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Wedding Higher Taxonomic Ranks with Metabolic Signatures Coded in Prokaryotic Genomes

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Wedding Higher Taxonomic Ranks with Metabolic Signatures Coded in Prokaryotic Genomes Wedding higher taxonomic ranks with metabolic signatures coded in prokaryotic genomes Gregorio Iraola*, Hugo Naya* Corresponding authors: E-mail: [email protected], [email protected] This PDF file includes: Supplementary Table 1 Supplementary Figures 1 to 4 Supplementary Methods SUPPLEMENTARY TABLES Supplementary Tab. 1 Supplementary Tab. 1. Full prediction for the set of 108 external genomes used as test. genome domain phylum class order family genus prediction alphaproteobacterium_LFTY0 Bacteria Proteobacteria Alphaproteobacteria Rhodobacterales Rhodobacteraceae Unknown candidatus_nasuia_deltocephalinicola_PUNC_CP013211 Bacteria Proteobacteria Gammaproteobacteria Unknown Unknown Unknown candidatus_sulcia_muelleri_PUNC_CP013212 Bacteria Bacteroidetes Flavobacteriia Flavobacteriales NA Candidatus Sulcia deinococcus_grandis_ATCC43672_BCMS0 Bacteria Deinococcus-Thermus Deinococci Deinococcales Deinococcaceae Deinococcus devosia_sp_H5989_CP011300 Bacteria Proteobacteria Unknown Unknown Unknown Unknown micromonospora_RV43_LEKG0 Bacteria Actinobacteria Actinobacteria Micromonosporales Micromonosporaceae Micromonospora nitrosomonas_communis_Nm2_CP011451 Bacteria Proteobacteria Betaproteobacteria Nitrosomonadales Nitrosomonadaceae Unknown nocardia_seriolae_U1_BBYQ0 Bacteria Actinobacteria Actinobacteria Corynebacteriales Nocardiaceae Nocardia nocardiopsis_RV163_LEKI01 Bacteria Actinobacteria Actinobacteria Streptosporangiales Nocardiopsaceae Nocardiopsis oscillatoriales_cyanobacterium_MTP1_LNAA0 Bacteria Cyanobacteria NA Oscillatoriales Unknown Unknown acetobacter_tropicalis_NBRC16470_BBMU0 Bacteria Proteobacteria Alphaproteobacteria Rhodospirillales Acetobacteraceae Acetobacter achromobacter_xylosoxidans_CF304_LFHA01 Bacteria Proteobacteria Betaproteobacteria Burkholderiales Alcaligenaceae Achromobacter acinetobacter_baumannii_Ab5_LANH000000000 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Moraxellaceae Acinetobacter actinobacillus_pleuropneumoniae_1022_JSVF0 Bacteria Proteobacteria Gammaproteobacteria Pasteurellales Pasteurellaceae Actinobacillus aeromonas_caviae_L12_JWJP01 Bacteria Proteobacteria Gammaproteobacteria Aeromonadales Aeromonadaceae Aeromonas alphaproteobacterium_Q1_BAYV01 Bacteria Proteobacteria Alphaproteobacteria Unknown Unknown Unknown amycolatopsis_orientalis_CPCC200066_JXRD01 Bacteria Actinobacteria Actinobacteria Pseudonocardiales Pseudonocardiaceae Amycolatopsis bacilli_bacterium_VT13104_LAZH01 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Unknown bacteroides_fragilis_BOB25_CP011073 Bacteria Bacteroidetes Bacteroidia Bacteroidales Bacteroidaceae Bacteroides bifidobacterium_adolescentis_150_LBHQ00000000 Bacteria Actinobacteria Actinobacteria Bifidobacteriales Bifidobacteriaceae Bifidobacterium bifidobacterium_angulatum_GT102_LAHN00000000 Bacteria Actinobacteria Actinobacteria Bifidobacteriales Bifidobacteriaceae Bifidobacterium brachymonas_chironomi_DSM19884_ARGE01 Bacteria Proteobacteria Betaproteobacteria Burkholderiales Comamonadaceae Unknown bradyrhizobium_japonicum_FN1_JGCL01 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Bradyrhizobiaceae Bradyrhizobium bradyrhizobium_sp_thb2_AUGA01 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Bradyrhizobiaceae Bradyrhizobium burkholderia_glathei_PML112 Bacteria Proteobacteria Betaproteobacteria Burkholderiales Burkholderiaceae Burkholderia cellulomonas_FA1_LBMY0 Bacteria Actinobacteria Actinobacteria Micrococcales Cellulomonadaceae Cellulomonas cellvibrio_mixtus_J38_ALBT0 Bacteria Proteobacteria Gammaproteobacteria Pseudomonadales Pseudomonadaceae Cellvibrio chlamydia_psittaci_HJ_JPIH01 Bacteria Chlamydiae Chlamydiia Chlamydiales Chlamydiaceae Chlamydia chromobacterium_subtsugae_MWU2920_LCWP0 Bacteria Proteobacteria Betaproteobacteria Neisseriales Chromobacteriaceae Chromobacterium citrobacter_rodentium_DBS100_JXUN0 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Citrobacter clavibacter_michiganensis_DOAB397 Bacteria Actinobacteria Actinobacteria Micrococcales Microbacteriaceae Clavibacter coxiella_brunetii_NLLimburg_JZWL0 Bacteria Proteobacteria Gammaproteobacteria Legionellales Coxiellaceae Coxiella cronobacter_sakazakii_CDC200903746_JZDO0 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Cronobacter deinococcus_sp_RL_JMQF01 Bacteria Deinococcus-Thermus Deinococci Deinococcales Deinococcaceae Deinococcus delftia_tsuruhatensis_MTQ3_LCZH01 Bacteria Proteobacteria Betaproteobacteria Burkholderiales Comamonadaceae Delftia dickeya_dianthicola_RNS049_APVF01 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Dickeya edwardsiella_piscicida_LADL05105_CP011364 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Edwardsiella enterobacter_cloacae_UW5_CP011798 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Enterobacter enterobacter_sp_54_JFHW01 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Enterobacter enterococcus_faecium_ATCC51559_JSVT0 Bacteria Firmicutes Bacilli Lactobacillales Enterococcaceae Enterococcus erwinia_tracheiphila_BuffGH_JXNU0 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Erwinia erythrobacter_vulgaris_O1_CCSI01 Bacteria Proteobacteria Alphaproteobacteria Sphingomonadales Erythrobacteraceae Erythrobacter flavobacterium_psychrophilum_FPG3_CP008207 Bacteria Bacteroidetes Flavobacteriia Flavobacteriales Flavobacteriaceae Flavobacterium flavobacterium_sp_83_JQMS0 Bacteria Bacteroidetes Flavobacteriia Flavobacteriales Flavobacteriaceae Flavobacterium francisella_tularensis_OR960246 Bacteria Proteobacteria Gammaproteobacteria Thiotrichales Francisellaceae Francisella frankia_DC12_LANG0 Bacteria Actinobacteria Actinobacteria Frankiales Frankiaceae Frankia fructobacillus_EFBN1_LDUY01 Bacteria Firmicutes Bacilli Lactobacillales Leuconostocaceae Unknown gardnerella_vaginalis_3549624_LFWD0 Bacteria Actinobacteria Actinobacteria Bifidobacteriales Bifidobacteriaceae Gardnerella geobacillus_Zgt1_LDPD01 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Geobacillus gluconobacter_oxydans_NL71_LCTG0 Bacteria Proteobacteria Alphaproteobacteria Rhodospirillales Acetobacteraceae Gluconobacter haemophilus_influenzae_MiHi64_JXMG0 Bacteria Proteobacteria Gammaproteobacteria Pasteurellales Pasteurellaceae Haemophilus hafnia_paralvei_GTAHAF03_JWGZ01 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Hafnia halomonas_lutea_DSM23508_ARKK01 Bacteria Proteobacteria Gammaproteobacteria Oceanospirillales Halomonadaceae Halomonas halomonas_MCTG39a_JQLV0 Bacteria Proteobacteria Gammaproteobacteria Oceanospirillales Halomonadaceae Halomonas hassallia_byssoidea_VB512170_JTCM0 Bacteria Cyanobacteria NA Nostocales Unknown Unknown jiangella_alkaliphila_KCTC19222_LBMC00000000 Bacteria Actinobacteria Actinobacteria Unknown Unknown Unknown kingella_kingae_KK247_CCJT0 Bacteria Proteobacteria Betaproteobacteria Neisseriales Neisseriaceae Kingella legionella_neumophila_Bnt314_BBUG0 Bacteria Proteobacteria Gammaproteobacteria Legionellales Legionellaceae Legionella leuconostoc_mesenteroides_LbE15_JAYN0 Bacteria Firmicutes Bacilli Lactobacillales Leuconostocaceae Leuconostoc leuconostoc_mesenteroides_P45_JRGZ0 Bacteria Firmicutes Bacilli Lactobacillales Leuconostocaceae Leuconostoc loktanella_hongkongensis_UST950701009PT_APGJ01 Bacteria Proteobacteria Alphaproteobacteria Rhodobacterales Rhodobacteraceae Loktanella lysinibacillus_xylanilyticus_DSM23493_LFXJ01 Bacteria Firmicutes Bacilli Bacillales Bacillaceae Lysinibacillus magnetospirillum_magnetotacticum_MS1_JXSL01 Bacteria Proteobacteria Alphaproteobacteria Rhodospirillales Rhodospirillaceae Magnetospirillum mannheimia_haemolytica_D174_CP006574 Bacteria Proteobacteria Gammaproteobacteria Pasteurellales Pasteurellaceae Mannheimia meiothermus_ruber_A_JXOP01 Bacteria Deinococcus-Thermus Deinococci Thermales Thermaceae Meiothermus mesorhizobium_loti_NZP2037_AQZP01 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Phyllobacteriaceae Mesorhizobium methylomicrobium_agile_ATCC34068_JPOJ0 Bacteria Proteobacteria Gammaproteobacteria Methylococcales Methylococcaceae Methylomicrobium micrococcus_sp_MSAsIII49_JXSP0 Bacteria Actinobacteria Actinobacteria Micrococcales Micrococcaceae Micrococcus microvirga_vignae_BR3299 Bacteria Proteobacteria Alphaproteobacteria Rhizobiales Unknown Unknown mycobacterium_tuberculosis_134152_LAVG00000000 Bacteria Actinobacteria Actinobacteria Corynebacteriales Mycobacteriaceae Mycobacterium Page 1 Supplementary Tab. 1 mycoplasma_gallinaceum_B20968B_CP011021 Bacteria Tenericutes Mollicutes Mycoplasmatales Mycoplasmataceae Mycoplasma mycrocystis_aeruginosa_NIES2549_CP011304 Bacteria Cyanobacteria NA Chroococcales NA Microcystis nocardia_seriolae_N2927_BAWD02 Bacteria Actinobacteria Actinobacteria Corynebacteriales Nocardiaceae Nocardia oenococcus_oeni_139_LCTM0 Bacteria Firmicutes Bacilli Lactobacillales Leuconostocaceae Oenococcus ornithobacterium_rhinotracheale_ORTUMN88_CP006828 Bacteria Bacteroidetes Flavobacteriia Flavobacteriales Flavobacteriaceae Ornithobacterium paenibacillus_wulumuqiensis_JCM30284_LAQP01 Bacteria Firmicutes Bacilli Bacillales Unknown Unknown pantoea_anthophila_112_JXXL01 Bacteria Proteobacteria Gammaproteobacteria Enterobacteriales Enterobacteriaceae Pantoea peptococcaceae_CEB3_LDXJ0 Bacteria Firmicutes Clostridia Clostridiales Unknown Unknown porphyromonas_canoris_COT108_JQZX0 Bacteria Bacteroidetes Bacteroidia
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