WormFlux: mechanistic analysis of C. elegans metabolism

Gene Overview

Name .....................................................	:	F31D4.9
Sequence ID .....................................................	:	F31D4.9
Status (?) Can be one of the following two: Curated (manually annotated or based on a curated SACURE result), or Not curated (SACURE result reported without manual check). .....................................................	:	Curated
KO (?) The KEGG orthology group (KO) that is associated with this gene. .....................................................	:	K03945NDUFA1; NADH dehydrogenase (ubiquinone) 1 alpha subcomplex subunit 1
Enzymes in the model (?) Enzymes that are part of the current metabolic network model. .....................................................	:	1.6.5.3names: NADH:ubiquinone reductase (H+-translocating);ubiquinone reductase;type 1 dehydrogenase;complex 1 dehydrogenase;coenzyme Q reductase;complex I (electron transport chain);complex I (mitochondrial electron transport);complex I (NADH:Q1 oxidoreductase);dihydronicotinamide adenine dinucleotide-coenzyme Q reductase;DPNH-coenzyme Q reductase;DPNH-ubiquinone reductase;mitochondrial electron transport complex 1;mitochondrial electron transport complex I;NADH coenzyme Q1 reductase;NADH-coenzyme Q oxidoreductase;NADH-coenzyme Q reductase;NADH-CoQ oxidoreductase;NADH-CoQ reductase;NADH-ubiquinone reductase;NADH-ubiquinone oxidoreductase;NADH-ubiquinone-1 reductase;reduced nicotinamide adenine dinucleotide-coenzyme Q reductase;NADH:ubiquinone oxidoreductase complex;NADH-Q6 oxidoreductase;electron transfer complex I;NADH2 dehydrogenase (ubiquinone), 1.6.99.3names: NADH dehydrogenase;cytochrome c reductase;type 1 dehydrogenase;beta-NADH dehydrogenase dinucleotide;diaphorase;dihydrocodehydrogenase I dehydrogenase;dihydronicotinamide adenine dinucleotide dehydrogenase;diphosphopyridine diaphorase;DPNH diaphorase;NADH diaphorase;NADH hydrogenase;NADH oxidoreductase;NADH-menadione oxidoreductase;reduced diphosphopyridine nucleotide diaphorase;NADH:cytochrome c oxidoreductase;NADH2 dehydrogenase;NADH:(acceptor) oxidoreductase
Other enzymes (?) Enzymes that are associated with this gene in the WormFlux database, but not included in the current network model. .....................................................	:	None
Model reactions (?) Reactions that are part of the current metabolic network model. See the bottom of this page for a table of reactions. .....................................................	:	RMC0184, RMC0007, RMC0006, RMC0008
Relevant model reactions (?) Model reactions that follow from the KEGG reactions associated with this gene, but that exclude this gene due to differences in reaction specificity or localization compared to the predictions for this gene. .....................................................	:	ERROR
Other reactions (?) KEGG reactions that are associated with this gene in the WormFlux database, but not included in the current network model. .....................................................	:	R02166

In WormPaths (?) Pathway maps where this gene is represented are listed here. .....................................................	:	Electron transport chain

External links

WBGene00009294

CELE_F31D4.9

Q9U3H4

► | Gene-KO-Enzyme-Reaction Associations (click to view)▼ | Gene-KO-Enzyme-Reaction Associations (click to hide)

SACURE (?) Associations established by SACURE (Systematic Annotation by CUration and REgression).

SACURE pipeline annotates genes based on a logistic function that converts evidence from multiple resources into a KEGG orthology decision, which is then associated with enzymes and reactions. False positives and false negatives of the logistic function are separated out during manual curation for making exceptional decisions.

See HELP in the upper menu for a description of the SACURE pipeline.

See below for a summary of association scores from SACURE.

Results (?) KO: Associated KEGG Orthology groups
Enzyme: Associated enzymes in EC numbering
Reactions: Associated reactions from KEGG reaction database.

Confidence level is indicated for each association as a function of overall SACURE score (a probability of true association; see below in the SACURE scores section). Score ranges for HIGH, MEDIUM, and LOW confidence levels are >0.99, 0.90-0.99, and 0.50-0.90, respectively. If an association is accepted with a probability less than 0.50 (due to an exceptional reason), then the confidence level is LOW.

Not determined indicates that annotation analysis resulted in no clear associations.

	ID - Confidence
KO	Not determined
Enzyme	Not determined
Reaction	Not determined

Comments

Based on the logistic function.
See scores from predictors and the logistic function below (SACURE summary).

Reconstruction (?) Associations established during the reconstruction process by lenient annotation, literature search, or gap-filling.

Results (?) KO: Associated KEGG Orthology groups
Enzyme: Associated enzymes in EC numbering
Reactions: Associated reactions from KEGG reaction database or custom reactions developed during reconstruction.

	ID - Confidence
KO	K03945 - Low
Enzyme	1.6.5.3 - Low 1.6.99.3 - Low
Reaction	R02163 - Low R00281 - Low R02166 - Low

Comments

KEGG and re-evaluation of computational annotation evidence (SW table has low but consistent scores for the KO in question).

► | SACURE Summary (click to view)▼ | SACURE scores (click to hide)

Score table (?) Association scores for KOs best matching to the query gene according to each annotation predictor, and for the accepted KO if there is any (rightmost columns).

The predictors are ordered in decreasing weight of contribution to the decision-making process in SACURE.

See above for the final decision on the annotation of this gene.

Predictor	Best scoring KOs	Best score	K03945	ERROR
KEGG (?) Score represents the annotation in KEGG database by June 2014. Takes a value of either 0 (KO is not associated with the query gene) or 1 (KO is associated with the query gene).	K03945	1	1	ERROR
Cluster (?) Score represents the degree of relatedness of a KO to the query gene based on the clustering in the phylogenetic tree of protein sequences (see below for the tree). Takes values from 0 to 1.	Not applicable	0.00	0.00	ERROR
myKEGG (?) Score represents the degree of relatedness of a KO to the query gene based on the Smith-Waterman alignment of protein sequence with most similar sequences from all organisms in the KEGG database. Takes values from 0 to 1. KOunknown indicates the score for sequences without any KO association in KEGG database.	Not applicable	0.00	0.00	ERROR
Tree (?) Score shows the degree of relatedness of a KO to the query gene based on the density of this KO in the phylogenetic tree of protein sequences (see below for the tree). Takes values from 0 to 2 as the score is normalized to the second best KO. KOunknown indicates the score for sequences without any KO association in KEGG database.	Not applicable	0.00	0.00	ERROR
KOG (?) Score indicates the absence or presence of a KO in association with one of the orthologs of the query gene according to a eukaryotic orthology database independent of KEGG (see HELP* in the upper menu for details). Takes a value of either 0 (absent) or 1 (present*).	Not applicable	0	0	ERROR
WormBase (?) Score represents matching between the KEGG descriptions of a KO (KO name and all related enzyme names) and the descriptions of the query gene in WormBase (gene overview and protein domains). Value is increased by 0.5 for every perfect word match and reduced by 0.1 for each character interruption. A non-matching word always creates a 0 score. WormBase description used for this gene was: NO DESCRIPTIONS FOUND	Not applicable	0.0	0.0	ERROR
Overall (?) Overall score from SACURE that represents the logistic-regression-based probability of acceptance of a KO in association with the query gene.	K03945	0.012	0.012	ERROR

► | Localization scores (click to view)▼ | Localization scores (click to hide)

Score table (?) Localization scores for proteins encoded by the query gene.

Each predictor is used to determine whether the protein is localized to mitochondria or other compartment.

Together with other genes and other predictors, these scores were used in the determination of the subcellular location of reactions associated with the query gene (see below for the reactions).

Predictor	Mitochondrial	Other
Mitoprot (?) Score represents the predicted probability that the protein is targeted to mitochondria (mitochondrial score) or not (other score) according to Mitoprot (click to reach). If multiple isofoms of the same protein are available the highest scores are shown for each compartment.	0.19	0.81
MitoMiner (?) Score evaluates the evidence for mitochondrial targeting based on the orthologs in 12 eukaryotic model organisms that are in the MitoMiner database (click to reach). If clear orthologs for the query gene are available in MitoMiner organisms, the score takes a value between 0 and 1 as a function of the ratio of orthologs that have hits (contributes to the mitochondrial score) or no hits (determines the other score) in the database. Mitochondrial score is also a function of the strength of the evidence for the orthologs found in the database (experimental evidence is given a higher weight than theoretical evidence during scoring).	0.00	0.33
UniProt (?) Score shows the subcellular localization of proteins encoded by this gene as reported in UniProt (click to reach) in October 2014. If a report is available, the score takes a value of either 0 (not reported to be localized to the pertaining compartment) or 1 (reported to be localized to the pertaining compartment).	Not available	Not available
Org. DB (?) Score shows the subcellular localization of proteins encoded by this gene as reported in Organelle Database (click to reach). If a report is available, the score takes a value of either 0 (not reported to be localized to the pertaining compartment) or 1 (reported to be localized to the pertaining compartment).	Not available	Not available

► | Phylogenetic tree (click to view)▼ | Phylogenetic tree (click to hide)

Not available

Reactions

Enzyme

Reactants

Products

Genes (?) Multiple genes are separated by OR (I) or AND (&).

I indicates that genes are redundant within the group (e.g. paralogs encoding the same enzyme).
& indicates that genes are non-redundant within the group (e.g. genes encoding different subunits of the same enzyme).

If there are multiple groups of genes, as in an enzyme complex with some enzymes associated with multiple genes, or in a case where the same enzyme is associated with different orthology groups with paralogs, each group with multiple genes is shown in parentheses.

Pathway

RMC0184Name: NADH:rhodoquinone oxidoreductase Type: Regular Location: Cytosol, Mitochondria KEGG ID: R00281 click to see details on this item	1.6.5.3Name: NADH:ubiquinone reductase (H+-translocating) Other names: ubiquinone reductase, type 1 dehydrogenase, complex 1 dehydrogenase, coenzyme Q reductase, complex I (electron transport chain), complex I (mitochondrial electron transport), complex I (NADH:Q1 oxidoreductase), dihydronicotinamide adenine dinucleotide-coenzyme Q reductase, DPNH-coenzyme Q reductase, DPNH-ubiquinone reductase, mitochondrial electron transport complex 1, mitochondrial electron transport complex I, NADH coenzyme Q1 reductase, NADH-coenzyme Q oxidoreductase, NADH-coenzyme Q reductase, NADH-CoQ oxidoreductase, NADH-CoQ reductase, NADH-ubiquinone reductase, NADH-ubiquinone oxidoreductase, NADH-ubiquinone-1 reductase, reduced nicotinamide adenine dinucleotide-coenzyme Q reductase, NADH:ubiquinone oxidoreductase complex, NADH-Q6 oxidoreductase, electron transfer complex I, NADH2 dehydrogenase (ubiquinone) click to see details on this item 1.6.99.3Name: NADH dehydrogenase Other names: cytochrome c reductase, type 1 dehydrogenase, beta-NADH dehydrogenase dinucleotide, diaphorase, dihydrocodehydrogenase I dehydrogenase, dihydronicotinamide adenine dinucleotide dehydrogenase, diphosphopyridine diaphorase, DPNH diaphorase, NADH diaphorase, NADH hydrogenase, NADH oxidoreductase, NADH-menadione oxidoreductase, reduced diphosphopyridine nucleotide diaphorase, NADH:cytochrome c oxidoreductase, NADH2 dehydrogenase, NADH:(acceptor) oxidoreductase click to see details on this item	rq9Name: Rhodoquinone-9 Formula: C53H81NO3 Charge: 0 click to see details on this item[m] + nadhName: Nicotinamide adenine dinucleotide - reduced Formula: C21H27N7O14P2 Charge: -2 click to see details on this item[m] + (5.0) hName: H+ Formula: H Charge: 1 click to see details on this item[m]	rq9h2Name: Rhodoquinonol-9 Formula: C53H83NO3 Charge: 0 click to see details on this item[m] + nadName: Nicotinamide adenine dinucleotide Formula: C21H26N7O14P2 Charge: -1 click to see details on this item[m] + (4.0) hName: H+ Formula: H Charge: 1 click to see details on this item[c]	(nduo-1 & nduo-2 & nduo-3 & nduo-4 & nduo-5 & nduo-6 & ndfl-4) & [F53F4.10 & (gas-1 \| nduf-2.2) & nuo-2 & nuo-1 & nuo-5 & nduf-7 & T20H4.5 & lpd-5 & nduf-5 & nduf-6] & [F31D4.9 & Y63D3A.7 & C33A12.1 & nuo-3 & F45H10.3 & Y54F10AM.5 & Y53G8AL.2 & nuo-4 & (F37C12.3 \| Y56A3A.19) & C34B2.8] & (F44G4.2 & C18E9.4 & nuo-6 & C25H3.9 & ZK809.3 & D2030.4 & Y51H1A.3 & C16A3.5 & F59C6.5 & Y71H2AM.4 & F42G8.10)	Electron transport chain
RMC0007Name: NADH:ubiquinone oxidoreductase Type: Regular Location: Cytosol, Mitochondria KEGG ID: R02163 click to see details on this item	1.6.5.3Name: NADH:ubiquinone reductase (H+-translocating) Other names: ubiquinone reductase, type 1 dehydrogenase, complex 1 dehydrogenase, coenzyme Q reductase, complex I (electron transport chain), complex I (mitochondrial electron transport), complex I (NADH:Q1 oxidoreductase), dihydronicotinamide adenine dinucleotide-coenzyme Q reductase, DPNH-coenzyme Q reductase, DPNH-ubiquinone reductase, mitochondrial electron transport complex 1, mitochondrial electron transport complex I, NADH coenzyme Q1 reductase, NADH-coenzyme Q oxidoreductase, NADH-coenzyme Q reductase, NADH-CoQ oxidoreductase, NADH-CoQ reductase, NADH-ubiquinone reductase, NADH-ubiquinone oxidoreductase, NADH-ubiquinone-1 reductase, reduced nicotinamide adenine dinucleotide-coenzyme Q reductase, NADH:ubiquinone oxidoreductase complex, NADH-Q6 oxidoreductase, electron transfer complex I, NADH2 dehydrogenase (ubiquinone) click to see details on this item 1.6.99.3Name: NADH dehydrogenase Other names: cytochrome c reductase, type 1 dehydrogenase, beta-NADH dehydrogenase dinucleotide, diaphorase, dihydrocodehydrogenase I dehydrogenase, dihydronicotinamide adenine dinucleotide dehydrogenase, diphosphopyridine diaphorase, DPNH diaphorase, NADH diaphorase, NADH hydrogenase, NADH oxidoreductase, NADH-menadione oxidoreductase, reduced diphosphopyridine nucleotide diaphorase, NADH:cytochrome c oxidoreductase, NADH2 dehydrogenase, NADH:(acceptor) oxidoreductase click to see details on this item	qName: Ubiquinone Formula: C14H18O4 Charge: 0 click to see details on this item[m] + nadhName: Nicotinamide adenine dinucleotide - reduced Formula: C21H27N7O14P2 Charge: -2 click to see details on this item[m] + hName: H+ Formula: H Charge: 1 click to see details on this item[c]	qh2Name: Ubiquinol Formula: C14H20O4 Charge: 0 click to see details on this item[m] + nadName: Nicotinamide adenine dinucleotide Formula: C21H26N7O14P2 Charge: -1 click to see details on this item[m]	(nduo-1 & nduo-2 & nduo-3 & nduo-4 & nduo-5 & nduo-6 & ndfl-4) & [F53F4.10 & (gas-1 \| nduf-2.2) & nuo-2 & nuo-1 & nuo-5 & nduf-7 & T20H4.5 & lpd-5 & nduf-5 & nduf-6] & [F31D4.9 & Y63D3A.7 & C33A12.1 & nuo-3 & F45H10.3 & Y54F10AM.5 & Y53G8AL.2 & nuo-4 & (F37C12.3 \| Y56A3A.19) & C34B2.8] & (F44G4.2 & C18E9.4 & nuo-6 & C25H3.9 & ZK809.3 & D2030.4 & Y51H1A.3 & C16A3.5 & F59C6.5 & Y71H2AM.4 & F42G8.10)	Electron transport chain
RMC0006Name: NADH:ubiquinone oxidoreductase Type: Regular Location: Cytosol, Mitochondria KEGG ID: R02163 click to see details on this item	1.6.5.3Name: NADH:ubiquinone reductase (H+-translocating) Other names: ubiquinone reductase, type 1 dehydrogenase, complex 1 dehydrogenase, coenzyme Q reductase, complex I (electron transport chain), complex I (mitochondrial electron transport), complex I (NADH:Q1 oxidoreductase), dihydronicotinamide adenine dinucleotide-coenzyme Q reductase, DPNH-coenzyme Q reductase, DPNH-ubiquinone reductase, mitochondrial electron transport complex 1, mitochondrial electron transport complex I, NADH coenzyme Q1 reductase, NADH-coenzyme Q oxidoreductase, NADH-coenzyme Q reductase, NADH-CoQ oxidoreductase, NADH-CoQ reductase, NADH-ubiquinone reductase, NADH-ubiquinone oxidoreductase, NADH-ubiquinone-1 reductase, reduced nicotinamide adenine dinucleotide-coenzyme Q reductase, NADH:ubiquinone oxidoreductase complex, NADH-Q6 oxidoreductase, electron transfer complex I, NADH2 dehydrogenase (ubiquinone) click to see details on this item 1.6.99.3Name: NADH dehydrogenase Other names: cytochrome c reductase, type 1 dehydrogenase, beta-NADH dehydrogenase dinucleotide, diaphorase, dihydrocodehydrogenase I dehydrogenase, dihydronicotinamide adenine dinucleotide dehydrogenase, diphosphopyridine diaphorase, DPNH diaphorase, NADH diaphorase, NADH hydrogenase, NADH oxidoreductase, NADH-menadione oxidoreductase, reduced diphosphopyridine nucleotide diaphorase, NADH:cytochrome c oxidoreductase, NADH2 dehydrogenase, NADH:(acceptor) oxidoreductase click to see details on this item	qName: Ubiquinone Formula: C14H18O4 Charge: 0 click to see details on this item[m] + nadhName: Nicotinamide adenine dinucleotide - reduced Formula: C21H27N7O14P2 Charge: -2 click to see details on this item[m] + (5.0) hName: H+ Formula: H Charge: 1 click to see details on this item[m]	qh2Name: Ubiquinol Formula: C14H20O4 Charge: 0 click to see details on this item[m] + nadName: Nicotinamide adenine dinucleotide Formula: C21H26N7O14P2 Charge: -1 click to see details on this item[m] + (4.0) hName: H+ Formula: H Charge: 1 click to see details on this item[c]	(nduo-1 & nduo-2 & nduo-3 & nduo-4 & nduo-5 & nduo-6 & ndfl-4) & [F53F4.10 & (gas-1 \| nduf-2.2) & nuo-2 & nuo-1 & nuo-5 & nduf-7 & T20H4.5 & lpd-5 & nduf-5 & nduf-6] & [F31D4.9 & Y63D3A.7 & C33A12.1 & nuo-3 & F45H10.3 & Y54F10AM.5 & Y53G8AL.2 & nuo-4 & (F37C12.3 \| Y56A3A.19) & C34B2.8] & (F44G4.2 & C18E9.4 & nuo-6 & C25H3.9 & ZK809.3 & D2030.4 & Y51H1A.3 & C16A3.5 & F59C6.5 & Y71H2AM.4 & F42G8.10)	Electron transport chain
RMC0008Name: NADH:ubiquinone oxidoreductase Type: Regular Location: Mitochondria KEGG ID: R02163 click to see details on this item	1.6.5.3Name: NADH:ubiquinone reductase (H+-translocating) Other names: ubiquinone reductase, type 1 dehydrogenase, complex 1 dehydrogenase, coenzyme Q reductase, complex I (electron transport chain), complex I (mitochondrial electron transport), complex I (NADH:Q1 oxidoreductase), dihydronicotinamide adenine dinucleotide-coenzyme Q reductase, DPNH-coenzyme Q reductase, DPNH-ubiquinone reductase, mitochondrial electron transport complex 1, mitochondrial electron transport complex I, NADH coenzyme Q1 reductase, NADH-coenzyme Q oxidoreductase, NADH-coenzyme Q reductase, NADH-CoQ oxidoreductase, NADH-CoQ reductase, NADH-ubiquinone reductase, NADH-ubiquinone oxidoreductase, NADH-ubiquinone-1 reductase, reduced nicotinamide adenine dinucleotide-coenzyme Q reductase, NADH:ubiquinone oxidoreductase complex, NADH-Q6 oxidoreductase, electron transfer complex I, NADH2 dehydrogenase (ubiquinone) click to see details on this item 1.6.99.3Name: NADH dehydrogenase Other names: cytochrome c reductase, type 1 dehydrogenase, beta-NADH dehydrogenase dinucleotide, diaphorase, dihydrocodehydrogenase I dehydrogenase, dihydronicotinamide adenine dinucleotide dehydrogenase, diphosphopyridine diaphorase, DPNH diaphorase, NADH diaphorase, NADH hydrogenase, NADH oxidoreductase, NADH-menadione oxidoreductase, reduced diphosphopyridine nucleotide diaphorase, NADH:cytochrome c oxidoreductase, NADH2 dehydrogenase, NADH:(acceptor) oxidoreductase click to see details on this item	[m] : qName: Ubiquinone Formula: C14H18O4 Charge: 0 click to see details on this item + nadhName: Nicotinamide adenine dinucleotide - reduced Formula: C21H27N7O14P2 Charge: -2 click to see details on this item + hName: H+ Formula: H Charge: 1 click to see details on this item	qh2Name: Ubiquinol Formula: C14H20O4 Charge: 0 click to see details on this item + nadName: Nicotinamide adenine dinucleotide Formula: C21H26N7O14P2 Charge: -1 click to see details on this item	(nduo-1 & nduo-2 & nduo-3 & nduo-4 & nduo-5 & nduo-6 & ndfl-4) & [F53F4.10 & (gas-1 \| nduf-2.2) & nuo-2 & nuo-1 & nuo-5 & nduf-7 & T20H4.5 & lpd-5 & nduf-5 & nduf-6] & [F31D4.9 & Y63D3A.7 & C33A12.1 & nuo-3 & F45H10.3 & Y54F10AM.5 & Y53G8AL.2 & nuo-4 & (F37C12.3 \| Y56A3A.19) & C34B2.8] & (F44G4.2 & C18E9.4 & nuo-6 & C25H3.9 & ZK809.3 & D2030.4 & Y51H1A.3 & C16A3.5 & F59C6.5 & Y71H2AM.4 & F42G8.10)	Electron transport chain

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