1. 4.2.1.3 enzyme   cis-aconitase
                      aconitase
                      aconitate hydratase
                      citrate(isocitrate) hydro-lyase

2. 4.2.1.36 enzyme   cis-homoaconitase
                      homoaconitase
                      homoaconitate hydratase
                      2-hydroxybutane-1,2,4-tricarboxylate hydro-lyase

3. 1.14.13.37 enzyme   (S)-cis-N-methyltetrahydroberberine 14-monooxygenase
                      (S)-cis-N-methyltetrahydroprotoberberine-14-hydroxylase
                      methyltetrahydroprotoberberine 14-hydroxylase
                      methyltetrahydroprotoberberine 14-monooxygenase
                      (S)-N-methylcanadine,NADPH:oxygen oxidoreductase (14-hydroxylating)

4. 1.1.1.228 enzyme   (+)-cis-sabinol dehydrogenase
                      (+)-cis-sabinol:NAD+ oxidoreductase
                      (+)-sabinol dehydrogenase

5. 1.3.1.66 enzyme   cis-dihydroethylcatechol dehydrogenase
                      cis-1,2-dihydro-3-ethylcatechol:NAD+ oxidoreductase

6. 2.1.1.122 enzyme   tetrahydroprotoberberine cis-N-methyltransferase
                      S-adenosyl-L-methionine:(S)-7,8,13,14-tetrahydroprotoberberine cis-N-methyltransferase
                      (S)-tetrahydroprotoberberine N-methyltransferase

7. 2.4.1.209 enzyme   cis-p-coumarate glucosyltransferase
                      UDP-glucose:cis-p-coumarate beta-D-glucosyltransferase

8. 2.5.1.20 enzyme   cis-prenyl transferase
                      rubber cis-polyprenylcistransferase
                      isopentenyl pyrophosphate cis-1,4-polyisoprenyl transferase
                      poly-cis-polyprenyl-diphosphate:isopentenyl-diphosphate polyprenylcistransferase
                      rubber allyltransferase
                      rubber polymerase
                      rubber prenyltransferase
                      rubber transferase

9. 3.3.2.3 enzyme   cis-epoxide hydrolase
                      epoxide hydratase
                      epoxide hydrolase
                      epoxide hydrolase
                      arene-oxide hydratase
                      aryl epoxide hydrase
                      xenobiotic epoxide hydrolase
                      trans-stilbene oxide hydrolase
                      benzo(a)pyrene-4,5-epoxide hydratase
                      benzo[a]pyrene-4,5-oxide hydratase

10. 3.3.2.9 enzyme   cis-epoxide hydrolase
                      mEH
                      epoxide hydrase
                      epoxide hydratase (ambiguous)
                      microsomal epoxide hydrase
                      microsomal epoxide hydrolase
                      arene-oxide hydratase (ambiguous)
                      aryl epoxide hydrase (ambiguous)
                      microsomal epoxide hydratase (ambiguous)
                      benzo(a)pyrene-4,5-epoxide hydratase
                      benzo[a]pyrene-4,5-oxide hydratase

11. 1.1.1.219 enzyme   cis-3,4-leucopelargonidin:NADP+ 4-oxidoreductase
                      dihydromyricetin reductase
                      dihydroquercetin reductase
                      NADPH-dihydromyricetin reductase
                      dihydroflavanol 4-reductase
                      dihydrokaempferol 4-reductase

12. 1.1.1.9 enzyme   2,3-cis-polyol(DPN) dehydrogenase (C3-5)
                      erythritol dehydrogenase
                      xylitol dehydrogenase
                      D-xylulose reductase
                      pentitol-DPN dehydrogenase
                      xylitol-2-dehydrogenase
                      NAD-dependent xylitol dehydrogenase
                      xylitol:NAD+ 2-oxidoreductase (D-xylulose-forming)

13. 1.3.1.19 enzyme   cis-benzene glycol dehydrogenase
                      cis-1,2-dihydrobenzene-1,2-diol dehydrogenase
                      cis-1,2-dihydrobenzene-1,2-diol:NAD+ oxidoreductase
                      cis-1,2-dihydrocyclohexa-3,5-diene (nicotinamide adenine  dinucleotide) oxidoreductase

14. 1.3.1.29 enzyme   (+)-cis-naphthalene dihydrodiol dehydrogenase
                      cis-dihydrodiol naphthalene dehydrogenase
                      cis-1,2-dihydro-1,2-dihydroxynaphthalene dehydrogenase
                      cis-1,2-dihydronaphthalene-1,2-diol:NAD+ 1,2-oxidoreductase
                      naphthalene dihydrodiol dehydrogenase

15. 1.3.1.37 enzyme   NADPH-dependent cis-enoyl-CoA reductase
                      acyl-CoA:NADP+ cis-2-oxidoreductase
                      cis-2-enoyl-CoA reductase (NADPH)
                      cis-2-enoyl-CoA reductase (NADPH2)
                      cis-2-enoyl-coenzyme A reductase
                      reductase, cis-2-enoyl coenzyme A

16. 1.3.1.49 enzyme   cis-3,4-dihydrophenanthrene-3,4-diol dehydrogenase
                      (+)-cis-3,4-dihydrophenanthrene-3,4-diol:NAD+ 3,4-oxidoreductase

17. 1.3.1.56 enzyme   cis-2,3-dihydrobiphenyl-2,3-diol dehydrogenase
                      cis-3-phenylcyclohexa-3,5-diene-1,2-diol:NAD+ oxidoreductase
                      2,3-dihydro-2,3-dihydroxybiphenyl dehydrogenase

18. 1.3.1.61 enzyme   terephthalate 1,2-cis-dihydrodiol dehydrogenase
                      cis-4,5-dihydroxycyclohexa-1(6),2-diene-1,4-dicarboxylate:NAD+ oxidoreductase (decarboxylating)

19. 1.3.1.64 enzyme   phthalate 4,5-cis-dihydrodiol dehydrogenase
                      cis-4,5-dihydroxycyclohexa-1(6),2-diene-1,2-dicarboxylate:NAD+ oxidoreductase

20. 2.4.1.215 enzyme   cis-zeatin O-beta-D-glucosyltransferase
                      UDP-glucose:cis-zeatin O-beta-D-glucosyltransferase

21. 3.1.1.63 enzyme   11-cis-retinol palmitate esterase
                      11-cis-retinyl-palmitate acylhydrolase
                      11-cis-retinyl-palmitate hydrolase
                      RPH

22. 4.1.1.6 enzyme   cis-aconitate carboxy-lyase
                      cis-aconitic decarboxylase (CAD)
                      aconitate decarboxylase

23. 5.2.1.1 enzyme   maleate cis-trans-isomerase
                      maleate isomerase

24. 5.2.1.2 enzyme   maleylacetone cis-trans-isomerase
                      4-maleylacetoacetate cis-trans-isomerase
                      maleylacetoacetate isomerase
                      maleylacetoacetic isomerase
                      maleylacetone isomerase

25. 5.2.1.4 enzyme   3-maleylpyruvate cis-trans-isomerase
                      maleylpyruvate isomerase

26. 5.2.1.8 enzyme   peptidylproline cis-trans-isomerase
                      peptidyl-prolyl cis-trans isomerase
                      PPIase
                      peptidylprolyl isomerase
                      peptide bond isomerase
                      cyclophilin [misleading, see comments]

27. 5.5.1.1 enzyme   cis,cis-muconate cycloisomerase
                      cis,cis-muconate-lactonizing enzyme
                      muconate cycloisomerase
                      muconate cycloisomerase I
                      muconate lactonizing enzyme
                      4-carboxymethyl-4-hydroxyisocrotonolactone lyase (decyclizing)
                      2,5-dihydro-5-oxofuran-2-acetate lyase (decyclizing)

28. 1.3.1.25 enzyme   cis-1,2-dihydroxycyclohexa-3,5-diene-1-carboxylate dehydrogenase
                      cis-1,2-dihydroxycyclohexa-3,5-diene-1-carboxylate:NAD+  oxidoreductase
                      DHBDH
                      dihydrodihydroxybenzoate dehydrogenase
                      2-hydro-1,2-dihydroxybenzoate dehydrogenase
                      1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase
                      3,5-cyclohexadiene-1,2-diol-1-carboxylate dehydrogenase
                      3,5-cyclohexadiene-1,2-diol-1-carboxylic acid dehydrogenase
                      (1R,6R)-1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate:NAD+ oxidoreductase (decarboxylating)

29. 1.3.1.60 enzyme   cis-1,2-dihydroxy-1,2-dihydrodibenzothiophene:NAD+ oxidoreductase
                      dibenzothiophene dihydrodiol dehydrogenase

30. 2.5.1.31 enzyme   di-trans,poly-cis-decaprenylcistransferase
                      di-trans,poly-cis-undecaprenyl-diphosphate synthase
                      di-trans,poly-cis-decaprenyl-diphosphate:isopentenyl-diphosphate undecaprenylcistransferase
                      UPP synthetase
                      bactoprenyl-diphosphate synthase
                      undecaprenyl diphosphate synthetase
                      undecaprenyl pyrophosphate synthetase
                      undecaprenyl-diphosphate synthase

31. 5.3.3.14 enzyme   trans-2,cis-3-decenoyl-ACP isomerase
                      trans-2-cis-3-decenoyl-ACP isomerase
                      FabM
                      beta-hydroxydecanoyl thioester dehydrase
                      trans-2-decenoyl-ACP isomerase
                      trans-2-decenoyl-[acyl-carrier protein] isomerase

32. 5.5.1.2 enzyme   3-carboxy-cis,cis-muconate cycloisomerase
                      3-carboxymuconolactone hydrolase
                      beta-carboxymuconate lactonizing enzyme
                      2-carboxy-2,5-dihydro-5-oxofuran-2-acetate lyase (decyclizing)

33. 5.5.1.5 enzyme   carboxy-cis,cis-muconate cyclase
                      3-carboxymuconate cyclase
                      3-carboxy-2,5-dihydro-5-oxofuran-2-acetate lyase (decyclizing)

34. 1.1.1.232 enzyme   (15S)-15-hydroxy-5,8,11-cis-13-trans-icosatetraenoate:NAD(P)+ 15-oxidoreductase
                      15-hydroxyeicosatetraenoate dehydrogenase
                      15-hydroxyicosatetraenoate dehydrogenase

35. 1.3.1.58 enzyme   cis-2,3-dihydroxy-2,3-dihydro-p-cumate:NAD+ oxidoreductase
                      2,3-dihydroxy-2,3-dihydro-p-cumate dehydrogenase

36. 1.3.1.67 enzyme   cis-1,2-dihydroxy-4-methylcyclohexa-3,5-diene-1-carboxylate  dehydrogenase
                      cis-1,2-dihydroxy-4-methylcyclohexa-3,5-diene-1-carboxylate:NAD(P)+ oxidoreductase (decarboxylating)

37. 5.2.1.3 enzyme   all-trans-retinal 11-cis-trans-isomerase
                      retinal isomerase
                      retinene isomerase
                      retinoid isomerase

38. 5.2.1.5 enzyme   linoleate delta12-cis-delta11-trans-isomerase
                      linoleate isomerase
                      linoleic acid isomerase

39. 5.2.1.7 enzyme   all-trans-retinol 11-cis-trans-isomerase
                      retinol isomerase
                      all-trans-retinol isomerase

40. 5.2.1.9 enzyme   2-trans,6-trans-farnesol 2-cis-trans-isomerase
                      farnesol isomerase
                      farnesol 2-isomerase

41. 5.2.1.10 enzyme   2-chloro-4-carboxymethylenebut-2-en-1,4-olide cis-trans-isomerase
                      chlorodienelactone isomerase
                      2-chlorocarboxymethylenebutenolide isomerase
                      2-chloro-4-carboxymethylenebut-2-en-1,4-olide isomerase

42. 5.2.1.6 enzyme   2-(2-furyl)-3-(5-nitro-2-furyl)acrylamide cis-trans-isomerase
                      furylfuramide isomerase

43. 5.3.3.3 enzyme   delta3-cis-delta2-trans-enoyl-CoA isomerase
                      vinylacetyl coenzyme A isomerase
                      vinylacetyl-CoA delta-isomerase
                      vinylacetyl coenzyme A delta-isomerase
                      vinylacetyl-CoA delta3-delta2-isomerase

44. 5.3.3.8 enzyme   delta3-cis-delta2-trans-enoyl-CoA isomerase
                      dodecenoyl-CoA delta3-cis-delta2-trans-isomerase
                      acetylene-allene isomerase
                      dodecenoyl-CoA isomerase
                      dodecenoyl-CoA delta-isomerase
                      dodecenoyl-CoA (3Z)-(2E)-isomerase

45. 1.2.1.45 enzyme   4-carboxy-2-hydroxy-cis,cis-muconate-6-semialdehyde:NADP+  oxidoreductase
                      4-carboxy-2-hydroxy-cis,cis-muconate-6-semialdehyde:NADP+ 6-oxidoreductase
                      2-hydroxy-4-carboxymuconate 6-semialdehyde dehydrogenase
                      4-carboxy-2-hydroxymuconate-6-semialdehyde dehydrogenase
                      alpha-hydroxy-gamma-carboxymuconic epsilon-semialdehyde  dehydrogenase

46. 5.3.3.13 enzyme   eicosapentaenoate cis-delta5,8,11,14,17-eicosapentaenoate  cis-delta5-trans-delta7,9-cis-delta14,17 isomerase
                      PFI
                      polyenoic fatty acid isomerase
                      (5Z,8Z,11Z,14Z,17Z)-eicosapentaenoate delta8,11-delta7,8-isomerase