Table 3 The 81 organisms included in the phylogenetic analysis. Full scientific names were abbreviated into three character notation (Abbr.) and their domain informations in phylogeny were also represented in single character that are Eubacteria (B), Archaea (A) and Eukaryota (E), respectively.
From: Construction of phylogenetic trees by kernel-based comparative analysis of metabolic networks
Abbr. | Domain | Organism | Abbr. | Domain | Organism |
|---|---|---|---|---|---|
Aae | B | Aquifex aeolicus | Mth | A | Methanobacterium thermoautotrophicum |
Ana | B | Anabaena sp. | Mtu | B | Mycobacterium tuberculosis H37Rv |
Atc | B | Agrobacterium tumefaciens C58 Cereon | Nma | B | Neisseria meningitidis serogroup A |
Ath | E | Arabidopsis thaliana | Nme | B | Neisseria meningitidis serogroup B |
Atu | B | Agrobacterium tumefaciens C58 UWash | Oih | B | Oceanobacillus iheyensis |
Bha | B | Bacillus halodurans | Pab | A | Pyrococcus abyssi |
Bme | B | Brucella melitensis | Pae | B | Pseudomonas aeruginosa |
Bsu | B | Bacillus subtilis | Pai | A | Pyrobaculum aerophilum |
Cac | B | Clostridium acetobutylicum | Pfu | A | Pyrococcus furiosus |
Ccr | B | Caulobacter crescentus | Pho | A | Pyrococcus horikoshii |
Cel | E | Caenorhabditis elegans | Pmu | B | Pasteurella multocida |
Cje | B | Campylobacter jejuni | Rno | E | Rattus norvegicus |
Cmu | B | Chlamydia muridarum | Rso | B | Ralstonia solanacearum |
Cpa | B | Chlamydophila pneumoniae AR39 | Sam | B | Staphylococcus aureus MW2 |
Cpe | B | Clostridium perfringens | Sau | B | Staphylococcus aureus N315 |
Cpj | B | Chlamydophila pneumoniae J138 | Sav | B | Staphylococcus aureus Mu50 |
Cpn | B | Chlamydophila pneumoniae CWL029 | Sce | E | Saccharomyces cerevisiae |
Cte | B | Chlorobium tepidum | Sco | B | Streptomyces coelicolor |
Ctr | B | Chlamydia trachomatis | Sme | B | Sinorhizobium meliloti |
Dme | E | Drosophila melanogaster | Spg | B | Streptococcus pyogenes M3 |
Dra | B | Deinococcus radiodurans | Spm | B | Streptococcus pyogenes M18 |
Ece | B | Escherichia coli O157 EDL933 | Spo | E | Schizosaccharomyces pombe |
Ecj | B | Escherichia coli K-12 W3110 | Spy | B | Streptococcus pyogenes |
Eco | B | Escherichia coli K-12 MG1655 | Sso | A | Sulfolobus solfataricus |
Ecs | B | Escherichia coli O157 Sakai | Stm | B | Salmonella typhimurium |
Fnu | B | Fusobacterium nucleatum | Sto | A | Sulfolobus tokodaii |
Hal | A | Halobacterium sp. | Sty | B | Salmonella typhi |
Hin | B | Haemophilus influenzae | Syn | B | Synechocystis sp. |
Hpj | B | Helicobacter pylori J99 | Tac | A | Thermoplasma acidophilum |
Hpy | B | Helicobacter pylori 26695 | Tel | B | Thermosynechococcus elongatus |
Hsa | E | Homo sapiens | Tma | B | Thermotoga maritima |
Lin | B | Listeria innocua | Tpa | B | Treponema pallidum |
Lla | B | Lactococcus lactis | Tte | B | Thermoanaerobacter tengcongensis |
Lmo | B | Listeria monocytogenes | Tvo | A | Thermoplasma volcanium |
Mac | A | Methanosarcina acetivorans | Vch | B | Vibrio cholerae |
Mja | A | Methanococcus jannaschii | Xax | B | Xanthomonas axonopodis |
Mle | B | Mycobacterium leprae | Xca | B | Xanthomonas campestris |
Mlo | B | Mesorhizobium loti | Xfa | B | Xylella fastidiosa |
Mma | A | Methanosarcina mazei | Ype | B | Yersinia pestis |
Mmu | E | Mus musculus | Ypk | B | Yersinia pestis KIM |
Mtc | B | Mycobacterium tuberculosis CDC1551 | Â | Â | Â |