(A) Multiple sequence alignment of PUG domains of N-glycanases (PNG1mm, PNG1dm), UBX domain-containing proteins (F13M7, CG5469), HOX domain containing proteins (F3M18, MLN1), UBA/Zinc-finger-domain-containing proteins (K24G6, T8011), and hypothetical zinc metalloproteinase (MXH1) and multiple sequence alignment of PUG-like domains in serine/threonine protein kinases / RNAses (F26K24, MJB20, K16H17, IRE1mm, ERN1, IRE1sc, YQG4, SPAC167, CG4583, RN5Ahs, RN5Amm). First column, protein names; second column, species names (at, Arabidopsis thaliana; ce,Caenorhabditis elegans; dm, Drosophila melanogaster; hs, Homo sapiens; mm, Mus musculus; pf,Plasmodium falciparum; sc, Saccharomyces cerevisiae;sp, Schizosaccharomyces pombe); third column, start of the domain in the respective sequences; rightmost column, database accession numbers. Conserved positively charged residues are shown in pink; conserved hydrophobic residues are shown in blue; other conserved residues are shown in bold. The predicted secondary structure taken from the consensus of the alignments (B/H, strand/helix predicted with expected average accuracy >82%; b/h, strand/helix predicted with expected average accuracy <82%) (Rost et al. 1994) is shownbelow, respectively (consistent secondary structure in bold letters). The consensus sequence (conserved in 80% of the sequences) for both alignments is shown below; s, l, p, h, c, -, L, N, and F indicate small, aliphatic, hydrophobic, polar, charged, negatively charged residues, conserved Leucines, Asparagine, and Phenylalanin. (B) Domain architecture of proteins containing the PUG domain (green) and the PUG-like domain (green dark horizontal pattern). Only proteins with distinct modular organizations are shown. The domain names are those of the Simple Modular Architecture Research Tool (http://smart.embl-heidelberg.de) (Schultz et al. 1998, 2000). C2H2, zinc finger C2H2 DNA-binding domain; PAW, domain in PNGases and other worm proteins; PQQ, β-propeller repeat; S_TKc, serine/threonine protein kinase catalytic domain; TGc, transglutaminase/protease-like homologs catalytic domain; UBA, biquitin-associated domain; UBCc, catalytic domain of ubiquitin-conjugating enzymes; UBX, domain present in ubiquitin regulatory proteins; TM, transmembrane region.
