mfd:Gene Product(s): Difference between revisions

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
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	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
edit table

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
edit table

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 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)
edit table

Domains/Motifs/Modification Sites

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

Type	Residues	Description	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]
edit table

<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:

edit table

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

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: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
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

References

[back to top]

See Help:References for how to manage references in EcoliWiki.

↑ ^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)
↑ ^2.0 ^2.1 ^2.2 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ 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
↑ ^6.0 ^6.1 ^6.2 ^6.3 Selby, CP & Sancar, A (1993) Molecular mechanism of transcription-repair coupling. Science 260 53-8 PubMed
↑ ^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
↑ ^8.0 ^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
↑ ^9.0 ^9.1 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
↑ Roberts, J & Park, JS (2004) Mfd, the bacterial transcription repair coupling factor: translocation, repair and termination. Curr. Opin. Microbiol. 7 120-5 PubMed
↑ 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
↑ ^12.0 ^12.1 ^12.2 ^12.3 Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

mfd:Gene Product(s): Difference between revisions

Latest revision as of 20:34, 17 February 2015

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

References

Categories

Navigation menu

@@ Line 35: / Line 35: @@
 *
 ****************************************************************************************** -->{{Product_nomenclature_help}}
-{|  id="Z46aa57857e25d"  class=" tableEdit Product_nomenclature_table"
+{|   id="Z46aa57857e25d"  class=" tableEdit Product_nomenclature_table"
 |-
@@ Line 44: / Line 44: @@
 !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
@@ Line 75: / Line 75: @@
 *
 ****************************************************************************************** -->{{Product_GO_help}}
-{|   id="P46aa57867c376"  class=" tableEdit GO_table_product dataTable"
+{| 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}}
-!|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:0005515
+GO:0006281
+|
+DNA repair
+|
+PMID:1763073
+|
+IMP: Inferred from Mutant Phenotype
+|
+|
+P
 |
-protein binding
 |
-PMID:16469698
+complete
+|-
 |
-IPI: Inferred from Physical Interaction
 |
-UniProtKB:P0A8V2
+GO:0006355
 |
-F
+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
 |
-Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
 |
 complete
@@ Line 105: / Line 162: @@
 nucleotide binding
 |
-GO_REF:0000004
+GOA:spkw<br />SP_KW:GO_REF:0000004
 |
 IEA: Inferred from Electronic Annotation
@@ Line 113: / Line 170: @@
 F
 |
-Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 124: / Line 181: @@
 nucleic acid binding
 |
-GO_REF:0000002<br />GO_REF:0000002
+GOA:interpro<br />GO_REF:0000002
 |
 IEA: Inferred from Electronic Annotation
 |
-InterPro:IPR001650<br />InterPro:IPR011545
+InterPro:IPR001650
 |
 F
 |
-Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
+Seeded from [[EcoCyc]] (v14.0)
+|
+complete
+|-
+|
+|
+GO:0003676
+|
+nucleic acid binding
+|
+GOA:interpro<br />GO_REF:0000002
+|
+IEA: Inferred from Electronic Annotation
+|
+InterPro:IPR011545
+|
+F
+|
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 143: / Line 219: @@
 DNA binding
 |
-GO_REF:0000004
+GOA:spkw<br />SP_KW:GO_REF:0000004
 |
 IEA: Inferred from Electronic Annotation
@@ Line 151: / Line 227: @@
 F
 |
-Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 162: / Line 238: @@
 damaged DNA binding
 |
-GO_REF:0000002
+GOA:interpro<br />GO_REF:0000002
 |
 IEA: Inferred from Electronic Annotation
@@ Line 170: / Line 246: @@
 F
 |
-Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
+Seeded from [[EcoCyc]] (v14.0)
+|
+complete
+|-
+|
+|
+GO:0003684
+|
+damaged DNA binding
+|
+GOA:interpro<br />GO_REF:0000002
+|
+IEA: Inferred from Electronic Annotation
+|
+InterPro:IPR005118
+|
+F
+|
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 181: / Line 276: @@
 transcription factor activity
 |
-GO_REF:0000002
+GOA:interpro<br />GO_REF:0000002
 |
 IEA: Inferred from Electronic Annotation
@@ Line 189: / Line 284: @@
 F
 |
-Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
+Seeded from [[EcoCyc]] (v14.0)
+|
+complete
+|-
+|
+|
+GO:0004386
+|
+helicase activity
+|
+GOA:interpro<br />GO_REF:0000002
+|
+IEA: Inferred from Electronic Annotation
+|
+InterPro:IPR001650
+|
+F
+|
+Seeded from [[EcoCyc]] (v14.0)
+|
+complete
+|-
+|
+|
+GO:0004386
+|
+helicase activity
+|
+GOA:interpro<br />GO_REF:0000002
+|
+IEA: Inferred from Electronic Annotation
+|
+InterPro:IPR004576
+|
+F
+|
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 200: / Line 333: @@
 helicase activity
 |
-GO_REF:0000002<br />GO_REF:0000004
+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
+|
+GOA:interpro<br />GO_REF:0000002
 |
 IEA: Inferred from Electronic Annotation
 |
-InterPro:IPR001650<br />SP_KW:KW-0347
+InterPro:IPR001650
 |
 F
 |
-Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 219: / Line 390: @@
 ATP binding
 |
-GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000002<br />GO_REF:0000004
+GOA:interpro<br />GO_REF:0000002
 |
 IEA: Inferred from Electronic Annotation
 |
-InterPro:IPR001650<br />InterPro:IPR004576<br />InterPro:IPR011545<br />SP_KW:KW-0067
+InterPro:IPR004576
 |
 F
 |
-Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 234: / Line 405: @@
 |
-GO:0006281
+GO:0005524
+|
+ATP binding
+|
+GOA:interpro<br />GO_REF:0000002
+|
+IEA: Inferred from Electronic Annotation
+|
+InterPro:IPR005118
 |
-DNA repair
+F
 |
-PMID:1763073
+Seeded from [[EcoCyc]] (v14.0)
 |
-IMP: Inferred from Mutant Phenotype
+complete
+|-
 |
 |
-P
+GO:0005524
+|
+ATP binding
+|
+GOA:interpro<br />GO_REF:0000002
+|
+IEA: Inferred from Electronic Annotation
+|
+InterPro:IPR011545
+|
+F
 |
-Seeded from EcoCyc 12.5 <ref name = 'LIB:EcoCyc12.5'/>
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 253: / Line 443: @@
 |
-GO:0006355
+GO:0005524
+|
+ATP binding
+|
+GOA:spkw<br />SP_KW:GO_REF:0000004
+|
+IEA: Inferred from Electronic Annotation
+|
+SP_KW:KW-0067
 |
-regulation of transcription, DNA-dependent
+F
 |
-PMID:8465200
+Seeded from [[EcoCyc]] (v14.0)
 |
-IDA: Inferred from Direct Assay
+complete
+|-
 |
+|
+GO:0006281
+|
+DNA repair
+|
+GOA:interpro<br />GO_REF:0000002
+|
+IEA: Inferred from Electronic Annotation
+|
+InterPro:IPR004576
 |
 P
 |
-Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 272: / Line 481: @@
 |
-GO:0006974
+GO:0006281
 |
-response to DNA damage stimulus
+DNA repair
 |
-PMID:8465200
+GOA:interpro<br />GO_REF:0000002
 |
-IDA: Inferred from Direct Assay
+IEA: Inferred from Electronic Annotation
 |
+InterPro:IPR005118
 |
 P
 |
-Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 291: / Line 500: @@
 |
-GO:0008026
+GO:0006281
 |
-ATP-dependent helicase activity
+DNA repair
 |
-GO_REF:0000002
+GOA:spkw<br />SP_KW:GO_REF:0000004
 |
 IEA: Inferred from Electronic Annotation
 |
-InterPro:IPR011545
+SP_KW:KW-0234
 |
-F
+P
 |
-Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 310: / Line 519: @@
 |
-GO:0016787
+GO:0006355
 |
-hydrolase activity
+regulation of transcription, DNA-dependent
 |
-GO_REF:0000004
+GOA:interpro<br />GO_REF:0000002
 |
 IEA: Inferred from Electronic Annotation
 |
-SP_KW:KW-0378
+InterPro:IPR003711
 |
-F
+P
 |
-Seeded from EcoCyc <ref name = 'LIB:EcoCyc13.0'/>
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
@@ Line 329: / Line 538: @@
 |
-GO:0000716
+GO:0006974
 |
-transcription-coupled nucleotide-excision repair, DNA damage recognition
+response to DNA damage stimulus
 |
-PMID:15063847
+GOA:spkw<br />SP_KW:GO_REF:0000004
 |
-IDA: Inferred from Direct Assay
+IEA: Inferred from Electronic Annotation
 |
+SP_KW:KW-0227
 |
 P
+|
+Seeded from [[EcoCyc]] (v14.0)
+|
+complete
+|-
 |
+|
+GO:0008026
+|
+ATP-dependent helicase activity
+|
+GOA:interpro<br />GO_REF:0000002
+|
+IEA: Inferred from Electronic Annotation
+|
+InterPro:IPR011545
+|
+F
+|
+Seeded from [[EcoCyc]] (v14.0)
 |
 complete
 |-
 |
 |
-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
 |- class="tableEdit_footer"
@@ Line 377: / Line 605: @@
 *
 ****************************************************************************************** -->{{Product_interactions_help}}
-{|   id="Y46aa578d15fd5"  class=" tableEdit Product_interactions_table dataTable"
+{| 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}}
 !|Partner Type!!Partner!!Notes!!References!!Evidence
@@ Line 468: / Line 696: @@
 |
 Experiment(s):EBI-1138903<br />
+|-
+|
+Protein
+|
+tdcC
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.0
+|-
+|
+Protein
+|
+yffB
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.0
 |- class="tableEdit_footer"
@@ Line 486: / Line 736: @@
 *
 ****************************************************************************************** -->{{Product_localization_help}}
-{|   id="B46a7ea7d8df88"  class=" tableEdit Product_localization_table"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="B46a7ea7d8df88"  class=" tableEdit Product_localization_table"
 |- {{table heading style}}
-!|Compartment!!Description!!Evidence!!Source!!Notes
+!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
 |- class="tableEdit_footer"
@@ Line 511: / Line 761: @@
 *
 ****************************************************************************************** -->{{Product_physical_properties_help}}
-{|  id="Y46aa578ed0dad"  class=" tableEdit Product_phys_prop_table"
+{|   id="Y46aa578ed0dad"  class=" tableEdit Product_phys_prop_table"
+|-
+!align=left {{table heading style}} |Name
+||
 |-
@@ Line 569: / Line 823: @@
 *
 ****************************************************************************************** -->{{Product_domains_motifs_help}}
-{|   id="Y46aa578f398c3"  class=" tableEdit Product_motif_table dataTable"
+{| 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}}
 !|Type!!Residues!!Description!!Notes!!References
+|-
+|
+Domain
+|
+..766
+|
+[http://pfam.janelia.org/family/PF00270 PF00270  DEAD/DEAH box helicase]
+|
+|
+PMID:19920124
+|-
+|
+Domain
+|
+..907
+|
+[http://pfam.janelia.org/family/PF00271 PF00271  Helicase conserved C-terminal domain]
+|
+|
+PMID:19920124
+|-
+|
+Domain
+|
+..573
+|
+[http://pfam.janelia.org/family/PF02559 PF02559  CarD-like/TRCF domain]
+|
+|
+PMID:19920124
+|-
+|
+Domain
+|
+..1105
+|
+[http://pfam.janelia.org/family/PF03461 PF03461  TRCF domain]
+|
+|
+PMID:19920124
 |- class="tableEdit_footer"
@@ Line 594: / Line 892: @@
 *
 ****************************************************************************************** -->{{Product_structure_help}}
-{|  id="Z46aa578f86356"  class=" tableEdit Product_structure_table"
+{|   id="Z46aa578f86356"  class=" tableEdit Product_structure_table"
 |-
@@ Line 607: / Line 905: @@
 ||
 View models at:
-* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=recA 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=recA&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)
 |- class="tableEdit_footer"
@@ Line 652: / Line 948: @@
 *
 ****************************************************************************************** -->{{Product_resources_help}}
-{|   id="U46aa5790c2646"  class=" tableEdit Product_resource_table"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="U46aa5790c2646"  class=" tableEdit Product_resource_table"
 |- {{table_heading_style}}
 !|Resource type!!Source!!Notes/Reference
@@ Line 674: / Line 970: @@
 *
 ****************************************************************************************** -->{{Gene_accessions_help}}
-{|   id="W46aa57911b787"  class=" tableEdit Gene_accessions_table"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="W46aa57911b787"  class=" tableEdit Gene_accessions_table"
 |- {{table_heading_style}}
 !|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://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11619-MONOMER EcoCyc:EG11619-MONOMER]
+[http://www.ncbi.nlm.nih.gov/protein/NP_415632.1 GeneID:945681]
 |
+Escherichia coli str. K-12 substr. MG1655
+|-
+|
+[[ASAP]]
+|
+ASAP:ABE-0003763
+|
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
+|-
+|
+[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
+|
+[http://www.uniprot.org/uniprot/P30958 UniProtKB/Swiss-Prot:P30958]
+|
+Escherichia coli str. K-12 substr. MG1655
+|-
+|
+[[EcoCyc]]
+|
+EcoCyc:EG11619
+|
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
 |-
 |
-[http://swissmodel.expasy.org/repository/ SwissModel] ([[SwissModel|EcoliWiki Page]])
+[[EcoGene]]
 |
-[http://swissmodel.expasy.org/repository/smr.php?job=2&sptr_ac=P30958 SwissModel:P30958]
+EcoGene:EG11619
 |
+''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:P30958|UniProt:P30958]]
+[http://www.ncbi.nlm.nih.gov/gene?term=945681 GeneID:945681]
 |
+Escherichia coli str. K-12 substr. MG1655
 |-
 |
-[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
+[[RegulonDB]]
 |
-[http://pfam.sanger.ac.uk/family?acc=PF02559 PFAM:PF02559]
+RegulonDB:ECK120001567
 |
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
 |-
 |
-[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_415632 RefSeq:NP_415632]
+EchoBASE:EB1576
 |
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
 |- class="tableEdit_footer"
@@ Line 731: / Line 1,055: @@
 *
 ****************************************************************************************** -->
-{|   id="Q46a7ea85c5f14"  class=" tableEdit Links_table"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Q46a7ea85c5f14"  class=" tableEdit Links_table"
 |- {{table_heading_style}}
 !|Name!!URL!!Comments
@@ Line 752: / Line 1,076: @@
 {{BacktoTop}}
 [[Category:Proteins]]
-[[Category:GO:0006350_!_transcription]][[Category:GO:0005737_!_cytoplasm]][[Category:Products with structures in PDB]]

mfd:Gene Product(s): Difference between revisions

Latest revision as of 20:34, 17 February 2015

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

References

Categories

Navigation menu

Search