ykfJ:Gene Product(s): Difference between revisions

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|{{Sub}}[[#Localization |Localization]]
|{{Sub}}[[#Localization |Localization]]
|{{Sub}}[[#Sequence|Sequence]]
|{{Sub}}[[#Sequence|Sequence]]
|{{Sub}}[[#Domains/Motifs/Modification Sites|Domains]]
|{{Sub}}[[#Structure|Structure]]
|{{Sub}}[[#Structure|Structure]]
|{{Sub}}[[#Gene Product Resources|Resources]]
|{{Sub}}[[#Gene Product Resources|Resources]]
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!{{table heading style}} |Standard name
!align=left {{table heading style}} |Standard name
|
||
YkfJ product
YkfJ  
|-
|-
!{{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
|
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conserved protein product<ref name='LIB:Riley_2006'/>, YkfJ product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, B0235 product<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''conserved protein<ref name='LIB:Riley_2006'/>, YkfJ<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, B0235<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK0236, JW0225, b0235''
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!{{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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hypothetical protein<ref name='LIB:EcoCyc10.6'/>; conserved protein<ref name='LIB:EcoCyc11.1'/>
hypothetical protein<ref name='LIB:EcoCyc10.6'/>; conserved protein<ref name='LIB:EcoCyc11.1'/>


|-
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!{{table heading style}} |EC number (for enzymes)
!align=left {{table heading style}} |EC number (for enzymes)
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===Notes===
===Notes===
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<big>'''Gene Ontology'''</big><br />{{Product_GO_help}}<!--box uid=421aa90e079fa326b6494f812ad13e79.20068.S46aa24fa4009e-->
<big>'''Gene Ontology'''</big><br /><!--box uid=421aa90e079fa326b6494f812ad13e79.20068.S46aa24fa4009e-->
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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
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!Partner Type!!Partner!!Notes
!|Partner Type!!Partner!!Notes!!References!!Evidence
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Protein
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btuD<br />
|
 
|
PMID:16606699
|
Experiment(s):EBI-1135979<br />
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Protein
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rpmB<br />
|
 
|
PMID:16606699
|
Experiment(s):EBI-1135979<br />
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Protein
|
groL<br />
|
 
|
PMID:16606699
|
Experiment(s):EBI-1135979<br />
|-
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Protein
|
rplB<br />
|
 
|
PMID:16606699
|
Experiment(s):EBI-1135979<br />
|-
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Protein
|
ybiI<br />
|
 
|
PMID:16606699
|
Experiment(s):EBI-1135979<br />
|-
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Protein
|
yfiM<br />
|
 
|
PMID:16606699
|
Experiment(s):EBI-1135979<br />
|-
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Protein
|
chaB<br />
|
 
|
PMID:16606699
|
Experiment(s):EBI-1135979<br />
|-
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Protein
|
rpsI<br />
|
 
|
PMID:16606699
|
Experiment(s):EBI-1135979<br />
 
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===Notes===
===Notes===
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!align=left {{table heading style}} |Name
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!{{table heading style}} |Sequence
!align=left {{table heading style}} |Sequence
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[http://biocyc.org/ECOLI/sequence-aa?object=G6119-MONOMER at EcoCyc]  
[http://biocyc.org/ECOLI/sequence-aa?object=G6119-MONOMER at EcoCyc]  
<pre>MEWYMGKYIR PLSDAVFTIA SDDLWIESLA IQQLHTTANL PNMQRVVGMP DLHPGRGYPI
<pre>MEWYMGKYIR PLSDAVFTIA SDDLWIESLA IQQLHTTANL PNMQRVVGMP DLHPGRGYPI
GAAFFSVGRF YPARRRGNGA GNRNGPLL</pre>  
GAAFFSVGRF YPARRRGNGA GNRNGPLL</pre>  
|-
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!{{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Length
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9.82 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
88
|-
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!{{table heading style}} |pI
!align=left {{table heading style}} |Mol. Wt
|
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9.82 kDa
|-
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!{{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |pI
|
||
16960 (calc based on 4 Y, 2 W, and 0 C residues)  
10.2 (calculated)
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!align=left {{table heading style}} |Extinction coefficient
||
16,960 (calc based on 4 Y, 2 W, and 0 C residues)
 
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==Domains/Motifs/Modification Sites==
 
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<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span><table>
<tr align="left" valign="top">
<td><!--box uid=421aa90e079fa326b6494f812ad13e79.20068.X46aa24fcc6e1b-->
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!Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
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Domain
|
13..74
|
[http://pfam.janelia.org/family/PF01139 PF01139  Uncharacterized protein family UPF0027]
|
 
|
PMID:19920124
 
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<td>
<!-- motifs column 2-->
<motif_map/>
</td>
</tr>
</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>ykfJ
<beststructure>
562</beststructure>
gene=ykfJ
 
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=ykfJ&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P75675 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=ykfJ&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P75675 PSI-PRED (P75675)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P75675 Genomes TO Protein (P75675)] (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
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===Notes===
===Notes===
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-
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[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/protein/ GeneID:944924]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P75675 UniProtKB/Swiss-Prot:P75675]
|
Escherichia coli str. K-12 substr. MG1655
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6119-MONOMER EcoCyc:G6119-MONOMER]
[http://www.ncbi.nlm.nih.gov/gene?term=944924 GeneID:944924]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
[[EcoCyc]]
|
|
[[uniprot:P75675|UniProt:P75675]] 
EcoCyc:
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|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_414770 RefSeq:NP_414770] 
RegulonDB:ECK120002739
|
|
''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=P75675 ModBase:P75675] 
EchoBASE:
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
===Notes===
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===Categories===
===Categories===
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[[Category:Proteins]]
[[Category:Pfam:PF01139_!_Uncharacterized protein family UPF0027]]

Latest revision as of 20:23, 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

YkfJ

Synonyms

conserved protein[1], YkfJ[2][1], B0235[2][1] , ECK0236, JW0225, b0235

Product description

hypothetical protein[2]; conserved protein[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
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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

btuD

PMID:16606699[4]

Experiment(s):EBI-1135979

Protein

rpmB

PMID:16606699[4]

Experiment(s):EBI-1135979

Protein

groL

PMID:16606699[4]

Experiment(s):EBI-1135979

Protein

rplB

PMID:16606699[4]

Experiment(s):EBI-1135979

Protein

ybiI

PMID:16606699[4]

Experiment(s):EBI-1135979

Protein

yfiM

PMID:16606699[4]

Experiment(s):EBI-1135979

Protein

chaB

PMID:16606699[4]

Experiment(s):EBI-1135979

Protein

rpsI

PMID:16606699[4]

Experiment(s):EBI-1135979
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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 

MEWYMGKYIR PLSDAVFTIA SDDLWIESLA IQQLHTTANL PNMQRVVGMP DLHPGRGYPI
GAAFFSVGRF YPARRRGNGA GNRNGPLL
Length

88

Mol. Wt

9.82 kDa

pI

10.2 (calculated)

Extinction coefficient

16,960 (calc based on 4 Y, 2 W, and 0 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

13..74

PF01139 Uncharacterized protein family UPF0027

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=ykfJ 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)

GeneID:944924

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P75675

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:944924

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002739

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:

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. ↑ 4.0 4.1 4.2 4.3 4.4 4.5 4.6 4.7 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  5. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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