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 (V_g).

The number of organisms in the respective cluster is stated as N_spec. 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