Supplemental Material Ann Rheum Dis Doi: 10.1136/Annrheumdis

BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) Ann Rheum Dis

Supplementary Tables

Supp table 7 SNPs and indels conserved between RA-assoicated S. parasalivarius isolates Supp table 8 Encoded proteins identified as conserved between RA-associated S. parasalivarius isolates and absent from non-RA isolate 2.1 Supp table 9 SNPs and indels conserved between low inflammatory RA-associated S. parasalivarius isolates Supp table 10 SNPs and indels absent from between low inflammatory RA-associated S. parasalivarius isolates Supp table 11 Encoded proteins conserved between low inflammatory RA-associated S. parasalivarius isolates Supp table 12 Encoded proteins absent low inflammatory RA-associated S. parasalivarius isolates

Moentadj R, et al. Ann Rheum Dis 2021; 80:573–581. doi: 10.1136/annrheumdis-2020-219009 BMJ Publishing Group Limited (BMJ) disclaims all liability and responsibility arising from any reliance Supplemental material placed on this supplemental material which has been supplied by the author(s) Ann Rheum Dis

Supplementary Table 7. SNPs and indels conserved between RA-assoicated S. parasalivarius isolates Home S. parasalivarius isolates S. salivarius CCH5-D3contig Position ReferenceAllele AlternateAllele 2.1 3.1 9.1 10.1 15.1 16.1 17.1 21.1 22.1 23.2 11.1 Class Risk Feature1 ProteinID Description Mutation Coding change NZ_LSIW01000011_33529_CA_TC 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00365 WP_060971273.1 DUF1958 domain-containing protein c.1215_1216delTGinsGA p.AsnGly405LysSer NZ_LSIW01000011_33535_TC_CT 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00365 WP_060971273.1 DUF1958 domain-containing protein c.1209_1210delGAinsAG p.Asn404Asp NZ_LSIW01000011_33541_C_T 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00365 WP_060971273.1 DUF1958 domain-containing protein c.1204G>A p.Ala402Thr NZ_LSIW01000011_35142_T_G 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00370 WP_013990637.1 cation transporter c.1029A>C p.Gln343His NZ_LSIW01000012_5927_T_G 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00435 WP_060971284.1 transcriptional regulator c.9T>G p.His3Gln NZ_LSIW01000023_1500_A_G 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00550 WP_021143879.1 pyridoxal 5'-phosphate synthase glutaminase subunit PdxT c.364A>G p.Asn122Asp NZ_LSIW01000023_1508_C_A 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00550 WP_021143879.1 pyridoxal 5'-phosphate synthase glutaminase subunit PdxT c.372C>A p.Asp124Glu NZ_LSIW01000024_452_C_G 1 1 1 1 missense_variant MODERATE AX662_RS00555 hypothetical protein c.119G>C p.Arg40Pro NZ_LSIW01000026_14569_TAGCG_CAGCA 1 1 1 missense_variant MODERATE AX662_RS00635 WP_060971300.1 amidohydrolase c.252_256delTAGCGinsCAGCA p.Asp86Asn NZ_LSIW01000026_22159_A_C 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00670 WP_060971305.1 phosphomevalonate kinase c.203A>C p.Glu68Ala NZ_LSIW01000026_22699_T_A 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00670 WP_060971305.1 phosphomevalonate kinase c.743T>A p.Val248Glu NZ_LSIW01000026_57987_TT_CC 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00830 WP_060971331.1 DNA topoisomerase IV subunit A c.162_163delTTinsCC p.Tyr55His NZ_LSIW01000026_9532_CTACAAA_TTGCAAC 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00600 WP_060971296.1 glucosamine-6-phosphate deaminase c.643_649delCTACAAAinsTTGCAAC p.Asn217His NZ_LSIW01000028_11188_T_C 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00900 WP_060971341.1 adenosine deaminase c.347T>C p.Ile116Thr NZ_LSIW01000028_11538_TTGA_CTGG 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00900 WP_060971341.1 adenosine deaminase c.697_700delTTGAinsCTGG p.Lys234Glu NZ_LSIW01000028_19455_TAAGGAATTG_GCAAGAACTC 1 1 1 1 missense_variant MODERATE AX662_RS00940 WP_060971348.1 ABC transporter ATP-binding protein c.1314_1323delTAAGGAATTGinsGCAAGAACTC p.AspLys438GluGln NZ_LSIW01000028_20333_T_A 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00945 WP_060971349.1 ABC transporter ATP-binding protein c.463T>A p.Phe155Ile NZ_LSIW01000028_20962_G_T 1 1 1 1 missense_variant MODERATE AX662_RS00945 WP_060971349.1 ABC transporter ATP-binding protein c.1092G>T p.Glu364Asp NZ_LSIW01000028_21449_G_T 1 1 1 missense_variant MODERATE AX662_RS00945 WP_060971349.1 ABC transporter ATP-binding protein c.1579G>T p.Gly527Cys NZ_LSIW01000028_22235_AGAT_TGAA 1 1 1 missense_variant MODERATE AX662_RS00955 WP_060971350.1 D-alanine--poly(phosphoribitol) ligase subunit 1 c.300_303delAGATinsTGAA p.Asp101Glu NZ_LSIW01000028_23589_T_A 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00960 WP_060971351.1 D-alanyl-lipoteichoic acid biosynthesis protein DltB c.107T>A p.Phe36Tyr NZ_LSIW01000028_23695_TA_CG 1 1 1 1 1 missense_variant MODERATE AX662_RS00960 WP_060971351.1 D-alanyl-lipoteichoic acid biosynthesis protein DltB c.213_214delTAinsCG p.Ile72Val NZ_LSIW01000028_24146_G_A 1 1 1 missense_variant MODERATE AX662_RS00960 WP_060971351.1 D-alanyl-lipoteichoic acid biosynthesis protein DltB c.664G>A p.Ala222Thr NZ_LSIW01000028_25547_T_G 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00970 WP_060971352.1 D-alanyl-lipoteichoic acid biosynthesis protein DltD c.568T>G p.Ser190Ala NZ_LSIW01000028_29763_TCGA_GTGG 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00980 WP_060971354.1 aminodeoxychorismate synthase, component I c.1253_1256delTCGAinsCCAC p.ValGlu418AlaThr NZ_LSIW01000028_31415_TAG_CAA 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00985 WP_004182017.1 hypothetical protein c.251_253delTAGinsCAA p.ValVal84AlaIle NZ_LSIW01000028_3756_A_G 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00855 WP_060971334.1 DNA gyrase subunit A c.2446A>G p.Asn816Asp NZ_LSIW01000028_4339_AAAAA_GAAGG 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00860 WP_060971335.1 class A sortase c.561_565delAAAAAinsGAAGG p.Ile189Val NZ_LSIW01000028_4369_GA_AG 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00860 WP_060971335.1 class A sortase c.591_592delGAinsAG p.Ile198Val NZ_LSIW01000028_54999_AAA_GAC 1 1 1 1 1 missense_variant MODERATE AX662_RS01095 WP_060971363.1 bifunctional DnaQ family exonuclease/ATP-dependent helicase c.1320_1322delAAAinsGAC p.Asn441Thr NZ_LSIW01000028_56408_G_T 1 1 1 1 1 1 missense_variant MODERATE AX662_RS01100 WP_037600738.1 hypothetical protein c.85G>T p.Val29Leu NZ_LSIW01000028_56491_CATAAGGACC_TATTAAGACT 1 1 1 1 1 1 missense_variant MODERATE AX662_RS01100 WP_037600738.1 hypothetical protein c.168_177delCATAAGGACCinsTATTAAGACT p.Arg58Lys NZ_LSIW01000028_56561_A_G 1 1 1 1 1 1 missense_variant MODERATE AX662_RS01100 WP_037600738.1 hypothetical protein c.238A>G p.Ser80Gly NZ_LSIW01000028_56588_A_G 1 1 1 1 1 1 missense_variant MODERATE AX662_RS01100 WP_037600738.1 hypothetical protein c.265A>G p.Met89Val NZ_LSIW01000028_56607_T_A 1 1 1 1 1 1 missense_variant MODERATE AX662_RS01100 WP_037600738.1 hypothetical protein c.284T>A p.Val95Glu NZ_LSIW01000028_56686_G_T 1 1 1 1 1 1 missense_variant MODERATE AX662_RS01100 WP_037600738.1 hypothetical protein c.363G>T p.Glu121Asp NZ_LSIW01000028_5791_GGTC_AATT 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00870 WP_060971336.1 DUF1002 domain-containing protein c.699_702delGGTCinsAATT p.Val234Ile NZ_LSIW01000028_5810_G_A 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00870 WP_060971336.1 DUF1002 domain-containing protein c.718G>A p.Asp240Asn NZ_LSIW01000028_5899_GAG_AAC 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00870 WP_060971336.1 DUF1002 domain-containing protein c.807_809delGAGinsAAC p.Ser270Thr NZ_LSIW01000028_6208_C_G 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00875 WP_060971337.1 divalent metal cation transporter c.7C>G p.Gln3Glu NZ_LSIW01000028_6221_T_C 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00875 WP_060971337.1 divalent metal cation transporter c.20T>C p.Phe7Ser NZ_LSIW01000028_6920_A_T 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00875 WP_060971337.1 divalent metal cation transporter c.719A>T p.Tyr240Phe NZ_LSIW01000028_8045_A_G 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00885 WP_060971338.1 FAD:protein FMN transferase c.826T>C p.Cys276Arg NZ_LSIW01000028_8530_C_G 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS00885 WP_060971338.1 FAD:protein FMN transferase c.341G>C p.Arg114Pro NZ_LSIW01000036_32851_T_C 1 1 1 1 1 1 missense_variant MODERATE AX662_RS01330 WP_060971395.1 hypothetical protein c.467T>C p.Val156Ala NZ_LSIW01000036_39956_TAAAC_AAAAA 1 1 1 missense_variant MODERATE AX662_RS01380 WP_060971404.1 HXXEE domain-containing protein c.326_330delGTTTAinsTTTTT p.SerLeu109IlePhe NZ_LSIW01000036_40022_CACATGA_AATATGG 1 1 1 missense_variant MODERATE AX662_RS01380 WP_060971404.1 HXXEE domain-containing protein c.258_264delTCATGTGinsCCATATT p.Val88Ile NZ_LSIW01000036_40054_T_C 1 1 1 1 1 1 missense_variant MODERATE AX662_RS01380 WP_060971404.1 HXXEE domain-containing protein c.232A>G p.Thr78Ala NZ_LSIW01000036_40176_A_G 1 1 1 1 missense_variant MODERATE AX662_RS01380 WP_060971404.1 HXXEE domain-containing protein c.110T>C p.Leu37Pro NZ_LSIW01000036_40185_A_G 1 1 1 1 missense_variant MODERATE AX662_RS01380 WP_060971404.1 HXXEE domain-containing protein c.101T>C p.Val34Ala NZ_LSIW01000036_40284_AT_A 1 1 1 frameshift_variant&start_lost HIGH AX662_RS01380 WP_060971404.1 HXXEE domain-containing protein c.1delA p.Met1fs NZ_LSIW01000036_40337_TTTGACC_CTGGACA 1 1 1 missense_variant MODERATE AX662_RS01385 WP_060971405.1 TetR/AcrR family transcriptional regulator c.534_540delGGTCAAAinsTGTCCAG p.Lys180Gln NZ_LSIW01000036_40386_GTC_CTG 1 1 1 1 missense_variant MODERATE AX662_RS01385 WP_060971405.1 TetR/AcrR family transcriptional regulator c.489_491delGACinsCAG p.Thr164Ser NZ_LSIW01000036_40403_GTTGGTT_ATGGCTG 1 1 1 missense_variant MODERATE AX662_RS01385 WP_060971405.1 TetR/AcrR family transcriptional regulator c.468_474delAACCAACinsCAGCCAT p.ThrAsn157SerHis NZ_LSIW01000036_40465_TCTCA_CGTCG 1 1 1 1 missense_variant MODERATE AX662_RS01385 WP_060971405.1 TetR/AcrR family transcriptional regulator c.408_412delTGAGAinsCGACG p.GluLys137AspGlu NZ_LSIW01000036_40506_TTCAGT_CGCAGC 1 1 1 missense_variant MODERATE AX662_RS01385 WP_060971405.1 TetR/AcrR family transcriptional regulator c.366_371delACTGAAinsGCTGCG p.Lys124Arg NZ_LSIW01000036_40834_TT_CA 1 1 1 missense_variant MODERATE AX662_RS01385 WP_060971405.1 TetR/AcrR family transcriptional regulator c.42_43delAAinsTG p.Thr15Ala NZ_LSIW01000036_40848_ATT_CTA 1 1 1 missense_variant MODERATE AX662_RS01385 WP_060971405.1 TetR/AcrR family transcriptional regulator c.27_29delAATinsTAG p.GlnIle9HisSer NZ_LSIW01000036_41293_C_A 1 1 1 1 missense_variant MODERATE AX662_RS01390 WP_060971406.1 cation transporter c.321C>A p.Asp107Glu NZ_LSIW01000036_41317_GT_CA 1 1 1 1 missense_variant MODERATE AX662_RS01390 WP_060971406.1 cation transporter c.345_346delGTinsCA p.MetPhe115IleIle NZ_LSIW01000036_41807_T_C 1 1 1 1 missense_variant MODERATE AX662_RS01390 WP_060971406.1 cation transporter c.835T>C p.Cys279Arg NZ_LSIW01000036_41842_CAGTC_AG 1 1 1 1 1 1 missense variant&disruptive inf MODERATE AX662_RS01390 WP_060971406.1 cation transporter c.870_874delCAGTCinsAG p.Ser291_Gln292delinsGlu NZ_LSIW01000036_41852_CATGGACATGATCACCACC_GAGCAGCAAA 1 1 1 1 missense variant&disruptive inf MODERATE AX662_RS01390 WP_060971406.1 cation transporter c.880_898delCATGGACATGATCACCACCinsGAGCAGCAAA p.His294_His300delinsGluGlnGlnAsn NZ_LSIW01000036_42210_GAGCGTCGGTC_ACGCATCAGTA 1 1 1 1 missense_variant MODERATE AX662_RS01395 WP_060971407.1 ferrochelatase c.218_228delGAGCGTCGGTCinsACGCATCAGTA p.Arg73His NZ_LSIW01000036_42405_AAGA_GTGAACACG 1 1 1 1 frameshift variant&missense va HIGH AX662_RS01395 WP_060971407.1 ferrochelatase c.413_416delAAGAinsGTGAACACG p.Gln138fs NZ_LSIW01000036_42413_TCACTTCTTC_ACTCT 1 1 1 1 frameshift variant&missense va HIGH AX662_RS01395 WP_060971407.1 ferrochelatase c.421_430delTCACTTCTTCinsACTCT p.Ser141fs NZ_LSIW01000036_42464_G_A 1 1 1 1 1 1 missense_variant MODERATE AX662_RS01395 WP_060971407.1 ferrochelatase c.472G>A p.Gly158Arg NZ_LSIW01000036_42606_C_A 1 1 1 missense_variant MODERATE AX662_RS01395 WP_060971407.1 ferrochelatase c.614C>A p.Thr205Asn NZ_LSIW01000036_42797_G_A 1 1 1 1 missense_variant MODERATE AX662_RS01395 WP_060971407.1 ferrochelatase c.805G>A p.Ala269Thr NZ_LSIW01000036_42830_T_A 1 1 1 missense_variant MODERATE AX662_RS01395 WP_060971407.1 ferrochelatase c.838T>A p.Ser280Thr NZ_LSIW01000036_42898_A_T 1 1 1 1 1 1 missense_variant MODERATE AX662_RS01395 WP_060971407.1 ferrochelatase c.906A>T p.Gln302His NZ_LSIW01000036_42942_C_T 1 1 1 missense_variant MODERATE AX662_RS01395 WP_060971407.1 ferrochelatase c.950C>T p.Thr317Ile NZ_LSIW01000036_43272_G_A 1 1 1 1 1 1 missense_variant MODERATE AX662_RS01400 Zn-dependent alcohol dehydrogenase c.94G>A p.Val32Ile NZ_LSIW01000036_43467_G_T 1 1 1 missense_variant MODERATE AX662_RS01400 Zn-dependent alcohol dehydrogenase c.289G>T p.Ala97Ser NZ_LSIW01000036_43564_T_A 1 1 1 stop_gained HIGH AX662_RS01400 Zn-dependent alcohol dehydrogenase c.386T>A p.Leu129* NZ_LSIW01000036_43615_A_C 1 1 1 missense_variant MODERATE AX662_RS01400 Zn-dependent alcohol dehydrogenase c.437A>C p.His146Pro NZ_LSIW01000036_43738_A_G 1 1 1 missense_variant MODERATE AX662_RS01400 Zn-dependent alcohol dehydrogenase c.560A>G p.Gln187Arg NZ_LSIW01000036_43816_T_A 1 1 1 1 1 missense_variant MODERATE AX662_RS01400 Zn-dependent alcohol dehydrogenase c.638T>A p.Val213Glu NZ_LSIW01000036_43822_T_A 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS01400 Zn-dependent alcohol dehydrogenase c.644T>A p.Leu215Gln NZ_LSIW01000036_43848_GAGGC_AAGGT 1 1 1 missense_variant MODERATE AX662_RS01400 Zn-dependent alcohol dehydrogenase c.670_674delGAGGCinsAAGGT p.GluAla224LysVal NZ_LSIW01000036_43878_A_G 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS01400 Zn-dependent alcohol dehydrogenase c.700A>G p.Arg234Gly NZ_LSIW01000036_43921_AGCG_GGCA 1 1 1 missense_variant MODERATE AX662_RS01400 Zn-dependent alcohol dehydrogenase c.743_746delAGCGinsGGCA p.GlnArg248ArgGln NZ_LSIW01000036_43960_ACGC_CCGT 1 1 1 1 missense_variant MODERATE AX662_RS01400 Zn-dependent alcohol dehydrogenase c.782_785delACGCinsCCGT p.AspAla261AlaVal NZ_LSIW01000036_44031_C_T 1 1 1 stop_gained HIGH AX662_RS01400 Zn-dependent alcohol dehydrogenase c.853C>T p.Arg285* NZ_LSIW01000036_44101_C_T 1 1 1 missense_variant MODERATE AX662_RS01400 Zn-dependent alcohol dehydrogenase c.923C>T p.Ala308Val NZ_LSIW01000036_44158_G_A 1 1 1 1 1 missense_variant MODERATE AX662_RS01400 Zn-dependent alcohol dehydrogenase c.980G>A p.Arg327Lys NZ_LSIW01000037_1852_T_G 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS01440 WP_060971413.1 hypothetical protein c.73T>G p.Leu25Val NZ_LSIW01000037_1949_CG_TA 1 1 1 missense_variant MODERATE AX662_RS01440 WP_060971413.1 hypothetical protein c.170_171delCGinsTA p.Ala57Val NZ_LSIW01000037_48146_G_A 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS01660 WP_002890668.1 YggS family pyridoxal phosphate-dependent enzyme c.7G>A p.Val3Ile NZ_LSIW01000037_5256_A_G 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS01465 WP_060971416.1 Cof-type HAD-IIB family hydrolase c.97A>G p.Lys33Glu NZ_LSIW01000039_2074_AGCC_GGCT 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS02165 WP_060971502.1 ATPase c.429_432delGGCTinsAGCC p.Met143Ile NZ_LSIW01000052_1213_A_G 1 1 1 1 1 1 missense_variant MODERATE AX662_RS02540 WP_060971539.1 transcriptional regulator c.706T>C p.Tyr236His NZ_LSIW01000052_2543_TA_GT 1 1 1 1 1 1 missense_variant MODERATE AX662_RS02545 WP_060971540.1 RDD family protein c.426_427delTAinsGT p.Ile143Phe NZ_LSIW01000052_2957_T_G 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS02550 WP_048675419.1 multidrug resistance efflux transporter family protein c.177T>G p.Asn59Lys NZ_LSIW01000052_3326_AG_GC 1 1 1 1 1 1 missense_variant MODERATE AX662_RS02550 WP_048675419.1 multidrug resistance efflux transporter family protein c.546_547delAGinsGC p.Glu183Gln NZ_LSIW01000052_4240_TTCTAAACT_GCCTAGCCC 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS02555 WP_060971541.1 glycosyl hydrolase family 32 c.285_293delTTCTAAACTinsGCCTAGCCC p.HisSerLysLeu95GlnProSerPro NZ_LSIW01000052_4256_CCT_TCA 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS02555 WP_060971541.1 glycosyl hydrolase family 32 c.301_303delCCTinsTCA p.Pro101Ser NZ_LSIW01000052_4264_GGA_AGT 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS02555 WP_060971541.1 glycosyl hydrolase family 32 c.309_311delGGAinsAGT p.Glu104Val NZ_LSIW01000052_4314_G_A 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS02555 WP_060971541.1 glycosyl hydrolase family 32 c.359G>A p.Gly120Glu NZ_LSIW01000052_4353_AAACC_TAACG 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS02555 WP_060971541.1 glycosyl hydrolase family 32 c.398_402delAAACCinsTAACG p.Glu133Val NZ_LSIW01000052_4469_AAGGTTGATGGC_CAGGCTGACGGT 1 1 1 1 1 1 missense_variant MODERATE AX662_RS02555 WP_060971541.1 glycosyl hydrolase family 32 c.514_525delAAGGTTGATGGCinsCAGGCTGACGGT p.LysVal172GlnAla NZ_LSIW01000052_4547_GTT_ATC 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS02555 WP_060971541.1 glycosyl hydrolase family 32 c.592_594delGTTinsATC p.Val198Ile NZ_LSIW01000052_4621_CAGTAAC_TAGCGAT 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS02555 WP_060971541.1 glycosyl hydrolase family 32 c.666_672delCAGTAACinsTAGCGAT p.Asn224Asp NZ_LSIW01000052_4699_A_T 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS02555 WP_060971541.1 glycosyl hydrolase family 32 c.744A>T p.Gln248His NZ_LSIW01000052_4950_AG_CC 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS02555 WP_060971541.1 glycosyl hydrolase family 32 c.995_996delAGinsCC p.Glu332Ala NZ_LSIW01000052_5097_G_A 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS02555 WP_060971541.1 glycosyl hydrolase family 32 c.1142G>A p.Ser381Asn NZ_LSIW01000052_6494_A_G 1 1 1 1 1 missense_variant MODERATE AX662_RS02555 WP_060971541.1 glycosyl hydrolase family 32 c.2539A>G p.Thr847Ala NZ_LSIW01000054_15888_ATCTTG_TGCTTA 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS10275 WP_082757388.1 hypothetical protein c.133_138delATCTTGinsTGCTTA p.Ile45Cys NZ_LSIW01000054_16319_A_C 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS02675 WP_060971550.1 biotin transporter BioY c.340T>G p.Leu114Val NZ_LSIW01000054_16343_T_C 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS02675 WP_060971550.1 biotin transporter BioY c.316A>G p.Lys106Glu NZ_LSIW01000054_16538_TAGCGAAGGTCTGG_CAGCAAAAGTTTGC 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS02675 WP_060971550.1 biotin transporter BioY c.108_121delCCAGACCTTCGCTAinsGCAAACTTTTGCTG p.Ile41Val NZ_LSIW01000054_16987_G_A 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS02680 WP_060971551.1 hypothetical protein c.53C>T p.Thr18Ile NZ_LSIW01000054_17424_T_A 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS02690 WP_060971552.1 divalent metal cation transporter c.1321A>T p.Ile441Phe NZ_LSIW01000054_18142_AGTTGGT_CGCTGGC 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS02690 WP_060971552.1 divalent metal cation transporter c.597_603delACCAACTinsGCCAGCG p.Thr201Ala NZ_LSIW01000054_18990_G_C 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS02695 WP_045768909.1 hypothetical protein c.49G>C p.Val17Leu NZ_LSIW01000054_4128_T_C 1 1 1 1 1 1 missense_variant MODERATE AX662_RS02610 WP_037603918.1 sodium-independent anion transporter c.892T>C p.Phe298Leu NZ_LSIW01000054_5114_G_C 1 1 1 1 1 1 missense_variant MODERATE AX662_RS02615 WP_003093491.1 TIGR03943 family protein c.653C>G p.Thr218Arg NZ_LSIW01000058_128357_C_T 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS03450 WP_060971616.1 YitT family protein c.59G>A p.Arg20Lys NZ_LSIW01000058_128799_A_G 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS03455 WP_060971617.1 aspartate--tRNA ligase c.1361T>C p.Val454Ala NZ_LSIW01000058_149026_C_T 1 1 1 1 1 1 missense_variant MODERATE AX662_RS03575 WP_013991330.1 DHH family phosphoesterase c.34G>A p.Val12Ile NZ_LSIW01000058_150111_A_T 1 1 1 1 1 1 missense_variant MODERATE AX662_RS03580 WP_060971631.1 tRNA uridine-5-carboxymethylaminomethyl(34) synthesis enzyme MnmG c.924T>A p.Asp308Glu NZ_LSIW01000058_75660_G_A 1 1 1 missense_variant MODERATE AX662_RS03125 WP_060971601.1 hypothetical protein c.131C>T p.Ala44Val NZ_LSIW01000058_79221_CG_TA 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS03135 WP_060971603.1 bifunctional acetaldehyde-CoA/alcohol dehydrogenase c.189_190delCGinsTA p.Val64Ile NZ_LSIW01000060_102052_T_G 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS04150 WP_060971696.1 hypothetical protein c.241A>C p.Ile81Leu NZ_LSIW01000060_102063_GT_AA 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS04150 WP_060971696.1 hypothetical protein c.229_230delACinsTT p.Thr77Leu NZ_LSIW01000060_105145_A_T 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS04170 WP_060971698.1 excinuclease ABC subunit UvrA c.2029T>A p.Ser677Thr NZ_LSIW01000060_109765_A_G 1 1 1 1 1 1 missense_variant MODERATE AX662_RS04185 WP_060971701.1 DUF4300 domain-containing protein c.497A>G p.Asn166Ser NZ_LSIW01000060_118640_C_G 1 1 1 1 1 1 missense_variant MODERATE AX662_RS04225 WP_060971704.1 DNA polymerase I c.990G>C p.Glu330Asp NZ_LSIW01000060_119174_ATTATCA_GTTTTCG 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS04225 WP_060971704.1 DNA polymerase I c.450_456delTGATAATinsCGAAAAC p.Asp151Glu NZ_LSIW01000060_12045_A_G 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS03740 WP_021143683.1 pantetheine-phosphate adenylyltransferase c.449T>C p.Val150Ala NZ_LSIW01000060_122662_A_T 1 1 1 1 1 1 missense_variant MODERATE AX662_RS04235 WP_060971706.1 colicin V production protein c.193T>A p.Leu65Ile NZ_LSIW01000060_150835_AA_GC 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS04390 WP_060971727.1 TatD family deoxyribonuclease c.352_353delTTinsGC p.Phe118Ala NZ_LSIW01000060_152028_A_T 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS04400 WP_037599064.1 thioredoxin c.25T>A p.Ser9Thr NZ_LSIW01000060_17472_CTACT_TTACC 1 1 1 1 1 1 missense_variant MODERATE AX662_RS03770 WP_060971653.1 amino acid ABC transporter substrate-binding protein c.79_83delAGTAGinsGGTAA p.SerArg27GlyLys NZ_LSIW01000060_43138_C_A 1 1 1 1 missense_variant MODERATE AX662_RS03895 WP_060971666.1 ATP-dependent helicase c.876G>T p.Glu292Asp NZ_LSIW01000060_58012_T_G 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS03965 WP_060971674.1 helicase-exonuclease AddAB subunit AddA c.2896A>C p.Lys966Gln NZ_LSIW01000060_73930_AATG_GATT 1 1 1 1 1 missense_variant MODERATE AX662_RS04015 WP_060971680.1 hypothetical protein c.286_289delCATTinsAATC p.HisSer96AsnPro NZ_LSIW01000060_84047_T_C 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS04065 WP_060971724.1 DNA helicase RecG c.1183A>G p.Lys395Glu NZ_LSIW01000069_1329_CAAGGTTGCT_TAAGTCCGCA 1 1 1 1 1 missense_variant MODERATE AX662_RS04460 WP_060971729.1 chorismate mutase c.120_129delCAAGGTTGCTinsTAAGTCCGCA p.Val42Ser NZ_LSIW01000069_1763_TAC_CAG 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS04465 WP_060971730.1 anthranilate synthase component I c.196_198delTACinsCAG p.Tyr66Gln NZ_LSIW01000069_7475_AGCTGAG_GGCAGAT 1 1 1 1 missense_variant MODERATE AX662_RS04495 WP_060971734.1 tryptophan synthase subunit alpha c.354_360delAGCTGAGinsGGCAGAT p.Glu120Asp NZ_LSIW01000069_8725_G_T 1 1 1 1 1 1 missense_variant MODERATE AX662_RS04500 WP_060971735.1 CopY/TcrY family copper transport repressor c.91G>T p.Ala31Ser NZ_LSIW01000069_9226_A_C 1 1 1 1 1 1 missense_variant MODERATE AX662_RS04505 WP_060971736.1 copper-translocating P-type ATPase c.157A>C p.Thr53Pro NZ_LSIW01000072_46081_A_G 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS04960 WP_060971782.1 tRNA uridine-5-carboxymethylaminomethyl(34) synthesis GTPase MnmE c.1051A>G p.Lys351Glu NZ_LSIW01000077_65555_A_G 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS05420 WP_060971845.1 16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB c.409A>G p.Asn137Asp NZ_LSIW01000081_10309_TTG_CTC 1 1 1 missense_variant MODERATE AX662_RS05515 WP_060971852.1 SAM-dependent methyltransferase c.559_561delCAAinsGAG p.Gln187Glu NZ_LSIW01000081_10372_AGAGTGA_GGAATTG 1 1 1 missense_variant MODERATE AX662_RS05515 WP_060971852.1 SAM-dependent methyltransferase c.492_498delTCACTCTinsCAATTCC p.His165Asn NZ_LSIW01000081_10745_T_C 1 1 1 missense_variant MODERATE AX662_RS05515 WP_060971852.1 SAM-dependent methyltransferase c.125A>G p.His42Arg NZ_LSIW01000081_16790_A_T 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS05530 WP_060971855.1 aspartate carbamoyltransferase catalytic subunit c.32T>A p.Ile11Lys NZ_LSIW01000081_22470_C_T 1 1 1 1 1 1 missense_variant MODERATE AX662_RS05560 WP_060971856.1 MFS transporter c.304G>A p.Ala102Thr NZ_LSIW01000081_22629_A_C 1 1 1 missense_variant MODERATE AX662_RS05560 WP_060971856.1 MFS transporter c.145T>G p.Ser49Ala NZ_LSIW01000081_28741_GCAAT_CTAAC 1 1 1 1 1 1 missense_variant MODERATE AX662_RS05595 WP_060971863.1 peptidylprolyl isomerase c.671_675delGCAATinsCTAAC p.Gly224Ala NZ_LSIW01000081_29954_T_C 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS05600 WP_060971864.1 PTS beta-glucoside transporter subunit EIIBCA c.814A>G p.Ile272Val NZ_LSIW01000081_32379_G_T 1 1 1 1 missense_variant MODERATE AX662_RS05610 WP_060971866.1 amino acid permease c.793C>A p.Leu265Ile NZ_LSIW01000081_32566_AAAGCCG_GAAACCT 1 1 1 1 1 1 missense_variant MODERATE AX662_RS05610 WP_060971866.1 amino acid permease c.600_606delCGGCTTTinsAGGTTTC p.His200Gln NZ_LSIW01000081_32585_GAAAGG_TTAAGA 1 1 1 1 1 1 missense_variant MODERATE AX662_RS05610 WP_060971866.1 amino acid permease c.582_587delCCTTTCinsTCTTAA p.Ser196Asn NZ_LSIW01000081_32667_T_C 1 1 1 1 1 1 missense_variant MODERATE AX662_RS05610 WP_060971866.1 amino acid permease c.505A>G p.Ile169Val NZ_LSIW01000081_33887_T_C 1 1 1 1 missense_variant MODERATE AX662_RS05620 WP_060971867.1 glycine--tRNA ligase subunit beta c.1780A>G p.Thr594Ala NZ_LSIW01000092_25521_CT_AC 1 1 1 1 1 1 missense_variant MODERATE AX662_RS06025 WP_060971905.1 nucleotidyltransferase c.207_208delAGinsGT p.Ala70Ser NZ_LSIW01000092_25989_C_G 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS06030 WP_060971906.1 class I SAM-dependent methyltransferase c.486G>C p.Glu162Asp NZ_LSIW01000092_26086_AT_GC 1 1 1 1 1 1 missense_variant MODERATE AX662_RS06030 WP_060971906.1 class I SAM-dependent methyltransferase c.388_389delATinsGC p.Ile130Ala NZ_LSIW01000092_26195_C_T 1 1 1 1 1 1 missense_variant MODERATE AX662_RS06030 WP_060971906.1 class I SAM-dependent methyltransferase c.280G>A p.Asp94Asn NZ_LSIW01000092_26240_A_C 1 1 1 1 1 1 missense_variant MODERATE AX662_RS06030 WP_060971906.1 class I SAM-dependent methyltransferase c.235T>G p.Ser79Ala NZ_LSIW01000092_27300_TTC_ATT 1 1 1 1 1 1 missense_variant MODERATE AX662_RS06040 WP_060971908.1 HAD family hydrolase c.345_347delGAAinsAAT p.Asn116Ile NZ_LSIW01000095_2139_A_G 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS06295 flagellar biosynthesis protein FliS c.746T>C p.Phe249Ser NZ_LSIW01000097_111344_A_C 1 1 1 1 1 1 missense_variant MODERATE AX662_RS06820 WP_060971998.1 ABC transporter permease c.808T>G p.Ser270Ala NZ_LSIW01000097_112014_CTC_TTT 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS06820 WP_060971998.1 ABC transporter permease c.136_138delGAGinsAAA p.Glu46Lys NZ_LSIW01000097_1133_CG_AC 1 1 1 missense_variant MODERATE AX662_RS06315 WP_060971933.1 N-acetyltransferase c.292_293delCGinsGT p.Arg98Val NZ_LSIW01000097_1141_A_T 1 1 1 missense_variant MODERATE AX662_RS06315 WP_060971933.1 N-acetyltransferase c.285T>A p.Ser95Arg NZ_LSIW01000097_1149_AAGTAGCAAGC_TAGTCGTAATT 1 1 1 missense_variant MODERATE AX662_RS06315 WP_060971933.1 N-acetyltransferase c.267_277delGCTTGCTACTTinsAATTACGACTA p.LeuAlaThrLeu90IleThrThrIle NZ_LSIW01000097_1178_CT_TG 1 1 1 missense_variant MODERATE AX662_RS06315 WP_060971933.1 N-acetyltransferase c.247_248delAGinsCA p.Arg83Gln NZ_LSIW01000097_118178_T_C 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS06855 WP_060972002.1 dihydroxyacetone kinase subunit DhaK c.842A>G p.Glu281Gly NZ_LSIW01000097_1188_G_A 1 1 1 missense_variant MODERATE AX662_RS06315 WP_060971933.1 N-acetyltransferase c.238C>T p.His80Tyr NZ_LSIW01000097_121825_AC_CT 1 1 1 missense_variant MODERATE AX662_RS06870 WP_060972005.1 hypothetical protein c.96_97delGTinsAG p.Ser33Ala NZ_LSIW01000097_55561_G_A 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS06570 WP_060971962.1 glucosyl transferase c.3077G>A p.Arg1026Lys NZ_LSIW01000097_55779_T_A 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS06575 WP_060971963.1 glutathione peroxidase c.7T>A p.Ser3Thr NZ_LSIW01000097_56102_TAAAA_AAAAC 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS06575 WP_060971963.1 glutathione peroxidase c.330_334delTAAAAinsAAAAC p.Lys112Gln NZ_LSIW01000097_65345_T_C 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS06635 WP_060971971.1 glyoxalase c.686A>G p.Glu229Gly NZ_LSIW01000097_65350_G_T 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS06635 WP_060971971.1 glyoxalase c.681C>A p.Asp227Glu NZ_LSIW01000097_93178_TC_CT 1 1 1 missense_variant MODERATE AX662_RS06750 WP_060971985.1 alpha-glucosidase c.1602_1603delGAinsAG p.Met535Val NZ_LSIW01000097_94433_A_T 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS06750 WP_060971985.1 alpha-glucosidase c.348T>A p.Asp116Glu NZ_LSIW01000098_125_A_G 1 1 1 1 1 1 missense_variant MODERATE AX662_RS06920 ABC transporter c.125A>G p.Gln42Arg NZ_LSIW01000098_56_C_T 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS06920 ABC transporter c.56C>T p.Thr19Ile NZ_LSIW01000113_22860_A_G 1 1 1 1 1 1 missense_variant MODERATE AX662_RS07350 WP_060972056.1 1-phosphofructokinase c.787A>G p.Ser263Gly NZ_LSIW01000113_30721_A_G 1 1 1 1 1 1 missense_variant MODERATE AX662_RS07380 WP_060972061.1 tRNA 4-thiouridine(8) synthase ThiI c.1093A>G p.Lys365Glu NZ_LSIW01000113_37253_A_C 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS07420 WP_060972066.1 DegV family protein c.737A>C p.Glu246Ala NZ_LSIW01000113_84287_GA_AG 1 1 1 missense_variant MODERATE AX662_RS07610 WP_060972090.1 hypothetical protein c.1729_1730delGAinsAG p.Asp577Ser NZ_LSIW01000133_1322_A_G 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS08165 WP_060972140.1 ComF family protein c.103T>C p.Tyr35His NZ_LSIW01000133_150362_C_T 1 1 1 missense_variant MODERATE AX662_RS08900 WP_060972219.1 RIP metalloprotease RseP c.1025G>A p.Ser342Asn NZ_LSIW01000133_150559_AC_GT 1 1 1 missense_variant MODERATE AX662_RS08900 WP_060972219.1 RIP metalloprotease RseP c.827_828delGTinsAC p.Ser276Asn NZ_LSIW01000133_150567_T_G 1 1 1 missense_variant MODERATE AX662_RS08900 WP_060972219.1 RIP metalloprotease RseP c.820A>C p.Lys274Gln NZ_LSIW01000133_151029_TT_CC 1 1 1 missense_variant MODERATE AX662_RS08900 WP_060972219.1 RIP metalloprotease RseP c.357_358delAAinsGG p.Asn120Asp NZ_LSIW01000133_151077_C_T 1 1 1 missense_variant MODERATE AX662_RS08900 WP_060972219.1 RIP metalloprotease RseP c.310G>A p.Val104Ile NZ_LSIW01000133_153102_A_C 1 1 1 missense_variant MODERATE AX662_RS08915 WP_022496558.1 protein translocase subunit YajC c.325T>G p.Ser109Ala NZ_LSIW01000133_1532_A_G 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS08170 WP_060972141.1 helicase c.1193T>C p.Leu398Pro NZ_LSIW01000133_1911_G_A 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS08170 WP_060972141.1 helicase c.814C>T p.Leu272Phe NZ_LSIW01000133_20450_AGAAG_CGAAA 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS08255 WP_060972150.1 haloacid dehalogenase c.2078_2082delCTTCTinsTTTCG p.Ala693Val NZ_LSIW01000133_20687_ATT_GTC 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS08255 WP_060972150.1 haloacid dehalogenase c.1843_1845delAATinsGAC p.Asn615Asp NZ_LSIW01000133_20699_ATCTGCC_GGCAGCT 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS08255 WP_060972150.1 haloacid dehalogenase c.1827_1833delGGCAGATinsAGCTGCC p.Asp611Ala NZ_LSIW01000133_20928_TT_CG 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS08255 WP_060972150.1 haloacid dehalogenase c.1603_1604delAAinsCG p.Lys535Arg NZ_LSIW01000133_21072_T_A 1 1 1 1 1 missense_variant MODERATE AX662_RS08255 WP_060972150.1 haloacid dehalogenase c.1460A>T p.Tyr487Phe NZ_LSIW01000133_2132_A_C 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS08170 WP_060972141.1 helicase c.593T>G p.Ile198Ser NZ_LSIW01000133_24677_T_C 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS08265 WP_060972152.1 UDP-N-acetylmuramoyl-L-alanyl-D-glutamate--L-lysine ligase c.305T>C p.Val102Ala NZ_LSIW01000133_2947_A_G 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS08175 WP_060972142.1 YigZ family protein c.169A>G p.Ile57Val NZ_LSIW01000133_31345_G_T 1 1 1 1 1 1 missense_variant MODERATE AX662_RS08290 WP_002883776.1 hypothetical protein c.300C>A p.Asp100Glu NZ_LSIW01000133_31976_G_A 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS08300 WP_002886615.1 transcription termination/antitermination protein NusA c.1178C>T p.Thr393Ile NZ_LSIW01000133_3312_T_G 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS08175 WP_060972142.1 YigZ family protein c.534T>G p.Asp178Glu NZ_LSIW01000133_33518_G_T 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS08305 WP_060972155.1 ribosome maturation factor RimP c.175C>A p.Leu59Ile NZ_LSIW01000133_3362_A_C 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS08175 WP_060972142.1 YigZ family protein c.584A>C p.Asn195Thr NZ_LSIW01000133_4799_G_T 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS08185 WP_060972144.1 CBS domain-containing protein c.442C>A p.Pro148Thr NZ_LSIW01000133_70162_T_C 1 1 1 missense_variant MODERATE AX662_RS08490 WP_060972175.1 ABC transporter ATP-binding protein c.343A>G p.Lys115Glu NZ_LSIW01000133_70490_T_A 1 1 1 1 1 missense_variant MODERATE AX662_RS08490 WP_060972175.1 ABC transporter ATP-binding protein c.15A>T p.Lys5Asn NZ_LSIW01000133_72228_A_G 1 1 1 1 1 missense_variant MODERATE AX662_RS08500 WP_060972176.1 cobalamin biosynthesis protein CbiM c.32T>C p.Met11Thr NZ_LSIW01000133_72400_A_G 1 1 1 1 1 missense_variant MODERATE AX662_RS08505 WP_060972177.1 urease accessory protein UreD c.703T>C p.Ser235Pro

NZ_LSIW01000133_74215_TGTTA_AGTTG 1 1 1 missense_variant MODERATE AX662_RS08515 WP_060972178.1 urease accessory protein UreF c.243_247delTAACAinsCAACT p.Ile83Leu NZ_LSIW01000133_74226_A_G 1 1 1 missense_variant MODERATE AX662_RS08515 WP_060972178.1 urease accessory protein UreF c.236T>C p.Val79Ala NZ_LSIW01000133_77774_T_C 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS08540 WP_060972181.1 acid-activated urea channel c.170A>G p.Asp57Gly NZ_LSIW01000133_78375_AG_GA 1 1 1 1 missense_variant MODERATE AX662_RS08545 WP_060972182.1 DUF4173 domain-containing protein c.25_26delAGinsGA p.Ser9Asp NZ_LSIW01000133_78441_C_T 1 1 1 1 missense_variant MODERATE AX662_RS08545 WP_060972182.1 DUF4173 domain-containing protein c.91C>T p.Leu31Phe NZ_LSIW01000133_78450_G_C 1 1 1 1 missense_variant MODERATE AX662_RS08545 WP_060972182.1 DUF4173 domain-containing protein c.100G>C p.Asp34His NZ_LSIW01000133_78503_CGTGG_TGTGT 1 1 1 1 missense_variant MODERATE AX662_RS08545 WP_060972182.1 DUF4173 domain-containing protein c.153_157delCGTGGinsTGTGT p.Ala53Ser NZ_LSIW01000133_78518_ATATA_GTATG 1 1 1 1 1 1 missense_variant MODERATE AX662_RS08545 WP_060972182.1 DUF4173 domain-containing protein c.168_172delATATAinsGTATG p.Ile58Val NZ_LSIW01000133_78564_G_C 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS08545 WP_060972182.1 DUF4173 domain-containing protein c.214G>C p.Val72Leu NZ_LSIW01000133_80062_G_A 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS08550 WP_060972183.1 DUF805 domain-containing protein c.64C>T p.Pro22Ser NZ_LSIW01000133_87210_A_G 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS08580 WP_002889909.1 Trk system potassium transporter TrkA c.1318A>G p.Ile440Val NZ_LSIW01000139_11055_CGT_TGC 1 1 1 1 1 1 missense_variant MODERATE AX662_RS09005 WP_060972230.1 dihydropteroate synthase c.759_761delCGTinsTGC p.Val254Ala NZ_LSIW01000139_5465_T_C 1 1 1 missense_variant MODERATE AX662_RS08975 WP_060972228.1 hypothetical protein c.1298T>C p.Val433Ala NZ_LSIW01000142_1216_G_T 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS09185 WP_060972252.1 dextran-binding lectin A c.1474C>A p.Leu492Ile NZ_LSIW01000142_1279_T_C 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS09185 WP_060972252.1 dextran-binding lectin A c.1411A>G p.Ile471Val NZ_LSIW01000142_1532_A_T 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS09185 WP_060972252.1 dextran-binding lectin A c.1158T>A p.Asp386Glu NZ_LSIW01000142_5799_AG_CA 1 1 1 1 1 missense_variant MODERATE AX662_RS09190 WP_060972253.1 YSIRK signal domain/LPXTG anchor domain surface protein c.1139_1140delCTinsTG p.Ala380Val NZ_LSIW01000142_5886_TTCGTAA_GTTGTAT 1 1 1 1 1 missense_variant MODERATE AX662_RS09190 WP_060972253.1 YSIRK signal domain/LPXTG anchor domain surface protein c.1047_1053delTTACGAAinsATACAAC p.Glu351Asn NZ_LSIW01000142_5918_C_A 1 1 1 1 1 missense_variant MODERATE AX662_RS09190 WP_060972253.1 YSIRK signal domain/LPXTG anchor domain surface protein c.1021G>T p.Ala341Ser NZ_LSIW01000142_5927_C_T 1 1 1 1 1 missense_variant MODERATE AX662_RS09190 WP_060972253.1 YSIRK signal domain/LPXTG anchor domain surface protein c.1012G>A p.Glu338Lys NZ_LSIW01000142_5938_ACG_GCA 1 1 1 1 1 1 missense_variant MODERATE AX662_RS09190 WP_060972253.1 YSIRK signal domain/LPXTG anchor domain surface protein c.999_1001delCGTinsTGC p.Val334Ala NZ_LSIW01000168_621_C_T 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS09735 WP_060972332.1 NADH oxidase c.859G>A p.Glu287Lys NZ_LSIW01000172_36693_A_G 1 1 1 1 1 1 missense_variant MODERATE AX662_RS09935 WP_060972351.1 cysteine desulfurase c.1006A>G p.Ile336Val NZ_LSIW01000172_40263_CA_AC 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS09955 WP_002883609.1 Hsp33 family molecular chaperone HslO c.818_819delCAinsAC p.Thr273Asn NZ_LSIW01000172_41864_A_C 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS09965 WP_038675197.1 transcriptional regulator c.419A>C p.Lys140Thr NZ_LSIW01000172_43275_A_G 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS09975 WP_049529339.1 metal ABC transporter permease c.685A>G p.Ile229Val NZ_LSIW01000172_43773_AGAT_GGAA 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS09980 malate transporter c.207_210delAGATinsGGAA p.Asp70Glu NZ_LSIW01000172_43789_G_A 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS09980 malate transporter c.223G>A p.Ala75Thr NZ_LSIW01000172_43836_C_A 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS09980 malate transporter c.270C>A p.Ser90Arg NZ_LSIW01000172_44054_A_G 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS09980 malate transporter c.488A>G p.Lys163Arg NZ_LSIW01000172_44140_GGT_AAG 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS09980 malate transporter c.574_576delGGTinsAAG p.Gly192Lys NZ_LSIW01000172_44147_CTG_TTA 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS09980 malate transporter c.581_583delCTGinsTTA p.SerGly194PheSer NZ_LSIW01000172_44215_G_A 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS09980 malate transporter c.649G>A p.Gly217Ser NZ_LSIW01000172_44309_G_A 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS09980 malate transporter c.743G>A p.Cys248Tyr NZ_LSIW01000172_44314_TGTTTAC_CGTATAT 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS09980 malate transporter c.748_754delTGTTTACinsCGTATAT p.CysLeu250ArgIle NZ_LSIW01000172_44326_ACCT_GCCC 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS09980 malate transporter c.760_763delACCTinsGCCC p.ThrSer254AlaPro NZ_LSIW01000172_44347_A_G 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS09980 malate transporter c.781A>G p.Thr261Ala NZ_LSIW01000172_44368_TGCC_GGCT 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS09980 malate transporter c.802_805delTGCCinsGGCT p.CysHis268GlyTyr NZ_LSIW01000176_16186_T_A 1 1 1 1 1 missense_variant MODERATE AX662_RS10135 WP_037597738.1 ABC transporter permease c.817T>A p.Leu273Met NZ_LSIW01000176_6343_G_A 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS10095 WP_060972356.1 GNAT family N-acetyltransferase c.130G>A p.Asp44Asn

Supplementary Table 8. Encoded proteins identified as conserved between RA-associated S. parasalivarius isolates and absent from non-RA isolate 2.1 Home S. parasalivarius isolates S. salivarius Annotation 2.1 3.1 9.1 10.1 15.1 16.1 17.1 21.1 22.1 23.2 11.1 Putative multidrug resistance efflux transporter OACCDLOP_01651฀OACCNCBGCKJJ_02025฀NCBG BOLGAICL_01700฀BOLGAEKMIGMNK_00710 JFMDMGNA_00133 AGDNAGMJ_02000 NOHGDGDB_01448฀NOHGDGDB_01447 hypothetical protein BKLDJMND_01301 KDGOJIBD_01173 EKMIGMNK_00790 JFMDMGNA_00058 AGDNAGMJ_01068 NOHGDGDB_01719 Beta-galactosidase BKLDJMND_01302 KDGOJIBD_01174 EKMIGMNK_00791 JFMDMGNA_00057 AGDNAGMJ_01067 NOHGDGDB_01718 Lactose permease BKLDJMND_01303 KDGOJIBD_01175 EKMIGMNK_00792 JFMDMGNA_00056 AGDNAGMJ_01066 NOHGDGDB_01717 Maltose epimerase BKLDJMND_01304 KDGOJIBD_01176 EKMIGMNK_00793 JFMDMGNA_00055 AGDNAGMJ_01065 NOHGDGDB_01716 Galactose-1-phosphate uridylyltransferase BKLDJMND_01306 KDGOJIBD_01178 EKMIGMNK_00795 JFMDMGNA_00053 AGDNAGMJ_01063 NOHGDGDB_01714 Galactokinase BKLDJMND_01307 KDGOJIBD_01179 EKMIGMNK_00796 JFMDMGNA_00052 AGDNAGMJ_01062 NOHGDGDB_01713 HTH-type transcriptional regulator LacR BKLDJMND_01308 KDGOJIBD_01180 EKMIGMNK_00797 JFMDMGNA_00051 AGDNAGMJ_01061 NOHGDGDB_01712

Supplementary Table 9. SNPs and indels conserved between low inflammatory RA-associated S. parasalivarius isolates Home S. parasalivarius isolates S. salivarius CCH5-D3contig_Position_ReferenceAllele_AlternateAllele 2.1 3.1 9.1 10.1 15.1 16.1 17.1 21.1 22.1 23.2 11.1 Class Risk Feature1 ProteinID Description EggNOG description Mutation Coding change COG code NZ_LSIW01000003_24181_GGAC_TGAA 1 1 missense_variant MODERATE AX662_RS00145 WP_060971246.1 alcohol dehydrogenase AdhP alcohol dehydrogenase c.48_51delGGACinsTGAA p.Asp17Glu NZ_LSIW01000003_25574_T_A 1 1 missense_variant MODERATE AX662_RS00150 WP_060971247.1 N-acetyltransferase COG1670 Acetyltransferases, including N-acetylases of ribosomal proteins c.140T>A p.Met47Lys NZ_LSIW01000003_25593_TGAA_AAAT 1 1 missense_variant MODERATE AX662_RS00150 WP_060971247.1 N-acetyltransferase COG1670 Acetyltransferases, including N-acetylases of ribosomal proteins c.159_162delTGAAinsAAAT p.AspGlu53GluAsn NZ_LSIW01000003_25606_G_C 1 1 missense_variant MODERATE AX662_RS00150 WP_060971247.1 N-acetyltransferase COG1670 Acetyltransferases, including N-acetylases of ribosomal proteins c.172G>C p.Val58Leu NZ_LSIW01000003_3663_GCTATAATTATAA_G 1 1 1 1 conservative_inframe_deletion MODERATE AX662_RS00040 WP_060971234.1 CAP domain-containing protein nuclear chromosome segregation c.274_285delAACTATAATTAT p.Asn92_Tyr95del NZ_LSIW01000003_4537_CGCTA_GGCAT 1 1 missense_variant MODERATE AX662_RS00040 WP_060971234.1 CAP domain-containing protein nuclear chromosome segregation c.1137_1141delCGCTAinsGGCAT p.Met381Leu NZ_LSIW01000003_4552_GGAA_AGAT 1 1 missense_variant MODERATE AX662_RS00040 WP_060971234.1 CAP domain-containing protein nuclear chromosome segregation c.1152_1155delGGAAinsAGAT p.Glu385Asp NZ_LSIW01000003_9412_GGGGC_AGGAG 1 1 1 missense_variant MODERATE AX662_RS00065 WP_060971237.1 dipeptidase Dipeptidase c.411_415delGGGGCinsAGGAG p.Gln139Glu NZ_LSIW01000003_9626_G_A 1 1 1 missense_variant MODERATE AX662_RS00065 WP_060971237.1 dipeptidase Dipeptidase c.625G>A p.Asp209Asn NZ_LSIW01000011_8908_ATGGA_GTGGT 1 1 missense_variant MODERATE AX662_RS00240 WP_060971255.1 LytR family transcriptional regulator Cell envelope-like function transcriptional attenuator common domain protein c.836_840delATGGAinsGTGGT p.Asp279Gly NZ_LSIW01000011_8973_A_C 1 1 missense_variant MODERATE AX662_RS00240 WP_060971255.1 LytR family transcriptional regulator Cell envelope-like function transcriptional attenuator common domain protein c.901A>C p.Lys301Gln NZ_LSIW01000011_9263_T_A 1 1 missense_variant MODERATE AX662_RS00240 WP_060971255.1 LytR family transcriptional regulator Cell envelope-like function transcriptional attenuator common domain protein c.1191T>A p.Asn397Lys NZ_LSIW01000011_9490_AAAGC_CAAGT 1 1 missense_variant MODERATE AX662_RS00240 WP_060971255.1 LytR family transcriptional regulator Cell envelope-like function transcriptional attenuator common domain protein c.1418_1422delAAAGCinsCAAGT p.Glu473Ala NZ_LSIW01000011_9640_C_A 1 1 missense_variant MODERATE AX662_RS00245 WP_002890887.1 tyrosine protein phosphatase Capsular polysaccharide biosynthesis protein c.107C>A p.Thr36Lys NZ_LSIW01000011_9724_A_C 1 1 missense_variant MODERATE AX662_RS00245 WP_002890887.1 tyrosine protein phosphatase Capsular polysaccharide biosynthesis protein c.191A>C p.Glu64Ala NZ_LSIW01000012_4178_GGCAAATCCG_AGCAGAACCA 1 1 1 1 missense_variant MODERATE AX662_RS00425 WP_060971283.1 N-acetyltransferase COG0454 Histone acetyltransferase HPA2 and related acetyltransferases c.234_243delCGGATTTGCCinsTGGTTCTGCT p.Phe80Ser NZ_LSIW01000012_5945_GAATTTAGGGT_AAATATGGGGC 1 1 missense_variant MODERATE AX662_RS00435 WP_060971284.1 transcriptional regulator Helix-turn-helix domain c.27_37delGAATTTAGGGTinsAAATATGGGGC p.LeuGlyPhe11MetGlyLeu NZ_LSIW01000014_512_G_T 1 1 1 1 missense_variant MODERATE AX662_RS00490 hypothetical protein c.260C>A p.Pro87Gln NZ_LSIW01000017_100_G_A 1 1 missense_variant MODERATE AX662_RS10205 hypothetical protein c.301C>T p.His101Tyr NZ_LSIW01000017_243_G_T 1 1 missense_variant MODERATE AX662_RS10205 hypothetical protein c.158C>A p.Thr53Asn NZ_LSIW01000017_56_TTCCACAAATAC_CTTCAAAAACGA 1 1 missense_variant MODERATE AX662_RS10205 hypothetical protein c.334_345delGTATTTGTGGAAinsTCGTTTTTGAAG p.ValPheValGlu112SerPheLeuLys NZ_LSIW01000026_18220_TG_CT 1 1 missense_variant MODERATE AX662_RS00650 WP_048676085.1 alpha/beta hydrolase alpha/beta hydrolase fold c.561_562delTGinsCT p.Gly188Cys NZ_LSIW01000026_19761_G_A 1 1 missense_variant MODERATE AX662_RS00655 WP_060971302.1 pyridine nucleotide-disulfide oxidoreductase Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family c.1160G>A p.Gly387Glu NZ_LSIW01000026_2255_C_T 1 1 missense_variant MODERATE AX662_RS00575 WP_013990980.1 BCCT family transporter Belongs to the BCCT transporter (TC 2.A.15) family c.110C>T p.Ser37Phe NZ_LSIW01000026_48827_T_C 1 1 missense_variant MODERATE AX662_RS00780 WP_060971324.1 dihydrofolate reductase Key enzyme in folate metabolism Catalyzes an essential reaction for de novo glycine and puc.440T>C p.Val147Ala NZ_LSIW01000026_5424_CAGC_AAGT 1 1 missense_variant MODERATE AX662_RS00585 WP_060971293.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.1362_1365delCAGCinsAAGT p.Asp454Glu NZ_LSIW01000026_5940_TC_CA 1 1 missense_variant MODERATE AX662_RS00590 WP_060971294.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.129_130delTCinsCA p.Leu44Ile NZ_LSIW01000026_5996_CC_AT 1 1 missense_variant MODERATE AX662_RS00590 WP_060971294.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.185_186delCCinsAT p.Ala62Asp NZ_LSIW01000026_6018_TGCTCG_CGCCCA 1 1 missense_variant MODERATE AX662_RS00590 WP_060971294.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.207_212delTGCTCGinsCGCCCA p.Arg71His NZ_LSIW01000026_6165_TGAG_CGAT 1 1 missense_variant MODERATE AX662_RS00590 WP_060971294.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.354_357delTGAGinsCGAT p.Glu119Asp NZ_LSIW01000026_6286_G_A 1 1 missense_variant MODERATE AX662_RS00590 WP_060971294.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.475G>A p.Val159Ile NZ_LSIW01000026_6311_CCTTG_TCTTA 1 1 missense_variant MODERATE AX662_RS00590 WP_060971294.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.500_504delCCTTGinsTCTTA p.Ala167Val NZ_LSIW01000028_10253_CGTAC_TGTAT 1 1 1 missense_variant MODERATE AX662_RS00895 WP_060971340.1 glutathione-dependent disulfide-bond oxidoreductase Glutathione S-transferase c.413_417delGTACGinsATACA p.Arg138His NZ_LSIW01000028_11078_TA_CG 1 1 missense_variant MODERATE AX662_RS00900 WP_060971341.1 adenosine deaminase Catalyzes the hydrolytic deamination of adenine to hypoxanthine. Plays an important role in c.237_238delTAinsCG p.Ile80Val NZ_LSIW01000028_18286_A_C 1 1 1 missense_variant MODERATE AX662_RS00940 WP_060971348.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.145A>C p.Lys49Gln NZ_LSIW01000028_18297_CTTTT_GTTTA 1 1 1 missense_variant MODERATE AX662_RS00940 WP_060971348.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.156_160delCTTTTinsGTTTA p.Leu54Met NZ_LSIW01000028_18313_G_C 1 1 1 missense_variant MODERATE AX662_RS00940 WP_060971348.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.172G>C p.Val58Leu NZ_LSIW01000028_18401_TGTTGACT_GTTTAACC 1 1 1 missense_variant MODERATE AX662_RS00940 WP_060971348.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.260_267delTGTTGACTinsGTTTAACC p.Val87Gly NZ_LSIW01000028_18422_CGAAA_AGAAG 1 1 missense_variant MODERATE AX662_RS00940 WP_060971348.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.281_285delCGAAAinsAGAAG p.Ala94Glu NZ_LSIW01000028_18767_G_A 1 1 missense_variant MODERATE AX662_RS00940 WP_060971348.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.626G>A p.Gly209Asp NZ_LSIW01000028_18778_C_G 1 1 missense_variant MODERATE AX662_RS00940 WP_060971348.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.637C>G p.Arg213Gly NZ_LSIW01000028_18901_G_A 1 1 1 missense_variant MODERATE AX662_RS00940 WP_060971348.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.760G>A p.Val254Ile NZ_LSIW01000028_18932_GTGGG_CTGGT 1 1 missense_variant MODERATE AX662_RS00940 WP_060971348.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.791_795delGTGGGinsCTGGT p.Gly264Ala NZ_LSIW01000028_19343_GAAAT_AAAAC 1 1 missense_variant MODERATE AX662_RS00940 WP_060971348.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.1202_1206delGAAATinsAAAAC p.Arg401Lys NZ_LSIW01000028_19505_AAGAC_GGGAT 1 1 1 missense_variant MODERATE AX662_RS00940 WP_060971348.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.1364_1368delAAGACinsGGGAT p.Lys455Arg NZ_LSIW01000028_3854_G_A 1 1 missense_variant MODERATE AX662_RS00860 WP_060971335.1 class A sortase Sortase (surface protein transpeptidase) c.76G>A p.Val26Ile NZ_LSIW01000028_54549_AGCC_GTCT 1 1 1 1 missense_variant MODERATE AX662_RS01095 WP_060971363.1 bifunctional DnaQ family exonuclease/ATP-dependent helicase helicase involved in DNA repair and perhaps also replication c.870_873delAGCCinsGTCT p.Ala291Ser NZ_LSIW01000028_56107_TAT_CAC 1 1 missense_variant MODERATE AX662_RS01095 WP_060971363.1 bifunctional DnaQ family exonuclease/ATP-dependent helicase helicase involved in DNA repair and perhaps also replication c.2428_2430delTATinsCAC p.Tyr810His NZ_LSIW01000028_59654_TT_AC 1 1 missense_variant MODERATE AX662_RS01115 WP_060971364.1 hypothetical protein c.253_254delTTinsAC p.Phe85Thr NZ_LSIW01000028_59705_C_G 1 1 missense_variant MODERATE AX662_RS01115 WP_060971364.1 hypothetical protein c.304C>G p.Gln102Glu NZ_LSIW01000028_6738_C_A 1 1 stop_gained HIGH AX662_RS00875 WP_060971337.1 divalent metal cation transporter Mn2 and Fe2 transporters of the NRAMP family c.537C>A p.Tyr179* NZ_LSIW01000028_9035_T_A 1 1 1 1 missense_variant MODERATE AX662_RS00890 WP_060971339.1 bifunctional oligoribonuclease/PAP phosphatase NrnA domain protein c.767A>T p.Gln256Leu NZ_LSIW01000028_9881_TTAGATA_ATTAGATC 1 1 1 frameshift variant&stop lost&splice HIGH AX662_RS00895 WP_060971340.1 glutathione-dependent disulfide-bond oxidoreductase Glutathione S-transferase c.783_789delTATCTAAinsGATCTAAT p.Asp261fs NZ_LSIW01000028_9931_TG_CA 1 1 1 missense_variant MODERATE AX662_RS00895 WP_060971340.1 glutathione-dependent disulfide-bond oxidoreductase Glutathione S-transferase c.738_739delCAinsTG p.Asn247Asp NZ_LSIW01000036_33654_T_C 1 1 1 missense_variant MODERATE AX662_RS01335 WP_060971396.1 ABC transporter permease cobalt transport c.671T>C p.Leu224Pro NZ_LSIW01000036_34964_A_G 1 1 1 missense_variant MODERATE AX662_RS01345 WP_060971398.1 ABC transporter ATP-binding protein ABC transporter, ATP-binding protein c.388A>G p.Thr130Ala NZ_LSIW01000036_35722_TTA_CTC 1 1 1 missense_variant MODERATE AX662_RS01350 nicotinamide mononucleotide transporter c.191_193delTTAinsCTC p.LeuIle64ProLeu NZ_LSIW01000036_35736_GC_AT 1 1 missense_variant MODERATE AX662_RS01350 nicotinamide mononucleotide transporter c.205_206delGCinsAT p.Ala69Ile NZ_LSIW01000036_35746_TTAACC_CTAGCT 1 1 missense_variant MODERATE AX662_RS01350 nicotinamide mononucleotide transporter c.215_220delTTAACCinsCTAGCT p.ValAsnLeu72AlaSerPhe NZ_LSIW01000036_35758_TTC_CTT 1 1 missense_variant MODERATE AX662_RS01350 nicotinamide mononucleotide transporter c.227_229delTTCinsCTT p.PheHis76SerTyr NZ_LSIW01000036_35769_ATCCG_GTCAA 1 1 missense_variant MODERATE AX662_RS01350 nicotinamide mononucleotide transporter c.238_242delATCCGinsGTCAA p.IleArg80ValAsn NZ_LSIW01000036_35778_CGCC_AGCT 1 1 stop_gained HIGH AX662_RS01350 nicotinamide mononucleotide transporter c.247_250delCGCCinsAGCT p.ArgGln83* NZ_LSIW01000036_35790_GTTC_TTAT 1 1 missense_variant MODERATE AX662_RS01350 nicotinamide mononucleotide transporter c.259_262delGTTCinsTTAT p.ValPro87LeuSer NZ_LSIW01000036_35820_T_C 1 1 1 missense_variant MODERATE AX662_RS01350 nicotinamide mononucleotide transporter c.289T>C p.Trp97Arg NZ_LSIW01000036_35828_G_A 1 1 stop_gained HIGH AX662_RS01350 nicotinamide mononucleotide transporter c.297G>A p.Trp99* NZ_LSIW01000036_35877_AGCC_TGCT 1 1 missense_variant MODERATE AX662_RS01350 nicotinamide mononucleotide transporter c.346_349delAGCCinsTGCT p.SerHis116CysTyr NZ_LSIW01000036_35887_A_G 1 1 missense_variant MODERATE AX662_RS01350 nicotinamide mononucleotide transporter c.356A>G p.Tyr119Cys NZ_LSIW01000036_36215_TTCAA_CTCTC 1 1 missense_variant MODERATE AX662_RS01355 WP_060971399.1 Rrf2 family transcriptional regulator Transcriptional regulator c.69_73delTTCAAinsCTCTC p.Lys25Gln NZ_LSIW01000036_36224_TCTGGCTGAGAGC_ATTAGCTATTAGT 1 1 missense_variant MODERATE AX662_RS01355 WP_060971399.1 Rrf2 family transcriptional regulator Transcriptional regulator c.78_90delTCTGGCTGAGAGCinsATTAGCTATTAGT p.Glu29Ile NZ_LSIW01000036_36308_T_G 1 1 missense_variant MODERATE AX662_RS01355 WP_060971399.1 Rrf2 family transcriptional regulator Transcriptional regulator c.162T>G p.His54Gln NZ_LSIW01000036_36391_A_G 1 1 1 missense_variant MODERATE AX662_RS01355 WP_060971399.1 Rrf2 family transcriptional regulator Transcriptional regulator c.245A>G p.Asn82Ser NZ_LSIW01000036_36460_GA_CT 1 1 missense_variant MODERATE AX662_RS01355 WP_060971399.1 Rrf2 family transcriptional regulator Transcriptional regulator c.314_315delGAinsCT p.Gly105Ala NZ_LSIW01000036_36515_CCAG_TCAC 1 1 missense_variant MODERATE AX662_RS01355 WP_060971399.1 Rrf2 family transcriptional regulator Transcriptional regulator c.369_372delCCAGinsTCAC p.Gln124His NZ_LSIW01000036_36557_T_G 1 1 missense_variant MODERATE AX662_RS01355 WP_060971399.1 Rrf2 family transcriptional regulator Transcriptional regulator c.411T>G p.Asp137Glu NZ_LSIW01000036_36675_TACTTAT_ATCATAC 1 1 1 missense_variant MODERATE AX662_RS01360 WP_060971400.1 NADP-dependent oxidoreductase nadph quinone reductase c.21_27delTACTTATinsATCATAC p.Thr8Ser NZ_LSIW01000036_36715_A_G 1 1 missense_variant MODERATE AX662_RS01360 WP_060971400.1 NADP-dependent oxidoreductase nadph quinone reductase c.61A>G p.Ile21Val NZ_LSIW01000036_36764_CA_TT 1 1 missense_variant MODERATE AX662_RS01360 WP_060971400.1 NADP-dependent oxidoreductase nadph quinone reductase c.110_111delCAinsTT p.Ala37Val NZ_LSIW01000036_36982_T_G 1 1 missense_variant MODERATE AX662_RS01360 WP_060971400.1 NADP-dependent oxidoreductase nadph quinone reductase c.328T>G p.Ser110Ala NZ_LSIW01000036_37008_TTCAAAT_GTCAGAC 1 1 missense_variant MODERATE AX662_RS01360 WP_060971400.1 NADP-dependent oxidoreductase nadph quinone reductase c.354_360delTTCAAATinsGTCAGAC p.Asn120Asp NZ_LSIW01000036_37084_GCTG_TCTA 1 1 missense_variant MODERATE AX662_RS01360 WP_060971400.1 NADP-dependent oxidoreductase nadph quinone reductase c.430_433delGCTGinsTCTA p.AlaGly144SerSer NZ_LSIW01000036_37152_AGC_GGG 1 1 missense_variant MODERATE AX662_RS01360 WP_060971400.1 NADP-dependent oxidoreductase nadph quinone reductase c.498_500delAGCinsGGG p.Ala167Gly NZ_LSIW01000036_37198_AAT_GAG 1 1 1 missense_variant MODERATE AX662_RS01360 WP_060971400.1 NADP-dependent oxidoreductase nadph quinone reductase c.544_546delAATinsGAG p.Asn182Glu NZ_LSIW01000036_37306_G_A 1 1 missense_variant MODERATE AX662_RS01360 WP_060971400.1 NADP-dependent oxidoreductase nadph quinone reductase c.652G>A p.Glu218Lys NZ_LSIW01000036_37541_A_G 1 1 missense_variant MODERATE AX662_RS01360 WP_060971400.1 NADP-dependent oxidoreductase nadph quinone reductase c.887A>G p.Lys296Arg NZ_LSIW01000036_37686_T_C 1 1 missense_variant MODERATE AX662_RS01365 WP_060971401.1 alpha/beta hydrolase Alpha/beta hydrolase family c.14T>C p.Ile5Thr NZ_LSIW01000036_37695_A_C 1 1 1 missense_variant MODERATE AX662_RS01365 WP_060971401.1 alpha/beta hydrolase Alpha/beta hydrolase family c.23A>C p.Asn8Thr NZ_LSIW01000036_37712_G_C 1 1 1 missense_variant MODERATE AX662_RS01365 WP_060971401.1 alpha/beta hydrolase Alpha/beta hydrolase family c.40G>C p.Glu14Gln NZ_LSIW01000036_37878_T_C 1 1 missense_variant MODERATE AX662_RS01365 WP_060971401.1 alpha/beta hydrolase Alpha/beta hydrolase family c.206T>C p.Val69Ala NZ_LSIW01000036_37934_TTTGTAA_GTTATAG 1 1 missense_variant MODERATE AX662_RS01365 WP_060971401.1 alpha/beta hydrolase Alpha/beta hydrolase family c.262_268delTTTGTAAinsGTTATAG p.PheValLys88ValIleGlu NZ_LSIW01000036_38008_GG_CA 1 1 missense_variant MODERATE AX662_RS01365 WP_060971401.1 alpha/beta hydrolase Alpha/beta hydrolase family c.336_337delGGinsCA p.MetVal112IleIle NZ_LSIW01000036_38016_TCC_ACA 1 1 missense_variant MODERATE AX662_RS01365 WP_060971401.1 alpha/beta hydrolase Alpha/beta hydrolase family c.344_346delTCCinsACA p.IleGln115AsnLys NZ_LSIW01000036_38235_A_C 1 1 1 missense_variant MODERATE AX662_RS01365 WP_060971401.1 alpha/beta hydrolase Alpha/beta hydrolase family c.563A>C p.Glu188Ala NZ_LSIW01000036_38255_G_C 1 1 1 missense_variant MODERATE AX662_RS01365 WP_060971401.1 alpha/beta hydrolase Alpha/beta hydrolase family c.583G>C p.Ala195Pro NZ_LSIW01000036_38353_GGATA_CGACC 1 1 missense_variant MODERATE AX662_RS01365 WP_060971401.1 alpha/beta hydrolase Alpha/beta hydrolase family c.681_685delGGATAinsCGACC p.Lys229Gln NZ_LSIW01000036_38536_A_G 1 1 missense_variant MODERATE AX662_RS01370 WP_060971402.1 dehydrogenase Belongs to the short-chain dehydrogenases reductases (SDR) family c.26A>G p.Asp9Gly NZ_LSIW01000036_38577_GCC_ACT 1 1 missense_variant MODERATE AX662_RS01370 WP_060971402.1 dehydrogenase Belongs to the short-chain dehydrogenases reductases (SDR) family c.67_69delGCCinsACT p.Ala23Thr NZ_LSIW01000036_38594_GGTT_TGTC 1 1 missense_variant MODERATE AX662_RS01370 WP_060971402.1 dehydrogenase Belongs to the short-chain dehydrogenases reductases (SDR) family c.84_87delGGTTinsTGTC p.Gln28His NZ_LSIW01000036_38617_A_C 1 1 1 missense_variant MODERATE AX662_RS01370 WP_060971402.1 dehydrogenase Belongs to the short-chain dehydrogenases reductases (SDR) family c.107A>C p.His36Pro NZ_LSIW01000036_38641_A_G 1 1 missense_variant MODERATE AX662_RS01370 WP_060971402.1 dehydrogenase Belongs to the short-chain dehydrogenases reductases (SDR) family c.131A>G p.Gln44Arg NZ_LSIW01000036_38677_TT_CA 1 1 missense_variant MODERATE AX662_RS01370 WP_060971402.1 dehydrogenase Belongs to the short-chain dehydrogenases reductases (SDR) family c.167_168delTTinsCA p.Phe56Ser NZ_LSIW01000036_38708_GGATGTC_TGAGGTT 1 1 missense_variant MODERATE AX662_RS01370 WP_060971402.1 dehydrogenase Belongs to the short-chain dehydrogenases reductases (SDR) family c.198_204delGGATGTCinsTGAGGTT p.GluAsp66AspGlu NZ_LSIW01000036_38725_T_C 1 1 missense_variant MODERATE AX662_RS01370 WP_060971402.1 dehydrogenase Belongs to the short-chain dehydrogenases reductases (SDR) family c.215T>C p.Val72Ala NZ_LSIW01000036_38754_GTCGA_ATCGG 1 1 missense_variant MODERATE AX662_RS01370 WP_060971402.1 dehydrogenase Belongs to the short-chain dehydrogenases reductases (SDR) family c.244_248delGTCGAinsATCGG p.ValAsp82IleGly NZ_LSIW01000036_38806_C_T 1 1 missense_variant MODERATE AX662_RS01370 WP_060971402.1 dehydrogenase Belongs to the short-chain dehydrogenases reductases (SDR) family c.296C>T p.Ala99Val NZ_LSIW01000036_38861_G_T 1 1 missense_variant MODERATE AX662_RS01370 WP_060971402.1 dehydrogenase Belongs to the short-chain dehydrogenases reductases (SDR) family c.351G>T p.Met117Ile NZ_LSIW01000036_38895_G_T 1 1 missense_variant MODERATE AX662_RS01370 WP_060971402.1 dehydrogenase Belongs to the short-chain dehydrogenases reductases (SDR) family c.385G>T p.Ala129Ser NZ_LSIW01000036_39056_C_A 1 1 missense_variant MODERATE AX662_RS01370 WP_060971402.1 dehydrogenase Belongs to the short-chain dehydrogenases reductases (SDR) family c.546C>A p.Phe182Leu NZ_LSIW01000036_39066_A_G 1 1 missense_variant MODERATE AX662_RS01370 WP_060971402.1 dehydrogenase Belongs to the short-chain dehydrogenases reductases (SDR) family c.556A>G p.Ser186Gly NZ_LSIW01000036_39189_AATT_GATC 1 1 missense_variant MODERATE AX662_RS01370 WP_060971402.1 dehydrogenase Belongs to the short-chain dehydrogenases reductases (SDR) family c.679_682delAATTinsGATC p.Asn227Asp NZ_LSIW01000036_39309_T_A 1 1 missense_variant MODERATE AX662_RS01370 WP_060971402.1 dehydrogenase Belongs to the short-chain dehydrogenases reductases (SDR) family c.799T>A p.Phe267Ile NZ_LSIW01000036_39511_AGATG_GGATT 1 1 1 missense_variant MODERATE AX662_RS01375 WP_060971403.1 hypothetical protein c.265_269delCATCTinsAATCC p.HisLeu89AsnPro NZ_LSIW01000036_39584_GA_TG 1 1 missense_variant MODERATE AX662_RS01375 WP_060971403.1 hypothetical protein c.195_196delTCinsCA p.Leu66Ile NZ_LSIW01000036_39602_AG_GC 1 1 1 missense_variant MODERATE AX662_RS01375 WP_060971403.1 hypothetical protein c.177_178delCTinsGC p.PheSer59LeuPro NZ_LSIW01000036_39608_A_G 1 1 missense_variant MODERATE AX662_RS01375 WP_060971403.1 hypothetical protein c.172T>C p.Phe58Leu NZ_LSIW01000036_40790_A_T 1 1 missense_variant MODERATE AX662_RS01385 WP_060971405.1 TetR/AcrR family transcriptional regulator Transcriptional regulator, TetR family c.87T>A p.His29Gln NZ_LSIW01000036_44843_A_C 1 1 missense_variant MODERATE AX662_RS01405 WP_060971408.1 CopY/TcrY family copper transport repressor Copper transport repressor, CopY TcrY family c.206A>C p.Lys69Thr NZ_LSIW01000036_45749_G_A 1 1 1 1 1 missense_variant MODERATE AX662_RS01415 WP_060971409.1 copper-translocating P-type ATPase P-type ATPase c.316G>A p.Gly106Ser NZ_LSIW01000036_45818_AT_TG 1 1 1 1 1 missense_variant MODERATE AX662_RS01415 WP_060971409.1 copper-translocating P-type ATPase P-type ATPase c.385_386delATinsTG p.Met129Trp NZ_LSIW01000036_46889_ATA_GTG 1 1 1 1 1 missense_variant MODERATE AX662_RS01415 WP_060971409.1 copper-translocating P-type ATPase P-type ATPase c.1456_1458delATAinsGTG p.Ile486Val NZ_LSIW01000036_47268_G_A 1 1 1 missense_variant MODERATE AX662_RS01415 WP_060971409.1 copper-translocating P-type ATPase P-type ATPase c.1835G>A p.Ser612Asn NZ_LSIW01000036_47522_A_C 1 1 1 missense_variant MODERATE AX662_RS01415 WP_060971409.1 copper-translocating P-type ATPase P-type ATPase c.2089A>C p.Ile697Leu NZ_LSIW01000037_133089_TC_GG 1 1 1 missense_variant MODERATE AX662_RS02005 WP_060971480.1 NAD(P)-dependent oxidoreductase Belongs to the short-chain dehydrogenases reductases (SDR) family c.550_551delTCinsGG p.Ser184Gly NZ_LSIW01000037_133097_CA_TG 1 1 1 missense_variant MODERATE AX662_RS02005 WP_060971480.1 NAD(P)-dependent oxidoreductase Belongs to the short-chain dehydrogenases reductases (SDR) family c.558_559delCAinsTG p.Asn187Asp NZ_LSIW01000037_133230_G_T 1 1 1 missense_variant MODERATE AX662_RS02005 WP_060971480.1 NAD(P)-dependent oxidoreductase Belongs to the short-chain dehydrogenases reductases (SDR) family c.691G>T p.Ala231Ser NZ_LSIW01000037_133264_AC_GA 1 1 1 missense_variant MODERATE AX662_RS02005 WP_060971480.1 NAD(P)-dependent oxidoreductase Belongs to the short-chain dehydrogenases reductases (SDR) family c.725_726delACinsGA p.His242Arg NZ_LSIW01000037_133452_TTGTAG_CTGTGT 1 1 1 missense_variant MODERATE AX662_RS02010 WP_060971481.1 class I SAM-dependent methyltransferase Methyltransferase domain c.134_139delTTGTAGinsCTGTGT p.LeuValAla45ProValSer NZ_LSIW01000037_2019_TGCCA_GGTCC 1 1 missense_variant MODERATE AX662_RS01440 WP_060971413.1 hypothetical protein c.240_244delTGCCAinsGGTCC p.AlaLys81ValGln NZ_LSIW01000037_2031_CG_AA 1 1 missense_variant MODERATE AX662_RS01440 WP_060971413.1 hypothetical protein c.252_253delCGinsAA p.AspVal84GluMet NZ_LSIW01000037_2041_ATC_GTT 1 1 1 missense_variant MODERATE AX662_RS01440 WP_060971413.1 hypothetical protein c.262_264delATCinsGTT p.Ile88Val NZ_LSIW01000037_47785_T_C 1 1 missense_variant MODERATE AX662_RS01655 WP_060971437.1 cell division protein FtsZ Essential cell division protein that forms a contractile ring structure (Z ring) at the future cell dc.971T>C p.Val324Ala NZ_LSIW01000037_50027_C_A 1 1 missense_variant MODERATE AX662_RS01675 WP_060971439.1 RNA-binding protein conserved protein, contains S4-like domain c.340C>A p.Leu114Ile NZ_LSIW01000037_5981_T_G 1 1 1 1 missense_variant MODERATE AX662_RS01465 WP_060971416.1 Cof-type HAD-IIB family hydrolase hydrolase c.822T>G p.Asp274Glu NZ_LSIW01000039_1957_GTT_ATG 1 1 1 1 missense_variant MODERATE AX662_RS02165 WP_060971502.1 ATPase E1-E2 ATPase c.547_549delAACinsCAT p.Asn183His NZ_LSIW01000039_1966_CTTA_TCTG 1 1 1 1 missense_variant MODERATE AX662_RS02165 WP_060971502.1 ATPase E1-E2 ATPase c.537_540delTAAGinsCAGA p.Lys180Arg NZ_LSIW01000051_31632_TT_CG 1 1 1 1 missense_variant MODERATE AX662_RS02445 WP_014633793.1 hypothetical protein c.477_478delTTinsCG p.Phe160Val NZ_LSIW01000052_2155_TC_CA 1 1 missense_variant MODERATE AX662_RS02545 WP_060971540.1 RDD family protein RDD family c.38_39delTCinsCA p.Ile13Thr NZ_LSIW01000052_2227_C_G 1 1 missense_variant MODERATE AX662_RS02545 WP_060971540.1 RDD family protein RDD family c.110C>G p.Ala37Gly NZ_LSIW01000052_2381_TTTT_CTTG 1 1 missense_variant MODERATE AX662_RS02545 WP_060971540.1 RDD family protein RDD family c.264_267delTTTTinsCTTG p.Phe89Leu NZ_LSIW01000052_2391_AC_GG 1 1 missense_variant MODERATE AX662_RS02545 WP_060971540.1 RDD family protein RDD family c.274_275delACinsGG p.Thr92Gly NZ_LSIW01000052_2402_ACTTC_GCTTG 1 1 missense_variant MODERATE AX662_RS02545 WP_060971540.1 RDD family protein RDD family c.285_289delACTTCinsGCTTG p.Gln97Glu NZ_LSIW01000052_2453_TACCATT_CGTCATC 1 1 missense_variant MODERATE AX662_RS02545 WP_060971540.1 RDD family protein RDD family c.336_342delTACCATTinsCGTCATC p.Thr113Val NZ_LSIW01000052_2558_CC_AA 1 1 missense_variant MODERATE AX662_RS02545 WP_060971540.1 RDD family protein RDD family c.441_442delCCinsAA p.Leu148Ile NZ_LSIW01000052_2569_CC_TG 1 1 missense_variant MODERATE AX662_RS02545 WP_060971540.1 RDD family protein RDD family c.452_453delCCinsTG p.Ser151Leu NZ_LSIW01000052_2586_ATG_TTT 1 1 missense_variant MODERATE AX662_RS02545 WP_060971540.1 RDD family protein RDD family c.469_471delATGinsTTT p.Met157Phe NZ_LSIW01000052_2602_AGAGG_GGAGA 1 1 missense_variant MODERATE AX662_RS02545 WP_060971540.1 RDD family protein RDD family c.485_489delAGAGGinsGGAGA p.Lys162Arg NZ_LSIW01000052_2937_G_A 1 1 missense_variant MODERATE AX662_RS02550 WP_048675419.1 multidrug resistance efflux transporter family protein membrane c.157G>A p.Ala53Thr NZ_LSIW01000052_2947_C_T 1 1 1 missense_variant MODERATE AX662_RS02550 WP_048675419.1 multidrug resistance efflux transporter family protein membrane c.167C>T p.Ala56Val NZ_LSIW01000052_3390_GTGATCTTA_TTGCTTTTG 1 1 1 missense_variant MODERATE AX662_RS02550 WP_048675419.1 multidrug resistance efflux transporter family protein membrane c.610_618delGTGATCTTAinsTTGCTTTTG p.ValIle204LeuLeu NZ_LSIW01000052_3403_T_C 1 1 missense_variant MODERATE AX662_RS02550 WP_048675419.1 multidrug resistance efflux transporter family protein membrane c.623T>C p.Val208Ala NZ_LSIW01000052_3412_TAACGGATT_GTGCAGATG 1 1 missense_variant MODERATE AX662_RS02550 WP_048675419.1 multidrug resistance efflux transporter family protein membrane c.632_640delTAACGGATTinsGTGCAGATG p.ValThrAspSer211GlyAlaAspAla NZ_LSIW01000052_4098_CAA_AAG 1 1 missense_variant MODERATE AX662_RS02555 WP_060971541.1 glycosyl hydrolase family 32 Belongs to the glycosyl hydrolase 32 family c.143_145delCAAinsAAG p.ProIle48GlnVal NZ_LSIW01000052_4118_G_A 1 1 missense_variant MODERATE AX662_RS02555 WP_060971541.1 glycosyl hydrolase family 32 Belongs to the glycosyl hydrolase 32 family c.163G>A p.Ala55Thr NZ_LSIW01000052_4140_AGG_CTCCTCAAGCGGAGC 1 1 1 1 missense variant&disruptive inframe MODERATE AX662_RS02555 WP_060971541.1 glycosyl hydrolase family 32 Belongs to the glycosyl hydrolase 32 family c.185_187delAGGinsCTCCTCAAGCGGAGC p.Glu62_Val63delinsAlaProGlnAlaGluLeu NZ_LSIW01000052_4191_C_A 1 1 missense_variant MODERATE AX662_RS02555 WP_060971541.1 glycosyl hydrolase family 32 Belongs to the glycosyl hydrolase 32 family c.236C>A p.Pro79Gln NZ_LSIW01000052_4271_GC_AT 1 1 missense_variant MODERATE AX662_RS02555 WP_060971541.1 glycosyl hydrolase family 32 Belongs to the glycosyl hydrolase 32 family c.316_317delGCinsAT p.Ala106Ile NZ_LSIW01000052_4297_AA_GG 1 1 missense_variant MODERATE AX662_RS02555 WP_060971541.1 glycosyl hydrolase family 32 Belongs to the glycosyl hydrolase 32 family c.342_343delAAinsGG p.Thr115Ala NZ_LSIW01000052_4303_CCAAG_GCAAA 1 1 missense_variant MODERATE AX662_RS02555 WP_060971541.1 glycosyl hydrolase family 32 Belongs to the glycosyl hydrolase 32 family c.348_352delCCAAGinsGCAAA p.AsnGlnAla116LysGlnThr NZ_LSIW01000052_4342_AACG_GCAATCT 1 1 missense variant&conservative inframMODERATE AX662_RS02555 WP_060971541.1 glycosyl hydrolase family 32 Belongs to the glycosyl hydrolase 32 family c.387_390delAACGinsGCAATCT p.Thr130delinsGlnSer NZ_LSIW01000052_4825_CGACT_TGACG 1 1 missense_variant MODERATE AX662_RS02555 WP_060971541.1 glycosyl hydrolase family 32 Belongs to the glycosyl hydrolase 32 family c.870_874delCGACTinsTGACG p.Ser292Ala NZ_LSIW01000052_4972_ACTCGTA_TCTTGTG 1 1 missense_variant MODERATE AX662_RS02555 WP_060971541.1 glycosyl hydrolase family 32 Belongs to the glycosyl hydrolase 32 family c.1017_1023delACTCGTAinsTCTTGTG p.Lys339Asn NZ_LSIW01000052_5069_A_G 1 1 missense_variant MODERATE AX662_RS02555 WP_060971541.1 glycosyl hydrolase family 32 Belongs to the glycosyl hydrolase 32 family c.1114A>G p.Thr372Ala NZ_LSIW01000054_22395_A_G 1 1 1 missense_variant MODERATE AX662_RS02710 WP_060971555.1 LysM domain-containing protein LysM domain c.790A>G p.Lys264Glu NZ_LSIW01000054_22415_CCA_ACG 1 1 1 missense_variant MODERATE AX662_RS02710 WP_060971555.1 LysM domain-containing protein LysM domain c.810_812delCCAinsACG p.AsnHis270LysArg NZ_LSIW01000054_22471_T_C 1 1 missense_variant MODERATE AX662_RS02710 WP_060971555.1 LysM domain-containing protein LysM domain c.866T>C p.Val289Ala NZ_LSIW01000054_22613_TGACGCT_CGACACC 1 1 missense_variant MODERATE AX662_RS02710 WP_060971555.1 LysM domain-containing protein LysM domain c.1008_1014delTGACGCTinsCGACACC p.Ala338Thr NZ_LSIW01000054_22624_ACAGGGATA_GCAACGGAG 1 1 missense_variant MODERATE AX662_RS02710 WP_060971555.1 LysM domain-containing protein LysM domain c.1019_1027delACAGGGATAinsGCAACGGAG p.AsnArgAspSer340SerAsnGlyGly NZ_LSIW01000054_5338_TC_CT 1 1 1 1 1 missense_variant MODERATE AX662_RS02615 WP_003093491.1 TIGR03943 family protein TIGR03943 family c.428_429delGAinsAG p.Arg143Lys NZ_LSIW01000058_118299_GATTCGG_AATCCGT 1 1 1 1 1 missense_variant MODERATE AX662_RS03400 WP_060971610.1 replication-associated recombination protein A ATPase related to the helicase subunit of the Holliday junction resolvase c.1245_1251delCCGAATCinsACGGATT p.Asp415Glu NZ_LSIW01000058_132858_G_C 1 1 1 missense_variant MODERATE AX662_RS10305 PTS beta-glucoside transporter subunit IIABC c.446C>G p.Ala149Gly NZ_LSIW01000058_133277_TTTCGGCCCTA_CTTCTGTCCTG 1 1 missense_variant MODERATE AX662_RS10305 PTS beta-glucoside transporter subunit IIABC c.17_27delTAGGGCCGAAAinsCAGGACAGAAG p.IleGlyPro6ThrGlyGln NZ_LSIW01000058_8302_T_C 1 1 missense_variant MODERATE AX662_RS02785 WP_060971563.1 argininosuccinate synthase Belongs to the argininosuccinate synthase family. Type 1 subfamily c.316A>G p.Lys106Glu NZ_LSIW01000058_8455_C_T 1 1 missense_variant MODERATE AX662_RS02785 WP_060971563.1 argininosuccinate synthase Belongs to the argininosuccinate synthase family. Type 1 subfamily c.163G>A p.Val55Ile NZ_LSIW01000058_9662_G_C 1 1 missense_variant MODERATE AX662_RS02790 WP_002885796.1 DNA-binding response regulator Response regulator of the LytR AlgR family c.644C>G p.Thr215Ser NZ_LSIW01000060_111695_CGT_TAC 1 1 missense_variant MODERATE AX662_RS04205 WP_060971702.1 hypothetical protein c.117_119delCGTinsTAC p.Val40Thr NZ_LSIW01000060_111748_C_G 1 1 missense_variant MODERATE AX662_RS04205 WP_060971702.1 hypothetical protein c.170C>G p.Thr57Arg NZ_LSIW01000060_111845_CCAAAA_TCATAG 1 1 missense_variant MODERATE AX662_RS04205 WP_060971702.1 hypothetical protein c.267_272delCCAAAAinsTCATAG p.GlnAsn90HisSer NZ_LSIW01000060_111891_A_G 1 1 missense_variant MODERATE AX662_RS04205 WP_060971702.1 hypothetical protein c.313A>G p.Asn105Asp NZ_LSIW01000060_112013_A_T 1 1 missense_variant MODERATE AX662_RS04205 WP_060971702.1 hypothetical protein c.435A>T p.Glu145Asp NZ_LSIW01000060_112056_GTCAGCCA_ACCAGTCG 1 1 missense_variant MODERATE AX662_RS04205 WP_060971702.1 hypothetical protein c.478_485delGTCAGCCAinsACCAGTCG p.ValSerHis160ThrSerArg NZ_LSIW01000060_112320_G_A 1 1 missense_variant MODERATE AX662_RS04205 WP_060971702.1 hypothetical protein c.742G>A p.Val248Ile NZ_LSIW01000060_112402_ACTTC_GCTTT 1 1 1 missense_variant MODERATE AX662_RS04205 WP_060971702.1 hypothetical protein c.824_828delACTTCinsGCTTT p.Asn275Ser NZ_LSIW01000060_112523_A_T 1 1 missense_variant MODERATE AX662_RS04205 WP_060971702.1 hypothetical protein c.945A>T p.Lys315Asn NZ_LSIW01000060_11920_GGAAAAG_AGCAAAC 1 1 missense_variant MODERATE AX662_RS03735 WP_060971651.1 PDZ domain-containing protein Belongs to the peptidase S16 family c.93_99delCTTTTCCinsGTTTGCT p.Ser33Ala NZ_LSIW01000060_124486_ACTC_CCTT 1 1 1 1 1 missense_variant MODERATE AX662_RS04250 WP_060971708.1 signal peptidase I Belongs to the peptidase S26 family c.96_99delACTCinsCCTT p.Leu32Phe NZ_LSIW01000060_16250_T_G 1 1 1 1 1 missense_variant MODERATE AX662_RS03765 WP_060971652.1 amino acid ABC transporter permease ABC transporter (Permease c.55A>C p.Ile19Leu NZ_LSIW01000060_68434_T_C 1 1 1 missense_variant MODERATE AX662_RS03985 WP_060971678.1 hypothetical protein c.767A>G p.Asp256Gly NZ_LSIW01000060_68911_TTG_CTA 1 1 1 missense_variant MODERATE AX662_RS03985 WP_060971678.1 hypothetical protein c.288_290delCAAinsTAG p.Asn97Ser NZ_LSIW01000060_73532_TGAAC_CGCAT 1 1 missense_variant MODERATE AX662_RS04015 WP_060971680.1 hypothetical protein membrane c.683_687delGTTCAinsATGCG p.SerSer228AsnAla NZ_LSIW01000060_74960_T_C 1 1 missense_variant MODERATE AX662_RS04025 WP_060971682.1 hypothetical protein response to antibiotic c.1651A>G p.Ser551Gly NZ_LSIW01000060_81234_AGTCAGA_GCTCAAG 1 1 1 1 missense_variant MODERATE AX662_RS04050 WP_060971686.1 DUF2975 domain-containing protein c.204_210delTCTGACTinsCTTGAGC p.Thr70Ser NZ_LSIW01000060_82996_GAATAGTACT_CAGTAATATC 1 1 1 1 missense_variant MODERATE AX662_RS04060 WP_060971688.1 hypothetical protein c.195_204delAGTACTATTCinsGATATTACTG p.ValLeuPhe66IleLeuLeu NZ_LSIW01000060_83037_G_A 1 1 1 1 missense_variant MODERATE AX662_RS04060 WP_060971688.1 hypothetical protein c.163C>T p.Leu55Phe NZ_LSIW01000069_1343_AGGCTAG_GGGCGAA 1 1 missense_variant MODERATE AX662_RS04460 WP_060971729.1 chorismate mutase Chorismate mutase c.134_140delAGGCTAGinsGGGCGAA p.GlnAlaSer45ArgAlaAsn NZ_LSIW01000069_14714_A_G 1 1 missense_variant MODERATE AX662_RS04530 WP_060971738.1 amino acid ABC transporter ATP-binding protein abc transporter atp-binding protein c.211A>G p.Ser71Gly NZ_LSIW01000072_22571_CC_TG 1 1 missense_variant MODERATE AX662_RS04850 WP_060971771.1 tyrosine recombinase XerS Site-specific tyrosine recombinase, which acts by catalyzing the cutting and rejoining of the rec.804_805delCCinsTG p.Leu269Val NZ_LSIW01000072_54434_A_G 1 1 1 1 missense_variant MODERATE AX662_RS04995 WP_060971787.1 orotidine-5'-phosphate decarboxylase Catalyzes the decarboxylation of orotidine 5'- monophosphate (OMP) to uridine 5'-monophoc.64T>C p.Phe22Leu NZ_LSIW01000072_68347_GTGAG_ATGAT 1 1 missense_variant MODERATE AX662_RS05050 WP_060971797.1 hypothetical protein Psort location CytoplasmicMembrane, score c.268_272delGTGAGinsATGAT p.ValSer90MetIle NZ_LSIW01000072_71480_T_C 1 1 1 missense_variant MODERATE AX662_RS05060 WP_060971799.1 iron-siderophore ABC transporter substrate-binding protein ABC-type enterochelin transport system, periplasmic component c.551A>G p.Lys184Arg NZ_LSIW01000072_71687_T_C 1 1 missense_variant MODERATE AX662_RS05060 WP_060971799.1 iron-siderophore ABC transporter substrate-binding protein ABC-type enterochelin transport system, periplasmic component c.344A>G p.Asn115Ser NZ_LSIW01000072_71799_CTAA_GGAG 1 1 missense_variant MODERATE AX662_RS05060 WP_060971799.1 iron-siderophore ABC transporter substrate-binding protein ABC-type enterochelin transport system, periplasmic component c.229_232delTTAGinsCTCC p.Asp78His NZ_LSIW01000072_71808_T_C 1 1 missense_variant MODERATE AX662_RS05060 WP_060971799.1 iron-siderophore ABC transporter substrate-binding protein ABC-type enterochelin transport system, periplasmic component c.223A>G p.Asn75Asp NZ_LSIW01000072_73265_T_A 1 1 missense_variant MODERATE AX662_RS05065 WP_060971800.1 restriction endonuclease subunit R Type III restriction enzyme, res subunit c.526T>A p.Leu176Ile NZ_LSIW01000072_73461_A_G 1 1 1 1 missense_variant MODERATE AX662_RS05065 WP_060971800.1 restriction endonuclease subunit R Type III restriction enzyme, res subunit c.722A>G p.Gln241Arg NZ_LSIW01000072_73503_G_A 1 1 missense_variant MODERATE AX662_RS05065 WP_060971800.1 restriction endonuclease subunit R Type III restriction enzyme, res subunit c.764G>A p.Arg255Lys NZ_LSIW01000072_73661_G_T 1 1 missense_variant MODERATE AX662_RS05065 WP_060971800.1 restriction endonuclease subunit R Type III restriction enzyme, res subunit c.922G>T p.Ala308Ser NZ_LSIW01000072_73671_A_C 1 1 missense_variant MODERATE AX662_RS05065 WP_060971800.1 restriction endonuclease subunit R Type III restriction enzyme, res subunit c.932A>C p.Asn311Thr NZ_LSIW01000072_73922_A_G 1 1 missense_variant MODERATE AX662_RS05065 WP_060971800.1 restriction endonuclease subunit R Type III restriction enzyme, res subunit c.1183A>G p.Asn395Asp NZ_LSIW01000072_74050_G_A 1 1 missense_variant MODERATE AX662_RS05065 WP_060971800.1 restriction endonuclease subunit R Type III restriction enzyme, res subunit c.1311G>A p.Met437Ile NZ_LSIW01000072_74102_A_G 1 1 1 1 missense_variant MODERATE AX662_RS05065 WP_060971800.1 restriction endonuclease subunit R Type III restriction enzyme, res subunit c.1363A>G p.Ile455Val NZ_LSIW01000072_74940_C_T 1 1 missense_variant MODERATE AX662_RS05065 WP_060971800.1 restriction endonuclease subunit R Type III restriction enzyme, res subunit c.2201C>T p.Ala734Val NZ_LSIW01000072_75032_TCC_GCT 1 1 missense_variant MODERATE AX662_RS05065 WP_060971800.1 restriction endonuclease subunit R Type III restriction enzyme, res subunit c.2293_2295delTCCinsGCT p.Ser765Ala NZ_LSIW01000072_75162_T_A 1 1 missense_variant MODERATE AX662_RS05065 WP_060971800.1 restriction endonuclease subunit R Type III restriction enzyme, res subunit c.2423T>A p.Leu808Gln NZ_LSIW01000072_75169_A_G 1 1 missense_variant MODERATE AX662_RS05065 WP_060971800.1 restriction endonuclease subunit R Type III restriction enzyme, res subunit c.2430A>G p.Ile810Met NZ_LSIW01000072_75353_G_A 1 1 missense_variant MODERATE AX662_RS05065 WP_060971800.1 restriction endonuclease subunit R Type III restriction enzyme, res subunit c.2614G>A p.Val872Ile NZ_LSIW01000072_75787_CATTG_TATTA 1 1 missense_variant MODERATE AX662_RS05070 WP_060971801.1 phosphoglycolate phosphatase HAD hydrolase, family IA, variant 1 c.261_265delCATTGinsTATTA p.Glu89Lys NZ_LSIW01000072_76288_T_G 1 1 missense_variant MODERATE AX662_RS05075 WP_060971802.1 phosphorylase Phosphorylase superfamily c.701A>C p.Asp234Ala NZ_LSIW01000072_76499_G_T 1 1 1 1 1 missense_variant MODERATE AX662_RS05075 WP_060971802.1 phosphorylase Phosphorylase superfamily c.490C>A p.Leu164Ile NZ_LSIW01000072_76775_TCG_ACA 1 1 missense_variant MODERATE AX662_RS05075 WP_060971802.1 phosphorylase Phosphorylase superfamily c.212_214delCGAinsTGT p.ThrThr71MetSer NZ_LSIW01000072_76795_G_C 1 1 missense_variant MODERATE AX662_RS05075 WP_060971802.1 phosphorylase Phosphorylase superfamily c.194C>G p.Thr65Ser NZ_LSIW01000072_76827_A_T 1 1 1 1 missense_variant MODERATE AX662_RS05075 WP_060971802.1 phosphorylase Phosphorylase superfamily c.162T>A p.Asp54Glu NZ_LSIW01000072_77871_G_A 1 1 missense_variant MODERATE AX662_RS05085 WP_060971803.1 ABC transporter permease ABC transporter c.1043C>T p.Ala348Val NZ_LSIW01000072_77999_CA_AG 1 1 missense_variant MODERATE AX662_RS05085 WP_060971803.1 ABC transporter permease ABC transporter c.914_915delTGinsCT p.Met305Thr NZ_LSIW01000072_78234_G_C 1 1 missense_variant MODERATE AX662_RS05085 WP_060971803.1 ABC transporter permease ABC transporter c.680C>G p.Ala227Gly NZ_LSIW01000072_78537_T_C 1 1 1 missense_variant MODERATE AX662_RS05085 WP_060971803.1 ABC transporter permease ABC transporter c.377A>G p.Asp126Gly NZ_LSIW01000072_78565_C_T 1 1 missense_variant MODERATE AX662_RS05085 WP_060971803.1 ABC transporter permease ABC transporter c.349G>A p.Val117Ile NZ_LSIW01000072_78682_T_G 1 1 missense_variant MODERATE AX662_RS05085 WP_060971803.1 ABC transporter permease ABC transporter c.232A>C p.Lys78Gln NZ_LSIW01000072_78712_A_C 1 1 missense_variant MODERATE AX662_RS05085 WP_060971803.1 ABC transporter permease ABC transporter c.202T>G p.Phe68Val NZ_LSIW01000072_78769_GCTTAACAGTCACC_ACTTGACATTTACA 1 1 missense_variant MODERATE AX662_RS05085 WP_060971803.1 ABC transporter permease ABC transporter c.132_145delGGTGACTGTTAAGCinsTGTAAATGTCAAGT p.Thr46Asn NZ_LSIW01000072_78883_T_C 1 1 missense_variant MODERATE AX662_RS05085 WP_060971803.1 ABC transporter permease ABC transporter c.31A>G p.Ile11Val NZ_LSIW01000072_79100_CCATCAACTCT_TGATTAATTCC 1 1 missense_variant MODERATE AX662_RS05090 WP_060971804.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.522_532delAGAGTTGATGGinsGGAATTAATCA p.MetAla177IleThr NZ_LSIW01000072_79280_CT_AC 1 1 missense_variant MODERATE AX662_RS05090 WP_060971804.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.351_352delAGinsGT p.Ala118Ser NZ_LSIW01000072_79296_AGATGAC_TGTTGTT 1 1 missense_variant MODERATE AX662_RS05090 WP_060971804.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.330_336delGTCATCTinsAACAACA p.SerSer111ThrThr NZ_LSIW01000072_79331_T_G 1 1 missense_variant MODERATE AX662_RS05090 WP_060971804.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.301A>C p.Lys101Gln NZ_LSIW01000072_79343_GCAA_CCAG 1 1 missense_variant MODERATE AX662_RS05090 WP_060971804.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.286_289delTTGCinsCTGG p.Gln97Glu NZ_LSIW01000072_79434_ATTT_GTGG 1 1 missense_variant MODERATE AX662_RS05090 WP_060971804.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.195_198delAAATinsCCAC p.GluAsn65AspHis NZ_LSIW01000072_79543_T_C 1 1 1 missense_variant MODERATE AX662_RS05090 WP_060971804.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.89A>G p.Glu30Gly NZ_LSIW01000072_79941_T_C 1 1 missense_variant MODERATE AX662_RS05095 hypothetical protein c.395A>G p.Glu132Gly NZ_LSIW01000072_80001_C_T 1 1 missense_variant MODERATE AX662_RS05095 hypothetical protein c.335G>A p.Arg112Lys NZ_LSIW01000072_80030_C_T 1 1 missense_variant MODERATE AX662_RS05095 hypothetical protein c.306G>A p.Met102Ile NZ_LSIW01000072_80121_G_A 1 1 missense_variant MODERATE AX662_RS05095 hypothetical protein c.215C>T p.Ser72Phe NZ_LSIW01000072_80175_ATATCCA_GTAGCCT 1 1 missense_variant MODERATE AX662_RS05095 hypothetical protein c.155_161delTGGATATinsAGGCTAC p.LeuAspIle52GlnAlaThr NZ_LSIW01000077_64678_G_T 1 1 missense_variant MODERATE AX662_RS05415 WP_060971842.1 methionyl-tRNA formyltransferase Attaches a formyl group to the free amino group of methionyl-tRNA(fMet). The formyl group c.457G>T p.Ala153Ser NZ_LSIW01000077_64712_C_G 1 1 missense_variant MODERATE AX662_RS05415 WP_060971842.1 methionyl-tRNA formyltransferase Attaches a formyl group to the free amino group of methionyl-tRNA(fMet). The formyl group c.491C>G p.Thr164Ser NZ_LSIW01000077_64966_AAT_GAC 1 1 missense_variant MODERATE AX662_RS05415 WP_060971842.1 methionyl-tRNA formyltransferase Attaches a formyl group to the free amino group of methionyl-tRNA(fMet). The formyl group c.745_747delAATinsGAC p.Asn249Asp NZ_LSIW01000077_64973_C_T 1 1 missense_variant MODERATE AX662_RS05415 WP_060971842.1 methionyl-tRNA formyltransferase Attaches a formyl group to the free amino group of methionyl-tRNA(fMet). The formyl group c.752C>T p.Ala251Val NZ_LSIW01000077_66094_TCCA_CGCC 1 1 missense_variant MODERATE AX662_RS05420 WP_060971845.1 16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB Specifically methylates the cytosine at position 967 (m5C967) of 16S rRNA c.948_951delTCCAinsCGCC p.Pro317Ala NZ_LSIW01000081_26713_GCG_CTT 1 1 1 missense_variant MODERATE AX662_RS05590 WP_060971862.1 hypothetical protein c.1069_1071delCGCinsAAG p.Arg357Lys NZ_LSIW01000081_34518_GGCCG_TGCCC 1 1 missense_variant MODERATE AX662_RS05620 WP_060971867.1 glycine--tRNA ligase subunit beta Glycyl-tRNA synthetase beta subunit c.1145_1149delCGGCCinsGGGCA p.Thr382Arg NZ_LSIW01000081_45125_T_G 1 1 1 missense_variant MODERATE AX662_RS05665 WP_060971872.1 N-acetylmuramoyl-L-alanine amidase amidase activity c.603A>C p.Glu201Asp NZ_LSIW01000081_9928_T_A 1 1 missense_variant MODERATE AX662_RS05510 WP_060971851.1 efflux RND transporter periplasmic adaptor subunit Belongs to the membrane fusion protein (MFP) (TC 8.A.1) family c.123A>T p.Lys41Asn NZ_LSIW01000092_23093_T_A 1 1 missense_variant MODERATE AX662_RS06010 WP_060971902.1 ATP-dependent Clp protease ATP-binding subunit ATP-dependent Clp protease ATP-binding subunit c.189A>T p.Gln63His NZ_LSIW01000092_24948_T_C 1 1 1 1 1 missense_variant MODERATE AX662_RS06025 WP_060971905.1 nucleotidyltransferase Belongs to the UPF0348 family c.781A>G p.Ile261Val NZ_LSIW01000092_25430_T_A 1 1 1 1 1 missense_variant MODERATE AX662_RS06025 WP_060971905.1 nucleotidyltransferase Belongs to the UPF0348 family c.299A>T p.Asp100Val NZ_LSIW01000095_1276_C_A 1 1 1 missense_variant MODERATE AX662_RS06295 flagellar biosynthesis protein FliS c.1609G>T p.Ala537Ser NZ_LSIW01000095_2191_T_A 1 1 1 missense_variant MODERATE AX662_RS06295 flagellar biosynthesis protein FliS c.694A>T p.Thr232Ser NZ_LSIW01000095_2273_TGACA_AGACT 1 1 1 missense_variant MODERATE AX662_RS06295 flagellar biosynthesis protein FliS c.608_612delTGTCAinsAGTCT p.Leu203Gln NZ_LSIW01000095_2551_TAGCC_CAGCT 1 1 1 missense_variant MODERATE AX662_RS06295 flagellar biosynthesis protein FliS c.330_334delGGCTAinsAGCTG p.Thr112Ala NZ_LSIW01000097_10842_GGC_AGT 1 1 missense_variant MODERATE AX662_RS06360 WP_060971942.1 DNA-binding response regulator COG2197 Response regulator containing a CheY-like receiver domain and an HTH DNA-bindin c.118_120delGCCinsACT p.Ala40Thr NZ_LSIW01000097_112097_A_T 1 1 missense_variant MODERATE AX662_RS06820 WP_060971998.1 ABC transporter permease Efflux ABC transporter, permease protein c.55T>A p.Phe19Ile NZ_LSIW01000097_123462_TTCC_CTCG 1 1 missense_variant MODERATE AX662_RS06875 WP_060972006.1 M13 family peptidase Peptidase family M13 c.606_609delGGAAinsCGAG p.Met202Ile NZ_LSIW01000097_13573_G_T 1 1 missense_variant MODERATE AX662_RS06375 WP_060971945.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.88C>A p.Gln30Lys NZ_LSIW01000097_55251_A_G 1 1 1 missense_variant MODERATE AX662_RS06570 WP_060971962.1 glucosyl transferase dextransucrase activity c.2767A>G p.Asn923Asp NZ_LSIW01000097_62832_AAATTCC_GAATATA 1 1 missense_variant MODERATE AX662_RS06615 WP_060972013.1 DUF3169 domain-containing protein Protein of unknown function (DUF3169) c.564_570delGGAATTTinsTATATTC p.Glu189Ile NZ_LSIW01000097_62885_TCA_GCT 1 1 missense_variant MODERATE AX662_RS06615 WP_060972013.1 DUF3169 domain-containing protein Protein of unknown function (DUF3169) c.515_517delTGAinsAGC p.LeuIle172GlnLeu NZ_LSIW01000097_62901_GCGAA_TCGAT 1 1 missense_variant MODERATE AX662_RS06615 WP_060972013.1 DUF3169 domain-containing protein Protein of unknown function (DUF3169) c.497_501delTTCGCinsATCGA p.Phe166Tyr NZ_LSIW01000097_62911_AT_GA 1 1 missense_variant MODERATE AX662_RS06615 WP_060972013.1 DUF3169 domain-containing protein Protein of unknown function (DUF3169) c.490_491delATinsTC p.Ile164Ser NZ_LSIW01000097_62917_GA_AC 1 1 missense_variant MODERATE AX662_RS06615 WP_060972013.1 DUF3169 domain-containing protein Protein of unknown function (DUF3169) c.484_485delTCinsGT p.Ser162Val NZ_LSIW01000097_62941_AT_GC 1 1 missense_variant MODERATE AX662_RS06615 WP_060972013.1 DUF3169 domain-containing protein Protein of unknown function (DUF3169) c.460_461delATinsGC p.Ile154Ala NZ_LSIW01000097_62983_AA_GC 1 1 missense_variant MODERATE AX662_RS06615 WP_060972013.1 DUF3169 domain-containing protein Protein of unknown function (DUF3169) c.418_419delTTinsGC p.Phe140Ala NZ_LSIW01000097_63026_T_A 1 1 missense_variant MODERATE AX662_RS06615 WP_060972013.1 DUF3169 domain-containing protein Protein of unknown function (DUF3169) c.376A>T p.Ser126Cys NZ_LSIW01000097_63038_C_T 1 1 missense_variant MODERATE AX662_RS06615 WP_060972013.1 DUF3169 domain-containing protein Protein of unknown function (DUF3169) c.364G>A p.Val122Ile NZ_LSIW01000097_63053_GTAAA_ACAAG 1 1 missense_variant MODERATE AX662_RS06615 WP_060972013.1 DUF3169 domain-containing protein Protein of unknown function (DUF3169) c.345_349delTTTACinsCTTGT p.Pro117Ser NZ_LSIW01000097_63062_AGATT_TGATG 1 1 missense_variant MODERATE AX662_RS06615 WP_060972013.1 DUF3169 domain-containing protein Protein of unknown function (DUF3169) c.336_340delAATCTinsCATCA p.Leu114Met NZ_LSIW01000097_63099_T_A 1 1 missense_variant MODERATE AX662_RS06615 WP_060972013.1 DUF3169 domain-containing protein Protein of unknown function (DUF3169) c.303A>T p.Lys101Asn NZ_LSIW01000097_63110_C_T 1 1 missense_variant MODERATE AX662_RS06615 WP_060972013.1 DUF3169 domain-containing protein Protein of unknown function (DUF3169) c.292G>A p.Val98Ile NZ_LSIW01000097_63225_AGAAC_TGAGT 1 1 missense_variant MODERATE AX662_RS06615 WP_060972013.1 DUF3169 domain-containing protein Protein of unknown function (DUF3169) c.173_177delGTTCTinsACTCA p.Gly58Asp NZ_LSIW01000097_63235_T_A 1 1 missense_variant MODERATE AX662_RS06615 WP_060972013.1 DUF3169 domain-containing protein Protein of unknown function (DUF3169) c.167A>T p.Tyr56Phe NZ_LSIW01000097_63247_G_T 1 1 missense_variant MODERATE AX662_RS06615 WP_060972013.1 DUF3169 domain-containing protein Protein of unknown function (DUF3169) c.155C>A p.Thr52Lys NZ_LSIW01000097_63258_AGATTGA_GGTTTGG 1 1 missense_variant MODERATE AX662_RS06615 WP_060972013.1 DUF3169 domain-containing protein Protein of unknown function (DUF3169) c.138_144delTCAATCTinsCCAAACC p.Ser48Thr NZ_LSIW01000097_63272_T_G 1 1 missense_variant MODERATE AX662_RS06615 WP_060972013.1 DUF3169 domain-containing protein Protein of unknown function (DUF3169) c.130A>C p.Ile44Leu NZ_LSIW01000097_63376_AATCTTTT_GATCGTTC 1 1 missense_variant MODERATE AX662_RS06615 WP_060972013.1 DUF3169 domain-containing protein Protein of unknown function (DUF3169) c.19_26delAAAAGATTinsGAACGATC p.LysArgPhe7GluArgSer NZ_LSIW01000097_63388_G_T 1 1 missense_variant MODERATE AX662_RS06615 WP_060972013.1 DUF3169 domain-containing protein Protein of unknown function (DUF3169) c.14C>A p.Pro5Gln NZ_LSIW01000097_63608_TC_GA 1 1 missense_variant MODERATE AX662_RS06620 WP_002885361.1 transcriptional regulator transcriptional c.5_6delGAinsTC p.Arg2Ile NZ_LSIW01000097_63688_GCCCT_CA 1 1 missense variant&disruptive inframe MODERATE AX662_RS06625 WP_060971969.1 hypothetical protein c.242_246delAGGGCinsTG p.Glu81_Gly82delinsVal NZ_LSIW01000097_63722_C_A 1 1 missense_variant MODERATE AX662_RS06625 WP_060971969.1 hypothetical protein c.212G>T p.Cys71Phe NZ_LSIW01000097_63735_C_T 1 1 missense_variant MODERATE AX662_RS06625 WP_060971969.1 hypothetical protein c.199G>A p.Glu67Lys

NZ_LSIW01000097_63765_T_C 1 1 missense_variant MODERATE AX662_RS06625 WP_060971969.1 hypothetical protein c.169A>G p.Ile57Val NZ_LSIW01000097_63838_TCGTC_CCCTT 1 1 missense_variant MODERATE AX662_RS06625 WP_060971969.1 hypothetical protein c.92_96delGACGAinsAAGGG p.ArgArg31LysGly NZ_LSIW01000097_80600_T_C 1 1 missense_variant MODERATE AX662_RS06710 WP_060972014.1 hypothetical protein Tetratricopeptide repeat c.952A>G p.Ser318Gly NZ_LSIW01000097_80974_C_A 1 1 missense_variant MODERATE AX662_RS06710 WP_060972014.1 hypothetical protein Tetratricopeptide repeat c.578G>T p.Ser193Ile NZ_LSIW01000097_81116_A_G 1 1 missense_variant MODERATE AX662_RS06710 WP_060972014.1 hypothetical protein Tetratricopeptide repeat c.436T>C p.Cys146Arg NZ_LSIW01000097_84156_T_G 1 1 missense_variant MODERATE AX662_RS06715 WP_060971982.1 beta-galactosidase #NAME? c.986A>C p.Lys329Thr NZ_LSIW01000101_4148_ATTCTCT_GTACTCC 1 1 1 missense_variant MODERATE AX662_RS07020 WP_060972023.1 Cardiolipin synthetase Hep Hag repeat protein c.528_534delAGAGAATinsGGAGTAC p.Asn178Tyr NZ_LSIW01000101_4295_GGCTGCTA_TGCTACTG 1 1 1 missense_variant MODERATE AX662_RS07020 WP_060972023.1 Cardiolipin synthetase Hep Hag repeat protein c.380_387delTAGCAGCCinsCAGTAGCA p.ValAla127AlaVal NZ_LSIW01000104_10375_C_T 1 1 missense_variant MODERATE AX662_RS07110 WP_060972035.1 TetR/AcrR family transcriptional regulator transcriptional regulator c.236G>A p.Gly79Glu NZ_LSIW01000104_1081_C_T 1 1 1 1 1 missense_variant MODERATE AX662_RS07050 WP_002885897.1 hypothetical protein Bacterial lipoprotein c.286C>T p.Pro96Ser NZ_LSIW01000104_11712_A_G 1 1 missense_variant MODERATE AX662_RS07115 WP_060972036.1 MFS transporter Major facilitator superfamily c.931A>G p.Ile311Val NZ_LSIW01000104_11719_A_G 1 1 missense_variant MODERATE AX662_RS07115 WP_060972036.1 MFS transporter Major facilitator superfamily c.938A>G p.Asp313Gly NZ_LSIW01000104_11823_G_C 1 1 missense_variant MODERATE AX662_RS07115 WP_060972036.1 MFS transporter Major facilitator superfamily c.1042G>C p.Glu348Gln NZ_LSIW01000104_12799_T_C 1 1 missense_variant MODERATE AX662_RS07120 DUF4767 domain-containing protein c.1247A>G p.Lys416Arg NZ_LSIW01000104_12835_T_C 1 1 stop_lost HIGH AX662_RS07120 DUF4767 domain-containing protein c.1211A>G p.Ter404Trpext*? NZ_LSIW01000104_1387_G_T 1 1 1 1 1 missense_variant MODERATE AX662_RS07055 WP_002886034.1 hypothetical protein c.73G>T p.Ala25Ser NZ_LSIW01000104_17918_C_G 1 1 missense_variant MODERATE AX662_RS07150 WP_060972040.1 DegV domain-containing protein EDD domain protein, DegV family c.436C>G p.Leu146Val NZ_LSIW01000104_17925_CT_GC 1 1 missense_variant MODERATE AX662_RS07150 WP_060972040.1 DegV domain-containing protein EDD domain protein, DegV family c.443_444delCTinsGC p.Ala148Gly NZ_LSIW01000104_21086_TA_GG 1 1 1 missense_variant MODERATE AX662_RS07165 WP_060972043.1 alpha/beta hydrolase hydrolases or acyltransferases (alpha beta hydrolase superfamily) c.330_331delTAinsCC p.Ile111Leu NZ_LSIW01000104_21114_TATATCG_AATTTCA 1 1 1 missense_variant MODERATE AX662_RS07165 WP_060972043.1 alpha/beta hydrolase hydrolases or acyltransferases (alpha beta hydrolase superfamily) c.297_303delCGATATAinsTGAAATT p.Asp100Glu NZ_LSIW01000104_21174_TAAAGCAAAT_GATTGCTAAC 1 1 missense_variant MODERATE AX662_RS07165 WP_060972043.1 alpha/beta hydrolase hydrolases or acyltransferases (alpha beta hydrolase superfamily) c.234_243delATTTGCTTTAinsGTTAGCAATC p.PheAlaLeu79LeuAlaIle NZ_LSIW01000104_21201_CT_TG 1 1 1 1 missense_variant MODERATE AX662_RS07165 WP_060972043.1 alpha/beta hydrolase hydrolases or acyltransferases (alpha beta hydrolase superfamily) c.215_216delAGinsCA p.Glu72Ala NZ_LSIW01000104_2175_A_T 1 1 1 1 1 missense_variant MODERATE AX662_RS07060 WP_048674351.1 CPBP family intramembrane metalloprotease CAAX protease self-immunity c.334T>A p.Ser112Thr NZ_LSIW01000104_2451_G_A 1 1 1 1 1 missense_variant MODERATE AX662_RS07060 WP_048674351.1 CPBP family intramembrane metalloprotease CAAX protease self-immunity c.58C>T p.Leu20Phe NZ_LSIW01000104_2460_T_A 1 1 1 1 1 missense_variant MODERATE AX662_RS07060 WP_048674351.1 CPBP family intramembrane metalloprotease CAAX protease self-immunity c.49A>T p.Thr17Ser NZ_LSIW01000104_3049_TTGG_CTGC 1 1 missense_variant MODERATE AX662_RS07070 WP_060972027.1 TetR/AcrR family transcriptional regulator TetR family transcriptional regulator c.537_540delCCAAinsGCAG p.Asp179Glu NZ_LSIW01000104_3204_G_C 1 1 missense_variant MODERATE AX662_RS07070 WP_060972027.1 TetR/AcrR family transcriptional regulator TetR family transcriptional regulator c.385C>G p.Arg129Gly NZ_LSIW01000104_9746_TG_GT 1 1 1 1 missense_variant MODERATE AX662_RS07105 WP_060972034.1 DUF4300 domain-containing protein Domain of unknown function (DUF4300) c.7_8delCAinsAC p.His3Thr NZ_LSIW01000109_116_ACTA_GCTT 1 1 missense_variant MODERATE AX662_RS07210 WP_082757403.1 amino acid ABC transporter permease ABC transporter (permease) c.509_512delTAGTinsAAGC p.LeuVal170GlnAla NZ_LSIW01000113_12011_A_G 1 1 missense_variant MODERATE AX662_RS07295 WP_060972052.1 [acyl-carrier-protein] S-malonyltransferase Malonyl CoA-acyl carrier protein transacylase c.158A>G p.Glu53Gly NZ_LSIW01000113_26835_CGACGG_TTACGA 1 1 missense_variant MODERATE AX662_RS07365 WP_060972058.1 bifunctional folylpolyglutamate synthase/dihydrofolate synthase Belongs to the folylpolyglutamate synthase family c.981_986delCCGTCGinsTCGTAA p.Arg329Lys NZ_LSIW01000113_34082_AGA_GGT 1 1 missense_variant MODERATE AX662_RS07395 WP_060972064.1 N-acetyltransferase acetyltransferase c.297_299delAGAinsGGT p.Glu100Val NZ_LSIW01000113_82998_T_C 1 1 1 missense_variant MODERATE AX662_RS07610 WP_060972090.1 hypothetical protein GBS Bsp-like repeat c.440T>C p.Val147Ala NZ_LSIW01000113_83337_G_A 1 1 1 missense_variant MODERATE AX662_RS07610 WP_060972090.1 hypothetical protein GBS Bsp-like repeat c.779G>A p.Ser260Asn NZ_LSIW01000113_83343_A_C 1 1 1 missense_variant MODERATE AX662_RS07610 WP_060972090.1 hypothetical protein GBS Bsp-like repeat c.785A>C p.Asn262Thr NZ_LSIW01000113_83366_AC_GT 1 1 1 missense_variant MODERATE AX662_RS07610 WP_060972090.1 hypothetical protein GBS Bsp-like repeat c.808_809delACinsGT p.Thr270Val NZ_LSIW01000133_147312_AAGATCG_GACATCA 1 1 1 1 missense_variant MODERATE AX662_RS08890 WP_060972218.1 ABC transporter permease ABC transporter c.267_273delCGATCTTinsTGATGTC p.Leu91Val NZ_LSIW01000133_1680_C_T 1 1 1 1 1 missense_variant MODERATE AX662_RS08170 WP_060972141.1 helicase Superfamily II DNA RNA helicase required for DNA uptake (late competence protein) c.1045G>A p.Glu349Lys NZ_LSIW01000133_19873_A_G 1 1 missense_variant MODERATE AX662_RS08255 WP_060972150.1 haloacid dehalogenase cation transport ATPase c.2659T>C p.Phe887Leu NZ_LSIW01000133_2592_G_A 1 1 1 1 missense_variant MODERATE AX662_RS08170 WP_060972141.1 helicase Superfamily II DNA RNA helicase required for DNA uptake (late competence protein) c.133C>T p.Arg45Trp NZ_LSIW01000133_26487_T_G 1 1 missense_variant MODERATE AX662_RS08270 peptidoglycan branched peptide synthesis protein c.625A>C p.Ile209Leu NZ_LSIW01000133_26492_G_T 1 1 missense_variant MODERATE AX662_RS08270 peptidoglycan branched peptide synthesis protein c.620C>A p.Ala207Asp NZ_LSIW01000133_26515_A_C 1 1 missense_variant MODERATE AX662_RS08270 peptidoglycan branched peptide synthesis protein c.597T>G p.Asp199Glu NZ_LSIW01000133_26561_T_A 1 1 stop_lost HIGH AX662_RS08270 peptidoglycan branched peptide synthesis protein c.551A>T p.Ter184Leuext*? NZ_LSIW01000133_26733_C_T 1 1 missense_variant MODERATE AX662_RS08270 peptidoglycan branched peptide synthesis protein c.379G>A p.Glu127Lys NZ_LSIW01000133_26828_A_G 1 1 missense_variant MODERATE AX662_RS08270 peptidoglycan branched peptide synthesis protein c.284T>C p.Val95Ala NZ_LSIW01000133_27056_T_C 1 1 missense_variant MODERATE AX662_RS08270 peptidoglycan branched peptide synthesis protein c.56A>G p.Asn19Ser NZ_LSIW01000133_5536_TCTTA_CCTTG 1 1 missense_variant MODERATE AX662_RS08190 WP_037600374.1 ABC transporter ATP-binding protein COG0410 ABC-type branched-chain amino acid transport systems, ATPase component c.546_550delTAAGAinsCAAGG p.Thr184Ala NZ_LSIW01000133_56174_G_A 1 1 1 1 missense_variant MODERATE AX662_RS08425 WP_060972166.1 16S rRNA (guanine(527)-N(7))-methyltransferase RsmG Ribosomal RNA small subunit methyltransferase G c.46G>A p.Asp16Asn NZ_LSIW01000133_7731_G_C 1 1 1 1 1 missense_variant MODERATE AX662_RS08200 WP_037600371.1 branched-chain amino acid ABC transporter permease Belongs to the binding-protein-dependent transport system permease family c.71C>G p.Ala24Gly NZ_LSIW01000133_78640_C_G 1 1 1 missense_variant MODERATE AX662_RS08545 WP_060972182.1 DUF4173 domain-containing protein Domain of unknown function (DUF4173) c.290C>G p.Ala97Gly NZ_LSIW01000142_5708_GG_CA 1 1 missense_variant MODERATE AX662_RS09190 WP_060972253.1 YSIRK signal domain/LPXTG anchor domain surface protein Glucan-binding protein C c.1230_1231delCCinsTG p.Gln411Glu NZ_LSIW01000142_5729_C_T 1 1 missense_variant MODERATE AX662_RS09190 WP_060972253.1 YSIRK signal domain/LPXTG anchor domain surface protein Glucan-binding protein C c.1210G>A p.Ala404Thr NZ_LSIW01000143_10252_AGCT_CATG 1 1 missense_variant MODERATE AX662_RS09290 WP_060972274.1 CPBP family intramembrane metalloprotease CAAX protease self-immunity c.693_696delAGCTinsCATG p.Ala232Met NZ_LSIW01000143_13378_AATATCC_GACGTCT 1 1 missense_variant MODERATE AX662_RS09305 WP_060972269.1 sugar O-acetyltransferase Maltose O-acetyltransferase c.264_270delGGATATTinsAGACGTC p.Ile90Val NZ_LSIW01000143_16216_TCT_GCC 1 1 missense_variant MODERATE AX662_RS09315 WP_060972271.1 glutamine amidotransferase domain protein c.2574_2576delAGAinsGGC p.Glu859Ala NZ_LSIW01000168_1840_C_T 1 1 1 missense_variant MODERATE AX662_RS09740 WP_003096870.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.1465G>A p.Val489Ile NZ_LSIW01000176_7229_A_G 1 1 missense_variant MODERATE AX662_RS10100 WP_060972357.1 DUF1934 domain-containing protein Domain of unknown function (DUF1934) c.67A>G p.Thr23Ala

Supplementary Table 10. SNPs and indels absent from between low inflammatory RA-associated S. parasalivarius isolates Home S. parasalivarius isolates S. salivarius CCH5-D3contig Position ReferenceAllele AlternateAllele 2.1 3.1 9.1 10.1 15.1 16.1 17.1 21.1 22.1 23.2 11.1 Class Risk Feature1 ProteinID Description EggNOG description Mutation Coding change NZ_LSIW01000003_25506_T_A 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS00150 WP 060971247.1 N-acetyltransferase COG1670 Acetyltransferases, including N-acetylases of ribosomal proteins c.72T>A p.Phe24Leu NZ_LSIW01000003_25544_C_T 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS00150 WP 060971247 1 N-acetyltransferase COG1670 Acetyltransferases, including N-acetylases of ribosomal proteins c.110C>T p.Thr37Ile NZ_LSIW01000011_25002_AA_TC 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS00315 WP 060971264 1 HAD family hydrolase Sucrose-6F-phosphate phosphohydrolase c.637_638delAAinsTC p.Asn213Ser NZ_LSIW01000011_25008_GCA_TCC 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS00315 WP 060971264.1 HAD family hydrolase Sucrose-6F-phosphate phosphohydrolase c.643_645delGCAinsTCC p.Ala215Ser NZ_LSIW01000011_25044_A_C 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS00315 WP 060971264 1 HAD family hydrolase Sucrose-6F-phosphate phosphohydrolase c.679A>C p.Ile227Leu NZ_LSIW01000012_3931_AGTCC_GGTCA 1 1 1 1 1 1 missense_variant MODERATE AX662 RS00425 WP 060971283 1 N-acetyltransferase COG0454 Histone acetyltransferase HPA2 and related acetyltransferases c.486_490delGGACTinsTGACC p.Cys164Arg NZ_LSIW01000012_3961_T_C 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS00425 WP 060971283.1 N-acetyltransferase COG0454 Histone acetyltransferase HPA2 and related acetyltransferases c.460A>G p.Asn154Asp NZ_LSIW01000012_4147_C_G 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS00425 WP 060971283 1 N-acetyltransferase COG0454 Histone acetyltransferase HPA2 and related acetyltransferases c.274G>C p.Glu92Gln NZ_LSIW01000012_4178_GGCAAATCCG_AGCAGAACCT 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS00425 WP 060971283 1 N-acetyltransferase COG0454 Histone acetyltransferase HPA2 and related acetyltransferases c.234_243delCGGATTTGCCinsAGGTTCTGCT p.Phe80Ser NZ_LSIW01000012_4317_GCC_TCT 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS00425 WP 060971283.1 N-acetyltransferase COG0454 Histone acetyltransferase HPA2 and related acetyltransferases c.102_104delGGCinsAGA p.Ala35Asp NZ_LSIW01000012_5630_A_G 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS10200 hypothetical protein c.56T>C p.Leu19Ser NZ_LSIW01000012_5659_CGG_TGA 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS10200 hypothetical protein c.25_27delCCGinsTCA p.Pro9Ser NZ_LSIW01000023_1200_AA_GC 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS00550 WP 021143879.1 pyridoxal 5'-phosphate synthase glutaminase subunit PdxT Catalyzes the hydrolysis of glutamine to glutamate and ammonia as part of the biosynthesis of pyrc.64_65delAAinsGC p.Lys22Ala NZ_LSIW01000026_17550_C_T 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS00645 WP 048676088 1 hypothetical protein c.290C>T p.Thr97Ile NZ_LSIW01000026_19761_GAATT_AAATC 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS00655 WP 060971302 1 pyridine nucleotide-disulfide oxidoreductase Belongs to the class-I pyridine nucleotide-disulfide oxidoreductase family c.1160_1164delGAATTinsAAATC p.Gly387Glu NZ_LSIW01000026_6023_G_A 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS00590 WP 060971294.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.212G>A p.Arg71His NZ_LSIW01000028_17581_A_G 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS00935 WP 060971347.1 lysozyme family protein lytic transglycosylase activity c.82A>G p.Ile28Val NZ_LSIW01000028_19326_GG_AA 1 1 1 1 1 1 missense_variant MODERATE AX662 RS00940 WP 060971348 1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.1185_1186delGGinsAA p.Asp396Asn NZ_LSIW01000028_19333_A_C 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS00940 WP 060971348.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.1192A>C p.Lys398Gln NZ_LSIW01000028_19343_G_A 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS00940 WP 060971348 1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.1202G>A p.Arg401Lys NZ_LSIW01000028_54364_GCG_TCT 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS01095 WP 060971363 1 bifunctional DnaQ family exonuclease/ATP-dependent helicase helicase involved in DNA repair and perhaps also replication c.685_687delGCGinsTCT p.Ala229Ser NZ_LSIW01000028_54437_G_A 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS01095 WP 060971363.1 bifunctional DnaQ family exonuclease/ATP-dependent helicase helicase involved in DNA repair and perhaps also replication c.758G>A p.Arg253Lys NZ_LSIW01000028_54543_AGCACAAGCC_GGCGCAATCT 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS01095 WP 060971363 1 bifunctional DnaQ family exonuclease/ATP-dependent helicase helicase involved in DNA repair and perhaps also replication c.864_873delAGCACAAGCCinsGGCGCAATCT p.Ala291Ser NZ_LSIW01000028_55121_CCTTA_GCTTG 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS01095 WP 060971363 1 bifunctional DnaQ family exonuclease/ATP-dependent helicase helicase involved in DNA repair and perhaps also replication c.1442_1446delCCTTAinsGCTTG p.Thr481Ser NZ_LSIW01000028_59655_T_C 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS01115 WP 060971364.1 hypothetical protein c.254T>C p.Phe85Ser NZ_LSIW01000028_9135_C_T 1 1 1 1 1 1 missense_variant MODERATE AX662 RS00890 WP 060971339 1 bifunctional oligoribonuclease/PAP phosphatase NrnA domain protein c.667G>A p.Val223Ile NZ_LSIW01000034_1257_G_A 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS01155 WP 060971368 1 glucosyl transferase dextransucrase activity c.1219G>A p.Val407Ile NZ_LSIW01000036_32745_A_T 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS01330 WP 060971395.1 hypothetical protein Psort location CytoplasmicMembrane, score c.361A>T p.Ile121Phe NZ_LSIW01000036_33101_G_A 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS01335 WP 060971396 1 ABC transporter permease cobalt transport c.118G>A p.Ala40Thr NZ_LSIW01000036_33937_G_A 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS01340 WP 060971397 1 ABC transporter ATP-binding protein ABC transporter c.184G>A p.Val62Met NZ_LSIW01000036_35605_AT_A 1 1 1 1 1 1 1 1 frameshift_variant HIGH AX662_RS01350 nicotinamide mononucleotide transporter c.78delT p.His27fs NZ_LSIW01000036_35625_A_G 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS01350 nicotinamide mononucleotide transporter c.94A>G p.Asn32Asp NZ_LSIW01000036_35658_G_A 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS01350 nicotinamide mononucleotide transporter c.127G>A p.Val43Ile NZ_LSIW01000036_35688_C_T 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS01350 nicotinamide mononucleotide transporter c.157C>T p.Pro53Ser NZ_LSIW01000036_35722_T_C 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS01350 nicotinamide mononucleotide transporter c.191T>C p.Leu64Pro NZ_LSIW01000036_35734_GTG_ATA 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS01350 nicotinamide mononucleotide transporter c.203_205delGTGinsATA p.CysAla68TyrThr NZ_LSIW01000037_10144_G_A 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS01485 WP 060971419.1 type I restriction endonuclease subunit R Subunit R is required for both nuclease and ATPase activities, but not for modification c.1151G>A p.Gly384Glu NZ_LSIW01000037_10689_G_A 1 1 1 1 1 1 missense_variant MODERATE AX662 RS01485 WP 060971419.1 type I restriction endonuclease subunit R Subunit R is required for both nuclease and ATPase activities, but not for modification c.1696G>A p.Val566Met NZ_LSIW01000037_10735_G_A 1 1 1 1 1 1 missense_variant MODERATE AX662 RS01485 WP 060971419 1 type I restriction endonuclease subunit R Subunit R is required for both nuclease and ATPase activities, but not for modification c.1742G>A p.Gly581Asp NZ_LSIW01000037_134063_G_A 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS02015 WP 060971482.1 N-acetyltransferase acetyltransferase c.33G>A p.Met11Ile NZ_LSIW01000037_134259_C_T 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS02015 WP 060971482 1 N-acetyltransferase acetyltransferase c.229C>T p.His77Tyr NZ_LSIW01000037_15996_TG_CT 1 1 1 1 1 1 missense_variant MODERATE AX662 RS01510 WP 060971424 1 hypothetical protein Phage derived protein Gp49-like (DUF891) c.238_239delTGinsCT p.Trp80Leu NZ_LSIW01000037_16434_T_A 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS01520 WP 060971425.1 type I restriction-modification system subunit M type I restriction-modification system c.6T>A p.Asp2Glu NZ_LSIW01000037_17876_G_A 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS01520 WP 060971425.1 type I restriction-modification system subunit M type I restriction-modification system c.1448G>A p.Gly483Glu NZ_LSIW01000037_3354_A_T 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS01450 WP 022495771 1 aminoacyl-tRNA deacylase Belongs to the prolyl-tRNA editing family. YbaK EbsC subfamily c.60T>A p.Asn20Lys NZ_LSIW01000037_4124_T_A 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS01455 WP 060971414.1 N-acetylmuramoyl-L-alanine amidase Glycosyl hydrolase, family 25 c.305A>T p.Gln102Leu NZ_LSIW01000037_4146_TA_CG 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS01455 WP 060971414 1 N-acetylmuramoyl-L-alanine amidase Glycosyl hydrolase, family 25 c.282_283delTAinsCG p.Ile95Val NZ_LSIW01000037_4302_G_T 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS01455 WP 060971414 1 N-acetylmuramoyl-L-alanine amidase Glycosyl hydrolase, family 25 c.127C>A p.Leu43Ile NZ_LSIW01000037_50023_GCTGC_ACTGA 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS01675 WP 060971439.1 RNA-binding protein conserved protein, contains S4-like domain c.336_340delGCTGCinsACTGA p.Leu114Ile NZ_LSIW01000037_5883_G_A 1 1 1 1 1 1 missense_variant MODERATE AX662 RS01465 WP 060971416 1 Cof-type HAD-IIB family hydrolase hydrolase c.724G>A p.Val242Ile NZ_LSIW01000037_5937_A_G 1 1 1 1 1 1 missense_variant MODERATE AX662 RS01465 WP 060971416 1 Cof-type HAD-IIB family hydrolase hydrolase c.778A>G p.Ile260Val NZ_LSIW01000037_5997_A_C 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS01465 WP 060971416.1 Cof-type HAD-IIB family hydrolase hydrolase c.838A>C p.Lys280Gln NZ_LSIW01000037_6104_GA_AG 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS01470 WP 021144400.1 hypothetical protein COG2141 Coenzyme F420-dependent N5,N10-methylene tetrahydromethanopterin reductase and c.560_561delTCinsCT p.Val187Ala NZ_LSIW01000037_7393_T_C 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS01475 WP 060971417 1 DUF2974 domain-containing protein Protein of unknown function (DUF2974) c.619T>C p.Ser207Pro NZ_LSIW01000037_93091_C_T 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS01850 hypothetical protein c.881C>T p.Ala294Val NZ_LSIW01000051_31633_T_G 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS02445 WP 014633793 1 hypothetical protein c.478T>G p.Phe160Val NZ_LSIW01000052_1043_TAGT_AAGA 1 1 1 1 1 1 missense_variant MODERATE AX662 RS02540 WP 060971539 1 transcriptional regulator sequence-specific DNA binding c.873_876delACTAinsTCTT p.Lys291Asn NZ_LSIW01000052_1063_C_G 1 1 1 1 missense_variant MODERATE AX662 RS02540 WP 060971539.1 transcriptional regulator sequence-specific DNA binding c.856G>C p.Glu286Gln NZ_LSIW01000052_2144_GATTT_AATTA 1 1 1 1 1 1 missense_variant MODERATE AX662 RS02545 WP 060971540.1 RDD family protein RDD family c.27_31delGATTTinsAATTA p.Leu11Ile NZ_LSIW01000052_2210_TATTA_CATTC 1 1 1 1 1 1 missense_variant MODERATE AX662 RS02545 WP 060971540 1 RDD family protein RDD family c.93_97delTATTAinsCATTC p.Ile33Leu NZ_LSIW01000052_2227_C_T 1 1 1 1 1 1 missense_variant MODERATE AX662 RS02545 WP 060971540.1 RDD family protein RDD family c.110C>T p.Ala37Val NZ_LSIW01000052_2241_G_A 1 1 1 1 1 1 missense_variant MODERATE AX662 RS02545 WP 060971540 1 RDD family protein RDD family c.124G>A p.Gly42Ser NZ_LSIW01000052_2406_C_G 1 1 1 1 1 1 missense_variant MODERATE AX662 RS02545 WP 060971540 1 RDD family protein RDD family c.289C>G p.Gln97Glu NZ_LSIW01000052_2504_TTTC_CTTA 1 1 1 1 1 1 missense_variant MODERATE AX662 RS02545 WP 060971540.1 RDD family protein RDD family c.387_390delTTTCinsCTTA p.Phe130Leu NZ_LSIW01000052_2569_CCT_TGC 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS02545 WP 060971540 1 RDD family protein RDD family c.452_454delCCTinsTGC p.Ser151Leu NZ_LSIW01000052_2627_ACA_CCG 1 1 1 1 1 1 missense_variant MODERATE AX662 RS02545 WP 060971540 1 RDD family protein RDD family c.510_512delACAinsCCG p.His171Arg NZ_LSIW01000052_3639_C_T 1 1 1 1 1 1 missense_variant MODERATE AX662 RS02550 WP 048675419.1 multidrug resistance efflux transporter family protein membrane c.859C>T p.Leu287Phe NZ_LSIW01000052_397_GTA_G 1 1 1 1 1 1 frameshift_variant HIGH AX662_RS10255 NAD(P)H oxidoreductase c.230_231delTA p.Ile77fs NZ_LSIW01000052_7453_AG_CT 1 1 1 1 1 1 missense_variant MODERATE AX662 RS02555 WP 060971541 1 glycosyl hydrolase family 32 Belongs to the glycosyl hydrolase 32 family c.3498_3499delAGinsCT p.Ala1167Ser NZ_LSIW01000052_7466_A_C 1 1 1 1 1 1 missense_variant MODERATE AX662 RS02555 WP 060971541.1 glycosyl hydrolase family 32 Belongs to the glycosyl hydrolase 32 family c.3511A>C p.Lys1171Gln NZ_LSIW01000054_189_CAGC_TAGA 1 1 1 1 1 1 missense_variant MODERATE AX662 RS02585 WP 060971543 1 hypothetical protein c.38_41delCAGCinsTAGA p.AlaAla13ValGlu NZ_LSIW01000054_251_AA_GC 1 1 1 1 1 1 missense_variant MODERATE AX662 RS02585 WP 060971543 1 hypothetical protein c.100_101delAAinsGC p.Asn34Ala NZ_LSIW01000054_34_TAAGT_CAAGC 1 1 1 1 1 1 stop_lost HIGH AX662 RS10270 WP 082757387.1 deoxyribodipyrimidine photolyase Pyrimidine dimer DNA glycosylase c.34_38delTAAGTinsCAAGC p.TerVal12GlnAlaext*? NZ_LSIW01000054_70_CCCA_TCCT 1 1 1 1 1 1 stop_gained HIGH AX662 RS10270 WP 082757387.1 deoxyribodipyrimidine photolyase Pyrimidine dimer DNA glycosylase c.70_73delCCCAinsTCCT p.ProArg24* NZ_LSIW01000054_83_GCT_ACC 1 1 1 1 1 1 missense_variant MODERATE AX662 RS10270 WP 082757387 1 deoxyribodipyrimidine photolyase Pyrimidine dimer DNA glycosylase c.83_85delGCTinsACC p.CysCys28TyrArg NZ_LSIW01000058_113652_A_C 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS03360 WP 060971609.1 putative sulfate exporter family transporter membrane c.595T>G p.Ser199Ala NZ_LSIW01000058_114063_C_A 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS03360 WP 060971609.1 putative sulfate exporter family transporter membrane c.184G>T p.Ala62Ser NZ_LSIW01000058_114209_G_A 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS03360 WP 060971609 1 putative sulfate exporter family transporter membrane c.38C>T p.Ala13Val NZ_LSIW01000058_114664_G_T 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS03365 WP 014635150.1 XRE family transcriptional regulator sequence-specific DNA binding c.410C>A p.Pro137Gln NZ_LSIW01000058_114678_C_A 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS03365 WP 014635150.1 XRE family transcriptional regulator sequence-specific DNA binding c.396G>T p.Met132Ile NZ_LSIW01000058_115687_A_G 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS03375 WP 048788676 1 replication initiation protein Replication initiation factor c.167A>G p.Lys56Arg NZ_LSIW01000058_115961_T_A 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS03375 WP 048788676.1 replication initiation protein Replication initiation factor c.441T>A p.Asp147Glu NZ_LSIW01000058_118913_A_G 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS03400 WP 060971610 1 replication-associated recombination protein A ATPase related to the helicase subunit of the Holliday junction resolvase c.637T>C p.Phe213Leu NZ_LSIW01000058_131256_CACGC_TACGT 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS03465 WP 060971619 1 histidine--tRNA ligase histidyl-tRNA synthetase c.720_724delGCGTGinsACGTA p.Ala242Thr NZ_LSIW01000058_132849_T_C 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS10305 PTS beta-glucoside transporter subunit IIABC c.455A>G p.Glu152Gly NZ_LSIW01000058_147865_T_C 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS03575 WP 013991330.1 DHH family phosphoesterase signaling protein consisting of a modified GGDEF domain and a DHH domain c.1195A>G p.Ile399Val NZ_LSIW01000060_59258_A_T 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS03965 WP 060971674 1 helicase-exonuclease AddAB subunit AddA ATP-dependent helicase nuclease subunit A c.1650T>A p.Asp550Glu NZ_LSIW01000060_67728_TAAG_ACTA 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS03985 WP 060971678.1 hypothetical protein c.1470_1473delCTTAinsTAGT p.Leu491Ser NZ_LSIW01000060_69603_TGGGACTCC_AGGAACATG 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS03995 WP 004183421 1 serine/threonine protein kinase c.676_684delGGAGTCCCAinsCATGTTCCT p.Gly226His NZ_LSIW01000060_69689_T_C 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS03995 WP 004183421 1 serine/threonine protein kinase c.598A>G p.Ile200Val NZ_LSIW01000060_84321_A_C 1 1 1 1 1 1 missense_variant MODERATE AX662 RS04065 WP 060971724.1 DNA helicase RecG Critical role in recombination and DNA repair. Helps process Holliday junction intermediates to matc.909T>G p.Phe303Leu NZ_LSIW01000060_9053_C_T 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS03715 WP 060971647 1 sodium:proton antiporter NhaP-type Na H and K H antiporters c.67G>A p.Val23Ile NZ_LSIW01000060_92372_C_T 1 1 1 1 1 1 missense_variant MODERATE AX662 RS04100 WP 060971692 1 mannose-6-phosphate isomerase, class I mannose-6-phosphate isomerase c.670G>A p.Val224Ile NZ_LSIW01000069_19668_A_C 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS04555 WP 060971742.1 TIGR02206 family membrane protein Integral membrane protein (intg_mem_TP0381) c.457A>C p.Lys153Gln NZ_LSIW01000069_3020_AG_CC 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS04470 WP 002951622 1 type 1 glutamine amidotransferase anthranilate c.101_102delAGinsCC p.Lys34Thr NZ_LSIW01000072_56496_C_A 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05005 WP 082757395 1 dihydroorotate dehydrogenase electron transfer subunit Responsible for channeling the electrons from the oxidation of dihydroorotate from the FMN redox c.7G>T p.Val3Phe NZ_LSIW01000072_57333_G_T 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05010 WP 060971790.1 DJ-1 family protein DJ-1 family c.30C>A p.Asp10Glu NZ_LSIW01000072_57676_G_A 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05015 WP 060971791 1 hypothetical protein TraX protein c.620C>T p.Ala207Val NZ_LSIW01000072_57812_GGAG_CGAT 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05015 WP 060971791 1 hypothetical protein TraX protein c.481_484delCTCCinsATCG p.LeuLeu161IleVal NZ_LSIW01000072_58160_C_A 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05015 WP 060971791.1 hypothetical protein TraX protein c.136G>T p.Ala46Ser NZ_LSIW01000072_68151_CGGCA_TGGGC 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05050 WP 060971797.1 hypothetical protein Psort location CytoplasmicMembrane, score c.72_76delCGGCAinsTGGGC p.Ile26Leu NZ_LSIW01000072_68175_AC_GT 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05050 WP 060971797 1 hypothetical protein Psort location CytoplasmicMembrane, score c.96_97delACinsGT p.Leu33Phe NZ_LSIW01000072_68259_TGT_GGC 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05050 WP 060971797.1 hypothetical protein Psort location CytoplasmicMembrane, score c.180_182delTGTinsGGC p.Val61Ala NZ_LSIW01000072_68633_AACCG_GGCCT 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05050 WP 060971797 1 hypothetical protein Psort location CytoplasmicMembrane, score c.554_558delAACCGinsGGCCT p.Lys185Arg NZ_LSIW01000072_68771_A_G 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05050 WP 060971797 1 hypothetical protein Psort location CytoplasmicMembrane, score c.692A>G p.Lys231Arg NZ_LSIW01000072_68807_T_C 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05050 WP 060971797.1 hypothetical protein Psort location CytoplasmicMembrane, score c.728T>C p.Val243Ala NZ_LSIW01000072_68884_ATGTCACTC_TTGACTCTG 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05050 WP 060971797 1 hypothetical protein Psort location CytoplasmicMembrane, score c.805_813delATGTCACTCinsTTGACTCTG p.MetSer269LeuThr NZ_LSIW01000072_69398_C_T 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05050 WP 060971797 1 hypothetical protein Psort location CytoplasmicMembrane, score c.1319C>T p.Ala440Val NZ_LSIW01000072_69608_TGCA_GGCG 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05050 WP 060971797.1 hypothetical protein Psort location CytoplasmicMembrane, score c.1529_1532delTGCAinsGGCG p.MetGln510ArgArg NZ_LSIW01000072_70212_G_A 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05055 WP 060971798 1 MATE family efflux transporter Mate efflux family protein c.538G>A p.Val180Ile NZ_LSIW01000073_41_A_T 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS05100 fibronectin-binding protein c.41A>T p.Tyr14Phe NZ_LSIW01000077_12571_TT_CA 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05175 WP 037611854.1 large conductance mechanosensitive channel protein MscL Channel that opens in response to stretch forces in the membrane lipid bilayer. May participate in tc.105_106delAAinsTG p.Ser36Gly NZ_LSIW01000077_61825_T_A 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05410 WP 060971841 1 primosomal protein N' Involved in the restart of stalled replication forks Recognizes and binds the arrested nascent DNA cc.18T>A p.His6Gln NZ_LSIW01000077_61876_GGTACCG_TATCCCT 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05410 WP 060971841 1 primosomal protein N' Involved in the restart of stalled replication forks Recognizes and binds the arrested nascent DNA cc.69_75delGGTACCGinsTATCCCT p.Val24Ile NZ_LSIW01000081_22112_A_T 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05560 WP 060971856.1 MFS transporter c.662T>A p.Leu221Gln NZ_LSIW01000081_22123_ATCGT_GTTGC 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05560 WP 060971856 1 MFS transporter c.647_651delACGATinsGCAAC p.HisAsp216ArgAsn NZ_LSIW01000081_25112_C_T 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05575 WP 060971859 1 ABC transporter ATP-binding protein AAA domain, putative AbiEii toxin, Type IV TA system c.191G>A p.Gly64Asp NZ_LSIW01000081_27288_CTACA_TTACG 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05590 WP 060971862.1 hypothetical protein c.492_496delTGTAGinsCGTAA p.Gly166Ser NZ_LSIW01000081_29186_C_T 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05600 WP 060971864 1 PTS beta-glucoside transporter subunit EIIBCA pts system c.1582G>A p.Ala528Thr NZ_LSIW01000081_42448_A_C 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05645 WP 060971869 1 cell surface protein amidase activity c.303T>G p.Asn101Lys NZ_LSIW01000081_42498_A_C 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05645 WP 060971869.1 cell surface protein amidase activity c.253T>G p.Ser85Ala NZ_LSIW01000081_42504_T_G 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05645 WP 060971869 1 cell surface protein amidase activity c.247A>C p.Lys83Gln NZ_LSIW01000081_42567_G_A 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05645 WP 060971869 1 cell surface protein amidase activity c.184C>T p.Pro62Ser NZ_LSIW01000081_42605_ACTC_GCCT 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05645 WP 060971869.1 cell surface protein amidase activity c.143_146delGAGTinsAGGC p.ArgVal48LysAla NZ_LSIW01000081_50650_GC_AA 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS05700 WP 060971876 1 dTMP kinase Phosphorylation of dTMP to form dTDP in both de novo and salvage pathways of dTTP synthesis c.384_385delGCinsTT p.His129Tyr NZ_LSIW01000091_1709_T_C 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS10360 ISL3 family transposase c.142A>G p.Ile48Val NZ_LSIW01000092_24946_AAT_GGC 1 1 1 1 1 1 missense_variant MODERATE AX662 RS06025 WP 060971905.1 nucleotidyltransferase Belongs to the UPF0348 family c.781_783delATTinsGCC p.Ile261Ala NZ_LSIW01000093_122_C_T 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS06180 WP 082757398 1 amino acid ABC transporter permease ABC transporter (permease) c.506G>A p.Ser169Asn NZ_LSIW01000094_19564_TGCC_AGCT 1 1 1 1 1 1 1 1 stop_gained HIGH AX662_RS06290 cell surface-associated protein c.773_776delGGCAinsAGCT p.TrpGln258* NZ_LSIW01000094_5188_A_T 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS06210 WP 004182627.1 tRNA (adenosine(37)-N6)-dimethylallyltransferase MiaA Catalyzes the transfer of a dimethylallyl group onto the adenine at position 37 in tRNAs that read cc.858T>A p.His286Gln NZ_LSIW01000097_11653_G_T 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS06365 WP 060971943 1 histidine kinase Histidine kinase c.400C>A p.Leu134Met NZ_LSIW01000097_123537_AGGGG_GGGAC 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS06875 WP 060972006 1 M13 family peptidase Peptidase family M13 c.530_534delCCCCTinsGTCCC p.Thr177Ser NZ_LSIW01000097_12444_TACGAT_CACTAG 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS06370 WP 060971944.1 ABC transporter permease ABC-2 type transporter c.334_339delATCGTAinsCTAGTG p.Ile112Leu NZ_LSIW01000097_131904_GG_TT 1 1 1 1 1 missense_variant MODERATE AX662 RS06905 WP 060972010 1 hypothetical protein c.82_83delCCinsAA p.Pro28Lys NZ_LSIW01000097_2673_C_T 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS06325 WP 060971935 1 antibiotic ABC transporter permease ABC-2 family transporter protein c.397G>A p.Val133Ile NZ_LSIW01000097_58116_C_G 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS06590 WP 060971965.1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.631G>C p.Glu211Gln NZ_LSIW01000097_58407_G_T 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS06590 WP 060971965 1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.340C>A p.Gln114Lys NZ_LSIW01000097_58424_T_C 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS06590 WP 060971965 1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.323A>G p.Asn108Ser NZ_LSIW01000097_58822_TGG_AGA 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS06595 WP 060971966.1 TetR family transcriptional regulator WHG domain c.495_497delCCAinsTCT p.Gln166Leu NZ_LSIW01000097_58932_A_T 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS06595 WP 060971966 1 TetR family transcriptional regulator WHG domain c.387T>A p.Asp129Glu NZ_LSIW01000097_60234_TT_CA 1 1 1 1 missense_variant MODERATE AX662 RS06600 WP 060971967 1 aldo/keto reductase Aldo keto reductase c.156_157delAAinsTG p.Asn53Asp NZ_LSIW01000099_491_CGT_TGC 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS06930 choline-binding protein c.307_309delACGinsGCA p.Thr103Ala NZ_LSIW01000099_499_T_C 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS06930 choline-binding protein c.301A>G p.Thr101Ala NZ_LSIW01000100_1379_CGCTG_TGCTA 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS06935 WP 060972016 1 GHKL domain-containing protein GHKL domain c.1221_1225delCAGCGinsTAGCA p.Val409Ile NZ_LSIW01000103_338_C_T 1 1 1 1 1 missense_variant MODERATE AX662_RS07035 ISL3 family transposase c.329C>T p.Ala110Val NZ_LSIW01000103_361_GTA_ATG 1 1 1 1 1 missense_variant MODERATE AX662_RS07035 ISL3 family transposase c.352_354delGTAinsATG p.Val118Met NZ_LSIW01000104_20094_T_G 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS07160 WP 060972042 1 DUF4336 domain-containing protein Domain of unknown function (DUF4336) c.514A>C p.Ile172Leu NZ_LSIW01000104_20156_T_G 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS07160 WP 060972042.1 DUF4336 domain-containing protein Domain of unknown function (DUF4336) c.452A>C p.Asn151Thr NZ_LSIW01000104_20866_T_C 1 1 1 1 1 1 missense_variant MODERATE AX662 RS07165 WP 060972043 1 alpha/beta hydrolase hydrolases or acyltransferases (alpha beta hydrolase superfamily) c.551A>G p.Glu184Gly NZ_LSIW01000104_20878_TTAT_GAAG 1 1 1 1 1 1 missense_variant MODERATE AX662 RS07165 WP 060972043 1 alpha/beta hydrolase hydrolases or acyltransferases (alpha beta hydrolase superfamily) c.536_539delATAAinsCTTC p.TyrLys179SerSer NZ_LSIW01000104_20932_T_A 1 1 1 1 1 1 missense_variant MODERATE AX662 RS07165 WP 060972043.1 alpha/beta hydrolase hydrolases or acyltransferases (alpha beta hydrolase superfamily) c.485A>T p.Tyr162Phe NZ_LSIW01000104_21045_C_A 1 1 1 1 1 1 missense_variant MODERATE AX662 RS07165 WP 060972043 1 alpha/beta hydrolase hydrolases or acyltransferases (alpha beta hydrolase superfamily) c.372G>T p.Leu124Phe NZ_LSIW01000104_44_CCGC_TCGT 1 1 1 1 1 1 missense_variant MODERATE AX662_RS07040 hypothetical protein c.184_187delGCGGinsACGA p.AlaGlu62ThrLys NZ_LSIW01000113_27277_AG_CA 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS07365 WP 060972058.1 bifunctional folylpolyglutamate synthase/dihydrofolate synthase Belongs to the folylpolyglutamate synthase family c.543_544delCTinsTG p.Ser182Ala NZ_LSIW01000113_34017_AAA_GAG 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS07395 WP 060972064 1 N-acetyltransferase acetyltransferase c.232_234delAAAinsGAG p.Lys78Glu NZ_LSIW01000113_86403_A_T 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS07620 WP 060972092 1 hypothetical protein c.199A>T p.Thr67Ser NZ_LSIW01000113_86536_A_AAGTTGGAGG 1 1 1 1 1 1 1 1 disruptive inframe inse MODERATE AX662 RS07620 WP 060972092.1 hypothetical protein c.337_338insGAGGAGTTG p.Val112_Glu113insGlyGlyVal NZ_LSIW01000114_1857_A_G 1 1 1 1 1 1 missense_variant MODERATE AX662 RS07625 WP 060972095 1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.1651A>G p.Ile551Val NZ_LSIW01000114_2310_CA_TG 1 1 1 1 1 1 missense_variant MODERATE AX662 RS07630 WP 060972096 1 ABC transporter ATP-binding protein abc transporter atp-binding protein c.369_370delCAinsTG p.Thr124Ala NZ_LSIW01000133_140820_C_A 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS08860 WP 060972215.1 RluA family pseudouridine synthase Responsible for synthesis of pseudouridine from uracil c.810C>A p.Asp270Glu NZ_LSIW01000133_145681_C_T 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS08890 WP 060972218 1 ABC transporter permease ABC transporter c.1904G>A p.Arg635Lys NZ_LSIW01000133_34021_TCCCGC_GCCCAG 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS08310 WP 060972156 1 LytR family transcriptional regulator Transcriptional c.1073_1078delGCGGGAinsCTGGGC p.GlyGlyThr358AlaGlyPro NZ_LSIW01000133_57800_T_C 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS08430 WP 079119914.1 ATPase V COG0168 Trk-type K transport systems, membrane components c.890T>C p.Val297Ala NZ_LSIW01000133_78972_G_C 1 1 1 1 1 1 missense_variant MODERATE AX662 RS08545 WP 060972182 1 DUF4173 domain-containing protein Domain of unknown function (DUF4173) c.622G>C p.Val208Leu NZ_LSIW01000137_3174_G_A 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS08950 serine protease c.3173G>A p.Arg1058Lys NZ_LSIW01000137_4207_T_A 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS08950 serine protease c.4206T>A p.Ser1402Arg NZ_LSIW01000137_6197_T_G 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662_RS08950 serine protease c.6196T>G p.Cys2066Gly NZ_LSIW01000138_136_GGT_AGC 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS08955 WP 060972226 1 IS30 family transposase Integrase c.826_828delACCinsGCT p.Thr276Ala NZ_LSIW01000143_13550_ATTTGG_CATTGT 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS09305 WP 060972269.1 sugar O-acetyltransferase Maltose O-acetyltransferase c.93_98delCCAAATinsACAATG p.AsnGlnMet31LysGlnTrp NZ_LSIW01000143_13564_GGATTTAGCT_TGAGCTGGCC 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS09305 WP 060972269 1 sugar O-acetyltransferase Maltose O-acetyltransferase c.75_84delAGCTAAATCCinsGGCCAGCTCA p.Lys27Ser NZ_LSIW01000143_13612_C_G 1 1 1 1 1 1 1 1 1 missense_variant MODERATE AX662 RS09305 WP 060972269 1 sugar O-acetyltransferase Maltose O-acetyltransferase c.36G>C p.Glu12Asp

Supplementary Table 11. Encoded proteins conserved between low inflammatory RA-associated S. parasalivarius isolates Home S. parasalivarius isolates S. salivarius Annotation 2.1 3.1 9.1 10.1 15.1 16.1 17.1 21.1 22.1 23.2 11.1 EggNOG description (21.1) COG code (21.1) Bacterial regulatory proteins, tetR family EKMIGMNK_00061 JFMDMGNA_02023 transcriptional regulator K Transcription Multidrug resistance protein Stp EKMIGMNK_00062 JFMDMGNA_01091 Major facilitator superfamily P Inorganic ion transport and metabolism tRNA-Glu(ttc) BKLDJMND_01948 KDGOJIBD_01950 EKMIGMNK_00360 JFMDMGNA_01981 hypothetical protein EKMIGMNK_00584 JFMDMGNA_00868 NOHGDGDB_00211 hypothetical protein EKMIGMNK_00712 JFMDMGNA_00131 hypothetical protein EKMIGMNK_00718 JFMDMGNA_00126 NOHGDGDB_01451฀NOHGDGDB_01450 Aminoacyltransferase FemB EKMIGMNK_01228 JFMDMGNA_00694 protein involved in methicillin resistance V Defense mechanisms hypothetical protein EKMIGMNK_01251 JFMDMGNA_01178 Glycosyl transferase family 2 EKMIGMNK_01252 JFMDMGNA_01177 Glycosyltransferase group 2 family protein S Function unknown hypothetical protein EKMIGMNK_01253 JFMDMGNA_01176 Uncharacterized conserved protein (DUF2304) S Function unknown Polyprenol monophosphomannose synthase EKMIGMNK_01254 JFMDMGNA_01175 group 2 family protein M Cell wall/membrane/envelope biogenesis putative glycosyltransferase EpsJ EKMIGMNK_01256 JFMDMGNA_01173 Glycosyltransferase, group 2 family protein M Cell wall/membrane/envelope biogenesis Glucosyl transferase GtrII EKMIGMNK_01259 JFMDMGNA_01170 Glucosyl transferase GtrII S Function unknown hypothetical protein BKLDJMND_01158 KDGOJIBD_00683 EKMIGMNK_01272 JFMDMGNA_01157 hypothetical protein EKMIGMNK_01363 JFMDMGNA_00824 NOHGDGDB_00177 putative glycosyltransferase EpsJ MKKDFLNB_00845 EKMIGMNK_01455 JFMDMGNA_00521 NOHGDGDB_00766 Glycosyltransferase like family 2 M Cell wall/membrane/envelope biogenesis Purine nucleoside phosphorylase DeoD-type BKLDJMND_00919 KDGOJIBD_01030 EKMIGMNK_01485 JFMDMGNA_00610 NOHGDGDB_00856 Phosphorylase superfamily F Nucleotide transport and metabolism Fatty acid metabolism regulator protein EKMIGMNK_01486 JFMDMGNA_00611 NOHGDGDB_00857 Bacterial regulatory proteins, tetR family K Transcription Inner membrane transport permease YbhR EKMIGMNK_01487 JFMDMGNA_00612 NOHGDGDB_00858 ABC transporter V Defense mechanisms putative ABC transporter ATP-binding protein YbhF EKMIGMNK_01488 JFMDMGNA_00613 NOHGDGDB_00859 abc transporter atp-binding protein V Defense mechanisms hypothetical protein EKMIGMNK 01489฀EK JFMDMGNA_00614฀JFMDMGNA_00615 hypothetical protein EKMIGMNK_01491 JFMDMGNA_00616 NOHGDGDB_00860 protein with an alpha beta hydrolase fold G Carbohydrate transport and metabolism Pyruvate oxidase EKMIGMNK_01492 JFMDMGNA_00617 NOHGDGDB_00861 Belongs to the TPP enzyme family E Amino acid transport and metabolism putative copper-exporting P-type ATPase V BKLDJMND_00918 KDGOJIBD_01029 EKMIGMNK_01493 JFMDMGNA_00618 NOHGDGDB_00862 P-type ATPase P Inorganic ion transport and metabolism Cupredoxin-like domain protein BKLDJMND_00917 KDGOJIBD_01028 EKMIGMNK_01494 JFMDMGNA_00619 NOHGDGDB_00863 cog cog4633 S Function unknown Transcriptional repressor CopY BKLDJMND_00916 KDGOJIBD_01027 EKMIGMNK_01495 JFMDMGNA_00620 NOHGDGDB_00864 Copper transport repressor, CopY TcrY family K Transcription hypothetical protein EKMIGMNK_01501 JFMDMGNA_00626 NOHGDGDB_00870 3-oxoacyl-[acyl-carrier-protein] reductase FabG EKMIGMNK_01502 JFMDMGNA_00627 NOHGDGDB_00871 Belongs to the short-chain dehydrogenases reductases (SDR) family I Lipid transport and metabolism 2-hydroxy-6-oxo-6-(2'-aminophenyl)hexa-2,4-dienoic acid hydrolase EKMIGMNK_01503 JFMDMGNA_00628 NOHGDGDB 00872฀N Alpha/beta hydrolase family I Lipid transport and metabolism Alcohol dehydrogenase EKMIGMNK_01504 JFMDMGNA_00629 NOHGDGDB_00874 nadph quinone reductase C Energy production and conversion Putative HTH-type transcriptional regulator YwnA EKMIGMNK_01505 JFMDMGNA_00630 NOHGDGDB_00875 Transcriptional regulator K Transcription

Supplementary Table 12. Encoded proteins absent low inflammatory RA-associated S. parasalivarius isolates Home

S. parasalivarius isolates S. salivarius Annotation 2.1 3.1 9.1 10.1 15.1 16.1 17.1 21.1 22.1 23.2 11.1 EggNOG description (23.2) COG code (23.2) Helix-turn-helix domain protein FCGJDEJI_00863 MKKDFLNB_00716 BKLDJMND_01935 KDGOJIBD_01923 OACCDLOP_02120 NCBGCKJJ_02103 BOLGAICL_02112 AGDNAGMJ_00186 Integrase L Replication, recombination and repair Putative multidrug export ATP-binding/permease protein FCGJDEJI_00387 MKKDFLNB_02108 OACCDLOP_02061 NCBGCKJJ_02091 BOLGAICL_02086 AGDNAGMJ_00285 ABC transporter transmembrane region V Defense mechanisms putative ABC transporter ATP-binding protein YxlF FCGJDEJI_00386 MKKDFLNB_02107 OACCDLOP_02060 NCBGCKJJ_02092 BOLGAICL_02085 AGDNAGMJ_00286 abc transporter atp-binding protein V Defense mechanisms hypothetical protein FCGJDEJI_00385 MKKDFLNB_02106 NCBGCKJJ_02093 BOLGAICL_02084 AGDNAGMJ_00287 ABC-type transport system involved in multi-copper enzyme maturation, permease component S Function unknown HTH-type transcriptional repressor BepR FCGJDEJI_00384 MKKDFLNB_02105 OACCDLOP_02007 NCBGCKJJ_02022 BOLGAICL_00001 AGDNAGMJ_00288 Bacterial regulatory proteins, tetR family K Transcription hypothetical protein FCGJDEJI_00372 MKKDFLNB_00344 BKLDJMND_00383 KDGOJIBD_01513 NCBGCKJJ_00921 BOLGAICL_01536 AGDNAGMJ_00431 acid-resistance membrane protein FCGJDEJI_00681 MKKDFLNB_00124 BKLDJMND_00732 KDGOJIBD_00330 OACCDLOP_00198 NCBGCKJJ_00371 BOLGAICL_01070 AGDNAGMJ_00606 NOHGDGDB_01104 Short repeat of unknown function (DUF308) S Function unknown hypothetical protein FCGJDEJI_00680 MKKDFLNB_00123 OACCDLOP_00197 NCBGCKJJ_00370 BOLGAICL_01071 AGDNAGMJ_00607 NOHGDGDB_01101 membrane S Function unknown hypothetical protein FCGJDEJI_01572 MKKDFLNB_01637 OACCDLOP_00907 NCBGCKJJ_01227 BOLGAICL_00625 AGDNAGMJ_00752 NOHGDGDB_00085 DNA-binding transcriptional repressor PuuR FCGJDEJI_00464 MKKDFLNB_00979 BKLDJMND_00170 KDGOJIBD_01204 OACCDLOP_01941 NCBGCKJJ_00560 BOLGAICL_00343 AGDNAGMJ_01561 Helix-turn-helix domain K Transcription hypothetical protein FCGJDEJI_01777 MKKDFLNB_00935 OACCDLOP_00557 NCBGCKJJ_01127 BOLGAICL_00884 AGDNAGMJ_01695 the current gene model (or a revised gene model) may contain a frame shift S Function unknown hypothetical protein FCGJDEJI_01783 MKKDFLNB_00941 BKLDJMND_00910 KDGOJIBD_01021 OACCDLOP_00563 NCBGCKJJ_01121 BOLGAICL_00890 AGDNAGMJ_01701 DDE domain protein FCGJDEJI_01785 MKKDFLNB_00943 BKLDJMND_00909 KDGOJIBD_01020 OACCDLOP_00564 NCBGCKJJ_01120 BOLGAICL_00891 AGDNAGMJ_01703 DDE domain L Replication, recombination and repair PII-type proteinase FCGJDEJI_00853 MKKDFLNB_00726 BKLDJMND_01218 KDGOJIBD_01090 OACCDLOP_01643 NCBGCKJJ_00684 BOLGAICL_01324 AGDNAGMJ_01870 Belongs to the peptidase S8 family O Posttranslational modification, protein turnover, chaperones General stress protein 14 FCGJDEJI_00854 MKKDFLNB_00725 BKLDJMND_01929 KDGOJIBD_01917 OACCDLOP_01644 NCBGCKJJ_02072 BOLGAICL_01707 AGDNAGMJ_01871 general stress protein S Function unknown

Moentadj R, et al. Ann Rheum Dis 2021; 80:573–581. doi: 10.1136/annrheumdis-2020-219009