Fig. 5
From: Identification of RAG-like transposons in protostomes suggests their ancient bilaterian origin
Alignment of RAG1L sequences from protostomes and deuterostomes. RAG1L sequences from 3 deuterostomes (the cephalochordate amphioxus (Bbe), echinoderm purple sea urchin (Spu), and hemichordate P. flava (Pfl)), 2 mollusk RAGL_B subfamilies (eastern oyster (Cvi) and pearly oyster (Pim)), and a nemertean N. geniculatus RAGL_D family representative (Nge) were aligned to mouse (Mmu) RAG1. Domains, sequence motifs, secondary structure assignment (helices - wavy lines; beta sheet - arrows, other - straight line), protein-protein and protein-DNA contact interactions (within 5 Å) displayed above the alignment derive from the BbeRAG1L cryo-EM structure (PDB: 6B40). Acidic catalytic residues, red; active site residue mouse H795, purple; zinc coordinating residues within ZDD (*) and ZnC2 and ZnH2 (#) are indicated above the sequences. Locations at which coding sequences span exon boundaries are underlined. Amino acid color code: hydrophobic aliphatic, yellow; hydrophobic aromatic, orange; positively charged, blue; negatively charged, red; neutral polar, light blue; glycine and prolines, grey; cysteine, purple; histidine, dark purple.
Sequences displayed are BbeRAG1L_B (GenBank: KJ748699.1), PflRAG1L_B (TSA:GDGM01438088.1), SpuRAG1L_B_Ech1 (Uniprot: Q45ZT6), and CviRAG1L_B_Biv1_0007, PimRAG1L_B_Biv2_3145, and NgeRAG1L_D_2322 from this study (Additional file 7: Alignment S1a).