README.md

RetroPath2.0 parameters for Carotene

Below are listed the RetroPath2.0 parameters in order to reproduce the carotene results. See "RetroPath2.0_tutorial" file for a step-by-step guide.

Input
- Pathway length: 5
- Source: path to "carotene/source.csv" file (beta-carotene)
- Sink: path to "carotene/sink.csv" file (all E. coli compounds)
- Rules: path to "carotene/rules.csv" file (see Rules section)
Output
- Result folder: path to the desired output folder (should exists before execution)
Result expected
- The generated metabolic graph (.json file in the result folder) can be visualized using the Scope Viewer.

Rules have been selected according to references. Below enzymes, EC numbers and associated MNXR IDs for each step:

Enzyme: GGPP synthase
- EC number(s): 2.5.1.29
- MetaNetX reactions: MNXR55435
Enzyme: phytoene synthase
- EC number(s): 2.5.1.32
- MetaNetX reactions: MNXR71200, MNXR70495, MNXR15602, MNXR8603, MNXR87812, MNXR67228
Enzyme: phytoene desaturase
- EC number(s): 1.3.99.31, 1.3.99.28
- MetaNetX reactions: MNXR26357, MNXR26773, MNXR26774
Enzyme: lycopene cyclase
- EC number(s): 5.5.1.19
- MetaNetX reactions: MNXR15454, MNXR16029, MNXR60336, MNXR17616, MNXR9555,