| PF00016 | RuBisCO_large | Ribulose bisphosphate carboxylase large chain, catalytic domain | P04718 |
| PF00071 | Ras | Ras family | Q09914 |
| PF00072 | Response_reg | Response regulator receiver domain | Q9RZA5 |
| PF00074 | RnaseA | Pancreatic ribonuclease | P61823 |
| PF00075 | RNase_H | RNase H | P04585 |
| PF00076 | RRM_1 | RNA recognition motif | P08579 |
| PF00077 | RVP | Retroviral aspartyl protease | P12497 |
| PF00078 | RVT_1 | Reverse transcriptase (RNA-dependent DNA polymerase) | P0A3U0 |
| PF00101 | RuBisCO_small | Ribulose bisphosphate carboxylase, small chain | P00870 |
| PF00154 | RecA | recA bacterial DNA recombination protein | A0A485JBB4 |
| PF00161 | RIP | Ribosome inactivating protein | P02879 |
| PF00163 | Ribosomal_S4 | Ribosomal protein S4/S9 N-terminal domain | P0A7V8 |
| PF00164 | Ribosom_S12_S23 | Ribosomal protein S12/S23 | A0A0F1AUC4 |
| PF00177 | Ribosomal_S7 | Ribosomal protein S7p/S5e | P02359 |
| PF00181 | Ribosomal_L2 | Ribosomal Proteins L2, RNA binding domain | P0CT70 |
| PF00189 | Ribosomal_S3_C | Ribosomal protein S3, C-terminal domain | B7MCS9 |
| PF00203 | Ribosomal_S19 | Ribosomal protein S19 | S1EA57 |
| PF00237 | Ribosomal_L22 | Ribosomal protein L22p/L17e | O14339 |
| PF00238 | Ribosomal_L14 | Ribosomal protein L14p/L23e | P0CT60 |
| PF00239 | Resolvase | Resolvase, N terminal domain | Q5MPE7 |
| PF00252 | Ribosomal_L16 | Ribosomal protein L16p/L10e | Q09127 |
| PF00253 | Ribosomal_S14 | Ribosomal protein S14p/S29e | U9Y6H3 |
| PF00268 | Ribonuc_red_sm | Ribonucleotide reductase, small chain | Q81G55 |
| PF00276 | Ribosomal_L23 | Ribosomal protein L23 | Q10330 |
| PF00281 | Ribosomal_L5 | Ribosomal protein L5 | P0CT77 |
| PF00297 | Ribosomal_L3 | Ribosomal protein L3 | P40372 |
| PF00298 | Ribosomal_L11 | Ribosomal protein L11, RNA binding domain | A0A6A5Q275 |
| PF00301 | Rubredoxin | Rubredoxin | P00269 |
| PF00312 | Ribosomal_S15 | Ribosomal protein S15 | D8EB41 |
| PF00317 | Ribonuc_red_lgN | Ribonucleotide reductase, all-alpha domain | P03190 |
| PF00318 | Ribosomal_S2 | Ribosomal protein S2 | J7QM75 |
| PF00327 | Ribosomal_L30 | Ribosomal protein L30p/L7e | P17937 |
| PF00333 | Ribosomal_S5 | Ribosomal protein S5, N-terminal domain | P0A7W1 |
| PF00338 | Ribosomal_S10 | Ribosomal protein S10p/S20e | V0ANK5 |
| PF00347 | Ribosomal_L6 | Ribosomal protein L6 | Q10232 |
| PF00355 | Rieske | Rieske [2Fe-2S] domain | A0A1S3TB49 |
| PF00366 | Ribosomal_S17 | Ribosomal protein S17 | P0DOY7 |
| PF00380 | Ribosomal_S9 | Ribosomal protein S9/S16 | A0A1X3LT86 |
| PF00398 | RrnaAD | Ribosomal RNA adenine dimethylase | Q8WVM0 |
| PF00410 | Ribosomal_S8 | Ribosomal protein S8 | D7XKZ3 |
| PF00411 | Ribosomal_S11 | Ribosomal protein S11 | A0A0H3PWX2 |
| PF00415 | RCC1 | Regulator of chromosome condensation (RCC1) repeat | Q9FN03 |
| PF00416 | Ribosomal_S13 | Ribosomal protein S13/S18 | A0A7U9IV78 |
| PF00424 | REV | REV protein (anti-repression trans-activator protein) | P04616 |
| PF00428 | Ribosomal_60s | 60s Acidic ribosomal protein | P05317 |
| PF00444 | Ribosomal_L36 | Ribosomal protein L36 | A0A0E2L017 |
| PF00445 | Ribonuclease_T2 | Ribonuclease T2 family | Q45U61 |
| PF00453 | Ribosomal_L20 | Ribosomal protein L20 | B7MAS6 |
| PF00466 | Ribosomal_L10 | Ribosomal protein L10 | Q9USZ6 |
| PF00468 | Ribosomal_L34 | Ribosomal protein L34 | B7MGC4 |
| PF00471 | Ribosomal_L33 | Ribosomal protein L33 | F4NQ61 |
| PF00472 | RF-1 | RF-1 domain | P0A7I0 |
| PF00480 | ROK | ROK family | A4JE13 |
| PF00542 | Ribosomal_L12 | Ribosomal protein L7/L12 C-terminal domain | P52815 |
| PF00545 | Ribonuclease | ribonuclease | P00651 |
| PF00554 | RHD_DNA_bind | Rel homology DNA-binding domain | Q00653 |
| PF00562 | RNA_pol_Rpb2_6 | RNA polymerase Rpb2, domain 6 | C4QZQ7 |
| PF00566 | RabGAP-TBC | Rab-GTPase-TBC domain | Q9P0N9 |
| PF00572 | Ribosomal_L13 | Ribosomal protein L13 | O42991 |
| PF00573 | Ribosomal_L4 | Ribosomal protein L4/L1 family | Q9P784 |
| PF00581 | Rhodanese | Rhodanese-like domain | Q16762 |
| PF00615 | RGS | Regulator of G protein signaling domain | Q3ZT31 |
| PF00616 | RasGAP | GTPase-activator protein for Ras-like GTPase | P21359 |
| PF00617 | RasGEF | RasGEF domain | Q07889 |
| PF00618 | RasGEF_N | RasGEF N-terminal motif | Q07889 |
| PF00620 | RhoGAP | RhoGAP domain | P27986 |
| PF00621 | RhoGEF | RhoGEF domain | Q92974 |
| PF00623 | RNA_pol_Rpb1_2 | RNA polymerase Rpb1, domain 2 | C4R4Y0 |
| PF00636 | Ribonuclease_3 | Ribonuclease III domain | Q9VCU9 |
| PF00638 | Ran_BP1 | RanBP1 domain | A0A1L8HGL2 |
| PF00639 | Rotamase | PPIC-type PPIASE domain | Q13526 |
| PF00652 | Ricin_B_lectin | Ricin-type beta-trefoil lectin domain | A0A3S6Q0Y2 |
| PF00665 | rve | Integrase core domain | Q72498 |
| PF00673 | Ribosomal_L5_C | ribosomal L5P family C-terminus | P0CT77 |
| PF00680 | RdRP_1 | Viral RNA-dependent RNA polymerase | P0DTD1 |
| PF00687 | Ribosomal_L1 | Ribosomal protein L1p/L10e family | Q9UT32 |
| PF00773 | RNB | RNB domain | Q8IYB7 |
| PF00788 | RA | Ras association (RalGDS/AF-6) domain | Q9NZL6 |
| PF00825 | Ribonuclease_P | Ribonuclease P | P0A7Y8 |
| PF00827 | Ribosomal_L15e | Ribosomal L15 | O74895 |
| PF00828 | Ribosomal_L27A | Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A | P36585 |
| PF00829 | Ribosomal_L21p | Ribosomal prokaryotic L21 protein | P60492 |
| PF00830 | Ribosomal_L28 | Ribosomal L28 family | A0A1X3JA73 |
| PF00831 | Ribosomal_L29 | Ribosomal L29 protein | O74904 |
| PF00832 | Ribosomal_L39 | Ribosomal L39 protein | P05767 |
| PF00833 | Ribosomal_S17e | Ribosomal S17 | P02407 |
| PF00834 | Ribul_P_3_epim | Ribulose-phosphate 3 epimerase family | Q9I5T1 |
| PF00848 | Ring_hydroxyl_A | Ring hydroxylating alpha subunit (catalytic domain) | B7WRJ9 |
| PF00853 | Runt | Runt domain | Q13950 |
| PF00861 | Ribosomal_L18p | Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast | E3PKY8 |
| PF00866 | Ring_hydroxyl_B | Ring hydroxylating beta subunit | B7WRJ8 |
| PF00886 | Ribosomal_S16 | Ribosomal protein S16 | C3SYP2 |
| PF00900 | Ribosomal_S4e | Ribosomal family S4e | P0CX35 |
| PF00910 | RNA_helicase | RNA helicase | P08617 |
| PF00929 | RNase_T | Exonuclease | A0R1E6 |
| PF00935 | Ribosomal_L44 | Ribosomal protein L44 | Q9UTI8 |
| PF00940 | RNA_pol | DNA-dependent RNA polymerase | P00573 |
| PF00945 | Rhabdo_ncap | Rhabdovirus nucleocapsid protein | Q9YZ24 |
| PF00974 | Rhabdo_glycop_FD | Rhabdovirus spike glycoprotein fusion domain | P08667 |
| PF00978 | RdRP_2 | RNA dependent RNA polymerase | P03317 |
| PF01000 | RNA_pol_A_bac | RNA polymerase Rpb3/RpoA insert domain | C4R7L2 |
| PF01015 | Ribosomal_S3Ae | Ribosomal S3Ae family | P33442 |
| PF01016 | Ribosomal_L27 | Ribosomal L27 protein | P0A7L8 |
| PF01020 | Ribosomal_L40e | Ribosomal L40e family | P0CH08 |
| PF01030 | Recep_L_domain | Receptor L domain | P00533 |
| PF01042 | Ribonuc_L-PSP | Endoribonuclease L-PSP | A0A7M7GBQ0 |
| PF01051 | Rep3_N | Initiator Replication protein, WH1 | P03856 |
| PF01084 | Ribosomal_S18 | Ribosomal protein S18 | A0A0E2KXL3 |
| PF01090 | Ribosomal_S19e | Ribosomal protein S19e | P07280 |
| PF01092 | Ribosomal_S6e | Ribosomal protein S6e | P0CX37 |
| PF01137 | RTC | RNA 3'-terminal phosphate cyclase | Q08096 |
| PF01138 | RNase_PH | 3' exoribonuclease family, domain 1 | P05055 |
| PF01139 | RtcB | tRNA-splicing ligase RtcB | O59245 |
| PF01157 | Ribosomal_L21e | Ribosomal protein L21e | Q9UUC1 |
| PF01158 | Ribosomal_L36e | Ribosomal protein L36e | O94658 |
| PF01159 | Ribosomal_L6e | Ribosomal protein L6e | P79071 |
| PF01163 | RIO1 | RIO domain | P40160 |
| PF01165 | Ribosomal_S21 | Ribosomal protein S21 | A0A0E2L2J1 |
| PF01191 | RNA_pol_Rpb5_C | RNA polymerase Rpb5, C-terminal domain | C4R3P8 |
| PF01192 | RNA_pol_Rpb6 | RNA polymerase Rpb6 | C4R1V1 |
| PF01193 | RNA_pol_L | RNA polymerase Rpb3/Rpb11 dimerisation domain | C4R7L2 |
| PF01194 | RNA_pol_N | RNA polymerases N / 8 kDa subunit | C4R009 |
| PF01196 | Ribosomal_L17 | Ribosomal protein L17 | A0A1X3LC97 |
| PF01197 | Ribosomal_L31 | Ribosomal protein L31 | P0A7M9 |
| PF01198 | Ribosomal_L31e | Ribosomal protein L31e | Q9URX6 |
| PF01199 | Ribosomal_L34e | Ribosomal protein L34e | O42846 |
| PF01200 | Ribosomal_S28e | Ribosomal protein S28e | Q3E7X9 |
| PF01201 | Ribosomal_S8e | Ribosomal protein S8e | Q9UU79 |
| PF01245 | Ribosomal_L19 | Ribosomal protein L19 | V0AJX1 |
| PF01246 | Ribosomal_L24e | Ribosomal protein L24e | Q10353 |
| PF01247 | Ribosomal_L35Ae | Ribosomal protein L35Ae | Q9USG6 |
| PF01248 | Ribosomal_L7Ae | Ribosomal protein L7Ae/L30e/S12e/Gadd45 family | O13672 |
| PF01249 | Ribosomal_S21e | Ribosomal protein S21e | P0C0V8 |
| PF01250 | Ribosomal_S6 | Ribosomal protein S6 | C3SFQ7 |
| PF01251 | Ribosomal_S7e | Ribosomal protein S7e | P26786 |
| PF01280 | Ribosomal_L19e | Ribosomal protein L19e | P05734 |
| PF01281 | Ribosomal_L9_N | Ribosomal protein L9, N-terminal domain | V0YZK9 |
| PF01282 | Ribosomal_S24e | Ribosomal protein S24e | P0CX31 |
| PF01283 | Ribosomal_S26e | Ribosomal protein S26e | P39938 |
| PF01294 | Ribosomal_L13e | Ribosomal protein L13e | O74175 |
| PF01330 | RuvA_N | RuvA N terminal domain | Q51425 |
| PF01351 | RNase_HII | Ribonuclease HII | Q2FZ38 |
| PF01365 | RYDR_ITPR | RIH domain | P29994 |
| PF01386 | Ribosomal_L25p | Ribosomal L25p family | D7XH79 |
| PF01402 | RHH_1 | Ribbon-helix-helix protein, copG family | P9WJ87 |
| PF01421 | Reprolysin | Reprolysin (M12B) family zinc metalloprotease | Q9UNA0 |
| PF01424 | R3H | R3H domain | D0VX24 |
| PF01446 | Rep_1 | Replication protein | |
| PF01525 | Rota_NS26 | Rotavirus NS26 | |
| PF01599 | Ribosomal_S27 | Ribosomal protein S27a | P05759 |
| PF01632 | Ribosomal_L35p | Ribosomal protein L35 | P0A7Q1 |
| PF01649 | Ribosomal_S20p | Ribosomal protein S20 | C3TRH7 |
| PF01655 | Ribosomal_L32e | Ribosomal protein L32 | P79015 |
| PF01667 | Ribosomal_S27e | Ribosomal protein S27 | P35997 |
| PF01694 | Rhomboid | Rhomboid family | P09391 |
| PF01719 | Rep_OBD | Plasmid replication protein, origin binding domain | P13921 |
| PF01765 | RRF | Ribosome recycling factor | P75161 |
| PF01775 | Ribosomal_L18A | Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A | P0CT68 |
| PF01776 | Ribosomal_L22e | Ribosomal L22e protein family | Q09668 |
| PF01777 | Ribosomal_L27e | Ribosomal L27e protein family | O14388 |
| PF01778 | Ribosomal_L28e | Ribosomal L28e protein family | Q9UTE6 |
| PF01779 | Ribosomal_L29e | Ribosomal L29e protein family | Q92366 |
| PF01780 | Ribosomal_L37ae | Ribosomal L37ae protein family | Q9HGL8 |
| PF01781 | Ribosomal_L38e | Ribosomal L38e protein family | Q9USR7 |
| PF01782 | RimM | RimM N-terminal domain | P44568 |
| PF01783 | Ribosomal_L32p | Ribosomal L32p protein family | D7XI28 |
| PF01815 | Rop | Rop protein | P03051 |
| PF01857 | RB_B | Retinoblastoma-associated protein B domain | P28749 |
| PF01858 | RB_A | Retinoblastoma-associated protein A domain | P28749 |
| PF01868 | RNase_P-MRP_p29 | Ribonuclease P/MRP, subunit p29 | P38336 |
| PF01872 | RibD_C | RibD C-terminal domain | A0A0H3FX83 |
| PF01876 | RNase_P_p30 | RNase P subunit p30 | P38786 |
| PF01877 | RNA_binding | RNA binding | O58738 |
| PF01900 | RNase_P_Rpp14 | Rpp14/Pop5 family | P28005 |
| PF01907 | Ribosomal_L37e | Ribosomal protein L37e | P05733 |
| PF01929 | Ribosomal_L14e | Ribosomal protein L14 | O94238 |
| PF01947 | Rv2949c-like | Chorismate pyruvate-lyase Rv2949c-like | O28875 |
| PF02009 | RIFIN | Rifin | C0H5N9 |
| PF02010 | REJ | REJ domain | |
| PF02014 | Reeler | Reeler domain | Q9HCB6 |
| PF02026 | RyR | RyR domain | E9Q401 |
| PF02027 | RolB_RolC | RolB/RolC glucosidase family | Q57530 |
| PF02033 | RBFA | Ribosome-binding factor A | Q8N0V3 |
| PF02042 | RWP-RK | RWP-RK domain | |
| PF02075 | RuvC | Crossover junction endodeoxyribonuclease RuvC | Q9RX75 |
| PF02082 | Rrf2 | Iron-dependent Transcriptional regulator | Q9L132 |
| PF02115 | Rho_GDI | RHO protein GDP dissociation inhibitor | P52566 |
| PF02123 | RdRP_4 | Viral RNA-directed RNA-polymerase | B3F2X2 |
| PF02132 | RecR_ZnF | RecR, Cys4-zinc finger domain | Q5SHY0 |
| PF02144 | Rad1 | Repair protein Rad1/Rec1/Rad17 | O60671 |
| PF02145 | Rap_GAP | Rap/ran-GAP | P49815 |
| PF02196 | RBD | Raf-like Ras-binding domain | P15056 |
| PF02197 | RIIa | Regulatory subunit of type II PKA R-subunit | F1QK17 |
| PF02257 | RFX_DNA_binding | RFX DNA-binding domain | Q68CP9 |
| PF02267 | Rib_hydrolayse | ADP-ribosyl cyclase | P28907 |
| PF02334 | RTP | Replication terminator protein | P0CI76 |
| PF02341 | RbcX | RbcX protein | O86418 |
| PF02382 | RTX | N-terminal domain in RTX protein | P0DKX7 |
| PF02410 | RsfS | Ribosomal silencing factor during starvation | Q96EH3 |
| PF02453 | Reticulon | Reticulon | Q99P72 |
| PF02482 | Ribosomal_S30AE | Sigma 54 modulation protein / S30EA ribosomal protein | P0AD49 |
| PF02486 | Rep_trans | Replication initiation factor | P19529 |
| PF02508 | Rnf-Nqr | Rnf-Nqr subunit, membrane protein | A0A085QWM0 |
| PF02517 | Rce1-like | Type II CAAX prenyl endopeptidase Rce1-like | Q6LZY8 |
| PF02565 | RecO_C | Recombination protein O C terminal | Q9RW50 |
| PF02576 | RimP_N | RimP N-terminal domain | P0A8A8 |
| PF02631 | RecX_HTH2 | RecX, second three-helix domain | Q1WV04 |
| PF02646 | RmuC | RmuC family | |
| PF02714 | RSN1_7TM | Calcium-dependent channel, 7TM region, putative phosphate | Q5TKG1 |
| PF02755 | RPEL | RPEL repeat | Q9C0D0 |
| PF02759 | RUN | RUN domain | Q9BQS8 |
| PF02788 | RuBisCO_large_N | Ribulose bisphosphate carboxylase large chain, N-terminal domain | P04718 |
| PF02813 | Retro_M | Retroviral M domain | P03354 |
| PF02867 | Ribonuc_red_lgC | Ribonucleotide reductase, barrel domain | M1PRZ0 |
| PF02915 | Rubrerythrin | Rubrerythrin | F9VPE5 |
| PF03055 | RPE65 | Retinal pigment epithelial membrane protein | Q9TXT9 |
| PF03085 | RAP-1 | Rhoptry-associated protein 1 (RAP-1) | |
| PF03089 | RAG2 | Recombination activating protein 2 | P21784 |
| PF03090 | Replicase | Replicase family | |
| PF03118 | RNA_pol_A_CTD | Bacterial RNA polymerase, alpha chain C terminal domain | P9WGZ1 |
| PF03193 | RsgA_GTPase | RsgA GTPase | P39286 |
| PF03214 | RGP | Reversibly glycosylated polypeptide | |
| PF03215 | Rad17 | Rad17 P-loop domain | P32641 |
| PF03216 | Rhabdo_ncap_2 | Rhabdovirus nucleoprotein | |
| PF03248 | Rer1 | Rer1 family | |
| PF03259 | Robl_LC7 | Roadblock/LC7 domain | Q9Y2Q5 |
| PF03297 | Ribosomal_S25 | S25 ribosomal protein | Q3E792 |
| PF03428 | RP-C | Replication protein C N-terminal domain | |
| PF03432 | Relaxase | MobA/VirD2-like, nuclease domain | |
| PF03527 | RHS | RHS protein | Q87PI5 |
| PF03528 | Rabaptin | Rabaptin | |
| PF03652 | RuvX | Holliday junction resolvase | Q9RRI2 |
| PF03668 | RapZ-like_N | RapZ-like N-terminal domain | P0A894 |
| PF03719 | Ribosomal_S5_C | Ribosomal protein S5, C-terminal domain | P0A7W1 |
| PF03725 | RNase_PH_C | 3' exoribonuclease family, domain 2 | P05055 |
| PF03732 | Retrotrans_gag | Retrotransposon gag protein | |
| PF03737 | RraA-like | Aldolase/RraA | Q9FBS9 |
| PF03763 | Remorin_C | Remorin, C-terminal region | |
| PF03766 | Remorin_N | Remorin, N-terminal region | |
| PF03787 | RAMPs | RAMP superfamily | A0A401FT36 |
| PF03834 | Rad10 | Binding domain of DNA repair protein Ercc1 (rad10/Swi10) | P07992 |
| PF03835 | Rad4 | Rad4 transglutaminase-like domain | P14736 |
| PF03836 | RasGAP_C | RasGAP C-terminus | |
| PF03837 | RecT | RecT family | P03698 |
| PF03838 | RecU | Recombination protein U | P39792 |
| PF03868 | Ribosomal_L6e_N | Ribosomal protein L6, N-terminal domain | G1SKF7 |
| PF03870 | RNA_pol_Rpb8 | RNA polymerase Rpb8 | C4R273 |
| PF03871 | RNA_pol_Rpb5_N | RNA polymerase Rpb5, N-terminal domain | C4R3P8 |
| PF03872 | RseA_N | Anti sigma-E protein RseA, N-terminal domain | P38107 |
| PF03873 | RseA_C | Anti sigma-E protein RseA, C-terminal domain | P38107 |
| PF03874 | RNA_pol_Rpb4 | RNA polymerase Rpb4 | C4R2U9 |
| PF03939 | Ribosomal_L23eN | Ribosomal protein L23, N-terminal domain | Q10330 |
| PF03946 | Ribosomal_L11_N | Ribosomal protein L11, N-terminal domain | A0A6A5Q275 |
| PF03947 | Ribosomal_L2_C | Ribosomal Proteins L2, C-terminal domain | P0CT70 |
| PF03948 | Ribosomal_L9_C | Ribosomal protein L9, C-terminal domain | V0YZK9 |
| PF04002 | RadC | RadC-like JAB domain | Q8KES1 |
| PF04025 | RemA-like | Extracellular matrix regulatory protein A-like | A4IM41 |
| PF04032 | Rpr2 | RNAse P Rpr2/Rpp21/SNM1 subunit domain | P40993 |
| PF04034 | Ribo_biogen_C | Ribosome biogenesis protein, C-terminal | E1QU22 |
| PF04055 | Radical_SAM | Radical SAM superfamily | Q9CZX0 |
| PF04057 | Rep-A_N | Replication factor-A protein 1, N-terminal domain | P27694 |
| PF04059 | RRM_2 | RNA recognition motif 2 | P08965 |
| PF04078 | Rcd1 | Cell differentiation family, Rcd1-like | Q92600 |
| PF04084 | RecA-like_ORC2 | Origin recognition complex subunit 2 RecA-like domain | P32833 |
| PF04090 | Rrn11 | RNA polymerase I-specific transcription initiation factor Rrn11 | Q04712 |
| PF04098 | Rad52_Rad22 | Rad52/22 family double-strand break repair protein | P43351 |
| PF04139 | Rad9 | Rad9 | Q99638 |
| PF04181 | RPAP2_Rtr1 | Rtr1/RPAP2 family | Q8IXW5 |
| PF04221 | RelB | RelB antitoxin | Q47150 |
| PF04246 | RseC_MucC | Positive regulator of sigma(E), RseC/MucC | |
| PF04308 | RNaseH_like | Ribonuclease H-like | |
| PF04321 | RmlD_sub_bind | RmlD substrate binding domain | C9K1F1 |
| PF04353 | Rsd_AlgQ | Regulator of RNA polymerase sigma(70) subunit, Rsd/AlgQ | P0AFX4 |
| PF04378 | RsmJ | Ribosomal RNA large subunit methyltransferase D, RlmJ | P37634 |
| PF04381 | RdgC | Putative exonuclease, RdgC | Q9HYX7 |
| PF04423 | Rad50_zn_hook | Rad50 zinc hook motif | P58301 |
| PF04437 | RINT1_TIP1 | RINT-1/TIP-1 family | Q75B58 |
| PF04479 | RTA1 | RTA1 like protein | |
| PF04506 | Rft-1 | Rft protein | |
| PF04527 | Retinin_C | Drosophila Retinin like protein | |
| PF04560 | RNA_pol_Rpb2_7 | RNA polymerase Rpb2, domain 7 | C4QZQ7 |
| PF04561 | RNA_pol_Rpb2_2 | RNA polymerase Rpb2, domain 2 | C4QZQ7 |
| PF04563 | RNA_pol_Rpb2_1 | RNA polymerase beta subunit | C4QZQ7 |
| PF04565 | RNA_pol_Rpb2_3 | RNA polymerase Rpb2, domain 3 | C4QZQ7 |
| PF04566 | RNA_pol_Rpb2_4 | RNA polymerase Rpb2, domain 4 | C4QZQ7 |
| PF04567 | RNA_pol_Rpb2_5 | RNA polymerase Rpb2, domain 5 | C4QZQ7 |
| PF04589 | RFX1_trans_act | RFX1 transcription activation region | |
| PF04597 | Ribophorin_I | Ribophorin I | P04843 |
| PF04607 | RelA_SpoT | Region found in RelA / SpoT proteins | A0A1B0VBT5 |
| PF04641 | Rtf2 | Rtf2 RING-finger | |
| PF04683 | Rpn13_ADRM1_Pru | Proteasome complex subunit Rpn13, Pru domain | A0A6A5PTW0 |
| PF04698 | Rab_eff_C | Rab effector MyRIP/melanophilin C-terminus | |
| PF04712 | Radial_spoke | Radial spokehead-like protein | Q01657 |
| PF04758 | Ribosomal_S30 | Ribosomal protein S30 | P0CX33 |
| PF04796 | RepA_C | Plasmid encoded RepA protein | |
| PF04801 | RPC5 | RPC5 protein | P36121 |
| PF04824 | Rad21_Rec8 | Conserved region of Rad21 / Rec8 like protein | Q12158 |
| PF04825 | Rad21_Rec8_N | N terminus of Rad21 / Rec8 like protein | P30776 |
| PF04851 | ResIII | Type III restriction enzyme, res subunit | P19447 |
| PF04901 | RAMP | Receptor activity modifying family | O60894 |
| PF04939 | RRS1 | Ribosome biogenesis regulatory protein (RRS1) | Q08746 |
| PF04950 | RIBIOP_C | 40S ribosome biogenesis protein Tsr1 and BMS1 C-terminal | Q07381 |
| PF04957 | RMF | Ribosome modulation factor | P0AFW2 |
| PF04983 | RNA_pol_Rpb1_3 | RNA polymerase Rpb1, domain 3 | C4R4Y0 |
| PF04989 | RMNT_CmcI | Rhamnosyl O-methyltransferase/CmcI | B5GLB3 |
| PF04990 | RNA_pol_Rpb1_7 | RNA polymerase Rpb1, domain 7 | C4R4Y0 |
| PF04992 | RNA_pol_Rpb1_6 | RNA polymerase Rpb1, domain 6 | C4R4Y0 |
| PF04997 | RNA_pol_Rpb1_1 | RNA polymerase Rpb1, domain 1 | C4R4Y0 |
| PF04998 | RNA_pol_Rpb1_5 | RNA polymerase Rpb1, domain 5 | C4R4Y0 |
| PF05000 | RNA_pol_Rpb1_4 | RNA polymerase Rpb1, domain 4 | C4R4Y0 |
| PF05001 | RNA_pol_Rpb1_R | RNA polymerase Rpb1 C-terminal repeat | C4R4Y0 |
| PF05025 | RbsD_FucU | RbsD / FucU transport protein family | A0A0H2ZNZ5 |
| PF05045 | RgpF | Rhamnan synthesis protein F | |
| PF05062 | RICH | RICH domain | P27951 |
| PF05082 | Rop-like | Rop-like | A1KYE3 |
| PF05104 | Rib_recp_KP_reg | Ribosome receptor lysine/proline rich region | |
| PF05132 | RNA_pol_Rpc4 | RNA polymerase III RPC4 | P25441 |
| PF05140 | ResB | ResB-like family | Q7VHG9 |
| PF05158 | RNA_pol_Rpc34 | RNA polymerase Rpc34 subunit | P32910 |
| PF05162 | Ribosomal_L41 | Ribosomal protein L41 | P0CX86 |
| PF05172 | RRM_Nup35 | Nup53/35/40-type RNA recognition motif | Q8NFH5 |
| PF05177 | RCSD | RCSD region | |
| PF05183 | RdRP | RNA dependent RNA polymerase | Q9Y7G6 |
| PF05189 | RTC_insert | RNA 3'-terminal phosphate cyclase (RTC), insert domain | Q08096 |
| PF05327 | RRN3 | RNA polymerase I specific transcription initiation factor RRN3 | Q9NYV6 |
| PF05336 | rhaM | L-rhamnose mutarotase | F0Q4R9 |
| PF05433 | Rick_17kDa_Anti | Glycine zipper 2TM domain | D2AGE2 |
| PF05443 | ROS_MUCR | ROS/MUCR transcriptional regulator protein | Q04152 |
| PF05491 | RuvB_C | RuvB C-terminal winged helix domain | Q51426 |
| PF05496 | RuvB_N | Holliday junction DNA helicase RuvB P-loop domain | Q5M2B1 |
| PF05498 | RALF | Rapid ALkalinization Factor (RALF) | Q9FZA0 |
| PF05508 | Ran-binding | RanGTP-binding protein | |
| PF05526 | R_equi_Vir | Rhodococcus equi virulence-associated protein | B4F366 |
| PF05593 | RHS_repeat | RHS Repeat | Q87PI5 |
| PF05608 | RTE1 | RTE1-like | |
| PF05633 | ROH1-like | Protein ROH1-like | |
| PF05645 | RNA_pol_Rpc82 | RNA polymerase III subunit RPC82 | P32349 |
| PF05659 | RPW8 | Arabidopsis broad-spectrum mildew resistance protein RPW8 | Q9FKZ1 |
| PF05691 | Raffinose_syn | Raffinose synthase or seed imbibition protein Sip1 | Q8RX87 |
| PF05732 | RepL | Firmicute plasmid replication protein (RepL) | |
| PF05755 | REF | Rubber elongation factor protein (REF) | |
| PF05773 | RWD | RWD domain | Q9P2K8 |
| PF05797 | Rep_4 | Yeast trans-acting factor (REP1/REP2) | |
| PF05817 | Ribophorin_II | Ribophorin II N-terminal domain | P04844 |
| PF05866 | RusA | Endodeoxyribonuclease RusA | P0AG74 |
| PF05879 | RHD3_GTPase | Root hair defective 3 GTP-binding protein (RHD3) GTPase domain | Q9C0L9 |
| PF05914 | RIB43A | RIB43A | Q9H4K1 |
| PF06001 | RING_CBP-p300 | CREB-binding protein/p300, atypical RING domain | Q09472 |
| PF06020 | Roughex | Drosophila roughex protein | |
| PF06026 | Rib_5-P_isom_A | Ribose 5-phosphate isomerase A (phosphoriboisomerase A) | B2FT30 |
| PF06045 | Rhamnogal_lyase | Rhamnogalacturonate lyase family | |
| PF06085 | Rz1 | Lipoprotein Rz1 precursor | |
| PF06098 | Radial_spoke_3 | Radial spoke protein 3 | A8J2J7 |
| PF06102 | RRP36 | rRNA biogenesis protein RRP36 | |
| PF06116 | RinB | Transcriptional activator RinB | |
| PF06134 | RhaA | L-rhamnose isomerase (RhaA) | Q9KCL9 |
| PF06271 | RDD | RDD family | |
| PF06296 | RelE | RelE toxin of RelE / RelB toxin-antitoxin system | Q9KMA6 |
| PF06379 | RhaT | L-rhamnose-proton symport protein (RhaT) | |
| PF06405 | RCC_reductase | Red chlorophyll catabolite reductase (RCC reductase) | Q8LDU4 |
| PF06459 | RR_TM4-6 | Ryanodine Receptor TM 4-6 | E9Q401 |
| PF06479 | Ribonuc_2-5A | Ribonuclease 2-5A | A5H025 |
| PF06504 | RepC | Replication protein C (RepC) | |
| PF06534 | RGM_C | Repulsive guidance molecule (RGM) C-terminus | Q6NW40 |
| PF06535 | RGM_N | Repulsive guidance molecule (RGM) N-terminus | Q6NW40 |
| PF06624 | RAMP4 | Ribosome associated membrane protein RAMP4 | |
| PF06815 | RVT_connect | Reverse transcriptase connection domain | P04585 |
| PF06817 | RVT_thumb | Reverse transcriptase thumb domain | P04585 |
| PF06830 | Root_cap | Root cap | |
| PF06870 | RNA_pol_I_A49 | A49-like RNA polymerase I associated factor | Q9GZS1 |
| PF06877 | RraB | Regulator of ribonuclease activity B | Q9KUU1 |
| PF06883 | RNA_pol_Rpa2_4 | RNA polymerase I, Rpa2 specific domain | Q9H9Y6 |
| PF06926 | Rep_Org_C | Putative replisome organiser protein C-terminus | |
| PF06954 | Resistin | Resistin | Q99P86 |
| PF06956 | RtcR | Regulator of RNA terminal phosphate cyclase | |
| PF06959 | RecQ5 | RecQ helicase protein-like 5 (RecQ5) | |
| PF06962 | rRNA_methylase | Putative rRNA methylase | Q2FXG9 |
| PF06970 | RepA_N | Replication initiator protein A (RepA) N-terminus | D2JDC3 |
| PF07035 | RMC1_C | Regulator of MON1-CCZ1 complex, C-terminal | |
| PF07064 | RIC1 | RIC1 | |
| PF07073 | ROF | Modulator of Rho-dependent transcription termination (ROF) | A0A0H3ADN9 |
| PF07218 | RAP1 | Rhoptry-associated protein 1 (RAP-1) | |
| PF07288 | RpoY | RNA polymerase epsilon subunit | O31718 |
| PF07326 | RCS1 | Regulator of chromosome segregation 1 | |
| PF07494 | Reg_prop | Two component regulator propeller | Q89YR8 |
| PF07497 | Rho_RNA_bind | Rho termination factor, RNA-binding domain | P0AG30 |
| PF07498 | Rho_N | Rho termination factor, N-terminal domain | P0AG30 |
| PF07499 | RuvA_C | RuvA, C-terminal domain | P66746 |
| PF07506 | RepB | RepB plasmid partitioning protein | |
| PF07508 | Recombinase | Recombinase | Q928V6 |
| PF07521 | RMMBL | Zn-dependent metallo-hydrolase RNA specificity domain | P9WGZ9 |
| PF07547 | RSD-2 | RSD-2 N-terminal domain | |
| PF07634 | RtxA | RtxA repeat | |
| PF07711 | RabGGT_insert | Rab geranylgeranyl transferase alpha-subunit, insert domain | Q08602 |
| PF07727 | RVT_2 | Reverse transcriptase (RNA-dependent DNA polymerase) | |
| PF07807 | RED_C | RED-like protein C-terminal region | Q13123 |
| PF07808 | RED_N | RED-like protein N-terminal region | Q13123 |
| PF07809 | RTP801_C | RTP801 C-terminal region | Q9NX09 |
| PF07834 | RanGAP1_C | RanGAP1 C-terminal domain | P46060 |
| PF07850 | Renin_r | Renin receptor-like transmembrane spanning segment | A0A1B0GVW0 |
| PF07878 | RHH_5 | CopG-like RHH_1 or ribbon-helix-helix domain, RHH_5 | |
| PF07890 | Rrp15p | Rrp15p | Q06511 |
| PF07964 | Red1 | Rec10 / Red1 | |
| PF07999 | RHSP | Retrotransposon hot spot protein, P-loop domain | |
| PF08048 | RepA1_leader | Tap RepA1 leader peptide | |
| PF08067 | ROKNT | ROKNT (NUC014) domain | P61978 |
| PF08069 | Ribosomal_S13_N | Ribosomal S13/S15 N-terminal domain | P05756 |
| PF08071 | RS4NT | RS4NT (NUC023) domain | P0CX35 |
| PF08079 | Ribosomal_L30_N | Ribosomal L30 N-terminal domain | P17937 |
| PF08081 | RBM1CTR | RBM1CTR (NUC064) family | |
| PF08161 | RRP12_HEAT | Ribosomal RNA-processing protein 12, HEAT repeats | Q5JTH9 |
| PF08167 | RIX1 | rRNA processing/ribosome biogenesis | C9JFV4 |
| PF08169 | RBB1NT | RBB1NT (NUC162) domain | P29374 |
| PF08203 | RNA_polI_A14 | Yeast RNA polymerase I subunit RPA14 | Q9P7P1 |
| PF08208 | RNA_polI_A34 | DNA-directed RNA polymerase I subunit RPA34.5 | O15446 |
| PF08228 | RNase_P_pop3 | RNase P subunit Pop3 | P53833 |
| PF08284 | RVP_2 | Retroviral aspartyl protease | |
| PF08292 | RNA_pol_Rbc25 | RNA polymerase III subunit Rpc25 | P35718 |
| PF08339 | RTX_C | RTX C-terminal domain | |
| PF08343 | RNR_N | Ribonucleotide reductase N-terminal | P50620 |
| PF08373 | RAP | RAP domain | |
| PF08375 | Rpn3_C | Proteasome regulatory subunit C-terminal | O43242 |
| PF08423 | Rad51 | Rad51 | O74036 |
| PF08428 | Rib | Rib domain | Q5FIM8 |
| PF08443 | RimK | RimK-like ATP-grasp domain | O74429 |
| PF08454 | RIH_assoc | RyR and IP3R Homology associated | P29994 |
| PF08471 | Ribonuc_red_2_N | Class II vitamin B12-dependent ribonucleotide reductase | Q3J3H6 |
| PF08477 | Roc | Ras of Complex, Roc, domain of DAPkinase | Q5S007 |
| PF08497 | Radical_SAM_N | Radical SAM N-terminal | |
| PF08504 | RunxI | Runx inhibition domain | |
| PF08512 | Rttp106-like_middle | Histone chaperone Rttp106-like, middle domain | F2QNN8 |
| PF08519 | RFC1 | Replication factor RFC1 C terminal domain | P38630 |
| PF08524 | rRNA_processing | rRNA processing | |
| PF08534 | Redoxin | Redoxin | G0S1P8 |
| PF08542 | Rep_fac_C | Replication factor C C-terminal domain | P40348 |
| PF08561 | Ribosomal_L37 | Mitochondrial ribosomal protein L37 | Q6P161 |
| PF08579 | RPM2 | Mitochondrial ribonuclease P subunit (RPM2) | |
| PF08584 | Ribonuc_P_40 | Ribonuclease P 40kDa (Rpp40) subunit | O75818 |
| PF08585 | RMI1_N_C | RMI1, N-terminal OB-fold domain | Q9H7E2 |
| PF08586 | Rsc14 | RSC complex, Rsc14/Ldb7 subunit | P38210 |
| PF08591 | RNR_inhib | Ribonucleotide reductase inhibitor | |
| PF08595 | RXT2_N | RXT2-like, N-terminal | |
| PF08605 | Rad9_Rad53_bind | Fungal Rad9-like Rad53-binding | |
| PF08615 | RNase_H2_suC | Ribonuclease H2 non-catalytic subunit (Ylr154p-like) | Q8TDP1 |
| PF08620 | RPAP1_C | RPAP1-like, C-terminal | |
| PF08621 | RPAP1_N | RPAP1-like, N-terminal | |
| PF08633 | Rox3 | Rox3 mediator complex subunit | A0A6A5Q3S8 |
| PF08642 | Rxt3 | Histone deacetylation protein Rxt3 | |
| PF08646 | Rep_fac-A_C | Replication factor-A C terminal domain | D2CVN6 |
| PF08652 | RAI1 | RAI1 like PD-(D/E)XK nuclease | O70348 |
| PF08658 | Rad54_N | Rad54 N terminal | |
| PF08661 | Rep_fac-A_3 | Replication factor A protein 3 | A0A0U8UFF4 |
| PF08673 | RsbU_N | Phosphoserine phosphatase RsbU, N-terminal domain | P40399 |
| PF08675 | RNA_bind | RNA binding domain | Q8VDG3 |
| PF08678 | Rsbr_N | Rsbr N terminal | Q92DC6 |
| PF08724 | Rep_N | Rep protein catalytic domain like | A3F778 |
| PF08730 | Rad33 | Rad33 | Q04231 |
| PF08737 | Rgp1 | Rgp1 | |
| PF08777 | RRM_3 | RNA binding motif | Q4G0J3 |
| PF08784 | RPA_C | Replication protein A C terminal | P15927 |
| PF08808 | RES | RES domain | Q88K57 |
| PF08912 | Rho_Binding | Rho Binding | Q28021 |
| PF08924 | Rv2525c_GlyHyd-like | Rv2525c-like, glycoside hydrolase-like domain | P95028 |
| PF08934 | Rb_C | Rb C-terminal domain | P28749 |
| PF08962 | Rv2632c-like | Rv2632c-like | P9WLS3 |
| PF09128 | RGS-like | Regulator of G protein signalling-like domain | Q9ES67 |
| PF09187 | RdDM_RDM1 | RNA-directed DNA methylation 1 | Q9LUJ3 |
| PF09197 | Rap1-DNA-bind | Rap1, DNA-binding | P11938 |
| PF09202 | Rio2_N | Rio2, N-terminal | P40160 |
| PF09231 | RDV-p3 | Rice dwarf virus p3 | P22472 |
| PF09243 | Rsm22 | Mitochondrial small ribosomal subunit Rsm22 | P36056 |
| PF09273 | Rubis-subs-bind | Rubisco LSMT substrate-binding | Q86TU7 |
| PF09284 | RhgB_N | Rhamnogalacturonan lyase B, N-terminal | Q00019 |
| PF09311 | Rab5-bind | Rabaptin-like protein | Q15276 |
| PF09357 | RteC | RteC protein | |
| PF09382 | RQC | RQC domain | Q14191 |
| PF09414 | RNA_ligase | RNA ligase | D2W2Z5 |
| PF09456 | RcsC | RcsC Alpha-Beta-Loop (ABL) | P0DMC5 |
| PF09457 | RBD-FIP | FIP domain | Q7L804 |
| PF09468 | RNase_H2-Ydr279 | Ydr279p protein family (RNase H2 complex component) wHTH domain | Q5TBB1 |
| PF09491 | RE_AlwI | AlwI restriction endonuclease | A3FEV7 |
| PF09499 | RE_ApaLI | ApaLI-like restriction endonuclease | |
| PF09504 | RE_Bsp6I | Bsp6I restriction endonuclease | |
| PF09510 | Rtt102p | Rtt102p-like transcription regulator protein | P53330 |
| PF09511 | RNA_lig_T4_1 | RNA ligase | G0S6G2 |
| PF09516 | RE_CfrBI | CfrBI restriction endonuclease | |
| PF09517 | RE_Eco29kI | Eco29kI restriction endonuclease | Q46944 |
| PF09518 | RE_HindIII | HindIII restriction endonuclease | P43870 |
| PF09519 | RE_HindVP | HindVP restriction endonuclease | |
| PF09520 | RE_TdeIII | Type II restriction endonuclease, TdeIII | |
| PF09521 | RE_NgoPII | NgoPII restriction endonuclease | |
| PF09522 | RE_R_Pab1 | R.Pab1 restriction endonuclease | G8ZFZ3 |
| PF09545 | RE_AccI | AccI restriction endonuclease | |
| PF09549 | RE_Bpu10I | Bpu10I restriction endonuclease | Q5D6Y4 |
| PF09552 | RE_BstXI | BstXI restriction endonuclease | |
| PF09553 | RE_Eco47II | Eco47II restriction endonuclease | |
| PF09554 | RE_HaeII | HaeII restriction endonuclease | |
| PF09556 | RE_HaeIII | HaeIII restriction endonuclease | |
| PF09561 | RE_HpaII | HpaII restriction endonuclease | |
| PF09562 | RE_LlaMI | LlaMI restriction endonuclease | |
| PF09563 | RE_LlaJI | LlaJI restriction endonuclease | |
| PF09564 | RE_NgoBV | NgoBV restriction endonuclease | P50183 |
| PF09565 | RE_NgoFVII | NgoFVII restriction endonuclease N-terminal PLD domain | Q5F9M9 |
| PF09566 | RE_SacI | SacI restriction endonuclease | Q83VS8 |
| PF09567 | RE_MamI | MamI restriction endonuclease | |
| PF09568 | RE_MjaI | MjaI restriction endonuclease | |
| PF09569 | RE_ScaI | ScaI restriction endonuclease | |
| PF09570 | RE_SinI | SinI restriction endonuclease | Q8YYB7 |
| PF09571 | RE_XcyI | XcyI restriction endonuclease | |
| PF09572 | RE_XamI | XamI restriction endonuclease | |
| PF09573 | RE_TaqI | TaqI restriction endonuclease | |
| PF09632 | Rac1 | Rac1-binding domain | Q93KQ6 |
| PF09665 | RE_Alw26IDE | Type II restriction endonuclease (RE_Alw26IDE) | |
| PF09744 | RH1 | RILP homology 1 domain | |
| PF10036 | RLL | RNA transcription, translation and transport factor protein | Q9Y224 |
| PF10074 | RovC_DNA-bd | T6SS, Transcription factor, DNA binding domain | A0A0H3B5N9 |
| PF10079 | Rossmann-like_BshC | Bacillithiol biosynthesis BshC, N-terminal Rossmann-like domain | P55342 |
| PF10099 | RskA_C | Anti-sigma-K factor rskA, C-terminal | |
| PF10127 | RlaP | RNA repair pathway DNA polymerase beta family | |
| PF10134 | RPA | Replication initiator protein A | |
| PF10135 | Rod-binding | Rod binding protein | |
| PF10150 | RNase_E_G | Ribonuclease E/G family | P21513 |
| PF10165 | Ric8 | Guanine nucleotide exchange factor synembryn | Q80XE1 |
| PF10214 | Rrn6_beta-prop | Rrn6, beta-propeller | P32786 |
| PF10247 | Romo1 | Reactive mitochondrial oxygen species modulator 1 | |
| PF10257 | RAI16-like | Retinoic acid induced 16-like protein | |
| PF10259 | Rogdi_lz | Rogdi leucine zipper containing protein | Q9GZN7 |
| PF10262 | Rdx | Rdx family | Q82LK9 |
| PF10304 | RTP1_C2 | Required for nuclear transport of RNA pol II C-terminus 2 | |
| PF10356 | RRG7 | Required for respiratory growth protein 7 | |
| PF10363 | RTP1_C1 | Required for nuclear transport of RNA pol II C-terminus 1 | |
| PF10370 | Rv2993c-like_N | Rv2993c-like, N-terminal | A0QUY6 |
| PF10378 | RRM | Putative RRM domain | |
| PF10385 | RNA_pol_Rpb2_45 | RNA polymerase beta subunit external 1 domain | P9WGY9 |
| PF10413 | Rhodopsin_N | Amino terminal of the G-protein receptor rhodopsin | P02699 |
| PF10443 | RNA12 | RNA12 protein | |
| PF10493 | Rod_C | Rough deal protein C-terminal region | P50748 |
| PF10501 | Ribosomal_L50 | Ribosomal subunit 39S | Q8N5N7 |
| PF10522 | RII_binding_1 | RII binding domain | Q12802 |
| PF10579 | Rapsyn_N | Rapsyn N-terminal myristoylation and linker region | |
| PF10598 | RRM_4 | RNA recognition motif of the spliceosomal PrP8 | Q6P2Q9 |
| PF10602 | RPN7 | 26S proteasome subunit RPN7 | Q15008 |
| PF10657 | RC-P840_PscD | Photosystem P840 reaction centre protein PscD | Q8KEP5 |
| PF10680 | RRN9 | RNA polymerase I specific transcription initiation factor | P53437 |
| PF10681 | Rot1 | Chaperone for protein-folding within the ER, fungal | |
| PF10723 | RepB-RCR_reg | Replication regulatory protein RepB | |
| PF10727 | Rossmann-like | Rossmann-like domain | |
| PF10843 | RGI1 | Respiratory growth induced protein 1 | P40043 |
| PF11002 | RDM | RFPL defining motif (RDM) | |
| PF11058 | Ral | Antirestriction protein Ral | |
| PF11083 | Relaxase_C | C-terminal helical hairpin domain from relaxase | |
| PF11109 | RFamide_26RFa | Orexigenic neuropeptide Qrfp/P518 | |
| PF11316 | Rhamno_transf | Putative rhamnosyl transferase | |
| PF11407 | RestrictionMunI | Type II restriction enzyme MunI | P43642 |
| PF11423 | Repressor_Mnt | Regulatory protein Mnt | P03049 |
| PF11461 | RILP | Rab interacting lysosomal protein | Q969X0 |
| PF11463 | R-HINP1I | R.HinP1I restriction endonuclease | Q5I6E6 |
| PF11464 | Rbsn | Rabenosyn Rab binding domain | Q9H1K0 |
| PF11465 | Receptor_2B4 | Natural killer cell receptor 2B4 | Q07763 |
| PF11469 | Ribonucleas_3_2 | Ribonuclease III | Q8U363 |
| PF11487 | RestrictionSfiI | Type II restriction enzyme SfiI | O52512 |
| PF11495 | Regulator_TrmB | Archaeal transcriptional regulator TrmB | Q8U3H1 |
| PF11511 | RhodobacterPufX | Intrinsic membrane protein PufX | P26240 |
| PF11548 | Receptor_IA-2 | Protein-tyrosine phosphatase receptor IA-2 | Q92932 |
| PF11574 | Rpf1_C | Resuscitation-promoting factor Rpf1, C-terminal | Q6NIK0 |
| PF11608 | RRM_MARF1 | MARF1, RNA recognition motif 1 | Q9Y4F3 |
| PF11626 | Rap1_C | TRF2-interacting telomeric protein/Rap1 - C terminal domain | P11938 |
| PF11648 | RIG-I_C-RD | C-terminal domain of RIG-I | O95786 |
| PF11705 | RNA_pol_3_Rpc31 | DNA-directed RNA polymerase III subunit Rpc31 | P17890 |
| PF11747 | RebB | Killing trait | |
| PF11776 | RcnB | Nickel/cobalt transporter regulator | A6TBK4 |
| PF11800 | RP-C_C | Replication protein C C-terminal region | |
| PF11826 | RctB_central | Vibrionales, replication initiator protein RctB, central region | Q9KNG2 |
| PF11835 | RRM_8 | RRM-like domain | Q8WVV9 |
| PF11891 | RETICULATA-like | Protein RETICULATA-related | |
| PF11967 | RecO_N | Recombination protein O N terminal | Q9RW50 |
| PF11976 | Rad60-SLD | Ubiquitin-2 like Rad60 SUMO-like | P63165 |
| PF11977 | RNase_Zc3h12a | Zc3h12a-like Ribonuclease NYN domain | Q5DTV4 |
| PF12042 | RP1-2 | Tubuliform egg casing silk strands structural domain | Q2LC34 |
| PF12072 | RNase_Y_N | RNase Y N-terminal region | |
| PF12122 | Rhomboid_N | Cytoplasmic N-terminal domain of rhomboid serine protease | P09391 |
| PF12136 | RNA_pol_Rpo13 | RNA polymerase Rpo13 subunit HTH domain | Q4JAJ6 |
| PF12137 | RapA_C | RNA polymerase recycling family C-terminal | P60240 |
| PF12174 | RST | RCD1-SRO-TAF4 (RST) plant domain | F4K4L7 |
| PF12231 | Rif1_N | Rap1-interacting factor 1 N terminal | P29539 |
| PF12234 | Rav1p_C | RAVE protein 1 C terminal | |
| PF12273 | RCR | Chitin synthesis regulation, resistance to Congo red | |
| PF12300 | RhlB | ATP-dependent RNA helicase RhlB | |
| PF12328 | Rpp20 | Rpp20 subunit of nuclear RNase MRP and P | P38291 |
| PF12331 | Rad26-like_helical_rpts | Rad26-like, helical repeats | G2QDY6 |
| PF12334 | rOmpB_passenger | Rickettsia outer membrane protein B, passenger domain | |
| PF12338 | RbcS | Ribulose-1,5-bisphosphate carboxylase small subunit | E3WDK7 |
| PF12368 | Rhodanese_C | Rhodanase C-terminal | |
| PF12560 | RAG1_imp_bd | RAG1 importin binding | P15919 |
| PF12606 | RELT | Tumour necrosis factor receptor superfamily member 19 | |
| PF12614 | RRF_GI | Ribosome recycling factor | |
| PF12647 | RNHCP | RNHCP domain | |
| PF12651 | RHH_3 | Ribbon-helix-helix domain | W9BQC4 |
| PF12721 | RHIM | RIP homotypic interaction motif | Q9Y572 |
| PF12768 | Rax2 | Rax2 C-terminal beta propeller domain | |
| PF12791 | RsgI_N | Anti-sigma factor N-terminus | A3DBH1 |
| PF12906 | RINGv | RING-variant domain | P40318 |
| PF12923 | RRP7 | Ribosomal RNA-processing protein 7 (RRP7) C-terminal domain | Q9Y3A4 |
| PF12940 | RAG1 | Recombination-activation protein 1 (RAG1), recombinase | P15919 |
| PF13032 | RNaseH_pPIWI_RE | RNaseH domain of pPIWI_RE | |
| PF13114 | RecO_N_2 | RecO N terminal | Q0PC17 |
| PF13145 | Rotamase_2 | PPIC-type PPIASE domain | Q8CVC6 |
| PF13333 | rve_2 | Integrase core domain | |
| PF13341 | RAG2_PHD | RAG2 PHD domain | P21784 |
| PF13375 | RnfC_N | RnfC Barrel sandwich hybrid domain | |
| PF13397 | RbpA | RNA polymerase-binding protein | F2RBH1 |
| PF13446 | RPT | A repeated domain in UCH-protein | |
| PF13456 | RVT_3 | Reverse transcriptase-like | Q9HSF6 |
| PF13464 | RodZ_C | RodZ C-terminal domain | |
| PF13467 | RHH_4 | Ribbon-helix-helix domain | Q7VY20 |
| PF13482 | RNase_H_2 | RNase_H superfamily | |
| PF13540 | RCC1_2 | Regulator of chromosome condensation (RCC1) repeat | Q9LX29 |
| PF13574 | Reprolysin_2 | Metallo-peptidase family M12B Reprolysin-like | O14672 |
| PF13582 | Reprolysin_3 | Metallo-peptidase family M12B Reprolysin-like | A0A5H1ZR49 |
| PF13583 | Reprolysin_4 | Metallo-peptidase family M12B Reprolysin-like | O86049 |
| PF13616 | Rotamase_3 | PPIC-type PPIASE domain | Q81U45 |
| PF13655 | RVT_N | N-terminal domain of reverse transcriptase | Q8DMK2 |
| PF13656 | RNA_pol_L_2 | RNA polymerase Rpb3/Rpb11 dimerisation domain | C4R3Z5 |
| PF13683 | rve_3 | Integrase core domain | |
| PF13688 | Reprolysin_5 | Metallo-peptidase family M12 | P54355 |
| PF13707 | RloB | RloB-like protein | |
| PF13806 | Rieske_2 | Rieske-like [2Fe-2S] domain | O53675 |
| PF13814 | Replic_Relax | Replication-relaxation | |
| PF13877 | RPAP3_C | Potential Monad-binding region of RPAP3 | Q9H6T3 |
| PF13881 | Rad60-SLD_2 | Ubiquitin-2 like Rad60 SUMO-like | Q9SW27 |
| PF13890 | Rab3-GTPase_cat | Rab3 GTPase-activating protein catalytic subunit | |
| PF13893 | RRM_5 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | P40567 |
| PF13901 | RH_dom | Rubicon Homology Domain | Q92622 |
| PF13902 | R3H-assoc | R3H-associated N-terminal domain | |
| PF13967 | RSN1_TM | Late exocytosis, associated with Golgi transport | Q5TKG1 |
| PF14200 | RicinB_lectin_2 | Ricin-type beta-trefoil lectin domain-like | A0A4V1G8Q1 |
| PF14204 | Ribosomal_L18_c | Ribosomal L18 C-terminal region | P52822 |
| PF14223 | Retrotran_gag_2 | gag-polypeptide of LTR copia-type | |
| PF14239 | RRXRR | RRXRR protein | |
| PF14243 | R2K_3 | ATP-grasp domain, R2K clade family 3 | |
| PF14244 | Retrotran_gag_3 | gag-polypeptide of LTR copia-type | |
| PF14361 | RsbRD_N | RsbT co-antagonist protein rsbRD N-terminal domain | |
| PF14374 | Ribos_L4_asso_C | 60S ribosomal protein L4 C-terminal domain | Q9P784 |
| PF14401 | RLAN | RimK-like ATPgrasp N-terminal domain | |
| PF14473 | RD3 | RD3 protein | Q7Z3Z2 |
| PF14474 | RTC4 | RTC4-like domain | |
| PF14511 | RE_EcoO109I | Type II restriction endonuclease EcoO109I | |
| PF14538 | Raptor_N | Raptor N-terminal CASPase like domain | Q8N122 |
| PF14574 | RACo_C_ter | C-terminal domain of RACo the ASKHA domain | Q3ACS2 |
| PF14615 | Rsa3 | Ribosome-assembly protein 3 | |
| PF14616 | Rua1_C | Transcription regulator Rua1, C-terminal | |
| PF14621 | RFX5_DNA_bdg | RFX5 DNA-binding domain | |
| PF14622 | Ribonucleas_3_3 | Ribonuclease-III-like | P0A7Y0 |
| PF14626 | RNase_Zc3h12a_2 | Zc3h12a-like Ribonuclease NYN domain | |
| PF14655 | RAB3GAP2_N | Rab3 GTPase-activating protein regulatory subunit N-terminus | |
| PF14656 | RAB3GAP2_C | Rab3 GTPase-activating protein regulatory subunit C-terminus | |
| PF14663 | RasGEF_N_2 | Rapamycin-insensitive companion of mTOR RasGEF_N domain | Q6R327 |
| PF14664 | RICTOR_N | Rapamycin-insensitive companion of mTOR, N-term | Q6R327 |
| PF14665 | RICTOR_phospho | Rapamycin-insensitive companion of mTOR, phosphorylation-site | Q6R327 |
| PF14666 | RICTOR_M | Rapamycin-insensitive companion of mTOR, middle domain | Q6R327 |
| PF14668 | RICTOR_V | Rapamycin-insensitive companion of mTOR, domain 5 | Q6R327 |
| PF14693 | Ribosomal_TL5_C | Ribosomal protein TL5, C-terminal domain | Q5SHZ1 |
| PF14700 | RPOL_N | DNA-directed RNA polymerase N-terminal | P00573 |
| PF14726 | RTTN_N | Rotatin, an armadillo repeat protein, centriole functioning | |
| PF14752 | RBP_receptor | Retinol binding protein receptor | F1RAX4 |
| PF14759 | Reductase_C | Reductase C-terminal | Q47QF8 |
| PF14760 | Rnk_N | Rnk N-terminus | P0AFW4 |
| PF14766 | RPA_interact_N | Replication protein A interacting N-terminal | |
| PF14767 | RPA_interact_M | Replication protein A interacting middle | |
| PF14768 | RPA_interact_C | Replication protein A interacting C-terminal | |
| PF14847 | Ras_bdg_2 | Ras-binding domain of Byr2 | |
| PF14876 | RSF | Respiratory growth transcriptional regulator | |
| PF14948 | RESP18 | RESP18 domain | |
| PF14996 | RMP | Retinal Maintenance | |
| PF14998 | Ripply | Transcription Regulator | |
| PF15035 | Rootletin | Ciliary rootlet component, centrosome cohesion | |
| PF15089 | Redic1-like | Regulator of DNA class I crossover intermediates 1-like | |
| PF15151 | RGCC | Response gene to complement 32 protein family | |
| PF15165 | REC114-like | Meiotic recombination protein REC114-like | Q9CWH4 |
| PF15201 | Rod_cone_degen | Progressive rod-cone degeneration | |
| PF15208 | Rab15_effector | Rab15 effector | Q6BDI9 |
| PF15250 | Raftlin | Raftlin | |
| PF15289 | RFXA_RFXANK_bdg | Regulatory factor X-associated C-terminal binding domain | O00287 |
| PF15303 | RNF111_N | E3 ubiquitin-protein ligase Arkadia N-terminus | |
| PF15319 | RHINO | RAD9, RAD1, HUS1-interacting nuclear orphan protein | |
| PF15320 | RAM | mRNA cap methylation, RNMT-activating mini protein | Q9BTL3 |
| PF15361 | RIC3 | Resistance to inhibitors of cholinesterase homologue 3 | |
| PF15449 | Retinal | Retinal protein | |
| PF15459 | RRP14 | 60S ribosome biogenesis protein Rrp14 | P36080 |
| PF15519 | RBM39linker | linker between RRM2 and RRM3 domains in RBM39 protein | |
| PF15628 | RRM_DME | RRM in Demeter | Q9SJQ6 |
| PF15696 | RAD51_interact | RAD51 interacting motif | |
| PF15725 | RCDG1 | Renal cancer differentiation gene 1 protein | |
| PF15828 | RDD1 | Required for drug-induced death protein 1 | |
| PF15926 | RNF220 | E3 ubiquitin-protein ligase RNF220 | |
| PF15933 | RnlB_antitoxin | Antitoxin to bacterial toxin RNase LS or RnlA | P52130 |
| PF15935 | RnlA_toxin | RNase LS, bacterial toxin | P52129 |
| PF15968 | RexB | Membrane-anchored ion channel, Abi component | |
| PF15969 | RexA | Intracellular sensor of Lambda phage, Abi component | |
| PF16099 | RMI1_C | Recq-mediated genome instability protein 1, C-terminal OB-fold | Q9H9A7 |
| PF16100 | RMI2 | RecQ-mediated genome instability protein 2 | Q96E14 |
| PF16124 | RecQ_Zn_bind | RecQ zinc-binding | O94762 |
| PF16179 | RHD_dimer | Rel homology dimerisation domain | Q00653 |
| PF16180 | RelB_leu_zip | RelB leucine zipper | |
| PF16181 | RelB_transactiv | RelB transactivation domain | |
| PF16199 | Radical_SAM_C | Radical_SAM C-terminal domain | Q9CZX0 |
| PF16205 | Ribosomal_S17_N | Ribosomal_S17 N-terminal | P0CX47 |
| PF16207 | RAWUL | RAWUL domain RING finger- and WD40-associated ubiquitin-like | Q9BSM1 |
| PF16294 | RSB_motif | RNSP1-SAP18 binding (RSB) motif | |
| PF16320 | Ribosomal_L12_N | Ribosomal protein L7/L12 dimerisation domain | P52815 |
| PF16321 | Ribosom_S30AE_C | Sigma 54 modulation/S30EA ribosomal protein C terminus | Q2G055 |
| PF16358 | RcsF | RcsF lipoprotein | P69411 |
| PF16359 | RcsD_ABL | RcsD-ABL domain | P39838 |
| PF16367 | RRM_7 | RNA recognition motif | Q8NE35 |
| PF16473 | Rv2179c-like | 3'-5' exoribonuclease Rv2179c-like domain | A0A045JQ63 |
| PF16512 | RhoGAP-FF1 | p190-A and -B Rho GAPs FF domain | Q9NRY4 |
| PF16524 | RisS_PPD | Periplasmic domain of Sensor histidine kinase RisS | Q3JRA3 |
| PF16550 | RPN13_C | UCH-binding domain | Q16186 |
| PF16611 | RGS12_us2 | Unstructured region between RBD and GoLoco | |
| PF16612 | RGS12_usC | C-terminal unstructured region of RGS12 | |
| PF16613 | RGS12_us1 | Unstructured region of RGS12 | |
| PF16614 | RhoGEF67_u2 | Unstructured region two on RhoGEF 6 and 7 | |
| PF16615 | RhoGEF67_u1 | Unstructured region one on RhoGEF 6 and 7 | |
| PF16658 | RF3_C | Class II release factor RF3, C-terminal domain | B2FR00 |
| PF16684 | ResT-TelK_cat | Telomere resolvase ResT/TelK catalytic domain | Q7CWV1 |
| PF16704 | Rab_bind | Rab binding domain | Q8IWJ2 |
| PF16717 | RAC_head | Ribosome-associated complex head domain | P32527 |
| PF16727 | REV1_C | DNA repair protein REV1 C-terminal domain | Q9UBZ9 |
| PF16745 | RsgA_N | RsgA N-terminal domain | Q9KX08 |
| PF16751 | RsdA_SigD_bd | Anti-sigma-D factor RsdA to sigma factor binding region | P9WJ71 |
| PF16762 | RHH_6 | Ribbon-helix-helix domain | Q8NL33 |
| PF16770 | RTT107_BRCT_5 | Regulator of Ty1 transposition protein 107 BRCT domain | P38850 |
| PF16771 | RTT107_BRCT_6 | Regulator of Ty1 transposition protein 107 BRCT domain | P38850 |
| PF16777 | RHH_7 | Transcriptional regulator, RHH-like, CopG | Q9ZLR7 |
| PF16786 | RecA_dep_nuc | Recombination enhancement, RecA-dependent nuclease | P35926 |
| PF16793 | RepB_primase | RepB DNA-primase N-terminal domain | Q52349 |
| PF16810 | RXLR | RXLR phytopathogen effector protein, Avirulence activity | G4ZLE6 |
| PF16842 | RRM_occluded | Occluded RNA-recognition motif | P49960 |
| PF16900 | REPA_OB_2 | Replication protein A OB domain | P27694 |
| PF16906 | Ribosomal_L26 | Ribosomal proteins L26 eukaryotic, L24P archaeal | U3PYE6 |
| PF16971 | RcpB | Rough colony protein B, tight adherence - tad - subunit | |
| PF16976 | RcpC | Flp pilus assembly protein RcpC/CpaB | |
| PF16992 | RNA_pol_RpbG | DNA-directed RNA polymerase, subunit G | Q4JAY4 |
| PF17066 | RITA | RBPJ-interacting and tubulin associated protein | |
| PF17067 | RPS31 | Ribosomal protein S31e | Q9SJU8 |
| PF17068 | RRG8 | Required for respiratory growth protein 8 mitochondrial | |
| PF17069 | RSRP | Arginine/Serine-Rich protein 1 | |
| PF17075 | RRT14 | Regular of rDNA transcription protein 14 | P40470 |
| PF17126 | RsmF_methylt_CI | RsmF rRNA methyltransferase first C-terminal domain | Q5SII2 |
| PF17135 | Ribosomal_L18 | Ribosomal protein 60S L18 and 50S L18e | Q10192 |
| PF17136 | ribosomal_L24 | Ribosomal proteins 50S L24/mitochondrial 39S L24 | A0A1X3KWX7 |
| PF17144 | Ribosomal_L5e | Ribosomal large subunit proteins 60S L5, and 50S L18 | P52822 |
| PF17184 | Rit1_C | Rit1 N-terminal domain | |
| PF17190 | RecG_N | RecG N-terminal helical domain | Q9WY48 |
| PF17191 | RecG_wedge | RecG wedge domain | |
| PF17208 | RBR | RNA binding Region | |
| PF17215 | Rrp44_S1 | S1 domain | Q08162 |
| PF17216 | Rrp44_CSD1 | Rrp44-like cold shock domain | Q8IYB7 |
| PF17241 | Retrotran_gag_4 | Ty5 Gag N-terminal region | |
| PF17378 | REC104 | Meiotic recombination protein REC104 | |
| PF17460 | RP854 | Uncharacterized protein RP854 | |
| PF17542 | RP853 | Uncharacterized RP853 | |
| PF17650 | RACo_linker | RACo linker region | Q3ACS2 |
| PF17651 | Raco_middle | RACo middle region | Q3ACS2 |
| PF17659 | RADX | RPA-related protein RADX | |
| PF17716 | RIMC1 | RAB7A-interacting MON1-CCZ1 complex subunit 1 | |
| PF17720 | RLIG1 | RNA ligase 1 | |
| PF17723 | RHH_8 | Ribbon-Helix-Helix transcriptional regulator family | |
| PF17756 | RET_CLD1 | RET Cadherin like domain 1 | A8E7C6 |
| PF17768 | RecJ_OB | RecJ OB domain | D0EM60 |
| PF17770 | RNase_J_C | Ribonuclease J C-terminal domain | P9WGZ9 |
| PF17777 | RL10P_insert | Insertion domain in 60S ribosomal protein L10P | Q9USZ6 |
| PF17781 | RPN1_RPN2_N | RPN1 N-terminal domain | Q13200 |
| PF17797 | RL | RL domain | F1NBW0 |
| PF17799 | RRM_Rrp7 | Rrp7 RRM-like N-terminal domain | P25368 |
| PF17812 | RET_CLD3 | RET Cadherin like domain 3 | A8E7C6 |
| PF17813 | RET_CLD4 | RET Cadherin like domain 4 | A8E7C6 |
| PF17875 | RPA43_OB | RPA43 OB domain in RNA Pol I | Q3B726 |
| PF17917 | RT_RNaseH | RNase H-like domain found in reverse transcriptase | P03355 |
| PF17919 | RT_RNaseH_2 | RNase H-like domain found in reverse transcriptase | Q99315 |
| PF17946 | RecC_C | RecC C-terminal domain | P07648 |
| PF17975 | RNR_Alpha | Ribonucleotide reductase alpha domain | Q59490 |
| PF18004 | RPN2_C | 26S proteasome regulatory subunit RPN2 C-terminal domain | Q99460 |
| PF18007 | Rv3651-like_N | Rv3651-like, N-terminal | I6YCP0 |
| PF18030 | Rimk_N | RimK PreATP-grasp domain | Q88AZ9 |
| PF18051 | RPN1_C | 26S proteasome non-ATPase regulatory subunit RPN1 C-terminal | Q13200 |
| PF18052 | Rx_N | Rx N-terminal domain | S5ABD6 |
| PF18055 | RPN6_N | 26S proteasome regulatory subunit RPN6 N-terminal domain | O00231 |
| PF18062 | RE_AspBHI_N | Restriction endonuclease AspBHI N-terminal | Q5ZW53 |
| PF18087 | RuBisCo_chap_C | Rubisco Assembly chaperone C-terminal domain | Q8YLP6 |
| PF18098 | RPN5_C | 26S proteasome regulatory subunit RPN5 C-terminal domain | O00232 |
| PF18106 | Rol_Rep_N | Rolling Circle replication initiation protein N-terminal domain | |
| PF18111 | RPGR1_C | Retinitis pigmentosa G-protein regulator interacting C-terminal | Q96KN7 |
| PF18113 | Rbx_binding | Rubredoxin binding C-terminal domain | Q9HTK9 |
| PF18119 | RIG-I_C | RIG-I receptor C-terminal domain | O95786 |
| PF18125 | RlmM_FDX | RlmM ferredoxin-like domain | P0ADR6 |
| PF18148 | RGS_DHEX | Regulator of G-protein signalling DHEX domain | P49802 |
| PF18187 | RIF5_SNase_1 | TbRIF5 SNase domain 1 | |
| PF18189 | RIF5_SNase_2 | TbRIF5 SNase domain 2 | |
| PF18215 | Rtt106_N | Histone chaperone Rtt106 N-terminal domain | P40161 |
| PF18248 | RalF_SCD | RalF C-terminal Sec-7 capping domain | Q8RT31 |
| PF18261 | Rpn9_C | Rpn9 C-terminal helix | Q04062 |
| PF18267 | Rubredoxin_C | Rubredoxin NAD+ reductase C-terminal domain | Q8WU10 |
| PF18278 | RANK_CRD_2 | Receptor activator of the NF-KB cysteine-rich repeat domain 2 | O35305 |
| PF18282 | RAP80_UIM | RAP80 N-terminal ubiquitin interaction motif | Q5U5Q9 |
| PF18299 | R2K_2 | ATP-grasp domain, R2K clade family 2 | |
| PF18311 | Rrp40_N | Exosome complex exonuclease Rrp40 N-terminal domain | Q08285 |
| PF18326 | RFX5_N | RFX5 N-terminal domain | P48382 |
| PF18367 | Rv2175c_C | Rv2175c C-terminal domain of unknown function | O53509 |
| PF18370 | RGI_lyase | Rhamnogalacturonan I lyases beta-sheet domain | Q65KY4 |
| PF18386 | ROQ_II | Roquin II domain | Q4VGL6 |
| PF18431 | RNAse_A_bac | Bacterial CdiA-CT RNAse A domain | |
| PF18444 | RRM_9 | RNA recognition motif | Q99257 |
| PF18465 | Rieske_3 | Rieske 3Fe-4S | Q6VAL8 |
| PF18471 | Ribosomal_L27_C | Ribosomal L27 protein C-terminal domain | P12687 |
| PF18497 | RNase_3_N | Ribonuclease III N-terminal domain | Q02555 |
| PF18501 | REC1 | Alpha helical recognition lobe domain | A0A182DWE3 |
| PF18503 | RPN6_C_helix | 26S proteasome subunit RPN6 C-terminal helix domain | O00231 |
| PF18506 | RelB-like | RelB Antitoxin | P0CL56 |
| PF18515 | Rh5 | Rh5 coiled-coil domain | Q8IFM5 |
| PF18516 | RuvC_1 | RuvC nuclease domain | A0A182DWE3 |
| PF18528 | Ret2_MD | RNA editing 3' terminal uridylyl transferase 2 middle domain | Q86MV5 |
| PF18541 | RuvC_III | RuvC endonuclease subdomain 3 | C9X1G5 |
| PF18561 | Regnase_1_C | Endoribonuclease Regnase 1/ ZC3H12 C-terminal domain | Q5D1E7 |
| PF18578 | Raf1_N | Rubisco accumulation factor 1 alpha helical domain | Q8YLP6 |
| PF18579 | Raf1_HTH | Rubisco accumulation factor 1 helix turn helix domain | Q8YLP6 |
| PF18602 | Rap1a | Rap1a immunity proteins | A0A083ZID3 |
| PF18614 | RNase_II_C_S1 | RNase II-type exonuclease C-terminal S1 domain | Q9RYD0 |
| PF18621 | Rv3651-like_middle | Rv3651-like, middle domain | I6YCP0 |
| PF18634 | RXLR_WY | RXLR phytopathogen effector protein WY-domain | D0NBE6 |
| PF18643 | RE_BsaWI | BsaWI restriction endonuclease type 2 | Q9KHV6 |
| PF18755 | RAMA | Restriction Enzyme Adenine Methylase Associated | Q3TV65 |
| PF18768 | RNPP_C | RNPP family C-terminal domain | Q45782 |
| PF18801 | RapH_N | response regulator aspartate phosphatase H, N terminal | E9RIY6 |
| PF18957 | RibLong | Long Rib domain | Q5FIM8 |
| PF18993 | Rv0078B | Rv0078B-related antitoxin | |
| PF19034 | RnlA-toxin_DBD | RNase LS, bacterial toxin DBD domain | P52129 |
| PF19192 | Response_reg_2 | Response receiver domain | |
| PF19198 | RsaA_NTD | RsaA N-terminal domain | A0A0H3C8J1 |
| PF19238 | Radical_SAM_2 | Radical SAM-like domain | |
| PF19296 | RelA_AH_RIS | RelA/SpoT, AH and RIS domains | O54408 |
| PF19322 | RKP_N | E3 ubiquitin-protein ligase RKP N-terminus | |
| PF19325 | RNF152_C | E3 ubiquitin-protein ligase RNF152 C-terminus | |
| PF19332 | RNF180_C | E3 ubiquitin-protein ligase RNF180 C-terminus | |
| PF19402 | RamS | Lanthionine-containing peptide SapB precursor RamS | |
| PF19417 | RnlA_toxin_N | RNase LS, bacterial toxin N-terminal | P52129 |
| PF19432 | RME-8_N | DNAJ protein RME-8 N-terminal | |
| PF19518 | RhoGAP_pG1_pG2 | p190RhoGAP, pG1 and pG2 domains | |
| PF19533 | Rab3-GAP_cat_C | Rab3 GTPase-activating protein catalytic subunit C-terminal | |
| PF19725 | RPC5_C | DNA-directed RNA polymerase III subunit RPC5 C-terminal | Q9NVU0 |
| PF19778 | RE_endonuc | Endonuclease domain | Q5ZND2 |
| PF19833 | RecG_dom3_C | ATP-dependent DNA helicase RecG, domain 3, C-terminal | Q9WY48 |
| PF19839 | RHH_9 | Ribbon-helix-helix protein | |
| PF19864 | Radical_SAM_N2 | Radical SAM proteins, N-terminal | |
| PF20199 | RepSA | Replication initiator protein, pSAM2 | |
| PF20381 | Rv1476 | Membrane protein Rv1476 | |
| PF20401 | Rhomboid_2 | Rhomboid-like protein | |
| PF20412 | RALGAPB_N | RALGAPB N-terminal domain | |
| PF20445 | RHS_N | Retrotransposon hot spot proteins N-terminal | |
| PF20514 | ROXA-like_wH | ROXA-like winged helix | P27431 |
| PF20639 | Rrn6_K-rich | RRN6, K-rich C-terminal domain | |
| PF20640 | Rrn6_HB | Rrn6, helical bundle domain | |
| PF20644 | Rrn7_cyclin_N | Rrn7/TAF1B, N-terminal cyclin domain | |
| PF20645 | Rrn7_cyclin_C | Rrn7/TAF1B, C-terminal cyclin domain | |
| PF20731 | RE_NgoFVII_C | NgoFVII C-terminal B3-like DNA-binding domain | |
| PF20748 | RecJ_C_Deinoc | RecJ C-terminal domain, Deinococci | |
| PF20833 | RNase_E_G_Thio | RNase E/G, Thioredoxin-like domain | |
| PF20842 | Rax2_2 | Rax2 second domain | |
| PF20843 | Rax2_3 | Rax2 third domain | |
| PF20859 | RHA1_ro05818_N | Hypothetical protein RHA1_ro05818, N-terminal helical domain | |
| PF20874 | Relaxase_M | Relaxase central domain | |
| PF20878 | REST_helical | Helical region in REST corepressor | |
| PF20912 | RPC3_helical | DNA-directed RNA polymerase III subunit RPC3, helical hairpin domain | |
| PF20924 | RLIP76_Ral-bd | RLIP76, Ral binding domain | |
| PF20945 | RMP1 | Ribonuclease MRP protein subunit RMP1 | |
| PF21000 | RMI1_N_N | RMI1, N-terminal helical domain | |
| PF21016 | RlmN_N | Ribosomal RNA large subunit methyltransferase N-terminal domain | |
| PF21022 | Rap-GAP_dimer | Rap/Ran-GAP protein dimerization domain | |
| PF21029 | RMC1_N | Regulator of MON1-CCZ1 complex, N-terminal | |
| PF21033 | RMD1-3 | Regulator of microtubule dynamics protein 1-3 | |
| PF21043 | Rv3651-like_C | Rv3651-like, C-terminal domain | |
| PF21046 | Rad26-like_C | Rad26-like, C-terminal domain | |
| PF21048 | Rad26-like_N | Rad26-like, N-terminal domain | |
| PF21054 | RUBC_PIKBD | Rubicon, PI3K-binding domain | |
| PF21096 | RecA_C | RecA C-terminal domain | |
| PF21119 | RYDR_Jsol | Ryanodine receptor junctional solenoid repeat | |
| PF21154 | RPN7_PSMD6_C | 26S proteasome regulatory subunit RPN7/PSMD6 C-terminal helix | |
| PF21175 | RecR_C | RecR, C-terminal | |
| PF21176 | RecR_HhH | RecR, helix-hairpin-helix | |
| PF21185 | RecD_N | RecBCD enzyme subunit RecD, N-terminal domain | |
| PF21205 | Rep3_C | Initiator Rep protein, WH2 | |
| PF21206 | Roquin_1_2-like_ROQ | Roquin 1/2-like, ROQ domain | |
| PF21210 | RNA_helicase_helical | Putative ATP-dependent RNA helicase, helical bundle | |
| PF21220 | RecQ-1-like_HTH | RecQ-1-like, helix-turn-helix domain | |
| PF21228 | RuBisCO_activase_AAA_helical | Ribulose bisphosphate carboxylase/oxygenase activase, AAA, helical | |
| PF21233 | RIOX1_C_WH | Ribosomal oxygenase 1, C-terminal winged helix domain | |
| PF21239 | RLMM_N | Ribosomal RNA large subunit methyltransferase M, N-terminal | |
| PF21251 | Ribosomal_uS5m_N | Small ribosomal subunit protein uS5m, N-terminal | |
| PF21259 | Rgg_C | HTH-type transcriptional regulator Rgg, C-terminal domain | |
| PF21261 | RRP40_N_mamm | Mammalian exosome complex component RRP40, N-terminal | |
| PF21262 | RRP40_S1 | Exosome complex component RRP40, S1 domain | |
| PF21266 | RRP4_S1 | RRP4, S1 domain | |
| PF21274 | Rng_hyd_C | Aromatic-ring hydroxylase, C-terminal | |
| PF21293 | RNAseD_HRDC_C | Ribonuclease D, C-terminal HRDC domain | |
| PF21348 | RGL11_C | Rhamnogalacturonan lyase family 11, C-terminal domain | |
| PF21349 | RUBY_RBDX | Rubrerythrin, rubredoxin-like domain | |
| PF21411 | Rap1_C_Sp | S. pombe DNA-binding protein Rap1, C-terminal | |
| PF21419 | RoxA-like_Cyt-c | RoxA-like, cytochrome c-like | |
| PF21449 | RIF2_ASCE | RIF2, ASCE domain | |
| PF21450 | RIF2_lid | RIF2, AAA+ lid domain | |
| PF21471 | Reelin_subrepeat-B | Reelin subrepeat B | |
| PF21505 | RPN2_N | 26S proteasome subunit RPN2, N-terminal domain | |
| PF21531 | Rv2175c_wHTH | DNA-binding protein Rv2175c, wHTH domain | |
| PF21534 | Rost | Protein rolling stone | |
| PF21557 | RhaB_D2 | Alpha-L-rhamnosidase, domain D2 | |
| PF21559 | Reb1_MybAD | DNA-binding protein reb1, Myb-associated domain | |
| PF21668 | RPOC_hybrid | DNA-directed RNA polymerase subunit beta', hybrid domain | |
| PF21712 | RASSF8-10_RA | Ras association domain-containing protein 8/10, RA domain | |
| PF21735 | RtxA_C | C-terminal repeat from RTX toxins | |
| PF21736 | REC102 | REC102 protein | |
| PF21761 | RedAm-like_C | NADPH-dependent reductive aminase-like, C-terminal domain | |
| PF21794 | RAD51D_N | RAD51D, N-terminal domain | |
| PF21811 | RdfA | Rod-determining factor A | |
| PF21859 | Replitron_HUH | Replitron, HUH endonuclease domain | |
| PF21860 | Replitron_C | Replitron, C-terminal domain | |
| PF21861 | RepB_C | Replication protein RepB, C-terminal | |
| PF21887 | RhiE_B | RhiE branching domain | |
| PF21960 | RCF1-5-like_lid | RCF1/5-like, AAA+ ATPase lid domain | |
| PF21981 | RecX_HTH3 | RecX, third three-helix domain | |
| PF21982 | RecX_HTH1 | RecX, first three-helix domain | |
| PF21989 | RA_2 | RA like domain | |
| PF21995 | RNR-II_ins_dom | B12-dependent ribonucleotide reductase, insertion domain | |
| PF22020 | RlmL_1st | RlmL ferredoxin-like domain | |
| PF22021 | RbmA-like_FnIII | RbmA-like, FnIII domain | |
| PF22047 | RecJ_C | Single-stranded-DNA-specific exonuclease RecJ C-terminal domain | |
| PF22078 | Ribosomal_bL9m_C | Large ribosomal subunit protein bL9m C-terminal domain | |
| PF22179 | RickCE_cat | RickCE-like, catalytic domain | |
| PF22180 | RH3_dom | RH3 domain | |
| PF22189 | RickCE_N | RickCE N-terminal | |
| PF22225 | RavZ_C | RavZ C-terminal PI3P-binding domain | |
| PF22234 | Rv2466c-like | Mycothiol-dependent nitroreductase Rv2466c | |
| PF22238 | RIP_P131-like | RIP/P131 family | |
| PF22286 | RHG20_PH | Rho GTPase-activating protein 20, PH domain | |
| PF22330 | Rib_mS39_PPR | Small ribosomal subunit protein mS39, PPR | |
| PF22336 | RhiE-like_linker | RhiE-like, KS-MAT linker domain | |
| PF22448 | RepB_primase_C | RepB DNA-primase C-terminal helical domain | |
| PF22458 | RsmF-B_ferredox | Methyltr_RsmF/B-like, ferredoxin-like domain | |
| PF22469 | RavJ_Peptidase | RavJ, Peptidase domain | |
| PF22477 | RepD-like_N | Replication initiation protein, N-terminal | |
| PF22505 | RNase_J_b_CASP | Ribonuclease J, beta-CASP domain | |
| PF22534 | RFC_C | Replication factor C subunit 3, C-terminal domain | |
| PF22540 | RET_CRD | RET, Cysteine Rich Domain | |
| PF22543 | Rieske_4 | Soluble Rieske-type ferredoxin | |
| PF22558 | REase-ARP | Restriction Endonuclease associating with ARP | |
| PF22601 | RIM2a_ZnF | RIM2-alpha zinc finger | |
| PF22603 | RAE1_2_domI_C | RAE1/2 domain I, C-terminal region | |
| PF22618 | RskA_N | Anti-sigma-K factor RskA, N-terminal domain | |
| PF22660 | RS_preATP-grasp-like | Ribonucleotide synthetase preATP-grasp domain | |
| PF22682 | Ribosomal_uL24m-like | Large ribosomal subunit protein uL24m | |
| PF22802 | RsiG | RsiG-like | |
| PF22808 | RhopH3_C | RhopH3 C-terminal domain | |
| PF22877 | RRM_Thc1 | Thc1, RRM domain | |
| PF22935 | RM44_endonuclase | Large ribosomal subunit protein mL44, endonuclease domain | |
| PF22961 | RECK-like_N | Reversion-inducing cysteine-rich with Kazal motifs, N-terminal | |
| PF22968 | RNF34L-like_3rd | E3 ubiquitin-protein ligase rififylin-like domain | |
| PF22976 | RRM_10 | RRM domain | |
| PF22981 | RM2_Med14 | Mediator of RNA polymerase II transcription subunit 14, RM2 | |
| PF22983 | RM8_Med14 | Mediator of RNA polymerase II transcription subunit 14, RM8 | |
| PF22984 | RM6_Med14 | Mediator of RNA polymerase II transcription subunit 14, RM6 | |
| PF22994 | RSC4_Ig_like | RSC4 Ig-like domain | |
| PF23010 | RA_3 | PHLPP protein RA domain | |
| PF23016 | RsmI_C | RsmI C-terminal HTH domain | |
| PF23057 | RBD_ZCCHC3_1st | ZCCHC3, first RNA-binding domain | |
| PF23058 | RBD_ZCCHC3_2nd | ZCCHC3, second RNA-binding domain | |
| PF23085 | RRM_PARP14_3 | PARP14, third RRM domain | |
| PF23222 | RRM_PARP14_1 | PAR14-like, first RRM domain | |
| PF23245 | RRM_PARP14_2 | PARP14, second RRM domain | |
| PF23268 | RIN1 | RIN1-like domain | |
| PF23321 | R1_ABCA1 | ABCA1-like, C-terminal R1 regulatory domain | |
| PF23343 | REP_ORF2-G2P | Replication-associated protein ORF2/G2P | |
| PF23348 | RDM3_C | RDM3 beta-solenoid | |
| PF23436 | RabGap-TBC_2 | RabGAP TBC domain | |
| PF23566 | RTG2_C | RTG2 C-terminal domain | |
| PF23594 | RPN11_C | 26S proteasome regulatory subunit RPN11 C-terminal domain | |
| PF23666 | Rcc01698_C | Host specificity protein-like, C-terminal | |
| PF23674 | RYYR-CCHC | RYYR-CCHC domain | |
| PF23705 | RxLR_effector | RxLR effector | |
| PF23706 | Rv1893 | Rv1893-like | |
| PF23714 | Rv3627c_N | Carboxypeptidase Rv3627c-like, N-terminal domain | |
| PF23750 | RsgI_M | Anti-sigma factor RsgI-like central domain | |
| PF23807 | RHH_10 | Ribbon-helix-helix protein | |
| PF23860 | Ribophorin_II_3rd | Ribophorin II third domain | |
| PF23861 | Ribophorin_II_2nd | Ribophorin II second domain | |
| PF24065 | REV3_N | DNA polymerase zeta catalytic subunit, N-terminal | |
| PF24099 | RBD_DGKtheta | Diacylglycerol kinase theta, RNA-binding domain-like | |
| PF24162 | RUS6_N | Protein root UVB sensitive 6, N-terminal | |
| PF24235 | RHG29_45_N | Rho GTPase-activating protein 29/45 N-terminal | |
| PF24435 | RRM_NFXL1 | NFXL1 RRM-like domain | |
| PF24447 | RE_BanI | Type II restriction enzyme BanI | |
| PF24456 | RHD_RETREG1-3 | RETREG1-3/ARL6IP-like, N-terminal reticulon-homology domain | |
| PF24475 | RBD_DEAH11 | DEAH11-like, RNA-binding domain | |
| PF24504 | Rod_N | Rod, N-terminal | |
| PF24553 | Rv0428c_C | Probable histone acetyltransferase Rv0428c C-terminal | |
| PF24572 | RBD_RDR6 | RNA-dependent RNA polymerase 6, RNA-binding domain | |
| PF24577 | RDR6_2nd | RNA-dependent RNA polymerase 6 second domain | |
| PF24600 | RavZ_cat | RavZ catalytic domain | |
| PF24637 | RRM_DEAH11 | DEAH11 RRM domain | |
| PF24764 | rva_4 | Integrase core domain | |
| PF24785 | RXYLT1_C | RXYLT1 C-terminal domain | |
| PF24786 | RXYLT1_N | RXYLT1 N-terminal domain | |
| PF24810 | RBD_LARS1 | Leucine--tRNA ligase, RagD-binding domain | |
| PF24833 | Rhabdo_glycop_CD | Rhabdovirus spike glycoprotein G central domain | |