Table 2.
Genes of L. lactis WFLU12 potentially involved in increased metabolites.
| Metabolite | Gene description | EC number | Gene name | Locus tag | Gene type# |
|---|---|---|---|---|---|
| 2-Hydroxy-4-methylvaleric acid | L-2-hydroxyisocaproate dehydrogenase | 1.1.1.- | Prokka_01454 | Dispensable | |
| 3-Hydroxybutyric acid | 3-hydroxyisobutyrate dehydrogenase | EC 1.1.1.31 | mmsB | Prokka_00965 | Dispensable |
| 3-Hydroxybutyric acid | 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9) | EC 2.3.1.16 EC 2.3.1.9 | atoB_1 | Prokka_02419 | Core |
| 3-Hydroxybutyric acid | 3-ketoacyl-CoA thiolase (EC 2.3.1.16) @ Acetyl-CoA acetyltransferase (EC 2.3.1.9) | EC 2.3.1.16 EC 2.3.1.9 | atoB_2 | Prokka_00418 | Dispensable |
| AMP | Adenine phosphoribosyltransferase | EC 2.4.2.7 | apt | Prokka_01595 | Core |
| AMP | Adenylosuccinate lyase | EC 4.3.2.2 | purB | Prokka_00224 | Core |
| AMP, thiamine | Adenylate kinase | EC 2.7.4.3 | adk | Prokka_00825 | Core |
| Ascorbic acid | PTS system, ascorbate-specific IIC component | EC:2.7.1.194 | ulaC | Prokka_00208 | Dispensable |
| Ascorbic acid | PTS system, ascorbate-specific IIA component | ulaA | Prokka_00206 | Dispensable | |
| Carboxymethyllysine | N5-(carboxyethyl)ornithine synthase | EC:1.5.1.24 | ceo | Prokka_01676 | Core |
| Citric acid | Aconitate hydratase | EC 4.2.1.3 | acnA | Prokka_01615 | Core |
| Citric acid | Citrate synthase (si) | EC 2.3.3.1 | gltA | Prokka_01614 | Core |
| Citrulline | Acetylglutamate kinase | EC:2.7.2.8 | argB | Prokka_01842 | Core |
| Citrulline | Acetylornithine deacetylase | EC:3.5.1.16 | argE | Prokka_01527 | Core |
| Citrulline | Acetylornithine/N-succinyldiaminopimelate aminotransferase | EC:2.6.1.11 2.6.1.17 | argD | Prokka_01841 | Dispensable |
| Citrulline | Alanine-synthesizing transaminase | EC:2.6.1.66 2.6.1.2 | alaA | Prokka_01171 | Core |
| Citrulline | Arginine deiminase | EC:3.5.3.6 | arcA | Prokka_00791 | Core |
| Citrulline | Argininosuccinate lyase | EC:4.3.2.1 | argH | Prokka_01135 | Core |
| Citrulline | Carbamate kinase | EC:2.7.2.2 | arcC | Prokka_00276 | Core |
| Citrulline | Carbamate kinase | EC:2.7.2.3 | arcC | Prokka_00787 | Core |
| Citrulline | Carbamate kinase | EC:2.7.2.4 | arcC | Prokka_00788 | Core |
| Citrulline | Carbamoyl-phosphate synthase large subunit | EC:6.3.5.5 | carB | Prokka_00118 | Core |
| Citrulline | Carbamoyl-phosphate synthase small subunit | EC:6.3.5.5 | carA | Prokka_00181 | Core |
| Citrulline | Glutamate N-acetyltransferase / amino-acid N-acetyltransferase | EC:2.3.1.35 EC:2.3.1.1 | argJ | Prokka_01840 | Dispensable |
| Citrulline | Glutamine synthetase | EC:6.3.1.2 | glnA | Prokka_00951 | Dispensable |
| Citrulline | N-acetyl-gamma-glutamyl-phosphate reductase | EC:1.2.1.38 | argC | Prokka_01839 | Core |
| Citrulline | Argininosuccinate synthase | EC:6.3.4.5 | argG | Prokka_01134 | Core |
| Citrulline | Ornithine carbamoyltransferase | EC:2.1.3.3 | argF | Prokka_00790 | Core |
| Citrulline | Ornithine carbamoyltransferase | EC:2.1.3.4 | argF | Prokka_01843 | Core |
| Cysteic acid | L-serine dehydratase | EC:4.3.1.17 | sdaA | Prokka_01865 | Core |
| Cysteic acid | L-serine dehydratase | EC:4.3.1.18 | sdaB | Prokka_01866 | Core |
| Cysteic acid | Phosphoadenosine phosphosulfate reductase | EC:1.8.4.8 | cysH | Prokka_02147 | Dispensable |
| Cysteic acid | Phosphoadenosine phosphosulfate reductase | EC:1.8.4.8 | cysH | Prokka_02536 | Dispensable |
| Cysteic acid | Sulfite exporter TauE/SafE | Prokka_00969 | Dispensable | ||
| Cysteic acid | Aspartate aminotransferase | EC 2.6.1.1 | aspB | Prokka_00474 | Core |
| Cysteine desulfurase | Cysteine desulfurase | EC:2.8.1.7 | iscS | Prokka_00504 | Core |
| Cysteine desulfurase | Cysteine desulfurase | EC:2.8.1.8 | iscS | Prokka_01482 | Core |
| FAD_divalent | 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase | EC:3.1.3.104 | ycsE | Prokka_00365 | Core |
| FAD_divalent | 6,7-dimethyl-8-ribityllumazine synthase | EC:2.5.1.78 | ribH | Prokka_02055 | Core |
| FAD_divalent | Diaminohydroxyphosphoribosylaminopyrimidine deaminase / 5-amino-6-(5-phosphoribosylamino)uracil reductase | EC:3.5.4.26 EC:1.1.1.193 | ribD | Prokka_02052 | Core |
| FAD_divalent | FMN hydrolase / 5-amino-6-(5-phospho-D-ribitylamino)uracil phosphatase | EC:3.1.3.102 EC:3.1.3.104 | ybjI | Prokka_00055 | Dispensable |
| FAD_divalent | Riboflavin kinase / FMN adenylyltransferase | EC:2.7.1.26 EC:2.7.7.2 | ribF | Prokka_02136 | Core |
| FAD_divalent | Riboflavin synthase | EC:2.5.1.9 | ribE | Prokka_02053 | Core |
| FAD_divalent | 3,4-dihydroxy 2-butanone 4-phosphate synthase / GTP cyclohydrolase II | EC:4.1.99.12 EC:3.5.4.25 | ribBA | Prokka_02054 | Core |
| Fumaric acid | Fumarate reductase, flavoprotein subunit precursor | EC 1.3.99.1 | Prokka_01381 | Core | |
| Glucose 1-phosphate | Phosphoglucomutase | EC 5.4.2.2 | pgmB | Prokka_01441 | Core |
| Glutathione (GSSG)_divalent | Glutathione peroxidase | EC 1.11.1.9 | gpx | Prokka_00119 | Core |
| Glutathione (GSSG)_divalent | Glutathione reductase | EC 1.8.1.7 | gor | Prokka_01883 | Core |
| Glycerol 3-phosphate | 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase | EC:5.4.2.11 | PGAM | Prokka_00347 | Core |
| Glycerol 3-phosphate | 2,3-bisphosphoglycerate-dependent phosphoglycerate mutase | EC:5.4.2.12 | PGAM | Prokka_01350 | Core |
| Glycerol 3-phosphate | Phosphoglycerate kinase | EC 2.7.2.3 | pgk | Prokka_01250 | Core |
| Guanosine | Purine nucleoside phosphorylase | EC 2.4.2.1 | deoD | Prokka_01998 | Core |
| Hydroxyproline | Pyrroline-5-carboxylate reductase | EC:1.5.1.2 | proC | Prokka_00530 | Core |
| Hydroxyproline | Pyrroline-5-carboxylate reductase | EC:1.5.1.3 | proC | Prokka_02427 | Dispensable |
| Inosine | Adenosine deaminase | EC:3.5.4.4 | add | Prokka_01301 | Dispensable |
| Inosine | Cytidine deaminase | EC:3.5.4.5 | cdd | Prokka_02546 | Core |
| Malic acid | malate dehydrogenase | EC 1.1.1.38 | maeA | Prokka_01968 | Core |
| Methionine sulfoxide | Peptide-methionine (R)-S-oxide reductase | EC:1.8.4.12 | msrB | Prokka_01199 | Core |
| Methionine sulfoxide | Peptide-methionine (S)-S-oxide reductase | EC:1.8.4.11 | msrA | Prokka_00761 | Core |
| Methionine sulfoxide | Peptide-methionine (S)-S-oxide reductase | EC:1.8.4.12 | msrA | Prokka_02442 | Dispensable |
| N8-Acetylspermidine | diamine N-acetyltransferase | EC:2.3.1.57 | speG | Prokka_00195 | Dispensable |
| N-Acetylglucosamine 1-phosphate | N-acetylglucosamine-1-phosphate uridyltransferase / Glucosamine-1-phosphate N-acetyltransferase | EC 2.7.7.23 /EC 2.3.1.157 | glmU | Prokka_00529 | Core |
| N-Acetylglutamic acid | N-acetylglutamate synthase | EC 2.3.1.1 | Nags | Prokka_01559 | Core |
| N-Acetylneuraminic acid | Phosphoglucosamine mutase | EC 5.4.2.10 | glmM | Prokka_01436 | Core |
| Nicotinamide | NAD+ kinase | EC 2.7.1.23 | ppnK | Prokka_01377 | Core |
| Nicotinamide | NAD+ synthetase | EC 6.3.1.5 | nadE | Prokka_02113 | Dispensable |
| Nicotinamide | Nicotinate-nucleotide adenylyltransferase | EC 2.7.7.18 | nadD | Prokka_02109 | Core |
| Nicotinamide | N-Ribosylnicotinamide phosphorylase | EC 2.4.2.1 | deoD | Prokka_01998 | Core |
| Nicotinamide | Nicotinate phosphoribosyltransferase | EC 6.3.4.21 | pncB | Prokka_02111 | Core |
| Taurine | Glutamate decarboxylase | EC 4.1.1.15 | gadB | Prokka_00031 | Dispensable |
| Thiamine | 1-deoxy-D-xylulose-5-phosphate synthase | EC:2.2.1.7 | dxs | Prokka_00257 | Dispensable |
| Thiamine | 1-deoxy-D-xylulose-5-phosphate synthase | EC:2.2.1.8 | dxs | Prokka_02507 | Dispensable |
| Thiamine | Cysteine desulfurase / selenocysteine lyase | EC:2.8.1.7 | sufS | Prokka_00426 | Core |
| Thiamine | Hydroxyethylthiazole kinase | EC:2.7.1.50 | thiM | Prokka_02295 | Core |
| Thiamine | Ribosome biogenesis GTPase / thiamine phosphate phosphatase | EC:3.6.1.- 3.1.3.100 | rsgA | Prokka_00641 | Core |
| Thiamine | Thiaminase (transcriptional activator TenA) | EC:3.5.99.2 | tenA | Prokka_00414 | Core |
| Thiamine | Thiamine-phosphate pyrophosphorylase | EC:2.5.1.3 | thiE | Prokka_02293 | Core |
| Thiamine | tRNA uracil 4-sulfurtransferase | EC:2.8.1.4 | thiI | Prokka_01389 | Core |
| Thiamine | Hydroxymethylpyrimidine/phosphomethylpyrimidine kinase | EC:2.7.1.49 EC:2.7.4.7 | thiD | Prokka_02294 | Core |
# Genes were identified based on pan-genome analysis using genome sequence of 20 L. lactis strains including the strain WFLU12 (Nguyen and Kim, 2018). The 19 strains include bacteria isolated from dairy product, UL8, C10, UC063, 275, 229, Il1403, 184, KLDS 4.0325, and SO; plant, AI-06, KF147, and NCDO 2118; meat, UC08 and UC11; drain water, IO-01; fermented food, A12; and human, CV56.