Table 2.
Annotated genes of the upper funneling pathway based on the eLignin database (Brink et al. 2019) and potential genes involved in lignin degradation
| Gene ID | Database | Database no. | Locus | Pathway | E-value |
|---|---|---|---|---|---|
| Genes involved in the funneling pathway lignin degradation (eLignin Database) | |||||
| Vanillin dehydrogenase | SwissProt | O69763 | Chromosome 2 | Vanillin to vanillic acid | 2.3e-196 |
| Feruloyl-CoA synthase | PHI | PHI:341Z, Q8XT88 | Chromosome 1 and 2 | Ferulic acid to feruloyl-CoA | 1.2e-112 |
| Enoyl-CoA Hydratase/lyase | SwissProt | Q2RQ36 | Chromosome 1 | p-Coumaroyl-CoA to 4-hydroxybenzaldehyde | 1.4e-36 |
| Hydroxybenzoate 3-Monooxygenase | SwissProt, Non-Redundant Protein Database | Q6SSJ6, WP_012433227.1 | Chromosome 1, 2, and 3 | 4-Hydroxybenzoic acid to protocatechuic acid | 7.0e-214; 2.6e-221 |
| Benzoate 1, 2-dioxygenase | Non-Redundant Protein Database | WP_012432614.1 | Chromosome 1 and 3 | Benzoic acid to 3,5-cyclohexadiene-1,2-diol-1-carboxylate | 6.1e-267 |
| 1,6-Dihydroxycyclohexa-2,4-diene-1-carboxylate dehydrogenase | SwissProt | P07772 | Chromosome 1 and 3 | 3,5-Cyclohexadiene-1,2-diol-1-carboxylate to catechol | 9.6e-77 |
| Catechol 1,2-dioxygenase | SwissProt | O33950 | Chromosome 3 | Catechol to cis,cis-muconic acid | 2.1e-144 |
| Catechol 2,3-dioxygenase | COG, Non-Redundant Protein Database | YP_559607, YP_00135324, YP_003280458, YP_004682700, YP_560354, WP_062170910.1 | Chromosome 3 | Catechol + O2 → (2Z,4E)-2-hydroxy-6-oxohexa-2,4-dienoate | 7.8e-68; 3.0e-45; 5.7e-65; 1.5e-109;4.0e-64; 4.3e-155 |
| Potential genes involved in lignin degradation | |||||
| Vanillate O-demethylase oxidoreductase |
Non-Redundant Protein Database SwissProt |
Chromosome 1 and 3 | Vanillic acid to catecholic structures, protocatechuate and gallate (Kamimura et al. 2017) |
2.1e-154; 1.3e-165; 4.1e-93 |
|
| Enoyl-CoA Hydratase/isomerase | COG, Non-Redundant Protein Database, SwissProt | YP_001413905, YP_002798614, YP_554216, YP_554155, YP_556021, YP_555851, YP_004680815, YP_005026757, YP_559584, WP_005793322.1, WP_028231531.1, WP_035521646.1, WP_011492940.1, WP_012426569.1, WP_012427501.1, WP_012404161.1, WP_030102796.1, WP_028194277.1, WP_069266866.1, WP_064271658.1, WP_012431551.1, WP_012431843.1, WP_035551717.1, WP_012432712.1, WP_035997457.1, WP_011489469.1, WP_011489931.1, WP_012434439.1, SDH36466.1, SDB90530.1, SAL69706.1, SAL32406.1, G4V4T7, O34893 | Chromosome 1, 2, and 3 | Feruloyl-SCoA to vanillin and acetyl-SCoA (Gasson et al. 1998) | 5.0e-66; 1.0e-130; 1.6e-201; 1.7e-163; 1.1e-58; 3.5e-123; 2.6e-135; 7.1e-52; 0; 2.4e-130; 1.5e-132; 4.0e-138; 4.2e-157; 1.6e-139; 9.6e-143; 3.7e-131; 4.6e-137; 9.5e-154; 2.4e-98; 1.0e-139; 5.7e-165; 1.4e-138; 4.6e-151; 7.8e-131; 1.3e-136; 4.7e-139; 3.4e-137; 3.5e-134; 2.5e-116; 2.8e-123; 4.3e-116; 6.7e-54; 2.5e-46 |
| Benzaldehyde dehydrogenase | Non-Redundant Protein Database | WP_028221099.1 | Chromosome 3 | Syringyl lignin catabolism (Kamimura et al. 2017) | 2.7e-236 |
| Benzoyl-CoA oxygenase/reductase | Non-Redundant Protein Database | WP_012433680.1 | Chromosome 3 | Putative genes assisting lignin breakdown (Kumar et al. 2018) | 1.2e-240 |