Table 2:
Comparative assessment of existing carbon fixation enzymes of rTCA cycle in 23 strains of Mycobacterium tuberculosis.
| *KO | Enzyme description | *EC | No of strains | Enzymes encoding genes in Mtb strains |
||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| S1 | S2 | S3 | S4 | S5 | S6 | S7 | S8 | S9 | S10 | S11 | S12 | S13 | S14 | S15 | S16 | S17 | S18 | S19 | S20 | S21 | S22 | S23 | ||||
| (A) ko00710: carbon fixation in photosynthetic organisms |
||||||||||||||||||||||||||
| K00024 | Malate dehydrogenase (MDH) | EC:1.1.1.37 | 23 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K00134 | Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) | EC:1.2.1.12 | 22 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K00615 | Transketolase (TK) | EC:2.2.1.1 | 22 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K00927 | Phosphoglycerate kinase (PGK) | EC:2.7.2.3 | 22 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K01006 | Pyruvate,orthophosphate dikinase (ppdK) | EC:2.7.9.1 | 24 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 2 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K01624 | Fructose-bisphosphate aldolase, class II (FBA) | EC:4.1.2.13 | 23 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K01783 | Ribulose-phosphate 3-epimerase (rpe) | EC:5.1.3.1 | 22 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K01803 | Triosephosphate isomerase (TIM) | EC:5.3.1.1 | 22 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K01808 | Ribose 5-phosphate isomerase B (rpiB) | EC:5.3.1.6 | 22 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K02446 | Fructose-1,6-bisphosphatase II (glpX) | EC:3.1.3.11 | 20 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| (B) ko00720: carbon fixation pathways in prokaryotes |
||||||||||||||||||||||||||
| K00024 | Malate dehydrogenase (MDH) | EC:1.1.1.37 | 23 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K00031 | Isocitrate dehydrogenase (IDH) | EC:1.1.1.42 | 23 | 2 | 3 | 2 | 2 | 2 | 1 | 2 | 2 | 2 | 2 | 2 | 2 | 1 | 2 | 2 | 2 | 2 | 2 | 1 | 2 | 2 | 2 | 2 |
| K00174 | 2-oxoglutarate ferredoxin oxidoreductase subunit alpha (korA) | EC:1.2.7.3 | 22 | 1 | 1 | 2 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K00175 | 2-oxoglutarate ferredoxin oxidoreductase subunit beta (korB) | EC:1.2.7.3 | 22 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K00239 | Succinate dehydrogenase flavoprotein subunit (sdhA) | EC:1.3.99.1 | 23 | 2 | 2 | 1 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 1 | 2 | 1 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 |
| K00240 | Succinate dehydrogenase iron-sulfur subunit (sdhB) | EC:1.3.99.1 | 23 | 2 | 2 | 2 | 2 | 2 | 1 | 2 | 2 | 2 | 2 | 2 | 2 | 3 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 |
| K00241 | Succinate dehydrogenase cytochrome b556 subunit (sdhC) | EC:1.3.99.1 | 23 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K00242 | Succinate dehydrogenase membrane anchor subunit (sdhD) | EC:1.3.99.1 | 23 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K00244 | Fumarate reductase flavoprotein subunit (frdA) | EC:1.3.99.1 | 21 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K00245 | Fumarate reductase flavoprotein subunit (frdB) | EC:1.3.99.1 | 23 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K00246 | Fumarate reductase subunit C (frdC) | EC:1.3.99.1 | 23 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K00247 | Fumarate reductase subunit D (frdD) | EC:1.3.99.1 | 23 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K00626 | Acetyl-CoA C-acetyltransferase | EC:2.3.1.9 | 23 | 9 | 10 | 7 | 9 | 9 | 8 | 10 | 10 | 10 | 9 | 8 | 10 | 7 | 11 | 8 | 10 | 10 | 10 | 9 | 11 | 8 | 10 | 11 |
| K00925 | Acetate kinase (ackA) | EC:2.7.2.1 | 22 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K01006 | Pyruvate,orthophosphate dikinase (ppdK) | EC:2.7.9.1 | 23 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 2 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K01491 | Methylenetetrahydrofolate dehydrogenase (NADP+) / Methenyltetrahydrofolate cyclohydrolase (fold) | EC:1.5.1.5 EC:3.5.4.9 |
22 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K01679 | Fumarate hydratase, class II | EC:4.2.1.2 | 20 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K01681 | Aaconitate hydratase (ACO) | EC:4.2.1.3 | 19 | 1 | 1 | 0 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K01782 | 3-hydroxyacyl-CoA dehydrogenase / enoyl-CoA hydratase / 3-hydroxybutyryl-CoA epimerase (fadJ) | EC:1.1.1.35 EC:4.2.1.17 EC:5.1.2.3 |
23 | 1 | 1 | 2 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 2 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K01847 | Methylmalonyl-CoA mutase (MUTB) | EC:5.4.99.2 | 20 | 2 | 2 | 0 | 2 | 3 | 1 | 2 | 2 | 2 | 2 | 2 | 2 | 0 | 2 | 0 | 2 | 2 | 2 | 2 | 2 | 2 | 2 | 2 |
| K01895 | Acetyl-CoA synthetase (ACSS) | EC:6.2.1.1 | 22 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K01902 | Succinyl-CoA synthetase alpha subunit (sucD) | EC:6.2.1.5 | 23 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K01903 | Succinyl-CoA synthetase beta subunit (sucC) | EC:6.2.1.5 | 23 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K01958 | Pyruvate carboxylase (PC) | EC:6.4.1.1 | 21 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K01963 | Acetyl-CoA carboxylase carboxyl transferase subunit beta (accD) | EC:6.4.1.2 | 21 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K01965 | Propionyl-CoA carboxylase alpha chain (PCCA) | EC:6.4.1.3 | 20 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 0 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K01966 | Propionyl-CoA carboxylase beta chain (PCCB) | EC:6.4.1.3 | 22 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K03518 | Carbon-monoxide dehydrogenase small subunit | EC:1.2.99.2 | 20 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 |
| K03519 | Carbon-monoxide dehydrogenase medium subunit | EC:1.2.99.2 | 19 | 1 | 0 | 2 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 |
| K03520 | Carbon-monoxide dehydrogenase large subunit | EC:1.2.99.2 | 20 | 1 | 1 | 2 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 1 | 2 | 1 | 1 | 1 | 0 | 1 | 1 | 1 | 1 |
| K05606 | Methylmalonyl-CoA/ethylmalonyl-CoA epimerase (MCEE) | EC:5.1.99.1 | 22 | 1 | 1 | 0 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| K13788 | Phosphate acetyltransferase (PTA) | EC:2.3.1.8 | 23 | 1 | 1 | 2 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
Strain-wise comparisons showed that most of the strains (except for a few strains that lack either one or two genes) contain genes encoding for respective enzymes in both pathways. *KO: KEGG orthologs; *EC number: Enzyme commission number; *Mycobacterium tuberculosis (strains): given below. S1: CCDC5180 uid161941; S2: H37Rv uid170532; S3: Haarlem3 NITR202 uid202216; S4: CDC1551 uid57775; S5: CCDC5079 uid161943; S6: RGTB423 uid162179; S7: CTRI 2 uid161997; S8: KZN 4207 uid83619; S9: CCDC5079_uid203790; S10: Beijing NITR203 uid197218; S11: EAI5 NITR206 uid202218; S12: F11 uid58417; S13: RGTB327 uid157907; S14: Erdman ATCC 35801 uid193763; S15: CAS NITR204 uid202217; S16: EAI5 uid212307; S17: KZN 605 uid54947; S18: UT205 uid162183; S19: H37Rv uid57777; S20: H37Ra uid58853; S21: Haarlem uid54453; S22: KZN 1435 uid59069; S23: uid185758.