Reconstruction of ancestral protein sequences and its applications

Cai, Wei; Pei, Jimin; Grishin, Nick V

doi:10.1186/1471-2148-4-33

BMC Ecology and Evolution

Table 3 Ancestral sequence reconstruction accuracy by different programs

From: Reconstruction of ancestral protein sequences and its applications

Root Seq.	Tree	Leaf Node Num.	Methods
			ANCESCON			PAML		PHYLIP $				PAUP*
			α _ML	α _AB	-α	+α	-α	+L +α	-L +α	+L -α	-L -α
1em2	pii1	25	0.45	0.32	0.35	0.41	0.37	0.29	0.27	0.21	0.29	0.26
1g9o	pii1	25	0.56	0.46	0.47	0.53	0.53	0.51	0.54	0.40	0.51	0.47
1rgg	pii1	25	0.60	0.42	0.47	0.60	0.62	0.47	0.58	0.32	0.56	0.47
1sgt	pii1	25	0.38	0.34	0.33	0.33	0.32	0.32	0.33	0.27	0.33	0.32
1zm2	pii1	25	0.33	0.29	0.3	0.28	0.25	0.21	0.25	0.21	0.27	0.16
2a8v	pii1	25	0.62	0.45	0.42	0.56	0.55	0.44	0.46	0.28	0.50	0.36
2ctb	pii1	25	0.53	0.40	0.39	0.41	0.38	0.24	0.24	0.21	0.29	0.22
Average accuracy			0.496	0.383	0.390	0.446	0.431	0.354	0.381	0.271	0.393	0.323
2ctb	gef	27	0.54	0.37	0.38	0.35	0.35	0.29	0.17	0.24	0.22	0.22
2ctb	LacI	54	0.66	0.64	0.57	0.44	0.37	0.49	0.35	0.42	0.33	0.34
2ctb	pdz	39	0.54	0.41	0.42	0.44	0.39	0.22	0.34	0.18	0.32	0.22
2ctb	ph	30	0.79	0.74	0.75	0.53	0.55	0.45	0.25	0.43	0.37	0.32
2ctb	pii1	25	0.53	0.40	0.39	0.41	0.38	0.24	0.24	0.21	0.29	0.22
2ctb	ptb	29	0.58	0.39	0.43	0.39	0.38	0.29	0.23	0.26	0.24	0.23
2ctb	sh2	34	0.61	0.42	0.40	0.43	0.40	0.30	0.22	0.20	0.27	0.22
2ctb	sh3	43	0.83	0.82	0.80	0.62	0.55	0.69	0.45	0.66	0.46	0.54
2ctb	GST	140	0.76	0.73	0.73	@	@	#	#	0.47	0.38	0.33
Average accuracy^&			0.635	0.524	0.518	0.451	0.421	0.371	0.281	0.325	0.313	0.289
1em2	pdz	39	0.45	0.35	0.36	0.44	0.44	0.29	0.43	0.23	0.4	0.24
1g9o	pii1	25	0.56	0.46	0.47	0.53	0.53	0.51	0.54	0.40	0.51	0.47
1rgg	sh2	34	0.64	0.48	0.46	0.61	0.61	0.56	0.59	0.34	0.6	0.41
1sgt	gef	27	0.49	0.39	0.40	0.48	0.44	0.42	0.44	0.36	0.45	0.41
1zm2	ptb	29	0.66	0.47	0.48	0.57	0.57	0.53	0.51	0.32	0.52	0.41
2a8v	ph	30	0.81	0.78	0.81	0.71	0.74	0.60	0.61	0.50	0.65	0.50
2ctb	LacI	54	0.66	0.64	0.57	0.44	0.37	0.49	0.35	0.42	0.33	0.34
Average accuracy			0.610	0.510	0.507	0.540	0.529	0.486	0.496	0.367	0.494	0.397
Probability^Δ				0.0026	0.0023	0.0248	0.0328	0.0007	0.0168	0.0001	0.0143	0.0005

All root sequences are taken from PDB database and the names listed in the table are PDB IDs.
Tree topologies for gef (guanine nucleotide exchange factor), LacI (PurR/LacI family of bacterial transcription factors), pdz, ph, pii1 (a signal transduction protein), ptb, sh2, sh3 and GST (glutathione S-transferase) are inferred from multiple sequence alignments chosen from Pfam database (version 7.3).
All tree topologies are generated from real alignments and the distances are rescaled in order to make the trees comparable.
The value in this table represents the accuracy of reconstruction, i.e. the fraction of correctly reconstructed sites for the root sequence. The best reconstruction accuracy in each test is shown in bold.
α_MLmeans that the site-specific rate factors were estimated by maximum likelihood method.
α_ABmeans that the site-specific rate factors were estimated by our empirical equation based on the given alignment (for details see Methods).
-α means that the rate factors were not considered in reconstruction.
+α means that the rate factors were considered in reconstruction.
+L means that branch lengths of the input tree were used in reconstruction, while -L means that branch lengths were estimated by the reconstruction program itself.
@: tree topology for GST had 140 leaf nodes that were too many for PAML to run through.
^$: rate factors estimated by PAML were used by PHYLIP in ancestral sequence reconstruction.
#: tree topology for GST had 140 leaf nodes, which were too many for PAML to estimate rate factors for GST.
^&:GST is excluded in calculation of the average.
^Δ: paired t-test method [40] was used to estimate the one-tail probability between ANCESCON and the other three reconstruction methods.

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