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  • ? : A single character. E.g., trehalose?phosphatase covers both trehalose phosphatase and trehalose-phosphatase, of which, only the latter fits the nomenclature used in this database.
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Network Biomass WormPaths
FBAFlux Balance Analysis PEAPathway Enrichment Analysis
Gene Overview
Name ..................................................... : ogdh-1
Sequence ID ..................................................... : T22B11.5
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. ..................................................... : K00164OGDH sucA; 2-oxoglutarate dehydrogenase E1 component [EC:1.2.4.2]
Enzymes in the model (?) Enzymes that are part of the current metabolic network model. ..................................................... : 1.2.4.2names: oxoglutarate dehydrogenase (succinyl-transferring);2-ketoglutarate dehydrogenase;2-oxoglutarate dehydrogenase;2-oxoglutarate: lipoate oxidoreductase;2-oxoglutarate:lipoamide 2-oxidoreductase (decarboxylating and acceptor-succinylating);alpha-ketoglutarate dehydrogenase;alphaketoglutaric acid dehydrogenase;alpha-ketoglutaric dehydrogenase;alpha-oxoglutarate dehydrogenase;AKGDH;OGDC;ketoglutaric dehydrogenase;oxoglutarate decarboxylase;oxoglutarate dehydrogenase;oxoglutarate dehydrogenase (lipoamide)
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.
.....................................................
: RMC0003, RMC0014
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. ..................................................... : R08549, R01700, R01933

In WormPaths (?) Pathway maps where this gene is represented are listed here. ..................................................... : Lysine degradation, TCA cycle
► | Gene-KO-Enzyme-Reaction Associations (click to view)▼ | Gene-KO-Enzyme-Reaction Associations (click to hide)
► | 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 K00164 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).
K00164 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.
K00164 1.00 1.00 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.
K00164 0.99 0.99 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.
K00164 2.00 2.00 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).
K00164 K15791 1 1 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:

"2-oxoglutarate dehydrogenase, E1 component $ Dehydrogenase E1 component $ Dehydrogenase, E1 component $ Phosphorylation site $ Transketolase, pyrimidine binding $ Transketolase-like, pyrimidine-binding $$ The T22B11.5 gene encodes an ortholog of the human gene OGDH, which when mutated leads to alpha-ketoglutarate deficiency (OMIM:203740); the T22B11.5 protein is predicted to be mitochondrial with 68% accuracy."
K00164 K00658 1.4 1.0 ERROR
Overall (?) Overall score from SACURE that represents the logistic-regression-based probability of acceptance of a KO in association with the query gene. K00164 1.000 1.000 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.
0.97 0.03
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).
0.93 0.09
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).
1 0
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).
1 0
► | Phylogenetic tree (click to view)▼ | Phylogenetic tree (click to hide)
K00164 VER:phi OGDH (R) K00164 MAM:shr OGDH (R) K00164 HSA:hsa OGDHL (R) K00164 INV:bfo BRAFLDRAFT_130310 (R) K00164 DME:dme Nc73EF (R) K00164 ART:phu Phum_PHUM601630 (R) K00164 NEM:cbr CBG01737 (R) KO-TBD CEL:cel ogdh-1 (SUBJECT) K00164 PRO:mbr MONBRDRAFT_39301 (R) K00164 PLA:vcn ogd1 (R) K00164 ATH:ath AT5G65750 (R) K00164 BAC:tmo sucA (R) K00164 SCE:sce KGD1 (R) K00164 FUN:ure UREG_05316 (R) K15791 CEL:cel ZK836.2 (P) 0.1
Sequence labels indicate KO, taxonomy or model organism, organism name (if taxonomic group), and gene name, respectively. CEL, C. elegans; HSA, H. sapiens; DME, D. melanogaster; ATH, A. thaliana; SCE, S. cerevisiae; BAC, bacteria; ARC, archaea; PRO, protists; FUN, fungi; PLA, plants; INV, invertebrates; NEM, nematodes; ART, arthropods; VER, vertebrates; MAM, mammals. Parenthetical information for organisms other than CEL indicates whether the genes are introduced as best matches (B) or reciprocal best hits (R) to the query gene. Parenthetical information for CEL indicates whether the genes are introduced as paralogues (P) of the query gene or as reciprocal best matches to one of the other organisms in the tree (B). Organism abbreviations are from KEGG.
Reactions
ID 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
1.2.4.2Name: oxoglutarate dehydrogenase (succinyl-transferring)
Other names: 2-ketoglutarate dehydrogenase, 2-oxoglutarate dehydrogenase, 2-oxoglutarate: lipoate oxidoreductase, 2-oxoglutarate:lipoamide 2-oxidoreductase (decarboxylating and acceptor-succinylating), alpha-ketoglutarate dehydrogenase, alphaketoglutaric acid dehydrogenase, alpha-ketoglutaric dehydrogenase, alpha-oxoglutarate dehydrogenase, AKGDH, OGDC, ketoglutaric dehydrogenase, oxoglutarate decarboxylase, oxoglutarate dehydrogenase, oxoglutarate dehydrogenase (lipoamide)

click to see details on this item

2.3.1.61Name: dihydrolipoyllysine-residue succinyltransferase
Other names: dihydrolipoamide S-succinyltransferase, dihydrolipoamide succinyltransferase, dihydrolipoic transsuccinylase, dihydrolipolyl transsuccinylase, dihydrolipoyl transsuccinylase, lipoate succinyltransferase (Escherichia coli), lipoic transsuccinylase, lipoyl transsuccinylase, succinyl-CoA:dihydrolipoamide S-succinyltransferase, succinyl-CoA:dihydrolipoate S-succinyltransferase, enzyme-dihydrolipoyllysine:succinyl-CoA S-succinyltransferase

click to see details on this item

1.8.1.4Name: dihydrolipoyl dehydrogenase
Other names: LDP-Glc, LDP-Val, dehydrolipoate dehydrogenase, diaphorase, dihydrolipoamide dehydrogenase, dihydrolipoamide:NAD+ oxidoreductase, dihydrolipoic dehydrogenase, dihydrothioctic dehydrogenase, lipoamide dehydrogenase (NADH), lipoamide oxidoreductase (NADH), lipoamide reductase, lipoamide reductase (NADH), lipoate dehydrogenase, lipoic acid dehydrogenase, lipoyl dehydrogenase, protein-6-N-(dihydrolipoyl)lysine:NAD+ oxidoreductase

click to see details on this item
1.2.4.2Name: oxoglutarate dehydrogenase (succinyl-transferring)
Other names: 2-ketoglutarate dehydrogenase, 2-oxoglutarate dehydrogenase, 2-oxoglutarate: lipoate oxidoreductase, 2-oxoglutarate:lipoamide 2-oxidoreductase (decarboxylating and acceptor-succinylating), alpha-ketoglutarate dehydrogenase, alphaketoglutaric acid dehydrogenase, alpha-ketoglutaric dehydrogenase, alpha-oxoglutarate dehydrogenase, AKGDH, OGDC, ketoglutaric dehydrogenase, oxoglutarate decarboxylase, oxoglutarate dehydrogenase, oxoglutarate dehydrogenase (lipoamide)

click to see details on this item

2.3.1.61Name: dihydrolipoyllysine-residue succinyltransferase
Other names: dihydrolipoamide S-succinyltransferase, dihydrolipoamide succinyltransferase, dihydrolipoic transsuccinylase, dihydrolipolyl transsuccinylase, dihydrolipoyl transsuccinylase, lipoate succinyltransferase (Escherichia coli), lipoic transsuccinylase, lipoyl transsuccinylase, succinyl-CoA:dihydrolipoamide S-succinyltransferase, succinyl-CoA:dihydrolipoate S-succinyltransferase, enzyme-dihydrolipoyllysine:succinyl-CoA S-succinyltransferase

click to see details on this item

1.8.1.4Name: dihydrolipoyl dehydrogenase
Other names: LDP-Glc, LDP-Val, dehydrolipoate dehydrogenase, diaphorase, dihydrolipoamide dehydrogenase, dihydrolipoamide:NAD+ oxidoreductase, dihydrolipoic dehydrogenase, dihydrothioctic dehydrogenase, lipoamide dehydrogenase (NADH), lipoamide oxidoreductase (NADH), lipoamide reductase, lipoamide reductase (NADH), lipoate dehydrogenase, lipoic acid dehydrogenase, lipoyl dehydrogenase, protein-6-N-(dihydrolipoyl)lysine:NAD+ oxidoreductase

click to see details on this item
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