Table 4. Inventory of methylotrophy and nitrogen metabolism metabolic modules.
| Enzyme/pathway/ Ecotype (strain) | Methylophilus methylotrophus Brown (5) | Methylophilus methylotrophus White (1) | Methylophilaceae 11 (11) | Methylophilaceae 11 (1P/1) | Methylophilaceae 7 (73s) | Methylotenera mobilis 13 (13) | Methylotenera mobilis JLW8 (JLW8) | Methylotenera versatilis 301 (301) | Methylovorus glucosotrophus SIP3–4 (3–4) |
| mxaFJGI (1)* | 1 | 1 | 1 | 1 | 1 | 1 | 0 | 0 | 1 |
| xoxF (copies) | 3 | 3 | 2 | 2 | 2 | 3 | 2 | 3 | 4 |
| Accessory (mxaRSACKL(D) gene copies** (2) | 4 | 4 | 4 | 4 | 4 | 4 | 2 | 2 | 3 |
| pqqA (copies) (1, 2) | 5 | 5 | 5 | 5 | 12 | 4 | 3 | 5 | 5 |
| pqqBCDEEFG (1, 2) | 1 | 1 | 1 | 1 | 1# | 1 | 1 | 1 | 1 |
| MADH genes (mauFBEDAGLMNO) (3) | 0 | 1 | 0 | 0 | 1 | 0 | 1 | 0 | 0 |
| N-methylglumatate pathway genes (mgdABCD, gma, mgsABC) (4) | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 1 | 1 |
| fae (copies) (5) | 1 | 1 | 2 | 2 | 0 | 2 | 2 | 2 | 2 |
| fae2 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| fae3 | 1 | 1 | 0 | 0 | 0 | 0 | 0 | 1 | 1 |
| H4MPT pathway genes (fhcABCD, mptG, mtdB, orfY, mch, orf5,7,17,1,9, pabB, orf22, 19, 20, afp) (5) | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| Formate dehydrogenase 1 genes (fdh1ABCDE) (7) | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| Formate dehydrogenase 4 genes (fdh4AB) (7) | 1 | 1 | 0 | 0 | 0 | 0 | 1 | 0 | 1 |
| Assimilatory RuMP cycle genes(hps1, hps2, hpi, tal, pgi, zwf, pgl, edd, eda, tkt, rpe, ppi)§ (9) | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| gndA (8) | 1 | 1 | 1 | 1 | 1 | 0 | 0 | 0 | 1 |
| gndB (8) | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 0 |
| Methylcitric acid cycle genes (prpCBD, cyl1, maoC, cyl2, gntR, mdh, sdhABCD, cyl3, prpE, fum, can) | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| Assimilatory nitrate reductase (nap) gene copies | 2 | 2 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| Respiratory nitrate reductase (narABC) | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
| Nitrite reductase (NADP; nirBD) gene copies | 2 | 2 | 1 | 1 | 1 | 1 | 1 | 1 | 1 |
| Nitrite reductase (copper; nirK) | 0 | 0 | 0 | 0 | 0 | 1 | 1 | 0 | 0 |
| Nitric oxide reductase (norBD) | 0 | 1¶ | 0 | 0 | 0 | 1 | 1 | 0 | 0 |
| Nitrous oxide reductase (nosZ) | 0 | 0 | 0 | 0 | 0 | 1 | 0 | 0 | 0 |
*Numbers in parentheses correspond to numbering of metabolic modules in Figure S1 in File S1.
**mxaD is only present in one copy, as part of the cluster directly downstream of mxaFJGI and is not present in strains JLW8 or 301 that are devoid of mxaFJGI.
#
Additional copies of pqqDE are present in this genome clustered with one of the copies of pqqA, as part of a genomic island. These are divergent and likely laterally transferred.
§
Two homologs of ppi are present.
¶
This organism only encodes NorB (not NorD).