Table 2.
Selected Genes Associated with Clade 3
| KOa | pb | Gene Description |
|---|---|---|
| Catabolism of 4-hydroxyphenylacetic acid | ||
| K02508 | 1.4E-02 | hpaA; 4-hydroxyphenylacetate 3-monooxygenase operon regulatory protein |
| K00483 | 3.6E-04 | hpaB; 4-hydroxyphenylacetate 3-monooxygenase |
| K00484 | 3.6E-04 | hpaC; flavin reductase (NADH) |
| K00455 | 3.6E-04 | hpaD; 3,4-dihydroxyphenylacetate 2,3-dioxygenase |
| K00151 | 3.6E-04 | hpaE; 5-carboxymethyl-2-hydroxymuconic-semialdehyde dehydrogenase |
| K01826 | 3.6E-04 | hpaF; 5-carboxymethyl-2-hydroxymuconate isomerase |
| K05921 | 3.6E-04 | hpaG; 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase |
| K02509 | 3.6E-04 | hpaH; 2-oxo-hept-3-ene-1,7-dioate hydratase |
| K02510 | 3.6E-04 | hpaI; 4-hydroxy-2-oxoheptanedioate aldolase |
| K02511 | 1.4E-02 | hpaX; 4-hydroxyphenylacetate permease |
| Aerobic catabolism of phenylacetic acid | ||
| K00146 | 8.2E-05 | feaB; phenylacetaldehyde dehydrogenase |
| K02609 | 5.2E-03 | paaA; ring-1,2-phenylacetyl-CoA epoxidase subunit |
| K02610 | 8.2E-05 | paaB; ring-1,2-phenylacetyl-CoA epoxidase subunit |
| K02611 | 8.2E-05 | paaC; ring-1,2-phenylacetyl-CoA epoxidase subunit |
| K02612 | 8.2E-05 | paaD; ring-1,2-phenylacetyl-CoA epoxidase subunit |
| K02613 | 8.2E-05 | paaE; ring-1,2-phenylacetyl-CoA epoxidase subunit |
| K01692 | 8.2E-05 | paaF; enoyl-CoA hydratase |
| K15866 | 8.2E-05 | paaG; 2-(1,2-epoxy-1,2-dihydrophenyl) acetyl-CoA isomerase |
| K02614 | 8.2E-05 | paaI; acyl-CoA thioesterase |
| K02615 | 8.2E-05 | paaJ; acetyl-CoA acetyltransferase |
| K01912 | 8.2E-05 | paaK; phenylacetate-CoA ligase |
| K02616 | 8.2E-05 | paaX; phenylacetic acid degradation operon negative regulatory protein |
| K02617 | 2.9E-08 | paaY; phenylacetic acid degradation protein |
| K02618 | 8.2E-05 | paaZ; oxepin-CoA hydrolase / 3-oxo-5, 6-dehydrosuberyl-CoA semialdehyde dehydrogenase |
| K00276 | 8.2E-05 | tynA; primary-amine oxidase |
| Phenylpropanoate/cinnamate degradation | ||
| K05711 | 1.5E-06 | hcaB; 2,3-dihydroxy-2,3-dihydrophenylpropionate dehydrogenase |
| K05710 | 1.5E-06 | hcaC; 3-phenylpropionate/trans-cinnamate dioxygenase ferredoxin subunit |
| K00529 | 1.5E-06 | hcaD; 3-phenylpropionate/trans-cinnamate dioxygenase ferredoxin reductase subunit |
| K05708 | 1.5E-06 | hcaE; 3-phenylpropionate/trans-cinnamate dioxygenase alpha subunit |
| K05709 | 3.3E-05 | hcaF; 3-phenylpropionate/trans-cinnamate dioxygenase beta subunit |
| K05817 | 1.5E-06 | hcaR; hca operon transcriptional activator |
| K05712 | 6.0E-04 | mhpA; 3-(3-hydroxy-phenyl)propionate hydroxylase |
| K05713 | 6.0E-04 | mhpB; 2,3-dihydroxyphenylpropionate 1,2-dioxygenase |
| K05714 | 6.0E-04 | mhpC; 2-hydroxy-6-ketonona-2,4-dienedioic acid hydrolase |
| K02554 | 6.0E-04 | mhpD; 2-keto-4-pentenoate hydratase |
| K01666 | 6.0E-04 | mhpE; 4-hydroxy 2-oxovalerate aldolase |
| K04073 | 6.0E-04 | mhpF; acetaldehyde dehydrogenase |
| homology to the hydrogenase hyc operon | ||
| K12136 | 1.5E-06 | hyfA; hydrogenase-4 component A |
| K12137 | 1.5E-06 | hyfB; hydrogenase-4 component B |
| K12138 | 1.5E-06 | hyfC; hydrogenase-4 component C |
| K12139 | 1.5E-06 | hyfD; hydrogenase-4 component D |
| K12140 | 1.5E-06 | hyfE; hydrogenase-4 component E |
| K12141 | 1.5E-06 | hyfF; hydrogenase-4 component F |
| K12143 | 3.3E-05 | hyfF; hydrogenase-4 component H |
| K12142 | 1.5E-06 | hyfG; hydrogenase-4 component G |
| K12144 | 1.5E-06 | hyfI; hydrogenase-4 component I |
| K12145 | 1.5E-06 | hyfJ; hydrogenase-4 component J |
| K12146 | 1.5E-06 | hyfR; hydrogenase-4 transcriptional activator |
a
KEGG orthology (KO) identifier
b
p is calculated as two-tailed Fisher’s exact probability. A complete gene list with p values is found in Table S2.