Table 2.
Organisms with no identifiable TA
| Organism | Size of chromosome (Mb) | Organism lifestyle | Toxin pseudogenes detectedb |
|---|---|---|---|
| Archaea | |||
| All archaea analyzed have TA loci | |||
| Gram-positive bacteria | |||
| Mycobacterium_leprae | 3.3 | Obligate host-associated | + |
| Tropheryma_whipplei_Twist | 0.9 | Obligate host-associated | − |
| Tropheryma_whipplei_TW08_27 | 0.9 | Obligate host-associated | − |
| Chlamydia_muridarum | 1.1 | Obligate host-associated | − |
| Chlamydia_trachomatis | 1.0 | Obligate host-associated | − |
| Chlamydophila_caviae_GPIC | 1.2 | Obligate host-associated | − |
| Chlamydophila_pneumoniae_CWL029 | 1.2 | Obligate host-associated | − |
| Chlamydophila_pneumoniae_TW_183 | 1.2 | Obligate host-associated | − |
| Chlamydophila_pneumoniae_AR39 | 1.2 | Obligate host-associated | − |
| Chlamydophila_pneumoniae_J138 | 1.2 | Obligate host-associated | − |
| Prochlorococcus_marinus | 1.8 | Obligate host-associated | − |
| Mycoplasma_gallisepticum | 1.0 | Obligate host-associated | − |
| Mycoplasma_genitalium | 0.6 | Obligate host-associated | − |
| Mycoplasma_penetrans | 1.4 | Obligate host-associated | − |
| Mycoplasma_pneumoniae | 0.8 | Obligate host-associated | − |
| Mycoplasma_pulmonis | 1.0 | Obligate host-associated | + |
| Ureaplasma_urealyticum | 0.8 | Obligate host-associated | − |
| Lactococcus_lactis | 2.4 | Fastidious lifestyle | − |
| Thermosynechococcus_elongatus | 2.6 | Thermophilic and phototropic | − |
| Gram-negativea | |||
| Rickettsia_prowazekii | 1.1 | Obligate host-associated | − |
| Campylobacter_jejuni | 1.6 | Habitat is the lower bowel | − |
| Helicobacter_hepaticus | 1.8 | Habitat is the lower bowel | + |
| Buchnera_sp_APS | 0.6 | Obligate host-associated | − |
| Buchnera_aphidicola | 0.6 | Obligate host-associated | − |
| Buchnera_aphidicola_Sg | 0.6 | Obligate host-associated | − |
| Wigglesworthia_brevipalpis | 0.7 | Obligate host-associated | − |
| Borrelia_burgdorferi | 0.9 | Obligate host-associated | − |
| Treponema_pallidum | 1.1 | Obligate host-associated | + |
| Thermotoga_maritima | 1.9 | Thermophilic | − |
| Haemophilus_ducreyi_35000HP | 1.7 | Obligate human pathogen, extracellular | − |
| Pasteurella_multocida | 2.3 | Pathogen—grows best on blood–agar | + |
aThe deep branching Aquifex_aeolicus and Thermotoga_maritima were here classified as Gram-negative bacteria for simplicity.
bSearch for pseudogenes was done with TBLASTN using individual chromosome sequences as search spaces and all toxin GIs (Table S2) as query sequences.