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A B C D Supplementary Figure 1 Supplementary Figure 1 A B 50.0% Without MK and UQ 50.0% Without MK and UQ 40.0% With MK and/or UQ 40.0% With MK and/or UQ 30.0% 30.0% 20.0% 20.0% 10.0% 10.0% % of predicted proteomes proteomes % of predicted % of predicted proteomes proteomes % of predicted 0.0% 0.0% Oxygen Requirements Habitats C D 40.0% Without complete MK/UQ 40.0% Without complete MK/UQ pathways pathways Without any type of 30.0% 30.0% Without any type of quinones quinones 20.0% 20.0% 10.0% 10.0% % of predicted proteomes proteomes % of predicted % of predicted proteomes proteomes % of predicted 0.0% 0.0% Oxygen Requirements Habitats Supplementary Figure 2 rrnAC0837 rrnAC0838 rrnAC0841 rrnAC0843 rrnAC0844 rrnAC0845 Haloarcula marismortui ATCC 43049 menF menD dnaJ' menB menE' menC' menA' ~720.8K ~731.2K NP2724A NP2726A NP2730A NP2734A NP2736A NP2738A Natronomonas pharaonis DSM 2160 menF menD menB menA menC menE ~1.32M ~1.33M HQ1872A HQ1873A HQ1874A HQ1875A HQ1876A Haloquadratum walsbyi DSM 16790 menF menD menB menA menC ~1.06M ~1.07M Hbor_17630 Hbor_17640 Hbor_17670 Hbor_17690 Hbor_17700 Halogeometricum borinquense DSM 11551 menF menD menB menA menC ~1.69M ~1.70M VNG1083G VNG1081G VNG1079G VNG1075G VNG1074G VNG1073G Halobacterium sp. NRC-1 menF' menD' menB' opuD' menA' menC' menE' ~830.6K ~821.2K OE2566R OE2563R OE2561R OE2559R OE2558R OE2555R Halobacterium salinarum R1 menF' menD' menB' opuD' menA' menC' menE' ~822.6K ~813.2K HVO_1470 HVO_1469 HVO_1465 HVO_1462 HVO_1461 Haloferax volcanii DS2 menF' menD' menB' trxB' menA' menC' ~1.34M ~1.33M Htur_1784 Htur_1783 Htur_1780 Htur_1776 Htur_1775 Htur_1774X Haloterrigena turkmenica DSM 5511 menF' menD' menB' menA' menC' menE' ~1.86M ~1.84M Nmag_3570 Nmag_3569 Nmag_3561 Nmag_3557 Nmag_3556 Nmag_3555 Natrialba magadii ATCC 43099 menF' menD' dnaJ' ~5.2K menB' menA' menC' menE' ~3.71M ~3.69M Huta_0814 Huta_0815 Huta_0395 Huta_0394 Huta_0393 Huta_0392 Halorhabdus utahensis DSM 12940 menF menD dnaJ' menB' menA' menC' menE' ~792K ~796K ~389K ~384.8K Hmuk_0041 Hmuk_2248 Hmuk_2249 Hmuk_2250 Hmuk_2252 Hmuk_2535 ~2.12M Halomicrobium mukohataei DSM 12286 menF' menE' menC' menA' menB' ~269K menD' ~37.9K ~2.44M Supplementary Figure 3. The genetic architectures of the classical MK pathway in the genomes of family Halobacteriaceae. The loci numbers are displayed above the arrows denoting different genes. The approximate physical distances in chromosome between two genes or clusters are displayed between bars under arrows. Supplementary Figure 3 Korarchaeum cryptofilum Korarchaeota 1 Picrophilus torridus 81 50 Staphylothermus marinus Thermoplasma volcanium Euryarchaeota Thermofilum pendens 0.97 1 Thermoplasma acidophilum Supplementary Figure 2. Phylogeny of A Crenarchaeota B Acidilobus saccharovorans Cyanothece sp. ATCC 51142 Cyanobacteria o-succinylbenzoate synthase (MenC). Aeropyrum pernix 0.95 Natranaerobius thermophilus Picrophilus torridus 0.58 Gemmatimonas aurantiaca Gemmatimonadetes This phylogeny was calculated from an 100 Thermoplasma volcanium Euryarchaeota Pectobacterium atrosepticum 100 Thermoplasma acidophilum 0.98 1 Lactobacillus rhamnosus amino acid alignment of 123 sequences Paludibacter propionicigenes Bacteroidetes Bacillus subtilis 86 Pectobacterium atrosepticum Enterococcus faecalis Firmicutes Lactobacillus rhamnosus 1 Listeria monocytogenes and 853 sites (including ambiguous 99 Listeria monocytogenes Thermaerobacter marianensis Enterococcus faecalis Firmicutes 1 0.68 Korarchaeum cryptofilum Korarchaeota alignments). There were 49 sequences of 0.71 Acidilobus saccharovorans Bacillus subtilis 0.93 Staphylothermus marinus Natranaerobius thermophilus Crenarchaeota mandelate racemase used as multiple 68 Cyanothece sp. ATCC 51142 Cyanobacteria 10.81 Thermofilum pendens Thermaerobacter marianensis Firmicutes Aeropyrum pernix outgroup. These outgroup sequences Isosphaera pallida Planctomycetes 0.96 Koribacter versatilis 1 Streptosporangium roseum Actinobacteria 0.74 Solibacter usitatus Acidobacteria Acidobacterium capsulatum distributed in 10 phyla. Sequences from Chloroflexus aurantiacus Chloroflexi 0.97 58 Solibacter usitatus 0.83 Paludibacter propionicigenes Bacteroidetes archaea displayed in red. Bootstrap Koribacter versatilis Acidobacteria Isosphaera pallida Planctomycetes 86 Acidobacterium capsulatum 0.99 Chloroflexus aurantiacus Chloroflexi 0.57 Streptosporangium roseum Truepera radiovictrix 0.5 Actinobacteria values above 49% are shown as Truepera radiovictrix Thermus thermophilus 100 0.98 0.99 Thermus thermophilus Oceanithermus profundus Deinococcus-Thermus percentages of 1000 replicates. The scale 99 0.99 Oceanithermus profundus Deinococcus-Thermus Deinococcus geothermalis 1 54 Deinococcus radiodurans 50 Deinococcus radiodurans bar denotes the number of substitutions 0.61 Deinococcus geothermalis 54 Rhodobacter capsulatus Proteobacteria 1 Rhodobacter capsulatus Gemmatimonas aurantiaca 1 Proteobacteria Gemmatimonadetes Thermomonospora curvata per site. Thermomonospora curvata Actinobacteria Actinobacteria 0.89 Acidimicrobium ferrooxidans 99 Acidimicrobium ferrooxidans Alicyclobacillus acidocaldarius Alicyclobacillus acidocaldarius Firmicutes Firmicutes 0.99 Exiguobacterium sibiricum Exiguobacterium sibiricum Ignicoccus hospitalis Crenarchaeota Ignicoccus hospitalis Crenarchaeota 1 100 Proteobacteria Proteobacteria Leadbetterella byssophila Leadbetterella byssophila 0.51 0.88 Spirosoma linguale 62 Chitinophaga pinensis 0.66 Gramella forsetii Bacteroidetes Gramella forsetii Bacteroidetes 1 0.99 0.99 Chitinophaga pinensis Spirosoma linguale 0.95 83 Haliangium ochraceum 100 Haliangium ochraceum 1 100 Pirellula staleyi Pirellula staleyi Rhodopirellula baltica Planctomycetes Rhodopirellula baltica Planctomycetes 0.99 Planctomyces brasiliensis 83 Planctomyces brasiliensis 66 0.99 Nostoc sp. PCC 7120 91 Synechococcus sp. JA-2-3B'a(2-13) 1 1 Cyanothece sp. PCC 8802 72 Synechococcus elongatus Cyanobacteria Cyanobacteria Synechococcus elongatus Cyanothece sp. PCC 8802 0.99 0.97 0.99 Synechococcus sp. JA-2-3B'a(2-13) 59 53 Nostoc sp. PCC 7120 74 Stigmatella aurantiaca 0.75 Stigmatella aurantiaca Oceanithermus profundus Deinococcus-Thermus Oceanithermus profundus Deinococcus-Thermus Pantoea sp. At-9b Pantoea sp. At-9b 0.78 Accumulibacter phosphatis Accumulibacter phosphatis 0.85 Salinibacter ruber Bacteroidetes Thermomicrobium roseum 0.56 Thermomicrobium roseum Chloroflexi Chloroflexi 94 Sphaerobacter thermophilus 0.96 Sphaerobacter thermophilus Stigmatella aurantiaca Proteobacteria 1 Stigmatella aurantiaca Proteobacteria Salinibacter ruber Bacteroidetes Halorhabdus utahensis Halorhabdus utahensis 0.56 1 Natrialba magadii 100 Halobacterium sp. NRC-1 0.9 Haloterrigena turkmenica 1 57 Halobacterium salinarum Natronomonas pharaonis 97 100 Haloterrigena turkmenica 1 Haloarcula marismortui Natrialba magadii 1 Halomicrobium mukohataei 87 Natronomonas pharaonis 0.95 Euryarchaeota Euryarchaeota 0.99 Haloferax volcanii 60 Halorubrum lacusprofundi Haloquadratum walsbyi Halogeometricum borinquense 0.99 Halogeometricum borinquense Haloquadratum walsbyi 0.77 0.98 Halorubrum lacusprofundi Haloferax volcanii Halobacterium sp. NRC-1 Halomicrobium mukohataei 1 Halobacterium salinarum 100 Haloarcula marismortui Mandelate racemase (Outgroup) Mandelate racemase (Outgroup) 0.5 0.5.
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