Suppl Table 4 - V5 Bacterial genomes and mRNAs.xlsx - PLOS

Table S4. Bacteria mRNA (and other non-‐rRNA) gene sequences from V5. ["n" indicates information not specified in the NCBI GenBank database.]

454 Sequence ID GKJWQY101AGGHX GKJWQY101BLAHS GKJWQY101BM4QM GKJWQY101BHEK2 GKJWQY101ALVRX GKJWQY101B2Q7Z GKJWQY101BJIYE GKJWQY101BP0TD GKJWQY101B2BHA GKJWQY101AE43F GKJWQY101A68QX GKJWQY101AH1E9 GKJWQY101BPEIQ GKJWQY101AFA5U GKJWQY101A4K6T GKJWQY101AAOCE GKJWQY101B0JWH GKJWQY101BKG7S GKJWQY101A5PQZ GKJWQY101A65QS GKJWQY101BB5IP GKJWQY101BC0IC GKJWQY101AQ51G GKJWQY101AV3CT GKJWQY101ASGX9 GKJWQY101A6R2G GKJWQY101BURAB GKJWQY101BLJAK GKJWQY101APUX9 GKJWQY101A2KCQ GKJWQY101ANZOF GKJWQY101BUUW5 GKJWQY101BQQMF GKJWQY101BGIIN GKJWQY101B2ENG GKJWQY101BHBKI GKJWQY101AJ2KZ GKJWQY101A4I0Z GKJWQY101BS0NP GKJWQY101AN552 GKJWQY101AWOSS GKJWQY101AP6Y7 GKJWQY101BYSCO GKJWQY101BJIPK GKJWQY101BZXZT GKJWQY101BEOT5 GKJWQY101ABFUA GKJWQY101A91OF GKJWQY101A8VQ6 GKJWQY101ASMWQ GKJWQY101BB7VS GKJWQY101ADTE9 GKJWQY101AIKHU GKJWQY101A4H47 GKJWQY101AXWLH GKJWQY101BYVV6 GKJWQY101AGPF8 GKJWQY101AQPZB GKJWQY101ACHK0 GKJWQY101BXWGA GKJWQY101BY2F1 GKJWQY101A5ZEU GKJWQY101APB60 GKJWQY101BC039 GKJWQY101ATFBR GKJWQY101BRVHX GKJWQY101BYL6X GKJWQY101AWOW9

Q length Q start Q end 545 5 506 571 66 567 251 3 199 433 5 376 500 5 174 448 36 408 542 38 541 550 202 550 504 342 439 573 18 571 413 315 358 507 161 482 456 17 410 502 380 494 615 4 148 567 19 512 576 227 572 547 17 512 510 4 427 554 23 549 574 5 569 557 16 556 597 5 571 587 19 581 573 17 503 571 5 570 566 21 523 582 5 398 573 5 569 591 17 589 303 4 68 565 17 562 393 18 342 310 18 247 246 18 200 544 18 518 595 18 592 576 19 574 584 64 582 561 4 559 589 4 587 476 18 421 548 7 537 572 1 569 586 18 571 555 20 329 587 17 582 548 15 506 567 32 251 163 29 136 233 67 184 305 19 271 277 4 217 553 333 381 352 18 320 360 16 277 340 16 279 526 5 383 426 24 349 568 157 184 480 18 443 261 8 214 447 5 401 546 335 540 558 5 556 334 19 280 559 4 543 290 5 221

e-‐value %-‐ident 0 97% 2E-‐172 89% 2E-‐75 93% 0 98% 2E-‐82 100% 3E-‐140 91% 3E-‐180 90% 1E-‐80 83% 1E-‐39 98% 0 91% 0.0000002 93% 2E-‐83 85% 0 96% 8E-‐27 87% 2E-‐29 85% 3E-‐136 85% 4E-‐115 89% 6E-‐148 86% 4E-‐124 86% 0 95% 0 94% 3E-‐175 88% 0 88% 0 93% 2E-‐173 90% 0 94% 2E-‐92 80% 1E-‐144 91% 4E-‐170 87% 0 94% 2E-‐15 92% 0 93% 4E-‐78 84% 3E-‐89 93% 4E-‐62 91% 0 96% 0 89% 0 88% 0 91% 0 88% 0 87% 8E-‐156 92% 7E-‐167 87% 0 92% 0 94% 8E-‐132 95% 0 89% 0 91% 4E-‐45 83% 1E-‐40 95% 2E-‐40 93% 2E-‐90 91% 4E-‐92 96% 4E-‐10 94% 3E-‐104 90% 7E-‐41 79% 4E-‐43 80% 2E-‐68 80% 8E-‐61 81% 0.002 100% 1E-‐124 86% 4E-‐92 97% 1E-‐158 92% 3E-‐17 76% 0 90% 8E-‐85 89% 0 90% 2E-‐80 92%

%-‐sim 97% 89% 93% 98% 100% 91% 90% 83% 98% 91% 93% 85% 96% 87% 85% 85% 89% 86% 86% 95% 94% 88% 88% 93% 90% 94% 80% 91% 87% 94% 92% 93% 84% 93% 91% 96% 89% 88% 91% 88% 87% 92% 87% 92% 94% 95% 89% 91% 83% 95% 93% 91% 96% 94% 90% 79% 80% 80% 81% 100% 86% 97% 92% 76% 90% 89% 90% 92%

GI number 31789410 117647674 140843962 111147037 119951388 41019279 145301903 118168627 76556220 133909243 24413764 260644157 118764602 295793053 291516109 257473675 295105686 108764099 256007408 38200856 68262661 237757549 256687298 119947346 183579876 162952245 119953846 54013472 110816552 269095543 212548595 188593544 291513545 254946573 283814236 294979899 52214156 60491031 29342101 149931032 149935098 34398108 294471613 255340365 146152184 149770655 255342900 295083795 269787736 37508091 171696371 218169741 256588085 256592529 146740642 147849409 33633126 47118315 242955773 111610610 47606667 186463002 47118302 17134864 146740643 146740638 158303474 284809060

Domain Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria

Phylum Acidobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Bacteroidetes Bacteroidetes Bacteroidetes Bacteroidetes Bacteroidetes Bacteroidetes Bacteroidetes Bacteroidetes Bacteroidetes Bacteroidetes Bacteroidetes Bacteroidetes Bacteroidetes Bacteroidetes Bacteroidetes Bacteroidetes Bacteroidetes Bacteroidetes Chloroflexi Cyanobacteria Cyanobacteria Cyanobacteria Cyanobacteria Cyanobacteria Cyanobacteria Cyanobacteria Cyanobacteria Cyanobacteria Cyanobacteria Cyanobacteria Cyanobacteria Cyanobacteria Cyanobacteria Cyanobacteria Cyanobacteria Cyanobacteria Cyanobacteria Cyanobacteria

Class / Order n Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Actinobacteria Bacteroidia Bacteroidia Bacteroidia Cytophagia Cytophagia Flavobacteria Bacteroidia Bacteroidia Bacteroidia Bacteroidia Bacteroidia Bacteroidia Bacteroidia Flavobacteria Flavobacteria Flavobacteria Sphingobacteria Bacteroidia Thermomicrobia Gloeobacteria Chroococcales Chroococcales Chroococcales Chroococcales Chroococcales Chroococcales Chroococcales Chroococcales Nostocales Nostocales Nostocales Nostocales Nostocales Nostocales Oscillatoriales Prochlorales n n

Description Uncultured Acidobacteria bacterium clone 38c7 genomic sequence Acidothermus cellulolyticus 11B strain 11B, complete genome Corynebacterium glutamicum R DNA, complete genome Frankia alni str. ACN14A chromosome, complete sequence Arthrobacter aurescens TC1 plasmid TC1, complete sequence Micromonospora echinospora ATCC 15835 gentamicin biosynthesis gene cluster, complete sequence Salinispora tropica CNB-‐440, complete genome Mycobacterium smegmatis str. MC2 155, complete genome Propionibacterium freudenreichii subsp. shermanii fba2 gene for fructose-‐bisphosphate aldolase class I Saccharopolyspora erythraea NRRL2338 complete genome Streptomyces coelicolor A3(2) complete genome; segment 9/29 Streptomyces scabiei 87.22 complete genome Bifidobacterium adolescentis ATCC 15703 DNA, complete genome Bifidobacterium animalis subsp. lactis V9, complete genome Bifidobacterium longum longum F8 draft genome Eggerthella lenta DSM 2243, complete genome Gordonibacter pamelaeae 7-‐10-‐1-‐bT draft genome Rubrobacter xylanophilus DSM 9941, complete genome Acidimicrobium ferrooxidans DSM 10331, complete genome Corynebacterium diphtheriae gravis NCTC13129, complete genome; segment 7/8 Corynebacterium jeikeium K411 complete genome Corynebacterium kroppenstedtii DSM 44385, complete genome Kytococcus sedentarius DSM 20547, complete genome Arthrobacter aurescens TC1, complete genome Kocuria rhizophila DC2201 DNA, complete genome Renibacterium salmoninarum ATCC 33209, complete genome Mycobacterium vanbaalenii PYR-‐1, complete genome Nocardia farcinica IFM 10152 DNA, complete genome Rhodococcus jostii RHA1, complete genome Sanguibacter keddieii DSM 10542, complete genome Candidatus Azobacteroides pseudotrichonymphae genomovar. CFP2 DNA, complete genome Porphyromonas gingivalis ATCC 33277 DNA, complete genome Alistipes shahii WAL 8301 draft genome Dyadobacter fermentans DSM 18053, complete genome Spirosoma linguale DSM 74, complete genome Zunongwangia profunda SM-‐A87, complete genome Bacteroides fragilis YCH46 DNA, complete genome Bacteroides fragilis NCTC 9343, complete genome Bacteroides thetaiotaomicron VPI-‐5482, complete genome Bacteroides vulgatus ATCC 8482, complete genome Parabacteroides distasonis ATCC 8503, complete genome Porphyromonas gingivalis W83, complete genome Prevotella ruminicola 23, complete genome Flavobacteriaceae bacterium 3519-‐10, complete genome Flavobacterium johnsoniae UW101, complete genome Flavobacterium psychrophilum JIP02/86 complete genome Pedobacter heparinus DSM 2366, complete genome Bacteroides xylanisolvens XB1A draft genome Sphaerobacter thermophilus DSM 20745 chromosome 2, complete sequence Gloeobacter violaceus PCC 7421 DNA, complete genome Cyanothece sp. ATCC 51142 circular chromosome, complete sequence Cyanothece sp. PCC 7424, complete genome Cyanothece sp. PCC 8802, complete genome Cyanothece sp. PCC 8802 plasmid pP880203, complete sequence Synechococcus rubescens SAG 3.81 partial ribosomal RNA operon, strain SAG 3.81 Synechococcus sp. RCC307 genomic DNA sequence Synechococcus sp. WH8102 complete genome; segment 6/7 Thermosynechococcus elongatus BP-‐1 DNA, complete genome Fremyella diplosiphon Fd33 light-‐indpendent protochlorophyllide oxidoreductase subunit B (chlB) gene, complete cds Fremyella diplosiphon Fd33 phycobilisome linker-‐core protein (apcC) and phycocyanobilin oxidoreductase (pcyA) genes, complete cds; cpc2 and cpc1 operons, Fremyella diplosiphon TspO-‐like protein, hypothetical protein, NblA-‐1 (nblA), CpeB (cpeB), CpeA (cpeA), CpeY (cpeY), and CpeZ (cpeZ) genes, complete cds Nostoc punctiforme PCC 73102, complete genome Nostoc sp. PCC 7120 DNA, complete genome Nostoc sp. PCC 7120 plasmid pCC7120delta DNA, complete sequence Microcoleus chthonoplastes PCC 7420 partial ribosomal RNA operon, strain PCC 7420 Prochlorothrix hollandica SAG 10.89 partial ribosomal RNA operon, strain SAG 10.89 Acaryochloris marina MBIC11017, complete genome Cyanobacterium UCYN-‐A, complete genome

GKJWQY101BQ48U GKJWQY101BJ44C GKJWQY101BQPKI GKJWQY101AKAL4 GKJWQY101AKQUQ GKJWQY101AQDCE GKJWQY101A2UHA GKJWQY101AWMCZ GKJWQY101AQZAT GKJWQY101ACEUC GKJWQY101AA6R0 GKJWQY101B2DJZ GKJWQY101ANNC9 GKJWQY101A6VHS GKJWQY101BLJ1O GKJWQY101AHEDV GKJWQY101BC6PS GKJWQY101AMO9E GKJWQY101A9OD0 GKJWQY101ADA2E GKJWQY101BLMTA GKJWQY101BI8YA GKJWQY101A2WZI GKJWQY101AKANV GKJWQY101ALDHC GKJWQY101A6FQL GKJWQY101AF275 GKJWQY101A5HHI GKJWQY101A7KUH GKJWQY101BXGNS GKJWQY101AFNBN GKJWQY101A2ND4 GKJWQY101BVGTG GKJWQY101A2QNZ GKJWQY101AIT3S GKJWQY101BVSNC GKJWQY101BIJGR GKJWQY101AVTLD GKJWQY101AR4X1 GKJWQY101AX0O9 GKJWQY101APBWG GKJWQY101BXM9C GKJWQY101B17VM GKJWQY101AF4EN GKJWQY101AIZHR GKJWQY101B2AHH GKJWQY101BNDMO GKJWQY101BBVTI GKJWQY101AXQ8R GKJWQY101ASAUF GKJWQY101BZHXT GKJWQY101BN6EO GKJWQY101A440I GKJWQY101A2M8L GKJWQY101AM35J GKJWQY101BMIJM GKJWQY101BMULU GKJWQY101BL46W GKJWQY101BIMJV GKJWQY101AZ6PA GKJWQY101AKUVY GKJWQY101AL2EY GKJWQY101BOYUA GKJWQY101AKXQT GKJWQY101BWB1P GKJWQY101AIN1W GKJWQY101A2H1I GKJWQY101BFXEC GKJWQY101BFH4F GKJWQY101ACCFZ GKJWQY101AIPY1 GKJWQY101BXUBT

481 613 556 539 222 479 548 545 611 378 423 416 607 591 463 181 383 334 479 517 376 641 582 345 261 507 567 374 203 493 518 505 546 477 370 236 305 316 537 546 500 573 233 544 472 421 405 484 580 575 548 577 454 595 538 565 441 622 561 461 246 563 408 538 559 569 561 525 563 548 586 538

5 18 19 17 18 17 5 26 79 6 5 18 25 5 5 30 13 134 5 5 5 193 14 100 17 18 23 5 5 5 18 5 4 17 24 18 24 127 18 25 18 12 16 18 23 14 57 5 4 5 5 18 3 5 5 1 5 12 5 109 18 5 5 18 18 5 29 18 60 22 18 1

412 609 546 497 177 414 238 543 551 334 386 364 557 575 368 142 79 282 477 472 330 226 578 142 182 504 362 271 159 378 511 355 543 422 324 199 146 276 537 207 322 555 192 542 409 374 351 441 576 528 548 573 188 588 537 560 385 498 558 412 204 556 365 531 552 564 521 522 395 545 585 516

1E-‐169 0 2E-‐88 6E-‐158 7E-‐74 0 6E-‐98 3E-‐156 4E-‐140 1E-‐103 4E-‐163 6E-‐147 4E-‐95 0 6E-‐157 2E-‐43 3E-‐20 1E-‐58 0 0 7E-‐86 0.000001 0 0.00003 8E-‐79 0 6E-‐173 9E-‐105 4E-‐71 0 1E-‐169 5E-‐143 0 0 1E-‐93 9E-‐83 4E-‐48 1E-‐67 0 1E-‐74 6E-‐118 1E-‐115 1E-‐86 0 3E-‐135 1E-‐138 1E-‐59 0 0 0 0 0 5E-‐83 0 0 0 0 8E-‐167 6E-‐168 7E-‐107 2E-‐75 0 1E-‐178 0 0 0 6E-‐173 0 2E-‐167 0 0 0

93% 88% 79% 88% 99% 98% 95% 86% 87% 88% 94% 94% 80% 93% 95% 96% 96% 95% 100% 99% 85% 100% 96% 91% 99% 99% 99% 93% 99% 99% 89% 93% 97% 98% 88% 98% 96% 99% 100% 95% 93% 82% 100% 98% 90% 92% 82% 99% 92% 95% 93% 90% 97% 93% 96% 95% 98% 89% 86% 90% 95% 91% 98% 97% 97% 94% 89% 99% 99% 99% 98% 93%

93% 88% 79% 88% 99% 98% 95% 86% 87% 88% 94% 94% 80% 93% 95% 96% 96% 95% 100% 99% 85% 100% 96% 91% 99% 99% 99% 93% 99% 99% 89% 93% 97% 98% 88% 98% 96% 99% 100% 95% 93% 82% 100% 98% 90% 92% 82% 99% 92% 95% 93% 90% 97% 93% 96% 95% 98% 89% 86% 90% 95% 91% 98% 97% 97% 94% 89% 99% 99% 99% 98% 93%

219862254 56684969 75699950 110164990 146740644 290469363 294979666 226319394 154350369 225785631 218540569 221237819 37903989 157679556 226092535 111182492 283481151 111182490 15146028 15146030 120400324 195537732 183223999 116090851 3582195 116108977 116106497 23094784 113120160 225724295 25307955 168994879 182628304 209539788 21905618 158139258 149901357 295317476 110673209 295089810 223928079 125712750 256797400 167830502 291556121 291529795 114336511 229264291 56908016 152022606 47118318 145902672 294346812 294799901 225184640 168990106 42632302 289169617 171988566 229467163 261280339 222119372 222420101 68445725 289178903 72493824 158967071 116103724 190711126 103422338 116092543 262396937

Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria

Cyanobacteria Cyanobacteria Cyanobacteria Cyanobacteria Cyanobacteria Deinococcus-‐Thermus Deinococcus-‐Thermus Deinococcus-‐Thermus Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes

n n n n Oscillatoriales Deinococci Deinococci Deinococci Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli

Cyanothece sp. PCC 7425, complete genome Synechococcus elongatus PCC 6301 DNA, complete genome Anabaena variabilis ATCC 29413, complete genome Trichodesmium erythraeum IMS101, complete genome Spirulina sp. PCC 6313 partial ribosomal RNA operon, strain PCC 6313 Meiothermus ruber DSM 1279, complete genome Chain A, Initiation Complex Of 70s Ribosome With Two Trnas And Mrna. This Entry 3i9e Contains 50s Ribosomal Subunit Of Molecule A. The 30s Ribosomal Sub Deinococcus deserti VCD115 plasmid 1, complete sequence Bacillus amyloliquefaciens FZB42, complete genome Bacillus cereus 03BB102, complete genome Bacillus cereus G9842, complete genome Bacillus cereus Q1, complete genome Bacillus cereus strain BGSC 6A5 rrnB operon, complete sequence Bacillus pumilus SAFR-‐032, complete genome Brevibacillus brevis NBRC 100599 DNA, complete genome Enterococcus avium clone EPE8_4 genomic sequence Enterococcus faecium partial plasmid pVEF4, strain 399/F98/A4 Enterococcus gallinarum clone EPE8_2 genomic sequence Lactobacillus delbrueckii subsp. bulgaricus ISL5 transposase gene, complete cds Lactobacillus delbrueckii subsp. lactis ISL6 transposase gene, complete cds Lactobacillus johnsonii strain ATCC 33200 exopolysaccharide biosynthesis gene cluster, complete sequence Lactobacillus plantarum L137 plasmid pLTK13 DNA, complete genome Lactobacillus reuteri JCM 1112 DNA, complete genome Oenococcus oeni PSU-‐1, complete genome Lactococcus lactis strain DPC3147 plasmid pMRC01, complete sequence Lactococcus lactis subsp. cremoris SK11 plasmid 4, complete sequence Lactococcus lactis subsp. cremoris SK11, complete genome Streptococcus agalactiae NEM316 complete genome, segment 3 Streptococcus macedonicus strain ACA-‐DC 198 putative relaxase gene, complete cds; macedocin gene cluster, complete sequence; McdK (mcdK), McdR (mcdR Streptococcus pneumoniae P1031, complete genome Streptococcus pneumoniae R6, complete genome Streptococcus pneumoniae Hungary19A-‐6, complete genome Streptococcus pneumoniae CGSP14, complete genome Streptococcus pyogenes NZ131, complete genome Streptococcus pyogenes MGAS315, complete genome Alkaliphilus oremlandii OhILAs, complete genome Clostridium beijerinckii NCIMB 8052, complete genome Clostridium botulinum F str. 230613, complete genome Clostridium perfringens ATCC 13124, complete genome Clostridium saccharolyticum-‐like K10 draft genome Clostridium sp. enrichment culture clone 7-‐14 genomic sequence Clostridium thermocellum ATCC 27405, complete genome Anaerococcus prevotii DSM 20548, complete genome Finegoldia magna ATCC 29328 DNA, complete genome Eubacterium siraeum V10Sc8a draft genome Eubacterium siraeum 70/3 draft genome Syntrophomonas wolfei subsp. wolfei str. Goettingen, complete genome Bacillus anthracis str. A0248, complete genome Bacillus clausii KSM-‐K16 DNA, complete genome Bacillus cereus subsp. cytotoxis NVH 391-‐98, complete genome Bacillus halodurans C-‐125 DNA, complete genome Bacillus licheniformis ATCC 14580, complete genome Bacillus megaterium QM B1551, complete genome Bacillus megaterium DSM319, complete genome Bacillus subtilis subsp. subtilis str. 168 complete genome Lysinibacillus sphaericus C3-‐41, complete genome Oceanobacillus iheyensis HTE831 DNA, complete genome Listeria seeligeri serovar 1/2b str. SLCC3954 complete genome Exiguobacterium sibiricum 255-‐15, complete genome Exiguobacterium sp. AT1b, complete genome Paenibacillus sp. Y412MC10, complete genome Macrococcus caseolyticus JCSC5402 DNA, complete genome Staphylococcus carnosus subsp. carnosus TM300 complete genome Staphylococcus haemolyticus JCSC1435 DNA, complete genome Staphylococcus lugdunensis HKU09-‐01, complete genome Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305 DNA, complete genome Lactobacillus acidophilus NCFM, complete genome Lactobacillus casei ATCC 334, complete genome Lactobacillus casei BL23 complete genome, strain BL23 Lactobacillus delbrueckii subsp. bulgaricus ATCC 11842 complete genome Lactobacillus delbrueckii subsp. bulgaricus ATCC BAA-‐365, complete genome Lactobacillus johnsonii FI9785, complete genome

GKJWQY101AKKWT GKJWQY101A9FF7 GKJWQY101APN55 GKJWQY101BF89U GKJWQY101A6GDN GKJWQY101AZ303 GKJWQY101AUKS3 GKJWQY101A3SPW GKJWQY101AB8GR GKJWQY101BZH5I GKJWQY101AH1ID GKJWQY101BI2WE GKJWQY101AYWCN GKJWQY101BOVEU GKJWQY101A1CSL GKJWQY101BNM0N GKJWQY101AYWMX GKJWQY101AOC8C GKJWQY101BE4ZG GKJWQY101BX0WB GKJWQY101AUKJZ GKJWQY101BDY1Q GKJWQY101ARORW GKJWQY101AHKOV GKJWQY101BGGHX GKJWQY101BUKAI GKJWQY101BPUIN GKJWQY101AW8QY GKJWQY101ALG3R GKJWQY101ATSIV GKJWQY101BNDWM GKJWQY101A40TK GKJWQY101AO1P2 GKJWQY101A44JY GKJWQY101BQCZD GKJWQY101BQTA7 GKJWQY101AYGQY GKJWQY101AKXDF GKJWQY101BCTZL GKJWQY101BBYCY GKJWQY101BCX1D GKJWQY101BSTMC GKJWQY101BWHUV GKJWQY101AEIGL GKJWQY101BJ7Q1 GKJWQY101AANQS GKJWQY101AP35G GKJWQY101BYYCA GKJWQY101BA89J GKJWQY101BFWYL GKJWQY101AR683 GKJWQY101AMU20 GKJWQY101A8WXN GKJWQY101B0JOO GKJWQY101BM98Q GKJWQY101BQAGF GKJWQY101BTYHD GKJWQY101A2KY0 GKJWQY101BXWSP GKJWQY101A06LP GKJWQY101ACT2K GKJWQY101A2BN5 GKJWQY101BL1SN GKJWQY101A24D1 GKJWQY101BNAXW GKJWQY101A2W2H GKJWQY101A5D79 GKJWQY101BU6EL GKJWQY101A4300 GKJWQY101A91EV GKJWQY101ADWXG GKJWQY101AU0ML

451 586 556 570 151 492 528 574 544 545 551 560 564 558 395 430 285 305 596 552 542 551 494 564 576 560 555 590 326 593 572 418 622 561 544 480 563 588 587 569 600 564 584 570 563 765 369 271 207 285 223 257 563 229 303 532 557 541 521 569 476 538 555 418 568 537 603 555 358 205 416 283

18 5 5 5 13 16 3 5 5 5 5 5 5 21 4 107 5 17 18 1 17 5 18 5 17 18 18 23 18 7 5 4 6 7 9 18 24 18 5 17 15 27 5 18 17 8 18 5 18 18 3 18 18 65 4 4 13 18 15 18 108 10 18 3 15 34 129 14 5 20 27 7

307 583 554 564 119 431 525 574 516 410 544 557 559 556 362 383 253 260 590 504 488 485 447 555 568 560 555 587 259 583 571 370 618 541 543 427 559 579 534 526 598 564 572 559 560 284 305 223 127 240 155 106 515 198 217 471 343 484 449 569 435 424 465 362 560 489 555 548 306 160 347 239

7E-‐92 0 4E-‐145 0 4E-‐39 0 0 0 0 3E-‐170 0 0 0 0 1E-‐172 6E-‐142 7E-‐105 2E-‐115 0 1E-‐174 6E-‐173 0 4E-‐79 0 0 0 0 0 5E-‐112 0 0 7E-‐141 0 0 0 0 2E-‐163 0 0 0 0 0 0 0 0 2E-‐108 3E-‐104 1E-‐106 8E-‐43 2E-‐105 2E-‐69 8E-‐24 0 9E-‐58 3E-‐78 3E-‐151 3E-‐96 2E-‐138 5E-‐94 0 5E-‐98 2E-‐163 0 6E-‐92 0 3E-‐161 1E-‐160 0 1E-‐108 5E-‐40 7E-‐131 4E-‐102

88% 97% 84% 99% 95% 96% 99% 100% 93% 94% 97% 98% 97% 97% 98% 100% 95% 98% 95% 89% 90% 95% 80% 91% 99% 94% 100% 94% 98% 87% 88% 92% 86% 94% 92% 95% 87% 91% 89% 96% 90% 91% 89% 91% 94% 93% 91% 99% 96% 98% 99% 91% 91% 98% 92% 88% 87% 86% 82% 94% 87% 92% 98% 84% 88% 90% 91% 93% 91% 89% 94% 96%

88% 97% 84% 99% 95% 96% 99% 100% 93% 94% 97% 98% 97% 97% 98% 100% 95% 98% 95% 89% 90% 95% 80% 91% 99% 94% 100% 94% 98% 87% 88% 92% 86% 94% 92% 95% 87% 91% 89% 96% 90% 91% 89% 91% 94% 93% 91% 99% 96% 98% 99% 91% 91% 98% 92% 88% 87% 86% 82% 94% 87% 92% 98% 84% 88% 90% 91% 93% 91% 89% 94% 96%

254044096 259648365 78609255 90820184 295831662 13400022 124491690 281374316 22535226 225700893 288730948 157074445 254996425 225726369 19913450 292557464 222113012 188497817 110681940 160426828 238871336 238874104 219536331 283951607 269093698 295112306 257152781 257149867 15487824 223928104 291523683 291526582 291520697 295092884 295114602 291558333 291541372 295107714 291543184 291545299 291548560 295098739 291532143 20095250 257048753 156773414 156774261 156770305 156776473 156769021 156770979 156768878 156773397 156773640 156773646 156770997 156770867 156775997 156770975 156768872 156775471 156768589 156772425 156773609 156774731 156769665 156768004 156767585 193083711 193084530 193084460 193084613


Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Firmicutes Fusobacteria Fusobacteria n n n n n n n n n n n n n n n n n n n n n n n n n n n

Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Bacilli Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Negativicutes Negativicutes Bacilli Bacilli Bacilli Bacilli Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Clostridia Erysipelotrichi Negativicutes Fusobacteria _class_ Fusobacteria _class_ n n n n n n n n n n n n n n n n n n n n n n n n n n n

Lactobacillus plantarum JDM1, complete genome Lactobacillus rhamnosus ATCC 53103 DNA, complete genome Lactobacillus sakei strain 23K complete genome Lactobacillus salivarius UCC118, complete genome Leuconostoc kimchii IMSNU 11154, complete genome Lactococcus lactis subsp. lactis Il1403, complete genome Lactococcus lactis subsp. cremoris MG1363, complete genome Lactococcus lactis subsp. lactis KF147, complete genome Streptococcus agalactiae 2603V/R, complete genome Streptococcus equi subsp. zooepidemicus H70, complete genome Streptococcus gallolyticus UCN34 complete genome Streptococcus gordonii str. Challis substr. CH1, complete genome Streptococcus mutans NN2025 DNA, complete genome Streptococcus pneumoniae Taiwan19F-‐14, complete genome Streptococcus pyogenes MGAS8232, complete genome Streptococcus suis GZ1, complete genome Streptococcus uberis 0140J complete genome Clostridium botulinum E3 str. Alaska E43, complete genome Clostridium perfringens SM101, complete genome Clostridium phytofermentans ISDg, complete genome Eubacterium eligens ATCC 27750, complete genome Eubacterium rectale ATCC 33656, complete genome Desulfitobacterium hafniense DCB-‐2, complete genome Acidaminococcus fermentans DSM 20731, complete genome Veillonella parvula DSM 2008, complete genome Enterococcus sp. 7L76 draft genome Lactobacillus rhamnosus Lc 705 plasmid sequence, strain Lc 705 Lactobacillus rhamnosus Lc 705 whole genome sequence, strain Lc 705 Lactobacillus sakei rrnA operon and rrnB operon, partial sequence Clostridium sp. enrichment culture clone 7-‐25 genomic sequence Eubacterium rectale DSM 17629 draft genome Eubacterium rectale M104/1 draft genome Coprococcus catus GD/7 draft genome Coprococcus sp. ART55/1 draft genome Clostridiales sp. SM4/1 draft genome Clostridiales sp. SSC/2 draft genome Ruminococcus bromii L2-‐63 draft genome Ruminococcus obeum A2-‐162 draft genome Ruminococcus sp. 18P13 draft genome Ruminococcus sp. SR1/5 draft genome Ruminococcus torques L2-‐14 draft genome Eubacterium cylindroides T2-‐87 draft genome Megamonas hypermegale ART12/1 draft genome Fusobacterium nucleatum subsp. nucleatum ATCC 25586, complete genome Leptotrichia buccalis DSM 1135, complete genome Uncultured bacterium clone LM0ACA6ZE09FM1 genomic sequence Uncultured bacterium clone HA0AAA18ZA07FM1 genomic sequence Uncultured bacterium clone LM0ABA36ZC08RM1 genomic sequence Uncultured bacterium clone LM0ACA9ZB08RM1 genomic sequence Uncultured bacterium clone LM0ABA7ZF10FM1 genomic sequence Uncultured bacterium clone LM0ABA6ZE04RM1 genomic sequence Uncultured bacterium clone LM0ABA5ZG02FM1 genomic sequence Uncultured bacterium clone LM0ACA6ZD02FM1 genomic sequence Uncultured bacterium clone LM0ACA9ZC05FM1 genomic sequence Uncultured bacterium clone LM0ACA9ZC11FM1 genomic sequence Uncultured bacterium clone LM0ABA6ZG02RM1 genomic sequence Uncultured bacterium clone LM0ABA5ZA11RM1 genomic sequence Uncultured bacterium clone LM0ACA3ZE01RM1 genomic sequence Uncultured bacterium clone LM0ABA6ZD12RM1 genomic sequence Uncultured bacterium clone LM0ABA5ZF07FM1 genomic sequence Uncultured bacterium clone LM0ACA21ZE06RM1 genomic sequence Uncultured bacterium clone LM0ABA40ZF05FM1 genomic sequence Uncultured bacterium clone LM0ACA2ZF10FM1 genomic sequence Uncultured bacterium clone LM0ACA8ZH09FM1 genomic sequence Uncultured bacterium clone LM0ACA1ZH04RM1 genomic sequence Uncultured bacterium clone LM0ABA1ZF09RM1 genomic sequence Uncultured bacterium clone LM0ABA31ZH10FM1 genomic sequence Uncultured bacterium clone LM0ABA2ZC09FM1 genomic sequence Uncultured bacterium AD12-‐C5 genomic sequence Uncultured bacterium ARCTIC38_F_05 genomic sequence Uncultured bacterium ARCTIC47_D_06 genomic sequence Uncultured bacterium HF0070_34E11 genomic sequence

GKJWQY101ANMYP GKJWQY101AHOJC GKJWQY101BI2JO GKJWQY101ANG5G GKJWQY101A9FHD GKJWQY101BLR88 GKJWQY101AH7PE GKJWQY101B18KD GKJWQY101AM37K GKJWQY101A17ME GKJWQY101AECX4 GKJWQY101BZ6F8 GKJWQY101A2QNX GKJWQY101BM4AZ GKJWQY101BNW14 GKJWQY101AXA5Z GKJWQY101BWIJY GKJWQY101AOB4M GKJWQY101A8S8N GKJWQY101BSJWR GKJWQY101BVQQU GKJWQY101BKAYD GKJWQY101BJH0Q GKJWQY101BD56T GKJWQY101BY5FD GKJWQY101AKOGB GKJWQY101B1UIB GKJWQY101AXTWR GKJWQY101AZQX2 GKJWQY101BH4I5 GKJWQY101BYYVG GKJWQY101A407X GKJWQY101B1OHM GKJWQY101A41PE GKJWQY101BT4ZY GKJWQY101AWPDP GKJWQY101BKKTZ GKJWQY101BD5KR GKJWQY101BMECY GKJWQY101AH347 GKJWQY101BE4R0 GKJWQY101BDY6H GKJWQY101AYMDQ GKJWQY101A2HLQ GKJWQY101B0GZZ GKJWQY101BQDY9 GKJWQY101A4OMR GKJWQY101BV2AQ GKJWQY101BU6BN GKJWQY101AX6T2 GKJWQY101BERYH GKJWQY101BHVBO GKJWQY101BRU7O GKJWQY101BRQ7P GKJWQY101ARU2K GKJWQY101AJPHZ GKJWQY101AGSJB GKJWQY101BYMZF GKJWQY101ATYDP GKJWQY101BSXCF GKJWQY101AL6DG GKJWQY101ATZNT GKJWQY101BUXBD GKJWQY101BRVHF GKJWQY101A14H0 GKJWQY101AHOIZ GKJWQY101BSA8U GKJWQY101BM00X GKJWQY101ASBL2 GKJWQY101BATJM GKJWQY101BQWCO GKJWQY101ASXGJ

93 335 400 545 225 506 431 574 544 572 530 569 544 443 408 445 548 528 551 566 585 576 560 570 536 575 569 530 535 552 588 528 297 569 567 568 579 585 519 608 362 568 317 209 540 536 527 541 504 494 547 505 505 560 500 518 496 548 385 501 481 193 461 354 579 503 613 551 563 570 376 515

23 1 5 17 5 5 9 14 86 18 4 18 7 18 20 53 18 193 5 11 18 4 16 62 3 18 17 18 18 2 16 4 18 7 24 17 21 18 17 20 215 20 20 31 171 18 191 123 38 18 24 5 21 134 434 63 5 17 15 54 5 44 372 21 23 10 19 21 18 18 66 371

60 273 337 544 141 501 388 492 508 570 522 566 423 341 353 386 457 432 547 564 580 571 557 565 531 572 562 455 529 550 586 523 247 567 531 566 575 585 477 87 242 550 270 165 203 476 527 216 404 391 479 505 489 394 480 472 429 68 328 453 436 158 459 316 576 497 610 550 545 563 220 468

7E-‐10 1E-‐102 1E-‐104 0 2E-‐24 0 3E-‐164 8E-‐172 8E-‐117 0 9E-‐176 3E-‐176 6E-‐163 2E-‐121 6E-‐92 8E-‐126 6E-‐118 6E-‐93 0 0 3E-‐166 0 0 0 0 2E-‐152 0 6E-‐128 0 7E-‐177 0 0 1E-‐112 0 0 0 0 0 0 1E-‐20 0.001 1E-‐135 1E-‐102 5E-‐55 0.000003 0 6E-‐118 2E-‐23 7E-‐112 1E-‐75 6E-‐78 1E-‐99 1E-‐84 5E-‐64 0.0000002 4E-‐50 0 4E-‐10 7E-‐136 4E-‐134 3E-‐130 1E-‐50 4E-‐10 1E-‐142 0 9E-‐176 0 0 0 0 8E-‐11 2E-‐17

100% 92% 88% 89% 83% 97% 94% 90% 85% 90% 88% 88% 92% 91% 86% 91% 85% 93% 92% 94% 86% 93% 95% 95% 92% 85% 90% 86% 92% 87% 91% 93% 99% 89% 96% 96% 89% 99% 96% 96% 100% 84% 94% 96% 100% 92% 90% 89% 87% 81% 79% 81% 80% 85% 91% 77% 99% 93% 95% 89% 87% 99% 82% 98% 91% 90% 91% 91% 96% 97% 76% 85%

100% 92% 88% 89% 83% 97% 94% 90% 85% 90% 88% 88% 92% 91% 86% 91% 85% 93% 92% 94% 86% 93% 95% 95% 92% 85% 90% 86% 92% 87% 91% 93% 99% 89% 96% 96% 89% 99% 96% 96% 100% 84% 94% 96% 100% 92% 90% 89% 87% 81% 79% 81% 80% 85% 91% 77% 99% 93% 95% 89% 87% 99% 82% 98% 91% 90% 91% 91% 96% 97% 76% 85%

193084646 193084638 193083728 62945638 83595892 146260146 62860402 156777063 156769510 156767597 156769699 156767618 156767628 156768405 156770664 156770556 156768500 156770596 156770864 156768827 156770902 156771060 156769048 156773064 156775970 156776145 156776214 156776216 156773440 156773475 156773480 156776331 193084596 193083707 193083717 193084603 193084608 193084619 193084621 193084601 91199943 283436255 67003493 240266805 146189981 219944660 111606883 221739013 86284380 190694918 227339586 227337257 30407155 25168258 158328513 119372524 32263857 221161990 56676665 42414566 82943940 288926859 145322317 188532098 170658659 47118328 119376152 83574254 292676846 98975575 115421100 38707361


n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n Planctomycetes Planctomycetes Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria

n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n n Planctomycetacia Planctomycetacia Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Alphaproteobacteria Betaproteobacteria Betaproteobacteria

Uncultured bacterium HF0200_39L23 genomic sequence Uncultured bacterium HF4000_48A13 genomic sequence Uncultured bacterium KM3-‐47-‐A6 genomic sequence Uncultured bacterium zdt-‐25h14 clone zdt-‐25h14, complete sequence Uncultured marine bacterium Ant4E12, partial genomic sequence Uncultured soil bacterium clone M53 similar to beta-‐lactamase genomic sequence Uncultured bacterium zdt-‐44a23 clone zdt-‐44a23, complete sequence Uncultured bacterium clone HA0AAA17ZD02RM1 genomic sequence Uncultured bacterium clone HA0AAA7ZF01FM1 genomic sequence Uncultured bacterium clone LM0ABA2ZD09FM1 genomic sequence Uncultured bacterium clone LM0ABA2ZE04RM1 genomic sequence Uncultured bacterium clone LM0ABA2ZG05FM1 genomic sequence Uncultured bacterium clone LM0ABA2ZH11FM1 genomic sequence Uncultured bacterium clone LM0ABA39ZA06FM1 genomic sequence Uncultured bacterium clone LM0ABA40ZH07RM1 genomic sequence Uncultured bacterium clone LM0ABA4ZC09RM1 genomic sequence Uncultured bacterium clone LM0ABA4ZD05FM1 genomic sequence Uncultured bacterium clone LM0ABA4ZH01RM1 genomic sequence Uncultured bacterium clone LM0ABA5ZA06RM1 genomic sequence Uncultured bacterium clone LM0ABA5ZA12FM1 genomic sequence Uncultured bacterium clone LM0ABA5ZE03RM1 genomic sequence Uncultured bacterium clone LM0ABA7ZF03RM1 genomic sequence Uncultured bacterium clone LM0ABA8ZA06FM1 genomic sequence Uncultured bacterium clone LM0ACA28ZD06FM1 genomic sequence Uncultured bacterium clone LM0ACA3ZB06RM1 genomic sequence Uncultured bacterium clone LM0ACA5ZC04RM1 genomic sequence Uncultured bacterium clone LM0ACA6ZA05RM1 genomic sequence Uncultured bacterium clone LM0ACA6ZA08RM1 genomic sequence Uncultured bacterium clone LM0ACA6ZH03FM1 genomic sequence Uncultured bacterium clone LM0ACA7ZC10FM1 genomic sequence Uncultured bacterium clone LM0ACA7ZD04FM1 genomic sequence Uncultured bacterium clone LM0ACA7ZE02RM1 genomic sequence Uncultured bacterium 2.6_D6 genomic sequence Uncultured bacterium AD12-‐A11 genomic sequence Uncultured bacterium AD84-‐H10 genomic sequence Uncultured bacterium HF0010_04H24 genomic sequence Uncultured bacterium HF0010_10C01 genomic sequence Uncultured bacterium HF0500_12O04 genomic sequence Uncultured bacterium HF0500_24B12 genomic sequence Uncultured bacterium JM9_G5 genomic sequence Kuenenia stuttgartiensis genome fragment KUST_E (5 of 5) Pirellula staleyi DSM 6068, complete genome Brevundimonas sp. SD212 carotenoid biosynthesis gene cluster (orf1, crtW, crtY, crtI, crtB, orf6, orf7, crtE, idi, crtZ, crtG, orf12), complete cds Bartonella grahamii as4aup, complete genome Bradyrhizobium sp. ORS278,complete sequence Methylobacterium nodulans ORS 2060, complete genome Aminobacter aminovorans partial gapA gene for glyceraldehyde-‐3-‐phosphate dehydrogenase, strain DSM 10368 Agrobacterium vitis S4 plasmid pAtS4e, complete sequence Rhizobium etli CFN 42 plasmid p42e, complete sequence Rhizobium etli CIAT 652, complete genome Rhizobium sp. NGR234, complete genome Rhizobium sp. NGR234 plasmid pNGR234b, complete sequence Sinorhizobium meliloti 1021 complete chromosome Sinorhizobium meliloti 1021 plasmid pSymA, complete sequence Azorhizobium caulinodans ORS 571 DNA, complete genome Paracoccus denitrificans PD1222 chromosome 1, complete sequence Paracoccus sp. Ol18 plasmid pOL18 rrn operon, complete sequence Rhodobacter sphaeroides KD131 chromosome 2, complete sequence Ruegeria pomeroyi DSS-‐3, complete genome Acetobacter pasteurianus partial ITS1, strain CCM 3606 Magnetospirillum magneticum AMB-‐1 DNA, complete genome Rhodospirillum centenum SW, complete genome Novosphingobium aromaticivorans DSM 12444 plasmid pNL2, complete sequence Sphingobium chungbukense rrnC operon, complete sequence Methylobacterium radiotolerans JCM 2831 plasmid pMRAD01, complete sequence Mesorhizobium loti MAFF303099 DNA, complete genome Paracoccus denitrificans PD1222 chromosome 2, complete sequence Rhodospirillum rubrum ATCC 11170, complete genome Sphingobium japonicum UT26S DNA, chromosome 2, complete genome Sphingopyxis alaskensis RB2256, complete genome Bordetella avium 197N complete genome Burkholderia anthina pANT1 plasmid ORF3 for hypothetical protein, strain BHS1

GKJWQY101BJCLG GKJWQY101AL5GX GKJWQY101BS6QI GKJWQY101BN6XJ GKJWQY101BCW7I GKJWQY101BXETD GKJWQY101AHRMM GKJWQY101BS6LH GKJWQY101BQ51J GKJWQY101AK7G8 GKJWQY101BIKNE GKJWQY101AJROG GKJWQY101B2KTE GKJWQY101AW7FS GKJWQY101BKTPD GKJWQY101A7HUP GKJWQY101BOC0B GKJWQY101AXXBZ GKJWQY101BYX8F GKJWQY101A4LWM GKJWQY101B17TY GKJWQY101AGP17 GKJWQY101ATCIB GKJWQY101AD239 GKJWQY101AG8TI GKJWQY101AX6PV GKJWQY101BLFSC GKJWQY101AQ5RN GKJWQY101AEFDT GKJWQY101BLFW7 GKJWQY101AVDT3 GKJWQY101B3I7Y GKJWQY101BISXY GKJWQY101A2RQ4 GKJWQY101AVQQS GKJWQY101A7KK6 GKJWQY101AN6A1 GKJWQY101ATI2M GKJWQY101A2EXF GKJWQY101AR8JF GKJWQY101ACR3I GKJWQY101AML8K GKJWQY101A8SDV GKJWQY101BJ0XY GKJWQY101BMVH7 GKJWQY101ADZWX GKJWQY101A5AS0 GKJWQY101AF69O GKJWQY101AYZFU GKJWQY101AULKC GKJWQY101AOYQY GKJWQY101BJB7H GKJWQY101ASOB7 GKJWQY101A55T9 GKJWQY101AQVXX GKJWQY101BJFYS GKJWQY101AZO3V GKJWQY101AX65L GKJWQY101ALTT0 GKJWQY101ASWG9 GKJWQY101ACB0K GKJWQY101ARN9L GKJWQY101A9KUB GKJWQY101AGMLE GKJWQY101ALGOA GKJWQY101BWYXQ

511 499 486 105 562 510 534 508 519 502 401 413 243 510 537 554 511 498 547 503 497 539 517 350 459 517 544 548 566 540 547 506 575 553 550 487 562 440 323 379 481 373 547 460 413 379 229 551 278 321 489 400 495 550 253 507 560 589 576 515 278 358 568 576 548 338

155 279 17 5 74 18 5 5 141 18 18 25 4 61 17 10 18 5 24 18 18 17 18 18 5 19 18 18 24 18 51 18 18 5 11 18 23 5 32 18 18 18 23 5 12 7 5 4 24 5 4 5 119 25 21 5 18 5 18 17 18 17 5 20 18 8

511 313 453 67 193 215 308 505 502 469 348 376 129 278 533 508 391 442 547 500 341 500 514 201 405 513 528 545 563 534 545 506 571 551 275 272 555 407 265 332 416 335 460 399 299 356 197 548 176 36 456 271 292 496 216 462 452 588 572 430 227 310 556 556 548 275

0 0.00001 0 5E-‐17 3E-‐16 1E-‐39 9E-‐32 1E-‐144 7E-‐18 9E-‐106 1E-‐153 1E-‐133 8E-‐49 2E-‐37 0 0 4E-‐179 0 0 0 2E-‐151 0 0 2E-‐90 2E-‐102 3E-‐151 0 0 0 0 1E-‐159 0 0 1E-‐150 8E-‐112 9E-‐91 2E-‐133 5E-‐103 1E-‐72 1E-‐137 5E-‐158 8E-‐135 0 6E-‐127 2E-‐122 2E-‐115 3E-‐77 0 2E-‐41 0.000007 0 4E-‐103 1E-‐29 5E-‐149 5E-‐61 0 0 0 0 0 1E-‐77 4E-‐148 0 1E-‐155 0 5E-‐82

100% 97% 95% 94% 81% 82% 77% 85% 73% 83% 97% 92% 95% 81% 93% 93% 98% 98% 96% 92% 97% 97% 96% 100% 84% 87% 95% 91% 96% 90% 88% 98% 99% 85% 95% 91% 84% 84% 88% 95% 92% 94% 98% 88% 95% 89% 94% 97% 88% 100% 98% 93% 82% 87% 89% 99% 95% 93% 97% 97% 93% 99% 91% 86% 90% 88%

100% 97% 95% 94% 81% 82% 77% 85% 73% 83% 97% 92% 95% 81% 93% 93% 98% 98% 96% 92% 97% 97% 96% 100% 84% 87% 95% 91% 96% 90% 88% 98% 99% 85% 95% 91% 84% 84% 88% 95% 92% 94% 98% 88% 95% 89% 94% 97% 88% 100% 98% 93% 82% 87% 89% 99% 95% 93% 97% 97% 93% 99% 91% 86% 90% 88%

13625778 126238441 237502667 295438061 295434944 83649860 83652219 91685338 171192370 206593202 120587178 121551644 295794626 294338440 48428765 34105712 66731897 161594571 254667570 77964193 77965403 77968738 295441430 288237308 30407127 30407128 221728669 120604516 91695138 133737197 71845263 186660182 260222220 90823168 262076673 219952977 82617838 78217452 34483186 237499037 120322793 167351963 117610791 219994503 261835099 145316543 291551905 291197582 150953431 295647398 53749768 256794767 83630956 261412053 247533203 108733343 49529273 71037566 148570901 226717097 190684944 63253978 283472039 117607074 226525288 187424568

Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria Bacteria

Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Proteobacteria Verrucomicrobia Verrucomicrobia

Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Betaproteobacteria Deltaproteobacteria Deltaproteobacteria Deltaproteobacteria Deltaproteobacteria Deltaproteobacteria Epsilonproteobacteria Gammaproteobacteria Gammaproteobacteria Gammaproteobacteria Gammaproteobacteria Gammaproteobacteria Gammaproteobacteria Gammaproteobacteria Gammaproteobacteria Gammaproteobacteria Gammaproteobacteria Gammaproteobacteria Gammaproteobacteria Gammaproteobacteria Gammaproteobacteria Gammaproteobacteria Gammaproteobacteria Gammaproteobacteria Gammaproteobacteria Gammaproteobacteria Gammaproteobacteria Gammaproteobacteria Gammaproteobacteria Gammaproteobacteria Gammaproteobacteria n n Verrucomicrobiae

Burkholderia cepacia acyl-‐homoserine lactone synthase BviI (bviI) and transcriptional activator BviR (bviR) genes, complete cds Burkholderia mallei NCTC 10247 chromosome II, complete sequence Burkholderia pseudomallei MSHR346 chromosome I, complete sequence Burkholderia sp. CCGE1002 chromosome 2, complete sequence Burkholderia sp. CCGE1002 chromosome 1, complete sequence Burkholderia thailandensis E264 chromosome II, complete sequence Burkholderia thailandensis E264 chromosome I, complete sequence Burkholderia xenovorans LB400 chromosome 1, complete sequence Polynucleobacter necessarius subsp. necessarius STIR1, complete genome Ralstonia solanacearum strain IPO1609 Genome Draft Acidovorax citrulli AAC00-‐1, complete genome Verminephrobacter eiseniae EF01-‐2, complete genome Thiomonas intermedia K12, complete genome Thiomonas sp. str. 3As, chromosome, complete genome Collimonas fungivorans fosmid CFUFOS26, complete sequence Chromobacterium violaceum ATCC 12472, complete genome Neisseria meningitidis MC58, complete genome Neisseria meningitidis 053442, complete genome Neisseria meningitidis alpha14 complete genome Burkholderia sp. 383 chromosome 3, complete sequence Burkholderia sp. 383 chromosome 1, complete sequence Burkholderia sp. 383, complete sequence Burkholderia sp. CCGE1002 plasmid pBC201, complete sequence Cupriavidus metallidurans CH34 megaplasmid, complete sequence Ralstonia solanacearum GMI1000 chromosome complete sequence Ralstonia solanacearum GMI1000 megaplasmid complete sequence Acidovorax ebreus TPSY, complete genome Acidovorax sp. JS42, complete genome Polaromonas sp. JS666, complete genome Herminiimonas arsenicoxydans chromosome, complete sequence Dechloromonas aromatica RCB, complete genome Burkholderia vietnamiensis strain CBMB40 nitrogenase molybdenum-‐iron protein beta chain-‐like (nifK) gene, partial sequence Curvibacter putative symbiont of Hydra magnipapillata genomic scaffold HmaUn_WGA71069_1 Pelobacter carbinolicus DSM 2380, complete genome Haliangium ochraceum DSM 14365, complete genome Anaeromyxobacter dehalogenans 2CP-‐1, complete genome Uncultured delta proteobacterium DeepAnt-‐32C6 fosmid, complete sequence Desulfovibrio alaskensis G20, complete genome Wolinella succinogenes, complete genome; segment 4/7 Tolumonas auensis DSM 9187, complete genome Marinobacter aquaeolei VT8, complete genome Shewanella halifaxensis HAW-‐EB4, complete genome Shewanella sp. ANA-‐3, complete genome Thioalkalivibrio sp. HL-‐EbGR7, complete genome Halothiobacillus neapolitanus c2, complete genome Enterobacter sp. 638, complete genome Erwinia amylovora CFBP1430 complete genome Erwinia amylovora ATCC 49946 chromosomal sequence Klebsiella pneumoniae subsp. pneumoniae MGH 78578, complete sequence Legionella pneumophila 2300/99 Alcoy, complete genome Legionella pneumophila str. Paris complete genome Kangiella koreensis DSM 16069, complete genome Hahella chejuensis KCTC 2396, complete genome Aggregatibacter actinomycetemcomitans D11S-‐1, complete genome Aggregatibacter aphrophilus NJ8700, complete genome Pseudomonas syringae pv. syringae strain UMAF0158 mangotoxin production gene cluster and rrn operon, partial sequence Acinetobacter sp. ADP1 complete genome Psychrobacter arcticus 273-‐4, complete genome Psychrobacter sp. PRwf-‐1, complete genome Azotobacter vinelandii DJ, complete genome Cellvibrio japonicus Ueda107, complete genome Pseudomonas syringae pv. syringae B728a, complete genome Xanthomonas albilineans str. GPE PC73, chromosome, complete genome Magnetococcus sp. MC-‐1, complete genome Uncultured Verrucomicrobia bacterium clone 118 genomic sequence Akkermansia muciniphila ATCC BAA-‐835, complete genome