mfd:Gene Product(s): Difference between revisions

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!align=left {{table heading style}} |Synonyms
!align=left {{table heading style}} |Synonyms
||
||
transcription-repair coupling factor<ref name='LIB:Riley_2006'/>, B1114<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Mfd<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, TRCF<ref name='LIB:EcoCyc11.1'/><ref name='LIB:Riley_2006'/>  
''transcription-repair coupling factor<ref name='LIB:Riley_2006'/>, B1114<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, Mfd<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, TRCF<ref name='LIB:EcoCyc11.1'/><ref name='LIB:Riley_2006'/> , ECK1100, JW1100, b1114''
|-
|-
!align=left {{table heading style}} |Product description
!align=left {{table heading style}} |Product description
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transcription-repair coupling factor<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>
transcription-repair coupling factor<ref name='LIB:EcoCyc10.6'/><ref name='LIB:EcoCyc11.1'/>


Transcription repair coupling factor<ref name='LIB:EcoGene'/>
|-
|-
!align=left {{table heading style}} |EC number (for enzymes)
!align=left {{table heading style}} |EC number (for enzymes)
||
||
*


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{{Product_nomenclature_help}}
 
<protect><!--Nomenclature_notes--></protect>
<protect><!--Nomenclature_notes--></protect>
===Notes===
===Notes===
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{{BacktoTop}}
{{BacktoTop}}
<protect>
<protect>
<big>'''Gene Ontology'''</big><br />{{Product_GO_help}}<!--box uid=421aa90e079fa326b6494f812ad13e79.22136.P46aa57867c376-->
<big>'''Gene Ontology'''</big><br /><!--box uid=421aa90e079fa326b6494f812ad13e79.22136.P46aa57867c376-->
<!--
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{|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="P46aa57867c376"  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
|-  
|-  
|
|


|
|
[[Category:GO:0005515_!_protein_binding]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0005515_!_protein_binding GO:0005515]
GO:0006281
|
DNA repair
|
PMID:1763073
|
IMP: Inferred from Mutant Phenotype
|
 
|
|
protein binding
P
|[[PMID:16469698]]<ref name=PMID:16469698/>
|
|
IPI: Inferred from Physical Interaction
 
|
|
[http://www.uniprot.org/uniprot/P0A8V2 UniProtKB:P0A8V2]
complete
|-
|
 
|
GO:0006355
|
regulation of transcription, DNA-dependent
|
PMID:8465200
|
IDA: Inferred from Direct Assay
|
 
|
P
|
 
|
complete
|-
|
 
|
GO:0006974
|
response to DNA damage stimulus
|
PMID:8465200
|
IDA: Inferred from Direct Assay
|
 
|
P
|
 
|
complete
|-
|
 
|
GO:0000716
|
transcription-coupled nucleotide-excision repair, DNA damage recognition
|
PMID:8465200
|
IDA: Inferred from Direct Assay
|
 
|
P
|
 
|
complete
|-
|
 
|
GO:0000166
|
nucleotide binding
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0547
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 99: Line 177:


|
|
[[Category:GO:0000166_!_nucleotide_binding]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0000166_!_nucleotide_binding GO:0000166]
GO:0003676
|
|
nucleotide binding
nucleic acid binding
|
|
[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000004 GO_REF:0000004]
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.uniprot.org/keywords/KW-0547 SP_KW:KW-0547]
InterPro:IPR001650
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 118: Line 196:


|
|
[[Category:GO:0003676_!_nucleic_acid_binding]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0003676_!_nucleic_acid_binding GO:0003676]
GO:0003676
|
|
nucleic acid binding
nucleic acid binding
|
|
[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000002 GO_REF:0000002]<br />[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000002 GO_REF:0000002]
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR001650 InterPro:IPR001650]<br />[http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR011545 InterPro:IPR011545]
InterPro:IPR011545
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 137: Line 215:


|
|
[[Category:GO:0003677_!_DNA_binding]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0003677_!_DNA_binding GO:0003677]
GO:0003677
|
|
DNA binding
DNA binding
|
|
[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000004 GO_REF:0000004]
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0238
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-  
|
 
|
GO:0003684
|
damaged DNA binding
|
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.uniprot.org/keywords/KW-0238 SP_KW:KW-0238]
InterPro:IPR004576
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 156: Line 253:


|
|
[[Category:GO:0003684_!_damaged_DNA_binding]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0003684_!_damaged_DNA_binding GO:0003684]
GO:0003684
|
|
damaged DNA binding
damaged DNA binding
|
|
[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000002 GO_REF:0000002]
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR004576 InterPro:IPR004576]
InterPro:IPR005118
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 175: Line 272:


|
|
[[Category:GO:0003700_!_transcription_factor_activity]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0003700_!_transcription_factor_activity GO:0003700]
GO:0003700
|
|
transcription factor activity
transcription factor activity
|
|
[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000002 GO_REF:0000002]
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR003711
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-  
|
 
|
GO:0004386
|
helicase activity
|
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR003711 InterPro:IPR003711]
InterPro:IPR001650
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 194: Line 310:


|
|
[[Category:GO:0004386_!_helicase_activity]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0004386_!_helicase_activity GO:0004386]
GO:0004386
|
|
helicase activity
helicase activity
|
|
[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000002 GO_REF:0000002]<br />[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000004 GO_REF:0000004]
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR001650 InterPro:IPR001650]<br />[http://www.uniprot.org/keywords/KW-0347 SP_KW:KW-0347]
InterPro:IPR004576
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 213: Line 329:


|
|
[[Category:GO:0005524_!_ATP_binding]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0005524_!_ATP_binding GO:0005524]
GO:0004386
|
helicase activity
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR005118
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0004386
|
helicase activity
|
GOA:spkw<br />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
ATP binding
|
|
[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000002 GO_REF:0000002]<br />[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000002 GO_REF:0000002]<br />[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000002 GO_REF:0000002]<br />[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000004 GO_REF:0000004]
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR001650 InterPro:IPR001650]<br />[http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR004576 InterPro:IPR004576]<br />[http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR011545 InterPro:IPR011545]<br />[http://www.uniprot.org/keywords/KW-0067 SP_KW:KW-0067]
InterPro:IPR001650
|
|
F
F
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 232: Line 386:


|
|
[[Category:GO:0006281_!_DNA_repair]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0006281_!_DNA_repair GO:0006281]
GO:0005524
|
ATP binding
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR004576
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0005524
|
ATP binding
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR005118
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0005524
|
ATP binding
|
GOA:interpro<br />GO_REF:0000002
|
IEA: Inferred from Electronic Annotation
|
InterPro:IPR011545
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0005524
|
ATP binding
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
IEA: Inferred from Electronic Annotation
|
SP_KW:KW-0067
|
F
|
Seeded from [[EcoCyc]] (v14.0)
|
complete
|-
|
 
|
GO:0006281
|
|
DNA repair
DNA repair
|
|
[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000002 GO_REF:0000002]<br />[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000004 GO_REF:0000004]
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR004576 InterPro:IPR004576]<br />[http://www.uniprot.org/keywords/KW-0234 SP_KW:KW-0234]
InterPro:IPR004576
|
|
P
P
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 251: Line 481:


|
|
[[Category:GO:0006355_!_regulation_of_transcription,_DNA-dependent]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0006355_!_regulation_of_transcription,_DNA-dependent GO:0006355]
GO:0006281
|
|
regulation of transcription, DNA-dependent
DNA repair
|
|
[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000002 GO_REF:0000002]
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR003711 InterPro:IPR003711]
InterPro:IPR005118
|
|
P
P
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 270: Line 500:


|
|
[[Category:GO:0006974_!_response_to_DNA_damage_stimulus]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0006974_!_response_to_DNA_damage_stimulus GO:0006974]
GO:0006281
|
|
response to DNA damage stimulus
DNA repair
|
|
[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000004 GO_REF:0000004]
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.uniprot.org/keywords/KW-0227 SP_KW:KW-0227]
SP_KW:KW-0234
|
|
P
P
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 289: Line 519:


|
|
[[Category:GO:0008026_!_ATP-dependent_helicase_activity]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0008026_!_ATP-dependent_helicase_activity GO:0008026]
GO:0006355
|
|
ATP-dependent helicase activity
regulation of transcription, DNA-dependent
|
|
[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000002 GO_REF:0000002]
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.ebi.ac.uk/interpro/DisplayIproEntry?ac=IPR011545 InterPro:IPR011545]
InterPro:IPR003711
|
|
F
P
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
Line 308: Line 538:


|
|
[[Category:GO:0016787_!_hydrolase_activity]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0016787_!_hydrolase_activity GO:0016787]
GO:0006974
|
|
hydrolase activity
response to DNA damage stimulus
|
|
[http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000004 GO_REF:0000004]
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
IEA: Inferred from Electronic Annotation
|
|
[http://www.uniprot.org/keywords/KW-0378 SP_KW:KW-0378]
SP_KW:KW-0227
|
|
F
P
|
|
Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
Seeded from [[EcoCyc]] (v14.0)
|
|
complete  
complete  
|-  
|-  
|
|
 
|
|
[[Category:GO:0006350_!_transcription]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0006350_!_transcription GO:0006350]
GO:0008026
|
|
transcription
ATP-dependent helicase activity
|
|
GOA:interpro<br />GO_REF:0000002
|
|
IEA: Inferred from Electronic Annotation
|
|
InterPro:IPR011545
|
|
P
F
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete
|-  
|-  
|
|
 
|
|
[[Category:GO:0005737_!_cytoplasm]][http://gowiki.tamu.edu/wiki/index.php/Category:GO:0005737_!_cytoplasm GO:0005737]
GO:0016787
|
|
cytoplasm
hydrolase activity
|
|
GOA:spkw<br />SP_KW:GO_REF:0000004
|
|
IEA: Inferred from Electronic Annotation
|
|
SP_KW:KW-0378
|
|
C
F
|
|
Seeded from EcoCyc 11.1<ref name='LIB:EcoCyc11.1'/>.  
Seeded from [[EcoCyc]] (v14.0)
|
|
required fields missing 
complete


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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.22136.P46aa57867c376&page=22136&pagename={{FULLPAGENAMEE}}&type=&template=GO_table_product edit table]</span> || || || || || || || ||
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****************************************************************************************** -->{{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="Y46aa578d15fd5"  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 382: Line 612:
Protein
Protein
|
|
[[tdcC:Gene_Product(s)|tdcC]]<br />
tdcC<br />
|
|


|[[PMID:15690043]]<ref name=PMID:15690043/>
|
|
Experiment(s):[http://www.ebi.ac.uk/iintact/search/do/search?searchString=EBI-893742 EBI-893742]<br />  
PMID:15690043
|
Experiment(s):EBI-893742<br />  
|-  
|-  
|
|
Protein
Protein
|
|
[[yffB:Gene_Product(s)|yffB]]<br />
yffB<br />
|
|


|[[PMID:15690043]]<ref name=PMID:15690043/>
|
|
Experiment(s):[http://www.ebi.ac.uk/iintact/search/do/search?searchString=EBI-893742 EBI-893742]<br />  
PMID:15690043
|
Experiment(s):EBI-893742<br />
|-
|
Protein
|
ihfA<br />
|
 
|
PMID:16606699
|
Experiment(s):EBI-1138903<br />
|-
|
Protein
|
rpsM<br />
|
 
|
PMID:16606699
|
Experiment(s):EBI-1138903<br />
|-
|
Protein
|
yeeT<br />
|
 
|
PMID:16606699
|
Experiment(s):EBI-1138903<br />
|-
|
Protein
|
rplB<br />
|
 
|
PMID:16606699
|
Experiment(s):EBI-1138903<br />
|-  
|
Protein
|
stpA<br />
|


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PMID:16606699
|
Experiment(s):EBI-1138903<br />
|-
|
Protein
|
nfrA<br />
|
 
|
PMID:16606699
|
Experiment(s):EBI-1138903<br />
|-
|
Protein
|
tdcC
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.0
|-
|
Protein
|
yffB
|
 
|
PMID:19402753
|
LCMS(ID Probability):99.0
 
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<!--Function_notes--></protect>
<!--Function_notes--></protect>
===Notes===
===Notes===
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|- {{table heading style}}
|- {{table heading style}}
!|Compartment!!Description!!Evidence!!Notes
!|Compartment!!Description!!Evidence!!Reference/Source!!Notes


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{|   id="Y46aa578ed0dad" class=" tableEdit Product_phys_prop_table"
 
|-
!align=left {{table heading style}} |Name
||


|-
|-
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NEKGGVIEFA EKNHVNPAWL IGLLQKQPQH YRLDGPTRLK FIQDLSERKT RIEWVRQFMR
NEKGGVIEFA EKNHVNPAWL IGLLQKQPQH YRLDGPTRLK FIQDLSERKT RIEWVRQFMR
ELEENAIA</pre>  
ELEENAIA</pre>  
|-
!align=left {{table heading style}} |Length
||
1,148
|-
|-
!align=left {{table heading style}} |Mol. Wt
!align=left {{table heading style}} |Mol. Wt
||
||
129.98 kDa (calc) <ref name='LIB:EcoCyc10.6'/>
129.985 kDa
|-
|-
!align=left {{table heading style}} |pI
!align=left {{table heading style}} |pI
||
||
6.1 (calculated)
|-
|-
!align=left {{table heading style}} |Extinction coefficient
!align=left {{table heading style}} |Extinction coefficient
||
||
95230 - 96105 (calc based on 27 Y, 10 W, and 7 C residues)  
95,230 - 96,105 (calc based on 27 Y, 10 W, and 7 C residues)


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<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span>
 
<!--box uid=421aa90e079fa326b6494f812ad13e79.22136.Y46aa578f398c3-->
<span id="Domains/Motifs/Modification Sites"><big>'''Domains/Motifs/Modification Sites'''</big></span><table>
<tr align="left" valign="top">
<td><!--box uid=421aa90e079fa326b6494f812ad13e79.22136.Y46aa578f398c3-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Y46aa578f398c3"  class=" tableEdit Product_motif_table dataTable"   
|- {{table heading style}}
|- {{table heading style}}
!|Type!!Residues!!Description!!Notes
!|Type!!Residues!!Description!!Notes!!References
|-
|
Domain
|
602..766
|
[http://pfam.janelia.org/family/PF00270 PF00270  DEAD/DEAH box helicase]
|
 
|
PMID:19920124
|-
|
Domain
|
832..907
|
[http://pfam.janelia.org/family/PF00271 PF00271  Helicase conserved C-terminal domain]
|
 
|
PMID:19920124
|-  
|-  
|
|
Domain
Domain
|
|
615 - 776
476..573
|
[http://pfam.janelia.org/family/PF02559 PF02559  CarD-like/TRCF domain]
|
|
[[interpro:IPR014021|Helicase ATP-binding]]
 
|
|
[http://www.uniprot.org/uniprot/P30958#section_features UniProt:P30958]
PMID:19920124
|-  
|-  
|
|
Domain
Domain
|
|
798 - 951
1005..1105
|
[http://pfam.janelia.org/family/PF03461 PF03461  TRCF domain]
|
|
[[interpro:IPR001650|Helicase C-terminal]]
 
|
|
[http://www.uniprot.org/uniprot/P30958#section_features UniProt:P30958]
PMID:19920124


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{{Product_domains_motifs_help}}
<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>mfd
<beststructure>
562</beststructure>
gene=mfd
 
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=mfd&sub=keywordSearc EcoliPredict]
* [http://www.proteinmodelportal.org/query/uniprot/P30958 Protein Model Portal]
* [http://modbase.compbio.ucsf.edu/modbase-cgi/model_search.cgi?searchmode=default&displaymode=moddetail&searchproperties=ALL&searchvalue=mfd&organism=562&organismtext= ModBase]
* [http://bioinf.cs.ucl.ac.uk/genome3d/read?uniprot_id=P30958 PSI-PRED (P30958)]
* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P30958 Genomes TO Protein (P30958)] (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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|- {{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/16129077 GI:16129077]
|
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_415632.1 GeneID:945681]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[ASAP]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11619-MONOMER EcoCyc:EG11619-MONOMER]
ASAP:ABE-0003763
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://swissmodel.expasy.org/repository/ SwissModel] ([[SwissModel|EcoliWiki Page]])  
[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
|
|
[http://swissmodel.expasy.org/repository/smr.php?job=2&sptr_ac=P30958 SwissModel:P30958]
[http://www.uniprot.org/uniprot/P30958 UniProtKB/Swiss-Prot:P30958]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
[[EcoCyc]]
|
|
[[uniprot:P30958|UniProt:P30958]]
EcoCyc:EG11619
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://pfam.sanger.ac.uk/family?acc=PF02559 PFAM:PF02559]
EcoGene:EG11619
|
|
''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_415632 RefSeq:NP_415632]
[http://www.ncbi.nlm.nih.gov/gene?term=945681 GeneID:945681]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://modbase.compbio.ucsf.edu ModBase] ([[ModBase|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://salilab.org/modbase/searchbyid?databaseID=P30958 ModBase:P30958]
RegulonDB:ECK120001567
|
|
''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=2B2N PDB:2B2N]
EchoBASE:EB1576
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments


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{{BacktoTop}}
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</noinclude>
===Categories===
===Categories===
{{BacktoTop}}
{{BacktoTop}}
[[Category:Proteins]]
[[Category:Proteins]]
[[Category:GO:0006350_!_transcription]][[Category:GO:0005737_!_cytoplasm]][[Category:Products with structures in PDB]]

Latest revision as of 20:34, 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

Mfd

Synonyms

transcription-repair coupling factor[1], B1114[2][1], Mfd[2][1], TRCF[3][1] , ECK1100, JW1100, b1114

Product description

transcription-repair coupling factor[2][3]

Transcription repair coupling factor[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:0006281

DNA repair

PMID:1763073[5]

IMP: Inferred from Mutant Phenotype

P

complete

GO:0006355

regulation of transcription, DNA-dependent

PMID:8465200[6]

IDA: Inferred from Direct Assay

P

complete

GO:0006974

response to DNA damage stimulus

PMID:8465200[6]

IDA: Inferred from Direct Assay

P

complete

GO:0000716

transcription-coupled nucleotide-excision repair, DNA damage recognition

PMID:8465200[6]

IDA: Inferred from Direct Assay

P

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:IPR001650

F

Seeded from EcoCyc (v14.0)

complete

GO:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011545

F

Seeded from EcoCyc (v14.0)

complete

GO:0003677

DNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0238

F

Seeded from EcoCyc (v14.0)

complete

GO:0003684

damaged DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004576

F

Seeded from EcoCyc (v14.0)

complete

GO:0003684

damaged DNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005118

F

Seeded from EcoCyc (v14.0)

complete

GO:0003700

transcription factor activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003711

F

Seeded from EcoCyc (v14.0)

complete

GO:0004386

helicase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001650

F

Seeded from EcoCyc (v14.0)

complete

GO:0004386

helicase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004576

F

Seeded from EcoCyc (v14.0)

complete

GO:0004386

helicase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005118

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:IPR001650

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004576

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005118

F

Seeded from EcoCyc (v14.0)

complete

GO:0005524

ATP binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011545

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:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004576

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR005118

P

Seeded from EcoCyc (v14.0)

complete

GO:0006281

DNA repair

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0234

P

Seeded from EcoCyc (v14.0)

complete

GO:0006355

regulation of transcription, DNA-dependent

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003711

P

Seeded from EcoCyc (v14.0)

complete

GO:0006974

response to DNA damage stimulus

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0227

P

Seeded from EcoCyc (v14.0)

complete

GO:0008026

ATP-dependent helicase activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011545

F

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

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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

tdcC

PMID:15690043[7]

Experiment(s):EBI-893742

Protein

yffB

PMID:15690043[7]

Experiment(s):EBI-893742

Protein

ihfA

PMID:16606699[8]

Experiment(s):EBI-1138903

Protein

rpsM

PMID:16606699[8]

Experiment(s):EBI-1138903

Protein

yeeT

PMID:16606699[8]

Experiment(s):EBI-1138903

Protein

rplB

PMID:16606699[8]

Experiment(s):EBI-1138903

Protein

stpA

PMID:16606699[8]

Experiment(s):EBI-1138903

Protein

nfrA

PMID:16606699[8]

Experiment(s):EBI-1138903

Protein

tdcC

PMID:19402753[9]

LCMS(ID Probability):99.0

Protein

yffB

PMID:19402753[9]

LCMS(ID Probability):99.0

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Notes

Mfd is involved in transcription-coupled repair[6][10]. Mfd is is an ATPase that can release stalled or paused RNA polymerases from DNA lesions, including thymine dimers and abasic sites[11]

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 

MPEQYRYTLP VKAGEQRLLG ELTGAACATL VAEIAERHAG PVVLIAPDMQ NALRLHDEIS
QFTDQMVMNL ADWETLPYDS FSPHQDIISS RLSTLYQLPT MQRGVLIVPV NTLMQRVCPH
SFLHGHALVM KKGQRLSRDA LRTQLDSAGY RHVDQVMEHG EYATRGALLD LFPMGSELPY
RLDFFDDEID SLRVFDVDSQ RTLEEVEAIN LLPAHEFPTD KAAIELFRSQ WRDTFEVKRD
PEHIYQQVSK GTLPAGIEYW QPLFFSEPLP PLFSYFPANT LLVNTGDLET SAERFQADTL
ARFENRGVDP MRPLLPPQSL WLRVDELFSE LKNWPRVQLK TEHLPTKAAN ANLGFQKLPD
LAVQAQQKAP LDALRKFLET FDGPVVFSVE SEGRREALGE LLARIKIAPQ RIMRLDEASD
RGRYLMIGAA EHGFVDTVRN LALICESDLL GERVARRRQD SRRTINPDTL IRNLAELHIG
QPVVHLEHGV GRYAGMTTLE AGGITGEYLM LTYANDAKLY VPVSSLHLIS RYAGGAEENA
PLHKLGGDAW SRARQKAAEK VRDVAAELLD IYAQRAAKEG FAFKHDREQY QLFCDSFPFE
TTPDQAQAIN AVLSDMCQPL AMDRLVCGDV GFGKTEVAMR AAFLAVDNHK QVAVLVPTTL
LAQQHYDNFR DRFANWPVRI EMISRFRSAK EQTQILAEVA EGKIDILIGT HKLLQSDVKF
KDLGLLIVDE EHRFGVRHKE RIKAMRANVD ILTLTATPIP RTLNMAMSGM RDLSIIATPP
ARRLAVKTFV REYDSMVVRE AILREILRGG QVYYLYNDVE NIQKAAERLA ELVPEARIAI
GHGQMREREL ERVMNDFHHQ RFNVLVCTTI IETGIDIPTA NTIIIERADH FGLAQLHQLR
GRVGRSHHQA YAWLLTPHPK AMTTDAQKRL EAIASLEDLG AGFALATHDL EIRGAGELLG
EEQSGSMETI GFSLYMELLE NAVDALKAGR EPSLEDLTSQ QTEVELRMPS LLPDDFIPDV
NTRLSFYKRI ASAKTENELE EIKVELIDRF GLLPDPARTL LDIARLRQQA QKLGIRKLEG
NEKGGVIEFA EKNHVNPAWL IGLLQKQPQH YRLDGPTRLK FIQDLSERKT RIEWVRQFMR
ELEENAIA
Length

1,148

Mol. Wt

129.985 kDa

pI

6.1 (calculated)

Extinction coefficient

95,230 - 96,105 (calc based on 27 Y, 10 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

602..766

PF00270 DEAD/DEAH box helicase

PMID:19920124[12]

Domain

832..907

PF00271 Helicase conserved C-terminal domain

PMID:19920124[12]

Domain

476..573

PF02559 CarD-like/TRCF domain

PMID:19920124[12]

Domain

1005..1105

PF03461 TRCF domain

PMID:19920124[12]

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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=mfd 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:16129077

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945681

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003763

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P30958

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11619

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11619

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945681

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001567

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1576

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. ↑ Selby, CP et al. (1991) Escherichia coli mfd mutant deficient in "mutation frequency decline" lacks strand-specific repair: in vitro complementation with purified coupling factor. Proc. Natl. Acad. Sci. U.S.A. 88 11574-8 PubMed
  6. ↑ 6.0 6.1 6.2 6.3 Selby, CP & Sancar, A (1993) Molecular mechanism of transcription-repair coupling. Science 260 53-8 PubMed
  7. ↑ 7.0 7.1 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
  8. ↑ 8.0 8.1 8.2 8.3 8.4 8.5 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
  9. ↑ 9.0 9.1 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
  10. ↑ Roberts, J & Park, JS (2004) Mfd, the bacterial transcription repair coupling factor: translocation, repair and termination. Curr. Opin. Microbiol. 7 120-5 PubMed
  11. ↑ Smith, AJ & Savery, NJ (2008) Effects of the bacterial transcription-repair coupling factor during transcription of DNA containing non-bulky lesions. DNA Repair (Amst.) 7 1670-9 PubMed
  12. ↑ 12.0 12.1 12.2 12.3 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

Categories

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