Table 1.
Predicted genes involved in xenobiotics degradation based on KEGG pathway analysis (Fig. 4, Fig. 5, Fig. 6, Fig. 7).
| KEGG xenobiotic degradation pathway/KEGG symbol | Strain name | KEGG protein name/KO | Reference gene/Uniport or PDB accession | Identity/query cover (%) |
|---|---|---|---|---|
| Steroid | Glutamicibacter protophormiae NG4 | |||
| choD | cholesterol oxidase/K03333 | Nr-database/TDW30780.1 | cholesterol oxidase (55.68/97) | |
| kstD | 3-oxosteroid 1-dehydrogenase/K05898 | Swissprot/Q04616.3 | 3-oxosteroid 1-dehydrogenase/(41.92/97) | |
| kshA/kshB | 3-ketosteroid 9alpha-monooxygenase subunit A and B/K15982 and K15983 | Swissprot/B6V6V5.1 Swissprot/A0R525.1 |
3-ketosteroid 9alpha-monooxygenase subunit A/(69.40/92) 3-ketosteroid 9alpha-monooxygenase subunit B/(59.01/96) |
|
| hsaA | 3-hydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione monooxygenase/K16047 | Nr-database/WP_204676060.1 | Hydroxylase/(100/100) | |
| hsaC | 3,4-dihydroxy-9,10-secoandrosta-1,3,5(10)-triene-9,17-dione 4,5-dioxygenase/K16049 | Nr-database/ALD65327.1 | Extradiol dioxygenase/(96.44/100) | |
| fadD3 | HIP---CoA ligase/K18687 | Swissprot//Q0S7V5.1 | HIP---CoA ligase/(49.16/97) | |
| Benzoate | Arthrobacter sp. 7749 | |||
| benA, benB and benC | benzoate 1,2-dioxygenase alpha, beta and reductase subunit/K05549, K05550, K05784 | Swissprot/P07769.2 Swissprot/P07770.1 Swissprot/P23101.1 |
benzoate 1,2-dioxygenase alpha/(67.89/93) benzoate 1,2-dioxygenase beta (63.98/89) Toluate 1,2-dioxygenase electron transfer component/(54.49/64) |
|
| benD | dihydroxycyclohexadiene carboxylate dehydrogenase/K05783 | Swissprot/P07772.2 | 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase/(59.92/92) | |
| catA | catechol 1,2-dioxygenase/K03381 | Swissprot/P95607.1 | catechol 1,2-dioxygenase/(56.99/95) | |
| catC | muconolactone delta-isomerase/K03464 | Swissprot/O33947.1 | Muconolactone Delta-isomerase (59.78/100) | |
| pcaD | 3-oxoadipate enol-lactonase/K01055 | Swissprot/P00632.3 | 3-oxoadipate enol-lactonase/(35.29/87) | |
| pcaIJ | 3-oxoadipate CoA-transferase alpha and beta subunit/K01031 and K01032 | Swissprot/Q01103.2 Swissprot/P0A101.2 |
3-oxoadipate CoA-transferase alpha/(65.26/95) 3-oxoadipate CoA-transferase beta (59.15/96) |
|
| fadA, fadI | acetyl-CoA acyltransferase/K00632 | Swissprot/Q5E8X7.2 | 3-ketoacyl-CoA thiolase (42.35/94) | |
| catE | catechol 2,3-dioxygenase/K07104 | Swissprot/P54721.2 | catechol 2,3-dioxygenase/(34.93/91) | |
| dmpD, xylF | 2-hydroxymuconate-semialdehyde hydrolase/K10216 | Swissprot/P19076.1 | 2-hydroxymuconate-semialdehyde hydrolase/(40.38/89) | |
| mhpD | 2-keto-4-pentenoate hydratase/K02554 | Swissprot/Q13VU0.1 | 2-keto-4-pentenoate hydratase (41.41/97) | |
| mhpE | 4-hydroxy 2-oxovalerate aldolase/K01666 | Swissprot/Q0RXC3.1 | 4-hydroxy 2-oxovalerate aldolase (65.45/96) | |
| mhpF | acetaldehyde dehydrogenase/K04073 | Swissprot/Q0S4F9.1 | acetaldehyde dehydrogenase (59.80/96) | |
| 4-hydroxybenzoate | Glutamicibacter protophormiae NG4 | |||
| pobA | p-hydroxybenzoate 3-monooxygenase/K00481 | Swissprot/8WEQ_A | p-hydroxybenzoate 3-monooxygenase/(63.36/98) | |
| pcaG and pcaH | protocatechuate 3,4-dioxygenase, alpha and beta subunit/K00448 and K00449 | Swissprot/P20371.3 Swissprot/P15110.1 |
protocatechuate 3,4-dioxygenase, alpha subunit/(41.50/93) protocatechuate 3,4-dioxygenase, beta subunit/(56.81/76) |
|
| pcaB | 3-carboxy-cis,cis-muconate cycloisomerase/K01857 | Swissprot/Q9I6Q8.1 | 3-carboxy-cis,cis-muconate cycloisomerase/(42.27/92) | |
| pcaC | 4-carboxymuconolactone decarboxylase/K01607 | Swissprot/P20370.2 | 4-carboxymuconolactone decarboxylase/(44.53/92) | |
| pcaD | 3-oxoadipate enol-lactonase/K01055 | Swissprot/P00632.3 | 3-oxoadipate enol-lactonase/(35/90) | |
| pcaIJ | 3-oxoadipate CoA-transferase alpha and beta subunit/K01031 and K01032 | Swissprot/Q01103.2 Swissprot/P0A101.2 |
3-oxoadipate CoA-transferase alpha subunit/(67.61/95) 3-oxoadipate CoA-transferase beta subunit/(64/92) |
|
| fadA, fadI | acetyl-CoA acyltransferase/K00632 | Swissprot/ | ||
| ligA and ligB | Arthrobacter alpinus ERGS4:06 | protocatechuate 4,5-dioxygenase alpha and beta subunit/K04100 and K04101 | Swissprot/P22635.1 Swissprot/P22636.1 |
protocatechuate 4,5-dioxygenase alpha/(56.91/93) protocatechuate 4,5-dioxygenase beta/(60.21/100) |
| ligC | 4-carboxy-2-hydroxymuconate semialdehyde dehydrogenase/K10219 | Swissprot/Q9KWL3.1 | 4-carboxy-2-hydroxymuconate semialdehyde dehydrogenase (67.41/99) | |
| ligI | 2-pyrone-4,6-dicarboxylate hydrolase/K10221 | Swissprot/Q93PS7.1 | 2-pyrone-4,6-dicarboxylate hydrolase/(63.46/99) | |
| galD | 4-oxalomesaconate tautomerase/K16514 | Swissprot/Q88JY0.1 | 4-oxalomesaconate tautomerase/(57.94/98) | |
| ligJ | 4-oxalomesaconate hydratase/K10220 | Swissprot/G2IQQ5.1 | 2-keto-4-carboxy-3-hexenedioate hydratase/(75.52/100) | |
| ligK, galC | 4-carboxy-4-hydroxy-2-oxoadipate aldolase/K10218 | Swissprot/G2IQQ8.1 | 4-carboxy-4-hydroxy-2-oxoadipate aldolase/(59.01/97) | |
| Toluene | Arthrobacter sp. 7749 | |||
| E1.1.1.90 | aryl-alcohol dehydrogenase/K00055 | Swissprot/P39849.1 | aryl-alcohol dehydrogenase/(50.14/99) | |
| xylC | benzaldehyde dehydrogenase (NAD+)/K00141 | Swissprot/P43503.1 | benzaldehyde dehydrogenase (NAD+)/(49.69/99) | |
| benA-xylX, benB-xylY, and benC-xylZ |
benzoate 1,2-dioxygenase alpha, beta and reductase subunit/K05549, K05550, K05784 | Swissprot/P07769.2 Swissprot/P07770.1 Swissprot/P23101.1 |
benzoate 1,2-dioxygenase alpha/(67.89/93) benzoate 1,2-dioxygenase beta (63.98/89) Toluate 1,2-dioxygenase electron transfer component/(54.49/64) |
|
| benD-xylL | dihydroxycyclohexadiene carboxylate dehydrogenase/K05783 | Swissprot/P07772.2 | 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase/(59.92/92) | |
| catA- | catechol 1,2-dioxygenase/K03381 | Swissprot/P95607.1 | catechol 1,2-dioxygenase/(56.99/95) | |
| catC | muconolactone delta-isomerase/K03464 | Swissprot/O33947.1 | Muconolactone Delta-isomerase (59.78/100) | |
| pcaD | 3-oxoadipate enol-lactonase/K01055 | Swissprot/P00632.3 | 3-oxoadipate enol-lactonase/(35.29/87) | |
| pcaIJ | 3-oxoadipate CoA-transferase alpha and beta subunit/K01031 and K01032 | Swissprot/Q01103.2 Swissprot/P0A101.2 |
3-oxoadipate CoA-transferase alpha/(65.26/95) 3-oxoadipate CoA-transferase beta (59.15/96) |
|
| fadA, fadI | acetyl-CoA acyltransferase/K00632 | Swissprot/Q5E8X7.2 | 3-ketoacyl-CoA thiolase (42.35/94) | |
| catE, dmpB-xylE | catechol 2,3-dioxygenase/K07104 | Swissprot/P54721.2 | catechol 2,3-dioxygenase/(34.93/91) | |
| dmpD, xylF | 2-hydroxymuconate-semialdehyde hydrolase/K10216 | Swissprot/P19076.1 | 2-hydroxymuconate-semialdehyde hydrolase/(40.38/89) | |
| mhpD | 2-keto-4-pentenoate hydratase/K02554 | Swissprot/Q13VU0.1 | 2-keto-4-pentenoate hydratase (41.41/97) | |
| mhpE | 4-hydroxy 2-oxovalerate aldolase/K01666 | Swissprot/Q0RXC3.1 | 4-hydroxy 2-oxovalerate aldolase (65.45/96) | |
| mhpF | acetaldehyde dehydrogenase/K04073 | Swissprot/Q0S4F9.1 | acetaldehyde dehydrogenase (59.80/96) | |
| p-Xylene | Arthrobacter sp. 7749 | |||
| E1.1.1.90 | aryl-alcohol dehydrogenase/K00055 | Swissprot/P39849.1 | aryl-alcohol dehydrogenase/(50.14/99) | |
| xylC | benzaldehyde dehydrogenase (NAD+)/K00141 | Swissprot/P43503.1 | benzaldehyde dehydrogenase (NAD+)/(49.69/99) | |
| benA-xylX, benB-xylY, and benC-xylZ |
Benzoate/toluate 1,2-dioxygenase alpha, beta and reductase subunit/K05549, K05550, K05784 | Swissprot/P07769.2 Swissprot/P07770.1 Swissprot/P23101.1 |
benzoate 1,2-dioxygenase alpha/(67.89/93) benzoate 1,2-dioxygenase beta (63.98/89) Toluate 1,2-dioxygenase electron transfer component/(54.49/64) |
|
| benD-xylL | dihydroxycyclohexadiene carboxylate dehydrogenase/K05783 | Swissprot/P07772.2 | 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase/(59.92/92) | |
| dmpB, xylE | 3,4-dihydroxyphenylacetate 2,3-dioxygenase/K00446 | Pdb/1Q0C_A | homoprotocatechuate 2,3-dioxygenase/(86.26/98) | |
| dmpD, xylF | 2-hydroxymuconate-semialdehyde hydrolase/K10216 | Swissprot/P19076.1 | 2-hydroxymuconate-semialdehyde hydrolase/(40.38/89) | |
| o-Xylene/m-Xylene | Arthrobacter sp. 7749 | |||
| E1.1.1.90 | aryl-alcohol dehydrogenase/K00055 | Swissprot/P39849.1 | aryl-alcohol dehydrogenase/(50.14/99) | |
| xylC | benzaldehyde dehydrogenase (NAD+)/K00141 | Swissprot/P43503.1 | benzaldehyde dehydrogenase (NAD+)/(49.69/99) | |
| benA-xylX, benB-xylY, and benC-xylZ |
Benzoate/toluate 1,2-dioxygenase alpha, beta and reductase subunit/K05549, K05550, K05784 | Swissprot/P07769.2 Swissprot/P07770.1 Swissprot/P23101.1 |
benzoate 1,2-dioxygenase alpha/(67.89/93) benzoate 1,2-dioxygenase beta (63.98/89) Toluate 1,2-dioxygenase electron transfer component/(54.49/64) |
|
| benD-xylL | dihydroxycyclohexadiene carboxylate dehydrogenase/K05783 | Swissprot/P07772.2 | 1,6-dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase/(59.92/92) | |
| dmpB, xylE | 3,4-dihydroxyphenylacetate 2,3-dioxygenase/K00446 | Pdb/1Q0C_A | homoprotocatechuate 2,3-dioxygenase/(86.26/98) | |
| mhpD | 2-keto-4-pentenoate hydratase/K02554 | Swissprot/Q13VU0.1 | 2-keto-4-pentenoate hydratase (41.41/97) | |
| mhpE | 4-hydroxy 2-oxovalerate aldolase/K01666 | Swissprot/Q0RXC3.1 | 4-hydroxy 2-oxovalerate aldolase (65.45/96) | |
| mhpF | acetaldehyde dehydrogenase/K04073 | Swissprot/Q0S4F9.1 | acetaldehyde dehydrogenase (59.80/96) | |
| Phenanthrene | Pseudarthrobacter phenanthrenivorans Sphe3 | |||
| nidA | ring-hydroxylating dioxygenase, large terminal subunit/K11943 | Pdb/2B1X_A | naphthalene dioxygenase large subunit/(74.41/96) | |
| phdI | 1-hydroxy-2-naphthoate 1,2-dioxygenasee/K11948 | Swissprot/O24721.2 | 1-hydroxy-2-naphthoate 1,2-dioxygenasee/(85.53/100) | |
| phdJ | 4-(2-carboxyphenyl)-2-oxobut-3-enoate aldolase/K11949 | Swissprot/Q79EM8.1 | Trans-2′-carboxybenzalpyruvate hydratase-aldolase (94.28/96) | |
| phdK | 2-formylbenzoate dehydrogenase/K18275 | Swissprot/Q79EM7.1 | 2-formylbenzoate dehydrogenase/(73.54/99) | |
| phtAb | phthalate 3,4-dioxygenase subunit beta/K18252 | Nr-database/MCU1563476.1 | phthalate 3,4-dioxygenase subunit beta/(89.05/100) | |
| phtC | 3,4-dihydroxyphthalate decarboxylase/K18256 | Nr-database/MCW2683780.1 | 3,4-dihydroxyphthalate decarboxylase (61.25/99) | |
| pcaG and pcaH | protocatechuate 3,4-dioxygenase, alpha and beta subunit/K00448 and K00449 | Swissprot/P00436.3 Swissprot/P15110.1 |
protocatechuate 3,4-dioxygenase alpha chain (39.90/97) protocatechuate 3,4-dioxygenase beta chain (55.35/73) |
|
| Azathioprene (prodrug) | Arthrobacter crystallopoietes DSM 20117 | |||
| hprT, hpt, HPRT1 | hypoxanthine phosphoribosyltransferase/K00760 | Swissprot/Q839B2.1 | hypoxanthine phosphoribosyltransferase/(52.81/97) | |
| IMPDH, guaB | inosine-5′-monophosphate dehydrogenase/K00088 | Swissprot/Q8G3N6.1 | inosine-5′-monophosphate dehydrogenase/(65.65/98) | |
| guaA, GMPS | GMP synthase (glutamine-hydrolysing)/K01951 | Nr-database/WP_074702029.1 | glutamine amidotransferas (100/100) | |
| Capecitabine (Prodrug) | Arthrobacter crystallopoietes DSM 20117 | |||
| cdd, CDA | cytidine deaminase/K01489 | Swissprot/P9WPH2.1 | cytidine deaminase/(56.35/75) | |
| deoA, TYMP | thymidine phosphorylase/K00758 | Swissport/P9WFS0.1 | thymidine phosphorylase/(62.59/98) | |
| tdk, TK | thymidine kinase/K00857 | Swissprot/Q5QWC7.1 | thymidine kinase/(45.45/98) | |
| ndk, NME | nucleoside diphosphate kinase/K00940 | Swissport/P36010.1 | nucleoside diphosphate kinase (61.19/97) | |
| DPYS, dht, hydA | Dihydropyrimidinase/K01464 | Swissprot/Q14117.1 | Dihydropyrimidinase (32.46/93) | |
| UPB1, pydC | N-carbamoylputrescine amidase/K01431 | Swissprot/Q9XGI9.1 | N-carbamoylputrescine amidase/(40.78/96) | |
| 5-Fluorouridine | Arthrobacter crystallopoietes DSM 20117 | |||
| udk, UCK | uridine kinase/K00876 | Nr-database/WP_074702196.1 | uridine kinase/(100/100) | |
| ndk, NME | nucleoside diphosphate kinase/K00940 | Swissprot/P36010.1 | nucleoside diphosphate kinase/(61.19/97) | |