MAR02517 should not be associated with the CTSA gene

[JonathanRob]

Description of the issue:

As identified by a user, MAR02517 is currently associated to only the CTSA gene (encoding Cathepsin A, a serine protease). This reaction involves fatty acid elongation and should not be associated with CTSA - it is not supported in literature/databases, and the only reference currently associated with the reaction is irrelevant.

Furthermore, it appears that the EC number associated with the reaction (3.1.2.2) is also incorrect.

Proposed solution

• [ ] Remove CTSA from the MAR02517 gene rule.
• [ ] Update the MAR02517 gene rule such that it is associated with the correct gene(s).
• [ ] Correct the MAR02517 EC number.
• Remove the MAR02517 reaction.

I hereby confirm that I have:

• Checked that a similar issue does not exist already

[haowang-bioinfo]

Update the MAR02517 gene rule such that it is associated with the correct gene(s).

@JonathanRob what are the correct genes?

[JonathanRob]

It seems like the correct genes should be the ELOVL genes, but the process takes place in (the membrane of) the endoplasmic reticulum. The MAR02517 reaction (the subject of this issue) is located in the lysosome, which is an odd place for a fatty acid elongation reaction to occur.

Human-GEM has two reactions that are equivalent to MAR02517 but located in different compartments: MAR02519 in the endoplasmic reticulum, and MAR02190 in the cytoplasm. These reactions are associated with some or all of the ELOVL genes, and although the cytoplasm location is questionable, it is at least not an isolated/dead-end reaction.

The lysosomal MAR02517 reaction is isolated, where its substrates malonyl-CoA[l] and palmitoyl-CoA[l], and product 3-oxooctadecanoyl-CoA[l] do not participate in any other reactions.

Given this, I would instead recommend that we just remove the MAR02517 reaction.

[haowang-bioinfo]

@JonathanRob based on your investigation, MAR02517 seem to be formulated in wrong compartment, GPR, EC number, and reference. Please go ahead to remove it.

In addition, the EC number of MAR02519 should then be corrected to 2.3.1.199.

[haowang-bioinfo]

fixed in #432