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AdditionalFile1.txt
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Sugars other than glucose:
Xylose
K01805 xylA; xylose isomerase [EC:5.3.1.5]
K00854 xylB, XYLB; xylulokinase [EC:2.7.1.17]
Arabinose
K01804 araA; L-arabinose isomerase [EC:5.3.1.4]
K00853 araB; L-ribulokinase [EC:2.7.1.16]
Galactose
K01785 galM, GALM; aldose 1-epimerase [EC:5.1.3.3]
K00849 galK; galactokinase [EC:2.7.1.6]
K00965 galT, GALT; UDPglucose--hexose-1-phosphate uridylyltransferase [EC:2.7.7.12]
K01784 galE, GALE; UDP-glucose 4-epimerase [EC:5.1.3.2]
K17716 capD; UDP-glucose 4-epimerase [EC:5.1.3.2]
Fructose
K00844 HK; hexokinase [EC:2.7.1.1], OR
K00847 E2.7.1.4, scrK; fructokinase [EC:2.7.1.4]
Mannose
K01809 manA, MPI; mannose-6-phosphate isomerase [EC:5.3.1.8], OR
K15916 pgi-pmi; glucose/mannose-6-phosphate isomerase [EC:5.3.1.9 5.3.1.8], OR
K16011 algA, xanB, rfbA, wbpW, pslB; mannose-1-phosphate guanylyltransferase / mannose-6-phosphate isomerase [EC:2.7.7.13 5.3.1.8]
Amino acids:
Alanine
K00814 GPT, ALT; alanine transaminase [EC:2.6.1.2], OR
K14260 alaA; alanine-synthesizing transaminase [EC:2.6.1.66 2.6.1.2], OR
K00830 AGXT; alanine-glyoxylate transaminase / serine-glyoxylate transaminase / serine-pyruvate transaminase [EC:2.6.1.44 2.6.1.45 2.6.1.51], OR
K00827 AGXT2; alanine-glyoxylate transaminase / (R)-3-amino-2-methylpropionate-pyruvate transaminase [EC:2.6.1.44 2.6.1.40], OR
K14272 GGAT; glutamate--glyoxylate aminotransferase [EC:2.6.1.4 2.6.1.2 2.6.1.44]
Aspartate
K01744 aspA; aspartate ammonia-lyase [EC:4.3.1.1]
Asparagine
K05597 aspQ, ansB, ansA; glutamin-(asparagin-)ase [EC:3.5.1.38], OR
K01424 E3.5.1.1, ansA, ansB; L-asparaginase [EC:3.5.1.1], OR
K13051 ASRGL1, iaaA; L-asparaginase / beta-aspartyl-peptidase [EC:3.5.1.1 3.4.19.5]
Glutamine
K01425 glsA, GLS; glutaminase [EC:3.5.1.2], OR
K23265 purQ; phosphoribosylformylglycinamidine synthase subunit PurQ / glutaminase [EC:6.3.5.3 3.5.1.2], OR
K05597 aspQ, ansB, ansA; glutamin-(asparagin-)ase [EC:3.5.1.38]
Glutamate
K15371 GDH2; glutamate dehydrogenase [EC:1.4.1.2], OR
K00260 gudB, rocG; glutamate dehydrogenase [EC:1.4.1.2], OR
K00261 GLUD1_2, gdhA; glutamate dehydrogenase (NAD(P)+) [EC:1.4.1.3], OR
K00262 E1.4.1.4, gdhA; glutamate dehydrogenase (NADP+) [EC:1.4.1.4]
Glycine
K00281 GLDC, gcvP; glycine dehydrogenase [EC:1.4.4.2]
K00282 gcvPA; glycine dehydrogenase subunit 1 [EC:1.4.4.2]
K00283 gcvPB; glycine dehydrogenase subunit 2 [EC:1.4.4.2]
K00605 gcvT, AMT; aminomethyltransferase [EC:2.1.2.10]
K00382 DLD, lpd, pdhD; dihydrolipoamide dehydrogenase [EC:1.8.1.4]
K02437 gcvH, GCSH; glycine cleavage system H protein
Serine
K17989 SDS, SDH, CHA1; L-serine/L-threonine ammonia-lyase [EC:4.3.1.17 4.3.1.19], OR
K01752 E4.3.1.17, sdaA, sdaB, tdcG; L-serine dehydratase [EC:4.3.1.17]
Threonine
K17989 SDS, SDH, CHA1; L-serine/L-threonine ammonia-lyase [EC:4.3.1.17 4.3.1.19], OR
K01754 E4.3.1.19, ilvA, tdcB; threonine dehydratase [EC:4.3.1.19]
Cysteine
K01758 CTH; cystathionine gamma-lyase [EC:4.4.1.1], OR
K17217 mccB; cystathionine gamma-lyase / homocysteine desulfhydrase [EC:4.4.1.1 4.4.1.2], OR
K00816 CCBL; kynurenine---oxoglutarate transaminase / cysteine-S-conjugate beta-lyase / glutamine---phenylpyruvate transaminase [EC:2.6.1.7 4.4.1.13 2.6.1.64], OR
K01760 metC; cysteine-S-conjugate beta-lyase [EC:4.4.1.13], OR
K14155 patB, malY; cysteine-S-conjugate beta-lyase [EC:4.4.1.13]
Methionine
K01761 E4.4.1.11; methionine-gamma-lyase [EC:4.4.1.11]
Arginine
K01476 E3.5.3.1, rocF, arg; arginase [EC:3.5.3.1]
K00819 rocD, OAT; ornithine--oxo-acid transaminase [EC:2.6.1.13]
K00294 E1.2.1.88; 1-pyrroline-5-carboxylate dehydrogenase [EC:1.2.1.88], OR
K13821 putA; RHH-type transcriptional regulator, proline utilization regulon repressor / proline dehydrogenase / delta 1-pyrroline-5-carboxylate dehydrogenase [EC:1.5.5.2 1.2.1.88]
Proline
K00318 PRODH, fadM, putB; proline dehydrogenase [EC:1.5.5.2]
K00294 E1.2.1.88; 1-pyrroline-5-carboxylate dehydrogenase [EC:1.2.1.88], OR
K13821 putA; RHH-type transcriptional regulator, proline utilization regulon repressor / proline dehydrogenase / delta 1-pyrroline-5-carboxylate dehydrogenase [EC:1.5.5.2 1.2.1.88]
Histidine
K01745 hutH, HAL; histidine ammonia-lyase [EC:4.3.1.3]
K01712 hutU, UROC1; urocanate hydratase [EC:4.2.1.49]
K01468 hutI, AMDHD1; imidazolonepropionase [EC:3.5.2.7]
K01479 hutG; formiminoglutamase [EC:3.5.3.8]
Oxidative phosphorylation
Cytochrome aa3 complex:
K02277 coxD, ctaF; cytochrome c oxidase subunit IV [EC:7.1.1.9]
K02276 coxC, ctaE; cytochrome c oxidase subunit III [EC:7.1.1.9]
K02274 coxA, ctaD; cytochrome c oxidase subunit I [EC:7.1.1.9]
K15408 coxAC; cytochrome c oxidase subunit I+III [EC:7.1.1.9]
K02275 coxB, ctaC; cytochrome c oxidase subunit II [EC:7.1.1.9]
Cytochrome cbb3 complex:
K00404 ccoN; cytochrome c oxidase cbb3-type subunit I [EC:7.1.1.9]
K00405 ccoO; cytochrome c oxidase cbb3-type subunit II
K15862 ccoNO; cytochrome c oxidase cbb3-type subunit I/II [EC:7.1.1.9]
K00407 ccoQ; cytochrome c oxidase cbb3-type subunit IV
K00406 ccoP; cytochrome c oxidase cbb3-type subunit III
Cytochrome bd:
K00425 cydA; cytochrome bd ubiquinol oxidase subunit I [EC:7.1.1.7]
K00426 cydB; cytochrome bd ubiquinol oxidase subunit II [EC:7.1.1.7]
Nitrogen
DNRA (nirBD or nrfAH)
K00362 nirB; nitrite reductase (NADH) large subunit [EC:1.7.1.15]
K00363 nirD; nitrite reductase (NADH) small subunit [EC:1.7.1.15]
K03385 nrfA; nitrite reductase (cytochrome c-552) [EC:1.7.2.2]
K15876 nrfH; cytochrome c nitrite reductase small subunit
Denitrification (narGHI or napAB + nirK or nirS + norBC + nosZ)
K00370 narG, narZ, nxrA; nitrate reductase / nitrite oxidoreductase, alpha subunit [EC:1.7.5.1 1.7.99.-]
K00371 narH, narY, nxrB; nitrate reductase / nitrite oxidoreductase, beta subunit [EC:1.7.5.1 1.7.99.-]
K00374 narI, narV; nitrate reductase gamma subunit [EC:1.7.5.1 1.7.99.-]
K02567 napA; nitrate reductase (cytochrome) [EC:1.9.6.1]
K02568 napB; nitrate reductase (cytochrome), electron transfer subunit
K00368 nirK; nitrite reductase (NO-forming) [EC:1.7.2.1]
K15864 nirS; nitrite reductase (NO-forming) / hydroxylamine reductase [EC:1.7.2.1 1.7.99.1]
K04561 norB; nitric oxide reductase subunit B [EC:1.7.2.5]
K02305 norC; nitric oxide reductase subunit C
K00376 nosZ; nitrous-oxide reductase [EC:1.7.2.4]
Short chain fatty acids
D-Lactate
K00102 LDHD, dld; D-lactate dehydrogenase (cytochrome) [EC:1.1.2.4], OR
K18930 dld; D-lactate dehydrogenase
L-lactate
K00101 lldD; L-lactate dehydrogenase (cytochrome) [EC:1.1.2.3]
Propionate
Step 1
K01895 ACSS1_2, acs; acetyl-CoA synthetase [EC:6.2.1.1], OR
K01908 ACSS3, prpE; propionyl-CoA synthetase [EC:6.2.1.17], OR
K01026 pct; propionate CoA-transferase [EC:2.8.3.1], OR
K01905 acdA; acetate---CoA ligase (ADP-forming) subunit alpha [EC:6.2.1.13] and
K22224 acdB; acetate---CoA ligase (ADP-forming) subunit beta [EC:6.2.1.13], OR
K24012 acdAB; acetate---CoA ligase (ADP-forming) [EC:6.2.1.13], OR
K00925 ackA; acetate kinase [EC:2.7.2.1] and
K00625 E2.3.1.8, pta; phosphate acetyltransferase [EC:2.3.1.8], OR
K13788 pta; phosphate acetyltransferase [EC:2.3.1.8], OR
K15024 K15024; putative phosphotransacetylase [EC:2.3.1.8]
Step 2
K01965 PCCA, pccA; propionyl-CoA carboxylase alpha chain [EC:6.4.1.3] and
K01966 PCCB, pccB; propionyl-CoA carboxylase beta chain [EC:6.4.1.3 2.1.3.15], OR
K03416 E2.1.3.1-5S; methylmalonyl-CoA carboxyltransferase 5S subunit [EC:2.1.3.1], OR
K11263 bccA, pccA; acetyl-CoA/propionyl-CoA carboxylase, biotin carboxylase, biotin carboxyl carrier protein [EC:6.4.1.2 6.4.1.3 6.3.4.14], OR
K15036 K15036; acetyl-CoA/propionyl-CoA carboxylase [EC:6.4.1.2 6.4.1.3 2.1.3.15], OR
K17489 E2.1.3.1-12S; methylmalonyl-CoA carboxyltransferase 12S subunit [EC:2.1.3.1], OR
K17490 E2.1.3.1-1.3S; methylmalonyl-CoA carboxyltransferase 1.3S subunit [EC:2.1.3.1], OR
K19312 pccB; acetyl-CoA/propionyl-CoA carboxylase carboxyl transferase subunit [EC:6.4.1.2 6.4.1.3 2.1.3.15]
Step 3
K05606 MCEE, epi; methylmalonyl-CoA/ethylmalonyl-CoA epimerase [EC:5.1.99.1]
Step 4
K01847 MUT; methylmalonyl-CoA mutase [EC:5.4.99.2], OR
K01849 E5.4.99.2B, mcmA2; methylmalonyl-CoA mutase, C-terminal domain [EC:5.4.99.2] and
K01848 E5.4.99.2A, mcmA1; methylmalonyl-CoA mutase, N-terminal domain [EC:5.4.99.2]
Step 5
K01902 sucD; succinyl-CoA synthetase alpha subunit [EC:6.2.1.5] and
K01903 sucC; succinyl-CoA synthetase beta subunit [EC:6.2.1.5]
Butyrate
Step 1
K00929 buk; butyrate kinase [EC:2.7.2.7] and
K00634 ptb; phosphate butyryltransferase [EC:2.3.1.19], OR
K01034 atoD; acetate CoA/acetoacetate CoA-transferase alpha subunit [EC:2.8.3.8 2.8.3.9] and
K01035 atoA; acetate CoA/acetoacetate CoA-transferase beta subunit [EC:2.8.3.8 2.8.3.9], OR
K23756 ACSM1;medium-chain acyl-CoA ligase / lipoate-activating enzyme [EC:6.2.1.2]
Step 2
K00248 ACADS, bcd; butyryl-CoA dehydrogenase [EC:1.3.8.1]
Step 3
K01782 fadJ; 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxybutyryl-CoA epimerase [EC:1.1.1.35 4.2.1.17 5.1.2.3], OR
K01692 paaF, echA; enoyl-CoA hydratase [EC:4.2.1.17], OR
K01715 crt; enoyl-CoA hydratase [EC:4.2.1.17], OR
K17865 croR; 3-hydroxybutyryl-CoA dehydratase [EC:4.2.1.55]
Step 4
K00023 phbB; acetoacetyl-CoA reductase [EC:1.1.1.36], OR
K00074 paaH, hbd, fadB, mmgB; 3-hydroxybutyryl-CoA dehydrogenase [EC:1.1.1.157], OR
K07516 fadN; 3-hydroxyacyl-CoA dehydrogenase [EC:1.1.1.35]
Step 5
K00626 ACAT, atoB; acetyl-CoA C-acetyltransferase [EC:2.3.1.9]
Acetate
Step 1
K00625 E2.3.1.8, pta; phosphate acetyltransferase [EC:2.3.1.8], OR
K00925 ackA; acetate kinase [EC:2.7.2.1] and
K13788 pta; phosphate acetyltransferase [EC:2.3.1.8], OR
K15024 K15024; putative phosphotransacetylase [EC:2.3.1.8]
K01895 ACSS1_2, acs; acetyl-CoA synthetase [EC:6.2.1.1], OR
Step 2
K14138 acsB; acetyl-CoA synthase [EC:2.3.1.169]
Step 3
K15023 acsE; 5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase [EC:2.1.1.258]
Step 4
K00297 metF, MTHFR; methylenetetrahydrofolate reductase (NADPH) [EC:1.5.1.20]
Step 5 and 6
K01491 folD; methylenetetrahydrofolate dehydrogenase (NADP+) / methenyltetrahydrofolate cyclohydrolase [EC:1.5.1.5 3.5.4.9]
Step 7
K01938 fhs; formate--tetrahydrofolate ligase [EC:6.3.4.3]
Step 8
K05299 fdhA; formate dehydrogenase (NADP+) alpha subunit [EC:1.17.1.10] and
K15022 fdhB; formate dehydrogenase (NADP+) beta subunit [EC:1.17.1.10]
Step 9
K00198 cooS, acsA; anaerobic carbon-monoxide dehydrogenase catalytic subunit [EC:1.2.7.4] and
K00196 cooF; anaerobic carbon-monoxide dehydrogenase iron sulfur subunit
WLP (all need to be present)
K15023 acsE; 5-methyltetrahydrofolate corrinoid/iron sulfur protein methyltransferase [EC:2.1.1.258]
K00297 metF, MTHFR; methylenetetrahydrofolate reductase (NADPH) [EC:1.5.1.20]
K01491 folD; methylenetetrahydrofolate dehydrogenase (NADP+) / methenyltetrahydrofolate cyclohydrolase [EC:1.5.1.5 3.5.4.9]
K01938 fhs; formate--tetrahydrofolate ligase [EC:6.3.4.3]
K05299 fdhA; formate dehydrogenase (NADP+) alpha subunit [EC:1.17.1.10]
K15022 fdhB; formate dehydrogenase (NADP+) beta subunit [EC:1.17.1.10]
K00198 cooS, acsA; anaerobic carbon-monoxide dehydrogenase catalytic subunit [EC:1.2.7.4]
K00197 cdhE, acsC; acetyl-CoA decarbonylase/synthase, CODH/ACS complex subunit gamma [EC:2.1.1.245]
K00194 cdhD, acsD; acetyl-CoA decarbonylase/synthase, CODH/ACS complex subunit delta [EC:2.1.1.245]
K14138 acsB; acetyl-CoA synthase [EC:2.3.1.169]
rTCA
System 1 (1 enzyme)
K01648 ACLY; ATP citrate (pro-S)-lyase [EC:2.3.3.8], OR
K15230 aclA; ATP-citrate lyase alpha-subunit [EC:2.3.3.8], and
K15231 aclB; ATP-citrate lyase beta-subunit [EC:2.3.3.8]
system 2 (two enzymes all three should be present)
K15232 ccsA; citryl-CoA synthetase large subunit [EC:6.2.1.18]
K15233 ccsB; citryl-CoA synthetase small subunit
K15234 ccl; citryl-CoA lyase [EC:4.1.3.34]
Calvin (all three need to be present)
K01601 rbcL, cbbL; ribulose-bisphosphate carboxylase large chain [EC:4.1.1.39]
K01602 rbcS, cbbS; ribulose-bisphosphate carboxylase small chain [EC:4.1.1.39]
K00855 PRK, prkB; phosphoribulokinase [EC:2.7.1.19]
Benzoyl-CoA degradation, benzoyl-CoA => 3-hydroxypimeloyl-CoA
Need badA + bcrABCD/ or bamBC + dch + had + oah
K04110 badA; benzoate-CoA ligase [EC:6.2.1.25]
K04112 bcrC, badD; benzoyl-CoA reductase subunit C [EC:1.3.7.8]
K04113 bcrB, badE; benzoyl-CoA reductase subunit B [EC:1.3.7.8]
K04114 bcrA, badF; benzoyl-CoA reductase subunit A [EC:1.3.7.8]
K04115 bcrD, badG; benzoyl-CoA reductase subunit D [EC:1.3.7.8]
K19515 bamB; benzoyl-CoA reductase subunit BamB [EC:1.3.-.-]
K19516 bamC; benzoyl-CoA reductase subunit BamC [EC:1.3.-.-]
K07537 dch; cyclohexa-1,5-dienecarbonyl-CoA hydratase [EC:4.2.1.100]
K07538 had; 6-hydroxycyclohex-1-ene-1-carbonyl-CoA dehydrogenase [EC:1.1.1.368]
K07539 oah; 6-oxocyclohex-1-ene-carbonyl-CoA hydrolase [EC:3.7.1.21]
Benzoate degradation, cyclohexanecarboxylic acid =>pimeloyl-CoA
need all of them to be present
K04116 aliA; cyclohexanecarboxylate-CoA ligase [EC:6.2.1.-]
K04117 aliB; cyclohexanecarboxyl-CoA dehydrogenase [EC:1.3.99.-]
K07534 badK; cyclohex-1-ene-1-carboxyl-CoA hydratase [EC:4.2.1.-]
K07535 badH; 2-hydroxycyclohexanecarboxyl-CoA dehydrogenase [EC:1.1.1.-]
K07536 badI; 2-ketocyclohexanecarboxyl-CoA hydrolase [EC:3.1.2.-]
K04118 E1.3.1.62; pimeloyl-CoA dehydrogenase [EC:1.3.1.62]
beta-Oxidation
Step 1
Any of these
K01897 ACSL, fadD; long-chain acyl-CoA synthetase [EC:6.2.1.3]
K15013 ACSBG; long-chain-fatty-acid--CoA ligase ACSBG [EC:6.2.1.3]
K00232 E1.3.3.6, ACOX1, ACOX3; acyl-CoA oxidase [EC:1.3.3.6]
K00249 ACADM, acd; acyl-CoA dehydrogenase [EC:1.3.8.7]
K00255 ACADL; long-chain-acyl-CoA dehydrogenase [EC:1.3.8.8]
K06445 fadE; acyl-CoA dehydrogenase [EC:1.3.99.-]
K09479 ACADVL; very long chain acyl-CoA dehydrogenase [EC:1.3.8.9]
Step 2
either of these
K01692 paaF, echA; enoyl-CoA hydratase [EC:4.2.1.17]
K07511 ECHS1; enoyl-CoA hydratase [EC:4.2.1.17]
K13767 fadB; enoyl-CoA hydratase [EC:4.2.1.17]
Step 3
either of these
K00022 HADH; 3-hydroxyacyl-CoA dehydrogenase [EC:1.1.1.35]
K07516 fadN; 3-hydroxyacyl-CoA dehydrogenase [EC:1.1.1.35]
OR step 2 and 3 combined
either of these
K01825 fadB; 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxybutyryl-CoA epimerase / enoyl-CoA isomerase [EC:1.1.1.35 4.2.1.17 5.1.2.3 5.3.3.8]
K01782 fadJ; 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxybutyryl-CoA epimerase [EC:1.1.1.35 4.2.1.17 5.1.2.3]
K07515 HADHA; enoyl-CoA hydratase / long-chain 3-hydroxyacyl-CoA dehydrogenase [EC:4.2.1.17 1.1.1.211]
K07514 EHHADH; enoyl-CoA hydratase / 3-hydroxyacyl-CoA dehydrogenase / 3,2-trans-enoyl-CoA isomerase [EC:4.2.1.17 1.1.1.35 5.3.3.8]
K10527 MFP2; enoyl-CoA hydratase/3-hydroxyacyl-CoA dehydrogenase [EC:4.2.1.17 1.1.1.35 1.1.1.211]
Last step
either of these
K00632 fadA, fadI; acetyl-CoA acyltransferase [EC:2.3.1.16]
K07513 ACAA1; acetyl-CoA acyltransferase 1 [EC:2.3.1.16]
K07508 ACAA2; acetyl-CoA acyltransferase 2 [EC:2.3.1.16]
K07509 HADHB; acetyl-CoA acyltransferase [EC:2.3.1.16]
Sometimes this is needed
K00626 ACAT, atoB; acetyl-CoA C-acetyltransferase [EC:2.3.1.9]