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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 (2) #888

Open JHL-452b opened 4 weeks ago

JHL-452b commented 4 weeks ago

Current behavior:

24 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
ENSG00000119673 P49753 MAR06453: 5-carboxy-gamma-chromanol + ATP + CoA + 2.0 H2O + NAD+ + O2 --> AMP + gamma-carboxyethyl-hydroxychroman + 2.0 H+ + H2O2 + 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 ENSG00000119673 encodes an enzyme that catalyzes the hydrolysis of acyl-CoAs into free fatty acids and CoA, specifically targeting long-chain acyl CoAs such as hexadecanoyl-CoA, tetradecanoyl-CoA, octadecanoyl-CoA, and others. The provided reaction involves the transformation of 5-carboxy-gamma-chromanol with ATP, CoA, H2O, NAD+, and O2 into AMP, gamma-carboxyethyl-hydroxychroman, H+, H2O2, NADH, PPi, and propanoyl-CoA, which involves different substrates and products. Thus, the gene and the reaction are not related. No
ENSG00000171954 Q6NT55 MAR06466: 13-hydroxy-gamma-tocopherol + H+ + 2.0 NADPH + 2.0 O2 --> 13-carboxy-gamma-tocopherol + 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 hydroxylation of ultra-long-chain fatty acyls, specifically contributing to the synthesis of omega-hydroxy-ultra-long chain fatty acylceramides. This process is crucial for ceramide biosynthesis and the permeability barrier of the stratum corneum. The reactions catalyzed by this enzyme involve the conversion of fatty acids using NADPH and molecular oxygen. The reaction provided, describing the conversion of 13-hydroxy-gamma-tocopherol to 13-carboxy-gamma-tocopherol, does not align with the described functions or substrates of ENSG00000171954. Thus, the gene is not relevant to this reaction. No
ENSG00000171954 Q6NT55 MAR06467: 13-hydroxy-gamma-tocopherol + H+ + 2.0 NADPH + 2.0 O2 --> 13-carboxy-gamma-tocopherol + 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 a cytochrome P450 monooxygenase involved in epidermal ceramide biosynthesis, catalyzing omega-hydroxylation of ultra-long-chain fatty acyls (C28-C36). However, the reaction provided involves the conversion of 13-hydroxy-gamma-tocopherol to 13-carboxy-gamma-tocopherol, which is unrelated to ceramide biosynthesis and the omega-hydroxylation process mediated by the gene's protein product. No
ENSG00000136881 Q14032 MAR06471: 11-carboxy-gamma-chromanol + ATP + CoA + 2.0 H2O + NAD+ + O2 --> 9-carboxy-gamma-chromanol + acetyl-CoA + AMP + 2.0 H+ + H2O2 + NADH + PPi 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 primarily functions in the amidation of bile acids with taurine and glycine, as well as in the hydrolysis and conjugation of various acyl-CoA derivatives. However, the reaction provided involves substrates such as 11-carboxy-gamma-chromanol, ATP, CoA, NAD+, and O2, resulting in products like 9-carboxy-gamma-chromanol, acetyl-CoA, AMP, H2O2, NADH, and PPi. These substrates and products are unrelated to the bile acid metabolism and acyl-CoA hydrolysis or conjugation activities associated with ENSG00000136881, indicating the gene's irrelevance to the given reaction. No
ENSG00000184227 Q86TX2 MAR06471: 11-carboxy-gamma-chromanol + ATP + CoA + 2.0 H2O + NAD+ + O2 --> 9-carboxy-gamma-chromanol + acetyl-CoA + AMP + 2.0 H+ + H2O2 + NADH + PPi 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 for an enzyme that catalyzes the hydrolysis of acyl-CoAs into free fatty acids and coenzyme A (CoASH), specifically targeting saturated and unsaturated long chain fatty acyl-CoAs (C12-C20). The provided reaction involves the conversion of 11-carboxy-gamma-chromanol to 9-carboxy-gamma-chromanol with the involvement of ATP, CoA, NAD+, and O2, producing acetyl-CoA, AMP, H2O2, NADH, and PPi. This reaction does not involve the hydrolysis of acyl-CoAs into free fatty acids and CoASH, and thus is not related to the catalytic activity of the gene ENSG00000184227. No
ENSG00000097021 O00154 MAR06471: 11-carboxy-gamma-chromanol + ATP + CoA + 2.0 H2O + NAD+ + O2 --> 9-carboxy-gamma-chromanol + acetyl-CoA + AMP + 2.0 H+ + H2O2 + NADH + PPi 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 ENSG00000097021 encodes an enzyme that catalyzes the hydrolysis of various acyl-CoAs into free fatty acids and CoA. Its specific catalytic activities involve breaking down fatty acyl-CoAs with chain lengths ranging from C8 to C18, which is supported by multiple PubMed sources. On the other hand, the provided reaction involves multiple substrates and products, including 11-carboxy-gamma-chromanol, ATP, CoA, H2O, NAD+, O2, 9-carboxy-gamma-chromanol, acetyl-CoA, AMP, H+, H2O2, NADH, and PPi, which does not align with the enzyme's known function of hydrolyzing specific acyl-CoAs. Hence, the gene and the reaction are not related. No
ENSG00000119673 P49753 MAR06471: 11-carboxy-gamma-chromanol + ATP + CoA + 2.0 H2O + NAD+ + O2 --> 9-carboxy-gamma-chromanol + acetyl-CoA + AMP + 2.0 H+ + H2O2 + NADH + PPi 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 ENSG00000119673 encodes an enzyme that catalyzes the hydrolysis of acyl-CoAs into free fatty acids and coenzyme A (CoASH), specifically targeting long-chain acyl CoAs. This involves reactions that convert molecules like hexadecanoyl-CoA, tetradecanoyl-CoA, octadecanoyl-CoA, etc., into their corresponding fatty acids and CoA. However, the reaction in question involves a different set of substrates and products, including 11-carboxy-gamma-chromanol, ATP, CoA, H2O, NAD+, O2, 9-carboxy-gamma-chromanol, acetyl-CoA, AMP, H+, H2O2, NADH, and PPi, which are not related to the specific function of hydrolyzing acyl-CoAs described for the gene. Thus, there is no overlap between the enzymatic function of the gene product and the reaction provided. No
ENSG00000138029 P55084 MAR06472: 9-carboxy-gamma-chromanol + ATP + CoA + 2.0 H2O + NAD+ + O2 --> 7-carboxy-gamma-chromanol + AMP + 2.0 H+ + H2O2 + 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 ENSG00000138029 encodes for the mitochondrial trifunctional enzyme involved in the mitochondrial beta-oxidation pathway, which catalyzes the last three reactions of breaking down long-chain fatty acids into acetyl-CoA. The reactions catalyzed by this enzyme involve different acyl-CoA substrates and produce 3-oxoacyl-CoA intermediates and CoA, with different chain lengths specified in the provided annotation. In contrast, the reaction provided involves 9-carboxy-gamma-chromanol, ATP, CoA, H2O, NAD+, and O2 producing 7-carboxy-gamma-chromanol, AMP, H2O2, NADH, PPi, and propanoyl-CoA, which is not related to the beta-oxidation of fatty acids or the functions of the mitochondrial trifunctional enzyme. No
ENSG00000084754 P40939 MAR06472: 9-carboxy-gamma-chromanol + ATP + CoA + 2.0 H2O + NAD+ + O2 --> 7-carboxy-gamma-chromanol + AMP + 2.0 H+ + H2O2 + 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 ENSG00000084754 encodes the mitochondrial trifunctional enzyme subunit alpha (HADHA), which is involved in the mitochondrial beta-oxidation pathway, specifically catalyzing the last three reactions in the breakdown of long-chain fatty acids into acetyl-CoA. The provided reaction involves substrates and products related to a different biochemical process, which includes 9-carboxy-gamma-chromanol, ATP, CoA, and NAD+, and results in the production of 7-carboxy-gamma-chromanol, AMP, H2O2, NADH, and propanoyl-CoA. None of these substrates or products are associated with the catalytic activities or known functions of HADHA, which primarily focuses on fatty acid metabolism and acylation of monolysocardiolipin. Therefore, the gene and the provided reaction are not related. No
ENSG00000143554 Q5K4L6 MAR06473: 7-carboxy-gamma-chromanol + ATP + CoA + 2.0 H2O + NAD+ + O2 --> 5-carboxy-gamma-chromanol + acetyl-CoA + AMP + 2.0 H+ + H2O2 + NADH + PPi 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 ENSG00000143554 encodes a protein that functions primarily as an acyl-CoA ligase, catalyzing the ATP-dependent formation of fatty acyl-CoA using long-chain fatty acids (LCFA) and very-long-chain fatty acids (VLCFA) as substrates. The catalytic activities provided indicate involvement in reactions that form various fatty acyl-CoA molecules through the consumption of ATP, CoA, and the corresponding fatty acid substrates. However, the given reaction involves 7-carboxy-gamma-chromanol, ATP, CoA, H2O, NAD+, and O2, resulting in the production of 5-carboxy-gamma-chromanol, acetyl-CoA, AMP, H+, H2O2, NADH, and PPi. This reaction does not correlate with the enzymatic functions or substrates (fatty acids) associated with the gene, indicating it is not relevant to the provided gene¡¯s known functions. No
ENSG00000097021 O00154 MAR06484: 11-carboxy-alpha-chromanol + ATP + CoA + 2.0 H2O + NAD+ + O2 --> 9-carboxy-alpha-chromanol + acetyl-CoA + AMP + 2.0 H+ + H2O2 + NADH + PPi 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 ENSG00000097021 encodes an enzyme that catalyzes the hydrolysis of various fatty acyl-CoAs, yielding free fatty acids and CoA. The specific reactions it catalyzes involve water and different fatty acyl-CoAs such as hexadecanoyl-CoA, octanoyl-CoA, dodecanoyl-CoA, and others. In contrast, the provided reaction involves compounds like 11-carboxy-alpha-chromanol, ATP, CoA, NAD+, and O2, and produces products such as 9-carboxy-alpha-chromanol, acetyl-CoA, AMP, H+, H2O2, NADH, and PPi, which are not within the substrate specificity or catalytic scope of the enzyme encoded by ENSG00000097021. Therefore, the gene and the reaction are unrelated based on their functional annotations and described activities. No
ENSG00000119673 P49753 MAR06486: 9-carboxy-alpha-chromanol + ATP + CoA + 2.0 H2O + NAD+ + O2 --> 7-carboxy-alpha-chromanol + AMP + 2.0 H+ + H2O2 + 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 ENSG00000119673 encodes an enzyme that catalyzes the hydrolysis of acyl-CoAs into free fatty acids and coenzyme A (CoASH), focusing primarily on long chain acyl CoAs (C14-C20). In contrast, the provided reaction involves the conversion of 9-carboxy-alpha-chromanol, ATP, CoA, H2O, NAD+, and O2 into 7-carboxy-alpha-chromanol, AMP, H+, H2O2, NADH, PPi, and propanoyl-CoA, which is not related to the hydrolysis of acyl-CoAs into free fatty acids and CoASH. Therefore, the gene and the reaction are not related. No
ENSG00000136881 Q14032 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 ENSG00000136881 catalyzes the amidation of bile acids with taurine and glycine, as well as acts as an acyl-CoA thioesterase involved in hydrolyzing various acyl-CoAs. However, the reaction provided involves the conversion of 13-carboxy-alpha-tocotrienol involving ATP, CoA, water, and NAD+, leading to the production of 11-carboxy-alpha-tocotrienol, AMP, protons, NADH, PPi, and propanoyl-CoA, which is not related to the functions or catalytic activities of the ENSG00000136881 gene product. No
ENSG00000177465 Q8N9L9 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 ENSG00000177465 catalyzes the hydrolysis of various acyl-CoA derivatives (e.g., succinyl-CoA, glutaryl-CoA, long chain saturated acyl-CoAs), converting them into CoA and their respective fatty acids. The provided reaction involves the transformation of 11-carboxy-alpha-tocotrienol to 9-carboxy-alpha-tocotrienol, along with the production of acetyl-CoA, AMP, H+, H2O2, NADH, and PPi, which does not align with any of the catalytic activities associated with the gene ENSG00000177465. Therefore, the functions and catalysis detailed for this gene do not intersect with the provided reaction. No
ENSG00000119673 P49753 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 ENSG00000119673 encodes an enzyme that catalyzes the hydrolysis of acyl-CoAs into free fatty acids and coenzyme A (CoASH), specifically targeting long chain acyl CoAs such as hexadecanoyl-CoA, tetradecanoyl-CoA, octadecanoyl-CoA, and other similar substrates. The provided reaction involves the conversion of 7-carboxy-alpha-tocotrienol and other substrates into 5-carboxy-alpha-chromanol and other products, which is not among the reactions catalyzed by the enzyme encoded by ENSG00000119673. Therefore, the gene is not relevant to the reaction provided. No
ENSG00000104325 Q16698 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 ENSG00000104325 encodes an enzyme that functions in the mitochondrial beta-oxidation pathway of unsaturated fatty enoyl-CoA esters, catalyzing the NADP-dependent reduction of various dienoyl-CoA substrates. The provided reaction involves the conversion of 7-carboxy-alpha-tocotrienol to 5-carboxy-alpha-chromanol, among other reactants and products, which is unrelated to the enzyme's role in fatty acid metabolism. Therefore, the gene and the reaction are not related. No
ENSG00000104325 Q16698 MAR06448: 11-carboxy-gamma-tocotrienol + ATP + CoA + 2.0 H2O + NAD+ + O2 --> 9-carboxy-gamma-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 ENSG00000104325 encodes an auxiliary enzyme of beta-oxidation, which catalyzes the NADP-dependent reduction of 2,4-dienoyl-CoA to trans-3-enoyl-CoA, participating in the metabolism of unsaturated fatty enoyl-CoA esters. The reaction mentioned involves the conversion of 11-carboxy-gamma-tocotrienol into 9-carboxy-gamma-tocotrienol and other products, which does not match the specific catalytic activities described for the gene ENSG00000104325. Therefore, the gene and the reaction are not related. No
ENSG00000097021 O00154 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 ENSG00000097021 encodes for an enzyme that catalyzes the hydrolysis of various acyl-CoAs into free fatty acids and coenzyme A (CoASH). The enzyme has a broad specificity towards fatty acyl-CoAs with chain lengths of C8-C18, including but not limited to palmitoyl-CoA, octanoyl-CoA, and octadecenoyl-CoA. The provided reaction involves the conversion of 9-carboxy-gamma-tocotrienol to 7-carboxy-gamma-tocotrienol and several other products, a process that includes ATP, NAD+, and CoA and results in the formation of AMP, NADH, PPi, and propanoyl-CoA. This reaction involves neither the substrates nor the products identified in the gene's annotated catalytic activities, indicating different substrate specificity and reaction mechanism. Therefore, based on the gene¡¯s known functions, it does not participate in the provided reaction, making it unrelated. No
ENSG00000143554 Q5K4L6 MAR06453: 5-carboxy-gamma-chromanol + ATP + CoA + 2.0 H2O + NAD+ + O2 --> AMP + gamma-carboxyethyl-hydroxychroman + 2.0 H+ + H2O2 + 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 ENSG00000143554 encodes an enzyme that primarily functions as an acyl-CoA ligase, catalyzing the ATP-dependent formation of fatty acyl-CoA from long-chain and very-long-chain fatty acids. The various catalytic activities described for this enzyme involve reactions that convert specific fatty acids, ATP, and CoA into their respective acyl-CoA derivatives with the concomitant production of AMP and diphosphate. However, the reaction provided involves the conversion of 5-carboxy-gamma-chromanol, ATP, CoA, H2O, and NAD+ into gamma-carboxyethyl-hydroxychroman, AMP, H+, H2O2, NADH, PPi, and propanoyl-CoA, which does not involve the substrates or products typically associated with the enzyme encoded by this gene. Therefore, based on the annotation of the gene, it does not appear to be relevant to the given reaction. No
ENSG00000143554 Q5K4L6 MAR06471: 11-carboxy-gamma-chromanol + ATP + CoA + 2.0 H2O + NAD+ + O2 --> 9-carboxy-gamma-chromanol + acetyl-CoA + AMP + 2.0 H+ + H2O2 + NADH + PPi 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 ENSG00000143554 encodes an enzyme that primarily catalyzes the ATP-dependent formation of fatty acyl-CoA using long-chain fatty acids and very-long-chain fatty acids as substrates. It facilitates the transport of these fatty acids across membranes. The provided reaction, however, involves the conversion of 11-carboxy-gamma-chromanol to 9-carboxy-gamma-chromanol along with the production of acetyl-CoA, AMP, H+, H2O2, NADH, and PPi. This reaction does not align with the gene's documented catalytic activities, which mainly involve fatty acid substrates and the resultant fatty acyl-CoA products. No
ENSG00000138796 Q16836 MAR06484: 11-carboxy-alpha-chromanol + ATP + CoA + 2.0 H2O + NAD+ + O2 --> 9-carboxy-alpha-chromanol + acetyl-CoA + AMP + 2.0 H+ + H2O2 + NADH + PPi 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 ENSG00000138796 encodes a mitochondrial fatty acid beta-oxidation enzyme that catalyzes the third step of the beta-oxidation cycle, specifically targeting medium and short-chain 3-hydroxy fatty acyl-CoAs, and plays a role in controlling insulin secretion. The reactions catalyzed by this enzyme involve the conversion of (3S)-3-hydroxyacyl-CoA to 3-oxoacyl-CoA with NAD+ as a coenzyme. However, the provided reaction involves 11-carboxy-alpha-chromanol and is distinct in its substrates and products (e.g., acetyl-CoA, AMP, H2O2), indicating that it is not part of the pathways facilitated by the gene's associated enzyme activities. Therefore, the gene does not align with the provided reaction. No
ENSG00000171954 Q6NT55 MAR06444: 13-hydroxy-gamma-tocotrienol + H+ + 2.0 NADPH + 2.0 O2 --> 13-carboxy-gamma-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 a cytochrome P450 monooxygenase that primarily functions in the omega-hydroxylation of ultra-long-chain fatty acids for ceramide synthesis, contributing to the epidermal permeability barrier. The catalytic activities described involve hydroxylation of fatty acids such as triacontanoate and omega-methyl-ultra-long-chain fatty acids. In contrast, the reaction provided involves the conversion of 13-hydroxy-gamma-tocotrienol to 13-carboxy-gamma-tocotrienol, a different substrate and pathway not related to the gene's annotated function or its associated enzymatic activities. No
ENSG00000242612 Q9NUI1 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 ENSG00000242612 encodes an enzyme that functions in the beta-oxidation pathway, participating specifically in the degradation of unsaturated fatty enoyl-CoA esters in peroxisomes. It catalyzes the NADP-dependent reduction of dienoyl-CoA to enoyl-CoA. The provided reaction involves the conversion of 7-carboxy-gamma-tocotrienol to 5-carboxy-gamma-chromanol, producing acetyl-CoA, AMP, H+, H2O2, and PPi. This reaction does not involve dienoyl-CoA substrates or the NADP-dependent reduction process characteristic of the gene's function, hence the gene is not relevant to the reaction. No
ENSG00000161533 Q15067 MAR06484: 11-carboxy-alpha-chromanol + ATP + CoA + 2.0 H2O + NAD+ + O2 --> 9-carboxy-alpha-chromanol + acetyl-CoA + AMP + 2.0 H+ + H2O2 + NADH + PPi 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 ENSG00000161533 is involved in the catalysis of the initial and rate-limiting step of peroxisomal beta-oxidation of very-long-chain fatty acids, converting saturated acyl-CoAs to trans-enoyl-CoAs while producing hydrogen peroxide (H2O2). The provided reaction, however, involves the transformation of 11-carboxy-alpha-chromanol to 9-carboxy-alpha-chromanol, along with ATP, CoA, NAD+, and O2 producing acetyl-CoA, AMP, NADH, PPi, H2O, H2O2, and H+. These two processes involve different substrates and products, indicating that the gene is not relevant to this reaction. No
Devlin-Moyer commented 3 weeks ago

I brought up similar issues with MAR06432, MAR06433, MAR06435, MAR06448, MAR06450, MAR06451, MAR06471, MAR06472, MAR06473, MAR06484, and MAR06486 in #738