| Domain | Name | Category | Type |
| IPR001656 | Pseudouridine synthase, TruD | Family | Family |
| IPR011760 | Pseudouridine synthase, TruD, insertion domain | Domain | Domain |
| IPR020103 | Pseudouridine synthase, catalytic domain superfamily | Family | Homologous superfamily |
| IPR020119 | Pseudouridine synthase TruD, conserved site | Site | Conserved site |
| IPR042214 | Pseudouridine synthase, TruD, catalytic domain | Family | Homologous superfamily |