Fix/hexanoate

[pranasag]

Main improvements in this PR:

This PR addresses #716 by removing the hexanoate MAM03684c species, and swapping hexanoic acid MAM02120c where applicable.

Changes done:

• Added mitochondrial and peroxisomal versions of MAM02120c, MAM02120m and MAM02120x, respectively
• Species MAM03684c, MAM03684m, MAM03684x, and MAM03684e have been removed
• Removed reactions of hexanoate activation (MAR09949), transport (MAR11292) and exchange (MAR11293), which are duplicate to MAR11544, MAR00167, and MAR09811, respectively
• In reactions MAR10374, MAR10377, MAR11290, MAR11291, MAR20040, hexanoate was changed to hexanoic acid
• Set reaction MAR10377 irreversible, as explained in Short- and medium-chain fatty acids don't have hydrolysis rxns #689
• updated GPRs of MAR10377 and MAR10374 with ENSG00000101473 and ENSG00000123130, respectively

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

[haowang-bioinfo]

looks nice - please also merge annotation MAM03684 into MAM02120, such as the BiGG id

[pranasag]

Good spot - added the BiGG id to MAM02120. This was the only annotation missing (MAM02120 was way more complete than MAM03684.

[haowang-bioinfo]

good work

[haowang-bioinfo]

if there is any evidence supporting an irreversible MAR10377?

[pranasag]

It involves hydrolyzing a high-energy bond, so the short answer is "thermodynamics". This traces back to the issues reported by Devlin Moyer and me (#527, #689), where [rightfully] setting reactions irreversible required additional fixes elsewhere

[haowang-bioinfo]

thanks for the clarification - may the GPR be updated with any ACOTs (#689), such as ACOT4 or ACOT6?

[pranasag]

For the peroxisomal reaction MAR10377, the best candidate is ACOT8 (ENSG00000101473), as ACOT4 and ACOT6 are known to be rather specific to certain acyl-CoAs. Alongside, mitochondrial reaction MAR10374 was also missing a GPR, I suggest ACOT9 (ENSG00000123130) since mitochondrial ACOTs with known specificity (ACOT2, ACOT7, and THEM5) are specific to very long-chain FAs.

[haowang-bioinfo]

makes sense - please go ahead to implementation