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Merged
madeline-scyphers merged 4 commits into from
Oct 26, 2026
Merged

Package/oct 21 rules update #60

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108c09b
package(rules): Oct 21 rules update
madeline-scyphers Oct 21, 2026
51c2e2b
package(rules): update rules
madeline-scyphers Oct 26, 2026
a179035
Add BOM to rules files
madeline-scyphers Oct 26, 2026
f49df2a
recover corruprted text
madeline-scyphers Oct 26, 2026
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2 changes: 1 addition & 1 deletion src/dram_rules/data/rules.tsv
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
name long_name alias rule group
name long_name alias rule group
M00001 "Glycolysis (Embden-Meyerhof pathway), glucose => pyruvate" m1 "path_steps([K00844 | K12407 | K00845 | K25026 | K00886 | K08074 | K00918],
[K01810 | K06859 | K13810 | K15916],
[K00850 | K16370 | K21071 | K24182 | K00918],
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45 changes: 24 additions & 21 deletions src/dram_rules/data/rules_ag.tsv
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Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
name rule module group notes
name rule module group notes
Cellulose @Cellulose Carbon Transformations Polymer Cellulose-associated hydrolytic and oxidative enzymes; includes endoglucanases, cellobiohydrolases, and LPMOs.
Hemicellulose @Hemicellulose Carbon Transformations Polymer Includes xylan, mannan, xyloglucan, and galactan-associated enzymes.
Pectin @Pectin Carbon Transformations Polymer Includes polygalacturonases, pectin/pectate lyases, and enzymes targeting pectin side chains.
Expand Down Expand Up @@ -49,22 +49,22 @@ DNRA NrfA only, NO2 To NH4 @nrfA Inorganic Nitrogen Transformation Dissimilatory
Urea Transport K11963 Nutrient Transporters Selected Nitrogen Transporters
Ammonium Transport K03320 Nutrient Transporters Selected Nitrogen Transporters
Nitrate/Nitrite Transporter K02575 Nutrient Transporters Selected Nitrogen Transporters
Oxygen Reduction - Low Affinity [percent(50,@CytochromeCOxidase)|percent(50,@CytochromeAa3600MenaquinolOxidase)|percent(50,@CytochromeOUbiquinolOxidase)] Other Respiratory Redox Processes Respiratory Redox Processes Oxygen Reduction
Oxygen Reduction - High Affinity [@percent50CytochromeBDUbiquinolOxidase|@percent50CytochromeCOxidaseCBB3] Other Respiratory Redox Processes Respiratory Redox Processes Oxygen Reduction
Iron Oxidation @IronOxidation Other Respiratory Redox Processes Iron Reduction and Oxidation
Iron Reduction @IronReduction Other Respiratory Redox Processes Iron Reduction and Oxidation
Sulfur Oxidation @sulfateoxidizer Other Respiratory Redox Processes Sulfur Reduction and Oxidation
Sulfate Reduction @Sulfatereducer Other Respiratory Redox Processes Sulfur Reduction and Oxidation
Non-sulfate-sulfur-reduction @Non-sulfate-sulfur-reduction Other Respiratory Redox Processes Sulfur Reduction and Oxidation
Phototrophy @phototroph Other Metabolic Systems
Obligate Fermenter @Fermenter Other Metabolic Systems
Hydrogenase @HydrogenUse Other Metabolic Systems
ATP synthase at_least(4, PRESENCE, [K02111,K02112,K02113,K02114,K02115,K02108,K02109,K02110])|at_least(5, PRESENCE, [K02117,K02118,K02119,K02120,K02121,K02122,K02107,K02123,K02124])|at_least(10, PRESENCE, [K02132,K02133,K02136,K02134,K02135,K02137,K02126,K02127,K02128,K02138,K02129,K01549,K02130,K02139,K02140,K02141,K02131,K02142,K02143,K02125])|at_least(7, PRESENCE, [K02145,K02147,K02148,K02149,K02150,K02151,K02152,K02144,K02154,K03661,K02155,K02146,K02153,K03662]) Other Metabolic Systems
Candidate Extracellular Aspartic Peptidases A01 Nutrient Assimilation and Transport Organic Nitrogen Mineralization Hydrolyze peptide bonds in proteins using an aspartic acid catalytic mechanism. Selected MEROPS families include extracellular proteases; confirm cellular localization.
Candidate Extracellular Cysteine Peptidases C01 | C10 | C25 Nutrient Assimilation and Transport Organic Nitrogen Mineralization Hydrolyze proteins and peptides using a cysteine catalytic mechanism. Selected families include extracellular and intracellular enzymes; confirm cellular localization.
Candidate Extracellular Glutamic Peptidases G01 Nutrient Assimilation and Transport Organic Nitrogen Mineralization Hydrolyze proteins using a glutamic acid catalytic mechanism, including secreted fungal proteases. Confirm cellular localization.
Candidate Extracellular Metallo Peptidases M04 | M09 | M10 | M12 | M36 Nutrient Assimilation and Transport Organic Nitrogen Mineralization Hydrolyze proteins and peptides using metal-dependent catalysis. Selected families include extracellular proteases; confirm cellular localization.
Candidate Extracellular Serine Peptidases S01 | S08 | S53 Nutrient Assimilation and Transport Organic Nitrogen Mineralization Hydrolyze proteins and peptides using a serine catalytic mechanism. Selected families include secreted and intracellular proteases; confirm cellular localization.
Oxygen Reduction - Low Affinity [percent(50,@CytochromeCOxidase)|percent(50,@CytochromeAa3600MenaquinolOxidase)|percent(50,@CytochromeOUbiquinolOxidase)] Other Respiratory Redox Processes Respiratory Redox Processes Oxygen Reduction
Oxygen Reduction - High Affinity [@percent50CytochromeBDUbiquinolOxidase|@percent50CytochromeCOxidaseCBB3] Other Respiratory Redox Processes Respiratory Redox Processes Oxygen Reduction
Iron Oxidation @IronOxidation Other Respiratory Redox Processes Iron Reduction and Oxidation
Iron Reduction @IronReduction Other Respiratory Redox Processes Iron Reduction and Oxidation
Sulfur Oxidation @sulfateoxidizer Other Respiratory Redox Processes Sulfur Reduction and Oxidation
Sulfate Reduction @Sulfatereducer Other Respiratory Redox Processes Sulfur Reduction and Oxidation
Non-sulfate-sulfur-reduction @Non-sulfate-sulfur-reduction Other Respiratory Redox Processes Sulfur Reduction and Oxidation
Phototrophy @PhototrophAllTypes Other Metabolic Systems
Obligate Fermenter @Fermenter Other Metabolic Systems
Hydrogenase @HydrogenUse Other Metabolic Systems
ATP synthase at_least(4, PRESENCE, [K02111,K02112,K02113,K02114,K02115,K02108,K02109,K02110])|at_least(5, PRESENCE, [K02117,K02118,K02119,K02120,K02121,K02122,K02107,K02123,K02124])|at_least(10, PRESENCE, [K02132,K02133,K02136,K02134,K02135,K02137,K02126,K02127,K02128,K02138,K02129,K01549,K02130,K02139,K02140,K02141,K02131,K02142,K02143,K02125])|at_least(7, PRESENCE, [K02145,K02147,K02148,K02149,K02150,K02151,K02152,K02144,K02154,K03661,K02155,K02146,K02153,K03662]) Other Metabolic Systems
Candidate Extracellular Aspartic Peptidases @ExtracellularAspartic Nutrient Assimilation and Transport Organic Nitrogen Mineralization Hydrolyze peptide bonds in proteins using an aspartic acid catalytic mechanism. Selected MEROPS families include extracellular proteases; confirm cellular localization.
Candidate Extracellular Cysteine Peptidases @ExtracellularCysteine Nutrient Assimilation and Transport Organic Nitrogen Mineralization Hydrolyze proteins and peptides using a cysteine catalytic mechanism. Selected families include extracellular and intracellular enzymes; confirm cellular localization.
Candidate Extracellular Glutamic Peptidases @ExtracellularGlutamic Nutrient Assimilation and Transport Organic Nitrogen Mineralization Hydrolyze proteins using a glutamic acid catalytic mechanism, including secreted fungal proteases. Confirm cellular localization.
Candidate Extracellular Metallo Peptidases @ExtracellularMetallo Nutrient Assimilation and Transport Organic Nitrogen Mineralization Hydrolyze proteins and peptides using metal-dependent catalysis. Selected families include extracellular proteases; confirm cellular localization.
Candidate Extracellular Serine Peptidases @ExtracellularSerine Nutrient Assimilation and Transport Organic Nitrogen Mineralization Hydrolyze proteins and peptides using a serine catalytic mechanism. Selected families include secreted and intracellular proteases; confirm cellular localization.
Urease @Urease Nutrient Assimilation and Transport Organic Nitrogen Mineralization Hydrolyzes urea to ammonia and carbon dioxide, contributing directly to N mineralization. Can be intracellular, cell-associated, or extracellular; confirm cellular localization.
Amidase K01426 Nutrient Assimilation and Transport Organic Nitrogen Mineralization Hydrolyzes amides to release ammonia and corresponding organic acids, contributing to N mineralization. Often intracellular; confirm cellular localization.
Formamidase K01455 Nutrient Assimilation and Transport Organic Nitrogen Mineralization Hydrolyzes formamide to formate and ammonia, contributing to N mineralization. Typically intracellular; confirm cellular localization.
Expand Down Expand Up @@ -96,16 +96,19 @@ Arsenite Oxidation Potential @ArseniteOxidation Environmental Adaptation Other M
Arsenate Reduction Potential @ArsenateReductionPotential Environmental Adaptation Other Metal and Trace Element Transformation and Resistance Converts As(V) to As(III), potentially increasing mobility and plant exposure; ArsC (K00537, K03741) mediates cellular detoxification and may not result in substantial environmental As(III) release.
Arsenic Methylation @ArsenicMethylation Environmental Adaptation Other Metal and Trace Element Transformation and Resistance Produces methylated arsenic species with variable toxicity, mobility, and plant uptake.
Mercury Reduction @MercuryReduction Environmental Adaptation Other Metal and Trace Element Transformation and Resistance MerA reduces Hg(II) to volatile Hg(0), affecting mercury mobility and atmospheric release.
Mercury Export @MercuryExport Environmental Adaptation Other Metal and Trace Element Transformation and Resistance
Mercury Methylation @MercuryMethylation Environmental Adaptation Other Metal and Trace Element Transformation and Resistance HgcA indicates potential for methylmercury production, increasing toxicity and bioaccumulation risk.
Organic Mercury Degradation @OrganomercuryDegradation Environmental Adaptation Other Metal and Trace Element Transformation and Resistance MerB cleaves organomercury compounds, including methylmercury, releasing Hg(II).
Copper Efflux @CopperEfflux Environmental Adaptation Other Metal and Trace Element Transformation and Resistance Detects microbial copper export systems associated with resistance to excess copper from fungicides, manure, and other agricultural inputs.
Zinc/Cadmium/Cobalt/Nickel Efflux @CadmiumZincEfflux |@DivalentMetalEfflux | @NickelCobaltEfflux | @CobaltZincCadmiumEfflux Environmental Adaptation Other Metal and Trace Element Transformation and Resistance
Chromium/Silver Efflux @ChromateEfflux |@SilverEfflux Environmental Adaptation Other Metal and Trace Element Transformation and Resistance
Atrazine Degradation Pathway K05394 & K03382 & K08710 Environmental Adaptations Possible Pesticide Degradation AtzA, AtzB, and AtzC catalyze sequential atrazine degradation to cyanuric acid. Does not indicate complete mineralization.
Initial 2,4-D Degradation K06912 Environmental Adaptations Possible Pesticide Degradation TfdA, which initiates 2,4-D herbicide degradation to 2,4-dichlorophenol. Does not indicate complete degradation or mineralization
Initial Pyrethroid Degradation K20992 Environmental Adaptations Possible Pesticide Degradation Pyrethroid hydrolase (PytH) cleaves ester bonds in pyrethroid insecticides. Indicates potential degradation, not complete mineralization.
Sugar Derived [K00697 & K01087] | [K01236 & K06044] | K05343 | [K00009 & K19270] Environmental Adaptations Potential Osmoprotection
Glycosylated [K03692 & K05978] | [K05947 & K07026] | K18818 Environmental Adaptations Potential Osmoprotection
Amino Acid Derived [K00931 & K00147 & K00286] | [K06718 & K00836 & K06720] Environmental Adaptations Potential Osmoprotection
Glycine betaine related [[K00108 | K11440] & K00130] | [K18896 & K18897] Environmental Adaptations Potential Osmoprotection
Superoxide @Superoxide Environmental Adaptations Oxidative Defense
Peroxide-catalase @Peroxide-catalase Environmental Adaptations Oxidative Defense
Peroxide-peroxiredoxin @Peroxide-peroxiredoxin Environmental Adaptations Oxidative Defense
Compatible-Solutes: Trehalose Synthesis @TrehaloseSynthesis Environmental Adaptation Osmoregulation
Compatible-Solutes: Other Sugar-Derived Compounds Synthesis @SugarDerivedCompatibleSoluteSynthesis Environmental Adaptation Osmoregulation
Compatible-Solutes: Ectoine Synthesis @EctoineSynthesis Environmental Adaptation Osmoregulation
Compatible-Solutes: Glycine Betaine Synthesis @GlycineBetaineSynthesis Environmental Adaptation Osmoregulation
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