DOI: 10.5061/dryad.mv185
title: Data from: Robustness of predictions of extremely thermally stable proteins in ancient organisms

description: A number of studies have addressed the environmental temperatures
 experienced by ancient life. Computational studies using a non-homogeneous
 evolution model have estimated ancestral G + C contents of ribosomal RNAs
 and the amino acid compositions of ancestral proteins, generating
 hypotheses regarding the mesophilic last universal common ancestor. In
 contrast, our previous study computationally reconstructed ancestral amino
 acid sequences of nucleoside diphosphate kinases using a homogeneous model
 and then empirically resurrected the ancestral proteins. The thermal
 stabilities of these ancestral proteins were equivalent to or greater than
 those of extant homologous thermophilic proteins, supporting the
 thermophilic universal ancestor theory. In this study, we re-inferred
 ancestral sequences using a dataset from which hyperthermophilic sequences
 were excluded. We also re-inferred ancestral sequences using a
 non-homogeneous evolution model. The newly reconstructed ancestral
 proteins are still thermally stable, further supporting the hypothesis
 that the ancient organisms contained thermally stable proteins and
 therefore that they were thermophilic.
description: Amino acid sequence of
 reconstructed archaeal ancestral NDK, Arc3nhAmino acid sequence of
 Arc3nh, a last archaeal common ancestor of nucleoside diphosphate kinase
 inferred using a non-homogeneous evolution modelArc3nh.txtAmino acid sequence of reconstructed archaeal ancestral NDK, Arc4nhAmino acid sequence of Arc4nh, a last archaeal common ancestor of nucleoside diphosphate kinase inferred using a non-homogeneous evolution model.Arc4nh.txtAmino acid sequence of reconstructed archaeal ancestral NDK, Arc6Amino acid sequence of Arc6, a last archaeal common ancestor of nucleoside diphosphate kinase inferred from a dataset without hyperthermophilic sequences.Arc6.txtAmino acid sequence of reconstructed archaeal and bacterial ancestral NDK, ArcBac7Amino acid sequence of ArcBac7, a last archaeal and bacterial ancestor of nucleoside diphosphate kinase inferred from a dataset without hyperthermophilic sequences.ArcBac7.txtAmino acid sequence of reconstructed bacterial ancestral NDK, Bac3nhAmino acid sequence of Bac3nh, a last bacterial common ancestor of nucleoside diphosphate kinase inferred using a non-homogeneous evolution model.Bac3nh.txtAmino acid sequence of reconstructed bacterial ancestral NDK, Bac4nhAmino acid sequence of Bac4nh, a last bacterial common ancestor of nucleoside diphosphate kinase inferred using a non-homogeneous evolution model.Bac4nh.txtAmino acid sequence of reconstructed bacterial ancestral NDK, Bac6Amino acid sequence of Bac6, a last bacterial common ancestor of nucleoside diphosphate kinase inferred from a dataset without hyperthermophilic sequences.Bac6.txtAmino acid sequence of reconstructed last universal common ancestral NDK, Com3nhAmino acid sequence of Com3nh, a last universal common ancestor of nucleoside diphosphate kinase inferred using a non-homogeneous evolution model.Com3nh.txtAmino acid sequence of reconstructed last universal common ancestral NDK, Com4nhAmino acid sequence of Com4nh, a last universal common ancestor of nucleoside diphosphate kinase inferred using a non-homogeneous evolution model.Com4nh.txt