TABLE 3.
Distribution of genes encoding relevant proteins involved in xenobiotics degradation in the BP8 metagenome.
| Activity | K Number | EC | Name | Paracoccus sp. BP8 | Chryseobacterium sp. BP8.2 | Parapedobacter sp. BP8.3 | Microbacteriaceae bacterium BP8.4 | O. intermedium BP8.5 |
| Benzoate and related compounds metabolism | ||||||||
| Benzoate/toluate 1,2- dioxygenase | K05549 K05550 K05784 | 1.14.12.10 1.18.1.- | benA-xylX benB-xylY benC-xylZ | 1 1 1 | – – – | – – – | – – – | – – – |
| Dihydroxyclohexadiene carboxylate dehydrogenase | K05783 | 1.3.1.25 | benD-xylL | 1 | – | – | – | – |
| p-Hydroxybenzoate 3-monooxygenase | K00481 | 1.14.13.2 | pobA | 1 | – | – | – | 1 |
| Catechol 1,2-dioxygenase | K03381 | 1.13.11.1 | catA | 1 | – | – | – | – |
| Catechol 2,3-dioxygenase | K07104 | 1.13.11.2 | catE | 1 | – | – | 1 | 1 |
| Protocatechuate 3,4-dioxygenase | K00448 K00449 | 1.13.11.3 | pcaG-pcaH | 1 1 | – – | – – | – – | 1 1 |
| Muconate cycloisomerase | K01856 | 5.5.1.1 | catB | 1 | – | – | 1 | – |
| 3-Carboxy-cis,cis-muconate cycloisomerase | K01857 | 5.5.1.2 | pcaB | 1 | – | – | – | 1 |
| Muconolactone isomerase | K01856 | 5.3.3.4 | catC | 1 | – | – | – | – |
| 4-Carboxymuconolactone decarboxylase | K01607 | 4.1.1.44 | pcaC | 2 | – | – | – | 1 |
| Enol-lactone hydrolase | K01055 | 3.1.1.24 | pcaD | 3 | – | – | – | 1 |
| β-ketoadipate:succyinyl- CoA transferase, | K01031 K01032 | 2.8.3.6 | pcaI-pcaJ | 1 1 | – – | – – | – – | 2 1 |
| β-ketoadipyl-CoA thiolase | K00632 | 2.3.1.16 | pcaF | – | 1 | 1 | 1 | 1 |
| 2-Oxopent-4-enoate hydratase (benzoate) | K02554 | 4.2.1.80 | mhpD | – | – | – | 1 | – |
| 4-Hydroxy 2-oxovalerate aldolase | K01666 | 4.1.3.39 | mhpE | – | – | – | 2 | – |
| Acetaldehyde dehydrogenase | K04073 | 1.2.1.10 | mhpF | – | – | – | 2 | – |
| 4-Methoxybenzoate monooxygenase (O-demethylating) | K22553 | 1.14.99.15 | CYP199A2 | 1 | – | – | – | – |
| Carboxymethylene butanolidase | K01061 | 3.1.1.45 | clcD | – | – | – | 1 | 1 |
| 4-Hydroxybenzoate decarboxylase | K03186 | 4.1.1.61 | ubiX | 2 | – | 1 | – | 1 |
| Amidase | K01426 | 3.5.1.4 | amiE | 1 | – | – | 1 | 1 |
| Benzoyl phosphate phosphohydrolase | K01512 | 3.6.1.7 | acyP | – | – | 1 | 1 | – |
| 2,4-Dichlorophenol 6-monooxygenase | K10676 | 1.14.13.20 | tfdB | 1 | – | – | – | – |
| 2-Haloacid dehalogenase | K01560 | 3.8.1.2 | 2 | – | – | – | 1 | |
| Alkanes metabolism | ||||||||
| Alkane 1-monooxygenase | K00496 | 1.14.15.3 | alkB1_B2 alkM | 2 | – | – | – | – |
| Ferredoxin NAD+ reductase component | K00529 | 1.18.1.3 | hcaD | 2 | – | – | – | 1 |
| Unspecific monooxygenase | K00493 | 1.14.14.1 | 2 | – | – | – | 1 | |
| Long-chain-alkane monooxygenase | K20938 | 1.14.14.28 | LadA | – | – | – | 1 | – |
| Alcohol dehydrogenase propanol preferring | K13953 | 1.1.1.1 | adhP | 2 | – | 1 | – | 1 |
| Aldehyde dehydrogenase (NAD+ dependent) | K00128 | 1.2.1.3 | ALDH | 6 | 2 | – | – | 3 |
| Aldehyde dehydrogenase (NADP dependent) | K14519 | 1.2.1.4 | aldH | – | 1 | – | – | – |
| Lipocalin family protein | K03098 | – | Blc | – | 1 | 1 | – | 1 |
| Long chain fatty acid transport protein | K06076 | – | fadL | 1 | – | – | – | – |
| N-methylpyrrolidone metabolism | ||||||||
| N-methylhydantoin amidohydrolase | K01473 K01474 | 3.5.2.14 | nmpA nmpB | 5 5 | – – | – – | – 1 | 1 – |
| Aminoacid oxidase | – | – | nmpC | 3 | – | – | 2 | 1 |
| Succinate-semialdehyde dehydrogenase | K00135 | 1.2.1.16 | nmpF | 7 | – | 1 | 2 | 1 |
| Isopropanol metabolism | ||||||||
| aAlcohol dehydrogenase propanol preferring | K13953 | 1.1.1.- | adh1 | 1 | – | – | – | – |
| Alcohol dehydrogenase bAldehyde dehydrogenase | K18369 K00138 K10854 | 1.1.1.- 1.2.1.- | adh2 adh3 acxB | 2 1 1 | – – – | – – – | – 1 – | – – – |
| Acetone carboxylase | K10855 K10856 | 6.4.1.6 | acxA acxC | 1 1 | – – | – – | – – | 1 – |
| 3-Oxoacid-CoA transferase | K01028 K01029 | 2.8.3.5 | 1 1 | 1 1 | 1 1 | 1 1 | – – | |
| Acetoacetate-CoA ligase | K01907 | 6.2.1.16 | acsA | – | – | – | – | 1 |
| Acetyl-CoA C-acetyltransferase | K00626 | 2.3.1.9 | atoB | 10 | 1 | 1 | 3 | 5 |
| Glycol ethers and polypropylene glycols metabolism | ||||||||
| cAlcohol dehydrogenase, | – | 1.1.1.- | pegdh | 3 | – | – | – | 3 |
| dAldehyde dehydrogenase | – | 1.2.1.3 | pegC | 3 | – | – | 1 | – |
| Glycolate oxidase | K00104 K11472 K11473 | 1.1.3.15 | glcD glcE glcF | 1 1 1 | – – – | – – – | – – 1 | 2 1 1 |
| Superoxide dismutase | K04564 K04565 | 1.15.1.1 | SOD2 SOD1 | – 1 | 1 1 | 3 – | 1 – | 1 – |
| Dye decoloring peroxidase | K15733 | 1.11.1.19 | DyP | 1 | – | – | 1 | – |
| Glutathione S-transferase | K00799 | 2.5.1.18 | gst | 11 | – | – | – | 8 |
| Acyl Co-A synthetase | K01897 | 6.2.1.3 | ACSL | 2 | 3 | 2 | 2 | 1 |
| S-(hydroxymethyl) glutathione dehydrogenase | K00121 | 1.1.1.284 | frmA | 3 | – | – | – | 2 |
| S-formylglutathione hydrolase | K01070 | 3.1.2.12 | fghA | 1 | – | – | – | 1 |
aAdh1 was identified by BLAST analysis using the adh1 sequence (Acc. num. BAD03962.1) reported for Gordonia sp. TY-5 (Kotani et al., 2003) as query (Query cover >99%; E-value = 4E-42; Identity 34%). The gene accession number in the BP8 metagenome is RQP06405.1. bAdh3 genes were identified by BLAST analysis using the adh3 sequence (Acc. num. BAD03965.1) reported for Gordonia sp. TY-5 (Kotani et al., 2003) as query (Query cover = 97%; E-value = 1E-97; Identity = 38.8%). The gene accession numbers in the BP8 metagenome are RQP06404.1 and RQP13157.1. These genes were classified as aldehyde dehydrogenases by KEGG, similarly as described in Kotani et al. (2003). cPegdh genes were identified by BLAST analysis using the polyethylene glycol dehydrogenase sequence (pegdh) from Sphingopyxis terrae (Acc. num. BAB61732) (Ohta et al., 2006) as query (Query cover = 97%; E-value = 2.0E-122; Identity = 38.5%). The gene accession numbers in the BP8 metagenome are RQP05609.1, RQP06903.1, RQP07092.1, RQP19606.1, RQP18819.1, RQP20974.1. dPegc genes were identified by BLAST using polyethylene glycol aldehyde dehydrogenase sequence from Sphingopyxis macrogoltabida (Acc. num. BAF98449.1) (Tani et al., 2007) as query (Query cover = 98%; E-value = 1.0E-80; Identity = 38%; Similarity = 56%). The gene accession numbers in the BP8 metagenome are RQP06197.1, RQP04172.1, RQP06015.1, RQP13157.1. Only RQP06197.1 was identified as K00128 by KEGG.