UbiA MenA

fig|563192.3.peg.990 fig|457398.5.peg.2833 1.000

fig|563192.3.peg.466 fig|537012.5.peg.2837 fig|411479.10.peg.142

fig|457393.3.peg.3338 fig|585543.3.peg.380 1.000

0.792 0.892

fig|349741.6.peg.1697 - gapped fig|649754.3.peg.866

fig|411466.7.peg.992 0.996

fig|398513.5.peg.1583 fig|518634.7.peg.1486 fig|548480.3.peg.661

fig|565040.3.peg.1716 fig|537937.5.peg.1190 fig|206672.9.peg.1709 fig|565042.3.peg.1665 0.987

fig|411481.5.peg.692 fig|547043.8.peg.224 fig|518635.7.peg.1318

fig|473819.7.peg.221 fig|391904.8.peg.2237

fig|566552.6.peg.1136 0.955

0.996

fig|561180.4.peg.1005 fig|442563.4.peg.450 0.967

0.902 0.984 0.984

0.978 0.010

fig|742821.3.peg.283 - gapped fig|469610.4.peg.252

0.999

fig|762983.3.peg.89 fig|471881.3.peg.1144

fig|471874.6.peg.3326 fig|521000.6.peg.1707

fig|520999.6.peg.3300 fig|500637.6.peg.491 fig|500637.6.peg.7164 0.839

fig|471881.3.peg.1142 fig|469613.3.peg.4110 fig|500638.3.peg.2921 0.994

fig|500639.8.peg.4107 fig|469608.3.peg.4886 fig|99287.12.peg.4311 fig|386585.9.peg.5079 fig|457400.3.peg.2036 fig|457401.3.peg.4466 fig|511145.12.peg.4048 fig|409438.11.peg.4396 fig|469598.5.peg.4674 fig|364106.8.peg.4404 fig|469595.3.peg.4563

fig|500640.5.peg.4618 0.843

1.000 0.769 0.283 0.951 0.989

0.683

fig|469589.3.peg.1146 fig|457388.5.peg.2787 fig|469591.4.peg.2123 fig|435591.13.peg.1540 fig|469592.4.peg.2567 fig|563193.3.peg.2694

fig|537006.5.peg.1125 fig|411477.4.peg.2834 fig|537006.5.peg.1126 1.000

fig|888832.3.peg.532 fig|537011.5.peg.2484 fig|537011.5.peg.3102 0.999

fig|449673.7.peg.2733 fig|665953.3.peg.1781 fig|483216.6.peg.319

fig|537012.5.peg.4917 fig|471870.8.peg.4691 fig|585543.3.peg.2496 fig|411479.10.peg.1765 fig|457393.3.peg.2962 0.353

0.998

fig|457424.5.peg.3914 fig|295405.11.peg.3561 fig|469587.3.peg.3626 fig|457392.3.peg.2991 fig|272559.17.peg.3572

fig|226186.12.peg.2067 fig|469586.3.peg.3246

fig|483215.6.peg.1445 fig|469590.5.peg.3335 fig|702443.3.peg.1371 fig|411476.11.peg.1053 fig|457390.3.peg.3585 fig|556259.3.peg.3678

fig|411901.7.peg.3568 fig|702444.3.peg.4491 fig|457387.3.peg.1326 fig|469588.3.peg.1735 fig|556258.5.peg.3344 fig|585544.3.peg.31 fig|702447.3.peg.2771 fig|657309.4.peg.126 0.834

0.911 0.939

fig|742725.3.peg.1308 fig|435590.9.peg.1705 fig|702446.3.peg.265 fig|457394.3.peg.4139 fig|469593.3.peg.4667 fig|457395.6.peg.4334 fig|483217.6.peg.231 fig|457391.3.peg.4348

fig|547042.5.peg.1543 fig|470145.6.peg.2627 fig|484018.6.peg.3417 0.871

0.987 0.759 0.704 0.453 0.985 0.993

0.727 0.993 0.925

fig|665943.3.peg.2890 fig|657308.3.peg.3081

fig|469615.3.peg.558 fig|469605.3.peg.1266 fig|469602.3.peg.1670 fig|469606.3.peg.717

fig|469603.3.peg.1383 fig|556264.3.peg.1014 fig|457405.3.peg.1668 0.984

1.000

fig|324831.13.peg.1760 fig|257314.6.peg.1815

fig|525338.3.peg.2342

fig|471881.3.peg.1145 0.963

fig|586220.3.peg.1341 fig|491074.3.peg.1707 fig|525278.3.peg.2031 fig|525310.3.peg.101 fig|525327.3.peg.278 fig|525318.3.peg.19 fig|525278.3.peg.86 fig|491074.3.peg.2502 fig|657310.3.peg.432 fig|749518.3.peg.1487 fig|362948.14.peg.1100 fig|525364.3.peg.978

fig|525325.3.peg.1250 fig|334390.5.peg.1217 fig|557436.4.peg.1094 fig|585517.3.peg.1506 fig|548485.3.peg.916 fig|557433.4.peg.1130 fig|491077.3.peg.1652 fig|525341.3.peg.1221 0.999

fig|525309.3.peg.1010 fig|525365.3.peg.1178 fig|575595.3.peg.1004 0.989

0.993 0.952 0.945 0.808 0.992

fig|387344.15.peg.1549

fig|585506.3.peg.985 fig|220668.9.peg.959

fig|525338.3.peg.1657 0.891

0.855 0.620 0.927 0.788 0.713 0.991 0.836

fig|525367.9.peg.627 fig|224308.113.peg.3959 0.957

fig|457416.3.peg.1676 fig|450749.3.peg.1402 1.000

0.956 0.785

fig|658664.3.peg.2752 fig|556268.6.peg.2272

fig|556269.4.peg.1008 0.927

0.980

fig|575587.3.peg.376 fig|469613.3.peg.2740

fig|500638.3.peg.116 0.589

fig|500639.8.peg.2467 fig|469608.3.peg.4217 fig|364106.8.peg.4488 fig|469598.5.peg.3324 fig|457401.3.peg.3312 fig|511145.12.peg.4157 fig|457400.3.peg.314 fig|409438.11.peg.4513 fig|386585.9.peg.5246

fig|99287.12.peg.4454 fig|469595.3.peg.4401 fig|500640.5.peg.4409 fig|471881.3.peg.3331 fig|520999.6.peg.1468

fig|500637.6.peg.2465 fig|500637.6.peg.6923 fig|521000.6.peg.17

fig|471874.6.peg.3746 0.990

0.311 0.959 0.859 0.990

fig|500635.8.peg.1449 fig|657316.3.peg.1682 0.995

fig|457398.5.peg.2595 fig|411464.8.peg.2008 1.000

fig|742725.3.peg.1930 fig|888826.3.peg.1565 fig|864566.3.peg.1076 1.000

fig|556267.4.peg.915 fig|537970.9.peg.1538

fig|537972.5.peg.1533 0.998

fig|537971.5.peg.1298 fig|613026.4.peg.1062 0.657

0.191 0.997 0.884

0.328 0.949 1.000

0.1

Figure S3. Maximum-likelihood tree for the UbiA, MenA, and MqnP proteins. MenA proteins were used as outgroup. Their co-occurrence in genomes with quinone biosynthesis pathways is shown by different colours. The SEED identifiers for proteins are shown; for their sequences, see the file Sequences S1 in the Supplementary materials.

UbiA MenA

MqnP