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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 Starch and sucrose metabolism #858

Open JHL-452b opened 1 month ago

JHL-452b commented 1 month ago

Current behavior:

25 genes are discovered to be uncorrelated with their corresponding reactions in Starch and sucrose metabolism

Gene UniProtID Reaction GPR Correlation Manually check
ENSG00000092529 P20807 MAR03989: H2O + maltose --> 2.0 glucose ENSG00000092529 or ENSG00000171298 or ENSG00000214013 or ENSG00000257335 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000092529 encodes a calcium-regulated non-lysosomal thiol-protease with broad endopeptidase activity and is involved in the proteasome-independent degradation of proteins such as p53/TP53. However, the reaction provided, which converts H2O and maltose into glucose, is specific to the enzymatic activity of hydrolases like maltase, not endopeptidases. Therefore, the gene's function and the given biochemical reaction are unrelated. No
ENSG00000142102 Q32M88 MAR04837: H2O + trehalose --> 2.0 glucose ENSG00000118094 or ENSG00000142102 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000142102 encodes an enzyme that catalyzes the hydrolysis of glucose from the disaccharide unit linked to hydroxylysine residues in collagen and collagen-like proteins. This specific reaction involves modifying collagen structures. However, the provided reaction is the hydrolysis of trehalose into glucose, which does not involve collagen or hydroxylysine residues, indicating that the gene's function is unrelated to this reaction. No
ENSG00000174876 P0DTE7 MAR08572: H2O + maltoheptaose --> fructose + maltohexaose ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000174876 encodes a calcium-binding enzyme involved in the hydrolysis of internal (1->4)-alpha-D-glucosidic bonds in polysaccharides, producing maltose, isomaltose, glucose, and dextrins. However, the provided reaction involves the conversion of maltoheptaose to fructose and maltohexaose, which is not catalyzed by the enzyme specified by the gene. Therefore, the gene and the reaction are not related. No
ENSG00000187733 P0DTE8 MAR08572: H2O + maltoheptaose --> fructose + maltohexaose ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000187733 codes for an enzyme that catalyzes the hydrolysis of internal (1->4)-alpha-D-glucosidic bonds in starch, producing maltose, isomaltose, glucose, and dextrins. However, the reaction given (H2O + maltoheptaose --> fructose + maltohexaose) does not align with this activity, as it involves the production of fructose, which is unrelated to the enzymatic activity described for the gene. No
ENSG00000187733 P0DTE8 MAR08574: H2O + maltohexaose --> fructose + maltopentaose ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000187733 encodes a calcium-binding enzyme that catalyzes the hydrolysis of internal (1->4)-alpha-D-glucosidic bonds in polysaccharides, yielding maltose, isomaltose, glucose, and dextrins. However, the reaction described involves the conversion of maltohexaose to fructose and maltopentaose, which does not involve the hydrolysis of (1->4)-alpha-D-glucosidic bonds catalyzed by the enzyme from the gene. Thus, the given gene and the specific reaction are not related. No
ENSG00000187733 P0DUB6 MAR08576: H2O + maltopentaose --> fructose + maltotetraose ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000187733 encodes for an enzyme that catalyzes the hydrolysis of (1->4)-alpha-D-glucosidic bonds in polysaccharides, mainly producing maltose, isomaltose, glucose, and dextrins. However, the provided reaction involves the hydrolysis of maltopentaose to produce fructose and maltotetraose, which does not align with the known catalytic activity of the enzyme encoded by this gene. Therefore, the gene and the reaction are not related. No
ENSG00000174876 P0DUB6 MAR08578: H2O + maltotetraose --> fructose + maltotriose ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000174876 encodes a calcium-binding enzyme that catalyzes the hydrolysis of internal (1->4)-alpha-D-glucosidic bonds in polysaccharides, resulting in products like maltose, isomaltose, and dextrins. However, the reaction provided (H2O + maltotetraose --> fructose + maltotriose) does not match this catalytic activity. The enzyme described does not produce fructose as a reaction product, indicating that the gene and the specific reaction are not related. No
ENSG00000187733 P0DTE8 MAR08578: H2O + maltotetraose --> fructose + maltotriose ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000187733 encodes for a calcium-binding enzyme involved in the hydrolysis of internal (1->4)-alpha-D-glucosidic bonds in polysaccharides, producing maltose, isomaltose, glucose, and dextrins. However, the reaction provided involves the conversion of maltotetraose into fructose and maltotriose, which does not align with the described function and catalytic activity of the gene product. Therefore, they are not related. No
ENSG00000174876 P0DUB6 MAR08580: H2O + maltotriose --> fructose + maltose ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The annotated gene, ENSG00000174876, catalyzes the endohydrolysis of (1->4)-alpha-D-glucosidic linkages in polysaccharides, producing maltose, isomaltose, glucose, and dextrins. However, the given reaction, H2O + maltotriose --> fructose + maltose, involves the production of fructose which is not a product of the enzyme's catalytic activity according to the provided function and catalytic activity information. Hence, the gene and the reaction are not related. No
ENSG00000174876 P0DTE7 MAR08580: H2O + maltotriose --> fructose + maltose ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000174876 encodes for a calcium-binding enzyme that catalyzes the hydrolysis of internal (1->4)-alpha-D-glucosidic bonds in polysaccharides, specifically starch, to produce maltose, isomaltose, glucose, and dextrins. However, the reaction provided (H2O + maltotriose --> fructose + maltose) does not involve the hydrolysis of (1->4)-alpha-D-glucosidic linkages nor the formation of the products typically generated by the enzyme encoded by ENSG00000174876. Therefore, the gene and the reaction are not related. No
ENSG00000187733 P0DTE8 MAR08580: H2O + maltotriose --> fructose + maltose ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000187733 encodes an enzyme that catalyzes the hydrolysis of internal (1->4)-alpha-D-glucosidic bonds in polysaccharides, yielding products such as maltose, isomaltose, glucose, and dextrins, as supported by PubMed:12527308. However, the reaction indicated (H2O + maltotriose --> fructose + maltose) does not align with the enzyme's known catalytic activity, which involves breaking (1->4)-alpha-D-glucosidic linkages but does not produce fructose as a product. No
ENSG00000174876 P0DUB6 MAR08582: H2O + maltose --> 2.0 fructose ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000174876 encodes a calcium-binding enzyme that catalyzes the hydrolysis of internal (1->4)-alpha-D-glucosidic bonds in polysaccharides, resulting in maltose, isomaltose, glucose, and dextrins. However, the reaction given is "H2O + maltose --> 2.0 fructose," which describes the conversion of maltose to fructose. This reaction does not involve the hydrolysis of (1->4)-alpha-D-glucosidic bonds, implying that the enzyme encoded by this gene does not participate in the provided reaction. No
ENSG00000174876 P0DTE7 MAR08582: H2O + maltose --> 2.0 fructose ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000174876 encodes for an enzyme that catalyzes the hydrolysis of (1->4)-alpha-D-glucosidic bonds in starch, producing maltose, isomaltose, glucose, and dextrins. However, the reaction provided (H2O + maltose --> 2.0 fructose) is not related to the activity of this enzyme, as it does not involve the hydrolysis of (1->4)-alpha-D-glucosidic bonds or the production of the specified products. The annotated function and catalytic activity of the gene do not match the specified reaction. No
ENSG00000187733 P0DUB6 MAR08582: H2O + maltose --> 2.0 fructose ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000187733 encodes a calcium-binding enzyme that catalyzes the hydrolysis of internal (1->4)-alpha-D-glucosidic bonds in polysaccharides, producing maltose, isomaltose, glucose, and dextrins. The described reaction (H2O + maltose --> 2.0 fructose) does not align with the gene's annotated catalytic activity, as the gene is not involved in converting maltose to fructose but rather in breaking down glucosidic bonds in polysaccharides. No
ENSG00000187733 P0DTE8 MAR08582: H2O + maltose --> 2.0 fructose ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000187733 encodes an enzyme that catalyzes the hydrolysis of (1->4)-alpha-D-glucosidic bonds in polysaccharides, producing maltose, isomaltose, glucose, and dextrins. However, the reaction described (H2O + maltose --> 2.0 fructose) is not consistent with the enzyme's function, as it does not involve the breakdown of maltose into fructose and does not match the enzyme's catalytic activity. No
ENSG00000237763 P0DUB6 MAR08582: H2O + maltose --> 2.0 fructose ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000237763 encodes a calcium-binding enzyme involved in starch digestion, catalyzing the hydrolysis of (1->4)-alpha-D-glucosidic bonds in polysaccharides, yielding products like maltose, isomaltose, glucose, and dextrins. However, the reaction provided (H2O + maltose --> 2.0 fructose) is not related to this enzyme¡¯s function, as it involves the conversion of maltose to fructose, not the hydrolysis of glucosidic bonds in polysaccharides. No
ENSG00000021488 P82251 MAR00072: glycogenin G4G7 + 8.0 H2O --> 8.0 glucose + Glycogen, Structure 4 (Glycogenin-1,6-{2[1,4-Glc], [1,4-Glc]}) (ENSG00000021488 and ENSG00000138079) or ENSG00000168003 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000021488 is associated with the function of forming a transporter complex with SLC3A1 to mediate the exchange between cationic and neutral amino acids. It is involved in processes such as the reabsorption of L-cystine and dibasic amino acids in renal proximal tubules. The listed catalytic activities include various amino acid exchanges involving L-arginine and other amino acids. However, the provided reaction involves glycogenin and the conversion of glycogenin G4G7 with water to glucose and Glycogen, Structure 4, which is not related to the amino acid transport and exchange functions of the gene ENSG00000021488. No
ENSG00000138079 Q07837 MAR00072: glycogenin G4G7 + 8.0 H2O --> 8.0 glucose + Glycogen, Structure 4 (Glycogenin-1,6-{2[1,4-Glc], [1,4-Glc]}) (ENSG00000021488 and ENSG00000138079) or ENSG00000168003 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation: The gene ENSG00000138079 functions as a chaperone facilitating biogenesis and trafficking of transporter heteromers, specifically involved in amino acid transport systems, while the reaction provided involves the conversion of glycogenin and water to glucose and glycogen, which pertains to carbohydrate metabolism. There is no direct relation between the gene's described role in amino acid transport and the glycogen metabolism reaction. No
ENSG00000237763 P0DUB6 MAR08568: H2O + maltodecaose --> fructose + maltononaose ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000237763 encodes an enzyme that catalyzes the hydrolysis of internal (1->4)-alpha-D-glucosidic bonds in polysaccharides, resulting in the production of maltose, isomaltose, glucose, and dextrins. However, the reaction provided involves the conversion of maltodecaose to fructose and maltononaose, which is not catalyzed by the enzyme associated with this gene. The enzyme's specific catalysis does not match the reaction described, indicating a lack of relevance. No
ENSG00000187733 P0DTE8 MAR08576: H2O + maltopentaose --> fructose + maltotetraose ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000187733 encodes for an enzyme that catalyzes the hydrolysis of internal (1->4)-alpha-D-glucosidic bonds in polysaccharides, primarily yielding maltose, isomaltose, glucose, and dextrins. In contrast, the reaction described involves the conversion of maltopentaose into fructose and maltotetraose, which do not align with the described catalytic activity or products of the enzyme. No
ENSG00000174876 P0DTE7 MAR08578: H2O + maltotetraose --> fructose + maltotriose ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The annotated gene ENSG00000174876 encodes a calcium-binding enzyme involved in starch digestion by catalyzing the hydrolysis of internal (1->4)-alpha-D-glucosidic bonds in polysaccharides, yielding maltose, isomaltose, glucose, and dextrins. However, the provided reaction, H2O + maltotetraose --> fructose + maltotriose, does not match the enzyme's described catalytic activity, which does not produce fructose. Therefore, the gene is not relevant to the reaction provided. No
ENSG00000174876 P0DUB6 MAR08574: H2O + maltohexaose --> fructose + maltopentaose ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000174876 encodes an enzyme that catalyzes the hydrolysis of (1->4)-alpha-D-glucosidic bonds in starch, producing maltose, isomaltose, glucose, and dextrins. However, the reaction given involves the conversion of maltohexaose to fructose and maltopentaose, which does not align with the enzyme's known catalytic activity and substrates. No
ENSG00000237763 P0DUB6 MAR08578: H2O + maltotetraose --> fructose + maltotriose ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000237763 encodes a calcium-binding enzyme that initiates starch digestion by catalyzing the hydrolysis of internal (1->4)-alpha-D-glucosidic bonds. The reaction provided involves the conversion of H2O and maltotetraose to fructose and maltotriose, which does not match the enzyme's function of breaking (1->4)-alpha-D-glucosidic bonds in polysaccharides. Therefore, the gene and the reaction are not related. No
ENSG00000187733 P0DUB6 MAR08580: H2O + maltotriose --> fructose + maltose ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000187733 encodes for a calcium-binding enzyme that catalyzes the hydrolysis of internal (1->4)-alpha-D-glucosidic bonds in polysaccharides, yielding maltose, isomaltose, glucose, and dextrins. However, the provided reaction converts maltotriose to fructose and maltose, which does not align with the catalytic activity of the enzyme encoded by this gene. Therefore, they are not related. No
ENSG00000237763 P0DUB6 MAR08580: H2O + maltotriose --> fructose + maltose ENSG00000120563 or ENSG00000174876 or ENSG00000187733 or ENSG00000237763 or ENSG00000240038 or ENSG00000243480 Pending No, the gene is not relevant to the reaction provided. Analysis and explanation. The gene ENSG00000237763 encodes for a calcium-binding enzyme that catalyzes the hydrolysis of (1->4)-alpha-D-glucosidic bonds in polysaccharides, producing maltose, isomaltose, glucose, and dextrins. However, the provided reaction involves the conversion of H2O and maltotriose into fructose and maltose, which differs from the enzyme's known activity of breaking down polysaccharides and does not align with its specified catalytic function. No
feiranl commented 1 month ago

delete MAR08580,MAR08578,MAR08576,MAR08574,MAR08572,MAR08582,MAR08568,MAR08576,MAR08578,MAR08574, since non of these genes are related to produce fructose. Please go aheand to make those changes for other rxns too.