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. 2024 Nov 20;13:RP96695. doi: 10.7554/eLife.96695

Table 2. Analysis of the genomic changes detected in the mutation accumulation experiment using whole genome sequencing.

Chromosome position Sample Reference Mutation AA mutation Gene code UniProt protein name Gene ontology (GO) Experiment
5214897 cip_b A AG Leu87 frameshift 148stop MSMEG_5116 Uncharacterized protein N/A Mutation accumulation (MA)
3614832 cip_b C T Pro139Leu MSMEG_3554 N5,N10-methylene-tetrahydromethanopterin reductase xidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [GO:0016705]
2208516 cip_b G GA Leu282 frameshift 283stop MSMEG_2133 Uncharacterized protein N/A
5861538 cip_c G GC Leu168 frameshift MSMEG_5792 UPF0678 fatty acid-binding protein-like protein MSMEG_5792/MSMEI_5639 intracellular transport [GO:0046907]
3415264 cip_c T TC Leu206 frameshift 257stop MSMEG_3338 Oxidoreductase, FAD/FMN-binding FMN binding [GO:0010181]; oxidoreductase activity [GO:0016491]
2033295 cip_c A AG Leu72 frameshift 258stop MSMEG_1954 ABC1 family protein N/A
1988098 cip_c A AG N/A Intergenic region intergenic N/A
1533730 inh_b C CTCG Asp201_INSERTION MSMEG_1431 Cytochrome P450-terp (EC 1.14.-.-) heme binding [GO:0020037]; iron ion binding [GO:0005506]; monooxygenase activity [GO:0004497]; oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen [GO:0016705]
994997 inh_C G A N/A intergenic N/A
5777585 inh_C C T Val99Met MSMEG_5688 Regulatory protein, MarR GO:0003700 DNA-binding transcription factor activity; GO:0006355 regulation of DNA-templated transcription
1508883 mmc_a C G Ala300Ala (neutral) MSMEG_1407 N/A N/A
4598387 mmc_a C G Ala371Arg MSMEG_4513 Polyketide synthase transferase activity, transferring acyl groups [GO:0016746]
6786854 mmc_a G A Trp104stop MSMEG_6740 1-aminocyclopropane-1-carboxylate deaminase (EC 3.5.99.7) 1-aminocyclopropane-1-carboxylate deaminase activity [GO:0008660]; pyridoxal phosphate binding [GO:0030170]; amine catabolic process [GO:0009310]
5313643 mmc_c C T N/A intergenic N/A N/A
1865825 mock_b G GC Ala351 frameshift MSMEG_1780 Natural resistance-associated macrophage protein metal ion transmembrane transporter activity; metal ion transport; membrane;
3722101 mock_b A C Asn185Thr MSMEG_3656 ABC transporter, permease/ATP-binding protein
58213 mock_c T TC N/A MSMEG_0037 tRNA-Leu N/A
4104684 mock_c T C Val70Ala MSMEG_4033 TetR-family protein transcriptional regulator GO:0006350, Sequence-specific dna binding transcription factor activity, Regulation of transcription, dna-dependent
5118524 mock_c C CG Asp89 frameshift 143stop MSMEG_5021 Alcohol dehydrogenase, zinc-containing Oxidoreductase activity, Zinc ion binding, Oxidation-reduction process
5217666 mock_g G A Thr200Thr (neutral) MSMEG_5119 L-glutamate gamma-semialdehyde dehydrogenase Mitochondrial matrix, Oxidation-reduction process, Proline biosynthetic process, 1-pyrroline-5-carboxylate dehydrogenase activity
2970975 mock_i T C Arg155Gly MSMEG_2908 2-Keto-3-deoxy-gluconate kinase kinase activity [GO:0016301]
2970982 mock_i C T Arg153Glu MSMEG_2908 2-Keto-3-deoxy-gluconate kinase kinase activity [GO:0016301]
3306164 mock_i G A Glu1151Glu (neutral) MSMEG_3225 Ferredoxin-dependent glutamate synthase 1 (EC 1.4.7.1) 3 iron, 4 sulfur cluster binding [GO:0051538]; glutamate synthase (ferredoxin) activity [GO:0016041]; metal ion binding [GO:0046872]; glutamate biosynthetic process [GO:0006537]; glutamine metabolic process [GO:0006541] Mutation accumulation (MA)
5805844 mock_i C T Val237Val (neutral) MSMEG_5721 Acetyl-CoA acetyltransferase transferase activity, transferring acyl groups other than amino-acyl groups [GO:0016747]
4987517 mock_j G A Leu30Leu (neutral) MSMEG_4890 Alkyl hydroperoxide reductase AhpD (EC 1.11.1.28) (Alkylhydroperoxidase AhpD) alkyl hydroperoxide reductase activity [GO:0008785]; hydroperoxide reductase activity [GO:0032843]; peroxidase activity [GO:0004601]; peroxiredoxin activity [GO:0051920]; response to oxidative stress [GO:0006979]
6406902 mock_j T TG N/A intergenic N/A N/A
491016 mock_k C T N/A intergenic N/A N/A
2287781 mock_k G A Gly199Asp MSMEG_2207 Beta-ketothiolase transferase activity, transferring acyl groups other than amino-acyl groups [GO:0016747]
3438752 rif_a A AC Arg17 frameshift 175stop MSMEG_3366 Isonitrile hydratase, putative N/A
5773058 rif_a C T Glu67Lys MSMEG_5682 Uncharacterized protein integral component of membrane [GO:0016021]
6220187 CIPB0.3 G T Trp53Cys MSMEG_6151 Alpha/beta hydrolase fold-1 epoxide hydrolase activity [GO:0004301] Fluctuation assay with CIP treatment