Supplementary Data McLean et al. 2018

Supplementary Data

Evidence of independent acquisition and adaption of ultra-small to human hosts across the highly diverse yet reduced genomes of the phylum Saccharibacteria a Department of Periodontics, University of Washington, Seattle, WA, 98195, USA b Department of Microbiology, University of Washington, Seattle, WA, 98195, USA c Department of Microbiology, The Forsyth Institute, Cambridge, Massachusetts 02142 dDepartment of Microbiology, The Ohio State University, Columbus, OH, USA

This PDF contains:

Supplementary Tables (separate file with tabs for each table)

• Supplementary Table 1 | Genomic properties, sources and genome curation. • Supplementary Table 2 | Proposed names and taxonomic placement of genomes. • Supplementary Table 3 | Single copy ribosomal marker occurrence across genomes. • Supplementary Table 4 | Raw data for Figure 2a percentage of genome coverage from mapped metagenomics read sets to newly available genomes. • Supplementary Table 5 | Clusters of orthologous percentage distribution across genomes compared to mutualistic and parasitic bacteria indicating loss or gain of functional capacities. • Supplementary Table 6 | Core shared among full/ near complete genomes of Saccharibacteria • Supplementary Table 7 | Unique genes among each of the G5, G6, G3 and G1 genomes of Oral Saccharibacteria.

Supplemental Data

• Supplemental Figure 1 | Full matrix of AAI, orthologous genes and percent orthologous fraction provided for each genome pair in Figure 2.

• Supplemental Data File 1 | Newick 16S RAXML tree. publically available genomes were manually curated to remove contaminating contigs from the submitted sequences delineated with columns for original (grey and red text) and curated properties (purple highlighting). CheckM assembly check results are presented. Completeness is normally based on 117 single core marker genes of bacterial genomes and not the recognized reduced genomes like the CPR with Supplementary Table 1| Genomic properties, sources and genome curation. Genome properties assessed for assemblies from this study and publically available/published genomes of Saccharibacteria. Some known marker genes that are missing therefore completeness are underestimated. S_aal RAAC3 GWC2 GWC2 RAAC3 TM7_ EAM_G5_2_HOT_35 TM7_ EAM_G5_1_HOT_356 TM7c TM7_S2_ Type_Strain_TM7x HOT_952 TM7_S1_ TM7_ANC_38.39_G1_1 TM7_G1_3_12Alb TM7_S7_ TM7_CMJM_G6_1_HOT_870 TM7_KMM_G3_1_HOT_351 TM7_G3_2_Rum_HOT_351B TM7_ EAM_G5_1_HOT_356 TM7c TM7_S2_ Type_Strain_TM7x HOT_952 TM7_S1_ TM7_ANC_38.39_G1_1 TM7_G1_3_12Alb TM7_S7_ TM7_CMJM_G6_1_HOT_870 TM7_KMM_G3_1_HOT_351 TM7_G3_2_Rum_HOT_351B S_aal TM7_ EAM_G5_2_HOT_35 6 6 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G6 G3 G3 G5 G5 G1 G1 G1 G1 G1 G1 G1 G1 G1 G1 G6 G3 G3 G5 G5 Group Designation Group Designation * completeness is based on bacterial genomes and not reduced CPR genomes with known marker genes that are missing therefore completeness are underestimated. RN213 CP007496.1 Environmental,Sludereactor PRJNA241438 Environmental,groundwater PopulationEnrichment SRR957739,38 PopulationEnrichment SRP064209 PRJNA216965 Albertsenetal.2013 PRJNA289925 Kantoretal.2013 CP005957.1 CP006915.1 PRJNA201542 PRJNA217186 SRP064209 SRP064209 PRJNA289925 PRJNA289925 PRJNA19085 SRS013946 PRJNA48479 2236661025 2236661021 2236661026

# scaffolds: Derived from Bioproject/IMG ID 129 102 189 105 73 71 17 29 24 35 1 1 1 1 6

1013781 1038683 Derived from SRA/Accession 141643 705126 845464 232758 136145 107046 Longest contig: 49198 66761 61213 37832 22786 40211 90811 IMG publicrelease IMG publicrelease IMG publicrelease rw ta.05Pplto nihetEnvironmental,groundwater PopulationEnrichment Brown etal.2015 Marcy etal2007 This Study This Study This Study This Study This Study This Study This Study He etal.

GC: New Genome Reference 0.48 0.44 0.49 0.43 0.47 0.48 0.32 0.40 0.50 0.51 0.39 0.47 0.48 0.49 0.46 ouainErcmn HomoSapiens,OralCavity Population Enrichment Population Enrichment ouainErcmn HomoSapiens,OralCavity HomoSapiens,OralCavity Population Enrichment Population Enrichment HomoSapiens,OralCavity HomoSapiens,OralCavity Population Enrichment Population Enrichment nce a utr HomoSapiens,OralCavity Eniched LabCulture utvtdSri HomoSapiens,OralCavity Cultivated Single Cell Single Cell Single Cell Single Cell

GC std Uncultured Type 0.03 0.00 0.00 0.00 0.04 0.03 0.02 0.01 0.01 0.01 0.05 0.03 0.02 0.00 0.00 Homo Sapiens,OralCavity Homo Sapiens,OralCavity Homo Sapiens,OralCavity Homo Sapiens,OralCavity Moose ,Rumen CheckM Results Coding density: Host, Habitat .9161189 0 99 474 0 46525887 No 8473 29598 141645 105 7.41 54 29598 108 8392 161 106 0.89 0.93 0.91 0.92 .37 6 00 0 35 919 5 01 35 10661 13650 40214 856 1.95 59 19440 13650 23288 108 5485 107790 171 10501 2888 161 73 1.72 75 72 0.89 23288 0.93 58 36810 171 15580 104 17 30417 36 171 21170 171 0.90 24 0.89 35 0.90 0.90 .0191423 848 860 6120746 2445 1.39 4863 29 23007 8055 2631 108 6.03 3676 38 5880 161 171 4786 58 129 102 0.91 2431 0.90 104 189 0.90 0.91 0.90 1038683 362 45176 1465 1306322 038 1056 1013781 71960129 630 474179 84298167 968 81 781472 557 456864 018711 705138 921 845464 # contigs: Original Genome Size AN A656 607 625762 NA NA NA AN A763 786 756930 607 NA 462105 NA NA NA NA NA 671 730081 681 NA 740987 NA NA NA NA NA AN A535 535 563755 719 NA 726940 NA NA NA NA NA 1 1 6 1 1 7 705126 171 0.00 66 ##### 108 845464 161 121157 171 6 ###18###6 0.93 67 ##### 108 ###### 161 ###### 171 # markers: Original Gene Count

Mean contig length: Original Scaffold Count 1 1 1 088 1092 1038683 038 1056 1013781 719587 474179 98871181664 711 56404 599808 473 400460 416614 1007 889708 018711 705138 921 845464 117 117 117 117 117 117 117 117 # marker sets: Curated Genome size (This study): ## 500 2753 018753 No 705138 705138 705138 12 0.00 65 ##### 0.00 63 ##### 78 404 741810158 No 5486 17081 49198 27 0.43 24 17080 30420 50725 0.00 107047 65 73 70435 1.71 57 50725 32 517 038213058 No 5880 13320 37832 50 1.71 35 13320 ## 50.00 65 ##### 14 700 698331821171 31148 90813 36 0.00 57 31148 N50 (contigs): # Curated Gene Count

Completeness*: Curated Genome Size Change 0 0 0 0

Contamination:

# ambiguous bases: 0 0 0 0 0 0 038 038 1013781 1013781 1013781 088 088 1038683 1038683 1038683 444856 845464 845464 845464 378161 121157 176314 232758 31574536810 70435 136145 11 0537 No 3676 8055 61213 Longest scaffold:

N50 (scaffolds):

Mean scaffold length: Yes Yes Yes Yes Yes Yes Yes Yes Yes Yes Metagenome bin Supplementary Table 2| Proposed names and novel taxonomic levels based on phlyogenomic relationships of Saccharibacteria genomes using combined information from 16S rRNA phylogeny, concatenated marker gene trees (Figure 1 and Extended Data Figure 1) as well the average amino acid comparisons (Figure 3 and Supplemental Figure 1) between genomes. Strain_Name Alias GroupName Phylum Class Order Family Genus Strain Full Species strain Type_Strain_TM7x HOT_952 TM7x G1_1_TM7x Bacteria Saccharibacteria Saccharimonia Nanosynbacterales Nanosynbacteraceae Nanosynbacter Lyticus Type_Strain_TM7x HOT_952 Nanosynbacter Lyticus Type_Strain_TM7x HOT_952 TM7_S2_ TM7_S2 G1_2_S2 Bacteria Saccharibacteria Saccharimonia Nanosynbacterales Nanosynbacteraceae Nanosynbacter sp. TM7_S2_ Nanosynbacter sp. TM7_S2_ TM7_G1_3_12Alb TM7_12A_lb G1_3_12Alb Bacteria Saccharibacteria Saccharimonia Nanosynbacterales Nanosynbacteraceae Nanosynbacter sp. TM7_G1_3_12Alb Nanosynbacter sp. TM7_G1_3_12Alb TM7c TM7_c G1_4_TM7c Bacteria Saccharibacteria Saccharimonia Nanosynbacterales Nanosynbacteraceae Nanosynbacter sp. TM7c Nanosynbacter sp. TM7c TM7_S7_ TM7_S7 G1_5_S7 Bacteria Saccharibacteria Saccharimonia Saccharimonales Sacchiramonaceaea Nanosynbacter sp. TM7_S7_ Nanosynbacter sp. TM7_S7_ TM7_S1_ TM7_S1 G1_6_S1 Bacteria Saccharibacteria Saccharimonia Saccharimonales Sacchiramonaceaea Nanosynbacter sp. TM7_S1_ Nanosynbacter sp. TM7_S1_

TM7_ANC_38.39_G1_1 ANC_38.39 Bacteria Saccharibacteria Saccharimonia Saccharimonales Sacchiramonaceaea Nanosynbacter sp. TM7_ANC_38.39_G1_1 Nanosynbacter sp. TM7_ANC_38.39_G1_1

TM7_ EAM_G5_1_HOT_356 TM7_9Asb G5_1_EAM Bacteria Saccharibacteria Nanoperiomorbia Nanoperiomorbales Nanoperiomorbaceae Nanoperiomorbus periodonticus TM7_ EAM_G5_1_HOT_356 Nanoperiomorbus periodonticus TM7_ EAM_G5_1_HOT_356 TM7_ EAM_G5_2_HOT_356 TM7_12Asb G5_2_EAM Bacteria Saccharibacteria Nanoperiomorbia Nanoperiomorbales Nanoperiomorbaceae Nanoperiomorbus periodonticus TM7_ EAM_G5_2_HOT_356 Nanoperiomorbus periodonticus TM7_ EAM_G5_2_HOT_356

TM7_CMJM_G6_1_HOT_870 TM7_G6 G6_1_CMJM Bacteria Saccharibacteria Nanosyncoccalia Nanogingivales Nanogingivalaceae Nanogingivalis gingivitcus TM7_CMJM_G6_1_HOT_870 Nanogingivalis gingivitcus TM7_CMJM_G6_1_HOT_870

TM7_KMM_G3_1_HOT_351 TM7_G3 G3_1_KMM Bacteria Saccharibacteria Nanosyncoccalia Nanosyncoccales Nanosyncoccacae Nanosyncoccus nanoralicus TM7_KMM_G3_1_HOT_351 Nanosyncoccus nanoralicus TM7_KMM_G3_1_HOT_351 TM7_G3_2_Rum_HOT_351B TM7_G32_Rum G3_2_Rum Bacteria Saccharibacteria Nanosyncoccalia Nanosyncoccales Nanosyncoccacae Nanosyncoccus alces TM7_G3_2_Rum_HOT_351B Nanosyncoccus alces TM7_G3_2_Rum_HOT_351B

Strain_Name Name Derivation Genome Derived From %GC Notes Type_Strain_TM7x HOT_952 Syn=symbiosis Lyticus=lysis Cultured as Epibiont on Actinomyces 44.5 TM7_S2_ Single Cell MDA 46.8 TM7_G1_3_12Alb Metagenome (PRJNA289925; SRP064209) 48.2 TM7c Single Cell MDA 39.1 TM7_S7_ Single Cell MDA 48.2 TM7_S1_ Single Cell MDA 46.8

Ancient Calculus Sample TM7_ANC_38.39_G1_1 (SRASRR957738,SRR957739) 48.1 Dalheim B61 skeleton; label: B61

TM7_ EAM_G5_1_HOT_356 morbus = disease Metagenome (PRJNA289925; SRP064209) 50.8 TM7_ EAM_G5_2_HOT_356 Metagenome (PRJNA289925; SRP064209) 50.5

TM7_CMJM_G6_1_HOT_870 gingivalicus= found on gingiva HMP Sample (SRS013946) 32.3

TM7_KMM_G3_1_HOT_351 coccus = shape Lab Enrichment Culture Metagenome 40.3 TM7_G3_2_Rum_HOT_351B Alces = moose Moose Rumen metagenome 43 Supplementary Table 3|Single copy ribosomal marker gene occurrence across genomes. RAAC3 S.aalborgensis TM7_GWC2 TM7x ANC_38.39 TM7_12A_lb TM7_S1 TM7_S2 TM7_S7 TM7c_ Gene gene name Annotation No. isolates No. sequences Avg sequences per isolate Min group size nuc Max group size nuc Avg group size nuc TM7_EAM_G5_2_HOT_357 TM7_EAM_G5_1_HOT_356 TM7_CMJM_G6_1_HOT_870 TM7_KMM_G3_1_HOT_351 TM7_G3_2_Rum_HOT_351B group_471 50S ribosomal protein L29,group_471 7 7 1 206 236 222 group_980 50S ribosomal protein L29,group_980 2 2 1 299 299 299 pnp 30S ribosomal protein S1,pnp 14 25 2 1043 2174 1539 rplA 50S ribosomal protein L1,rplA 14 14 1 620 1094 987 rplB 50S ribosomal protein L2,rplB 12 12 1 836 848 839 rplC 50S ribosomal protein L3,rplC 12 12 1 611 638 618 rplD 50S ribosomal protein L4,rplD 12 12 1 587 623 608 rplE 50S ribosomal protein L5,rplE 12 12 1 572 626 585 rplF 50S ribosomal protein L6,rplF 14 14 1 410 542 528 rplJ 50S ribosomal protein L10,rplJ 13 14 1 509 599 528 rplK 50S ribosomal protein L11,rplK 13 13 1 425 428 425 rplL 50S ribosomal protein L7/L12,rplL 13 14 1 365 383 375 rplM 50S ribosomal protein L13,rplM 13 13 1 425 446 433 rplN 50S ribosomal protein L14,rplN 11 11 1 368 368 368 rplO 50S ribosomal protein L15,rplO 15 16 1 221 506 463 rplP 50S ribosomal protein L16,rplP 12 12 1 413 419 414 rplQ 50S ribosomal protein L17,rplQ 13 13 1 383 446 404 rplR 50S ribosomal protein L18,rplR 15 15 1 329 356 347 rplS 50S ribosomal protein L19,rplS 11 11 1 428 524 496 rplT 50S ribosomal protein L20,rplT 13 13 1 341 353 344 rplU 50S ribosomal protein L21,rplU 13 13 1 242 311 301 rplV 50S ribosomal protein L22,rplV 12 12 1 386 464 418 rplW 50S ribosomal protein L23,rplW 12 12 1 308 401 324 rplX 50S ribosomal protein L24,rplX 13 13 1 227 323 302 rplY 50S ribosomal protein L25,rplY 7 7 1 680 767 716 rpmA 50S ribosomal protein L27,rpmA 10 10 1 272 272 272 rpmB 50S ribosomal protein L28,rpmB 13 13 1 188 227 206 rpmC 50S ribosomal protein L29,rpmC 1 1 1 185 185 185 rpmE2 50S ribosomal protein L31 type B,rpmE2 11 11 1 308 404 348 rpmG 50S ribosomal protein L33,rpmG 12 13 1 206 221 212 rpmH 50S ribosomal protein L34,rpmH 4 4 1 137 137 137 rpmI 50S ribosomal protein L35,rpmI 13 13 1 194 197 194 rpsB 30S ribosomal protein S2,rpsB 12 12 1 236 746 671 rpsC 30S ribosomal protein S3,rpsC 12 12 1 626 644 635 rpsD 30S ribosomal protein S4,rpsD 13 13 1 617 626 617 rpsE 30S ribosomal protein S5,rpsE 14 15 1 575 683 622 rpsF 30S ribosomal protein S6,rpsF 11 11 1 305 377 353 rpsG 30S ribosomal protein S7,rpsG 12 12 1 476 479 478 rpsH 30S ribosomal protein S8,rpsH 13 13 1 401 401 401 rpsI 30S ribosomal protein S9,rpsI 14 14 1 398 401 398 rpsJ 30S ribosomal protein S10,rpsJ 13 13 1 311 326 319 rpsK 30S ribosomal protein S11,rpsK 14 14 1 269 437 393 rpsL 30S ribosomal protein S12,rpsL 12 12 1 410 413 412 rpsM 30S ribosomal protein S13,rpsM 14 14 1 386 386 386 rpsN2 Alternate 30S ribosomal protein S14,rpsN2 13 13 1 266 269 268 rpsO 30S ribosomal protein S15,rpsO 12 12 1 266 302 269 rpsP 30S ribosomal protein S16,rpsP 12 12 1 332 422 375 rpsQ 30S ribosomal protein S17,rpsQ 12 12 1 269 377 319 rpsR 30S ribosomal protein S18,rpsR 13 13 1 194 209 199 rpsS 30S ribosomal protein S19,rpsS 12 12 1 263 293 269 rpsT 30S ribosomal protein S20,rpsT 12 12 1 251 401 354 rpsU 30S ribosomal protein S21,rpsU 14 16 1 215 257 224 healthy subjects downloaded from the Human Microbiome Project DACC). Supplementary Table 4| Raw data for Figure 2a percentage of genome coverage from mapped metagenomics read sets to newly available genomes. Ancient Neanderthal dental calculus (48,000 years), through to modern body sites in health and disease from published datasets (SRS samples from TM7_CMJM_G6_1_HOT_870 TM7_G3_2_Rum_HOT_351B TM7_ EAM_G5_1_HOT_356 TM7_ EAM_G5_2_HOT_35 TM7_KMM_G3_1_HOT_351 TM7_ANC_38.39_G1_1 TM7_G1_3_12Alb SR1 _345 1OR1 TM7_S7 TM7_S2 Name TM7x TM7c 6 24.1 36.9 19.1 14.7 15.5 0.3 4.6 6.9 0.5 0.2 1.5

9 ELSIDRON1L7 0.2 0.1 0.1 0.1 0 0 0 0 0 0 0 0 SPYNEWL8 0.2 5.2 1.7 0.2 1.2 0.4 0.3 0.1 0.2 0 0 0 SPYOLD_L7L8 23.7 23.5 36.1 21.5 17.4 97.1 11.8 22.8 2.2 3.2 0.8 0.1 SRR957738 28.3 26.6 43.2 24.6 18.9 15.9 26.5 5.5 3.7 0.8 0.1 99 SRR957739 57.3 52.3 35.7 57.7 60.9 5.1 0.1 0.8 6.4 34 0 0 012B_TGACCA 58.9 24.3 0.3 0.1 2.2 1.4 2.3 2.3 0.3 0.2 0.2 0.3 SRS104521_Subgingival_Plaque 61.5 18.6 1.4 0.4 3.6 1.2 6.5 0.4 0.2 0.2 0.8

3 SRS079308_Supragingival_Plaque 3.8 4.2 7.8 4.2 2.6 2.3 4.5 3.8 0.3 0.9 3.5

3 SRS049988_Buccal_Mucosa 11.7 0.1 1.6 4.2 0.9 0.6 1.1 0.4 0.3 0.7

0 0 SRS062878_Hard_Palate 0.4 0.7 9.1 1.8 3.2 1.6 0.9 8.3 0.3 0.3 46

3 SRS097905_Throat 26.8 87.5 0.2 1.5 1.5 0.5 0.7 0.8 0.4 0.1 0.3 0.2 SRS144374_Attached_Keratinized_Gingiva 93.1 79.5 0.8 1.3 9.9 6.4 2.1 3.8 1.8 1.2 0.9 0.6 SRS144560_Tongue_Dorsum 53.9 21.7 23.2 15.8 50.2 28.8 29.4 10.8 9.8 5.9 7.8 0.1 SRS147126_Saliva 11.4 1.1 6.5 8.4 3.6 1.3 1.8 0.8 1.6 0.1 4.3 0.5 SRS147149_Palatine_Tonsils 10.3 0.6 8.2 8.8 1.6 2.4 4.9 0.9 0.4 2.5 0.4

3 SRS077322_Anterior_Nares 0.1 0.1 0.1 0.1 0.2 0.1 0.1 0.1 0.1 0 0 0 SRS071988_Ileal_Pouch 25.6 58.3 0.6 1.5 1.6 1.2 1.7 0.6 0.3 0.4 0.5

1 SRS098640_Mid_Vagina 0.1 0.1 0.1 0 0 0 0 0 0 0 0 0 SRS075975_Vaginal_Introitus 0.4 3.4 0.7 1.7 0.6 1.2 4.4 0.8 0.3 0.5 1.4 0.2 SRS023466_Posterior_Fornix 0.6 0.3 1.1 0.8 1.1 8.5 0.3 0.4 0.4 2.9 0.6

3 SRS301868_Stool 0.1 0.1 0.2 0.4 0.1 0.1 0.2 0.2 0.3 0.2 0 0 SRS143565_Right_Antecubital_Fossa 0.1 0.2 0.1 0.1 0.1 0.1 0.1 0 0 0 0 0 SRS072200_Nasopharynx 0.1 0.1 0 0 0 0 0 0 0 0 0 0 SRS072331_Blood 0.5 0.3 0.7 0.8 0.7 0.6 0.6 0.3 0.4 0.4 0.6 0.6 SRS077863_Left_Retroauricular_Crease 0.5 0.5 0.5 0.6 0.6 0.7 0.8 0.3 0.4 0.5 0.5 0.6 SRS078434_Right_Retroauticular_Crease Supplementary Table 5| COG distribution percentage across genomes for functionally annotated genes within mutualistic and parasitic bacteria (from Merhej et al. (20) ) from environmental and oral Saccharibacteria groups highlight enrichment of genes with functions in defense mechanisms, translation, replication/recombination and lack of those involved with amino acids, lipid and energy production and conservation supporting the reduced functional capacity and host dependent lifestyle (Supplemental to Figure 3).

COG Categories FHA (n = 85)*HD (n = 125)*FL (n = 192)*OI (n = 40)* TM7_full_oral(avg)TM7_full_ENVl(avg)TM7_ EAM_G5_2_HOT_357TM7_ EAM_G5_1_HOT_356TM7_CMJM_G6_1_HOT_870TM7_KMM_G3_1_HOT_351TM7_G3_2_Rum_HOT_351B TM7x ANC 12Alb S1 S2 S7 GWC2 S.aal RAAC3 TM7c GWA2 Berkel Kazan SR1 RNA processing and modification A 0.1 0.1 0.1 0.1 0.2 0.2 0.3 0.3 0.3 0.0 0.2 0.2 0.0 0.0 0.0 0.3 0.2 0.2 0.2 0.2 0.4 0.0 0.0 0.0 0.0 Chromatine structure and dynamics B 0.0 0.0 0.1 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.2 Energy production and conversion C 6.7 6.8 6.9 7.9 2.3 3.5 1.3 1.3 1.9 3.3 3.1 3.0 3.1 3.1 3.8 2.4 2.5 3.9 4.2 4.0 1.8 4.6 4.1 0.6 3.6 control, cell division, chromosome partitioningD 1.3 1.4 1.2 1.8 2.2 2.0 2.0 2.3 2.4 2.7 2.0 1.9 1.6 2.0 1.7 1.8 3.1 2.0 1.6 1.9 2.5 1.0 1.9 2.5 1.3 Amino acid transport and metabolism E 9.1 8.7 9.9 6.4 2.6 2.4 1.5 1.8 3.8 3.3 2.9 2.5 3.5 2.0 3.3 2.4 3.5 1.1 2.6 2.1 3.6 4.3 2.8 1.9 1.1 Nucleotide transport and metabolism F 3.2 3.4 3.2 4.3 3.0 4.2 2.6 3.1 2.2 4.2 2.7 3.4 4.1 2.4 2.1 3.9 4.6 3.0 4.9 3.2 5.8 7.2 3.5 4.1 3.8 Carbohydrate transport and metabolism G 6.7 6.3 6.1 3.9 4.1 4.6 4.8 3.6 4.8 2.7 4.3 4.7 4.1 2.7 4.6 5.1 5.0 5.6 4.3 4.2 4.3 5.0 4.3 1.4 2.3 Coenzyme transport and metabolism H 4.9 5.2 5.1 6.5 0.6 1.5 0.3 0.0 0.5 1.2 1.1 0.6 0.8 2.4 0.8 0.9 0.8 1.8 1.2 1.7 1.1 1.2 0.5 0.3 1.5 Lipid transport and metabolism I 3.5 3.6 3.8 4.2 0.3 0.7 0.3 0.3 0.3 0.0 0.7 0.2 0.4 1.2 0.4 0.0 0.6 1.0 0.3 0.6 1.1 0.7 0.9 0.6 0.8 Translation, ribosomal structure and biogenesis J 8.5 10.1 7.3 18.9 23.3 17.2 22.4 22.9 26.1 25.2 22.1 20.8 18.3 22.7 20.8 16.0 16.9 16.7 17.5 18.8 15.8 15.1 17.1 26.2 20.6 Transcription K 6.3 5.9 7.6 3.8 4.1 3.5 4.1 3.6 4.3 4.5 4.3 3.6 4.3 5.1 3.8 3.6 3.6 3.6 3.8 4.2 2.5 4.1 4.7 5.2 4.4 Replication, recombination and repair L 9.6 9.6 6.5 9.2 11.8 11.0 13.0 13.5 11.6 10.0 12.3 10.4 11.3 8.6 9.2 11.5 11.1 9.8 11.3 11.8 11.2 10.6 10.5 13.5 10.7 Cell wall/membrane/envelope biogenesis M 6.6 6.5 6.0 6.3 7.1 9.6 4.6 4.6 8.9 6.7 8.9 9.1 9.0 10.2 10.0 7.3 8.6 7.9 7.3 9.9 13.3 7.9 11.7 12.2 9.0 Cell motility N 2.7 2.5 2.5 1.3 0.0 0.0 0.0 0.0 0.0 0.0 0.2 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.2 0.0 0.0 0.0 Posttranslational modification, protein turnover, chaperonesO 4.4 4.7 4.4 6.3 6.3 5.4 6.6 6.6 5.6 6.4 5.8 6.6 5.1 3.5 4.2 5.4 5.8 5.7 5.7 6.1 4.0 7.0 5.4 5.0 6.1 Inorganic transport and metabolism P 5.3 5.1 5.9 3.6 1.5 2.4 1.0 1.3 1.1 2.4 1.3 2.1 2.7 0.8 1.7 1.8 1.5 2.3 3.5 2.3 1.4 1.7 1.2 1.1 3.6 Secondary metabolites biosynthesis, transport and catabolismQ 1.9 1.8 2.3 1.0 0.1 0.4 0.3 0.0 0.0 0.0 0.2 0.0 0.4 0.0 0.8 0.9 0.2 0.8 0.3 0.2 0.4 0.7 0.7 0.0 1.0 Function unknown S 11.0 10.4 12.1 7.0 17.9 21.4 19.1 20.9 15.1 16.4 17.7 18.5 19.1 22.0 21.3 26.6 21.9 23.4 20.8 19.9 21.6 20.6 21.9 19.9 22.7 Signal transduction mechanisms T 3.4 3.1 4.8 1.7 2.8 2.4 4.1 3.6 2.7 2.1 1.8 2.8 2.5 3.5 3.3 2.4 2.5 2.8 2.4 2.3 2.2 2.2 2.8 0.6 1.7 Intracellular trafficking, secretion, and vesicular transportU 3.5 3.7 2.9 4.8 2.0 2.2 2.0 1.5 2.4 2.1 1.8 2.3 2.1 1.6 1.3 0.9 1.7 2.0 1.9 1.9 2.9 2.4 2.9 2.5 2.1 Defense mechanisms V 1.2 1.1 1.4 0.4 5.0 3.3 6.9 6.9 3.8 4.2 3.4 4.9 5.5 5.1 5.0 4.5 4.0 4.1 4.0 3.2 1.8 1.7 1.7 1.7 1.5

OI corresponds to obligate intracellular, FHA corresponds to facultative host-associated, HD corresponds to all host-dependent, FL corresponds to free-living bacteria * Data from Merhej et al. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2688493/table/T1/

COG Categories TM7x: 570 genesTM7_full_oral(avg) in COGTM7_full_ENVl(avg)Parasites*: Mutualists*756 genes in : 512COG genes in COG Energy production and conversion C 3.0 2.3 3.5 7.5 7.6 Cell cycle control, cell division, chromosome partitioningD 1.9 2.2 2.0 1.6 1.8 Amino acid transport and metabolism E 2.5 2.6 2.4 5.2 7.8 Nucleotide transport and metabolism F 3.4 3.0 4.2 3.8 4.7 Carbohydrate transport and metabolism G 4.7 4.1 4.6 3.5 4.0 Coenzyme transport and metabolism H 0.6 0.6 1.5 5.9 6.0 Lipid transport and metabolism I 0.2 0.3 0.7 4.1 3.2 Translation, ribosomal structure and biogenesis J 20.8 23.3 17.2 16.7 21.0 Transcription K 3.6 4.1 3.5 3.2 3.3 Replication, recombination and repair L 10.4 11.8 11.0 7.6 7.8 Cell wall/membrane/envelope biogenesis M 9.1 7.1 9.6 5.8 5.1 Cell motility N 0.0 0.0 0.0 1.2 1.6 Posttranslational modification, protein turnover, chaperonesO 6.6 6.3 5.4 6.0 6.2 Inorganic ion transport and metabolism P 2.1 1.5 2.4 3.4 3.2 Signal transduction mechanisms T 2.8 2.8 2.4 1.8 0.6 Intracellular trafficking, secretion, and vesicular transportU 2.3 2.0 2.2 4.8 3.5 Defense mechanisms V 4.9 5.0 3.3 0.5 0.4

* Data from Merhej et al. Supplementary Table 6| Core genes shared among full/ near complete genomes of Saccharibacteria. Genomes from G1, G5, G6, G3 groups were compared which included 2 Environmental G1 representatives and 4 Oral (G1, G5,G6, G3) resulting in 201 core genes.

RAAC3_032|S.aal_032|TM7_G52|G6_V1 |G3_Oral|TM7x 30S ribosomal protein S1_rps1_ 30S ribosomal protein S10_rpsJ_ 30S ribosomal protein S11_rpsK_ 30S ribosomal protein S12_rpsL_ 30S ribosomal protein S13_rpsM_ 30S ribosomal protein S15_rpsO_ 30S ribosomal protein S16_rpsP_ 30S ribosomal protein S17_rpsQ_ 30S ribosomal protein S18_rpsR_ 30S ribosomal protein S19_rpsS_ 30S ribosomal protein S20_rpsT_ 30S ribosomal protein S21_rpsU_ 30S ribosomal protein S3_rpsC_ 30S ribosomal protein S4_rpsD_ 30S ribosomal protein S5_rpsE_ 30S ribosomal protein S6_rpsF_ 30S ribosomal protein S7_rpsG_ 30S ribosomal protein S8_rpsH_ 30S ribosomal protein S9_rpsI_ 50S ribosomal protein L1_rplA_ 50S ribosomal protein L10_rplJ_ 50S ribosomal protein L11_rplK_ 50S ribosomal protein L13_rplM_ 50S ribosomal protein L14_rplN_ 50S ribosomal protein L15_rplO_ 50S ribosomal protein L16_rplP_ 50S ribosomal protein L17_rplQ_ 50S ribosomal protein L18_rplR_ 50S ribosomal protein L19_rplS_ 50S ribosomal protein L2_rplB_ 50S ribosomal protein L20_rplT_ 50S ribosomal protein L21_rplU_ 50S ribosomal protein L22_rplV_ 50S ribosomal protein L23_rplW_ 50S ribosomal protein L24_rplX_ 50S ribosomal protein L28_rpmB_ 50S ribosomal protein L3_rplC_ 50S ribosomal protein L35_rpmI_ 50S ribosomal protein L4_rplD_ 50S ribosomal protein L5_rplE_ 50S ribosomal protein L6_rplF_ 50S ribosomal protein L7/L12_rplL_ AAA-like domain protein_group_176_ AAA-like domain protein_group_177_ Alanine--tRNA ligase_alaS_ Alternate 30S ribosomal protein S14_rpsN2_ Aminopeptidase N_pepN_ Aquaporin Z_aqpZ_ Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B_gatB_ ATP-dependent Clp protease ATP-binding subunit ClpC_clpC_ ATP-dependent Clp protease proteolytic subunit_clpP_ ATP-dependent zinc metalloprotease FtsH_ftsH_ Bacterial membrane flanked domain protein_group_458_ Bifunctional PGK/TIM_pgk/tpi_ Cell division protein FtsZ_ftsZ_ Chaperone protein DnaK_dnaK_ Chromosomal replication initiator protein DnaA_dnaA_ Competence protein A_ftsA_2_ Competence protein ComM_comM_ Crossover junction RuvC_ruvC_ Cysteine desulfurase_iscS_ D-allulose-6-phosphate 3-epimerase_rpe_ Diadenosine hexaphosphate hydrolase_ndx1_ Disulfide bond formation protein D precursor_bdbD_ Divergent PAP2 family protein_group_473_ DNA gyrase subunit A_gyrA_ DNA gyrase subunit B_gyrB_ DNA polymerase I_ thermostable_polA_ DNA polymerase III subunit beta_dnaN_ DNA polymerase III subunit delta_group_440_ DNA polymerase III subunit tau_dnaX_2_ DNA repair protein RecO_recO_ DNA SpoIIIE_spoIIIE_ DNA-directed RNA polymerase subunit alpha_rpoA_ Elongation factor Ts_tsf_ 7 large subunit_xseA_ Exodeoxyribonuclease_exoA_ FK506-binding protein_fbp_ Formamidopyrimidine-DNA glycosylase_mutM_ GDP-mannose-dependent alpha-(1-6)-phosphatidylinositol monomannoside mannosyltransferase_pimB_ Glutamyl-tRNA(Gln) amidotransferase subunit A_gatA_ Glutamyl-tRNA(Gln) amidotransferase subunit C_gatC_ Glutaredoxin_group_345_ Glycine--tRNA ligase_glyQS_ GTPase Der_der_ heat shock protein GrpE_grpE_ Heat-inducible transcription repressor HrcA_hrcA_ Holliday junction ATP-dependent DNA helicase RuvA_ruvA_ Holliday junction ATP-dependent DNA helicase RuvB_ruvB_ hypothetical protein_CARKD_ hypothetical protein_ftsL_ hypothetical protein_ftsQ_ hypothetical protein_mprA_ hypothetical protein_surA_ Inorganic pyrophosphatase_ppa_ Leucine--tRNA ligase_leuS_ Lysine--tRNA ligase_lysS_ and cobalt efflux protein CorC_corC_ Membrane protein insertase YidC_yidC_ Membrane protein of unknown function_group_374_ metal-dependent hydrolase_group_464_ Metalloprotease MmpA_mmpA_ Methionine aminopeptidase 1_map_ Methionine--tRNA ligase_metG_ Methionyl-tRNA formyltransferase_fmt_ N-acetylmuramoyl-L-alanine amidase sle1 precursor_sle1_ Peptide chain release factor 2_prfB_ Peptide deformylase 1_def1_ Peptidyl-tRNA hydrolase_pth_ Phenylalanine--tRNA alpha subunit_pheS_ Phenylalanine--tRNA ligase beta subunit_pheT_ pheromone autoinducer 2 transporter_tqsA_ Photosystem I assembly protein Ycf3_ycf3_ preprotein translocase subunit SecA_secA_ preprotein translocase subunit SecE_secE_ preprotein translocase subunit SecG_group_373_ preprotein translocase subunit SecY_secY_ Primosomal protein N'_priA_ Proline--tRNA ligase_proS_ putative aminodeoxychorismate lyase_group_233_ putative chromosome-partitioning protein ParB_parB_ putative YcfH_ycfH_ putative peptidoglycan biosynthesis protein MurJ_murJ_ putative ribose-5-phosphate B_rpiB_ putative RNA methyltransferase_rlmCD_ putative sugar EpsL_epsL_ Putative transcriptional regulator YvhJ_yvhJ_ putative transcriptional regulatory protein TcrX_tcrX_ putative transcriptional regulatory protein/MSMEI_2866_pmpR_ putative tRNA-dihydrouridine synthase_dus_ Pyruvate kinase_pyk_ 3_rnc_ Ribonuclease HII_rnhB_ Ribonuclease J 1_rnjA_ protein component_rnpA_ Ribonuclease Y_rny_ Ribosomal large subunit pseudouridine synthase D_rluA_ Ribosomal RNA small subunit A_rsmA_ Ribosomal small subunit pseudouridine synthase A_rsuA_ -recycling factor_frr_ Sensor histidine kinase YycG_resE_1_ Sensor protein kinase WalK_yycG_1_ Serine--tRNA ligase_serS_ Sigma 54 modulation protein / S30EA ribosomal protein_yvyD_ Signal peptidase I T_sipT_ Single-stranded DNA-binding protein_ssb_ Sortase family protein_group_288_ Sporulation initiation inhibitor protein Soj_soj_ SsrA-binding protein_smpB_ Stress-induced bacterial acidophilic repeat motif protein_group_474_ Teichoic acid translocation permease protein TagG_tagG_ Teichoic acids export ATP-binding protein TagH_tagH_ Thioredoxin reductase_trxB_ Threonine--tRNA ligase_thrS_ Transcription elongation factor GreA_greA_ Transcriptional repressor NrdR_nrdR_ Translation initiation factor IF-3_infC_ tRNA (guanine-N(1)-)-methyltransferase_trmD_ tRNA dimethylallyltransferase_miaA_ tRNA pseudouridine synthase B_truB_ tRNA threonylcarbamoyladenosine biosynthesis protein TsaB_tsaB_ tRNA-specific 2-thiouridylase MnmA_mnmA_ tRNA(Ile)-lysidine synthase_tilS_ Tryptophan--tRNA ligase_trpS_ Type 4 prepilin-like leader peptide-processing enzyme_comC_ Type II secretion system protein F_epsF_ Tyrosine recombinase XerC_xerC_ UDP-N-acetylmuramoylalanine--D-glutamate ligase_murD_ Undecaprenyl-diphosphatase_uppP_ UvrABC system protein C_uvrC_ hypothetical protein_group_376_ hypothetical protein_group_393_ hypothetical protein_group_398_ hypothetical protein_group_410_ hypothetical protein_group_411_ hypothetical protein_group_412_ hypothetical protein_group_415_ hypothetical protein_group_443_ hypothetical protein_group_451_ hypothetical protein_group_452_ hypothetical protein_group_453_ hypothetical protein_group_455_ hypothetical protein_group_456_ hypothetical protein_group_460_ hypothetical protein_group_463_ hypothetical protein_group_470_ hypothetical protein_group_475_ hypothetical protein_group_485_ hypothetical protein_group_491_ hypothetical protein_group_501_ hypothetical protein_group_503_ hypothetical protein_group_505_ hypothetical protein_group_509_ hypothetical protein_group_523_ hypothetical protein_group_560_ hypothetical protein_group_561_ hypothetical protein_group_562_ hypothetical protein_group_567_ hypothetical protein_group_581_ hypothetical protein_group_584_ hypothetical protein_group_585_ Supplementary Table 7| Unique genes among the G5, G6, G3 and G1 genomes of Oral Saccharibacteria. Unique genes comparing full/ near complete genomes of four representatives from the G1-G6 groups. G5_TM7_ EAM_G5_2_HOT_356 G6_TM7_CMJM_G6_1_HOT_870 G3_TM7_KMM_G3_1_HOT_351 G1_TM7x Type_Strain_TM7x HOT_952 1_4-alpha-glucan branching GlgB_glgB_1_ Valine--tRNA ligase_group_132_valS 14.7 kDa -like protein_group_1091_rnhA_1 1-deoxy-D-xylulose-5-phosphate synthase_dxs_ 1_4-alpha-glucan branching enzyme GlgB_glgB_2_ UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase_group_261_murF2-succinyl-6-hydroxy-2_4-cyclohexadiene-1-carboxylate synthase_group_1130_menH1_4-alpha-glucan branching enzyme GlgB_glgB_ 23S rRNA (guanosine-2'-O-)-methyltransferase_group_828_ Type II secretion system protein E_epsE_ ABC transporter ATP-binding protein NatA_natA_ 3-oxoacyl-[acyl-carrier-protein] reductase FabG1_fabG1_ 30S ribosomal protein S1_group_155_rpsA Transcriptional regulatory protein TcrA_tcrA_ Acetyltransferase YpeA_ypeA_1_ 6-phospho-5-dehydro-2-deoxy-D-gluconate aldolase_iolJ_ 4_5:9_10-diseco-3-hydroxy-5_9_17-trioxoandrosta-1(10)_2-diene-4-oate hydrolase_hsaD_Transcriptional regulatory protein QseB_qseB_ Adenosine monophosphate-protein transferase NmFic_group_1162_ ABC transporter ATP-binding protein uup_uup_ 50S ribosomal protein L29_group_892_ Transcription elongation factor GreA_greA_1_ Adenylate kinase_adk_2_ Alkaline synthesis sensor protein PhoR_phoR_ 6-phosphogluconate dehydrogenase_ decarboxylating_gnd_ Signal transduction histidine-protein kinase ArlS_group_53_arlSADP-ribosyl-[dinitrogen reductase] glycohydrolase_draG_ Alpha/beta family protein_group_1288_ ABC-2 family transporter protein_group_803_ Sensor histidine kinase ResE_resE_2_ Alkyl hydroperoxide reductase subunit C_ahpC_ Alpha/beta hydrolase family protein_group_1297_ Adenosine monophosphate-protein transferase SoFic_group_518_ S-adenosylmethionine:tRNA ribosyltransferase-isomerase_queA_Alpha-monoglucosyldiacylglycerol synthase_group_103_ ATP synthase epsilon chain_atpC_ Adenosine monophosphate-protein transferase SoFic_group_519_ rRNA adenine N-6-methyltransferase_ermA1_ Alpha-monoglucosyldiacylglycerol synthase_group_104_ ATP synthase gamma chain_atpG_ Antitoxin MazE_mazE_ putative pyridine nucleotide-disulfide RclA_rclA_Arylsulfate sulfotransferase AssT_assT_ ATP synthase subunit a_atpB_ aspartoacylase_group_811_ putative glycosyltransferase EpsJ_group_320_epsJ ATP-dependent DNA helicase PcrA_group_144_pcrA ATP synthase subunit alpha_atpA_ Bacterial inner membrane protein_group_889_ putative AAA domain-containing protein_group_92_ Bacitracin export ATP-binding protein BceA_group_28_bceA ATP synthase subunit b_atpF_ Bifunctional hemolysin/adenylate cyclase precursor_cya_ putative ABC transporter ATP-binding protein_group_32_ Bacitracin export permease protein BceB_bceB_1_ ATP synthase subunit beta_atpD_ Calcium-transporting ATPase_group_122_ Phosphoserine phosphatase 1_pspA_ Bacitracin export permease protein BceB_bceB_2_ ATP-dependent RNA helicase HrpB_hrpB_ CorA-like Mg2 transporter protein_group_572_ Phosphoglucomutase_pgcA_ Beta-(1-->2)glucan export ATP-binding/permease protein NdvA_ndvA_ATP-dependent zinc metalloprotease FtsH 4_ftsH4_ CRISPR-associated Cas1_cas1_ Phenyllactate dehydrogenase_fldH_ Bifunctional (p)ppGpp synthase/hydrolase RelA_relA_2_ Autolysin_lytA_ CRISPR-associated endonuclease Cas9_cas9_ Nudix hydrolase_group_987_ Bifunctional (p)ppGpp synthase/hydrolase RelA_relA_1_ BNR/Asp-box repeat protein_group_1301_ CRISPR-associated endonuclease 2_cas9-2_ Lipoteichoic acid synthase 1_ltaS1_ Capsule biosynthesis protein CapA_capA_ Calcium-transporting ATPase 1_group_121_ CRISPR-associated Cas2_cas2_ Lipid II:glycine glycyltransferase_group_1058_femX Cell division ATP-binding protein FtsE_group_18_ftsE CDP-alcohol phosphatidyltransferase_group_1222_ CTP synthase_pyrG_ GTP-binding protein TypA/BipA_typA_ Cell division protein ZipA_zipA_ cell division protein MraZ_group_1220_ cysteine desulfurase activator complex subunit SufD_group_823_ Glycerophosphoryl diester phosphodiesterase_ugpQ_ Curved DNA-binding protein_cbpA_ Chaperone protein ClpB 1_clpB1_ D-alanyl-D-alanine endopeptidase_group_928_ Exodeoxyribonuclease 7 small subunit_xseB_ Decaprenyl-phosphate phosphoribosyltransferase_group_1064_ Competence protein A_group_242_ Divergent AAA domain protein_group_831_ Elongation factor 4_lepA_2_ Demethylmenaquinone methyltransferase_menG_ Copper-exporting P-type ATPase A_copA_ Divergent AAA domain protein_group_855_ Deoxyuridine 5'-triphosphate nucleotidohydrolase_dut_ DNA-directed RNA polymerase subunit beta_rpoB_1_ CYTH domain protein_group_767_ DNA adenine methyltransferase YhdJ_yhdJ_ Chaperone protein DnaJ_dnaJ_2_ Ethanolamine utilization protein EutD_eutD_ CYTH domain protein_group_768_ DNA mismatch repair protein_group_858_ ATP-dependent DNA helicase RecG_group_204_recG Exopolysaccharide phosphotransferase CpsY_cpsY_ D-alanyl-D-alanine carboxypeptidase_vanYB_ DNA polymerase III subunit delta_group_406_ Alpha-D-glucose 1-phosphate phosphatase YihX_yihX_ Glutamine--fructose-6-phosphate aminotransferase [isomerizing]_glmS_Daunorubicin/doxorubicin resistance ATP-binding protein DrrA_drrA_ DNA polymerase IV_dinB_ 2_3-bisphosphoglycerate-dependent phosphoglycerate mutase_group_248_gpmAHigh-affinity zinc uptake system membrane protein ZnuB_znuB_ Dihydroorotate dehydrogenase (quinone)_pyrD_ DSBA-like thioredoxin domain protein_group_213_ hypothetical protein_group_1000_ L-glutamine:2-deoxy-scyllo-inosose aminotransferase_btrR_ DNA topoisomerase I_group_1329_ Eco47II restriction endonuclease_group_905_ hypothetical protein_group_999_ Macrolide export ATP-binding/permease protein MacB_macB_ DNA-binding response regulator MtrA_mtrA_ EcoKI restriction-modification system protein HsdS_group_793_ hypothetical protein_group_998_ PhoH-like protein_group_1166_ dTDP-4-dehydrorhamnose reductase_rmlD_1_ Elongation factor Tu_group_65_tuf hypothetical protein_group_997_ Phosphoglucosamine mutase_glmM_ dTDP-4-dehydrorhamnose reductase_rmlD_2_ Endonuclease III_nth_ hypothetical protein_group_996_ Phosphorylated carbohydrates phosphatase_group_1083_ EcoKI restriction-modification system protein HsdS_group_765_ exodeoxyribonuclease VII small subunit_group_903_ hypothetical protein_group_995_ Putative multidrug export ATP-binding/permease protein_group_19_ EcoKI restriction-modification system protein HsdS_group_766_ FemAB family protein_group_486_ hypothetical protein_group_994_ putative periplasmic iron-binding protein_group_1112_ Elongation factor Tu_tuf_ Fic/DOC family protein_group_520_ hypothetical protein_group_993_ Ribose-phosphate pyrophosphokinase_prs_ Endoglucanase C307 precursor_group_1328_ FtsX-like permease family protein_group_280_ hypothetical protein_group_992_ rRNA adenine N-6-methyltransferase_erm_ Eukaryotic phosphomannomutase_group_1271_ FtsX-like permease family protein_group_533_ hypothetical protein_group_991_ Rubrerythrin-1_rbr1_ F0F1 ATP synthase subunit C_group_1232_ FtsX-like permease family protein_group_534_ hypothetical protein_group_990_ S-adenosylmethionine synthase_metK_ F0F1 ATP synthase subunit delta_group_1234_ FtsX-like permease family protein_group_535_ hypothetical protein_group_989_ Thymidine kinase_tdk_ Ferric uptake regulator family protein_group_1299_ FtsX-like permease family protein_group_788_ hypothetical protein_group_988_ Thymidylate synthase_thyA_ Flavohemoprotein_hmp_ GDSL-like /Acylhydrolase_group_837_ hypothetical protein_group_985_ Translation initiation factor IF-2_group_68_infB FtsX-like permease family protein_group_281_ GMP synthase [glutamine-hydrolyzing]_guaA_ hypothetical protein_group_984_ Type II secretion system protein E_group_97_epsE General stress protein A_gspA_ GTP-binding protein TypA/BipA_group_71_typA hypothetical protein_group_983_ Xylulose-5-phosphate phosphoketolase_xpkA_ Glucan endo-1_3-beta-glucosidase A1 precursor_glcA_ Ham1 family protein_group_875_ hypothetical protein_group_125_ hypothetical protein_group_1065_ Gluconeogenesis factor_group_1219_ Helix-turn-helix domain protein_group_884_ hypothetical protein_group_981_ hypothetical protein_group_1066_ Glucose-1-phosphate thymidylyltransferase 1_rmlA1_ Hemolysin secretion protein D_ chromosomal_hlyD_ hypothetical protein_group_980_ hypothetical protein_group_1067_ Glycerol-3-phosphate cytidylyltransferase_tagD_ HTH-type transcriptional regulator IscR_iscR_ hypothetical protein_group_979_ hypothetical protein_group_1068_ GTP-binding protein TypA/BipA_group_73_typA Inner membrane protein YiaH_yiaH_ hypothetical protein_group_978_ hypothetical protein_group_1070_ Hemolysin C_tlyC_ Integrase core domain protein_group_894_ hypothetical protein_group_977_ hypothetical protein_group_1073_ Hypoxanthine-guanine phosphoribosyltransferase_hpt_ Isoleucine--tRNA ligase 2_group_198_ileS2 hypothetical protein_group_976_ hypothetical protein_group_1074_ Inner membrane transport permease YbhS_ybhS_ L_D-transpeptidase catalytic domain_group_914_ hypothetical protein_group_975_ hypothetical protein_group_1075_ Integral membrane protein TerC family protein_group_1226_ Lipoprotein-releasing system ATP-binding protein LolD_lolD_4_ hypothetical protein_group_974_ hypothetical protein_group_1076_ KAP family P-loop domain protein_group_1341_ Lipoprotein-releasing system ATP-binding protein LolD_lolD_2_ hypothetical protein_group_973_ hypothetical protein_group_1077_ Lipoteichoic acid synthase 2_ltaS2_ Lipoprotein-releasing system ATP-binding protein LolD_lolD_3_ hypothetical protein_group_972_ hypothetical protein_group_1078_ Lysine--tRNA ligase_group_173_lysS Listeria-Bacteroides repeat domain (List_Bact_rpt)_group_888_ hypothetical protein_group_971_ hypothetical protein_group_1079_ Magnesium transport protein CorA_corA_1_ Macrolide export ATP-binding/permease protein MacB_macB_2_ hypothetical protein_group_970_ hypothetical protein_group_1081_ Magnesium transport protein CorA_corA_2_ Modification methylase BspRI_bspRIM_ hypothetical protein_group_969_ hypothetical protein_group_1082_ Mannosylfructose-phosphate synthase_mfpsA_ Modification methylase HaeIII_haeIIIM_ hypothetical protein_group_967_ hypothetical protein_group_1084_ Mercuric reductase_group_270_merA mRNA interferase PemK_pemK_ hypothetical protein_group_966_ hypothetical protein_group_1085_ Methylated-DNA--protein-cysteine methyltransferase_group_1191_ogt Murein DD-endopeptidase MepH precursor_mepH_ hypothetical protein_group_964_ hypothetical protein_group_1086_ molybdenum biosynthesis protein A_group_1345_ NlpC/P60 family protein_group_869_ hypothetical protein_group_963_ hypothetical protein_group_1087_ Multi-copper polyphenol oxidoreductase laccase_group_1305_ Nucleoside 2-deoxyribosyltransferase_group_841_ hypothetical protein_group_962_ hypothetical protein_group_1088_ NAD-dependent malic enzyme_group_1275_ Peptidase M16 inactive domain protein_group_252_ hypothetical protein_group_961_ hypothetical protein_group_1090_ NADH pyrophosphatase_group_1250_ Protein of unknown function (Hypoth_ymh)_group_791_ hypothetical protein_group_960_ hypothetical protein_group_1092_ nucleoside triphosphate pyrophosphohydrolase_group_117_ Pullulanase precursor_pulA_ hypothetical protein_group_959_ hypothetical protein_group_1093_ Peptidoglycan-N-acetylmuramic acid deacetylase PdaC_pdaC_ putative ABC transporter ATP-binding protein_group_35_ hypothetical protein_group_958_ hypothetical protein_group_1094_ Phosphotransferase enzyme family protein_group_769_ putative ABC transporter ATP-binding protein_group_36_ hypothetical protein_group_957_ hypothetical protein_group_1097_ PKD domain protein_group_760_ putative ABC transporter ATP-binding protein_group_6_ hypothetical protein_group_956_ hypothetical protein_group_1098_ Poly-beta-1_6-N-acetyl-D-glucosamine synthase_pgaC_ putative ABC transporter ATP-binding protein YxlF_yxlF_ hypothetical protein_group_955_ hypothetical protein_group_1099_ Polysaccharide biosynthesis protein_group_1351_ putative ABC transporter ATP-binding protein/MT2552_group_7_ hypothetical protein_group_954_ hypothetical protein_group_1102_ putative ABC transporter ATP-binding protein_group_11_ putative aminodeoxychorismate lyase_group_165_ hypothetical protein_group_953_ hypothetical protein_group_1103_ putative ABC transporter ATP-binding protein_group_12_ putative BsuMI modification methylase subunit YdiO_ydiO_ hypothetical protein_group_952_ hypothetical protein_group_1104_ putative ABC transporter ATP-binding protein YbhF_ybhF_ Putative glycosyltransferase CsbB_csbB_ hypothetical protein_group_951_ hypothetical protein_group_1106_ putative ABC transporter ATP-binding protein YjjK_yjjK_ putative kinase inhibitor protein_group_789_ hypothetical protein_group_950_ hypothetical protein_group_1107_ putative aminodeoxychorismate lyase_group_166_ Putative mutator protein MutT4_group_112_mutT4 hypothetical protein_group_949_ hypothetical protein_group_1108_ putative dTDP-4-dehydrorhamnose 3_5-epimerase_rfbC_ Putative NAD(P)H nitroreductase/MT3217_group_857_ hypothetical protein_group_948_ hypothetical protein_group_1110_ Putative F0F1-ATPase subunit (ATPase_gene1)_group_1230_ putative oxidoreductase_group_832_ hypothetical protein_group_265_ hypothetical protein_group_1111_ putative glycosyl transferase_group_108_ Regulator of chromosome condensation (RCC1) repeat protein_group_338_ hypothetical protein_group_946_ hypothetical protein_group_1115_ putative glycosyl transferase_group_1295_ Regulator of chromosome condensation (RCC1) repeat protein_group_562_ hypothetical protein_group_945_ hypothetical protein_group_1116_ Putative multidrug export ATP-binding/permease protein_group_14_ Ribonuclease H_rnhA_1_ hypothetical protein_group_944_ hypothetical protein_group_1117_ putative nucleotide-binding protein_group_1262_ Ribonuclease H_rnhA_2_ hypothetical protein_group_469_ hypothetical protein_group_1118_ putative permease_group_1225_ RNA polymerase sigma factor_group_171_ hypothetical protein_group_942_ hypothetical protein_group_1119_ Putative serine protease HtrA_group_1261_htrA shikimate kinase_group_838_ hypothetical protein_group_941_ hypothetical protein_group_1120_ Putative type-1 specificity protein MG438_group_1340_ Signal transduction histidine-protein kinase ArlS_arlS_ hypothetical protein_group_940_ hypothetical protein_group_1121_ Pyridoxamine 5'-phosphate oxidase_group_1183_ Sortase family protein_group_360_ hypothetical protein_group_84_ hypothetical protein_group_1122_ Regulator of chromosome condensation (RCC1) repeat protein_group_335_ Spore protein SP21_hspA_2_ hypothetical protein_group_83_ hypothetical protein_group_1123_ Regulator of chromosome condensation (RCC1) repeat protein_group_336_ Toxin RTX-I translocation ATP-binding protein_apxIB_ hypothetical protein_group_1030_ hypothetical protein_group_1124_ Reverse transcriptase (RNA-dependent DNA polymerase)_group_1339_ Transcriptional activator protein CopR_copR_ hypothetical protein_group_266_ hypothetical protein_group_1125_ Ribonucleoside-diphosphate reductase NrdZ_nrdZ_ Transcriptional activator protein CzcR_czcR_ hypothetical protein_group_947_ hypothetical protein_group_1126_ Ribonucleoside-diphosphate reductase subunit beta_nrdB_ Transcriptional regulator PadR-like family protein_group_787_ hypothetical protein_group_943_ hypothetical protein_group_1127_ RNA pyrophosphohydrolase_group_115_ Translation initiation factor IF-2_group_72_infB hypothetical protein_group_1025_ hypothetical protein_group_1128_ RNA pyrophosphohydrolase_rppH_ TrbC/VIRB2 family protein_group_79_ hypothetical protein_group_491_ hypothetical protein_group_1129_ Sensor histidine kinase YycG_yycG_1_ Type I restriction enzyme EcoKI M protein_hsdM_ hypothetical protein_group_1032_ hypothetical protein_group_1131_ Sortase family protein_group_221_ Uracil DNA glycosylase superfamily protein_group_829_ hypothetical protein_group_939_ hypothetical protein_group_1132_ Superoxide dismutase [Mn]_sodA_ hypothetical protein_group_187_ hypothetical protein_group_164_ hypothetical protein_group_1133_ Thioredoxin-1_trxA_ hypothetical protein_group_188_ hypothetical protein_group_1038_ hypothetical protein_group_1134_ Threonylcarbamoyl-AMP synthase_ywlC_ hypothetical protein_group_189_ hypothetical protein_group_982_ hypothetical protein_group_1135_ Transcription elongation factor GreA_greA_2_ hypothetical protein_group_190_ hypothetical protein_group_1005_ hypothetical protein_group_1136_ Transcriptional regulator WhiB4_whiB4_ hypothetical protein_group_191_ hypothetical protein_group_127_ hypothetical protein_group_1137_ Transcriptional regulatory protein CusR_cusR_ hypothetical protein_group_192_ hypothetical protein_group_128_ hypothetical protein_group_1138_ Transcriptional repressor CopY_copY_ hypothetical protein_group_193_ hypothetical protein_group_1062_ hypothetical protein_group_1139_ Transcriptional repressor NrdR_nrdR_1_ hypothetical protein_group_215_ hypothetical protein_group_1061_ hypothetical protein_group_1140_ Transketolase 1_tktA_ hypothetical protein_group_216_ hypothetical protein_group_1060_ hypothetical protein_group_1141_ tRNA (guanosine(18)-2'-O)-methyltransferase_trmH_1_ hypothetical protein_group_217_ hypothetical protein_group_1057_ hypothetical protein_group_1143_ Type I restriction enzyme EcoKI M protein_group_210_hsdM hypothetical protein_group_218_ hypothetical protein_group_1056_ hypothetical protein_group_1144_ Type II secretion system protein E_group_94_xpsE_1 hypothetical protein_group_219_ hypothetical protein_group_1055_ hypothetical protein_group_1145_ Type II secretion system protein E_xpsE_3_ hypothetical protein_group_223_ hypothetical protein_group_1054_ hypothetical protein_group_1146_ Type II secretion system protein F_epsF_2_ hypothetical protein_group_224_ hypothetical protein_group_1053_ hypothetical protein_group_1147_ Type II secretion system protein G precursor_xcpT_ hypothetical protein_group_225_ hypothetical protein_group_1052_ hypothetical protein_group_1148_ Type-1 restriction enzyme R protein_hsdR_1_ hypothetical protein_group_232_ hypothetical protein_group_1051_ hypothetical protein_group_1149_ Tyrosine recombinase XerC_xerC_2_ hypothetical protein_group_233_ hypothetical protein_group_1050_ hypothetical protein_group_1150_ undecaprenyl pyrophosphate phosphatase_group_1290_ hypothetical protein_group_234_ hypothetical protein_group_1049_ hypothetical protein_group_1151_ Undecaprenyl-phosphate mannosyltransferase_group_109_ hypothetical protein_group_235_ hypothetical protein_group_1048_ hypothetical protein_group_1152_ UTP--glucose-1-phosphate uridylyltransferase_group_273_gtaB hypothetical protein_group_236_ hypothetical protein_group_1047_ hypothetical protein_group_1153_ UTP--glucose-1-phosphate uridylyltransferase_galU_ hypothetical protein_group_264_ hypothetical protein_group_1046_ hypothetical protein_group_1154_ UvrABC system protein A_uvrA_ hypothetical protein_group_377_ hypothetical protein_group_1045_ hypothetical protein_group_1155_ UvrABC system protein B_group_205_uvrB hypothetical protein_group_378_ hypothetical protein_group_1044_ hypothetical protein_group_1157_ VIT family protein_group_1327_ hypothetical protein_group_380_ hypothetical protein_group_1043_ hypothetical protein_group_1158_ Vitamin K epoxide reductase family protein_group_1201_ hypothetical protein_group_381_ hypothetical protein_group_1042_ hypothetical protein_group_1159_ Zinc-specific metallo-regulatory protein_zur_ hypothetical protein_group_382_ hypothetical protein_group_1041_ hypothetical protein_group_1160_ hypothetical protein_group_1173_ hypothetical protein_group_556_ hypothetical protein_group_1040_ hypothetical protein_group_1163_ hypothetical protein_group_1174_ hypothetical protein_group_557_ hypothetical protein_group_1039_ hypothetical protein_group_1164_ hypothetical protein_group_1175_ hypothetical protein_group_558_ hypothetical protein_group_126_ hypothetical protein_group_1165_ hypothetical protein_group_1176_ hypothetical protein_group_561_ hypothetical protein_group_1037_ hypothetical protein_group_1167_ hypothetical protein_group_1178_ hypothetical protein_group_563_ hypothetical protein_group_1035_ hypothetical protein_group_1168_ hypothetical protein_group_1179_ hypothetical protein_group_650_ hypothetical protein_group_1034_ hypothetical protein_group_1169_ hypothetical protein_group_1180_ hypothetical protein_group_651_ hypothetical protein_group_1033_ hypothetical protein_group_1170_ hypothetical protein_group_1184_ hypothetical protein_group_652_ hypothetical protein_group_186_ hypothetical protein_group_1171_ hypothetical protein_group_1185_ hypothetical protein_group_653_ hypothetical protein_group_1031_ hypothetical protein_group_1172_ hypothetical protein_group_1187_ hypothetical protein_group_655_ hypothetical protein_group_85_ hypothetical protein_group_133_ hypothetical protein_group_1188_ hypothetical protein_group_656_ hypothetical protein_group_1029_ hypothetical protein_group_134_ hypothetical protein_group_1189_ hypothetical protein_group_662_ hypothetical protein_group_1027_ hypothetical protein_group_135_ hypothetical protein_group_1190_ hypothetical protein_group_663_ hypothetical protein_group_1026_ hypothetical protein_group_136_ hypothetical protein_group_1192_ hypothetical protein_group_670_ hypothetical protein_group_492_ hypothetical protein_group_137_ hypothetical protein_group_1193_ hypothetical protein_group_671_ hypothetical protein_group_1024_ hypothetical protein_group_138_ hypothetical protein_group_1195_ hypothetical protein_group_676_ hypothetical protein_group_1023_ hypothetical protein_group_139_ hypothetical protein_group_1196_ hypothetical protein_group_677_ hypothetical protein_group_1022_ hypothetical protein_group_140_ hypothetical protein_group_1197_ hypothetical protein_group_679_ hypothetical protein_group_1021_ hypothetical protein_group_141_ hypothetical protein_group_1198_ hypothetical protein_group_680_ hypothetical protein_group_1020_ hypothetical protein_group_158_ hypothetical protein_group_1199_ hypothetical protein_group_681_ hypothetical protein_group_1019_ hypothetical protein_group_229_ hypothetical protein_group_1200_ hypothetical protein_group_682_ hypothetical protein_group_1018_ hypothetical protein_group_230_ hypothetical protein_group_1202_ hypothetical protein_group_683_ hypothetical protein_group_1017_ hypothetical protein_group_500_ hypothetical protein_group_1203_ hypothetical protein_group_684_ hypothetical protein_group_1016_ hypothetical protein_group_501_ hypothetical protein_group_1204_ hypothetical protein_group_697_ hypothetical protein_group_1015_ hypothetical protein_group_502_ hypothetical protein_group_1205_ hypothetical protein_group_698_ hypothetical protein_group_1014_ hypothetical protein_group_503_ hypothetical protein_group_1206_ hypothetical protein_group_701_ hypothetical protein_group_1013_ hypothetical protein_group_504_ hypothetical protein_group_1207_ hypothetical protein_group_702_ hypothetical protein_group_1012_ hypothetical protein_group_505_ hypothetical protein_group_1208_ hypothetical protein_group_75_ hypothetical protein_group_1011_ hypothetical protein_group_506_ hypothetical protein_group_1209_ hypothetical protein_group_777_ hypothetical protein_group_1010_ hypothetical protein_group_507_ hypothetical protein_group_1211_ hypothetical protein_group_778_ hypothetical protein_group_1009_ hypothetical protein_group_607_ hypothetical protein_group_1212_ hypothetical protein_group_779_ hypothetical protein_group_1008_ hypothetical protein_group_609_ hypothetical protein_group_1213_ hypothetical protein_group_780_ hypothetical protein_group_1006_ hypothetical protein_group_643_ hypothetical protein_group_1214_ hypothetical protein_group_781_ hypothetical protein_group_123_ hypothetical protein_group_644_ hypothetical protein_group_1215_ hypothetical protein_group_782_ hypothetical protein_group_1004_ hypothetical protein_group_645_ hypothetical protein_group_1216_ hypothetical protein_group_783_ hypothetical protein_group_1003_ hypothetical protein_group_749_ hypothetical protein_group_1217_ hypothetical protein_group_784_ hypothetical protein_group_1002_ hypothetical protein_group_750_ hypothetical protein_group_1221_ hypothetical protein_group_786_ hypothetical protein_group_1001_ Inner membrane protein YrbG_yrbG_ hypothetical protein_group_1224_ hypothetical protein_group_790_ hypothetical protein_group_1227_ hypothetical protein_group_792_ hypothetical protein_group_1228_ hypothetical protein_group_794_ hypothetical protein_group_1229_ hypothetical protein_group_795_ hypothetical protein_group_1237_ hypothetical protein_group_796_ hypothetical protein_group_1238_ hypothetical protein_group_797_ hypothetical protein_group_1239_ hypothetical protein_group_798_ hypothetical protein_group_1240_ hypothetical protein_group_799_ hypothetical protein_group_1241_ hypothetical protein_group_80_ hypothetical protein_group_1242_ hypothetical protein_group_800_ hypothetical protein_group_1244_ hypothetical protein_group_801_ hypothetical protein_group_1245_ hypothetical protein_group_804_ hypothetical protein_group_1248_ hypothetical protein_group_805_ hypothetical protein_group_1249_ hypothetical protein_group_806_ hypothetical protein_group_1252_ hypothetical protein_group_808_ hypothetical protein_group_1253_ hypothetical protein_group_810_ hypothetical protein_group_1255_ hypothetical protein_group_812_ hypothetical protein_group_1256_ hypothetical protein_group_814_ hypothetical protein_group_1257_ hypothetical protein_group_815_ hypothetical protein_group_1258_ hypothetical protein_group_817_ hypothetical protein_group_1259_ hypothetical protein_group_818_ hypothetical protein_group_1260_ hypothetical protein_group_820_ hypothetical protein_group_1263_ hypothetical protein_group_824_ hypothetical protein_group_1264_ hypothetical protein_group_825_ hypothetical protein_group_1265_ hypothetical protein_group_826_ hypothetical protein_group_1266_ hypothetical protein_group_827_ hypothetical protein_group_1267_ hypothetical protein_group_830_ hypothetical protein_group_1268_ hypothetical protein_group_833_ hypothetical protein_group_1269_ hypothetical protein_group_834_ hypothetical protein_group_1270_ hypothetical protein_group_835_ hypothetical protein_group_1272_ hypothetical protein_group_836_ hypothetical protein_group_1273_ hypothetical protein_group_839_ hypothetical protein_group_1274_ hypothetical protein_group_840_ hypothetical protein_group_1276_ hypothetical protein_group_842_ hypothetical protein_group_1277_ hypothetical protein_group_843_ hypothetical protein_group_1278_ hypothetical protein_group_844_ hypothetical protein_group_1279_ hypothetical protein_group_845_ hypothetical protein_group_1280_ hypothetical protein_group_846_ hypothetical protein_group_1281_ hypothetical protein_group_847_ hypothetical protein_group_1283_ hypothetical protein_group_848_ hypothetical protein_group_1286_ hypothetical protein_group_849_ hypothetical protein_group_1287_ hypothetical protein_group_850_ hypothetical protein_group_1289_ hypothetical protein_group_851_ hypothetical protein_group_1291_ hypothetical protein_group_852_ hypothetical protein_group_1292_ hypothetical protein_group_853_ hypothetical protein_group_1293_ hypothetical protein_group_854_ hypothetical protein_group_1294_ hypothetical protein_group_856_ hypothetical protein_group_1296_ hypothetical protein_group_859_ hypothetical protein_group_1300_ hypothetical protein_group_860_ hypothetical protein_group_1302_ hypothetical protein_group_861_ hypothetical protein_group_1303_ hypothetical protein_group_862_ hypothetical protein_group_1306_ hypothetical protein_group_863_ hypothetical protein_group_1307_ hypothetical protein_group_864_ hypothetical protein_group_1308_ hypothetical protein_group_865_ hypothetical protein_group_1310_ hypothetical protein_group_866_ hypothetical protein_group_1311_ hypothetical protein_group_867_ hypothetical protein_group_1312_ hypothetical protein_group_868_ hypothetical protein_group_1313_ hypothetical protein_group_870_ hypothetical protein_group_1314_ hypothetical protein_group_871_ hypothetical protein_group_1315_ hypothetical protein_group_872_ hypothetical protein_group_1316_ hypothetical protein_group_873_ hypothetical protein_group_1317_ hypothetical protein_group_874_ hypothetical protein_group_1318_ hypothetical protein_group_876_ hypothetical protein_group_1319_ hypothetical protein_group_877_ hypothetical protein_group_1320_ hypothetical protein_group_878_ hypothetical protein_group_1321_ hypothetical protein_group_879_ hypothetical protein_group_1323_ hypothetical protein_group_882_ hypothetical protein_group_1324_ hypothetical protein_group_883_ hypothetical protein_group_1325_ hypothetical protein_group_885_ hypothetical protein_group_1326_ hypothetical protein_group_886_ hypothetical protein_group_1330_ hypothetical protein_group_887_ hypothetical protein_group_1332_ hypothetical protein_group_890_ hypothetical protein_group_1333_ hypothetical protein_group_891_ hypothetical protein_group_1334_ hypothetical protein_group_893_ hypothetical protein_group_1337_ hypothetical protein_group_895_ hypothetical protein_group_1338_ hypothetical protein_group_896_ hypothetical protein_group_1342_ hypothetical protein_group_897_ hypothetical protein_group_1343_ hypothetical protein_group_898_ hypothetical protein_group_1349_ hypothetical protein_group_904_ hypothetical protein_group_185_ hypothetical protein_group_906_ hypothetical protein_group_226_ hypothetical protein_group_907_ hypothetical protein_group_337_ hypothetical protein_group_908_ hypothetical protein_group_383_ hypothetical protein_group_909_ hypothetical protein_group_757_ hypothetical protein_group_910_ hypothetical protein_group_758_ hypothetical protein_group_912_ hypothetical protein_group_759_ hypothetical protein_group_913_ hypothetical protein_group_761_ hypothetical protein_group_915_ hypothetical protein_group_762_ hypothetical protein_group_916_ hypothetical protein_group_770_ hypothetical protein_group_917_ hypothetical protein_group_773_ hypothetical protein_group_918_ hypothetical protein_group_774_ hypothetical protein_group_919_ hypothetical protein_group_82_ hypothetical protein_group_920_ hypothetical protein_group_921_ hypothetical protein_group_922_ hypothetical protein_group_923_ hypothetical protein_group_924_ hypothetical protein_group_925_ hypothetical protein_group_926_ hypothetical protein_group_927_ hypothetical protein_group_929_ hypothetical protein_group_930_ hypothetical protein_group_931_ hypothetical protein_group_932_ hypothetical protein_group_933_ hypothetical protein_group_934_ hypothetical protein_group_935_ hypothetical protein_group_936_ hypothetical protein_group_937_

Supplemental Figure 1 | Full matrix of AAI, orthologous genes and percent orthologous fraction provided for each genome pair in Figure 2.