table s1

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2130087..2168671. 38585. 58.7. PflQ2. 3552-3598. 3598. 3596. 3597. Phage lysogen. Pseudomonas fulva 12-X. NC_015556.1. 2257605..2363077. 105473.
TABLE S1

Organism Acidovorax sp. KKS102 Acinetobacter baumannii AB0057 Acinetobacter baumannii AYE Acinetobacter baumannii D1279779 Acinetobacter baumannii Naval-57 Acinetobacter baumannii OIFC137 Acinetobacter guillouiae MSP4-18 Acinetobacter gyllenbergii MTCC 11365 Acinetobacter lwoffii SH145 Acinetobacter radioresistens SK82 Acinetobacter sp. NBRC100985 Acinetobacter sp. WC-743 Agrobacterium sp. H13-3 Aliivibrio salmonicida LFI1238 Alteromonas macleodii Balearic Sea AD45 Alteromonas macleodii str. 'Deep ecotype' (Island 1) Alteromonas macleodii str. 'Deep ecotype' (Island 2) Bradyrhizobium sp. BTAi1 Burkholderia cenocepacia H111 Burkholderia gladioli BSR3 Caulobacter sp. K31 Colwellia psychrerythraea 34H Escherichia coli 101-1 Escherichia coli 3003 Escherichia coli B171 Escherichia coli ETEC H10407 Escherichia coli KTE41 Escherichia coli O157H7 str. EC4115 Escherichia coli PA40 Escherichia coli STEC_H.1.8 Glaciecola mesophila KMM 241 Herbaspirillium sp. CF444 Hoeflea phototrophica DFL-43 Hyphomonas neptunium ATCC 15444 Kingella oralis ATCC 51147 Labrenzia alexandrii DFL-11 Mesorhizobium opportunistum WSM2075 Neisseria meningitidis 73696 Neisseria meningitidis ATCC 13091 Pandoraea sp. SD6-2 Paracoccus denitrificans PD1222 Parvibaculum lavamentivorans DS-1 Phaeobacter gallaeciensis DSM 17395 Phenylobacterium zucineum HLK1 Pseudoalteromonas tunicata D2 Pseudogulbenkiania sp. NH8B Pseudomonas aeruginosa MSH-10 Pseudomonas aeruginosa PA7 Pseudomonas chlororaphis O6 Pseudomonas fluorescens BRIP34879 Pseudomonas fluorescens Q2-87 Pseudomonas fulva 12-X Pseudomonas protegens CHA0 Pseudomonas protegens Pf-5 Pseudomonas pseudoalcaligenes KF707 Pseudomonas putida GB-1 Pseudomonas putida H8234 Pseudomonas putida S16 Pseudomonas resinovorans NBRC 106553 Pseudomonas sp. GM60 Pseudomonas sp. GM74 Pseudomonas sp. GM80 Pseudomonas sp. P179 Pseudomonas synxantha BG33R Pseudomonas syringae pv. avellanae str. ISPaVe037 Rhizobium lupini HPC(L) Rhodobacteraceae bacterium KLH11 Rhodomicrobium vannielii ATCC 17100† Ruegeria sp. R11 Shewanella baltica OS155 Shewanella baltica OS185

Accession Version NC_018708.1 NC_011586.1 NC_010410.1 NC_020547.2 AMFP01000033.1 AFDK01000002.1 ASQG01000039.1 ASQH01000014.1 NZ_GG705066.1 NZ_ACVR01000072.1 NZ_BAEB01000006.1 AMFQ01000090.1 NC_015183.1 NC_011312.1 NC_018679.1 NC_011138.2 NC_011138.2 NC_009485.1 CAFQ01000015.1 NC_015381.1 NC_010338.1 NC_003910.7 NZ_AAMK02000006.1 AFAF02000002.1 NZ_AAJX02000004.1 NC_017633.1 ASUF01000002.1 NC_011353.1 AKLQ01000063.1 AFDY01000049.1 BAEP01000023.1 NZ_AKJW01000015.1 NZ_ABIA02000005.1 NC_008358.1 ACJW02000002.1 NZ_EQ973121.1 NC_015675.1 APTR01000030.1 NZ_AEEF01000001.1 AQOU01000038.1 NC_008686.1 NC_009719.1 NZ_ABIF01000015.1 NC_011144.1 NZ_AAOH01000003.1 NC_016002.1 ASWW01000003.1 NC_009656.1 NZ_AHOT01000027.1 AMZW01000089.1 AGBM01000001.1 NC_015556.1 NC_021237.1 CP000076.1 AJMR01000228.1 NC_010322.1 CP005976.1 NC_015733.1 NC_021499 NZ_AKJI01000047.1 AKJG01000046.1 NZ_AKJD01000246.1 AQFO01000014.1 NZ_CM001514.1 AKCK01000055.1 AMQQ01000004.1 NZ_DS999531.1 NC_014664.1 NZ_DS999054.1 NC_009052.1 NC_009665.1

Island Name G08abn G08aye D1279779_RGP05

ϕ VS1

Island 10

RGP56 Prophage 3 Prophage 2

Prophage 03

Coordinates 2635879..2647205 686242..709787 3240071..3263741 595655..642997 158876..205485 3406689..3448088 23019..61244 31583..54268 22884..55777 64274..94100 68257..94432 137442..162473 1437021..1478152 428180..437090 3848848..3868705 3651333..3677013 3721852..3747532 3464601..3604950 36888..83895 2106016..2128524 1999331..2184138 364208..384624 51324..79125 362630..409709 51511..95437 4684277..4723914 42719..83413 5179273..5190127 54348..65206 31089..83492 158489..187213 60763..69441 330659..363334 269653..283801 776377..811527 523596..529163 4428933..4582578 40652..84499 40927..82652 40667..49678 1388784..1523382 1096727..1154718 17762..54815 2656855..2791880 381923..420459 558446..601013 839103..894227 2411812..2468822 770994..829360 14881..50242 2130087..2168671 2257605..2363077 2253742..2290680 2206875..2248336 412242..525826 1936916..1981735 1761316..1814709 1947645..1989806 3872818..3943813 90198..107498 100576..146826 17402..64255 388699..441269 1852442..1863492 118856..135069 165839..208803 2330944..2379161 1918261..1967577 541627..590903 4210997..4253441 866082..908384

Size (bp) G+C (%) 11327 61.6 23546 37.7 23671 37.7 47343 37.3 46610 39.2 41400 37.8 38226 39.1 22686 39.2 32894 40.0 29827 40.4 26172 36.2 25032 38.3 41132 56.6 8911 33.9 19858 38.6 25681 41.0 25681 41.0 140350 62.7 47008 61.3 22509 57.0 184808 66.5 20417 36.1 27802 50.8 47080 50.9 43927 50.5 39638 50.0 40695 51.0 10855 46.1 10859 46.1 52404 52.8 28725 40.2 8679 50.7 32676 57.4 14149 55.4 35151 53.7 5568 47.6 153646 59.9 43848 51.9 41726 51.1 9012 56.5 134599 61.8 57992 58.9 37054 54.4 135026 67.7 38537 43.9 42568 62.8 55125 62.1 57011 62.8 58367 59.0 35362 56.3 38585 58.7 105473 58.8 36939 58.4 41462 58.9 113585 61.8 44820 60.9 53394 60.2 42162 59.2 70966 62.1 17301 52.8 46251 57.0 46854 58.1 52571 61.5 11051 52.2 16214 50.7 42965 56.3 48218 55.4 49317 60.3 49277 56.7 42445 46.0 42303 46.2

Locus Tag C380 AB57 ABAYE ABD1 ACINNAV57 ACIN3137_A L291 L293 HMPREF0017 ACIRA0001 ACT4_006 ACINWC743 AGROH133 VSALI AMBAS45 MADE MADE BBta I35 bgla_1g Caul CPS EC1011 EC3003 EcB171 ETEC WGC ECH74115 ECPA40 ECSTECH18 GMES PMI16 HPDFL43 HNE GCWU000324 SADFL11 Mesop NM73696 HMPREF0602 C266 Pden Plav RGBS107 PHZ_c PTD2 NH8B LE46 PSPA7 PchlO6 A986 PflQ2 Psefu PFLCHA0_c PFL ppKF707 PputGB1 L483 PPS PCA10 PM132 PMI34 PMI37 HMPREF1224 PseBG33 Pav037 C241 RKLH11 Rvan RR11 Sbal Shew185

CDS 12130-12220 0641-0666 3198-3233 05270-05690 0588-0630 3137-3319 2552-2589 1364-1388 02541-02567 0075-0114 00690-00890 3553-3576 06152-06219 0388-0399 16335-16445 1016775-1016910 1017135-1017275 3310-3456 1589-1653 18670-18900 2043-1864 0353-0383 3356-3393 4528-4592 0688-0730 4359-4304 00045-00108 5530-5551 5484-5503 5069-5153 1194-1222 00553-00564 10257-10387 0283-0293 01205-01259 1138-2029 4302-4443 0415-0353 0052-0118 17541-17581 1420-1548 1004-1050 16878-16743 2343-2442 08004-08264 0534-0598 1516-1588 2362-2435 2091-2179 15166-15361 3552-3598 2114-2205 20300-20720 1975-2023 4047-4141 1710-1763 08090-08470 1736-1780 35880-35170 02372-02396 01891-01945 05674-05731 06117-06055 1689-1699 1760-1772 02694-02994 310-1236 1748-1799 404-1812 3585-3633 0722-0774

dusA int 12220 12195 0641 0644 3223 3221 05270 05280 0588 0590 3319 3320 2552 2553 1364 1365 02541 02542 0114 0113 00690 00700 3553 3554 06152 06153 0399 0398 16335 16340 1016775 1016780 1017275 1017270 3456 3455 1589 1590 18670 18690 2043 2042 0353 0354 3393 3392 4592 4591 0730 0729 4359 4358 00108 00107 5551 5550 5503 5502 5153 5152 1222 1221 00564 00563 10257 10262 0293 0292 01259 01258 1138 2278 4443 4442 0415 0414 0118 0117 17541 17546 1420 1421 1050 1049 16743 16748 2343 2344 08264 08259 0598 0597 1516 1517 2362 2363 2091 2093 15166 15171 3598 3596 2114 2115 20300 20310 1975 1976 4047 4048 1710 1711 08090 08095 1736 1737 35880 35870 02396 02395 01891 01892 05731 05730 06117 06116 1689 1691 1772 1771 02694 02699 310 1807 1748 1749 1812 3187 3585 3586 0774 0773

prtN 0643 3220 05290 0589 3321 2554 02543 0109 00710

3310 18680 0369 3358 4530 0670 4308 00048 5532 5485 5071

01207

17581

08009 0589 01518 2364 2092 15176 3597 2116 20320

1712 08100 1739 35850 02394 01894 05729 06115 1690

3025 1797 3620 0734

Putative genomic island function(s) Phage lysogen Copper resistance Copper resistance Type I restriction-modification, arginine succinyltransferase pathway Type I restriction-modification, pyrimidine utilisation pathway Copper and arsenic resistance Arsenic, chromium and heavy metal resistance Arsenic and heavy metal resistance, ferrous iron transport Type I restriction-modification, potassium transport Phage lysogen Type II restriction-modification, DNA helicase Arsenic resistance, ferric iron uptake, metabolism Phage lysogen Phage remnant Phage remnant Type I restriction-modification, ISAma4 transposase Type I restriction-modification, ISAma4 transposase Conjugal transfer, cationic metal resistance, DNA replication and maintenance Phage lysogen Phage lysogen Conjugal transfer, carbonaceous compound degradation, multiple integrases Phage remnant, ISCps1 transposase Phage lysogen Phage lysogen Phage lysogen Phage lysogen Phage lysogen Phage remnant Phage remnant Phage lysogen, IS3 transposase, tRNAs genes Type I restriction-modification Phage remnant Metabolism Unknown Phage lysogen Degraded genomic island Conjugal transfer, cytochrome biogenesis Phage lysogen Phage lysogen Unknown Conjugal transfer Pseudoazurin production, nitrogen oxide metabolism Metabolism Type IV secretion system, various metabolic enzymes Phage lysogen Phage lysogen Phage lysogen Phage lysogen Phage lysogen Phage lysogen Phage lysogen Conjugal transfer, DNA replication and maintenance Phage lysogen Phage lysogen Conjugal transfer, amino acid metabolism, DNA replication and partitioning Phage lysogen Phage lysogen Phage lysogen Arsenic resistance, metabolism Phage remnant Phage lysogen Phage lysogen Phage lysogen Unknown Phage remnant Phage lysogen, tRNA-Met Phage lysogen Conjugal transfer, various transposases Phage lysogen Phage lysogen Phage lysogen

Organism Shewanella baltica OS195 Shewanella baltica OS223 Shewanella denitrificans OS217 Shewanella sp. MR-7 Sinorhizobium fredii HH103 Sinorhizobium fredii USDA 257 Sinorhizobium medicae WSM419 Sinorhizobium meliloti AK83 Sinorhizobium meliloti BL225C Sinorhizobium meliloti SM11 Starkeya novella DSM 506 Variovorax paradoxus S110 Vibrio cholerae O1 str. EM-1676A Vibrio cholerae TMA 21 Vibrio mimicus VM223 Vibrio parahaemolyticus BB22OP Vibrio shilonii AK1 Vibrio sinaloensis DSM 21326 Vibrio sp. 16 Vibrio sp. RC341 Vibrio splendidus 12B01 Xanthomonas albilineans GPE PC73 Xenorhabdus bovienii SS-2004 †: Secondary attR site at 1987629..1987644

Accession Version NC_009997.1 NC_011663.1 NC_007954.1 NC_008322.1 HE616890.1 NC_018000.1 NC_009636.1 NC_015590.1 CP002740.1 CP001830.1 NC_014217.1 NC_012791.1 APFY01000090.1 NZ_ACHY01000008.1 NZ_ADAJ01000005.1 NC_019955.1 NZ_ABCH01000029.1 NZ_AEVT01000002.1 DS999366.1 NZ_ACZT01000016.1 NZ_AAMR01000034.1 NC_013722.1 NC_013892.1

Island Name

Coordinates 903068..946900 883717..926065 3867007..3909462 820506..853673 1772042..1814196 4359830..4364587 1717430..1768028 1828582..1877761 1728034..1776517 2406519..2454942 882664..907567 2202985..2265954 11544..48041 9867..38075 215734..227834 2860513..2893508 6437..42147 63274..77654 11141..26033 6993..19073 7414..21480 219708..271808 3797963..3840279

Size (bp) G+C (%) 43833 45.3 42349 46.1 42456 45.3 33168 48.6 42155 62.0 4758 57.5 50599 61.2 49180 60.8 48484 61.2 48424 60.9 24904 66.5 62970 64.1 36498 42.7 28209 43.9 12101 46.6 32996 49.8 35711 43.5 14381 45.9 14893 47.0 12081 46.3 14067 44.0 52101 59.9 42317 48.3

Locus Tag Sbal195 Sba1223 Sden Shewmr7 SFHH103 USDA257_c Smed Sinme SinmeB SM11_chr Snov Vapar VCEM1676A VCB VMA VPBB VSAK1 VISI1226 VPMS16 VCJ V12B01 XALc XBJ1

CDS 0751-0806 0742-0799 3232-3281 0699-0746 01636-01689 41740-41790 1621-1683 1811-1876 1656-1716 1426-1491 0848-0872 2059-2122 000425-000456 000225-000242 000316-000303 2545-2586 13606-13831 20525-20665 1054-1081 000612-000632 10660-10775 0171-0242 3925-3991

dusA 0806 0799 3232 0746 01636 41740 1621 1811 1656 1491 0872 2122 000456 000225 000316 2545 13606 20665 1081 000612 10660 0242 3925

int 0805 0798 3233 0745 01637 41750 1622 1812 1657 1490 0871 2121 000455 000226 000315 2546 13611 20660 1080 000613 10665 0241 3926

prtN 0763 0759 3273 0703 01689 1680 1873 1714 1426

000241 2550 13636 20540 1074 10760 3991

Putative genomic island function(s) Phage lysogen Phage lysogen, ISSba2 tranposase Phage lysogen Phage lysogen Phage lysogen Degraded genomic island, DNA ligase Phage lysogen Phage lysogen Phage lysogen Phage lysogen Alkanesulphonate metabolism DNA replication Fimbrial biogenesis Conjugal transfer Phage remnant, DNA replication Phage lysogen Phage lysogen Phage lysogen Unknown Phage remnant, DNA replication Phage remnant, DNA replication Phage lysogen Phage lysogen, tRNA-Phe