FMWO d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Nitrosomonadaceae g Nitrosomonas s Nitrosomonas mobilis 1/1-272

FMWO d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Nitrosomonadaceae g Nitrosomonas s Nitrosomonas mobilis 2/1-272

FOID d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Nitrosomonadaceae g Nitrosomonas s Nitrosomonas europaea 1/1-272

GCA 002869885 1 ASM286988v1 1 methane 002869885 monooxygenase/ammonia protein 1 NitrospiraPLY24690 GCA sp CG24C monooxygenase /1-274A subunit

GCA GCA 900167395 1 IMG-taxon 2582581324 annotated assembly protein SKA09313 1 ammonia monooxygenase NitrosomonassubunitA europaea /1-272

GCA 900111725 1 IMG-taxon 2671180133 annotated assembly protein SET51056 1 ammonia monooxygenase subunit NitrosomonasA europaea /1-272

GCA 900106625 1 IMG-taxon 2671180134 annotated assembly protein SDW98167 1 ammonia monooxygenase subunitA Nitrosomonas europaea /1-272

FNOY d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Nitrosomonadaceae g Nitrosomonas s Nitrosomonas halophila 1/1-274

GCA 900107165 1 IMG-taxon 2675903041 annotated assembly protein SDZ04661 1 ammonia monooxygenase subunitA Nitrosomonas halophila /1-274

GCA 900106875 1 IMG-taxon 2671180081 annotated assembly protein SDX13811 1 ammonia monooxygenase subunit A Nitrosomonas eutropha /1-272

GCA 900100815 1 IMG-taxon 2671180129 annotated assembly protein SCX29452 1 ammonia monooxygenase subunit A Nitrosomonas eutropha /1-272

FNYF d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Nitrosomonadaceae g Nitrosomonas s Nitrosomonas eutropha 1/1-272 GCA 900108975 1 IMG-taxon 2671180128 annotated assembly protein SEJ33789 1 ammonia monooxygenase subunit A Nitrosomonas eutropha /1-272 FPBL d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Nitrosomonadaceae g Nitrosomonas s Nitrosomonas eutropha A 1/1-272

GCA 000009145 1ASM914v1 protein CAD85974 1Ammonia monooxygenase subunit A Nitrosomonas europaeaATCC 19718 /1-272

GCA 900116685 1 IMG-taxon 2671180072 annotated assembly protein SFU84057 1 ammonia monooxygenase subunit A Nitrosomonas eutropha /1-272

GCA 900103035 1 NSMM protein SCZ86996 1Ammonia monooxygenase acetylene-binding Nitrosomonas mobilis /1-272 GCA 900113925 1 IMG-taxon 2675903040 annotated assembly protein SFJ09834 1 methane/ammonia monooxygenase subunit A Nitrosomonas sp Nm34 /1-274

GCA 001567435 1ASM156743v1 protein KXK49931 1 ammonia monooxygenase subunitA Nitrosomonas europaea /1-272 FOUF d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Nitrosomonadaceae g Nitrosomonas s Nitrosomonas nitrosa 1/1-274 GCA 900106545 1 IMG-taxon 2675903044 annotated assembly protein SDX19239 1 methane/ammoniaGCA 900114795 1 IMG-taxon monooxygenase 2671180218 annotatedsubunit A assembly Nitrosomonas protein SFM93401communis 1 ammonia/1-274 monooxygenase subunit A Nitrosomonas nitrosa /1-274

GCA 000014765 1 ASM1476v1 protein ABI60535 1 ammonia monooxygenase subunit A Nitrosomonas eutropha C91 /1-272

FNNH d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Nitrosomonadaceae g Nitrosomonas s Nitrosomonas communis 1/1-274

FOUB d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Nitrosomonadaceae g Nitrosomonas s Nitrosomonas communis A 1/1-274

GCA 900107335 1 IMG-taxon 2675903036 annotated assembly protein SDZ18871 1 methane/ammonia monooxygenase subunit A Nitrosomonas sp Nm58 /1-274

GCA 900100485 1 IMG-taxon 2675903038GCA 900114745 annotated 1 assembly IMG-taxon protein 2675903043 SDI11441 annotated 1 methane/ammonia assembly protein monooxygenase SFN18330 1 ammonia subunit monooxygenase A Nitrosomonas subunit sp Nm132 A Nitrosomonas /1-274 communis /1-274

GCA 900111165 1 IMG-taxon 2675903037 annotated assembly protein SER65150 1 methane/ammonia monooxygenase subunit A Nitrosomonas sp Nm51 /1-274 FOIA d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Nitrosomonadaceae g Nitrosomonas s Nitrosomonas marina A 1/1-274 GCA 900107265 1 IMG-taxon 2675903042 annotated assembly protein SDZ11758 1 ammonia monooxygenase subunit A Nitrosomonas sp Nm33 /1-274

GCA 001007935 1 ASM100793v1 protein AKH39468 1 ammonia monooxygenase Nitrosomonas communis /1-274

GCA 900111605 1 IMG-taxon 2671180135 annotated assembly protein SES99874 1 ammonia monooxygenase subunit A Nitrosomonas marina /1-274

GCA 900110145 1 IMG-taxon 2671180082 annotated assembly protein SEN26221 1 ammonia monooxygenase subunit A Nitrosomonas marina /1-274 FOCP d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Nitrosomonadaceae g Nitrosomonas s Nitrosomonas marina 1/1-274

FNPJ d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Nitrosomonadaceae g Nitrosomonas s 1/1-274 FOSP d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Nitrosomonadaceae g Nitrosomonas s Nitrosomonas aestuarii 1/1-274

GCA 900112825 1 IMG-taxon 2675903035 annotated assembly protein SFE33608 1 methane/ammonia monooxygenase subunit A Nitrosomonas sp Nm166 /1-274 GCA 900114305 1 IMG-taxon 2671180137 annotated assembly protein SFK36912 1 ammonia monooxygenase subunit A Nitrosomonas aestuarii /1-274

GCA 900108305 1 IMG-taxon 2671180130 annotated assembly protein SEF78994 1 ammonia monooxygenase subunit A Nitrosomonas ureae /1-274

GCA 900215345 1 IMG-taxon 2734482144 annotated assembly protein SOD20748 1 methane/ammonia monooxygenase subunit A Nitrosomonas ureae /1-274 GCA 000175095 2 ASM17509v2 protein ADZ27404 1 methane monooxygenase/ammonia monooxygenase subunit A Nitrosomonas sp AL212 /1-274

GCA 900111055 1 IMG-taxon 2675903039 annotated assembly protein SEQ25651 1 methane/ammonia monooxygenase subunit A Nitrosomonas ureae /1-274 GCA 001455205 1 ASM145520v1 protein ALQ52180 1 methane monooxygenase/ammonia monooxygenase subunit A Nitrosomonas ureae /1-274

GCA 002869895 1 ASM286989v1 protein PLY22682 1 methane monooxygenase/ammonia monooxygenase subunit A Nitrospira sp CG24E /1-269

GCA 002869925 1 ASM286992v1 protein PLY35005 1 methane monooxygenase/ammonia monooxygenase subunit A Nitrospira sp CG24A /1-271 GCA 002869925 1 ASM286992v1 protein PLY35005 1 methane monooxygenase/ammonia monooxygenase subunit A Nitrospira sp CG24A /1-239 OCMU d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Nitrosomonadaceae g Nitrosomonas s Nitrosomonas ureae 1/1-274

OCMU d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Nitrosomonadaceae g Nitrosomonas s Nitrosomonas ureae 3/1-274

CZPZ d Bacteria p Nitrospirota c Nitrospiria o Nitrospirales f Nitrospiraceae g Nitrospira s Nitrospira nitrificans 1/1-273

GCA 002083565 1 ASM208356v1 protein OQW57195 1 methane monooxygenase/ammonia monooxygenase subunit A Nitrospira sp ST-bin4 /1-274 GCA 001458775 1 COMA2 protein CUS38627 1 Ammonia monooxygenase subunit A Candidatus Nitrospira nitrificans /1-273 FJVM d Bacteria p Nitrospirota c Nitrospiria o Nitrospirales f Nitrospiraceae g Nitrospira s 1/1-274GCA 002869845 1 ASM286984v1 protein PLY29908 1 methane monooxygenase/ammonia monooxygenase subunit A Nitrospira sp CG24B /1-272 OCMU d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Nitrosomonadaceae g Nitrosomonas s Nitrosomonas ureae 2/1-274 GCA 002083405 1 ASM208340v1 protein OQW37964 1 methane monooxygenase/ammonia monooxygenase subunit A Nitrospira sp SG-bin2 /1-274

GCA 002083365 1 ASM208336v1 protein OQW38018 1 methane monooxygenase/ammonia monooxygenase subunit A Nitrospira sp SG-bin1 /1-272

GCA 001458695 1 NiCh1 protein CUQ66826 1 Ammonia monooxygenase subunit A Candidatus Nitrospira inopinata /1-274 FJVN d Bacteria p Nitrospirota c Nitrospiria o Nitrospirales f Nitrospiraceae g Nitrospira s Nitrospira moscoviensis A 1/1-274 GCA 002083355 ASM208335v11 protein OQW36130 1 methane monooxygenase/ammonia monooxygenase subunit A Nitrospira sp HN-bin3 /1-274 CZQA d Bacteria p Nitrospirota c Nitrospiria o Nitrospirales f Nitrospiraceae g Nitrospira s Nitrospira nitrosa 2/1-274 CZQA d Bacteria p Nitrospirota c Nitrospiria o Nitrospirales f Nitrospiraceae g Nitrospira s Nitrospira nitrosa 1/1-274 GCA 001458735 1 COMA1 protein CUS38424 1 Ammonia monooxygenase subunit A Candidatus Nitrospira nitrosa /1-274 GCA 002254365 1 ASM225436v1 protein OYT21943 1 methane monooxygenase/ammonia monooxygenase subunit A Nitrospira sp UW-LDO-01 /1-274 Tree scale: 1 GCA 000219585 1 ASM21958v1 protein AEJ02636 1 methane monooxygenase/ammonia monooxygenase subunit A Nitrosomonas sp Is79A3 /1-274

GCA 003011925 1 ASM301192v1 protein PSJ15838 1 methane monooxygenase/ammonia monooxygenase subunit A Nitrosomonas sp APG5 /1-274 GCA 900106555 1 IMG-taxon 2671180131 annotated assembly protein SDX61716 1 ammonia monooxygenase subunit A Nitrosomonas oligotropha /1-274

GCA 900110385 1 IMG-taxon 2671180132 annotated assembly protein SEP15831 1 ammonia monooxygenase subunit A Nitrosomonas oligotropha /1-274

FNOE d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Nitrosomonadaceae g Nitrosomonas s Nitrosomonas oligotropha 1/1-274

FOXN d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Nitrosomonadaceae g Nitrosomonas s Nitrosomonas cryotolerans 2/1-274

FOXN d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Nitrosomonadaceae g Nitrosomonas s Nitrosomonas cryotolerans 1/1-274 GCA 900143275 1 IMG-taxon 2588253501 annotated assembly protein SIO41207 1 ammonia monooxygenase subunit A Nitrosomonas cryotolerans ATCC 49181 /1-274

GCA 900115725 1 IMG-taxon 2671180136 annotated assembly protein SFQ18048 1 ammonia monooxygenase subunit A Nitrosomonas cryotolerans /1-274

GCA 900142705 1 IMG-taxon 2671180073 annotated assembly protein SHL56793 1 ammonia monooxygenase subunit A Nitrosospira sp Nsp11 /1-274

GCA 900103145 1 IMG-taxon 2671180080 annotated assembly protein SDA13048 1 ammonia monooxygenase subunit A Nitrosospira sp Nsp18 /1-274

GCA 900100985 1 IMG-taxon 2671180077 annotated assembly protein SCX63633 1 ammonia monooxygenase subunit A Nitrosospira sp Nsp1 /1-274

PHCV d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Rhodocyclaceae g Rugosibacter s 2/1-245 GCA 002842395 1 ASM284239v1 protein PKO83758 1 methane monooxygenase/ammonia monooxygenase subunit A Betaproteobacteria bacterium HGW-Betaproteobacteria-11 /1-245 GCA 900215485 1 IMG-taxon 2721756095 annotated assembly protein SOD40998 1 ammonia monooxygenase subunit A Nitrosovibrio sp Nv4 /1-274 FMUF d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Nitrosomonadaceae g Nitrosospira s 1/1-274

GCA 900110495 1 IMG-taxon 2675903143 annotated assembly protein SEO89261 1 ammonia monooxygenase subunit A Nitrosovibrio sp Nv6 /1-274

AYLO d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methyloglobulus s Methyloglobulus morosus 3/1-267 GCA 001644115 1 ASM164411v1 protein OAI07208 1 methane monooxygenase/ammonia monooxygenase subunit A Methylomonas methanica /1-246 FOVY d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Nitrosomonadaceae g Nitrosospira s Nitrosospira briensis A 1/1-274 GCA 001644035 1 ASM164403v1 protein OAI08303 1 methane monooxygenase/ammonia monooxygenase subunit A Methylomonas methanica /1-246 DLHW d Bacteria p Proteobacteria c GammaproteobacteriaLUUG d o Bacteria Methylococcales p Proteobacteria f Methylomonadaceae c Gammaproteobacteria g Methyloglobulus o Methylococcaless 3/1-253 f Methylomonadaceae g Methylomonas s Methylomonas methanica A 3/1-247 LUUG d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methylomonas s Methylomonas methanica A 2/1-245

GCA 002441955AZXK d Bacteria 1 ASM244195v1 p Proteobacteria protein ATG91943c Gammaproteobacteria 1 methane monooxygenase/ammonia o Methylococcales f Methylomonadaceae monooxygenase subunit g Methylomonas A Methylomonas s 2/1-244 koyamae /1-234 GCA 900115325 1 IMG-taxon 2671180070 annotated assembly protein SFO12665 1 ammonia monooxygenase subunit A Nitrosospira briensis /1-274 PHSP d MKMCBacteria d p Bacteria Proteobacteria p Proteobacteria c Gammaproteobacteria c Gammaproteobacteria o Methylococcales o Methylococcales f Methylomonadaceae f Methylomonadaceae g KS41 s 2/1-250 g Methylomonas s Methylomonas koyamae A 2/1-244 GCA 000214275 3 ASM21427v3 protein EIC29219 1 Ammonia monooxygenase Methylomicrobium album BG8 /1-234 GCA 002890675 1 ASM289067v1 protein PNE12180 1 methane monooxygenase/ammonia monooxygenase subunit A Beijerinckiaceae bacterium /1-246 DLHW d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methyloglobulus s 1/1-238

GCA 900113575 1 IMG-taxon 2671180078 annotated assembly protein SFH38457 1 ammonia monooxygenase subunit A Nitrosospira sp Nsp14 /1-274 JYNS d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylococcaceae g Methyloterricola s Methyloterricola oryzae 3/1-250 GCA 900108135 1 IMG-taxon 2671180127 annotated assembly protein SEF68642 1 ammonia monooxygenase subunit A Nitrosospira multiformis ATCC 25196 /1-274 ARCT d BacteriaGCA p Proteobacteria001644125 1 ASM164412v1c Alphaproteobacteria protein o OAI30590 Rhizobiales 1 methanef Beijerinckiaceae monooxygenase/ammonia g Methylocystis s Methylocystis monooxygenase rosea subunit1/1-247 A Methylosinus sp R-45379 /1-249 ARCT d BacteriaGCA p Proteobacteria002117405 1 ASM211740v1c Alphaproteobacteria protein o ARN79806Rhizobiales 1f Beijerinckiaceaemethane monooxygenase/ammonia g Methylocystis s Methylocystis monooxygenase rosea 3/1-235 subunit A Methylocystis bryophila /1-249

GCA 000196355 1 ASM19635v1 protein ABB76052 1 ammonia monooxygenase subunit A Nitrosospira multiformis ATCC 25196 /1-274 GCA 900107715 1 IMG-taxon 2671180074 annotated assembly protein SEA41232 1 ammonia monooxygenase subunit A Nitrosospira multiformis /1-274

FNQL d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Nitrosomonadaceae g Nitrosospira s Nitrosospira multiformis 1/1-274 GCA 002716545 1 ASM271654v1 protein MBG95493 1 methane monooxygenase/ammonia monooxygenase subunit A Cycloclasticus sp /1-238 GCA 002700385 1 ASM270038v1 protein MAV31088 1 methane monooxygenase/ammonia monooxygenase subunit A Cycloclasticus sp /1-238

GCA 900110185 1 IMG-taxon 2671180076 annotated assembly protein SEN16582 1 ammonia monooxygenase subunit A Nitrosospira multiformis /1-274

FOCT d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Nitrosomonadaceae g Nitrosospira s Nitrosospira multiformis A 1/1-274 GCA 002842395 1 ASM284239v1 protein PKO84334 1 methane monooxygenase/ammonia monooxygenase subunit A Betaproteobacteria bacterium HGW-Betaproteobacteria-11 /1-244 DEIG d Bacteria p PHCVProteobacteria d Bacteria c Gammaproteobacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Cycloclasticaceae o Betaproteobacteriales g UBA2780 f Rhodocyclaceae s 1/1-248 g Rugosibacter s 1/1-253

GCA 002795245 1 ASM279524v1 protein PJG53672GCA 900111015 1 methane 1 IMG-taxonmonooxygenase/ammonia 2616644811 annotated monooxygenase assembly subunit protein A SEQ84470Bradyrhizobium 1 ammonia sp INPA54B monooxygenase /1-232 subunit A Solimonas aquatica /2-256 GCA 002953135 1 ASM295313v1 proteinFOFS AUW60608 d Bacteria 1 methane p Proteobacteria monooxygenase/ammonia c Gammaproteobacteria monooxygenase o Nevskiales subunit f NevskiaceaeA plasmid Sphingobium g Solimonas sp sSCG-1 Solimonas /1-237 aquatica 1/1-250 GCA 900111585 1 IMG-taxon 2671180069 annotated assembly protein SES62907 1 ammonia monooxygenase subunit A Nitrosospira multiformis /1-274 PAKU d Bacteria p Proteobacteria c Gammaproteobacteria o Nevskiales f Nevskiaceae g Polycyclovorans s 2/1-236 PAKU d Bacteria p Proteobacteria c Gammaproteobacteria o Nevskiales f Nevskiaceae g Polycyclovorans s 1/2-265 GCA 001770905 1 ASM177090v1 protein OGB13554 1 hypothetical protein A3I64 13755 Burkholderiales bacterium RIFCSPLOWO2 02 FULL 67 64 /2-264 FOHI d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Nitrosomonadaceae g Nitrosospira s Nitrosospira multiformis B 1/1-274 GCA 001772135 1 ASM177213v1 protein OGB44611 1 hypothetical protein A3E51 20820 Burkholderiales bacterium RIFCSPHIGHO2 12 FULL 67 38 /2-264 GCA 001770965 1 ASM177096v1 protein OGB95759 1 hypothetical protein A3G82 11060 Burkholderiales bacterium RIFCSPLOWO2 12 FULL 67 210 /2-264

FPBZ d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Nitrosomonadaceae g Nitrosospira s Nitrosospira multiformis C 1/1-274

GCA 900116835 1 IMG-taxon 2671180079 annotated assembly protein SFU60960 1 ammonia monooxygenase subunit A Nitrosospira multiformis /1-274 GCA 002727615 1 ASM272761v1 protein MBT35706 1 methane monooxygenase/ammonia monooxygenase subunit A Rickettsiales bacterium /1-247

1.0

GCA 900094605 1 IMG-taxon 2617270735 annotated assembly protein SCB45705 1 methane/ammonia monooxygenase subunit A Bradyrhizobium shewense /1-248 GCA 900109785 1 IMG-taxon 2671180071 annotated assembly protein SEL05413 1 ammonia monooxygenase subunit A Nitrosovibrio tenuis /1-274 0.7 GCA 002936975 1 ASM293697v1 protein PPQ14299 1 methane monooxygenase/ammonia monooxygenase subunit A Bradyrhizobium sp AC87j1 /1-248 LNDV d Bacteria p ProteobacteriaGCA 002068095 c Gammaproteobacteria 1 ASM206809v1 o Betaproteobacterialesprotein OPY96798 1 hypotheticalf Ga0077523 protein g Ga0077526 A5906 01120s 1/1-249 Bradyrhizobium sp BR10280 /1-245 LJYG d Bacteria p Proteobacteria c Alphaproteobacteria o Rhizobiales f Xanthobacteraceae g Bradyrhizobium s Bradyrhizobium manausense 1/1-267 GCA 001440035 1 ABySSBR3351v1 protein KRQ16351 1 hypothetical protein AOQ71 05115 Bradyrhizobium manausense /1-245 FOBH d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Nitrosomonadaceae g Nitrosospira s Nitrosospira tenuis 1/1-274 1.0

0.10.50.9

0.4 1.0 GCA 001899235 1 ASM189923v1 protein OJY07900 1 methane monooxygenase/ammonia monooxygenase subunit A Nitrosospira sp 56-18 /1-274 0.9 1.0 0.9

0.9 GCA 900102495 1 IMG-taxon 2671180042 annotated assembly protein SCY45393 1 ammonia monooxygenase subunit A Nitrosospira sp Nl5 /1-274 0.9

0.4 GCA 900103165 1 IMG-taxon 2667527227 annotated assembly protein SDR01399 1 ammonia monooxygenase subunit A Nitrosospira multiformis /1-274 1.0

1.0 GCA 900101945 1 IMG-taxon 2671180075 annotated assembly protein SCX92723 1 ammonia monooxygenase subunit A Nitrosospira sp Nsp13 /1-274 1.0

1.0 0.30.1 0.11.00.9 1.00.90.60.3 1.01.0 MPMI d Bacteria p UBP10 c GR-WP33-30 o bin18AQXZ f bin18 d Bacteriag bin18 sp 1/1-231Actinobacteriota c Actinobacteria o Corynebacteriales f Corynebacteriaceae g Smaragdicoccus s Smaragdicoccus niigatensis 1/2-240 FMVD d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Nitrosomonadaceae g Nitrosospira s Nitrosospira multiformis D 1/1-274 0.7 AQXZ d Bacteria p Actinobacteriota c Actinobacteria o Corynebacteriales f Corynebacteriaceae g Smaragdicoccus s Smaragdicoccus niigatensis 1/1-225 0.60.70.1 0.9 0.7 1.0 1.0 1.0 0.3 1.0 1.0 0.6 GCA 000355765 4 ASM35576v4 protein ASL24810 1 methane monooxygenase/ammonia monooxygenase subunit A Nitrosospira lacus /1-274 1.0 1.01.0 1.0 0.9 0.50.7 0.9 0.9 0.8 0.9 0.9 0.40.90.20.80.8 1.00.9 1.00.90.9 1.0 1.0 GCA 000832065 1 ASM83206v1 protein KIO48008 1 ammonia monooxygenase Nitrosospira sp NpAV /1-274 0.71.0 1.0 1.01.0 1.00.20.61.00.80.81.0 1.0 1.0 0.10.50.81.00.81.01.00.91.00.9 1.0 0.30.90.90.91.00.80.60.70.70.9 0.9 1.0 GCA 000389985 1 1 0 proteinGCA EON22010 GCA002887815 000266905 1 particulate 1 ASM288781v1 1 ASM26690v1butane monooxygenase protein protein PND54403 AFM20519 subunit 1 methane A 1 Nocardioides Ammonia monooxygenase/ammonia monooxygenase sp CF8 /1-229 plasmid monooxygenase Mycobacterium subunit chubuense A Mycobacterium NBB4 /3-244 sp ENV421 /1-226 0.9 0.8 1.01.0 1.0 GCA 000230895 3 ASM23089v3 protein AEV73581 1 Ammonia monooxygenase Mycobacterium rhodesiae NBB3 /2-243 0.8 GCA 002157835 1 ASM215783v1 protein ART74457 1 methane monooxygenase/ammonia monooxygenase subunit A plasmid Mycobacterium dioxanotrophicus /5-236 1.0 1.0 0.9 MPMI d Bacteria p UBP10 c GR-WP33-30 o bin18 f bin18 g bin18 s 2/15-263

JZDQ d Bacteria p Actinobacteriota c Actinobacteria o Propionibacteriales f Nocardioidaceae g Nocardioides s Nocardioides luteus 1/1-220 1.0 GCA 000192415 1 Noca bact Broad 1 V1 protein EGD43187 1 methane monooxygenase A subunit Nocardioidaceae bacterium Broad-1 /1-236 1.0 GCA 000960475 2 ASM96047v2 protein OIJ27996 1 methane monooxygenase Nocardioides luteus /1-236

1.0 JYIJ d Bacteria p Actinobacteriota c Actinobacteria o Streptomycetales f Streptomycetaceae A g Streptomyces F s Streptomyces F thermoautotrophicus 1/1-220 GCA 001543925 1 ASM154392v1 protein KWX00979 1 Particulate methane monooxygenase A-subunit Streptomyces thermoautotrophicus /7-249 GCA 001543895 1 ASM154389v1 protein KWX04684 1 methane monooxygenase Streptomyces thermoautotrophicus /7-249 1.0 GCA 001543915 1 ASM154391v1 protein KWX06881 1 methane monooxygenase Streptomyces thermoautotrophicus /7-249 1.0

1.0 1.0 0.4 1.0 1.0 0.9 1.0 1.00.3 1.0 1.0 0.9 1.0 1.0 1.0 1.0 1.0

0.8 0.9 0.9 1.0 1.0 1.0 0.9 1.0 1.0 GCA 002162695 1 ASM216269v1 protein OUR81281 1 methane monooxygenase/ammonia monooxygenase subunit A Cycloclasticus sp 46 120 T64 /1-247 GCA 002163215 1 ASM216321v1 protein OUR67821 1 methane monooxygenase/ammonia monooxygenase subunit A Cycloclasticus sp 46 83 sub15 T18 /1-247 GCA 002101235 1 ASM210123v1 protein ORU93661 1 methane monooxygenase/ammonia monooxygenase subunit A Cycloclasticus sp symbiont of Bathymodiolus heckerae /1-247 0.9 GCA 002162705 1 ASM216270v1 protein OUR85102 1 methane monooxygenase/ammonia monooxygenase subunit A Cycloclasticus sp 44 32 T64 /1-247 0.8 1.0 GCA 002101205 1 ASM210120v1 protein ORU91033 1 methane monooxygenase/ammonia monooxygenase subunit A Cycloclasticus sp symbiont of Poecilosclerida sp N /1-240 GCA 002101225 1 ASM210122v1 protein ORU89476 1 methane monooxygenase/ammonia monooxygenase subunit A Cycloclasticus sp symbiont of Poecilosclerida sp M /1-245 GCA 002401815 1 ASM240181v1 protein PCI68422 1 methane monooxygenase/ammonia monooxygenase subunit A Piscirickettsiaceae bacterium /1-247 GCA 002733135 1 ASM273313v1 protein PHS73401 1 methane monooxygenase/ammonia monooxygenase subunit A Cycloclasticus sp /1-247 1.0 1.0 0.71.00.70.70.4 1.0 0.8 0.8 0.9 1.0 GCA 002746135 1 ASM274613v1 protein PCJ38281 1 methane monooxygenase/ammonia monooxygenase subunit A Cellvibrionales bacterium /1-237 1.0 GCA 002162755 1 ASM216275v1 protein OUS17543 1 hypothetical protein A9Q88 02975 Gammaproteobacteria bacterium 50 400 T64 /1-237 0.9 1.0 1.00.80.8 1.0 MAAS d Bacteria p Proteobacteria c Gammaproteobacteria o Pseudomonadales f Porticoccaceae g 50-400-T64 s 1/1-237 DJFY d Bacteria p Proteobacteria c Gammaproteobacteria o Pseudomonadales f Porticoccaceae g HB2-32-21 s 1/1-237 GCA 002162825 1 ASM216282v1 protein OUS09231 1 hypothetical protein A9Q90 04105 Gammaproteobacteria bacterium 54 18 T64 /1-234 1.0 1.0 GCA 002162815 1 ASM216281v1 protein OUS10042 1 hypothetical protein A9Q89 11910 Gammaproteobacteria bacterium 53 120 T64 /1-234 0.9 0.70.9 1.0 0.4 1.0 0.9 1.0 0.9 0.80.6 0.9 AQQV d Bacteria p Proteobacteria c Gammaproteobacteria o Nevskiales f Oceanococcaceae g Oceanococcus s Oceanococcus atlanticus 1/1-248 1.0 GCA 002706265 1 ASM270626v1 protein MAY26629 1 methane monooxygenase/ammonia monooxygenase subunit A Polycyclovorans sp /1-242 1.0 1.0 1.0 FOFS d Bacteria p Proteobacteria c Gammaproteobacteria o Nevskiales f Nevskiaceae g Solimonas s Solimonas aquatica 2/1-248 1.0 GCA 900111015 1 IMG-taxon 2616644811 annotated assembly protein SEQ16222 1 methane/ammonia monooxygenase subunit A Solimonas aquatica /1-238 1.00.3 1.0 DCVY d Bacteria p Proteobacteria c Gammaproteobacteria o Betaproteobacteriales f Burkholderiaceae g Acidovorax B s Acidovorax B delafieldii 1/1-249 0.9 1.0 0.8 GCA 001770895 LSIH1 ASM177089v1 d Bacteria p proteinProteobacteria OGB49382 c Gammaproteobacteria 1 hypothetical protein o A2W72 Betaproteobacteriales 07305 Burkholderiales f Burkholderiaceae bacterium RIFCSPLOWO2 g Acidovorax s 12Acidovorax 67 14 /1-241 delafieldii 1/1-246 GCA 000576245 1 T4 protein EWS66135 1 Particulate methane monooxygenase beta subunit Hydrogenophaga sp T4 /1-249 1.0 1.0 0.8

0.7 1.0 1.0 DJFZ d Bacteria p Proteobacteria c Gammaproteobacteria o UBA5859 f UBA5859 g UBA5859 s 2/1-246 DHQP d Bacteria p Proteobacteria c Gammaproteobacteria o UBA5335 f UBA5335 g UBA5335 s 1/1-243

0.7 1.0 1.0 1.0 DGOX d Bacteria p Proteobacteria c Gammaproteobacteria o Ga0077536 f UBA981 g UBA981 s 1/1-246

0.8

0.5 1.0

1.0 0.8 DFBZ d Bacteria p Proteobacteria c Gammaproteobacteria o Pseudomonadales f UBA3067 g UBA3067 s 1/1-241 1.0 DFBZ d Bacteria p Proteobacteria c Gammaproteobacteria o Pseudomonadales f UBA3067 g UBA3067 s 2/1-246 0.7 1.0

1.0 DJFZ d Bacteria p Proteobacteria c Gammaproteobacteria o UBA5859 f UBA5859 g UBA5859 s 1/1-245 GCA 002401525 1 ASM240152v1 protein PCI52101 1DEIQ methane d Bacteria monooxygenase/ammonia p Proteobacteria c Gammaproteobacteria monooxygenase subunit o UBA2770A Moraxellaceae f UBA2770 bacterium g UBA2770 /1-244 s 1/1-230 0.9

1.0 1.0 1.0 NVVB d Bacteria p Proteobacteria c Gammaproteobacteria o Pseudomonadales f UBA3067 g GCA-002402085 s 1/1-244

1.0 1.0 NVVB d Bacteria p Proteobacteria c Gammaproteobacteria o PseudomonadalesDHQP d Bacteria f UBA3067p Proteobacteria g GCA-002402085 c Gammaproteobacteria s 2/7-250 o UBA5335 f UBA5335 g UBA5335 s 2/6-244 0.90.70.5 1.0 0.9 0.9 0.5 0.9 GCA 002402085 1 ASM240208v1 protein PCJ15356 1 methane monooxygenase/ammonia monooxygenase subunit A Gammaproteobacteria bacterium /1-244 0.90.5 0.91.0 1.0 0.30.5 0.7 1.0 0.9 1.0 0.40.90.50.00.20.60.60.80.91.01.0 1.01.0 GCA 001644025 1 ASM164402v1 protein OAI18234 1 methane monooxygenase/ammonia monooxygenase subunit A Methylomonas koyamae /1-246 0.80.60.40.80.20.90.91.0 0.6 0.20.9 0.8 1.0 0.50.9 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 1.0 0.9 0.91.0 GCA 001856095 1 ASM185609v1 protein OHX37424 1 methane monooxygenase/ammonia monooxygenase subunit A Methylomonas sp LWB /1-246 1.0 1.0 1.0 0.8 0.3 MKMC d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methylomonas s Methylomonas koyamae A 1/1-246 1.0 0.81.0 1.00.20.1 1.01.0 0.8 1.0 DKAI d Bacteria p Myxococcota c UBA9160 o UBA9160 f UBA6930 g UBA6930 s 1/1-248 1.0 LUUF d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methylomonas s Methylomonas methanica 2/1-243 0.51.00.8 1.00.9 0.7 LUUF d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methylomonas s Methylomonas methanica 1/1-246 1.01.0 1.0 1.0 GCA 000785705 2 ASM78570v2 protein AMK77276 1 methane monooxygenase/ammonia monooxygenase subunit A Methylomonas denitrificans /1-246 1.0 1.0

GCA 001644045 1 ASM164404v1 protein OAH97776 1 methane monooxygenase/ammonia monooxygenase subunit A Methylomonas methanica /1-246

1.0 JAFS d Bacteria p Verrucomicrobiota c Verrucomicrobiae o Methylacidiphilales f Methylacidiphilaceae g LP2A s 2/1-240 GCA 002083615 1 ASM208361v1 proteinAZXK d OQW67450 Bacteria p Proteobacteria 1 methane monooxygenase/ammonia c Gammaproteobacteria monooxygenaseo Methylococcales subunit f Methylomonadaceae A Proteobacteria gbacterium Methylomonas ST bin11 s 1/1-246 /1-246 JQNX d Bacteria p Verrucomicrobiota c Verrucomicrobiae o Methylacidiphilales f Methylacidiphilaceae g Methylacidiphilum s Methylacidiphilum kamchatkense 2/1-245 0.9 1.0

1.00.61.0 0.2 0.60.80.8 CAHT d Bacteria p Verrucomicrobiota c Verrucomicrobiae o Methylacidiphilales f Methylacidiphilaceae g Methylacidiphilum s Methylacidiphilum fumariolicum 2/1-238 0.8 GCA 000297415 1 ASM29741v1 protein CCG92750 1 PmoA1 Methylacidiphilum fumariolicum SolV /1-239 LUUG d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methylomonas s Methylomonas methanica A 1/1-246 JQNX d Bacteria p Verrucomicrobiota c Verrucomicrobiae o Methylacidiphilales f Methylacidiphilaceae g Methylacidiphilum s Methylacidiphilum kamchatkense 4/1-243 1.0 GCA 001644095 1 ASM164409v1 protein OAI27352 1 methane monooxygenase/ammonia monooxygenase subunit A Methylomonas koyamae /1-246

GCA 001644685 1 ASM164468v1 protein ANE57196 1 methane monooxygenase/ammonia monooxygenase subunit A Methylomonas sp DH-1 /1-246 GCA 002441955 1 ASM244195v1 protein ATG92172 1 methane/ammonia monooxygenase subunit A Methylomonas koyamae /1-246 1.0 1.00.9 0.9

LUUJ d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methylomonas s Methylomonas koyamae 1/1-246 1.0

GCA 001644135 1 ASM164413v1 protein OAI14146 1 methane monooxygenase/ammonia monooxygenase subunit A Methylomonas koyamae /1-246

LUUJ d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methylomonas s Methylomonas koyamae 2/1-257 GCA 002928965 1 ASM292896v1 protein PPD33405 1 methane monooxygenase/ammonia monooxygenase subunit A Methylomonas sp /1-246 NSJN d Bacteria p Methylomirabilota c Methylomirabilia o Methylomirabilales f Methylomirabilaceae g Methylomirabilis s Methylomirabilis oxyfera A 1/1-242

GCA 002834115 1 ASM283411v1 protein PKD39891 1 methane monooxygenase/ammonia monooxygenase subunit A Methylomonas sp Kb3 /1-246 GCA 000091165 1 ASM9116v1 protein CBE69519 1 Particulate methane monooxygenase A-subunit PMO Candidatus Methylomirabilis oxyfera /1-241 NSJM d Bacteria p Methylomirabilota c Methylomirabilia o Methylomirabilales f Methylomirabilaceae g Methylomirabilis s 1/1-242 JQNXJQNX d Bacteriad Bacteria p Verrucomicrobiota p Verrucomicrobiota c Verrucomicrobiae c Verrucomicrobiae o Methylacidiphilales o Methylacidiphilales f Methylacidiphilaceae f Methylacidiphilaceae g Methylacidiphilum g Methylacidiphilum s Methylacidiphilum s Methylacidiphilum kamchatkense kamchatkense 1/1-248 3/1-260 GCA 000214665GCA 1 ASM21466v1 002929135 1protein ASM292913v1 AEF98753 protein 1 methane PPD54121 monooxygenase/ammonia 1 methane monooxygenase/ammonia monooxygenase monooxygenase subunit A Methylomonas subunit A methanica Methylomonas MC09 sp /1-246 /1-246 GCA 000817245 1 ASM81724v1 protein KIE59428 1 particulate methane monooxygenase Methylacidiphilum kamchatkense Kam1 /1-248 CAHTCAHT d Bacteria d Bacteria p Verrucomicrobiota p Verrucomicrobiota c Verrucomicrobiae c Verrucomicrobiae o Methylacidiphilales o Methylacidiphilales f Methylacidiphilaceae f Methylacidiphilaceae g Methylacidiphilum g Methylacidiphilum s Methylacidiphilum s Methylacidiphilum fumariolicum fumariolicum 1/1-248 3/1-260 GCA 002929015 1 ASM292901v1 protein PPD37238 1 methane monooxygenase/ammonia monooxygenase subunit A Methylomonas sp /1-246 GCA 000297415 1 ASM29741v1 protein CCG92189 1 Methane monooxygenase subunit beta Methylacidiphilum fumariolicum SolV /1-248

GCA 002928855 1 ASM292885v1 protein PPD22290 1 methane monooxygenase/ammonia monooxygenase subunit A Methylomonas sp /1-246 d Bacteria p Proteobacteria c Gammaproteobacteria o Nitrosococcales f Nitrosococcaceae g Nitrosococcus s Nitrosococcus halophilus 1/1-248 GCA 000024725 1 ASM2472v1GCA 002356115 protein 1 ADE13856 ASM235611v1 1 methane protein monooxygenase/ammonia BAW80891 1 methane monooxygenasemonooxygenase/ammonia subunit A Nitrosococcus monooxygenase halophilus subunit Nc A 4 Candidatus/1-247 Nitrosoglobus terrae /1-247 GCA 001644015 1 ASM164401v1 protein OAI10795 1 methane monooxygenase/ammonia monooxygenase subunit A Methylomonas lenta /1-246 d Bacteria p Proteobacteria c Gammaproteobacteria o Nitrosococcales f Nitrosococcaceae g Nitrosoglobus s Nitrosoglobus terrae 1/1-247

LUUI d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methylomonas s Methylomonas lenta 1/1-257 GCA 000143085 1 ASM14308v1 protein ADJ27588 1 methane monooxygenase/ammonia monooxygenase subunit A Nitrosococcus watsonii C-113 /1-243 GCA 000012805d Bacteria p 1 Proteobacteria ASM1280v1 protein c Gammaproteobacteria ABA58955 1 ammonia o Nitrosococcales monooxygenase f Nitrosococcaceaesubunit A / particulate g Nitrosococcus methane monooxygenase s Nitrosococcus PmoA watsonii subunit 1/1-247 Nitrosococcus oceani ATCC 19707 /1-247 GCA 000740745 1 ASM74074v1 protein KFI18754 1 ammonia monooxygenase Nitrosococcus oceani C-27 /1-247 GCA 000155655 1 ASM15565v1 protein EDZ67928 1 methane monooxygenase/ammonia monooxygenase subunit A Nitrosococcus oceani AFC27 /1-227 GCA 000740735 1 ASM74073v1 protein KFI21872 1 ammonia monooxygenase Nitrosococcus oceani /1-247 JPON d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methylomarinum s Methylomarinum vadi 1/1-246 JPGN d Bacteria p Proteobacteria c Gammaproteobacteria o Nitrosococcales f Nitrosococcaceae g Nitrosococcus s Nitrosococcus oceani 1/1-247

BDMN d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methyloprofundus s 1/1-246 AVFK d Bacteria p Proteobacteria c Alphaproteobacteria o Azospirillales f Azospirillaceae g Skermanella s Skermanella aerolata 1/2-251 GCA 000936425 1 ASM93642v1 protein KJB91180 1 ammonia monooxygenase Skermanella aerolata KACC 11604 /2-251

GCA 002189065 1 ASM218906v1 protein GAW86063 1 methane/ammonia monooxygenase subunit A Bathymodiolus platifrons methanotrophic gill symbiont /1-246

GCA 002890675 1 ASM289067v1 protein PNE09675 1 methane monooxygenase/ammonia monooxygenase subunit A Beijerinckiaceae bacterium /1-242 GCA 002928495 1 ASM292849v1 protein PPC90499 1 methane monooxygenase/ammonia monooxygenase subunit A Methylobacter sp /1-246

LPUF d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methyloprofundus s Methyloprofundus sedimenti 1/1-245 ATXB d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylothermaceae g Methylohalobius s Methylohalobius crimeensis 2/1-247 PHSP d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g KS41 s 1/1-246 JQKO d BacteriaGCA p Proteobacteria900114285 1 IMG-taxonc Alphaproteobacteria 2675903028 o Rhizobiales annotated fassembly Beijerinckiaceae protein g SFK40498 Methylocapsa 1 methane/ammonia s Methylocapsa aurea monooxygenase 1/1-243 subunit A Methylocapsa palsarum /1-239 GCA 001566965 1 2044C megahit protein KXJ41239 1 methane monooxygenase/ammonia monooxygenase subunitA Methylothermaceae bacteria B42 /1-247 GCA 002072955 1 ASM207295v1 protein OQK15452 1 methane monooxygenase/ammonia monooxygenase subunit A Methyloprofundus sedimenti /1-245 LSNW d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylothermaceae g B42 s 1/1-247 ATYA d Bacteria p Proteobacteria c Alphaproteobacteria o Rhizobiales f Beijerinckiaceae g Methylocapsa s Methylocapsa acidiphila 1/1-239 MUGK d Bacteria p Proteobacteria c Gammaproteobacteria o UBA7966 f UBA7966 g USCg-Taylor s 1/1-246 FOSN d Bacteria p Proteobacteria c Alphaproteobacteria o Rhizobiales f Beijerinckiaceae g Methylocapsa s Methylocapsa palsarum 1/1-239 GCA 002928745 1 ASM292874v1 protein PPD05193 1 methane monooxygenase/ammonia monooxygenase subunit A Methylobacter sp /1-246 GCA 002007425 1 USCg1 0 protein OOO02385 1 Particulate methane monooxygenase beta subunit Chromatiales bacterium USCg Taylor /1-246

JYNS d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylococcaceae g Methyloterricola s Methyloterricola oryzae 2/1-247 JYNS d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylococcaceae g Methyloterricola s Methyloterricola oryzae 1/1-247

GCA 900094635 1 BAZMOX protein SCN46754 1 Particulate methane monooxygenase A-subunit methanotrophic endosymbiont of Bathymodiolus azoricus Menez Gwen /1-246 BBDL d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylococcaceae g Methylogaea s Methylogaea oryzae 1/1-259 GCA 002928995 1 ASM292899v1 protein PPD34918 1 methane monooxygenase/ammonia monooxygenase subunit A Methylomonas sp /1-246

DBZZ d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g UBA1147 s 1/1-269 GCA 002928915 1 ASM292891v1 protein PPD19313 1 methane monooxygenase/ammonia monooxygenase subunit A Methylobacter sp /1-246

AZUO d Bacteria p Proteobacteria c Alphaproteobacteria o Rhizobiales f Beijerinckiaceae g Methylosinus s 1/1-235 AZUO d Bacteria p Proteobacteria c Alphaproteobacteria o Rhizobiales f Beijerinckiaceae g Methylosinus s 2/1-235 JQNK d Bacteria p Proteobacteria c Alphaproteobacteria o Rhizobiales f Beijerinckiaceae g Methylosinus s Methylosinus sp1 2/1-258 JQNK d Bacteria p Proteobacteria c Alphaproteobacteria o Rhizobiales f Beijerinckiaceae g Methylosinus s Methylosinus sp1 1/1-258

ADVE d Bacteria p Proteobacteria c Alphaproteobacteria o Rhizobiales f Beijerinckiaceae g Methylosinus s Methylosinus trichosporium 1/1-245 GCA 001675455 1 ASM167545v1 protein OBS50573 1 methane monooxygenase/ammonia monooxygenase subunit A Methylosinus sp 3S-1 /1-245 ADVE d Bacteria p Proteobacteria c Alphaproteobacteria o Rhizobiales f Beijerinckiaceae g Methylosinus s Methylosinus trichosporium 2/1-245 GCA 002752655 1 ASM275265v1 protein ATQ68209 1 methane monooxygenase/ammonia monooxygenase subunitAJTV A Methylosinus d Bacteria trichosporium p Proteobacteria OB3b /1-245 c Alphaproteobacteria o Rhizobiales f Beijerinckiaceae g Methylocystis s Methylocystis parvus 1/5-247 AJTV d Bacteria p Proteobacteria c Alphaproteobacteria o Rhizobiales f Beijerinckiaceae g Methylocystis s Methylocystis parvus 2/1-246

JQNK d Bacteria p Proteobacteria c Alphaproteobacteria o Rhizobiales f Beijerinckiaceae g Methylosinus s Methylosinus sp1 3/1-244 AZUO d Bacteria p Proteobacteria c Alphaproteobacteria o Rhizobiales f Beijerinckiaceae g Methylosinus s 3/1-244

AEVM d Bacteria p Proteobacteria c Alphaproteobacteria o Rhizobiales f Beijerinckiaceae g Methylocystis s 2/1-274 GCA 900163755 1 ASM90016375v1 protein SJM94736 1 Particulate methane monooxygenase beta subunit Crenothrix polyspora /1-247 AEVM d Bacteria p Proteobacteria c Alphaproteobacteria o Rhizobiales f Beijerinckiaceae g Methylocystis s 1/1-274 ARCT d Bacteria p Proteobacteria c Alphaproteobacteria o Rhizobiales f Beijerinckiaceae g Methylocystis s Methylocystis rosea 2/1-237 GCA 000304315 1 Msp SC2 protein CCJ08985 1 Particulate methane monooxygenase subunit A Methylocystis sp SC2 /1-245 GCA 001423645 1 Leaf161 protein KQR42957 1 methane monooxygenase/ammonia monooxygenase subunitA Microbacterium sp Leaf161 /1-245

FUKI d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Crenothrix s Crenothrix polyspora A 1/1-247

FUKI d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Crenothrix s Crenothrix polyspora A 2/1-243

FUKJ d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Crenothrix s Crenothrix polyspora 2/1-243 GCA 000496735 2 MKO1 protein ESS72026 1 particulate methane monooxygenase beta subunit Methyloglobulus morosus KoM1 /1-247 FUKJ d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Crenothrix s Crenothrix polyspora 1/1-247

DLHW d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methyloglobulus s 2/1-235

AYLO d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g MethyloglobulusGCA 000963695 1 Methcu1 s Methyloglobulus 0 protein KJV05401 morosus 1 ammonia 1/1-247 monooxygenase Methylococcaceae bacterium Sn10-6 /1-247

AYLO d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methyloglobulus s Methyloglobulus morosus 2/1-243

JPOJ d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methylomicrobium s Methylomicrobium agile 1/1-247 GCA 000214275 3 ASM21427v3 protein EIC31239 1 methane monooxygenase/ammonia monooxygenase subunit A Methylomicrobium album BG8 /1-247

AFJF d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methylomicrobium s Methylomicrobium album 1/1-247

AFJF d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methylomicrobium s Methylomicrobium album 2/1-243 AZUN d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methylosarcina s Methylosarcina lacus 1/1-247 JPOJ d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methylomicrobium s Methylomicrobium agile 2/1-243

ARCU d Bacteria p Proteobacteria c Gammaproteobacteria o MethylococcalesGCA 002929035 1 f ASM292903v1Methylomonadaceae protein PPD42224 g Methylosarcina 1 methane monooxygenase/ammoniaA s Methylosarcina A fibrata monooxygenase 1/1-239 subunit A Methylobacter sp /1-247

GCA 002209385 1 ASM220938v1 protein ASF47706 1 methane monooxygenase/ammonia monooxygenase subunit A Methylovulum psychrotolerans /1-247

GCA 002923755AQZU 1 dASM292375v1 Bacteria p Proteobacteria protein POZ52442 c Gammaproteobacteria 1 methane monooxygenase/ammonia o Methylococcales f Methylomonadaceae monooxygenase subunitg Methylovulum A Methylovulum s Methylovulum psychrotolerans miyakonenseMBQZ d Bacteria/1-247 1/1-247 p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g UBA4132 s 1/1-246

PGZD d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g roteobacteria-3-A s 1/1-246 ATYJ d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methylobacter s Methylobacter luteus 2/1-236

ATYJ d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methylobacter s Methylobacter luteus 1/1-246

JQKS d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methylobacter s Methylobacter marinus 1/1-247

JQKS d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methylobacter s Methylobacter marinus 2/1-236 GCA 002256685 1 ASM225668v1 protein OYV20797 1 ammonia monooxygenase subunit A Methylococcaceae bacterium NSP1-2 /1-246 GCA 002134785 1 ASM213478v1 protein OTE95784 1 methane monooxygenase/ammonia monooxygenase subunit A Crenothrix sp D3 /1-246

GCA 002256705 1 ASM225670v1 protein OYV16785 1 ammonia monooxygenase subunit A Methylococcaceae bacterium NSM2-1 /1-246 GCA 002934365 1 ASM293436v1 protein PPK64111 1 methane/ammoniaGCA 002256465 monooxygenase 1 ASM225646v1 subunit protein OYV16745A Methylobacter 1 ammonia tundripaludummonooxygenase subunit /1-247 A Methylococcaceae bacterium NSP1-1 /1-246

MPSY d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g OPU3-GD-OMZ s 1/1-247 JQNS d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methylobacter s Methylobacter whittenburyi 1/1-247

MSCV d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylococcaceae g Methylocaldum s 1/1-252 JQNS d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methylobacter s Methylobacter whittenburyi 2/1-243 GCA 000968535 1 ASM96853v1 protein CCE22213 1 particulate methane monooxygenase A subunit Methylomicrobium alcaliphilum 20Z /1-246

GCA 000008325 1 ASM832v1 protein AAU92182 1 methane monooxygenase A subunit Methylococcus capsulatus str Bath /1-247

AEGW d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methylobacter A s Methylobacter A tundripaludum 1/1-246 GCA 000190755 3 ASM19075v3 protein EGW23568 1 methane monooxygenase/ammonia monooxygenase subunit A Methylobacter tundripaludum SV96 /1-246

AEGW Bacteriad p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methylobacter A s Methylobacter A tundripaludum 2/1-236

AOTL d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylomonadaceae g Methylomicrobium A s Methylomicrobium A buryatense 1/1-247

AUKJ d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylococcaceae g Methylococcus s Methylococcus capsulatus 1/1-247

FXAM d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylococcaceae g Methylomagnum s Methylomagnum ishizawai 2/1-263

FXAM d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylococcaceae g Methylomagnum s Methylomagnum ishizawai 1/1-263

FXAM d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylococcaceae g Methylomagnum s Methylomagnum ishizawai 3/1-245

ATXX d Bacteria p Proteobacteria c Gammaproteobacteria o Methylococcales f Methylococcaceae g Methylocaldum s Methylocaldum szegediense 1/1-247

GCA 002843155 1 ASM284315v1 protein PKM12779 1 methane monooxygenase/ammonia monooxygenase subunit A Gammaproteobacteria bacterium HGW-Gammaproteobacteria-3 /1-246

GCA 900155475 1 IMG-taxon 2593339134 annotated assembly protein SMF97267 1 methane/ammonia monooxygenase subunit A Methylomagnum ishizawai /1-247