ybjX:Gene Product(s): Difference between revisions

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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
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conserved protein<ref name='LIB:Riley_2006'/>, B0877<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YbjX<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''conserved protein<ref name='LIB:Riley_2006'/>, B0877<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YbjX<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK0868, JW0861, b0877''
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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{|   id="I46aa48a976c1a"  class=" tableEdit GO_table_product dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="I46aa48a976c1a"  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
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{|   id="S46aa48a9e9da0"  class=" tableEdit Product_interactions_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="S46aa48a9e9da0"  class=" tableEdit Product_interactions_table dataTable"   
|- {{table heading style}}
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!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
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Protein
Protein
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|
[[rpmC:Gene_Product(s)|rpmC]]
rpmC
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Protein
Protein
|
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[[rpmG:Gene_Product(s)|rpmG]]
rpmG
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Protein
Protein
|
|
[[rpmB:Gene_Product(s)|rpmB]]
rpmB
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Protein
Protein
|
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[[rpsA:Gene_Product(s)|rpsA]]
rpsA
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Protein
Protein
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[[rplJ:Gene_Product(s)|rplJ]]
rplJ
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Protein
Protein
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[[rplT:Gene_Product(s)|rplT]]
rplT
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Protein
Protein
|
|
[[rplO:Gene_Product(s)|rplO]]
rplO
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Protein
Protein
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|
[[rplE:Gene_Product(s)|rplE]]
rplE
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Protein
Protein
|
|
[[rfaD:Gene_Product(s)|rfaD]]
rfaD
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|


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PMID:19402753
PMID:19402753
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MALDI(Z-score):38.502110  
MALDI(Z-score):38.502110  
|-  
|-  
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Protein
Protein
|
|
[[rplU:Gene_Product(s)|rplU]]
rplU
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Protein
Protein
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[[tufB:Gene_Product(s)|tufB]]
tufB
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PMID:19402753
PMID:19402753
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MALDI(Z-score):20.676555  
MALDI(Z-score):20.676555  
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|-  
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Protein
Protein
|
|
[[rplI:Gene_Product(s)|rplI]]
rplI
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Protein
Protein
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[[rplF:Gene_Product(s)|rplF]]
rplF
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Protein
Protein
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[[rplQ:Gene_Product(s)|rplQ]]
rplQ
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Protein
Protein
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[[rpsF:Gene_Product(s)|rpsF]]
rpsF
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Protein
Protein
|
|
[[hupB:Gene_Product(s)|hupB]]
hupB
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Protein
Protein
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[[rplS:Gene_Product(s)|rplS]]
rplS
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Protein
Protein
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[[rplM:Gene_Product(s)|rplM]]
rplM
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Protein
Protein
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[[hupA:Gene_Product(s)|hupA]]
hupA
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Protein
Protein
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[[rpsD:Gene_Product(s)|rpsD]]
rpsD
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Protein
Protein
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[[rpsM:Gene_Product(s)|rpsM]]
rpsM
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Protein
Protein
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[[rplX:Gene_Product(s)|rplX]]
rplX
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Protein
Protein
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[[rpsC:Gene_Product(s)|rpsC]]
rpsC
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Protein
Protein
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[[rplA:Gene_Product(s)|rplA]]
rplA
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Protein
Protein
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[[rplB:Gene_Product(s)|rplB]]
rplB
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Protein
Protein
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[[srmB:Gene_Product(s)|srmB]]
srmB
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PMID:19402753
PMID:19402753
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MALDI(Z-score):24.880466  
MALDI(Z-score):24.880466  
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Protein
Protein
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[[dnaJ:Gene_Product(s)|dnaJ]]
dnaJ
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Protein
Protein
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[[rplD:Gene_Product(s)|rplD]]
rplD
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Protein
Protein
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[[yfiF:Gene_Product(s)|yfiF]]
yfiF
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LCMS(ID Probability):97.8 MALDI(Z-score):7.664643  
LCMS(ID Probability):97.8 MALDI(Z-score):7.664643  
|-
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Protein
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rnr
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PMID:19402753
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MALDI(Z-score):26.041938
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Protein
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rplL
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PMID:19402753
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LCMS(ID Probability):99.6


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{|   id="O46a7da6eee7ac"  class=" tableEdit Product_localization_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O46a7da6eee7ac"  class=" tableEdit Product_localization_table"   
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!|Compartment!!Description!!Evidence!!Source!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes


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{|  id="U46aa48abadaf6"  class=" tableEdit Product_phys_prop_table"   
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!align=left {{table heading style}} |Name
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{|   id="W46aa48ac15a38"  class=" tableEdit Product_motif_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="W46aa48ac15a38"  class=" tableEdit Product_motif_table dataTable"   
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!|Type!!Residues!!Description!!Notes!!References
!|Type!!Residues!!Description!!Notes!!References
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View models at:
View models at:
* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=recA EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P75829 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=recA&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P75829 PSI-PRED (P75829)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P75829 Genomes TO Protein (P75829)] (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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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="G46aa48acaf08d"  class=" tableEdit Product_resource_table"   
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!|Resource type!!Source!!Notes/Reference
!|Resource type!!Source!!Notes/Reference
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{|   id="Z46aa48ad0712c"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46aa48ad0712c"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|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/protein/16128845 GI:16128845]
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Escherichia coli str. K-12 substr. MG1655
|-
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[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
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[http://www.ncbi.nlm.nih.gov/protein/NP_415398.1 GeneID:946025]
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Escherichia coli str. K-12 substr. MG1655
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[[ASAP]]
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ASAP:ABE-0002982
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6463-MONOMER EcoCyc:G6463-MONOMER]
[http://www.uniprot.org/uniprot/P75829 UniProtKB/Swiss-Prot:P75829]
|
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Escherichia coli str. K-12 substr. MG1655
|-
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[[EcoCyc]]
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EcoCyc:G6460
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[[EcoGene]]
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EcoGene:EG13693
|
''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]])
|
|
[http://www.uniprot.org/uniprot/P75829 UniProt:P75829]
[http://www.ncbi.nlm.nih.gov/gene?term=946025 GeneID:946025]
|
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Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[RegulonDB]]
|
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[http://pfam.janelia.org/protein/P75829 Pfam:P75829]
RegulonDB:ECK120003060
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
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[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
[[EchoBASE]]
|
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[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_415398 RefSeq:NP_415398]
EchoBASE:EB3457
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="G46a7da738b608"  class=" tableEdit Links_table"   
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!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:31, 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

YbjX

Synonyms

conserved protein[1], B0877[2][1], YbjX[2][1] , ECK0868, JW0861, b0877

Product description

conserved protein[2][3]

Function unknown, homologous to somA (S.t.) and virK (S.f.)[4]

EC number (for enzymes)


edit table


Notes

Function

[back to top]


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:0006974

response to DNA damage stimulus

PMID:11967071[5]

IEP: Inferred from Expression Pattern

P

complete

edit table

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

lpdA

PMID:15690043[6]

Experiment(s):EBI-879208

Protein

pssA

PMID:15690043[6]

Experiment(s):EBI-879208

Protein

rplA

PMID:15690043[6]

Experiment(s):EBI-879208, EBI-882921

Protein

rplB

PMID:15690043[6]

Experiment(s):EBI-879208, EBI-882921

Protein

rplC

PMID:15690043[6]

Experiment(s):EBI-879208, EBI-882921

Protein

rplD

PMID:15690043[6]

Experiment(s):EBI-879208, EBI-882921

Protein

rplE

PMID:15690043[6]

Experiment(s):EBI-879208, EBI-882921

Protein

rplF

PMID:15690043[6]

Experiment(s):EBI-879208, EBI-882921

Protein

rplM

PMID:15690043[6]

Experiment(s):EBI-879208, EBI-882921

Protein

rplV

PMID:15690043[6]

Experiment(s):EBI-879208

Protein

rpoC

PMID:15690043[6]

Experiment(s):EBI-879208

Protein

rpsA

PMID:15690043[6]

Experiment(s):EBI-879208, EBI-882921

Protein

rpsB

PMID:15690043[6]

Experiment(s):EBI-879208, EBI-882921

Protein

rpsC

PMID:15690043[6]

Experiment(s):EBI-879208, EBI-882921

Protein

rpsD

PMID:15690043[6]

Experiment(s):EBI-879208

Protein

rpsG

PMID:15690043[6]

Experiment(s):EBI-879208, EBI-882921

Protein

srmB

PMID:15690043[6]

Experiment(s):EBI-879208

Protein

tufA

PMID:15690043[6]

Experiment(s):EBI-879208, EBI-882921

Protein

rnr

PMID:15690043[6]

Experiment(s):EBI-879208

Protein

rluB

PMID:15690043[6]

Experiment(s):EBI-879208

Protein

rplX

PMID:15690043[6]

Experiment(s):EBI-882921

Protein

rpmB

PMID:15690043[6]

Experiment(s):EBI-882921

Protein

rpmC

PMID:15690043[6]

Experiment(s):EBI-882921

Protein

rpmG

PMID:15690043[6]

Experiment(s):EBI-882921

Protein

rpsE

PMID:15690043[6]

Experiment(s):EBI-882921

Protein

rpsF

PMID:15690043[6]

Experiment(s):EBI-882921

Protein

rpsM

PMID:15690043[6]

Experiment(s):EBI-882921

Protein

rpsS

PMID:15690043[6]

Experiment(s):EBI-882921

Protein

rpsT

PMID:15690043[6]

Experiment(s):EBI-882921

Protein

aceF

PMID:15690043[6]

Experiment(s):EBI-882921

Protein

dnaJ

PMID:15690043[6]

Experiment(s):EBI-882921

Protein

hupA

PMID:15690043[6]

Experiment(s):EBI-882921

Protein

hupB

PMID:15690043[6]

Experiment(s):EBI-882921

Protein

rplI

PMID:15690043[6]

Experiment(s):EBI-882921

Protein

rplJ

PMID:15690043[6]

Experiment(s):EBI-882921

Protein

rplL

PMID:15690043[6]

Experiment(s):EBI-882921

Protein

rplO

PMID:15690043[6]

Experiment(s):EBI-882921

Protein

rplQ

PMID:15690043[6]

Experiment(s):EBI-882921

Protein

rplS

PMID:15690043[6]

Experiment(s):EBI-882921

Protein

rplT

PMID:15690043[6]

Experiment(s):EBI-882921

Protein

rplU

PMID:15690043[6]

Experiment(s):EBI-882921

Protein

perM

PMID:16606699[7]

Experiment(s):EBI-1138231

Protein

yciH

PMID:16606699[7]

Experiment(s):EBI-1138231

Protein

rplB

PMID:16606699[7]

Experiment(s):EBI-1138231

Protein

appY

PMID:16606699[7]

Experiment(s):EBI-1138231

Protein

groL

PMID:16606699[7]

Experiment(s):EBI-1138231

Protein

mutH

PMID:16606699[7]

Experiment(s):EBI-1138231

Protein

rpmC

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

rpmG

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

rpmB

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

rpsA

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):21.224236

Protein

rplJ

PMID:19402753[8]

LCMS(ID Probability):99.4 MALDI(Z-score):3.385515

Protein

rplT

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

rplO

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

rplE

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):27.323521

Protein

rfaD

PMID:19402753[8]

MALDI(Z-score):38.502110

Protein

rplU

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

tufB

PMID:19402753[8]

MALDI(Z-score):20.676555

Protein

rplI

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

rplF

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):29.180248

Protein

rplQ

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

rpsF

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

hupB

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

rplS

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):2.654204

Protein

rplM

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):32.496120

Protein

hupA

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

rpsD

PMID:19402753[8]

LCMS(ID Probability):97.9 MALDI(Z-score):34.058088

Protein

rpsM

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

rplX

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

rpsC

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):26.378458

Protein

rplA

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):23.679102

Protein

rplB

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):37.287562

Protein

srmB

PMID:19402753[8]

MALDI(Z-score):24.880466

Protein

dnaJ

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

rplD

PMID:19402753[8]

LCMS(ID Probability):99.6 MALDI(Z-score):18.911757

Protein

yfiF

PMID:19402753[8]

LCMS(ID Probability):97.8 MALDI(Z-score):7.664643

Protein

rnr

PMID:19402753[8]

MALDI(Z-score):26.041938

Protein

rplL

PMID:19402753[8]

LCMS(ID Probability):99.6

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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 

MVKSTPCITI DFMNMSQLTE RTFTPSESLS SLSLFLSLAR GQCRPGKFWH RRSFRQKFLL
RSLIMPRLSV EWMNELSHWP NLNVLLTRQP RLPVRLHRPY LAANLSRKQL LEALRYHYAL
LRECMSAEEF SLYLNTPGLQ LAKLEGKNGE QFTLELTMMI SMDKEGDSTI LFRNSEGIPL
AEITFTLCEY QGKRTMFIGG LQGAKWEIPH QEIQNATKAC HGLFPKRLVM EAACLFAQRL
QVEQIIAVSN ETHIYRSLRY RDKEGKIHAD YNAFWESVGG VCDAERHYRL PAQIARKEIA
EIASKKRAEY RRRYEMLDAI QPQMATMFRG
Length

330

Mol. Wt

38.358 kDa

pI

9.7 (calculated)

Extinction coefficient

43,890 - 44,765 (calc based on 11 Y, 5 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

40..328

PF04393 Protein of unknown function (DUF535)

PMID:19920124[9]

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<motif_map/>

Structure
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Structures

<beststructure> gene=ybjX taxon=562,83333 </beststructure>

Models

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Structure figures

Notes

Gene Product Resources

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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:16128845

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946025

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002982

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P75829

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6460

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13693

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946025

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003060

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3457

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. ↑ Khil, PP & Camerini-Otero, RD (2002) Over 1000 genes are involved in the DNA damage response of Escherichia coli. Mol. Microbiol. 44 89-105 PubMed
  6. ↑ 6.00 6.01 6.02 6.03 6.04 6.05 6.06 6.07 6.08 6.09 6.10 6.11 6.12 6.13 6.14 6.15 6.16 6.17 6.18 6.19 6.20 6.21 6.22 6.23 6.24 6.25 6.26 6.27 6.28 6.29 6.30 6.31 6.32 6.33 6.34 6.35 6.36 6.37 6.38 6.39 6.40 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  7. ↑ 7.0 7.1 7.2 7.3 7.4 7.5 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  8. ↑ 8.00 8.01 8.02 8.03 8.04 8.05 8.06 8.07 8.08 8.09 8.10 8.11 8.12 8.13 8.14 8.15 8.16 8.17 8.18 8.19 8.20 8.21 8.22 8.23 8.24 8.25 8.26 8.27 8.28 8.29 8.30 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  9. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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