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SysBioChalmers / Human-GEM

The generic genome-scale metabolic model of Homo sapiens
https://sysbiochalmers.github.io/Human-GEM-guide/
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GPR curation for Vitamin A/B2/C/D/E metabolism (1) #887

Open JHL-452b opened 4 weeks ago

JHL-452b commented 4 weeks ago

Current behavior:

23 genes are discovered to be uncorrelated with their corresponding reactions in Vitamin A/B2/C/D/E metabolism.

Gene UniProtID Reaction GPR Correlation Manually check
ENSG00000170786 Q8N3Y7 MAR01690: 9-cis-retinol + NADP+ --> 9-cis-retinal + H+ + NADPH ENSG00000072042 or ENSG00000080511 or ENSG00000139988 or ENSG00000160439 or ENSG00000170786 or ENSG00000240857 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000170786 has been described to function as an oxidoreductase with a strong preference for NAD and it catalyzes the oxidation of all-trans-retinol to all-trans-retinaldehyde using NAD(+), but it shows no activity with 11-cis-retinol or 11-cis-retinaldehyde. The reaction provided involves 9-cis-retinol and NADP+, which are not substrates for the gene's specified catalytic activity, thus the gene does not relate to the reaction given. No
ENSG00000197594 P22413 MAR08968: FAD + H2O --> AMP + FMN + 2.0 H+ ENSG00000197594 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000197594 encodes a nucleotide pyrophosphatase that primarily hydrolyzes nucleoside 5' triphosphates to their corresponding monophosphates, releasing pyrophosphate. The gene is involved in bone mineralization, soft tissue calcification, and the regulation of purinergic signaling. The provided reaction, however, involves the conversion of FAD to AMP, FMN, and protons, which is not one of the catalytic activities associated with this gene. Therefore, the gene's function and the provided reaction are not related. No
ENSG00000159423 P30038 MAR01372: D-glucurono-6,3-lactone + 2.0 H2O + NAD+ --> D-glucarate + 3.0 H+ + NADH ENSG00000111275 or ENSG00000137124 or ENSG00000159423 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000159423 is involved in the irreversible conversion of delta-1-pyrroline-5-carboxylate (P5C) to glutamate, with the preferred substrate being glutamic gamma-semialdehyde. In contrast, the provided reaction describes the conversion of D-glucurono-6,3-lactone to D-glucarate. The substrates and products of the gene's function do not match those of the given reaction, indicating that they are unrelated. No
ENSG00000145476 Q6ZWL3 MAR02135: 25-hydroxyvitamin D3-26,23-lactol + O2 --> 25-hydroxyvitamin D3-26,23-lactone + H2O2 ENSG00000119723 or ENSG00000130649 or ENSG00000145476 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000145476 encodes a cytochrome P450 monooxygenase that is primarily involved in the omega-hydroxylation of polyunsaturated fatty acids (PUFAs) such as docosahexaenoate (DHA) and eicosapentaenoate (EPA) in the eye. It also hydroxylates saturated fatty acids like laurate, myristate, and palmitate. The reactions it catalyzes involve substrates like dodecanoate, tetradecanoate, hexadecanoate, eicosapentaenoate, and docosahexaenoate, and do not include the conversion of 25-hydroxyvitamin D3-26,23-lactol to 25-hydroxyvitamin D3-26,23-lactone. Therefore, the reaction provided is not associated with the gene's known functions or catalytical activities. No
ENSG00000119723 Q9Y2Z9 MAR02143: calcitetrol + H+ + NADPH + O2 --> 24-oxo-1alpha,25-dihydroxyvitamin D3 + 2.0 H2O + NADP+ ENSG00000119723 or ENSG00000130649 or ENSG00000145476 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000119723 encodes for an FAD-dependent monooxygenase required for ubiquinone biosynthesis, specifically catalyzing the hydroxylation of 3-hexaprenyl-4-hydroxybenzoic acid to 3-hexaprenyl-4,5-dihydroxybenzoic acid. However, the reaction provided involves the conversion of calcitetrol to 24-oxo-1alpha,25-dihydroxyvitamin D3, which does not relate to the hydroxylation process or substrates involved in ubiquinone biosynthesis. Therefore, the gene and the reaction are not related. No
ENSG00000119723 Q9Y2Z9 MAR02144: 24-oxo-1alpha,25-dihydroxyvitamin D3 + H+ + NADPH + O2 --> 24-oxo-1alpha,23,25-trihydroxyvitamin D3 + H2O + NADP+ ENSG00000119723 or ENSG00000130649 or ENSG00000145476 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000119723 encodes a FAD-dependent monooxygenase involved in ubiquinone biosynthesis, specifically catalyzing the hydroxylation of 3-hexaprenyl-4-hydroxybenzoic acid (HHB) to 3-hexaprenyl-4,5-dihydroxybenzoic acid (DHHB). The provided reaction involves a different substrate, 24-oxo-1alpha,25-dihydroxyvitamin D3, and its transformation into 24-oxo-1alpha,23,25-trihydroxyvitamin D3, which does not align with the functional activity of the gene's product. Therefore, the gene and the reaction are unrelated. No
ENSG00000119723 Q9Y2Z9 MAR02133: 23S,25,26-trihydroxyvitamin D3 + O2 --> 25-hydroxyvitamin D3-26,23-lactol + H2O2 ENSG00000119723 or ENSG00000130649 or ENSG00000145476 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000119723 encodes for an FAD-dependent monooxygenase that catalyzes the hydroxylation of 3-hexaprenyl-4-hydroxybenzoic acid (HHB) to 3-hexaprenyl-4,5-dihydroxybenzoic acid (DHHB) and participates in the biosynthesis of ubiquinone. However, the reaction provided involves the conversion of 23S,25,26-trihydroxyvitamin D3 to 25-hydroxyvitamin D3-26,23-lactol and is unrelated to the function of the monooxygenase described for the gene. No
ENSG00000145476 Q6ZWL3 MAR02136: 25-hydroxyvitamin D3-26,23-lactol + O2 --> 25-hydroxyvitamin D3-26,23-lactone + H2O2 ENSG00000119723 or ENSG00000130649 or ENSG00000145476 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000145476 encodes a cytochrome P450 monooxygenase involved in the omega-hydroxylation of polyunsaturated and saturated fatty acids such as docosahexaenoate, eicosapentaenoate, laurate, myristate, and palmitate, using molecular oxygen and NADPH. In contrast, the provided reaction involves the conversion of 25-hydroxyvitamin D3-26,23-lactol to 25-hydroxyvitamin D3-26,23-lactone, which does not involve fatty acids or the specific enzymatic activities described for this gene. Therefore, the gene and the reaction are not related. No
ENSG00000119723 Q9Y2Z9 MAR02130: 23s,25-dihydroxyvitamin D3 + H2O + NADP+ <=> calcidiol + H+ + NADPH + O2 ENSG00000119723 or ENSG00000130649 or ENSG00000145476 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000119723 encodes for an FAD-dependent monooxygenase involved in ubiquinone biosynthesis, specifically catalyzing the hydroxylation of 3-hexaprenyl-4-hydroxybenzoic acid (HHB) to 3-hexaprenyl-4,5-dihydroxybenzoic acid (DHHB). The reaction provided involves the conversion of 23s,25-dihydroxyvitamin D3 to calcidiol, which is unrelated to the gene's function of hydroxylating compounds in the ubiquinone biosynthesis pathway. No
ENSG00000119723 Q9Y2Z9 MAR02134: 23S,25,26-trihydroxyvitamin D3 + O2 --> 25-hydroxyvitamin D3-26,23-lactol + H2O2 ENSG00000119723 or ENSG00000130649 or ENSG00000145476 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000119723 encodes an FAD-dependent monooxygenase involved in the C5-ring hydroxylation during ubiquinone biosynthesis, specifically catalyzing the hydroxylation of 3-hexaprenyl-4-hydroxybenzoic acid (HHB) to 3-hexaprenyl-4,5-dihydroxybenzoic acid (DHHB). The provided reaction involves the conversion of 23S,25,26-trihydroxyvitamin D3 to 25-hydroxyvitamin D3-26,23-lactol and H2O2, which does not align with the gene's function in hydroxylation and ubiquinone biosynthesis. No
ENSG00000119723 Q9Y2Z9 MAR02135: 25-hydroxyvitamin D3-26,23-lactol + O2 --> 25-hydroxyvitamin D3-26,23-lactone + H2O2 ENSG00000119723 or ENSG00000130649 or ENSG00000145476 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000119723 encodes for a FAD-dependent monooxygenase involved in ubiquinone biosynthesis, specifically catalyzing the hydroxylation of 3-hexaprenyl-4-hydroxybenzoic acid (HHB) to 3-hexaprenyl-4,5-dihydroxybenzoic acid (DHHB). The provided reaction, however, involves the conversion of 25-hydroxyvitamin D3-26,23-lactol to 25-hydroxyvitamin D3-26,23-lactone, which does not relate to the function of the gene described, as it does not involve ubiquinone or hydroxylation of HHB. No
ENSG00000171954 Q6NT55 MAR06429: 13-hydroxy-alpha-tocotrienol + H+ + 2.0 NADPH + 2.0 O2 --> 13-carboxy-alpha-tocotrienol + 3.0 H2O + 2.0 NADP+ ENSG00000171903 or ENSG00000171954 or ENSG00000186115 or ENSG00000186526 or ENSG00000186529 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000171954 encodes for a cytochrome P450 monooxygenase involved in the omega-hydroxylation of ultra-long-chain fatty acyls (C28-C36) in the epidermal ceramide biosynthesis pathway. It catalyzes the hydroxylation of these fatty acids to form omega-hydroxy-ultra-long-chain fatty acylceramides. The reaction provided involves the conversion of 13-hydroxy-alpha-tocotrienol to 13-carboxy-alpha-tocotrienol, which is not related to the ceramide biosynthesis pathway or omega-hydroxylation of fatty acyls. Hence, the gene and the reaction are not related. No
ENSG00000184227 Q86TX2 MAR06432: 13-carboxy-alpha-tocotrienol + ATP + CoA + 2.0 H2O + NAD+ --> 11-carboxy-alpha-tocotrienol + AMP + 2.0 H+ + NADH + PPi + propanoyl-CoA ENSG00000060971 or ENSG00000072506 or ENSG00000084754 or ENSG00000087008 or ENSG00000097021 or ENSG00000101473 or ENSG00000119673 or ENSG00000127884 or ENSG00000130304 or ENSG00000133835 or ENSG00000136881 or ENSG00000138029 or ENSG00000138796 or ENSG00000140284 or ENSG00000143554 or ENSG00000157426 or ENSG00000161533 or ENSG00000167107 or ENSG00000167114 or ENSG00000167315 or ENSG00000176715 or ENSG00000177465 or ENSG00000184227 or ENSG00000242110 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000184227 encodes an enzyme that catalyzes the hydrolysis of various acyl-CoAs into free fatty acids and CoA, specifically targeting saturated and unsaturated long-chain fatty acyl-CoAs (C12-C20). The catalytic activities listed for the gene involve hydrolysis reactions that produce CoA and fatty acids from acyl-CoA substrates. However, the reaction provided involves the conversion of 13-carboxy-alpha-tocotrienol to 11-carboxy-alpha-tocotrienol along with ATP, CoA, H2O, and NAD+, yielding AMP, H+, NADH, PPi, and propanoyl-CoA. This reaction does not match any of the described activities of the gene, which are linked to fatty acyl-CoA hydrolysis, not transformations involving tocotrienol. Therefore, the gene and the reaction are not related. No
ENSG00000097021 O00154 MAR06433: 11-carboxy-alpha-tocotrienol + ATP + CoA + 2.0 H2O + NAD+ + O2 --> 9-carboxy-alpha-tocotrienol + acetyl-CoA + AMP + 2.0 H+ + H2O2 + NADH + PPi ENSG00000060971 or ENSG00000072506 or ENSG00000084754 or ENSG00000087008 or ENSG00000097021 or ENSG00000101473 or ENSG00000104325 or ENSG00000119673 or ENSG00000127884 or ENSG00000130304 or ENSG00000133835 or ENSG00000136881 or ENSG00000138029 or ENSG00000138796 or ENSG00000140284 or ENSG00000143554 or ENSG00000157426 or ENSG00000161533 or ENSG00000167107 or ENSG00000167114 or ENSG00000167315 or ENSG00000167969 or ENSG00000176715 or ENSG00000177465 or ENSG00000184227 or ENSG00000198721 or ENSG00000242110 or ENSG00000242612 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000097021 encodes an enzyme that catalyzes the hydrolysis of acyl-CoAs into free fatty acids and coenzyme A (CoASH). It primarily acts on fatty acyl-CoAs with chain lengths of C8-C18, such as palmitoyl-CoA, octanoyl-CoA, dodecanoyl-CoA, (9Z)-octadecenoyl-CoA, tetradecanoyl-CoA, decanoyl-CoA, and octadecanoyl-CoA. In contrast, the provided reaction converts 11-carboxy-alpha-tocotrienol into 9-carboxy-alpha-tocotrienol with the involvement of ATP, CoA, H2O, NAD+, O2, producing acetyl-CoA, AMP, H+, H2O2, NADH, and PPi. This reaction does not involve the hydrolysis of acyl-CoAs but rather a different biochemical process, indicating that the gene's function is not pertinent to this reaction. No
ENSG00000072506 Q99714 MAR06435: 7-carboxy-alpha-tocotrienol + ATP + CoA + 2.0 H2O + O2 --> 5-carboxy-alpha-chromanol + acetyl-CoA + AMP + H+ + H2O2 + PPi ENSG00000060971 or ENSG00000072506 or ENSG00000084754 or ENSG00000087008 or ENSG00000097021 or ENSG00000101473 or ENSG00000104325 or ENSG00000119673 or ENSG00000127884 or ENSG00000130304 or ENSG00000133835 or ENSG00000136881 or ENSG00000138029 or ENSG00000138796 or ENSG00000140284 or ENSG00000143554 or ENSG00000157426 or ENSG00000161533 or ENSG00000167107 or ENSG00000167114 or ENSG00000167315 or ENSG00000167969 or ENSG00000176715 or ENSG00000177465 or ENSG00000184227 or ENSG00000198721 or ENSG00000242110 or ENSG00000242612 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000072506 encodes a mitochondrial dehydrogenase enzyme involved in fatty acid beta-oxidation, branched-chain amino acid catabolism, and steroid metabolism. It catalyzes specific reactions such as the conversion of (S)-3-hydroxyacyl-CoA to 3-ketoacyl-CoA, oxidation of 3-hydroxy-2-methylbutanoyl-CoA, and oxidation of hydroxysteroids and bile acids. However, the reaction provided involves the conversion of 7-carboxy-alpha-tocotrienol to 5-carboxy-alpha-chromanol using ATP, CoA, water, and oxygen, which does not overlap with any of the functions or catalytic activities of the gene in question. Therefore, the gene is not relevant to this reaction. No
ENSG00000167969 P42126 MAR06435: 7-carboxy-alpha-tocotrienol + ATP + CoA + 2.0 H2O + O2 --> 5-carboxy-alpha-chromanol + acetyl-CoA + AMP + H+ + H2O2 + PPi ENSG00000060971 or ENSG00000072506 or ENSG00000084754 or ENSG00000087008 or ENSG00000097021 or ENSG00000101473 or ENSG00000104325 or ENSG00000119673 or ENSG00000127884 or ENSG00000130304 or ENSG00000133835 or ENSG00000136881 or ENSG00000138029 or ENSG00000138796 or ENSG00000140284 or ENSG00000143554 or ENSG00000157426 or ENSG00000161533 or ENSG00000167107 or ENSG00000167114 or ENSG00000167315 or ENSG00000167969 or ENSG00000176715 or ENSG00000177465 or ENSG00000184227 or ENSG00000198721 or ENSG00000242110 or ENSG00000242612 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000167969 encodes an enzyme involved in the isomerization of (3Z)- and (3E)-enoyl-CoA into (2E)-enoyl-CoA, which is a key step in fatty acid beta-oxidation. The provided reaction involves the conversion of 7-carboxy-alpha-tocotrienol to 5-carboxy-alpha-chromanol along with the production of acetyl-CoA, AMP, H+, H2O2, and PPi, which does not pertain to the isomerization process catalyzed by the enzyme encoded by the gene ENSG00000167969. Therefore, the gene is not relevant to the reaction provided. No
ENSG00000138796 Q16836 MAR06435: 7-carboxy-alpha-tocotrienol + ATP + CoA + 2.0 H2O + O2 --> 5-carboxy-alpha-chromanol + acetyl-CoA + AMP + H+ + H2O2 + PPi ENSG00000060971 or ENSG00000072506 or ENSG00000084754 or ENSG00000087008 or ENSG00000097021 or ENSG00000101473 or ENSG00000104325 or ENSG00000119673 or ENSG00000127884 or ENSG00000130304 or ENSG00000133835 or ENSG00000136881 or ENSG00000138029 or ENSG00000138796 or ENSG00000140284 or ENSG00000143554 or ENSG00000157426 or ENSG00000161533 or ENSG00000167107 or ENSG00000167114 or ENSG00000167315 or ENSG00000167969 or ENSG00000176715 or ENSG00000177465 or ENSG00000184227 or ENSG00000198721 or ENSG00000242110 or ENSG00000242612 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000138796 encodes an enzyme involved in mitochondrial fatty acid beta-oxidation, specifically catalyzing reactions for the oxidation of medium and short-chain 3-hydroxy fatty acyl-CoAs. The reactions include the conversion of (3S)-3-hydroxyacyl-CoA to 3-oxoacyl-CoA, (3S)-3-hydroxybutanoyl-CoA to acetoacetyl-CoA, (3S)-hydroxydecanoyl-CoA to 3-oxodecanoyl-CoA, and (3S)-hydroxyhexadecanoyl-CoA to 3-oxohexadecanoyl-CoA, all involving NAD+ and yielding NADH. However, the reaction provided involves 7-carboxy-alpha-tocotrienol, ATP, CoA, H2O, and O2, resulting in 5-carboxy-alpha-chromanol, acetyl-CoA, AMP, H+, H2O2, and PPi. This reaction is unrelated to the fatty acid beta-oxidation pathway and the specific catalytic activities of the enzyme encoded by the gene ENSG00000138796. No
ENSG00000136881 Q14032 MAR06450: 9-carboxy-gamma-tocotrienol + ATP + CoA + 2.0 H2O + NAD+ --> 7-carboxy-gamma-tocotrienol + AMP + 2.0 H+ + NADH + PPi + propanoyl-CoA ENSG00000060971 or ENSG00000072506 or ENSG00000084754 or ENSG00000087008 or ENSG00000097021 or ENSG00000101473 or ENSG00000119673 or ENSG00000127884 or ENSG00000130304 or ENSG00000133835 or ENSG00000136881 or ENSG00000138029 or ENSG00000138796 or ENSG00000140284 or ENSG00000143554 or ENSG00000157426 or ENSG00000161533 or ENSG00000167107 or ENSG00000167114 or ENSG00000167315 or ENSG00000176715 or ENSG00000177465 or ENSG00000184227 or ENSG00000242110 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000136881 encodes an enzyme that catalyzes the amidation of bile acids (BAs) with the amino acids taurine and glycine, as well as the hydrolysis of various acyl-CoA thioesters. The listed activities involve bile acid metabolism and the regulation of intracellular levels of free fatty acids. However, the provided reaction involves the conversion of 9-carboxy-gamma-tocotrienol to 7-carboxy-gamma-tocotrienol and does not involve bile acids or acyl-CoA derivatives, indicating that the gene product's specific enzymatic activities are not related to this reaction. Therefore, this gene is not relevant to the given reaction. No
ENSG00000184227 Q86TX2 MAR06451: 7-carboxy-gamma-tocotrienol + ATP + CoA + 2.0 H2O + O2 --> 5-carboxy-gamma-chromanol + acetyl-CoA + AMP + H+ + H2O2 + PPi ENSG00000060971 or ENSG00000072506 or ENSG00000084754 or ENSG00000087008 or ENSG00000097021 or ENSG00000101473 or ENSG00000104325 or ENSG00000119673 or ENSG00000127884 or ENSG00000130304 or ENSG00000133835 or ENSG00000136881 or ENSG00000138029 or ENSG00000138796 or ENSG00000140284 or ENSG00000143554 or ENSG00000157426 or ENSG00000161533 or ENSG00000167107 or ENSG00000167114 or ENSG00000167315 or ENSG00000167969 or ENSG00000176715 or ENSG00000177465 or ENSG00000184227 or ENSG00000198721 or ENSG00000242110 or ENSG00000242612 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000184227 encodes an enzyme that catalyzes the hydrolysis of various acyl-CoAs to free fatty acids and coenzyme A (CoASH). The reactions catalyzed by this enzyme are primarily hydrolytic processes involving long-chain fatty acyl-CoAs, such as hexadecanoyl-CoA, decanoyl-CoA, dodecanoyl-CoA, tetradecanoyl-CoA, octadecanoyl-CoA, eicosanoyl-CoA, (9Z)-octadecenoyl-CoA, (9Z)-hexadecenoyl-CoA, and (9E)-octadecenoyl-CoA. However, the provided reaction involves the conversion of 7-carboxy-gamma-tocotrienol into 5-carboxy-gamma-chromanol along with ATP, CoA, H2O, O2, producing acetyl-CoA, AMP, H+, H2O2, and PPi, which is not related to the hydrolysis of fatty acyl-CoAs catalyzed by the enzyme encoded by ENSG00000184227. Therefore, the gene and the reaction are not related. No
ENSG00000167969 P42126 MAR06451: 7-carboxy-gamma-tocotrienol + ATP + CoA + 2.0 H2O + O2 --> 5-carboxy-gamma-chromanol + acetyl-CoA + AMP + H+ + H2O2 + PPi ENSG00000060971 or ENSG00000072506 or ENSG00000084754 or ENSG00000087008 or ENSG00000097021 or ENSG00000101473 or ENSG00000104325 or ENSG00000119673 or ENSG00000127884 or ENSG00000130304 or ENSG00000133835 or ENSG00000136881 or ENSG00000138029 or ENSG00000138796 or ENSG00000140284 or ENSG00000143554 or ENSG00000157426 or ENSG00000161533 or ENSG00000167107 or ENSG00000167114 or ENSG00000167315 or ENSG00000167969 or ENSG00000176715 or ENSG00000177465 or ENSG00000184227 or ENSG00000198721 or ENSG00000242110 or ENSG00000242612 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000167969 is involved in the isomerization of enoyl-CoA species as part of fatty acid beta-oxidation, while the given reaction involves the conversion of 7-carboxy-gamma-tocotrienol to 5-carboxy-gamma-chromanol, which does not involve enoyl-CoA species or isomerization processes linked to fatty acid metabolism. Therefore, the gene and the reaction are unrelated. No
ENSG00000177465 Q8N9L9 MAR06451: 7-carboxy-gamma-tocotrienol + ATP + CoA + 2.0 H2O + O2 --> 5-carboxy-gamma-chromanol + acetyl-CoA + AMP + H+ + H2O2 + PPi ENSG00000060971 or ENSG00000072506 or ENSG00000084754 or ENSG00000087008 or ENSG00000097021 or ENSG00000101473 or ENSG00000104325 or ENSG00000119673 or ENSG00000127884 or ENSG00000130304 or ENSG00000133835 or ENSG00000136881 or ENSG00000138029 or ENSG00000138796 or ENSG00000140284 or ENSG00000143554 or ENSG00000157426 or ENSG00000161533 or ENSG00000167107 or ENSG00000167114 or ENSG00000167315 or ENSG00000167969 or ENSG00000176715 or ENSG00000177465 or ENSG00000184227 or ENSG00000198721 or ENSG00000242110 or ENSG00000242612 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000177465 encodes an enzyme that catalyzes the hydrolysis of various acyl-CoAs into free fatty acids and coenzyme A (CoASH). The annotated functions of this gene include hydrolyzing succinyl-CoA, glutaryl-CoA, various long-chain acyl-CoAs, and other specific CoA derivatives. However, the provided reaction involves 7-carboxy-gamma-tocotrienol, ATP, CoA, H2O, and O2, resulting in the formation of 5-carboxy-gamma-chromanol, acetyl-CoA, AMP, H+, H2O2, and PPi. This reaction does not involve the substrates or products typically associated with the catalysis performed by the enzyme encoded by ENSG00000177465, indicating that the gene is not relevant to the reaction described. No
ENSG00000119673 P49753 MAR06451: 7-carboxy-gamma-tocotrienol + ATP + CoA + 2.0 H2O + O2 --> 5-carboxy-gamma-chromanol + acetyl-CoA + AMP + H+ + H2O2 + PPi ENSG00000060971 or ENSG00000072506 or ENSG00000084754 or ENSG00000087008 or ENSG00000097021 or ENSG00000101473 or ENSG00000104325 or ENSG00000119673 or ENSG00000127884 or ENSG00000130304 or ENSG00000133835 or ENSG00000136881 or ENSG00000138029 or ENSG00000138796 or ENSG00000140284 or ENSG00000143554 or ENSG00000157426 or ENSG00000161533 or ENSG00000167107 or ENSG00000167114 or ENSG00000167315 or ENSG00000167969 or ENSG00000176715 or ENSG00000177465 or ENSG00000184227 or ENSG00000198721 or ENSG00000242110 or ENSG00000242612 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000119673 encodes an enzyme that functions in the hydrolysis of acyl-CoAs into free fatty acids and coenzyme A, specifically targeting long-chain acyl CoAs. Its catalytic activities are confined to reactions involving various acyl-CoAs and water, resulting in the production of CoA, H(+), and different fatty acids. In contrast, the provided reaction involves the conversion of 7-carboxy-gamma-tocotrienol, ATP, CoA, and other substrates into 5-carboxy-gamma-chromanol, acetyl-CoA, AMP, H(+), H2O2, and PPi. Since this reaction does not involve the hydrolysis of acyl-CoAs nor the production of free fatty acids and simply diverges from the specific enzyme functions as annotated, the gene is not relevant to the provided reaction. No
ENSG00000104325 Q16698 MAR06451: 7-carboxy-gamma-tocotrienol + ATP + CoA + 2.0 H2O + O2 --> 5-carboxy-gamma-chromanol + acetyl-CoA + AMP + H+ + H2O2 + PPi ENSG00000060971 or ENSG00000072506 or ENSG00000084754 or ENSG00000087008 or ENSG00000097021 or ENSG00000101473 or ENSG00000104325 or ENSG00000119673 or ENSG00000127884 or ENSG00000130304 or ENSG00000133835 or ENSG00000136881 or ENSG00000138029 or ENSG00000138796 or ENSG00000140284 or ENSG00000143554 or ENSG00000157426 or ENSG00000161533 or ENSG00000167107 or ENSG00000167114 or ENSG00000167315 or ENSG00000167969 or ENSG00000176715 or ENSG00000177465 or ENSG00000184227 or ENSG00000198721 or ENSG00000242110 or ENSG00000242612 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000104325 encodes an enzyme involved in the beta-oxidation of unsaturated fatty enoyl-CoA esters in mitochondria, specifically catalyzing NADP-dependent reductions of 2,4-dienoyl-CoA to trans-3-enoyl-CoA. However, the reaction provided involves the conversion of 7-carboxy-gamma-tocotrienol to 5-carboxy-gamma-chromanol and includes substrates and products such as ATP, CoA, acetyl-CoA, AMP, H2O2, and PPi, which are not associated with the enzyme's known function or catalytic activities. Therefore, the gene ENSG00000104325 and the reaction are not related. No
Devlin-Moyer commented 3 weeks ago

It does seem like ENSG00000197594 should not be associated with MAR08968; it looks like FLAD1 (ENSG00000160688) can catalyze that reaction according to this paper, so you could replace one with the other to make sure MAR08968 still has a GPR.

I brought up problems with the GPRs of MAR06432, MAR06433, MAR06435, MAR06450, and MAR06451 in #738

feiranl commented 1 week ago

Remove ENSG00000170786 from reaction MAR01690, as ENSG00000170786 is NADH-dependent, while the reaction requires NADPH as a cofactor. Retain other genes associated with MAR01690 that are NADPH-dependent, as they remain compatible with the reaction's NADPH requirements. Copy the reaction MAR01690, modify the cofactor to NADH, and add NAD as an alternative cofactor to accommodate NADH dependency, use ENSG00000170786 as GPR.

Keep ENSG00000159423 for reaction MAR01372. Retain ENSG00000171954 for reaction MAR06429 to maintain P450 diversity.

feiranl commented 1 week ago

Others seems fine to me! This issue basically deal with the cofactor specificity with the gene ENSG00000119723 encoding for an FAD-dependent monooxygenase required for ubiquinone biosynthesis, while it was been linked with a lot rxns with NAD(P)H related rxns.