WormFlux: mechanistic analysis of C. elegans metabolism

Reaction Overview

Model ID .....................................................

DGR0001

Name .....................................................

Bacterial peptide degradation

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.

iCEL1314

Comments

Represents degradation and amino acid composition of protein in the bacterial diet.

Listed genes are based on Geier et al. (2001) (https://doi.org/10.1046/j.1432-1327.1999.00679.x ) and probably encode a subset of proteolysis enzymes. According to Geier et al., aspartyl proteases are responsible for 90% of proteolytic activity in C. elegans extracts. Proteins encoded by the genes associated with this reaction were isolated and confirmed to be proteases in the same study.

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	Reaction

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