| 2OG-FeII_Oxy | PF03171 | 2OG-Fe(II) oxygenase superfamily | 2 | 2 |
| 2OG-FeII_Oxy_2 | PF13532 | 2OG-Fe(II) oxygenase superfamily | 45 | 45 |
| 2OG-FeII_Oxy_3 | PF13640 | 2OG-Fe(II) oxygenase superfamily | 1 | 1 |
| 5_3_exonuc | PF01367 | 5'-3' exonuclease, C-terminal SAM fold | 7 | 6 |
| 5_3_exonuc_N | PF02739 | 5'-3' exonuclease, N-terminal resolvase-like domain | 8 | 5 |
| 7kD_DNA_binding | PF02294 | 7kD DNA-binding domain | 26 | 19 |
| AAA | PF00004 | ATPase family associated with various cellular activities (AAA) | 53 | 49 |
| AAA_12 | PF13087 | AAA domain | 2 | 2 |
| AAA_14 | PF13173 | AAA domain | 1 | 1 |
| AAA_16 | PF13191 | AAA ATPase domain | 19 | 20 |
| AAA_19 | PF13245 | AAA domain | 6 | 6 |
| AAA_22 | PF13401 | AAA domain | 17 | 17 |
| AAA_23 | PF13476 | AAA domain | 9 | 9 |
| AAA_25 | PF13481 | AAA domain | 1 | 1 |
| AAA_29 | PF13555 | P-loop containing region of AAA domain | 2 | 2 |
| AAA_30 | PF13604 | AAA domain | 19 | 17 |
| AAA_31 | PF13614 | AAA domain | 5 | 2 |
| AAA_33 | PF13671 | AAA domain | 11 | 7 |
| ABC_tran | PF00005 | ABC transporter | 1 | 1 |
| AFT | PF08731 | Transcription factor AFT | 1 | 1 |
| AGOG | PF09171 | N-glycosylase/DNA lyase | 5 | 5 |
| AGT | PF11440 | DNA alpha-glucosyltransferase | 4 | 4 |
| AHSA1 | PF08327 | Activator of Hsp90 ATPase homolog 1-like protein | 1 | 1 |
| ANATO | PF01821 | Anaphylotoxin-like domain | 2 | 2 |
| AP2 | PF00847 | AP2 domain | 6 | 6 |
| APOBEC2 | PF18772 | APOBEC2 | 4 | 4 |
| AP_endonuc_2 | PF01261 | Xylose isomerase-like TIM barrel | 6 | 6 |
| ARID | PF01388 | ARID/BRIGHT DNA binding domain | 8 | 3 |
| ASXH | PF13919 | Asx homology domain | 1 | 1 |
| ATP-synt_ab | PF00006 | ATP synthase alpha/beta family, nucleotide-binding domain | 14 | 1 |
| Actin | PF00022 | Actin | 22 | 7 |
| Ada_Zn_binding | PF02805 | Metal binding domain of Ada | 2 | 2 |
| Adenine_glyco | PF03352 | Methyladenine glycosylase | 1 | 1 |
| Ago_PAZ | PF18309 | Argonaute PAZ domain | 23 | 21 |
| AlbA_2 | PF04326 | Putative DNA-binding domain | 2 | 1 |
| Amino_oxidase | PF01593 | Flavin containing amine oxidoreductase | 3 | 2 |
| Aminotran_1_2 | PF00155 | Aminotransferase class I and II | 4 | 4 |
| Ank_2 | PF12796 | Ankyrin repeats (3 copies) | 8 | 1 |
| Annexin | PF00191 | Annexin | 2 | 2 |
| Antiterm | PF03589 | Antitermination protein | 3 | 3 |
| AraR_C | PF19368 | AraR C-terminal winged HTH domain | 3 | 3 |
| Arb2 | PF09757 | Arb2 domain | 1 | 1 |
| Arc | PF03869 | Arc-like DNA binding domain | 6 | 6 |
| Arg_repressor | PF01316 | Arginine repressor, DNA binding domain | 5 | 5 |
| Arm-DNA-bind_1 | PF09003 | Bacteriophage lambda integrase, Arm DNA-binding domain | 4 | 3 |
| ArsC | PF03960 | ArsC family | 1 | 1 |
| AsiA | PF09010 | Anti-Sigma Factor A | 1 | 1 |
| B-block_TFIIIC | PF04182 | B-block binding subunit of TFIIIC | 3 | 3 |
| B3 | PF02362 | B3 DNA binding domain | 11 | 11 |
| BAF | PF02961 | Barrier to autointegration factor | 1 | 1 |
| BEN | PF10523 | BEN domain | 10 | 10 |
| BES1_N | PF05687 | BES1/BZR1 plant transcription factor, N-terminal | 8 | 8 |
| BET | PF17035 | Bromodomain extra-terminal - transcription regulation | 1 | 1 |
| BHD_1 | PF10403 | Rad4 beta-hairpin domain 1 | 16 | 13 |
| BHD_2 | PF10404 | Rad4 beta-hairpin domain 2 | 16 | 13 |
| BHD_3 | PF10405 | Rad4 beta-hairpin domain 3 | 16 | 13 |
| BRCA-2_OB3 | PF09104 | BRCA2, oligonucleotide/oligosaccharide-binding, domain 3 | 1 | 1 |
| BRCT | PF00533 | BRCA1 C Terminus (BRCT) domain | 33 | 9 |
| BRF1 | PF07741 | Brf1-like TBP-binding domain | 12 | 2 |
| BTD | PF09270 | Beta-trefoil DNA-binding domain | 17 | 15 |
| Bac_DNA_binding | PF00216 | Bacterial DNA-binding protein | 24 | 18 |
| Bac_DnaA | PF00308 | Bacterial dnaA protein | 1 | 1 |
| Bac_DnaA_C | PF08299 | Bacterial dnaA protein helix-turn-helix | 5 | 4 |
| Baculo_LEF-3 | PF05847 | Nucleopolyhedrovirus late expression factor 3 (LEF-3) | 2 | 2 |
| BamHI | PF02923 | Restriction endonuclease BamHI | 5 | 5 |
| BfiI_DBD | PF18243 | Metal-independent restriction enzyme BfiI DNA binding domain | 1 | 1 |
| BpuJI_N | PF11564 | Restriction endonuclease BpuJI - N terminal | 4 | 4 |
| BrkDBD | PF09607 | Brinker DNA-binding domain | 1 | 1 |
| Bromodomain | PF00439 | Bromodomain | 34 | 9 |
| Bse634I | PF07832 | Cfr10I/Bse634I restriction endonuclease | 13 | 13 |
| Bunya_nucleocap | PF00952 | Bunyavirus nucleocapsid (N) protein | 1 | 1 |
| C1_4 | PF07975 | TFIIH C1-like domain | 52 | 1 |
| C2-set_2 | PF08205 | CD80-like C2-set immunoglobulin domain | 2 | 2 |
| CBFB_NFYA | PF02045 | CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B | 9 | 8 |
| CBFD_NFYB_HMF | PF00808 | Histone-like transcription factor (CBF/NF-Y) and archaeal histone | 18 | 18 |
| CCT | PF06203 | CCT motif | 3 | 3 |
| CENP-B_N | PF04218 | CENP-B N-terminal DNA-binding domain | 1 | 1 |
| CENP-I | PF07778 | Mis6 | 6 | 1 |
| CENP-L | PF13092 | Kinetochore complex Sim4 subunit Fta1 | 6 | 6 |
| CENP-N | PF05238 | Kinetochore protein CHL4 like | 14 | 14 |
| CENP-S | PF15630 | CENP-S protein | 5 | 2 |
| CENP-T_C | PF15511 | Centromere kinetochore component CENP-T histone fold | 7 | 6 |
| CENP-W | PF15510 | CENP-W protein | 3 | 3 |
| CENP-X | PF09415 | CENP-S associating Centromere protein X | 5 | 2 |
| COE1_DBD | PF16422 | Transcription factor COE1 DNA-binding domain | 3 | 3 |
| CP2 | PF04516 | CP2 transcription factor | 1 | 1 |
| CPL | PF08144 | CPL (NUC119) domain | 1 | 1 |
| CR6_interact | PF10147 | Growth arrest and DNA-damage-inducible proteins-interacting protein 1 | 2 | 1 |
| CRISPR_Cas2 | PF09827 | CRISPR associated protein Cas2 | 17 | 15 |
| CRISPR_Cas9_WED | PF18061 | CRISPR-Cas9 WED domain | 12 | 12 |
| CRISPR_Cse1 | PF09481 | CRISPR-associated protein Cse1 (CRISPR_cse1) | 6 | 6 |
| CRISPR_Cse2 | PF09485 | CRISPR-associated protein Cse2 (CRISPR_cse2) | 6 | 5 |
| CRISPR_assoc | PF08798 | CRISPR associated protein | 7 | 3 |
| CSD | PF00313 | 'Cold-shock' DNA-binding domain | 5 | 5 |
| CTC1 | PF15489 | CST, telomere maintenance, complex subunit CTC1 | 5 | 4 |
| CUT | PF02376 | CUT domain | 4 | 4 |
| C_LFY_FLO | PF17538 | DNA Binding Domain (C-terminal) Leafy/Floricaula | 3 | 3 |
| CarD_CdnL_TRCF | PF02559 | CarD-like/TRCF domain | 23 | 18 |
| Cas3_C | PF18395 | Cas3 C-terminal domain | 5 | 5 |
| Cas5fv_helical | PF20158 | Cas5fv helical domain | 1 | 1 |
| Cas6b_C | PF17262 | Cas6b C-terminal domain | 1 | 1 |
| Cas6b_N | PF17955 | Cas6b N-terminal domain | 1 | 1 |
| Cas9-BH | PF16593 | Bridge helix of CRISPR-associated endonuclease Cas9 | 65 | 57 |
| Cas9_C | PF18525 | Cas9 C-terminal domain | 3 | 3 |
| Cas9_PI | PF16595 | PAM-interacting domain of CRISPR-associated endonuclease Cas9 | 65 | 65 |
| Cas9_PI2 | PF18070 | CRISPR-Cas9 PI domain | 13 | 11 |
| Cas9_REC | PF16592 | REC lobe of CRISPR-associated endonuclease Cas9 | 77 | 77 |
| Cas9_Topo | PF17894 | Topo homolgy domain in CRISPR-associated endonuclease Cas9 | 3 | 3 |
| Cas9_a | PF18470 | Cas9 alpha-helical lobe domain | 12 | 11 |
| Cas9_b_hairpin | PF17893 | CRISPR-associated endonuclease Cas9 beta-hairpin domain | 3 | 3 |
| Cas_CT1975 | PF09344 | CT1975-like protein | 6 | 6 |
| Cas_Cas1 | PF01867 | CRISPR associated protein Cas1 | 30 | 27 |
| Cas_Cas2CT1978 | PF09707 | CRISPR-associated protein (Cas_Cas2CT1978) | 16 | 16 |
| Cas_Cas4 | PF01930 | Domain of unknown function DUF83 | 11 | 10 |
| Cas_Cas5d | PF09704 | CRISPR-associated protein (Cas_Cas5) | 10 | 10 |
| Cas_Cas7 | PF05107 | CRISPR-associated protein Cas7 | 2 | 2 |
| Cas_Cmr3 | PF09700 | CRISPR-associated protein (Cas_Cmr3) | 1 | 1 |
| Cas_Cmr5 | PF09701 | CRISPR-associated protein (Cas_Cmr5) | 1 | 1 |
| Cas_Csa4 | PF09703 | CRISPR-associated protein (Cas_Csa4) | 2 | 2 |
| Cas_Csd1 | PF09709 | CRISPR-associated protein (Cas_Csd1) | 2 | 2 |
| Cas_Csn2 | PF09711 | CRISPR-associated protein (Cas_Csn2) | 3 | 3 |
| Cas_Csy1 | PF09611 | CRISPR-associated protein (Cas_Csy1) | 15 | 13 |
| Cas_Csy2 | PF09614 | CRISPR-associated protein (Cas_Csy2) | 15 | 11 |
| Cas_Csy3 | PF09615 | CRISPR-associated protein (Cas_Csy3) | 18 | 13 |
| Cas_Csy4 | PF09618 | CRISPR-associated protein (Cas_Csy4) | 17 | 1 |
| Cas_DxTHG | PF09455 | CRISPR-associated (Cas) DxTHG family | 1 | 1 |
| Cauli_VI | PF01693 | Caulimovirus viroplasmin | 1 | 1 |
| CcdA | PF07362 | Post-segregation antitoxin CcdA | 2 | 2 |
| Cdc13_OB2 | PF18691 | Cell division control protein 13, OB2 domain | 1 | 1 |
| Cdc6_C | PF09079 | CDC6, C terminal winged helix domain | 20 | 18 |
| Cdh1_DBD_1 | PF18196 | Chromodomain helicase DNA-binding domain 1 | 7 | 6 |
| Cep3 | PF16846 | Centromere DNA-binding protein complex CBF3 subunit B | 5 | 1 |
| Chordopox_A20R | PF05941 | Chordopoxvirus A20R protein | 2 | 1 |
| Chromo | PF00385 | Chromo (CHRromatin Organisation MOdifier) domain | 11 | 7 |
| Chromo_2 | PF18704 | Chromatin organization modifier domain 2 | 1 | 1 |
| Circo_capsid | PF02443 | Circovirus capsid protein | 2 | 2 |
| Cnd1 | PF12717 | non-SMC mitotic condensation complex subunit 1 | 4 | 4 |
| Cnd1_N | PF12922 | non-SMC mitotic condensation complex subunit 1, N-term | 3 | 3 |
| Cnd2 | PF05786 | Condensin complex subunit 2 | 8 | 8 |
| Cnd3 | PF12719 | Nuclear condensing complex subunits, C-term domain | 5 | 5 |
| CodY | PF06018 | CodY GAF-like domain | 2 | 1 |
| Cohesin_HEAT | PF12765 | HEAT repeat associated with sister chromatid cohesion | 5 | 5 |
| Couple_hipA | PF13657 | HipA N-terminal domain | 6 | 2 |
| Cren7 | PF11520 | Chromatin protein Cren7 | 13 | 13 |
| Cro | PF09048 | Cro | 3 | 3 |
| Csc2 | PF18320 | Csc2 Crispr | 1 | 1 |
| CtsR | PF05848 | CtsR N-terminal HTH domain | 1 | 1 |
| CtsR_C | PF17727 | CtsR C-terminal dimerization domain | 1 | 1 |
| Cytochrom_B_N_2 | PF13631 | Cytochrome b(N-terminal)/b6/petB | 3 | 3 |
| D5_N | PF08706 | D5 N terminal like | 2 | 2 |
| DBD_Tnp_Hermes | PF10683 | Hermes transposase DNA-binding domain | 5 | 5 |
| DBINO | PF13892 | DNA-binding domain | 11 | 2 |
| DDE_2 | PF02914 | Bacteriophage Mu transposase | 1 | 1 |
| DDE_Tnp_1 | PF01609 | Transposase DDE domain | 5 | 5 |
| DDE_Tnp_1_7 | PF13843 | Transposase IS4 | 2 | 2 |
| DDE_Tnp_Tn3 | PF01526 | Tn3 transposase DDE domain | 3 | 3 |
| DDHD | PF02862 | DDHD domain | 18 | 17 |
| DEAD | PF00270 | DEAD/DEAH box helicase | 48 | 38 |
| DEAD_2 | PF06733 | DEAD_2 | 56 | 2 |
| DEAD_assoc | PF08494 | DEAD/H associated | 1 | 1 |
| DHH | PF01368 | DHH family | 4 | 4 |
| DHHA1 | PF02272 | DHHA1 domain | 4 | 4 |
| DM | PF00751 | DM DNA binding domain | 1 | 1 |
| DNAPKcs_CC5 | PF19704 | DNA-PKcs, CC5 | 23 | 21 |
| DNAP_B_exo_N | PF08452 | DNA polymerase family B exonuclease domain, N-terminal | 1 | 1 |
| DNA_PPF | PF02916 | DNA polymerase processivity factor | 4 | 3 |
| DNA_alkylation | PF08713 | DNA alkylation repair enzyme | 24 | 24 |
| DNA_binding_1 | PF01035 | 6-O-methylguanine DNA methyltransferase, DNA binding domain | 12 | 12 |
| DNA_gyraseA_C | PF03989 | DNA gyrase C-terminal domain, beta-propeller | 8 | 1 |
| DNA_gyraseB | PF00204 | DNA gyrase B | 19 | 4 |
| DNA_gyraseB_C | PF00986 | DNA gyrase B subunit, carboxyl terminus | 70 | 69 |
| DNA_ligase_A_C | PF04679 | ATP dependent DNA ligase C terminal region | 33 | 21 |
| DNA_ligase_A_M | PF01068 | ATP dependent DNA ligase domain | 46 | 37 |
| DNA_ligase_A_N | PF04675 | DNA ligase N terminus | 33 | 24 |
| DNA_ligase_OB | PF03120 | NAD-dependent DNA ligase OB-fold domain | 2 | 2 |
| DNA_ligase_OB_2 | PF14743 | DNA ligase OB-like domain | 13 | 12 |
| DNA_ligase_ZBD | PF03119 | NAD-dependent DNA ligase C4 zinc finger domain | 2 | 2 |
| DNA_ligase_aden | PF01653 | NAD-dependent DNA ligase adenylation domain | 2 | 2 |
| DNA_methylase | PF00145 | C-5 cytosine-specific DNA methylase | 71 | 71 |
| DNA_mis_repair | PF01119 | DNA mismatch repair protein, C-terminal domain | 3 | 1 |
| DNA_photolyase | PF00875 | DNA photolyase | 13 | 13 |
| DNA_pol3_alpha | PF07733 | Bacterial DNA polymerase III alpha NTPase domain | 9 | 9 |
| DNA_pol3_beta | PF00712 | DNA polymerase III beta subunit, N-terminal domain | 4 | 4 |
| DNA_pol3_beta_2 | PF02767 | DNA polymerase III beta subunit, central domain | 4 | 4 |
| DNA_pol3_beta_3 | PF02768 | DNA polymerase III beta subunit, C-terminal domain | 4 | 1 |
| DNA_pol3_delt_C | PF14840 | Processivity clamp loader gamma complex DNA pol III C-term | 3 | 3 |
| DNA_pol3_delta | PF06144 | DNA polymerase III, delta subunit | 3 | 2 |
| DNA_pol3_delta2 | PF13177 | DNA polymerase III, delta subunit | 34 | 30 |
| DNA_pol3_finger | PF17657 | Bacterial DNA polymerase III alpha subunit finger domain | 9 | 8 |
| DNA_pol_A | PF00476 | DNA polymerase family A | 246 | 235 |
| DNA_pol_A_exo1 | PF01612 | 3'-5' exonuclease | 153 | 85 |
| DNA_pol_B | PF00136 | DNA polymerase family B | 208 | 184 |
| DNA_pol_B_2 | PF03175 | DNA polymerase type B, organellar and viral | 7 | 7 |
| DNA_pol_B_exo1 | PF03104 | DNA polymerase family B, exonuclease domain | 205 | 182 |
| DNA_pol_B_palm | PF14792 | DNA polymerase beta palm | 650 | 640 |
| DNA_pol_B_thumb | PF14791 | DNA polymerase beta thumb | 652 | 638 |
| DNA_pol_lambd_f | PF10391 | Fingers domain of DNA polymerase lambda | 644 | 635 |
| DNA_primase_S | PF01896 | DNA primase small subunit | 18 | 12 |
| DNA_primase_lrg | PF04104 | Eukaryotic and archaeal DNA primase, large subunit | 12 | 10 |
| DNA_processg_A | PF02481 | DNA recombination-mediator protein A | 1 | 1 |
| DNA_topoisoIV | PF00521 | DNA gyrase/topoisomerase IV, subunit A | 93 | 92 |
| DNApol3-delta_C | PF09115 | DNA polymerase III, delta subunit, C terminal | 3 | 3 |
| DNApol_Exo | PF18136 | DNA mitochondrial polymerase exonuclease domain | 16 | 9 |
| DOT1 | PF08123 | Histone methylation protein DOT1 | 13 | 3 |
| DRMBL | PF07522 | DNA repair metallo-beta-lactamase | 2 | 2 |
| DSHCT | PF08148 | DSHCT (NUC185) domain | 3 | 3 |
| DUF1706 | PF08020 | Protein of unknown function (DUF1706) | 1 | 1 |
| DUF1778 | PF08681 | Protein of unknown function (DUF1778) | 2 | 2 |
| DUF1870 | PF08965 | Domain of unknown function (DUF1870) | 1 | 1 |
| DUF1936 | PF09151 | Domain of unknown function (DUF1936) | 1 | 1 |
| DUF1998 | PF09369 | Domain of unknown function (DUF1998) | 3 | 3 |
| DUF2228 | PF10228 | Uncharacterised conserved protein (DUF2228) | 3 | 2 |
| DUF2258 | PF10015 | Uncharacterized protein conserved in archaea (DUF2258) | 1 | 1 |
| DUF2312 | PF10073 | Uncharacterized protein conserved in bacteria (DUF2312) | 2 | 2 |
| DUF2815 | PF10991 | Protein of unknown function (DUF2815) | 1 | 1 |
| DUF3378 | PF11858 | Domain of unknown function (DUF3378) | 1 | 1 |
| DUF3458 | PF11940 | Domain of unknown function (DUF3458) Ig-like fold | 16 | 7 |
| DUF3535 | PF12054 | Domain of unknown function (DUF3535) | 4 | 1 |
| DUF3591 | PF12157 | Protein of unknown function (DUF3591) | 16 | 11 |
| DUF3882 | PF07066 | Lactococcus phage M3 protein | 5 | 5 |
| DUF4152 | PF13680 | Protein of unknown function (DUF4152) | 5 | 5 |
| DUF4158 | PF13700 | Domain of unknown function (DUF4158) | 3 | 3 |
| DUF4918 | PF16265 | Domain of unknown function (DUF4918) | 3 | 3 |
| DUF5906 | PF19263 | Family of unknown function (DUF5906) | 2 | 1 |
| DUF6433 | PF20025 | Family of unknown function (DUF6433) | 5 | 5 |
| DUF659 | PF04937 | Protein of unknown function (DUF 659) | 5 | 5 |
| DUF790 | PF05626 | Protein of unknown function (DUF790) | 1 | 1 |
| DarT | PF14487 | ssDNA thymidine ADP-ribosyltransferase, DarT | 5 | 5 |
| DcpS_C | PF11969 | Scavenger mRNA decapping enzyme C-term binding | 10 | 10 |
| DdrB | PF12747 | DdrB-like protein | 2 | 2 |
| Denso_VP4 | PF02336 | Capsid protein VP4 | 1 | 1 |
| DevR | PF01905 | CRISPR-associated negative auto-regulator DevR/Csa2 | 2 | 2 |
| Dimer_Tnp_Tn5 | PF02281 | Transposase Tn5 dimerisation domain | 5 | 5 |
| Dimer_Tnp_hAT | PF05699 | hAT family C-terminal dimerisation region | 5 | 5 |
| Dna2 | PF08696 | DNA replication factor Dna2 | 2 | 2 |
| DnaB | PF00772 | DnaB-like helicase N terminal domain | 14 | 1 |
| DnaB_C | PF03796 | DnaB-like helicase C terminal domain | 23 | 22 |
| DnaJ_CXXCXGXG | PF00684 | DnaJ central domain | 1 | 1 |
| DnaT | PF17948 | DnaT DNA-binding domain | 2 | 2 |
| DpnI | PF06044 | Dam-replacing family | 2 | 1 |
| DpnI_C | PF17726 | Dam-replacing HTH domain | 2 | 2 |
| E2F_TDP | PF02319 | E2F/DP family winged-helix DNA-binding domain | 2 | 2 |
| EBV-NA1 | PF02905 | Epstein Barr virus nuclear antigen-1, DNA-binding domain | 6 | 6 |
| EF-hand_12 | PF17901 | EF-hand fold domain | 4 | 4 |
| EFG_C | PF00679 | Elongation factor G C-terminus | 3 | 1 |
| EFG_III | PF14492 | Elongation Factor G, domain III | 3 | 1 |
| EFG_IV | PF03764 | Elongation factor G, domain IV | 3 | 2 |
| EPL1 | PF10513 | Enhancer of polycomb-like | 2 | 1 |
| ERCC3_RAD25_C | PF16203 | ERCC3/RAD25/XPB C-terminal helicase | 55 | 52 |
| ERCC4 | PF02732 | ERCC4 domain | 7 | 5 |
| EVE | PF01878 | EVE domain | 1 | 1 |
| EXOSC1 | PF10447 | Exosome component EXOSC1/CSL4 | 2 | 2 |
| Eco57I | PF07669 | Eco57I restriction-modification methylase | 9 | 9 |
| EcoRI | PF02963 | Restriction endonuclease EcoRI | 7 | 7 |
| EcoRII-C | PF09019 | EcoRII C terminal | 4 | 4 |
| EcoRII-N | PF09217 | Restriction endonuclease EcoRII, N-terminal | 2 | 2 |
| Elf1 | PF05129 | Transcription elongation factor Elf1 like | 17 | 4 |
| EndIII_4Fe-2S | PF10576 | Iron-sulfur binding domain of endonuclease III | 21 | 20 |
| Endonuc-BglII | PF09195 | Restriction endonuclease BglII | 4 | 4 |
| Endonuc-BsobI | PF09194 | Restriction endonuclease BsobI | 1 | 1 |
| Endonuc-EcoRV | PF09233 | Restriction endonuclease EcoRV | 29 | 29 |
| Endonuc-FokI_C | PF09254 | Restriction endonuclease FokI, C terminal | 1 | 1 |
| Endonuc-HincII | PF09226 | Restriction endonuclease HincII | 18 | 18 |
| Endonuc-MspI | PF09208 | Restriction endonuclease MspI | 2 | 2 |
| Endonuc-PvuII | PF09225 | Restriction endonuclease PvuII | 5 | 5 |
| Endonuc-dimeris | PF09124 | T4 recombination endonuclease VII, dimerisation | 2 | 2 |
| Endonuc_BglI | PF14562 | Restriction endonuclease BglI | 1 | 1 |
| Endonuclease_1 | PF04231 | Endonuclease I | 2 | 2 |
| Endonuclease_5 | PF04493 | Endonuclease V | 17 | 17 |
| Endonuclease_7 | PF02945 | Recombination endonuclease VII | 4 | 4 |
| Endonuclease_NS | PF01223 | DNA/RNA non-specific endonuclease | 10 | 9 |
| Ets | PF00178 | Ets-domain | 70 | 70 |
| Ets1_N_flank | PF19525 | Ets1 N-terminal flanking region of Ets domain | 17 | 13 |
| Exc | PF07825 | Excisionase-like protein | 7 | 6 |
| Exo_endo_phos | PF03372 | Endonuclease/Exonuclease/phosphatase family | 81 | 81 |
| Exog_C | PF18026 | Endo/exonuclease (EXOG) C-terminal domain | 7 | 7 |
| Exonuc_V_gamma | PF04257 | Exodeoxyribonuclease V, gamma subunit | 18 | 13 |
| Exonuc_X-T_C | PF08411 | Exonuclease C-terminal | 6 | 6 |
| FAD_binding_7 | PF03441 | FAD binding domain of DNA photolyase | 13 | 13 |
| FANCI_HD1 | PF14679 | FANCI helical domain 1 | 12 | 10 |
| FANCI_S2 | PF14676 | FANCI solenoid 2 | 12 | 10 |
| FANCI_S3 | PF14677 | FANCI solenoid 3 | 12 | 8 |
| FANCI_S4 | PF14678 | FANCI solenoid 4 | 12 | 11 |
| FANC_SAP | PF18081 | Fanconi anemia-associated nuclease SAP domain | 5 | 5 |
| FTO_CTD | PF12934 | FTO C-terminal domain | 1 | 1 |
| FTO_NTD | PF12933 | FTO catalytic domain | 1 | 1 |
| FUR | PF01475 | Ferric uptake regulator family | 12 | 12 |
| FancD2 | PF14631 | Fanconi anaemia protein FancD2 nuclease | 12 | 11 |
| Fapy_DNA_glyco | PF01149 | Formamidopyrimidine-DNA glycosylase N-terminal domain | 104 | 103 |
| Fe_dep_repress | PF01325 | Iron dependent repressor, N-terminal DNA binding domain | 12 | 11 |
| FemAB | PF02388 | FemAB family | 4 | 4 |
| Flavi_DEAD | PF07652 | Flavivirus DEAD domain | 5 | 5 |
| FliT | PF05400 | Flagellar protein FliT | 1 | 1 |
| Flp_C | PF05202 | Recombinase Flp protein | 3 | 3 |
| Flp_N | PF03930 | Recombinase Flp protein N-terminus | 3 | 3 |
| Flu_NP | PF00506 | Influenza virus nucleoprotein | 2 | 2 |
| Flu_PA | PF00603 | Influenza RNA-dependent RNA polymerase subunit PA | 3 | 3 |
| FokI_C | PF02980 | Restriction endonuclease FokI, catalytic domain | 1 | 1 |
| FokI_N | PF02981 | Restriction endonuclease FokI, recognition domain | 1 | 1 |
| Forkhead | PF00250 | Forkhead domain | 39 | 39 |
| FtsK_SpoIIIE | PF01580 | FtsK/SpoIIIE family | 3 | 3 |
| FtsK_alpha | PF17854 | FtsK alpha domain | 3 | 3 |
| FtsK_gamma | PF09397 | Ftsk gamma domain | 1 | 1 |
| Furin-like | PF00757 | Furin-like cysteine rich region | 4 | 1 |
| GAGA | PF09237 | GAGA factor | 2 | 2 |
| GAS | PF13851 | Growth-arrest specific micro-tubule binding | 4 | 2 |
| GATA | PF00320 | GATA zinc finger | 17 | 16 |
| GCM | PF03615 | GCM motif protein | 1 | 1 |
| GEN1_C | PF18380 | Holliday junction resolvase Gen1 C-terminal domain | 5 | 1 |
| GFD1 | PF17331 | GFD1 mRNA transport factor | 2 | 2 |
| GIIM | PF08388 | Group II intron, maturase-specific domain | 6 | 6 |
| GIY-YIG | PF01541 | GIY-YIG catalytic domain | 2 | 2 |
| GTP_EFTU | PF00009 | Elongation factor Tu GTP binding domain | 3 | 1 |
| Gal4_dimer | PF03902 | Gal4-like dimerisation domain | 4 | 4 |
| GbpC | PF08363 | Glucan-binding protein C | 1 | 1 |
| GcrA | PF07750 | GcrA cell cycle regulator | 5 | 5 |
| Ge1_WD40 | PF16529 | WD40 region of Ge1, enhancer of mRNA-decapping protein | 2 | 2 |
| Gemini_AL1 | PF00799 | Geminivirus Rep catalytic domain | 4 | 4 |
| Gemini_coat | PF00844 | Geminivirus coat protein/nuclear export factor BR1 family | 1 | 1 |
| GerE | PF00196 | Bacterial regulatory proteins, luxR family | 16 | 16 |
| Glyco_transf_10 | PF00852 | Glycosyltransferase family 10 (fucosyltransferase) C-term | 3 | 3 |
| Glycos_transf_1 | PF00534 | Glycosyl transferases group 1 | 1 | 1 |
| GntR | PF00392 | Bacterial regulatory proteins, gntR family | 21 | 19 |
| Gti1_Pac2 | PF09729 | Gti1/Pac2 family | 3 | 3 |
| GyrI-like | PF06445 | GyrI-like small molecule binding domain | 23 | 2 |
| H2TH | PF06831 | Formamidopyrimidine-DNA glycosylase H2TH domain | 104 | 103 |
| HA2 | PF04408 | Helicase associated domain (HA2) | 12 | 12 |
| HAND | PF09110 | HAND | 4 | 1 |
| HARE-HTH | PF05066 | HB1, ASXL, restriction endonuclease HTH domain | 3 | 1 |
| HATPase_c_3 | PF13589 | Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase | 3 | 3 |
| HAT_KAT11 | PF08214 | Histone acetylation protein | 9 | 9 |
| HBB | PF06777 | Helical and beta-bridge domain | 56 | 3 |
| HD | PF01966 | HD domain | 6 | 5 |
| HDA2-3 | PF11496 | Class II histone deacetylase complex subunits 2 and 3 | 1 | 1 |
| HD_6 | PF18019 | HD domain | 5 | 5 |
| HEAT_2 | PF13646 | HEAT repeats | 10 | 6 |
| HHH | PF00633 | Helix-hairpin-helix motif | 25 | 25 |
| HHH_2 | PF12826 | Helix-hairpin-helix motif | 3 | 3 |
| HHH_4 | PF14490 | Helix-hairpin-helix containing domain | 2 | 2 |
| HHH_5 | PF14520 | Helix-hairpin-helix domain | 105 | 60 |
| HHH_6 | PF14579 | Helix-hairpin-helix motif | 9 | 9 |
| HHH_8 | PF14716 | Helix-hairpin-helix domain | 636 | 513 |
| HIN | PF02760 | HIN-200/IF120x domain | 11 | 11 |
| HIRAN | PF08797 | HIRAN domain | 4 | 4 |
| HIT | PF01230 | HIT domain | 4 | 4 |
| HLH | PF00010 | Helix-loop-helix DNA-binding domain | 41 | 41 |
| HMG_box | PF00505 | HMG (high mobility group) box | 65 | 54 |
| HMG_box_2 | PF09011 | HMG-box domain | 21 | 16 |
| HNF-1_N | PF04814 | Hepatocyte nuclear factor 1 (HNF-1), N terminus | 2 | 2 |
| HNH | PF01844 | HNH endonuclease | 9 | 4 |
| HNH_3 | PF13392 | HNH endonuclease | 1 | 1 |
| HNH_4 | PF13395 | HNH endonuclease | 87 | 18 |
| HPD | PF05044 | Homeo-prospero domain | 1 | 1 |
| HSA | PF07529 | HSA | 15 | 2 |
| HSF_DNA-bind | PF00447 | HSF-type DNA-binding | 16 | 12 |
| HTH_1 | PF00126 | Bacterial regulatory helix-turn-helix protein, lysR family | 7 | 7 |
| HTH_11 | PF08279 | HTH domain | 1 | 1 |
| HTH_17 | PF12728 | Helix-turn-helix domain | 2 | 2 |
| HTH_18 | PF12833 | Helix-turn-helix domain | 13 | 13 |
| HTH_19 | PF12844 | Helix-turn-helix domain | 1 | 4 |
| HTH_23 | PF13384 | Homeodomain-like domain | 4 | 4 |
| HTH_24 | PF13412 | Winged helix-turn-helix DNA-binding | 2 | 2 |
| HTH_27 | PF13463 | Winged helix DNA-binding domain | 4 | 3 |
| HTH_28 | PF13518 | Helix-turn-helix domain | 5 | 5 |
| HTH_29 | PF13551 | Winged helix-turn helix | 1 | 1 |
| HTH_3 | PF01381 | Helix-turn-helix | 57 | 51 |
| HTH_31 | PF13560 | Helix-turn-helix domain | 3 | 2 |
| HTH_35 | PF13693 | Winged helix-turn-helix DNA-binding | 1 | 1 |
| HTH_37 | PF13744 | Helix-turn-helix domain | 1 | 1 |
| HTH_45 | PF14947 | Winged helix-turn-helix | 1 | 1 |
| HTH_48 | PF17906 | HTH domain in Mos1 transposase | 6 | 5 |
| HTH_5 | PF01022 | Bacterial regulatory protein, arsR family | 8 | 8 |
| HTH_54 | PF18607 | ParA helix turn helix domain | 1 | 1 |
| HTH_56 | PF18662 | Cch helix turn helix domain | 1 | 1 |
| HTH_7 | PF02796 | Helix-turn-helix domain of resolvase | 17 | 17 |
| HTH_8 | PF02954 | Bacterial regulatory protein, Fis family | 26 | 25 |
| HTH_AsnC-type | PF13404 | AsnC-type helix-turn-helix domain | 5 | 5 |
| HTH_CodY | PF08222 | CodY helix-turn-helix domain | 2 | 2 |
| HTH_Crp_2 | PF13545 | Crp-like helix-turn-helix domain | 38 | 37 |
| HTH_IclR | PF09339 | IclR helix-turn-helix domain | 1 | 1 |
| HTH_OrfB_IS605 | PF12323 | Helix-turn-helix domain | 3 | 3 |
| HTH_ParB | PF17762 | HTH domain found in ParB protein | 5 | 5 |
| HTH_Tnp_Mu_1 | PF02316 | Mu DNA-binding domain | 2 | 2 |
| HTH_Tnp_Mu_2 | PF09039 | Mu DNA binding, I gamma subdomain | 1 | 1 |
| HTH_Tnp_Tc3_1 | PF11427 | Tc3 transposase | 2 | 2 |
| HTH_Tnp_Tc3_2 | PF01498 | Transposase | 1 | 1 |
| HTH_Tnp_Tc5 | PF03221 | Tc5 transposase DNA-binding domain | 1 | 1 |
| HTH_WhiA | PF02650 | WhiA C-terminal HTH domain | 2 | 1 |
| HTH_psq | PF05225 | helix-turn-helix, Psq domain | 1 | 1 |
| Hap4_Hap_bind | PF10297 | Minimal binding motif of Hap4 for binding to Hap2/3/5 | 2 | 2 |
| Helicase_C | PF00271 | Helicase conserved C-terminal domain | 126 | 111 |
| Helicase_C_2 | PF13307 | Helicase C-terminal domain | 59 | 11 |
| Helicase_C_3 | PF13625 | Helicase conserved C-terminal domain | 54 | 1 |
| Helitron_like_N | PF14214 | Helitron helicase-like domain at N-terminus | 1 | 1 |
| Herpes_Helicase | PF02689 | Helicase | 3 | 3 |
| Herpes_ICP4_N | PF03584 | Herpesvirus ICP4-like protein N-terminal region | 2 | 2 |
| Herpes_ori_bp | PF02399 | Origin of replication binding protein | 3 | 3 |
| Hfq | PF17209 | Hfq protein | 1 | 1 |
| HhH-GPD | PF00730 | HhH-GPD superfamily base excision DNA repair protein | 92 | 92 |
| HipA_C | PF07804 | HipA-like C-terminal domain | 6 | 6 |
| His_Me_b4a2 | PF18275 | His-Me finger endonuclease beta4-alpha2 domain | 2 | 2 |
| Histone | PF00125 | Core histone H2A/H2B/H3/H4 | 560 | 544 |
| Histone_H2A_C | PF16211 | C-terminus of histone H2A | 549 | 159 |
| Histone_HNS | PF00816 | H-NS histone family | 2 | 2 |
| Hjc | PF01870 | Archaeal holliday junction resolvase (hjc) | 3 | 3 |
| Hom_end | PF05204 | Homing endonuclease | 2 | 2 |
| Hom_end_hint | PF05203 | Hom_end-associated Hint | 2 | 2 |
| Homeobox_KN | PF05920 | Homeobox KN domain | 16 | 16 |
| Homeodomain | PF00046 | Homeodomain | 111 | 104 |
| Hormone_recep | PF00104 | Ligand-binding domain of nuclear hormone receptor | 10 | 2 |
| HsdM_N | PF12161 | HsdM N-terminal domain | 5 | 2 |
| Hus1 | PF04005 | Hus1-like protein | 12 | 2 |
| HxlR | PF01638 | HxlR-like helix-turn-helix | 2 | 2 |
| IBD | PF10416 | Transcription-initiator DNA-binding domain IBD | 2 | 2 |
| IL1 | PF00340 | Interleukin-1 / 18 | 1 | 1 |
| IL6 | PF00489 | Interleukin-6/G-CSF/MGF family | 2 | 2 |
| IMS | PF00817 | impB/mucB/samB family | 466 | 455 |
| IMS_C | PF11799 | impB/mucB/samB family C-terminal domain | 466 | 457 |
| IMS_HHH | PF11798 | IMS family HHH motif | 200 | 191 |
| INO80_Ies4 | PF08193 | INO80 complex subunit Ies4 | 2 | 2 |
| IN_DBD_C | PF00552 | Integrase DNA binding domain | 29 | 30 |
| IRF | PF00605 | Interferon regulatory factor transcription factor | 12 | 12 |
| Ig_3 | PF13927 | Immunoglobulin domain | 2 | 2 |
| Integrase_DNA | PF02920 | DNA binding domain of tn916 integrase | 2 | 2 |
| Integrase_H2C2 | PF17921 | Integrase zinc binding domain | 52 | 51 |
| Integrase_Zn | PF02022 | Integrase Zinc binding domain | 29 | 30 |
| Ion_trans_N | PF08412 | Ion transport protein N-terminal | 8 | 8 |
| IstB_IS21 | PF01695 | IstB-like ATP binding protein | 1 | 1 |
| KH_1 | PF00013 | KH domain | 11 | 10 |
| KH_5 | PF13184 | NusA-like KH domain | 29 | 1 |
| KORA | PF16509 | TrfB plasmid transcriptional repressor | 5 | 5 |
| KOW | PF00467 | KOW motif | 101 | 15 |
| KilA-N | PF04383 | KilA-N domain | 1 | 1 |
| KorB | PF08535 | KorB domain | 1 | 1 |
| Ku | PF02735 | Ku70/Ku80 beta-barrel domain | 29 | 29 |
| Ku_C | PF03730 | Ku70/Ku80 C-terminal arm | 29 | 26 |
| Ku_N | PF03731 | Ku70/Ku80 N-terminal alpha/beta domain | 29 | 29 |
| Ku_PK_bind | PF08785 | Ku C terminal domain like | 25 | 2 |
| LAG1-DNAbind | PF09271 | LAG1, DNA binding | 17 | 17 |
| LAGLIDADG_1 | PF00961 | LAGLIDADG endonuclease | 94 | 93 |
| LAGLIDADG_2 | PF03161 | LAGLIDADG DNA endonuclease family | 7 | 6 |
| LAGLIDADG_3 | PF14528 | LAGLIDADG-like domain | 19 | 18 |
| LAGLIDADG_WhiA | PF14527 | WhiA LAGLIDADG-like domain | 2 | 2 |
| LRR_12 | PF18837 | Leucine-rich repeat | 11 | 2 |
| LRR_4 | PF12799 | Leucine Rich repeats (2 copies) | 8 | 6 |
| LRR_8 | PF13855 | Leucine rich repeat | 12 | 11 |
| LacI | PF00356 | Bacterial regulatory proteins, lacI family | 42 | 42 |
| Lactamase_B_2 | PF12706 | Beta-lactamase superfamily domain | 1 | 1 |
| Lactonase | PF10282 | Lactonase, 7-bladed beta-propeller | 16 | 14 |
| Ldh_1_C | PF02866 | lactate/malate dehydrogenase, alpha/beta C-terminal domain | 3 | 3 |
| Ldh_1_N | PF00056 | lactate/malate dehydrogenase, NAD binding domain | 3 | 3 |
| Lectin_legB | PF00139 | Legume lectin domain | 7 | 7 |
| Leo1 | PF04004 | Leo1-like protein | 14 | 2 |
| LexA_DNA_bind | PF01726 | LexA DNA binding domain | 3 | 3 |
| Lgl_C | PF08596 | Lethal giant larvae(Lgl) like, C-terminal | 1 | 1 |
| Lhr_WH | PF19306 | Helicase Lhr winged helix domain | 3 | 3 |
| Linker_histone | PF00538 | linker histone H1 and H5 family | 43 | 41 |
| Lon_2 | PF13337 | Putative ATP-dependent Lon protease | 1 | 1 |
| LppC | PF04348 | LppC putative lipoprotein | 5 | 5 |
| LytTR | PF04397 | LytTr DNA-binding domain | 6 | 6 |
| MAGE | PF01454 | MAGE family | 1 | 1 |
| MBD | PF01429 | Methyl-CpG binding domain | 33 | 33 |
| MCM | PF00493 | MCM P-loop domain | 36 | 35 |
| MCM_OB | PF17207 | MCM OB domain | 37 | 20 |
| MH1 | PF03165 | MH1 domain | 20 | 23 |
| MRP-S24 | PF14955 | Mitochondrial ribosome subunit S24 | 2 | 1 |
| MSL2-CXC | PF16682 | CXC domain of E3 ubiquitin-protein ligase MSL2 | 2 | 2 |
| MT-A70 | PF05063 | MT-A70 | 1 | 1 |
| Mab-21 | PF03281 | Mab-21 protein | 38 | 37 |
| MafB19-deam | PF14437 | MafB19-like deaminase | 3 | 3 |
| MarR | PF01047 | MarR family | 12 | 12 |
| MarR_2 | PF12802 | MarR family | 12 | 12 |
| MatP | PF06303 | MatP N-terminal domain | 9 | 9 |
| MatP_C | PF17414 | MatP C-terminal ribbon-helix-helix domain | 9 | 9 |
| MazE_antitoxin | PF04014 | Antidote-toxin recognition MazE, bacterial antitoxin | 5 | 5 |
| Med19 | PF10278 | Mediator of RNA pol II transcription subunit 19 | 6 | 1 |
| MerR | PF00376 | MerR family regulatory protein | 7 | 7 |
| MerR-DNA-bind | PF09278 | MerR, DNA binding | 6 | 6 |
| MerR_1 | PF13411 | MerR HTH family regulatory protein | 36 | 36 |
| MerR_2 | PF13591 | MerR HTH family regulatory protein | 1 | 1 |
| MetJ | PF01340 | Met Apo-repressor, MetJ | 6 | 3 |
| Metallophos | PF00149 | Calcineurin-like phosphoesterase | 12 | 8 |
| Methylase_S | PF01420 | Type I restriction modification DNA specificity domain | 5 | 5 |
| MethyltransfD12 | PF02086 | D12 class N6 adenine-specific DNA methyltransferase | 15 | 15 |
| Methyltransf_1N | PF02870 | 6-O-methylguanine DNA methyltransferase, ribonuclease-like domain | 5 | 2 |
| Microvir_J | PF04726 | Microvirus J protein | 3 | 3 |
| MobA_MobL | PF03389 | MobA/MobL family | 1 | 1 |
| Mob_Pre | PF01076 | Plasmid recombination enzyme | 6 | 6 |
| MogR_DNAbind | PF12181 | DNA binding domain of the motility gene repressor (MogR) | 1 | 1 |
| MotCF | PF09158 | Bacteriophage T4 MotA, C-terminal | 2 | 2 |
| MqsA_antitoxin | PF15731 | Antitoxin component of bacterial toxin-antitoxin system, MqsA | 3 | 3 |
| MrcB_N | PF12102 | MrcB-like, N-terminal domain | 6 | 6 |
| Mrr_cat | PF04471 | Restriction endonuclease | 1 | 1 |
| Mu-transpos_C | PF09299 | Mu transposase, C-terminal | 6 | 5 |
| MukB | PF04310 | MukB N-terminal | 6 | 6 |
| MukE | PF04288 | MukE-like family | 6 | 6 |
| MukF_C | PF17193 | MukF C-terminal domain | 6 | 6 |
| MutH | PF02976 | DNA mismatch repair enzyme MutH | 3 | 3 |
| MutS_I | PF01624 | MutS domain I | 34 | 30 |
| MutS_II | PF05188 | MutS domain II | 34 | 1 |
| MutS_III | PF05192 | MutS domain III | 34 | 10 |
| MutS_IV | PF05190 | MutS family domain IV | 34 | 31 |
| MvaI_BcnI | PF15515 | MvaI/BcnI restriction endonuclease family | 4 | 4 |
| Myb_DNA-bind_5 | PF13873 | Myb/SANT-like DNA-binding domain | 1 | 1 |
| Myb_DNA-bind_6 | PF13921 | Myb-like DNA-binding domain | 13 | 13 |
| Myb_DNA-bind_7 | PF15963 | Myb DNA-binding like | 14 | 14 |
| Myb_DNA-binding | PF00249 | Myb-like DNA-binding domain | 58 | 37 |
| N6_Mtase | PF02384 | N-6 DNA Methylase | 44 | 41 |
| N6_N4_Mtase | PF01555 | DNA methylase | 2 | 2 |
| NAD2 | PF18782 | Novel AID APOBEC clade 2 | 16 | 15 |
| NAM | PF02365 | No apical meristem (NAM) protein | 3 | 3 |
| NDC10_II | PF16787 | Centromere DNA-binding protein complex CBF3 subunit, domain 2 | 3 | 3 |
| NDT80_PhoG | PF05224 | NDT80 / PhoG like DNA-binding family | 11 | 11 |
| NFACT-R_1 | PF05670 | NFACT protein RNA binding domain | 1 | 1 |
| NGF | PF00243 | Nerve growth factor family | 1 | 1 |
| NPHI_C | PF08469 | Nucleoside triphosphatase I C-terminal | 1 | 1 |
| NTP_transf_2 | PF01909 | Nucleotidyltransferase domain | 2 | 2 |
| NUC | PF18510 | Nuclease domain | 19 | 3 |
| NUC194 | PF08163 | NUC194 domain | 23 | 1 |
| NUDIX_4 | PF14815 | NUDIX domain | 16 | 16 |
| NUMOD3 | PF07460 | NUMOD3 motif | 2 | 2 |
| NUMOD4 | PF07463 | NUMOD4 motif | 1 | 1 |
| NaeI | PF09126 | Restriction endonuclease NaeI | 1 | 1 |
| Neil1-DNA_bind | PF09292 | Endonuclease VIII-like 1, DNA bind | 23 | 23 |
| NfI_DNAbd_pre-N | PF10524 | Nuclear factor I protein pre-N-terminus | 1 | 1 |
| NgoMIV_restric | PF09015 | NgoMIV restriction enzyme | 2 | 2 |
| NikR_C | PF08753 | NikR C terminal nickel binding domain | 2 | 2 |
| Nipped-B_C | PF12830 | Sister chromatid cohesion C-terminus | 5 | 5 |
| NotI | PF12183 | Restriction endonuclease NotI | 1 | 1 |
| NucS | PF01939 | Endonuclease NucS | 5 | 5 |
| NusG | PF02357 | Transcription termination factor nusG | 60 | 60 |
| OB_Dis3 | PF17849 | Dis3-like cold-shock domain 2 (CSD2) | 2 | 2 |
| OB_NTP_bind | PF07717 | Oligonucleotide/oligosaccharide-binding (OB)-fold | 12 | 12 |
| OGG_N | PF07934 | 8-oxoguanine DNA glycosylase, N-terminal domain | 33 | 20 |
| ORC2 | PF04084 | Origin recognition complex subunit 2 | 19 | 20 |
| ORC3_N | PF07034 | Origin recognition complex (ORC) subunit 3 N-terminus | 19 | 20 |
| ORC4_C | PF14629 | Origin recognition complex (ORC) subunit 4 C-terminus | 19 | 13 |
| ORC5_C | PF14630 | Origin recognition complex (ORC) subunit 5 C-terminus | 19 | 19 |
| ORC6 | PF05460 | Origin recognition complex subunit 6 (ORC6) | 18 | 8 |
| ORC_WH_C | PF18137 | Origin recognition complex winged helix C-terminal | 19 | 17 |
| Omega_Repress | PF07764 | Omega Transcriptional Repressor | 3 | 3 |
| OrfB_IS605 | PF01385 | Probable transposase | 9 | 9 |
| OrfB_Zn_ribbon | PF07282 | Putative transposase DNA-binding domain | 17 | 15 |
| P53 | PF00870 | P53 DNA-binding domain | 59 | 58 |
| PA-IIL | PF07472 | Fucose-binding lectin II (PA-IIL) | 1 | 1 |
| PAF | PF15715 | PCNA-associated factor histone like domain | 1 | 1 |
| PAPA-1 | PF04795 | PAPA-1-like conserved region | 7 | 4 |
| PARP_reg | PF02877 | Poly(ADP-ribose) polymerase, regulatory domain | 13 | 4 |
| PARP_regulatory | PF01358 | Poly A polymerase regulatory subunit | 1 | 1 |
| PAS | PF00989 | PAS fold | 11 | 3 |
| PAX | PF00292 | 'Paired box' domain | 4 | 4 |
| PAZ | PF02170 | PAZ domain | 2 | 2 |
| PAZ_siRNAbind | PF12212 | PAZ domain | 1 | 1 |
| PC4 | PF02229 | Transcriptional Coactivator p15 (PC4) | 10 | 10 |
| PCNA_C | PF02747 | Proliferating cell nuclear antigen, C-terminal domain | 36 | 32 |
| PCNA_N | PF00705 | Proliferating cell nuclear antigen, N-terminal domain | 36 | 32 |
| PD-C2-AF1 | PF09310 | POU domain, class 2, associating factor 1 | 1 | 1 |
| PDDEXK_1 | PF12705 | PD-(D/E)XK nuclease superfamily | 22 | 11 |
| PDDEXK_5 | PF11645 | PD-(D/E)XK endonuclease | 1 | 1 |
| PDEase_II | PF02112 | cAMP phosphodiesterases class-II | 1 | 1 |
| PDGF | PF00341 | PDGF/VEGF domain | 2 | 2 |
| PHD | PF00628 | PHD-finger | 38 | 1 |
| PHD_2 | PF13831 | PHD-finger | 1 | 1 |
| PHD_4 | PF16866 | PHD-finger | 2 | 1 |
| PHP | PF02811 | PHP domain | 9 | 1 |
| PH_18 | PF18469 | Pleckstrin homology domain | 5 | 5 |
| PIF1 | PF05970 | PIF1-like helicase | 16 | 16 |
| PIN_4 | PF13638 | PIN domain | 2 | 2 |
| PNK3P | PF08645 | Polynucleotide kinase 3 phosphatase | 5 | 5 |
| POT1 | PF02765 | Telomeric single stranded DNA binding POT1/CDC13 | 28 | 28 |
| POT1PC | PF16686 | ssDNA-binding domain of telomere protection protein | 35 | 35 |
| PPR_1 | PF12854 | PPR repeat | 1 | 1 |
| PPR_2 | PF13041 | PPR repeat family | 7 | 2 |
| PPV_E1_C | PF00519 | Papillomavirus helicase | 4 | 4 |
| PPV_E2_C | PF00511 | E2 (early) protein, C terminal | 4 | 4 |
| PQQ | PF01011 | PQQ enzyme repeat | 1 | 1 |
| PWWP | PF00855 | PWWP domain | 24 | 13 |
| PadR | PF03551 | Transcriptional regulator PadR-like family | 5 | 5 |
| ParB | PF08775 | ParB family | 5 | 5 |
| Parvo_NS1 | PF01057 | Parvovirus non-structural protein NS1 | 5 | 3 |
| Parvo_coat | PF00740 | Parvovirus coat protein VP2 | 8 | 7 |
| PemK_toxin | PF02452 | PemK-like, MazF-like toxin of type II toxin-antitoxin system | 3 | 3 |
| Penicillinase_R | PF03965 | Penicillinase repressor | 4 | 4 |
| Peptidase_S48 | PF03574 | Peptidase family S48 | 5 | 5 |
| Peripla_BP_3 | PF13377 | Periplasmic binding protein-like domain | 27 | 12 |
| Phage_CII | PF05269 | Bacteriophage CII protein | 2 | 2 |
| Phage_Coat_B | PF05356 | Inovirus Coat protein B | 2 | 2 |
| Phage_F | PF02305 | Capsid protein (F protein) | 3 | 3 |
| Phage_antitermQ | PF06530 | Phage antitermination protein Q | 4 | 3 |
| Phage_clamp_A | PF16790 | Bacteriophage clamp loader A subunit | 3 | 3 |
| Phage_endo_I | PF05367 | Phage endonuclease I | 1 | 1 |
| Phage_int_SAM_1 | PF02899 | Phage integrase, N-terminal SAM-like domain | 36 | 36 |
| Phage_int_SAM_4 | PF13495 | Phage integrase, N-terminal SAM-like domain | 1 | 1 |
| Phage_int_SAM_6 | PF18644 | Phage integrase SAM-like domain | 3 | 3 |
| Phage_integrase | PF00589 | Phage integrase family | 40 | 40 |
| PhdYeFM_antitox | PF02604 | Antitoxin Phd_YefM, type II toxin-antitoxin system | 4 | 4 |
| Phi-29_GP16_7 | PF06720 | Bacteriophage phi-29 early protein GP16.7 | 1 | 1 |
| Phi-29_GP4 | PF05464 | Phi-29-like late genes activator (early protein GP4) | 1 | 1 |
| Phosphodiest | PF01663 | Type I phosphodiesterase / nucleotide pyrophosphatase | 1 | 1 |
| Piwi | PF02171 | Piwi domain | 43 | 42 |
| Podovirus_Gp16 | PF05894 | Podovirus DNA encapsidation protein (Gp16) | 1 | 1 |
| PolC_DP2 | PF03833 | DNA polymerase II large subunit DP2 | 4 | 4 |
| Polyoma_lg_T_C | PF06431 | Polyomavirus large T antigen C-terminus | 1 | 2 |
| Pou | PF00157 | Pou domain - N-terminal to homeobox domain | 25 | 25 |
| Pox_A22 | PF04848 | Poxvirus A22 protein | 1 | 1 |
| Pox_A32 | PF04665 | Poxvirus A32 protein | 11 | 11 |
| Pox_RNA_Pol_22 | PF05273 | Poxvirus RNA polymerase 22 kDa subunit | 7 | 3 |
| Pox_Rap94 | PF03294 | RNA polymerase-associated transcription specificity factor, Rap94 | 5 | 2 |
| Pox_VERT_large | PF04441 | Poxvirus early transcription factor (VETF), large subunit | 1 | 1 |
| Pox_polyA_pol_C | PF12629 | Poxvirus poly(A) polymerase C-terminal domain | 1 | 1 |
| Pox_polyA_pol_N | PF12630 | Poxvirus poly(A) polymerase N-terminal domain | 1 | 1 |
| PriA_3primeBD | PF17764 | 3'DNA-binding domain (3'BD) | 7 | 7 |
| PriA_C | PF18074 | Primosomal protein N C-terminal domain | 2 | 2 |
| PriA_CRR | PF18319 | PriA DNA helicase Cys-rich region (CRR) domain | 2 | 1 |
| PriCT_1 | PF08708 | Primase C terminal 1 (PriCT-1) | 1 | 1 |
| Prim_Zn_Ribbon | PF08273 | Zinc-binding domain of primase-helicase | 9 | 4 |
| Pur_DNA_glyco | PF02245 | Methylpurine-DNA glycosylase (MPG) | 8 | 8 |
| Put_DNA-bind_N | PF06971 | Putative DNA-binding protein N-terminus | 5 | 5 |
| Pyr_excise | PF03013 | Pyrimidine dimer DNA glycosylase | 2 | 2 |
| R-HINP1I | PF11463 | R.HinP1I restriction endonuclease | 4 | 4 |
| RAG1 | PF12940 | Recombination-activation protein 1 (RAG1), recombinase | 43 | 43 |
| RAG2 | PF03089 | Recombination activating protein 2 | 35 | 32 |
| RAMA | PF18755 | Restriction Enzyme Adenine Methylase Associated | 2 | 2 |
| RAMPs | PF03787 | RAMP superfamily | 1 | 1 |
| RCC1 | PF00415 | Regulator of chromosome condensation (RCC1) repeat | 2 | 1 |
| REC1 | PF18501 | Alpha helical recognition lobe domain | 19 | 19 |
| REPA_OB_2 | PF16900 | Replication protein A OB domain | 3 | 3 |
| RE_AspBHI_N | PF18062 | Restriction endonuclease AspBHI N-terminal | 2 | 1 |
| RE_BsaWI | PF18643 | BsaWI restriction endonuclease type 2 | 3 | 3 |
| RE_Eco29kI | PF09517 | Eco29kI restriction endonuclease | 2 | 2 |
| RE_EcoO109I | PF14511 | Type II restriction endonuclease EcoO109I | 1 | 1 |
| RE_HindIII | PF09518 | HindIII restriction endonuclease | 7 | 7 |
| RE_NgoFVII | PF09565 | NgoFVII restriction endonuclease | 2 | 2 |
| RE_R_Pab1 | PF09522 | R.Pab1 restriction endonuclease | 5 | 4 |
| RE_SacI | PF09566 | SacI restriction endonuclease | 1 | 1 |
| RE_SinI | PF09570 | SinI restriction endonuclease | 2 | 2 |
| RFC1 | PF08519 | Replication factor RFC1 C terminal domain | 19 | 19 |
| RFX_DNA_binding | PF02257 | RFX DNA-binding domain | 3 | 1 |
| RHD_DNA_bind | PF00554 | Rel homology DNA-binding domain | 33 | 32 |
| RHD_dimer | PF16179 | Rel homology dimerisation domain | 31 | 30 |
| RHH_1 | PF01402 | Ribbon-helix-helix protein, copG family | 7 | 7 |
| RIG-I_C-RD | PF11648 | C-terminal domain of RIG-I | 1 | 1 |
| RL10P_insert | PF17777 | Insertion domain in 60S ribosomal protein L10P | 3 | 1 |
| RNA_helicase | PF00910 | RNA helicase | 2 | 2 |
| RNA_ligase | PF09414 | RNA ligase | 2 | 2 |
| RNA_pol | PF00940 | DNA-dependent RNA polymerase | 23 | 26 |
| RNA_pol_A_CTD | PF03118 | Bacterial RNA polymerase, alpha chain C terminal domain | 326 | 37 |
| RNA_pol_A_bac | PF01000 | RNA polymerase Rpb3/RpoA insert domain | 664 | 1 |
| RNA_pol_I_A49 | PF06870 | A49-like RNA polymerase I associated factor | 27 | 6 |
| RNA_pol_I_TF | PF04090 | RNA polymerase I specific initiation factor | 13 | 13 |
| RNA_pol_L | PF01193 | RNA polymerase Rpb3/Rpb11 dimerisation domain | 403 | 1 |
| RNA_pol_Rpb1_1 | PF04997 | RNA polymerase Rpb1, domain 1 | 674 | 650 |
| RNA_pol_Rpb1_2 | PF00623 | RNA polymerase Rpb1, domain 2 | 645 | 510 |
| RNA_pol_Rpb1_4 | PF05000 | RNA polymerase Rpb1, domain 4 | 669 | 1 |
| RNA_pol_Rpb1_5 | PF04998 | RNA polymerase Rpb1, domain 5 | 671 | 577 |
| RNA_pol_Rpb2_1 | PF04563 | RNA polymerase beta subunit | 628 | 486 |
| RNA_pol_Rpb2_2 | PF04561 | RNA polymerase Rpb2, domain 2 | 666 | 457 |
| RNA_pol_Rpb2_3 | PF04565 | RNA polymerase Rpb2, domain 3 | 673 | 565 |
| RNA_pol_Rpb2_6 | PF00562 | RNA polymerase Rpb2, domain 6 | 677 | 534 |
| RNA_pol_Rpb2_7 | PF04560 | RNA polymerase Rpb2, domain 7 | 674 | 532 |
| RNA_pol_Rpb5_N | PF03871 | RNA polymerase Rpb5, N-terminal domain | 284 | 142 |
| RNA_pol_Rpc34 | PF05158 | RNA polymerase Rpc34 subunit | 28 | 10 |
| RNA_pol_Rpc82 | PF05645 | RNA polymerase III subunit RPC82 | 28 | 14 |
| RNA_pol_Rpo13 | PF12136 | RNA polymerase Rpo13 subunit HTH domain | 1 | 1 |
| RNB | PF00773 | RNB domain | 2 | 2 |
| RNaseH_C | PF09293 | T4 RNase H, C terminal | 3 | 1 |
| RNase_H | PF00075 | RNase H | 215 | 198 |
| RNase_HII | PF01351 | Ribonuclease HII | 7 | 6 |
| RNase_PH | PF01138 | 3' exoribonuclease family, domain 1 | 2 | 2 |
| RNase_PH_C | PF03725 | 3' exoribonuclease family, domain 2 | 2 | 2 |
| RNase_P_p30 | PF01876 | RNase P subunit p30 | 6 | 4 |
| RNase_T | PF00929 | Exonuclease | 48 | 42 |
| RPOL_N | PF14700 | DNA-directed RNA polymerase N-terminal | 26 | 29 |
| RQC | PF09382 | RQC domain | 7 | 6 |
| RRM_1 | PF00076 | RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) | 61 | 46 |
| RRM_DME | PF15628 | RRM in Demeter | 3 | 3 |
| RRN9 | PF10680 | RNA polymerase I specific transcription initiation factor | 1 | 1 |
| RRXRR | PF14239 | RRXRR protein | 5 | 5 |
| RTP | PF02334 | Replication terminator protein | 4 | 4 |
| RT_RNaseH_2 | PF17919 | RNase H-like domain found in reverse transcriptase | 6 | 5 |
| RVT_1 | PF00078 | Reverse transcriptase (RNA-dependent DNA polymerase) | 199 | 190 |
| RVT_3 | PF13456 | Reverse transcriptase-like | 7 | 6 |
| RVT_N | PF13655 | N-terminal domain of reverse transcriptase | 2 | 1 |
| RVT_connect | PF06815 | Reverse transcriptase connection domain | 124 | 117 |
| RVT_thumb | PF06817 | Reverse transcriptase thumb domain | 125 | 118 |
| Rad1 | PF02144 | Repair protein Rad1/Rec1/Rad17 | 12 | 5 |
| Rad17 | PF03215 | Rad17 P-loop domain | 12 | 12 |
| Rad21_Rec8_N | PF04825 | N terminus of Rad21 / Rec8 like protein | 4 | 2 |
| Rad4 | PF03835 | Rad4 transglutaminase-like domain | 15 | 8 |
| Rad51 | PF08423 | Rad51 | 13 | 13 |
| Rad52_Rad22 | PF04098 | Rad52/22 family double-strand break repair protein | 2 | 2 |
| Rap1-DNA-bind | PF09197 | Rap1, DNA-binding | 8 | 8 |
| RbpA | PF13397 | RNA polymerase-binding protein | 25 | 24 |
| RdRP | PF05183 | RNA dependent RNA polymerase | 4 | 3 |
| RdRP_1 | PF00680 | Viral RNA-dependent RNA polymerase | 13 | 13 |
| RdRP_3 | PF00998 | Viral RNA dependent RNA polymerase | 1 | 1 |
| RdRP_4 | PF02123 | Viral RNA-directed RNA-polymerase | 1 | 1 |
| RecA | PF00154 | recA bacterial DNA recombination protein | 13 | 13 |
| RecC_C | PF17946 | RecC C-terminal domain | 13 | 13 |
| RecG_wedge | PF17191 | RecG wedge domain | 1 | 1 |
| RecJ_OB | PF17768 | RecJ OB domain | 3 | 2 |
| RecQ_Zn_bind | PF16124 | RecQ zinc-binding | 7 | 7 |
| RecT | PF03837 | RecT family | 2 | 2 |
| RecU | PF03838 | Recombination protein U | 1 | 1 |
| Recep_L_domain | PF01030 | Receptor L domain | 4 | 4 |
| Recombinase | PF07508 | Recombinase | 2 | 2 |
| RelE | PF06296 | RelE toxin of RelE / RelB toxin-antitoxin system | 1 | 1 |
| RepA_N | PF06970 | Replication initiator protein A (RepA) N-terminus | 1 | 1 |
| RepB_primase | PF16793 | RepB DNA-primase from phage plasmid | 1 | 1 |
| Rep_1B | PF17873 | Replicase polyprotein 1ab | 1 | 1 |
| Rep_2 | PF01719 | Plasmid replication protein | 1 | 1 |
| Rep_3 | PF01051 | Initiator Replication protein | 18 | 18 |
| Rep_N | PF08724 | Rep protein catalytic domain like | 10 | 6 |
| Rep_fac-A_C | PF08646 | Replication factor-A C terminal domain | 12 | 12 |
| Rep_fac_C | PF08542 | Replication factor C C-terminal domain | 34 | 21 |
| ResIII | PF04851 | Type III restriction enzyme, res subunit | 69 | 65 |
| Resolvase | PF00239 | Resolvase, N terminal domain | 10 | 10 |
| Response_reg | PF00072 | Response regulator receiver domain | 11 | 1 |
| RestrictionMunI | PF11407 | Type II restriction enzyme MunI | 1 | 1 |
| RestrictionSfiI | PF11487 | Type II restriction enzyme SfiI | 2 | 2 |
| Rho_N | PF07498 | Rho termination factor, N-terminal domain | 14 | 3 |
| Rho_RNA_bind | PF07497 | Rho termination factor, RNA-binding domain | 14 | 13 |
| Ribonuclease | PF00545 | ribonuclease | 2 | 2 |
| Ribonuclease_T2 | PF00445 | Ribonuclease T2 family | 1 | 1 |
| Ribos_L4_asso_C | PF14374 | 60S ribosomal protein L4 C-terminal domain | 1 | 1 |
| Ribosom_S12_S23 | PF00164 | Ribosomal protein S12/S23 | 35 | 2 |
| Ribosomal_L1 | PF00687 | Ribosomal protein L1p/L10e family | 1 | 1 |
| Ribosomal_L10 | PF00466 | Ribosomal protein L10 | 20 | 1 |
| Ribosomal_L13 | PF00572 | Ribosomal protein L13 | 36 | 1 |
| Ribosomal_L13e | PF01294 | Ribosomal protein L13e | 1 | 1 |
| Ribosomal_L14 | PF00238 | Ribosomal protein L14p/L23e | 36 | 1 |
| Ribosomal_L14e | PF01929 | Ribosomal protein L14 | 1 | 1 |
| Ribosomal_L15e | PF00827 | Ribosomal L15 | 3 | 1 |
| Ribosomal_L16 | PF00252 | Ribosomal protein L16p/L10e | 36 | 1 |
| Ribosomal_L18 | PF17135 | Ribosomal protein 60S L18 and 50S L18e | 3 | 1 |
| Ribosomal_L18A | PF01775 | Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A | 1 | 1 |
| Ribosomal_L19e | PF01280 | Ribosomal protein L19e | 3 | 1 |
| Ribosomal_L2 | PF00181 | Ribosomal Proteins L2, RNA binding domain | 36 | 1 |
| Ribosomal_L21e | PF01157 | Ribosomal protein L21e | 3 | 1 |
| Ribosomal_L22 | PF00237 | Ribosomal protein L22p/L17e | 36 | 1 |
| Ribosomal_L22e | PF01776 | Ribosomal L22e protein family | 1 | 1 |
| Ribosomal_L23 | PF00276 | Ribosomal protein L23 | 36 | 1 |
| Ribosomal_L23eN | PF03939 | Ribosomal protein L23, N-terminal domain | 1 | 1 |
| Ribosomal_L24e | PF01246 | Ribosomal protein L24e | 3 | 1 |
| Ribosomal_L26 | PF16906 | Ribosomal proteins L26 eukaryotic, L24P archaeal | 3 | 1 |
| Ribosomal_L27A | PF00828 | Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A | 36 | 1 |
| Ribosomal_L27e | PF01777 | Ribosomal L27e protein family | 1 | 1 |
| Ribosomal_L29e | PF01779 | Ribosomal L29e protein family | 1 | 1 |
| Ribosomal_L2_C | PF03947 | Ribosomal Proteins L2, C-terminal domain | 36 | 1 |
| Ribosomal_L3 | PF00297 | Ribosomal protein L3 | 36 | 1 |
| Ribosomal_L30 | PF00327 | Ribosomal protein L30p/L7e | 36 | 1 |
| Ribosomal_L30_N | PF08079 | Ribosomal L30 N-terminal domain | 1 | 1 |
| Ribosomal_L31e | PF01198 | Ribosomal protein L31e | 3 | 1 |
| Ribosomal_L32e | PF01655 | Ribosomal protein L32 | 3 | 1 |
| Ribosomal_L33 | PF00471 | Ribosomal protein L33 | 33 | 2 |
| Ribosomal_L34e | PF01199 | Ribosomal protein L34e | 1 | 1 |
| Ribosomal_L35Ae | PF01247 | Ribosomal protein L35Ae | 1 | 1 |
| Ribosomal_L35p | PF01632 | Ribosomal protein L35 | 33 | 1 |
| Ribosomal_L36e | PF01158 | Ribosomal protein L36e | 1 | 1 |
| Ribosomal_L37ae | PF01780 | Ribosomal L37ae protein family | 3 | 1 |
| Ribosomal_L37e | PF01907 | Ribosomal protein L37e | 3 | 1 |
| Ribosomal_L38e | PF01781 | Ribosomal L38e protein family | 1 | 1 |
| Ribosomal_L39 | PF00832 | Ribosomal L39 protein | 3 | 1 |
| Ribosomal_L4 | PF00573 | Ribosomal protein L4/L1 family | 36 | 1 |
| Ribosomal_L40e | PF01020 | Ribosomal L40e family | 2 | 1 |
| Ribosomal_L41 | PF05162 | Ribosomal protein L41 | 1 | 1 |
| Ribosomal_L44 | PF00935 | Ribosomal protein L44 | 3 | 1 |
| Ribosomal_L5 | PF00281 | Ribosomal protein L5 | 34 | 1 |
| Ribosomal_L5_C | PF00673 | ribosomal L5P family C-terminus | 34 | 1 |
| Ribosomal_L5e | PF17144 | Ribosomal large subunit proteins 60S L5, and 50S L18 | 3 | 1 |
| Ribosomal_L6 | PF00347 | Ribosomal protein L6 | 34 | 1 |
| Ribosomal_L6e | PF01159 | Ribosomal protein L6e | 1 | 1 |
| Ribosomal_L7Ae | PF01248 | Ribosomal protein L7Ae/L30e/S12e/Gadd45 family | 4 | 1 |
| Ribosomal_S10 | PF00338 | Ribosomal protein S10p/S20e | 38 | 2 |
| Ribosomal_S11 | PF00411 | Ribosomal protein S11 | 34 | 1 |
| Ribosomal_S13 | PF00416 | Ribosomal protein S13/S18 | 34 | 2 |
| Ribosomal_S15 | PF00312 | Ribosomal protein S15 | 37 | 2 |
| Ribosomal_S25 | PF03297 | S25 ribosomal protein | 1 | 1 |
| Ribosomal_S3Ae | PF01015 | Ribosomal S3Ae family | 1 | 1 |
| Ribosomal_S3_C | PF00189 | Ribosomal protein S3, C-terminal domain | 32 | 1 |
| Ribosomal_S5 | PF00333 | Ribosomal protein S5, N-terminal domain | 34 | 2 |
| Ribosomal_S7 | PF00177 | Ribosomal protein S7p/S5e | 35 | 2 |
| Ribosomal_S8e | PF01201 | Ribosomal protein S8e | 2 | 1 |
| Ribosomal_S9 | PF00380 | Ribosomal protein S9/S16 | 35 | 1 |
| Rif1_N | PF12231 | Rap1-interacting factor 1 N terminal | 1 | 1 |
| RnaseA | PF00074 | Pancreatic ribonuclease | 7 | 7 |
| Rrf2 | PF02082 | Iron-dependent Transcriptional regulator | 5 | 5 |
| RrnaAD | PF00398 | Ribosomal RNA adenine dimethylase | 4 | 4 |
| Rrp44_CSD1 | PF17216 | Rrp44-like cold shock domain | 2 | 2 |
| Rrp44_S1 | PF17215 | S1 domain | 2 | 2 |
| RsdA_SigD_bd | PF16751 | Anti-sigma-D factor RsdA to sigma factor binding region | 1 | 1 |
| RtcB | PF01139 | tRNA-splicing ligase RtcB | 1 | 1 |
| Rtt106 | PF08512 | Histone chaperone Rttp106-like | 7 | 6 |
| Runt | PF00853 | Runt domain | 19 | 19 |
| RusA | PF05866 | Endodeoxyribonuclease RusA | 1 | 1 |
| RuvA_C | PF07499 | RuvA, C-terminal domain | 13 | 4 |
| RuvA_N | PF01330 | RuvA N terminal domain | 7 | 5 |
| RuvB_C | PF05491 | RuvB C-terminal winged helix domain | 13 | 13 |
| RuvB_N | PF05496 | Holliday junction DNA helicase RuvB P-loop domain | 13 | 11 |
| RuvC | PF02075 | Crossover junction endodeoxyribonuclease RuvC | 2 | 2 |
| RuvC_1 | PF18516 | RuvC nuclease domain | 27 | 27 |
| RuvC_III | PF18541 | RuvC endonuclease subdomain 3 | 89 | 81 |
| SAD_SRA | PF02182 | SAD/SRA domain | 24 | 24 |
| SAP | PF02037 | SAP domain | 29 | 5 |
| SASP | PF00269 | Small, acid-soluble spore proteins, alpha/beta type | 1 | 1 |
| SBP_bac_1 | PF01547 | Bacterial extracellular solute-binding protein | 34 | 2 |
| SCP1201-deam | PF14428 | SCP1.201-like deaminase | 2 | 2 |
| SET | PF00856 | SET domain | 35 | 17 |
| SH2 | PF00017 | SH2 domain | 6 | 1 |
| SH3_11 | PF18103 | Retroviral integrase C-terminal SH3 domain | 51 | 51 |
| SH3_13 | PF18335 | ATP-dependent RecD-like DNA helicase SH3 domain | 13 | 10 |
| SH3_14 | PF18343 | Dda helicase SH3 domain | 3 | 3 |
| SLIDE | PF09111 | SLIDE | 4 | 1 |
| SMC_N | PF02463 | RecF/RecN/SMC N terminal domain | 14 | 12 |
| SMC_hinge | PF06470 | SMC proteins Flexible Hinge Domain | 8 | 1 |
| SNAPC1 | PF09808 | Small nuclear RNA activating complex (SNAPc), subunit 1 | 9 | 3 |
| SNAPC3 | PF12251 | snRNA-activating protein complex (SNAPc), subunit 3 | 9 | 9 |
| SNF2-rel_dom | PF00176 | SNF2-related domain | 66 | 60 |
| SOXp | PF12336 | SOX transcription factor | 6 | 6 |
| SPT16 | PF08644 | FACT complex subunit (SPT16/CDC68) | 7 | 7 |
| SRA | PF18491 | SET and RING associated domain | 2 | 2 |
| SRAP | PF02586 | SOS response associated peptidase (SRAP) | 12 | 12 |
| SRF-TF | PF00319 | SRF-type transcription factor (DNA-binding and dimerisation domain) | 16 | 16 |
| SSB | PF00436 | Single-strand binding protein family | 13 | 13 |
| SSrecog | PF03531 | Structure-specific recognition protein (SSRP1) | 7 | 2 |
| STAG | PF08514 | STAG domain | 3 | 2 |
| STAT_bind | PF02864 | STAT protein, DNA binding domain | 6 | 6 |
| SUIM_assoc | PF16619 | Unstructured region C-term to UIM in Ataxin3 | 2 | 2 |
| SbcD_C | PF12320 | Type 5 capsule protein repressor C-terminal domain | 5 | 4 |
| SelB-wing_2 | PF09106 | Elongation factor SelB, winged helix | 1 | 1 |
| SeqA | PF03925 | SeqA protein C-terminal domain | 4 | 4 |
| SfsA | PF03749 | Sugar fermentation stimulation protein RE domain | 1 | 1 |
| SfsA_N | PF17746 | SfsA N-terminal OB domain | 1 | 1 |
| Sgf11 | PF08209 | Sgf11 (transcriptional regulation protein) | 2 | 1 |
| Sigma54_AID | PF00309 | Sigma-54 factor, Activator interacting domain (AID) | 11 | 6 |
| Sigma54_CBD | PF04963 | Sigma-54 factor, core binding domain | 12 | 5 |
| Sigma54_DBD | PF04552 | Sigma-54, DNA binding domain | 14 | 14 |
| Sigma54_activat | PF00158 | Sigma-54 interaction domain | 2 | 2 |
| Sigma70_ner | PF04546 | Sigma-70, non-essential region | 66 | 18 |
| Sigma70_r1_2 | PF00140 | Sigma-70 factor, region 1.2 | 196 | 181 |
| Sigma70_r2 | PF04542 | Sigma-70 region 2 | 218 | 213 |
| Sigma70_r3 | PF04539 | Sigma-70 region 3 | 200 | 178 |
| Sigma70_r4 | PF04545 | Sigma-70, region 4 | 205 | 109 |
| Sigma70_r4_2 | PF08281 | Sigma-70, region 4 | 19 | 4 |
| Sin3a_C | PF16879 | C-terminal domain of Sin3a protein | 3 | 3 |
| Slx4 | PF09494 | Slx4 endonuclease | 2 | 1 |
| SnAC | PF14619 | Snf2-ATP coupling, chromatin remodelling complex | 20 | 2 |
| SoPB_HTH | PF18090 | Centromere-binding protein HTH domain | 3 | 3 |
| Spo0A_C | PF08769 | Sporulation initiation factor Spo0A C terminal | 1 | 1 |
| Spt5-NGN | PF03439 | Early transcription elongation factor of RNA pol II, NGN section | 34 | 24 |
| Spuma_A9PTase | PF03539 | Spumavirus aspartic protease (A9) | 3 | 2 |
| Sulf_coat_C | PF12193 | Sulfolobus virus coat protein C terminal | 4 | 4 |
| Sushi | PF00084 | Sushi repeat (SCR repeat) | 2 | 2 |
| Swi3 | PF07962 | Replication Fork Protection Component Swi3 | 5 | 5 |
| T-box | PF00907 | T-box | 10 | 10 |
| T4-Gluco-transf | PF09198 | Bacteriophage T4 beta-glucosyltransferase | 4 | 4 |
| TAF | PF02969 | TATA box binding protein associated factor (TAF) | 538 | 517 |
| TAF4 | PF05236 | Transcription initiation factor TFIID component TAF4 family | 14 | 2 |
| TAL_effector | PF03377 | TAL effector repeat | 34 | 32 |
| TBCA | PF02970 | Tubulin binding cofactor A | 1 | 1 |
| TBP | PF00352 | Transcription factor TFIID (or TATA-binding protein, TBP) | 123 | 119 |
| TCP | PF03634 | TCP family transcription factor | 6 | 6 |
| TCR | PF03638 | Tesmin/TSO1-like CXC domain, cysteine-rich domain | 1 | 1 |
| TEA | PF01285 | TEA/ATTS domain | 3 | 3 |
| TEBP_beta | PF07404 | Telomere-binding protein beta subunit (TEBP beta) | 14 | 14 |
| TERT_thumb | PF17984 | Telomerase reverse transcriptase thumb DNA binding domain | 14 | 14 |
| TFA2_Winged_2 | PF18121 | TFA2 Winged helix domain 2 | 51 | 19 |
| TFIIA | PF03153 | Transcription factor IIA, alpha/beta subunit | 50 | 32 |
| TFIIA_gamma_C | PF02751 | Transcription initiation factor IIA, gamma subunit | 68 | 1 |
| TFIIB | PF00382 | Transcription factor TFIIB repeat | 85 | 82 |
| TFIID-18kDa | PF02269 | Transcription initiation factor IID, 18kD subunit | 13 | 1 |
| TFIIE_alpha | PF02002 | TFIIE alpha subunit | 72 | 39 |
| TFIIF_alpha | PF05793 | Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) | 54 | 21 |
| TFIIF_beta | PF02270 | TFIIF, beta subunit HTH domain | 62 | 50 |
| TFR_dimer | PF04253 | Transferrin receptor-like dimerisation domain | 1 | 1 |
| TF_AP-2 | PF03299 | Transcription factor AP-2 | 2 | 2 |
| TF_Zn_Ribbon | PF08271 | TFIIB zinc-binding | 82 | 10 |
| THAP | PF05485 | THAP domain | 5 | 3 |
| TIMELESS | PF04821 | Timeless protein | 5 | 3 |
| TIP49 | PF06068 | TIP49 P-loop domain | 8 | 1 |
| TIR | PF01582 | TIR domain | 3 | 3 |
| TOPRIM_C | PF16898 | C-terminal associated domain of TOPRIM | 22 | 22 |
| TORC_N | PF12884 | Transducer of regulated CREB activity, N terminus | 2 | 2 |
| TPR_11 | PF13414 | TPR repeat | 8 | 1 |
| TPR_16 | PF13432 | Tetratricopeptide repeat | 15 | 1 |
| TPR_19 | PF14559 | Tetratricopeptide repeat | 8 | 1 |
| TRCF | PF03461 | TRCF domain | 11 | 1 |
| TSC22 | PF01166 | TSC-22/dip/bun family | 1 | 1 |
| T_Ag_DNA_bind | PF02217 | Origin of replication binding protein | 8 | 8 |
| Taq-exonuc | PF09281 | Taq polymerase, exonuclease | 72 | 8 |
| TaqI_C | PF12950 | TaqI-like C-terminal specificity domain | 36 | 36 |
| TatD_DNase | PF01026 | TatD related DNase | 1 | 1 |
| Telomerase_RBD | PF12009 | Telomerase ribonucleoprotein complex - RNA binding domain | 22 | 22 |
| Telomere_res | PF16684 | Telomere resolvase | 10 | 10 |
| Tenui_N | PF05733 | Tenuivirus/Phlebovirus nucleocapsid protein | 1 | 1 |
| Ter | PF05472 | DNA replication terminus site-binding protein (Ter protein) | 8 | 8 |
| TetR_C_1 | PF02909 | Tetracyclin repressor-like, C-terminal domain | 4 | 1 |
| TetR_C_32 | PF19344 | Tetracyclin repressor-like, C-terminal domain | 5 | 4 |
| TetR_C_33 | PF13305 | Tetracyclin repressor-like, C-terminal domain | 1 | 1 |
| TetR_C_6 | PF13977 | BetI-type transcriptional repressor, C-terminal | 7 | 1 |
| TetR_N | PF00440 | Bacterial regulatory proteins, tetR family | 40 | 39 |
| Tet_JBP | PF12851 | Oxygenase domain of the 2OGFeDO superfamily | 6 | 6 |
| Tfb2 | PF03849 | Transcription factor Tfb2 | 54 | 3 |
| Tfb2_C | PF18307 | Transcription factor Tfb2 (p52) C-terminal domain | 55 | 2 |
| Tfb5 | PF06331 | Transcription factor TFIIH complex subunit Tfb5 | 55 | 4 |
| ThaI | PF15514 | Restriction endonuclease ThaI | 1 | 1 |
| Thioredoxin | PF00085 | Thioredoxin | 19 | 4 |
| TniB | PF05621 | Bacterial TniB protein | 15 | 15 |
| TniQ | PF06527 | TniQ | 12 | 7 |
| Tnp_DNA_bind | PF14706 | Transposase DNA-binding | 5 | 5 |
| Tnp_P_element | PF12017 | Transposase protein | 2 | 2 |
| Tnp_P_element_C | PF12596 | 87kDa Transposase | 2 | 2 |
| Tnp_zf-ribbon_2 | PF13842 | DDE_Tnp_1-like zinc-ribbon | 2 | 2 |
| Topo_C_assoc | PF14370 | C-terminal topoisomerase domain | 16 | 16 |
| Topo_Zn_Ribbon | PF08272 | Topoisomerase I zinc-ribbon-like | 1 | 1 |
| Topoisom_I | PF01028 | Eukaryotic DNA topoisomerase I, catalytic core | 20 | 20 |
| Topoisom_I_N | PF02919 | Eukaryotic DNA topoisomerase I, DNA binding fragment | 16 | 16 |
| Topoisom_bac | PF01131 | DNA topoisomerase | 14 | 14 |
| Toprim | PF01751 | Toprim domain | 106 | 104 |
| Toprim_2 | PF13155 | Toprim-like | 9 | 4 |
| Toprim_3 | PF13362 | Toprim domain | 5 | 3 |
| Toprim_4 | PF13662 | Toprim domain | 8 | 1 |
| Toprim_N | PF08275 | DNA primase catalytic core, N-terminal domain | 9 | 8 |
| Tospo_nucleocap | PF01533 | Tospovirus nucleocapsid protein | 1 | 1 |
| Tower | PF09121 | Tower | 1 | 1 |
| TraI_2B | PF18340 | DNA relaxase TraI 2B/2B-like domain | 1 | 1 |
| Tra_M | PF05261 | TraM protein, DNA-binding | 2 | 2 |
| Trans_coact | PF16805 | Phage late-transcription coactivator | 1 | 1 |
| Trans_reg_C | PF00486 | Transcriptional regulatory protein, C terminal | 14 | 14 |
| Translin | PF01997 | Translin family | 1 | 1 |
| Transposase_1 | PF01359 | Transposase (partial DDE domain) | 5 | 4 |
| Transposase_mut | PF00872 | Transposase, Mutator family | 3 | 3 |
| TrmB | PF01978 | Sugar-specific transcriptional regulator TrmB | 4 | 4 |
| Trp_repressor | PF01371 | Trp repressor protein | 4 | 4 |
| TrwC | PF08751 | TrwC relaxase | 10 | 10 |
| Trypsin | PF00089 | Trypsin | 27 | 27 |
| Tudor-knot | PF11717 | RNA binding activity-knot of a chromodomain | 7 | 4 |
| Type2_restr_D3 | PF16902 | Type-2 restriction enzyme D3 domain | 1 | 1 |
| Type_ISP_C | PF18135 | Type ISP C-terminal specificity domain | 4 | 4 |
| Tyr-DNA_phospho | PF06087 | Tyrosyl-DNA phosphodiesterase | 10 | 5 |
| UCH | PF00443 | Ubiquitin carboxyl-terminal hydrolase | 5 | 2 |
| UDG | PF03167 | Uracil DNA glycosylase superfamily | 42 | 42 |
| UQ_con | PF00179 | Ubiquitin-conjugating enzyme | 8 | 2 |
| UvdE | PF03851 | UV-endonuclease UvdE | 1 | 1 |
| UvrA_DNA-bind | PF17755 | UvrA DNA-binding domain | 1 | 1 |
| UvrB | PF12344 | Ultra-violet resistance protein B | 8 | 1 |
| UvrB_inter | PF17757 | UvrB interaction domain | 19 | 5 |
| UvrD-helicase | PF00580 | UvrD/REP helicase N-terminal domain | 31 | 31 |
| UvrD_C | PF13361 | UvrD-like helicase C-terminal domain | 28 | 28 |
| UvrD_C_2 | PF13538 | UvrD-like helicase C-terminal domain | 31 | 28 |
| V-set | PF07686 | Immunoglobulin V-set domain | 41 | 17 |
| VP40 | PF07447 | Matrix protein VP40 | 1 | 1 |
| VRR_NUC | PF08774 | VRR-NUC domain | 13 | 9 |
| VWA | PF00092 | von Willebrand factor type A domain | 5 | 5 |
| VirDNA-topo-I_N | PF09266 | Viral DNA topoisomerase I, N-terminal | 3 | 3 |
| VirE | PF05272 | Virulence-associated protein E | 1 | 1 |
| Vir_act_alpha_C | PF10400 | Virulence activator alpha C-term | 5 | 1 |
| Viral_Rep | PF02407 | Putative viral replication protein | 5 | 3 |
| Viral_alk_exo | PF01771 | Viral alkaline exonuclease | 1 | 1 |
| Viral_helicase1 | PF01443 | Viral (Superfamily 1) RNA helicase | 3 | 3 |
| Vsr | PF03852 | DNA mismatch endonuclease Vsr | 2 | 2 |
| WD40 | PF00400 | WD domain, G-beta repeat | 67 | 16 |
| WGR | PF05406 | WGR domain | 16 | 16 |
| WHIM1 | PF15612 | WSTF, HB1, Itc1p, MBD9 motif 1 | 1 | 1 |
| WRKY | PF03106 | WRKY DNA -binding domain | 6 | 6 |
| WYL | PF13280 | WYL domain | 4 | 2 |
| Whib | PF02467 | Transcription factor WhiB | 6 | 5 |
| Whirly | PF08536 | Whirly transcription factor | 5 | 5 |
| XPA_C | PF05181 | XPA protein C-terminus | 15 | 15 |
| XPG_I | PF00867 | XPG I-region | 48 | 42 |
| XPG_N | PF00752 | XPG N-terminal domain | 48 | 44 |
| XRN_M | PF17846 | Xrn1 helical domain | 1 | 1 |
| XRN_N | PF03159 | XRN 5'-3' exonuclease N-terminus | 1 | 1 |
| Y1_Tnp | PF01797 | Transposase IS200 like | 12 | 12 |
| YL1 | PF05764 | YL1 nuclear protein | 1 | 1 |
| YTH | PF04146 | YT521-B-like domain | 4 | 4 |
| Ydc2-catalyt | PF09159 | Mitochondrial resolvase Ydc2 / RNA splicing MRS1 | 1 | 1 |
| YlqD | PF11068 | YlqD protein | 2 | 2 |
| YqaJ | PF09588 | YqaJ-like viral recombinase domain | 4 | 4 |
| Zap1_zf2 | PF18217 | Zap1 zinc finger 2 | 3 | 3 |
| Zn-C2H2_12 | PF18112 | Autophagy receptor zinc finger-C2H2 domain | 1 | 1 |
| Zn_clus | PF00172 | Fungal Zn(2)-Cys(6) binuclear cluster domain | 22 | 17 |
| Zn_ribbon_recom | PF13408 | Recombinase zinc beta ribbon domain | 2 | 2 |
| bCoV_S1_RBD | PF09408 | Betacoronavirus spike glycoprotein S1, receptor binding | 2 | 2 |
| bZIP_1 | PF00170 | bZIP transcription factor | 16 | 15 |
| bZIP_2 | PF07716 | Basic region leucine zipper | 20 | 20 |
| bZIP_Maf | PF03131 | bZIP Maf transcription factor | 9 | 9 |
| cNMP_binding | PF00027 | Cyclic nucleotide-binding domain | 36 | 23 |
| fn3 | PF00041 | Fibronectin type III domain | 4 | 4 |
| gp32 | PF08804 | gp32 DNA binding protein like | 1 | 1 |
| gp45-slide_C | PF09116 | gp45 sliding clamp, C terminal | 4 | 3 |
| mTERF | PF02536 | mTERF | 8 | 8 |
| pRN1_helical | PF13010 | Primase helical domain | 1 | 1 |
| preSET_CXC | PF18264 | CXC domain | 2 | 2 |
| rpo30_N | PF12410 | Poxvirus DNA dependent RNA polymerase 30kDa subunit | 7 | 3 |
| rve | PF00665 | Integrase core domain | 88 | 86 |
| rve_3 | PF13683 | Integrase core domain | 1 | 1 |
| ssDNA_TraI_N | PF18272 | single-stranded DNA binding TraI N-terminal subdomain | 1 | 1 |
| tRNA_anti-codon | PF01336 | OB-fold nucleic acid binding domain | 31 | 17 |
| ubiquitin | PF00240 | Ubiquitin family | 44 | 6 |
| z-alpha | PF02295 | Adenosine deaminase z-alpha domain | 21 | 21 |
| zf-C2H2 | PF00096 | Zinc finger, C2H2 type | 101 | 100 |
| zf-C2HC | PF01530 | Zinc finger, C2HC type | 3 | 2 |
| zf-C2HE | PF16278 | C2HE / C2H2 / C2HC zinc-binding finger | 14 | 14 |
| zf-C4 | PF00105 | Zinc finger, C4 type (two domains) | 96 | 95 |
| zf-C4_Topoisom | PF01396 | Topoisomerase DNA binding C4 zinc finger | 6 | 1 |
| zf-CCCH | PF00642 | Zinc finger C-x8-C-x5-C-x3-H type (and similar) | 1 | 1 |
| zf-CCHC | PF00098 | Zinc knuckle | 10 | 9 |
| zf-CHC2 | PF01807 | CHC2 zinc finger | 5 | 5 |
| zf-CXXC | PF02008 | CXXC zinc finger domain | 23 | 20 |
| zf-FPG_IleRS | PF06827 | Zinc finger found in FPG and IleRS | 82 | 78 |
| zf-H2C2_2 | PF13465 | Zinc-finger double domain | 130 | 130 |
| zf-H2C2_5 | PF13909 | C2H2-type zinc-finger domain | 6 | 6 |
| zf-His_Me_endon | PF05551 | Zinc-binding loop region of homing endonuclease | 7 | 7 |
| zf-LYAR | PF08790 | LYAR-type C2HC zinc finger | 3 | 3 |
| zf-PARP | PF00645 | Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region | 14 | 14 |
| zf-RING_UBOX | PF13445 | RING-type zinc-finger | 1 | 1 |
| zf-RanBP | PF00641 | Zn-finger in Ran binding protein and others | 6 | 2 |
| zf-U11-48K | PF05253 | U11-48K-like CHHC zinc finger | 7 | 7 |
| zf-WRNIP1_ubi | PF18279 | Werner helicase-interacting protein 1 ubiquitin-binding domain | 1 | 1 |
| zf-primase | PF09329 | Primase zinc finger | 2 | 1 |
| zf_Hakai | PF18408 | C2H2 Hakai zinc finger domain | 1 | 1 |