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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
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