ybaB: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'/>, B0471<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YbaB<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, DnaZ<ref name='LIB:EcoCyc11.1'/><ref name='LIB:Riley_2006'/>  
''conserved protein<ref name='LIB:Riley_2006'/>, B0471<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YbaB<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, DnaZ<ref name='LIB:EcoCyc11.1'/><ref name='LIB:Riley_2006'/> , ECK0465, JW0460, b0471''
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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conserved protein<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>
conserved protein<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>


Function unknown, in recR operon; may be involved in DNA repair<ref name='LIB:EcoGene'/>
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!align=left {{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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{{BacktoTop}}
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<protect>
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<big>'''Gene Ontology'''</big><br />{{Product_GO_help}}<!--box uid=421aa90e079fa326b6494f812ad13e79.20609.U46aa31fe5a0b3-->
<big>'''Gene Ontology'''</big><br /><!--box uid=421aa90e079fa326b6494f812ad13e79.20609.U46aa31fe5a0b3-->
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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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[[Category:GO:0006950_!_response_to_stress]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0006950_!_response_to_stress GO:0006950]
GO:0003677
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response to stress
DNA binding
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PMID:19594923
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IDA: Inferred from Direct Assay
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P
F
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Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.
 
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required fields missing 
complete


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|- {{table heading style}}
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!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
|-
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Protein
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deaD<br />
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PMID:15690043
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Experiment(s):EBI-892236<br />
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Protein
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wzxC<br />
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PMID:15690043
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Experiment(s):EBI-892236<br />
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Protein
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ychN<br />
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PMID:15690043
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Experiment(s):EBI-892236<br />
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Protein
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rplT<br />
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PMID:16606699
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Experiment(s):EBI-1136788<br />
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Protein
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nadE<br />
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PMID:16606699
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Experiment(s):EBI-1136788<br />
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Protein
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intB<br />
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PMID:16606699
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Experiment(s):EBI-1136788<br />
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Protein
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inaA<br />
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PMID:16606699
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Experiment(s):EBI-1136788<br />
|-
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Protein
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deaD
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PMID:19402753
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LCMS(ID Probability):99.6
|-
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Protein
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ychN
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PMID:19402753
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LCMS(ID Probability):99.6
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Protein
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wzxC
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PMID:19402753
|
LCMS(ID Probability):99.6


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===Notes===
===Notes===
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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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<pre>MFGKGGLGNL MKQAQQMQEK MQKMQEEIAQ LEVTGESGAG LVKVTINGAH NCRRVEIDPS
<pre>MFGKGGLGNL MKQAQQMQEK MQKMQEEIAQ LEVTGESGAG LVKVTINGAH NCRRVEIDPS
LLEDDKEMLE DLVAAAFNDA ARRIEETQKE KMASVSSGMQ LPPGFKMPF</pre>  
LLEDDKEMLE DLVAAAFNDA ARRIEETQKE KMASVSSGMQ LPPGFKMPF</pre>  
|-
!align=left {{table heading style}} |Length
||
109
|-
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!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
12.01 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
12.014 kDa
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!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
4.9 (calculated)
|-
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!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
0 - 125 (calc based on 0 Y, 0 W, and 1 C residues)  
0 - 125 (calc based on 0 Y, 0 W, and 1 C residues)


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<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span>
 
<!--box uid=421aa90e079fa326b6494f812ad13e79.20609.P46aa3203c641a-->
<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span><table>
<tr align="left" valign="top">
<td><!--box uid=421aa90e079fa326b6494f812ad13e79.20609.P46aa3203c641a-->
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!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-
|
Domain
|
11..102
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[http://pfam.janelia.org/family/PF02575 PF02575  Uncharacterised BCR, YbaB family COG0718]
|
 
|
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>ybaB
<beststructure>
562</beststructure>
gene=ybaB
 
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=ybaB&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P0A8B5 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=ybaB&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P0A8B5 PSI-PRED (P0A8B5)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P0A8B5 Genomes TO Protein (P0A8B5)] (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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===Notes===
===Notes===
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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]])
|
[http://www.ncbi.nlm.nih.gov/protein/16128455 GI:16128455]
|
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://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11100-MONOMER EcoCyc:EG11100-MONOMER]
[http://www.ncbi.nlm.nih.gov/protein/NP_415004.1 GeneID:945104]
|
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Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
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ASAP:ABE-0001636
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P0A8B5 UniProtKB/Swiss-Prot:P0A8B5]
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
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[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
[[EcoCyc]]
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[[uniprot:P0A8B5|UniProt:P0A8B5]]
EcoCyc:EG11100
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
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[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://pfam.sanger.ac.uk/family?acc=PF02575 PFAM:PF02575]
EcoGene:EG11100
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
|
[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_415004 RefSeq:NP_415004]
[http://www.ncbi.nlm.nih.gov/gene?term=945104 GeneID:945104]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://modbase.compbio.ucsf.edu ModBase] ([[ModBase|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://salilab.org/modbase/searchbyid?databaseID=P0A8B5 ModBase:P0A8B5]
RegulonDB:ECK120001088
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://www.rcsb.org/pdb PDB] ([[PDB|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://www.rcsb.org/pdb/cgi/explore.cgi?pdbId=1PUG PDB:1PUG]
EchoBASE:EB1092
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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===Categories===
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[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0006950_!_response to stress]][[Category:Products with structures in PDB]]

Latest revision as of 20:26, 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

YbaB

Synonyms

conserved protein[1], B0471[2][1], YbaB[2][1], DnaZ[3][1] , ECK0465, JW0460, b0471

Product description

conserved protein[2][3]

Function unknown, in recR operon; may be involved in DNA repair[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:0003677

DNA binding

PMID:19594923[5]

IDA: Inferred from Direct Assay

F

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

deaD

PMID:15690043[6]

Experiment(s):EBI-892236

Protein

wzxC

PMID:15690043[6]

Experiment(s):EBI-892236

Protein

ychN

PMID:15690043[6]

Experiment(s):EBI-892236

Protein

rplT

PMID:16606699[7]

Experiment(s):EBI-1136788

Protein

nadE

PMID:16606699[7]

Experiment(s):EBI-1136788

Protein

intB

PMID:16606699[7]

Experiment(s):EBI-1136788

Protein

inaA

PMID:16606699[7]

Experiment(s):EBI-1136788

Protein

deaD

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

ychN

PMID:19402753[8]

LCMS(ID Probability):99.6

Protein

wzxC

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 

MFGKGGLGNL MKQAQQMQEK MQKMQEEIAQ LEVTGESGAG LVKVTINGAH NCRRVEIDPS
LLEDDKEMLE DLVAAAFNDA ARRIEETQKE KMASVSSGMQ LPPGFKMPF
Length

109

Mol. Wt

12.014 kDa

pI

4.9 (calculated)

Extinction coefficient

0 - 125 (calc based on 0 Y, 0 W, and 1 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

11..102

PF02575 Uncharacterised BCR, YbaB family COG0718

PMID:19920124[9]

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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=ybaB 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:16128455

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945104

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001636

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P0A8B5

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11100

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11100

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945104

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001088

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1092

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 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. ↑ 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. ↑ Cooley, AE et al. (2009) DNA-binding by Haemophilus influenzae and Escherichia coli YbaB, members of a widely-distributed bacterial protein family. BMC Microbiol. 9 137 PubMed
  6. ↑ 6.0 6.1 6.2 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 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  8. ↑ 8.0 8.1 8.2 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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