Table 3 Genomics-driven prediction of genes encoding peripheral and central catabolic pathways for aromatic compound degradation in Variovorax sp. PAMC26660
Gene | KEGG orthology ID | Locus Tag | Function | Reference gene/UniprotKBÂ or PDB accession | Identity/query cover (%) |
|---|---|---|---|---|---|
4-hydroxybenzoate | |||||
 pobA | K00481 | 5874025_5875206 | 4-hydroxybenzoate 3-monooxygenase | pobA/Q03298.1 | 67.26/99 |
Protocatechuate | |||||
 pcaG | K00448 | 1485975_1486583 | protocatechuate 3,4-dioxygenase, alpha subunit | pcxA/P15109.1 | 61.46/94 |
 pcaH | K00449 | 1485224_1485958 | protocatechuate 3,4-dioxygenase, beta subunit | pcxB/P15110.1 | 73.04/94 |
 pcaB | K01857 | 5194953_5196167 | 3-carboxy-cis,cis-muconate cycloisomerase | pcaB/P32427.3 | 45.79/88 |
 pcaC | K01607 | 5196164_5196598 | 4-carboxymuconolactone decarboxylase | DC4C/P20370.2 | 34.92/87 |
 pcaD | K01055 | 5197818_5198582 | 3-oxoadipate enol-lactonase | ELH2/P00632.3 | 37.71/92 |
 pcaI | K01031 | 1440608_1441309 | 3-oxoadipate CoA-transferase, alpha subunit | pcaI/Q01103.2 | 70.70/92 |
 pcaJ | K01032 | 1439964_1440611 | 3-oxoadipate CoA-transferase, beta subunit | pcaJ/P0A101.2 | 68.87/98 |
 atoB | K00626 | 1438732_1439937 | acetyl-CoA C-acetyltransferase | pcaF/Q43974.1 | 65.05/99 |
 fadA | K00632 | 3392309_3393505 3439178_3440368 5029514_5030647 | acetyl-CoA acyltransferase | fadA/O32177.1 fadA/O32177.1 fadA/Q010T4.1 | 50.64/98 45.45/99 50.77/99 |
Tyrosine | |||||
 tyrB | K00832 | 5638920_5640116 | aromatic-amino-acid transaminase | tyrB/P04693.1 | 52.39/99 |
Homogentisate | |||||
 hppD | K00457 | 1745226_1746353 | 4-hydroxyphenylpyruvate dioxygenase | hppD/P80064.1 | 59.4/96 |
 hmgA | K00451 | 2812778_2814088 | homogentisate 1,2-dioxygenase | hgd/Q1D8L9.1 | 63.81/96 |
 faaH | K16171 | 1772826_1773899 | fumarylacetoacetate hydrolase | faaH/3LZK_A | 58.26/92 |
 fahA | K01555 | 2810513_2811778 | fumarylacetoacetase | faaA/A5PKH3.1 | 47.12/94 |
Gentisate | |||||
 nagI | K00450 | 2892208_2893296 | gentisate 1,2-dioxygenase | GDO1/Q9S3U6.1 | 52.91/95 |
 nagL | K01801 | 5495938_5496576 | maleylacetoacetate isomerase/maleylpyruvate isomerase | nagL/O86043.1 | 46.45/99 |
 nagK | K16165 | 2893363_2894067 | fumarylpyruvate hydrolase | nagK/O86042.1 | 48.19/81 |
Phenylacetate | |||||
 paaK | K01912 | 4002663_4003976 | phenylacetate-CoA ligase | paaK/Q9L9C1.1 | 69.48/100 |
Phenylacetyl-CoA | |||||
 paaA | K02609 | 4001605_4002618 | ring-1,2-phenylacetyl-CoA epoxidase subunit PaaA | paaA/P76077.1 | 65.16/91 |
 paaB | K02610 | 4001306_4001608 | ring-1,2-phenylacetyl-CoA epoxidase subunit PaaB | paaB/P76078.1 | 65.56/90 |
 paaC | K02611 | 4000168_4000941 | ring-1,2-phenylacetyl-CoA epoxidase subunit PaaC | paaC/P76079.1 | 49.79/94 |
 paaD | K02612 | 3999644_4000168 | ring-1,2-phenylacetyl-CoA epoxidase subunit PaaD | paaD/P76080.2 | 43.68/96 |
 paaE | K02613 | 3998548_3999633 | ring-1,2-phenylacetyl-CoA epoxidase subunit PaaE | paaE/P76081.1 | 42.34/99 |
 paaG | K15866 | 4004803_4005606 | 2-(1,2-epoxy-1,2-dihydrophenyl) acetyl-CoA isomerase | paaG/P77467.1 | 55.13/98 |
 paaZ | K02618 | 3991275_3993326 | oxepin-CoA hydrolase / 3-oxo-5,6-dehydrosuberyl-CoA semialdehyde dehydrogenase | paaZ/P77455.1 | 58.74/99 |