V.0.5
V.0.5 Adds functions for sulfolipid biosynthesis (key gene sqdB) and C-P lyase
V.0.3. Adds retinal biosynthesis, sulfite dehydrogenase (quinone), hydrazine dehydrogenase, hydrazine synthase, DMSP/DMS/DMSO cycling, cobalamin biosynthesis, competence-related DNA transport, anaplerotic reactions
Nitrogen metabolism
	Dissimilatory nitrate reduction requires narGH K00370 + K00371 AND/OR napAB K02567 + K02568
	Nitrite oxidation requires nxrAB K00370 + K00371
	DNRA requires nirBD (K00362 + K00363) and/or nrfAH K03385 + K15876
	Denitrification step of nitrite reduction NO2 > NO requires nirK K00368 OR nirS K15864
	Denitrification step of nitric oxide reduction NO > N2O requires norBC K04561 + K02305
	Denitrification step of nitrous-oxide reduction N2O > N2 requires nosZ K00376
	Nitrogen fixation requires the nifKDH (K02586 + K02591 + K02588)
	Nitrification by bacteria hydroxylamine to nitrite NH2OH > NO2 requires hao K10535
	Nitrification ammonium to hydroxylamine NH4 > N2OH for detection, amoA (K10944) is essential and amoBC (K10945 + K10946) supports functional potential
	Anammox requires hydroxylamine oxidoreductase (K10535) and nirK or nirS (K00368 or K15864)
		hydrazine dehydrogenase K20935
		hydrazine synthase (K20932 + K20933 + K20934)


glycolysis as a pathway measured as a fraction of the following KOs: 
		phosphoglucomutase K01835
		glucose-6-phosphate isomerase K01810
		6-phosphofructokinase K00850 OR pyrophosphate--fructose-6-phosphate 1-phosphotransferase K00895
		fructose-bisphosphate aldolase K01623
		glyceraldehyde 3-phosphate dehydrogenase K00134 OR glyceraldehyde-3-phosphate dehydrogenase (NAD(P)) K00150
		phosphoglycerate kinase K00927
		2,3-bisphosphoglycerate-dependent phosphoglycerate mutase K01834 OR 2,3-bisphosphoglycerate-independent phosphoglycerate mutase K15633
		enolase K01689
		pyruvate kinase K00873 OR pyruvate, orthophosphate dikinase K01006

gluconeogenesis requires fructose-1,6-bisphosphatase K03841 to reverse reaction, also requires all other parts of glycolysis EXCEPT for K00850/K00895

TCA cycle as measured as a fraction of the following KOs:
		aconitate hydratase - 2 subunits K01681 & K01682
		isocitrate dehydrogenase K00031 OR isocitrate dehydrogenase (NAD+) K00030 OR isocitrate--homoisocitrate dehydrogenase K17753
		2-oxoglutarate/2-oxoacid ferredoxin oxidoreductase korAB essential K00174 + K00175 ALSO check for korCD K00177 & K00176
		succinyl-CoA synthetase K01899 + K01900 OR succinyl-CoA synthetase K01902 + K01903 OR succinyl-CoA:acetate CoA-transferase K18118
		fumarate reductase (K00244 + K00245 + K00246 + K00247) OR succinate dehydrogenase / fumarate reductase (K00239 + K00240 + K00241 + K00242) OR succinate dehydrogenase (ubiquinone) (K00234 + K00235 + K00236 + K00237)
		fumarate hydratase (K01677 + K01678 + K01679)
		malate dehydrogenase (quinone) K00116 OR K00025 OR K00026 OR K00024
		citrate synthase K01647

CBB cycle measured as a fraction of the following KOs:
		FIRST check and report presence of RuBisCo - ribulose-bisphosphate carboxylase (Type 1) two subunits K01601 + K01602
		Then check for 3 essential steps in canonical cycle:
		phosphoglycerate kinase K00927
		glyceraldehyde 3-phosphate dehydrogenase K00134 OR glyceraldehyde-3-phosphate dehydrogenase (NADP+) K05298 OR glyceraldehyde-3-phosphate dehydrogenase (NAD(P)) K00150
		phosphoribulokinase K00855
		Then check for ribulose regeneration (several alternative pathways):
		Option 1 - ribulose-phosphate 3-epimerase K01783 AND xylulose-5-phosphate/fructose-6-phosphate phosphoketolase K01621
		Option 2 - transketolase K00615	AND ribulose-phosphate 3-epimerase K01783
		Option 3 - transketolase K00615	AND ribose 5-phosphate isomerase A K01807
		Option 4 - fructose-bisphosphate aldolase, class I K01623 OR fructose-bisphosphate aldolase, class II K01624 OR fructose-bisphosphate aldolase, class I K11645
					transketolase K00615
					Some combination of these genes:
					fructose-1,6-bisphosphatase II / sedoheptulose-1,7-bisphosphatase K11532
					fructose-1,6-bisphosphatase I K03841 
					fructose-1,6-bisphosphatase II K02446

Reverse TCA cycle display completeness of TCA cycle, check for essential gene components:
		Requires
		Option 1 - ATP-citrate lyase K15230 + K15231
		Option 2 - citryl-CoA synthetase K15232 + K152333 AND citryl-CoA lyase K15234

Wood-Ljungdahl pathway requires some essential genes and pathway fraction:
		Essential:
		Option 1 (when fused) - acetyl-CoA decarbonylase/synthase complex subunit alpha K00192 AND carbon-monoxide dehydrogenase K00198 + K00196 OR carbon-monoxide dehydrogenase K03520 + K03518 + K03519
		Option 2 - CO-methylating acetyl-CoA synthase K14138 AND carbon-monoxide dehydrogenase K00198 + K03518 + K03519 + K03520
		Methyl branch:
		formate dehydrogenase K05299 + K15022
		formate--tetrahydrofolate ligase K01938
		methylenetetrahydrofolate dehydrogenase (NADP+) / methenyltetrahydrofolate cyclohydrolase K01491
		methylenetetrahydrofolate reductase (NADPH) K00297

3-hydroxypropionate pathway measured as a fraction of the following KOs:
	Two separate pathways cycling from acetyl-CoA
	Pathway 1:
		pyruvate ferredoxin oxidoreductase K00169 + K00170 + K00171 + K00172 + K03737
		pyruvate, orthophosphate dikinase K01006 OR pyruvate, water dikinase K01007
		phosphoenolpyruvate carboxylase K01595
		malate dehydrogenase K00024
		succinyl-CoA:(S)-malate CoA-transferase K14471 + K14472
		malyl-CoA/(S)-citramalyl-CoA lyase K08691
	Pathway 2:
		acetyl-CoA carboxylase, biotin carboxylase K02160 + K01961 + K01962 + K01963 + K01964 + K15037 + K15036 + K18603 + K18604 + K18605
		malonyl-CoA reductase / 3-hydroxypropionate dehydrogenase (NADP+) K14468 + K15017
		3-hydroxypropionate dehydrogenase (NADP+) K15039
		acrylyl-CoA reductase (NADPH) / 3-hydroxypropionyl-CoA dehydratase / 3-hydroxypropionyl-CoA synthetase K14469 + K15018
		3-hydroxypropionyl-coenzyme A dehydratase K15019
		acryloyl-coenzyme A reductase K15020
		malyl-CoA/(S)-citramalyl-CoA lyase K08691
		2-methylfumaryl-CoA hydratase K14449
		2-methylfumaryl-CoA isomerase K14470
		3-methylfumaryl-CoA hydratase K09709
		malyl-CoA/(S)-citramalyl-CoA lyase K08691

4-hydroxybutyrate/3-hydroxypropionate cycle measures as a fraction of the following KOs:
		Reference from Thaumarchaea -- incomplete in KOs
		acetyl-CoA carboxylase, biotin carboxylase K02160 + K01961 + K01962 + K01963 + K01964 + K15037 + K15036 + K18603 + K18604 + K18605
		malonic semialdehyde reductase K18602
		3-hydroxypropionyl-CoA synthetase (ADP-forming) K18594
		acrylyl-CoA reductase (NADPH) / 3-hydroxypropionyl-CoA dehydratase / 3-hydroxypropionyl-CoA synthetase K14469 + K15019
		propionyl-CoA carboxylase K15052 + K01964 + K15037 + K15036 + K18603 + K18604 + K18605
		methylmalonyl-CoA/ethylmalonyl-CoA epimerase K05606
		methylmalonyl-CoA mutase K01847 + K01848 + K01849
		4-hydroxybutyryl-CoA synthetase (ADP-forming) K18593
		4-hydroxybutyryl-CoA dehydratase / vinylacetyl-CoA-Delta-isomerase K14534
		enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase K15016
		acetyl-CoA C-acetyltransferase K00626

Carbon degradation - Each enzyme taken as a single entity:
		beta-glucosidase K05350
		beta-glucosidase K05349
		cellulase K01225
		cellulase K19668
		chitinase K01183
		bifunctional chitinase/lysozyme K13381
		basic endochitinase B K20547
		diacetylchitobiose deacetylase K03478 OR K18454
		beta-N-acetylhexosaminidase K01207
		pectinesterase K01051
		exo-poly-alpha-galacturonosidase K01213
		oligogalacturonide lyase K01730
		exopolygalacturonase K01184
		D-galacturonate isomerase K01812
		D-galacturonate epimerase K08679
		alpha-amylase K01176
		glucoamylase K01178  
		pullulanase K01200  

Chemotaxis (as determined by Tara) KO fraction above a certain threshold:
	K13924	 cheBR; two-component system, chemotaxis family, CheB/CheR fusion protein [EC:3.1.1.61 2.1.1.80]
	K00575	 cheR; chemotaxis protein methyltransferase CheR [EC:2.1.1.80]
	K03413	 cheY; two-component system, chemotaxis family, response regulator CheY
	K03412	 cheB; two-component system, chemotaxis family, response regulator CheB [EC:3.1.1.61]
	K03406	 mcp; methyl-accepting chemotaxis protein
	K03407	 cheA; two-component system, chemotaxis family, sensor kinase CheA [EC:2.7.13.3]
	K03415	 cheV; two-component system, chemotaxis family, response regulator CheV
	K03408	 cheW; purine-binding chemotaxis protein CheW

Flagellum biosynthesis (as determined by Tara) KO fraction above a certain threshold:
	K02409	 flagellar M-ring protein FliF
	K02401	 flagellar biosynthetic protein FlhB
	K02394	 flagellar P-ring protein precursor FlgI
	K02397	 flagellar hook-associated protein 3 FlgL
	K02396	 flagellar hook-associated protein 1 FlgK
	K02391	 flagellar basal-body rod protein FlgF
	K02390	 flagellar hook protein FlgE
	K02393	 flagellar L-ring protein precursor FlgH
	K02392	 flagellar basal-body rod protein FlgG
	K02386	 flagella basal body P-ring formation protein FlgA
	K02557	 chemotaxis protein MotB
	K02556	 chemotaxis protein MotA
	K02400	 flagellar biosynthesis protein FlhA
	K02418	 flagellar protein FliO/FliZ
	K02389	 flagellar basal-body rod modification protein FlgD
	K02412	 flagellum-specific ATP synthase [EC:3.6.3.14]
	K02387	 flagellar basal-body rod protein FlgB
	K02410	 flagellar motor switch protein FliG
	K02411	 flagellar assembly protein FliH
	K02416	 flagellar motor switch protein FliM
	K02417	 flagellar motor switch protein FliN/FliY
	K02407	 flagellar hook-associated protein 2
	K02406	 flagellin

Sulfur metabolism
	Assimilation
		K00392	 sir; sulfite reductase (ferredoxin) [EC:1.8.7.1]
		K00380 + K00381 cysJ; sulfite reductase (NADPH) flavoprotein alpha-component [EC:1.8.1.2] + cysI; sulfite reductase (NADPH) hemoprotein beta-component [EC:1.8.1.2]
	Reversible Dissimilatory
		K00958	sat; sulfate adenylyltransferase
		K00395 + K00394	aprB; adenylylsulfate reductase, subunit B [EC:1.8.99.2] + aprA; adenylylsulfate reductase, subunit A [EC:1.8.99.2]
		K11180 + K11181	dsrA; sulfite reductase, dissimilatory-type alpha subunit [EC:1.8.99.3] + dsrB; sulfite reductase, dissimilatory-type beta subunit [EC:1.8.99.3]
	Thiosulfate oxidation measured as a fraction of KOs:
		soxA K17222
		soxB K17224
		soxC K17225
		soxX K17223
		soxY K17226
		soxZ K17227
	Alternative thiosulfate oxidation
		K16936 doxA; thiosulfate dehydrogenase [quinone] small subunit [EC:1.8.5.2]
		K16937 doxD; thiosulfate dehydrogenase [quinone] large subunit [EC:1.8.5.2]
		K19713 tsdA; thiosulfate dehydrogenase [EC:1.8.2.2]
	Sulfur reduction (reversible reaction)
		K17219 sreA; sulfur reductase molybdopterin subunit
		K17220 sreB; sulfur reductase FeS subunit
		K17221 sreC; sulfur reductase membrane anchor
		K08352 psrA; thiosulfate reductase / polysulfide reductase chain A
		K08353 psrB; thiosulfate reductase electron transport protein
		K08354 psrC; thiosulfate reductase cytochrome b subunit
		K17993 hydA; sulfhydrogenase subunit alpha
		K17996 hydB; sulfhydrogenase subunit beta (sulfur reductase)
		K17995 hydG; sulfhydrogenase subunit gamma (sulfur reductase)
		K17994 hydD; sulfhydrogenase subunit delta
	Aerobic sulfur disproportionation
		K16952 sor; sulfur oxygenase/reductase [EC:1.13.11.55]
	K17725 sdo; sulfur dioxygenase
	K05301 sorB; sulfite dehydrogenase
	Sulfide oxidation
		K17218 sqr; sulfide:quinone oxidoreductase [EC:1.8.5.4]
		K17229 fccB; sulfide dehydrogenase [flavocytochrome c] flavoprotein chain
	Sulfite dehydrogenase (quinone)
		K21307 + K21308 + K21309 soeABC
	DMSP demethylation
		K17486 dmdA; dimethylsulfoniopropionate demethylase
	DMS dehydrogenase
		K16964 ddhA; dimethylsulfide dehydrogenase subunit alpha 
		K16965 ddhB; dimethylsulfide dehydrogenase subunit beta
		K16966 ddhC; dimethylsulfide dehydrogenase subunit gamma
	DMSO reductase
		K07306 dmsA; anaerobic dimethyl sulfoxide reductase subunit A
		K07307 dmsB; anaerobic dimethyl sulfoxide reductase subunit B (DMSO reductase iron- sulfur subunit)
		K07308 dmsC; anaerobic dimethyl sulfoxide reductase subunit C (DMSO reductase anchor subunit)

Methanogenesis
	Methanogenesis via methanol
		K14080 mtaA; [methyl-Co(III) methanol-specific corrinoid protein]:coenzyme M methyltransferase
		K04480 mtaB; methanol---5-hydroxybenzumidazolylcobamide Co-methyltransferase
		K14081 mtaC; methanol corrinoid protein
	Methanogenesis via dimethylamine
		K14082 mtbA; [methyl-Co(III) methylamine-specific corrinoid protein]:coenzyme M methyltransferase
		K16178 mtbB; dimethylamine---corrinoid protein Co-methyltransferase 
	Methanogenesis via dimethylsulfide, methanethiol, methylpropanoate
		K16954 mtsA; methylthiol:coenzyme M methyltransferase
		K16955 mtsB; methylated-thiol--corrinoid protein
	Methanogenesis via methylamine
		K16176 mtmB; monomethylamine methyltransferase
	Methanogenesis via trimethylamine
		K14083 mttB; trimethylamine methyltransferase
	Methanogenesis via acetate
		K00193 cdhC; acetyl-CoA decarbonylase/synthase complex subunit beta 
		K00194 cdhD; acetyl-CoA decarbonylase/synthase complex subunit delta 
		K00197 cdhE; acetyl-CoA decarbonylase/synthase complex subunit gamma
	Methanogenesis via CO2
		K00200 + K00201 + K00202 + K00203 + K11261 + K00205 fmdABCDEF; formylmethanofuran dehydrogenase
		K00200 + K00201 + K00202 + K00203 fwdABCD; tungsten-containing formylmethanofuran dehydrogenase
		K00672 ftr; formylmethanofuran--tetrahydromethanopterin N-formyltransferase 
		K01499 mch; methenyltetrahydromethanopterin cyclohydrolase
		K13942 hmd; 5,10-methenyltetrahydromethanopterin hydrogenase
		K00320 mer; 5,10-methylenetetrahydromethanopterin reductase
		K00577 + K00578 + K00579 + K00580 + K00581 + K00582 + K00583 + K00584 mtrABCDEFGH; tetrahydromethanopterin S-methyltransferase
	Coenzyme M reduction to methane
		K00399 + K00401 + K00402 mcrABCD; methyl-coenzyme M reductase
	Coenzyme B/Coenzyme M regeneration
		K03388 + K03389 + K03390 + K08264 + K08265 hdrABCDE; CoB-CoM heterodisulfide reductase
	Dimethylamine/trimethylamine dehydrogenase
		K00317 dmd-tmd; dimethylamine/trimethylamine dehydrogenase

Methane oxidation
	K16157 + K16158 + K16159 + K16161 mmoXYZC; soluble methane monooxygenase

Transporters
	K02040 + K02037 + K02038 + K02036 pstABCS; phosphate
	K02044 + K02042 + K02041 phnDEC; phosphonate
	K02064 + K02063 + K02062 tbpA,thiPQ; thiamin
	K06858 + K06073 + K06074 btuFCD; vitamin B12
	K11959 + K11960 + K11961 + K11962 + K11963 urtABCED; urea


Thiamin biosynthesis
	Generation of 2-[(2R,5Z)-2-carboxy-4-methylthiazol-5(2H)-ylidene]ethyl phosphate
		K03148 thiF; sulfur carrier protein ThiS adenylyltransferase
		K04487 iscS; cysteine desulfurase
		K03150 thiH; 2-iminoacetate synthase OR K03153 thiO; glycine oxidase
		K03151 thiI; thiamine biosynthesis protein ThiI
		K01662 dxs; 1-deoxy-D-xylulose-5-phosphate synthase
		K03149 thiG; thiazole synthase
		K10810 tenI; thiazole tautomerase OR THI4 K03146; thiamine thiazole synthase
	Generation of 4-amino-2-methyl-5-(diphosphomethyl)pyrimidine
		K18278 THI5; pyrimidine precursor biosynthesis enzyme OR K03147 thiC; phosphomethylpyrimidine synthase OR K00877 THI20; hydroxymethylpyrimidine/phosphomethylpyrimidine kinase / thiaminase OR K00941 thiD; hydroxymethylpyrimidine/phosphomethylpyrimidine kinase OR K14153 thiDE; hydroxymethylpyrimidine kinase / phosphomethylpyrimidine kinase / thiamine-phosphate diphosphorylase
		K00877 THI20; hydroxymethylpyrimidine/phosphomethylpyrimidine kinase / thiaminase OR K00941 thiD; hydroxymethylpyrimidine/phosphomethylpyrimidine kinase 
	Terminal biosynthesis
		K00788 thiE; thiamine-phosphate pyrophosphorylase OR K14153 thiDE; hydroxymethylpyrimidine kinase / phosphomethylpyrimidine kinase / thiamine-phosphate diphosphorylase OR K14154 THI6;thiamine-phosphate diphosphorylase / hydroxyethylthiazole kinase 
		K00946 thiL; thiamine-monophosphate kinase 

Riboflavin biosynthesis
	K02858 ribB; 3,4-dihydroxy 2-butanone 4-phosphate synthase OR K14652 ribAB; 3,4-dihydroxy 2-butanone 4-phosphate synthase / GTP cyclohydrolase II
	K00082 ribD2; 5-amino-6-(5-phosphoribosylamino)uracil reductase OR K11752 ribD; diaminohydroxyphosphoribosylaminopyrimidine deaminase / 5-amino-6-(5-phosphoribosylamino)uracil reductase 
	K00794 ribH; 6,7-dimethyl-8-ribityllumazine synthase
	K00793 ribE; riboflavin synthase
	Conversion to FMN and FAD (not included in script)
		K00861 RFK; riboflavin kinase OR K20884 FHY; riboflavin kinase / FMN hydrolase OR K11753 ribF; riboflavin kinase / FMN adenylyltransferase
		K14656 ribL; FAD synthetase OR K00953 FLAD1; FAD synthetase

Cobalamin biosynthesis
	K00798 pduO; cob(I)alamin adenosyltransferase OR K19221 cobA; cob(I)alamin adenosyltransferase
	K02232 cobQ; adenosylcobyric acid synthase
	K02225 cobC; cobalamin biosynthetic protein CobC
	K02227 cobD; adenosylcobinamide-phosphate synthase
	K02231 cobU; adenosylcobinamide kinase / adenosylcobinamide-phosphate guanylyltransferase
	If cobU is present, this function in the biosynthesis process has already been counted:
		K19712 cobY; adenosylcobinamide-phosphate guanylyltransferase
	K02233 cobV; adenosylcobinamide-GDP ribazoletransferase
	K02226 cobC; alpha-ribazole phosphatase
	K00768 cobT; nicotinate-nucleotide--dimethylbenzimidazole phosphoribosyltransferase

Oxidative phosphorylation (Nuo, ATPases)
	F-type ATPase
		K02111 + K02112 + K02115 + K02113 + K02114 + K02108 + K02109 + K02110 atpFBCHGDAE
	V-type ATPase
		K02117 + K02118 + K02119 + K02120 + K02121 + K02122 + K02107 + K02123 + K02124 ntpABCDEFIK,ahaH
	NADH-quinone oxidoreductase
		K00330 + K00331 + K00332 + K00333 + K00334 + K00335 + K00336 + K00337 + K00338 + K00339 + K00340 + K00341 + K00342 + K00343 nuoABCDEFGHIJKLMN
	NAD(P)H-quinone oxidoreductase
		K05574 + K05582 + K05581 + K05579 + K05572 + K05580 + K05578 + K05576 + K05577 + K05575 + K05573 + K05583 + K05584 + K05585 ndcABCDEFGHIJKLMN
	Cytochrome c oxidase, cbb3-type
		K00404 + K00405 + K00407 + K00406 ccoPQNO
	Cytochrome bd complex
		K00425 + K00426 cydAB
	cytochrome o ubiquinol oxidase
		K02300 + K02299 + K02298 + K02297 cyoABCD
	cytochrome c oxidase
		K02277 + K02276 + K02274 + K02275 coxABCD
	cytochrome aa3-600 menaquinol oxidase
		K02829 + K02828 + K02827 + K02826 qoxABCD
	ubiquinol-cytochrome c reductase
		K00411 petA; ubiquinol-cytochrome c reductase iron-sulfur subunit
		K00410 fbcH; ubiquinol-cytochrome c reductase cytochrome b/c1 subunit
	
Hydrogen redox
	K00437 + K18008 hydB2,hydA2; NiFe hydrogenase
	K18016 + K18017 + K18023 mbhLJK; membrane-bound hydrogenase
	K00533 + K00534 hupSL; ferrodoxin hydrogenase
	K05922 + K05927 hydA3,hydB3; hydrogen:quinone oxidoreductase
	K00436 + K18005 + K18006 + K18007 hoxHFUY; NAD-reducing hydrogenase
	K17992 + K18330 + K18331 + K18332 hndABCD; NADP-reducing hydrogenase
	K06282 + K06281 + K03620 hyaABC; NiFe hydrogenase Hyd-1

Photosynthesis
	Photosystem II (major reaction center proteins - 21 additional proteins possible as part of structure)
		K02703 + K02706 + K02705 + K02704 + K02707 + K02708
	Photosystem I
		K02689 + K02690 + K026891 + K02692 + K02693 + K02694 + K02696 + K02697 + K02698 + K02699 + K02700 + K08905 + K02695 + K02701 + K14332 + K02702
	Cytochrome b6/f complex
		K02635 + K02637 + K02634 + K02636 + K02642 + K02643 + K03689 + K02640
	Anoxygenic photosynthesis
		Anoxygenic reaction center II (pufML)
		K08929 + K08928
		Anoxygenic reaction center I (pscABCD)
		K08940 + K08941 + K08942 + K08943
	Retinal biosynthesis (necessary for proteorhodopsin)
		K06443 crtY; lycopene beta-cyclase
		K02291 crtB; 15-cis-phytoene/all-trans-phytoene synthase 
		K10027 crtI; phytoene desaturase 
		K13789 crtE; geranylgeranyl diphosphate synthase, type II

Entner-Doudoroff Pathway (to generate pyruvate, alt to glycolysis)
	K00036 G6PD; glucose-6-phosphate 1-dehydrogenase
	K01057 PGLS; 6-phosphogluconolactonase OR K07404 pgl; 6-phosphogluconolactonase
	Alternative to previous steps: K13937 H6PD; hexose-6-phosphate dehydrogenase
	K01690 edd; phosphogluconate dehydratase
	K01625 eda; 2-dehydro-3-deoxyphosphogluconate aldolase OR K17463 dgaF; 2-dehydro-3-deoxy-phosphogluconate aldolase OR K11395 kdpgA; 2-dehydro-3-deoxy-phosphogluconate/2-dehydro-3-deoxy-6-phosphogalactonate aldolase

Mixed Acid Fermentation (conversion of pyruvate to fermentation products)
	Pyruvate to Lactate
		K00016 LDH; L-lactate dehydrogenase
	Pyruvate to Formate + Acetyl-CoA
		K00656 pf1D; formate C-acetyltransferase
	Formate to CO2 & H2
		(K00122 + K00125 + K00126 + K00123 + K00124 + K00127 formate dehydrogenase)
	To Acetate
		Direct from pyruvate
			K00156 poxB; pyruvate dehydrogenase (quinone)
		Direct from pyruvate via Acetyl-P
			K00158 poxL; pyruvate oxidase + K01512 acyP; acylphosphatase
		Direct from acetyl-CoA
			K01067 ACH1; acetyl-CoA hydrolase
		From acetyl-CoA via Acetyl-P
			(K13788 pta; phosphate acetyltransferase OR K04020 eutD; phosphotransacetylase) + K01512 acyP; acylphosphatase
		From lactate
			K00467 lactate 2-monooxygenase
	To Ethanol
		Step 1 to Acetaldehyde from Acetate
			(K00128 + K14085 + K00149 aldehyde dehydrogenase (NAD+)) OR K00129 aldehyde dehydrogenase (NAD(P)+) OR K00138 aldB; aldehyde dehydrogenase
		Step 1 to Acetaldehyde from Acetyl-CoA (reversible)
			K00132 + K04072 + K04073 + K18366 + K04021 acetaldehyde dehydrogenase (acetylating)
		Step 2 to Ethanol from Acetaldehyde
			(K13951 OR K13980 OR K13952 OR K13953 OR K13954 OR K00001 OR K00121 OR K04072 OR K18857 alcohol dehydrogenase) OR (K14028 + K14029 methanol dehydrogenase (cytochrome c)) OR K00114 exaA; alcohol dehydrogenase (cytochrome c) OR K00002 adh; alcohol dehydrogenase (NADP+) OR K04022 eutG; alcohol dehydrogenase 	
	PEP to Succinate via OAA, malate & fumarate
		Step 1
			K01596 pckA; phosphoenolpyruvate carboxykinase (GTP) OR K20370 PEPCK; phosphoenolpyruvate carboxykinase (diphosphate) OR K01610 pckA; phosphoenolpyruvate carboxykinase (ATP)
		Step 2
			(K00025 + K00026 + K00024 malate dehydrogenase) OR K00051 malate dehydrogenase (NADP+) OR K00116 mqo; malate dehydrogenase (quinone)
		Step 3
			(K01676 + K01677 + K01678 + K01679 fumarate hydratase, class I)
		Step 4
			(K00244 + K00245 + K00246 + K00247 fumarate reductase flavoprotein)
Naphthalene degradation to salicylate
	K14579 + K14580 + K14578 + K14581 nahAabcd; naphthalene 1,2-dioxygenase (4 subunits)
	K14582 nahB; cis-1,2-dihydro-1,2-dihydroxynaphthalene/dibenzothiophene dihydrodiol dehydrogenase
	K14583 nahC; 1,2-dihydroxynaphthalene dioxygenase
	K14584 nahD; 2-hydroxychromene-2-carboxylate isomerase
	K14585 nahE; trans-o-hydroxybenzylidenepyruvate hydratase-aldolase 
	K00152 nahF; salicylaldehyde dehydrogenase

Biofilm formation
	K11935 + K11931 + K11936 + K11937 pgaABCD; biofilm PGA synthesis protein
	K13654 mcbR; GntR family transcriptional regulator, colanic acid and biofilm gene transcriptional regulator
	K12148 bssS; biofilm regulator BssS
	K13650 mcbA; MqsR-controlled colanic acid and biofilm protein A
	K04335 + K04334 + K04336 csgABC; curli fimbriae biosynthesis
	K12687 flu; antigen 43

Competence-related DNA transporter 
	Core components
	K02237  comEA; competence protein ComEA
	K01493  comEB; dCMP deaminase [EC:3.5.4.12]
	K02238  comEC; competence protein ComEC
	K02239  comER; competence protein ComER
	K02240  comFA; competence protein ComFA
	K02241  comFB; competence protein ComFB
	K02242  comFC; competence protein ComFC
	K02243  comGA; competence protein ComGA
	K02244  comGB; competence protein ComGB
	K02245  comGC; competence protein ComGC
	K02246  comGD; competence protein ComGD
	K02247  comGE; competence protein ComGE
	K02248  comGF; competence protein ComGF
	K02249  comGG; competence protein ComGG
	Related components
	K02250  comK; competence protein ComK
	K02251  comQ; competence protein ComQ
	K02252  comS; competence protein ComS
	K02253  comX; competence protein ComX
	K02254  comZ; competence protein ComZ
	Additional competence factors
	K12292	comA; ATP-binding cassette, subfamily C, bacterial, competence factor transporting protein [EC:3.4.22.-]
	K07680	comP; two-component system, NarL family, sensor histidine kinase ComP [EC:2.7.13.3]
	K12293	comB; competence factor transport accessory protein ComB
	K12415	comC; competence-stimulating peptide
	K12294	comD; two-component system, AgrA family, sensor histidine kinase ComD [EC:2.7.13.3]
	K12295	comE; two-component system, AgrA family, response regulator ComE
	K12296	comX1_2; competence protein ComX

Anaplerotic Reactions
	Glyoxylate shunt
	Requires the presence of both isocitrate lyase and malate synthase
	K01637	aceA; isocitrate lyase
	K01638	aceB; malate synthase
	Anaplerotic enzymes
	All reactions are reversible. Organisms can have 0-4 of the pathways
	K00029	maeB; malate dehydrogenase (oxaloacetate-decarboxylating) (NADP+) or 'malic' enzyme
	K01958	pyruvate carboxylase OR K01959 pycA + K01960 pycB; pyruvate carboxylase subunits A + B
	K01595	ppc; phosphoenolpyruvate carboxylase
	K01610	pckA; phosphoenolpyruvate carboxykinase (ATP) OR K01596 pckA; phosphoenolpyruvate carboxykinase (GTP) OR K20370 PEPCK; phosphoenolpyruvate carboxykinase (diphosphate)

Sulfolipid biosynthesis
	Two components SQD1/sqdB and SQD2 (SQD2 may not be present in bacteria/archaea but belongs to the CAZy GT4 family)
	K06118	sqdB; UDP-sulfoquinovose synthase 
	K06119	SQD2; sulfoquinovosyltransferase

C-P lyase
	There is key enzyme that performs the cleavage of methane from the C-bond PhnJ, but the entire pathway requires an operon that leads to synthesis of a ribosyl phosphonate
	The transporter for phosphonate phnCED is represented in the transporter subcategory
	K02043	phnF; GntR family transcriptional regulator, phosphonate transport system regulatory protein
	K06166	phnG; alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit 
	K06164	phnH; alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit 
	K06164	phnI; alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit 
	K06163	phnJ; alpha-D-ribose 1-methylphosphonate 5-phosphate C-P lyase
	K05781	phnK; putative phosphonate transport system ATP-binding protein
	K05780	phnL; alpha-D-ribose 1-methylphosphonate 5-triphosphate synthase subunit
	K06162	phnM; alpha-D-ribose 1-methylphosphonate 5-triphosphate diphosphatase
	k05775	phnN; ribose 1,5-bisphosphokinase
	k09994	phnO; aminoalkylphosphonate N-acetyltransferase
	K06167	phnP; phosphoribosyl 1,2-cyclic phosphate phosphodiesterase