Fix duplicated reactions

[sulheim]

Description of the issue:

The following reactions are duplicated in terms of substrates / products (but not gene annotation):

• GABTA and ABPYRATA
• CA2abc1 and AMEt

Figure out which one of these that should be deleted / modified / kept

To do:

If specific curations are proposed, generate a list of checkboxes of steps that should be followed to solve this issue:

• [ ] E.g. generate script for performing curation

I hereby confirm that:

• [x] This problem persists in the master branch of the repository
• [x] A similar issue does not already exist
• [x] I've considered asking this first in the Gitter chat room

[sulheim]

About the reactions

1. ABPYRATA

- name: 4-aminobutyrate aminotransferase
- metabolites:
  - 4abut_c: -1.0
  - ala__L_c: 1.0
  - pyr_c: -1.0
  - sucsal_c: 1.0
- gene_reaction_rule: SCO5676 or SCO7034
- ec-code: 2.6.1.19
- kegg.reaction: R10178

The EC-code and gene annotations matches R01648 and not R10178. However, since R01648 also is present in the model already (id: ABTA), I suggest to delete this reaction.

2. GABTA

- gene_reaction_rule: SCO5655
- biocyc: RXN-6902
- ec-code: 2.6.1.96

Keep this reaction in the model and annotate it with R10178.

3. CA2abc1

- name: calcium-transporting ATPase
- metabolites:
 - adp_c: 1.0
 - atp_c: -1.0
 - ca2_c: 1.0
 - ca2_e: -1.0
 - h2o_c: -1.0
 - h_c: 1.0
 - pi_c: 1.0
- gene_reaction_rule: SCO3216 or SCO4332
- biocyc: 3.6.3.8-RXN
- ec-code: 3.6.3.8
- metanetx.reaction: MNXR96435

Keep this reaction as is

4. AMEt

Clearly something wrong here. Metabolites identical to CA2abc1.

- name: Transport of S-Adenosyl-L-methionine via ABC system
- gene_reaction_rule: SCO4104 or SCO5481

From the newTransportRxns.csv file I find the reason for the error: The compartment is cytoplasm for the metabolite amet both as substrate and product (should be [e] on one side) amet[c] + ca2[e] + h2o[c] + atp[c] -> amet[c] + ca2[c] + adp[c] + pi[c] + h[c]

Both genes are found on TransportDB and annotated as TRIC - transporters.

[edkerk]

I agree, remove (1), update (2) and keep (3). For (4), are TRIC transporters active (using ATP) and transporting more than just Ca2+? This is not so clear from the provided link.