Figure 2

Amino acid sequence alignments for Gamera and LINEs. (a) Alignments were made using the CLUSTAL W program (Thompson et al, 1994). The Gamera sequence in the top line is heavily shaded, along with identical amino acid residues in the other four sequences. Lightly shaded residues are chemically similar amino acids. Grouping was: nonpolar, AFILMPVW; polar, CGNQSTY; basic, DE; acidic, HKR. Designations of sequences and their EMBL accession numbers are: Gamera, Gamera-cur1 of Oryzias curvinotus, AB081572; SjR2, the SjR2 element of the human blood fluke Schistosoma japonicum, AY027869; Swimmer, the Swimmer 1 element of the medaka fish, AF055641; L1Hs, the L1 element of human, U93569; PsCR1, the PsCR1 element of the turtle Platemys spixii, AB005891. (b) The aligned regions in panel (a) were reverse transcriptase domains. The range of the region in the case of human L1 is indicated by a bar under the overall structure of L1. It corresponds to amino acid positions 448-737 in ORF2 consisting of 1275 amino acids. The scheme was redrawn from Sassaman et al, (1997). Designations are: UTR. untranslated regions; ORF, open reading frame; EN, endonuclease domain; RT, reverse transcriptase domain.