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

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

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 ** ** ** ** **
  1. 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.