Fix/mito nuc trans

[Devlin-Moyer]

Main improvements in this PR:

As proposed in #694:

• Creates new gene entries for ENSG00000171612 (name: SLC25A33) and ENSG00000114120 (name: SLC25A36)
• Makes MAR08301 reversible and change its GPR to ENSG00000171612
• Removes MAR07823, MAR07926, MAR09019 and MAR04843
• Creates new reaction CTP [c] + CDP [m] <-> CTP [m] + CDP [c], GPR: ENSG00000114120
• Creates new reaction CTP [c] + CMP [m] <-> CTP [m] + CMP [c], GPR: ENSG00000114120
• Creates new reaction CTP [c] + dCTP [m] <-> CTP [m] + dCTP [c], GPR: ENSG00000114120
• Creates new reaction CTP [c] + dCDP [m] <-> CTP [m] + dCDP [c], GPR: ENSG00000114120
• Creates new reaction CTP [c] + dCMP [m] <-> CTP [m] + dCMP [c], GPR: ENSG00000114120
• Creates new reaction CTP [c] + GTP [m] <-> CTP [m] + GTP [c], GPR: ENSG00000114120
• Creates new reaction CTP [c] + GDP [m] <-> CTP [m] + GDP [c], GPR: ENSG00000114120
• Creates new reaction CTP [c] + GMP [m] <-> CTP [m] + GMP [c], GPR: ENSG00000114120
• Creates new reaction CTP [c] + dGTP [m] <-> CTP [m] + dGTP [c], GPR: ENSG00000114120
• Creates new reaction CTP [c] + dGDP [m] <-> CTP [m] + dGDP [c], GPR: ENSG00000114120
• Creates new reaction CTP [c] + dGMP [m] <-> CTP [m] + dGMP [c], GPR: ENSG00000114120
• Creates new reaction CTP [c] + ITP [m] <-> CTP [m] + ITP [c], GPR: ENSG00000114120
• Creates new reaction CTP [c] + IDP [m] <-> CTP [m] + IDP [c], GPR: ENSG00000114120
• Creates new reaction CTP [c] + IMP [m] <-> CTP [m] + IMP [c], GPR: ENSG00000114120
• Creates new reaction CTP [c] + UTP [m] <-> CTP [m] + UTP [c], GPR: ENSG00000114120 or ENSG00000171612
• Creates new reaction CTP [c] + UDP [m] <-> CTP [m] + UDP [c], GPR: ENSG00000114120
• Creates new reaction CTP [c] + UMP [m] <-> CTP [m] + UMP [c], GPR: ENSG00000114120
• Creates new reaction CTP [c] + dUTP [m] <-> CTP [m] + dUTP [c], GPR: ENSG00000114120
• Creates new reaction CTP [c] + dUDP [m] <-> CTP [m] + dUDP [c], GPR: ENSG00000114120
• Creates new reaction CTP [c] + dUMP [m] <-> CTP [m] + dUMP [c], GPR: ENSG00000114120
• Creates new reaction UTP [c] + CDP [m] <-> UTP [m] + CDP [c], GPR: ENSG00000171612
• Creates new reaction UTP [c] + dCTP [m] <-> UTP [m] + dCTP [c], GPR: ENSG00000171612
• Creates new reaction UTP [c] + dCDP [m] <-> UTP [m] + dCDP [c], GPR: ENSG00000171612
• Creates new reaction UTP [c] + GTP [m] <-> UTP [m] + GTP [c], GPR: ENSG00000171612
• Creates new reaction UTP [c] + GDP [m] <-> UTP [m] + GDP [c], GPR: ENSG00000171612
• Creates new reaction UTP [c] + dGTP [m] <-> UTP [m] + dGTP [c], GPR: ENSG00000171612
• Creates new reaction UTP [c] + dGDP [m] <-> UTP [m] + dGDP [c], GPR: ENSG00000171612
• Creates new reaction UTP [c] + ITP [m] <-> UTP [m] + ITP [c], GPR: ENSG00000171612
• Creates new reaction UTP [c] + dTTP [m] <-> UTP [m] + dTTP [c], GPR: ENSG00000171612
• Creates new reaction UTP [c] + dTDP [m] <-> UTP [m] + dTDP [c], GPR: ENSG00000171612
• Creates new reaction UTP [c] + UDP [m] <-> UTP [m] + UDP [c], GPR: ENSG00000171612
• Creates new reaction UTP [c] + dUTP [m] <-> UTP [m] + dUTP [c], GPR: ENSG00000171612
• Creates new reaction CTP [c] <-> CTP [m], GPR: ENSG00000114120 or ENSG00000171612
• Creates new reaction GTP [c] <-> GTP [m], GPR: ENSG00000114120 or ENSG00000171612
• Creates new reaction UTP [c] <-> UTP [m], GPR: ENSG00000114120 or ENSG00000171612

I hereby confirm that I have:

• Tested my code on my own computer for running the model
• Selected develop as a target branch
• Any removed reactions and metabolites have been moved to the corresponding deprecated identifier lists

[feiranl]

MAR20138 and MAR20139 are same. Please remove one.

[feiranl]

LGTM excep the duplicated rxn mentioned.

[haowang-bioinfo]

good job!

minor thing: the new reaction dTTP [c] <-> dTTP [m] listed in #694 was added as MAR20166 in this PR, but somehow missing in above message

[Devlin-Moyer]

MAR08301 already represented uniport of dTTP between the cytosol and mitochondria, so I didn't have to make a new reaction for it. I did have to make it reversible and associate it with SLC25A33, which is the second change listed in the PR message.

[haowang-bioinfo]

MAR08301 already represented uniport of dTTP between the cytosol and mitochondria, so I didn't have to make a new reaction for it. I did have to make it reversible and associate it with SLC25A33, which is the second change listed in the PR message.

wait, in that sense, this MAR20166 is duplicate to MAR08301, right?

[Devlin-Moyer]

oh whoops that is right; MAR20166 shouldn't have been added cuz it is redundant with MAR08301. I can fix that in like an hour or two

[haowang-bioinfo]

oh whoops that is right; MAR20166 shouldn't have been added cuz it is redundant with MAR08301. I can fix that in like an hour or two

ok, then take away existing MAR20166 and turn MAR20167 into new MAR20166, also make them consistent with reactons.tsv please

[haowang-bioinfo]

I wonder how this duplication pair (MAR20166 vs. MAR08301) was escaped from the memote test #672, any ideas? @mihai-sysbio

[mihai-sysbio]

I wonder how this duplication pair (MAR20166 vs. MAR08301) was escaped from the memote test #672, any ideas? @mihai-sysbio

Hmm that's interesting. Here is the official documentation of the function find_duplicate_reactions in Memote https://github.com/opencobra/memote/blob/4c08f46849628507ac8c4de56b5d6ec745feed0b/src/memote/support/basic.py#L433-L450

(MAR20166 vs. MAR08301) was escaped from the memote test

Those two are indeed duplicated, so they should have been detected. I would have to run that test locally to confirm if it indeed did not work, or if it simply skipped over failing the check in an informative way.

[haowang-bioinfo]

now this duplicate pair MAR08301:MAR20166 is captured by the updated yaml-validation action by #582