Comparative Genomic Analysis of a Methylorubrum rhodesianum MB200 Isolated from Biogas Digesters Provided New Insights into the Carbon Metabolism of Methylotrophic Bacteria
The central carbon metabolic pathways in M. rhodesianum strain MB200 and proposed EMC pathway containing partial propionate metabolic pathway based on our customized genomic and transcriptomic analyses. Genes encoding enzymes for each step are listed in . The common up– (red) and down– (blue) regulated genes are marked. SA: succinate; MA: methanol; FM: formaldehyde; MA_FM: methanol and formaldehyde; SA_FM: succinate and formaldehyde; EA: ethanol.
Publication
Comparative Genomic Analysis of a Methylorubrum rhodesianum MB200 Isolated from Biogas Digesters Provided New Insights into the Carbon Metabolism of Methylotrophic Bacteria. (2023) Xi Zhang, et al. Int J Mol Sci. 2023 Apr;24(8):7521. Figure: F5.| Organism | Group | Word | Match | Source | NCBI Symbol | NCBI ID |
|---|---|---|---|---|---|---|
| Drosophila melanogaster | Invertebrates | mal | MAL | ncbigene_symbol | mal | 33045 |
| Drosophila melanogaster | Invertebrates | mal | MAL | ncbigene_synonym | bs | 37890 |
| Drosophila melanogaster | Invertebrates | mal | MAL | ncbigene_synonym | Mrtf | 38338 |
| Drosophila melanogaster | Invertebrates | cal | CAL | ncbigene_symbol | cal | 247962 |
| Drosophila melanogaster | Invertebrates | cal | CAL | ncbigene_synonym | Cam | 36329 |
| Drosophila melanogaster | Invertebrates | mch | MCH | ncbigene_symbol | mch | 249741 |
| Drosophila melanogaster | Invertebrates | Ha | HA | ncbigene_symbol | ha | 251217 |
| Drosophila melanogaster | Invertebrates | fill | FILI | ncbigene_symbol | Fili | 5740472 |
| Drosophila melanogaster | Invertebrates | pur | PUR | ncbigene_symbol | pur | 252462 |
| Drosophila melanogaster | Invertebrates | phd | PHD | ncbigene_symbol | ph-d | 44889 |
| Drosophila melanogaster | Invertebrates | phd | PHD | ncbigene_synonym | Hph | 40633 |
| Drosophila melanogaster | Invertebrates | pie | PIE | ncbigene_symbol | pie | 44315 |
| Drosophila melanogaster | Invertebrates | gra | GRA | ncbigene_symbol | gra | 251211 |
| Drosophila melanogaster | Invertebrates | gra | GRA | ncbigene_synonym | grn | 40962 |
| Drosophila melanogaster | Invertebrates | gra | GRA | ncbigene_synonym | grape | 248538 |
| Drosophila melanogaster | Invertebrates | GCS | GCS | ncbigene_synonym | Gclc | 53581 |
| Drosophila melanogaster | Invertebrates | ap | AP | ncbigene_symbol | ap | 35509 |
| Drosophila melanogaster | Invertebrates | KE | KE | ncbigene_symbol | ke | 251554 |
| Drosophila melanogaster | Invertebrates | Rump | RUMP | ncbigene_symbol | rump | 41138 |
| Drosophila melanogaster | Invertebrates | Cycle | CYCLE | ncbigene_synonym | CycE | 34924 |
| Drosophila melanogaster | Invertebrates | Cycle | CYCLE | ncbigene_synonym | cyc | 40162 |
| Drosophila melanogaster | Invertebrates | AMI | AMI | ncbigene_symbol | ami | 43908 |
| Drosophila melanogaster | Invertebrates | AMI | AMI | ncbigene_synonym | so | 35662 |
| Drosophila melanogaster | Invertebrates | ell | ELL | ncbigene_synonym | Su(Tpl) | 40171 |
| Drosophila melanogaster | Invertebrates | pr | PR | ncbigene_symbol | pr | 35292 |
| Drosophila melanogaster | Invertebrates | pak | PAK | ncbigene_symbol | Pak | 44039 |
| Drosophila melanogaster | Invertebrates | pak | PAK | ncbigene_synonym | mbt | 32631 |
| Drosophila melanogaster | Invertebrates | mil | MIL | ncbigene_symbol | mil | 43343 |
| Drosophila melanogaster | Invertebrates | ad | AD | ncbigene_symbol | ad | 247742 |
| Drosophila melanogaster | Invertebrates | past | PAST | ncbigene_synonym | Past1 | 41569 |
| Drosophila melanogaster | Invertebrates | Aca | ACA | ncbigene_synonym | tRNA:Thr-TGT-1-1 | 3771902 |
| Drosophila melanogaster | Invertebrates | Aca | ACA | ncbigene_synonym | tRNA:Thr-TGT-2-1 | 3771937 |
| Drosophila melanogaster | Invertebrates | Aca | ACA | ncbigene_synonym | tRNA:Thr-TGT-2-2 | 3772144 |
| Drosophila melanogaster | Invertebrates | Aca | ACA | ncbigene_synonym | tRNA:Thr-TGT-2-5 | 3772291 |
| Drosophila melanogaster | Invertebrates | Aca | ACA | ncbigene_synonym | tRNA:Thr-TGT-2-4 | 19835230 |
| Drosophila melanogaster | Invertebrates | Aca | ACA | ncbigene_synonym | tRNA:Thr-TGT-2-3 | 19836221 |
| Drosophila melanogaster | Invertebrates | COA | COA | ncbigene_symbol | Coa | 248135 |
| Drosophila melanogaster | Invertebrates | Mey | MEY | ncbigene_symbol | mey | 43715 |
| Drosophila melanogaster | Invertebrates | EMC | EMC | ncbigene_symbol | emc | 38091 |
| Drosophila melanogaster | Invertebrates | dep | DEP | ncbigene_symbol | dep | 248306 |
| Drosophila melanogaster | Invertebrates | dep | DEP | ncbigene_synonym | DptA | 37183 |
| Drosophila melanogaster | Invertebrates | dep | DEP | ncbigene_synonym | dve | 37546 |
| Homo sapiens | Primates | mal | MAL | ncbigene_symbol | MAL | 4118 |
| Homo sapiens | Primates | mal | MAL | ncbigene_synonym | MRTFA | 57591 |
| Homo sapiens | Primates | mal | MAL | ncbigene_synonym | TIRAP | 114609 |
| Homo sapiens | Primates | mal | MA1 | ncbigene_synonym | PNMA1 | 9240 |
| Homo sapiens | Primates | axal | AXA1 | ncbigene_synonym | APTX | 54840 |
| Homo sapiens | Primates | cal | CAL | ncbigene_synonym | FBLIM1 | 54751 |
| Homo sapiens | Primates | cal | CAL | ncbigene_synonym | GOPC | 57120 |
| Homo sapiens | Primates | cal | CA1 | ncbigene_symbol | CA1 | 759 |
| Homo sapiens | Primates | mch | MCH | ncbigene_synonym | PMCH | 5367 |
| Homo sapiens | Primates | HiF | HIF | famplex_relations | HIF1A | 3091 |
| Homo sapiens | Primates | HiF | HIF | famplex_relations | EPAS1 | 2034 |
| Homo sapiens | Primates | HiF | HIF | famplex_relations | HIF3A | 64344 |
| Homo sapiens | Primates | HiF | HIF | famplex_relations | ARNT | 405 |
| Homo sapiens | Primates | HiF | HIF | famplex_relations | ARNT2 | 9915 |
| Homo sapiens | Primates | HiF | HIF | famplex_relations | BMAL1 | 406 |
| Homo sapiens | Primates | phd | PHD | ncbigene_synonym | PDC | 5132 |
| Homo sapiens | Primates | GCS | GCS | ncbigene_synonym | GCLC | 2729 |
| Homo sapiens | Primates | GCS | GCS | ncbigene_synonym | UGCG | 7357 |
| Homo sapiens | Primates | D-G6-p | DG6 | ncbigene_synonym | PGRMC2 | 10424 |
| Homo sapiens | Primates | ell | ELL | ncbigene_symbol | ELL | 8178 |
| Homo sapiens | Primates | aldi | ALDI | ncbigene_synonym | TMT1B | 196410 |
| Homo sapiens | Primates | pak | PAK | famplex_relations | PAK1 | 5058 |
| Homo sapiens | Primates | pak | PAK | famplex_relations | PAK2 | 5062 |
| Homo sapiens | Primates | pak | PAK | famplex_relations | PAK3 | 5063 |
| Homo sapiens | Primates | pak | PAK | famplex_relations | PAK4 | 10298 |
| Homo sapiens | Primates | pak | PAK | famplex_relations | PAK5 | 57144 |
| Homo sapiens | Primates | pak | PAK | famplex_relations | PAK6 | 56924 |
| Homo sapiens | Primates | past | PAST | ncbigene_synonym | EHD1 | 10938 |
| Homo sapiens | Primates | MIAT | MIAT | ncbigene_symbol | MIAT | 440823 |
| Homo sapiens | Primates | PHB | PHB | ncbigene_synonym | PHB1 | 5245 |
| Homo sapiens | Primates | Cak | CAK | ncbigene_synonym | DDR1 | 780 |
| Homo sapiens | Primates | Cak | CAK | ncbigene_synonym | CCNH | 902 |
| Homo sapiens | Primates | Cak | CAK | ncbigene_synonym | CDK7 | 1022 |
| Word | Match | MeSH | Name | ChEBI |
|---|---|---|---|---|
| CHOH | NA | mesh:C103208 | ||
| MELAN | NA | mesh:D058965 | ||
| methyl | NA | mesh:C031105 | ||
| formyl | NA | mesh:C053858 | ||
| formate | NA | mesh:D005561 | ||
| methylene HiF | NA | mesh:C471213 | ||
| Serine | NA | mesh:C047902 | ||
| Glycine | Glycine | mesh:D005998 | glycine | chebi:15428 |
| Ethanol | Ethanol | mesh:D000431 | ethanol | chebi:16236 |
| D-glacenate-P | Phlorhizin | mesh:D010695 | phlorizin | chebi:8113 |
| Glaceno-15-lactone-P | Lactones | mesh:D007783 | lactone | chebi:25000 |
| Pyruvate | NA | mesh:D011773 | ||
| Glejaldehyde | NA | |||
| Acetaldehyde | Acetaldehyde | mesh:D000079 | acetaldehyde | chebi:15343 |
| TCA | NA | mesh:C000589078 | ||
| Acetyl | NA | mesh:C011632 | ||
| Succinate | Succinates | mesh:D013386 | succinate | chebi:26806 |
| Succinyl-Ca | Calcium | mesh:D002118 | calcium atom | chebi:22984 |
| PHB | NA | mesh:C514366 | ||
| Ca | Calcium | mesh:D002118 | calcium atom | chebi:22984 |
| phosphate | NA | mesh:D010710 | ||
| R-3-Hydroxybutyl-Ca | Calcium | mesh:D002118 | calcium atom | chebi:22984 |
| (2R)-ethylmalery-Col | NA | mesh:C057112 | ||
| Mesaco-Ca | Calcium | mesh:D002118 | calcium atom | chebi:22984 |
Disease mentions
| Word | Match | MeSH | Name | DOID |
|---|---|---|---|---|
| MIAT | NA |