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  • List of Pfam domains:
      
					
Pfam release : 31.0 Pfam-A families : 16712 Date : 2017-02 Based on UniProtKB : 2016_10
Best resolution complexes of Pfam family representatives, bound with nucleic acid

List of Pfam families detected in NPIDB entries:
Pfam ID  Domain  # of entries  # of domains  # of bound domains 
  2OG-FeII_Oxy_2   2OG-Fe(II) oxygenase superfamily 44 46 45
  40S_S4_C   40S ribosomal protein S4 C-terminus 68 68 63
  40S_SA_C   40S ribosomal protein SA C-terminus 7 7 0
  4HBT   Thioesterase superfamily 1 4 0
  5_3_exonuc   5'-3' exonuclease, C-terminal SAM fold 5 6 5
  5_3_exonuc_N   5'-3' exonuclease, N-terminal resolvase-like domain 6 7 4
  7kD_DNA_binding   7kD DNA-binding domain 19 24 22
  AAA   ATPase family associated with various cellular activities (AAA) 5 18 16
  AAA_11   AAA domain 6 13 12
  AAA_12   AAA domain 6 8 7
  AAA_16   AAA ATPase domain 1 1 1
  AAA_21   AAA domain, putative AbiEii toxin, Type IV TA system 1 2 0
  AAA_22   AAA domain 4 9 4
  AAA_23   AAA domain 4 10 7
  AAA_30   AAA domain 7 12 10
  AAA_31   AAA domain 1 4 2
  AAA_33   AAA domain 12 30 21
  ABC_tran   ABC transporter 4 8 6
  ABC_tran_CTD   ABC transporter C-terminal domain 13 13 0
  ABC_tran_Xtn   ABC transporter 1 1 1
  Aconitase   Aconitase family (aconitate hydratase) 2 3 3
  Aconitase_C   Aconitase C-terminal domain 2 3 3
  Activator_LAG-3   Transcriptional activator LAG-3 1 1 0
  Ada_Zn_binding   Metal binding domain of Ada 2 2 2
  Adenine_glyco   Methyladenine glycosylase 1 1 1
  AF-4   AF-4 proto-oncoprotein 1 1 0
  AFT   Transcription factor AFT 1 4 4
  AGT   DNA alpha-glucosyltransferase 4 11 11
  Alba   Alba 3 7 4
  AlkA_N   AlkA N-terminal domain 12 39 0
  Amidase   Amidase 3 7 2
  Amino_oxidase   Flavin containing amine oxidoreductase 1 1 1
  ANAPC4_WD40   Anaphase-promoting complex subunit 4 WD40 domain 7 16 10
  Ank_2   Ankyrin repeats (3 copies) 6 14 4
  Ank_4   Ankyrin repeats (many copies) 1 1 0
  Ank_5   Ankyrin repeats (many copies) 3 4 2
  Anticodon_1   Anticodon-binding domain of tRNA 21 33 33
  AP2   AP2 domain 2 3 3
  APOBEC_N   APOBEC-like N-terminal domain 4 12 9
  Apolipoprotein   Apolipoprotein A1/A4/E domain 1 2 0
  AP_endonuc_2   Xylose isomerase-like TIM barrel 4 6 5
  Aquarius_N   Intron-binding protein aquarius N-terminus 1 1 0
  Arc   Arc-like DNA binding domain 4 16 16
  Arena_ncap_C   Arenavirus nucleocapsid C-terminal domain 5 5 5
  Arena_nucleocap   Arenavirus nucleocapsid N-terminal domain 2 8 8
  ArgoL1   Argonaute linker 1 domain 23 23 23
  ArgoL2   Argonaute linker 2 domain 23 23 9
  ArgoMid   Mid domain of argonaute 23 23 4
  ArgoN   N-terminal domain of argonaute 24 24 11
  Arg_repressor   Arginine repressor, DNA binding domain 5 23 23
  Arg_repressor_C   Arginine repressor, C-terminal domain 4 19 0
  Arg_tRNA_synt_N   Arginyl tRNA synthetase N terminal domain 4 6 4
  ARID   ARID/BRIGHT DNA binding domain 2 2 2
  Arm-DNA-bind_1   Bacteriophage lambda integrase, Arm DNA-binding domain 4 12 12
  Arm-DNA-bind_3   Arm DNA-binding domain 1 2 2
  AsnC_trans_reg   Lrp/AsnC ligand binding domain 1 1 0
  Asparaginase   Asparaginase, N-terminal 1 2 0
  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-binding domain 9 54 22
  ATP_bind_3   PP-loop family 1 2 2
  Autoind_bind   Autoinducer binding domain 2 8 0
  Auxin_resp   Auxin response factor 1 2 0
  A_deamin   Adenosine-deaminase (editase) domain 4 8 5
  B12-binding   B12 binding domain 1 8 0
  B12-binding_2   B12 binding domain 1 8 0
  B2   RNA binding protein B2 2 4 4
  B3   B3 DNA binding domain 1 2 2
  B3_4   B3/4 domain 2 4 2
  B5   tRNA synthetase B5 domain 2 4 0
  Bac_DnaA   Bacterial dnaA protein 1 4 4
  Bac_DnaA_C   Bacterial dnaA protein helix-turn-helix 4 9 5
  Bac_DNA_binding   Bacterial DNA-binding protein 19 44 40
  BAF   Barrier to autointegration factor 1 2 2
  BAH   BAH domain 7 20 2
  BamHI   Restriction endonuclease BamHI 5 12 11
  BCAS2   Breast carcinoma amplified sequence 2 (BCAS2) 3 4 3
  BEN   BEN domain 2 6 6
  BET   Bromodomain extra-terminal - transcription regulation 1 1 0
  Beta-Casp   Beta-Casp domain 1 4 4
  BHD_1   Rad4 beta-hairpin domain 1 3 3 3
  BHD_3   Rad4 beta-hairpin domain 3 3 3 3
  BP28CT   BP28CT (NUC211) domain 1 1 0
  BpuJI_N   Restriction endonuclease BpuJI - N terminal 4 5 5
  BRCA-2_helical   BRCA2, helical 1 1 0
  BRCA-2_OB1   BRCA2, oligonucleotide/oligosaccharide-binding, domain 1 1 1 0
  BRCA-2_OB3   BRCA2, oligonucleotide/oligosaccharide-binding, domain 3 1 1 1
  BRCT   BRCA1 C Terminus (BRCT) domain 1 1 1
  BRF1   Brf1-like TBP-binding domain 1 4 0
  Brix   Brix domain 1 1 1
  BrkDBD   Brinker DNA-binding domain 1 1 1
  Bromo_coat   Bromovirus coat protein 1 3 3
  Bse634I   Cfr10I/Bse634I restriction endonuclease 10 34 32
  BTD   Beta-trefoil DNA-binding domain 12 15 14
  Btz   CASC3/Barentsz eIF4AIII binding 5 17 9
  Bunya_nucleocap   Bunyavirus nucleocapsid (N) protein 5 24 24
  Bunya_RdRp   Bunyavirus RNA dependent RNA polymerase 2 2 2
  bZIP_1   bZIP transcription factor 11 23 22
  bZIP_2   Basic region leucine zipper 17 35 35
  bZIP_Maf   bZIP Maf transcription factor 6 14 12
  C1-set   Immunoglobulin C1-set domain 25 68 2
  C2-set_2   CD80-like C2-set immunoglobulin domain 4 8 5
  CAF1   CAF1 family ribonuclease 1 2 2
  CarD_CdnL_TRCF   CarD-like/TRCF domain 2 4 4
  Cas9-BH   Bridge helix of CRISPR-associated endonuclease Cas9 16 19 19
  Cas9_PI   PAM-interacting domain of CRISPR-associated endonuclease Cas9 14 17 17
  Cas9_REC   REC lobe of CRISPR-associated endonuclease Cas9 16 19 19
  Cas_Cas1   CRISPR associated protein Cas1 7 58 39
  Cas_Cas2CT1978   CRISPR-associated protein (Cas_Cas2CT1978) 7 16 8
  Cas_Cas5d   CRISPR-associated protein (Cas_Cas5) 7 11 11
  Cas_Cas6   CRISPR associated protein Cas6 4 7 7
  Cas_Cmr3   CRISPR-associated protein (Cas_Cmr3) 1 2 2
  Cas_Cmr5   CRISPR-associated protein (Cas_Cmr5) 1 2 2
  Cas_csx3   CRISPR-associated protein (Cas_csx3) 1 2 2
  Cas_Csy1   CRISPR-associated protein (Cas_Csy1) 1 1 1
  Cas_Csy2   CRISPR-associated protein (Cas_Csy2) 1 1 1
  Cas_Csy3   CRISPR-associated protein (Cas_Csy3) 1 7 7
  Cas_Csy4   CRISPR-associated protein (Cas_Csy4) 7 9 8
  Cas_CT1975   CT1975-like protein 7 68 67
  CAT_RBD   CAT RNA binding domain 1 2 2
  Cauli_VI   Caulimovirus viroplasmin 1 6 6
  CBFB_NFYA   CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B 2 2 2
  CBFD_NFYB_HMF   Histone-like transcription factor (CBF/NF-Y) and archaeal histone 4 7 7
  CBF_beta   Core binding factor beta subunit 9 17 0
  CcdA   Post-segregation antitoxin CcdA 2 4 4
  CDC45   CDC45-like protein 2 4 0
  Cdc6_C   CDC6, C terminal winged helix domain 4 5 5
  Cdd1   Pathogenicity locus 38 46 45
  CDT1_C   DNA replication factor Cdt1 C-terminal domain 2 2 0
  CENP-B_N   CENP-B N-terminal DNA-binding domain 1 1 1
  CENP-S   CENP-S protein 2 30 1
  CENP-T_C   Centromere kinetochore component CENP-T histone fold 145 309 305
  CENP-X   CENP-S associating Centromere protein X 2 30 8
  CHCH   CHCH domain 2 2 0
  Chordopox_A20R   Chordopoxvirus A20R protein 1 3 0
  Circo_capsid   Circovirus capsid protein 1 5 5
  Cir_N   N-terminal domain of CBF1 interacting co-repressor CIR 3 3 3
  Clp1   Pre-mRNA cleavage complex II protein Clp1 4 4 0
  CLP1_N   N-terminal beta-sandwich domain of polyadenylation factor 4 4 0
  CLP1_P   mRNA cleavage and polyadenylation factor CLP1 P-loop 4 4 4
  cNMP_binding   Cyclic nucleotide-binding domain 25 59 12
  CoA_binding   CoA binding domain 3 8 0
  COE1_DBD   Transcription factor COE1 DNA-binding domain 3 9 8
  COE1_HLH   Transcription factor COE1 helix-loop-helix domain 1 2 0
  Como_LCP   Large coat protein 2 2 1
  Como_SCP   Small coat protein 2 2 0
  Couple_hipA   HipA N-terminal domain 4 8 0
  CPL   CPL (NUC119) domain 1 1 1
  CPSF_A   CPSF A subunit region 11 13 0
  CR6_interact   Growth arrest and DNA-damage-inducible proteins-interacting protein 1 1 1 1
  Cren7   Chromatin protein Cren7 8 13 13
  CRISPR_assoc   CRISPR associated protein 13 25 25
  CRISPR_Cas6   CRISPR-associated endoribonuclease Cas6 5 12 12
  CRISPR_Cse1   CRISPR-associated protein Cse1 (CRISPR_cse1) 7 11 10
  CRISPR_Cse2   CRISPR-associated protein Cse2 (CRISPR_cse2) 7 22 6
  Cro   Cro 3 9 3
  Crp   Bacterial regulatory proteins, crp family 16 31 31
  CSD   'Cold-shock' DNA-binding domain 12 30 27
  CsrA   Global regulator protein family 9 26 26
  CTP-dep_RFKase   Domain of unknown function DUF120 1 2 0
  CtsR   Firmicute transcriptional repressor of class III stress genes (CtsR) 1 2 2
  Cucumo_2B   Cucumovirus protein 2B 2 6 6
  Cucumo_coat   Cucumovirus coat protein 1 3 0
  Cullin   Cullin family 2 3 0
  Cullin_Nedd8   Cullin protein neddylation domain 2 3 0
  CUT   CUT domain 3 4 4
  cwf21   cwf21 domain 4 4 0
  Cwf_Cwc_15   Cwf15/Cwc15 cell cycle control protein 5 10 5
  Cyclin_N   Cyclin, N-terminal domain 2 3 2
  Cytotoxic   Cytotoxic 1 1 1
  C_LFY_FLO   DNA Binding Domain (C-terminal) Leafy/Floricaula 1 2 2
  DALR_1   DALR anticodon binding domain 4 6 4
  DALR_2   DALR domain 1 1 1
  DAP3   Mitochondrial ribosomal death-associated protein 3 2 2 2
  DbpA   DbpA RNA binding domain 1 1 1
  DcpS_C   Scavenger mRNA decapping enzyme C-term binding 4 8 8
  DDE_Tnp_1   Transposase DDE domain 4 8 8
  DdrB   DdrB-like protein 2 10 8
  DEAD   DEAD/DEAH box helicase 55 124 104
  DEAD_2   DEAD_2 9 9 0
  Denso_VP4   Capsid protein VP4 1 1 1
  DHC_N1   Dynein heavy chain, N-terminal region 1 1 2 0
  DHH   DHH family 3 4 3
  DHHA1   DHHA1 domain 5 8 7
  DIM1   Mitosis protein DIM1 4 4 3
  Dimer_Tnp_Tn5   Transposase Tn5 dimerisation domain 4 8 8
  DKCLD   DKCLD (NUC011) domain 12 12 11
  DM   DM DNA binding domain 1 3 3
  Dna2   DNA replication factor Dna2 2 3 3
  DnaB   DnaB-like helicase N terminal domain 1 12 0
  DnaB_bind   DnaB-helicase binding domain of primase 1 2 0
  DnaB_C   DnaB-like helicase C terminal domain 1 12 12
  DNApol3-delta_C   DNA polymerase III, delta subunit, C terminal 3 6 0
  DNA_alkylation   DNA alkylation repair enzyme 17 17 17
  DNA_binding_1   6-O-methylguanine DNA methyltransferase, DNA binding domain 13 19 15
  DNA_gyraseB   DNA gyrase B 3 5 0
  DNA_gyraseB_C   DNA gyrase B subunit, carboxyl terminus 45 107 95
  DNA_III_psi   DNA polymerase III psi subunit 1 2 0
  DNA_ligase_aden   NAD-dependent DNA ligase adenylation domain 2 2 2
  DNA_ligase_A_C   ATP dependent DNA ligase C terminal region 2 2 2
  DNA_ligase_A_M   ATP dependent DNA ligase domain 4 7 7
  DNA_ligase_A_N   DNA ligase N terminus 2 2 2
  DNA_ligase_OB   NAD-dependent DNA ligase OB-fold domain 2 2 2
  DNA_ligase_OB_2   DNA ligase OB-like domain 2 5 5
  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger domain 2 2 2
  DNA_methylase   C-5 cytosine-specific DNA methylase 33 38 38
  DNA_photolyase   DNA photolyase 11 25 20
  DNA_pol3_alpha   Bacterial DNA polymerase III alpha subunit 8 12 11
  DNA_pol3_beta   DNA polymerase III beta subunit, N-terminal domain 4 8 3
  DNA_pol3_beta_2   DNA polymerase III beta subunit, central domain 4 8 3
  DNA_pol3_beta_3   DNA polymerase III beta subunit, C-terminal domain 4 8 0
  DNA_pol3_delta   DNA polymerase III, delta subunit 3 6 0
  DNA_pol3_delta2   DNA polymerase III, delta subunit 3 24 24
  DNA_pol3_delt_C   Processivity clamp loader gamma complex DNA pol III C-term 3 6 6
  DNA_pol3_gamma3   DNA polymerase III subunits gamma and tau domain III 3 18 0
  DNA_pol3_tau_5   DNA polymerase III tau subunit V interacting with alpha 1 1 0
  DNA_pol3_theta   DNA polymerase III, theta subunit 1 1 0
  DNA_pol_A   DNA polymerase family A 184 226 224
  DNA_pol_A_exo1   3'-5' exonuclease 17 18 17
  DNA_pol_B   DNA polymerase family B 143 197 192
  DNA_pol_B_2   DNA polymerase type B, organellar and viral 6 15 14
  DNA_pol_B_exo1   DNA polymerase family B, exonuclease domain 144 220 185
  DNA_pol_B_palm   DNA polymerase beta palm 389 434 421
  DNA_pol_B_thumb   DNA polymerase beta thumb 399 455 321
  DNA_pol_lambd_f   Fingers domain of DNA polymerase lambda 389 434 426
  DNA_PPF   DNA polymerase processivity factor 3 12 0
  DNA_primase_lrg   Eukaryotic and archaeal DNA primase, large subunit 2 4 4
  DNA_primase_S   DNA primase small subunit 1 2 2
  DNA_processg_A   DNA recombination-mediator protein A 1 2 2
  DNA_RNApol_7kD   DNA directed RNA polymerase, 7 kDa subunit 107 109 0
  DNA_topoisoIV   DNA gyrase/topoisomerase IV, subunit A 54 135 125
  DpnI   Dam-replacing family 2 3 3
  DSHCT   DSHCT (NUC185) domain 2 3 3
  dsrm   Double-stranded RNA binding motif 27 50 41
  DSS1_SEM1   DSS1/SEM1 family 1 1 0
  DUF1115   Protein of unknown function (DUF1115) 5 6 5
  DUF1713   Mitochondrial domain of unknown function (DUF1713) 2 2 2
  DUF1726   Domain of unknown function (DUF1726) 1 2 0
  DUF1730   Domain of unknown function (DUF1730) 3 8 0
  DUF1743   Domain of unknown function (DUF1743) 2 2 2
  DUF2209   Uncharacterized protein conserved in archaea (DUF2209) 2 2 0
  DUF2258   Uncharacterized protein conserved in archaea (DUF2258) 1 8 8
  DUF331   Domain of unknown function 1 1 1
  DUF3378   Domain of unknown function (DUF3378) 1 1 1
  DUF3578   Domain of unknown function (DUF3578) 3 6 6
  DUF3591   Protein of unknown function (DUF3591) 1 1 1
  DUF3692   CRISPR-associated protein 1 1 0
  DUF4114   Domain of unknown function (DUF4114) 1 1 0
  DUF4152   Protein of unknown function (DUF4152) 5 15 15
  DUF445   Protein of unknown function (DUF445) 1 1 1
  DUF4455   Domain of unknown function (DUF4455) 1 2 0
  DUF4496   Domain of unknown function (DUF4496) 6 7 5
  DUF4918   Domain of unknown function (DUF4918) 3 6 6
  DUF5323   Family of unknown function (DUF5323) 3 3 3
  DUF5328   Family of unknown function (DUF5328) 2 8 5
  DUF5467   Family of unknown function (DUF5467) 1 1 1
  DUF572   Family of unknown function (DUF572) 3 3 3
  DUF727   Protein of unknown function (DUF727) 1 1 1
  Dus   Dihydrouridine synthase (Dus) 4 8 8
  E2F_TDP   E2F/DP family winged-helix DNA-binding domain 2 4 4
  EAL   EAL domain 2 4 4
  EBV-NA1   Epstein Barr virus nuclear antigen-1, DNA-binding domain 1 2 2
  Eco57I   Eco57I restriction-modification methylase 9 16 16
  EcoRI   Restriction endonuclease EcoRI 6 12 12
  EcoRII-C   EcoRII C terminal 3 10 10
  EcoRII-N   Restriction endonuclease EcoRII, N-terminal 1 1 1
  ECR1_N   Exosome complex exonuclease RRP4 N-terminal region 8 12 0
  EFG_C   Elongation factor G C-terminus 52 52 4
  EFG_II   Elongation Factor G, domain II 41 41 10
  EFG_IV   Elongation factor G, domain IV 48 48 29
  EFP   Elongation factor P (EF-P) OB domain 2 2 0
  EFP_N   Elongation factor P (EF-P) KOW-like domain 2 2 2
  EFTUD2   116 kDa U5 small nuclear ribonucleoprotein component N-terminus 1 1 0
  EF_TS   Elongation factor TS 9 9 0
  eIF-1a   Translation initiation factor 1A / IF-1 23 23 22
  eIF-3c_N   Eukaryotic translation initiation factor 3 subunit 8 N-terminus 1 1 1
  eIF-5_eIF-2B   Domain found in IF2B/IF5 2 2 1
  eIF-6   eIF-6 family 8 8 1
  eIF2A   Eukaryotic translation initiation factor eIF2A 1 1 1
  eIF2_C   Initiation factor eIF2 gamma, C terminal 6 6 3
  eIF3g   Eukaryotic translation initiation factor 3 subunit G 1 1 0
  EIF_2_alpha   Eukaryotic translation initiation factor 2 alpha subunit 6 6 3
  Elong-fact-P_C   Elongation factor P, C-terminal 2 2 2
  EMG1   EMG1/NEP1 methyltransferase 4 8 6
  Endonuc-BglII   Restriction endonuclease BglII 4 8 8
  Endonuc-BsobI   Restriction endonuclease BsobI 1 2 2
  Endonuc-dimeris   T4 recombination endonuclease VII, dimerisation 2 4 4
  Endonuc-EcoRV   Restriction endonuclease EcoRV 30 62 62
  Endonuc-FokI_C   Restriction endonuclease FokI, C terminal 1 1 1
  Endonuc-HincII   Restriction endonuclease HincII 18 49 49
  Endonuc-MspI   Restriction endonuclease MspI 2 4 4
  Endonuc-PvuII   Restriction endonuclease PvuII 5 10 10
  Endonuclease_1   Endonuclease I 2 6 6
  Endonuclease_5   Endonuclease V 3 6 2
  Endonuclease_7   Recombination endonuclease VII 4 8 8
  Endonuclease_NS   DNA/RNA non-specific endonuclease 2 3 2
  Endonuc_BglI   Restriction endonuclease BglI 1 2 2
  EnY2   Transcription factor e(y)2 1 4 3
  ERCC3_RAD25_C   ERCC3/RAD25/XPB C-terminal helicase 7 7 4
  ERCC4   ERCC4 domain 6 19 9
  eRF1_1   eRF1 domain 1 6 6 5
  eRF1_2   eRF1 domain 2 6 6 3
  eRF1_3   eRF1 domain 3 6 6 3
  Ets   Ets-domain 38 69 69
  EVE   EVE domain 1 2 2
  Exc   Excisionase-like protein 4 10 9
  Exo70   Exo70 exocyst complex subunit 1 1 0
  Exonuc_VII_L   Exonuclease VII, large subunit 1 2 0
  Exonuc_V_gamma   Exodeoxyribonuclease V, gamma subunit 3 5 0
  Exonuc_X-T_C   Exonuclease C-terminal 6 18 18
  EXOSC1   Exosome component EXOSC1/CSL4 8 17 1
  Exo_endo_phos   Endonuclease/Exonuclease/phosphatase family 40 87 79
  FadR_C   FadR C-terminal domain 3 8 0
  FAD_binding_7   FAD binding domain of DNA photolyase 10 23 17
  Fapy_DNA_glyco   Formamidopyrimidine-DNA glycosylase N-terminal domain 74 95 95
  Fcf1   Fcf1 1 1 0
  FDX-ACB   Ferredoxin-fold anticodon binding domain 3 5 5
  FemAB   FemAB family 1 2 1
  FeoA   FeoA domain 1 8 0
  Fer4   4Fe-4S binding domain 2 2 0
  Fer4_16   4Fe-4S double cluster binding domain 3 8 4
  Fe_dep_repress   Iron dependent repressor, N-terminal DNA binding domain 6 28 28
  Fe_dep_repr_C   Iron dependent repressor, metal binding and dimerisation domain 6 28 0
  FHA   FHA domain 1 1 0
  Fibrillarin   Fibrillarin 9 26 15
  Filo_VP35   Filoviridae VP35 5 17 15
  FKBP_C   FKBP-type peptidyl-prolyl cis-trans isomerase 1 2 0
  Flavi_DEAD   Flavivirus DEAD domain 15 31 28
  Flavi_NS5   Flavivirus RNA-directed RNA polymerase 1 1 0
  Flexi_CP   Viral coat protein 2 26 26
  Flp_C   Recombinase Flp protein 3 12 12
  Flp_N   Recombinase Flp protein N-terminus 3 12 12
  Flu_NP   Influenza virus nucleoprotein 1 50 0
  Flu_NS1   Influenza non-structural protein (NS1) 1 2 2
  Flu_PA   Influenza RNA-dependent RNA polymerase subunit PA 8 10 10
  Flu_PB1   Influenza RNA-dependent RNA polymerase subunit PB1 8 10 8
  Flu_PB2   Influenza RNA-dependent RNA polymerase subunit PB2 7 8 6
  FokI_C   Restriction endonuclease FokI, catalytic domain 1 1 1
  FokI_N   Restriction endonuclease FokI, recognition domain 1 1 1
  Forkhead   Forkhead domain 15 29 29
  Formyl_trans_C   Formyl transferase, C-terminal domain 1 2 2
  Formyl_trans_N   Formyl transferase 1 2 2
  FOXP-CC   FOXP coiled-coil domain 1 1 0
  FtsJ   FtsJ-like methyltransferase 3 7 5
  Ftsk_gamma   Ftsk gamma domain 1 6 6
  FUR   Ferric uptake regulator family 4 12 12
  G-gamma   GGL domain 1 1 0
  G10   G10 protein 8 8 7
  GAD   GAD domain 5 11 2
  GAGA   GAGA factor 2 2 2
  Gag_spuma   Spumavirus gag protein 1 1 0
  Gal4_dimer   Gal4-like dimerisation domain 2 4 4
  Gar1   Gar1/Naf1 RNA binding region 4 4 0
  GATA   GATA zinc finger 16 27 25
  GatB_N   GatB/GatE catalytic domain 4 9 8
  GatB_Yqey   GatB domain 3 7 5
  Gcd10p   Gcd10p family 3 5 5
  GCD14   tRNA methyltransferase complex GCD14 subunit 3 4 2
  GCD14_N   tRNA methyltransferase complex GCD14 subunit N-term 3 4 2
  GCM   GCM motif protein 1 1 1
  GerE   Bacterial regulatory proteins, luxR family 9 28 28
  Glu-tRNAGln   Glu-tRNAGln amidotransferase C subunit 3 7 0
  GNAT_acetyltr_2   GNAT acetyltransferase 2 1 5 0
  GntR   Bacterial regulatory proteins, gntR family 10 24 24
  gp45-slide_C   gp45 sliding clamp, C terminal 3 12 2
  GreA_GreB   Transcription elongation factor, GreA/GreB, C-term 2 6 0
  GreA_GreB_N   Transcription elongation factor, N-terminal 2 6 0
  Gti1_Pac2   Gti1/Pac2 family 3 4 4
  GTP-bdg_M   GTP-binding GTPase Middle Region 1 1 1
  GTP-bdg_N   GTP-binding GTPase N-terminal 1 1 0
  GTP1_OBG   GTP1/OBG 1 1 1
  GTP_EFTU   Elongation factor Tu GTP binding domain 109 136 45
  GTP_EFTU_D2   Elongation factor Tu domain 2 108 112 70
  GTP_EFTU_D3   Elongation factor Tu C-terminal domain 40 44 29
  GTP_EFTU_D4   Elongation factor Tu domain 4 5 5 5
  GyrI-like   GyrI-like small molecule binding domain 8 18 0
  H2TH   Formamidopyrimidine-DNA glycosylase H2TH domain 74 95 93
  HA2   Helicase associated domain (HA2) 8 10 5
  HABP4_PAI-RBP1   Hyaluronan / mRNA binding family 17 17 17
  HAND   HAND 1 1 0
  HAT   HAT (Half-A-TPR) repeat 8 11 1
  HATPase_c   Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase 3 5 0
  HBB   Helical and beta-bridge domain 9 9 1
  HD   HD domain 4 16 11
  HD_assoc   Phosphohydrolase-associated domain 1 6 0
  HEAT_2   HEAT repeats 3 8 4
  Helicase_C   Helicase conserved C-terminal domain 80 156 136
  Helicase_C_2   Helicase C-terminal domain 9 9 2
  Helicase_RecD   Helicase 1 2 0
  Herpes_alk_exo   Herpesvirus alkaline exonuclease 2 2 2
  Hfq   Hfq protein 12 88 67
  HGTP_anticodon   Anticodon binding domain 12 30 18
  HHH   Helix-hairpin-helix motif 15 16 16
  HhH-GPD   HhH-GPD superfamily base excision DNA repair protein 75 106 106
  HHH_2   Helix-hairpin-helix motif 3 4 3
  HHH_4   Helix-hairpin-helix containing domain 2 3 3
  HHH_5   Helix-hairpin-helix domain 10 23 11
  HHH_6   Helix-hairpin-helix motif 8 12 8
  HHH_8   Helix-hairpin-helix domain 379 417 321
  HigB-like_toxin   RelE-like toxin of type II toxin-antitoxin system HigB 1 1 1
  HIN   HIN-200/IF120x domain 8 19 18
  HipA_C   HipA-like C-terminal domain 4 8 4
  HIRAN   HIRAN domain 2 6 6
  Histone   Core histone H2A/H2B/H3/H4 145 925 908
  Histone_H2A_C   C-terminus of histone H2A 145 308 3
  Histone_HNS   H-NS histone family 1 1 1
  HIT   HIT domain 3 9 9
  Hjc   Archaeal holliday junction resolvase (hjc) 3 6 4
  HLH   Helix-loop-helix DNA-binding domain 21 60 60
  HMG_box   HMG (high mobility group) box 23 48 47
  HMG_box_2   HMG-box domain 6 14 14
  HNF-1_N   Hepatocyte nuclear factor 1 (HNF-1), N terminus 2 4 4
  HNH_3   HNH endonuclease 1 1 1
  HNH_4   HNH endonuclease 16 17 1
  Homeobox   Homeobox domain 64 134 134
  Homeobox_KN   Homeobox KN domain 5 8 8
  Hom_end   Homing endonuclease 2 4 4
  Hom_end_hint   Hom_end-associated Hint 2 2 2
  Hormone_recep   Ligand-binding domain of nuclear hormone receptor 6 16 0
  HPD   Homeo-prospero domain 1 1 1
  HRDC   HRDC domain 6 7 2
  HsdM_N   HsdM N-terminal domain 1 2 0
  HSF_DNA-bind   HSF-type DNA-binding 10 25 19
  HTH_1   Bacterial regulatory helix-turn-helix protein, lysR family 2 12 12
  HTH_18   Helix-turn-helix domain 4 7 7
  HTH_19   Helix-turn-helix domain 3 8 8
  HTH_24   Winged helix-turn-helix DNA-binding 6 14 14
  HTH_27   Winged helix DNA-binding domain 8 54 53
  HTH_3   Helix-turn-helix 40 106 101
  HTH_31   Helix-turn-helix domain 2 4 4
  HTH_5   Bacterial regulatory protein, arsR family 2 8 8
  HTH_7   Helix-turn-helix domain of resolvase 16 33 33
  HTH_8   Bacterial regulatory protein, Fis family 22 44 44
  HTH_9   RNA polymerase III subunit RPC82 helix-turn-helix domain 1 1 0
  HTH_AraC   Bacterial regulatory helix-turn-helix proteins, AraC family 1 1 1
  HTH_AsnC-type   AsnC-type helix-turn-helix domain 1 1 1
  HTH_Crp_2   Crp-like helix-turn-helix domain 10 30 30
  HTH_IclR   IclR helix-turn-helix domain 1 4 4
  HTH_Tnp_Mu_1   Mu DNA-binding domain 1 1 1
  HTH_Tnp_Tc3_1   Tc3 transposase 2 2 2
  HTH_Tnp_Tc5   Tc5 transposase DNA-binding domain 1 1 1
  HutP   HutP 4 24 24
  HxlR   HxlR-like helix-turn-helix 1 2 2
  IBD   Transcription-initiator DNA-binding domain IBD 2 7 5
  IBN_N   Importin-beta N-terminal domain 1 2 0
  IclR   Bacterial transcriptional regulator 1 4 0
  IF-2   Translation-initiation factor 2 8 8 2
  IF3_C   Translation initiation factor IF-3, C-terminal domain 12 12 11
  IF3_N   Translation initiation factor IF-3, N-terminal domain 11 11 11
  IgG_binding_B   B domain 1 1 0
  Ig_3   Immunoglobulin domain 4 8 8
  IL6   Interleukin-6/G-CSF/MGF family 2 3 3
  Img2   Mitochondrial large subunit ribosomal protein (Img2) 3 3 2
  IMS   impB/mucB/samB family 309 392 389
  IMS_C   impB/mucB/samB family C-terminal domain 183 217 217
  IMS_HHH   IMS family HHH motif 156 228 223
  IncA   IncA protein 4 8 8
  Integrase_DNA   DNA binding domain of tn916 integrase 2 2 2
  Integrase_Zn   Integrase Zinc binding domain 5 38 6
  Intron_maturas2   Type II intron maturase 1 1 1
  Ints3   Integrator complex subunit 3 2 2 0
  IN_DBD_C   Integrase DNA binding domain 5 48 25
  IPPT   IPP transferase 7 26 26
  IRF   Interferon regulatory factor transcription factor 7 22 21
  Isy1   Isy1-like splicing family 3 3 3
  JAB   JAB1/Mov34/MPN/PAD-1 ubiquitin protease 1 1 0
  KH_1   KH domain 26 64 50
  KH_2   KH domain 476 477 63
  KH_5   NusA-like KH domain 4 6 6
  KH_6   KH domain 6 12 0
  KH_dom-like   KH-domain-like of EngA bacterial GTPase enzymes, C-terminal 1 1 1
  KilA-N   KilA-N domain 1 2 2
  KORA   TrfB plasmid transcriptional repressor 3 12 12
  KorB   KorB domain 1 4 4
  KOW   KOW motif 507 527 437
  KTI12   Chromatin associated protein KTI12 3 6 6
  Ku   Ku70/Ku80 beta-barrel domain 1 2 2
  Ku_C   Ku70/Ku80 C-terminal arm 1 2 1
  Ku_N   Ku70/Ku80 N-terminal alpha/beta domain 1 2 1
  L31   Mitochondrial ribosomal protein L31 1 1 0
  L51_S25_CI-B8   Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain 4 4 3
  La   La domain 7 13 12
  LacI   Bacterial regulatory proteins, lacI family 40 82 78
  Lactamase_B   Metallo-beta-lactamase superfamily 4 10 10
  Lactamase_B_2   Beta-lactamase superfamily domain 3 8 7
  LAG1-DNAbind   LAG1, DNA binding 12 15 14
  LAGLIDADG_1   LAGLIDADG endonuclease 64 163 161
  LAGLIDADG_2   LAGLIDADG DNA endonuclease family 6 8 8
  LAGLIDADG_3   LAGLIDADG-like domain 17 99 99
  Ldh_1_C   lactate/malate dehydrogenase, alpha/beta C-terminal domain 3 10 5
  Ldh_1_N   lactate/malate dehydrogenase, NAD binding domain 3 10 10
  Lectin_legB   Legume lectin domain 1 4 4
  LepA_C   GTP-binding protein LepA C-terminus 2 2 2
  Leucyl-specific   Leucine-tRNA synthetase-specific domain 3 6 0
  Levi_coat   Levivirus coat protein 31 97 90
  LexA_DNA_bind   LexA DNA binding domain 3 6 4
  LIM   LIM domain 1 2 0
  Linker_histone   linker histone H1 and H5 family 1 1 1
  LRR_4   Leucine Rich repeats (2 copies) 1 2 1
  LRR_8   Leucine rich repeat 10 121 48
  LRR_9   Leucine-rich repeat 7 8 2
  LSM   LSM domain 24 399 293
  LUC7   LUC7 N_terminus 284 284 276
  Lys   C-type lysozyme/alpha-lactalbumin family 2 7 7
  LytTR   LytTr DNA-binding domain 6 14 12
  L_protein_N   L protein N-terminus 2 2 0
  MA3   MA3 domain 8 8 0
  Mab-21   Mab-21 protein 10 16 16
  Macro   Macro domain 2 8 4
  MafB19-deam   MafB19-like deaminase 1 4 4
  Mago_nashi   Mago nashi protein 5 9 0
  MamL-1   MamL-1 domain 3 4 0
  MarR   MarR family 9 37 37
  MarR_2   MarR family 7 27 21
  MazE_antitoxin   Antidote-toxin recognition MazE, bacterial antitoxin 4 14 14
  MBD   Methyl-CpG binding domain 10 11 11
  MC1   Non-histone chromosomal protein MC1 1 1 1
  MCM   MCM2/3/5 family 4 24 14
  MCM_N   MCM N-terminal domain 5 36 0
  MCM_OB   MCM OB domain 5 36 12
  Med11   Mediator complex protein 2 2 0
  Med12-LCEWAV   Eukaryotic Mediator 12 subunit domain 2 2 2
  Med17   Subunit 17 of Mediator complex 2 2 0
  Med18   Med18 protein 2 2 0
  Med20   TATA-binding related factor (TRF) of subunit 20 of Mediator complex 2 2 0
  Med21   Subunit 21 of Mediator complex 1 1 0
  Med22   Surfeit locus protein 5 subunit 22 of Mediator complex 2 2 0
  Med31   SOH1 1 1 0
  Med4   Vitamin-D-receptor interacting Mediator subunit 4 1 1 0
  Med6   MED6 mediator sub complex component 2 2 0
  Med7   MED7 protein 1 2 0
  Med8   Mediator of RNA polymerase II transcription complex subunit 8 2 2 0
  Med9   RNA polymerase II transcription mediator complex subunit 9 1 2 0
  MEF2_binding   MEF2 binding 1 1 0
  MerR_1   MerR HTH family regulatory protein 15 41 40
  Metallophos   Calcineurin-like phosphoesterase 10 40 25
  Methylase_S   Type I restriction modification DNA specificity domain 1 2 2
  MethyltransfD12   D12 class N6 adenine-specific DNA methyltransferase 15 26 24
  Methyltransf_1N   6-O-methylguanine DNA methyltransferase, ribonuclease-like domain 4 9 0
  Methyltransf_31   Methyltransferase domain 1 2 2
  Methyltransf_4   Putative methyltransferase 1 1 1
  MetJ   Met Apo-repressor, MetJ 6 24 24
  Met_10   Met-10+ like-protein 2 3 3
  MH1   MH1 domain 10 27 27
  Mhr1   Transcriptional regulation of mitochondrial recombination 1 1 0
  Microvir_J   Microvirus J protein 2 2 2
  MIF4G   MIF4G domain 1 1 0
  Mitoc_L55   Mitochondrial ribosomal protein L55 1 1 0
  MMR_HSR1   50S ribosome-binding GTPase 8 9 5
  MMR_HSR1_Xtn   C-terminal region of MMR_HSR1 domain 4 4 0
  MMS1_N   Mono-functional DNA-alkylating methyl methanesulfonate N-term 11 13 0
  MobA_MobL   MobA/MobL family 1 1 1
  Mob_Pre   Plasmid recombination enzyme 6 7 7
  MogR_DNAbind   DNA binding domain of the motility gene repressor (MogR) 1 2 2
  MotCF   Bacteriophage T4 MotA, C-terminal 1 4 4
  MqsA_antitoxin   Antitoxin component of bacterial toxin-antitoxin system, MqsA 1 2 2
  MRP   Mitochondrial RNA binding protein MRP 1 2 2
  MRP-63   Mitochondrial ribosome protein 63 1 1 1
  MRP-L20   Mitochondrial ribosomal protein subunit L20 1 1 0
  MRP-L27   Mitochondrial ribosomal protein L27 2 2 1
  MRP-L28   Mitochondrial ribosomal protein L28 2 2 1
  MRP-L46   39S mitochondrial ribosomal protein L46 1 1 0
  MRP-L47   Mitochondrial 39-S ribosomal protein L47 (MRP-L47) 4 4 1
  MRP-L51   Mitochondrial ribosomal subunit 1 1 1
  MRP-S22   Mitochondrial 28S ribosomal protein S22 2 2 0
  MRP-S23   Mitochondrial ribosomal protein S23 2 2 2
  MRP-S24   Mitochondrial ribosome subunit S24 3 3 3
  MRP-S26   Mitochondrial ribosome subunit S26 2 2 2
  MRP-S27   Mitochondrial 28S ribosomal protein S27 1 1 1
  MRP-S28   Mitochondrial ribosomal subunit protein 2 2 2
  MRP-S31   Mitochondrial 28S ribosomal protein S31 2 2 0
  MRP-S32   Mitochondrial 28S ribosomal protein S32 1 1 1
  MRP-S33   Mitochondrial ribosomal subunit S27 2 2 2
  MRP-S34   Mitochondrial 28S ribosomal protein S34 2 2 2
  MRP-S35   Mitochondrial ribosomal protein MRP-S35 2 2 2
  MRP_L53   39S ribosomal protein L53/MRP-L53 1 1 1
  Mrr_cat   Restriction endonuclease 1 4 0
  Mrr_cat_2   Restriction endonuclease 1 2 0
  MSL2-CXC   CXC domain of E3 ubiquitin-protein ligase MSL2 2 6 6
  mTERF   mTERF 8 8 8
  MutH   DNA mismatch repair enzyme MutH 2 3 3
  MutS_I   MutS domain I 25 50 39
  MutS_II   MutS domain II 25 50 0
  MutS_III   MutS domain III 25 50 49
  MutS_IV   MutS family domain IV 25 46 44
  MutS_V   MutS domain V 25 50 0
  MvaI_BcnI   MvaI/BcnI restriction endonuclease family 4 10 10
  Myb_Cef   pre-mRNA splicing factor component 2 2 2
  Myb_DNA-binding   Myb-like DNA-binding domain 20 42 38
  Myb_DNA-bind_5   Myb/SANT-like DNA-binding domain 1 2 2
  Myb_DNA-bind_6   Myb-like DNA-binding domain 10 12 11
  Myc-LZ   Myc leucine zipper domain 2 4 0
  N36   36-mer N-terminal peptide of the N protein (N36) 3 4 4
  N6_Mtase   N-6 DNA Methylase 3 6 6
  N6_N4_Mtase   DNA methylase 1 2 2
  NaeI   Restriction endonuclease NaeI 1 2 2
  NAM   No apical meristem (NAM) protein 2 8 8
  NARP1   NMDA receptor-regulated protein 1 4 4 4
  NDC10_II   Centromere DNA-binding protein complex CBF3 subunit, domain 2 2 10 5
  NDT80_PhoG   NDT80 / PhoG like DNA-binding family 11 11 11
  Neil1-DNA_bind   Endonuclease VIII-like 1, DNA bind 5 15 15
  NGF   Nerve growth factor family 1 2 2
  NgoMIV_restric   NgoMIV restriction enzyme 2 6 6
  NHL   NHL repeat 2 15 15
  NikR_C   NikR C terminal nickel binding domain 1 8 4
  Nop   snoRNA binding domain, fibrillarin 17 42 41
  Nop10p   Nucleolar RNA-binding protein, Nop10p family 12 12 9
  NotI   Restriction endonuclease NotI 1 2 2
  NTP_transf_2   Nucleotidyltransferase domain 47 88 81
  NucS   Endonuclease NucS 5 10 10
  NUDIX   NUDIX domain 6 10 3
  NUDIX_2   Nucleotide hydrolase 4 12 9
  NUDIX_4   NUDIX domain 10 11 11
  NUMOD4   NUMOD4 motif 1 1 1
  NusA_N   NusA N-terminal domain 2 3 0
  NusB   NusB family 5 15 10
  NusG   Transcription termination factor nusG 1 1 1
  OAS1_C   2'-5'-oligoadenylate synthetase 1, domain 2, C-terminus 5 5 5
  OB_NTP_bind   Oligonucleotide/oligosaccharide-binding (OB)-fold 8 10 5
  OB_RNB   Ribonuclease B OB domain 1 1 0
  OGG_N   8-oxoguanine DNA glycosylase, N-terminal domain 30 32 1
  Omega_Repress   Omega Transcriptional Repressor 3 12 12
  ORC2   Origin recognition complex subunit 2 2 2 2
  ORC4_C   Origin recognition complex (ORC) subunit 4 C-terminus 2 2 2
  ORC5_C   Origin recognition complex (ORC) subunit 5 C-terminus 2 2 2
  P22_Cro   DNA-binding transcriptional regulator Cro 1 2 2
  P53   P53 DNA-binding domain 27 123 123
  P53_tetramer   P53 tetramerisation motif 4 16 0
  PA-IIL   Fucose-binding lectin II (PA-IIL) 1 1 0
  PADR1   PADR1 (NUC008) domain 4 8 0
  PAP_assoc   Cid1 family poly A polymerase 1 2 2
  PAP_central   Poly(A) polymerase central domain 1 1 1
  PAP_RNA-bind   Poly(A) polymerase predicted RNA binding domain 1 1 1
  Paramyxo_ncap   Paramyxovirus nucleocapsid protein 2 14 14
  ParB   ParB family 5 7 6
  ParBc   ParB-like nuclease domain 1 4 0
  ParE_toxin   ParE toxin of type II toxin-antitoxin system, parDE 2 2 2
  PARP   Poly(ADP-ribose) polymerase catalytic domain 4 8 0
  PARP_reg   Poly(ADP-ribose) polymerase, regulatory domain 4 8 0
  PARP_regulatory   Poly A polymerase regulatory subunit 4 6 3
  Parvo_coat   Parvovirus coat protein VP2 8 8 8
  PAS   PAS fold 4 8 2
  PAS_11   PAS domain 3 3 0
  PAS_3   PAS fold 3 3 0
  PAX   'Paired box' domain 4 6 6
  PAZ   PAZ domain 33 41 40
  PBP   Phosphatidylethanolamine-binding protein 3 3 0
  PC4   Transcriptional Coactivator p15 (PC4) 4 12 12
  PCI   PCI domain 1 2 0
  PCNA_C   Proliferating cell nuclear antigen, C-terminal domain 2 6 2
  PCNA_N   Proliferating cell nuclear antigen, N-terminal domain 2 6 3
  PCRF   PCRF domain 16 16 13
  PD-C2-AF1   POU domain, class 2, associating factor 1 1 2 2
  PDCD9   Mitochondrial 28S ribosomal protein S30 (PDCD9) 1 2 2
  PDDEXK_1   PD-(D/E)XK nuclease superfamily 7 14 6
  PDDEXK_5   PD-(D/E)XK endonuclease 1 4 2
  PemK_toxin   PemK-like, MazF-like toxin of type II toxin-antitoxin system 8 18 13
  Penicillinase_R   Penicillinase repressor 4 9 9
  Peptidase_A21   Peptidase family A21 1 8 1
  Peptidase_A6   Peptidase A6 family 7 21 7
  Peptidase_S24   Peptidase S24-like 4 8 0
  Peptidase_S29   Hepatitis C virus NS3 protease 2 4 0
  Peptidase_S48   Peptidase family S48 6 14 14
  Pept_tRNA_hydro   Peptidyl-tRNA hydrolase 1 2 2
  Peripla_BP_1   Periplasmic binding proteins and sugar binding domain of LacI family 1 4 0
  Peripla_BP_3   Periplasmic binding protein-like domain 30 65 0
  PH   PH domain 2 2 0
  Phage_CII   Bacteriophage CII protein 1 4 4
  Phage_clamp_A   Bacteriophage clamp loader A subunit 3 4 3
  Phage_coat   Phage PP7 coat protein 1 12 12
  Phage_endo_I   Phage endonuclease I 1 2 2
  Phage_F   Capsid protein (F protein) 2 3 3
  Phage_G   Major spike protein (G protein) 2 2 0
  Phage_integrase   Phage integrase family 29 108 108
  Phage_int_SAM_1   Phage integrase, N-terminal SAM-like domain 3 10 10
  Phage_int_SAM_4   Phage integrase, N-terminal SAM-like domain 23 88 88
  Phage_lysozyme   Phage lysozyme 1 1 0
  Phage_mat-A   Phage maturation protein 1 1 1
  Phage_NinH   Phage NinH protein 21 21 21
  PhdYeFM_antitox   Antitoxin Phd_YefM, type II toxin-antitoxin system 2 8 8
  Phe_tRNA-synt_N   Aminoacyl tRNA synthetase class II, N-terminal domain 2 4 4
  PHF5   PHF5-like protein 1 1 0
  Phi-29_GP16_7   Bacteriophage phi-29 early protein GP16.7 1 6 2
  Phi-29_GP4   Phi-29-like late genes activator (early protein GP4) 1 2 2
  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophosphatase 1 1 1
  PHP   PHP domain 10 15 0
  PIF1   PIF1-like helicase 3 4 4
  PIN   PIN domain 4 16 0
  PIN_4   PIN domain 5 5 0
  Piwi   Piwi domain 46 63 59
  Pkinase   Protein kinase domain 4 5 2
  Plug_translocon   Plug domain of Sec61p 7 7 0
  PMC2NT   PMC2NT (NUC016) domain 1 1 0
  Pneumovirus_M2   Pneumovirus matrix protein 2 (M2) 1 4 0
  Pneumo_ncap   Pneumovirus nucleocapsid protein 6 103 103
  PNK3P   Polynucleotide kinase 3 phosphatase 5 6 6
  PolC_DP2   DNA polymerase II large subunit DP2 12 12 9
  PolyA_pol   Poly A polymerase head domain 13 22 21
  PolyA_pol_RNAbd   Probable RNA and SrmB- binding site of polymerase A 13 22 16
  Polyketide_cyc2   Polyketide cyclase / dehydrase and lipid transport 1 1 1
  Polyoma_lg_T_C   Polyomavirus large T antigen C-terminus 2 10 10
  POT1   Telomeric single stranded DNA binding POT1/CDC13 22 47 30
  POT1PC   ssDNA-binding domain of telomere protection protein 12 12 12
  POTRA_1   POTRA domain, FtsQ-type 1 1 0
  Pou   Pou domain - N-terminal to homeobox domain 10 21 21
  Pox_polyA_pol   Poxvirus poly(A) polymerase nucleotidyltransferase domain 3 5 2
  Pox_polyA_pol_C   Poxvirus poly(A) polymerase C-terminal domain 3 5 4
  Pox_polyA_pol_N   Poxvirus poly(A) polymerase N-terminal domain 3 5 5
  PPR   PPR repeat 2 3 1
  PPR_1   PPR repeat 6 13 13
  PPR_2   PPR repeat family 6 35 27
  PPR_3   Pentatricopeptide repeat domain 2 7 7
  PPV_E1_C   Papillomavirus helicase 3 24 23
  PPV_E2_C   E2 (early) protein, C terminal 4 7 7
  PQQ_2   PQQ-like domain 1 4 2
  Pre-SET   Pre-SET motif 3 3 0
  PriCT_1   Primase C terminal 1 (PriCT-1) 1 2 2
  PRO8NT   PRO8NT (NUC069), PrP8 N-terminal domain 12 12 10
  PROCN   PROCN (NUC071) domain 13 13 10
  PROCT   PROCT (NUC072) domain 6 6 0
  Prok-RING_1   Prokaryotic RING finger family 1 2 6 0
  ProRS-C_1   Prolyl-tRNA synthetase, C-terminal 2 4 0
  Pro_isomerase   Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD 1 2 1
  Prp18   Prp18 domain 3 3 2
  Prp19   Prp19/Pso4-like 5 20 5
  PRP1_N   PRP1 splicing factor, N-terminal 1 2 0
  PRP3   pre-mRNA processing factor 3 (PRP3) 3 3 3
  Prp31_C   Prp31 C terminal domain 3 3 3
  PRP8_domainIV   PRP8 domain IV core 12 12 7
  PseudoU_synth_1   tRNA pseudouridine synthase 3 20 15
  PseudoU_synth_2   RNA pseudouridylate synthase 3 10 10
  PspA_IM30   PspA/IM30 family 3 5 4
  PSRP-3_Ycf65   Plastid and cyanobacterial ribosomal protein (PSRP-3 / Ycf65) 1 1 0
  PTS-HPr   PTS HPr component phosphorylation site 5 13 0
  PUA   PUA domain 16 18 15
  PUF   Pumilio-family RNA binding repeat 40 365 348
  PurA   PurA ssDNA and RNA-binding protein 1 1 1
  Pur_DNA_glyco   Methylpurine-DNA glycosylase (MPG) 5 6 6
  Put_DNA-bind_N   Putative DNA-binding protein N-terminus 3 8 8
  Pyr_excise   Pyrimidine dimer DNA glycosylase 2 3 3
  Qua1   Qua1 domain 2 4 0
  R-HINP1I   R.HinP1I restriction endonuclease 4 5 5
  Rad10   Binding domain of DNA repair protein Ercc1 (rad10/Swi10) 1 1 0
  Rad4   Rad4 transglutaminase-like domain 3 3 3
  Rad51   Rad51 2 6 6
  Radical_SAM   Radical SAM superfamily 2 4 4
  RAG1   Recombination-activation protein 1 (RAG1), recombinase 3 6 6
  RAG2   Recombination activating protein 2 3 6 2
  RAI1   RAI1 like PD-(D/E)XK nuclease 4 6 6
  RAMPs   RAMP superfamily 1 4 4
  Rap1-DNA-bind   Rap1, DNA-binding 3 4 4
  RapA_C   RNA polymerase recycling family C-terminal 1 2 0
  Ras   Ras family 2 4 4
  RbpA   RNA polymerase-binding protein 2 2 2
  RCC1   Regulator of chromosome condensation (RCC1) repeat 2 17 2
  RCC1_2   Regulator of chromosome condensation (RCC1) repeat 1 1 0
  RdRP_1   RNA dependent RNA polymerase 62 131 126
  RdRP_3   Viral RNA dependent RNA polymerase 15 16 16
  RdRP_4   Viral RNA-directed RNA-polymerase 7 8 8
  RdRP_5   Reovirus RNA-dependent RNA polymerase lambda 3 4 4 4
  RecA   recA bacterial DNA recombination protein 4 36 36
  RecG_N   RecG N-terminal helical domain 1 1 0
  RecG_wedge   RecG wedge domain 1 1 1
  Recombinase   Recombinase 1 4 4
  RecQ_Zn_bind   RecQ zinc-binding 5 7 7
  RecR   RecR protein 15 15 2
  RecU   Recombination protein U 1 4 4
  Regulator_TrmB   Archaeal transcriptional regulator TrmB 3 12 0
  RepA_N   Replication initiator protein A (RepA) N-terminus 1 8 3
  REPA_OB_2   Replication protein A OB domain 3 5 5
  RepB_primase   RepB DNA-primase from phage plasmid 1 1 1
  Rep_3   Initiator Replication protein 3 4 4
  Rep_fac-A_3   Replication factor A protein 3 2 4 0
  Rep_fac-A_C   Replication factor-A C terminal domain 3 5 5
  Rep_N   Rep protein catalytic domain like 4 14 14
  ResIII   Type III restriction enzyme, res subunit 29 38 34
  Resolvase   Resolvase, N terminal domain 8 25 23
  Response_reg   Response regulator receiver domain 5 14 0
  RestrictionMunI   Type II restriction enzyme MunI 1 2 2
  REV   REV protein (anti-repression trans-activator protein) 1 2 2
  RE_Eco29kI   Eco29kI restriction endonuclease 2 16 16
  RE_EcoO109I   Type II restriction endonuclease EcoO109I 1 2 2
  RE_HindIII   HindIII restriction endonuclease 7 32 32
  RE_NgoFVII   NgoFVII restriction endonuclease 2 4 4
  RE_R_Pab1   R.Pab1 restriction endonuclease 2 4 4
  RF-1   RF-1 domain 17 17 14
  RF3_C   Class II release factor RF3, C-terminal domain 3 3 3
  RFX_DNA_binding   RFX DNA-binding domain 1 2 2
  RGS   Regulator of G protein signaling domain 2 2 0
  Rhabdo_ncap   Rhabdovirus nucleocapsid protein 5 67 67
  RHD_dimer   Rel homology dimerisation domain 25 66 49
  RHD_DNA_bind   Rel homology DNA-binding domain 27 68 68
  RHH_1   Ribbon-helix-helix protein, copG family 3 24 24
  Rho_N   Rho termination factor, N-terminal domain 10 54 0
  Rho_RNA_bind   Rho termination factor, RNA-binding domain 10 57 30
  Rhv   picornavirus capsid protein 2 2 0
  Ribonuclease   ribonuclease 3 5 5
  Ribonuclease_3   Ribonuclease III domain 2 5 4
  Ribonuclease_P   Ribonuclease P 2 2 2
  Ribonuclease_T2   Ribonuclease T2 family 1 1 1
  Ribonucleas_3_3   Ribonuclease-III-like 12 25 14
  Ribonuc_2-5A   Ribonuclease 2-5A 1 2 0
  Ribosomal_60s   60s Acidic ribosomal protein 1 1 0
  Ribosomal_L1   Ribosomal protein L1p/L10e family 158 168 154
  Ribosomal_L10   Ribosomal protein L10 44 45 44
  Ribosomal_L11   Ribosomal protein L11, RNA binding domain 264 269 238
  Ribosomal_L11_N   Ribosomal protein L11, N-terminal domain 206 207 159
  Ribosomal_L12   Ribosomal protein L7/L12 C-terminal domain 19 24 13
  Ribosomal_L12_N   Ribosomal protein L7/L12 dimerisation domain 12 24 4
  Ribosomal_L13   Ribosomal protein L13 432 432 393
  Ribosomal_L13e   Ribosomal protein L13e 21 21 21
  Ribosomal_L14   Ribosomal protein L14p/L23e 438 438 397
  Ribosomal_L14e   Ribosomal protein L14 25 26 25
  Ribosomal_L15e   Ribosomal L15 94 94 74
  Ribosomal_L16   Ribosomal protein L16p/L10e 438 438 417
  Ribosomal_L17   Ribosomal protein L17 336 336 323
  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e 94 94 69
  Ribosomal_L18A   Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A 22 22 4
  Ribosomal_L18p   Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast 328 328 316
  Ribosomal_L18_c   Ribosomal L18 C-terminal region 43 43 42
  Ribosomal_L19   Ribosomal protein L19 331 331 315
  Ribosomal_L19e   Ribosomal protein L19e 96 96 71
  Ribosomal_L2   Ribosomal Proteins L2, RNA binding domain 450 450 427
  Ribosomal_L20   Ribosomal protein L20 335 335 323
  Ribosomal_L21e   Ribosomal protein L21e 94 94 73
  Ribosomal_L21p   Ribosomal prokaryotic L21 protein 331 331 320
  Ribosomal_L22   Ribosomal protein L22p/L17e 441 441 399
  Ribosomal_L22e   Ribosomal L22e protein family 21 21 4
  Ribosomal_L23   Ribosomal protein L23 439 439 402
  Ribosomal_L23eN   Ribosomal protein L23, N-terminal domain 21 21 4
  ribosomal_L24   Ribosomal proteins 50S L24/mitochondrial 39S L24 334 334 319
  Ribosomal_L24e   Ribosomal protein L24e 104 104 75
  Ribosomal_L25p   Ribosomal L25p family 331 332 316
  Ribosomal_L26   Ribosomal proteins L26 eukaryotic, L24P archaeal 102 102 80
  Ribosomal_L27   Ribosomal L27 protein 335 335 322
  Ribosomal_L27A   Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A 431 431 393
  Ribosomal_L27e   Ribosomal L27e protein family 21 21 4
  Ribosomal_L28   Ribosomal L28 family 295 295 294
  Ribosomal_L28e   Ribosomal L28e protein family 4 4 4
  Ribosomal_L29   Ribosomal L29 protein 435 435 399
  Ribosomal_L29e   Ribosomal L29e protein family 21 21 4
  Ribosomal_L2_C   Ribosomal Proteins L2, C-terminal domain 450 450 427
  Ribosomal_L3   Ribosomal protein L3 453 455 432
  Ribosomal_L30   Ribosomal protein L30p/L7e 443 443 421
  Ribosomal_L30_N   Ribosomal L30 N-terminal domain 40 40 36
  Ribosomal_L31   Ribosomal protein L31 203 203 138
  Ribosomal_L31e   Ribosomal protein L31e 99 99 71
  Ribosomal_L32e   Ribosomal protein L32 94 95 69
  Ribosomal_L32p   Ribosomal L32p protein family 336 336 319
  Ribosomal_L33   Ribosomal protein L33 326 326 304
  Ribosomal_L34   Ribosomal protein L34 331 331 313
  Ribosomal_L34e   Ribosomal protein L34e 23 23 5
  Ribosomal_L35Ae   Ribosomal protein L35Ae 21 21 4
  Ribosomal_L35p   Ribosomal protein L35 328 328 312
  Ribosomal_L36   Ribosomal protein L36 272 272 256
  Ribosomal_L36e   Ribosomal protein L36e 21 21 4
  Ribosomal_L37ae   Ribosomal L37ae protein family 95 104 70
  Ribosomal_L37e   Ribosomal protein L37e 94 94 74
  Ribosomal_L38e   Ribosomal L38e protein family 21 21 4
  Ribosomal_L39   Ribosomal L39 protein 95 95 75
  Ribosomal_L4   Ribosomal protein L4/L1 family 457 457 431
  Ribosomal_L40e   Ribosomal L40e family 25 26 7
  Ribosomal_L41   Ribosomal protein L41 23 23 6
  Ribosomal_L44   Ribosomal protein L44 96 104 77
  Ribosomal_L5   Ribosomal protein L5 430 431 412
  Ribosomal_L50   Ribosomal subunit 39S 2 2 1
  Ribosomal_L5e   Ribosomal large subunit proteins 60S L5, and 50S L18 117 186 177
  Ribosomal_L5_C   ribosomal L5P family C-terminus 430 432 411
  Ribosomal_L6   Ribosomal protein L6 450 900 848
  Ribosomal_L6e   Ribosomal protein L6e 40 74 72
  Ribosomal_L7Ae   Ribosomal protein L7Ae/L30e/S12e/Gadd45 family 228 297 272
  Ribosomal_L9_C   Ribosomal protein L9, C-terminal domain 243 243 24
  Ribosomal_L9_N   Ribosomal protein L9, N-terminal domain 279 279 264
  Ribosomal_S10   Ribosomal protein S10p/S20e 481 489 471
  Ribosomal_S11   Ribosomal protein S11 483 484 471
  Ribosomal_S13   Ribosomal protein S13/S18 476 478 465
  Ribosomal_S13_N   Ribosomal S13/S15 N-terminal domain 73 73 73
  Ribosomal_S14   Ribosomal protein S14p/S29e 477 480 450
  Ribosomal_S15   Ribosomal protein S15 488 490 475
  Ribosomal_S16   Ribosomal protein S16 404 405 393
  Ribosomal_S17   Ribosomal protein S17 481 482 469
  Ribosomal_S17e   Ribosomal S17 71 71 71
  Ribosomal_S17_N   Ribosomal_S17 N-terminal 68 68 68
  Ribosomal_S18   Ribosomal protein S18 407 411 394
  Ribosomal_S19   Ribosomal protein S19 479 479 468
  Ribosomal_S19e   Ribosomal protein S19e 72 72 72
  Ribosomal_S2   Ribosomal protein S2 479 558 540
  Ribosomal_S20p   Ribosomal protein S20 400 401 391
  Ribosomal_S21   Ribosomal protein S21 113 114 113
  Ribosomal_S21e   Ribosomal protein S21e 66 66 27
  Ribosomal_S24e   Ribosomal protein S24e 73 73 72
  Ribosomal_S25   S25 ribosomal protein 67 67 67
  Ribosomal_S26e   Ribosomal protein S26e 66 68 49
  Ribosomal_S27   Ribosomal protein S27a 68 70 51
  Ribosomal_S27e   Ribosomal protein S27 70 72 52
  Ribosomal_S28e   Ribosomal protein S28e 73 73 56
  Ribosomal_S30   Ribosomal protein S30 71 71 54
  Ribosomal_S30AE   Sigma 54 modulation protein / S30EA ribosomal protein 10 10 10
  Ribosomal_S3Ae   Ribosomal S3Ae family 71 71 71
  Ribosomal_S3_C   Ribosomal protein S3, C-terminal domain 475 476 465
  Ribosomal_S4   Ribosomal protein S4/S9 N-terminal domain 431 432 417
  Ribosomal_S4e   Ribosomal family S4e 72 72 72
  Ribosomal_S5   Ribosomal protein S5, N-terminal domain 482 483 468
  Ribosomal_S5_C   Ribosomal protein S5, C-terminal domain 482 483 470
  Ribosomal_S6   Ribosomal protein S6 407 409 392
  Ribosomal_S6e   Ribosomal protein S6e 73 73 73
  Ribosomal_S7   Ribosomal protein S7p/S5e 486 488 474
  Ribosomal_S7e   Ribosomal protein S7e 68 68 67
  Ribosomal_S8   Ribosomal protein S8 484 487 473
  Ribosomal_S8e   Ribosomal protein S8e 72 72 72
  Ribosomal_S9   Ribosomal protein S9/S16 481 482 469
  Ribosomal_TL5_C   Ribosomal protein TL5, C-terminal domain 206 207 155
  Ribosom_S12_S23   Ribosomal protein S12/S23 503 504 478
  Ribos_L4_asso_C   60S ribosomal protein L4 C-terminal domain 38 38 34
  Ricin_B_lectin   Ricin-type beta-trefoil lectin domain 1 2 0
  RIG-I_C-RD   C-terminal domain of RIG-I 25 53 53
  RIP   Ribosome inactivating protein 1 1 1
  RLI   Possible Fer4-like domain in RNase L inhibitor, RLI 2 2 1
  RMF   Ribosome modulation factor 2 2 2
  RMMBL   Zn-dependent metallo-hydrolase RNA specificity domain 5 12 9
  RnaseA   Pancreatic ribonuclease 7 11 11
  RNaseH_C   T4 RNase H, C terminal 1 1 1
  RNase_E_G   Ribonuclease E/G family 2 6 6
  RNase_H   RNase H 73 128 128
  RNase_HII   Ribonuclease HII 5 5 5
  RNase_H_2   RNase_H superfamily 3 4 4
  RNase_PH   3' exoribonuclease family, domain 1 9 54 21
  RNase_PH_C   3' exoribonuclease family, domain 2 9 42 7
  RNase_T   Exonuclease 33 82 74
  RNA_GG_bind   PHAX RNA-binding domain 1 1 1
  RNA_ligase   RNA ligase 2 4 4
  RNA_pol   DNA-dependent RNA polymerase 11 18 18
  RNA_polI_A14   Yeast RNA polymerase I subunit RPA14 6 12 0
  RNA_polI_A34   DNA-directed RNA polymerase I subunit RPA34.5 6 6 0
  RNA_pol_A_bac   RNA polymerase Rpb3/RpoA insert domain 163 279 0
  RNA_pol_A_CTD   Bacterial RNA polymerase, alpha chain C terminal domain 8 15 10
  RNA_pol_I_A49   A49-like RNA polymerase I associated factor 6 7 0
  RNA_pol_I_TF   RNA polymerase I specific initiation factor 1 1 1
  RNA_pol_L   RNA polymerase Rpb3/Rpb11 dimerisation domain 163 279 0
  RNA_pol_L_2   RNA polymerase Rpb3/Rpb11 dimerisation domain 107 109 0
  RNA_POL_M_15KD   RNA polymerases M/15 Kd subunit 105 107 0
  RNA_pol_N   RNA polymerases N / 8 kDa subunit 107 109 0
  RNA_pol_Rbc25   RNA polymerase III subunit Rpc25 1 1 0
  RNA_pol_Rpa2_4   RNA polymerase I, Rpa2 specific domain 6 6 0
  RNA_pol_Rpb1_1   RNA polymerase Rpb1, domain 1 163 221 157
  RNA_pol_Rpb1_2   RNA polymerase Rpb1, domain 2 163 214 161
  RNA_pol_Rpb1_3   RNA polymerase Rpb1, domain 3 163 194 0
  RNA_pol_Rpb1_4   RNA polymerase Rpb1, domain 4 163 194 3
  RNA_pol_Rpb1_5   RNA polymerase Rpb1, domain 5 163 261 177
  RNA_pol_Rpb1_6   RNA polymerase Rpb1, domain 6 98 100 0
  RNA_pol_Rpb1_7   RNA polymerase Rpb1, domain 7 98 100 0
  RNA_pol_Rpb1_R   RNA polymerase Rpb1 C-terminal repeat 1 1 0
  RNA_pol_Rpb2_1   RNA polymerase beta subunit 163 194 88
  RNA_pol_Rpb2_2   RNA polymerase Rpb2, domain 2 163 211 76
  RNA_pol_Rpb2_3   RNA polymerase Rpb2, domain 3 163 194 130
  RNA_pol_Rpb2_4   RNA polymerase Rpb2, domain 4 101 103 0
  RNA_pol_Rpb2_45   RNA polymerase beta subunit external 1 domain 56 85 0
  RNA_pol_Rpb2_5   RNA polymerase Rpb2, domain 5 101 103 0
  RNA_pol_Rpb2_6   RNA polymerase Rpb2, domain 6 163 194 132
  RNA_pol_Rpb2_7   RNA polymerase Rpb2, domain 7 163 194 129
  RNA_pol_Rpb4   RNA polymerase Rpb4 61 63 0
  RNA_pol_Rpb5_C   RNA polymerase Rpb5, C-terminal domain 107 109 0
  RNA_pol_Rpb5_N   RNA polymerase Rpb5, N-terminal domain 105 107 5
  RNA_pol_Rpb6   RNA polymerase Rpb6 163 194 0
  RNA_pol_Rpb8   RNA polymerase Rpb8 105 107 0
  RNA_pol_RpbG   DNA-directed RNA polymerase, subunit G 2 2 0
  RNA_pol_Rpc34   RNA polymerase Rpc34 subunit 1 1 0
  RNA_pol_Rpc4   RNA polymerase III RPC4 1 1 0
  RNA_pol_Rpc82   RNA polymerase III subunit RPC82 1 2 0
  RNA_pol_Rpo13   RNA polymerase Rpo13 subunit HTH domain 2 2 0
  RNA_replicase_B   RNA replicase, beta-chain 9 9 9
  RNB   RNB domain 8 9 8
  ROK   ROK family 1 4 0
  Rotavirus_VP1   Rotavirus VP1 C-terminal domain 7 8 6
  Rota_NSP3   Rotavirus non-structural protein NSP3 1 8 8
  RPOL_N   DNA-directed RNA polymerase N-terminal 11 21 21
  Rpp20   Rpp20 subunit of nuclear RNase MRP and P 1 1 1
  RPS31   Ribosomal protein S31e 1 1 1
  RQC   RQC domain 6 9 9
  RRF   Ribosome recycling factor 18 18 11
  Rrf2   Transcriptional regulator 3 6 6
  RRM_1   RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 184 369 286
  RRM_3   RNA binding motif 1 2 2
  RRM_4   RNA recognition motif of the spliceosomal PrP8 12 12 7
  RRM_5   RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 7 7 7
  RRM_7   RNA recognition motif 2 2 2
  RRM_occluded   Occluded RNA-recognition motif 2 3 3
  RRN3   RNA polymerase I specific transcription initiation factor RRN3 1 2 0
  Rrn6   RNA polymerase I-specific transcription-initiation factor 1 1 0
  RrnaAD   Ribosomal RNA adenine dimethylase 4 4 3
  rRNA_proc-arch   rRNA-processing arch domain 2 4 0
  Rrp44_CSD1   Rrp44-like cold shock domain 7 9 4
  Rrp44_S1   S1 domain 6 6 0
  RS4NT   RS4NT (NUC023) domain 72 72 72
  RsgA_GTPase   RsgA GTPase 3 3 3
  RTC   RNA 3'-terminal phosphate cyclase 3 4 3
  RTC_insert   RNA 3'-terminal phosphate cyclase (RTC), insert domain 3 4 0
  RTP   Replication terminator protein 4 10 10
  Runt   Runt domain 15 26 26
  RusA   Endodeoxyribonuclease RusA 1 4 2
  RuvA_C   RuvA, C-terminal domain 2 8 4
  RuvA_N   RuvA N terminal domain 2 8 0
  RuvC   Crossover junction endodeoxyribonuclease RuvC 1 2 2
  rve   Integrase core domain 12 62 17
  RVT_1   Reverse transcriptase (RNA-dependent DNA polymerase) 74 199 115
  RVT_3   Reverse transcriptase-like 1 2 2
  RVT_connect   Reverse transcriptase connection domain 46 152 109
  RVT_thumb   Reverse transcriptase thumb domain 46 152 72
  S1   S1 RNA binding domain 72 79 6
  S10_plectin   Plectin/S10 domain 65 65 65
  S4   S4 domain 481 552 533
  SAD_SRA   SAD/SRA domain 20 41 38
  SAM_2   SAM domain (Sterile alpha motif) 3 3 3
  SAP   SAP domain 4 8 8
  SART-1   SART-1 family 2 2 0
  Sas10_Utp3   Sas10/Utp3/C1D family 1 1 0
  SASP   Small, acid-soluble spore proteins, alpha/beta type 1 3 3
  SbcCD_C   Putative exonuclease SbcCD, C subunit 4 10 0
  SBDS   Shwachman-Bodian-Diamond syndrome (SBDS) protein 3 3 1
  SBDS_C   SBDS protein C-terminal domain 3 3 3
  SBP_bac_8   Bacterial extracellular solute-binding protein 2 3 0
  Sec61_beta   Sec61beta family 7 7 0
  Sec63   Sec63 Brl domain 6 12 4
  SecA_SW   SecA Wing and Scaffold domain 1 2 0
  SecE   SecE/Sec61-gamma subunits of protein translocation complex 10 10 0
  SecG   Preprotein translocase SecG subunit 2 2 0
  SecY   SecY translocase 11 11 11
  SelB-wing_2   Elongation factor SelB, winged helix 2 6 6
  SelB-wing_3   Elongation factor SelB, winged helix 4 11 8
  SepSecS   O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS 2 8 8
  SeqA   SeqA protein C-terminal domain 4 9 9
  SeqA_N   SeqA protein N-terminal domain 1 4 0
  Seryl_tRNA_N   Seryl-tRNA synthetase N-terminal domain 3 6 4
  SET   SET domain 4 4 0
  SF3b10   Splicing factor 3B subunit 10 (SF3b10) 1 1 0
  Sgf11   Sgf11 (transcriptional regulation protein) 1 4 3
  SH2   SH2 domain 4 11 0
  She2p   RNA binding protein She2p 2 8 8
  SHS2_Rpb7-N   SHS2 domain found in N terminus of Rpb7p/Rpc25p/MJ0397 67 69 0
  Sigma54_CBD   Sigma-54 factor, core binding domain 1 2 0
  Sigma54_DBD   Sigma-54, DNA binding domain 3 4 4
  Sigma70_ner   Sigma-70, non-essential region 4 10 0
  Sigma70_r1_2   Sigma-70 factor, region 1.2 45 67 64
  Sigma70_r2   Sigma-70 region 2 48 71 70
  Sigma70_r3   Sigma-70 region 3 44 64 51
  Sigma70_r4   Sigma-70, region 4 48 70 32
  Sigma70_r4_2   Sigma-70, region 4 1 2 2
  Sin_N   Sin-like protein conserved region 1 1 0
  SKIP_SNW   SKIP/SNW domain 8 8 7
  SLBP_RNA_bind   Histone RNA hairpin-binding protein RNA-binding domain 6 9 9
  Sld5   GINS complex protein 2 8 0
  SLD5_C   DNA replication complex GINS protein SLD5 C-terminus 2 2 0
  SLIDE   SLIDE 1 1 0
  Slu7   Pre-mRNA splicing Prp18-interacting factor 2 2 2
  SmpB   SmpB protein 9 14 11
  SNF2_N   SNF2 family N-terminal domain 4 6 4
  Somatomedin_B   Somatomedin B domain 1 2 0
  SOSSC   SOSS complex subunit C 1 1 0
  Spo0A_C   Sporulation initiation factor Spo0A C terminal 1 4 4
  SRC-1   Steroid receptor coactivator 1 2 0
  SRF-TF   SRF-type transcription factor (DNA-binding and dimerisation domain) 11 36 34
  SRP-alpha_N   Signal recognition particle, alpha subunit, N-terminal 1 1 1
  SRP14   Signal recognition particle 14kD protein 7 10 9
  SRP19   SRP19 protein 15 20 19
  SRP54   SRP54-type protein, GTPase domain 14 27 9
  SRP54_N   SRP54-type protein, helical bundle domain 14 26 3
  SRP68   RNA-binding signal recognition particle 68 3 4 4
  SRP72   SRP72 RNA-binding domain 1 2 2
  SRP9-21   Signal recognition particle 9 kDa protein (SRP9) 7 10 5
  SRPRB   Signal recognition particle receptor beta subunit 1 1 0
  SRP_SPB   Signal peptide binding domain 34 40 39
  SSB   Single-strand binding protein family 4 14 14
  Ssl1   Ssl1-like 5 5 0
  STAR_dimer   Homodimerisation region of STAR domain protein 1 2 0
  STAT_alpha   STAT protein, all-alpha domain 4 11 0
  STAT_bind   STAT protein, DNA binding domain 4 11 11
  SUI1   Translation initiation factor SUI1 14 14 14
  Sulf_coat_C   Sulfolobus virus coat protein C terminal 1 58 58
  SUV3_C   Mitochondrial degradasome RNA helicase subunit C terminal 1 1 0
  SWIRM   SWIRM domain 1 1 0
  SYF2   SYF2 splicing factor 5 5 5
  T-box   T-box 7 16 15
  T4-Gluco-transf   Bacteriophage T4 beta-glucosyltransferase 4 8 5
  TAF6_C   TAF6 C-terminal HEAT repeat domain 1 2 0
  TAF8_C   Transcription factor TFIID complex subunit 8 C-term 1 1 0
  TAFII55_N   TAFII55 protein conserved region 1 1 0
  TAL_effector   TAL effector repeat 23 527 515
  Tap-RNA_bind   Tap, RNA-binding 1 2 2
  Taq-exonuc   Taq polymerase, exonuclease 50 50 23
  TaqI_C   TaqI-like C-terminal specificity domain 9 16 16
  Tat   Transactivating regulatory protein (Tat) 1 1 1
  TatD_DNase   TatD related DNase 1 1 1
  Tau95   RNA polymerase III transcription factor (TF)IIIC subunit 4 4 2
  Taxilin   Myosin-like coiled-coil protein 2 3 3
  TBP   Transcription factor TFIID (or TATA-binding protein, TBP) 45 132 132
  TCR   Tesmin/TSO1-like CXC domain, cysteine-rich domain 2 5 5
  TEA   TEA/ATTS domain family 2 2 2
  TEBP_beta   Telomere-binding protein beta subunit (TEBP beta) 14 14 14
  Telomerase_RBD   Telomerase ribonucleoprotein complex - RNA binding domain 3 5 4
  Telomere_res   Telomere resolvase 3 4 4
  Tenui_N   Tenuivirus/Phlebovirus nucleocapsid protein 4 70 70
  Ter   DNA replication terminus site-binding protein (Ter protein) 8 8 8
  TetR_C   Tetracyclin repressor, C-terminal all-alpha domain 2 5 0
  TetR_C_11   Bacterial transcriptional repressor C-terminal 1 4 0
  TetR_C_13   Bacterial transcriptional repressor C-terminal 1 16 0
  TetR_C_4   YsiA-like protein, C-terminal region 1 4 0
  TetR_C_5   QacR-like protein, C-terminal region 1 4 0
  TetR_N   Bacterial regulatory proteins, tetR family 18 85 82
  Tet_JBP   Oxygenase domain of the 2OGFeDO superfamily 3 6 4
  Tfb2   Transcription factor Tfb2 5 10 0
  Tfb4   Transcription factor Tfb4 5 5 0
  Tfb5   Transcription factor TFIIH complex subunit Tfb5 7 7 1
  TFIIA   Transcription factor IIA, alpha/beta subunit 17 34 15
  TFIIA_gamma_C   Transcription initiation factor IIA, gamma subunit 17 17 0
  TFIIA_gamma_N   Transcription initiation factor IIA, gamma subunit, helical domain 17 17 0
  TFIIB   Transcription factor TFIIB repeat 19 44 36
  TFIIE_alpha   TFIIE alpha subunit 12 12 4
  TFIIE_beta   TFIIE beta subunit core domain 12 12 0
  TFIIF_alpha   Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) 14 14 3
  TFIIF_beta   Transcription initiation factor IIF, beta subunit 14 16 10
  TFIIS_C   Transcription factor S-II (TFIIS) 98 110 1
  TFIIS_M   Transcription factor S-II (TFIIS), central domain 13 13 0
  TF_Zn_Ribbon   TFIIB zinc-binding 15 27 9
  TGS   TGS domain 1 1 0
  TGT   Queuine tRNA-ribosyltransferase 3 10 6
  TGT_C1   C1 domain of tRNA-guanine transglycosylase dimerisation 1 2 2
  TGT_C2   Patch-forming domain C2 of tRNA-guanine transglycosylase 1 2 2
  ThaI   Restriction endonuclease ThaI 1 2 2
  THAP   THAP domain 3 3 3
  Thg1   tRNAHis guanylyltransferase 4 12 6
  Thg1C   Thg1 C terminal domain 4 12 10
  ThiI   Thiamine biosynthesis protein (ThiI) 3 6 5
  Thioredoxin   Thioredoxin 17 19 2
  Thrombin_light   Thrombin light chain 16 17 1
  THUMP   THUMP domain 3 6 6
  Thx   30S ribosomal protein Thx 267 267 259
  TIG   IPT/TIG domain 6 9 0
  TilS   TilS substrate binding domain 1 2 2
  TilS_C   TilS substrate C-terminal domain 1 2 2
  Tim44   Tim44-like domain 2 2 1
  TMV_coat   Virus coat protein (TMV like) 11 11 11
  Tna_leader   Tryptophanase operon leader peptide 1 1 1
  Tnp_DNA_bind   Transposase DNA-binding 4 8 8
  TNV_CP   Satellite tobacco necrosis virus coat protein 1 1 1
  TolA_bind_tri   TolA binding protein trimerisation 2 3 3
  Tombus_P19   Tombusvirus P19 core protein 4 8 8
  Topoisom_bac   DNA topoisomerase 9 14 14
  Topoisom_I   Eukaryotic DNA topoisomerase I, catalytic core 20 20 19
  Topoisom_I_N   Eukaryotic DNA topoisomerase I, DNA binding fragment 16 16 16
  Topo_C_assoc   C-terminal topoisomerase domain 16 16 15
  Topo_Zn_Ribbon   Topoisomerase I zinc-ribbon-like 1 2 2
  Toprim   Toprim domain 63 139 138
  Toprim_2   Toprim-like 1 2 0
  TOPRIM_C   C-terminal associated domain of TOPRIM 9 18 18
  Toprim_N   DNA primase catalytic core, N-terminal domain 1 2 2
  Torus   Torus domain 8 8 7
  Tospo_nucleocap   Tospovirus nucleocapsid protein 2 6 5
  Tower   Tower 1 1 1
  ToxN_toxin   Toxin ToxN, type III toxin-antitoxin system 3 10 10
  TPR_1   Tetratricopeptide repeat 7 7 0
  TPR_12   Tetratricopeptide repeat 9 10 0
  TPR_15   Tetratricopeptide repeat 3 3 3
  TPR_19   Tetratricopeptide repeat 4 4 4
  TPR_2   Tetratricopeptide repeat 1 1 0
  TraI   DNA helicase TraI 1 1 0
  TRAM   TRAM domain 1 2 2
  Translin   Translin family 3 36 15
  Transposase_1   Transposase (partial DDE domain) 5 10 10
  Trans_reg_C   Transcriptional regulatory protein, C terminal 9 43 21
  Tra_M   TraM protein, DNA-binding 1 8 8
  Trigger_N   Bacterial trigger factor protein (TF) 3 3 2
  TrmB   Sugar-specific transcriptional regulator TrmB 3 12 12
  tRNA-synt_1   tRNA synthetases class I (I, L, M and V) 21 59 43
  tRNA-synt_1b   tRNA synthetases class I (W and Y) 6 20 20
  tRNA-synt_1c   tRNA synthetases class I (E and Q), catalytic domain 27 37 36
  tRNA-synt_1c_C   tRNA synthetases class I (E and Q), anti-codon binding domain 18 18 17
  tRNA-synt_1d   tRNA synthetases class I (R) 4 10 6
  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain 1 1 1
  tRNA-synt_1g   tRNA synthetases class I (M) 8 10 4
  tRNA-synt_1_2   Leucyl-tRNA synthetase, Domain 2 13 20 20
  tRNA-synt_2   tRNA synthetases class II (D, K and N) 7 19 10
  tRNA-synt_2b   tRNA synthetase class II core domain (G, H, P, S and T) 10 26 18
  tRNA-synt_2c   tRNA synthetases class II (A) 2 4 2
  tRNA-synt_2d   tRNA synthetases class II core domain (F) 4 12 12
  tRNA_anti-codon   OB-fold nucleic acid binding domain 21 41 37
  tRNA_bind   Putative tRNA binding domain 2 4 0
  tRNA_bind_2   Possible tRNA binding domain 1 4 0
  tRNA_int_endo   tRNA intron endonuclease, catalytic C-terminal domain 1 4 4
  tRNA_int_endo_N   tRNA intron endonuclease, N-terminal domain 1 4 0
  tRNA_m1G_MT   tRNA (Guanine-1)-methyltransferase 3 6 6
  tRNA_Me_trans   tRNA methyl transferase 3 5 5
  tRNA_NucTran2_2   tRNA nucleotidyltransferase domain 2 putative 1 2 2
  tRNA_NucTransf2   tRNA nucleotidyltransferase, second domain 34 68 66
  tRNA_SAD   Threonyl and Alanyl tRNA synthetase second additional domain 3 5 1
  tRNA_U5-meth_tr   tRNA (Uracil-5-)-methyltransferase 2 4 4
  TROVE   TROVE domain 2 4 4
  TrpBP   Tryptophan RNA-binding attenuator protein 16 352 176
  Trp_repressor   Trp repressor protein 4 16 16
  TruB-C_2   Pseudouridine synthase II TruB, C-terminal 2 2 1
  TruB_C_2   tRNA pseudouridylate synthase B C-terminal domain 17 17 1
  TruB_N   TruB family pseudouridylate synthase (N terminal domain) 17 23 21
  TrwC   TrwC relaxase 9 12 12
  Trypsin   Trypsin 16 17 17
  Tudor-knot   RNA binding activity-knot of a chromodomain 1 2 2
  Tymo_coat   Tymovirus coat protein 3 9 5
  Type2_restr_D3   Type-2 restriction enzyme D3 domain 1 1 1
  Tyr-DNA_phospho   Tyrosyl-DNA phosphodiesterase 8 16 16
  T_Ag_DNA_bind   Origin of replication binding protein 7 20 20
  U-box   U-box domain 5 17 5
  U1snRNP70_N   U1 small nuclear ribonucleoprotein of 70kDa MW N terminal 3 7 5
  U5_2-snRNA_bdg   U5-snRNA binding site 2 of PrP8 12 12 10
  U6-snRNA_bdg   U6-snRNA interacting domain of PrP8 12 12 8
  ubiquitin   Ubiquitin family 2 6 3
  UCH   Ubiquitin carboxyl-terminal hydrolase 2 5 3
  UDG   Uracil DNA glycosylase superfamily 33 42 42
  UPF1_Zn_bind   RNA helicase (UPF2 interacting domain) 1 1 0
  UQ_con   Ubiquitin-conjugating enzyme 1 2 1
  UTRA   UTRA domain 1 2 0
  UvdE   UV-endonuclease UvdE 1 1 1
  UVR   UvrB/uvrC motif 2 4 0
  UvrB   Ultra-violet resistance protein B 4 6 0
  UvrD-helicase   UvrD/REP helicase N-terminal domain 18 37 37
  UvrD_C   UvrD-like helicase C-terminal domain 18 41 40
  UvrD_C_2   UvrD-like helicase C-terminal domain 9 15 11
  V-set   Immunoglobulin V-set domain 26 89 36
  Val_tRNA-synt_C   Valyl tRNA synthetase tRNA binding arm 2 4 4
  Viral_coat   Viral coat protein (S domain) 10 360 197
  Viral_helicase1   Viral (Superfamily 1) RNA helicase 1 4 4
  VirDNA-topo-I_N   Viral DNA topoisomerase I, N-terminal 3 3 3
  VP40   Matrix protein VP40 2 9 9
  VRR_NUC   VRR-NUC domain 9 18 11
  Vsr   DNA mismatch endonuclease Vsr 2 2 2
  VWA   von Willebrand factor type A domain 2 2 2
  WD40   WD domain, G-beta repeat 89 350 178
  WGR   WGR domain 4 8 8
  WHEP-TRS   WHEP-TRS domain 1 1 0
  WHIM1   WSTF, HB1, Itc1p, MBD9 motif 1 1 1 0
  Whirly   Whirly transcription factor 3 3 3
  WRKY   WRKY DNA -binding domain 1 1 1
  XPA_C   XPA protein C-terminus 7 14 14
  XPA_N   XPA protein N-terminal 7 14 0
  XPC-binding   XPC-binding domain 3 3 0
  XPG_I   XPG I-region 15 26 11
  XPG_N   XPG N-terminal domain 15 27 24
  Xpo1   Exportin 1-like protein 2 4 2
  XRN_N   XRN 5'-3' exonuclease N-terminus 1 1 1
  Y1_Tnp   Transposase IS200 like 10 26 26
  YEATS   YEATS family 1 1 0
  YoeB_toxin   YoeB-like toxin of bacterial type II toxin-antitoxin system 2 2 2
  YqaJ   YqaJ-like viral recombinase domain 3 9 9
  YTH   YT521-B-like domain 6 12 12
  z-alpha   Adenosine deaminase z-alpha domain 15 42 33
  ZapB   Cell division protein ZapB 5 8 7
  zf-C2H2   Zinc finger, C2H2 type 7 20 19
  zf-C2HC   Zinc finger, C2HC type 2 3 3
  zf-C2HE   C2HE / C2H2 / C2HC zinc-binding finger 7 17 16
  zf-C3HC4_2   Zinc finger, C3HC4 type (RING finger) 1 4 0
  zf-C4   Zinc finger, C4 type (two domains) 74 173 173
  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger 1 2 2
  zf-CCCH   Zinc finger C-x8-C-x5-C-x3-H type (and similar) 4 9 6
  zf-CCCH_2   RNA-binding, Nab2-type zinc finger 2 14 13
  zf-CCHC   Zinc knuckle 25 40 40
  zf-CXXC   CXXC zinc finger domain 15 16 16
  zf-Di19   Drought induced 19 protein (Di19), zinc-binding 1 2 2
  zf-FPG_IleRS   Zinc finger found in FPG and IleRS 66 72 69
  zf-H2C2_2   Zinc-finger double domain 58 150 150
  zf-His_Me_endon   Zinc-binding loop region of homing endonuclease 7 16 16
  zf-met   Zinc-finger of C2H2 type 1 1 1
  zf-nanos   Nanos RNA binding domain 2 2 2
  zf-PARP   Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region 10 34 34
  zf-primase   Primase zinc finger 1 1 0
  zf-RanBP   Zn-finger in Ran binding protein and others 1 1 1
  zf-RNPHF   RNPHF zinc finger 1 1 0
  zf-RRN7   Zinc-finger of RNA-polymerase I-specific TFIIB, Rrn7 1 1 0
  zf-TAZ   TAZ zinc finger 1 1 0
  zf-U1   U1 zinc finger 2 8 4
  zf-UBP   Zn-finger in ubiquitin-hydrolases and other protein 2 5 1
  zinc_ribbon_2   zinc-ribbon domain 1 1 1
  Zn-ribbon_8   Zinc ribbon domain 2 5 5
  Zn_clus   Fungal Zn(2)-Cys(6) binuclear cluster domain 12 28 28
  Zn_ribbon_recom   Recombinase zinc beta ribbon domain 1 4 4
© NPIDB team 2003 - 2017

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