{{#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	ndh
Gene Synonym(s)	ECK1095, b1109, JW1095^[1], JW1095
Product Desc.	NADH dehydrogenase II^[2]^[3] Respiratory NADH dehydrogenase II; NADH:ubiquinone oxidoreductase II; membrane-bound flavoprotein; cupric reductase^[4]
Product Synonyms(s)	respiratory NADH dehydrogenase 2/cupric reductase^[1], B1109^[2]^[1], Ndh^[2]^[1], NDH-2^[2]^[1], NADH dhII^[2]^[1] , ECK1095, JW1095, b1109
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ndh^[2], OP00217
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]

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	ndh
Mnemonic	NADH dehydrogenase
Synonyms	ECK1095, b1109, JW1095^[1], JW1095
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	25.12 minutes	MG1655: 1165308..1166612 <gbrowseImage> name=NC_000913:1165308..1166612 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1180662..1181966 <gbrowseImage> name=NC_012967:1180662..1181966 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1069233..1070537 <gbrowseImage> name=NC_012759:1069233..1070537 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1167662..1168966 <gbrowseImage> name=NC_007779:1167662..1168966 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 1220753..1222057 <gbrowseImage> name=NC_010473:1220753..1222057 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
Coding Start (SO:0000323)	MG1655	1165311	Edman degradation	PMID:6265208
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)	Reference	Availability	Comments
Δndh (Keio:JW1095)	deletion	deletion	PMID:16738554	Shigen
ndh::Tn5KAN-2 (FB20255)	Insertion at nt 1052 in Plus orientation		PMID:15262929	E. coli Genome Project:FB20255	does not contain pKD46
ndh-401				CGSC:7432
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
JW1095	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACTACGCCATTGAAAAAGAT Primer 2:CCATGCAACTTCAAACGCGGACG
15A8	Kohara Phage	Genobase	PMID:3038334
zce-726::Tn10	Linked marker	CAG12078 = CGSC7361^[5]	est. P1 cotransduction: 71% ^[6]
zcf-117::Tn10	Linked marker	CAG18463 = CGSC7363^[5]	est. P1 cotransduction: 13% ^[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:EG10649	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10649	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000642	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946792	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0643	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003746	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	Ndh
Synonyms	respiratory NADH dehydrogenase 2/cupric reductase^[1], B1109^[2]^[1], Ndh^[2]^[1], NDH-2^[2]^[1], NADH dhII^[2]^[1] , ECK1095, JW1095, b1109
Product description	NADH dehydrogenase II^[2]^[3] Respiratory NADH dehydrogenase II; NADH:ubiquinone oxidoreductase II; membrane-bound flavoprotein; cupric reductase^[4]
EC number (for enzymes)	1.16.1.-^[1] 1.6.99.3^[1]
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
NOT	GO:0005737	cytoplasm	PMID:6784762	IDA: Inferred from Direct Assay		C	Seeded from Riley et al 2006 ^[1]. NADH dehydrogenase II fractionates with cellular membranes.	complete
	GO:0006810	transport	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0813	P	Seeded from EcoCyc (v14.0)	complete
	GO:0009061	anaerobic respiration				P	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	GO:0050660	FAD binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001327	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	rpsC	PMID:16606699	Experiment(s):EBI-1138895
Protein	rpsI	PMID:16606699	Experiment(s):EBI-1138895
Protein	hldD	PMID:16606699	Experiment(s):EBI-1138895
Protein	ompL	PMID:16606699	Experiment(s):EBI-1138895
Protein	rplB	PMID:16606699	Experiment(s):EBI-1138895
Protein	alr	PMID:16606699	Experiment(s):EBI-1138895
Protein	tufB	PMID:19402753	MALDI(Z-score):19.246938
Protein	gnd	PMID:19402753	LCMS(ID Probability):99.6
Protein	rfaD	PMID:19402753	MALDI(Z-score):38.374327
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
plasma membrane			From EcoCyc^[3]
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 MTTPLKKIVI VGGGAGGLEM ATQLGHKLGR KKKAKITLVD RNHSHLWKPL LHEVATGSLD EGVDALSYLA HARNHGFQFQ LGSVIDIDRE AKTITIAELR DEKGELLVPE RKIAYDTLVM ALGSTSNDFN TPGVKENCIF LDNPHQARRF HQEMLNLFLK YSANLGANGK VNIAIVGGGA TGVELSAELH NAVKQLHSYG YKGLTNEALN VTLVEAGERI LPALPPRISA AAHNELTKLG VRVLTQTMVT SADEGGLHTK DGEYIEADLM VWAAGIKAPD FLKDIGGLET NRINQLVVEP TLQTTRDPDI YAIGDCASCP RPEGGFVPPR AQAAHQMATC AMNNILAQMN GKPLKNYQYK DHGSLVSLSN FSTVGSLMGN LTRGSMMIEG RIARFVYISL YRMHQIALHG YFKTGLMMLV GSINRVIRPR LKLH
Length	434
Mol. Wt	47.359 kDa
pI	9.2 (calculated)
Extinction coefficient	28,880 - 29,380 (calc based on 12 Y, 2 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
Initiator Methionine	1	Removed	UniProt:P00393
Domain	7..102	PF00070 Pyridine nucleotide-disulphide oxidoreductase		PMID:19920124
Domain	172..266	PF00070 Pyridine nucleotide-disulphide oxidoreductase		PMID:19920124
Domain	7..321	PF07992 Pyridine nucleotide-disulphide oxidoreductase		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=ndh 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:16129072	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946792	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003746	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P00393	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10649	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10649	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946792	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000642	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0643	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 MC4100	5.71E+02	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI		PMID:18304323
Protein	Ecoli K-12	58.781+/-0.795	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.126917178	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	13264	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
Protein	E. coli K-12 MG1655	925	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
Protein	E. coli K-12 MG1655	8557	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		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)
ndh
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_000913:1165288..1165328 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:b1109 (EcoliWiki Page)	NCBI GEO profiles for ndh
microarray	GenExpDB:b1109 (EcoliWiki Page)	Summary of data for ndh 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
	GFP Fusion	Intergenic region (1164833..1165357) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ03; Well:G4^[7]
edit table

Notes

Accessions Related to ndh Expression

[back to top]

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10649	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0643	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1109
EcoGene	EcoGene:EG10649	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000642	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003746	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]

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

Organism	Homologs (Statistics)	Comments
Arabidopsis thaliana	AT2G29990 (score: 1.000; bootstrap: 60%) AT1G07180 (score: 0.808) AT4G05020 (score: 0.194) AT4G28220 (score: 0.194) AT2G20800 (score: 0.178) AT4G21490 (score: 0.127)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00038111 (score: 1.000; bootstrap: 100%) WBGene00038112 (score: 0.752)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000012973 (score: 1.000; bootstrap: 89%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0190805 (score: 1.000; bootstrap: 81%) DDB0188774 (score: 0.232) DDB0168392 (score: 0.195) DDB0190809 (score: 0.171) DDB0201952 (score: 0.126)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000007614 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000015274 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q5W745 (score: 1.000; bootstrap: 57%) Q655G1 (score: 1.000; bootstrap: 59%) Q6YZ09 (score: 0.332) Q8H5X6 (score: 0.182) Q5QLT6 (score: 0.112)	From Inparanoid:20070104
Saccharomyces cerevisiae	YDL085W (score: 1.000; bootstrap: 100%) YMR145C (score: 0.550) YML120C (score: 0.280)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPBC9475c (score: 1.000; bootstrap: 100%) SPAC3A117 (score: 0.304)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000158126 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00025004001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	NDH	From SHIGELLACYC
E. coli O157	NDH	From ECOO157CYC
edit table

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)	PF00070 Pyridine nucleotide-disulphide oxidoreductase
Pfam (EcoliWiki Page)	PF00070 Pyridine nucleotide-disulphide oxidoreductase
Superfamily (EcoliWiki Page)	SUPERFAMILY:51905
Superfamily (EcoliWiki Page)	SUPERFAMILY:51905
Panther (EcoliWiki Page)	PTHR22915:SF6
Pfam (EcoliWiki Page)	PF07992 Pyridine nucleotide-disulphide oxidoreductase
EcoCyc	EcoCyc:EG10649	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10649	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000642	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0643	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003746	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.

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 ^1.11 ^1.12 ^1.13 ^1.14 ^1.15 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

ndh: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 ndh Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

Categories

Navigation menu

Search