Retrieve k_cat Report

Overview

Penalty Score Distribution

Score	Count	Percent
0	18	10.98%
1	7	4.27%
2	5	3.05%
3	17	10.37%
4	19	11.59%
5	33	20.12%
6	14	8.54%
7	3	1.83%
8	7	4.27%
9	2	1.22%
16	39	23.78%

Distribution of k_cat values (Stacked by Penalty Score)

Penalty Score

The penalty score evaluates how well a candidate k_cat entry fits the query enzyme and conditions. A lower score indicates a better match (0 = Best possible, 16 = No match).

Scoring process:

• Catalytic enzyme: Check if the reported enzyme matches the expected catalytic enzyme(s).
• Organism: Penalize mismatches between the source organism and the target organism.
• Enzyme variant: Exclude or penalize mutant/engineered variants (wildtype preferred).
• pH: Check whether the reported pH is consistent with the desired experimental range.
• Substrate: Verify substrate compatibility with the catalytic reaction.
• Temperature: Penalize deviations from the target temperature; if possible, adjust kcat values using the Arrhenius equation.

Score breakdown:

Criterion	Penalty
Substrate mismatch	+4
Catalytic enzyme mismatch	+3
Organism mismatch	+2
pH unknown	+1
pH out of range	+2
Temperature unknown	+1
Temperature out of range	+2
Enzyme variant unknown	+1

Candidates are then ranked by:

1. Lowest penalty-score
2. Highest sequence identity percentage to the target enzyme
3. Closest organism compared to the target organism.
4. Adjusted k_cat value (favoring the highest value by default)

Please check the documentation for more details on the scoring system and the retrieval process.

Notes

Please note that the number of rows may differ between the extraction and retrieval stages. Indeed, when a single reaction–enzyme combination is associated with multiple EC numbers, WILDkCAT automatically merges these rows after retrieval, keeping only the best entry according to the criteria described above. The EC number of the selected kcat is stored in the 'ec_code' column, while all EC numbers associated with the reaction are stored in the 'ec_codes' column.