GPR curation for Chondroitin sulfate degradation and Sulfur metabolism

[JHL-452b]

Current behavior:

9 genes are discovered to be uncorrelated with their corresponding reactions in Chondroitin sulfate degradation and Sulfur metabolism.

Gene	UniProtID	Reaction	GPR	Correlation	Manually check
ENSG00000104331	Q9NX62	MAR04187: H2O + PAPS --> adenylyl sulfate + Pi	ENSG00000104331 or ENSG00000162813	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. According to the annotation, the gene ENSG00000104331 encodes an enzyme with 3'-nucleotidase activity that specifically hydrolyzes adenosine 3',5'-bisphosphate (PAP) to adenosine 5'-monophosphate (AMP) and phosphate. This enzyme does not act on 3'-phosphoadenosine 5'-phosphosulfate (PAPS) or various inositol phosphate substrates. Therefore, it is not involved in the reaction provided (H2O + PAPS --> adenylyl sulfate + Pi), indicating the gene's function does not relate to the specified reaction.	No
ENSG00000108602	P30838	MAR04842: SAM --> activated methyl group + SAH	ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The provided gene, ENSG00000108602, encodes an aldehyde dehydrogenase (ALDH) enzyme that primarily catalyzes the oxidation of aldehydes to carboxylates, using NAD+ as a cofactor. The specific reactions mentioned involve aldehyde substrates and their conversion to fatty acids. In contrast, the reaction given, "SAM --> activated methyl group + SAH," pertains to the conversion of S-adenosylmethionine (SAM) to S-adenosylhomocysteine (SAH), a methylation process. This reaction does not involve the metabolism of aldehydes, which is the primary function of the ALDH enzyme encoded by ENSG00000108602. Thus, the gene does not relate to the provided reaction.	No
ENSG00000204386	Q99519	MAR07530: chondroitin sulfate C (GalNAc6S-GlcA), degradation product 3 + H2O --> chondroitin sulfate C (GalNAc6S-GlcA), degradation product 4 + H+ + sulfate	ENSG00000064601 and ENSG00000141012 and ENSG00000170266 and ENSG00000204386	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000204386 encodes an enzyme that catalyzes the removal of sialic acid residues from glycoproteins and glycolipids. However, the reaction described involves the degradation of chondroitin sulfate C, which does not involve sialic acid residues but involves the hydrolysis of a different substrate, resulting in the release of H2O, H+, and sulfate. Hence, the function of the gene does not relate to the chondroitin sulfate C degradation reaction.	No
ENSG00000204386	Q99519	MAR07542: chondroitin sulfate D (GlcNAc6S-GlcA2S), free chain + H2O --> chondroitin sulfate D (GlcNAc6S-GlcA2S), degradation product 1 + H+ + sulfate	ENSG00000064601 and ENSG00000141012 and ENSG00000170266 and ENSG00000204386	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000204386 encodes an enzyme that catalyzes the removal of sialic acid moieties from glycoproteins and glycolipids, with a preference for alpha 2-3 and alpha 2-6 sialyl linkages. However, the reaction provided involves the degradation of chondroitin sulfate D, which is a different type of polysaccharide, and does not involve sialic acid moieties. Therefore, the enzyme encoded by this gene does not catalyze the reaction described.	No
ENSG00000204386	Q99519	MAR07560: chondroitin sulfate E (GalNAc4,6diS-GlcA), degradation product 1 + H2O --> chondroitin sulfate E (GalNAc4,6diS-GlcA), degradation product 2 + H+ + sulfate	ENSG00000064601 and ENSG00000141012 and ENSG00000170266 and ENSG00000204386	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The given gene (ENSG00000204386) encodes a protein that catalyzes the removal of sialic acid moieties from glycoproteins and glycolipids, with a preference for alpha 2-3 and alpha 2-6 sialyl linkages. The reaction described involves the degradation of chondroitin sulfate E and does not pertain to the hydrolysis of sialic acid residues. Therefore, the gene products do not participate in the provided reaction.	No
ENSG00000204386	Q99519	MAR07526: chondroitin sulfate C (GalNAc6S-GlcA), free chain + H2O --> chondroitin sulfate C (GalNAc6S-GlcA), degradation product 1 + H+ + sulfate	ENSG00000064601 and ENSG00000141012 and ENSG00000170266 and ENSG00000204386	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000204386 encodes an enzyme that catalyzes the hydrolysis of terminal sialic acid residues from glycoproteins and glycolipids. The provided reaction, however, describes the degradation of chondroitin sulfate C, which involves cleaving a different substrate (GalNAc6S-GlcA) and producing different degradation products including H+ and sulfate. Therefore, the gene's annotated function does not align with the described reaction mechanism.	No
ENSG00000204386	Q99519	MAR07547: chondroitin sulfate D (GlcNAc6S-GlcA2S), degradation product 4 + H2O --> chondroitin sulfate D (GlcNAc6S-GlcA2S), degradation product 5 + H+ + sulfate	ENSG00000064601 and ENSG00000141012 and ENSG00000170266 and ENSG00000204386	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000204386 encodes for an enzyme that catalyzes the removal of sialic acid moieties from glycoproteins and glycolipids, specifically hydrolyzing alpha-(2->3)-, alpha-(2->6)-, and alpha-(2->8)- glycosidic linkages of terminal sialic acid residues. On the other hand, the provided reaction involves the degradation of chondroitin sulfate D, resulting in the formation of degradation products along with water, a proton, and sulfate. There is no mention of sialic acid or glycosidic linkages in chondroitin sulfate D, and thus, the gene's function and the specific enzymatic activity it encodes are not related to this reaction.	No
ENSG00000135702	Q9GZS9	MAR07369: keratan sulfate I biosynthesis, precursor 34 + PAPS --> H+ + keratan sulfate I biosynthesis, precursor 35 + PAP	ENSG00000135702 or ENSG00000140835 or ENSG00000175040 or ENSG00000183196	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000135702 encodes a sulfotransferase enzyme that specifically catalyzes the transfer of sulfate to the position 6 of non-reducing N-acetylglucosamine (GlcNAc) residues and O-linked sugars of mucin-type acceptors. However, the given reaction involves the biosynthesis of keratan sulfate I, which the gene's enzyme has no activity toward. Therefore, the gene's function does not align with the reaction described.	No
ENSG00000106304	P38567	MAR07503: chondroitin sulfate A (GalNAc4S-GlcA), free chain + 2.0 H2O --> chondroitin sulfate A (GalNAc4S-GlcA), degradation product 2 + H+ + N-acetylgalactosamine + sulfate	ENSG00000049860 or ENSG00000068001 or ENSG00000106302 or ENSG00000106304 or ENSG00000114378 or ENSG00000169660 or ENSG00000186792 or ENSG00000213614	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000106304 encodes a protein involved in sperm-egg adhesion by digesting hyaluronic acid, whereas the reaction involves the hydrolysis of chondroitin sulfate A. The functions and substrates of the gene product and the reaction are different, indicating no relevance between them.	No

[hhl-24]

All of these seem fine to me.