refactor: update general kcat database

[edkerk]

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Description of the new feature:

By repurposing some of the DLKcat code, construct a JSON file similar as in DLKcat. This JSON contains k_cat values from BRENDA and SABIO-RK databases, and could be run every 6-12 months.

In contrast to the current DLKcat code, some filtering steps should be skipped, to (a) keep specific activities; (b) keep cases where no amino acid sequence could be assigned to. By doing so, this kcat database can be used in GECKO's fuzzy matching approach. The file thereby replaces the max_Kcat and max_SA files that GECKO currently uses.

This JSON file should be loaded into MATLAB, to be used in GECKO fuzzy matching (which is refactored in a separate Issue).

However, if the purpose of this file is only used for GECKO's fuzzy matching, then we might as well stick with the existing max_Kcat and max_SA files? Let's keep this Issue on hold for now.

[mihai-sysbio]

I'm not totally sure on the scope of the issue: is it about creating a local k_cat file or about how that file is used by GECKO? Perhaps it would be easier to discuss verbally and write up conclusions.

[edkerk]

Both about the actual file and how it is used. But it sounds like GotEnzymes will also be able to provide such a file (did not know this when opening this issue), so this issue will most likely be addressed when GECKO and GotEnzymes can work together.

[edkerk]

Does not strictly have to be JSON, but it should be flat-text so that it is diff-able.

[edkerk]

For reference, this is what GotEnzymes output looks like (showing only the first 28 lines here):

{"enzymes":[{"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R04770","ec_number":"4.4.1.1;4.4.1.11","compound":"C00109","kcat_values":1.1646},
{"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R04770","ec_number":"4.4.1.1;4.4.1.11","compound":"C00014","kcat_values":4.2309},
{"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R09366","ec_number":"4.4.1.1;4.4.1.13","compound":"C05703","kcat_values":1.5564},
{"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R00782","ec_number":"4.4.1.1;4.4.1.13;4.4.1.28","compound":"C00022","kcat_values":0.7785},
{"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R09366","ec_number":"4.4.1.1;4.4.1.13","compound":"C00022","kcat_values":0.7785},
{"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R02408","ec_number":"4.4.1.1;4.4.1.13;4.4.1.35","compound":"C01962","kcat_values":2.2991},
{"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R04930","ec_number":"4.4.1.1","compound":"C00109","kcat_values":1.1646},
{"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R00782","ec_number":"4.4.1.1;4.4.1.13;4.4.1.28","compound":"C00283","kcat_values":2.2484},
{"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R09366","ec_number":"4.4.1.1;4.4.1.13","compound":"C00014","kcat_values":4.2309},
{"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R02408","ec_number":"4.4.1.1;4.4.1.13;4.4.1.35","compound":"C00022","kcat_values":0.7785},
{"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R04930","ec_number":"4.4.1.1","compound":"C05699","kcat_values":1.3478},
{"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R09366","ec_number":"4.4.1.1;4.4.1.13","compound":"C05689","kcat_values":1.3304},
{"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R04930","ec_number":"4.4.1.1","compound":"C00014","kcat_values":4.2309},
{"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R04770","ec_number":"4.4.1.1;4.4.1.11","compound":"C05703","kcat_values":1.5564},
{"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R02408","ec_number":"4.4.1.1;4.4.1.13;4.4.1.35","compound":"C00014","kcat_values":4.2309},
{"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R02408","ec_number":"4.4.1.1;4.4.1.13;4.4.1.35","compound":"C00491","kcat_values":1.0792},
{"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R01001","ec_number":"4.4.1.1","compound":"C02291","kcat_values":0.476},
{"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R04770","ec_number":"4.4.1.1;4.4.1.11","compound":"C05335","kcat_values":1.4882},
{"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R01001","ec_number":"4.4.1.1","compound":"C00014","kcat_values":4.2309},
{"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R01001","ec_number":"4.4.1.1","compound":"C00109","kcat_values":1.1646},
{"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R01001","ec_number":"4.4.1.1","compound":"C00097","kcat_values":0.1704}
{"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R00782","ec_number":"4.4.1.1;4.4.1.13;4.4.1.28","compound":"C00097","kcat_values":0.1704}
{"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R00782","ec_number":"4.4.1.1;4.4.1.13;4.4.1.28","compound":"C00014","kcat_values":4.2309}
{"gene":"YAL012W","organism":"sce","domain":"E","ko":"K01758","reaction_id":"R04930","ec_number":"4.4.1.1","compound":"C05688","kcat_values":0.7746}
{"gene":"YAL023C","organism":"sce","domain":"E","ko":"K00728","reaction_id":"R11399","ec_number":"2.4.1.109","compound":"C03862","kcat_values":5.6405}
{"gene":"YAL023C","organism":"sce","domain":"E","ko":"K00728","reaction_id":"R11399","ec_number":"2.4.1.109","compound":"C00110","kcat_values":5.1653}
{"gene":"YAL023C","organism":"sce","domain":"E","ko":"K00728","reaction_id":"R04072","ec_number":"2.4.1.109","compound":"C03862","kcat_values":5.6405}
{"gene":"YAL023C","organism":"sce","domain":"E","ko":"K00728","reaction_id":"R04072","ec_number":"2.4.1.109","compound":"C00110","kcat_values":5.1653}

[mihai-sysbio]

Just a note, the above is without having exposed a purpose-built API. Therefore, my recommendation would be to see that as a foundation to build a more compact and potentially more usable response.

[mihai-sysbio]

Here is the link to the promised API https://metabolicatlas.org/api/v2/#/GotEnzymes