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Table S2. Proteins from core proteome found in M pneumonia complexes. COMPLEX_NAME Aminoacyl-tRNA synthetase complex Aminoacyl-tRNA synthetase complex Aminoacyl-tRNA synthetase complex Aminoacyl-tRNA synthetase complex Aminoacyl-tRNA synthetase complex Aminoacyl-tRNA synthetase complex ATP synthase complex GENE Cohesin like complex COMPLEX_FUNCTION Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Energy production and conversion Cell division and chromosome partitioning Cell division and chromosome partitioning Complex 1 Function unknown Mpn195 Complex 1 Apt Complex 105 Function unknown DNA replication, recombination and repair DNA replication, recombination and repair Complex 106 Function unknown Fba Complex 108 Complex 108 Complex 110 Complex 110 Function unknown Function unknown Function unknown Function unknown Prs ArgS RpsM TpiA Complex 112 Complex 114 Complex 114 Complex 116 Function unknown Transcription Transcription Function unknown Mpn521 RpoD DnaK Tuf Complex 13 Function unknown AcpS Complex 13 Function unknown GidA Complex 13 Complex 19 Complex 20 Complex 22 Function unknown Function unknown Function unknown Function unknown Mpn563 ThyA DnaG Pth Complex 22 Function unknown Mpn547 Complex 23 Function unknown Mpn547 Complex 24 Complex 25 Complex 25 Function unknown Function unknown Function unknown Mpn525 HprK Mpn241 Cohesin like complex Complex 100 PheT UNIPROT_NAME Fructose-bisphosphate aldolase Signal recognition particle protein Phenylalanyl-tRNA synthetase ? chain Phenylalanyl-tRNA synthetase ? chain ThrS Threonyl-tRNA synthetase TyrS AtpF Tyrosyl-tRNA synthetase ATP synthase B chain precursor UvrB UvrABC system protein B Lon ATP-dependent protease La Uncharacterized protein MG181 homolog Adenine phosphoribosyltransferase Holliday junction ATPdependent DNA helicase RuvB Fba Ffh PheS RuvB UvrA UvrABC system protein A Fructose-bisphosphate aldolase Ribose-phosphate pyrophosphokinase Arginyl-tRNA synthetase 30S ribosomal protein S13 Triosephosphate isomerase Uncharacterized tRNA/rRNA methyltransferase MG346 homolog RNA polymerase ? factor RpoD Chaperone protein DnaK Elongation factor Tu Holo-[acyl carrier protein] synthase tRNA uridine 5carboxymethylaminomethyl modification enzyme Uncharacterized GTP-binding protein MG384 homolog Thymidylate synthase DNA primase Peptidyl-tRNA hydrolase Uncharacterized protein MG369 homolog Uncharacterized protein MG369 homolog Uncharacterized protein MG349 homolog HPr kinase/phosphorylase Uncharacterized protein Mpn569 MG103 homolog HPr kinase/phosphorylase Trigger factor 50S ribosomal protein L16 UvrABC system protein B Putative Holliday junction resolvase Probable tRNA modification GTPase TrmE Uncharacterized deoxyribonuclease MG009 homolog Threonyl-tRNA synthetase Guanylate kinase Peptide deformylase Alanyl-tRNA synthetase Putative metalloprotease Mpn569 Eno Enolase TpiA Triosephosphate isomerase ATP synthase B chain precursor Guanylate kinase Peptide deformylase 30S ribosomal protein S14 type Z Complex 26 Complex 32 Complex 33 Complex 33 Function unknown Function unknown Function unknown Function unknown HprK Tig RplP UvrB Complex 33 Function unknown Mpn418 Complex 36 Function unknown TrmE Complex 36 Complex 36 Complex 4 Complex 4 Complex 4 Function unknown Function unknown Function unknown Function unknown Function unknown Carbohydrate transport and metabolism Carbohydrate transport and metabolism Carbohydrate transport and metabolism Mpn009 ThrS Gmk Def AlaS AtpF Gmk Def Complex 51 Function unknown Function unknown Function unknown Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Complex 56 Complex 61 Function unknown Function unknown Mpn071 Nfo Complex 62 Complex 64 Function unknown Function unknown DeoD Efp Complex 67 Function unknown Mpn350 Complex 67 GreA Complex 7 Function unknown Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Complex 72 Function unknown Mpn047 Complex 74 Function unknown PtsI Complex 75 Complex 75 Function unknown Function unknown Mpn461 Cmk Complex 78 Complex 83 Function unknown Function unknown MsrB SerS Complex 85 Function unknown GpmI Complex 46 Complex 46 Complex 46 Complex 48 Complex 5 Complex 5 Complex 51 Complex 7 Complex 7 Complex 7 RpsZ ThrS Upp Threonyl-tRNA synthetase UPF0011 protein MG056 homolog Probable endonuclease 4 Purine nucleoside phosphorylase DeoD-type Elongation factor P UPF0078 membrane protein Mpn350 Transcription elongation factor GreA Uracil phosphoribosyltransferase DeoA Thymidine phosphorylase InfB Translation initiation factor IF-2 RbfA Ribosome-binding factor A Uncharacterized protein MG037 homolog Phosphoenolpyruvate-protein phosphotransferase Uncharacterized protein MG323 homolog Cytidylate kinase Peptide methionine sulfoxide reductase Seryl-tRNA synthetase 2,3-bisphosphoglycerateindependent phosphoglycerate mutase Complex 88 Complex 90 Complex 90 Complex 91 Complex 92 Complex 96 Complex 98 Complex 99 Cytidine deaminationribosome complex Cytidine deaminationribosome complex DNA Polymerase III ? complex DNA Polymerase III ? complex DNA Polymerase III core complex DNA Polymerase III core complex DNA Polymerase III core complex DNA Polymerase III core complex DNA Polymerase III core complex DNA Primase complex DNA Primase complex DNA Primase complex DNA Recombination complex DNA Recombination complex DNA Recombination complex DNA Recombination complex DnaA complex Dnak-GrpE complex Glycolytic enzyme complex 1 Glycolytic enzyme complex 1 Glycolytic enzyme complex 2 Glycolytic enzyme complex 2 Glycolytic enzyme complex 2 Glycolytic enzyme Function unknown DNA replication, recombination and repair DNA replication, recombination and repair Prs Function unknown Carbohydrate transport and metabolism Translation, ribosomal structure and biogenesis Function unknown Function unknown Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis DNA replication, recombination and repair DNA replication, recombination and repair DNA replication, recombination and repair DNA replication, recombination and repair DNA replication, recombination and repair SecA DNA replication, recombination and repair DNA replication, recombination and repair DNA replication, recombination and repair DNA replication, recombination and repair DNA replication, recombination and repair DNA replication, recombination and repair DNA replication, recombination and repair DNA replication, recombination and repair DNA replication, recombination and repair DNA replication, recombination and repair Posttranslational modification, protein turnover, chaperones Carbohydrate transport and metabolism Carbohydrate transport and metabolism Carbohydrate transport and metabolism Carbohydrate transport and metabolism Carbohydrate transport and metabolism Carbohydrate transport and UvrC Ribose-phosphate pyrophosphokinase Mpn259 UvrABC system protein C Uncharacterized GTP-binding protein MG384 homolog Preprotein translocase subunit SecA Uncharacterized protein MG120 homolog ArgS EngA AlaS Arginyl-tRNA synthetase GTP-binding protein EngA Alanyl-tRNA synthetase Cdd Cytidine deaminase RplL 50S ribosomal protein L7/L12 Uncharacterized protein MG007 homolog Mpn563 Mpn007 DnaX Gcp DNA polymerase III subunit ?/? Probable O-sialoglycoprotein endopeptidase DnaG DNA primase DnaE Mpn014 DNA polymerase III subunit ? tRNA uridine 5carboxymethylaminomethyl modification enzyme Uncharacterized GTP-binding protein MG384 homolog Uncharacterized protein MG010 homolog Uncharacterized protein MG010 homolog Ung Uracil-DNA glycosylase ProS Prolyl-tRNA synthetase Mpn424 UPF0122 protein Mpn424 RecA Protein RecA RecA Protein RecA Chromosomal replication initiator protein dnaA GidA Mpn563 Mpn014 DnaA DnaK Fba Pyk Chaperone protein DnaK Fructose-bisphosphate aldolase HrcA Pyruvate kinase Heat-inducible transcription repressor GlyQS Glycyl-tRNA synthetase Nox Pgk Probable NADH oxidase Phosphoglycerate kinase complex 2 Glycolytic enzyme complex 2 Glycolytic enzyme complex 2 L29-S12 complex L29-S12 complex Peptidase complex Peptidase complex Peptidase complex Phenylalanine-tRNA synthetase complex Phenylalanine-tRNA synthetase complex Phosphotransfer system complex Protein chaperone complex Protein chaperone complex Protein chaperone complex Protein chaperone complex Protein chaperone complex Protein chaperone complex Protein chaperone complex Pyruvate dehydrogenase complex Pyruvate dehydrogenase complex Pyruvate dehydrogenase complex Pyruvate dehydrogenase complex Pyruvate dehydrogenase complex Pyruvate dehydrogenase complex Restriction enzyme complex metabolism Carbohydrate transport and metabolism Carbohydrate transport and metabolism Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Amino acid transport and metabolism DnaK Chaperone protein DnaK Eno Enolase RpmC 50S ribosomal protein L29 RpsL Metabolism Posttranslational modification, protein turnover, chaperones Posttranslational modification, protein turnover, chaperones Posttranslational modification, protein turnover, chaperones Posttranslational modification, protein turnover, chaperones Posttranslational modification, protein turnover, chaperones Posttranslational modification, protein turnover, chaperones Posttranslational modification, protein turnover, chaperones Mpn268 30S ribosomal protein S12 Phosphate import ATP-binding protein PstB 2,3-bisphosphoglycerateindependent phosphoglycerate mutase Cell division protease FtsH homolog Phenylalanyl-tRNA synthetase ? chain Phenylalanyl-tRNA synthetase ? chain Putative phosphotransferase enzyme IIB component HrcA Heat-inducible transcription repressor HrcA GlyQS Glycyl-tRNA synthetase Nox Probable NADH oxidase Pgk Phosphoglycerate kinase DnaK Chaperone protein DnaK RplJ 50S ribosomal protein L10 Mpn547 Uncharacterized protein MG369 homolog Metabolism Tmk Thymidylate kinase Metabolism TrmE Metabolism Mpn009 Probable tRNA modification GTPase TrmE Uncharacterized deoxyribonuclease MG009 homolog Metabolism PdhB Pyruvate dehydrogenase E1 component subunit ? Metabolism PdhA Pyruvate dehydrogenase E1 component subunit ? Metabolism ThrS Threonyl-tRNA synthetase Defense mechanisms RpmI 50S ribosomal protein L35 Amino acid transport and metabolism Amino acid transport and metabolism Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis PstB GpmI FtsH PheS PheT Restriction enzyme complex Restriction enzyme complex Restriction enzyme complex Ribonucleosidediphosphate reductase complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Defense mechanisms Adk Adenylate kinase Defense mechanisms DnaB Defense mechanisms FtsH Replicative DNA helicase Cell division protease FtsH homolog Metabolism Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis NrdE Ribonucleoside-diphosphate reductase ? subunit Tmk Thymidylate kinase InfC Translation initiation factor IF-3 RplT NusA 50S ribosomal protein L20 Transcription elongation protein NusA InfB Translation initiation factor IF-2 RplC 50S ribosomal protein L3 RplD 50S ribosomal protein L4 RplW 50S ribosomal protein L23 RplB 50S ribosomal protein L2 RpsS 30S ribosomal protein S19 RpsC 30S ribosomal protein S3 RplP 50S ribosomal protein L16 RpsQ 30S ribosomal protein S17 RplX 50S ribosomal protein L24 RplE RpsZ 50S ribosomal protein L5 30S ribosomal protein S14 type Z RpsH 30S ribosomal protein S8 RplF 50S ribosomal protein L6 RpsE 30S ribosomal protein S5 RpmJ 50S ribosomal protein L36 RpsM 30S ribosomal protein S13 RplQ 50S ribosomal protein L17 RpsB 30S ribosomal protein S2 RplK 50S ribosomal protein L11 RplA 50S ribosomal protein L1 Pth Peptidyl-tRNA hydrolase RpsL 30S ribosomal protein S12 Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex Ribosome complex RNA polymerase complex RNA polymerase complex RNA polymerase complex RNA polymerase complex RNA polymerase complex RNA polymerase complex RNA polymerase complex RNA polymerase complex RNA polymerase complex RNA polymerase complex RNA polymerase complex RNA polymerase Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis RpsG 30S ribosomal protein S7 RpsF 30S ribosomal protein S6 RpsR PgsA 30S ribosomal protein S18 CDP-diacylglycerol-glycerol-3phosphate 3phosphatidyltransferase RpmA 50S ribosomal protein L27 RpsD 30S ribosomal protein S4 EngA GTP-binding protein EngA IleS RuvB Isoleucyl-tRNA synthetase Holliday junction ATPdependent DNA helicase RuvB RplJ 50S ribosomal protein L10 RplL 50S ribosomal protein L7/L12 RpsT 30S ribosomal protein S20 ThrS Threonyl-tRNA synthetase RpsI 30S ribosomal protein S9 RpsO 30S ribosomal protein S15 Frr Ribosome recycling factor RplS 50S ribosomal protein L19 RpsP 30S ribosomal protein S16 Tuf Elongation factor Tu Uncharacterized deoxyribonuclease MG009 homolog Uncharacterized protein MG010 homolog Transcription Mpn009 Transcription Mpn014 Transcription Mpn067 Transcription NusA Protein MG054 homolog Transcription elongation protein NusA Transcription InfB Translation initiation factor IF-2 Transcription RpmC Transcription RpsZ 50S ribosomal protein L29 30S ribosomal protein S14 type Z Transcription InfA Transcription RpoA Translation initiation factor IF-1 DNA-directed RNA polymerase ? chain Transcription RplK 50S ribosomal protein L11 Transcription Transcription TrpS RpoD Tryptophanyl-tRNA synthetase RNA polymerase ? factor RpoD complex RNA polymerase complex RNA polymerase complex RNA polymerase complex RNA polymerase complex RNA polymerase complex ScpA-ThyA complex Translation elongation factor complex Translation elongation factor complex Translation elongation factor complex Translation elongation factor complex Translation elongation factor complex Translation elongation factor complex Translation elongation factor complex ?-A) Transcription GlyQS Glycyl-tRNA synthetase Transcription RecA Transcription RpoC Transcription RpoB Protein RecA DNA-directed RNA polymerase ?' chain DNA-directed RNA polymerase ? chain Transcription Metabolism Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis Translation, ribosomal structure and biogenesis RplL ThyA 50S ribosomal protein L7/L12 Thymidylate synthase Tmk Thymidylate kinase RplB 50S ribosomal protein L2 RpmC 50S ribosomal protein L29 RplK 50S ribosomal protein L11 RpsL 30S ribosomal protein S12 Tsf Elongation factor Ts Tuf Elongation factor Tu
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