Table 1.
Key metabolic pathways and CBB cycle‐associated genes in Ca. Methylomirabilis iodofontis.
| Pathway | Locus tag | Gene | Enzyme | Similaritya to gene of M. oxyfera (%) | Top hit (similarity)a |
|---|---|---|---|---|---|
| Oxygenic denitrification | bin‐48‐10‐cds15 | napB | Nitrate reductase cytochrome c‐type subunit NapB | 77.0 | M. limnetica (83.5%) |
| bin‐48‐10‐cds16 | napA | Periplasmic nitrate reductase NapA | 89.1 | M. limnetica (92.5%) | |
| bin‐48‐132‐cds1 | nirS | Nitrite reductase (NO‐forming) | 88.5 | M. limnetica (97.8%) | |
| bin‐48‐55‐cds1b | nod | Putative nitric oxide dismutase | 83.8 | M. limnetica (93.4%) | |
| bin‐48‐326‐cds1b | nod | Putative nitric oxide dismutase | 91.0 | M. limnetica (99.3%) | |
| Methane oxidation | Missing | pmoCAB | Particulate methane monooxygenase | ||
| bin‐48‐119‐cds7 | mxaF | Methanol dehydrogenase | 96.4 | M. limnetica (97%) | |
| Missing | fea | Formaldehyde activating enzyme | |||
| bin‐48‐146‐cds2 | fhcD | Formylmethanofuran tetrahydromethanopterin formyltransferase | 93.4 | M. oxyfera (93.4%) | |
| bin‐48‐153‐cds5 | folD | Methylene H4F dehydrogenase | 89.6 | M. limnetica (94.7%) | |
| bin‐48‐154‐cds2 | fdhA | Formate dehydrogenase major subunit | 87.9 | M. limnetica (91.1%) | |
| bin‐48‐7‐cds14 | fdhD | Formate dehydrogenase accessory protein | 89.2 | M. limnetica (93.3%) | |
| CBB cycle | bin‐48‐50‐cds5 | rbcL | Ribulose bisphosphate carboxylase, large chain, N‐terminal | 87.5 | M. limnetica (92.4%) |
| bin‐48‐99‐cds1 | rbcL | Ribulose‐bisphosphate carboxylase, large chain | 96.9 | M. limnetica (97.6%) | |
| Missing | rbcS | Ribulose‐bisphosphate carboxylase, small chain | |||
| bin‐48‐166‐cds1 | pgk | Phosphoglycerate kinase | 94.1 | M. oxyfera (94.1%) | |
| bin‐48‐242‐cds3 | pgk | Phosphoglycerate kinase | 87.2 | M. limnetica (95.2%) | |
| bin‐48‐108‐cds1 | gap | Glyceraldehyde 3‐phosphate dehydrogenase | 87.2 | M. limnetica (96.6%) | |
| bin‐48‐166‐cds2 | gap | Glyceraldehyde‐3‐phosphate dehydrogenase (NAD(P)) | 88.0 | M. limnetica (98.8%) | |
| bin‐48‐242‐cds2 | tpi | Triosephosphate isomerase | 81.9 | M. limnetica (93.4%) | |
| bin‐48‐242‐cds3 | tpi | Triosephosphate isomerase | 87.2 | M. limnetica (95.2%) | |
| bin‐48‐99‐cds4 | fbb | Fructose‐bisphosphate aldolase | ND | M. limnetica (95.6%) | |
| bin‐48‐99‐cds3 | fbp | Fructose‐1,6‐bisphosphatase I | 87.3 | M. limnetica (94.4%) | |
| bin‐48‐108‐cds3 | glpX | Fructose‐1,6‐bisphosphatase II | 91.1 | AOM enrichment (92.0%) | |
| bin‐48‐96‐cds4 | tkt | Transketolase | ND | AOM enrichment (78.6) | |
| bin‐48‐108‐cds2 | tkt | Transketolase | 89.3 | M. limnetica (95.5) | |
| bin‐48‐17‐cds6 | xfp | Xylulose‐5‐phosphate/fructose‐6‐phosphate phosphoketolase | ND | AOM enrichment (85.0) | |
| bin‐48‐99‐cds2 | rpiA | Ribose 5‐phosphate isomerase A | 89.0 | M. limnetica (91.8) | |
| bin‐48‐34‐cds1 | prk | Phosphoribulokinase | 94.8 | M. limnetica (97.4) | |
| Iodate reduction | bin‐48‐25‐cds2 | idrP2 | Cytochrome c peroxidase | 34.1 | Environmental MAG (58.5%) |
| bin‐48‐25‐cds3 | idrP1 | Cytochrome c peroxidase | 34.1 | Chloroflexi bac. (61.1%) | |
| bin‐48‐25‐cds4 | idrB | Arsenite oxidase small subunit | ND | Rhodocyclaceae bac. (55.7%) | |
| bin‐48‐25‐cds5 | idrA | Arsenite oxidase large subunit | 25.2 | Plancetomycetaceae bac. (65.4%) |
a
Based on amino acid sequence.
b
The two Nod sequences have 26 residual overlap and can be assembled, resulting in one complete M. iodofontis Nod. ND, no significant similarity found.