GPR curation for Retinol metabolism/Riboflavin metabolism

[JHL-452b]

Current behavior:

18 genes are discovered to be uncorrelated with their corresponding reactions in Retinol metabolism/Riboflavin metabolism

Gene	UniProtID	Reaction	GPR	Correlation	Manually check
ENSG00000147576	Q8IWW8	MAR06631: NAD+ + retinol --> H+ + NADH + retinal	ENSG00000025423 or ENSG00000135437 or ENSG00000147576 or ENSG00000170786 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 ENSG00000147576 encodes a protein that catalyzes the oxidation of gamma-hydroxybutyrate to succinic semialdehyde and the reduction of 2-ketoglutarate to D-2-hydroxyglutarate. It also acts on D,L-3-hydroxyisobutyrate and L-3-hydroxybutyrate with lower activity. This gene's catalytic activities do not involve the conversion of NAD+ and retinol to retinal, NADH, and H+, which is the provided reaction. Therefore, the gene ENSG00000147576 and the provided reaction are not related.	No
ENSG00000204195	Q58HT5	MAR06635: PC-LD pool + retinol --> 1-lysolecithin pool + retinyl-ester	ENSG00000062282 or ENSG00000114113 or ENSG00000114115 or ENSG00000121207 or ENSG00000147160 or ENSG00000185000 or ENSG00000204195	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000204195 encodes an acyltransferase that specifically catalyzes the formation of ester bonds between fatty alcohols and fatty acyl-CoAs to form wax monoesters. It shows strong preferences for particular substrates, such as decyl alcohol and saturated acyl-CoAs, as detailed in various catalytic activities involving different fatty alcohols and fatty acyl-CoAs (PubMed:15671038). The provided reaction, PC-LD pool + retinol --> 1-lysolecithin pool + retinyl-ester, involves the esterification of retinol which does not correspond to the described activities of the acyltransferase encoded by the gene. Thus, the gene's function does not align with the reaction provided.	No
ENSG00000170786	Q8N3Y7	MAR06638: 11-cis-retinal + H+ + NADH <=> 11-cis-retinol + NAD+	ENSG00000025423 or ENSG00000135437 or ENSG00000139547 or ENSG00000140522 or ENSG00000157326 or ENSG00000170786 or ENSG00000187630 or ENSG00000265203	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000170786 encodes an enzyme with oxidoreductase activity that specifically functions on all-trans-retinol to convert it to all-trans-retinaldehyde with NAD(+) as a cofactor, as supported by multiple references (PubMed:18926804). However, the reaction provided involves the conversion of 11-cis-retinal to 11-cis-retinol with NADH as a cofactor, which is not a recognized activity of the enzyme encoded by ENSG00000170786. Additionally, the enzyme has no activity with 11-cis-retinol or 11-cis-retinaldehyde as substrates, further confirming the irrelevance.	No
ENSG00000163684	O95059	MAR06640: retinol --> anhydroretinol + H2O	ENSG00000163684 or ENSG00000244486	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000163684 encodes a component of ribonuclease P, which is a ribonucleoprotein complex involved in generating mature tRNA molecules by cleaving their 5'-ends. This function is unrelated to the mentioned reaction, which involves the conversion of retinol to anhydroretinol and the production of water. Therefore, the gene and the reaction are not related.	No
ENSG00000155016	Q7Z449	MAR06657: H+ + NADPH + O2 + retinoate --> 18-hydroxy-all-trans-retinoate + H2O + NADP+	ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000155016 encodes a cytochrome P450 monooxygenase, which is involved in the metabolism of arachidonic acid and its conjugates. Its known activities include hydroxylation of long-chain fatty acids and oxidation of the indole ring of N-arachidonoyl-serotonin. The provided reaction involves the conversion of retinoate to 18-hydroxy-all-trans-retinoate, a reaction that falls outside the specified functional parameters of this gene's enzymatic activities. Therefore, based on the gene's documented functions, it is not related to the given reaction.	No
ENSG00000137869	P11511	MAR06657: H+ + NADPH + O2 + retinoate --> 18-hydroxy-all-trans-retinoate + H2O + NADP+	ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000137869 encodes for a cytochrome P450 monooxygenase that catalyzes the conversion of C19 androgens to C18 estrogens, and other related reactions involving estrogen and androgen metabolism. However, the provided reaction involves the conversion of retinoate to 18-hydroxy-all-trans-retinoate, which does not fall under the scope of reactions catalyzed by this gene as per the provided annotations. Thus, there is no direct relevance between the gene and the specified reaction.	No
ENSG00000134184	P09488	MAR06661: 13-cis-retinoate <=> retinoate	ENSG00000134184	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000134184 is involved in catalyzing the conjugation of reduced glutathione to exogenous and endogenous hydrophobic electrophiles, including reactions involving prostaglandins A2 and J2, as well as other hepoxilin-related compounds. The reaction provided, which is the isomerization of 13-cis-retinoate to retinoate, does not involve glutathione conjugation or the substrates handled by the gene's encoded enzyme. Thus, the gene's function and catalytic activities do not align with the described reaction.	No
ENSG00000121039	Q8IZV5	MAR06670: 4-oxo-9-cis-retinoate + H+ + NADPH <=> 9-cis-4-oxo-13,14-dihydro-retinoate + NADP+	ENSG00000087076 or ENSG00000099377 or ENSG00000100867 or ENSG00000109854 or ENSG00000121039 or ENSG00000138400 or ENSG00000139988 or ENSG00000145439 or ENSG00000159692 or ENSG00000160439 or ENSG00000164039 or ENSG00000167733 or ENSG00000170426 or ENSG00000170786 or ENSG00000176387 or ENSG00000183921 or ENSG00000184860 or ENSG00000186153 or ENSG00000187134 or ENSG00000197894 or ENSG00000198074 or ENSG00000198189 or ENSG00000198610 or ENSG00000204228 or ENSG00000227471 or ENSG00000240857	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000121039 encodes for a retinol dehydrogenase that specifically converts all-trans-retinol to all-trans-retinal using NADP+ and has no activity towards other forms of retinol. The provided reaction involves the conversion of 4-oxo-9-cis-retinoate to 9-cis-4-oxo-13,14-dihydro-retinoate, which does not involve all-trans-retinol or all-trans-retinal and also specifies different substrates and reaction products. Therefore, the protein encoded by ENSG00000121039 is not relevant to this reaction.	No
ENSG00000087076	Q9BPX1	MAR06670: 4-oxo-9-cis-retinoate + H+ + NADPH <=> 9-cis-4-oxo-13,14-dihydro-retinoate + NADP+	ENSG00000087076 or ENSG00000099377 or ENSG00000100867 or ENSG00000109854 or ENSG00000121039 or ENSG00000138400 or ENSG00000139988 or ENSG00000145439 or ENSG00000159692 or ENSG00000160439 or ENSG00000164039 or ENSG00000167733 or ENSG00000170426 or ENSG00000170786 or ENSG00000176387 or ENSG00000183921 or ENSG00000184860 or ENSG00000186153 or ENSG00000187134 or ENSG00000197894 or ENSG00000198074 or ENSG00000198189 or ENSG00000198610 or ENSG00000204228 or ENSG00000227471 or ENSG00000240857	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000087076 encodes for an enzyme with NAD-dependent 17-beta-hydroxysteroid dehydrogenase activity, primarily converting oestradiol to oestrone and acting on 5-androstene-3-beta,17-beta-diol. The reactions catalyzed by this enzyme involve steroid hormones and NAD(NADH) as cofactors. However, the reaction provided involves 4-oxo-9-cis-retinoate and NADPH, which is not a substrate or cofactor associated with the enzyme's activity as described. Therefore, based on the gene's function and catalytic activity annotations, it is not relevant to the reaction involving 4-oxo-9-cis-retinoate and NADPH.	No
ENSG00000099377	Q9H2F3	MAR06670: 4-oxo-9-cis-retinoate + H+ + NADPH <=> 9-cis-4-oxo-13,14-dihydro-retinoate + NADP+	ENSG00000087076 or ENSG00000099377 or ENSG00000100867 or ENSG00000109854 or ENSG00000121039 or ENSG00000138400 or ENSG00000139988 or ENSG00000145439 or ENSG00000159692 or ENSG00000160439 or ENSG00000164039 or ENSG00000167733 or ENSG00000170426 or ENSG00000170786 or ENSG00000176387 or ENSG00000183921 or ENSG00000184860 or ENSG00000186153 or ENSG00000187134 or ENSG00000197894 or ENSG00000198074 or ENSG00000198189 or ENSG00000198610 or ENSG00000204228 or ENSG00000227471 or ENSG00000240857	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000099377 encodes an enzyme that plays a crucial role in the biosynthesis of hormonal steroids, specifically involved in bile acid synthesis and the degradation of 7-alpha,25-dihydroxycholesterol. The enzyme catalyzes reactions involving 7-alpha-hydroxycholesterol and related sterols. However, the provided reaction involves 4-oxo-9-cis-retinoate and NADPH, which are not substrates or products in any of the catalytic activities listed for this gene. Therefore, the gene is not related to the provided reaction.	No
ENSG00000147576	Q8IWW8	MAR06633: NAD+ + retinol --> H+ + NADH + retinal	ENSG00000025423 or ENSG00000135437 or ENSG00000147576 or ENSG00000170786 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 ENSG00000147576 encodes a protein that catalyzes the oxidation of gamma-hydroxybutyrate to succinic semialdehyde and the reduction of 2-ketoglutarate to D-2-hydroxyglutarate. It also acts on D,L-3-hydroxyisobutyrate and L-3-hydroxybutyrate. However, the provided reaction involves the oxidation of retinol to retinal using NAD+ as a cofactor, which is not among the reactions catalyzed by the gene's protein product. Thus, the gene and the reaction are not related.	No
ENSG00000100867	Q13268	MAR06670: 4-oxo-9-cis-retinoate + H+ + NADPH <=> 9-cis-4-oxo-13,14-dihydro-retinoate + NADP+	ENSG00000087076 or ENSG00000099377 or ENSG00000100867 or ENSG00000109854 or ENSG00000121039 or ENSG00000138400 or ENSG00000139988 or ENSG00000145439 or ENSG00000159692 or ENSG00000160439 or ENSG00000164039 or ENSG00000167733 or ENSG00000170426 or ENSG00000170786 or ENSG00000176387 or ENSG00000183921 or ENSG00000184860 or ENSG00000186153 or ENSG00000187134 or ENSG00000197894 or ENSG00000198074 or ENSG00000198189 or ENSG00000198610 or ENSG00000204228 or ENSG00000227471 or ENSG00000240857	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000100867 encodes an NADPH-dependent oxidoreductase that catalyzes the reduction of specific dicarbonyl compounds and displays minor hydroxysteroid dehydrogenase activity toward bile acids. However, it does not show any activity with retinoids as substrates, which makes it unrelated to the reaction of converting 4-oxo-9-cis-retinoate to 9-cis-4-oxo-13,14-dihydro-retinoate. Therefore, the gene¡¯s function does not align with the reaction specified.	No
ENSG00000170786	Q8N3Y7	MAR08709: 11-cis-retinal + H+ + NADPH <=> 11-cis-retinol + NADP+	ENSG00000025423 or ENSG00000135437 or ENSG00000139547 or ENSG00000140522 or ENSG00000157326 or ENSG00000170786 or ENSG00000187630 or ENSG00000265203	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000170786 encodes for an oxidoreductase that is active in both oxidative and reductive directions with a strong preference for NAD. It catalyzes the oxidation of all-trans-retinol to all-trans-retinaldehyde with NAD(+) as a cofactor. However, this enzyme shows no activity with 11-cis-retinol or 11-cis-retinaldehyde as substrates, irrespective of whether NAD(+)/NADH or NADP(+)/NADPH are used. The provided reaction involves 11-cis-retinal and NADPH, which are substrates for which the enzyme encoded by this gene exhibits no activity, thus making the gene irrelevant to the provided reaction.	No
ENSG00000186377	Q8N118	MAR06658: H+ + NADPH + O2 + retinoate --> 18-hydroxy-all-trans-retinoate + H2O + NADP+	ENSG00000021461 or ENSG00000100197 or ENSG00000106258 or ENSG00000108242 or ENSG00000130649 or ENSG00000134716 or ENSG00000137869 or ENSG00000138061 or ENSG00000138109 or ENSG00000138115 or ENSG00000140465 or ENSG00000140505 or ENSG00000142973 or ENSG00000155016 or ENSG00000160868 or ENSG00000160870 or ENSG00000165841 or ENSG00000167600 or ENSG00000171903 or ENSG00000186160 or ENSG00000186204 or ENSG00000186377 or ENSG00000186526 or ENSG00000197408 or ENSG00000197446 or ENSG00000197838 or ENSG00000198077 or ENSG00000255974	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000186377 encodes a cytochrome P450 monooxygenase that catalyzes the epoxidation of the last double bond of the arachidonoyl moiety of anandamide, modulating endocannabinoid signaling. The associated reaction involves N-(5Z,8Z,11Z,14Z-eicosatetraenoyl)-ethanolamine, O2, and NADPH--hemoprotein reductase. However, the provided reaction involves retinoate, NADPH, and O2 to produce 18-hydroxy-all-trans-retinoate, which does not correlate with the gene's described function or established catalytic activity.	No
ENSG00000155893	Q8TE99	MAR06507: FMN + H2O --> Pi + riboflavin	ENSG00000014257 or ENSG00000102575 or ENSG00000142513 or ENSG00000155893 or ENSG00000162836 or ENSG00000183760	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000155893 encodes a protein responsible for the 2-O-dephosphorylation of xylose in the glycosaminoglycan-protein linkage region of proteoglycans. It specifically regulates the maturation of glycosaminoglycan (GAG) chains by catalyzing the removal of phosphate from xylose. In contrast, the reaction provided, FMN + H2O --> Pi + riboflavin, involves the hydrolysis of FMN to yield phosphate (Pi) and riboflavin. This reaction does not pertain to the activities associated with GAG-protein linkage or xylose dephosphorylation. Hence, the gene is not relevant to the given reaction.	No
ENSG00000162836	Q9NPH0	MAR06507: FMN + H2O --> Pi + riboflavin	ENSG00000014257 or ENSG00000102575 or ENSG00000142513 or ENSG00000155893 or ENSG00000162836 or ENSG00000183760	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000162836 encodes an enzyme that hydrolyzes lysophosphatidic acid containing a medium length fatty acid chain to the corresponding monoacylglycerol. The reactions catalyzed by this enzyme involve the conversion of lysophosphatidic acid to monoacylglycerol and phosphate. However, the provided reaction describes a different process: the conversion of FMN and water to phosphate and riboflavin. This reaction does not involve lysophosphatidic acid or monoacylglycerol and therefore does not relate to the function or catalytic activity of the gene ENSG00000162836.	No
ENSG00000102575	P13686	MAR06507: FMN + H2O --> Pi + riboflavin	ENSG00000014257 or ENSG00000102575 or ENSG00000142513 or ENSG00000155893 or ENSG00000162836 or ENSG00000183760	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000102575 is involved in osteopontin/bone sialoprotein dephosphorylation and catalyzes reactions involving a phosphate monoester and water, yielding an alcohol and phosphate. However, the provided reaction involves the conversion of FMN to riboflavin and phosphate, which does not align with the specific dephosphorylation function of the gene.	No
ENSG00000112874	Q9BQG2	MAR20117: FAD + H2O --> AMP + FMN + 2.0 H+	ENSG00000112874	Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The provided gene, ENSG00000112874, encodes an mRNA decapping enzyme. The functional annotation indicates that this enzyme specifically removes NAD caps from mRNAs and hydrolyzes NAD(H) and NADPH molecules to various products. However, the reaction given is "FAD + H2O --> AMP + FMN + 2.0 H+", which involves the hydrolysis of FAD to FMN and AMP. The gene described does not have any known activity involving FAD hydrolysis, and thus is not relevant to the provided reaction.	No