
{{BacktoTop}}
 
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</noinclude>
===Categories===
===Categories===
{{BacktoTop}}
{{BacktoTop}}
[[Category:Proteins]]
[[Category:Proteins]]
[[Category:Pfam:PF00920_!_Dehydratase family]]

Latest revision as of 20:23, 17 February 2015

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Nomenclature

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Standard name

YagF

Synonyms

CP4-6 prophage; predicted dehydratase[1], B0269[2][1], YagF[2][1] , ECK0270, JW0262, b0269

Product description

putative dehydratase[2]; CP4-6 prophage; predicted dehydratase[3]

Function unknown, CP4-6 putative prophage remnant[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:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000581

F

Seeded from EcoCyc (v14.0)

complete

GO:0003824

catalytic activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020558

F

Seeded from EcoCyc (v14.0)

complete

GO:0008152

metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR000581

P

Seeded from EcoCyc (v14.0)

complete

GO:0008152

metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR020558

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

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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 

MTIEKIFTPQ DDAFYAVITH AAGPQGALPL TPQMLMESPS GNLFGMTQNA GMGWDANKLT
GKEVLIIGTQ GGIRAGDGRP IALGYHTGHW EIGMQMQAAA KEITRNGGIP FAAFVSDPCD
GRSQGTHGMF DSLPYRNDAA IVFRRLIRSL PTRRAVIGVA TCDKGLPATM IALAAMHDLP
TILVPGGATL PPTVGEDAGK VQTIGARFAN HELSLQEAAE LGCRACASPG GGCQFLGTAG
TSQVVAEALG LALPHSALAP SGQAVWLEIA RQSARAVSEL DSRGITTRDI LSDKAIENAM
VIHAAFGGST NLLLHIPAIA HAAGCTIPDV EHWTRINRKV PRLVSVLPNG PDYHPTVRAF
LAGGVPEVML HLRDLGLLHL DAMTVTGQTV GENLEWWQAS ERRARFRQCL REQDGVEPDD
VILPPEKAKA KGLTSTVCFP TGNIAPEGSV IKATAIDPSV VGEDGVYHHT GRVRVFVSEA
QAIKAIKREE IVQGDIMVVI GGGPSGTGME ETYQLTSALK HISWGKTVSL ITDARFSGVS
TGACFGHVSP EALAGGPIGK LRDNDIIEIA VDRLTLTGSV NFIGTADNPL TPEEGARELA
RRQTHPDLHA HDFLPDDTRL WAALQSVSGG TWKGCIYDTD KIIEVINAGK KALGI
Length

655

Mol. Wt

69.399 kDa

pI

6.4 (calculated)

Extinction coefficient

59,930 - 61,180 (calc based on 7 Y, 9 W, and 10 C residues)

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Domains/Motifs/Modification Sites

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Type Residues Description Notes References

Domain

63..635

PF00920 Dehydratase family

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=yagF 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:16128254

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:944928

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000923

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P77596

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6141

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13345

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:944928

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002761

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3129

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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