TABLE 2.
Key genes involved in metabolism, auxin biosynthesis, phosphate solubilization, and antibiotic resistance in HgT21
| Process/activity | No. of Contig | ID | Enzyme |
|---|---|---|---|
| Carbohydrate and polyalcohol metabolism | |||
| d-Raffinose | 3 | 4652 | Alpha-galactosidase (EC 3.2.1.22) |
| 15 | 330 | Alpha-galactosidase (EC 3.2.1.22) | |
| d-xylose | 3 | 3729 | Xylose isomerase (EC 5.3.1.5) |
| 3 | 3730 | Xylulose kinase (EC 2.7.1.17) | |
| d-galactose | 3 | 4652 | Alpha-galactosidase (EC 3.2.1.22) |
| 15 | 330 | Alpha-galactosidase (EC 3.2.1.22) | |
| 3 | 3772 | Beta-galactosidase (EC 3.2.1.23) | |
| 3 | 4022 | Beta-galactosidase (EC 3.2.1.23) | |
| d-ribose | 2 | 2867 | Ribose 5-phosphate isomerase A (EC 5.3.1.6) |
| 2 | 3551 | Ribose 5-phosphate isomerase B (EC 5.3.1.6) | |
| 4 | 4918 | Ribose 5-phosphate isomerase B (EC 5.3.1.6) | |
| Lactose | 3 | 3772 | Beta-galactosidase (EC 3.2.1.23) |
| 3 | 4022 | Beta-galactosidase (EC 3.2.1.23) | |
| 10 | 16 | d-Tagatose 3-epimerase | |
| Saccharose/sucrose | 5 | 5078 | 6-Phosphogluconolactonase (EC 3.1.1.31) |
| 1 | 1987 | 6-Phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) | |
| 2 | 2601 | 6-Phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) | |
| 2 | 3187 | 6-Phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44) | |
| 2 | 2867 | Ribose 5-phosphate isomerase A (EC 5.3.1.6) | |
| 2 | 3551 | Ribose 5-phosphate isomerase B (EC 5.3.1.6) | |
| 4 | 4918 | Ribose 5-phosphate isomerase B (EC 5.3.1.6) | |
| 991 | 1443 | Sucrose-6-phosphate hydrolase (EC 3.2.1.B3) | |
| 1 | 1534 | Sucrose-6-phosphate hydrolase (EC 3.2.1.B3) | |
| 20 | 2473 | Sucrose-6-phosphate hydrolase (EC 3.2.1.B3) | |
| 21 | 2475 | Sucrose-6-phosphate hydrolase (EC 3.2.1.B3) | |
| 2 | 3492 | Sucrose-6-phosphate hydrolase (EC 3.2.1.B3) | |
| 2 | 3500 | Sucrose-6-phosphate hydrolase (EC 3.2.1.B3) | |
| 2 | 3153 | Phosphoenolpyruvate-protein phosphotransferase of PTS system (EC 2.7.3.9) | |
| d-Maltose | 17 | 377 | Maltose O-acetyltransferase (EC 2.3.1.79) |
| 2 | 2505 | Maltose operon transcriptional repressor MalR, LacI family | |
| 3 | 4173 | Maltose O-acetyltransferase (EC 2.3.1.79) | |
| 3 | 4272 | Maltose/maltodextrin ABC transporter, substrate binding periplasmic protein MalE | |
| 9 | 5741 | Maltose O-acetyltransferase (EC 2.3.1.79) | |
| d-Trehalose | 2 | 2802 | PTS system, trehalose-specific IIB component (EC 2.7.1.69)/PTS system, trehalose-specific IIC component (EC 2.7.1.69) |
| 2 | 2803 | Trehalose-6-phosphate hydrolase (EC 3.2.1.93) | |
| 2 | 2804 | Trehalose operon transcriptional repressor | |
| d-Sorbitol | 3 | 4198 | Sorbitol-6-phosphate 2-dehydrogenase (EC 1.1.1.140) |
| 6 | 5294 | Glucitol/sorbitol-specific transport protein GutA | |
| 6 | 5295 | Sorbitol dehydrogenase (EC 1.1.1.14) | |
| d-Mannitol | 2 | 2862 | Putative transcriptional antiterminator, BglG family/PTS system, mannitol/fructose-specific IIA component (EC 2.7.1.69) |
| 13 | 241 | Mannitol-1-phosphate 5-dehydrogenase (EC 1.1.1.17) | |
| 13 | 242 | Mannitol operon activator, BglG family | |
| 13 | 243 | PTS system, mannitol-specific IIC component (EC 2.7.1.69)/PTS system, mannitol-specific IIB component (EC 2.7.1.69)/PTS system, mannitol-specific IIA component | |
| Starch hydrolysis | 3 | 4365 | Alpha-amylase (EC 3.2.1.1) |
| 4 | 5002 | Cytoplasmic alpha-amylase (EC 3.2.1.1) | |
| Metabolism of proteins, amino acids and others | |||
| Acetoin production | 3 | 3747 | Acetoin dehydrogenase E1 component alpha-subunit (EC 1.2.4.-) |
| 3 | 3748 | Acetoin dehydrogenase E1 component beta-subunit (EC 1.2.4.-) | |
| 3 | 3749 | Dihydrolipoamide acetyltransferase component (E2) of acetoin dehydrogenase complex (EC 2.3.1) | |
| 3 | 3750 | Dihydrolipoamide dehydrogenase of acetoin dehydrogenase (EC 1.8.1.4) | |
| 3 | 3751 | Transcriptional activator of acetoin dehydrogenase operon AcoR | |
| 3 | 3752 | 2,3-Butanediol dehydrogenase, R-alcohol forming, (R)- and (S)-acetoin-specific (EC 1.1.1.4) | |
| Casein hydrolysis | 1 | 1494 | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) |
| 1 | 2167 | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | |
| 4 | 4812 | ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) | |
| Cytochrome oxidase | 1 | 1256 | Cytochrome oxidase biogenesis protein Sco1/SenC/PrrC, putative copper metallochaperone |
| Lysine descarboxylase | 14 | 256 | Arginine decarboxylase (EC 4.1.1.19)/Lysine decarboxylase (EC 4.1.1.18) |
| 3 | 3933 | Lysine decarboxylase family | |
| Ornithine descarboxilase | 2 | 2528 | Ornithine carbamoyltransferase (EC 2.1.3.3) |
| 2 | 2507 | Ornithine aminotransferase (EC 2.6.1.13) | |
| Arginine dihydrolase 1 | 2 | 3203 | Arginine decarboxylase (EC 4.1.1.19) |
| 14 | 256 | Arginine decarboxylase (EC 4.1.1.19)/lysine decarboxylase (EC 4.1.1.18) | |
| Alanine arylamidase | 1 | 686 | N-acetylmuramoyl-l-alanine amidase (EC 3.5.1.28) |
| 1 | 1212 | N-acetylmuramoyl-l-alanine amidase (EC 3.5.1.28) | |
| 1 | 1688 | N-acetylmuramoyl-l-alanine amidase | |
| 1 | 2095 | N-acetylmuramoyl-l-alanine amidase (EC 3.5.1.28) | |
| 1 | 2201 | N-acetylmuramoyl-l-alanine amidase (EC 3.5.1.28) | |
| 2 | 2903 | N-acetylmuramoyl-l-alanine amidase | |
| 3 | 3925 | N-acetylmuramoyl-l-alanine amidase (EC 3.5.1.28) | |
| 3 | 3928 | N-acetylmuramoyl-l-alanine amidase (EC 3.5.1.28) | |
| 3 | 4105 | N-acetylmuramoyl-l-alanine amidase | |
| Tyrosine arylamidase | 1 | 2373 | Aminopeptidase S (Leu, Val, Phe, Tyr preference) (EC 3.4.11.24) |
| Beta galactosidase | 3 | 4022 | Beta-galactosidase (EC 3.2.1.23) |
| 3 | 3772 | Beta-galactosidase (EC 3.2.1.23) | |
| Alpha galactosidase | 15 | 330 | Alpha-galactosidase (EC 3.2.1.22) |
| 3 | 4652 | Alpha-galactosidase (EC 3.2.1.22) | |
| Alpha glucosidase | 2 | 3289 | Alpha-glucosidase (EC 3.2.1.20) |
| 1 | 1533 | Alpha-glucosidase (EC 3.2.1.20) | |
| N-acetyl-d-glucosaminidase | 18 | 386 | Spore cortex-lytic enzyme, N-acetylglucosaminidase SleL (EC 3.2.1.-) |
| 2 | 3351 | Spore peptidoglycan hydrolase (N-acetylglucosaminidase) (EC 3.2.1) | |
| Urease | 1 | 2274 | Urease gamma subunit (EC 3.5.1.5) |
| 1 | 2275 | Urease beta subunit (EC 3.5.1.5) | |
| 1 | 2276 | Urease alpha subunit (EC 3.5.1.5) | |
| 1 | 2277 | Urease accessory protein UreE | |
| 1 | 2278 | Urease accessory protein UreF | |
| 1 | 2279 | Urease accessory protein UreG | |
| 1 | 2280 | Urease accessory protein UreD | |
| Auxin biosynthesis | |||
| IAA synthesis | 2 | 3619 | Acetolactate synthase large subunit (EC 2.2.1.6) |
| 2 | 2637 | Alpha-acetolactate decarboxylase (EC 4.1.1.5) | |
| 2 | 2638 | Acetolactate synthase, catabolic (EC 2.2.1.6) | |
| 1 | 614 | Acetolactate synthase large subunit (EC 2.2.1.6) | |
| 1 | 615 | Acetolactate synthase small subunit (EC 2.2.1.6) | |
| 3 | 3752 | 2,3-butanediol dehydrogenase, R-alcohol forming, (R)- and (S)-acetoin-specific (EC 1.1.1.4) | |
| 1 | 1836 | 2,3-butanediol dehydrogenase, R-alcohol forming, (R)- and (S)-acetoin-specific (EC 1.1.1.4) | |
| 3 | 3691 | Glycerol dehydrogenase (EC 1.1.1.6) | |
| Phosphate solubilization | |||
| 2 | 3621 | Glucose dehydrogenase (pyrroloquinoline-quinone) | |
| 2 | 3622 | Glucose dehydrogenase (pyrroloquinoline-quinone) | |
| 7 | 5440 | l-lactate dehydrogenase (EC 1.1.1.27) | |
| 2 | 3087 | Predicted l-lactate dehydrogenase, Fe-S oxidoreductase subunit YkgE | |
| 2 | 3088 | Predicted l-lactate dehydrogenase, iron-sulfur cluster-binding subunit YkgF | |
| 2 | 3089 | Predicted l-lactate dehydrogenase, hypothetical protein subunit YkgG | |
| 1 | 2185 | Citrate synthase (si) (EC 2.3.3.1) | |
| 1 | 544 | Citrate synthase (si) (EC 2.3.3.1) | |
| 3 | 4390 | Manganese-dependent inorganic pyrophosphatase (EC 3.6.1.1) | |
| 1 | 548 | Alkaline phosphatase synthesis transcriptional regulatory protein PhoP | |
| 1 | 2268 | Alkaline phosphatase | |
| 2 | 2484 | Alkaline phosphatase-like protein | |
| 2 | 3067 | Alkaline phosphatase (EC 3.1.3.1) | |
| 2 | 3367 | Alkaline phosphatase (EC 3.1.3.1) | |
| 2 | 3581 | Alkaline phosphatase like protein | |
| 4 | 5006 | Alkaline phosphatase (EC 3.1.3.1) | |
| Antibiotic resistance | |||
| 1 | 478 | Metallo-beta-lactamase family protein | |
| 1 | 1333 | Metallo-beta-lactamase family protein | |
| 1 | 1899 | Beta-lactamase class A | |
| 2 | 2615 | Metallo-beta-lactamase family protein | |
| 2 | 3330 | Beta-lactamase (EC 3.5.2.6) | |
| 2 | 3410 | Beta-lactamase (EC 3.5.2.6) | |
| 2 | 3473 | Metallo-beta-lactamase family protein | |
| 2 | 3657 | Beta-lactamase class C and other penicillin binding proteins | |
| 3 | 4280 | Metal-dependent hydrolases of the beta-lactamase superfamily I; PhnP protein | |
| 4 | 5011 | Zn-dependent hydrolase (beta-lactamase superfamily) | |
| 7 | 5353 | Metal-dependent hydrolases of the beta-lactamase superfamily I; PhnP protein |