Table 1. Maximum likelihood trees from 19,050,992 protein sequences from 5,433 bacterial and 212 archaeal species were calculated for clusters obtained by MCL, yielding 101,422 trees with at least four sequences and two taxonomic groups present. Each of the 101,422 trees were assigned a protein label according to the NCBI sequence header that was represented the most. On the left panel all trees were annotated and sorted according to their verticality score for the genes (Vg).
The number of organisms in the respective cluster is stated as Nspec. On the right panel the same values are stated only for conserved protein families–determined by average branch length ≤ 0.1.
| All 101,422 protein families | The 8,547 most conserved protein families | |||||
|---|---|---|---|---|---|---|
| Vg | Protein family | Nspec | V | Protein family | Nspec | |
| Most vertical | ||||||
| 24.00 | 30S ribosomal protein S10 | 5,646 | 24.00 | 30S ribosomal protein S10 | 5,646 | |
| 23.00 | 30S ribosomal protein S11 | 5,652 | 23.00 | 30S ribosomal protein S11 | 5,652 | |
| 22.30 | Asp/glu–tRNA amidotransferase subunit B | 4,269 | 22.30 | Asp/glu–tRNA amidotransferase subunit B | 4,269 | |
| 22.00 | 50S ribosomal protein L1 | 5,650 | 22.00 | 50S ribosomal protein L1 | 5,650 | |
| 21.89 | Alanine–tRNA ligase | 5,598 | 21.89 | Alanine–tRNA ligase | 5,598 | |
| 21.57 | 50S ribosomal protein L2 | 5,616 | 21.57 | 50S ribosomal protein L2 | 5,616 | |
| 20.93 | Sec family type I SRPa protein | 5,571 | 20.93 | Sec family type I SRPa protein | 5,571 | |
| 20.88 | 30S ribosomal protein S5 | 5,653 | 20.88 | 30S ribosomal protein S5 | 5,653 | |
| 19.82 | Translation elongation factor G | 5,624 | 19.82 | Translation elongation factor G | 5,624 | |
| 19.55 | DNA-directed RNA polymerase subunit beta | 5,300 | 19.55 | DNA-directed RNA polymerase subunit beta | 5,300 | |
| 19.32 | tRNA methylthiotransferase MiaB | 4,764 | 18.86 | Translation initiation factor IF-2 | 5,379 | |
| 18.94 | Signal recognition particle-docking protein FtsY | 5,525 | 18.80 | Histidine–tRNA ligase | 5,627 | |
| 18.86 | Translation initiation factor IF-2 | 5,379 | 18.76 | DNA gyrase subunit A | 5,467 | |
| 18.80 | Histidine–tRNA ligase | 5,627 | 18.00 | 50S ribosomal protein L14 | 5,655 | |
| 18.76 | DNA gyrase subunit A | 5,467 | 18.00 | Methionine–tRNA ligase | 5,587 | |
| 18.03 | tRNA pseudouridine synthase B | 5,434 | 17.98 | Excinuclease ABC subunit B | 5,411 | |
| 18.00 | 50S ribosomal protein L14 | 5,655 | 17.96 | DNA-directed RNA polymerase subunit alpha | 5,431 | |
| 18.00 | Methionine–tRNA ligase | 5,587 | 17.93 | CTP synthetase | 5,433 | |
| 17.98 | Excinuclease ABC subunit B | 5,411 | 17.88 | 30S ribosomal protein S8 | 5,653 | |
| 17.96 | DNA-directed RNA polymerase subunit alpha | 5,431 | 17.85 | Preprotein translocase subunit SecA | 5,395 | |
| Most lateral | ||||||
| 0 | Heavy metal-responsive transcriptional regulator | 2,392 | 0 | SDH cyt b556 large subunit | 2,344 | |
| 0 | SDH cyt b556 large subunit | 2,344 | 0 | RnfH family protein | 2,004 | |
| 0 | Anaerobic ribo.-triPb reductase activating protein | 2,078 | 0 | Hypothetical protein | 1,964 | |
| 0 | Thiol:disulfide interchange protein DsbC | 1,952 | 0 | Amino acid ABC transporter permease | 1,666 | |
| 0 | RnfH family protein | 2,004 | 0 | Succinate dehydrogenase, HMc anchor protein | 1,800 | |
| 0 | Disulfide bond formation protein B 1 | 1,808 | 0 | LysR family transcriptional regulator | 1,267 | |
| 0 | Hypothetical protein | 1,964 | 0 | Hypothetical protein | 1,688 | |
| 0 | Amino acid ABC transporter permease | 1,666 | 0 | Maleylacetoacetate isomerase | 1,430 | |
| 0 | LysR family transcriptional regulator | 1,431 | 0 | Sigma-E factor regulatory protein RseB | 1,599 | |
| 0 | Succinate dehydrogenase, HMc anchor protein | 1,800 | 0 | tRNA synthase TrmP | 1,567 | |
| 0 | LysR family transcriptional regulator | 1,267 | 0 | tRNA 5-methoxyuridine(34) synthase CmoB | 1,525 | |
| 0 | Hypothetical protein | 1,688 | 0 | Chemotaxis phosphatase CheZ family protein | 1,483 | |
| 0 | Maleylacetoacetate isomerase | 1,430 | 0 | Hypothetical protein | 1,505 | |
| 0 | Sigma-E factor regulatory protein RseB | 1,599 | 0 | Hypothetical protein | 1,345 | |
| 0 | tRNA synthase TrmP | 1,567 | 0 | Outer membrane protein assembly protein | 1,301 | |
| 0 | tRNA 5-methoxyuridine(34) synthase CmoB | 1,525 | 0 | Deoxyribonuclease I | 1,269 | |
| 0 | Chemotaxis phosphatase CheZ family protein | 1,483 | 0 | Formate dehydrogenase accessory protein FdhE | 1,241 | |
| 0 | Hypothetical protein | 1,505 | 0 | Flagellar export protein FliJ | 1,208 | |
| 0 | Hypothetical protein | 1,345 | 0 | Hypothetical protein | 1,200 | |
| 0 | Hypothetical protein | 1,325 | 0 | Hypothetical protein | 1,179 | |
Notes
a SRP protein–general secretory pathway protein signal recognition particle protein
b ribo.-triP–ribonucleoside-triphosphate
c HM–hydrophobic membrane