Category:Papers with tracks in Gbrowse

2013-08-06T15:54:44Z

Thomaspd:

EcoliWiki strives to make all ''E. coli'' data available, [[EcoliWiki:Wish List|in the long run]]. We are working on putting the data from many papers into our genome browser, [http://heptamer.tamu.edu/cgi-bin/gb2/gbrowse/MG1655/ available here]. This category might be called "Papers we want to put into Gbrowse" instead. For more information, see each paper's page.

To add papers to this list, add the tag:
<nowiki>Category:Papers with tracks in Gbrowse</nowiki>

If you would like to see your data as a viewable track in Gbrowse, feel free to contact us at [mailto:ecoliwiki@gmail.com ecoliwiki@gmail.com].

To access datasets:
* Select desired dataset(s) by clicking on checkboxes in the table below, or the "Check all" box at the top of the table.
** You can filter the table entries first by typing a keyword in the search box below.
* Once you have selected at least one dataset, buttons will appear to allow you to view the data in the context of the relevant genome assembly. Just click on one of these buttons.
<gbrowse_summary/>

<pmidsummary/>
== See also ==
* [[:Category:Papers with data to add as GBrowse tracks]]
* [[:Category:Custom GBrowse tracks]]
* [[Help:Gbrowse]]
== References ==
{{RefHelp}}<references/>
[[Category:GBrowse]]

rho:Gene Product(s)

2011-08-05T17:01:40Z

Thomaspd: Table edited by Thomaspd via TableEdit

{{#css:Suppresslinks.css}}<css>{{:Suppresslinks.css}}</css>
<noinclude>{{TabsTop}}
{{Tab|Quickview|rho}}{{Tab|Gene|rho}}{{Tab On|Gene Product(s)|rho}}{{Tab|Expression|rho}}{{Tab|Evolution|rho}}{{Tab|On One Page|rho}}{{TabsBottom}}
{|
|-
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Function |Function]]
|{{Sub}}[[#Interactions |Interactions]]
|{{Sub}}[[#Localization |Localization]]
|{{Sub}}[[#Sequence|Sequence]]
|{{Sub}}[[#Domains/Motifs/Modification Sites|Domains]]
|{{Sub}}[[#Structure|Structure]]
|{{Sub}}[[#Gene Product Resources|Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Links |Links]]
|{{Sub}}[[#References| References]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
</noinclude>
==Nomenclature==

{{Product_nomenclature_help}}
{| id="A46ab0358a9201" class=" tableEdit Product_nomenclature_table"

|-
!align=left {{table heading style}} |Standard name
||
Rho
|-
!align=left {{table heading style}} |Synonyms
||
transcription termination factor<ref name='LIB:Riley_2006'/>, B3783<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, RnsC<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Tsu<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Sun<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, NusD<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Psu<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, SbaA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, PsuA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, NitA<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Rho<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>
|-
!align=left {{table heading style}} |Product description
||
transcription termination factor Rho; polarity suppressor<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>;

Component of [[:Category:Complex:transcription termination factor Rho|transcription termination factor Rho]]<ref name='LIB:EcoCyc11.1'/>

Transcription termination factor Rho; bicyclomycin target<ref name='LIB:EcoGene'/>
|-
!align=left {{table heading style}} |EC number (for enzymes)
||

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|}


<protect></protect>
===Notes===

==Function==
{{BacktoTop}}
<protect>
<big>'''Gene Ontology'''</big> 
{{Product_GO_help}}
{| id="Q46ab035aca7e9" class=" tableEdit GO_table_product dataTable"
|- {{table_heading_style}}
!|Qualifier!!GO ID!!GO term name!!Reference(s)!!Evidence Code!!with/from!!Aspect!!Notes!!Status
|-
|

|
GO:0000166
|
nucleotide binding
|
GOA:interpro GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR003593
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0000166
|
nucleotide binding
|
GOA:spkw SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0547
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0003676
|
nucleic acid binding
|
GOA:interpro GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR011129
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0003715
|
transcription termination factor activity
|
GOA:interpro GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR004665
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0003715
|
transcription termination factor activity
|
GOA:interpro GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR011112
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0003715
|
transcription termination factor activity
|
GOA:interpro GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR011113
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0003723
|
RNA binding
|
GOA:interpro GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR011113
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0003723
|
RNA binding
|
GOA:spkw SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0694
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0004386
|
helicase activity
|
GOA:spkw SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0347
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0005524
|
ATP binding
|
GOA:interpro GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR004665
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0005524
|
ATP binding
|
GOA:spkw SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0067
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0006350
|
transcription
|
GOA:spkw SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0804
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0006353
|
transcription termination
|
GOA:interpro GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR004665
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0006353
|
transcription termination
|
GOA:interpro GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR011112
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0006353
|
transcription termination
|
GOA:interpro GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR011113
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0006353
|
transcription termination
|
GOA:spkw SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0806
|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0016787
|
hydrolase activity
|
GOA:spkw SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0378
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0017111
|
nucleoside-triphosphatase activity
|
GOA:interpro GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR003593
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|

|
GO:0031555
|
transcriptional attenuation
|
PMID:2423505
|
IMP: Inferred from Mutant Phenotype
|

|
P
|
Seeded from [[EcoCyc]] (v14.0)
|
complete

|- class="tableEdit_footer"
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|}


<big>'''Interactions'''</big>

{{Product_interactions_help}}
{| id="X46ab0366f3cc2" class=" tableEdit Product_interactions_table dataTable"
|- {{table heading style}}
!|Partner Type!!Partner!!Notes!!References!!Evidence
|-
|
Protein
|
Subunits of [[:Category:Complex:transcription termination factor Rho|transcription termination factor Rho]]
|
could be indirect
|

|

|-
|
Protein
|
tufA 
|

|
PMID:15690043
|
Experiment(s):EBI-884347 
|-
|
Protein
|
gsp 
|

|
PMID:15690043
|
Experiment(s):EBI-891277 
|-
|
Protein
|
menF 
|

|
PMID:15690043
|
Experiment(s):EBI-891277 
|-
|
Protein
|
rplC 
|

|
PMID:15690043
|
Experiment(s):EBI-891277 
|-
|
Protein
|
rplL 
|

|
PMID:15690043
|
Experiment(s):EBI-891277 
|-
|
Protein
|
rpsB 
|

|
PMID:15690043
|
Experiment(s):EBI-891277 
|-
|
Protein
|
yhbY 
|

|
PMID:15690043
|
Experiment(s):EBI-891277 
|-
|
Protein
|
uspG 
|

|
PMID:16606699
|
Experiment(s):EBI-1146678 
|-
|
Protein
|
[[yhbY:Gene_Product(s)|yhbY]]
|

|
PMID:19402753
|
LCMS(ID Probability):99.0 MALDI(Z-score):27.463697
|-
|
Protein
|
[[tufB:Gene_Product(s)|tufB]]
|

|
PMID:19402753
|
MALDI(Z-score):20.423130
|-
|
Protein
|
[[rplD:Gene_Product(s)|rplD]]
|

|
PMID:19402753
|
LCMS(ID Probability):99.0 MALDI(Z-score):17.053160

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|}


</protect>
===Notes===

==Localization==

{{Product_localization_help}}
{| id="E46a88dea00e77" class=" tableEdit Product_localization_table"
|- {{table heading style}}
!|Compartment!!Description!!Evidence!!Source!!Notes

|- class="tableEdit_footer"
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|}


<protect></protect>

===Notes===

==Structure and Physical Properties==
{{BacktoTop}}
<protect>
<big>'''Physical Properties'''</big>

{{Product_physical_properties_help}}
{| id="I46ab036973cca" class=" tableEdit Product_phys_prop_table"

|-
!align=left {{table heading style}} |Sequence
||
[http://biocyc.org/ECOLI/sequence-aa?object=EG10845-MONOMER at EcoCyc]
<pre>MNLTELKNTP VSELITLGEN MGLENLARMR KQDIIFAILK QHAKSGEDIF GDGVLEILQD
GFGFLRSADS SYLAGPDDIY VSPSQIRRFN LRTGDTISGK IRPPKEGERY FALLKVNEVN
FDKPENARNK ILFENLTPLH ANSRLRMERG NGSTEDLTAR VLDLASPIGR GQRGLIVAPP
KAGKTMLLQN IAQSIAYNHP DCVLMVLLID ERPEEVTEMQ RLVKGEVVAS TFDEPASRHV
QVAEMVIEKA KRLVEHKKDV IILLDSITRL ARAYNTVVPA SGKVLTGGVD ANALHRPKRF
FGAARNVEEG GSLTIIATAL IDTGSKMDEV IYEEFKGTGN MELHLSRKIA EKRVFPAIDY
NRSGTRKEEL LTTQEELQKM WILRKIIHPM GEIDAMEFLI NKLAMTKTND DFFEMMKRS</pre>
|-
!align=left {{table heading style}} |Length
||
419
|-
!align=left {{table heading style}} |Mol. Wt
||
47.005 kDa
|-
!align=left {{table heading style}} |pI
||
7.2 (calculated)
|-
!align=left {{table heading style}} |Extinction coefficient
||
15,930 - 16,055 (calc based on 7 Y, 1 W, and 1 C residues)

|- class="tableEdit_footer"
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|}


<big>'''Domains/Motifs/Modification Sites'''</big><table>
<tr align="left" valign="top">
<td>
{{Product_domains_motifs_help}}
{| id="R46ab0369ea2fd" class=" tableEdit Product_motif_table dataTable"
|- {{table heading style}}
!|Type!!Residues!!Description!!Notes!!References
|-
|
Domain
|
157..365
|
[http://pfam.janelia.org/family/PF00006 PF00006 ATP synthase alpha/beta family, nucleotide-binding domain]
|

|
PMID:19920124
|-
|
Domain
|
49..126
|
[http://pfam.janelia.org/family/PF07497 PF07497 Rho termination factor, RNA-binding domain]
|

|
PMID:19920124
|-
|
Domain
|
5..47
|
[http://pfam.janelia.org/family/PF07498 PF07498 Rho termination factor, N-terminal domain]
|

|
PMID:19920124

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|}
</td>
<td>


<motif_map/>
</td>
</tr>
</table>

<table><tr valign='top'><td>
<big>'''Structure'''</big> 

{{Product_structure_help}}
{| id="P46ab036a58da6" class=" tableEdit Product_structure_table"

|-
!align=left {{table heading style}} |Structures
||
<beststructure>
gene=rho
taxon=562,83333
</beststructure>
|-
!align=left {{table heading style}} |Models
||
View models at:
* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=recA EcoliPredict]
* [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/psipred/ PSI-PRED]
* [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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|}


</td><td></protect>
==== Structure figures ====

<protect>
</td><tr><table></protect>
===Notes===

==Gene Product Resources==
{{BacktoTop}}

{{Product_resources_help}}
{| id="T46ab036d62e3d" class=" tableEdit Product_resource_table"
|- {{table_heading_style}}
!|Resource type!!Source!!Notes/Reference
|-
|

|
[http://www.ebi.ac.uk/chebi/searchId.do?chebiId=60584 bicyclomycin]
|
Chemical inhibitor of Rho

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|}


<protect></protect>
===Notes===

==Accessions in Other Databases==
{{BacktoTop}}

{{Gene_accessions_help}}
{| id="F46ab036dc7256" class=" tableEdit Gene_accessions_table"
|- {{table_heading_style}}
!|Database!!Accession!!Notes
|-
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10845-MONOMER EcoCyc:EG10845-MONOMER]
|

|-
|
[http://swissmodel.expasy.org/repository/ SwissModel] ([[SwissModel|EcoliWiki Page]])
|
[http://swissmodel.expasy.org/repository/smr.php?job=2&sptr_ac=P0AG30 SwissModel:P0AG30]
|

|-
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P0AG30 UniProt:P0AG30]
|

|-
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
|
[http://pfam.janelia.org/protein/P0AG30 Pfam:P0AG30]
|

|-
|
[http://www.ncbi.nlm.nih.gov/RefSeq/ RefSeq] ([[RefSeq|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=NP_418230 RefSeq:NP_418230]
|

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<protect></protect>
===Notes===

==Links==
{{BacktoTop}}


{| id="B46a88df32dd8e" class=" tableEdit Links_table"
|- {{table_heading_style}}
!|Name!!URL!!Comments

|- class="tableEdit_footer"
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|}


<noinclude>
==References==
{{BacktoTop}}
{{RefHelp}}
<references />
__NOTOC__
===Categories===
{{BacktoTop}}
[[Category:Proteins]]

User:Thomaspd

2010-09-22T20:03:41Z

Thomaspd: Table edited by Thomaspd via TableEdit

Click "edit table" in the last row to add information to the table. Click [[Help:Adding_your_information|here]] to find out how to add more information to your user page.



{| id="I4c9a5ea1e9200" class=" tableEdit User_info_table"

|-
!align=left |Name (Last, First)
||
Thomas, Paul
|-
!align=left |Organization
||
University of Southern California
|-
!align=left |Position
||
Assoc Professor
|-
!align=left |Address
||

|-
!align=left |Contact Info
||
*pdthomas@usc.edu
|-
!align=left |Website(s)
||
http://uscnorriscancer.usc.edu/about/leadership/pauldthomas.html
|-
!align=left |Interests
||
Evolution of genes and biological systems; use of knowledge of model organisms in human health
|-
!align=left |Genes
||

|-
!align=left |Lab members
||

|- class="tableEdit_footer"
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==References==
{{RefHelp}}
<references/>

EcoliWiki - User contributions [en]

Category:Papers with tracks in Gbrowse

rho:Gene Product(s)

User:Thomaspd