ybaP: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'/>, B0482<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YbaP<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''conserved protein<ref name='LIB:Riley_2006'/>, B0482<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YbaP<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK0476, JW0471, b0482''
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!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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putative ligase<ref name='LIB:EcoCyc10.6'/>; conserved protein<ref name='LIB:EcoCyc11.1'/>
putative ligase<ref name='LIB:EcoCyc10.6'/>; conserved protein<ref name='LIB:EcoCyc11.1'/>


Function unknown<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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<big>'''Gene Ontology'''</big><br />{{Product_GO_help}}<!--box uid=421aa90e079fa326b6494f812ad13e79.20635.W46aa32b54fb90-->
<big>'''Gene Ontology'''</big><br /><!--box uid=421aa90e079fa326b6494f812ad13e79.20635.W46aa32b54fb90-->
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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!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
|-
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Protein
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ybaK<br />
|
|
PMID:16606699
|
Experiment(s):EBI-1136849<br />
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Protein
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appY<br />
|
|
PMID:16606699
|
Experiment(s):EBI-1136849<br />
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Protein
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sucB<br />
|
|
PMID:16606699
|
Experiment(s):EBI-1136849<br />
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Protein
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carA<br />
|
|
PMID:16606699
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Experiment(s):EBI-1136849<br />
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Protein
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zwf<br />
|
|
PMID:16606699
|
Experiment(s):EBI-1136849<br />
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Protein
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tatE<br />
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|
PMID:16606699
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Experiment(s):EBI-1136849<br />
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Protein
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glpD<br />
|
|
PMID:16606699
|
Experiment(s):EBI-1136849<br />
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Protein
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groL<br />
|
|
PMID:16606699
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Experiment(s):EBI-1136849<br />
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Protein
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dnaK<br />
|


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PMID:16606699
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Experiment(s):EBI-1136849<br />
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Protein
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sdhA<br />
|
 
|
PMID:16606699
|
Experiment(s):EBI-1136849<br />
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Protein
|
hisJ<br />
|
 
|
PMID:16606699
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Experiment(s):EBI-1136849<br />
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Protein
|
yibK<br />
|
 
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PMID:16606699
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Experiment(s):EBI-1136849<br />
 
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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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DTLTHWHTNA RLLQQMMSWW LNAPPQNNDI TLPNTFSQSL YDVLMHQRNL AWRDKLRAMP
DTLTHWHTNA RLLQQMMSWW LNAPPQNNDI TLPNTFSQSL YDVLMHQRNL AWRDKLRAMP
PGRYVVAVGA LHLYGEGNLP QMLR</pre>  
PGRYVVAVGA LHLYGEGNLP QMLR</pre>  
|-
!align=left {{table heading style}} |Length
||
264
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
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29.9 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
29.903 kDa
|-
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!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
6.7 (calculated)
|-
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!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
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48930 - 49055 (calc based on 7 Y, 7 W, and 1 C residues)  
48,930 - 49,055 (calc based on 7 Y, 7 W, and 1 C residues)


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<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span>
 
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<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span><table>
<tr align="left" valign="top">
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!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-
|
Domain
|
26..264
|
[http://pfam.janelia.org/family/PF07446 PF07446  GumN protein]
|
 
|
PMID:19920124


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<td>
<!-- motifs column 2-->
<motif_map/>
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</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>ybaP
<beststructure>
562</beststructure>
gene=ybaP
 
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=ybaP&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P77301 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=ybaP&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P77301 PSI-PRED (P77301)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P77301 Genomes TO Protein (P77301)] (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 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
|-  
|-  
|
|
[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=G6258-MONOMER EcoCyc:G6258-MONOMER]
[http://www.ncbi.nlm.nih.gov/protein/16128466 GI:16128466]
|
|
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_415015.1 GeneID:945124]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
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ASAP:ABE-0001673
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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/P77301 UniProtKB/Swiss-Prot:P77301]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
EcoCyc:G6258
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EcoGene]]
|
EcoGene:EG13244
|
''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:P77301|UniProt:P77301]]
[http://www.ncbi.nlm.nih.gov/gene?term=945124 GeneID:945124]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://pfam.sanger.ac.uk/family?acc=PF07446 PFAM:PF07446]
RegulonDB:ECK120002866
|
|
''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]]
|
|
[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_415015 RefSeq:NP_415015]
EchoBASE:EB3033
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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===Notes===
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===Categories===
===Categories===
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[[Category:Proteins]]
[[Category:Proteins]]
[[Category:Pfam:PF07446_!_GumN protein]]

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

YbaP

Synonyms

conserved protein[1], B0482[2][1], YbaP[2][1] , ECK0476, JW0471, b0482

Product description

putative ligase[2]; conserved protein[3]

Function unknown[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
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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

ybaK

PMID:16606699[5]

Experiment(s):EBI-1136849

Protein

appY

PMID:16606699[5]

Experiment(s):EBI-1136849

Protein

sucB

PMID:16606699[5]

Experiment(s):EBI-1136849

Protein

carA

PMID:16606699[5]

Experiment(s):EBI-1136849

Protein

zwf

PMID:16606699[5]

Experiment(s):EBI-1136849

Protein

tatE

PMID:16606699[5]

Experiment(s):EBI-1136849

Protein

glpD

PMID:16606699[5]

Experiment(s):EBI-1136849

Protein

groL

PMID:16606699[5]

Experiment(s):EBI-1136849

Protein

dnaK

PMID:16606699[5]

Experiment(s):EBI-1136849

Protein

sdhA

PMID:16606699[5]

Experiment(s):EBI-1136849

Protein

hisJ

PMID:16606699[5]

Experiment(s):EBI-1136849

Protein

yibK

PMID:16606699[5]

Experiment(s):EBI-1136849
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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 

MDLLYRVKTL WAALRGNHYT WPAIDITLPG NRHFHLIGSI HMGSHDMAPL PTRLLKKLKN
ADALIVEADV STSDTPFANL PACEALEERI SEEQLQNLQH ISQEMGISPS LFSTQPLWQI
AMVLQATQAQ KLGLRAEYGI DYQLLQAAKQ QHKPVIELEG AENQIAMLLQ LPDKGLALLD
DTLTHWHTNA RLLQQMMSWW LNAPPQNNDI TLPNTFSQSL YDVLMHQRNL AWRDKLRAMP
PGRYVVAVGA LHLYGEGNLP QMLR
Length

264

Mol. Wt

29.903 kDa

pI

6.7 (calculated)

Extinction coefficient

48,930 - 49,055 (calc based on 7 Y, 7 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

26..264

PF07446 GumN protein

PMID:19920124[6]

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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=ybaP 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:16128466

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945124

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001673

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P77301

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6258

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13244

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945124

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002866

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3033

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. ↑ 5.00 5.01 5.02 5.03 5.04 5.05 5.06 5.07 5.08 5.09 5.10 5.11 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  6. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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