Fig. 2. Amino acid alignment of human, macaque, rat, mouse, dog, rabbit, sheep, cow, pig, chicken, turkey, zebrafish and Atlantic cod PepT1. Multiple sequence alignment was generated using Clustal W 1.82 using the tool at the www.ebi.ac.uk/clustalw web site with the following (default) parameters: Matrix=Gonnet 250, Gap Open=10, End Gaps=–1, Gap Extension=0.2, Gap Distances=4. Putative transmembrane segments (Ia to XII) were predicted using the TMHMM 2.0 program (TMHMM Server v. 2.0 at http://www.cbs.dtu.dk/services/TMHMM-2.0/), which is part of the Simple Modular Architecture Research Tool (SMART; at http://www.expasy.org/prosite/), and are indicated by grey-boxed double-headed broken arrows (with darker grey designating the core stretch of amino acids within each putative TMHMM-predicted transmembrane segment that is shared by at least two of the aligned sequences). Within each sequence, the topological location of each TMHMM2-predicted transmembrane helix is specifically underlined. Potential phosphorylation (solid triangle, protein kinase C; solid circle, protein kinase A) and N-glycosylation (Y) sites are indicated and correspondently highlighted in dark grey, light grey and dark green, respectively, along the sequences where found. The proposed `PTR2 family proton/oligopeptide symporters signature 1' motif (PROSITE pattern: PS01022; amino acid residues 77–101 in Atlantic cod PepT1) and `PTR2 family proton/oligopeptide symporters signature 2' motif (PROSITE pattern: PS01023; amino acid residues 170–182 in Atlantic cod PepT1) are highlighted in black. Individual amino acid residues identified by site-directed mutagenesis in PepT1 proteins from various mammalian species and found to be either involved in transport activity or responsible for incorrect synthesis and/or transport of the protein to the plasma membrane are indicated in red (for details, see Table 1).