nemR:Gene Product(s): Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older edit
No edit summary
touch table
 
(26 intermediate revisions by 2 users not shown)
Line 35: Line 35:
*  
*  
****************************************************************************************** -->{{Product_nomenclature_help}}
****************************************************************************************** -->{{Product_nomenclature_help}}
{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  
{|   id="G46aa745b4687d" class=" tableEdit Product_nomenclature_table"


|-
|-
Line 44: Line 44:
!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
predicted DNA-binding transcriptional regulator<ref name='LIB:Riley_2006'/>, B1649<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YdhM<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>  
''predicted DNA-binding transcriptional regulator<ref name='LIB:Riley_2006'/>, B1649<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, YdhM<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK1645, JW5874, ydhM, b1649''
|-
|-
!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
Line 55: Line 55:
*
*


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23335.G46aa745b4687d&page=23335&pagename={{FULLPAGENAMEE}}&type=1&template=Product_nomenclature_table edit table] ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23335.G46aa745b4687d&page=23335&pagename={{FULLPAGENAMEE}}&type=1&template=Product_nomenclature_table edit table]</span> ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.23335.G46aa745b4687d-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.23335.G46aa745b4687d-->
Line 74: Line 74:
*  
*  
****************************************************************************************** -->{{Product_GO_help}}
****************************************************************************************** -->{{Product_GO_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="L46aa745c4d3c4"  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
|-
|
 
|
GO:0006355
|
regulation of transcription, DNA-dependent
|
GO_REF:0000002<br />GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR001647<br />SP_KW:KW-0805
|
P
|
Seeded from EcoCyc
|
complete
|-
|
 
|
GO:0003677
|
DNA binding
|
GO_REF:0000002<br />GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR012287<br />SP_KW:KW-0238
|
F
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
|
complete
|-  
|-  
|
|
Line 123: Line 85:
transcription factor activity
transcription factor activity
|
|
GO_REF:0000002
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
Line 131: Line 93:
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 138: Line 100:


|
|
GO:0005515
GO:0003700
|
|
protein binding
transcription factor activity
|
|
PMID:15690043
PMID:15556475
|
|
IPI: Inferred from Physical Interaction
ISS: Inferred from Sequence or Structural Similarity
|
|
UniProtKB:P04951
Swiss-Prot:P0ACS9
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 157: Line 119:


|
|
GO:0006350
GO:0003700
|
|
transcription
transcription factor activity
|
|
GO_REF:0000004
PMID:18567656
|
|
IEA: Inferred from Electronic Annotation
IDA: Inferred from Direct Assay
|
SP_KW:KW-0804
|
P
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
|
complete
|-
|
|


|
GO:0030528
|
transcription regulator activity
|
GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR011075
|
|
F
F
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 195: Line 138:


|
|
GO:0045449
GO:0016566
|
regulation of transcription
|
GO_REF:0000002<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
specific transcriptional repressor activity
|
|
InterPro:IPR011075<br />InterPro:IPR012287
PMID:15556475
|
|
P
ISS: Inferred from Sequence or Structural Similarity
|
|
Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
Swiss-Prot:P0ACS9
|
complete
|-  
|
 
|
GO:0003677
|
DNA binding
|
GO_REF:0000002<br />GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR012287<br />SP_KW:KW-0238
|
|
F
F
|
|
Seeded from EcoCyc
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 233: Line 157:


|
|
GO:0003700
GO:0016566
|
transcription factor activity
|
|
GO_REF:0000002
specific transcriptional repressor activity
|
|
IEA: Inferred from Electronic Annotation
PMID:18567656
|
|
InterPro:IPR001647
IDA: Inferred from Direct Assay
|
F
|
Seeded from EcoCyc
|
complete
|-
|
|


|
GO:0005515
|
protein binding
|
PMID:15690043
|
IPI: Inferred from Physical Interaction
|
UniProtKB:P04951
|
|
F
F
|
|
Seeded from EcoCyc
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 271: Line 176:


|
|
GO:0006350
GO:0032582
|
|
transcription
negative regulation of gene-specific transcription
|
|
GO_REF:0000004
PMID:15556475
|
|
IEA: Inferred from Electronic Annotation
ISS: Inferred from Sequence or Structural Similarity
|
|
SP_KW:KW-0804
Swiss-Prot:P0ACS9
|
|
P
P
|
|
Seeded from EcoCyc
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 290: Line 195:


|
|
GO:0030528
GO:0032582
|
transcription regulator activity
|
GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
negative regulation of gene-specific transcription
|
|
InterPro:IPR011075
PMID:18567656
|
|
F
IDA: Inferred from Direct Assay
|
Seeded from EcoCyc
|
complete
|-
|
|


|
GO:0045449
|
regulation of transcription
|
GO_REF:0000002<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR011075<br />InterPro:IPR012287
|
|
P
P
|
|
Seeded from EcoCyc
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23335.L46aa745c4d3c4&page=23335&pagename={{FULLPAGENAMEE}}&type=&template=GO_table_product edit table] || || || || || || || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23335.L46aa745c4d3c4&page=23335&pagename={{FULLPAGENAMEE}}&type=&template=GO_table_product edit table]</span> || || || || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.23335.L46aa745c4d3c4-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.23335.L46aa745c4d3c4-->
Line 338: Line 224:
*  
*  
****************************************************************************************** -->{{Product_interactions_help}}
****************************************************************************************** -->{{Product_interactions_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="P46aa746008ce3"  class=" tableEdit Product_interactions_table dataTable"   
|- {{table heading style}}
|- {{table heading style}}
!|Partner Type!!Partner!!Notes!!References!!Evidence
!|Partner Type!!Partner!!Notes!!References!!Evidence
Line 352: Line 238:
|
|
Experiment(s):EBI-890408<br />  
Experiment(s):EBI-890408<br />  
|-
|
Protein
|
kdsB
|
|
PMID:19402753
|
LCMS(ID Probability):99.4


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23335.P46aa746008ce3&page=23335&pagename={{FULLPAGENAMEE}}&type=&template=Product_interactions_table edit table] || || || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23335.P46aa746008ce3&page=23335&pagename={{FULLPAGENAMEE}}&type=&template=Product_interactions_table edit table]</span> || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.23335.P46aa746008ce3-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.23335.P46aa746008ce3-->
Line 370: Line 267:
*  
*  
****************************************************************************************** -->{{Product_localization_help}}
****************************************************************************************** -->{{Product_localization_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="C46a8065d66698"  class=" tableEdit Product_localization_table"   
|- {{table heading style}}
|- {{table heading style}}
!|Compartment!!Description!!Evidence!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23335.C46a8065d66698&page=23335&pagename={{FULLPAGENAMEE}}&type=&template=Product_localization_table edit table] || || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23335.C46a8065d66698&page=23335&pagename={{FULLPAGENAMEE}}&type=&template=Product_localization_table edit table]</span> || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.23335.C46a8065d66698-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.23335.C46a8065d66698-->
Line 395: Line 292:
*  
*  
****************************************************************************************** -->{{Product_physical_properties_help}}
****************************************************************************************** -->{{Product_physical_properties_help}}
{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"
{|   id="S46aa7461dc559" class=" tableEdit Product_phys_prop_table"
 
|-
!align=left {{table heading style}} |Name
||


|-
|-
Line 422: Line 323:
17,420 - 18,170 (calc based on 8 Y, 1 W, and 6 C residues)
17,420 - 18,170 (calc based on 8 Y, 1 W, and 6 C residues)


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23335.S46aa7461dc559&page=23335&pagename={{FULLPAGENAMEE}}&type=1&template=Product_phys_prop_table edit table] ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23335.S46aa7461dc559&page=23335&pagename={{FULLPAGENAMEE}}&type=1&template=Product_phys_prop_table edit table]</span> ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.23335.S46aa7461dc559-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.23335.S46aa7461dc559-->
Line 437: Line 338:
*  
*  
****************************************************************************************** -->{{Product_domains_motifs_help}}
****************************************************************************************** -->{{Product_domains_motifs_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="M46aa74624d7d5"  class=" tableEdit Product_motif_table dataTable"   
|- {{table heading style}}
|- {{table heading style}}
!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-
|
Domain
|
13..59
|
[http://pfam.janelia.org/family/PF00440 PF00440  Bacterial regulatory proteins, tetR family]
|
 
|
PMID:19920124


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23335.M46aa74624d7d5&page=23335&pagename={{FULLPAGENAMEE}}&type=&template=Product_motif_table edit table] || || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23335.M46aa74624d7d5&page=23335&pagename={{FULLPAGENAMEE}}&type=&template=Product_motif_table edit table]</span> || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.23335.M46aa74624d7d5-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.23335.M46aa74624d7d5-->
Line 463: Line 375:
*  
*  
****************************************************************************************** -->{{Product_structure_help}}
****************************************************************************************** -->{{Product_structure_help}}
{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  
{|   id="W46a8065f045fd" class=" tableEdit Product_structure_table"


|-
|-
Line 476: Line 388:
||
||
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/P67430 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=P67430 PSI-PRED (P67430)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P67430 Genomes TO Protein (P67430)] (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)


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23335.W46a8065f045fd&page=23335&pagename={{FULLPAGENAMEE}}&type=1&template=Product_structure_table edit table] ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23335.W46a8065f045fd&page=23335&pagename={{FULLPAGENAMEE}}&type=1&template=Product_structure_table edit table]</span> ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.23335.W46a8065f045fd-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.23335.W46a8065f045fd-->
Line 521: Line 431:
*  
*  
****************************************************************************************** -->{{Product_resources_help}}
****************************************************************************************** -->{{Product_resources_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O46aa746306782"  class=" tableEdit Product_resource_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Resource type!!Source!!Notes/Reference
!|Resource type!!Source!!Notes/Reference


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23335.O46aa746306782&page=23335&pagename={{FULLPAGENAMEE}}&type=&template=Product_resource_table edit table] || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23335.O46aa746306782&page=23335&pagename={{FULLPAGENAMEE}}&type=&template=Product_resource_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.23335.O46aa746306782-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.23335.O46aa746306782-->
Line 543: Line 453:
*  
*  
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="V46aa74635c40a"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|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://www.ncbi.nlm.nih.gov/protein/145698269 GI:145698269]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[http://www.ncbi.nlm.nih.gov/protein NCBI (Protein)] ([[NCBI (Protein)|EcoliWiki Page]])
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6889-MONOMER EcoCyc:G6889-MONOMER]
[http://www.ncbi.nlm.nih.gov/protein/NP_416166.3 GeneID:946166]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
ASAP:ABE-0005514
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
[http://www.uniprot.org/uniprot/P67430 UniProtKB/Swiss-Prot:P67430]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[EcoCyc]]
|
EcoCyc:G6889
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
[[EcoGene]]
|
|
[[uniprot:P67430|UniProt:P67430]]
EcoGene:EG13947
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI (Gene)] ([[NCBI (Gene)|EcoliWiki Page]])
|
|
[http://pfam.sanger.ac.uk/family?acc=PF00440 PFAM:PF00440]
[http://www.ncbi.nlm.nih.gov/gene?term=946166 GeneID:946166]
|
|
Escherichia coli str. K-12 substr. 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_416166 RefSeq:NP_416166]
RegulonDB:ECK120003478
|
|
''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=P67430 ModBase:P67430]
EchoBASE:EB3705
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23335.V46aa74635c40a&page=23335&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table] || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23335.V46aa74635c40a&page=23335&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.23335.V46aa74635c40a-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.23335.V46aa74635c40a-->
Line 600: Line 538:
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46a806628adec"  class=" tableEdit Links_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Name!!URL!!Comments
!|Name!!URL!!Comments


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23335.Z46a806628adec&page=23335&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table] || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.23335.Z46a806628adec&page=23335&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.23335.Z46a806628adec-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.23335.Z46a806628adec-->
Line 621: Line 559:
{{BacktoTop}}
{{BacktoTop}}
[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0006355_!_regulation of transcription, DNA-dependent]]

Latest revision as of 20:41, 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

YdhM

Synonyms

predicted DNA-binding transcriptional regulator[1], B1649[2][1], YdhM[2][1] , ECK1645, JW5874, ydhM, b1649

Product description

hypothetical protein[2]; predicted DNA-binding transcriptional regulator[3]. YdhM binding to the ydhM-nemA promoter is reduced by addition of NEM. Genomic SELEX identifies a binding site for YdhM in the ydhM-nemA promoter region. [4]

EC number (for enzymes)
edit table

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Notes

Function

[back to top]


Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki. 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:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001647

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

PMID:15556475[5]

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P0ACS9

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

PMID:18567656[4]

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0016566

specific transcriptional repressor activity

PMID:15556475[5]

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P0ACS9

F

Seeded from EcoCyc (v14.0)

complete

GO:0016566

specific transcriptional repressor activity

PMID:18567656[4]

IDA: Inferred from Direct Assay

F

Seeded from EcoCyc (v14.0)

complete

GO:0032582

negative regulation of gene-specific transcription

PMID:15556475[5]

ISS: Inferred from Sequence or Structural Similarity

Swiss-Prot:P0ACS9

P

Seeded from EcoCyc (v14.0)

complete

GO:0032582

negative regulation of gene-specific transcription

PMID:18567656[4]

IDA: Inferred from Direct Assay

P

Seeded from EcoCyc (v14.0)

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

kdsB

PMID:15690043[6]

Experiment(s):EBI-890408

Protein

kdsB

PMID:19402753[7]

LCMS(ID Probability):99.4

edit table

See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
edit table

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.


Notes

Structure and Physical Properties

[back to top]


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 

MNKHTEHDTR EHLLATGEQL CLQRGFTGMG LSELLKTAEV PKGSFYHYFR SKEAFGVAML
ERHYAAYHQR LTELLQSGEG NYRDRILAYY QQTLNQFCQH GTISGCLTVK LSAEVCDLSE
DMRSAMDKGA RGVIALLSQA LENGRENHCL TFCGEPLQQA QVLYALWLGA NLQAKISRSF
EPLENALAHV KNIIATPAV
Length

199

Mol. Wt

22.275 kDa

pI

3.5 (calculated)

Extinction coefficient

17,420 - 18,170 (calc based on 8 Y, 1 W, and 6 C residues)

edit table

See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

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..59

PF00440 Bacterial regulatory proteins, tetR family

PMID:19920124[8]

edit table
See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

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

Models

View models at:

edit table

See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structure figures

Notes

Gene Product Resources

[back to top]


See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
edit table

See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Notes

Accessions in Other Databases

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:145698269

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:946166

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005514

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P67430

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:G6889

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13947

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:946166

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003478

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3705

Escherichia coli str. K-12 substr. MG1655

edit table

See Help:Product_accessions for help entering or editing information in this section of EcoliWiki.

Notes

Links

[back to top]


See Help:Links_table for how to enter or edit information in this section of EcoliWiki.



References

[back to top]


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 Umezawa, Y et al. (2008) The uncharacterized transcription factor YdhM is the regulator of the nemA gene, encoding N-ethylmaleimide reductase. J. Bacteriol. 190 5890-7 PubMed
  5. ↑ 5.0 5.1 5.2 Pérez-Rueda, E et al. (2004) Phylogenetic distribution of DNA-binding transcription factors in bacteria and archaea. Comput Biol Chem 28 341-50 PubMed
  6. ↑ Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  7. ↑ Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  8. ↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

[back to top]


Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=nemR:Gene_Product(s)&oldid=1493582"