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Network Biomass WormPaths
FBAFlux Balance Analysis PEAPathway Enrichment Analysis
Reaction Overview
Model ID ..................................................... : RMC0094
Name ..................................................... : Beta oxidation of intermediary fatty acid C16:3 (mitochondrial)
Type (?)

One of the following categories:

Regular: Regular enzymatic reactions that do not fit in any special categories below
Biomass: Reactions that represent the assembly of the worm biomass
Degradation: Reactions that represent the degradation of the bacterial diet
Demand: Reactions that consume products in the compartment that they are produced
Sink: Reactions that can not only consume but also provide a metabolite in a particular compartment (e.g., storage reactions)
Transport: Reactions that transport material between different compartments
Exchange: Reactions that exchange metabolites with the environment
.....................................................
: Regular
KEGG ID (?) Reactions in KEGG database that match this reaction.

Multiple IDs typically indicate that the model reaction is a merged reaction.
.....................................................
: R00392, R04319, R03224, R02685, R01778, R00391
Is in PRIME model (?) Indicates whether the reaction is part of the PRIME model, which is the basis (minimum model) for proper biomass/energy generation and compartmentalization. ..................................................... : Yes
Reversibility ..................................................... : Irreversible
Localization ..................................................... : Mitochondria
Other annotation ..................................................... : See tabular representation below.
Comments
  • Merged oxidation reaction down to a C14 with a set degradation pathway.
  • Gene sets follow the order of enzyme sets. The gene for 1.3.1.34 is based on PMID: 11025529.
  • Reaction for 5.3.3.8 is not in the list of KEGG reactions as specific matches are not available for this enzyme in the KEGG database.
  • See also note #10 and note #8.
  • Protein localization: based on pathway.
  • Reversibility: based on pathway.

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

    Score table (?) Localization scores for this reaction. Predictors use information at three levels: specific protein associated with the reaction, generic enzyme associated with the reaction, and the reaction itself.

    Each predictor is used to determine whether the reaction takes place in mitochondria or other compartment.

    "Not available" indicates that no score was available for the corresponding gene, enzyme, or reaction in the relevant database.

    Predictor Mitochondrial Other Weight
    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. Probability values >0.95 are multiplied by 2 as a bonus for the score.

    If multiple proteins are associated with the reaction, the maximum score for each compartment is presented. See corresponding gene pages (see table below) for the scores of individual proteins.
    2.00 1.91 2.0
    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).

    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).

    If multiple proteins are associated with the reaction, the maximum score for each compartment is presented. See corresponding gene pages (see table below) for the scores of individual proteins.
    1.00 0.67 1.5 Specific
    protein
    UniProt (?) Score shows the subcellular localization of proteins encoded by this gene as reported in UniProt (click to reach) in October 2014.

    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).

    If multiple proteins are associated with the reaction, the maximum score for each compartment is presented. See corresponding gene pages (see table below) for the scores of individual proteins.
    1 1 1.0
    Org. DB (?) Score shows the subcellular localization of proteins encoded by this gene as reported in Organelle Database (click to reach).

    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).

    If multiple proteins are associated with the reaction, the maximum score for each compartment is presented. See corresponding gene pages (see table below) for the scores of individual proteins.
    1 0 1.0
    BRENDA (?) Score represents the proportion of proteins experimentally localized to the indicated compartment as reported in the BRENDA database (click to reach) for the generic enzyme associated with this reaction. If one of the reported localization experiments for a compartment is carried out in C. elegans, a score of 1.0 is granted regardless of reports from other organisms.

    If multiple enzymes are associated with the reaction, the maximum score for each compartment is presented.
    0.94 0.70 1.0 Generic enzyme
    BiGG (?) Score represents 0.5 times the number of eukaryotic models with the indicated compartment for this reaction in the BiGG database. Since there are two eukaryotic models, the maximum score is 1.0. Not available Not available 1.5 Reaction
    FBA (?) Score shows whether the reaction is useful when it is placed in the indicated compartment based on flux balance analysis. A score of 0 generally indicates no flux carrying capacity, while 1 indicates that the reaction can carry flux. In some cases, a score of 0 also indicates flux carrying as part of a looping pathway, as a looping flux flow does not warrant the contribution of the reaction to metabolic processes in a comparment. If the flux also contributes to biomass or energy generation when placed in the pertaining compartment, a bonus score of 1 is added to reach a maximum score of 2.

    This score is valid only for PRIME model reactions, and therefore, is "not applicable" to others.
    1 0 2.0
    Overall (?) Obtained by multiplying each score by the corresponding weight and summing the products. A value >6.2 is considered as sufficient evidence for localization to the pertaining compartment. If neither compartment reaches this threshold, the greater score decides. However, if two scores are within 1.2 of each other, reaction is considered to be localized to both compartments. If FBA score is not available, the first threshold is reduced to 4.2. Exceptions (i.e., cases when these rules are overridden by other criteria) are idicated in general comments to the reaction. 10.4 6.5
    ► | Reversibility scores (click to view)▼ | Reversibility scores (click to hide)

    Score tables (?) Reaction directionality scores for the KEGG reaction(s) that are associated with this model reaction. Different sources are used and evidence is culminated for each direction with respect to the KEGG reaction (click reaction IDs to reach relevant KEGG pages).

    Reaction
    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
    1.3.8.7Name: medium-chain acyl-CoA dehydrogenase
    Other names: fatty acyl coenzyme A dehydrogenase (ambiguous), acyl coenzyme A dehydrogenase (ambiguous), acyl dehydrogenase (ambiguous), fatty-acyl-CoA dehydrogenase (ambiguous), acyl CoA dehydrogenase (ambiguous), general acyl CoA dehydrogenase (ambiguous), medium-chain acyl-coenzyme A dehydrogenase, acyl-CoA:(acceptor) 2,3-oxidoreductase (ambiguous), ACADM (gene name).

    click to see details on this item

    5.3.3.8Name: dodecenoyl-CoA isomerase
    Other names: dodecenoyl-CoA Delta-isomerase, Delta3-cis-Delta2-trans-enoyl-CoA isomerase, acetylene-allene isomerase, dodecenoyl-CoA Delta-isomerase, dodecenoyl-CoA Delta3-cis-Delta2-trans-isomerase

    click to see details on this item

    1.3.1.34Name: 2,4-dienoyl-CoA reductase (NADPH)
    Other names: 4-enoyl-CoA reductase (NADPH), 4-enoyl coenzyme A (reduced nicotinamide adenine dinucleotide phosphate) reductase, 4-enoyl-CoA reductase, 2,4-dienoyl-CoA reductase (NADPH)

    click to see details on this item

    4.2.1.17Name: enoyl-CoA hydratase
    Other names: enoyl hydrase, unsaturated acyl-CoA hydratase, beta-hydroxyacyl-CoA dehydrase, beta-hydroxyacid dehydrase, hydratase, enoyl coenzyme A, acyl coenzyme A hydrase, crotonase, crotonyl hydrase, 2-octenoyl coenzyme A hydrase, enoyl coenzyme A hydratase, 2-enoyl-CoA hydratase, short-chain enoyl-CoA hydratase, ECH, trans-2-enoyl-CoA hydratase, enoyl coenzyme A hydrase (D), enoyl coenzyme A hydrase (L), short chain enoyl coenzyme A hydratase, D-3-hydroxyacyl-CoA dehydratase, enol-CoA hydratase

    click to see details on this item

    1.1.1.211Name: long-chain-3-hydroxyacyl-CoA dehydrogenase
    Other names: beta-hydroxyacyl-CoA dehydrogenase, long-chain 3-hydroxyacyl coenzyme A dehydrogenase, 3-hydroxyacyl-CoA dehydrogenase, LCHAD

    click to see details on this item

    1.1.1.35Name: 3-hydroxyacyl-CoA dehydrogenase
    Other names: beta-hydroxyacyl dehydrogenase, beta-keto-reductase, 3-keto reductase, 3-hydroxyacyl coenzyme A dehydrogenase, beta-hydroxyacyl-coenzyme A synthetase, beta-hydroxyacylcoenzyme A dehydrogenase, beta-hydroxybutyrylcoenzyme A dehydrogenase, 3-hydroxyacetyl-coenzyme A dehydrogenase, L-3-hydroxyacyl coenzyme A dehydrogenase, L-3-hydroxyacyl CoA dehydrogenase, beta-hydroxyacyl CoA dehydrogenase, 3beta-hydroxyacyl coenzyme A dehydrogenase, 3-hydroxybutyryl-CoA dehydrogenase, beta-ketoacyl-CoA reductase, beta-hydroxy acid dehydrogenase, 3-L-hydroxyacyl-CoA dehydrogenase, 3-hydroxyisobutyryl-CoA dehydrogenase, 1-specific DPN-linked beta-hydroxybutyric dehydrogenase

    click to see details on this item

    2.3.1.16Name: acetyl-CoA C-acyltransferase
    Other names: beta-ketothiolase, 3-ketoacyl-CoA thiolase, KAT, beta-ketoacyl coenzyme A thiolase, beta-ketoacyl-CoA thiolase, beta-ketoadipyl coenzyme A thiolase, beta-ketoadipyl-CoA thiolase, 3-ketoacyl CoA thiolase, 3-ketoacyl coenzyme A thiolase, 3-ketoacyl thiolase, 3-ketothiolase, 3-oxoacyl-CoA thiolase, 3-oxoacyl-coenzyme A thiolase, 6-oxoacyl-CoA thiolase, acetoacetyl-CoA beta-ketothiolase, acetyl-CoA acyltransferase, ketoacyl-CoA acyltransferase, ketoacyl-coenzyme A thiolase, long-chain 3-oxoacyl-CoA thiolase, oxoacyl-coenzyme A thiolase, pro-3-ketoacyl-CoA thiolase, thiolase I, 2-methylacetoacetyl-CoA thiolase [misleading]

    click to see details on this item
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