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Table 1 Species and taxonomic groups represented in the genome sequence dataset. The taxonomic information is from the NCBI Taxonomy database [85] and the three-letter code for the organisms is from KEGG [24]

From: High precision multi-genome scale reannotation of enzyme function by EFICAz

ARCHAEA

Euryarchaeota: mja mmp mac mma mth mka afu hal hma tac tvo pto pho pab pfu tko

Crenarchaeota: ape sso sto pai

Nanoarchaeota: neq

BACTERIA

Proteobacteria, Alphaproteobacteria: rpr rty rco wol wbm ama eru erw erg mlo sme atu atc bme bms bja rpa bhe bqu ccr sil zmo gox

Proteobacteria, Betaproteobacteria: nme nma ngo cvi rso bma bps bpe bpa bbr neu eba

Proteobacteria, Gammaproteobacteria: eco ecj ece ecs ecc sty stt spt stm ype ypk ypm yps sfl sfx eca plu buc bas bab wbr bfl hin hdu pmu msu xfa xft xcc xac xoo vch vvu vvy vpa vfi ppr pae ppu pst aci son ilo cbu lpn lpf lpp mca ftu

Proteobacteria, delta/epsilon subdivision: hpy hpj hhe wsu cje cjr gsu dvu bba dps

Firmicutes, Bacilli: bsu bha ban bar baa bat bce bca bcz btk bli bld bcl oih gka sau sav sam sar sas sac sep ser lmo lmf lin lla spy spm spg sps spa spn spr sag san smu stc stl lpl ljo lac efa

Firmicutes, Clostridia: cac cpe ctc tte

Firmicutes, Mollicutes: mge mpn mpu mpe mga mmy mmo mhy uur poy mfl

Firmicutes, Actinobacteria: mtu mtc mbo mle mpa cgl cef nfa cdi sco sma twh tws lxx pac blo sth

Fusobacteria: fnu

Planctomycetes: rba

Chlamydiae/Verrucomicrobia group: ctr cmu cpn cpa cpj cpt cca pcu

Spirochaetes: bbu bga tpa tde lil lic

Bacteroidetes/Chlorobi group: cte bth bfr pgi

Cyanobacteria: syn syw syc tel gvi ana pma pmm pmt

Chloroflexi: det

Deinococcus-Thermus: dra tth ttj

Aquificae: aae

Thermotogae: tma

EUKARYA

Fungi/Metazoa group: hsa1 mmu1 rno1 dre1 dme cel

Viridiplantae: ath osa1

Rhodophyta: cme

Fungi/Metazoa group: sce ago cal spo ecu

Mycetozoa: ddi1

Alveolata: pfa cpv1 cho1

Euglenozoa: tbr1 lma1

  1. 1Incomplete genome project. aae: Aquifex aeolicus, aci: Acinetobacter sp. ADP1, afu: Archaeoglobus fulgidus, ago: Ashbya gossypii, ama: Anaplasma marginale, ana: Anabaena sp. PCC7120, ape: Aeropyrum pernix, atc: Agrobacterium tumefaciens C58 (Cereon), ath: Arabidopsis thaliana, atu: Agrobacterium tumefaciens C58 (UWash/Dupont), baa: Bacillus anthracis A2012, bab: Buchnera aphidicola Bp, ban: Bacillus anthracis Ames, bar: Bacillus anthracis Ames 0581, bas: Buchnera aphidicola Sg, bat: Bacillus anthracis Sterne, bba: Bdellovibrio bacteriovorus, bbr: Bordetella bronchiseptica, bbu: Borrelia burgdorferi, bca: Bacillus cereus ATCC 10987, bce: Bacillus cereus ATCC 14579, bcl: Bacillus clausii, bcz: Bacillus cereus ZK, bfl: Blochmannia floridanus, bfr: Bacteroides fragilis, bga: Borrelia garinii, bha: Bacillus halodurans, bhe: Bartonella henselae, bja: Bradyrhizobium japonicum, bld: Bacillus licheniformis DSM13, bli: Bacillus licheniformis ATCC 14580, blo: Bifidobacterium longum, bma: Burkholderia mallei, bme: Brucella melitensis, bms: Brucella suis, bpa: Bordetella parapertussis, bpe: Bordetella pertussis, bps: Burkholderia pseudomallei, bqu: Bartonella quintana, bsu: Bacillus subtilis, bth: Bacteroides thetaiotaomicron, btk: Bacillus thuringiensis, buc: Buchnera aphidicola APS, cac: Clostridium acetobutylicum, cal: Candida albicans, cbu: Coxiella burnetii, cca: Chlamydophila caviae, ccr: Caulobacter crescentus, cdi: Corynebacterium diphtheriae, cef: Corynebacterium efficiens, cel: Caenorhabditis elegans, cgl: Corynebacterium glutamicum, cho: Cryptosporidium hominis, cje: Campylobacter jejuni NCTC11168, cjr: Campylobacter jejuni RM1221, cme: Cyanidioschyzon merolae, cmu: Chlamydia mu ridarum, cpa: Chlamydophila pneumoniae AR39, cpe: Clostridium perfringens, cpj: Chlamydophila pneumoniae J138, cpn: Chlamydophila pneumoniae CWL029, cpt: Chlamydophila pneumoniae TW183, cpv: Cryptosporidium parvum, ctc: Clostridium tetani E88, cte: Chlorobium tepidum, ctr: Chlamydia trachomatis, cvi: Chromobacterium violaceum, ddi: Dictyostelium discoideum, det: Dehalococcoides ethenogenes, dme: Drosophila melanogaster, dps: Desulfotalea psychrophila, dra: Deinococcus radiodurans, dre: Danio rerio, dvu: Desulfovibrio vulgaris Hildenborough, eba: Azoarcus sp. EbN1, eca: Erwinia carotovora, ecc: Escherichia coli CFT073, ece: Escherichia coli O157 EDL933, ecj: Escherichia coli K-12 W3110, eco: Escherichia coli K-12 MG1655, ecs: Escherichia coli O157 Sakai, ecu: Encephalitozoon cuniculi, efa: Enterococcus faecalis, erg: Ehrlichia ruminantium Gardel, eru: Ehrlichia ruminantium Welgevonden (South Africa), erw: Ehrlichia ruminantium Welgevonden (France), fnu: Fusobacterium nucleatum, ftu: Francisella tularensis, gka: Geobacillus kaustophilus, gox: Gluconobacter oxydans, gsu: Geobacter sulfurreducens, gvi: Gloeobacter violaceus, hal: Halobacterium sp. NRC-1, hdu: Haemophilus ducreyi, hhe: Helicobacter hepaticus, hin: Haemophilus influenzae, hma: Haloarcula marismortui, hpj: Helicobacter pylori J99, hpy: Helicobacter pylori 26695, hsa: Homo sapiens, ilo: Idiomarina loihiensis, lac: Lactobacillus acidophilus, lic: Leptospira interrogans serovar Copenhageni, lil: Leptospira interrogans serovar lai, lin: Listeria innocua, ljo: Lactobacillus johnsonii, lla: Lactococcus lactis, lma: Leishmania major, lmf: Listeria monocytogenes F2365, lmo: Listeria monocytogenes EGD-e, lpf: Legionella pneumophila Lens, lpl: Lactobacillus plantarum, lpn: Legionella pneumophila Philadelphia 1, lpp: Legionella pneumophila Paris, lxx: Leifsonia xyli xyli CTCB07, mac: Methanosarcina acetivorans, mbo: Mycobacterium bovis, mca: Methylococcus capsulatus, mfl: Mesoplasma florum, mga: Mycoplasma gallisepticum, mge: Mycoplasma genitalium, mhy: Mycoplasma hyopneumoniae, mja: Methanococcus jannaschii, mka: Methanopyrus kandleri, mle: Mycobacterium leprae, mlo: Mesorhizobium loti, mma: Methanosarcina mazei, mmo: Mycoplasma mobile, mmp: Methanococcus maripaludis, mmu: Mus musculus, mmy: Mycoplasma mycoides, mpa: Mycobacterium avium paratuberculosis, mpe: Mycoplasma penetrans, mpn: Mycoplasma pneumoniae, mpu: Mycoplasma pulmonis, msu: Mannheimia succiniciproducens, mtc: Mycobacterium tuberculosis CDC1551, mth: Methanobacterium thermoautotrophicum, mtu: Mycobacterium tuberculosis H37Rv, neq: Nanoarchaeum equitans, neu: Nitrosomonas europaea, nfa: Nocardia farcinica, ngo: Neisseria gonorrhoeae, nma: Neisseria meningitidis Z2491 (serogroup A), nme: Neisseria meningitidis MC58 (serogroup B), oih: Oceanobacillus iheyensis, osa: Oryza sativa, pab: Pyrococcus abyssi, pac: Propionibacterium acnes, pae: Pseudomonas aeruginosa, pai: Pyrobaculum aerophilum, pcu: Parachlamydia sp. UWE25, pfa: Plasmodium falciparum, pfu: Pyrococcus furiosus, pgi: Porphyromonas gingivalis, pho: Pyrococcus horikoshii, plu: Photorhabdus luminescens, pma: Prochlorococcus marinus SS120, pmm: Prochlorococcus marinus MED4, pmt: Prochlorococcus marinus MIT9313, pmu: Pasteurella multocida, poy: Phytoplasma sp. onion yellows, ppr: Photobacterium profundum, ppu: Pseudomonas putida, pst: Pseudomonas syringae, pto: Picrophilus torridus, rba: Rhodopirellula baltica, rco: Rickettsia conorii, rno: Rattus norvegicus, rpa: Rhodopseudomonas palustris CGA009, rpr: Rickettsia prowazekii, rso: Ralstonia solanacearum GMI1000, rty: Rickettsia typhi, sac: Staphylococcus aureus COL, sag: Streptococcus agalactiae 2603, sam: Staphylococcus aureus MW2, san: Streptococcus agalactiae NEM316, sar: Staphylococcus aureus MRSA252, sas: Staphylococcus aureus MSSA476, sau: Staphylococcus aureus N315, sav: Staphylococcus aureus Mu50, sce: Saccharomyces cerevisiae, sco: Streptomyces coelicolor, sep: Staphylococcus epidermidis ATCC 12228, ser: Staphylococcus epidermidis RP62A, sfl: Shigella flexneri 301, sfx: Shigella flexneri 2457T, sil: Silicibacter pomeroyi, sma: Streptomyces avermitilis, sme: Sinorhizobium meliloti, smu: Streptococcus mutans, son: Shewanella oneidensis, spa: Streptococcus pyogenes MGAS10394, spg: Streptococcus pyogenes MGAS315, spm: Streptococcus pyogenes MGAS8232, spn: Streptococcus pneumoniae TIGR4, spo: Schizosaccharomyces pombe, spr: Streptococcus pneumoniae R6, sps: Streptococcus pyogenes SSI-1, spt: Salmonella enterica serovar Paratyphi A, spy: Streptococcus pyogenes SF370, sso: Sulfolobus solfataricus, stc: Streptococcus thermophilus CNRZ1066, sth: Symbiobacterium thermophilum, stl: Streptococcus thermophilus LMG18311, stm: Salmonella typhimurium LT2, sto: Sulfolobus tokodaii, stt: Salmonella enterica serovar typhi Ty2, sty: Salmonella typhi CT18, syc: Synechococcus sp. PCC6301, syn: Synechocystis sp. PCC6803, syw: Synechococcus sp. WH8102, tac: Thermoplasma acidophilum, tbr: Trypanosoma brucei, tde: i, tel: Thermosynechococcus elongatus, tko: Thermococcus kodakaraensis, tma: Thermotoga maritima, tpa: Treponema pallidum, tte: Thermoanaerobacter tengcongensis, tth: Thermus thermophilus HB27, ttj: Thermus thermophilus HB8, tvo: Thermoplasma volcanium, twh: Tropheryma whipplei Twist, tws: Tropheryma whipplei TW08/27, uur: Ureaplasma urealyticum, vch: Vibrio cholerae, vfi: Vibrio fischeri, vpa: Vibrio parahaemolyticus, vvu: Vibrio vulnificus CMCP6, vvy: Vibrio vulnificus YJ016, wbm: Wolbachia endosymbiont strain TRS of Brugia malayi, wbr: Wigglesworthia brevipalpis, wol: Wolbachia wMel, wsu: Wolinella succinogenes, xac: Xanthomonas axonopodis, xcc: Xanthomonas campestris, xfa: Xylella fastidiosa 9a5c, xft: Xylella fastidiosa Temecula1, xoo: Xanthomonas oryzae, ype: Yersinia pestis CO92, ypk: Yersinia pestis KIM, ypm: Yersinia pestis Mediaevails, yps: Yersinia pseudotuberculosis, zmo: Zymomonas mobilis.
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BMC Genomics

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