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The unique family of membrane-bound proton-pumping inorganic pyro-phosphatases, involving pyrophosphate as the alternative to ATP, was investigated by characterizing 166 members of the UniProtKB⁄Swiss-Prot + UniProtKB⁄TrEMBL databases and available completed genomes, using sequence comparisons and a hidden Markov model based upon a conserved 57-residue region in the loop between transmembrane segments 5 and 6. | ỊFEBS Journal Analysis of ancient sequence motifs in the H -PPase family Joel Hedlund1 Roberto Cantoni2 3 4 Margareta Baltscheffsky2 Herrick Baltscheffsky2 and Bengt Persson1 4 1 IFM Bioinformatics Linkoping University Sweden 2 Department of Biochemistry and Biophysics Arrhenius Laboratories Stockholm University Sweden 3 Department of PhysicalSciences Federico II University of Naples Italy 4 Department of Celland Molecular Biology CMB Programme for Genomics and Bioinformatics Karolinska Institutet Stockholm Sweden Keywords bioinformatics hidden Markov models molecular evolution proteinaceous amino acids pyrophosphatase Correspondence B. Persson IFM Bioinformatics Linkoping University S-581 83 Linkoping Sweden Fax 46 13 137 568 Tel 46 13 282 983 E-mail bpn@ifm.liu.se These authors contributed equally to this work Received 9 August 2006 revised 26 September 2006 accepted 27 September 2006 doi 10.1111 j.1742-4658.2006.05514.x The unique family of membrane-bound proton-pumping inorganic pyrophosphatases involving pyrophosphate as the alternative to ATP was investigated by characterizing 166 members of the UniProtKB Swiss-Prot UniProtKB TrEMBL databases and available completed genomes using sequence comparisons and a hidden Markov model based upon a conserved 57-residue region in the loop between transmembrane segments 5 and 6. The hidden Markov model was also used to search the approximately one million sequences recently reported from a large-scale sequencing project of organisms in the Sargasso Sea resulting in additional 164 partial pyrophosphatase sequences. The strongly conserved 57-residue region was found to contain two nonapeptidyl sequences mainly consisting of the four very early proteinaceous amino acid residues Gly Ala Val and Asp compatible with an ancient origin of the inorganic pyrophosphatases. The nonapeptide patterns have charged amino acid residues at positions 1 5 and 9 are apparent binding sites for the substrate and parts of the active site and .
