diff --git a/README.md b/README.md index fc7c4da..fb6b6f3 100644 --- a/README.md +++ b/README.md @@ -30,6 +30,10 @@ If you use brendapy in your project cite and [![DOI](https://zenodo.org/badge/199438774.svg)](https://zenodo.org/badge/latestdoi/199438774) +**Funding** +Matthias König is supported by the Federal Ministry of Education and Research (BMBF, Germany) +within the research network Systems Medicine of the Liver (**LiSyM**, grant number 031L0054). + ## Installation `brendapy` is available from [pypi](https://pypi.python.org/pypi/brendapy) ``` @@ -42,6 +46,7 @@ Examples are provided in [./brendapy/examples.py](./brendapy/examples.py) or in ```python from brendapy import BrendaParser, BrendaProtein + def parse_proteins_for_ec(): """Parse the protein entries for a given EC number in BRENDA. @@ -49,7 +54,7 @@ def parse_proteins_for_ec(): """ brenda = BrendaParser() ec = "1.1.1.1" - proteins = brenda.parse_proteins(ec) + proteins = brenda.get_proteins(ec) print(f"{len(proteins)} proteins for EC {ec} in BRENDA") print(f"Protein identifier: {proteins.keys()}") @@ -68,60 +73,2288 @@ if __name__ == "__main__": 167 proteins for EC 1.1.1.1 in BRENDA Protein identifier: dict_keys([1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127, 128, 129, 130, 131, 132, 133, 134, 135, 136, 137, 138, 139, 140, 141, 142, 143, 144, 145, 146, 147, 148, 149, 150, 151, 152, 153, 154, 155, 156, 157, 158, 159, 160, 161, 162, 163, 164, 165, 166, 167]) -------------------------------------------------------------------------------- -Protein ID 8 -EC 1.1.1.1 -Organism Homo sapiens -Source Tissue ['liver', 'hepatocyte', 'retina', 'stomach', 'more', 'skin', 'hepatoma cell', 'serum', 'adenocarcinoma cell', 'aorta', 'esophagus', 'blood serum', 'colorectum', 'cervical cancer cell', 'pancreas', 'uterus', 'kidney', 'lung', 'cornea', 'testis'] -Localisation ['cytosol'] -NSP [['all-trans-retinol + NAD+ = all-trans-retinal + NADH', '#8# ADH4 might be involved in biosynthesis of retinoic acid <124>'], ['all-trans-retinol + NAD+ = all-trans-retinal + NADH', '#8# ADH4 might be involved in biosynthesis of retinoic acid <124>'], ['ethanol + NAD+ = acetaldehyde + NADH', '#5# role of the major liver isoenzyme A2 in ethanol metabolism <48>; #41# plays an important role in the metabolism of ethanol <102>; #8# chi-ADH plays an important role in the metabolism of long chain alcohols and aldehydes <21>; #8# the anodic enzyme form may contribute significantly to alcohol elimination in man, particularly at high concentrations when the other enzyme species are saturated <18>; #8# the enzyme plays a significant role in first-pass metabolism of ethanol in human <96>; #8# enzyme is responsible for the major ethanol oxidation capacity in the body. The products acetaldehyde and NADH are responsible for the most of the toxic effects and metabolic disturbances produced by ethanol ingestion <10>; #10# rate-limiting step of the alcoholic fermentation <122>; #5# DH3 plays an important role in systemic ethanol metabolism at higher levels of blood ethanol through activation by cytoplasmic solution hydrophobicity <141>'], ['ethanol + NAD+ = acetaldehyde + NADH', '#5# role of the major liver isoenzyme A2 in ethanol metabolism <48>; #41# plays an important role in the metabolism of ethanol <102>; #8# chi-ADH plays an important role in the metabolism of long chain alcohols and aldehydes <21>; #8# the anodic enzyme form may contribute significantly to alcohol elimination in man, particularly at high concentrations when the other enzyme species are saturated <18>; #8# the enzyme plays a significant role in first-pass metabolism of ethanol in human <96>; #8# enzyme is responsible for the major ethanol oxidation capacity in the body. The products acetaldehyde and NADH are responsible for the most of the toxic effects and metabolic disturbances produced by ethanol ingestion <10>; #10# rate-limiting step of the alcoholic fermentation <122>; #5# DH3 plays an important role in systemic ethanol metabolism at higher levels of blood ethanol through activation by cytoplasmic solution hydrophobicity <141>'], ['ethanol + NAD+ = acetaldehyde + NADH', '#5# role of the major liver isoenzyme A2 in ethanol metabolism <48>; #41# plays an important role in the metabolism of ethanol <102>; #8# chi-ADH plays an important role in the metabolism of long chain alcohols and aldehydes <21>; #8# the anodic enzyme form may contribute significantly to alcohol elimination in man, particularly at high concentrations when the other enzyme species are saturated <18>; #8# the enzyme plays a significant role in first-pass metabolism of ethanol in human <96>; #8# enzyme is responsible for the major ethanol oxidation capacity in the body. The products acetaldehyde and NADH are responsible for the most of the toxic effects and metabolic disturbances produced by ethanol ingestion <10>; #10# rate-limiting step of the alcoholic fermentation <122>; #5# DH3 plays an important role in systemic ethanol metabolism at higher levels of blood ethanol through activation by cytoplasmic solution hydrophobicity <141>'], ['isobutyramide + NAD+ = ? {r}', ''], ['1-butanol + NAD+ = butanal + NADH + H+', ''], ['1-butanol + NAD+ = butanal + NADH + H+ {r}', ''], ['TADH is a NAD(H)-dependent enzyme and shows a very broad substrate spectrum producing exclusively the (S)-enantiomer in high enantiomeric excess', '#10# constitutive enzyme <94>; #42# key enzyme in ethanol production <68>; #52# one constitutive enzyme, ADH-MI and one inducible enzyme, ADH-MII <82>; #53# enzyme may be involved in the metabolism of dietary wax esters in salmonid fish <59>; #78# the enzyme oxidizes alcohols to aldehydes or ketones both for detoxification and metabolic purposes <38>; #36# involvement in the development of male hamster reproductive system <47>; #60# alcohol dehydrogenase activity may not limit alcohol supply for ester production during ripening <146>; #41# activity is severely reduced towards aliphatic alcohols of more than 8 carbon atoms for the free enzyme, but not so with immobilized HLAD, exhibiting an activity towards C22 and C24 aliphatic alcohols higher than 50% of the highest value, obtained with C8 <204>; #8# differences in the activities of total ADH and class I ADH isoenzyme between cancer liver tissues and healthy hepatocytes may be a factor in ethanol metabolism disorders, which can intensify carcinogenesis <180>; #112# TADH is a NAD(H)-dependent enzyme and shows a very broad substrate spectrum producing exclusively the (S)-enantiomer in high enantiomeric excess (more than 99%) during asymmetric reduction of ketones <197>; #123# the physiological direction of the catalytic reaction is reduction rather than oxidation <219>'], ['TADH is a NAD(H)-dependent enzyme and shows a very broad substrate spectrum producing exclusively the (S)-enantiomer in high enantiomeric excess', '#10# constitutive enzyme <94>; #42# key enzyme in ethanol production <68>; #52# one constitutive enzyme, ADH-MI and one inducible enzyme, ADH-MII <82>; #53# enzyme may be involved in the metabolism of dietary wax esters in salmonid fish <59>; #78# the enzyme oxidizes alcohols to aldehydes or ketones both for detoxification and metabolic purposes <38>; #36# involvement in the development of male hamster reproductive system <47>; #60# alcohol dehydrogenase activity may not limit alcohol supply for ester production during ripening <146>; #41# activity is severely reduced towards aliphatic alcohols of more than 8 carbon atoms for the free enzyme, but not so with immobilized HLAD, exhibiting an activity towards C22 and C24 aliphatic alcohols higher than 50% of the highest value, obtained with C8 <204>; #8# differences in the activities of total ADH and class I ADH isoenzyme between cancer liver tissues and healthy hepatocytes may be a factor in ethanol metabolism disorders, which can intensify carcinogenesis <180>; #112# TADH is a NAD(H)-dependent enzyme and shows a very broad substrate spectrum producing exclusively the (S)-enantiomer in high enantiomeric excess (more than 99%) during asymmetric reduction of ketones <197>; #123# the physiological direction of the catalytic reaction is reduction rather than oxidation <219>']] -Turnover Number [['-999', 'more', 'turnover-numbers for the class I isoenzymes with the substrates ethanol, methanol, ethylene glycol, benzyl alcohol, octanol, cyclohexanol and 16-hydroxyhexadecanoic acid <13>; Km-values of active-site Co(II)substituted enzyme <31>; kinetics of ethanol oxidation <63>; kcat for isozymes ADH1, and ADH4 for all retinoid substrates in forward and reverse reaction <119>; kcat for isozymes ADH1B1, ADH1B2, and ADH4 for all retinoid substrates in forward and reverse reaction <119>; effects of tert-butanol, butyramide, valeramide and capronamide on turnover-number of ethanol <141>; kinetic data füor wild-type enzyme and chimeric enzyme created by insertion of an RTX domain from the adenylate cyclase of Bordetella pertussis into a loop near the catalytic active site of the thermostable alcohol dehydrogenase D (AdhD) from Pyrococcus furiosus <289>'], ['0.55', 'all-trans-retinal', 'pH 7.5, 25C, isozyme ADH1B2 <107>'], ['0.4', 'all-trans-retinol', ''], ['8', 'Pentanol', ''], ['0.7', 'ethanol', 'pH 7.5, anodic enzyme form <18>'], ['0.7', 'butanol', 'pH 7.5, anodic enzyme form <18>'], ['0.9', 'all-trans-retinol', 'pH 7.5, 25C, isozyme ADH4 <107>'], ['0.04', 'Octanol', 'recombinant allozyme Val308, pH 7.5, 25C <115>'], ['16', 'Pentanol', ''], ['2.5', 'ethanol', 'per active site <12>'], ['2.5', '3,4-dihydro-retinol', 'pH 7.5, 25C, isozyme ADH4 <107>'], ['6.17', '16-hydroxyhexadecanoate', ''], ['20', '4-oxo-retinal', 'pH 7.5, 25C, isozyme ADH4 <107>'], ['4', 'ethanol', 'isoenzyme alpha,gamma1 <13>'], ['4', '12-hydroxydodecanoate', ''], ['0.11', 'retinol', 'recombinant allozyme Val308, pH 7.5, 25C <115>'], ['3.83', 'ethanol', 'isoenzyme gamma1,gamma1 <13>'], ['4.33', 'Octanol', 'isoenzyme alpha,gamma1 <13>'], ['0.167', 'ethanol', 'recombinant allozyme Ile308, pH 7.5, 25C <115>'], ['0.167', '4-oxo-retinal', 'pH 7.5, 25C, isozyme ADH1B1 <107>'], ['0.183', '1-Pentanol', ''], ['0.583', 'Cyclohexanol', ''], ['0.75', '2-propanol', ''], ['0.75', 'ethylene glycol', ''], ['2.83', '1-Octanol', ''], ['2.83', '2-deoxy-D-ribose', ''], ['2.83', '4-hydroxy-retinol', 'pH 7.5, 25C, isozyme ADH1B2 <107>'], ['7.5', '3-Phenyl-1-propanol', ''], ['3.33', 'octanal', ''], ['7.33', 'Octanol', ''], ['0.333', '12-Hydroxydodecanoic acid', ''], ['2.17', '(S)-2-butanol', ''], ['0.018', 'all-trans-retinal', 'pH 7.5, 25C, isozyme ADH1B1 <107>'], ['0.092', '4-hydroxy-retinol', 'pH 7.5, 25C, isozyme ADH1B1 <107>'], ['0.25', 'all-trans-retinol', 'pH 7.5, 25C, isozyme ADH1B2 <107>'], ['0.667', 'Pentanol', 'pH 7.5, anodic enzyme form <18>'], ['0.038', 'Octanol', 'recombinant allozyme Ile308, pH 7.5, 25C <115>'], ['2.95', '12-hydroxydodecanoate', ''], ['8.33', 'Octanol', ''], ['9.17', 'benzyl alcohol', ''], ['0.22', '3,4-dihydro-retinal', 'pH 7.5, 25C, isozyme ADH1B2 <107>'], ['4.67', 'benzyl alcohol', 'isoenzyme alpha,gamma1 <13>'], ['17.2', 'Propanol', ''], ['0.245', 'Pentanol', ''], ['0.717', 'NAD+', 'pH 7.5, anodic enzyme form <18>'], ['1.83', 'all-trans-retinal', 'pH 7.5, 25C, isozyme ADH4 <107>'], ['1.83', 'tryptophol', ''], ['0.102', 'methanol', ''], ['0.467', 'Vanillyl alcohol', ''], ['0.683', '3-Pyridylcarbinol', 'pH 7.5, anodic enzyme form <18>'], ['1.22', '3,4-dihydro-retinal', 'pH 7.5, 25C, isozyme ADH4 <107>'], ['3.03', '12-hydroxydodecanoate', ''], ['7.83', 'ethanol', ''], ['7.83', '4-oxo-retinal', 'pH 7.5, 25C, isozyme ADH1B2 <107>'], ['8.67', 'Vanillyl alcohol', ''], ['10.2', 'ethanol', 'pH 10.0, anodic enzyme form <18>'], ['19.5', 'Hexanol', ''], ['30.7', 'ethanol', ''], ['34.8', 'butanol', ''], ['0.175', 'ethanol', 'recombinant allozyme Val308, pH 7.5, 25C <115>'], ['0.028', 'all-trans-retinol', 'pH 7.5, 25C, isozyme ADH1B1 <107>'], ['0.087', 'retinol', 'recombinant allozyme Ile308, pH 7.5, 25C <115>'], ['34.2', '4-hydroxy-retinol', 'pH 7.5, 25C, isozyme ADH4 <107>'], ['0.088', '3,4-dihydro-retinol', 'pH 7.5, 25C, isozyme ADH1B2 <107>']] -Km [['-999', 'more', 'kinetics <117,121>; pH-dependence of Km-value <89>; kinetics of ethanol oxidation <63>; kinetics of native and modified enzyme with coenzyme analogues <54>; Km-values of active-site Co(II)substituted enzyme <31>; Km values for the class I isoenzymes with the substrates ethanol, methanol, ethylene glycol, benzyl alcohol, octanol, cyclohexanol and 16-hydroxyhexadecanoic acid <13>; steady-state kinetics <116>; detailed kinetic mechanism, steady-state kinetics for wild-type and mutant enzymes, investigation of pH-dependency <111>; detailed kinetics, computational analysis of the reaction mechanism <130>; Km for isozymes ADH1, and ADH4 for all retinoid substrates in forward and reverse reaction <119>; Km for isozymes ADH1B1, ADH1B2, and ADH4 for all retinoid substrates in forward and reverse reaction <119>; Michaelis-Menten kinetics <105,226,288>; steady-state kinetics, kinetic mechanism <124>; steady-state kinetics, MW 25 kDa <115>; wild-type and mutant forms of the 3 isozymes, steady-state kinetics, detailed kinetic analysis, at different pH values and temperatures <120>; effects of tert-butanol, butyramide, valeramide and capronamide on KM-value for ethanol <141>; kinetic data füor wild-type enzyme and chimeric enzyme created by insertion of an RTX domain from the adenylate cyclase of Bordetella pertussis into a loop near the catalytic active site of the thermostable alcohol dehydrogenase D (AdhD) from Pyrococcus furiosus <289>'], ['10.6', 'ethanol', 'recombinant allozyme Val308, pH 7.5, 25C <115>'], ['0.06', '16-hydroxyhexadecanoate', '0.1 M glycine-NaOH buffer, pH 10.0, 25C <14>'], ['0.55', '1-Octanol', ''], ['0.004', '4-hydroxy-retinol', 'pH 7.5, 25C, isozyme ADH1B1 <107>'], ['0.012', 'all-trans-retinal', 'pH 7.5, 25C, isozyme ADH1B2 <107>'], ['0.012', 'retinol', 'recombinant allozyme Val308, pH 7.5, 25C <115>'], ['0.008', 'Cyclohexanol', 'isoenzyme alpha,gamma1 <13>'], ['0.013', 'NAD+', 'isoenzyme alpha,alpha <16,17>'], ['0.049', 'ethanol', 'isoenzyme beta1,beta1 <17>'], ['0.015', '4-hydroxy-retinol', 'pH 7.5, 25C, isozyme ADH4 <107>'], ['0.018', '11-cis-retinol', 'isozyme ADH1B2, pH 7.5, 25C <119>'], ['0.022', 'NAD+', ''], ['0.027', '5beta-Pregnan-3beta-ol-20-one', 'pH 7.3, 37C, ADH1C*2 (gamma2gamma2) <116>'], ['0.027', '4-oxo-retinal', 'pH 7.5, 25C, isozyme ADH1B2 <107>'], ['0.032', '3-Phenyl-1-propanol', '0.1 M glycine-NaOH buffer, pH 10.0, 25C <14>'], ['0.09', 'Pentanol', '0.1 M glycine-NaOH buffer, pH 10.0, 25C <14>'], ['0.025', 'NAD+', ''], ['0.025', '4-oxo-retinal', 'pH 7.5, 25C, isozyme ADH1B1 <107>'], ['0.025', '3,4-dihydro-retinal', 'pH 7.5, 25C, isozyme ADH1B2 <107>'], ['0.2', 'tryptophol', '0.1 M glycine-NaOH buffer, pH 10.0, 25C <14>'], ['1', 'ethanol', 'isoenzyme gamma1,gamma1 <15>'], ['0.009', 'all-trans-retinol', ''], ['0.009', 'Octanol', 'recombinant allozyme Ile308, pH 7.5, 25C <115>'], ['0.023', 'all-trans-retinol', 'pH 7.5, 25C, isozyme ADH4 <107>'], ['0.023', '9-cis-retinol', 'isozyme ADH1B2, pH 7.5, 25C <119>'], ['0.25', '5beta-cholanic acid-3-one', 'pH 7.3, 37C, ADH1C*2 (gamma2gamma2) <116>'], ['0.28', 'Pentanol', ''], ['0.0025', 'NADH', ''], ['0.8', 'Octanol', ''], ['2.4', 'octanal', ''], ['1.8', 'ethanol', ''], ['0.23', '12-hydroxydodecanoate', '0.1 M glycine-NaOH buffer, pH 10.0, 25C <14>'], ['0.028', '3,4-dihydro-retinol', 'pH 7.5, 25C, isozyme ADH4 <107>'], ['0.15', 'benzyl alcohol', ''], ['0.0036', '5alpha-androstan-17beta-ol-3-one', 'pH 7.3, 37C, ADH1C*2 (gamma2gamma2) <116>'], ['0.0036', '5beta-pregnan-3,20-dione', 'pH 7.3, 37C, ADH1C*2 (gamma2gamma2) <116>'], ['0.011', 'NADH', 'isoenzyme alpha,alpha <16>'], ['0.011', 'all-trans-retinal', 'pH 7.5, 25C, isozyme ADH1B1 <107>'], ['0.011', 'retinol', 'recombinant allozyme Ile308, pH 7.5, 25C <115>'], ['0.011', '9-cis-retinol', 'isozyme ADH1B1, pH 7.5, 25C <119>'], ['0.011', '4-hydroxy-retinol', 'pH 7.5, 25C, isozyme ADH1B2 <107>'], ['1.2', 'Octanol', ''], ['4.3', 'acetaldehyde', 'isoenzyme alpha,alpha <15>'], ['0.007', 'NADH', 'isoenzyme gamma1,gamma1 <16>'], ['0.007', 'benzyl alcohol', '0.1 M glycine-NaOH buffer, pH 10.0, 25C <14>'], ['0.007', 'Octanol', '0.1 M glycine-NaOH buffer, pH 10.0, 25C <14>'], ['0.033', 'all-trans-retinol', 'isozyme ADH1B2, pH 7.5, 25C <119>; pH 7.5, 25C, isozyme ADH1B2 <107>'], ['0.034', 'all-trans-retinal', 'pH 7.5, 25C, isozyme ADH4 <107>'], ['0.034', 'Vanillyl alcohol', '0.1 M glycine-NaOH buffer, pH 10.0, 25C <14>'], ['0.08', 'Octanol', 'isoenzyme alpha,gamma1 <13>'], ['0.085', 'acetaldehyde', 'isoenzyme beta1,beta1 <15>; isoenzyme beta1,beta1, 0.1 M sodium phosphate buffer, pH 7.5, at 25 C <20>'], ['0.84', 'ethanol', 'isoenzyme beta2,beta2, 0.1 M sodium phosphate buffer, pH 7.5, 25C <20>'], ['0.017', '4-oxo-retinal', 'pH 7.5, 25C, isozyme ADH4 <107>'], ['0.046', '5beta-androstan-17beta-ol-3-one', 'pH 7.3, 37C, ADH1C*2 (gamma2gamma2) <116>'], ['0.33', 'acetaldehyde', 'isoenzyme gamma1,gamma1 <15>'], ['0.13', 'Hexanol', ''], ['0.34', 'NAD+', ''], ['0.024', '3,4-dihydro-retinol', 'pH 7.5, 25C, isozyme ADH1B2 <107>'], ['0.035', '11-cis-retinol', 'isozyme ADH1B1, pH 7.5, 25C <119>'], ['0.048', '12-hydroxydodecanoate', ''], ['9', 'ethanol', 'recombinant allozyme Ile308, pH 7.5, 25C <115>'], ['17', 'Hexanol', ''], ['0.026', '3,4-dihydro-retinal', 'pH 7.5, 25C, isozyme ADH4 <107>'], ['0.63', 'ethanol', 'isoenzyme gamma2,gamma2 <15>'], ['11', 'Vanillyl alcohol', ''], ['1.6', 'ethanol', 'isoenzyme beta1,beta1 <17>'], ['4.2', 'ethanol', 'isoenzyme alpha,alpha <15,17>'], ['0.016', 'Octanol', 'recombinant allozyme Val308, pH 7.5, 25C <115>'], ['0.056', '12-Hydroxydodecanoic acid', ''], ['0.91', 'Propanol', ''], ['50', 'ethylene glycol', 'isoenzyme alpha,gamma1 <13>'], ['260', 'NADH', 'isoenzyme beta3,beta3, 0.1 M sodium phospahte buffer, pH 7.5, 25C <20>'], ['0.047', '12-hydroxydodecanoate', ''], ['150', 'methanol', 'isoenzyme alpha,gamma1 <13>'], ['0.24', 'acetaldehyde', 'isoenzyme gamma2,gamma2 <15>; isoenzymes beta2,beta2 <15>; isoenzyme beta2,beta2, 0.1 M sodium phosphate buffer, pH 7.5, 25C <20>'], ['0.24', 'butanol', ''], ['0.94', 'ethanol', 'isoenzyme beta2,beta2 <15>'], ['10.4', 'methanol', ''], ['3.4', 'acetaldehyde', 'isoenzyme beta3,beta3, 0.1 M sodium phospahte buffer, pH 7.5, 25C <20>'], ['6.4', 'NADH', 'isoenzyme beta1,beta1, 0.1 M sodium phosphate buffer, pH 7.5, at 25 C <20>'], ['0.044', 'Pentanol', ''], ['0.058', '5beta-androstan-3beta-ol-17-one', 'pH 7.3, 37C, ADH1C*2 (gamma2gamma2) <116>'], ['0.0064', 'NADH', 'isoenzyme beta1,beta1 <16>'], ['36', 'ethanol', 'isoenzyme beta3,beta3, 0.1 M sodium phospahte buffer, pH 7.5, 25C <20>'], ['120', 'ethanol', '0.1 M glycine-NaOH buffer, pH 10.0, 25C <14>'], ['120', '(S)-2-butanol', ''], ['7.4', 'NAD+', 'isoenzyme beta1,beta1, 0.1 M sodium phosphate buffer, pH 7.5, at 25 C <20>'], ['18', 'ethanol', ''], ['23', 'Cyclohexanol', 'isoenzyme beta1,beta1 <13>'], ['3.2', 'ethanol', 'isoenzyme gamma1,gamma1 <17>'], ['27', '1-Pentanol', ''], ['210', 'Cyclohexanol', '0.1 M glycine-NaOH buffer, pH 10.0, 25C <14>'], ['290', 'ethylene glycol', '0.1 M glycine-NaOH buffer, pH 10.0, 25C <14>'], ['0.0074', 'NAD+', 'isoenzyme beta1,beta1 <17>; isoenzyme beta2,beta2 <16>'], ['0.0087', 'NAD+', 'isoenzyme gamma2,gamma2 <16,17>'], ['0.79', 'butanol', ''], ['180', 'NAD+', 'isoenzyme beta2,beta2, 0.1 M sodium phosphate buffer, pH 7.5, 25C <20>'], ['310', '2-deoxy-D-ribose', '0.1 M glycine-NaOH buffer, pH 10.0, 25C <14>'], ['1.39', 'Propanol', ''], ['0.0079', 'NAD+', 'isoenzyme gamma1,gamma1 <16,17>'], ['105', 'NADH', 'isoenzyme beta2,beta2, 0.1 M sodium phosphate buffer, pH 7.5, 25C <20>'], ['560', '2-propanol', '0.1 M glycine-NaOH buffer, pH 10.0, 25C <14>'], ['710', 'NAD+', 'isoenzyme beta3,beta3, 0.1 M sodium phospahte buffer, pH 7.5, 25C <20>'], ['1.5', 'ethanol', 'isoenzyme alpha,alpha <17>; mutant C257L, pH 8.0, 60C <246>'], ['0.45', 'ethanol', ''], ['0.18', 'NAD+', 'isoenzyme beta1,beta1 <16>; 65C, pH 10.5 <218>'], ['0.105', 'NADH', 'isoenzyme beta2,beta2 <16>; cosubstrate acetoin, pH 6.0, 70C <243>'], ['1.7', 'ethanol', 'isoenzyme III <79>; isoenzyme alpha,gamma1 <13>; isoenzyme gamma2,gamma2 <17>'], ['0.063', 'NAD+', 'recombinant allozyme Ile308, pH 7.5, 25C <115>; 45C, pH 8.8, cosubstrate: 2,3-butanediol, wild-type enzyme <290>'], ['0.022', 'ethanol', '70C, pH 9.0, 50 mM Tris-HCl, 4 M NaCl <181>; isoenzyme beta1,beta1, 0.1 M sodium phosphate buffer, pH 7.5, at 25 C <20>'], ['0.03', 'all-trans-retinol', 'isoenzyme BB-ADH <95>; isozyme ADH1B1, pH 7.5, 25C <119>; pH 7.5, 25C, isozyme ADH1B1 <107>'], ['28', 'ethanol', ''], ['0.074', 'NAD+', 'oxidation of ethanol <99>; recombinant allozyme Val308, pH 7.5, 25C <115>'], ['0.1', '12-hydroxydodecanoate', '']] -Specific Activity [['3.3', ''], ['0.6', ''], ['0.65', ''], ['1.47', ''], ['1.3', '']] -Cofactors [] -Inhibitors [['4-Methylpyrazole', '1 mM, 31% inhibition <23>; class III enzyme is completely insensitive to inhibition <11,16>; poor inhibitor, class II isoenzyme <14>; no inhibition by 12 mM <21>; competitive against ethanol <96>'], ['1,10-phenanthroline', ''], ['pyrazole', '0.05 mM, 50% inhibition <10>; no inhibition at 1.0 mM <23>'], ['NADP+', ''], ['4-bromopyrazole', ''], ['4-pentylpyrazole', ''], ['sulfonic acid', ''], ['8-Amino-6-methoxyquinoline', ''], ['4-cyanopyrazole', ''], ['4-nitropyrazole', ''], ['4-octylpyrazole', ''], ['4-propylpyrazole', ''], ['all-trans-retinal', 'product inhibition <124>'], ['4-androsten-3,17-dione', 'competitive against substrate cyclohexanone <116>'], ['3-butylthiolan 1-oxide', 'dead-end inhibitor to the enzyme-cofactor complex, inhibition of oxidation reaction <116>'], ['5alpha-androstan-17beta-ol-3-one', 'i.e. 5alpha-dihydrotestosterone, allosteric, competitive against substrate cyclohexanone, noncompetitive against NAD+ nd ethanol <116>'], ['N-cyclopentyl-N-cyclobutylformamide', 'inhibits isozyme alphaalpha, complex structure <109>'], ['N-benzylformamide', 'inhibits isozyme beta(1)beta(1) <109>'], ['N-heptylformamide', 'inhibits isozyme beta(1)beta(1) <109>'], ['N-1-methylheptylformamide', 'inhibits isozyme gamma(2)gamma(2) <109>'], ['all-trans-retinoic acid', 'weak feedback inhibition <124>'], ['cimetidine', '0.2 mM, 2.5% inhibition of hepatic allotype ADH1B*1/*1 activity, 12% inhibition of hepatic allotype ADH1B*2/*2 activity <273>'], ['acetaminophen', '0.5 mM, 16% inhibition of hepatic allotype ADH1B*1/*1 activity, 6.1% inhibition of hepatic allotype ADH1B*2/*2 activity <273>'], ['Acetylsalicylate', '1 mM, 4.4% inhibition of hepatic allotype ADH1B*1/*1 activity, 2.8% inhibition of hepatic allotype ADH1B*2/*2 activity <273>'], ['salicylate', '1.5 mM, 12% inhibition of hepatic allotype ADH1B*1/*1 activity, 31% inhibition of hepatic allotype ADH1B*2/*2 activity <273>'], ['trifluoroethanol', 'competitive against retinol, noncompetitive against NAD+ <124>'], ['dipicolinic acid', ''], ['EDTA', ''], ['Isobutyramide', 'substrate inhibition, competitive against retinol, noncompetitive against NADH <124>'], ["2,2'-bipyridine", ''], ['4-iodopyrazole', ''], ['8-hydroxyquinoline 5-sulfonic acid', ''], ['4-methoxypyrazole', '1 mM, 28% inhibition <23>'], ['13% relative activity at 10%', 'competitive, stabilizes the retinoid compounds, elevates the Km values of the substrates, most effective at 0.1% w/v <107>']] -Ki [['0.014', '5alpha-androstan-17beta-ol-3-one', 'pH 7.3, 37C, versus ethanol <116>'], ['0.028', '5alpha-androstan-17beta-ol-3-one', 'pH 7.3, 37C, versus NAD+ <116>'], ['0.0047', '5alpha-androstan-17beta-ol-3-one', 'pH 7.3, 37C, versus cyclohexanone <116>'], ['0.0047', '4-androsten-3,17-dione', 'pH 7.3, 37C, versus cyclohexanone <116>'], ['-999', 'more', 'inhibition kinetics <116>']] -Metal Ions [['Zn2+', 'catalytic zinc <109>'], ['Zinc', 'enzyme contains 7.59 zinc atoms per molecule <96>; contains 3.8 mol of Zn per mol of protein <16,45>; zinc containing enzyme <12>; from beta1gamma1 and gamma1gamma1 isoenzyme the active-site zinc is extracted much more slowly than from beta1beta1 isoenzyme. Characterization of active-site-specific zinc-depleted and reconstituted cobalt(II) alcohol dehydrogenase <19>; contains 3.7 gatom of zinc per mol of enzyme <23>; 3.6-4.2 gatom of zinc per mol <21>']] -References [124, 150, 180, 186, 191, 194, 206, 228, 229, 273] -Pubmed {124: '<124> Chou, C.F.; Lai, C.L.; Chang, Y.C.; Duester, G.; Yin, S.J.: Kinetic mechanism of human class IV alcohol dehydrogenase functioning as retinol dehydrogenase. J. Biol. Chem. (2002) 277, 25209-25216. {Pubmed:11997393}', 150: '<150> Jelski, W.; Chrostek, L.; Markiewicz, W.; Szmitkowski, M.: Activity of alcohol dehydrogenase (ADH) isoenzymes and aldehyde dehydrogenase (ALDH) in the sera of patients with breast cancer. J. Clin. Lab. Anal. (2006) 20, 105-108. {Pubmed:16721836}', 180: '<180> Jelski, W.; Zalewski, B.; Szmitkowski, M.: The activity of class I, II, III, and IV alcohol dehydrogenase (ADH) isoenzymes and aldehyde dehydrogenase (ALDH) in liver cancer. Digest. Dis. Sci. (2008) 53, 2550-2555. {Pubmed:18224440}', 186: '<186> Jelski, W.; Zalewski, B.; Szmitkowski, M.: Alcohol dehydrogenase (ADH) isoenzymes and aldehyde dehydrogenase (ALDH) activity in the sera of patients with liver cancer. J. Clin. Lab. Anal. (2008) 22, 204-209. {Pubmed:18484658}', 191: '<191> Jelski, W.; Chrostek, L.; Szmitkowski, M.: The activity of class I, II, III, and IV of alcohol dehydrogenase isoenzymes and aldehyde dehydrogenase in pancreatic cancer. Pancreas (2007) 35, 142-146. {Pubmed:17632320}', 194: '<194> Jelski, W.; Szmitkowski, M.: Alcohol dehydrogenase (ADH) and aldehyde dehydrogenase (ALDH) in the cancer diseases. Clin. Chim. Acta (2008) 395, 1-5. {Pubmed:18505683}', 206: '<206> Jelski, W.; Orywal, K.; Panek, B.; Gacko, M.; Mroczko, B.; Szmitkowski, M.: The activity of class I, II, III and IV of alcohol dehydrogenase (ADH) isoenzymes and aldehyde dehydrogenase (ALDH) in the wall of abdominal aortic aneurysms. Exp. Mol. Pathol. (2009) 87, 59-62. {Pubmed:19332052}', 228: '<228> Ostberg, L.J.; Stroemberg, P.; Hedberg, J.J.; Persson, B.; Hoeoeg, J.O.: Analysis of mammalian alcohol dehydrogenase 5 (ADH5): Characterisation of rat ADH5 with comparisons to the corresponding human variant. Chem. Biol. Interact. (2013) 202, 97-103. {Pubmed:23159888}', 229: '<229> Orywal, K.; Jelski, W.; Zdrodowski, M.; Szmitkowski, M.: The activity of class I, II, III and IV alcohol dehydrogenase isoenzymes and aldehyde dehydrogenase in cervical cancer. Clin. Biochem. (2011) 44, 1231-1234. {Pubmed:21784063}', 273: '<273> Chi, Y.C.; Lee, S.L.; Lai, C.L.; Lee, Y.P.; Lee, S.P.; Chiang, C.P.; Yin, S.J.: Ethanol oxidation and the inhibition by drugs in human liver, stomach and small intestine: Quantitative assessment with numerical organ modeling of alcohol dehydrogenase isozymes. Chem. Biol. Interact. (2016) 258, 134-141. {Pubmed:27544634}'} --------------------------------------------------------------------------------- -Protein ID 106 -EC 1.1.1.1 -Organism Homo sapiens -Source Tissue ['liver', 'buccal mucosa'] -Localisation ['cytosol'] -NSP [] -Turnover Number [] -Km [['0.00024', '1-formyl-8-methylpyrene', 'isozyme ADH2, at 21-23C <214>'], ['0.0005', '1-formylpyrene', 'isozyme ADH1C, at 21-23C <214>'], ['0.0009', '1-formyl-6-methylpyrene', 'isozyme ADH1C, at 21-23C <214>'], ['0.001', '4-formylpyrene', 'isozyme ADH1C, at 21-23C <214>'], ['0.001', '4-hydroxymethylpyrene', 'isozyme ADH1C, at 21-23C <214>'], ['0.012', '1-formylpyrene', 'isozyme ADH2, at 21-23C <214>'], ['0.04', '4-hydroxymethylpyrene', 'isozyme ADH2, at 21-23C <214>'], ['0.009', '2-formylpyrene', 'isozyme ADH3, at 21-23C <214>'], ['0.00055', '1-formylpyrene', 'isozyme ADH3, at 21-23C <214>'], ['0.0021', '2-formylpyrene', 'isozyme ADH1C, at 21-23C <214>'], ['0.0021', '4-formylpyrene', 'isozyme ADH3, at 21-23C <214>'], ['0.00031', '1-hydroxymethyl-8-methylpyrene', 'isozyme ADH3, at 21-23C <214>'], ['0.39', '1-Octanol', 'isozyme ADH3, at 21-23C <214>'], ['0.076', '1-hydroxymethylpyrene', 'isozyme ADH2, at 21-23C <214>'], ['0.77', 'ethanol', 'isozyme ADH1C, at 21-23C <214>'], ['0.00057', '1-hydroxymethyl-6-methylpyrene', 'isozyme ADH3, at 21-23C <214>'], ['0.34', 'acetaldehyde', 'isozyme ADH1C, at 21-23C <214>'], ['0.0029', '2-formylpyrene', 'isozyme ADH2, at 21-23C <214>'], ['0.059', '1-hydroxymethyl-8-methylpyrene', 'isozyme ADH1C, at 21-23C <214>'], ['26', 'acetaldehyde', 'isozyme ADH2, at 21-23C <214>'], ['0.0044', '2-hydroxymethylpyrene', 'isozyme ADH2, at 21-23C <214>'], ['33', 'ethanol', 'isozyme ADH2, at 21-23C <214>'], ['0.0064', '1-hydroxymethyl-6-methylpyrene', 'isozyme ADH2, at 21-23C <214>'], ['0.0064', '1-hydroxymethyl-8-methylpyrene', 'isozyme ADH2, at 21-23C <214>'], ['0.0038', '4-formylpyrene', 'isozyme ADH2, at 21-23C <214>'], ['0.0038', '1-formyl-6-methylpyrene', 'isozyme ADH3, at 21-23C <214>'], ['9.6', 'octanal', 'isozyme ADH3, at 21-23C <214>'], ['0.106', '2-hydroxymethylpyrene', 'isozyme ADH3, at 21-23C <214>'], ['0.00059', '1-hydroxymethylpyrene', 'isozyme ADH3, at 21-23C <214>'], ['0.00032', '1-formyl-6-methylpyrene', 'isozyme ADH2, at 21-23C <214>'], ['0.00075', '1-hydroxymethylpyrene', 'isozyme ADH1C, at 21-23C <214>'], ['0.00131', '1-formyl-8-methylpyrene', 'isozyme ADH1C, at 21-23C <214>'], ['0.00048', '2-hydroxymethylpyrene', 'isozyme ADH1C, at 21-23C <214>'], ['0.00037', '4-hydroxymethylpyrene', 'isozyme ADH3, at 21-23C <214>'], ['0.00115', '1-hydroxymethyl-6-methylpyrene', 'isozyme ADH1C, at 21-23C <214>'], ['0.00149', '1-formyl-8-methylpyrene', 'isozyme ADH3, at 21-23C <214>']] -Specific Activity [] -Cofactors [] -Inhibitors [['4-Methylpyrazole', ''], ['50%', 'ethanol competitively inhibits the oxidation of 1-hydroxymethylpyrene by ADH1C and ADH3 <214>'], ['50%', 'DMSO inhibits isozyme ADH2-catalysed oxidation in an uncompetitive mode and reduction in a mixed mode <214>; DMSO inhibits isozymes ADH1C-catalysed oxidation in an uncompetitive mode and reduction in a mixed mode, no inhibition is detected with isozyme ADH3 <214>']] -Ki [['1.7', 'ethanol', 'isozyme ADH1C, using 1-hydroxymethylpyrene as substrate <214>'], ['1470', 'ethanol', 'isozyme ADH3, using 1-hydroxymethylpyrene as substrate <214>']] -Metal Ions [] -References [214] -Pubmed {214: '<214> Kollock, R.; Frank, H.; Seidel, A.; Meinl, W.; Glatt, H.: Oxidation of alcohols and reduction of aldehydes derived from methyl- and dimethylpyrenes by cDNA-expressed human alcohol dehydrogenases. Toxicology (2008) 245, 65-75. {Pubmed:18242813}'} --------------------------------------------------------------------------------- -Protein ID 109 -EC 1.1.1.1 -Organism Homo sapiens -Source Tissue ['buccal mucosa'] -Localisation ['cytosol'] -NSP [] -Turnover Number [] -Km [['0.00028', '1-hydroxymethyl-6-methylpyrene', 'isozyme ADH4, at 21-23C <214>'], ['0.033', '2-hydroxymethylpyrene', 'isozyme ADH4, at 21-23C <214>'], ['0.0016', '1-hydroxymethyl-8-methylpyrene', 'isozyme ADH4, at 21-23C <214>'], ['0.00092', '1-formylpyrene', 'isozyme ADH4, at 21-23C <214>'], ['0.0029', '4-hydroxymethylpyrene', 'isozyme ADH4, at 21-23C <214>'], ['0.0069', '2-formylpyrene', 'isozyme ADH4, at 21-23C <214>'], ['3.6', 'ethanol', 'isozyme ADH4, at 21-23C <214>'], ['0.000035', '1-formyl-8-methylpyrene', 'isozyme ADH4, at 21-23C <214>'], ['12.7', 'acetaldehyde', 'isozyme ADH4, at 21-23C <214>'], ['0.0283', '1-hydroxymethylpyrene', 'isozyme ADH4, at 21-23C <214>'], ['0.00048', '4-formylpyrene', 'isozyme ADH4, at 21-23C <214>'], ['0.000036', '1-formyl-6-methylpyrene', 'isozyme ADH4, at 21-23C <214>']] -Specific Activity [] -Cofactors [] -Inhibitors [['4-Methylpyrazole', ''], ['50%', 'ethanol competitively inhibits the oxidation of 1-hydroxymethylpyrene by ADH4 <214>'], ['50%', 'DMSO inhibits isozymes ADH4-catalysed oxidation in an uncompetitive mode and reduction in a mixed mode <214>']] -Ki [['3.3', 'ethanol', 'isozyme ADH4, using 1-hydroxymethylpyrene as substrate <214>']] -Metal Ions [] -References [214] -Pubmed {214: '<214> Kollock, R.; Frank, H.; Seidel, A.; Meinl, W.; Glatt, H.: Oxidation of alcohols and reduction of aldehydes derived from methyl- and dimethylpyrenes by cDNA-expressed human alcohol dehydrogenases. Toxicology (2008) 245, 65-75. {Pubmed:18242813}'} +OrderedDict([('protein_id', 8), + ('ec', '1.1.1.1'), + ('organism', 'Homo sapiens'), + ('AP', [{'data': 'medicine', 'refs': [8, 24]}]), + ('CF', + [{'data': 'NAD+', + 'refs': [1, + 2, + 3, + 4, + 5, + 6, + 7, + 8, + 9, + 10, + 11, + 12, + 13, + 14, + 15, + 16, + 17, + 18, + 19, + 21, + 22, + 23, + 24, + 27, + 28, + 32, + 33, + 34, + 36, + 38, + 39, + 41, + 42, + 43, + 44, + 45, + 46, + 47, + 48, + 50, + 51, + 52, + 53, + 55, + 59, + 60, + 61, + 63, + 64, + 66, + 67, + 68, + 69, + 70, + 71, + 72, + 73, + 74, + 75, + 76, + 77, + 78, + 79, + 80, + 81, + 82, + 83, + 84, + 85, + 86, + 87, + 88, + 90, + 91, + 92, + 93, + 94, + 95, + 96, + 98, + 105, + 106, + 107, + 108, + 109, + 110, + 111, + 112, + 113, + 114, + 115, + 119, + 122, + 123, + 124, + 125, + 126, + 127, + 128, + 129, + 130, + 133, + 137, + 138, + 139, + 140, + 142, + 143, + 150, + 153, + 161, + 162, + 163, + 166]}, + {'data': 'NADH', + 'refs': [1, + 2, + 3, + 4, + 5, + 6, + 8, + 9, + 10, + 11, + 12, + 13, + 14, + 15, + 16, + 17, + 18, + 19, + 21, + 22, + 23, + 24, + 27, + 28, + 29, + 32, + 33, + 36, + 38, + 39, + 40, + 41, + 42, + 43, + 44, + 45, + 46, + 47, + 48, + 52, + 53, + 54, + 55, + 59, + 61, + 63, + 64, + 67, + 68, + 69, + 70, + 72, + 73, + 74, + 75, + 76, + 77, + 78, + 79, + 80, + 81, + 82, + 83, + 84, + 85, + 88, + 89, + 90, + 93, + 115, + 119, + 122, + 123, + 124, + 125, + 126, + 127, + 128, + 136, + 137, + 138, + 141, + 144, + 147, + 149, + 153, + 156, + 157, + 161, + 162, + 163, + 164]}]), + ('EN', + [{'data': 'A93F', 'refs': [8]}, + {'data': 'S48T', 'refs': [8]}, + {'data': 'V141L', 'refs': [8]}]), + ('IN', + [{'data': '4-Methylpyrazole', + 'refs': [5, + 7, + 8, + 27, + 34, + 36, + 41, + 43, + 46, + 66, + 73, + 79, + 106, + 109]}, + {'data': '1,10-phenanthroline', + 'refs': [5, 8, 12, 18, 26, 36, 42, 43, 68, 73, 79, 92, 101]}, + {'data': 'pyrazole', + 'refs': [5, 8, 9, 10, 12, 19, 43, 46, 69, 78, 79, 88]}, + {'data': 'NADP+', 'refs': [8]}, + {'data': '4-bromopyrazole', 'refs': [8]}, + {'data': '4-pentylpyrazole', 'refs': [8]}, + {'data': 'sulfonic acid', 'refs': [8]}, + {'data': '8-Amino-6-methoxyquinoline', 'refs': [8]}, + {'data': '4-cyanopyrazole', 'refs': [8]}, + {'data': '4-nitropyrazole', 'refs': [8]}, + {'data': '4-octylpyrazole', 'refs': [8]}, + {'data': '4-propylpyrazole', 'refs': [8]}, + {'data': 'all-trans-retinal', 'refs': [8]}, + {'data': '4-androsten-3,17-dione', 'refs': [8]}, + {'data': '3-butylthiolan 1-oxide', 'refs': [8]}, + {'data': '5alpha-androstan-17beta-ol-3-one', 'refs': [8]}, + {'data': 'N-cyclopentyl-N-cyclobutylformamide', 'refs': [8]}, + {'data': 'N-benzylformamide', 'refs': [8]}, + {'data': 'N-heptylformamide', 'refs': [8]}, + {'data': 'N-1-methylheptylformamide', 'refs': [8]}, + {'data': 'all-trans-retinoic acid', 'refs': [8]}, + {'data': 'cimetidine', 'refs': [8]}, + {'data': 'acetaminophen', 'refs': [8]}, + {'data': 'Acetylsalicylate', 'refs': [8]}, + {'data': 'salicylate', 'refs': [8]}, + {'data': 'trifluoroethanol', 'refs': [8, 10]}, + {'data': 'dipicolinic acid', 'refs': [8, 10, 79]}, + {'data': 'EDTA', + 'refs': [8, 18, 26, 43, 46, 48, 55, 57, 58, 61, 79, 112, 124]}, + {'data': 'Isobutyramide', 'refs': [8, 41]}, + {'data': "2,2'-bipyridine", 'refs': [8, 43]}, + {'data': '4-iodopyrazole', 'refs': [8, 46]}, + {'data': '8-hydroxyquinoline 5-sulfonic acid', 'refs': [8, 79]}, + {'data': '4-methoxypyrazole', 'refs': [8, 9, 10, 12, 36]}, + {'data': 'Tween 80', 'refs': [8, 99, 112]}]), + ('KI', + [{'data': '0.014 {5alpha-androstan-17beta-ol-3-one}', + 'refs': [8]}, + {'data': '0.028 {5alpha-androstan-17beta-ol-3-one}', + 'refs': [8]}, + {'data': '0.0047 {5alpha-androstan-17beta-ol-3-one}', + 'refs': [8]}, + {'data': '0.0047 {4-androsten-3,17-dione}', 'refs': [8]}, + {'data': '0.014 {5alpha-androstan-17beta-ol-3-one}', + 'refs': [8]}, + {'data': '0.028 {5alpha-androstan-17beta-ol-3-one}', + 'refs': [8]}, + {'data': '0.0047 {5alpha-androstan-17beta-ol-3-one}', + 'refs': [8]}, + {'data': '0.0047 {4-androsten-3,17-dione}', 'refs': [8]}, + {'data': '0.014 {5alpha-androstan-17beta-ol-3-one}', + 'refs': [8]}, + {'data': '0.028 {5alpha-androstan-17beta-ol-3-one}', + 'refs': [8]}, + {'data': '0.0047 {5alpha-androstan-17beta-ol-3-one}', + 'refs': [8]}, + {'data': '0.0047 {4-androsten-3,17-dione}', 'refs': [8]}]), + ('KM', + [{'data': '10.6 {ethanol}', 'refs': [7, 8]}, + {'data': '0.06 {16-hydroxyhexadecanoate}', 'refs': [8]}, + {'data': '0.55 {1-Octanol}', 'refs': [8]}, + {'data': '0.004 {4-hydroxy-retinol}', 'refs': [8]}, + {'data': '0.012 {all-trans-retinal}', 'refs': [8]}, + {'data': '0.012 {retinol}', 'refs': [8]}, + {'data': '0.008 {Cyclohexanol}', 'refs': [8]}, + {'data': '0.013 {NAD+}', 'refs': [8]}, + {'data': '0.049 {ethanol}', 'refs': [8]}, + {'data': '0.015 {4-hydroxy-retinol}', 'refs': [8]}, + {'data': '0.018 {11-cis-retinol}', 'refs': [8]}, + {'data': '0.022 {NAD+}', 'refs': [8]}, + {'data': '0.027 {5beta-Pregnan-3beta-ol-20-one}', 'refs': [8]}, + {'data': '0.027 {4-oxo-retinal}', 'refs': [8]}, + {'data': '0.032 {3-Phenyl-1-propanol}', 'refs': [8]}, + {'data': '0.09 {Pentanol}', 'refs': [8]}, + {'data': '0.025 {NAD+}', 'refs': [8]}, + {'data': '0.025 {4-oxo-retinal}', 'refs': [8]}, + {'data': '0.025 {3,4-dihydro-retinal}', 'refs': [8]}, + {'data': '0.2 {tryptophol}', 'refs': [8]}, + {'data': '1 {ethanol}', 'refs': [8]}, + {'data': '0.009 {all-trans-retinol}', 'refs': [8]}, + {'data': '0.009 {Octanol}', 'refs': [8]}, + {'data': '0.023 {all-trans-retinol}', 'refs': [8]}, + {'data': '0.023 {9-cis-retinol}', 'refs': [8]}, + {'data': '0.25 {5beta-cholanic acid-3-one}', 'refs': [8]}, + {'data': '0.28 {Pentanol}', 'refs': [8]}, + {'data': '0.0025 {NADH}', 'refs': [8]}, + {'data': '0.8 {Octanol}', 'refs': [8]}, + {'data': '2.4 {octanal}', 'refs': [8]}, + {'data': '1.8 {ethanol}', 'refs': [8]}, + {'data': '0.23 {12-hydroxydodecanoate}', 'refs': [8]}, + {'data': '0.028 {3,4-dihydro-retinol}', 'refs': [8]}, + {'data': '0.15 {benzyl alcohol}', 'refs': [8]}, + {'data': '0.0036 {5alpha-androstan-17beta-ol-3-one}', + 'refs': [8]}, + {'data': '0.0036 {5beta-pregnan-3,20-dione}', 'refs': [8]}, + {'data': '0.011 {NADH}', 'refs': [8]}, + {'data': '0.011 {all-trans-retinal}', 'refs': [8]}, + {'data': '0.011 {retinol}', 'refs': [8]}, + {'data': '0.011 {9-cis-retinol}', 'refs': [8]}, + {'data': '0.011 {4-hydroxy-retinol}', 'refs': [8]}, + {'data': '1.2 {Octanol}', 'refs': [8]}, + {'data': '4.3 {acetaldehyde}', 'refs': [8]}, + {'data': '0.007 {NADH}', 'refs': [8]}, + {'data': '0.007 {benzyl alcohol}', 'refs': [8]}, + {'data': '0.007 {Octanol}', 'refs': [8]}, + {'data': '0.033 {all-trans-retinol}', 'refs': [8]}, + {'data': '0.034 {all-trans-retinal}', 'refs': [8]}, + {'data': '0.034 {Vanillyl alcohol}', 'refs': [8]}, + {'data': '0.08 {Octanol}', 'refs': [8]}, + {'data': '0.085 {acetaldehyde}', 'refs': [8]}, + {'data': '0.84 {ethanol}', 'refs': [8]}, + {'data': '0.017 {4-oxo-retinal}', 'refs': [8]}, + {'data': '0.046 {5beta-androstan-17beta-ol-3-one}', 'refs': [8]}, + {'data': '0.33 {acetaldehyde}', 'refs': [8]}, + {'data': '0.13 {Hexanol}', 'refs': [8]}, + {'data': '0.34 {NAD+}', 'refs': [8]}, + {'data': '0.024 {3,4-dihydro-retinol}', 'refs': [8]}, + {'data': '0.035 {11-cis-retinol}', 'refs': [8]}, + {'data': '0.048 {12-hydroxydodecanoate}', 'refs': [8]}, + {'data': '9 {ethanol}', 'refs': [8]}, + {'data': '17 {Hexanol}', 'refs': [8]}, + {'data': '0.026 {3,4-dihydro-retinal}', 'refs': [8]}, + {'data': '0.63 {ethanol}', 'refs': [8]}, + {'data': '11 {Vanillyl alcohol}', 'refs': [8]}, + {'data': '1.6 {ethanol}', 'refs': [8]}, + {'data': '4.2 {ethanol}', 'refs': [8]}, + {'data': '0.016 {Octanol}', 'refs': [8]}, + {'data': '0.056 {12-Hydroxydodecanoic acid}', 'refs': [8]}, + {'data': '0.91 {Propanol}', 'refs': [8]}, + {'data': '50 {ethylene glycol}', 'refs': [8]}, + {'data': '260 {NADH}', 'refs': [8]}, + {'data': '0.047 {12-hydroxydodecanoate}', 'refs': [8]}, + {'data': '150 {methanol}', 'refs': [8]}, + {'data': '0.24 {acetaldehyde}', 'refs': [8]}, + {'data': '0.24 {butanol}', 'refs': [8]}, + {'data': '0.94 {ethanol}', 'refs': [8]}, + {'data': '10.4 {methanol}', 'refs': [8]}, + {'data': '3.4 {acetaldehyde}', 'refs': [8]}, + {'data': '6.4 {NADH}', 'refs': [8]}, + {'data': '0.044 {Pentanol}', 'refs': [8]}, + {'data': '0.058 {5beta-androstan-3beta-ol-17-one}', 'refs': [8]}, + {'data': '0.0064 {NADH}', 'refs': [8]}, + {'data': '36 {ethanol}', 'refs': [8]}, + {'data': '120 {ethanol}', 'refs': [8]}, + {'data': '120 {', 'refs': [8]}, + {'data': '7.4 {NAD+}', 'refs': [8]}, + {'data': '18 {ethanol}', 'refs': [8]}, + {'data': '23 {Cyclohexanol}', 'refs': [8]}, + {'data': '3.2 {ethanol}', 'refs': [8]}, + {'data': '27 {1-Pentanol}', 'refs': [8]}, + {'data': '210 {Cyclohexanol}', 'refs': [8]}, + {'data': '290 {ethylene glycol}', 'refs': [8]}, + {'data': '0.0074 {NAD+}', 'refs': [8]}, + {'data': '0.0087 {NAD+}', 'refs': [8]}, + {'data': '0.79 {butanol}', 'refs': [8]}, + {'data': '180 {NAD+}', 'refs': [8]}, + {'data': '310 {2-deoxy-D-ribose}', 'refs': [8]}, + {'data': '1.39 {Propanol}', 'refs': [8]}, + {'data': '0.0079 {NAD+}', 'refs': [8]}, + {'data': '105 {NADH}', 'refs': [8]}, + {'data': '560 {2-propanol}', 'refs': [8]}, + {'data': '710 {NAD+}', 'refs': [8]}, + {'data': '1.5 {ethanol}', 'refs': [8, 119]}, + {'data': '0.45 {ethanol}', 'refs': [8, 12, 127]}, + {'data': '0.18 {NAD+}', 'refs': [8, 124]}, + {'data': '0.105 {NADH}', 'refs': [8, 150]}, + {'data': '1.7 {ethanol}', 'refs': [8, 16]}, + {'data': '0.063 {NAD+}', 'refs': [8, 23]}, + {'data': '0.022 {ethanol}', 'refs': [8, 31]}, + {'data': '0.03 {all-trans-retinol}', 'refs': [8, 36]}, + {'data': '28 {ethanol}', 'refs': [8, 36]}, + {'data': '0.074 {NAD+}', 'refs': [8, 55]}, + {'data': '0.1 {12-hydroxydodecanoate}', 'refs': [8, 9]}]), + ('LO', + [{'data': 'cytosol', + 'refs': [7, 8, 24, 27, 34, 50, 61, 66, 106, 109]}]), + ('ME', + [{'data': 'Zn2+', + 'refs': [5, + 6, + 8, + 10, + 13, + 26, + 27, + 41, + 44, + 46, + 61, + 87, + 94, + 110, + 111, + 122, + 149, + 161]}, + {'data': 'Zinc', + 'refs': [5, + 8, + 9, + 12, + 14, + 18, + 36, + 41, + 42, + 43, + 46, + 55, + 68, + 79, + 103, + 104, + 105]}]), + ('MW', + [{'data': '40000', + 'refs': [1, + 8, + 9, + 10, + 36, + 42, + 53, + 79, + 80, + 92, + 106, + 109, + 112, + 131, + 132, + 153]}, + {'data': '78000', 'refs': [8]}, + {'data': '78000-85000', 'refs': [8]}, + {'data': '79000-84000', 'refs': [8]}, + {'data': '82700', 'refs': [8]}, + {'data': '42000', 'refs': [8, 23, 61, 68, 69, 70]}, + {'data': '41000', 'refs': [8, 36]}]), + ('NSP', + [{'data': 'all-trans-retinol + NAD+ = all-trans-retinal + NADH', + 'refs': [5, 8]}, + {'data': 'all-trans-retinol + NAD+ = all-trans-retinal + NADH', + 'refs': [5, 8]}, + {'data': 'ethanol + NAD+ = acetaldehyde + NADH', + 'refs': [5, 8, 10, 31, 41]}, + {'data': 'ethanol + NAD+ = acetaldehyde + NADH', + 'refs': [5, 8, 10, 31, 41]}, + {'data': 'ethanol + NAD+ = acetaldehyde + NADH', + 'refs': [5, 8, 10, 31, 41]}, + {'data': 'isobutyramide + NAD+ = ? {r}', 'refs': [8]}, + {'data': '1-butanol + NAD+ = butanal + NADH + H+', 'refs': [8]}, + {'data': '1-butanol + NAD+ = butanal + NADH + H+ {r}', + 'refs': [8]}]), + ('PHO', + [{'data': '7.5', 'refs': [3, 5, 8, 10, 46, 55, 75]}, + {'data': '8.5', 'refs': [3, 8, 18, 46, 61, 90, 128]}, + {'data': '8', + 'refs': [4, + 8, + 18, + 25, + 41, + 48, + 72, + 114, + 115, + 119, + 132, + 136, + 151]}, + {'data': '10.5', 'refs': [5, 8, 9, 20, 73, 122, 132]}, + {'data': '7.4', 'refs': [8]}, + {'data': '7-7.5', 'refs': [8]}, + {'data': '7.6', 'refs': [8]}, + {'data': '8.5-8.8', 'refs': [8]}, + {'data': '10-10.5', 'refs': [8]}, + {'data': '7', + 'refs': [8, 10, 52, 89, 122, 137, 138, 139, 163, 164]}, + {'data': '10.8', 'refs': [8, 12]}, + {'data': '10', 'refs': [8, 18, 42, 88, 124, 129, 133, 161]}, + {'data': '5.9', 'refs': [8, 29]}, + {'data': '7.3', 'refs': [8, 41]}, + {'data': '10.4', 'refs': [8, 47]}]), + ('PHR', + [{'data': '8-10.5', 'refs': [8]}, + {'data': '8-12', 'refs': [8, 31, 47]}]), + ('PHS', [{'data': '7-10.6', 'refs': [8]}]), + ('SA', + [{'data': '3.3', 'refs': [8]}, + {'data': '0.6', 'refs': [8]}, + {'data': '0.65', 'refs': [8]}, + {'data': '1.47', 'refs': [8]}, + {'data': '1.3', 'refs': [8, 9]}]), + ('SP', + [{'data': 'ethanol + NAD+ = acetaldehyde + NADH', + 'refs': [4, + 5, + 7, + 8, + 9, + 10, + 12, + 13, + 14, + 18, + 19, + 21, + 24, + 27, + 28, + 31, + 32, + 34, + 36, + 41, + 42, + 43, + 45, + 47, + 50, + 52, + 53, + 55, + 58, + 61, + 66, + 67, + 68, + 69, + 70, + 71, + 72, + 73, + 75, + 79, + 80, + 81, + 82, + 83, + 88, + 90, + 98]}, + {'data': 'ethanol + NAD+ = acetaldehyde + NADH', + 'refs': [4, + 5, + 7, + 8, + 9, + 10, + 12, + 13, + 14, + 18, + 19, + 21, + 24, + 27, + 28, + 31, + 32, + 34, + 36, + 41, + 42, + 43, + 45, + 47, + 50, + 52, + 53, + 55, + 58, + 61, + 66, + 67, + 68, + 69, + 70, + 71, + 72, + 73, + 75, + 79, + 80, + 81, + 82, + 83, + 88, + 90, + 98]}, + {'data': 'ethanol + NAD+ = acetaldehyde + NADH', + 'refs': [4, + 5, + 7, + 8, + 9, + 10, + 12, + 13, + 14, + 18, + 19, + 21, + 24, + 27, + 28, + 31, + 32, + 34, + 36, + 41, + 42, + 43, + 45, + 47, + 50, + 52, + 53, + 55, + 58, + 61, + 66, + 67, + 68, + 69, + 70, + 71, + 72, + 73, + 75, + 79, + 80, + 81, + 82, + 83, + 88, + 90, + 98]}, + {'data': 'propan-2-ol + NAD+ = acetone + NADH', + 'refs': [4, + 8, + 10, + 12, + 14, + 18, + 38, + 41, + 42, + 46, + 55, + 70, + 72, + 75, + 78]}, + {'data': 'propan-2-ol + NAD+ = acetone + NADH', + 'refs': [4, + 8, + 10, + 12, + 14, + 18, + 38, + 41, + 42, + 46, + 55, + 70, + 72, + 75, + 78]}, + {'data': 'propanol + NADH = propionaldehyde + NADH', + 'refs': [4, + 8, + 10, + 12, + 18, + 19, + 38, + 42, + 46, + 53, + 55, + 67, + 70, + 78, + 81, + 82]}, + {'data': 'propanol + NADH = propionaldehyde + NADH {}', + 'refs': [4, + 8, + 10, + 12, + 18, + 19, + 38, + 42, + 46, + 53, + 55, + 67, + 70, + 78, + 81, + 82]}, + {'data': 'butan-2-ol + NAD+ = butan-2-one + NADH', + 'refs': [4, 8, 18, 36, 38, 41, 46, 53, 70, 72, 75, 78, 82]}, + {'data': 'butan-2-ol + NAD+ = butan-2-one + NADH', + 'refs': [4, 8, 18, 36, 38, 41, 46, 53, 70, 72, 75, 78, 82]}, + {'data': 'butanol + NAD+ = butyraldehyde + NADH', + 'refs': [4, + 8, + 9, + 10, + 12, + 18, + 36, + 38, + 41, + 42, + 46, + 53, + 67, + 69, + 72, + 75, + 78, + 81, + 82, + 83]}, + {'data': 'butanol + NAD+ = butyraldehyde + NADH', + 'refs': [4, + 8, + 9, + 10, + 12, + 18, + 36, + 38, + 41, + 42, + 46, + 53, + 67, + 69, + 72, + 75, + 78, + 81, + 82, + 83]}, + {'data': '7-cis-retinol + NAD+ = 7-cis-retinal + NADH', + 'refs': [5, 8]}, + {'data': 'octanol + NAD+ = octanal + NADH', 'refs': [5, 8]}, + {'data': 'ethanol + NAD+ = acetaldehyde + NADH + H+', + 'refs': [5, + 8, + 10, + 20, + 31, + 41, + 42, + 46, + 48, + 51, + 57, + 71, + 86, + 91, + 92, + 94, + 95, + 99, + 100, + 102, + 105, + 106, + 107, + 108, + 109, + 110, + 111, + 112, + 119, + 125, + 126, + 127, + 132, + 133, + 136, + 137, + 138, + 139, + 155, + 161, + 163]}, + {'data': 'ethanol + NAD+ = acetaldehyde + NADH + H+', + 'refs': [5, + 8, + 10, + 20, + 31, + 41, + 42, + 46, + 48, + 51, + 57, + 71, + 86, + 91, + 92, + 94, + 95, + 99, + 100, + 102, + 105, + 106, + 107, + 108, + 109, + 110, + 111, + 112, + 119, + 125, + 126, + 127, + 132, + 133, + 136, + 137, + 138, + 139, + 155, + 161, + 163]}, + {'data': 'ethanol + NAD+ = acetaldehyde + NADH + H+', + 'refs': [5, + 8, + 10, + 20, + 31, + 41, + 42, + 46, + 48, + 51, + 57, + 71, + 86, + 91, + 92, + 94, + 95, + 99, + 100, + 102, + 105, + 106, + 107, + 108, + 109, + 110, + 111, + 112, + 119, + 125, + 126, + 127, + 132, + 133, + 136, + 137, + 138, + 139, + 155, + 161, + 163]}, + {'data': 'all-trans-retinol + NAD+ = all-trans-retinal + NADH', + 'refs': [5, 8, 36, 41]}, + {'data': 'all-trans-retinol + NAD+ = all-trans-retinal + NADH', + 'refs': [5, 8, 36, 41]}, + {'data': 'hexanol + NAD+ = n-hexanal + NADH', + 'refs': [5, 8, 36, 41, 42, 70, 83]}, + {'data': 'hexanol + NAD+ = n-hexanal + NADH', + 'refs': [5, 8, 36, 41, 42, 70, 83]}, + {'data': 'ethylene glycol + NAD+ = ? + NADH', + 'refs': [5, 8, 38, 69]}, + {'data': 'ethylene glycol + NAD+ = ? + NADH', + 'refs': [5, 8, 38, 69]}, + {'data': '9-cis-retinol + NAD+ = 9-cis-retinal + NADH', + 'refs': [5, 8, 41]}, + {'data': '11-cis-retinol + NAD+ = 11-cis-retinal + NADH', + 'refs': [5, 8, 41]}, + {'data': '13-cis-retinol + NAD+ = 13-cis-retinal + NADH', + 'refs': [5, 8, 41]}, + {'data': 'pentanal + NAD+ = pentanone + NADH', + 'refs': [5, 8, 41, 43, 70, 79]}, + {'data': 'methanol + NAD+ = formaldehyde + NADH + H+', + 'refs': [5, + 8, + 9, + 12, + 18, + 38, + 42, + 43, + 52, + 53, + 57, + 58, + 69, + 70, + 79, + 83, + 88, + 99, + 100, + 111]}, + {'data': 'methanol + NAD+ = formaldehyde + NADH + H+', + 'refs': [5, + 8, + 9, + 12, + 18, + 38, + 42, + 43, + 52, + 53, + 57, + 58, + 69, + 70, + 79, + 83, + 88, + 99, + 100, + 111]}, + {'data': 'methanol + NAD+ = formaldehyde + NADH + H+', + 'refs': [5, + 8, + 9, + 12, + 18, + 38, + 42, + 43, + 52, + 53, + 57, + 58, + 69, + 70, + 79, + 83, + 88, + 99, + 100, + 111]}, + {'data': 'methanol + NAD+ = formaldehyde + NADH + H+', + 'refs': [5, + 8, + 9, + 12, + 18, + 38, + 42, + 43, + 52, + 53, + 57, + 58, + 69, + 70, + 79, + 83, + 88, + 99, + 100, + 111]}, + {'data': 'benzyl alcohol + NAD+ = benzaldehyde + NADH', + 'refs': [5, 8, 9, 18, 36, 41, 46, 58, 69]}, + {'data': 'benzyl alcohol + NAD+ = benzaldehyde + NADH', + 'refs': [5, 8, 9, 18, 36, 41, 46, 58, 69]}, + {'data': 'benzyl alcohol + NAD+ = benzaldehyde + NADH', + 'refs': [5, 8, 9, 18, 36, 41, 46, 58, 69]}, + {'data': 'cyclohexanol + NAD+ = cyclohexanone + NADH', + 'refs': [5, 8, 9, 18, 36, 43, 67, 69, 78, 81, 83]}, + {'data': 'cyclohexanol + NAD+ = cyclohexanone + NADH', + 'refs': [5, 8, 9, 18, 36, 43, 67, 69, 78, 81, 83]}, + {'data': 'octan-1-ol + NAD+ = n-octanal + NADH', + 'refs': [5, 8, 9, 18, 38, 42, 43, 69, 70, 83]}, + {'data': '3-phenyl-1-propanol + NAD+ = 3-phenyl-1-propanone + ' + 'NADH {}', + 'refs': [8]}, + {'data': '3-phenyl-1-propanol + NAD+ = 3-phenyl-1-propanone + ' + 'NADH', + 'refs': [8]}, + {'data': 'isobutyl alcohol + NAD+ = ? + NADH', 'refs': [8]}, + {'data': 'isopentenyl alcohol + NAD+ = isopentanone + NADH', + 'refs': [8]}, + {'data': '16-hydroxyhexadecanoate + NAD+ = 16-oxohexadecanoic ' + 'acid + NADH', + 'refs': [8]}, + {'data': 'vanillyl alcohol + NAD+ = vanillin + NADH', + 'refs': [8]}, + {'data': 'tryptophol + NAD+ = ? + NADH', 'refs': [8]}, + {'data': '2-deoxy-D-ribose + NAD+ = ? + NADH', 'refs': [8]}, + {'data': '17beta-hydroxyetiocholan-3-one + NAD+ = ' + 'ethiocholan-3,17-dione + NADH', + 'refs': [8]}, + {'data': 'phenylalaninol + NAD+ = ? + NADH', 'refs': [8]}, + {'data': 'digitose + NAD+ = ? + NADH', 'refs': [8]}, + {'data': '3-pyridylcarbinol + NAD+ = pyridine-3-carbaldehyde + ' + 'NADH', + 'refs': [8]}, + {'data': 'trans-4-', 'refs': [8]}, + {'data': 'retinol + NAD+ = retinal + NADH', 'refs': [8]}, + {'data': '5alpha-pregnan-3beta-ol-20-one + NAD+ = ' + '5alpha-pregnan-3,20-dione + NADH', + 'refs': [8]}, + {'data': 'isobutyramide + NAD+ = ? {r}', 'refs': [8]}, + {'data': '3,4-dihydro-retinol + NAD+ = 3,4-dihydro-retinal {r}', + 'refs': [8]}, + {'data': '4-hydroxy-retinol + NAD+ = 4-oxo-retinal + NADH {r}', + 'refs': [8]}, + {'data': '5beta-cholanic acid-3-one + NADH = 5beta-cholanic ' + 'acid-3-ol + NAD+', + 'refs': [8]}, + {'data': '5beta-pregnan-3,20-dione + NADH = ?', 'refs': [8]}, + {'data': '5beta-pregnan-3beta-ol-20-one + NAD+ = ' + '5beta-pregnan-3,20-dione + NADH', + 'refs': [8]}, + {'data': 'hexanol + NAD+ = hexanal + NADH', 'refs': [8]}, + {'data': '4-methoxy-1-naphthaldehyde + NAD+ = ' + '4-methoxy-1-naphthyl alcohol + NADH + H+', + 'refs': [8]}, + {'data': '4-methoxy-1-naphthaldehyde + NADH + H+ = ' + '4-methoxynaphthalene-1-carbaldehyde + NAD+', + 'refs': [8]}, + {'data': '6-methoxy-2-naphthaldehyde + NADH + H+ = ' + '6-methoxy-2-naphthyl alcohol + NAD+', + 'refs': [8]}, + {'data': '6-methoxy-2-naphthaldehyde + NADH + H+ =', + 'refs': [8]}, + {'data': 'm-nitrobenzaldehyde + NAD+ = m-nitrobenzyl alcohol + ' + 'NADH + H+', + 'refs': [8]}, + {'data': 'n-butanol + NAD+ = butylaldehyde + NADH + H+', + 'refs': [8]}, + {'data': 'n-butanol + NAD+ = butylaldehyde + NADH + H+ {r}', + 'refs': [8]}, + {'data': 'p-nitrobenzaldehyde + NADH + H+ = p-nitrobenzyl ' + 'alcohol + NAD+', + 'refs': [8]}, + {'data': 'retinal + NADH + H+ = retinol + NAD+', 'refs': [8]}, + {'data': '4-methoxy-1-naphthaldehyde + NAD+ = ' + '4-methoxy-1-naphthol + NADH + H+', + 'refs': [8]}, + {'data': '4-nitrosodimethylaniline + NAD+ = ? + NADH + H+', + 'refs': [8]}, + {'data': '6-methoxy-2-naphthaldehyde + NADH + H+ = ' + '6-methoxy-2-naphtol + NAD+', + 'refs': [8]}, + {'data': 'n-butanol + NAD+ = n-butanal + NADH', 'refs': [8, 10]}, + {'data': 'n-butanol + NAD+ = n-butanal + NADH {r}', + 'refs': [8, 10]}, + {'data': 'benzyl alcohol + NAD+ = benzaldehyde + NADH + H+', + 'refs': [8, + 10, + 41, + 46, + 47, + 57, + 71, + 95, + 96, + 105, + 112, + 113, + 119, + 132, + 142]}, + {'data': 'benzyl alcohol + NAD+ = benzaldehyde + NADH + H+', + 'refs': [8, + 10, + 41, + 46, + 47, + 57, + 71, + 95, + 96, + 105, + 112, + 113, + 119, + 132, + 142]}, + {'data': 'cyclohexanone + NADH + H+ = cyclohexanol + NAD+', + 'refs': [8, 124, 143]}, + {'data': 'cyclohexanone + NADH + H+ = cyclohexanol + NAD+', + 'refs': [8, 124, 143]}, + {'data': '3-nitrobenzaldehyde + NADH + H+ = 3-nitrobenzyl ' + 'alcohol + NAD+', + 'refs': [8, 128]}, + {'data': '3-nitrobenzaldehyde + NADH + H+ = 3-nitrobenzyl ' + 'alcohol + NAD+', + 'refs': [8, 128]}, + {'data': '1-butanol + NAD+ = butanal + NADH + H+', + 'refs': [8, + 31, + 48, + 57, + 92, + 96, + 98, + 105, + 110, + 111, + 112, + 127, + 132, + 161]}, + {'data': '1-butanol + NAD+ = butanal + NADH + H+', + 'refs': [8, + 31, + 48, + 57, + 92, + 96, + 98, + 105, + 110, + 111, + 112, + 127, + 132, + 161]}, + {'data': '5beta-androstan-3beta-ol-17-one + NAD+ = ' + '5beta-androstan-3,17-dione + NADH', + 'refs': [8, 41]}, + {'data': '5beta-androstan-17beta-ol-3-one + NAD+ = ' + '5beta-androstan-3,17-dione + NADH', + 'refs': [8, 41]}, + {'data': 'octan-2-ol + NAD+ = octan-2-one + NADH', + 'refs': [8, 41, 70, 78]}, + {'data': 'furfuryl alcohol + NAD+ = furfural + NADH', + 'refs': [8, 42]}, + {'data': 'furfuryl alcohol + NAD+ = furfural + NADH', + 'refs': [8, 42]}, + {'data': '5alpha-androstan-17beta-ol-3-one + NADH + H+ = ' + '3beta,17beta-dihydroxy-5alpha-androstan + NAD+ {}', + 'refs': [8, 9]}, + {'data': '5alpha-androstan-17beta-ol-3-one + NADH + H+ = ' + '3beta,17beta-dihydroxy-5alpha-androstan + NAD+', + 'refs': [8, 9]}, + {'data': 'm-nitrobenzaldehyde + NADH + H+ = m-nitrobenzyl ' + 'alcohol + NAD+', + 'refs': [8, 9]}, + {'data': 'm-nitrobenzaldehyde + NADH + H+ = m-nitrobenzyl ' + 'alcohol + NAD+', + 'refs': [8, 9]}, + {'data': 'pentanol + NAD+ = n-pentanal + NADH', + 'refs': [8, 9, 12, 18, 19, 38, 42, 67, 68, 69, 78, 81]}, + {'data': '12-hydroxydodecanoate + NAD+ = 12-oxododecanoic acid ' + '+ NADH', + 'refs': [8, 9, 36, 69]}, + {'data': '12-hydroxydodecanoate + NAD+ = 12-oxododecanoic acid ' + '+ NADH', + 'refs': [8, 9, 36, 69]}, + {'data': 'octanal + NADH + H+ = octanol + NAD+', + 'refs': [8, 9, 69]}]), + ('ST', + [{'data': 'liver', + 'refs': [1, + 2, + 5, + 8, + 9, + 12, + 36, + 41, + 43, + 53, + 59, + 69, + 73, + 79, + 80, + 83, + 106, + 130, + 131]}, + {'data': 'hepatocyte', 'refs': [5, 8]}, + {'data': 'retina', 'refs': [5, 8]}, + {'data': 'stomach', 'refs': [5, 8, 9, 84]}, + {'data': 'skin', 'refs': [8]}, + {'data': 'hepatoma cell', 'refs': [8]}, + {'data': 'serum', 'refs': [8]}, + {'data': 'adenocarcinoma cell', 'refs': [8]}, + {'data': 'aorta', 'refs': [8]}, + {'data': 'esophagus', 'refs': [8]}, + {'data': 'blood serum', 'refs': [8]}, + {'data': 'colorectum', 'refs': [8]}, + {'data': 'cervical cancer cell', 'refs': [8]}, + {'data': 'pancreas', 'refs': [8, 9]}, + {'data': 'uterus', 'refs': [8, 9]}, + {'data': 'kidney', 'refs': [8, 9]}, + {'data': 'lung', 'refs': [8, 9]}, + {'data': 'cornea', 'refs': [8, 9]}, + {'data': 'testis', 'refs': [8, 9, 36]}]), + ('SU', + [{'data': '?', + 'refs': [1, + 8, + 14, + 15, + 24, + 25, + 31, + 73, + 80, + 85, + 98, + 103, + 104, + 126, + 131, + 149, + 151, + 153, + 158]}, + {'data': 'dimer', + 'refs': [3, + 4, + 5, + 8, + 9, + 10, + 12, + 16, + 18, + 19, + 20, + 21, + 26, + 36, + 41, + 42, + 44, + 45, + 46, + 53, + 61, + 67, + 68, + 69, + 72, + 75, + 78, + 79, + 81, + 88, + 100, + 149, + 161]}, + {'data': 'More', 'refs': [8, 27, 48, 124]}]), + ('SY', + [{'data': 'alcohol dehydrogenase 1', 'refs': [5, 8, 10]}, + {'data': 'ADH', + 'refs': [5, + 8, + 10, + 13, + 27, + 37, + 41, + 46, + 61, + 71, + 87, + 88, + 91, + 95, + 105, + 108, + 111, + 112, + 125, + 126, + 166]}, + {'data': 'ALDH', 'refs': [8]}, + {'data': 'ADH1C*1', 'refs': [8]}, + {'data': 'ADH1C*2', 'refs': [8]}, + {'data': 'aldehyde dehydrogenase', 'refs': [8]}, + {'data': 'class III ADH', 'refs': [8]}, + {'data': 'class I ADH', 'refs': [8]}, + {'data': 'class II ADH', 'refs': [8]}, + {'data': 'class IV ADH', 'refs': [8]}, + {'data': 'ADH1B', 'refs': [8]}, + {'data': 'ADH1', 'refs': [8, 10, 96, 98, 113, 114, 136, 162]}, + {'data': 'ADH4', 'refs': [8, 102, 104, 109, 139]}]), + ('TN', + [{'data': '0.55 {all-trans-retinal}', 'refs': [8]}, + {'data': '0.4 {all-trans-retinol}', 'refs': [8]}, + {'data': '8 {Pentanol}', 'refs': [8]}, + {'data': '0.7 {ethanol}', 'refs': [8]}, + {'data': '0.7 {butanol}', 'refs': [8]}, + {'data': '0.9 {all-trans-retinol}', 'refs': [8]}, + {'data': '0.04 {Octanol}', 'refs': [8]}, + {'data': '16 {Pentanol}', 'refs': [8]}, + {'data': '2.5 {ethanol}', 'refs': [8]}, + {'data': '2.5 {3,4-dihydro-retinol}', 'refs': [8]}, + {'data': '6.17 {16-hydroxyhexadecanoate}', 'refs': [8]}, + {'data': '20 {4-oxo-retinal}', 'refs': [8]}, + {'data': '4 {ethanol}', 'refs': [8]}, + {'data': '4 {12-hydroxydodecanoate}', 'refs': [8]}, + {'data': '0.11 {retinol}', 'refs': [8]}, + {'data': '3.83 {ethanol}', 'refs': [8]}, + {'data': '4.33 {Octanol}', 'refs': [8]}, + {'data': '0.167 {ethanol}', 'refs': [8]}, + {'data': '0.167 {4-oxo-retinal}', 'refs': [8]}, + {'data': '0.183 {1-Pentanol}', 'refs': [8]}, + {'data': '0.583 {Cyclohexanol}', 'refs': [8]}, + {'data': '0.75 {2-propanol}', 'refs': [8]}, + {'data': '0.75 {ethylene glycol}', 'refs': [8]}, + {'data': '2.83 {1-Octanol}', 'refs': [8]}, + {'data': '2.83 {2-deoxy-D-ribose}', 'refs': [8]}, + {'data': '2.83 {4-hydroxy-retinol}', 'refs': [8]}, + {'data': '7.5 {3-Phenyl-1-propanol}', 'refs': [8]}, + {'data': '3.33 {octanal}', 'refs': [8]}, + {'data': '7.33 {Octanol}', 'refs': [8]}, + {'data': '0.333 {12-Hydroxydodecanoic acid}', 'refs': [8]}, + {'data': '2.17 {', 'refs': [8]}, + {'data': '0.018 {all-trans-retinal}', 'refs': [8]}, + {'data': '0.092 {4-hydroxy-retinol}', 'refs': [8]}, + {'data': '0.25 {all-trans-retinol}', 'refs': [8]}, + {'data': '0.667 {Pentanol}', 'refs': [8]}, + {'data': '0.038 {Octanol}', 'refs': [8]}, + {'data': '2.95 {12-hydroxydodecanoate}', 'refs': [8]}, + {'data': '8.33 {Octanol}', 'refs': [8]}, + {'data': '9.17 {benzyl alcohol}', 'refs': [8]}, + {'data': '0.22 {3,4-dihydro-retinal}', 'refs': [8]}, + {'data': '4.67 {benzyl alcohol}', 'refs': [8]}, + {'data': '17.2 {Propanol}', 'refs': [8]}, + {'data': '0.245 {Pentanol}', 'refs': [8]}, + {'data': '0.717 {NAD+}', 'refs': [8]}, + {'data': '1.83 {all-trans-retinal}', 'refs': [8]}, + {'data': '1.83 {tryptophol}', 'refs': [8]}, + {'data': '0.102 {methanol}', 'refs': [8]}, + {'data': '0.467 {Vanillyl alcohol}', 'refs': [8]}, + {'data': '0.683 {3-Pyridylcarbinol}', 'refs': [8]}, + {'data': '1.22 {3,4-dihydro-retinal}', 'refs': [8]}, + {'data': '3.03 {12-hydroxydodecanoate}', 'refs': [8]}, + {'data': '7.83 {ethanol}', 'refs': [8]}, + {'data': '7.83 {4-oxo-retinal}', 'refs': [8]}, + {'data': '8.67 {Vanillyl alcohol}', 'refs': [8]}, + {'data': '10.2 {ethanol}', 'refs': [8]}, + {'data': '19.5 {Hexanol}', 'refs': [8]}, + {'data': '30.7 {ethanol}', 'refs': [8]}, + {'data': '34.8 {butanol}', 'refs': [8]}, + {'data': '0.175 {ethanol}', 'refs': [8]}, + {'data': '0.028 {all-trans-retinol}', 'refs': [8]}, + {'data': '0.087 {retinol}', 'refs': [8]}, + {'data': '34.2 {4-hydroxy-retinol}', 'refs': [8]}, + {'data': '0.088 {3,4-dihydro-retinol}', 'refs': [8]}]), + ('TO', + [{'data': '25', 'refs': [5, 8, 10, 25, 40, 61]}, + {'data': '30-37', 'refs': [8, 41]}]), + ('TS', [{'data': '23', 'refs': [8]}]), + ('references', + {1: {'info': 'Talbot, B.G.; Qureshi, A.A.; Cohen, R.; Thirion, ' + 'J.P.: Purification and properties of two distinct ' + 'groups of ADH isozymes from Chinese hamster liver. 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(2007) 349, ' + '1337-1340.', + 'pubmed': ''}})]) -------------------------------------------------------------------------------- ``` -## Funding -Matthias König is supported by the Federal Ministry of Education and Research (BMBF, Germany) -within the research network Systems Medicine of the Liver (**LiSyM**, grant number 031L0054). - ## Release notes +### 0.2.0 +* unittests and continuous integration +* complete refactoring of parser +* supporting full set of information + ### 0.1.0 * initial release of updated parser --- diff --git a/brendapy/_version.py b/brendapy/_version.py index daa98c8..da0f7c5 100644 --- a/brendapy/_version.py +++ b/brendapy/_version.py @@ -1,7 +1,4 @@ """ Definition of version string. """ -__version__ = "0.1.2" - -PROGRAM_VERSION = __version__ -PROGRAM_NAME = 'brendapy' +__version__ = "0.2.0" diff --git a/brendapy/examples.py b/brendapy/examples.py index 141cb26..b9540ae 100644 --- a/brendapy/examples.py +++ b/brendapy/examples.py @@ -11,11 +11,11 @@ def parse_proteins_for_ec(): """ brenda = BrendaParser() ec = "1.1.1.1" - proteins = brenda.parse_proteins(ec) + proteins = brenda.get_proteins(ec) print(f"{len(proteins)} proteins for EC {ec} in BRENDA") print(f"Protein identifier: {proteins.keys()}") - print("-"*80) + print("-" * 80) for p in proteins.values(): if p.organism == "Homo sapiens": print(p) diff --git a/brendapy/parser.py b/brendapy/parser.py index 6ad46de..dc17489 100644 --- a/brendapy/parser.py +++ b/brendapy/parser.py @@ -1,5 +1,51 @@ """ -Module for parsing the BRENDA ENZYME information from flat file +Module for parsing the BRENDA ENZYME information from flat file. +The following information is available: + + AC activating compound + AP application + CF cofactor + CL cloned + CR crystallization + EN engineering + EXP expression + GI general information on enzyme + GS general stability + IC50 IC-50 Value + ID EC-class + IN inhibitors + KKM Kcat/KM-Value substrate in {...} + KI Ki-value inhibitor in {...} + KM KM-value substrate in {...} + LO localization + ME metals/ions + MW molecular weight + NSP natural substrates/products reversibilty information in {...} + OS oxygen stability + OSS organic solvent stability + PHO pH-optimum + PHR pH-range + PHS pH stability + PI isoelectric point + PM posttranslation modification + PR protein + PU purification + RE reaction catalyzed + RF references + REN renatured + RN accepted name (IUPAC) + RT reaction type + SA specific activity + SN synonyms + SP substrates/products reversibilty information in {...} + SS storage stability + ST source/tissue + SU subunits + SY systematic name + TN turnover number substrate in {...} + TO temperature optimum + TR temperature range + TS temperature stability """ import os import re @@ -12,20 +58,44 @@ class BrendaParser(object): - """ Parser for BRENDA information.""" + """ Parser for BRENDA information. + + The parser reads the BRENDA flat file into the + parts for the ec numbers. Via the BrendaParser the + information for the ec numbers can be accesses. + """ + + BRENDA_KEYS = { + "AC", "AP", "CF", "CL", "CR", "EN", "EXP", "GI", "GS", "IC50", + "ID", "IN", "KKM", "KI", "KM", "LO", "ME", "MW", "NSP", "OS", + "OSS", "PHO", "PHR", "PHS", "PI", "PM", "PR", "PU", "RE", "RF", + "REN", "RN", "RT", "SA", "SN", "SP", "SS", "ST", "SU", "SY", "TN", + "TO", "TR", "TS" + } + PATTERN_RF = re.compile(r"^<(\d+?)> (.+) {Pubmed:\s*(\d*)\s*}") + PATTERN_ALL = re.compile(r"^#([,\d\s]+?)#(.+)<([,\d\s]+)>") def __init__(self, brenda_file=BRENDA_FILE): - """ Initialize the parser. - Parses the BRENDA file + """ Initialize parser and parse BRENDA file. :param brenda_file: BRENDA text file """ self.brenda_file = brenda_file self.ec_text = BrendaParser.parse_entry_strings(self.brenda_file) - # self.ec_proteins = self.parse_proteins() + self.ec_data = OrderedDict() # only parse on demand + + def keys(self): + """ Available ec keys. - @classmethod - def parse_entry_strings(cls, filename): + Information for these EC numbers is available in the + parser object. + + :return: list of ec numbers + """ + return self.ec_text.keys() + + @staticmethod + def parse_entry_strings(filename): """ Reads the string entries from BRENDA file. :param filename: BRENDA database download @@ -33,16 +103,18 @@ def parse_entry_strings(cls, filename): """ logging.info(f"`parse_entry_strings` from `{filename}`") ec_data = OrderedDict() - start = "ID\t" - end = "///" + in_entry = False data_lines = [] # read BRENDA file with open(filename, 'r') as bf: for line in bf.readlines(): + if line.startswith("*") or len(line) == 0: + continue + # start of entry - if line.startswith(start): + if line.startswith("ID\t"): in_entry = True ec = BrendaParser._get_ec_from_line(line) data_lines = [line] @@ -50,154 +122,107 @@ def parse_entry_strings(cls, filename): if in_entry: data_lines.append(line) # end of entry - if in_entry and line.startswith(end): + if in_entry and line.startswith("///"): in_entry = False entry = "".join(data_lines) entry.replace('\xef\xbf\xbd', " ") + # store entry ec_data[ec] = entry + data_lines = [] return ec_data - @property - def keys(self): - """ Available ec keys. - :return: - """ - return self.ec_text.keys() - - @staticmethod - def _get_ec_from_line(line): - ec = line.strip().split("\t")[1].strip() - ec = ec.split(" ")[0] - if utils.is_ec_number(ec): - return ec - else: - return None + @utils.timeit + def parse_info_dicts(self): + """ Parses all info dicts. - # ------------------------------ - # Parse information from entry - # ------------------------------ - @staticmethod - def parse_info(bid, ec_info): - """ Get information from ec_str for given BRENDA id (bids are listed below). - - AC activating compound - AP application - CF cofactor - CL cloned - CR crystallization - EN engineering - EXP expression - GI general information on enzyme - GS general stability - IC50 IC-50 Value - ID EC-class - IN inhibitors - KKM Kcat/KM-Value substrate in {...} - KI Ki-value inhibitor in {...} - KM KM-value substrate in {...} - LO localization - ME metals/ions - MW molecular weight - NSP natural substrates/products reversibilty information in {...} - OS oxygen stability - OSS organic solvent stability - PHO pH-optimum - PHR pH-range - PHS pH stability - PI isoelectric point - PM posttranslation modification - PR protein - PU purification - RE reaction catalyzed - RF references - REN renatured - RN accepted name (IUPAC) - RT reaction type - SA specific activity - SN synonyms - SP substrates/products reversibilty information in {...} - SS storage stability - ST source/tissue - SU subunits - SY systematic name - TN turnover number substrate in {...} - TO temperature optimum - TR temperature range - TS temperature stability - - :param bid: BRENDA key - :param ec_info: BRENDA information string for EC - :return: + This takes around ~15s and prepares all proteins. """ - def starts_with_string(line, string): - start = [string + "\t", string + " "] - for item in start: - if line.startswith(item): - return True - return False - - results = [] - lines = ec_info.split("\n") - in_item = False - L = len(bid) - - for line in lines: - # read first entry - if not in_item and starts_with_string(line, bid): - item = line[L+1:] - in_item = True - - elif in_item is True: - # entries longer than one line - if starts_with_string(line, ''): - item += " " + line.strip() - - # write entries if next entry begins - elif starts_with_string(line, bid): - results.append(item) - - item = line[L+1:] - # write last entry - elif len(line) == 0: - results.append(item) - break - - return [item.replace('\t', ' ') for item in results] + d = OrderedDict() + for ec, ec_string in self.ec_text.items(): + d[ec] = BrendaParser._parse_info_dict(ec, ec_string) + return d @staticmethod - def parse_info_dict(ec_str): + def _parse_info_dict(ec, ec_str): """ :return: """ - keys = { - "AC", "AP", "CF", "CL", "CR", "EN", "EXP", "GI", "GS", "IC50", - "ID", "IN", "KKM", "KI", "KM", "LO", "ME", "MW", "NSP", "OS", - "OSS", "PHO", "PHR", "PHS", "PI", "PM", "PR", "PU", "RE", "RF", - "REN", "RN", "RT", "SA", "SN", "SP", "SS", "ST", "SU", "SY", "TN", - "TO", "TR", "TS" - } - results = defaultdict(list) + results = defaultdict(OrderedDict) + + def store_item(bid, item): + """ Store parsed item for bid. + :param bid: + :param item: + :return: + """ + if bid == "ID": + results[bid] = item + elif bid in {"RN", "RE", "RT", "SN"}: + if isinstance(results[bid], OrderedDict): + results[bid] = {item} + else: + results[bid].add(item) + elif bid == "RF": + match = BrendaParser.PATTERN_RF.match(item) + if match: + rid, info, pubmed = match.group(1), match.group(2), match.group(3) + rid = int(rid) # integer keys for all references + results[bid][rid] = { + # 'id': rid, + 'info': info, + 'pubmed': pubmed, + } + else: + logging.error(f"{ec}_{bid}: could not be parsed: `{item}`") + else: + match = BrendaParser.PATTERN_ALL.match(item) + if match: + ids, data, refs = match.group(1), match.group(2), match.group(3) + ids = ids.replace(' ', ",") # fix the missing comma in ids + refs = ids.replace(' ', ",") # fix the missing comma in refs + ids = [int(token) for token in ids.split(',')] + # get rid of brackets + info = { + 'data': data.split('(')[0].strip(), + 'refs': [int(token) for token in refs.split(',')] + } + if info['data'] in ['more', 'more = ?', '-999 {more}', '-999']: + logging.info(f"{ec}_{bid}: `more` information not stored: {info}") + return + if len(info['data']) == 0: + logging.info(f"{ec}_{bid}: `empty` information not stored: {info}") + return + + for pid in ids: + if bid == "PR": + results[bid][pid] = info + else: + if pid in results[bid]: + results[bid][pid].append(info) + else: + results[bid][pid] = [info] + else: + if bid == "SY" and item[0] != '#': + logging.info(f"{ec}_{bid}: generic synonyms are not stored: {item}") + else: + logging.error(f"{ec}_{bid}: could not be parsed: `{item}`") def parse_bid_item(line): tokens = line.split("\t") bid = tokens[0].strip() item = "\t".join(tokens[1:]) - print(bid, item) return bid, item - # combine lines into entries + # parse entries from line lines = ec_str.split("\n") - in_item = False for line in lines: - print(line) - # read initial line of entry if not in_item: if len(line) > 0 and not line.startswith("\t"): bid, item = parse_bid_item(line) - if bid in keys: + if bid in BrendaParser.BRENDA_KEYS: in_item = True else: in_item = False @@ -211,76 +236,47 @@ def parse_bid_item(line): # write entries if next entry begins elif len(line) > 0 and not line.startswith("\t"): # store old entry - results[bid].append(item.replace('\t', ' ')) + store_item(bid, item) + in_item = False # create new entry bid, item = parse_bid_item(line) - if bid in keys: + if bid in BrendaParser.BRENDA_KEYS: in_item = True else: - in_item = False + logging.error(f"{ec}_{bid}: BRENDA key not supported in line: `{line}`") item = None # write last entry elif len(line) == 0: - results[bid].append(item.replace('\t', ' ')) + store_item(bid, item) + in_item = False return results @staticmethod - def is_id_in_entry(id, entry): - """ Returns True if ID is in Entry, False otherwise. - - ID list always starts with '#' and ends with '#' - Entries are separated by comma. - Solution with regular expressions searching for - #3# and #3,4,5,6# patterns - """ - pattern = r"#[\d,]+#" - items = re.findall(pattern, entry) - ids = [] - for item in items: - ids.extend( - [id for id in item[1:-1].split(",") - if id != '' and id.isdigit()] - ) - # Is ID in IDlist ? - ids = [int(id) for id in ids] - return id in ids - - @staticmethod - def get_entry_with_id(id, entry_list): - """ Returns an entry list of the entries in which the id is found - Information for proteins can be collected. - Use the filterfunction: isIDinEntry(ID) - """ - return [entry for entry in entry_list - if BrendaParser.is_id_in_entry(id, entry)] - - def parse_all_proteins(self): - proteins_all = {} - for ec in self.ec_text.keys(): - proteins_all[ec] = self.parse_proteins(ec) - return proteins_all + def _get_ec_from_line(line): + ec = line.strip().split("\t")[1].strip() + ec = ec.split(" ")[0] + if utils.is_ec_number(ec): + return ec + else: + return None - def parse_proteins(self, ec): + def get_proteins(self, ec): """ Parses all BRENDA proteins for given EC number. :param ec: - :return: dict of proteins (key, protein) + :return: OrderedDict of BRENDA proteins """ - ec_str = self.ec_text[ec] - entries = self.parse_info("PR", ec_str) - - # get the protein ids from the proteins - protein_keys = set() - for entry in entries: - tokens = entry.split("#") - protein_keys.add(int(tokens[1])) + # process text data for ec if not already existing + if ec not in self.ec_data: + self.ec_data[ec] = BrendaParser._parse_info_dict(ec, ec_str=self.ec_text[ec]) + ec_data = self.ec_data[ec] proteins = {} - for key in protein_keys: - proteins[key] = BrendaProtein(ec, key, ec_str) + for key in ec_data['PR'].keys(): + proteins[key] = BrendaProtein(ec=ec, key=key, data=ec_data) return proteins @@ -307,454 +303,66 @@ class BrendaProtein(object): "Inhibitors", "Ki", "Metal ions", "References" ] - def __init__(self, ec, id, ec_string): + def __init__(self, ec, key, data): """ Protein object is initialized with ec number 'ec', id (number of entry for ec in Brenda) and ec_string which contains the data for the protein. """ - self.ec = ec - self.protein_id = id - self.ec_string = ec_string - self.organism = self.get_organism() - self.gene = self.get_swissprot_gene() - self.references = self.get_references() - self.reaction = self.get_reaction() - self.source_tissue = self.get_source_tissue() - self.localisation = self.get_localication() - self.natural_substrate_product = self.get_natural_substrate_product() - self.substrate_product = self.get_substrate_product() - self.turnover_number = self.get_turnover_number() - self.km = self.getKm() - self.specific_activity = self.getSpecificActivity() - self.cofactors = self.getCofactors() - self.inhibitors = self.getInhibitors() - self.ki = self.getKi() - self.metal_ions = self.getMetalIons() - self.pubmed = self.get_pubmed() + self.data = OrderedDict([ + ('protein_id', key), + ('ec', ec), + ('organism', data['PR'][key]['data']), + ]) + reference_ids = set(data['PR'][key]['refs']) + for bid in [ + "AC", "AP", "CF", "CL", "CR", "EN", "EXP", "GI", "GS", "IC50", + "ID", "IN", "KKM", "KI", "KM", "LO", "ME", "MW", "NSP", "OS", + "OSS", "PHO", "PHR", "PHS", "PI", "PM", "PR", "PU", "RE", "RF", + "REN", "RN", "RT", "SA", "SN", "SP", "SS", "ST", "SU", "SY", "TN", + "TO", "TR", "TS" + ]: + if bid in ["ID", "PR", "RN", "RE", "RT", "SN", "RF"]: + continue + info = data[bid].get(key, None) + if info: + # print(bid, info) + self.data[bid] = info + for item in info: + reference_ids.update(item['refs']) + + # FIXME: some mentioned references are missing + self.data['references'] = {ref_id: data['RF'].get(ref_id, None) for ref_id in reference_ids} + + @property + def protein_id(self): + return self.data['protein_id'] + + @property + def ec(self): + return self.data['ec'] + + @property + def organism(self): + return self.data['organism'] + + @property + def source_tissues(self): + return [item['data'] for item in self.data["ST"]] + + @property + def kms(self): + return [item['data'] for item in self.data["KM"]] + + @property + def kis(self): + return [item['data'] for item in self.data["KM"]] + + @property + def references(self): + return self.data['references'] def __str__(self): """String representation. """ - lines = [] - data = OrderedDict([ - ("Protein ID", self.protein_id), - ("EC", self.ec), - ("Organism", self.organism), - ("Source Tissue", self.source_tissue), - ("Localisation", self.localisation), - ("NSP", self.natural_substrate_product), - ("Turnover Number", self.turnover_number), - ("Km", self.km), - ("Specific Activity", self.specific_activity), - ("Cofactors", self.cofactors), - ("Inhibitors", self.inhibitors), - ("Ki", self.ki), - ("Metal Ions", self.metal_ions), - ("References", self.references), - ("Pubmed", self.pubmed), - ]) - for (field, info) in data.items(): - lines.append(field.ljust(20) + str(info)) - return "\n".join(lines) - - def get_organism(self): - """ Sets organism information from protein """ - pr_entries = BrendaParser.parse_info("PR", self.ec_string) - entry = BrendaParser.get_entry_with_id(self.protein_id, pr_entries) - items = entry[0].split(" ") - if len(items[2]) > 0 and items[2][0] != "Q": - organism = items[1] + " " + items[2] - else: - organism = items[1] - return organism - - def get_swissprot_gene(self): - """ Sets gene information for protein """ - pr_entries = BrendaParser.parse_info("PR", self.ec_string) - # Get Entries for id - entry = BrendaParser.get_entry_with_id(self.protein_id, pr_entries) - items = entry[0].split(" ") - gene = [items[-3], items[-2]] - return gene - - def get_reaction(self): - """ Sets reaction for protein - - FIXME: What is this ? Still necessary ? - """ - pass - - def get_source_tissue(self): - """ Sets source tissue for protein """ - st_entries = BrendaParser.parse_info("ST", self.ec_string) - - entries = BrendaParser.get_entry_with_id(self.protein_id, st_entries) - tissues = [] - - def get_tissue(entry): - pattern = r"#.*?# .*? \(" - tmp = re.findall(pattern, entry) - if not tmp: - pattern = r"#.*?# .* <" - tmp = re.findall(pattern, entry) - tmp = tmp[0].split("#") - tissue = tmp[-1][:-1].strip() - return tissue - - for entry in entries: - tissues.append(get_tissue(entry)) - return tissues - - def get_localication(self): - """ Sets localisation for protein """ - lo_entries = BrendaParser.parse_info("LO", self.ec_string) - entries = BrendaParser.get_entry_with_id(self.protein_id, lo_entries) - localisation = [] - - def get_loc(entry): - pattern = r"^#.*?# .* <" - tmp = re.findall(pattern, entry) - if not tmp: - pattern = r"^#.*?# .* (" - tmp = re.findall(pattern, entry) - tmp = tmp[0].split("#") - loc = tmp[2][:-1].strip() - return loc - - for entry in entries: - localisation.append(get_loc(entry)) - return localisation - - def get_natural_substrate_product(self): - """ Sets natural substrate, product for protein """ - nsp_entries = BrendaParser.parse_info("NSP", self.ec_string) - entries = BrendaParser.get_entry_with_id(self.protein_id, nsp_entries) - nsp = [] - - def get_reaction(entry): - """ Gets the natural reaction equation """ - pattern = r"#.*?# .* \(" - tmp = re.findall(pattern, entry) - if not tmp: - pattern = r"#.*?# .* <" - tmp = re.findall(pattern, entry) - if not tmp: - tmp = re.findall(r"#.*?# .*", entry) - tmp = tmp[0].split("#") - reaction = tmp[-1][:-1].strip() - return reaction - - def get_info(entry): - """ Gets additional information """ - pattern = r"\(.*\)" - tmp = re.findall(pattern, entry) - if tmp: - info = tmp[0][1:-1] - else: - info = '' - if not BrendaParser.is_id_in_entry(self.protein_id, info): - info = '' - return info - - for entry in entries: - nsp.append( - [get_reaction(entry), get_info(entry)] - ) - return nsp - - def get_substrate_product(self): - """ Sets substrate, product for protein - - Additional substrate, product information - TODO: not implemented (information not very important) - """ - sp_entries = BrendaParser.parse_info("SP", self.ec_string) - entries = BrendaParser.get_entry_with_id(self.protein_id, sp_entries) - - return [] - - def get_turnover_number(self): - """ Sets the turnover numbers for the proteins """ - tn_entries = BrendaParser.parse_info("TN", self.ec_string) - entries = BrendaParser.get_entry_with_id(self.protein_id, tn_entries) - - tn = [] - - def getTN(entry): - """ gets the turnover value """ - pattern = r"#.*?# \d*.\d*.* {" - tmp = re.findall(pattern, entry) - tmp = tmp[0].split("#") - tn = tmp[-1][:-1].strip() - return tn - - def getSubstrate(entry): - """ gets the coresponding value """ - pattern = r"{.*}" - tmp = re.findall(pattern, entry) - substrate = tmp[0][1:-1] - return substrate - - def getAddInfo(entry): - """ gets addtional information for the tn value """ - info = '' - pattern = r"\(.*\)" - tmp = re.findall(pattern, entry) - if tmp: - info = tmp[0][1:-1].replace("\xb0", "") - if not BrendaParser.is_id_in_entry(self.protein_id, info): - info = '' - else: - info = re.sub("#.*?#", "", info).strip() - return info - - # Get the information from the entries - for entry in entries: - tn.append([getTN(entry), getSubstrate(entry), getAddInfo(entry)]) - return tn - - def getKm(self): - """ Sets the Km values of the proteins """ - km_entries = BrendaParser.parse_info("KM", self.ec_string) - entries = BrendaParser.get_entry_with_id(self.protein_id, km_entries) - # print entries - km = [] - - def getKM(entry): - """ gets the turnover value """ - pattern = r"#.*?# \d*.\d*.* {" - tmp = re.findall(pattern, entry) - tmp = tmp[0].split("#") - km = tmp[-1][:-1].strip() - return km - - def getSubstrate(entry): - """ gets the coresponding value """ - pattern = r"{.*}" - tmp = re.findall(pattern, entry) - substrate = tmp[0][1:-1] - return substrate - - def getAddInfo(entry): - """ gets addtional information for the tn value """ - info = '' - pattern = r"\(.*\)" - tmp = re.findall(pattern, entry) - if tmp: - info = tmp[0][1:-1].replace("\xb0", "") - if not BrendaParser.is_id_in_entry(self.protein_id, info): - info = '' - else: - info = re.sub("#.*?#", "", info).strip() - return info - - for entry in entries: - km.append([getKM(entry), getSubstrate(entry), getAddInfo(entry)]) - # print km[-1] - return km - - def getSpecificActivity(self): - """ Sets the specific activity of the proteins """ - sa_entries = BrendaParser.parse_info("SA", self.ec_string) - entries = BrendaParser.get_entry_with_id(self.protein_id, sa_entries) - # print entries - sa = [] - - def getSA(entry): - """ gets value of specific activity """ - pattern = r"#.*# \d*.\d*.* \(" - tmp = re.findall(pattern, entry) - if not tmp: - tmp = re.findall(r"#.*?# \d*.\d*.* <", entry) - if not tmp: - tmp = re.findall(r"#.*?# -\d*.\d*.* \(", entry) - if not tmp: - tmp = re.findall(r"#.*?# -\d*.\d*.* <", entry) - tmp = tmp[0].split("#") - sa = tmp[-1][:-1].strip() - return sa - - def getAddInfo(entry): - """ gets additional information for the sa value """ - info = '' - pattern = r"\(.*\)" - tmp = re.findall(pattern, entry) - if tmp: - info = tmp[0][1:-1] - if not BrendaParser.is_id_in_entry(self.protein_id, info): - info = '' - else: - info = re.sub("#.*?#", "", info).strip() - return info - - for entry in entries: - sa.append([getSA(entry), getAddInfo(entry)]) - # print sa[-1] - return sa - - def getCofactors(self): - """ Sets the cofactors of the proteins """ - co_entries = BrendaParser.parse_info("CF", self.ec_string) - entries = BrendaParser.get_entry_with_id(self.protein_id, co_entries) - # print entries - co = [] - - def getCF(entry): - """ Gets the cofactor from entry. """ - pattern = r"#.*?# .* \(" - tmp = re.findall(pattern, entry) - if not tmp: - pattern = r"#.*?# .* <" - tmp = re.findall(pattern, entry) - tmp = tmp[0].split("#") - cf = tmp[-1][:-1].strip() - return cf - - def getAddInfo(entry): - """ Gets additional information for the cofactor """ - info = '' - pattern = r"\(.*\)" - tmp = re.findall(pattern, entry) - if tmp: - info = tmp[0][1:-1] - info = [item for item in info.split(';') - if BrendaParser.is_id_in_entry(self.protein_id, item)] - info = [re.sub(r"#.*?#", "", item).strip() for item in info] - return "; ".join(info) - - for entry in entries: - co.append([getCF(entry), getAddInfo(entry)]) - # print co[-1] - return co - - def getInhibitors(self): - """ Sets the inhinitors of the proteins """ - in_entries = BrendaParser.parse_info("IN", self.ec_string) - entries = BrendaParser.get_entry_with_id(self.protein_id, in_entries) - # print entries - inhibitors = [] - - def getIN(entry): - """ Gets the inhibitor from entry. """ - pattern = r"#.*?# .* \(" - tmp = re.findall(pattern, entry) - if not tmp: - pattern = r"#.*?# .* <" - tmp = re.findall(pattern, entry) - tmp = tmp[0].split("#") - inhibitor = tmp[-1][:-1].strip() - return inhibitor - - def getAddInfo(entry): - """ Gets additional information for the inhibitor """ - info = '' - pattern = r"\(.*\)" - tmp = re.findall(pattern, entry) - if tmp: - info = tmp[0][1:-1] - info = [item for item in info.split(';') - if BrendaParser.is_id_in_entry(self.protein_id, item)] - info = [re.sub(r"#.*?#", "", item).strip() for item in info] - return "; ".join(info) - - for entry in entries: - inhibitors.append([getIN(entry), getAddInfo(entry)]) - # print inhibitors[-1] - return inhibitors - - def getKi(self): - """ Sets the Ki values of the proteins """ - ki_entries = BrendaParser.parse_info("KI", self.ec_string) - entries = BrendaParser.get_entry_with_id(self.protein_id, ki_entries) - # print entries - ki = [] - - def getKI(entry): - """ gets the turnover value """ - pattern = r"#.*?# \d*.\d*.* {" - tmp = re.findall(pattern, entry) - # print entry - tmp = tmp[0].split("#") - ki = tmp[-1][:-1].strip() - return ki - - def getSubstrate(entry): - """ gets the coresponding value """ - pattern = r"{.*}" - tmp = re.findall(pattern, entry) - substrate = tmp[0][1:-1] - return substrate - - def getAddInfo(entry): - """ gets addtional information for the tn value """ - info = '' - pattern = r"\(.*\)" - tmp = re.findall(pattern, entry) - if tmp: - info = tmp[0][1:-1].replace("\xb0", "") - if not BrendaParser.is_id_in_entry(self.protein_id, info): - info = '' - else: - info = re.sub("#.*?#", "", info).strip() - return info - - for entry in entries: - ki.append([getKI(entry), getSubstrate(entry), getAddInfo(entry)]) - # print ki[-1] - return ki - - def getMetalIons(self): - """ Sets the metal ions of the proteins """ - me_entries = BrendaParser.parse_info("ME", self.ec_string) - entries = BrendaParser.get_entry_with_id(self.protein_id, me_entries) - # print entries - me = [] - - def getME(entry): - """ Gets the metal ions from entry. """ - pattern = r"#.*?# .* \(" - tmp = re.findall(pattern, entry) - if not tmp: - pattern = r"#.*?# .* <" - tmp = re.findall(pattern, entry) - tmp = tmp[0].split("#") - me_ion = tmp[-1][:-1].strip() - return me_ion - - def getAddInfo(entry): - """ Gets additional information for the cofactor """ - info = '' - pattern = r"\(.*\)" - tmp = re.findall(pattern, entry) - if tmp: - info = tmp[0][1:-1] - info = [item for item in info.split(';') - if BrendaParser.is_id_in_entry(self.protein_id, item)] - info = [re.sub(r"#.*?#", "", item).strip() for item in info] - return "; ".join(info) - - for entry in entries: - me.append([getME(entry), getAddInfo(entry)]) - # print me[-1] - return me - - def get_references(self): - """ Parse the reference integers from the protein entries.""" - pr_entries = BrendaParser.parse_info("PR", self.ec_string) - # Get Entries for id - entry = BrendaParser.get_entry_with_id(self.protein_id, pr_entries) - items = entry[0].split(" ") - references = items[-1].replace("<", "").replace(">", "").split(",") - return [int(ref) for ref in references] - - def get_pubmed(self): - """ Gets information about the cited pubmed references. - So the given data in the protein objects can be validated - """ - rf_entries = BrendaParser.parse_info("RF", self.ec_string) - pubmeds = {} - for ref_id in self.references: - entry = rf_entries[ref_id-1] - pubmeds[ref_id] = entry - - return pubmeds + from pprint import pformat + return pformat(self.data) diff --git a/brendapy/tests/test_brenda.py b/brendapy/tests/test_brenda.py index f53f430..60fe7c6 100644 --- a/brendapy/tests/test_brenda.py +++ b/brendapy/tests/test_brenda.py @@ -1,8 +1,11 @@ import pytest +import logging from brendapy import BrendaParser, BrendaProtein from brendapy.settings import BRENDA_FILE +BRENDA_PARSER = BrendaParser() + def test_parsing(): brenda = BrendaParser() @@ -16,54 +19,41 @@ def test_parsing_from_file(): assert "1.1.1.1" in brenda.ec_text -def test_protein(): +def test_protein1(): """ Test the proteinBRENDA module """ - brenda = BrendaParser() - ec = "1.1.1.1" - proteins = brenda.parse_proteins(ec) + proteins = BRENDA_PARSER.get_proteins(ec) assert proteins assert len(proteins) == 167 def test_protein_detail1(): - brenda = BrendaParser() - ec = "1.1.1.1" - ec_str = brenda.ec_text[ec] - protein = BrendaProtein(ec=ec, id=1, ec_string=ec_str) + proteins = BRENDA_PARSER.get_proteins(ec="1.1.1.1") + protein = proteins[1] + assert protein - assert 'liver' in protein.source_tissue + assert 'liver' in protein.source_tissues assert protein.organism == "Gallus gallus" assert 44 in protein.references - assert len(protein.pubmed) == 1 def test_protein_detail2(): - brenda = BrendaParser() - ec = "1.1.1.1" - ec_str = brenda.ec_text[ec] - protein = BrendaProtein(ec=ec, id=4, ec_string=ec_str) + proteins = BRENDA_PARSER.get_proteins("1.1.1.1") + protein = proteins[4] + assert protein assert protein.organism == "Drosophila melanogaster" - assert 8 in protein.references - assert len(protein.pubmed) == 7 -''' -def test_all_proteins(): - brenda = BrendaParser() - for ec in brenda.keys(): - print(ec) - proteins = brenda.parse_proteins(ec) - def test_info_dict(): - brenda = BrendaParser() ec = "1.1.1.2" - ec_str = brenda.ec_text[ec] - d = brenda.parse_info_dict(ec_str) - from pprint import pprint - pprint(d) - import json - assert False -''' + ec_str = BRENDA_PARSER.ec_text[ec] + d = BRENDA_PARSER._parse_info_dict(ec, ec_str) + assert d + + +@pytest.mark.parametrize("ec", BRENDA_PARSER.keys()) +def test_proteins_for_ec(ec): + proteins = BRENDA_PARSER.get_proteins(ec) + assert proteins is not None diff --git a/brendapy/utils.py b/brendapy/utils.py index 1557009..b70690d 100644 --- a/brendapy/utils.py +++ b/brendapy/utils.py @@ -1,3 +1,5 @@ +import time + def is_ec_number(ec): """Tests if given string 'ec' is EC number. @@ -10,3 +12,20 @@ def is_ec_number(ec): if not number.isdigit(): return False return True + + +def timeit(method): + """ Timing decorator. """ + def timed(*args, **kw): + ts = time.time() + result = method(*args, **kw) + te = time.time() + + if 'log_time' in kw: + name = kw.get('log_name', method.__name__.upper()) + kw['log_time'][name] = int((te - ts) * 1000) + else: + print('%r %2.2f ms' % (method.__name__, (te - ts) * 1000)) + return result + + return timed diff --git a/tox.ini b/tox.ini index 84b029f..1d71f41 100644 --- a/tox.ini +++ b/tox.ini @@ -12,4 +12,4 @@ skip_install = True deps = pep8 commands = - pep8 --show-source brendapy \ No newline at end of file + pep8 --show-source brendapy --ignore=E501 \ No newline at end of file