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Taxonomic profiling and metagenome analysis of a microbial community from a habitat contaminated with industrial discharges
Microbial Ecology
Varun Shah, Martha Zakrzewski, Daniel Wibberg, Felix Eikmeyer, Andreas Schlüter and Datta Madamwar*
*Corresponding author:- E-mail: [email protected]
Tel: +91-02692-229380; Fax: +91-02692-231042/236475
Affiliation: BRD School of Biosciences, Sardar Patel Maidan, Vadtal Road, Satellite Campus, Post Box No. 39,
Sardar Patel University, Vallabh Vidyanagar - 388 120, Anand, Gujarat, India.
47
Legends to supplementary
Figure S1 The rarefaction curves at rank phylum (a) and rank genus (b) for all the three microbial classification (RDP, CARMA and LCA)
Table S2 Selected gene ontology (GO) terms relevant to xenobiotic biodegradation are described
Table S3 Selected cluster of orthologous groups of proteins (COGs) playing a role in xenobiotic biodegradation are described
Table S4 Selected protein family members (Pfam) relevant in xenobiotic biodegradation are described
Table S5 Enzymes identified in metagenome sequences and also characterized in UM-BBD (University of Minnesota Biocatalysis/Biodegradation Database) for xenobiotic biodegradation along with their possible reactions and pathways are described
48
a
49
b
Fig. S1
50
Table S2: Selected gene ontology (GO) terms relevant to xenobiotic biodegradation are described.
GO terms
0005975
0006096
0016787
0016740
0005215
0016829
0006099
0009055
0033014
0006807
0016866
0008901
0006725
0008137
0008113
0008410
0006979
0015109
0015703
0015948
0016836
0004109
0004096
0004089
0000103
0019438
0009325
0008940
0004455
0004129
0006790
0006097
0016833
Description
Carbohydrate metabolic process
Glycolysis
Hydrolase activity
Transferase
Transporter
Lyase
TCA cycle
Electron carrier activity
Tetrapyrrole biosynthetic process
N compound metabolic process
Intramolecular transferase
Ferredoxin hydrogenase activity
Cellular aromatic compound metabolic process
NADH dehrogenase (ubiquinone)
Peptide methionine-(S)-oxide reductase
CoA transferase activity
Response to oxidative stress
Chromate transmembrane transporter
Chromate transport
Methanogenesis
Hydro lyase
Coproporphyrinogen oxidase
Catalase
Carbonate dehydratase
Sulfate assimilation
Aromatic compounds biosynthetic process
Nitrate reductase complex
Nitrate reductase activity
Ketol-acid reductoisomerase activity
Cytochrome c-oxidase
Sulfur metabolic process
Glyoxylate cycles
Oxo-acid lyase
51
0004781
0004497
0004602
0015105
0016846
0009375
0004174
0016840
0008146
0046685
0004601
0006801
0004597
0018492
0019645
0018759
0008827
0018822
0004301
0004784
0019439
0045482
0008937
0046413
0018836
0003937
0016811
0016705, 0016616,
0016651, 0016712,
0016625, 0016620,
0016655, 0016669,
0016614 and 0016730
0018576
0016813
Sulfate adenyl transferase activity (ATP)
Monooxygenase activity
Glutathione peroxidase
Arsenite transmembrane transporter
Carbon-sulfur lyase
Ferredoxin hydrogenase
Electron transferring flavoprotein dehydrogenase
C-N lyase
Sulfotransferase
Response to arsenic
Peroxidase
Superoxide metabolic
Peptide-aspartate β-dioxygenase activity
Carbon monoxide dehydrogenase
Anaerobic electron transport chain
Methenyltetrahydromethanopterin cyclohydrolase activity
Cytochrome O ubiquinol oxidase
Nitrile hydratase
Epoxide hydrolase
Superoxide dismutase
Aromatic compound catabolic process
Trichodiene synthase
Ferredoxin reductase
Organomercury catabolic process
Alkyl mercury lyase
IMP cyclohydrolase activity
Hydrolase activity
Oxidoreductase activity
Catechol I
Hydrolase activity
52
Table S3: Selected cluster of orthologous groups of proteins (COGs) playing a role in xenobiotic biodegradation are described.
COG category/
COG no.
C
COG1032
COG0247
COG0437
COG1905
COG0526
COG0778
COG0543
COG1145
COG1007
COG0348
COG1251
COG0852
COG0649
COG1008
COG0731
COG1005
COG0377
COG1034
COG0713
COG2181
COG0674
COG1013
COG1144
COG1014
COG2710
COG1347
COG3259
COG2080
Description
Energy production and conversion
Fe-S oxidoreductases family 2
Fe-S oxidoreductases
Fe-S-cluster-containing hydrogenase components 1
NADH:ubiquinone oxidoreductase 24 kD subunit
Thiol-disulfide isomerase and thioredoxins
Nitroreductase
2-polyprenylphenol hydroxylase and related flavodoxin oxidoreductases
Ferredoxin 2
NADH:ubiquinone oxidoreductase subunit 2 (chain N)
Polyferredoxin
NAD(P)H-nitrite reductase
NADH:ubiquinone oxidoreductase 27 kD subunit
NADH:ubiquinone oxidoreductase 49 kD subunit 7
NADH:ubiquinone oxidoreductase subunit 4 (chain M)
Fe-S oxidoreductases
NADH:ubiquinone oxidoreductase subunit 1 (chain H)
NADH:ubiquinone oxidoreductase 20 kD subunit and related Fe-S oxidoreductases
NADH dehydrogenase/NADH:ubiquinone oxidoreductase 75 kD subunit (chain G)
NADH:ubiquinone oxidoreductase subunit 11 or 4L (chain K)
Nitrate reductase gamma subunit
Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, alpha subunit
Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, beta subunit
Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, delta subunit
Pyruvate:ferredoxin oxidoreductase and related 2-oxoacid:ferredoxin oxidoreductases, gamma subunit
Nitrogenase molybdenum-iron protein, alpha and beta chains
Na+-transporting NADH:ubiquinone oxidoreductase subunit 4
Coenzyme F420-reducing hydrogenase, alpha subunit
Aerobic-type carbon monoxide dehydrogenase, small subunit CoxS/CutS homologs
53
COG2878
COG1148
COG0243
COG1902
P
COG2059
COG0659
COG3256
COG2897
COG0607
COG3420
COG3142
COG2920
COG0715
COG0600
H
COG0043
COG0163
COG0382
COG2227
COG0147
COG0512
Q
COG1228
COG1225
T
COG0589
R
COG2070
O
COG3634
Predicted alternative beta subunit of Na+-transporting NADH:ubiquinone oxidoreductase
Heterodisulfide reductase, subunit A and related polyferredoxins
Anaerobic dehydrogenases, typically selenocysteine-containing
NADH:flavin oxidoreductases, Old Yellow Enzyme family
Inorganic ion transport and metabolism
Chromate transport protein ChrA
Sulfate permease and related transporters (MFS superfamily)
Nitric oxide reductase large subunit
Rhodanese-related sulfurtransferases
Rhodanese-related sulfurtransferases
Nitrous oxidase accessory protein
Uncharacterized protein involved in copper resistance
Sulfite reductase, gamma subunit
ABC-type nitrate/sulfonate/taurine/bicarbonate transport systems, periplasmic components
ABC-type nitrate/sulfonate/taurine/bicarbonate transport systems, permease components
Coenzyme metabolism
3-polyprenyl-4-hydroxybenzoate decarboxylase and related decarboxylases
3-polyprenyl-4-hydroxybenzoate decarboxylase
4-hydroxybenzoate polyprenyltransferase and related prenyltransferases
2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase
Anthranilate/para-aminobenzoate synthases component I
Anthranilate/para-aminobenzoate synthases component II
Secondary metabolites biosynthesis, transport and catabolism
Imidazolonepropionase and related amidohydrolases
Peroxiredoxin
Signal transduction mechanisms
Universal stress protein UspA and related nucleotide-binding proteins
General function predictions only
Dioxygenases related to 2-nitropropane dioxygenase
Post translational modification, protein turnover, chaperones
Alkyl hydroperoxide reductase, large subunit
(E/H)
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Table S4: Selected protein family members (Pfam) relevant in xenobiotic biodegradation are described.
Pfam no.
PF01558
PF10695
PF01512
PF00909
PF01257
PF01475
PF03060
PF03807
PF02417
PF01625
PF00148
PF00174
PF01654
PF01544
PF04909
PF10589
PF02578
PF02028
PF02219
PF01970
PF04324
PF01977
PF00199
PF03150
PF01676
PF05690
PF02421
PF02322
PF02665
PF10588
PF02657
PF06983
PF01070
Description
Pyruvate ferredoxin/flavodoxin oxidoreductase (POR)
Cell-wall-associated hydrolase (Cw-hydrolase)
Respiratory-chain NADH dehydrogenase 51 Kd subunit (Complex1_51K)
Ammonium transporter family (Ammonium_transp)
Respiratory-chain NADH dehydrogenase 24 Kd subunit (Complex1_24kDa)
Ferric uptake regulator family (FUR)
2-nitropropane dioxygenase (NPD)
NADP oxidoreductase coenzyme F420-dependent (F420_oxidored)
Chromate transporter (Chromate_transp)
Peptide methionine sulfoxide reductase (PMSR)
Nitrogenase component 1 type Oxidoreductase (Oxidored_nitro)
Oxidoreductase molybdopterin binding domain (Oxidored_molyb)
Bacterial Cytochrome Ubiquinol Oxidase (Bac_Ubq_Cox)
CorA-like Mg2+ transporter protein (CorA)
Amidohydrolase (Amidohydro_2)
NADH-ubiquinone oxidoreductase-F iron-sulfur binding region (NADH_4Fe-4S)
Multi-copper polyphenol oxidoreductase laccase (Cu-oxidase_4)
BCCT family transporter (BCCT)
Methylenetetrahydrofolate reductase (MTHFR)
Tripartite tricarboxylate transporter TctA family (TctA)
BFD-like [2Fe-2S] binding domain (Fer2_BFD)
3-octaprenyl-4-hydroxybenzoate carboxy-lyase (UbiD)
Catalase (Catalase)
Di-haem cytochrome c peroxidase (CCP_MauG)
Metalloenzyme superfamily (Metalloenzyme)
Thiazole biosynthesis protein ThiG (ThiG)
Ferrous iron transport protein B (FeoB_N)
Cytochrome oxidase subunit II (Cyto_ox_2)
Nitrate reductase gamma subunit (Nitrate_red_gam)
NADH-ubiquinone oxidoreductase-G iron-sulfur binding region (NADH-G_4Fe-4S_3)
Fe-S metabolism associated domain (SufE)
3-demethylubiquinone-9 3-methyltransferase (3-dmu-9_3-mt)
FMN-dependent dehydrogenase (FMN_dh)
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PF04453
PF05896
PF07833
PF01794
PF02040
PF02335
PF00775
PF03594
PF01880
PF07664
PF05425
PF08770
PF00743
PF07879
PF05816
PF08376
PF02342
PF02613
PF04386
PF08803
PF05275
PF05187
PF02411
PF01322
PF02167
PF00685
PF09678
PF00848
PF03091
PF10399
PF05138
PF03892
PF06778
PF03597
PF00866
PF04234
Organic solvent tolerance protein (OstA_C)
Na(+)-translocating NADH-quinone reductase subunit A (NQRA) (NQRA)
Copper amine oxidase N-terminal domain (Cu_amine_oxidN1)
Ferric reductase like transmembrane component (Ferric_reduct)
Arsenical pump membrane protein (ArsB)
Cytochrome c552 (Cytochrom_C552)
Dioxygenase (Dioxygenase_C)
Benzoate membrane transport protein (BenE)
Desulfoferrodoxin (Desulfoferrodox)
Ferrous iron transport protein B C terminus (FeoB_C)
Copper resistance protein D (CopD)
Sulphur oxidation protein SoxZ (SoxZ)
Flavin-binding monooxygenase-like (FMO-like)
PHB/PHA accumulation regulator DNA-binding domain (PHB_acc_N)
Toxic anion resistance protein (TelA) (TelA)
Nitrate and nitrite sensing (NIT)
Bacterial stress protein (TerD)
Nitrate reductase delta subunit (Nitrate_red_del)
Stringent starvation protein B (SspB)
Putative mono-oxygenase ydhR (ydhR)
Copper resistance protein B precursor (CopB) (CopB)
Electron transfer flavoprotein-ubiquinone oxidoreductase (ETF_QO)
MerT mercuric transport protein (MerT)
Cytochrome C (Cytochrom_C_2)
Cytochrome C1 family (Cytochrom_C1)
Sulfotransferase domain (Sulfotransfer_1)
Cytochrome c oxidase caa3 assembly factor (Caa3_CtaG) (Caa3_CtaG)
Ring hydroxylating alpha subunit (catalytic domain) (Ring_hydroxyl_A)
CutA1 divalent ion tolerance protein (CutA1)
Ubiquitinol-cytochrome C reductase Fe-S subunit TAT signal (UCR_Fe-S_N)
Phenylacetic acid catabolic protein (PaaA_PaaC)
Nitrate reductase cytochrome c-type subunit (NapB) (NapB)
Chlorite dismutase (Chlor_dismutase)
Cytochrome oxidase maturation protein cbb3-type (CcoS)
Ring hydroxylating beta subunit (Ring_hydroxyl_B)
Copper resistance protein CopC (CopC)
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PF06240
PF06953
PF04261
PF03598
PF05233
PF10670
PF00080
PF05597
PF07357
PF10138
PF09828
PF08802
PF03626
PF08635
PF04444
PF02289
PF05099
PF06441
PF06099
PF09055
PF02943
PF03596
PF03284
PF07746
PF02979
PF01179
PF05494
PF07976
PF04896
PF09821
PF01058
PF02727
PF07858
PF03712
PF09242
Carbon monoxide dehydrogenase subunit G (CoxG) (COXG)
Arsenical resistance operon trans-acting repressor ArsD (ArsD)
Dyp-type peroxidase family (Dyp_perox)
CO dehydrogenase/acetyl-CoA synthase complex beta subunit (CdhC)
PHB accumulation regulatory domain (PHB_acc)
Nickel uptake substrate-specific transmembrane region (NikM)
Copper/zinc superoxide dismutase (SODC) (Sod_Cu)
Poly(hydroxyalcanoate) granule associated protein (phasin) (Phasin)
Dinitrogenase reductase ADP-ribosyltransferase (DRAT) (DRAT)
Tellurium resistance protein (Tellurium_res)
Chromate resistance exported protein (Chrome_Resist)
Cytochrome B6-F complex Fe-S subunit (CytB6-F_Fe-S)
Prokaryotic Cytochrome C oxidase subunit IV (COX4_pro)
Putative oxidoreductase C terminal (ox_reductase_C)
Catechol dioxygenase N terminus (Dioxygenase_N)
Cyclohydrolase (MCH) (MCH)
Tellurite resistance protein TerB (TerB)
Epoxide hydrolase N terminus (EHN)
Phenol hydroxylase subunit (Phenol_hyd_sub)
Nickel-containing superoxide dismutase (Sod_Ni)
Ferredoxin thioredoxin reductase catalytic beta chain (FeThRed_B)
Cadmium resistance transporter (Cad)
Phenazine biosynthesis protein A/B (PHZA_PHZB)
Aromatic-ring-opening dioxygenase LigAB
Nitrile hydratase
Copper amine oxidase
Toluene tolerance
Phenol hydroxylase
Ammonia monooxygenase/methane monooxygenase
ABC nitrate/sulfonate/bicarbonate family transporter
NADH ubiquinone oxidoreductase
Copper amine oxidase
Limonene-1
Copper type II ascorbate-dependent monooxygenase
Flavocytochrome c sulphide dehydrogenase
57
Table S5: Enzymes identified in metagenome sequences and also characterized in UM-BBD (University of Minnesota Biocatalysis/Biodegradation Database) for xenobiotic biodegradation along with their possible reactions and pathways are described.
Sr.
No.
1
2
3
4
5
Enzyme
Possible pathways
Catalyzed reaction(s)
Azoreductase
3-hydroxyacyl CoA dehydrogenase
Acetoacetyl CoA reductase
s-hydroxymethyl glutathione
dehydrogenase
Quinoprotein alcohol
dehydrogenase
Dye degradation pathway
Cyclohexane degradation pathway
Benzoate degradation pathway (anaerobic)
C1 Metabolic cycle pathway
From diazene to RNH2 + R’NH2
From (3S)-3-Hydroxyadipyl-CoA to 3-Oxoadipyl-CoA
From (3S)-3-Hydroxybutyryl-CoA to Acetoacetyl-CoA
From S-Hydroxymethylglutathione to S-Formylglutathione
1,2 Dichloroethane degradation pathway
C1 Metabolic cycle pathway
Hexahydro-1,3,5-trinitro-1,3,5-triazine degradation
pathway
1,3-Dichloropropene family degradation pathway
From 2-Chloroethanol to Chloroacetaldehyde
From Methanol to Formaldehyde
From Formate to Carbon Dioxide
6
Formate dehydrogenase
7
Aldehyde dehydrogenase
8
Aldehyde dehydrogenase (NAD+)
9
10
Aldehyde oxidase
Carbon monoxide dehydrogenase
11
12
2,5-Dichloro-2,5-cyclohexadiene1,4-diol dehydrogenase
Benzyl alcohol dehydrogenase
13
14
15
16
Enoyl CoA reductase
Benzoyl CoA reductase
4-hydroxy benzoyl CoA reductase
Trimethylamine dehydrogenase
1,2 Dichloroethane degradation pathway
Dodecyl sulphate degradation pathway
n-octane degradation pathway
Furfural degradation pathway
Thiocyanate degradation pathway
2,4,6 trinitrotoluene degradation pathway (anaerobic)
gamma-Hexachlorocyclohexane degradation pathway
Toluene degradation pathway
m-cresol degradation pathway
o-xylene degradation pathway
m-xylene degradation pathway
p-xylene degradation pathway
Cyclohexane degradation pathway
Benzoate degradation pathway (anaerobic)
Phenol degradation pathway (anaerobic)
N,N-Diethyl-m-toluamide degradation pathway
N-Methylmorpholine-N-oxide degradation pathway
From cis-3-Chloroallyl aldehyde to cis-3-Chloroacrylic acid
From trans-3-Chloroallyl aldehyde to trans-3-Chloroacrylic acid
From Chloroacetaldehyde to Chloroacetate
From Dodecanal to Lauric acid
From 1-Octanal to Octanoate
From Furfural to 2-Furoate
From Carbon Monoxide to Carbon Dioxide
From 2,4-Diamino-6-nitrotoluene to 2,4-Diamino-6hydroxylaminotoluene
From 2,5-Dichloro-2,5-cyclohexadiene-1,4-diol to 2,5Dichlorohydroquinone
From Benzyl alcohol to Benzaldehyde
From 3-Hydroxybenzyl alcohol to 3-Hydroxybenzaldehyde
From 2-Methylbenzyl alcohol to 2-Methylbenzaldehyde
From 3-Methylbenzyl alcohol to 3-Methylbenzaldehyde
From p-Methylbenzyl alcohol to p-Tolualdehyde
From Adipyl-CoA to 5-Carboxy-2-pentenoyl-CoA
From Benzoyl-CoA to Cyclohex-1,5-diene-1-carboxyl-CoA
From 4-Hydroxybenzoyl-CoA to Benzoyl-CoA
From Diethylamine to Acetaldehyde and Ethyl amine
From N-Methylmorpholine to Formaldehyde and Morpholine
58
17
Methylamine dehydrogenase
18
19
Trimethylamine-N-oxide reductase
Xenobiotic reductase
and Morpholine degradation pathway
Hexadecyltrimethylammonium chloride degradation
pathway
N,N-Diethyl-m-toluamide degradation pathway
2-Chloro-N-isopropylacetanilide degradation
pathway
Glyphosate degradation pathway
N-Methylmorpholine-N-oxide degradation pathway
Nitroglycerin degradation pathway
Pentaerythritol tetranitrate degradation pathway
20
NAD(P)H nitroreductase
2,4,6-Trinitrotoluene degradation pathway
(anaerobic/aerobic)
2,4 dinitrotoluene degradation pathway
21
22
2-Oxopropyl-CoM reductase
Dimethyl sulfoxide reductase
23
Dissimilatory sulfite reductase
Parathion degradation pathway (anaerobic/aerobic)
Propylene degradation pathway
Dimethyl sulfoxide and
Organosulfide cycle pathway
2,4,6-Trinitrotoluene degradation pathway
From Trimethylamine to Formaldehyde and Dimethylamine
From Ethyl amine to Acetaldehyde
From Isopropylamine to Acetaldehyde and Methane
From Methylamine to Formaldehyde
From N-Methylmorpholine-N-oxide to N-Methylmorpholine
From 1,2-Dinitroglycerol to 1-Mononitroglycerol or 2Mononitroglycerol
From 1,3-Dinitroglycerol to 1-Mononitroglycerol
From 1-Mononitroglycerol to Glycerol
From 2-Mononitroglycerol to Glycerol
From Nitroglycerin (NG) to 1,2-Dinitroglycerol or 1,3-Dinitroglycerol
From Pentaerythritol tetranitrate to Pentaerythritol trinitrate
From Pentaerythritol trinitrate to Pentaerythritol dinitrate
From 4-Amino-2,6-dinitrotoluene to 4-Amino-2-hydroxylamino-6nitrotoluene or 2,4-Diamino-6-nitrotoluene
From 2-Amino-4,6-dinitrotoluene to 2,6-Diamino-4-nitrotoluene or
2,4-Diamino-6-nitrotoluene
From 2,4-Dihydroxylamino-6-nitrotoluene to 4-Amino-2hydroxylamino-6-nitrotoluene
From 4-Hydroxylamino-2,6-dinitrotoluene to 4-Amino-2,6dinitrotoluene
From 2-Hydroxylamino-4,6-dinitrotoluene to 2-Amino-4,6dinitrotoluene
From 2,4,6-Trinitrotoluene to 4-Amino-2,6-dinitrotoluene or 2-Amino4,6-dinitrotoluene or 2-Hydroxylamino-4,6-dinitrotoluene
From 4-Amino-2-nitrotoluene to 2,4-Diaminotoluene
From 2-Amino-4-nitrotoluene to 2,4-Diaminotoluene
From 2,4-Dinitrotoluene to 4-Amino-2-nitrotoluene or 2-Amino-4nitrotoluene
From Parathion to Aminoparathion
From 2-Oxopropyl-CoM to Acetoacetate
From Dimethyl Sulfoxide to Dimethyl Sulfide
From 2,4-Diamino-6-hydroxylaminotoluene to 2,4,6-Triaminotoluene
59
24
25
26
27
28
Lignin peroxidase
Alkyl hydroperoxide reductase
Cytochrome-c3 hydrogenase
2-Aminophenol 1,6 dioxygenase
Catechol 1,2 dioxygenase
(anaerobic)
Anthracene degradation pathway
n-octane degradation pathway
Chromium(VI) reduction pathway
Nitrobenzene degradation pathway
Nitrobenzene degradation pathway
Chlorobenzene degradation pathway
2,4-Dichlorophenoxyacetic acid degradation pathway
2-Mercaptobenzothiazole degradation pathway
4-Fluorobenzoate degradation pathway
(anaerobic/aerobic)
3-Fluorobenzoate degradation pathway
p-Xylene degradation pathway
Tetrachlorobenzene degradation pathway
1,2,4-Trichlorobenzene degradation pathway
(anaerobic/aerobic)
2-Mercaptobenzothiazole degradation pathway
29
Catechol 2,3 dioxygenase
Nitrobenzene degradation pathway
2,4-Dichlorophenoxyacetic acid degradation pathway
o-Xylene degradation pathway
Toluene degradation pathway
p-Xylene degradation pathway
30
31
32
33
34
35
Protocatechuate 3,4 dioxygenase
Protocatechuate 4,5 dioxygenase
Homogentisate 1,2-dioxygenase
2-Nitropropane dioxygenase
Chlorite dismutase
Ammonia monooxygenase
36
Phthalate 4,5-dioxygenase
2-Aminobenzenesulfonate degradation pathway
Styrene degradation pathway
Benzoate degradation via hydroxylation pathway
Benzoate degradation via hydroxylation pathway
Styrene degradation pathway
2-Nitropropane degradation pathway
Perchlorate degradation Pathway (anaerobic)
1,1,1-Trichloroethane degradation
pathway (anaerobic/aerobic)
Phthalate family degradation pathway
From Anthracene to 9,10-Anthraquinone
From Octane hydroperoxide to 1-Octanol
From Chromate to Chromium (III)
From 2-Aminophenol to 2-Aminomuconate semialdehyde
From Catechol to cis,cis-Muconate
From 3-Chlorocatechol to 2-Chloro-cis,cis-muconate
From 4-Chlorocatechol to 3-Chloro-cis,cis-muconate
From 6,7-Dihydroxy-2-mercaptobenzothiazole to 4-[2Carboxylatovinyl]-2-mercaptothiazole-5-carboxylate
From 4-Fluorocatechol to 3-Fluoro-cis,cis-muconate
From 3-Fluorocatechol to 2-Fluoro-cis,cis-muconate
From 4-Methylcatechol to 3-Methyl-cis,cis-hexadienedioate
From Tetrachlorocatechol to Tetrachloro-cis,cis-muconate
From 3,4,6-Trichlorocatechol to 2,3,5-Trichloro-cis,cis-muconate
From 2,6,7-Trihydroxybenzothiazole to 4-[2-Carboxylatovinyl]-2hydroxythiazole-5-carboxylate
From Catechol to 2-Hydroxy-cis,cis-muconate semialdehyde
From 4-Chlorocatechol to 5-Chloro-2-hydroxymuconic semialdehyde
From 3,4-Dimethylcatechol to 2-Hydroxy-5-methyl-6-oxohepta-2,4dienoate
From 3-Methylcatechol to cis,cis-2-Hydroxy-6-oxohept-2,4-dienoate
From 4-Methylcatechol to 2-Hydroxy-5-methyl-cis,cis-muconic
semialdehyde
From 3-Sulfocatechol to 2-Hydroxymuconate
From 3-Vinylcatechol to (2E,4Z)-2-Hydroxy-6-oxoocta-2,4,7-trienoate
From 3,4-Dihydroxybenzoate to 3-Carboxy-cis,cis-muconate
From Protocatechuate to 4-carboxy-2-hydroxymuconate semialdehyde
From Homogentisate to 4-Maleylacetoacetate
From 2-Nitropropane to Acetone
From Chlorite to Chloride
From Chloroethane to Acetaldehyde
From Phthalate to Phthalate-4,5-cis-dihydrodiol
60
37
Benzoate 1,2-dioxygenase
Benzoate degradation pathway
3-Flurobenzoate degradation pathway
4-Flurobenzoate degradation pathway
(anaerobic/aerobic)
p-xylene degradation pathway
38
39
Terephthalate 1,2-dioxygenase
Biphenyl dioxygenase
Phthalate family degradation pathway
Biphenyl degradation pathway
4-chlorobiphenyl degradation pathway
40
Nitrilotriacetate monooxygenase
41
Salicylate hydroxylase
Nitrilotriacetate degradation pathway
(anaerobic/aerobic)
Naphthalene degradation pathway
1-methylnaphthalene degradation pathway
2-methylnaphthalene degradation pathway
42
43
4-hydroxybenzoate 3monooxygenase
Phenol 2-monoxygenase
44
45
Vanillate monooxygenase
Unspecific monooxygenase
Benzoate degradation via hydroxylation pathway
Chlorobenzene degradation pathway
Phenol family degradation pathway
Nitrophenol family degradation pathway
(anaerobic/aerobic)
2,4 Dichlorobenzoate degradation
Benzyl sulfide degradation pathway
Methyl tert-butyl ether degradation pathway
Hexahydro-1,3,5-trinitro-1,3,5-triazine degradation
pathway
Morpholine degradation pathway
46
Alkane 1-monooxygenase
n-octane degradation pathway
Methyl tert-butyl ether degradation pathway
From Benzoate to cis-1,6-Dihydroxy-2,4-cyclohexadiene-1-carboxylic
acid
From 3-Fluorobenzoate to 3-Fluorocyclohexadiene-cis,cis-1,2-diol-1carboxylate or 5-Fluorocyclohexadiene-cis,cis-1,2-diol-1-carboxylate
From 4-Fluorobenzoate to 4-Fluorocyclohexadiene-cis,cis-1,2-diol-1carboxylate
From p-Toluate to 4-Methylcyclohexa-3,5-diene-1,2-cis-diol-1carboxylic acid
From Terephthalate to Terephthalate-1,2-cis-dihydrodiol
From Biphenyl to cis-2,3-Dihydro-2,3-dihydroxybiphenyl
From 4-Chlorobiphenyl to cis-2,3-Dihydro-2,3-dihydroxy-4'chlorobiphenyl
From Nitrilotriacetate to Glyoxylate and Iminodiacetate
From Salicylate to Catechol
From 3-Methylsalicylate to 3-Methylcatechol
From 4-Hydroxymethylsalicylate to 4-Hydroxymethylcatechol
From 4-Methylsalicylate to 4-Methylcatechol
4-hydroxybenzoate to 3,4-Dihydroxybenzoate
From 2-Chlorophenol to 3-Chlorocatechol
From Phenol to Catechol
From Hydroquinone to 1,2,4-Benzenetriol
From Resorcinol to 1,2,4-Benzenetriol
From Vanillate to 3,4-Dihydroxybenzoate and Formaldehyde
From Benzyl sulfoxide to Benzyl sulfone
From Methyl tert-butyl ether to tert-Butyl alcohol
From 1,3-Dinitro-1,2,3,4-tetrahydro-1,3,5-triazine to 1-Nitro-1,2dihydro-1,3,5-triazine
From Hexahydro-1,3,5-trinitro-1,3,5-triazine to 1,3-Dinitro-1,2,3,4tetrahydro-1,3,5-triazine
From Morpholine to 2-Hydroxymorpholine
From 2-Hydroxymorpholine to 2-(2-Aminoethoxy)acetaldehyde
From n-Octane to 1-Octanol
From tert-Butyl alcohol to 2-Methyl-2-hydroxy-1-propanol
From Methyl tert-butyl ether to tert-Butyl formate
61
47
48
Mercuric reductase
Nitrogenase
49
50
51
52
53
Arsenate reductase
Arsenite oxidase
Selenate reductase
Chromate reductase
Acetyl CoA C acyltransferase
54
55
Selenophosphate synthetase
Propionate CoA transferase
56
57
58
3-oxoadipate CoA transferase
Acetate CoA transferase
Glutaconate CoA transferase
59
60
Arylesterase
Dienelactone hydrolase
Organomercury degradation pathway
Acetylene degradation pathway
Thiocyanate degradation pathway
Arsonoacetate degradation pathway
Arsonoacetate degradation pathway
Selenate degradation pathway
Chromium (VI) reduction pathway
Nitrophenol family degradation pathway
(anaerobic/aerobic)
Selenate degradation pathway
Acrylonitrile degradation pathway
Styrene degradation pathway
Nitrophenol family degradation pathway
Benzoate degradation via CoA ligation pathway
Acrylonitrile degradation pathway
Styrene degradation pathway
4-hydroxyacetophenone degradation pathway
2,4 dichlorophenoxyacetic acid degradation pathway
2,4 dichlorotoluene degradation pathway
61
62
4-hydroxybenzoyl CoA
thioesterase
Aryldialkyl phosphatase
Chlorobenzene degradation pathway
1,2,4- trichlorobenzene degradation pathway
(aerobic/anaerobic)
4-fluorobenzoate degradation pathway
(aerobic/anaerobic)
Tetrachlorobenzene degradation pathway
2,4- dichlorobenzoate degradation pathway
Malathion degradation pathway
From Mercury (II) to Mercury
From Acetylene to Ethylene
From Carbonyl sulfide to Carbon Monoxide
From Arsenate to Arsenite
From Arsenite to Arsenate
From Selenate to Selenite
From Chromate to Chromium (III)
From 3-Oxoadipyl-CoA to Succinyl-CoA and Acetyl-CoA
From Hydrogen Selenide to Selenophosphate
From Lactoyl-CoA to L-Lactate
From Acetyl CoA and propanoate to acetate and propanoyl-CoA
From 3-Oxoadipate to 3-Oxoadipyl-CoA
From Acyl-CoA to Acetyl CoA
From Acrylate to Acrylyl-CoA
From acetyl-CoA and (E)-glutaconate to acetate and glutaconyl-1-CoA
From 4-Hydroxyphenyl acetate to Hydroquinone and Acetate
From cis-4-Carboxymethylenebut-2-en-4-olide to Maleylacetate
From cis-2-Chlorodienelactone to 2-Chloromaleylacetate
From 4-Methylenebut-2-en-4-olide to cis-Acetylacrylate
From 2-Chloro-3-methyl-cis/trans-dienelactone to 3-Chloro-2methylmaleylacetate
From 2-Chloro-5-methyl-cis-dienelactone to 2-Chloro-5methylmaleylacetate
From trans-4-Carboxymethylenebut-2-en-4-olide to Maleylacetate
From 2,5-Dichloro-carboxymethylenebut-2-en-4-olide to 2,5-Dichloro4-oxohex-2-enedioate
From 4-Fluoromuconolactone to Maleylacetate
From 2,3,5-Trichlorodienelactone to 2,3,5-Trichloromaleylacetic acid
From 4-Hydroxybenzoyl-CoA to 4-Hydroxybenzoate
From S-(Diethylsuccinyl)-phosphorothioate to Phosphate and Diethyl
2-mercaptosuccinate
62
Parathion degradation pathway
63
Epoxide hydrolase
Benzo(a)pyrene degradation pathway
64
Amidase
65
66
67
Allophanate hydrolase
6 aminohexanoate cyclic dimer
hydrolase
6 aminohexanoate dimer hydrolase
Acrylonitrile degradation pathway
Benzonitrile degradation pathway
Atrazine degradation pathway
Nylon degradation pathway
68
Nitrilase
69
Hydroxy dechloroatrazine
ethylaminohydrolase
70
N-isopropylammelide
isopropylamino hydrolase
Fumarylacetoacetase
2-hydroxy-6-oxo-6-phenylhexa2,4-dienoate hydrolase
71
72
Nylon degradation pathway
Benzonitrile degradation pathway
Z-phenylacetaldoxime degradation pathway
Atrazine degradation pathway
Atrazine degradation pathway
Styrene degradation pathway
Dibenzofuran degradation pathway
4-chlorobiphenyl degradation pathway
Biphenyl degradation pathway
73
N-ethyl ammeline chlorohydrolase
Atrazine degradation pathway
74
75
2-haloacid dehalogenase
Haloalkane dehalogenase
1,2 Dichloroethane degradation pathway
1,2 Dichloroethane degradation pathway
1,3 Dichloropropene degradation pathway
beta-1,2,3,4,5,6 – Hexachloro- cyclohexane
degradation pathway (aerobic/anaerobic)
From Paraoxon to p-Nitrophenol and Diethylphosphoric acid
From Parathion to Diethylthiophosphoric acid and p-Nitrophenol
From Aminoparathion to Diethylthiophosphoric acid and pAminophenol
From Benzo(a)pyrene-11,12-epoxide to Benzo(a)pyrene-trans-11,12dihydrodiol
From Acrylamide to Acrylate
From Benzamide to Benzoate
From Allophanate to Carbon Dioxide
From 6-Aminohexanoate Cyclic Dimer to 6-Aminohexanoate Linear
Dimer
From 6-Aminohexanoate (n) mer to 6-Aminohexanoate and 6Aminohexanoate (n-1) mer
From Benzonitrile to Benzoate
From Phenylacetonitrile to Phenylacetate
From 2-Chloro-4-hydroxy-6-amino-1,3,5-triazine to 2,4-Dihydroxy-6amino-1,3,5-triazine
From Hydroxyatrazine to N-Isopropylammelide and Ethyl amine
From 2,4-Dihydroxy-6-amino-1,3,5-triazine to Cyanuric acid
From N-Isopropylammelide to Cyanuric acid
From Fumarylacetoacetate to Fumarate and Acetoacetate
From 2-Hydroxy-6-oxo-6-(2-hydroxyphenyl)-hexa-2,4-dienoate to 2Oxopent-4-enoate and Salicylate
From 2-Hydroxy-6-oxo-6-(4'-chlorophenyl)-hexa-2,4-dienoate to cis-2Hydroxypenta-2,4-dienoate and 4-Chlorobenzoate
From 2-Hydroxy-6-oxo-6-phenylhexa-2,4-dienoate to cis-2Hydroxypenta-2,4-dienoate and Benzoate
From Deisopropylatrazine to Deisopropylhydroxyatrazine
From Deisopropyldeethylatrazine to 2-Chloro-4-hydroxy-6-amino1,3,5-triazine
From Chloroacetate to Glycolate
From 1,2-Dichloroethane to 2-Chloroethanol
From cis-1,3-Dichloropropene to cis-3-Chloro-2-propene-1-ol
From trans-1,3-Dichloropropene to trans-3-Chloro-2-propene-1-ol
From beta-1,2,3,4,5,6-Hexachlorocyclohexane to 2,3,4,5,6Pentachlorocyclohexanol
63
gamma-Hexachlorocyclohexane degradation
pathway
76
77
78
79
80
81
Atrazine chlorohydrolase
4,5 Dihydroxyphthalate
decarboxylase
4-Hydroxybenzoate decarboxylase
Glutaconyl CoA decarboxylase
4 Oxalocrotonate decarboxylase
4-hydroxyl 2 oxovalerate aldolase
82
Enoyl CoA hydratase
83
2 oxopent 4 enoate hydratase
84
Dienoyl CoA hydratase
85
86
Maleylacetoacetate isomerase
Muconate cycloisomerase
87
Chloromuconate cycloisomerase
1,2,3-Tribromopropane degradation pathway
Atrazine degradation pathway
Phthalate family degradation pathway
Phenol degradation pathway (anaerobic)
Benzoate degradation pathway (anaerobic)
2,4 dichlorophenoxyacetic acid degradation pathway
p-xylene degradation pathway
4-chlorobiphenyl, ethylbenzene, styrene and toluene
degradation pathway
Cyclohexane degradation pathway
Benzoate (anaerobic), Cyclopropane carboxylate
degradation pathway
Benzoate (anaerobic) degradation pathway
Gallate (anaerobic) degradation pathway
3-(4-Sulfophenyl)butyrate degradation pathway
p-xylene degradation pathway
4-chlorobiphenyl, ethylbenzene, styrene and toluene
degradation pathway
Benzoate (anaerobic) degradation pathway
Styrene degradation pathway
2,4 dichlorophenoxyacetic acid degradation pathway
4-fluorobenzoate degradation pathway
(aerobic/anaerobic)
p-xylene degradation pathway
Chlorobenzene degradation pathway
2,4 dichlorophenoxyacetic acid degradation pathway
From 2,4,5-Trichloro-2,5-cyclohexadiene-1-ol to 2,5-Dichloro-2,5cyclohexadiene-1,4-diol
From 1,3(R),4,6(R)-Tetrachloro-1,4-cyclohexadiene to 2,4,5-Trichloro2,5-cyclohexadiene-1-ol
From 1,2,3-Tribromopropane to 2,3-Dibromo-1-propanol
From Atrazine to Hydroxyatrazine
From 4,5-Dihydroxyphthalate to 3,4-Dihydroxybenzoate
From 4-Hydroxyphthalate to 3-Hydroxybenzoate
From Phenol to 4-hydroxybenzoate
From Glutaconyl-CoA to Crotonoyl-CoA
From 5-Chloro-2-hydroxymuconate to 5-Chloro-2-oxopent-4-enoate
From 4-Hydroxy-2-oxohexanoate to Pyruvate and Propanal
From 4-Hydroxy-2-oxovalerate to Pyruvate and Acetaldehyde
From 5-Carboxy-2-pentenoyl-CoA to (3S)-3-Hydroxyadipyl-CoA
From Crotonoyl-CoA to (3S)-3-Hydroxybutyryl-CoA
From 2,3-Didehydro-pimeloyl-CoA to 3-Hydroxypimelyl-CoA
From (3S)-3-Hydroxybutyryl-CoA to Crotonoyl-CoA
From 3-(4-Sulfophenyl)butyrate enoyl-CoA to 3-Hydroxy-3-(4sulfophenyl)butyryl-CoA
From 2-Oxohex-trans-4-enoate to 4-Hydroxy-2-oxohexanoate
From cis-2-Hydroxypenta-2,4-dienoate to 4-Hydroxy-2-oxovalerate
From Cyclohex-1,5-diene-1-carboxyl-CoA to 6-Hydroxycyclohex-1ene-1-carboxyl-CoA
From 4-Maleylacetoacetate to Fumarylacetoacetate
From 3-Chloro-cis,cis-muconate to 4-Methylenebut-2-en-4-olide
From 3-Fluoro-cis,cis-muconate to 4-Fluoromuconolactone
From 3-Methyl-cis,cis-hexadienedioate to 3-Methylmuconolactone
From 3-Methyl-cis,cis-hexadienedioate to 4-Methylmuconolactone
From 2-Chloro-cis,cis-muconate to trans-4-Carboxymethylenebut-2en-4-olide
From 3-Chloro-cis,cis-muconate to cis-4-Carboxymethylenebut-2-en4-olide
64
2,4 dichlorotoluene degradation pathway
1,4 Dichlorobenzene degradation pathway
Tetrachlorobenzene degradation pathway
1,2,4 Trichlorobenzene degradation pathway
88
Benzoate CoA ligase
Benzoate degradation pathway (anaerobic)
From 3,5-Dichloro-2-methylmuconolactone to 2-Chloro-3-methylcis/trans-dienelactone
From 3,5-Dichloro-3-methyl-cis,cis-muconate to 2-Chloro-5-methylcis-dienelactone
From 3,5-Dichloro-3-methyl-cis,cis-muconate to 3,5-Dichloro-2methylmuconolactone
From 2,5-Dichloro-cis,cis-muconate to trans-2-Chlorodienelactone
From Tetrachloro-cis,cis-muconate to 2,3,5-Trichlorodienelactone
From 2,3,5-Trichloro-cis,cis-muconate to 2,5-Dichlorocarboxymethylenebut-2-en-4-olide
From Benzoate to Benzoyl-CoA
65