{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

On One Page

Quickview |

Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Standard Name	torD
Gene Synonym(s)	ECK0989, b0998, JW0983^[1], JW0983
Product Desc.	chaperone protein for trimethylamine-N-oxide oxidoreductase I^[2]^[3] Redox enzyme maturation protein (REMP) for TorA; cytoplasmic chaperone for TorA activation; protects TorA TAT signal peptide from degradation^[4]
Product Synonyms(s)	chaperone involved in maturation of TorA subunit of trimethylamine N-oxide reductase system I^[1], B0998^[2]^[1], TorD^[2]^[1] , ECK0989, JW0983, b0998
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): torCAD^[2], OP00297, tor
Regulation/Activity
Quick Links
edit table

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]

TorD prepares the molybdoenzyme TorA for MGD cofactor insertion, independent of signal peptide binding. torD, dmsD and ycdY are paralogs. Overexpressed YdcY and DmsD interfere with apoTorA maturation by TorD, independent of the TorA signal peptide (Ilbert, 2004). Bifunctional TorD acts in MGD insertion and TorA export proof-reading, a step that insures only mature protein is exported.^[4]

Gene

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]

See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	torD
Mnemonic	Trimethylamine oxide reductase
Synonyms	ECK0989, b0998, JW0983^[1], JW0983
edit table

</protect>

Notes

Location(s) and DNA Sequence

[back to top]

<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	22.87 minutes	MG1655: 1061022..1061621 <gbrowseImage> name=NC_000913:1061022..1061621 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1078089..1078688 <gbrowseImage> name=NC_012967:1078089..1078688 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 963990..964589 <gbrowseImage> name=NC_012759:963990..964589 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1062221..1062820 <gbrowseImage> name=NC_007779:1062221..1062820 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1114950..1115549 <gbrowseImage> name=NC_010473:1114950..1115549 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
edit table

</protect>

Notes

Sequence Features

[back to top]

See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
edit table

Notes

Alleles and Phenotypes

[back to top]

See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Phenotype: Description	Reference	Availability	Comments
Strain DH10B		S46N	Nonsynonomous mutation	PMID:18245285	ASAP	This is a SNP in E. coli K-12 Strain DH10B
torD(del)(Keio:JW0983)	deletion	deletion		PMID:16738554	Shigen CGSC8970^[5]
torD7429(del)::kan				PMID:16738554	CGSC:103180
edit table

Notes

Genetic Interactions

[back to top]

Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
edit table

</protect>

Notes

Genetic Resources

[back to top]

See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW0983	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACCACGCTGACAGCACAACA Primer 2:CCTCTGTTTTGGTGGTCGCACTC
2F1	Kohara Phage	Genobase	PMID:3038334
5A12	Kohara Phage	Genobase	PMID:3038334
zcb-3059::Tn10	Linked marker	CAG12094 = CGSC7358^[5]	est. P1 cotransduction: 5% ^[6]
zcc-282::Tn10	Linked marker	CAG18466 = CGSC7359^[5]	est. P1 cotransduction: 95% ^[6]
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
EcoCyc	EcoCyc:EG12195	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12195	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002084	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945625	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2112	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003374	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Product(s)

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

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

Standard name	TorD
Synonyms	chaperone involved in maturation of TorA subunit of trimethylamine N-oxide reductase system I^[1], B0998^[2]^[1], TorD^[2]^[1] , ECK0989, JW0983, b0998
Product description	chaperone protein for trimethylamine-N-oxide oxidoreductase I^[2]^[3] Redox enzyme maturation protein (REMP) for TorA; cytoplasmic chaperone for TorA activation; protects TorA TAT signal peptide from degradation^[4]
EC number (for enzymes)
edit table

Notes

Function

[back to top]

<protect> 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_01150	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:0006457	protein folding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01150	P	Seeded from EcoCyc (v14.0)	complete
	GO:0008940	nitrate reductase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003765	F	Seeded from EcoCyc (v14.0)	complete
	GO:0009325	nitrate reductase complex	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003765	C	Seeded from EcoCyc (v14.0)	complete
	GO:0055114	oxidation reduction	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003765	P	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	PMID:9632735	IDA: Inferred from Direct Assay		C		complete
	GO:0042277	peptide binding	PMID:18522945	IMP: Inferred from Mutant Phenotype		F	TorD binds the TorA signal sequence (Figure 3).	complete
	GO:0005515	protein binding	PMID:18522945	IPI: Inferred from Physical Interaction	EcoliWiki:mobA	F		complete
	GO:0043546	molybdopterin cofactor binding	PMID:18522945	IMP: Inferred from Mutant Phenotype		F		complete
	GO:0051604	protein maturation	PMID:15723832	IEP: Inferred from Expression Pattern		P		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	rplW	PMID:19402753	LCMS(ID Probability):99.6
Protein	groS	PMID:19402753	LCMS(ID Probability):99.6
Protein	pta	PMID:19402753	LCMS(ID Probability):99.6
Protein	yajQ	PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):29.816468
edit table

</protect>

Notes

Localization

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

Compartment	Description	Evidence	Reference/Source	Notes
cytoplasm
edit table

Notes

Structure and Physical Properties

[back to top]

<protect> 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 MTTLTAQQIA CVYAWLAQLF SRELDDEQLT QIASAQMAEW FSLLKSEPPL TAAVNELENR IATLTVRDDA RLELAADFCG LFLMTDKQAA LPYASAYKQD EQEIKRLLVE AGMETSGNFN EPADHLAIYL ELLSHLHFSL GEGTVPARRI DSLRQKTLTA LWQWLPEFVA RCRQYDSFGF YAALSQLLLV LVECDHQNR
Length	199
Mol. Wt	22.573 kDa
pI	4.6 (calculated)
Extinction coefficient	30,940 - 31,440 (calc based on 6 Y, 4 W, and 4 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	Notes	References
Domain	14..172	PF02613 Nitrate reductase delta subunit		PMID:19920124
edit table

<motif_map/>

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

Structures

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

Models

View models at:

edit table

</protect>

Structure figures

</protect>

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:16128964	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945625	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003374	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P36662	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12195	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12195	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945625	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002084	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2112	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Expression

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

[back to top]

See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Notes	Reference(s)
Protein	E. coli K-12 MG1655	0^a	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	1^a	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	0^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
edit table

Notes

Transcription and Transcriptional Regulation

[back to top]

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

Transcription unit(s)
torCAD
edit table

Figure courtesy of RegulonDB

</protect>

Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

[back to top]

<protect><gbrowseImage> name=NC_000913:1061002..1061042 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

</protect>

Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

[back to top]

<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
edit table

Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b0998 (EcoliWiki Page)	NCBI GEO profiles for torD
microarray	GenExpDB:b0998 (EcoliWiki Page)	Summary of data for torD from multiple microarray studies
edit table

Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
edit table

Notes

Accessions Related to torD Expression

[back to top]

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12195	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2112	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0998
EcoGene	EcoGene:EG12195	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002084	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003374	Escherichia coli str. K-12 substr. MG1655
edit table

Notes

Links

[back to top]

Name	URL	Comments
edit table

Evolution

[back to top]

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]

<protect> See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
edit table

</protect>

Do-It-Yourself Web Tools

Notes

Families

[back to top]

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

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF02613 Nitrate reductase delta subunit
Superfamily (EcoliWiki Page)	SUPERFAMILY:89155
EcoCyc	EcoCyc:EG12195	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12195	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002084	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2112	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003374	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 ^1.4 ^1.5 ^1.6 ^1.7 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 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
↑ ^4.0 ^4.1 ^4.2 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 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

torD:On One Page

Quickview

Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to torD Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

Categories

Navigation menu

Search