fdhD:Gene Product(s): Difference between revisions

Standard name	FdhD
Synonyms	formate dehydrogenase formation protein^[1], B3895^[2]^[1], FdhD^[2]^[1] , ECK3888, JW3866, b3895
Product description	affects formate dehydrogenase-N^[2]^[3] Redox enzyme maturation protein (REMP) for FdnG/FdoG; required for formate dehydrogenase activity; probable cytoplasmic protein^[4]
EC number (for enzymes)
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Notes

Function

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

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
	GO:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00187	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	Seeded from EcoCyc (v14.0)	complete
	GO:0008863	formate dehydrogenase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003786	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009326	formate dehydrogenase complex	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003786	C	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	References	Evidence
Protein	aceE	PMID:15690043^[5]	Experiment(s):EBI-886164
Protein	aceF	PMID:15690043^[5]	Experiment(s):EBI-886164
Protein	iscS	PMID:15690043^[5]	Experiment(s):EBI-886164, EBI-887896
Protein	lpdA	PMID:15690043^[5]	Experiment(s):EBI-886164
Protein	lysU	PMID:15690043^[5]	Experiment(s):EBI-886164
Protein	rpsB	PMID:15690043^[5]	Experiment(s):EBI-886164
Protein	tatE	PMID:16606699^[6]	Experiment(s):EBI-1146919
Protein	gltJ	PMID:16606699^[6]	Experiment(s):EBI-1146919
Protein	lolB	PMID:16606699^[6]	Experiment(s):EBI-1146919
Protein	groL	PMID:16606699^[6]	Experiment(s):EBI-1146919
Protein	cspE	PMID:16606699^[6]	Experiment(s):EBI-1146919
Protein	yncC	PMID:16606699^[6]	Experiment(s):EBI-1146919
Protein	dapA	PMID:16606699^[6]	Experiment(s):EBI-1146919
Protein	atoA	PMID:16606699^[6]	Experiment(s):EBI-1146919
Protein	rpmB	PMID:16606699^[6]	Experiment(s):EBI-1146919
Protein	ahpC	PMID:16606699^[6]	Experiment(s):EBI-1146919
Protein	iscS	PMID:16606699^[6]	Experiment(s):EBI-1146919
Protein	ydfX	PMID:16606699^[6]	Experiment(s):EBI-1146919
Protein	map	PMID:19402753^[7]	MALDI(Z-score):38.741739
Protein	gatZ	PMID:19402753^[7]	MALDI(Z-score):23.393145
Protein	iscS	PMID:19402753^[7]	LCMS(ID Probability):99.6 MALDI(Z-score):46.320178
Protein	ibpB	PMID:19402753^[7]	MALDI(Z-score):35.294336
Protein	narJ	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	rpsN	PMID:19402753^[7]	LCMS(ID Probability):99.6
Protein	dnaJ	PMID:19402753^[7]	MALDI(Z-score):34.017231
Protein	groS	PMID:19402753^[7]	MALDI(Z-score):28.256905
Protein	lysU	PMID:19402753^[7]	MALDI(Z-score):25.833714
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Notes

Localization

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

Compartment	Description	Evidence	Reference/Source	Notes
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Notes

Structure and Physical Properties

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

Name
Sequence	at EcoCyc MKKTQRKEIE NVTNITGVRQ IELWRRDDLQ HPRLDEVAEE VPVALVYNGI SHVVMMASPK DLEYFALGFS LSEGIIESPR DIFGMDVVPS CNGLEVQIEL SSRRFMGLKE RRRALAGRTG CGVCGVEQLN DIGKPVQPLP FTQTFDLNKL DDALRHLNDF QPVGQLTGCT HAAAWMLPSG ELVGGHEDVG RHVALDKLLG RRSQEGESWQ QGAVLVSSRA SYEMVQKSAM CGVEILFAVS AATTLAVEVA ERCNLTLVGF CKPGRATVYT HPQRLSN
Length	277
Mol. Wt	30.558 kDa
pI	6.4 (calculated)
Extinction coefficient	22,460 - 23,335 (calc based on 4 Y, 3 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	38..276	PF02634 FdhD/NarQ family		PMID:19920124^[8]
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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=fdhD 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:16131735	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948393	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0012714	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P32177	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11859	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11859	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948393	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001790	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1805	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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

↑ ^1.0 ^1.1 ^1.2 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
↑ 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.
↑ ^5.0 ^5.1 ^5.2 ^5.3 ^5.4 ^5.5 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
↑ ^6.00 ^6.01 ^6.02 ^6.03 ^6.04 ^6.05 ^6.06 ^6.07 ^6.08 ^6.09 ^6.10 ^6.11 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
↑ ^7.0 ^7.1 ^7.2 ^7.3 ^7.4 ^7.5 ^7.6 ^7.7 ^7.8 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

fdhD:Gene Product(s): Difference between revisions

Latest revision as of 21:09, 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 44: / Line 44: @@
 !align=left {{table heading style}} |Synonyms
 ||
-formate dehydrogenase formation protein<ref name='LIB:Riley_2006'/>, B3895<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, FdhD<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>
+''formate dehydrogenase formation protein<ref name='LIB:Riley_2006'/>, B3895<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/>, FdhD<ref name='LIB:EcoCyc10.6'/><ref name='LIB:Riley_2006'/> , ECK3888, JW3866, b3895''
 |-
 !align=left {{table heading style}} |Product description
@@ Line 75: / Line 75: @@
 *
 ****************************************************************************************** -->{{Product_GO_help}}
-{|   id="I46ab0b43b82dd"  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="I46ab0b43b82dd"  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
 |-
 |
@@ Line 187: / Line 187: @@
 *
 ****************************************************************************************** -->{{Product_interactions_help}}
-{|   id="E46ab0b482bcde"  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="E46ab0b482bcde"  class=" tableEdit Product_interactions_table dataTable"
 |- {{table heading style}}
 !|Partner Type!!Partner!!Notes!!References!!Evidence
@@ Line 392: / Line 392: @@
 Protein
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-[[map:Gene_Product(s)|map]]
+map
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@@ Line 398: / Line 398: @@
 PMID:19402753
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- MALDI(Z-score):38.741739
+MALDI(Z-score):38.741739
+|-
+|
+Protein
+|
+gatZ
+|
+|
+PMID:19402753
+|
+MALDI(Z-score):23.393145
+|-
+|
+Protein
+|
+iscS
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6 MALDI(Z-score):46.320178
+|-
+|
+Protein
+|
+ibpB
+|
+|
+PMID:19402753
+|
+MALDI(Z-score):35.294336
+|-
+|
+Protein
+|
+narJ
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
+|-
+|
+Protein
+|
+rpsN
+|
+|
+PMID:19402753
+|
+LCMS(ID Probability):99.6
+|-
+|
+Protein
+|
+dnaJ
+|
+|
+PMID:19402753
+|
+MALDI(Z-score):34.017231
+|-
+|
+Protein
+|
+groS
+|
+|
+PMID:19402753
+|
+MALDI(Z-score):28.256905
+|-
+|
+Protein
+|
+lysU
+|
+|
+PMID:19402753
+|
+MALDI(Z-score):25.833714
 |- class="tableEdit_footer"
@@ Line 417: / Line 505: @@
 *
 ****************************************************************************************** -->{{Product_localization_help}}
-{|   id="S46a8940f43037"  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="S46a8940f43037"  class=" tableEdit Product_localization_table"
 |- {{table heading style}}
-!|Compartment!!Description!!Evidence!!Source!!Notes
+!|Compartment!!Description!!Evidence!!Reference/Source!!Notes
 |- class="tableEdit_footer"
@@ Line 443: / Line 531: @@
 ****************************************************************************************** -->{{Product_physical_properties_help}}
 {|   id="V46ab0b4a3aef7"  class=" tableEdit Product_phys_prop_table"
+|-
+!align=left {{table heading style}} |Name
+||
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@@ Line 485: / Line 577: @@
 *
 ****************************************************************************************** -->{{Product_domains_motifs_help}}
-{|   id="T46ab0b4ab3121"  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="T46ab0b4ab3121"  class=" tableEdit Product_motif_table dataTable"
 |- {{table heading style}}
 !|Type!!Residues!!Description!!Notes!!References
@@ Line 534: / Line 626: @@
 ||
 View models at:
-* [http://dragon.bio.purdue.edu/ecolpredict2/localsearch/cgi-bin/search3.cgi?q=recA EcoliPredict]
+* [http://www.proteinmodelportal.org/query/uniprot/P32177 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=P32177 PSI-PRED (P32177)]
-* [http://bioinf.cs.ucl.ac.uk/psipred/ PSI-PRED]
+* [http://spock.genes.nig.ac.jp/~genome/cgi-bin/gkeytext.pl.cgi?A&QUERY1=P32177 Genomes TO Protein (P32177)] (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 579: / Line 669: @@
 *
 ****************************************************************************************** -->{{Product_resources_help}}
-{|   id="L46ab0b4b8b06c"  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="L46ab0b4b8b06c"  class=" tableEdit Product_resource_table"
 |- {{table_heading_style}}
 !|Resource type!!Source!!Notes/Reference
@@ Line 601: / Line 691: @@
 *
 ****************************************************************************************** -->{{Gene_accessions_help}}
-{|   id="V46ab0b4bf14d7"  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="V46ab0b4bf14d7"  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://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11859-MONOMER EcoCyc:EG11859-MONOMER]
+[http://www.ncbi.nlm.nih.gov/protein/16131735 GI:16131735]
 |
+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_418331.1 GeneID:948393]
+|
+Escherichia coli str. K-12 substr. MG1655
+|-
+|
+[[ASAP]]
+|
+ASAP:ABE-0012714
+|
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
+|-
+|
+[http://www.pir.uniprot.org/ UniProt] ([[UniProt|EcoliWiki Page]])
+|
+[http://www.uniprot.org/uniprot/P32177 UniProtKB/Swiss-Prot:P32177]
+|
+Escherichia coli str. K-12 substr. MG1655
+|-
+|
+[[EcoCyc]]
+|
+EcoCyc:EG11859
+|
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
+|-
+|
+[[EcoGene]]
+|
+EcoGene:EG11859
+|
+''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]])
 |
-[http://www.uniprot.org/uniprot/P32177 UniProt:P32177]
+[http://www.ncbi.nlm.nih.gov/gene?term=948393 GeneID:948393]
 |
+Escherichia coli str. K-12 substr. MG1655
 |-
 |
-[http://pfam.sanger.ac.uk/ PFAM] ([[PFAM|EcoliWiki Page]])
+[[RegulonDB]]
 |
-[http://pfam.janelia.org/protein/P32177 Pfam:P32177]
+RegulonDB:ECK120001790
 |
+''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_418331 RefSeq:NP_418331]
+EchoBASE:EB1805
 |
+''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
 |- class="tableEdit_footer"
@@ Line 651: / Line 776: @@
 *
 ****************************************************************************************** -->
-{|   id="P46a894139a5ce"  class=" tableEdit Links_table"
+{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="P46a894139a5ce"  class=" tableEdit Links_table"
 |- {{table_heading_style}}
 !|Name!!URL!!Comments

fdhD:Gene Product(s): Difference between revisions

Latest revision as of 21:09, 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