diff --git a/src/dram_rules/data/rules.tsv b/src/dram_rules/data/rules.tsv index 0d39efc..ed80595 100644 --- a/src/dram_rules/data/rules.tsv +++ b/src/dram_rules/data/rules.tsv @@ -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], diff --git a/src/dram_rules/data/rules_ag.tsv b/src/dram_rules/data/rules_ag.tsv index 2dc2913..55f533f 100644 --- a/src/dram_rules/data/rules_ag.tsv +++ b/src/dram_rules/data/rules_ag.tsv @@ -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. @@ -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. @@ -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 diff --git a/src/dram_rules/data/rules_aquatic.tsv b/src/dram_rules/data/rules_aquatic.tsv index 44460dd..6ad3a86 100644 --- a/src/dram_rules/data/rules_aquatic.tsv +++ b/src/dram_rules/data/rules_aquatic.tsv @@ -1,124 +1,109 @@ -name rule rule_options module group notes -Plant Polymer Mixed @PlantPolymerMixed Carbon Processing polymer -Cellulose @Cellulose Carbon Processing polymer -Hemicellulose-Xylan @Hemicellulose-Xylan Carbon Processing polymer -Hemicellulose-Other @Hemicellulose-Other Carbon Processing polymer -Pectin @Pectin Carbon Processing polymer -Arabinogalactan @Arabinogalactan Carbon Processing polymer -Starch Specific @StarchSpecific Carbon Processing polymer -Starch/Glycogen @StarchGlycogen Carbon Processing polymer -Chitin @Chitin Carbon Processing polymer -Microbially-derived @Microbially-derived Carbon Processing polymer -Laminarin GH5;EC:3.2.1.39 | GH55;EC:3.2.1.39 | GH5;EC:3.2.1.58 | GH55;EC:3.2.1.58 Carbon Processing polymer-algae specific -Alginate PL14;EC:4.2.2.3 | PL15;EC:4.2.2.3 | PL17;EC:4.2.2.11 | PL17;EC:4.2.2.3 | PL18;EC:4.2.2.11 | PL18;EC:4.2.2.3 | PL31;EC:4.2.2.3 | PL32;EC:4.2.2.3 | PL36;EC:4.2.2.3 | PL38;EC:4.2.2.3 | PL38;EC:4.2.2.11 | PL39;EC:4.2.2.3 | PL39;EC:4.2.2.11 | PL41;EC:4.2.2.3 | PL5;EC:4.2.2.3 | PL6;EC:4.2.2.11 | PL6;EC:4.2.2.3 | PL7;EC:4.2.2.11 | PL7;EC:4.2.2.3 | PL8;EC:4.2.2.3 | PL44;EC:4.2.2.3 Carbon Processing polymer-algae specific -Agarose GH118;EC:3.2.1.81 | GH16;EC:3.2.1.81 | GH50;EC:3.2.1.81 | GH86;EC:3.2.1.81 | GH96;EC:3.2.1.158 Carbon Processing polymer-algae specific -Porphyran GH16;EC:3.2.1.178 Carbon Processing polymer-algae specific -Carrageenan GH150;EC:3.2.1.162 | GH16;EC:3.2.1.83 | GH82;EC:3.2.1.157 Carbon Processing polymer-algae specific -Fucoidan GH107;EC:3.2.1.212 | GH168;EC:3.2.1.211 | GH174;EC:3.2.1.- | GH187;EC:3.2.1.- | PL43;EC:4.2.2.- | GH107;EC:3.2.1.211 | GH168;EC:3.2.1.- Carbon Processing polymer-algae specific -Ulvan PL24;EC:4.2.2.- | PL25;EC:4.2.2.- | PL28;EC:4.2.2.- Carbon Processing polymer-algae specific -Funoran GH96;EC:3.2.1.222 Carbon Processing polymer-algae specific -Cellulose-derived @Cellulose-derived Carbon Processing oligomer -Hemicellulose-derived xylan @Hemicellulose-derived-xylan Carbon Processing oligomer -Hemicellulose-derived other @Hemicellulose-derived-other Carbon Processing oligomer -Pectin-derived @Pectin-derived Carbon Processing oligomer -Starch/Glycogen-derived @Starch-Glycogen-derived Carbon Processing oligomer -Chitin-derived @Chitin-derived Carbon Processing oligomer -Chitin / other-derived @Chitin-other-derived Carbon Processing oligomer -Alginate-derived PL14;EC:4.2.2.26 | PL15;EC:4.2.2.26 | PL17;EC:4.2.2.26 | PL6;EC:4.2.2.26 | PL7;EC:4.2.2.26 Carbon Processing oligomer -Agarose-derived GH117;EC:3.2.1.159 Carbon Processing oligomer -Cellobiose @Cellobiose Carbon Processing disaccharide -Maltose @Maltose Carbon Processing disaccharide -Sucrose @Sucrose Carbon Processing disaccharide -Trehalose @Trehalose Carbon Processing disaccharide -Lactose @Lactose Carbon Processing disaccharide -Xylan/Xylobiose @XylanXylobiose Carbon Processing disaccharide -Mannose/Mannobiose @Mannose-Mannobiose Carbon Processing disaccharide -Other disaccharides @Other-disaccharides Carbon Processing disaccharide -Glucose @Glucose Carbon Processing monosaccharide -Xylose @Xylose Carbon Processing monosaccharide -Arabinose @Arabinose Carbon Processing monosaccharide -Mannose @Mannose Carbon Processing monosaccharide -Galactose @Galactose Carbon Processing monosaccharide -Fructose @Fructose Carbon Processing monosaccharide -Rhamnose @Rhamnose Carbon Processing monosaccharide -N-Acetylglucosamine (Glc-NAc) @N-Acetylglucosamine Carbon Processing monosaccharide -Fucose @Fucose Carbon Processing monosaccharide -Acetate @Acetate-Final Carbon Processing low-molecular-weight-carbon -Butyrate @Butyrate-Final Carbon Processing low-molecular-weight-carbon -Propionate @Propionate-Final Carbon Processing low-molecular-weight-carbon -Ethanol/Alcohol @Ethanol Carbon Processing low-molecular-weight-carbon -Methanol @Methanol Carbon Processing low-molecular-weight-carbon -"Fatty Acid Degradation Beta-Oxidation " [k06445 | k00249 | k00255 | k09479] & [k13767 | k01825] & k00632 carbon processing medium carbon "for a genome to have fatty acid degradation capability via beta-oxidation, it should encode at least one acyl-coa dehydrogenase (fade,k06445,k00249,k00255,k09479), one enoyl-coa hydratase (fadb,k13767,k01825), and thiolase (fada,k00632) completing one full ≈í‚â§-oxidation cycle. " -Aerobic CH4 Oxidation @AerobicMethanotroph carbon processing little carbon "for a genome to have ch‚Äö√á√ë oxidation capability, it must encode at least one methane monooxygenase complex (pmmo or smmo), which catalyzes the conversion of methane to methanol. " -Alkane Tranformation (Archaeal) k00399 & k00401 & k00402 & k00421 & k00422 carbon processing little carbon "for a genome to have anaerobic alkane transformation capability, it should encode for a methyl-com reductase catalytic subunit (mcra, k00399). encoding for other subunits (mcrabcdg, k00399,k00401,k00402,k00421,k00422) is detected. this annotation will identify canonical mcr and divergent mcr or mcr-like sequences mapping to the same ko, performing an mcra phylogeny is recommended. presence of an mcr without phylogenetic placement can suggest multiple different metabolisms falling under anaerobic alkane transformation capability (various forms of methanogenesis, reverse methanogenesis, anaerobic alkane degradation). " -CO2 Fixation @CO2fixation carbon processing c fixation for a genome to have co‚Äö√á√á fixation capability via the acetyl-coa pathway, it should encode: the complete codh/acs complex (cdha, cdhb, cdhc, cdhd, and cdhe subunits), which together catalyze co‚Äö√á√á reduction to acetyl-coa. this is distinct from the wood-ljungdahl pathway row which additionally requires (eastern) methyl branch genes. -Wood-Ljungdahl Pathway @ReductiveAcetylCoAWoodLjungdahl carbon processing c fixation "for a genome to have wood-ljungdahl co2 fixation capability, it should encode the complete western brnach codh/acs complex for either the bacterial (k00198, k14138) or archaeal (k00192, k00195, k00193, k00194, k00197) and have at least one eastern/methyl branch entry point (fdha k01938 or fhs k05299). presence of both branches indicates full reductive acetyl-coa synthesis from co2 molecules. " -3-Hydroxypropionate/4-Hydroxybutyrate (3Hp/4Hb) Cycle @DicarboxylateHydroxybutyrate carbon processing c fixation for a genome to have 3hp/4hb co‚Äö√á√á fixation capability, it should encode all of the 3 following genes - 1) k14534, 2) either malonyl-coa reductase or acetyl-coa carboxylase (k15017, or k18603-5, respectively) 3) either k15039 and k18602) .presence of all three modules indicates complete autotrophic co‚Äö√á√á fixation via the 3hp/4hb cycle, something previously characteristic of crenarchaeota in marine sediments. -Calvin-Benson-Bassham (Cbb) Cycle @Calvin carbon processing c fixation "for a genome to have cbb cycle co‚Äö√á√á fixation capability it should encode ribulose-bisphosphate carboxylase large chain (rbcl, k01601), phosphoribulokinase (prk, k00855), and one ribulose-phosphate 3-epimerase (rpe, k01783) to differentiate the cbb cycle from the rhp metabolic pathway. " -Reductive Glycine Pathway @ReductiveGlycinePathway carbon processing c fixation "for a genome to have reductive glycine pathway co‚Äö√á√á fixation capabilit, it should encode at least 3 proteins/subunuts of the glycine cleavage system (k00283, k00282, k02437, and k00605) and at least 5 of the glycine reductase (k10671, k10672, k00384, k21577, k21576, k03671, and k10670). " -Rtca Cycle @ReductiveCitricAcid carbon processing c fixation "for a genome to have reductive tca cycle it should encode either 1 atp-citrate lyase (k15233 or k15232) or citryl-coa synthetase+citryl-coa lyase (k15233 or k15232, and k15234). " -Rump Pathway (Non-Methanogenic Methylotrophy Type I) [k08093 | k13831 | k13812] & k08094 & [k00093 | k23995 | k17066 | k14028 | k14029] carbon processing non-methanogenic methylotrophy "for a genome to have rump pathway methylotrophy capability it should encode hps (k08093,k13831,k13812) and phi (k08094) a methanol dehydrogenase (mdh, k00093,k23995,k17066,k14028,k14029) and at least one together these suggest capacity to convert methanol and formaledehyde into usable fructose 6-phosphate. " -Serine Pathway (Non-Methanogenic Methylotrophy Type Ii) k00830 & k00018 & k08691 carbon processing non-methanogenic methylotrophy "for a genome to have serine pathway methylotrophy capability it should encode serine-glyoxylate transaminase (sgt, k00830), hydroxypyruvate reductase (hpr, k00018), and malyl-coa lyase (mcl, k08691). additional encoding of serine hydroxymethyltransferase (shmt, k00600) further supports likelihood of having this pathway. " -Hydrogenotrophic Methanogenesis @hydrogenotrophic "{""include_when"":{""all_columns_present"":[""taxonomy""]}}" carbon processing methanogenesis "for a genome to have hydrogenotrophic methanogenesis capability it should encode the mcr complex (mcrabg, k00399+k00401+k00402), the mtr complex core subunits (mtra-e+h, k00577-k00581+k00584; mtrf/g omitted due to less consistent annotations), at least 2 of the 4 upper c1 pathway steps (ftr-k00672, mch-k01499, mtd-k00319 or hmd-k13942, mer-k00320), and at least one fwd/fmd subunit (k00200-k00205). this combination distinguishes hydrogenotrophic methanogens from obligate methylotrophic lineages (which lack mtr) and from aceticlastic methanogens (which lack the upper c1 pathway). anme archaea encode the same genes in reverse so performing an mcra phylogeny is highly recommended to confirm methanogenesis direction. methylotrophs that also do hydrogenotrophic methanogenesis e.g. canonical methanosarcinales) will present as matched to this row and ""methylotrophic and aceticlastic methanogenesis"". distinguishing between methanogenesis pathways via gene presence/absence is not recommended for genomes less than 90% complete. " -Methylotrophic Methanogenesis @methylotroph "{""include_when"":{""all_columns_present"":[""taxonomy""]}}" carbon processing methanogenesis "for a genome to have methylotrophic or aceticlastic methanogenesis capability it should encode the mcr complex (mcrabg, k00399+k00401+k00402) plus at least one substrate-specific entry point. i.e. methanol, methylamines, methylated sulfur, or acetate . for methanol potential enzymes are mtab (k04480), mtaa (k14080), or mtac (k14081); for methylamines potential enzymes are mtba (k14082), mtmb/monomethylamine methyltransferase (k16176), mtmc/monomethylamine corrinoid protein (k16177), mtbb/dimethylamine methyltransferase (k16178), mtbc/dimethylamine corrinoid protein (k16179), mttb/trimethylamine methyltransferase (k14083), or mttc/trimethylamine corrinoid protein (k14084); for methylated sulfur potential enzymes are mtsa (k16954) or mtsb (k16955); for acetate, enzymes are acka+pta (k00925+k00625) or acs (k01895), combined with codh/acs core subunits cdhc+cdhe+cdhd (k00193+k00197+k00194). here, aceticlastic methanogenesis overlaps with co2 fixation and wood-ljungdahl rows, but is distinguished with the presence of the mcr complex. performing an mcra phylogeny is recommended to distinguish between methanogenesis and anaerobic methanotrophy. distinguishing between methanogenesis pathways via gene presence/absence is not recommended for genomes less than 90% complete. " -Acetoclastic Methanogenesis @acetoclastic "{""include_when"":{""all_columns_present"":[""taxonomy""]}}" -N2O To N2 @NitrousOxideReductase inorganic nitrogen transformation n reduction the reduction of nitrous oxide (n‚Äö√á√áo) to dinitrogen gas (n‚Äö√á√á) is catalyzed by nitrous oxide reductase (nosz, k00376). presence of this gene indicates the potential for the final step of denitrification, converting n‚Äö√á√áo into n‚Äö√á√á. -NO3 To NO2 @NarNitrateReductase | @NapNitrateReductase inorganic nitrogen transformation n reduction nitrate reduction to nitrite can occur through either the membrane-bound nar system (k00370 and k00371, both required) or the periplasmic nap system (k02567 and k02568, both required). either system completes the nitrate transformation step. -DNRA @DNRA inorganic nitrogen transformation n reduction dnra reduces nitrate to ammonium through a two-step process: nitrate reduction via nar or nap systems, followed by nitrite reduction via nrf or nir enzymes. presence of one nitrate reductase system and one nitrite reductase system indicates dnra capability. -NO2 To NO @NitriteReductase inorganic nitrogen transformation n reduction nitrite reduction to nitric oxide (no) is carried out by either nirs (k00368) or nirk (k15864). presence of either gene indicates capacity for nitrate/nitrite reduction in denitrification. -NO To N2O @NitricOxideReductase inorganic nitrogen transformation n reduction the conversion of nitric oxide (no) to nitrous oxide (n‚Äö√á√áo) is catalyzed by nitric oxide reductase, encoded by norb (k04561) in bacteria or cyp55 (k15877) in fungi. presence of either gene indicates the capacity to perform this denitrification step -Aerobic Nitrite Oxidation @NitriteOxidoreductase inorganic nitrogen transformation nitrification aerobic nitrate oxidation (nitrite oxidation) is the second step of nitrification, where nitrite is oxidized to nitrate by the nxr complex (nxrab) under oxic conditions, completing the conversion of reduced nitrogen to its most oxidized form. -Aerobic Ammonium Oxidation @AerobicAmmoniaOxidizer inorganic nitrogen transformation nitrification aerobic ammonium oxidation converts ammonia to nitrite through sequential reactions catalyzed by ammonia monooxygenase and hydroxylamine oxidoreductase. presence of one ammonia monooxygenase subunit set and hydroxylamine oxidoreductase indicates this capability. -N2 Fixation @nitrogen-fixer inorganic nitrogen transformation nitrification nitrogen fixation converts atmospheric n‚Äö√á√á to ammonium through the nitrogenase enzyme complex. functional capacity is indicated by the presence of all subunits for either the mo-nitrogenase (nif) or the v-nitrogenase (vnf) system, as either complete complex can catalyze n‚Äö√á√á reduction. -Urease "@Urease " organic nitrogen transformation primary n transformation urea hydrolysis requires the full urease enzyme complex, composed of subunits urea (k01430), ureb (k01429), and urec (k01428). all three genes are needed to complete urea transformation to ammonium and co‚Äö√á√á. -Amidase k01426 organic nitrogen transformation mineralization presence of amidase enzyme -Phototroph-Oxygenic @Phototroph-Oxygenic light energy Phototroph -Phototroph-AnoxygenicType2 @Phototroph-AnoxygenicType2 light energy Phototroph -Phototroph-AnoxygenicType1 @Phototroph-AnoxygenicType1 light energy Phototroph -Phototroph-Rhodopsin K04641 light energy Rhodopsin -Extracellular Asparagine Peptidases n04 | n10 | n11 organic nitrogen transformation mineralization presence of any extracellular asparagine peptidase -Extracellular Aspartic Peptidases a01 | a02 | a05 | a08 | a11 | a22 | a24 | a26 | a28 | a31 | a32 | a37 organic nitrogen transformation mineralization presence of any extracellular aspartic peptidase -Extracellular Cysteine Peptidases c01 | c02 | c10 | c11 | c110 | c113 | c13 | c14 | c15 | c19 | c25 | c26 | c39 | c40 | c44 | c45 | c46 | c47 | c51 | c56 | c59 | c60 | c66 | c69 | c82 | c83 | c89 | c93 organic nitrogen transformation mineralization presence of any extracellular cysteine peptidase -Extracellular Glutamic Peptidases g01 organic nitrogen transformation mineralization presence of any extracellular glutamic peptidase -Extracellular Metallo Peptidases m01 | m02 | m03 | m04 | m05 | m06 | m07 | m08 | m09 | m10 | m11 | m12 | m13 | m14 | m15 | m16 | m17 | m18 | m19 | m20 | m23 | m24 | m26 | m28 | m30 | m32 | m34 | m35 | m36 | m38 | m41 | m42 | m43 | m44 | m48 | m49 | m50 | m54 | m55 | m56 | m57 | m60 | m61 | m64 | m66 | m67 | m72 | m73 | m74 | m75 | m76 | m78 | m79 | m81 | m82 | m84 | m85 | m86 | m88 | m93 | m96 | m97 | m98 organic nitrogen transformation mineralization presence of any extracellular metallo peptidase -Extracellular Serine Peptidases s01 | s06 | s08 | s09 | s10 | s11 | s12 | s13 | s14 | s15 | s16 | s24 | s26 | s28 | s33 | s37 | s41 | s45 | s46 | s49 | s50 | s51 | s53 | s54 | s55 | s59 | s60 | s66 | s73 organic nitrogen transformation mineralization presence of any extracellular serine peptidase -Extracellular Threonine Peptidases t01 | t02 | t03 | t05 | t07 organic nitrogen transformation mineralization presence of any extracellular threonine peptidase -Formamidase k01455 organic nitrogen transformation mineralization presence of formamidase enzyme -Mixed Peptidases p01 organic nitrogen transformation mineralization presence of any extracellular mixed peptidase -Unknown Peptidases u32 | u62 | u69 | u72 | u73 | u74 organic nitrogen transformation mineralization presence of any extracellular unknown catalytic type peptidase -Dissimilatory-Sulfate-Reduction @Sulfatereducer Sulfur Cycling Sulfide Production Dissimilatory sulfate reduction to sulfide (H2S); key souring mechanism in oil & gas systems. Requires adenylysulfate reductase (aprAB; K00394, K00395) and dissimilatory sulfite reductase (dsrAB; dsrA, dsrB). -Thiosulfate-Reduction-(Respiratory) at_least(2, PRESENCE, [K08352, K08353, K08354]) Sulfur Cycling Sulfide Production Respiratory thiosulfate reduction via the PhsABC thiosulfate reductase complex (phsA K08352, phsB K08353, phsC K08354). Requires at least 2 of 3 subunits to account for incomplete genome recovery in metagenomic data. Uses thiosulfate as terminal electron acceptor under anaerobic conditions. Found in Salmonella, Citrobacter, and diverse anaerobes. -Thiosulfate-Reduction-(Rhodanese) K01011 | Rhodanese Sulfur Cycling Sulfide Production Thiosulfate sulfurtransferase (rhodanese; K01011 rdl/glpE-type, K14180 mitochondrial-type) transfers sulfur from thiosulfate to cyanide or other acceptors, producing sulfite and thiocyanate. Also involved in sulfur relay and cyanide detoxification. Distinct from respiratory thiosulfate reduction ‚Äö√Ñ√Æ does not conserve energy via electron transport. Extremely widespread across bacteria and archaea so interpret cautiously; presence alone is not diagnostic of dedicated thiosulfate metabolism. -Sulfur-Oxidation-Sox [K17223 | K17222] & [K17226 | K17227] & K17224 Sulfur Cycling Sulfur Oxidation Oxidation of reduced sulfur compounds via the SOX multienzyme complex. SoxXA (K17223, K17222) initiate sulfur binding, SoxYZ (K17226, K17227) are the sulfur-carrying proteins, and SoxB (K17224) is the sulfate-releasing thiohydrolase. SoxCD (K17225, K22622) are optional and indicate complete oxidation to sulfate without intermediates. -Sulfur-Oxidation-Reverse-Dsr [K11180 | dsrA | K11181 | dsrB] & K27196 Sulfur Cycling Sulfur Oxidation Oxidation of stored sulfur globules via reverse-running DsrAB, distinguished from reductive DsrAB by co-occurrence with dsrL (K27196), an NADH-dependent oxidoreductase found exclusively in sulfur-oxidizing organisms. Both dsrA/dsrB (K11180/K11181) and dsrL (K27196) required. Found in Chlorobi, some Gammaproteobacteria, and Chromatiales. -Tetrathionate-Reduction at_least(2, PRESENCE, [K08359, K08358, K08357]) Sulfur Cycling S Transformations Tetrathionate reduction via the ttrABC system (ttrA K08359, ttrB K08358, ttrC K08357). At least 2 of 3 subunits required. Relevant as an alternative electron acceptor in anaerobic subsurface and industrial systems. -DMS/DMSP Cycling k28073 | k16953 | k28067 | k28068 | k28069 | k28072 | k17486 | [k20034 & k20035 & k20036] | k16967 | k16964 | k18277 | [k07306 & [k07307 | k00184] & [k07308 | k00185]] | k07811 sulfur cycling organic sulfur transformation "for a genome to have organosulfur cycling capacity it should encode ‚Äö√¢‚Ä¢1 enzyme for transforimg at least one of the following substrates: dmsp,dms,dmso,methanethiol,dmsop,mmpa . key enzymes and their substrates include: dmsp lyases (dddd-k28073, dddl-k16953, dddp-k28067, dddw-k28068, dddy-k28069, dddx-k28072) producing dms from dmsp. dmsp demethylase (dmda-k17486) producing mmpa from dmsp. mmpa demethylation enzymes,dmdbcd (k20034+k20035+k20036), producing methanethiol from mmpa. dms monooxygenase (dmoa-k16967) producing methanethiol from dms. dms dehydrogenase (ddha-k16964) or trimethylamine monooxygenase (tmm-k18277) oxidizing dms to dmso. dmso reductase complex, dmsabc (k07306 +k07307 or k00184 +k07308 or k00185), or trimethylamine n-oxide reductase (tora-k07811) reducing dmso back to dms. " -[Fefe] Group_A Hydrogenase FeFe_groupA energy metabolism [fefe] hydrogenases presence of [fefe] group_a hydrogenase -[Fefe] Group_B Hydrogenase FeFe_groupB energy metabolism [fefe] hydrogenases presence of [fefe] group_b hydrogenase -[Fefe] Group_C Hydrogenase FeFe_groupC energy metabolism [fefe] hydrogenases presence of [fefe] group_c hydrogenase -[Fefe] Group_E Hydrogenase FeFe_groupE energy metabolism [fefe] hydrogenases presence of [fefe] group_e hydrogenase -[Fefe] Group_F Hydrogenase FeFe_groupF energy metabolism [fefe] hydrogenases presence of [fefe] group_f hydrogenase -[Nife] Group_1 Hydrogenase NiFe_group1 energy metabolism [nife] hydrogenases presence of [nife] group_1 hydrogenase -[Nife] Group_2 Hydrogenase NiFe_group2 energy metabolism [nife] hydrogenases presence of [nife] group_2 hydrogenase -[Nife] Group_3 Hydrogenase NiFe_group3 energy metabolism [nife] hydrogenases presence of [nife] group_3 hydrogenase -[Nife] Group_4 Hydrogenase NiFe_group4 energy metabolism [nife] hydrogenases presence of [nife] group_4 hydrogenase -Arsenic k07755 | k08356 | k08355 | k00537 | k03741 | k11811 | k03892 | k03325 | k01551 | k03893 | arsd | aior-aoxr | aios-aoxs heavy metal tolerance box 16 presence of arsenic resistance, oxidation, reduction, methylation, and efflux genes (ars, aio) indicates microbial potential for arsenic detoxification and transformation. includes oxidation (aioa/b), reduction (arsc), methylation (arsm), efflux (arsa/b/d), and regulation (arsr, aior/s). -Cadmium k21903 | k21885 | k07665 | k07644 | k02483 | k22043 | k03088 | k24079 | k24078 | cadd | k15726 | k15727 | k15725 | cznb | k21133 | dmef | k08970 | k16264 | k01534 heavy metal tolerance box 16 presence of cadmium-associated resistance, regulation, and efflux genes indicates microbial potential for detoxification of cd¬¨‚⧂Äö√Ö‚à´ via efflux pumps (czc, czn, zitb, znta), transcriptional control (cadx, cmtr, czra, cusr/s), and sequestration or transport (cadd, dmef, cnr system), contributing to cadmium tolerance. -Cobalt k07644 | k02483 | ncrb | ncry | k23240 | k24073 | k24079 | k06042 | k03088 | k24078 | k03585 | k18138 | k18139 | cnrt | k03284 | corb | k06189 | k12951 | k15726 | k15727 | k15725 | dmef | dmer | k07785 | k08970 | k23243 | k16264 | k01534 heavy metal tolerance box 16 presence of cobalt resistance and transport genes indicates microbial capacity for co¬¨‚⧂Äö√Ö‚à´ detoxification, efflux, and regulation. includes transcriptional regulators (ncr, cnr, rcn), efflux systems (czc, dme, zitb, znta), transporters (cora/b/c, ctpd), and multi-component resistance operons (cme, cus, dmerf), enabling microbial adaptation to cobalt-rich or contaminated environments. -Magnesium k06042 | k03284 | corb | k06189 | k01531 | k06213 heavy metal tolerance box 16 presence of magnesium homeostasis and transport genes indicates microbial capacity for mg¬¨‚⧂Äö√Ö‚à´ uptake, export, and regulation. includes primary transporters (cora, mgta, corb/c), p-type atpases for active transport, and regulatory proteins involved in maintaining cytoplasmic mg¬¨‚⧂Äö√Ö‚à´ balance under metal or osmotic stress conditions. -Manganese k11924 | k12950 | k11707 | k03322 | k23242 | k11604 | k11607 | k11605 | k11606 heavy metal tolerance box 16 presence of manganese transport and regulatory genes indicates microbial capacity for mn¬¨‚⧂Äö√Ö‚à´ uptake, efflux, and homeostasis. includes import systems (mnth, mnta, yfeabcd), p-type atpases (ctpc), efflux channels (mntp), and regulatory proteins (mntr) that maintain intracellular mn¬¨‚⧂Äö√Ö‚à´ balance, protect against oxidative stress, and support metalloenzyme function. -Mercury k00221 | k00520 | k19057 | k08365 | k19058 | k19059 | k08364 | k08363 heavy metal tolerance box 16 presence of mercury resistance (mer) operon genes indicates microbial capacity for detoxification of inorganic and organic mercury compounds. includes transport and binding proteins (merc, mere, merf, merp, mert), regulatory components (merr, merd), and enzymes mediating reduction (mera) and cleavage of organomercurials (merb), collectively conferring hg¬¨‚⧂Äö√Ö‚à´ and methylmercury resistance. -Nickel ncrb | ncry | k07722 | k11328 | k23240 | k24073 | k24079 | k03088 | k11330 | k24078 | cnrt | k12951 | k15726 | k15727 | k15725 | cznb | dmef | dmer | hupe | k01552 | k15584 | k15585 | k15586 | k15587 | k10824 | k07241 | k11326 | k07785 | k08970 | k23243 heavy metal tolerance box 16 presence of nickel transport, efflux, and regulatory genes indicates microbial capacity for ni¬¨‚⧂Äö√Ö‚à´ acquisition, homeostasis, and detoxification. includes uptake systems (nikabcde, nixa, hupe), efflux pumps (czc, dme, cnr, nrs, rcn), cation diffusion facilitators (cnrt), and transcriptional regulators (ncr, nrs, nikr, rcnr) that maintain intracellular ni¬¨‚⧂Äö√Ö‚à´ balance and support ni-dependent metalloenzyme function under metal stress. -Silver silf | k07665 | k07644 | k17686 | k01533 | k07787 | k07798 | k07796 | k07810 | sile | k23254 heavy metal tolerance box 16 presence of silver resistance and efflux genes indicates microbial capacity for ag‚Äö√Ö‚à´ detoxification and homeostasis. includes multi-component efflux systems (sil, cus, cop), periplasmic chaperones (silf, sile, cusf), p-type atpases (silp, copa, copb), and two-component regulatory systems (cusrs) that coordinate ag‚Äö√Ö‚à´ sensing, transport, and reduction to mitigate toxicity in contaminated environments. -Zinc k21904 | zeva | k07803 | zint-yoda | k03765 | k21903 | k07644 | k02483 | k22043 | k13638 | k07713 | k07709 | k09823 | k03709 | k18324 | cadd | k12950 | k15726 | k15727 | k15725 | cznb | k21133 | k07799 | k07788 | k07789 | k11707 | k08970 | k11710 | k07238 | k16264 | k01534 | k09815 | k09816 | k09817 | k11708 | k11709 heavy metal tolerance box 16 presence of zinc resistance and homeostasis genes indicates microbial capacity for zn¬¨‚⧂Äö√Ö‚à´ uptake, sequestration, and efflux. includes import systems (znuabc, zipb, trob), regulators (zur, zrar/s, zntr, cadc/x), efflux transporters (czcabc, zitb, znta), metallothioneins and chaperones (smta, zint, zeva), and multidrug efflux systems (mdtabc) that together maintain intracellular zn¬¨‚⧂Äö√Ö‚à´ balance and mitigate metal stress. -Copper k07156 | k03926 | k06201 | k21609 | k07233 | pcoe | k07213 | k09796 | k19342 | cina | k14588 | cuto | k22552 | copl | copy-tcry | corr | k02483 | k21600 | k11923 | k07665 | k07644 | k19591 | k21601 | k21902 | k18992 | k18324 | k03585 | k18138 | k18139 | k17686 | k01533 | k07245 | copp | crda | k12954 | k12956 | k07787 | k07798 | k07796 | k07810 | k03820 | k06079 | hpcopa | mctb | k14166 | k08221 heavy metal tolerance box 16 presence of copper resistance, homeostasis, and transport genes indicates microbial potential for cu‚Äö√Ö‚à´/cu¬¨‚⧂Äö√Ö‚à´ detoxification, efflux, and redox regulation. this includes p-type atpases (copa, copb, ctpg, ctpv), multicopper oxidases (cueo, mco, cuto), periplasmic binding/chaperone systems (copc/d/z, pcoe, copl, cuer), regulatory systems (cusrs, cuer, corr, copy-tcry), and rnd/multidrug efflux complexes (cuscba, cmeabc, acrd, mctb), together facilitating copper detoxification and maintaining metal homeostasis under oxidative stress. -Iron k03594 | dpr-dps | dpsa | k02217 | k07229 | k03709 | pmra | pmrb | k02012 | k02011 | k02010 | k13283 | k16088 | k03322 | k01552 | pmrc | k06147 | k11604 | k11607 | k11605 | k11606 | k07224 heavy metal tolerance box 16 presence of iron storage, uptake, and efflux genes indicates microbial capacity for fe¬¨‚⧂Äö√Ö‚à´/fe¬¨‚â•‚Äö√Ö‚à´ homeostasis and oxidative stress mitigation. this includes ferritin-like storage proteins (bfra, pfr, dpr-dps), fe(ii)/fe(iii) transport and reduction systems (fbpabc, yfeabcd, fpta, yqjh, efeo), efflux pumps (fief), and regulatory elements (pmra/b/c, ider). collectively these confer resistance to iron overload, oxidative damage, and contribute to redox balancing. -Biofilms k19290 | k19291 | k19293 | k19294 | k19295 | k19296 | k11936 | k11937 | k21001 | k20997 | k25205 | k21461 stress adaptations box 17 "presence of alginate, psl, or pga/ica matrix biosynthesis genes indicates microbial capacity for biofilm formation, enhancing surface adhesion and persistence in marine environments. biofilm production supports microbial community stability, particle colonization, and resistance to physical disturbance in dynamic marine systems. " -Oxidative Stress k03782 | k04564 | k04565 | k01920 | k01921 | k05909 | k00421 | k05910 | k00431 | k00799 stress adaptations box 17 presence of oxidative stress defense genes (catalases, superoxide dismutases, glutathione biosynthesis enzymes, peroxidases, or laccases) indicates microbial potential to detoxify reactive oxygen species. this is relevant in marine microbes exposed to reactive oxygen species generated by chemical or biological oxidation systems and at oxic-anoxic interfaces. -Flagella k02406 & k02390 & k02409 & [k02394 | k02386] & k02393 & [k02556 | k02557 | k10564 | k21217 | k21218] & [k02410 | k02416] stress adaptations box 17 "for a genome to have bacterial flagella motility, it should encode flagellin (flic, k02406), hook protein (flge, k02390), m-ring membrane anchor (flif, k02409), one p-ring proteins (flgi, k02394 and flga, k02386), l-ring precursor (flgh, k02393), and at least one motor stator protein (mota-k02556, motb-k02557, motc-k10564, motd-k10564 , motx-k21217, or moty-k21218), at least one switch protein (flig-k02410 or flim-k02416). " -Reductive Dehalogenation k21566 | k21647 stress adaptations box 18 presence of reductive dehalogenases: cpra-k21566 and/or pcea-k21647 -C-P Lyase Complex @C-P-Lyase-Complex Phosphorus Acquisition and Metabolism Phosphorus Acquisition and Metabolism -Organic P Mineralization @Organic-P-Mineralization Phosphorus Acquisition and Metabolism Phosphorus Acquisition and Metabolism -Phytase @Phytase Phosphorus Acquisition and Metabolism Phosphorus Acquisition and Metabolism -Inorganic P Solubilization @Inorganic-P-Solubilization Phosphorus Acquisition and Metabolism Phosphorus Acquisition and Metabolism -High-affinity Pi uptake @High-affinity-Pi-uptake Phosphorus Acquisition and Metabolism Phosphorus Acquisition and Metabolism +name rule rule_options module group +Fucoidan GH107;3.2.1.212 | GH168;3.2.1.211 | GH174;3.2.1.- | GH187;3.2.1.- | PL43;4.2.2.- | GH107;3.2.1.211 | GH168;3.2.1.- Carbon Processing Polysaccharide Marine Algal +Ulvan PL24;4.2.2.- | PL25;4.2.2.- | PL28;4.2.2.- Carbon Processing Polysaccharide Marine Algal +Carrageenan GH150;3.2.1.162 | GH16;3.2.1.83 | GH82;3.2.1.157 Carbon Processing Polysaccharide Marine Algal +Porphyran GH16;3.2.1.178 Carbon Processing Polysaccharide Marine Algal +Funoran GH96;3.2.1.222 Carbon Processing Polysaccharide Marine Algal +Alginate PL14;4.2.2.3 | PL15;4.2.2.3 | PL17;4.2.2.11 | PL17;4.2.2.3 | PL18;4.2.2.11 | PL18;4.2.2.3 | PL31;4.2.2.3 | PL32;4.2.2.3 | PL36;4.2.2.3 | PL38;4.2.2.3 | PL38;4.2.2.11 | PL39;4.2.2.3 | PL39;4.2.2.11 | PL41;4.2.2.3 | PL5;4.2.2.3 | PL6;4.2.2.11 | PL6;4.2.2.3 | PL7;4.2.2.11 | PL7;4.2.2.3 | PL8;4.2.2.3 | PL44;4.2.2.3 Carbon Processing Polysaccharide Marine Algal +Agarose GH118;3.2.1.81 | GH16;3.2.1.81 | GH50;3.2.1.81 | GH86;3.2.1.81 | GH96;3.2.1.158 Carbon Processing Polysaccharide Marine Algal +Laminarin GH5;3.2.1.39 | GH55;3.2.1.39 | GH5;3.2.1.58 | GH55;3.2.1.58 Carbon Processing Polysaccharide Marine Algal +Cellulose @Cellulose Carbon Processing Polysaccharide Other +Hemicellulose @Hemicellulose-Xylan | @Hemicellulose-Other Carbon Processing Polysaccharide Other +Arabinogalactan @Arabinogalactan Carbon Processing Polysaccharide Other +Starch/Glycogen @StarchGlycogen | @StarchSpecific Carbon Processing Polysaccharide Other +Chitin @Chitin Carbon Processing Polysaccharide Other +Cellulose-Associated @BetaGlucosides Carbon Processing Oligomer +Hemicellulose-Associated @Xylooligosaccharides | @XyloglucanMannooligosaccharides | @XylanXylobiose Carbon Processing Oligomer +Storage-Associated @Fructooligosaccharides | @MaltooligosaccharidesAlphaGlucosides Carbon Processing Oligomer +Chitin and Related Oligosaccharides @Chitooligosaccharides | @NAcetylhexosaminides Carbon Processing Oligomer +Alginate-Associated PL14;4.2.2.26 | PL15;4.2.2.26 | PL17;4.2.2.26 | PL6;4.2.2.26 | PL7;4.2.2.26 Carbon Processing Oligomer +Agarose-Associated GH117;3.2.1.159 Carbon Processing Oligomer +Cellobiose @Cellobiose Carbon Processing Oligomer +Maltose @Maltose Carbon Processing Oligomer +Sucrose @Sucrose Carbon Processing Oligomer +Trehalose @Trehalose Carbon Processing Oligomer +Xylan/Xylobiose @XylanXylobiose Carbon Processing Oligomer +Mannose/Mannobiose @Mannose-Mannobiose Carbon Processing Oligomer +Glucose @Glucose Carbon Processing Monosaccharide +Xylose @Xylose Carbon Processing Monosaccharide +Arabinose @Arabinose Carbon Processing Monosaccharide +Mannose @Mannose Carbon Processing Monosaccharide +Galactose @Galactose Carbon Processing Monosaccharide +Fructose @Fructose Carbon Processing Monosaccharide +Rhamnose @Rhamnose Carbon Processing Monosaccharide +N-Acetylglucosamine (Glc-NAc) @N-Acetylglucosamine Carbon Processing Monosaccharide +Fucose @Fucose Carbon Processing Monosaccharide +Acetate @Acetate-Final Carbon Processing Low Molecular Weight Carbon +Butyrate @Butyrate-Final Carbon Processing Low Molecular Weight Carbon +Propionate @Propionate-Final Carbon Processing Low Molecular Weight Carbon +Ethanol/Alcohol @Ethanol Carbon Processing Low Molecular Weight Carbon +Methanol @Methanol Carbon Processing Low Molecular Weight Carbon +Hydrogenotrophic @hydrogenotrophic "{""include_when"":{""all_columns_present"":[""taxonomy""]}}" Carbon Processing One Carbon Metabolism +Acetoclastic @acetoclastic "{""include_when"":{""all_columns_present"":[""taxonomy""]}}" Carbon Processing One Carbon Metabolism +Methylotrophic @methylotroph "{""include_when"":{""all_columns_present"":[""taxonomy""]}}" Carbon Processing One Carbon Metabolism +Aerobic Methanotroph @AerobicMethanotroph Carbon Processing One Carbon Metabolism +Methanogen Or ANME @Methanogen "{""include_when"":{""all_columns_absent"":[""taxonomy""]}}" Carbon Processing One Carbon Metabolism +Anaerobic Oxidation of Methane @anaerobic-methanotrophic-Archaea Carbon Processing One Carbon Metabolism +Rump Pathway (Non-Methanogenic Methylotrophy Type I) [k08093 | k13831 | k13812] & k08094 & [k00093 | k23995 | k17066 | k14028 | k14029] Carbon Processing One Carbon Metabolism +Serine Pathway (Non-Methanogenic Methylotrophy Type Ii) k00830 & k00018 & k08691 Carbon Processing One Carbon +Calvin Cycle @Calvin Carbon Processing Carbon Fixation +Hydroxypropionate-Hydroxybutyrate Cycle @HydroxypropionateHydroxybutylate Carbon Processing Carbon Fixation +Dicarboxylate Hydroxybutyrate Cycle @DicarboxylateHydroxybutyrate Carbon Processing Carbon Fixation +Wood–Ljungdahl Pathway @ReductiveAcetylCoAWoodLjungdahl Carbon Processing Carbon Fixation +Phototroph All Types @PhototrophAllTypes Phototrophy Light Sensing and Energy +Phototroph- Oxygenic @Phototroph-Oxygenic Phototrophy Light Sensing and Energy +Phototroph- Anoxygenic @AnoxygenicTypeIISubtype | @AnoxygenicTypeIPscASubtype | @PotentialAnoxygenicDivergentTypeISubtype Phototrophy Light Sensing and Energy +Rhodopsin All Types @RhodopsinAllTypes Phototrophy Light Sensing and Energy +Bacteriorhodopsin Proton Pump Subtype @Bacteriorhodopsin Phototrophy Light Sensing and Energy +Oxygen - Low Affinity Use [percent(50,@CytochromeCOxidase)|percent(50,@CytochromeAa3600MenaquinolOxidase)|percent(50,@CytochromeOUbiquinolOxidase)] Respiratory Redox Processes Oxygen Reduction +Oxygen - High Affinity Use [@percent50CytochromeBDUbiquinolOxidase|@percent50CytochromeCOxidaseCBB3] Respiratory Redox Processes Oxygen Reduction +NO3 To NO2 @NarNitrateReductase|[@NapNitrateReductase] Respiratory Redox Processes Nitrogen Reduction +NO2 To NO @NitriteReductase Respiratory Redox Processes Nitrogen Reduction +NO To N2O @NitricOxideReductase Respiratory Redox Processes Nitrogen Reduction +N2O To N2 @NitrousOxideReductase Respiratory Redox Processes Nitrogen Reduction +DNRA, NO3 To NH4 @DNRA Respiratory Redox Processes Nitrogen Reduction +Aerobic Ammonium Oxidation @AerobicAmmoniaOxidizer Respiratory Redox Processes Nitrogen Oxidation +Aerobic Nitrite Oxidation @NitriteOxidoreductase Respiratory Redox Processes Nitrogen Oxidation +Anaerobic Ammonia Oxidation Anammox @Annamox Respiratory Redox Processes Nitrogen Oxidation +Dissimilatory-Sulfate-Reduction @Sulfatereducer Respiratory Redox Processes Sulfur Cycling +Thiosulfate-Reduction-(Respiratory) @ThiosulfateRed Respiratory Redox Processes Sulfur Cycling +Thiosulfate-Reduction-(Rhodanese) K01011 | Rhodanese Respiratory Redox Processes Sulfur Cycling +Sulfur-Oxidation-Sox @SoxXA & @SoxYZ & @SoxB Respiratory Redox Processes Sulfur Cycling +Sulfur-Oxidation-Reverse-Dsr @DsrABtypeo Respiratory Redox Processes Sulfur Cycling +Tetrathionate-Reduction @TetrathionateRed Respiratory Redox Processes Sulfur Cycling +[Fefe] Group_A Hydrogenase hmm@fefe_group_a_hydrogenase Other Energy Metabolisms Hydrogen Metabolism +[Fefe] Group_B Hydrogenase hmm@fefe_group_b_hydrogenase Other Energy Metabolisms Hydrogen Metabolism +[Fefe] Group_C Hydrogenase hmm@fefe_group_c_hydrogenase Other Energy Metabolisms Hydrogen Metabolism +[Fefe] Group_E Hydrogenase hmm@fefe_group_e_hydrogenase Other Energy Metabolisms Hydrogen Metabolism +[Fefe] Group_F Hydrogenase hmm@fefe_group_f_hydrogenase Other Energy Metabolisms Hydrogen Metabolism +[Nife] Group_1 Hydrogenase hmm@nife_group_1_hydrogenase Other Energy Metabolisms Hydrogen Metabolism +[Nife] Group_2 Hydrogenase hmm@nife_group_2_hydrogenase Other Energy Metabolisms Hydrogen Metabolism +[Nife] Group_3 Hydrogenase hmm@nife_group_3_hydrogenase Other Energy Metabolisms Hydrogen Metabolism +[Nife] Group_4 Hydrogenase hmm@nife_group_4_hydrogenase Other Energy Metabolisms Hydrogen Metabolism +Candidate Extracellular Aspartic Peptidases @ExtracellularAspartic Nutrient Acquisition Nitrogen Assimilation +Candidate Extracellular Cysteine Peptidases @ExtracellularCysteine Nutrient Acquisition Nitrogen Assimilation +Candidate Extracellular Glutamic Peptidases @ExtracellularGlutamic Nutrient Acquisition Nitrogen Assimilation +Candidate Extracellular Metallo Peptidases @ExtracellularMetallo Nutrient Acquisition Nitrogen Assimilation +Candidate Extracellular Serine Peptidases @ExtracellularSerine Nutrient Acquisition Nitrogen Assimilation +Urease @Urease Nutrient Acquisition Nitrogen Assimilation +Amidase K01426 Nutrient Acquisition Nitrogen Assimilation +Formamidase K01455 Nutrient Acquisition Nitrogen Assimilation +N2 Fixation @nitrogen-fixer Nutrient Acquisition Nitrogen Assimilation +Sulfur- DMS/DMSP Cycling K28073 | K16953 | K28067 | K28068 | K28069 | K28072 | K17486 | [K20034 & K20035 & K20036] | K16967 | K16964 | K18277 | [K07306 & [K07307 | K00184] & [K07308 | K00185]] | K07811 Nutrient Acquisition Other Nutrient Assimilations and Transformations +Phosphorus- C-P Lyase @C-P-Lyase-Complex Nutrient Acquisition Other Nutrient Assimilations and Transformations +Phosphorus- Organic Mineralization @Organic-P-Mineralization Nutrient Acquisition Other Nutrient Assimilations and Transformations +Phosphorus- Pi Uptake @High-affinity-Pi-uptake Nutrient Acquisition Other Nutrient Assimilations and Transformations +Copper Efflux @CopperEfflux Environmental Adaptation Heavy Metal Transformation and Resistance +Cobalt/Cadmium/Zinc/Ni Efflux @CadmiumZincEfflux | @DivalentMetalEfflux | @CobaltZincCadmiumEfflux | @NickelCobaltEfflux Environmental Adaptation Heavy Metal Transformation and Resistance +Mercury Reduction @MercuryReduction Environmental Adaptation Heavy Metal Transformation and Resistance +Organomercury Degradation @OrganomercuryDegradation Environmental Adaptation Heavy Metal Transformation and Resistance +Mercury Methylation @MercuryMethylation Environmental Adaptation Heavy Metal Transformation and Resistance +EpsProduction @EpsProduction Environmental Adaptation Biofilms & Attachment +QuorumSensing @QuorumSensing Environmental Adaptation Biofilms & Attachment +Motility @Motility Environmental Adaptation Biofilms & Attachment +Ion Homeostasis: K+ Uptake and Na+ Exclusion @IonBalance-saltinpotential Environmental Adaptation Osmoregulation +Compatible-Solutes: Glycine Betaine Synthesis @GlycineBetaineSynthesis Environmental Adaptation Osmoregulation +Compatible-Solutes: Ectoine Synthesis @EctoineSynthesis Environmental Adaptation Osmoregulation +Compatible-Solutes: Sugar Derived Synthesis @SugarDerivedCompatibleSoluteSynthesis Environmental Adaptation Osmoregulation +Compatible-Solutes: Methylated Transport @MethylatedCompatibleSoluteTransport Environmental Adaptation Osmoregulation +Compatible-Solutes: Ectoine Transport @EctoineTransport Environmental Adaptation Osmoregulation diff --git a/src/dram_rules/data/rules_bgc.tsv b/src/dram_rules/data/rules_bgc.tsv index b39cb3b..250a646 100644 --- a/src/dram_rules/data/rules_bgc.tsv +++ b/src/dram_rules/data/rules_bgc.tsv @@ -1,6 +1,5 @@ -name rule rule_options module group notes +name rule rule_options module group notes Calvin Cycle @Calvin Carbon Transformations Carbon Fixation -Reductive Citric Acid Cycle @ReductiveCitricAcid Carbon Transformations Carbon Fixation Hydroxypropionate-Hydroxybutyrate Cycle @HydroxypropionateHydroxybutylate Carbon Transformations Carbon Fixation Dicarboxylate Hydroxybutyrate Cycle @DicarboxylateHydroxybutyrate Carbon Transformations Carbon Fixation Wood-Ljungdahl Pathway @ReductiveAcetylCoAWoodLjungdahl Carbon Transformations Carbon Fixation @@ -56,7 +55,7 @@ Oxalate K01577 | K07749 Carbon Transformations Low Molecular Weight Carbon Formate K00656 Carbon Transformations Low Molecular Weight Carbon Methanol @Methanol Carbon Transformations Low Molecular Weight Carbon Ethanol/Alcohol @Ethanol Carbon Transformations Low Molecular Weight Carbon -Photosynthesis @phototroph Energy Conservation Photosynthesis +Photosynthesis @PhototrophAllTypes Energy Conservation Photosynthesis ETC: Complex I Nadh Dehydrogenase at_least(9, PRESENCE, [K00330,K00331,K00332,K00333,K13378,K13380,K00334,K00335,K00336,K00337,K00338,K00339,K00340,K00341,K00342,K15863,K00343])|at_least(7, PRESENCE, [K05574,K05582,K05581,K05579,K05572,K05580,K05578,K05576,K05577,K05575,K05573,K05583,K05584,K05585])|at_least(4, PRESENCE, [K03878,K03879,K03880,K03881,K03882,K03883,K03884])|at_least(6, PRESENCE, [K03934,K03935,K03936,K03937,K03938,K03939,K03940,K03941,K03942,K03943,K03944])|at_least(7, PRESENCE, [K03945,K03946,K03947,K03948,K03949,K03950,K03951,K03952,K03953,K03954,K03955,K03956,K11352,K11353])|at_least(6, PRESENCE, [K03957,K03958,K03959,K03960,K03961,K03962,K03963,K03964,K03965,K03966,K11351])|at_least(3, PRESENCE, [K00346,K00347,K00348,K00349,K00350,K00351]) Energy Conservation Respiratory Electron Transport and ATP Synthesis ETC: Complex II Succinate Dehydrogenase at_least(4, PRESENCE, [K00239,K00240,K00241,K00242,K00244,K00245,K00246,K00247,K18859,K18860])|at_least(2, PRESENCE, [K00234,K00235,K00236,K00237]) Energy Conservation Respiratory Electron Transport and ATP Synthesis Presence of a majority of an KEGG-derived Complex I variant, indicative of respiration ETC: Complex III Cytochrome Bc1 Complex at_least(4, PRESENCE, [K00412,K00413,K00410,K00411,K03891,K03889,K03890])|at_least(4, PRESENCE, [K00414,K00415,K00416,K00417,K00418,K00419,K00420])|at_least(2, PRESENCE, [K03886,K03887,K03888]) Energy Conservation Respiratory Electron Transport and ATP Synthesis Presence of a majority of an KEGG-derived Complex II variant, indicative of respiration @@ -83,7 +82,7 @@ Acetoclastic @acetoclastic "{""include_when"":{""all_columns_present"":[""taxono Methylotrophic @methylotroph "{""include_when"":{""all_columns_present"":[""taxonomy""]}}" Respiratory Redox Processes Methane Production and Oxidation For a genome to have acetoclastic methanogenesis potential, it must encode mcrA, part of the ACS_CODH complex, and either Acetate Kinase and Phosphotransacetylase OR Acetyl CoA Synthetase. There is a MANDATORY taxonomic requirement for this rule to run, and a MAG or genome must also belong to the genus Methanosarcina or the family Methanotrichaceae Aerobic Methanotroph @AerobicMethanotroph Respiratory Redox Processes Methane Production and Oxidation "For a genome to have methyltotrophic methanogenesis potential, it must encode mcrA and at least one substrate-demethylating corrinoid-dependent methyltransferase homolog ""MtxB""" Methanogen Or ANME @Methanogen "{""include_when"":{""all_columns_absent"":[""taxonomy""]}}" Respiratory Redox Processes Methane Production and Oxidation A genome that encodes adenylysulfate reductase and dissimilatory sulfite reductase -Anaerobic Oxidation of Methane @anaerobic-methanotrophic-Archaea Respiratory Redox Processes Methane Production and Oxidation For a genome to have CH‚Äö√Ñ√∂‚àö√ë‚àö‚àÇ‚Äö√†√∂‚àö¬∞‚Äö√†√∂‚àö¬¥ oxidation capability, it must encode at least one methane monooxygenase complex pMMO or sMMO, which catalyzes the conversion of methane to methanol ‚Äö√Ñ√∂‚àö√ë‚àö‚àÇ‚Äö√†√∂‚àö√´‚Äö√†√∂‚àö√ú the key diagnostic step of methanotrophy in soils. It must also encode any genes for denitrifcation narG, napA, nirK, nirS, norB +Anaerobic Oxidation of Methane @anaerobic-methanotrophic-Archaea Respiratory Redox Processes Methane Production and Oxidation For a genome to have CH₄ oxidation capability, it must encode at least one methane monooxygenase complex pMMO or sMMO, which catalyzes the conversion of methane to methanol — the key diagnostic step of methanotrophy in soils. It must also encode any genes for denitrifcation narG, napA, nirK, nirS, norB Possible Obligate Fermenter @Fermenter Other Metabolic Traits Other Metabolic Traits Hydrogenases @HydrogenUse Other Metabolic Traits Other Metabolic Traits Nitrogen Fixation @nitrogen-fixer Other Metabolic Traits Other Metabolic Traits @@ -91,6 +90,7 @@ Arsenite Oxidation Potential @ArseniteOxidation Environmental Adaptation Other 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). Possible Selenate Reduction @PossibleSelenateReduction Environmental Adaptation Other Metal and Trace Element Transformation and Resistance CopA (K17686) or CopB (K01533) copper-exporting ATPases, OR the complete CusABC efflux system consisting of CusA (K07787), CusB (K07798), AND CusC ]K07796). The rule requires only one ATPase or all three CusABC components. diff --git a/src/dram_rules/data/rules_common.tsv b/src/dram_rules/data/rules_common.tsv index d70312f..61d5064 100644 --- a/src/dram_rules/data/rules_common.tsv +++ b/src/dram_rules/data/rules_common.tsv @@ -1,34 +1,38 @@ -name alias rule - Acetate-Final @Acetate-1 | @Acetate-2 | @Acetate-3 | @Acetate-4 | @Acetate-5 Acetate-associated metabolism - Acetate-1 K24012 | [K01905 & K22224] Acetyl-CoA ↔ acetate; shared activity with propionate - Acetate-2 K01568 & [K00138 | K00128 | K14085 | K00149 | K00129] Pyruvate → acetaldehyde → acetate - Acetate-3 [K00625 | K13788 | K15024] & K00925 Acetyl-CoA ↔ acetyl-phosphate ↔ acetate - Acetate-4 K01621 & K00925 Xylulose-5-phosphate/fructose-6-phosphate → acetyl-phosphate → acetate - Acetate-5 K01895 | K01913 Acetate → acetyl-CoA; not acetate specific +name alias rule notes + Acetate-Final @Acetate-1 | @Acetate-2 | @Acetate-3 | @Acetate-4 | @Acetate-5 | @Acetate-6 Acetate-associated metabolism + Acetate-1 K24012 | [K01905 & K22224] Acetyl-CoA to acetate; shared activity with propionate + Acetate-2 K01568 & [K00138 | K00128 | K14085 | K00149 | K00129] Pyruvate to acetaldehyde to acetate + Acetate-3 [K00625 | K13788 | K15024] & K00925 Acetyl-CoA to acetyl-phosphate ↔ acetate + Acetate-4 K01621 & K00925 Xylulose-5-phosphate/fructose-6-phosphate to acetyl-phosphate to acetate + Acetate-5 K01895 | K01913 Acetate to acetyl-CoA; not acetate specific + Acetate-6 K00156 Pyruvate to acetate Propionate-Final @Propionate-1 | @Propionate-2 | @Propionate-3 | @Propionate-4 Propionate-associated metabolism - Propionate-1 [K01847 | [K01848 & K01849]] & K05606 & [K11264 | K18426] & @Propionate-terminal Succinyl-CoA → methylmalonyl-CoA → propionyl-CoA → propionate - Propionate-2 K20626 & K20627 & K00248 & @Propionate-terminal Lactate → lactoyl-CoA → acryloyl-CoA → propionyl-CoA → propionate - Propionate-3 K01699 & K13919 & K13920 & K13922 & @Propionate-terminal 1,2-Propanediol → propionaldehyde → propionyl-CoA → propionate - Propionate-4 K01908 Propionate → propionyl-CoA - Propionate-terminal K01026 | K24012 | [K01905 & K22224] | [K13923 & [K00932 | K19697]] Propionyl-CoA ↔ propionate; broad alternatives require pathway context + Propionate-1 [K01847 | [K01848 & K01849]] & K05606 & [K11264 | K18426 | [K01604 & K23351 & K20509]] & @Propionate-terminal Succinyl-CoA tomethylmalonyl-CoA to propionyl-CoA to propionate + Propionate-2 K20626 & K20627 & [K00248 | K20143] & @Propionate-terminal Lactate to lactoyl-CoA to acryloyl-CoA to propionyl-CoA to propionate + Propionate-3 K01699 & K13919 & K13920 & K13922 & @Propionate-terminal 1,2-Propanediol to propionaldehyde to propionyl-CoA to propionate + Propionate-4 K01908 Propionate to propionyl-CoA + Propionate-terminal K22214| K01026 | K24012 | [K01905 & K22224] | [K13923 & [K00932 | K19697]] Propionyl-CoA to propionate; broad alternatives require pathway context Butyrate-Final @Butyrate-1 | @Butyrate-2 | @Butyrate-3 Butyrate-associated metabolism - Butyrate-1 K00634 & K00929 Butyryl-CoA ↔ butyryl-phosphate ↔ butyrate - Butyrate-2 [[K01034 & K01035] | K19709] Acetyl-CoA ↔ butyryl-CoA ↔ butyrate through CoA transfer; context-supported, not uniquely specific - Butyrate-3 K01913 Butyrate → butyryl-CoA; not butyrate specific - Acetyl-CoAtoButyryl-CoA K00626 & [K00074 | K00022 | K07516 | K01825 | K01782 | K07514] & [K01692 | K01825 | K01782 | K07515 | K07514 | K07511 | K01715] & K00248 Acetyl-CoA ↔ acetoacetyl-CoA ↔ 3-hydroxybutyryl-CoA ↔ crotonyl-CoA ↔ butyryl-CoA + Butyrate-1 K00634 & K00929 & K00248 Butyryl-CoA to butyryl-phosphate to butyrate + Butyrate-2 [[K01034 & K01035] | K19709] Acetyl-CoA to butyryl-CoA to butyrate through CoA transfer; context-supported, not uniquely specific + Butyrate-3 K01913 Butyrate to butyryl-CoA; not butyrate specific + Acetyl-CoAtoButyryl-CoA K00626 & [K00074 | K00022 | K07516 | K01825 | K01782 | K07514] & [K01692 | K01825 | K01782 | K07515 | K07514 | K07511 | K01715] & K00248 Acetyl-CoA to acetoacetyl-CoA to 3-hydroxybutyryl-CoA to crotonyl-CoA to butyryl-CoA Lactate-Final @Lactate-1 | @Lactate-2 | @Lactate-3 | @Lactate-4 Lactate-associated metabolism - Lactate-1 K00016 Pyruvate ↔ L-lactate; NAD-dependent LDH - Lactate-2 K03778 Pyruvate ↔ D-lactate; NAD-dependent LDH - Lactate-3 K00101 | K29125 L-lactate → pyruvate; cytochrome-/quinone-dependent LDH - Lactate-4 K00102 D-lactate → pyruvate; cytochrome-dependent LDH - - phototroph @Phototroph-Oxygenic | @Phototroph-AnoxygenicType2 | @Phototroph-AnoxygenicType1 - Phototroph-Oxygenic [K02703 & K02706] & [K02689 & K02690] - Phototroph-AnoxygenicType2 K08928 & K08929 - Phototroph-AnoxygenicType1 K08940 + Lactate-1 K00016 Pyruvate to L-lactate; NAD-dependent LDH + Lactate-2 K03778 Pyruvate to D-lactate; NAD-dependent LDH + Lactate-3 K00101 | K29125 L-lactate to pyruvate; cytochrome-/quinone-dependent LDH + Lactate-4 K00102 D-lactate to pyruvate; cytochrome-dependent LDH + + PhototrophAllTypes PF00223 | [K08928 & K08929] + Phototroph-Oxygenic K02703 & K02706 & K02689 & K02690 + AnoxygenicTypeIISubtype K08928 & K08929 + AnoxygenicTypeIPscASubtype K08940 + PotentialAnoxygenicDivergentTypeISubtype PF00223 & not(@Phototroph-Oxygenic | @AnoxygenicTypeIISubtype | @AnoxygenicTypeIPscASubtype) + RhodopsinAllTypes PF01036 + Bacteriorhodopsin K04641 CO2fixation @Calvin | @ReductiveCitricAcid |@HydroxypropionateHydroxybutylate| @HydroxypropionateHydroxybutylate| @DicarboxylateHydroxybutyrate | @ReductiveAcetylCoAWoodLjungdahl | @ReductiveGlycinePathway Calvin @RibuloseBisphosphateCarboxylase&@CalvinCycle50p @@ -101,12 +105,19 @@ name alias rule HydrogenUse NiFe_group1 | NiFe_group2 | NiFe_group3 | NiFe_group4 | FeFe_groupA | FeFe_groupB | FeFe_groupC | FeFe_groupE | FeFe_groupF Fermenter not(@NegativeForFermenter) & [@Lactate-Final | @Ethanol | @Acetate-Final | @Butyrate-Final | @Propionate-Final] & [K00850 | K00873 | K01690 | K01625 | K00615 | K00616] - NegativeForFermenter @ETC50 | @Methanogen | @Denitrifier | @Sulfatereducer | @AerobicAmmoniaOxidizer | @Aerobe | @Microaerophillic | @phototroph | @Non-sulfate-sulfur-reduction | @IronReduction + NegativeForFermenter @ETC50 | @Methanogen | @Denitrifier | @Sulfatereducer | @AerobicAmmoniaOxidizer | @Aerobe | @Microaerophillic | @PhototrophAllTypes | @Non-sulfate-sulfur-reduction | @IronReduction | @SulfiteRed Denitrifier @ETC50 & [[@NarNitrateReductase | @NapNitrateReductase] | @NitriteReductase | @NitricOxideReductase | @NitrousOxideReductase] NitrousOxideReductase K00376 | EC:1.7.2.4 NitricOxideReductase K04561 | K15877 | EC:1.7.2.5 NitriteReductase K00368 | K15864 | EC:1.7.2.1 + AcetogenOrAcetateOxidizer @ReductiveAcetylCoAWoodLjungdahl_Bacterial & @AcetateKinase & @PhosphateAcetyltransferase & @AcetogenEnergyConservation & not(@Sulfatereducer) + AcetateKinase K00925 + PhosphateAcetyltransferase K13788|K00625 + AcetogenEnergyConservation @RNFcomplex | @ECHcomplex + RNFcomplex at_least(3, PRESENCE, [K03612,K03613,K03614,K03615,K03616,K03617]) + ECHcomplex at_least(3, PRESENCE, [K14086,K14087,K14088,K14089,K14090,K14091]) + Aerobe [@CytochromeCOxidase | @CytochromeAa3600MenaquinolOxidase | @CytochromeOUbiquinolOxidase] & @ETC50 CytochromeCOxidase K02275 | K02274 | K02276 | K15408 | K02277 CytochromeAa3600MenaquinolOxidase K02827 | K02826 | K02828 | K02829 @@ -164,21 +175,21 @@ name alias rule mtrCAB MtrA & @mtoAB & MtrC_TIGR03507 ExtABCD ExtA_pcc_cyt | ExtB_porin | ExtC_pcc_lp_cyt | ExtD_pcc_lp_cyt - IronOxidation [@Cyc2 | @mtoAB | @foxEYZ ] & [@Microaerophillic | @Aerobe | @Sulfatereducer | @Denitrifier | @phototroph] + IronOxidation [@Cyc2 | @mtoAB | @foxEYZ ] & [@Microaerophillic | @Aerobe | @Sulfatereducer | @Denitrifier | @PhototrophAllTypes] Cyc2 at_least(2, COUNTS, [Cyc2_repCluster1, Cyc2_repCluster2, Cyc2_repCluster3]) foxEYZ FoxE & FoxY & FoxZ mtoAB MtrB_TIGR03509 Sulfatereducer @DsrABtyper & [K00958 | K00394 |K00395] - DsrABtyper dsrAr | dsrBr - SulfiteRed dsrAr | dsrBr + DsrABtyper dsrAr | dsrBr | dsrAr_arch | dsrBr_arch + SulfiteRed @DsrABtyper TetrathionateRed at_least(2, PRESENCE, [K08359, K08358, K08357]) ThiosulfateRed at_least(2, PRESENCE, [K08352, K08353, K08354]) ElementalSRed at_least(2, PRESENCE, [K17219, K17220, K17221]) Non-sulfate-sulfur-reduction @TetrathionateRed |@ThiosulfateRed | @SulfiteRed | @ElementalSRed sulfateoxidizer [@DsrABtypeo | @SoeABC | @SorAB | @Sqr | @FccAB | @SoxXA | @SoxYZ | @SoxB | @SoxCD] & @ETC50 - DsrABtypeo K11180 | dsrA | dsrB | K11181 + DsrABtypeo dsrAo | dsrBo SoeABC K21307 | K21308 | K21309 SorAB K05301 | K00386 Sqr sqr_alignment | K17218 @@ -192,7 +203,7 @@ name alias rule Methanogen @MethylCoenzymeMReductase MethylCoenzymeMReductase @McrAor3999 | K00401 | K00402 notOtherMethanogen not(@OtherAjMethanogen) - OtherAjMethanogen @Sulfatereducer | @Denitrifier | @AerobicAmmoniaOxidizer |@Comammox | @Annamox | @phototroph | @ETC60 + OtherAjMethanogen @Sulfatereducer | @Denitrifier | @AerobicAmmoniaOxidizer |@Comammox | @Annamox | @PhototrophAllTypes | @ETC60 hydrogenotrophic [[[@Methanogen] & @ReductiveAcetylCoAWoodLjungdahl_Archaeal_MethylOnly & @TetrahydromethanopterinSMethyltransferase_MTRcomplex & [ @Frh_hydrogenase |@Mvh_hydrogenase |@Eha_hydrogenase |@Ehb_hydrogenase |@Fdo_hydrogenase |@FormateDehydrogenase_1|@FdhF|@FdhAB ]] | [[tax(o__Methanoflorentales)|tax(g__Methanobacterium_A)|tax(g__Methanobacterium_C)|tax(g__Methanobacterium_E)|tax(g__Methanobacterium_F)|tax(g__Methanobacterium)|tax(g__Methanobrevibacter_A)|tax(g__Methanobrevibacter)|tax(g__Methanothermobacter_A)|tax(g__Methanothermobacter)|tax(g__Methanothermus)|tax(f__Methanobacteriaceae)|tax(g__Methanocella_A)|tax(g__Methanocella)|tax(g__Methanooceanicella)|tax(o__Methanococcales)|tax(o__Methanomicrobiales)|tax(g__Methanopyrus)|tax(o__Nezhaarchaeales)|tax(g__Methanolacinia)|tax(g__Methanobacterium_B)|tax(g__Methanobacterium_D)|tax(g__Methanosarcina)] & not(tax(g__Methanosphaera))]] & not([@Methanogen] & [tax(g__Methanocomedens_A)|tax(g__Methanocomedens_B)|tax(g__Methanogaster_A)|tax(g__Methanogaster_B)|tax(g__Methanoperedens_A)|tax(g__Methanoperedens)|tax(g__ANME-1-THS)|tax(g__ANME1a)|tax(g__G60ANME1)|tax(g__Methanophaga)|tax(g__Methanovorans)|tax(g__Methanomarinus)|tax(g__Methanoxibalbensis)|tax(g__Methanospirare)|tax(g__Kmv04)|tax(g__Methanogaster_C)|tax(g__Methanogaster_D)|tax(g__CAZCRM01)|tax(g__UBA10536)|tax(g__Methanoxibalbensis)]) ReductiveAcetylCoAWoodLjungdahl_Archaeal_MethylOnly at_least(4, PRESENCE, [ @FormylmethanofuranDehydrogenase, @Formylmethanofuran-Tetrahydromethanopterin-N-formyltransferase, @MethenyltetraydromethanopterinCyclohydrolase, @MethelenetetraydromethanopterinDehydrogenaseand510-MethenyltetrahydromethanopterinHydrogenase , @510-MethylenetetrahydromethanopterinReductase ]) @@ -302,26 +313,63 @@ name alias rule Urease [K01428&K01429&K01430] ArsenicResistanceBroad K03893 | K03325 | K11811 | K07089 - ArsenicDetoxification [K00537 | K03741] & [K03893 | K03325] + ArsenateReductionDetox K00537 | K03741 + ArseniteExportDetox K03893 | K03325 ArseniteOxidation K08355 & K08356 RespiratoryArsenateReduction K28466 & K28467 ArsenicMethylation K07755 ArsenateReductionPotential K00537 | K03741 | [K28466 & K28467] - MercuryReduction K00520 - MercuryDetox K00520 & [K08363 | K19058 | K19059] + MercuryReduction K00520 | merA + MercuryExport [K08363 | K19058 | K19059] | [merC | merE | merF] MercuryMethylation HgcA OrganomercuryDegradation K00221 - GeneralHeavyMetalEfflux @CopperEfflux | @CadmiumZincEfflux | @DivalentMetalEfflux | @NickelCobaltEfflux | @ZincEfflux | @SilverEfflux | @ChromateEfflux - CopperEfflux K17686 | K01533 | [K07787 & K07798 & K07796] - CadmiumZincEfflux K01534 - DivalentMetalEfflux K15726 & K15727 & K15725 + GeneralHeavyMetalEfflux @CopperEfflux | @CadmiumZincEfflux | @DivalentMetalEfflux | @NickelCobaltEfflux | @CobaltZincCadmiumEfflux | @SilverEfflux | @ChromateEfflux + CopperEfflux K17686 | K01533 | [K07787 & K07798 & K07796] | copA | copB + CadmiumZincEfflux K01534 | zntA-yhhO + DivalentMetalEfflux [K15726 | czcA] & [K15727 | czcB] & [K15725 | czcC] NickelCobaltEfflux K08970 | [K11326 & K11327 & K11331] - ZincEfflux K16264 - SilverEfflux K23254 + CobaltZincCadmiumEfflux K16264 | zitB-ybgR ChromateEfflux K07240 + SilverResistance silF | silE + SilverEfflux K23254 | silP + ChromateReductase K19784 PossibleSelenateReduction @SelenateChlorateReduction | @SelenateReductionSrd - SelenateChlorateReduction K17050 & K17051 & K17052 + SelenateChlorateReduction K17050 & K17051 & K17052 SelenateReductionSrd K27874 & K27875 & K27876 + + ExtracellularAspartic A01 + ExtracellularCysteine C01 | C10 | C25 + ExtracellularGlutamic G01 + ExtracellularMetallo M04 | M09 | M10 | M12 | M36 + ExtracellularSerine S01 | S08 | S53 + + EpsProduction at_least(2, PRESENCE, [K20997, K21001, K21154, K25902, K25904, K25906, K25205, K21461]) + QuorumSensing [[K13060 | K13061] & [K18304 | K18099]] | K07173 | at_least(2, PRESENCE, [K10555, K10556, K10557, K10558]) + Motility [K02410 | K02411] & at_least(3, PRESENCE, [K02406, K02407, K02400, K02408, K02409, K02412, K02416, K02417, K02386, K02387, K02391, K02393, K02404, K02405]) + + IonBalance-saltinpotential [K01546 & K01547] | [K05565 & at_least(3, PRESENCE, [K05566, K05567, K05568, K05569, K05570, K05571])] | [K03499 & K03498] + GlycineBetaineSynthesis [[K00108 | K11440] & K00130] | [K18896 & K18897] + EctoineSynthesis K06718 & K00836 & K06720 + TrehaloseSynthesis [K00697 & K01087] | [K01236 & K06044] | K05343 + MannitolSynthesis [K00009 & K19270] + GlycosylatedSynthesis [K03692 & K05978] | [K05947 & K07026] | K18818 + SugarDerivedCompatibleSoluteSynthesis @TrehaloseSynthesis | @MannitolSynthesis |@GlycosylatedSynthesis + MethylatedCompatibleSoluteTransport K02168 | K03451 | K05245 | K03762 | K05020 | [K02000 & K02001 & K02002] | at_least(2, PRESENCE, [K05845, K05846, K05847]) | at_least(2, PRESENCE, [K10036, K10037, K10038]) + EctoineTransport at_least(2, PRESENCE, [K02028, K02029, K02030]) + SugarDerivedTransport at_least(2, PRESENCE, [K10227, K10228, K10229, K10230]) | at_least(2, PRESENCE, [K02783, K02781, K02782]) | K02798 | at_least(2, PRESENCE, [K10109, K10110, K10111]) | K17314 + + Tetracycline-inactivation 3000036 + Tetracycline-efflux 0010002 | 0010001 + Tetracycline-protection 0000002 + Macrolide-efflux 0010002 + Macrolide-inactivation 3000320 | 3000333 + Macrolide-alteration 3000560 + Beta-lactam-inactivation 3000059|3000056|3000069|3000066|3000020|3000057|3000021|3007721|3002998|3004192|3003000|3000068|3000067|3000058|3000043|3000073|3002384|3000014|3004824|3000083|3007696|3007697|3007704|3002994|3000015|3000091|3007723|3007735 + Sulfoamide-target-replacement 3000410 | 3000412 | 3000413 | 3004361 + Aminoglycoside-inactivation 3007419 | 3000114 | 3000322 | 3000345 | 3004275 | 3000126 | 3000127 | 3002601 + Aminoglycoside-alteration 3004271 | 3004272 + Aminoglycosde-efflux 3000491 | 3003841 + MultidrugEfflux 3003038 | 3003032 | 3000386 | 3000384 | 3000503 | 3000773 | 3000788 | 3000797 | 3000815 diff --git a/src/dram_rules/data/rules_eng_sys.tsv b/src/dram_rules/data/rules_eng_sys.tsv index b097004..ed383d6 100644 --- a/src/dram_rules/data/rules_eng_sys.tsv +++ b/src/dram_rules/data/rules_eng_sys.tsv @@ -1,99 +1,135 @@ -name rule rule_options module group notes -Dissimilatory-Sulfate-Reduction @Sulfatereducer Sulfur Cycling Sulfide Production Dissimilatory sulfate reduction to sulfide (H2S); key souring mechanism in oil & gas systems. Requires adenylysulfate reductase (aprAB; K00394, K00395) and dissimilatory sulfite reductase (dsrAB; dsrA, dsrB). -Thiosulfate-Reduction-(Respiratory) at_least(2, PRESENCE, [K08352, K08353, K08354]) Sulfur Cycling Sulfide Production Respiratory thiosulfate reduction via the PhsABC thiosulfate reductase complex (phsA K08352, phsB K08353, phsC K08354). Requires at least 2 of 3 subunits to account for incomplete genome recovery in metagenomic data. Uses thiosulfate as terminal electron acceptor under anaerobic conditions. Found in Salmonella, Citrobacter, and diverse anaerobes. -Thiosulfate-Reduction-(Rhodanese) K01011 | Rhodanese Sulfur Cycling Sulfide Production Thiosulfate sulfurtransferase (rhodanese; K01011 rdl/glpE-type, K14180 mitochondrial-type) transfers sulfur from thiosulfate to cyanide or other acceptors, producing sulfite and thiocyanate. Also involved in sulfur relay and cyanide detoxification. Distinct from respiratory thiosulfate reduction ‚Äö√Ñ√Æ does not conserve energy via electron transport. Extremely widespread across bacteria and archaea so interpret cautiously; presence alone is not diagnostic of dedicated thiosulfate metabolism. -Sulfur-Oxidation-Sox [K17223 | K17222] & [K17226 | K17227] & K17224 Sulfur Cycling Sulfur Oxidation Oxidation of reduced sulfur compounds via the SOX multienzyme complex. SoxXA (K17223, K17222) initiate sulfur binding, SoxYZ (K17226, K17227) are the sulfur-carrying proteins, and SoxB (K17224) is the sulfate-releasing thiohydrolase. SoxCD (K17225, K22622) are optional and indicate complete oxidation to sulfate without intermediates. -Sulfur-Oxidation-Reverse-Dsr [K11180 | dsrA | K11181 | dsrB] & K27196 Sulfur Cycling Sulfur Oxidation Oxidation of stored sulfur globules via reverse-running DsrAB, distinguished from reductive DsrAB by co-occurrence with dsrL (K27196), an NADH-dependent oxidoreductase found exclusively in sulfur-oxidizing organisms. Both dsrA/dsrB (K11180/K11181) and dsrL (K27196) required. Found in Chlorobi, some Gammaproteobacteria, and Chromatiales. -Tetrathionate-Reduction at_least(2, PRESENCE, [K08359, K08358, K08357]) Sulfur Cycling S Transformations Tetrathionate reduction via the ttrABC system (ttrA K08359, ttrB K08358, ttrC K08357). At least 2 of 3 subunits required. Relevant as an alternative electron acceptor in anaerobic subsurface and industrial systems. -Hydrogenotrophic-Methanogenesis @hydrogenotrophic "{""include_when"":{""all_columns_present"":[""taxonomy""]}}" Methane Production & Consumption Methane Production Methanogenesis from H2/CO2; dominant pathway in shale and anaerobic digesters. Requires McrA plus hydrogenotrophic pathway genes including F420-reducing hydrogenase subunits and methyl-CoM reductase components. -Acetoclastic-Methanogenesis @acetoclastic "{""include_when"":{""all_columns_present"":[""taxonomy""]}}" Methane Production & Consumption Methane Production Methanogenesis from acetate; requires McrA, ACS/CODH complex (K00193, K00194, K00197, K00198), and acetate activation via phosphotransacetylase-acetate kinase (K00925, K00625) or acetyl-CoA synthetase (K01895). Taxonomy filter recommended (Methanosarcina or Methanotrichaceae). -Methylotrophic-Methanogenesis @methylotroph "{""include_when"":{""all_columns_present"":[""taxonomy""]}}" Methane Production & Consumption Methane Production Methanogenesis from methylated substrates (methanol, methylamines, DMSP); McrA plus methyltransferase homologs (K04480, K14083, K16176, K16178, K25220, K16954, K25600, K25916, K26847). -Anaerobic-Methane-Oxidation-(ANME) @anaerobic-methanotrophic-Archaea "{""include_when"":{""all_columns_present"":[""taxonomy""]}}" Methane Production & Consumption Methane Oxidation Anaerobic oxidation of methane by ANME archaea; requires McrA with mandatory taxonomic filter for ANME genera. Taxonomy is essential to distinguish ANME from methanogens which share McrA. -Aerobic-Methane-Oxidation @AerobicMethanotroph Methane Production & Consumption Methane Oxidation Aerobic oxidation of methane via particulate methane monooxygenase (pMMO); HMMs cover diverse methanotroph lineages including Alphaproteobacteria, Gammaproteobacteria, NC10, Verrucomicrobia, and Actinobacteria. Relevant in oxic zones of engineered systems receiving methane inputs. -Fermentative-H2-(Fefe) FeFe_groupA | FeFe_groupB | FeFe_groupC | FeFe_groupE | FeFe_groupF Hydrogen Use FeFe Hydrogenases FeFe hydrogenases; primarily fermentative H2 production across all subgroups. Group A is the most common fermentative H2-producing hydrogenase; Group B is electron-bifurcating; Group C is putatively sensory; Groups E and F are found in anaerobic fungi and diverse anaerobes. All subgroups associated with anaerobic fermentative metabolism. -H2-Metabolism-Nife-Group-1 NiFe_group1 Hydrogen Use NiFe Hydrogenases NiFe group 1 hydrogenases; membrane-bound, predominantly H2 uptake linked to respiratory electron transport chain. Most characterized members are H2-consuming; functional inference for uncharacterized members is based on phylogeny. Key for cathodic depolarization MIC and energy conservation in H2-rich systems including underground hydrogen storage. -H2-Metabolism-Nife-Group-2 NiFe_group2 Hydrogen Use NiFe Hydrogenases NiFe group 2 hydrogenases; putative sensory/regulatory function detecting environmental H2 concentrations and regulating expression of other hydrogenases. Do not contribute directly to energy conservation. Functional characterization is limited relative to other NiFe groups. -H2-Metabolism-Nife-Group-3 NiFe_group3 Hydrogen Use NiFe Hydrogenases Cytoplasmic bidirectional NiFe hydrogenases capable of both H2 production and consumption depending on prevailing redox conditions. Involved in NADH and ferredoxin redox balancing during fermentation and anaerobic metabolism. The bidirectional nature means functional direction cannot be inferred from gene presence alone and is condition-dependent. -H2-Metabolism-Nife-Group-4 NiFe_group4 Hydrogen Use NiFe Hydrogenases Membrane-bound energy-conserving NiFe hydrogenases primarily involved in H2 evolution, coupled to ion pumping for energy conservation under anaerobic conditions. Found in strict anaerobes, acetogens, and methanogens. Relevant in anaerobic digesters, shale systems, and underground hydrogen storage where H2 production by microbial communities affects system chemistry and storage integrity. -Aerobic Ammonium Oxidation @AerobicAmmoniaOxidizer Nitrogen Cycling Nitrification+E27 Aerobic oxidation of ammonia to nitrite; first step of canonical two-step nitrification. Requires ammonia monooxygenase (amoA; K28504, K10945, K10946, or AmoA HMMs for beta/gammaproteobacterial and archaeal AOB) plus hydroxylamine oxidoreductase (hao; K10535). AmoA HMMs provide better phylogenetic resolution than K numbers alone. Excludes comammox Nitrospira which has a distinct AmoA lineage captured separately. -Aerobic Nitrite Oxidation @NitriteOxidoreductase Nitrogen Cycling Nitrification Aerobic oxidation of nitrite to nitrate; second step of nitrification via nitrite oxidoreductase (NXR). HMM-based detection is more specific than K number alone due to paralog confusion between NXR and NarGH. -Anammox @Annamox Nitrogen Cycling Anammox Anaerobic ammonium oxidation to dinitrogen gas. Requires nitrite reduction to NO (NirS K00368 or NirK K15864), hydrazine synthase complex (hzsA K20932, hzsB K20933, hzsC K20934 ‚Äö√Ñ√Æ all three required), and hydrazine dehydrogenase (hdh K20935). The HZS complex is essentially unique to anammox Planctomycetes making this a highly specific rule. -Comammox @Comammox Nitrogen Cycling Comammox Complete ammonia oxidation to nitrate by a single organism (comammox Nitrospira). Distinguished from canonical nitrification by the phylogenetically distinct comammox AmoA (amoa_Nitrospira_beta). Also requires nitrite oxidoreductase (nxr; K00370 or K00371) and hydrazine dehydrogenase (K20935) or equivalent. First predicted and confirmed in engineered systems including drinking water distribution systems, wastewater biofilters, and slow sand filters. -NO3 To NO2 @NarNitrateReductase | @NapNitrateReductase Nitrogen Cycling Denitrification First step of denitrification via membrane-bound nitrate reductase (NarGHI; NarG) or periplasmic nitrate reductase (NapAB; K02567, K02568). Also relevant in produced water injection systems where nitrate is added for souring control. -NO2 To NO @NitriteReductase Nitrogen Cycling Denitrification Second step of denitrification via NirS (cd1-type nitrite reductase; K00368) or NirK (copper-type nitrite reductase; K15864). -NO To N2O @NitricOxideReductase Nitrogen Cycling Denitrification Third step of denitrification via nitric oxide reductase ‚Äö√Ñ√Æ cNOR (K04561) or qNOR (K15877). -N2O To N2 @NitrousOxideReductase Nitrogen Cycling Denitrification Final step of complete denitrification via nitrous oxide reductase (nosZ; K00376). Presence indicates complete denitrification capacity. Absence with upstream denitrification genes present indicates N2O-producing incomplete denitrifier. -DNRA @DNRA Nitrogen Cycling DNRA Dissimilatory nitrate reduction to ammonium via nitrate reductase (NarGH K00370/K00371 or NapAB K02567/K02568) plus nitrite reductase (NrfAB K00362/K00363 or NirBD K03385/K15876). Competes with denitrification for nitrate; retains nitrogen in system rather than releasing N2. -Iron/Manganese/Selenium-Reduction @IronReduction Metals Metal Cycling Dissimilatory Fe(III), Mn(IV), and Se(VI) reduction via outer membrane cytochrome systems. The Mtr system (MtrCAB; Fe@MtrA, Fe@MtrB_TIGR03509, Fe@MtrC_TIGR03507) and Omc cytochromes (Fe@OmcS, Fe@OmcZ, Fe@OmcF) are the primary systems in Shewanella and Geobacter respectively. ExtABCD system found in other iron reducers. No unique diagnostic gene distinguishes Fe(III) from Mn(IV) or Se(VI) reduction ‚Äö√Ñ√Æ the same EET machinery reduces all three. HMMs from DRAM Fe@ database. -Iron-Oxidation @IronOxidation Metals Metal Cycling Ferrous iron oxidation for energy conservation. Cyc2 (outer membrane cytochrome, broad iron oxidizers; Fe@Cyc2), MtoAB (neutrophilic iron oxidizers; Fe@MtoA & Fe@MtoB), FoxEYZ (acidophilic iron oxidizers; Fe@FoxE & Fe@FoxY & Fe@FoxZ), PioA (photoferrotrophic iron oxidation; Fe@PioA). HMMs from FeGenie database. -Arsenate-Reduction-(Respiratory) K08355 & K08356 Metals Metal Cycling Respiratory arsenate reduction via the ArrAB complex (arrA K08355, arrB K08356); uses As(V) as terminal electron acceptor for anaerobic energy conservation. Distinct from detoxification arsenate reductase (arsC) which reduces As(V) to As(III) solely for efflux. Found in diverse anaerobes including Shewanella, Chrysiogenes, and Sulfurospirillum. Relevant in arsenic-rich subsurface and produced water systems. -Arsenite-Oxidation K08356 & K08355 Metals Metal Cycling Arsenite oxidase large subunit (aioA/aoxB; K08356) and small subunit (aioB/aoxA; K08355) oxidize As(III) to As(V). Can serve as lithotrophic energy conservation (electrons feed into quinone pool) or as detoxification. Both subunits required. Note: K08355 and K08356 are shared with respiratory arsenate reduction (arrAB) due to KEGG numbering ambiguity ‚Äö√Ñ√Æ interpret in genomic context. -Extracellular-Electron-Transfer-(Emic) [Fe@MtrA & Fe@MtrB_TIGR03509 & Fe@MtrC_TIGR03507] | Fe@OmcS | Fe@OmcZ Metals Metal Cycling Direct extracellular electron transfer (EET) from metal surface to microbial cell; primary mechanism of electrical MIC (EMIC). Mtr system (MtrCAB) in Shewanella requires all three subunits; OmcS and OmcZ are outer membrane cytochromes in Geobacter sufficient alone. Overlaps with Fe/Mn reduction rule ‚Äö√Ñ√Æ interpret in context of biofilm presence and metal surface contact. -Iron-Acquisition-(Ferrous,-Feo) [Fe@FeoB_N | Fe@FeoB_C | Fe@FeoB_Gate] & Fe@FeoA Metals Iron Acquisition Ferrous iron (Fe2+) uptake via the Feo system. FeoB_N, FeoB_C, FeoB_gate are domains of the same FeoB GTPase-gated membrane channel ‚Äö√Ñ√Æ any domain detection indicates FeoB presence. FeoA is the small accessory cytoplasmic protein required alongside FeoB. Primary Fe(II) uptake route under anaerobic/microaerobic conditions. HMMs from FeGenie. -Iron-Acquisition-(Ferric,-Fbp/Fut) at_least(2, PRESENCE, [[fbpA | FbpA-iron_binding_and_transport-rep], [fbpB | FbpB-FutB-iron_permease_fam1-rep], FbpC-iron_uptake_ATPase-rep]) | [FutC-iron_ABC_transporter_ATPase-rep & [FutA1-iron_ABC_transporter_iron-binding-rep | FutA2-iron_ABC_transporter_iron-binding-rep]] Metals Iron Acquisition Ferric iron (Fe3+) ABC transport systems. FbpABC (heterotrophic bacteria; requires at least 2 of 3 subunits for confident call). FutABC (cyanobacteria; requires ATPase FutC plus at least one substrate-binding protein FutA1 or FutA2). Relevant under oxic or iron-limited conditions. HMMs from FeGenie. -Arsenic-Resistance [arsC | K00537 | K03741] & [arsB | K03893 | acr3 | K03325] Metals Metal Detox Arsenate detoxification via arsenate reductase (arsC; K00537 glutaredoxin-type or K03741 thioredoxin-type) reducing As(V) to As(III), coupled with arsenite export via ArsB (K03893) or Acr3 (K03325) efflux pumps. ArsA ATPase (K01551) and ArsH (K11811) provide additional resistance capacity. Not respiratory ‚Äö√Ñ√Æ distinct from arrAB respiratory arsenate reduction in Metal Cycling. -Arsenic-Methylation K07755 Metals Metal Detox Arsenite S-adenosylmethionine methyltransferase (arsM; K07755) detoxifies arsenic via sequential methylation to organoarsenicals (monomethylarsenic, dimethylarsenic, trimethylarsine gas). Distinct detoxification strategy from efflux ‚Äö√Ñ√Æ volatilizes arsenic. Found in diverse bacteria and archaea including methanogens. -Copper-Resistance [copA | K17686 | copB | K01533 | [[cusA-ybdE | K07787] & [cusB | K07798] & [cusC-ylcB | K07796]]] & [cueO | K14588 | mco | K22552 | cusF-cusX | K07810] Metals Metal Detox Copper efflux via P-type ATPases (copA K17686 Cu+, copB K01533 Cu2+) or CusCBA RND efflux system (K07787, K07798, K07796) combined with periplasmic detoxification via cuproxidase CueO (K14588), multicopper oxidase Mco (K22552), or chaperone CusF (K07810). CopC (K07156) and CopD (K07245) are additional resistance proteins. -Mercury-Resistance [merA | K00520] & [merT | K08363 | merC | K19058 | merE | K19059 | merF] Metals Metal Detox Mercuric reductase (merA; K00520) reduces ionic Hg(II) to volatile Hg(0) requiring mercury import via MerT (K08363), MerC (K19058), MerE (K19059), or MerF. MerP (K08364) is a periplasmic Hg-binding protein. merB (K00221) additionally cleaves organomercury compounds. merR (K08365) and merD (K19057) are regulatory. Note merF lacks a confirmed K number ‚Äö√Ñ√Æ included in gene names only. -Chromate-Resistance K07240 | K19784 Metals Metal Detox Chromate efflux transporter (chrA; K07240) and chromate resistance protein (chrB; K19784). ChrA actively exports chromate from the cell. Relevant in industrial and mining-influenced systems with chromate contamination. -Cadmium/Zinc/Cobalt-Resistance at_least(2, PRESENCE, [czcA | K15726, czcB | K15727, czcC | K15725]) | [zntA-yhhO | K01534] | [zitB-ybgR | K16264] Metals Metal Detox Heavy metal efflux via CzcABC RND efflux system (K15726/K15727/K15725; at least 2 of 3 subunits required for metagenomic data) handling Cd/Zn/Co, ZntA P-type ATPase (K01534) for Zn/Cd export, or ZitB CDF transporter (K16264). CadX (K21903) and CzrB (K21133) are regulators. -Nickel/Cobalt-Resistance nrsA | K11326 | [rcnA-yohM | K08970] | K24079 | K24078 | [ctpD | K12951] Metals Metal Detox Nickel and cobalt efflux via NrsA (K11326), RcnA/NicO family (K08970), CnrY (K24079) and CnrR (K24078) of the CnrYXH/CnrCBA system, or CtpD P-type ATPase (K12951). Relevant in stainless steel corrosion environments and industrial bioreactors where nickel leaches from equipment. -Silver-Resistance silP | K23254 | silF | silE Metals Metal Detox Silver efflux via SilP P-type ATPase (K23254); SilF and SilE are periplasmic silver-binding proteins. K number only confirmed for silP; silF and silE lack confirmed K numbers. Relevant in engineered systems using silver-based antimicrobials. -Lead-Resistance pbrR | pbrT Metals Metal Detox Lead resistance via PbrR transcriptional regulator and PbrT Pb(II) membrane transporter. pbrR and pbrT lack confirmed K numbers in current KEGG ‚Äö√Ñ√Æ gene name identifiers used. Rule requires HMM development for reliable detection. -Acetate @Acetate-Final Fermentation End Products Organic Acids Acetate production via multiple fermentative routes: (1) oxidative decarboxylation of pyruvate to acetyl-CoA via pyruvate dehydrogenase (K00163, K00161, K00162), pyruvate ferredoxin oxidoreductase (K00174, K00175), or pyruvate formate lyase (K01568), followed by acetate release via acetate kinase/phosphotransacetylase (K01905, K22224, K24012); (2) direct aldehyde oxidation routes (K00138, K00128, K14085, K00149, K00129); or (3) acetyl-CoA hydrolysis (K01895, K01913). -Propionate @Propionate-Final Fermentation End Products Organic Acids Propionate production via three routes: (1) methylmalonyl-CoA pathway involving succinyl-CoA intermediates (K01899, K01900, K01902, K01903, K01847, K01849, K01848, K00140, K01895, K01908); (2) acrylate pathway via lactate (K01026, K20626, K20627, K00248, K00232); or (3) propionyl-CoA pathway (K01699, K13919, K13920, K13922). Key fermentation product and syntrophic substrate. -Butyrate @Butyrate-Final Fermentation End Products Organic Acids Butyrate production via multiple routes: (1) classical acetyl-CoA condensation pathway (K00626, K00074/K00022, K01692, K00209/K17829, K01034/K01035/K19709); (2) glutarate pathway (K00135/K08324/K00139/K17761, K00043/K08318/K18120/K18121, K18122, K14534); (3) lysine pathway (K01580, K13524/K07250/K14268/K00823/K16871); or (4) 4-aminobutyrate pathway (K01843). -Lactate @Lactate-Final Fermentation End Products Organic Acids Lactate production via three routes: (1) complete glycolytic route followed by lactate dehydrogenase (K00016); (2) lactate dehydrogenase alone (K00016) as minimal call; or (3) PTS sugar system route (K18124/K18125/K00115/K19813/K00117 & K01053 & K05308 & K11395/K18127 & K00016). Lactate is a primary fermentation product in Firmicutes and relevant as MIC organic acid, SRB substrate, and electron donor. -Formate K00656 | @FormateDehydrogenase_1 | @FormateDehydrogenase_2 | @FormateDehydrogenase_3 | @FormateDehydrogenase_4 | @FormateDehydrogenase_5 Fermentation End Products Organic Acids Formate production via pyruvate formate lyase (PFL; K00656) cleaving pyruvate to formate and acetyl-CoA under strictly anaerobic conditions, or via formate dehydrogenase ‚Äö√Ñ√Æ FDH-N subunits (K00122, K00123; both required) or FDH-H subunits (K00124, K00125, K00126; at least 2 required). Formate is a key interspecies electron/H2 carrier in syntrophic systems. -Succinate [K00244 | K00245] & [K00246 | K00247] Fermentation End Products Organic Acids Succinate production via fumarate reductase ‚Äö√Ñ√Æ catalytic subunits frdA/frdB (K00244, K00245) plus membrane anchor subunits frdC/frdD (K00246, K00247). Note fumarate reductase is also involved in other metabolisms beyond succinate production; interpret in context of broader fermentative metabolism. -Butanol [K00100 | K00544] & [K00634 & [K00929 | K01896]] Fermentation End Products Alcohols Butanol production via ABE fermentation pathway; requires butyryl-CoA formation (thiolase K00634 plus butyryl-CoA acetyltransferase K00929 or K01896) followed by reduction to butanol via butanol dehydrogenase (bdh; K00100) or NADH-dependent butanol dehydrogenase (K00544). Butyryl-CoA intermediate shared with butyrate pathway. Found predominantly in Clostridia. -Rhamnose @Rhamnose Carbon Transformations saccharide -Mannose @Mannose Carbon Transformations saccharide -Glucose @Glucose Carbon Transformations saccharide -Galactose @Galactose Carbon Transformations saccharide -Fucose @Fucose Carbon Transformations saccharide -Fructose @Fructose Carbon Transformations saccharide -Arabinose @Arabinose Carbon Transformations saccharide -Xylose @Xylose Carbon Transformations saccharide -Starch/Glycogen @StarchGlycogen Carbon Transformations polymer -Microbially-derived @Microbially-derived Carbon Transformations polymer -Hemicellulose @Hemicellulose Carbon Transformations polymer -Galactomannan (e.g., Guar-Gum) GH5;EC:3.2.1.78 | GH27;EC:3.2.1.22 | GH36;EC:3.2.1.22 Carbon Transformations polymer -Cellulose @Cellulose Carbon Transformations polymer -Protocatechuic-Acid [at_least(1, PRESENCE, [K04100,K04101]) & at_least(2, PRESENCE, [K10219, EC:1.1.1.312, K10221, K10220, K16515, K10218, K16514 ])] | [at_least(1, PRESENCE, [K00448,EC:1.13.11.3, K00449]) & at_least(2, PRESENCE, [K01607, EC:4.1.1.44, K01857, EC:5.5.1.2, K01055, EC:3.1.1.24, K01031])] Carbon Transformations oxygenated-aromatic -Catechol [[K03381|EC:1.13.11.1] & at_least(2, PRESENCE, [K01856, EC:5.5.1.1,K03464,EC:5.3.3.4,K01055,EC:3.1.1.24,K01031])] | [at_least(1, PRESENCE, [K00446,K07104]) & [K10216 | at_least(1, PRESENCE, [K10217,K01617,K01821]) ] & at_least(1, PRESENCE, [K02554,K01666,K18364,K18365])] Carbon Transformations oxygenated-aromatic -4-Methoxybenzoate K22553 Carbon Transformations oxygenated-aromatic -4-Hydroxybenzoate [K00481|EC:1.14.13.2|K04105|K20458|EC:6.2.1.27|EC:6.2.1.25|K04107|EC:1.1.7.11|K04108|K04109] Carbon Transformations oxygenated-aromatic -Cellobiose @Cellobiose Carbon Transformations oligosaccharide -Trehalose @Trehalose Carbon Transformations disaccharide -Maltose @Maltose Carbon Transformations disaccharide -Lactose @Lactose Carbon Transformations disaccharide -Sucrose @Sucrose Carbon Transformations disaccharide -Pah-Anaerobic NmsA Carbon Transformations hydrocarbons -Pah-Aerobic NdoB|NdoC|non_NdoB_type|K27540 Carbon Transformations hydrocarbons -Aromatic-Btex-Anaerobic AbcA_1|AbcA_2|EbdA|CmdA|BssA Carbon Transformations hydrocarbons -Aromatic-Btex-Aerobic TmoA_BmoA|TmoB_BmoB|TmoE|TomA1|TomA3|TomA4|DmpO|MAH_alpha|MAH_beta Carbon Transformations hydrocarbons -Alkane-Anaerobic AssA Carbon Transformations hydrocarbons -Alkane-Aerobic-Short-Chain pBmoA|pBmoB|pBmoC|sBmoX|sBmoY|sBmoZ|PrmA|PrmC Carbon Transformations hydrocarbons -Alkane-Aerobic-Med/Long-Chain AlkB|AlmA_GroupI|AlmA_GroupIII|CYP153|LadA_alpha|LadA_beta|LadB Carbon Transformations hydrocarbons -Methanol @Methanol Carbon Transformations LMWC -Ethanol/Alcohol @Ethanol Carbon Transformations LMWC -Ethylene-Glycol-Degradation [K00001 | K00121] & [K14085 | K00128 | K00149] Carbon Transformations LMWC Ethylene glycol degradation via glycolate oxidase (K11472) or diol dehydratase (K18394) for initial oxidation, followed by alcohol dehydrogenase (K00001, K00121) and aldehyde dehydrogenase (K14085, K00128, K00149). Ethylene glycol is used as antifreeze in pipelines and gas processing facilities. Note: K11472 and K18394 removed per curation. -Eps-Production K16566 | K16557 | K16556 | K16555 | K19290 | K19291 | K19293 | K19294 | K19295 | K19296 | K11936 | K11937 | K20997 | K21001 | K21154 | K25902 | K25904 | K25906 | K25205 | K21461 Biofilms & Attachment EPS Exopolysaccharide biosynthesis and biofilm matrix structural genes including alginate biosynthesis (alg genes; K16566, K16557, K16556, K16555), Psl polysaccharide biosynthesis (K19290-K19296), PGA/ICA poly-GlcNAc synthesis (pgaABCD/icaABCD; K11936, K11937), and additional EPS biosynthesis genes. Any single gene indicates EPS production capacity. Drives pipeline fouling and MIC in engineered systems. -Quorum-Sensing [[K13060 | K13061] & [K18304 | K18099]] | K07173 | at_least(2, PRESENCE, [K10555, K10556, K10557, K10558]) Biofilms & Attachment Quorum Sensing Quorum sensing via three systems: (1) AHL/LuxI-LuxR: LuxI-type AHL synthases lasI (K13060) or rhlI/cepI/tofI homologs (K13061) paired with LuxR-type receptors lasR (K18304) or rhlR homologs (K18099) ‚Äö√Ñ√Æ both synthase and receptor required; (2) AI-2/LuxS system: LuxS S-ribosylhomocysteine lyase (K07173) ‚Äö√Ñ√Æ widely conserved but interpret alone cautiously as it has metabolic roles beyond QS; (3) AI-2 import via Lsr ABC transporter: LsrB substrate-binding (K10555), LsrC permease (K10556), LsrD permease (K10557), LsrA ATPase (K10558) ‚Äö√Ñ√Æ at least 2 subunits required ‚Äö√Ñ√Æ indicates active AI-2 uptake and response capacity. -Motility [K02410 | K02411] & at_least(3, PRESENCE, [K02406, K02407, K02400, K02408, K02409, K02412, K02416, K02417, K02386, K02387, K02391, K02393, K02404, K02405]) Biofilms & Attachment Motility Flagellar motor (MotA K02410 or MotB K02411; at least one required) plus at least 3 structural/assembly genes from the flagellar complex. Required for surface approach and early biofilm attachment. Also relevant for chemotaxis toward carbon/electron donor sources in engineered systems. -Salt-In-Strategy-(K+-Accumulation) [K01546 | K01547 | K01548] | [K05565 & at_least(3, PRESENCE, [K05566, K05567, K05568, K05569, K05570, K05571])] | [K03315 | K07084] | at_least(2, PRESENCE, [K05559, K05560, K05561, K05562, K05563, K05564]) | [K03499 & K03498] Environmental Stress Response Osmoregulation Halophilic salt-in osmoadaptation via K+ accumulation and Na+ exclusion. KdpABC P-type ATPase (K01546-K01548) imports K+; KdpDE (K07646, K07667) sensor-regulator. Mrp/Mnh Na+:H+ antiporter (K05565-K05571; Mrp subunit K05565 required plus at least 3 others). PhaABCDEFG K+ transporter (K05559-K05564; at least 2 of 6). TrkA/TrkH constitutive K+ uptake (K03499 & K03498; both required). NhaC Na+:H+ antiporter (K03315 or K07084). Highly relevant in hypersaline produced waters (TDS >200 g/L). -Compatible-Solutes:-Methylated-(Synthesis) [[K00108 | K11440] & K00130] | [K18896 & K18897] Environmental Stress Response Osmoregulation Glycine betaine biosynthesis via two routes: (1) choline oxidation pathway ‚Äö√Ñ√Æ choline dehydrogenase (betA; K00108 or K11440) AND betaine-aldehyde dehydrogenase (betB; K00130); or (2) sequential N-methylation of glycine ‚Äö√Ñ√Æ glycine/sarcosine methyltransferase (K18896) AND sarcosine/dimethylglycine methyltransferase (K18897). -Compatible-Solutes:-Ectoine-(Synthesis) K06718 & K00836 & K06720 Environmental Stress Response Osmoregulation Ectoine biosynthesis via complete ectABC pathway: diaminobutyrate acetyltransferase (ectA; K06718), diaminobutyrate aminotransferase (ectB; K00836), ectoine synthase (ectC; K06720) ‚Äö√Ñ√Æ all three required. Ectoine hydroxylase (ectD; K10674) additionally produces hydroxyectoine with enhanced thermostability. Major compatible solute in halophilic bacteria. -Compatible-Solutes:-Sugars-(Synthesis) [K00697 & K01087] | K06044 | K01236 | K05342 | K05343 | K05947 | K00009 Environmental Stress Response Osmoregulation Biosynthesis of sugar-derived compatible solutes. Trehalose: OtsAB (K00697 & K01087; both required), TreYZ (K06044 or K01236), TreS (K05343), TreP (K05342). Mannosylglycerate: mpgSP (K05947). Mannitol: mtlD (K00009). Note K05342 and K05343 overlap with Trehalose Use row in Carbon Degradation. -Compatible-Solutes:-Methylated-(Transport) K02168 | K03451 | K05245 | K03762 | K05020 | [K02000 & K02001 & K02002] | at_least(2, PRESENCE, [K05845, K05846, K05847]) | at_least(2, PRESENCE, [K10036, K10037, K10038]) Environmental Stress Response Osmoregulation Transport of glycine betaine, choline, proline, and related methylated osmoprotectants. BetP/T/S BCCT transporter (K02168), carnitine/betaine antiporter (K05245), OpuD betaine transporter (K05020). ProVWX ABC transporter (K02000 & K02001 & K02002; all three required). OpuABC (K05845, K05846, K05847; at least 2 subunits). Glutamine ABC (K10036, K10037, K10038; at least 2 subunits). ProP MFS transporter (K03762); ProQ effector (K03607). -Compatible-Solutes:-Ectoine-(Transport) at_least(2, PRESENCE, [K02028, K02029, K02030]) Environmental Stress Response Osmoregulation Ectoine/hydroxyectoine uptake via EhuABC ABC transporter (EhuA ATPase K02028, EhuC/D permease K02029, EhuB substrate-binding protein K02030). At least 2 of 3 subunits required for metagenomic data. Organisms with transport but not synthesis genes are ectoine scavengers. -Compatible-Solutes:-Sugars-(Transport) at_least(2, PRESENCE, [K10227, K10228, K10229, K10230]) | at_least(2, PRESENCE, [K02783, K02781, K02782]) | K02798 | at_least(2, PRESENCE, [K10109, K10110, K10111]) | K17314 Environmental Stress Response Osmoregulation Sugar osmoprotectant transport. SmoEF ABC system (K10227-K10230; at least 2 subunits), SrlABE PTS (K02783, K02781, K02782; at least 2 subunits), mannitol PTS (mtlA; K02798). Trehalose: dedicated transporter (K17314) or maltose/trehalose ABC (K10109-K10111; at least 2 subunits). Organisms with transport but not synthesis genes scavenge solutes from environment. -Beta-Lactam-Resistance K18698 | K18699 | K18796 | K18767 | K18797 | K19097 | K19317 | K18768 | K18970 | K19316 | K22346 | K18795 | K19218 | K19217 | K18790 | K18791 | K19098 | K18792 | K19213 | K21276 | K18793 | K18971 | K22352 | K19209 Environmental Stress Response Antibiotic Resistance Beta-lactamase and penicillin-binding protein resistance genes conferring resistance to beta-lactam antibiotics (penicillins, cephalosporins, carbapenems). Major antibiotic resistance gene class in environmental microbiomes. -Macrolide-Resistance K00561 | K14336 | K15632 | K18230 | K18231 | K19349 | K19350 | K18232 | K19541 | K08217 Environmental Stress Response Antibiotic Resistance Macrolide resistance via efflux pumps, ribosomal methylases (erm genes), or macrolide esterases. -Tetracycline-Resistance K08151 | K08168 | K18214 | K18215 | K18218 | K18216 | K18217 | K19542 | K18233 | K18220 | K18221 Environmental Stress Response Antibiotic Resistance Tetracycline resistance via efflux pumps (tet efflux genes) or ribosomal protection proteins. -Sulfonamide-Resistance K18974 | K18824 | K18825 Environmental Stress Response Antibiotic Resistance Sulfonamide resistance via dihydropteroate synthase variants (sul1, sul2, sul3) insensitive to sulfonamide inhibition. Among the most commonly detected antibiotic resistance genes in wastewater and water treatment systems. -Biocide-Efflux-(General) K03585 | K18138 | [K18324 | 2.A.6.2.7_P24177] | [K18142 | 2.A.6.2.2_P31224] | [K03297 | 2.A.7.1] | [[K11814 | 2.A.7.1.6] & [K11815 | 2.A.7.1.6]] | [K18975 | 2.A.7.1.11] Environmental Stress Response Biocide Resistance Broad-spectrum efflux genes for biocide and multidrug resistance. MexA/membrane fusion protein (K03585), MATE efflux (K03400), MexB/RND pump (K18138), AcrD/RND pump (K18324), AcrF/RND pump (K18142), and SMR family pumps: Mmr (K03297), EbrA/EbrB paired SMR pump (K11814 & K11815), Ebr SMR pump (K18975). Aldehyde dehydrogenase (K14085) provides chemical detoxification capacity. RND pumps (2.A.6 TCDB family) provide broad substrate efflux relevant in oil and gas and wastewater systems. General row is superset of Aldehyde Resistance sub-row. -Aldehyde-Resistance K00149 | K14085 Environmental Stress Response Biocide Resistance Resistance to aldehyde biocides (e.g., glutaraldehyde, formaldehyde) mediated by aldehyde oxidoreductases and aldehyde:ferredoxin oxidoreductases (K00149, K14085), which detoxify reactive aldehyde compounds. -Qac-Resistance K08167 | K11741 Environmental Stress Response Biocide Resistance Resistance to quaternary ammonium compound (QAC) disinfectants mediated by multidrug efflux transporters (K08167, K11741) that export toxic biocides from the cell. -Oxidative-Stress-Resistance K04564|K04565|K04569|K03781|K03782|K24119|K03387|K04761|K13639|K13631|K00383|K01919|K03671|K00384|K03672|K10563|K03575|K03553|K04047|K03594|K02217|K03674|K03675|K03676|K07304|K07305|K04063|K11065|K03564|K00036|K00033|K00324|K00325|K19824|K04487|K05997|K09014|K09013|K09015|K11717|K02426|K03087|K03711|K13643|K01338|K04043|K05919|K01759|K00799|K01069|K10773|K10567|K03574|K01151|K03584|K01142|K09825|K23775|K04084|K01920 Environmental Stress Response Biocide Resistance Presence of oxidative stress response genes indicates microbial potential to detoxify reactive oxygen species through catalase‚Äö√Ñ√¨peroxidase, superoxide dismutase, glutathione biosynthesis, NADH peroxidase, or related genes/proteins, supporting survival under oxidative stress. +name rule rule_options module group notes +Calvin Cycle @Calvin Carbon Transformations Carbon Fixation +Hydroxypropionate-Hydroxybutyrate Cycle @HydroxypropionateHydroxybutylate Carbon Transformations Carbon Fixation +Dicarboxylate Hydroxybutyrate Cycle @DicarboxylateHydroxybutyrate Carbon Transformations Carbon Fixation +Wood–Ljungdahl Pathway @ReductiveAcetylCoAWoodLjungdahl Carbon Transformations Carbon Fixation +PAH – Anaerobic NmsA Carbon Transformations Hydrocarbon +PAH – Aerobic NdoB|NdoC|non_NdoB_type|K27540 Carbon Transformations Hydrocarbon +BTEX – Anaerobic AbcA_1|AbcA_2|EbdA|CmdA|BssA Carbon Transformations Hydrocarbon +BTEX – Aerobic TmoA_BmoA|TmoB_BmoB|TmoE|TomA1|TomA3|TomA4|DmpO|MAH_alpha|MAH_beta Carbon Transformations Hydrocarbon +Alkane – Anaerobic AssA Carbon Transformations Hydrocarbon +Alkane Long-Chain – Aerobic AlkB|AlmA_GroupI|AlmA_GroupIII|CYP153|LadA_alpha|LadA_beta|LadB Carbon Transformations Hydrocarbon +Alkane Short-Chain – Aerobic pBmoA|pBmoB|pBmoC|sBmoX|sBmoY|sBmoZ|PrmA|PrmC Carbon Transformations Hydrocarbon +Flavones at_least(2, PRESENCE, [D00001,K26178,D00003,K26177,EC:5.5.1.6,D00006,K22906,EC:3.7.1.4,D00009,K26176]) Carbon Transformations Oxygenated Aromatic +Ferulic-Acid at_least(1, PRESENCE, [D00038,K12508,EC:6.2.1.34,K18383]) Carbon Transformations Oxygenated Aromatic +Caffeic-Acid at_least(2, PRESENCE, [D00014,K22432,D00015,K22431,D00016,K22430,EC:1.3.1.108,D00017,D00018]) Carbon Transformations Oxygenated Aromatic +Syringate K15064 Carbon Transformations Oxygenated Aromatic +Vanillate K03862|K03863|K15066 Carbon Transformations Oxygenated Aromatic +Gallic-Acid at_least(2, PRESENCE, [K22958, K22959, K22960]) Carbon Transformations Oxygenated Aromatic +Coumarate D00039 Carbon Transformations Oxygenated Aromatic +Protocatechuic-Acid [at_least(1, PRESENCE, [K04100,K04101]) & at_least(2, PRESENCE, [K10219, EC:1.1.1.312, K10221, K10220, K16515, K10218, K16514 ])] | [at_least(1, PRESENCE, [K00448,EC:1.13.11.3, K00449]) & at_least(2, PRESENCE, [K01607, EC:4.1.1.44, K01857, EC:5.5.1.2, K01055, EC:3.1.1.24, K01031])] Carbon Transformations Oxygenated Aromatic +4-Methoxybenzoate K22553 Carbon Transformations Oxygenated Aromatic +4-Hydroxybenzoate [K00481|EC:1.14.13.2|K04105|K20458|EC:6.2.1.27|EC:6.2.1.25|K04107|EC:1.1.7.11|K04108|K04109] Carbon Transformations Oxygenated Aromatic +Catechol [[K03381|EC:1.13.11.1] & at_least(2, PRESENCE, [K01856, EC:5.5.1.1,K03464,EC:5.3.3.4,K01055,EC:3.1.1.24,K01031])] | [at_least(1, PRESENCE, [K00446,K07104]) & [K10216 | at_least(1, PRESENCE, [K10217,K01617,K01821]) ] & at_least(1, PRESENCE, [K02554,K01666,K18364,K18365])] Carbon Transformations Oxygenated Aromatic +Cellulose @Cellulose Carbon Transformations Polysaccharides +Hemicellulose @Hemicellulose-Xylan | @Hemicellulose-Other Carbon Transformations Polysaccharides +Galactomannan (e.g., Guar-Gum) GH5;EC:3.2.1.78 | GH27;EC:3.2.1.22 | GH36;EC:3.2.1.22 Carbon Transformations Polysaccharides +Xylan or Xylobiose (mixed size) @XylanXylobiose Carbon Transformations Polysaccharides +Pectin @Pectin Carbon Transformations Polysaccharides +Multiple Plant Polysaccharides @PlantPolymerMixed Carbon Transformations Polysaccharides can act on multiple plant polymers of hemicellulose, pectin, and cellulose +Starch/Glycogen @StarchGlycogen Carbon Transformations Polysaccharides +Chitin @Chitin Carbon Transformations Polysaccharides +Cellulose-Associated @BetaGlucosides Carbon Transformations Oligosaccharide β-Glucoside hydrolysis; may support cellulose-derived oligosaccharide utilization +Hemicellulose-Associated @Xylooligosaccharides | @XyloglucanMannooligosaccharides Carbon Transformations Oligosaccharide xylooligosaccharides and xyloglucan- or mannan-related oligosaccharides, potentially supporting hemicellulose-derived carbohydrate utilization. +Pectin-Associated @PecticOligosaccharides Carbon Transformations Oligosaccharide pectic oligosaccharides, potentially supporting utilization of pectin breakdown products. +Starch/Glycogen Associated @MaltooligosaccharidesAlphaGlucosides Carbon Transformations Oligosaccharide maltooligosaccharides and α-glucosides, potentially supporting utilization of starch- or glycogen-derived carbohydrates. +Chitin-Associated @Chitooligosaccharides | @NAcetylhexosaminides Carbon Transformations Oligosaccharide chitooligosaccharides and N-acetylhexosaminides, potentially supporting chitin-derived carbohydrate utilization. N-acetylhexosaminides may also originate from other glycoconjugates. +Other oligosaccharides @OtherGlycosidesOligosaccharides | @OligosaccharideOxidation | @Fructooligosaccharides Carbon Transformations Oligosaccharide Diverse glycoside and oligosaccharide transformations, including fructooligosaccharide utilization and oligosaccharide oxidation, that are not assigned to a single major polymer-associated group. +Cellobiose @Cellobiose Carbon Transformations Oligosaccharide Glucose disaccharide produced during cellulose breakdown; utilization does not imply direct cellulose degradation. +Maltose @Maltose Carbon Transformations Oligosaccharide Glucose disaccharide associated with starch and glycogen breakdown. +Sucrose @Sucrose Carbon Transformations Oligosaccharide Glucose–fructose disaccharide commonly found in plants; important for carbon transport and storage. +Trehalose @Trehalose Carbon Transformations Oligosaccharide Glucose disaccharide used for carbon storage and stress protection in many organisms. +Lactose @Lactose Carbon Transformations Oligosaccharide Galactose–glucose disaccharide; utilization indicates potential to process lactose or related β-galactosides. +Mannobiose or Mannose (mixed size) @Mannose-Mannobiose Carbon Transformations Oligosaccharide Mannose-containing carbohydrates associated with mannan and other glycans; calls may represent monosaccharide or disaccharide processing. +Glucose @Glucose Carbon Transformations Monosaccharide Central hexose used in carbohydrate metabolism. +Xylose @Xylose Carbon Transformations Monosaccharide Pentose commonly derived from xylan and other plant polysaccharides. +Arabinose @Arabinose Carbon Transformations Monosaccharide Pentose commonly found in plant cell-wall polysaccharides, including hemicellulose (e.g., arabinoxylan), arabinan, and pectin. +Mannose @Mannose Carbon Transformations Monosaccharide Hexose commonly found in plant cell-wall polysaccharides, including hemicellulose and pectin, as well as diverse glycoconjugates +Galactose @Galactose Carbon Transformations Monosaccharide Hexose found in plant cell-wall polysaccharides, including pectin (galactans) and some hemicelluloses, as well as other glycans. +Fructose @Fructose Carbon Transformations Monosaccharide Hexose found in sucrose and fructans (e.g., inulin and levan), as well as other carbohydrates. +Rhamnose @Rhamnose Carbon Transformations Monosaccharide Deoxyhexose commonly found in pectin (rhamnogalacturonans) and microbial polysaccharides. +N-Acetylglucosamine (Glc-NAc) @N-Acetylglucosamine Carbon Transformations Monosaccharide Amino sugar found in chitin (fungal cell walls), bacterial peptidoglycan, and other glycoconjugates. +SCFA-Propionate @Propionate-Final Carbon Transformations Low Molecular Weight Carbon +SCFA-Butyrate @Butyrate-Final Carbon Transformations Low Molecular Weight Carbon +SCFA-Acetate @Acetate-Final Carbon Transformations Low Molecular Weight Carbon +Succinate [K00244 | K00245] & [K00246 | K00247] Carbon Transformations Low Molecular Weight Carbon Succinate production via fumarate reductase — catalytic subunits frdA/frdB (K00244, K00245) plus membrane anchor subunits frdC/frdD (K00246, K00247). Note fumarate reductase is also involved in other metabolisms beyond succinate production; interpret in context of broader fermentative metabolism. +Oxalate K01577 | K07749 Carbon Transformations Low Molecular Weight Carbon +Formate K00656 Carbon Transformations Low Molecular Weight Carbon +Methanol @Methanol Carbon Transformations Low Molecular Weight Carbon +Ethanol/Alcohol @Ethanol Carbon Transformations Low Molecular Weight Carbon +Butanol [K00100 | K00544] & [K00634 & [K00929 | K01896]] Carbon Transformations Low Molecular Weight Carbon Butanol production via ABE fermentation pathway; requires butyryl-CoA formation (thiolase K00634 plus butyryl-CoA acetyltransferase K00929 or K01896) followed by reduction to butanol via butanol dehydrogenase (bdh; K00100) or NADH-dependent butanol dehydrogenase (K00544). Butyryl-CoA intermediate shared with butyrate pathway. Found predominantly in Clostridia. +Ethylene-Glycol-Degradation [K00001 | K00121] & [K14085 | K00128 | K00149] Carbon Transformations Low Molecular Weight Carbon Ethylene glycol degradation via glycolate oxidase (K11472) or diol dehydratase (K18394) for initial oxidation, followed by alcohol dehydrogenase (K00001, K00121) and aldehyde dehydrogenase (K14085, K00128, K00149). Ethylene glycol is used as antifreeze in pipelines and gas processing facilities. Note: K11472 and K18394 removed per curation. +Oxygen - Low Affinity Use [percent(50,@CytochromeCOxidase)|percent(50,@CytochromeAa3600MenaquinolOxidase)|percent(50,@CytochromeOUbiquinolOxidase)] Respiratory Redox Processes Oxygen Reduction +Oxygen - High Affinity Use [@percent50CytochromeBDUbiquinolOxidase|@percent50CytochromeCOxidaseCBB3] Respiratory Redox Processes Oxygen Reduction +NO3 To NO2 @NarNitrateReductase|[@NapNitrateReductase] Respiratory Redox Processes Nitrogen Reduction +NO2 To NO @NitriteReductase Respiratory Redox Processes Nitrogen Reduction +NO To N2O @NitricOxideReductase Respiratory Redox Processes Nitrogen Reduction +N2O To N2 @NitrousOxideReductase Respiratory Redox Processes Nitrogen Reduction +DNRA, NO3 To NH4 @DNRA Respiratory Redox Processes Nitrogen Reduction +DNRA NrfA only, NO2 To NH4 @nrfA Respiratory Redox Processes Nitrogen Reduction +Aerobic Ammonium Oxidation @AerobicAmmoniaOxidizer Respiratory Redox Processes Nitrogen Oxidation +Aerobic Nitrite Oxidation @NitriteOxidoreductase Respiratory Redox Processes Nitrogen Oxidation +Anaerobic Ammonia Oxidation Anammox @Annamox Respiratory Redox Processes Nitrogen Oxidation +Complete Ammonia Oxidation Comammox @Comammox Respiratory Redox Processes Nitrogen Oxidation +Iron Oxidation @IronOxidation Respiratory Redox Processes Dissimilatory Metal Reduction and Oxidation Ferrous iron oxidation for energy conservation. Cyc2 (outer membrane cytochrome, broad iron oxidizers; Fe@Cyc2), MtoAB (neutrophilic iron oxidizers; Fe@MtoA & Fe@MtoB), FoxEYZ (acidophilic iron oxidizers; Fe@FoxE & Fe@FoxY & Fe@FoxZ), PioA (photoferrotrophic iron oxidation; Fe@PioA). HMMs from FeGenie database. +Iron/Manganese/Selenium-Reduction @IronReduction Respiratory Redox Processes Dissimilatory Metal Reduction and Oxidation Dissimilatory Fe(III), Mn(IV), and potentially Se(VI) reduction via extracellular electron transfer (EET) systems, including MtrCAB in Shewanella (Fe@MtrA, Fe@MtrB_TIGR03509, Fe@MtrC_TIGR03507), Omc cytochromes in Geobacter (Fe@OmcS, Fe@OmcZ, Fe@OmcF), and ExtABCD in other iron reducers. These systems are not substrate-specific markers, so their presence does not distinguish Fe(III), Mn(IV), or Se(VI) reduction. HMMs from the DRAM Fe@ database +Arsenate Reduction @RespiratoryArsenateReduction Respiratory Redox Processes Dissimilatory Metal Reduction and Oxidation ArrAB-mediated dissimilatory arsenate reduction using As(V) as a terminal electron acceptor for anaerobic respiration +Selenate Reduction @SelenateReductionSrd Respiratory Redox Processes Dissimilatory Metal Reduction and Oxidation SrdABC-mediated dissimilatory selenate reduction using Se(VI) as a terminal electron acceptor for anaerobic respiration +Possible Selenate or Chlorate Reduction @PossibleSelenateReduction Respiratory Redox Processes Dissimilatory Metal Reduction and Oxidation Selenate/chlorate reductase (SerABC/ClrABC; K17050, K17051, K17052) — cannot distinguish selenate from chlorate reduction based on these KOs alone +Sulfur Oxidation @sulfateoxidizer Respiratory Redox Processes Sulfur Reduction and Oxidation +Sulfate Reduction @Sulfatereducer Respiratory Redox Processes Sulfur Reduction and Oxidation +Elemntal Sulfur Reduction @ElementalSRed Respiratory Redox Processes Sulfur Reduction and Oxidation +Thiosulfate-Reduction-(Respiratory) @ThiosulfateRed Respiratory Redox Processes Sulfur Reduction and Oxidation +Thiosulfate-Reduction-(Rhodanese) K01011 | Rhodanese Respiratory Redox Processes Sulfur Reduction and Oxidation +Tetrathionate-Reduction @TetrathionateRed Respiratory Redox Processes Sulfur Reduction and Oxidation +Hydrogenotrophic @hydrogenotrophic Respiratory Redox Processes Methane Production and Oxidation For a few genome to encode potential to oxidize carbon monoxide, it must encode either the aerobic or anaerobic carbon monoxide dehydrogenase and it anaerobic, NOT be an acetogen/use the Wood Ljungdahl pathway +Acetoclastic @acetoclastic Respiratory Redox Processes Methane Production and Oxidation For a genome to have hydrogneotrophic methanogenesis potential, it must encode mcrA, at least 4 genes of the methyl branch of the Wood-lungdahl pathway, part of the MTR complex, and at least one gene for any known hydrgenotrophic hdyrogenase. +Methylotrophic @methylotroph Respiratory Redox Processes Methane Production and Oxidation For a genome to have acetoclastic methanogenesis potential, it must encode mcrA, part of the ACS_CODH complex, and either Acetate Kinase and Phosphotransacetylase OR Acetyl CoA Synthetase. There is a MANDATORY taxonomic requirement for this rule to run, and a MAG or genome must also belong to the genus Methanosarcina or the family Methanotrichaceae +Aerobic Methanotroph @AerobicMethanotroph Respiratory Redox Processes Methane Production and Oxidation "For a genome to have methyltotrophic methanogenesis potential, it must encode mcrA and at least one substrate-demethylating corrinoid-dependent methyltransferase homolog ""MtxB""" +Methanogen Or ANME @Methanogen Respiratory Redox Processes Methane Production and Oxidation A genome that encodes adenylysulfate reductase and dissimilatory sulfite reductase +Anaerobic Oxidation of Methane @anaerobic-methanotrophic-Archaea Respiratory Redox Processes Methane Production and Oxidation For a genome to have CH₄ oxidation capability, it must encode at least one methane monooxygenase complex pMMO or sMMO, which catalyzes the conversion of methane to methanol — the key diagnostic step of methanotrophy in soils. It must also encode any genes for denitrifcation narG, napA, nirK, nirS, norB +Phototroph @PhototrophAllTypes Other Metabolic Traits Other Metabolic Traits +Possible Obligate Fermenter @Fermenter Other Metabolic Traits Other Metabolic Traits +Fermentative-H2-(Fefe) FeFe_groupA | FeFe_groupB | FeFe_groupC | FeFe_groupE | FeFe_groupF Other Metabolic Traits Other Metabolic Traits FeFe hydrogenases; primarily fermentative H2 production across all subgroups. Group A is the most common fermentative H2-producing hydrogenase; Group B is electron-bifurcating; Group C is putatively sensory; Groups E and F are found in anaerobic fungi and diverse anaerobes. All subgroups associated with anaerobic fermentative metabolism. +H2-Metabolism-Nife-Group-1 NiFe_group1 Other Metabolic Traits Other Metabolic Traits NiFe group 1 hydrogenases; membrane-bound, predominantly H2 uptake linked to respiratory electron transport chain. Most characterized members are H2-consuming; functional inference for uncharacterized members is based on phylogeny. Key for cathodic depolarization MIC and energy conservation in H2-rich systems including underground hydrogen storage. +H2-Metabolism-Nife-Group-2 NiFe_group2 Other Metabolic Traits Other Metabolic Traits NiFe group 2 hydrogenases; putative sensory/regulatory function detecting environmental H2 concentrations and regulating expression of other hydrogenases. Do not contribute directly to energy conservation. Functional characterization is limited relative to other NiFe groups. +H2-Metabolism-Nife-Group-3 NiFe_group3 Other Metabolic Traits Other Metabolic Traits Cytoplasmic bidirectional NiFe hydrogenases capable of both H2 production and consumption depending on prevailing redox conditions. Involved in NADH and ferredoxin redox balancing during fermentation and anaerobic metabolism. The bidirectional nature means functional direction cannot be inferred from gene presence alone and is condition-dependent. +H2-Metabolism-Nife-Group-4 NiFe_group4 Other Metabolic Traits Other Metabolic Traits Membrane-bound energy-conserving NiFe hydrogenases primarily involved in H2 evolution, coupled to ion pumping for energy conservation under anaerobic conditions. Found in strict anaerobes, acetogens, and methanogens. Relevant in anaerobic digesters, shale systems, and underground hydrogen storage where H2 production by microbial communities affects system chemistry and storage integrity. +Nitrogen Fixation @nitrogen-fixer Other Metabolic Traits Other Metabolic Traits 3 types of nitrogenase are covered by this, see trait rule +Detox Arsenic Reduction @ArsenateReductionDetox Environmental Adaptation Other Metal and Trace Element Transformation and Resistance ArsC-mediated detoxification. +Detox Arsenic Export @ArseniteExportDetox Environmental Adaptation Other Metal and Trace Element Transformation and Resistance ArsB/Acr3-mediated arsenite export. +Broad Arsenic Resistance @ArsenicResistanceBroad Environmental Adaptation Other Metal and Trace Element Transformation and Resistance Broad screening for arsenic resistance mechanisms. Overlaps with export intentionally. +Detox Arsenic Methylation @ArsenicMethylation Environmental Adaptation Other Metal and Trace Element Transformation and Resistance Arsenic transformation mechanism with arsM +Detox or Respiration Arsenite Oxidation @ArseniteOxidation Environmental Adaptation Other Metal and Trace Element Transformation and Resistance Arsenite oxidation metabolism with aioA, aioB, can be respiratory or detox depends on context +Detox Mercury Reduction @MercuryReduction Environmental Adaptation Other Metal and Trace Element Transformation and Resistance MerA-mediated reduction of Hg(II) to elemental Hg(0) for detoxification +Detox Mercury Export @MercuryExport Environmental Adaptation Other Metal and Trace Element Transformation and Resistance MerT/MerC/MerE-mediated mercury transport associated with resistance +Detox Organic Mercury Degradation @OrganomercuryDegradation Environmental Adaptation Other Metal and Trace Element Transformation and Resistance MerB-mediated cleavage of carbon–mercury bonds in organomercury compounds +Mercury Methylation @MercuryMethylation Environmental Adaptation Other Metal and Trace Element Transformation and Resistance HgcA-mediated methylation of inorganic mercury to methylmercury; HgcB supports this process +Detox Copper Export @CopperEfflux Environmental Adaptation Other Metal and Trace Element Transformation and Resistance Copper efflux mediated by copper-exporting ATPases and Cus-associated transport systems +Detox Cadmium/Zinc Export @CadmiumZincEfflux Environmental Adaptation Other Metal and Trace Element Transformation and Resistance Cadmium/zinc efflux mediated by a metal-exporting ATPase +Detox Divalent Metal Export @DivalentMetalEfflux Environmental Adaptation Other Metal and Trace Element Transformation and Resistance Divalent metal efflux mediated by a multicomponent RND transport system +Detox Nickel/Cobalt Export @NickelCobaltEfflux Environmental Adaptation Other Metal and Trace Element Transformation and Resistance Nickel/cobalt efflux mediated by metal resistance transporters +Detox Cobalt/Zinc/Cadmium Export @CobaltZincCadmiumEfflux Environmental Adaptation Other Metal and Trace Element Transformation and Resistance CzcD/ZitB-mediated cobalt, zinc, and cadmium efflux +Detox Silver Export @SilverEfflux Environmental Adaptation Other Metal and Trace Element Transformation and Resistance Silver efflux mediated by a silver resistance transporter +Detox Silver Resistance @SilverResistance Environmental Adaptation Other Metal and Trace Element Transformation and Resistance +Detox Chromate Export @ChromateEfflux Environmental Adaptation Other Metal and Trace Element Transformation and Resistance +Detox Chromate Reductase @ChromateReductase Environmental Adaptation Other Metal and Trace Element Transformation and Resistance ChrA-mediated chromate efflux for detoxification +Eps-Production @EpsProduction Environmental Adaptation Biofilms & Attachment Exopolysaccharide biosynthesis and biofilm matrix structural genes including alginate biosynthesis (alg genes; K16566, K16557, K16556, K16555), Psl polysaccharide biosynthesis (K19290-K19296), PGA/ICA poly-GlcNAc synthesis (pgaABCD/icaABCD; K11936, K11937), and additional EPS biosynthesis genes. Any single gene indicates EPS production capacity. Drives pipeline fouling and MIC in engineered systems. +Quorum-Sensing @QuorumSensing Environmental Adaptation Biofilms & Attachment Quorum sensing via three systems: (1) AHL/LuxI-LuxR: LuxI-type AHL synthases lasI (K13060) or rhlI/cepI/tofI homologs (K13061) paired with LuxR-type receptors lasR (K18304) or rhlR homologs (K18099) — both synthase and receptor required; (2) AI-2/LuxS system: LuxS S-ribosylhomocysteine lyase (K07173) — widely conserved but interpret alone cautiously as it has metabolic roles beyond QS; (3) AI-2 import via Lsr ABC transporter: LsrB substrate-binding (K10555), LsrC permease (K10556), LsrD permease (K10557), LsrA ATPase (K10558) — at least 2 subunits required — indicates active AI-2 uptake and response capacity. +Motility @Motility Environmental Adaptation Biofilms & Attachment Flagellar motor (MotA K02410 or MotB K02411; at least one required) plus at least 3 structural/assembly genes from the flagellar complex. Required for surface approach and early biofilm attachment. Also relevant for chemotaxis toward carbon/electron donor sources in engineered systems. +Ion Homeostasis: K+ Uptake and Na+ Exclusion @IonBalance-saltinpotential Environmental Adaptation Osmoregulation Halophilic salt-in osmoadaptation via K+ accumulation and Na+ exclusion. KdpABC P-type ATPase (K01546-K01548) imports K+; KdpDE (K07646, K07667) sensor-regulator. Mrp/Mnh Na+:H+ antiporter (K05565-K05571; Mrp subunit K05565 required plus at least 3 others). PhaABCDEFG K+ transporter (K05559-K05564; at least 2 of 6). TrkA/TrkH constitutive K+ uptake (K03499 & K03498; both required). NhaC Na+:H+ antiporter (K03315 or K07084). Highly relevant in hypersaline produced waters (TDS >200 g/L). +Compatible-Solutes: Glycine Betaine Synthesis @GlycineBetaineSynthesis Environmental Adaptation Osmoregulation Glycine betaine biosynthesis via two routes: (1) choline oxidation pathway — choline dehydrogenase (betA; K00108 or K11440) AND betaine-aldehyde dehydrogenase (betB; K00130); or (2) sequential N-methylation of glycine — glycine/sarcosine methyltransferase (K18896) AND sarcosine/dimethylglycine methyltransferase (K18897). +Compatible-Solutes: Ectoine Synthesis @EctoineSynthesis Environmental Adaptation Osmoregulation Ectoine biosynthesis via complete ectABC pathway: diaminobutyrate acetyltransferase (ectA; K06718), diaminobutyrate aminotransferase (ectB; K00836), ectoine synthase (ectC; K06720) — all three required. Ectoine hydroxylase (ectD; K10674) additionally produces hydroxyectoine with enhanced thermostability. Major compatible solute in halophilic bacteria. +Compatible-Solutes: Sugar Derived Synthesis @SugarDerivedCompatibleSoluteSynthesis Environmental Adaptation Osmoregulation Biosynthesis of sugar-derived compatible solutes. Trehalose: OtsAB (K00697 & K01087; both required), TreYZ (K06044 or K01236), TreS (K05343), TreP (K05342). Mannosylglycerate: mpgSP (K05947). Mannitol: mtlD (K00009). Note K05342 and K05343 overlap with Trehalose Use row in Carbon Degradation. +Compatible-Solutes: Methylated Transport @MethylatedCompatibleSoluteTransport Environmental Adaptation Osmoregulation Transport of glycine betaine, choline, proline, and related methylated osmoprotectants. BetP/T/S BCCT transporter (K02168), carnitine/betaine antiporter (K05245), OpuD betaine transporter (K05020). ProVWX ABC transporter (K02000 & K02001 & K02002; all three required). OpuABC (K05845, K05846, K05847; at least 2 subunits). Glutamine ABC (K10036, K10037, K10038; at least 2 subunits). ProP MFS transporter (K03762); ProQ effector (K03607). +Compatible-Solutes: Ectoine Transport @EctoineTransport Environmental Adaptation Osmoregulation Ectoine/hydroxyectoine uptake via EhuABC ABC transporter (EhuA ATPase K02028, EhuC/D permease K02029, EhuB substrate-binding protein K02030). At least 2 of 3 subunits required for metagenomic data. Organisms with transport but not synthesis genes are ectoine scavengers. +Superoxide @Superoxide Environmental Adaptation Oxidative defense +Peroxide-catalase @Peroxide-catalase Environmental Adaptation Oxidative defense +Peroxide-peroxiredoxin @Peroxide-peroxiredoxin Environmental Adaptation Oxidative defense +Aldehyde-Resistance K00149 | K14085 Environmental Adaptation Biocide Resistance Resistance to aldehyde biocides (e.g., glutaraldehyde, formaldehyde) mediated by aldehyde oxidoreductases and aldehyde:ferredoxin oxidoreductases (K00149, K14085), which detoxify reactive aldehyde compounds. +Qac-Resistance K08167 | K11741 Environmental Adaptation Biocide Resistance Resistance to quaternary ammonium compound (QAC) disinfectants mediated by multidrug efflux transporters (K08167, K11741) that export toxic biocides from the cell. +Biocide-Efflux-(General) K03585 | K18138 | [K18324 | 2.A.6.2.7_P24177] | [K18142 | 2.A.6.2.2_P31224] | [K03297 | 2.A.7.1] | [[K11814 | 2.A.7.1.6] & [K11815 | 2.A.7.1.6]] | [K18975 | 2.A.7.1.11] Environmental Adaptation Biocide Resistance Broad-spectrum efflux genes for biocide and multidrug resistance. MexA/membrane fusion protein (K03585), MATE efflux (K03400), MexB/RND pump (K18138), AcrD/RND pump (K18324), AcrF/RND pump (K18142), and SMR family pumps: Mmr (K03297), EbrA/EbrB paired SMR pump (K11814 & K11815), Ebr SMR pump (K18975). Aldehyde dehydrogenase (K14085) provides chemical detoxification capacity. RND pumps (2.A.6 TCDB family) provide broad substrate efflux relevant in oil and gas and wastewater systems. General row is superset of Aldehyde Resistance sub-row. +Beta-Lactam Inactivation @Beta-lactam-inactivation Environmental Adaptation Antibiotic Resistance +Tetracycline Inactivation @Tetracycline-inactivation Environmental Adaptation Antibiotic Resistance +Macroglide Inactivation @Macrolide-inactivation Environmental Adaptation Antibiotic Resistance +Aminoglycoside Inactivation @Aminoglycoside-inactivation Environmental Adaptation Antibiotic Resistance diff --git a/src/dram_rules/data/rules_gut.tsv b/src/dram_rules/data/rules_gut.tsv index e053f18..907b450 100644 --- a/src/dram_rules/data/rules_gut.tsv +++ b/src/dram_rules/data/rules_gut.tsv @@ -1,4 +1,4 @@ -name rule rule_options module group notes +name rule rule_options module group notes Mucin-O-glycan GH101;EC:3.2.1.97 | GH109;EC:3.2.1.49 | GH129;EC:3.2.1.49 | GH89;EC:3.2.1.50 Carbon Processing Host-associated glycan Host-N-glycan GH99;EC:3.2.1.198 | GH163;EC:3.2.1.- | GH18;EC:3.2.1.96 | GH85;EC:3.2.1.96 | GH99;EC:3.2.1.130 Carbon Processing Host-associated glycan Host-glycosphingolipid GH116;EC:3.2.1.45 | GH3;EC:3.2.1.45 | GH30;EC:3.2.1.45 Carbon Processing Host-associated glycan @@ -52,42 +52,49 @@ Methylotrophic Methanogen @methylotroph "{""include_when"":{""all_columns_presen Oxygen - Low Affinity Use [percent(50,@CytochromeCOxidase)|percent(50,@CytochromeAa3600MenaquinolOxidase)|percent(50,@CytochromeOUbiquinolOxidase)] Other Reductases Other Reductases Low affinity oxygen use indicates an aerobe and requires the presence of a low-affinity oxidase plus a majority of the elctron transport chain Oxygen - High Affinity Use [@percent50CytochromeBDUbiquinolOxidase|@percent50CytochromeCOxidaseCBB3] Other Reductases Other Reductases High affinity oxygen use indicates a microaerophile and requires the presence of a high-affinity oxidase plus a majority of the elctron transport chain Nitrate Reduction To Nitrite @NarNitrateReductase | @NapNitrateReductase Other Reductases Other Reductases Nitrate reduction to nitrite can occur through either the membrane-bound Nar system (K00370, K00371) or the periplasmic Nap system (K02567, K02568). Either system completes the nitrate transformation step. -Nitrous Oxide Reduction To Dinitrogen Gas @NitrousOxideReductase Other Reductases Other Reductases The reduction of nitrous oxide (N‚Äö√Ñ√∂‚àö√°‚àö√°O) to dinitrogen gas (N‚Äö√Ñ√∂‚àö√°‚àö√°) is catalyzed by nitrous oxide reductase (nosZ, K00376). Presence of this gene indicates the potential for the final step of denitrification, converting greenhouse gas N‚Äö√Ñ√∂‚àö√°‚àö√°O into inert atmospheric N‚Äö√Ñ√∂‚àö√°‚àö√°. +Nitrous Oxide Reduction To Dinitrogen Gas @NitrousOxideReductase Other Reductases Other Reductases The reduction of nitrous oxide (N₂O) to dinitrogen gas (N₂) is catalyzed by nitrous oxide reductase (nosZ, K00376). Presence of this gene indicates the potential for the final step of denitrification, converting greenhouse gas N₂O into inert atmospheric N₂. Sulfate Reduction @DsrABtyper Other Reductases Other Reductases A genome that encodes adenylysulfate reductase and dissimilatory sulfite reductase -Tetrathionate Reduction @TetrathionateRed Other Reductases Other Reductases Tetrathionate reductase complex (ttrABC): TtrA catalytic subunit (K08359), TtrB electron transfer subunit (K08358), TtrC membrane anchor (K08357). At least 2 of 3 subunits required to allow for incomplete genome recovery. Tetrathionate is generated in the inflamed gut from host-derived thiosulfate oxidation and is exploited as an electron acceptor by Salmonella enterica and other Enterobacteriaceae during inflammation, conferring a growth advantage. Rule mirrors Thiosulfate Reduction group ‚Äö√Ñ√∂‚àö√ë‚àö√Ü both are non-sulfate sulfur respiration pathways enriched during gut dysbiosis. +Tetrathionate Reduction @TetrathionateRed Other Reductases Other Reductases Tetrathionate reductase complex (ttrABC): TtrA catalytic subunit (K08359), TtrB electron transfer subunit (K08358), TtrC membrane anchor (K08357). At least 2 of 3 subunits required to allow for incomplete genome recovery. Tetrathionate is generated in the inflamed gut from host-derived thiosulfate oxidation and is exploited as an electron acceptor by Salmonella enterica and other Enterobacteriaceae during inflammation, conferring a growth advantage. Rule mirrors Thiosulfate Reduction group — both are non-sulfate sulfur respiration pathways enriched during gut dysbiosis. Fumarate Reduction at_least(2, PRESENCE, [K00244,K00245,K00246,K00247]) Other Reductases Other Reductases Requires at least two subunits of fumarate reductase -TMAO Reduction [K07811 & K03532] | [K07812 & K07821] Other Reductases Other Reductases TMAO reductase systems: TorA (K03532) or TorZ/BisZ (K07811) catalytic subunit paired with TorC (K03533) or TorY/BisC (K07821) cytochrome c subunit. Either complete reductase system (TorAC or TorZY) indicates anaerobic TMAO respiration capacity. TMAO is an abundant dietary-derived compound in fish and meat; gut Enterobacteriaceae reduce it to TMA, which is subsequently oxidized by the host liver to TMAO ‚Äö√Ñ√∂‚àö√ë‚àö√Ü connecting microbial metabolism to host cardiovascular risk. +TMAO Reduction [K07811 & K03532] | [K07812 & K07821] Other Reductases Other Reductases TMAO reductase systems: TorA (K03532) or TorZ/BisZ (K07811) catalytic subunit paired with TorC (K03533) or TorY/BisC (K07821) cytochrome c subunit. Either complete reductase system (TorAC or TorZY) indicates anaerobic TMAO respiration capacity. TMAO is an abundant dietary-derived compound in fish and meat; gut Enterobacteriaceae reduce it to TMA, which is subsequently oxidized by the host liver to TMAO — connecting microbial metabolism to host cardiovascular risk. Obligate Fermenter @Fermenter Other Metabolic Systems Other Metabolic Systems Hydrogen Use @HydrogenUse Other Metabolic Systems Other Metabolic Systems -Quorum Sensing [[K13060 | K13061] & [K18304 | K18099]] | K07173 | at_least(2, PRESENCE, [K10555, K10556, K10557, K10558]) Colonization & Persistence Colonization & Persistence Quorum sensing via three systems: (1) AHL/LuxI-LuxR: LuxI-type AHL synthases lasI (K13060) or rhlI/cepI/tofI homologs (K13061) paired with LuxR-type receptors lasR (K18304) or rhlR homologs (K18099) ‚Äö√Ñ√∂‚àö√ë‚àö√Ü both synthase and receptor required; (2) AI-2/LuxS system: LuxS S-ribosylhomocysteine lyase (K07173) ‚Äö√Ñ√∂‚àö√ë‚àö√Ü widely conserved but interpret alone cautiously as it has metabolic roles beyond QS; (3) AI-2 import via Lsr ABC transporter: LsrB substrate-binding (K10555), LsrC permease (K10556), LsrD permease (K10557), LsrA ATPase (K10558) ‚Äö√Ñ√∂‚àö√ë‚àö√Ü at least 2 subunits required ‚Äö√Ñ√∂‚àö√ë‚àö√Ü indicates active AI-2 uptake and response capacity. +Quorum Sensing [[K13060 | K13061] & [K18304 | K18099]] | K07173 | at_least(2, PRESENCE, [K10555, K10556, K10557, K10558]) Colonization & Persistence Colonization & Persistence Quorum sensing via three systems: (1) AHL/LuxI-LuxR: LuxI-type AHL synthases lasI (K13060) or rhlI/cepI/tofI homologs (K13061) paired with LuxR-type receptors lasR (K18304) or rhlR homologs (K18099) — both synthase and receptor required; (2) AI-2/LuxS system: LuxS S-ribosylhomocysteine lyase (K07173) — widely conserved but interpret alone cautiously as it has metabolic roles beyond QS; (3) AI-2 import via Lsr ABC transporter: LsrB substrate-binding (K10555), LsrC permease (K10556), LsrD permease (K10557), LsrA ATPase (K10558) — at least 2 subunits required — indicates active AI-2 uptake and response capacity. Motility [K02410 | K02411] & at_least(3, PRESENCE, [K02406, K02407, K02400, K02408, K02409, K02412, K02416, K02417, K02386, K02387, K02391, K02393, K02404, K02405]) Colonization & Persistence Colonization & Persistence Flagellar motor (MotA K02410 or MotB K02411; at least one required) plus at least 3 structural/assembly genes from the flagellar complex. Required for surface approach and early biofilm attachment. Also relevant for chemotaxis toward carbon/electron donor sources in engineered systems. Bile Acid Deconjugation K01442 Host Interaction Bile acid metabolism Presence of choloylglycine hydrolase (K01442), the canonical bile salt hydrolase (BSH), indicates capacity to deconjugate glycine- and taurine-conjugated bile acids to free bile acids and amino acids Bile acid 7α-dehydroxylation potential K15872 & K15870 Host Interaction Bile acid metabolism Indicates potential for individual bile acid hydroxyl/oxo transformations. A positive call does not establish complete epimerization or 7α-dehydroxylation. -Bile Acid Redox [K00076 | K22604 | K22605 | K22606 | K22607 | K23231] Host Interaction Bile acid metabolism Presence of at least one bile acid‚Äö√Ñ√∂‚àö√ë‚àö¬®active hydroxysteroid dehydrogenase indicates capacity to oxidize and epimerize bile acids at the 3 or 7 positions via oxo intermediates. These enzymes are essential for forming iso‚Äö√Ñ√∂‚àö√ë‚àö¬¥ and urso‚Äö√Ñ√∂‚àö√ë‚àö¬¥bile acids and for completing epi‚Äö√Ñ√∂‚àö√ë‚àö¬¥bile acid pathways in the human gut +Bile Acid Redox [K00076 | K22604 | K22605 | K22606 | K22607 | K23231] Host Interaction Bile acid metabolism Presence of at least one bile acid–active hydroxysteroid dehydrogenase indicates capacity to oxidize and epimerize bile acids at the 3 or 7 positions via oxo intermediates. These enzymes are essential for forming iso‑ and urso‑bile acids and for completing epi‑bile acid pathways in the human gut Menaquinone (K2) K02552 & K02551 & K02549 & K01661 & K01911 & K02548 Host Interaction Vitamin biosynthesis Co-occurrence of menF (K02552), menD (K02551), menC (K02549), menB (K01661), menE (K01911), and menA (K02548) represents the full classical menaquinone biosynthesis pathway from chorismate to polyprenylated menaquinone Folate K00796 & K00287 Host Interaction Vitamin biosynthesis Co-occurrence of dihydropteroate synthase (K00796) and dihydrofolate reductase (K00287) marks the minimal two-step folate synthesis/recycling module from p-aminobenzoate to tetrahydrofolate. Folate-prototrophic gut microbes (Lactobacillus reuteri, Bifidobacterium spp.) supply folate to the host and folate-auxotrophic microbiome members, supporting one-carbon metabolism and nucleotide synthesis. Thiamine K03147 & K00788 Host Interaction Vitamin biosynthesis Co-occurrence of thiamine-phosphate pyrophosphorylase (K03147/ThiE) and hydroxyethylthiazole kinase (K00788/ThiM) marks the minimal thiamine biosynthesis completion module. Thiamine-producing gut microbes contribute to host B1 supply and support TPP-dependent metabolic pathways in the microbiome. Full de novo synthesis requires additional ThiC/ThiG upstream enzymes not captured here; this rule flags thiamine phosphate assembly capacity. Biotin (B7) K01012 Host Interaction Vitamin biosynthesis Biotin synthase (K01012/BioB) catalyzes the final step of biotin biosynthesis, inserting a sulfur atom into dethiobiotin to form biotin (vitamin B7). Presence alone indicates biotin biosynthesis completion capacity. Biotin-prototrophic gut microbes (Fusobacterium nucleatum, some Bacteroides) contribute to colonic biotin supply; biotin is essential for carboxylase enzymes including pyruvate carboxylase and acetyl-CoA carboxylase. Niacin (B3) K03517 & K00278 & K00767 Host Interaction Vitamin biosynthesis Co-occurrence of aspartate oxidase (K03517/NadB), quinolinate synthase (K00278/NadA), and nicotinate-nucleotide pyrophosphorylase (K00767/NadC) marks the de novo NAD biosynthesis route from aspartate through quinolinate. Niacin/B3-prototrophic gut microbes produce nicotinamide and support luminal NAD+ precursor availability, relevant for host intestinal epithelial function and microbiome-host signaling via extracellular NAD+ metabolites. -Cobalamin (B12) [K00798 | K19221] & K02232 & [K02225 | K02227] & K02231 & K00768 & [K02226 | K22316] & K02233 Host Interaction Vitamin biosynthesis Presence of all core corrinoid loop assembly genes in KEGG module M00122 (cobyrinate a,c-diamide ‚Äö√Ñ√∂‚àö√∫‚àö‚↠cobalamin), with allowed alternatives at specific steps, indicates capacity for de novo completion of cobalamin (vitamin B12) biosynthesis. This marks high-confidence B12 producers in gut and rumen microbiomes, which can support cobalamin-dependent pathways in both microbes and the host. -Pantothenate (B5) [K00826 & K00606 & K00077 & K01579 & [K01918 | K13799]] | [K00606 & K00077 & K13367 & K00128 & K01918] Host Interaction Vitamin biosynthesis Presence of all core pantothenate biosynthesis genes from either the valine/aspartate route (M00119) or the 2‚Äö√Ñ√∂‚àö√ë‚àö¬¥oxoisovalerate/spermine route (M00913) indicates de novo vitamin B5 production capacity. -Pyridoxine (B6) K03472 & K03473 & K00831 & K00097 & K03474 & K00275 Host Interaction Vitamin biosynthesis Presence of all core genes in KEGG module M00124 (erythrose-4P ‚Äö√Ñ√∂‚àö√∫‚àö‚↠pyridoxal 5'-phosphate) indicates capacity for de novo vitamin B6 biosynthesis as PLP. In gut and rumen microbiomes, such B6 prototrophy is less prevalent than other B-vitamin pathways but supports amino acid metabolism and can provide B6 to auxotrophic microbes and the host -Riboflavin (B2) [[K01497 | K14652] & [[K01498 & K00082] | K11752] & [K22912 | K20860 | K20861 | K20862 | K21063 | K21064] & [K02858 | K14652] & K00794 & K00793 & [[K20884 & K22949] | K11753]] Host Interaction Vitamin biosynthesis Presence of all core genes in KEGG module M00125 (riboflavin biosynthesis, GTP ‚Äö√Ñ√∂‚àö√∫‚àö‚↠riboflavin/FM N/FAD) with allowed enzyme alternatives indicates capacity for de novo vitamin B2 biosynthesis. In gut and rumen microbiomes, such riboflavin prototrophy is an important microbial trait that supplies B2 for FMN/FAD cofactor production and can contribute to host vitamin status -Beta-Lactam Resistance K18698 | K18699 | K18796 | K18767 | K18797 | K19097 | K19317 | K18768 | K18970 | K19316 | K22346 | K18795 | K19218 | K19217 | K18790 | K18791 | K19098 | K18792 | K19213 | K21276 | K18793 | K18971 | K22352 | K19209 Host Interaction Antibiotic Resistance Potential Beta-lactamase and penicillin-binding protein resistance genes conferring resistance to beta-lactam antibiotics (penicillins, cephalosporins, carbapenems). Major antibiotic resistance gene class in environmental microbiomes. -Macrolide Resistance K00561 | K14336 | K15632 | K18230 | K18231 | K19349 | K19350 | K18232 | K19541 | K08217 Host Interaction Antibiotic Resistance Potential Macrolide resistance via efflux pumps, ribosomal methylases (erm genes), or macrolide esterases. -Tetracycline Resistance K08151 | K08168 | K18214 | K18215 | K18218 | K18216 | K18217 | K19542 | K18233 | K18220 | K18221 | 3000254 Host Interaction Antibiotic Resistance Potential Tetracycline resistance via efflux pumps (tet efflux genes) or ribosomal protection proteins. -Sulfonamide Resistance K18974 | K18824 | K18825 Host Interaction Antibiotic Resistance Potential Sulfonamide resistance via dihydropteroate synthase variants (sul1, sul2, sul3) insensitive to sulfonamide inhibition. Sulfonamide resistance genes are among the most prevalent antibiotic resistance determinants in human gut microbiomes, particularly in individuals with prior antibiotic exposure, and are frequently found on mobile genetic elements that co-carry other resistance genes. -Aminoglycoside Resistance K03395 | K18815 | K18816 | K00984 | K19272 | K10673 Host Interaction Antibiotic Resistance Potential Presence of aminoglycoside-modifying enzyme genes, including N-acetyltransferases (AAC(3), AAC(6‚Äö√Ñ√∂‚àö√ë‚Äö√¢¬ß)), O-nucleotidyltransferases (aadA, ANT(3¬¨‚Ć‚Äö√†¬¥); K00984), and O-phosphotransferases (APH(3‚Äö√Ñ√∂‚àö√ë‚Äö√¢¬ß), APH(3¬¨‚Ć‚Äö√†¬¥)), indicates resistance to aminoglycoside antibiotics via drug inactivation. Aminoglycoside resistance genes of these families are common in human and animal gut microbiomes and in the rumen, where they contribute substantially to the overall resistome +Cobalamin (B12) [K00798 | K19221] & K02232 & [K02225 | K02227] & K02231 & K00768 & [K02226 | K22316] & K02233 Host Interaction Vitamin biosynthesis Presence of all core corrinoid loop assembly genes in KEGG module M00122 (cobyrinate a,c-diamide → cobalamin), with allowed alternatives at specific steps, indicates capacity for de novo completion of cobalamin (vitamin B12) biosynthesis. This marks high-confidence B12 producers in gut and rumen microbiomes, which can support cobalamin-dependent pathways in both microbes and the host. +Pantothenate (B5) [K00826 & K00606 & K00077 & K01579 & [K01918 | K13799]] | [K00606 & K00077 & K13367 & K00128 & K01918] Host Interaction Vitamin biosynthesis Presence of all core pantothenate biosynthesis genes from either the valine/aspartate route (M00119) or the 2‑oxoisovalerate/spermine route (M00913) indicates de novo vitamin B5 production capacity. +Pyridoxine (B6) K03472 & K03473 & K00831 & K00097 & K03474 & K00275 Host Interaction Vitamin biosynthesis Presence of all core genes in KEGG module M00124 (erythrose-4P → pyridoxal 5'-phosphate) indicates capacity for de novo vitamin B6 biosynthesis as PLP. In gut and rumen microbiomes, such B6 prototrophy is less prevalent than other B-vitamin pathways but supports amino acid metabolism and can provide B6 to auxotrophic microbes and the host +Riboflavin (B2) [[K01497 | K14652] & [[K01498 & K00082] | K11752] & [K22912 | K20860 | K20861 | K20862 | K21063 | K21064] & [K02858 | K14652] & K00794 & K00793 & [[K20884 & K22949] | K11753]] Host Interaction Vitamin biosynthesis Presence of all core genes in KEGG module M00125 (riboflavin biosynthesis, GTP → riboflavin/FM N/FAD) with allowed enzyme alternatives indicates capacity for de novo vitamin B2 biosynthesis. In gut and rumen microbiomes, such riboflavin prototrophy is an important microbial trait that supplies B2 for FMN/FAD cofactor production and can contribute to host vitamin status +Tetracycline inactivation @Tetracycline-inactivation Host Interaction Antibiotic Resistance +Tetracycline efflux @Tetracycline-efflux Host Interaction Antibiotic Resistance +Tetracycline protection @Tetracycline-protection Host Interaction Antibiotic Resistance +Macrolide efflux @Macrolide-efflux Host Interaction Antibiotic Resistance +Macrolide inactivation @Macrolide-inactivation Host Interaction Antibiotic Resistance +Macrolide alteration @Macrolide-alteration Host Interaction Antibiotic Resistance +Beta-lactam inactivation @Beta-lactam-inactivation Host Interaction Antibiotic Resistance +Sulfoamide target-replacement @Sulfoamide-target-replacement Host Interaction Antibiotic Resistance +Aminoglycoside inactivation @Aminoglycoside-inactivation Host Interaction Antibiotic Resistance +Aminoglycoside alteration @Aminoglycoside-alteration Host Interaction Antibiotic Resistance +Aminoglycosde efflux @Aminoglycosde-efflux Host Interaction Antibiotic Resistance +Multidrug efflux @MultidrugEfflux Host Interaction Antibiotic Resistance Azo prodrug reduction K01118 Host Interaction Drug metabolism Prodrug activation: azoreductase (K01118) reduces azo-bond prodrugs (sulfasalazine, balsalazide) to release active 5-aminosalicylic acid (5-ASA) in the colon. Primary enzymatic mechanism by which IBD prodrugs are activated by gut microbiota. Presence indicates capacity to convert prodrugs to their active forms, with implications for inter-individual variation in drug response. 5-Fluorouracil reduction K17722 & K17723 Host Interaction Drug metabolism Chemotherapy inactivation: co-occurrence of cytosine deaminase (K17722) and uracil phosphoribosyltransferase (K17723) encodes the 5-fluorouracil (5-FU) inactivation pathway. Gut microbes expressing these enzymes can degrade 5-FU to inactive catabolites, potentially reducing drug efficacy. Relevant to colorectal cancer chemotherapy outcomes where microbiome composition affects 5-FU bioavailability. -Nitroreduction potential K10678 | K10679 Host Interaction Drug metabolism Nitro drug reduction: nitroreductase type I (K10678) or type II (K10679) reduces nitro groups in prodrugs such as metronidazole, nitrofurantoin, and tinidazole. Reductive activation converts these prodrugs to toxic intermediates that damage DNA. Paradoxically, acquired resistance in Helicobacter pylori and Bacteroides involves loss or mutation of these reductases ‚Äö√Ñ√∂‚àö√ë‚àö√Ü flagging presence indicates susceptibility to nitro-drug activation. +Nitroreduction potential K10678 | K10679 Host Interaction Drug metabolism Nitro drug reduction: nitroreductase type I (K10678) or type II (K10679) reduces nitro groups in prodrugs such as metronidazole, nitrofurantoin, and tinidazole. Reductive activation converts these prodrugs to toxic intermediates that damage DNA. Paradoxically, acquired resistance in Helicobacter pylori and Bacteroides involves loss or mutation of these reductases — flagging presence indicates susceptibility to nitro-drug activation. Levodopa decarboxylation potential K22330 Host Interaction Drug metabolism Presence of a tyrosine decarboxylase associated with microbial conversion of levodopa to dopamine. Indicates potential for this reaction; it does not establish broad neurological drug metabolism. -Quaternary Amines to TMA [K20038 & K20037] | K22443 | K21579 Host Interaction Other Organic N Transformations TMA production via three routes: (1) choline TMA-lyase complex cutC/cutD (K20038/K20037) ‚Äö√Ñ√∂‚àö√ë‚àö√Ü primary choline-to-TMA route; (2) carnitine oxygenase cntA (K22443) ‚Äö√Ñ√∂‚àö√ë‚àö√Ü L-carnitine cleavage; (3) glycine reductase grdH (K21579) ‚Äö√Ñ√∂‚àö√ë‚àö√Ü glycine betaine reduction. TMA is the gut microbial precursor of host-produced TMAO, a circulating metabolite associated with cardiovascular disease risk. All three routes are diet-substrate-dependent. +Quaternary Amines to TMA [K20038 & K20037] | K22443 | K21579 Host Interaction Other Organic N Transformations TMA production via three routes: (1) choline TMA-lyase complex cutC/cutD (K20038/K20037) — primary choline-to-TMA route; (2) carnitine oxygenase cntA (K22443) — L-carnitine cleavage; (3) glycine reductase grdH (K21579) — glycine betaine reduction. TMA is the gut microbial precursor of host-produced TMAO, a circulating metabolite associated with cardiovascular disease risk. All three routes are diet-substrate-dependent. Quaternary Amine Demethylation K25600 | K25220 Host Interaction Other Organic N Transformations -TMA Demethylation K14083 Host Interaction Other Organic N Transformations TMA demethylation via pyrrolysine-containing methyltransferases: MttB-type trimethylamine methyltransferase (K14083), MtgB glycine betaine methyltransferase (K25600), or EC:2.1.1.389 (dimethylamine/trimethylamine corrinoid methyltransferase). Removes a methyl group from TMA, reducing circulating TMA and potentially TMAO levels. Found in Methanomassiliicoccales archaea and some anaerobic bacteria. NOTE: EC:2.1.1.389 is not yet a KEGG K-number ‚Äö√Ñ√∂‚àö√ë‚àö√Ü confirm DRAM2 can accept EC:identifiers in rule engine. -Urease @Urease Host Interaction Other Organic N Transformations Urea hydrolysis requires the full urease enzyme complex composed of subunits ureC (K01428), ureB (K01429), and ureA (K01430). All three subunits are required for activity. In the gut, urease-positive organisms (Helicobacter pylori, Klebsiella pneumoniae, Proteus mirabilis) hydrolyze urea to ammonia and CO‚Äö√Ñ√∂‚àö√°‚àö√°, raising local pH and supporting colonization of acidic niches. In the rumen, urease activity by diverse Firmicutes and Proteobacteria is central to urea nitrogen recycling and represents a major route by which dietary or salivary urea re-enters the microbial nitrogen pool +TMA Demethylation K14083 Host Interaction Other Organic N Transformations TMA demethylation via pyrrolysine-containing methyltransferases: MttB-type trimethylamine methyltransferase (K14083), MtgB glycine betaine methyltransferase (K25600), or EC:2.1.1.389 (dimethylamine/trimethylamine corrinoid methyltransferase). Removes a methyl group from TMA, reducing circulating TMA and potentially TMAO levels. Found in Methanomassiliicoccales archaea and some anaerobic bacteria. NOTE: EC:2.1.1.389 is not yet a KEGG K-number — confirm DRAM2 can accept EC:identifiers in rule engine. +Urease @Urease Host Interaction Other Organic N Transformations Urea hydrolysis requires the full urease enzyme complex composed of subunits ureC (K01428), ureB (K01429), and ureA (K01430). All three subunits are required for activity. In the gut, urease-positive organisms (Helicobacter pylori, Klebsiella pneumoniae, Proteus mirabilis) hydrolyze urea to ammonia and CO₂, raising local pH and supporting colonization of acidic niches. In the rumen, urease activity by diverse Firmicutes and Proteobacteria is central to urea nitrogen recycling and represents a major route by which dietary or salivary urea re-enters the microbial nitrogen pool Iron Acquisition K19611 | K16090 | K16091 | K12545 | K16152 | K15721 | K16088 | K16089 | K16087 | K02014 Pathogenesis & Virulence Pathogenesis & Virulence Siderophore receptors (K19611/fepA, K16090/fiu, K16091/fecA), heme acquisition (K12545/hasA, K16152/hasR), siderophore/yersiniabactin receptors (K15721/fyuA), and iron complex TonB-dependent receptors (K16088, K16089, K16087, K02014). Broad outer-membrane iron uptake capacity. -Hemolysins K11005 | K11032 | K11038 | K10948 | K11139 Pathogenesis & Virulence Pathogenesis & Virulence Pore-forming hemolysins: HlyA (K11005), HlyII (K11032), leukocidin/Hlg family (K11038), and HlyC-family protein (K06189). Note: K06189 and K11005/K11032/K11038 are also present in Toxins row ‚Äö√Ñ√∂‚àö√ë‚àö√Ü expected overlap between hemolysin and toxin categories. +Hemolysins K11005 | K11032 | K11038 | K10948 | K11139 Pathogenesis & Virulence Pathogenesis & Virulence Pore-forming hemolysins: HlyA (K11005), HlyII (K11032), leukocidin/Hlg family (K11038), and HlyC-family protein (K06189). Note: K06189 and K11005/K11032/K11038 are also present in Toxins row — expected overlap between hemolysin and toxin categories. Pilus And Fimbrial Adhesion K07345 | K07349 | K07350 | K07352 | K02650 | K12790 | K12689 | K11038 | K13733 | K13732 | K14194 Pathogenesis & Virulence Pathogenesis & Virulence Surface attachment to gut epithelium via fimbrial and pilus systems. Epithelial Invasion at_least(2,PRESENCE, [K13285,K13287,K12679,K01387,K21449,K19231,K19232,K19233,K12678]) Pathogenesis & Virulence Pathogenesis & Virulence Active invasion of gut epithelial cells via multiple mechanisms. Type III Secretion System [K03219 | K03222 | K03224 | K03225 | K03230 | K04057] | [K15344 | K15345 | K15346] | [K23648 | K23651 | K23652 | K23653 | K23654 | K23655 | K23656 | K23657 | K23658] Pathogenesis & Virulence Pathogenesis & Virulence Type III secretion system capacity via structural components or secreted effectors diff --git a/src/dram_rules/data/summarize_sheets/assimilation_and_cofactor_metabolism.tsv b/src/dram_rules/data/summarize_sheets/assimilation_and_cofactor_metabolism.tsv index 99a511f..805192a 100644 --- a/src/dram_rules/data/summarize_sheets/assimilation_and_cofactor_metabolism.tsv +++ b/src/dram_rules/data/summarize_sheets/assimilation_and_cofactor_metabolism.tsv @@ -1,4 +1,4 @@ -topic_ecosystem module gene_id gene_description +topic_ecosystem module gene_id gene_description Assimilation nutrient aquistion Nitrogen fixation, organic nitrogen degradation, inorganic n assimilation K02588 nitrogenase iron protein [RN:R05185] Assimilation nutrient aquistion Nitrogen fixation, organic nitrogen degradation, inorganic n assimilation K02586 nitrogenase molybdenum-iron protein [EC:1.18.6.1] [RN:R05185] Assimilation nutrient aquistion Nitrogen fixation, organic nitrogen degradation, inorganic n assimilation K02591 nitrogenase molybdenum-iron protein [EC:1.18.6.1] [RN:R05185] diff --git a/src/dram_rules/data/summarize_sheets/cellular_machinery.tsv b/src/dram_rules/data/summarize_sheets/cellular_machinery.tsv index c53dbce..93fcc24 100644 --- a/src/dram_rules/data/summarize_sheets/cellular_machinery.tsv +++ b/src/dram_rules/data/summarize_sheets/cellular_machinery.tsv @@ -1,4 +1,4 @@ -topic_ecosystem module gene_id gene_description +topic_ecosystem module gene_id gene_description Motility Flagellar, Chemotaxis, Pili K02399 flagella synthesis protein FlgN Motility Flagellar, Chemotaxis, Pili K02413 flagellar FliJ protein Motility Flagellar, Chemotaxis, Pili K02422 flagellar protein FliS diff --git a/src/dram_rules/data/summarize_sheets/distill_ag.tsv b/src/dram_rules/data/summarize_sheets/distill_ag.tsv index 36f0d43..59681af 100644 --- a/src/dram_rules/data/summarize_sheets/distill_ag.tsv +++ b/src/dram_rules/data/summarize_sheets/distill_ag.tsv @@ -1,4 +1,4 @@ -gene_id gene_description module subheader topic_ecosystem notes +gene_id gene_description module subheader topic_ecosystem notes K02588 NifH; nitrogenase molybdenum-iron protein; ; [RN:R05185] Nitrogen Inorganic Transformations N2 Fixation ag K02586 NifD; nitrogenase molybdenum-iron protein alpha subunit; [EC:1.18.6.1]; [RN:R05185] Nitrogen Inorganic Transformations N2 Fixation ag K02591 NifK; nitrogenase molybdenum-iron protein beta subunit; [EC:1.18.6.1]; [RN:R05185] Nitrogen Inorganic Transformations N2 Fixation ag diff --git a/src/dram_rules/data/summarize_sheets/distill_aquatic.tsv b/src/dram_rules/data/summarize_sheets/distill_aquatic.tsv index 256434f..aaffbea 100644 --- a/src/dram_rules/data/summarize_sheets/distill_aquatic.tsv +++ b/src/dram_rules/data/summarize_sheets/distill_aquatic.tsv @@ -1,4 +1,4 @@ -gene_id gene_description pathway topic_ecosystem header subheader note reference +gene_id gene_description pathway topic_ecosystem header subheader note reference K04114 benzoyl-CoA reductase subunit A [EC:1.3.7.8] Anaerobic aromatic hydrocarbon degradation marine Carbon Processing Big Carbon K07540 benzylsuccinate synthase [EC:4.1.99.11] Anaerobic aromatic hydrocarbon degradation marine Carbon Processing Big Carbon AA10 AA10 (formerly CBM33) proteins are copper-dependent lytic polysaccharide monooxygenases (LPMOs); some proteins have been shown to act on chitin, others on cellulose; lytic cellulose monooxygenase (C1-hydroxylating) (EC 1.14.99.54); lytic cellulose monooxygenase (C4-dehydrogenating)(EC 1.14.99.56); lytic chitin monooxygenase (EC 1.14.99.53) Cellulose degradation marine Carbon Processing Big Carbon diff --git a/src/dram_rules/data/summarize_sheets/distill_bgc.tsv b/src/dram_rules/data/summarize_sheets/distill_bgc.tsv index 3363b07..561cae1 100644 --- a/src/dram_rules/data/summarize_sheets/distill_bgc.tsv +++ b/src/dram_rules/data/summarize_sheets/distill_bgc.tsv @@ -1,4 +1,4 @@ -gene_id gene_description module subheader topic_ecosystem note reference count pathway +gene_id gene_description module subheader topic_ecosystem note reference count pathway ExtABCD "Nutrient Cycling , Redox Ladder" Iron Reduction bgc FmnA fegenie db: HMM "Nutrient Cycling , Redox Ladder" Iron Reduction bgc MtrA fegenie db: HMM "Nutrient Cycling , Redox Ladder" Iron Reduction bgc diff --git a/src/dram_rules/data/summarize_sheets/distill_eng_sys.tsv b/src/dram_rules/data/summarize_sheets/distill_eng_sys.tsv index 275c7a3..ce4e1da 100644 --- a/src/dram_rules/data/summarize_sheets/distill_eng_sys.tsv +++ b/src/dram_rules/data/summarize_sheets/distill_eng_sys.tsv @@ -1,4 +1,4 @@ -gene_id gene_description module subheader topic_ecosystem notes +gene_id gene_description module subheader topic_ecosystem notes K00370 narG, nitrate reductase, alpha subunit [EC:1.7.99.-] [RN:R00798] Nitrogen Cycling Nitrification, Comammox, Denitrification, DNRA eng_sys Nitrite Oxidation to Nitrate (Nitrification), Complete Ammonia Oxidation (Comammox), Nitrate Reduction to Nitrite, DNRA (NO3 to NH4) K00371 narH, nitrate reductase, beta subunit [EC:1.7.99.-] [RN:R00798] Nitrogen Cycling Nitrification, Comammox, Denitrification, DNRA eng_sys Nitrite Oxidation to Nitrate (Nitrification), Complete Ammonia Oxidation (Comammox), Nitrate Reduction to Nitrite, DNRA (NO3 to NH4) K00149 aldehyde dehydrogenase family 9 member A1 Fermentation End Products Organic Acids, Alcohols, Other Carbon, Biocide Resistance eng_sys Acetate Production, Ethanol Production, Ethylene Glycol Degradation, Aldehyde Resistance diff --git a/src/dram_rules/data/summarize_sheets/distill_gut.tsv b/src/dram_rules/data/summarize_sheets/distill_gut.tsv index 901a4c3..717f279 100644 --- a/src/dram_rules/data/summarize_sheets/distill_gut.tsv +++ b/src/dram_rules/data/summarize_sheets/distill_gut.tsv @@ -1,4 +1,4 @@ -gene_id gene_description pathway module subheader topic_ecosystem +gene_id gene_description pathway module subheader topic_ecosystem K01182 sucrase-isomaltase [EC:3.2.1.48] Sucrose and starch metabolism (sucrase–isomaltase complex) Carbon Processing Sugars gut K01203 β-fructofuranosidase [EC:3.2.1.26] Fructose and mannose metabolism (β-fructofuranosidase) Carbon Processing Sugars gut K12047 sucrose phosphorylase [EC:2.4.1.7] Sucrose metabolism (sucrose phosphorylase) Carbon Processing Sugars gut diff --git a/src/dram_rules/data/summarize_sheets/energy_acquisition_bioenergetics.tsv b/src/dram_rules/data/summarize_sheets/energy_acquisition_bioenergetics.tsv index 3a168cf..b21b3d7 100644 --- a/src/dram_rules/data/summarize_sheets/energy_acquisition_bioenergetics.tsv +++ b/src/dram_rules/data/summarize_sheets/energy_acquisition_bioenergetics.tsv @@ -1,4 +1,4 @@ -topic_ecosystem module gene_id gene_description +topic_ecosystem module gene_id gene_description Carbon_Organic Trophic Organic Trophic Groups (polymer, sugar, LMOA) K01812 glucuronate isomerase Carbon_Organic Trophic Organic Trophic Groups (polymer, sugar, LMOA) K00041 tagaturonate reductase Carbon_Organic Trophic Organic Trophic Groups (polymer, sugar, LMOA) K01685 altronate hydrolase diff --git a/src/dram_rules/data/summarize_sheets/environmental_interaction_and_adaptation.tsv b/src/dram_rules/data/summarize_sheets/environmental_interaction_and_adaptation.tsv index b01e713..9c298c4 100644 --- a/src/dram_rules/data/summarize_sheets/environmental_interaction_and_adaptation.tsv +++ b/src/dram_rules/data/summarize_sheets/environmental_interaction_and_adaptation.tsv @@ -1,4 +1,4 @@ -topic_ecosystem module gene_id gene_description +topic_ecosystem module gene_id gene_description Defense System-Viral Crispr/phage resistance K07016 csm1, cas10; CRISPR-associated protein Csm1 Defense System-Viral Crispr/phage resistance K19138 csm2; CRISPR-associated protein Csm2 Defense System-Viral Crispr/phage resistance K09002 csm3; CRISPR-associated protein Csm3 diff --git a/src/dram_rules/data/traits_rules.tsv b/src/dram_rules/data/traits_rules.tsv index c9daedf..ef16115 100644 --- a/src/dram_rules/data/traits_rules.tsv +++ b/src/dram_rules/data/traits_rules.tsv @@ -1,5 +1,5 @@ -name rule rule_options topic_ecosystem -phototroph @phototroph traits +name rule rule_options topic_ecosystem +phototroph @PhototrophAllTypes traits CO2-fixation @CO2fixation traits hydrogen-metabolism @HydrogenUse traits obligate-fermenter @Fermenter traits diff --git a/src/dram_rules/make_product.py b/src/dram_rules/make_product.py index b841234..a1d0898 100644 --- a/src/dram_rules/make_product.py +++ b/src/dram_rules/make_product.py @@ -51,8 +51,8 @@ "default": Path(__file__).parent / "data/rules.tsv", "ag": Path(__file__).parent / "data/rules_ag.tsv", "bgc": Path(__file__).parent / "data/rules_bgc.tsv", - # "aquatic": Path(__file__).parent / "data/rules_aquatic.tsv", - # "eng_sys": Path(__file__).parent / "data/rules_eng_sys.tsv", + "aquatic": Path(__file__).parent / "data/rules_aquatic.tsv", + "eng_sys": Path(__file__).parent / "data/rules_eng_sys.tsv", "gut": Path(__file__).parent / "data/rules_gut.tsv", } @@ -452,6 +452,8 @@ def main( del raw_anno + output_dir.mkdir(parents=True, exist_ok=True) + if save_dataframes: for df_type, dfs_dict in dfs.items(): df = pl.concat( diff --git a/src/dram_rules/rule_parser/rules.py b/src/dram_rules/rule_parser/rules.py index ebbcb42..7794423 100644 --- a/src/dram_rules/rule_parser/rules.py +++ b/src/dram_rules/rule_parser/rules.py @@ -526,6 +526,18 @@ def parse_rule_expr(expr_str: str) -> Expr: pl.col(label_col).str.strip_chars(), pl.col(alias_col).str.strip_chars() ) + labels = ( + lf.filter(pl.col(label_col).is_not_null() & (pl.col(label_col) != "")) + .select(label_col) + .collect() + .to_series() + ) + duplicate_labels = labels.filter(labels.is_duplicated()).unique().sort().to_list() + if duplicate_labels: + raise RuleError( + f"Rule column '{label_col}' needs to be unique. Duplicate labels: {duplicate_labels}" + ) + rules = { a: b for a, b in lf.filter(~pl.col(label_col).is_null())