Precursor domains and conserved motifs. A, a precursor with an intein containing a homing endonuclease domain (gold) is depicted with intein splicing domain motifs (red) listed above and conserved residues that participate in catalysis listed below. Residues in intein motifs are numbered based on their position within each motif (green) as defined in InBase (). Residues specific to class 2 or 3 inteins are in lowercase, and only a subset of residues found at A:1 is depicted. Motifs A, B, F, and G have also been called N1, N2, C2, and C1, respectively (). Motifs C, D, E, and H are specific to certain homing endonucleases and are not shown. To simplify discussion of inteins in various precursors, residues in each part are numbered independently. Intein residues are numbered from the N to C terminus beginning with 1. Residues in the N- and C-exteins (blue) are numbered from the splice site outwards and include a minus sign for N-extein and a plus sign for C-extein residues. B, folding of the precursor forms the intein active site and initiates protein splicing. Homing endonuclease domains in larger inteins fold separately from the intein and extein domains. Association of extein fragments can influence precursor folding and active site architecture. X represents an oxygen or a sulfur atom.