GPR curation for Arginine and proline metabolism/Tyrosine metabolism

[JHL-452b]

Current behavior:

24 genes are discovered to be uncorrelated with their corresponding reactions in Arginine and proline metabolism/Tyrosine metabolism

Gene	UniProtID	Reaction	GPR	Correlation	Manually check
ENSG00000117592	P30041	MAR03391: dopamine + H2O2 --> dopamine-O-quinone + 2.0 H2O	ENSG00000005381 or ENSG00000117592	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000117592 encodes for a thiol-specific peroxidase with activities such as reducing hydrogen peroxide and organic hydroperoxides, phospholipase activity, and lysophospholipid acyltransferase activity. However, the provided reaction involves the conversion of dopamine and hydrogen peroxide to dopamine-O-quinone and water, which is not related to any of the catalytic activities or functions attributed to this gene. Therefore, the gene is not relevant to the reaction provided.	No
ENSG00000117305	P35914	MAR03935: formaldehyde + GSH <=> hydroxymethylglutathione	ENSG00000117305	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000117305 encodes for mitochondrial 3-hydroxymethyl-3-methylglutaryl-CoA lyase, which catalyzes the cleavage of (S)-3-hydroxy-3-methylglutaryl-CoA into acetyl-CoA and acetoacetate, a key step in ketogenesis and leucine catabolism. The reaction provided, formaldehyde + GSH <=> hydroxymethylglutathione, involves formaldehyde detoxification through glutathione conjugation, which is unrelated to the function and catalytic activity of the gene product of ENSG00000117305.	No
ENSG00000142920	Q96A70	MAR04191: arginine + H+ --> agmatine + CO2	ENSG00000142920	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000142920 encodes an Antizyme Inhibitor (AZI) protein, which regulates ornithine decarboxylase (ODC) activity and polyamine uptake. There is no mention of arginine or its conversion to agmatine and CO2 in the functions described. Therefore, the gene is not related to the reaction provided.	No
ENSG00000184254	P47895	MAR04683: H2O + NAD+ + phenylacetaldehyde --> 2.0 H+ + NADH + phenylacetate	ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000184254 catalyzes the NAD-dependent oxidation of aldehyde substrates such as all-trans-retinal and all-trans-13,14-dihydroretinal into their corresponding carboxylic acids. However, the reaction provided involves the conversion of phenylacetaldehyde to phenylacetate, which is not listed as a substrate specific to the gene. Therefore, the gene and the reaction are not related.	No
ENSG00000184254	P47895	MAR04685: H2O + NAD+ + phenylacetaldehyde --> 2.0 H+ + NADH + phenylacetate	ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000184254 encodes an enzyme that catalyzes the NAD-dependent oxidation of aldehyde substrates like all-trans-retinal and all-trans-13,14-dihydroretinal to their corresponding carboxylic acids. It has high specificity for all-trans-retinal and can also accept acetaldehyde as a substrate with lower affinity. However, the provided reaction involves the conversion of phenylacetaldehyde to phenylacetate, which is not among the substrates mentioned for the enzyme encoded by ENSG00000184254. Therefore, the gene is not relevant to the reaction provided.	No
ENSG00000184254	P47895	MAR04686: 2.0 H+ + NADPH + phenylacetate <=> H2O + NADP+ + phenylacetaldehyde	ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000184254 encodes an enzyme that catalyzes the NAD-dependent oxidation of aldehyde substrates, specifically all-trans-retinal and all-trans-13,14-dihydroretinal, to their corresponding carboxylic acids. However, the reaction provided involves the conversion of phenylacetate to phenylacetaldehyde using NADPH as a cofactor, which does not match the substrates or products associated with the enzyme encoded by ENSG00000184254. This indicates that the gene and the reaction are not related.	No
ENSG00000184254	P47895	MAR04687: 2.0 H+ + NADPH + phenylacetate <=> H2O + NADP+ + phenylacetaldehyde	ENSG00000006534 or ENSG00000108602 or ENSG00000132746 or ENSG00000184254	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000184254 encodes an enzyme that specifically catalyzes the NAD-dependent oxidation of aldehyde substrates such as all-trans-retinal and all-trans-13,14-dihydroretinal to their corresponding carboxylic acids. In contrast, the provided reaction involves the conversion of phenylacetate to phenylacetaldehyde, which does not match the substrates or reactions associated with the enzyme encoded by the gene. Thus, the gene and the reaction are not related.	No
ENSG00000118514	Q9H2A2	MAR06953: H2O + NAD+ + spermidine monoaldehyde 1 --> 2.0 H+ + NADH + putreanine	ENSG00000064763 or ENSG00000118514 or ENSG00000197601	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The function of the gene ENSG00000118514 involves catalyzing the NAD-dependent oxidation of 2-aminomuconic semialdehyde in the kynurenine pathway of L-tryptophan degradation. The provided reaction, however, involves the transformation of spermidine monoaldehyde into putreanine, which is not related to the kynurenine pathway or the specific catalytic activity of the gene product. Therefore, the gene and the reaction are not related.	No
ENSG00000064763	Q96K12	MAR06953: H2O + NAD+ + spermidine monoaldehyde 1 --> 2.0 H+ + NADH + putreanine	ENSG00000064763 or ENSG00000118514 or ENSG00000197601	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000064763 encodes an enzyme that catalyzes the reduction of long-chain fatty acyl-CoA to fatty alcohols using NADPH as a cofactor. It specifically acts on C16 or C18 saturated fatty acyl-CoA substrates and shows lower activity with shorter fatty acyl-CoA substrates. The provided reaction, however, involves the conversion of spermidine monoaldehyde to putreanine using NAD+ and H2O, which is not related to the fatty acid reduction activity of the gene product. Therefore, the gene does not play a role in the described reaction.	No
ENSG00000064763	Q96K12	MAR06954: H2O + NAD+ + spermidine monoaldehyde 2 --> 2.0 H+ + isoputreanine + NADH	ENSG00000064763 or ENSG00000118514 or ENSG00000197601	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000064763 encodes an enzyme that catalyzes the reduction of long-chain fatty acyl-CoA to fatty alcohols using NADPH as a cofactor, which is supported by multiple references and annotation evidence. The provided reaction, however, involves the conversion of spermidine monoaldehyde to isoputreanine using NAD+, producing H2O and NADH. These are distinct biochemical processes with different substrates, products, and cofactors, thus the gene is not related to the provided reaction.	No
ENSG00000064763	Q96K12	MAR06973: 2.0 H+ + NADH + spermic acid 1 <=> H2O + NAD+ + spermine monoaldehyde	ENSG00000064763 or ENSG00000118514 or ENSG00000197601	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000064763 catalyzes the reduction of long-chain fatty acyl-CoAs to long-chain primary fatty alcohols, as indicated by its functions (e.g., converting hexadecanoyl-CoA to hexadecan-1-ol). However, the provided reaction involves the conversion of spermic acid and NADH to spermine monoaldehyde and NAD+, which does not align with the functions and catalytic activities described for ENSG00000064763. Therefore, the gene and the reaction are not related.	No
ENSG00000198099	P08319	MAR08530: formaldehyde + GSH + NAD+ <=> formylglutathione + H+ + NADH	ENSG00000147576 or ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The listed gene ENSG00000198099 catalyzes several specific reactions involving the oxidation of retinols, long chain omega-hydroxy fatty acids, and benzoquinones, as detailed in the respective annotations. However, it does not catalyze the reaction involving formaldehyde, GSH, and NAD+ to form formylglutathione, H+, and NADH. Therefore, the annotated functions of the gene do not match the reaction provided.	No
ENSG00000196616	P00325	MAR08530: formaldehyde + GSH + NAD+ <=> formylglutathione + H+ + NADH	ENSG00000147576 or ENSG00000172955 or ENSG00000187758 or ENSG00000196344 or ENSG00000196616 or ENSG00000197894 or ENSG00000198099 or ENSG00000248144	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000196616 encodes an enzyme that catalyzes the NAD-dependent oxidation of all-trans-retinol and its derivatives such as all-trans-4-hydroxyretinol, as well as the NADH-dependent reduction of all-trans-retinal and its derivatives such as all-trans-4-oxoretinal. However, the reaction in question involves the conversion of formaldehyde, GSH, and NAD+ to formylglutathione, H+, and NADH, which is not related to any of the catalytic activities described for the enzyme encoded by this gene. Therefore, the gene ENSG00000196616 and the presented reaction are not related.	No
ENSG00000077498	P14679	MAR08630: 2.0 4-coumarate + O2 --> 2.0 caffeate	ENSG00000077498	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000077498 encodes a copper-containing oxidase involved in melanin biosynthesis, catalyzing the hydroxylation of tyrosine to DOPA and the oxidation of DOPA to DOPA-quinone, as well as other similar reactions. However, the reaction in question (2.0 4-coumarate + O2 --> 2.0 caffeate) involves the conversion of 4-coumarate to caffeate, which is not related to the enzymatic activities of the gene¡¯s product. Therefore, the gene and the reaction are not related.	No
ENSG00000131873	Q86X52	MAR12002: dopamine + UDP-glucuronate --> H+ + UDP + Dopamine-4-O-Glucuronide	(ENSG00000123989 and ENSG00000131873) or ENSG00000147408 or ENSG00000169826 or ENSG00000198108	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000131873 encodes an enzyme involved in the transfer of glucuronic acid and N-acetylgalactosamine to chondroitin polymer, whereas the reaction described involves the glucuronidation of dopamine, which is not related to the function of the encoded enzyme as per the annotation provided.	No
ENSG00000123989	Q8IZ52	MAR12002: dopamine + UDP-glucuronate --> H+ + UDP + Dopamine-4-O-Glucuronide	(ENSG00000123989 and ENSG00000131873) or ENSG00000147408 or ENSG00000169826 or ENSG00000198108	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000123989 encodes an enzyme with beta-1,3-glucuronic acid and beta-1,4-N-acetylgalactosamine transferase activity, involved in the elongation of chondroitin polymer. The catalytic activities listed for this gene involve specific substrates like UDP-N-acetyl-alpha-D-galactosamine and UDP-alpha-D-glucuronate in the synthesis of chondroitin sulfate chains. However, the reaction provided involves dopamine and UDP-glucuronate, resulting in the formation of dopamine-4-O-glucuronide, which does not fall under the described activities of the gene, indicating a different enzymatic process not related to chondroitin polymerization.	No
ENSG00000169826	Q8N6G5	MAR12002: dopamine + UDP-glucuronate --> H+ + UDP + Dopamine-4-O-Glucuronide	(ENSG00000123989 and ENSG00000131873) or ENSG00000147408 or ENSG00000169826 or ENSG00000198108	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000169826 encodes a protein that transfers N-acetylgalactosamine (GalNAc) from UDP-GalNAc to glucuronic acid (GlcUA) and is involved in the elongation of chondroitin chains. However, the provided reaction involves the glucuronidation of dopamine using UDP-glucuronate, which does not involve the transfer of GalNAc or the elongation of chondroitin chains. Therefore, the gene and the given reaction are not related.	No
ENSG00000198108	Q70JA7	MAR12002: dopamine + UDP-glucuronate --> H+ + UDP + Dopamine-4-O-Glucuronide	(ENSG00000123989 and ENSG00000131873) or ENSG00000147408 or ENSG00000169826 or ENSG00000198108	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000198108 encodes an enzyme with beta-1,3-glucuronic acid and beta-1,4-N-acetylgalactosamine transferase activity, which is involved in the elongation of chondroitin polymer chains. Its catalytic activities involve transferring glucuronic acid and N-acetylgalactosamine residues to specific substrates, but it does not catalyze the conversion of dopamine to dopamine-4-O-glucuronide as described in the provided reaction. Therefore, the gene and the mentioned reaction are unrelated.	No
ENSG00000147408	Q8TDX6	MAR12002: dopamine + UDP-glucuronate --> H+ + UDP + Dopamine-4-O-Glucuronide	(ENSG00000123989 and ENSG00000131873) or ENSG00000147408 or ENSG00000169826 or ENSG00000198108	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000147408 encodes an enzyme that transfers 1,4-N-acetylgalactosamine (GalNAc) from UDP-GalNAc to the non-reducing end of glucuronic acid (GlcUA), playing a role in chondroitin chain biosynthesis and cartilage formation. However, the provided reaction involves the conversion of dopamine and UDP-glucuronate to H+, UDP, and dopamine-4-O-glucuronide, which is unrelated to the function or catalytic activity described for this gene.	No
ENSG00000131873	Q86X52	MAR12003: dopamine + UDP-glucuronate --> H+ + UDP + Dopamine-3-O-Glucuronide	(ENSG00000123989 and ENSG00000131873) or ENSG00000147408 or ENSG00000169826 or ENSG00000198108	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000131873 encodes an enzyme with beta-1,3-glucuronic acid and beta-1,4-N-acetylgalactosamine transferase activities, specifically involved in the biosynthesis of chondroitin polymers. The catalytic activities described involve the addition of glucuronic acid and N-acetylgalactosamine residues to elongating chondroitin chains. However, the reaction provided involves the glucuronidation of dopamine to produce dopamine-3-O-glucuronide, which is a different biochemical pathway and uses a different enzyme activity (glucuronosyltransferase) not attributed to the gene in question. Therefore, the gene and the provided reaction are not related.	No
ENSG00000123989	Q8IZ52	MAR12003: dopamine + UDP-glucuronate --> H+ + UDP + Dopamine-3-O-Glucuronide	(ENSG00000123989 and ENSG00000131873) or ENSG00000147408 or ENSG00000169826 or ENSG00000198108	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000123989 is involved in the transfer of glucuronic acid (GlcUA) and N-acetylgalactosamine (GalNAc) to the chondroitin polymer as described in its catalytic activities, facilitating chondroitin polymerization. However, the provided reaction involves the conversion of dopamine and UDP-glucuronate to H+, UDP, and dopamine-3-O-glucuronide, which is not related to the functions or catalytic activities of the gene ENSG00000123989 that are specific to chondroitin polymerization processes.	No
ENSG00000169826	Q8N6G5	MAR12003: dopamine + UDP-glucuronate --> H+ + UDP + Dopamine-3-O-Glucuronide	(ENSG00000123989 and ENSG00000131873) or ENSG00000147408 or ENSG00000169826 or ENSG00000198108	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000169826 is involved in transferring 1,4-N-acetylgalactosamine (GalNAc) from UDP-GalNAc to the non-reducing end of glucuronic acid (GlcUA) and is essential for the addition of GalNAc to the core tetrasaccharide linker and elongation of chondroitin chains. The specified reaction, however, involves the conjugation of dopamine with UDP-glucuronate, producing UDP and Dopamine-3-O-Glucuronide, which does not involve the transfer of GalNAc nor the participation in processes related to chondroitin chains. Thus, the gene's function is not related to the provided reaction.	No
ENSG00000198108	Q70JA7	MAR12003: dopamine + UDP-glucuronate --> H+ + UDP + Dopamine-3-O-Glucuronide	(ENSG00000123989 and ENSG00000131873) or ENSG00000147408 or ENSG00000169826 or ENSG00000198108	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000198108 encodes for an enzyme with the function of transferring glucuronic acid (GlcUA) and N-acetylgalactosamine (GalNAc) to the non-reducing end of elongating chondroitin polymer. The catalytic activities described are all related to the synthesis and modification of complex polysaccharides, specifically chondroitin. In contrast, the reaction provided involves the glucuronidation of dopamine, which is a different biochemical pathway unrelated to chondroitin synthesis. Therefore, the functions and catalytic activities of the gene's product do not correspond to the reaction involving dopamine and UDP-glucuronate.	No
ENSG00000147408	Q8TDX6	MAR12003: dopamine + UDP-glucuronate --> H+ + UDP + Dopamine-3-O-Glucuronide	(ENSG00000123989 and ENSG00000131873) or ENSG00000147408 or ENSG00000169826 or ENSG00000198108	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000147408 encodes an enzyme that transfers 1,4-N-acetylgalactosamine (GalNAc) from UDP-GalNAc to glucuronic acid (GlcUA) at the non-reducing end of glucuronic acid, playing a role in chondroitin chain biosynthesis and cartilage formation. The reaction provided involves the conjugation of dopamine with UDP-glucuronate to form dopamine-3-O-Glucuronide, which is a different biochemical process. Therefore, the gene and the reaction are not related.	No

[feiranl]

LGTM! It basically remove the protein modification enzymes from the GPRs of simple metabolic reactions. but double check if removing this rxn would affect the metabolic tasks.