A class frequency mixture model that adjusts for site-specific amino acid frequencies and improves inference of protein phylogeny

Table 1 Statistical analyses of site-specific amino acid uniformity and state frequencies in 21 protein data sets.

Protein family	Taxa	Sites	Z-test (uniformity)				χ² test (states)
			Rate 1	Rate 2	Rate 3	Rate 4
Carboxyl_trans	36	212	0.97	**	0.05	*	**
CTP-synthetase	65	212	**	**	**	**	*
DNA topo IV	49	228	0.21	**	**	**	*
Filament	36	210	0.35	0.09	0.92	0.45	0.66
Glu_synth_NTN	40	253	**	**	**	**	0.01
HSP70	34	432	0.31	**	*	**	**
ILVD_EDD	51	310	0.20	*	**	**	**
MCM	40	220	0.66	*	*	0.11	**
MreB	32	275	0.50	0.10	**	*	0.03
Poty_coat	34	212	0.19	**	**	**	**
SecA	70	203	**	**	**	**	**
Usher	36	317	*	**	**	**	0.08
HSP90	54	459	**	**	**	**	**
NuoF	41	405	**	**	**	**	**
Cpn60	41	466	0.18	0.04	**	**	**
MPP	43	203	0.04	0.24	**	0.03	0.32
α-tubulin	54	375	**	*	**	**	*
β-tubulin	46	382	**	**	*	**	0.02
Actin	48	363	**	**	**	*	*
EF-1α	38	361	0.29	**	**	**	**
EF-2	37	669	**	**	**	**	**

P-values: ** < 0.001; * < 0.01. The protein family abbreviations are: Carboxyl_trans, acetyl-CoA carboxylase; Cpn60, 60-kDa chaperonin; DNA topo IV, DNA topoisomerase IV subunit A (GyrA); EF-1α, elongation factor 1α; EF2, elongation factor 2; Filament, intermediate filament protein; Glu_synth_NTN, Glutamate synthase aminotransferase; HSP70, 70-kDa heat shock protein; HSP90, 90-kDa heat shock protein; ILVD_EDD, dehydratase family proteins; NuoF, NADH dehydrogenase I chain F; MCM, minichromosome maintenance protein; MPP, mitochondrial processing peptidase sequences; MreB, a bacterial homolog of the eukaryotic actin; Poty_coat, potyvirus coat protein; Usher, Fimbrial usher protein.

ISSN: 2730-7182