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Network Biomass WormPaths
FBAFlux Balance Analysis PEAPathway Enrichment Analysis
WormClustClustering- and enrichment-based association of genes with the metabolic network
Reaction Overview
Model ID ..................................................... : DGR0016
Name ..................................................... : Bacterial lipa (inner LPS and first two monomers of outer section) degradation
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
..................................................... 		: Degradation
KEGG ID (?) Reactions in KEGG database that match this reaction.

Multiple IDs typically indicate that the model reaction is a merged reaction. ..................................................... 		: Not available
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 ..................................................... : Cytosol
Other annotation ..................................................... : See tabular representation below.
Comments
  • Represents the degradation and composition of lipid A in bacterial diet.
  • Also see note #27.

    • ► | 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.     		ERROR ERROR 2.0w
    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.     		ERROR ERROR 1.5w 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.     		ERROR ERROR 1.0w
    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.     		ERROR ERROR 1.0w
    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.     		ERROR ERROR 1.0w 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. ERROR ERROR 1.5w 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.     		ERROR ERROR 2.0w
    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. ERROR ERROR
    ► | 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).

    ERROR
    Source Forward Backward Reversible
    MetaCyc (?) Score of 1 represents the direction of the reaction as indicated in MetaCyc. ERROR ERROR ERROR
    SEED (?) Score of 1 represents the direction of the reaction as indicated in the SEED database. ERROR ERROR ERROR
    BiGG (?) Score represents 0.5 times the number of models with the indicated direction for this reaction in the BiGG database. ERROR ERROR ERROR
    BRENDA (?) Score represents the proportion of reactions with the indicated direction reported in the BRENDA database for the enzymes associated with this reaction. Only reactions with a reported direction were used in the calculation. ERROR ERROR ERROR
    Total (?) If no direction has >0.5 points, reaction is considered reversible. If the score of one direction with the highest score is more than 25% larger than the next highest score, the direction with the highest score is taken. Else, reaction is considered reversible. Exceptions (i.e., cases when these rules are overridden by other criteria) are idicated in general comments to the reaction. ERROR ERROR ERROR
    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
    DGR0016Name: Bacterial lipa (inner LPS and first two monomers of outer section) degradation
    Type: Degradation
    Location: Cytosol
    KEGG ID: NA

    click to see details on this item
    To be determined
    [c] : lipa_BACName: KDO(2)-lipid (A)
    Formula: C110H196N2O39P2
    Charge: -6




    click to see details on this item     + (4) nadhName: Nicotinamide adenine dinucleotide - reduced
    Formula: C21H27N7O14P2
    Charge: -2




    click to see details on this item     + (5) h2oName: H2O
    Formula: H2O
    Charge: 0




    click to see details on this item
    ddcaName: Dodecanoate (n-C12:0)
    Formula: C12H23O2
    Charge: -1




    click to see details on this item     + (5) ttdcaName: tetradecanoate (n-C14:0)
    Formula: C14H27O2
    Charge: -1




    click to see details on this item     + (4) nadName: Nicotinamide adenine dinucleotide
    Formula: C21H26N7O14P2
    Charge: -1




    click to see details on this item     + (2) r5pName: alpha-D-Ribose 5-phosphate
    Formula: C5H9O8P
    Charge: -2




    click to see details on this item     + (2) pyrName: Pyruvate
    Formula: C3H3O3
    Charge: -1




    click to see details on this item     + (2) gamName: D-Glucosamine
    Formula: C6H14NO5
    Charge: 1




    click to see details on this item
    Not determined
    Bacterial digestion
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