Back to Pfam families list
Pfam ID  Domain  PDB ID  Domain Kind  Res, A 
  2OG-FeII_Oxy_2   2OG-Fe(II) oxygenase superfamily 4zhn A:18-210 dna 1.33
  40S_S4_C   40S ribosomal protein S4 C-terminus 4ujp F:212-259 rna 2.80
  5_3_exonuc   5'-3' exonuclease, C-terminal SAM fold 3zda A:160-250 dna 1.50
  5_3_exonuc_N   5'-3' exonuclease, N-terminal resolvase-like domain 5hp4 A:21-190 dna 1.86
  7kD_DNA_binding   7kD DNA-binding domain 1xyi A:3-60 dna 1.45
  AAA   ATPase family associated with various cellular activities (AAA) 3u61 B:46-160 dna 3.20
  AAA_11   AAA domain 5ean A:724-799 dna 2.36
  AAA_12   AAA domain 5ean A:806-1020 dna 2.36
  AAA_16   AAA ATPase domain 2v1u A:32-185 dna 3.10
  AAA_22   AAA domain 2qby A:52-187 dna 3.35
  AAA_23   AAA domain 5dac A:6-1118 dna 2.50
  AAA_30   AAA domain 3gpl A:338-525 dna 2.50
  AAA_31   AAA domain 5u1j B:3-182 dna 2.95
  AAA_33   AAA domain 4qm6 B:10-144 rna 1.50
  ABC_tran   ABC transporter 3pih A:600-837 dna 2.90
  ABC_tran_Xtn   ABC transporter 3j5s D:230-312 rna 7.50
  Aconitase   Aconitase family (aconitate hydratase) 3snp A:58-564 rna 2.80
  Aconitase_C   Aconitase C-terminal domain 3snp B:692-821 rna 2.80
  Ada_Zn_binding   Metal binding domain of Ada 1u8b A:11-75 dna 2.10
  Adenine_glyco   Methyladenine glycosylase 2ofi A:6-182 dna 1.85
  AFT   Transcription factor AFT 4lmg B:51-108 dna 2.20
  AGT   DNA alpha-glucosyltransferase 1y8z A:1013-1368 dna 1.90
  Alba   Alba 3wbm C:10-74 rna 2.00
  Amidase   Amidase 3kfu H:19-448 rna 3.00
  Amino_oxidase   Flavin containing amine oxidoreductase 4xbf A:288-826 rna 2.80
  ANAPC4_WD40   Anaphase-promoting complex subunit 4 WD40 domain 5gxh A:395-480 rna 1.80
  Ank_2   Ankyrin repeats (3 copies) 4oav B:86-155 rna 2.10
  Ank_5   Ankyrin repeats (many copies) 4oav D:153-209 rna 2.10
  Anticodon_1   Anticodon-binding domain of tRNA 4arc A:698-827 rna 2.00
  AP2   AP2 domain 3igm A:64-117 dna 2.20
  APOBEC_N   APOBEC-like N-terminal domain 5td5 A:197-375 dna 1.72
  AP_endonuc_2   Xylose isomerase-like TIM barrel 2nq9 A:19-239 dna 1.45
  Arc   Arc-like DNA binding domain 1bdt C:4-50 dna 2.50
  Arena_ncap_C   Arenavirus nucleocapsid C-terminal domain 4gv3 A:363-543 rna 1.68
  Arena_nucleocap   Arenavirus nucleocapsid N-terminal domain 3t5n A:8-163 rna 1.79
  ArgoL1   Argonaute linker 1 domain 4z4d A:176-226 rna 1.60
  ArgoL2   Argonaute linker 2 domain 4z4d A:374-420 rna 1.60
  ArgoMid   Mid domain of argonaute 4w5o A:429-511 rna 1.80
  ArgoN   N-terminal domain of argonaute 4z4d A:36-166 rna 1.60
  Arg_repressor   Arginine repressor, DNA binding domain 3lap E:17-86 dna 2.15
  Arg_tRNA_synt_N   Arginyl tRNA synthetase N terminal domain 2zue A:4-90 rna 2.00
  Arm-DNA-bind_1   Bacteriophage lambda integrase, Arm DNA-binding domain 1z1b N:7-69 dna 3.80
  Arm-DNA-bind_3   Arm DNA-binding domain 3rmp A:3-78 dna 2.21
  ATP-synt_ab   ATP synthase alpha/beta family, nucleotide-binding domain 5jji A:158-365 rna 2.60
  ATP_bind_3   PP-loop family 3a2k B:20-205 rna 3.65
  A_deamin   Adenosine-deaminase (editase) domain 5ed1 A:370-691 rna 2.77
  B2   RNA binding protein B2 2az2 A:2-71 rna 2.60
  B3   B3 DNA binding domain 4ldx A:124-226 dna 2.90
  B3_4   B3/4 domain 2iy5 B:209-385 rna 3.10
  Bac_DnaA   Bacterial dnaA protein 3r8f D:79-295 dna 3.37
  Bac_DnaA_C   Bacterial dnaA protein helix-turn-helix 3pvv A:413-480 dna 2.00
  Bac_DNA_binding   Bacterial DNA-binding protein 1p71 A:1-90 dna 1.90
  BAF   Barrier to autointegration factor 2bzf A:2-88 dna 2.87
  BAH   BAH domain 4da4 B:935-1103 dna 2.60
  BamHI   Restriction endonuclease BamHI 3bam A:8-167 dna 1.80
  BCAS2   Breast carcinoma amplified sequence 2 (BCAS2) 5gmk t:1-175 rna 3.40
  BEN   BEN domain 4ix7 B:279-349 dna 1.58
  Beta-Casp   Beta-Casp domain 3ie1 A:228-351 rna 2.85
  BHD_1   Rad4 beta-hairpin domain 1 2qsh A:431-487 dna 2.81
  BHD_3   Rad4 beta-hairpin domain 3 2qsh A:551-625 dna 2.81
  BpuJI_N   Restriction endonuclease BpuJI - N terminal 2vla A:2-274 dna 1.30
  BRCA-2_OB3   BRCA2, oligonucleotide/oligosaccharide-binding, domain 3 1mje A:2971-3105 dna 3.50
  Brix   Brix domain 5jpq c:93-267 rna 7.30
  Bromo_coat   Bromovirus coat protein 1cwp B:27-190 rna 3.20
  Bse634I   Cfr10I/Bse634I restriction endonuclease 3dvo A:48-332 dna 1.89
  BTD   Beta-trefoil DNA-binding domain 3iag C:205-354 dna 2.00
  Btz   CASC3/Barentsz eIF4AIII binding 2j0s T:169-217 rna 2.21
  Bunya_nucleocap   Bunyavirus nucleocapsid (N) protein 4jng A:7-229 rna 2.12
  Bunya_RdRp   Bunyavirus RNA dependent RNA polymerase 5amr A:596-1353 rna 2.57
  bZIP_1   bZIP transcription factor 5t01 A:252-313 dna 1.89
  bZIP_2   Basic region leucine zipper 1gu4 B:270-323 dna 1.80
  bZIP_Maf   bZIP Maf transcription factor 2wt7 B:214-302 dna 2.30
  C1-set   Immunoglobulin C1-set domain 3agv B:348-432 rna 2.15
  C2-set_2   CD80-like C2-set immunoglobulin domain 3s59 B:124-219 dna 2.80
  CAF1   CAF1 family ribonuclease 2a1r B:3-263 rna 2.60
  CarD_CdnL_TRCF   CarD-like/TRCF domain 4xls M:4-112 dna 4.01
  Cas9-BH   Bridge helix of CRISPR-associated endonuclease Cas9 5b2r B:62-94 hybrid 2.00
  Cas9_PI   PAM-interacting domain of CRISPR-associated endonuclease Cas9 5b2r B:1102-1358 hybrid 2.00
  Cas9_REC   REC lobe of CRISPR-associated endonuclease Cas9 5b2r B:177-712 hybrid 2.00
  Cas_Cas1   CRISPR associated protein Cas1 5dlj A:122-240 dna 2.60
  Cas_Cas2CT1978   CRISPR-associated protein (Cas_Cas2CT1978) 5dlj E:3-78 dna 2.60
  Cas_Cas5d   CRISPR-associated protein (Cas_Cas5) 5h9f J:4-215 hybrid 2.45
  Cas_Cas6   CRISPR associated protein Cas6 3qjl A:93-237 rna 2.70
  Cas_Cmr3   CRISPR-associated protein (Cas_Cmr3) 3x1l B:101-321 hybrid 2.10
  Cas_Cmr5   CRISPR-associated protein (Cas_Cmr5) 3x1l F:6-150 hybrid 2.10
  Cas_csx3   CRISPR-associated protein (Cas_csx3) 3wzi B:15-90 rna 2.90
  Cas_Csy1   CRISPR-associated protein (Cas_Csy1) 5uz9 A:46-415 rna 3.40
  Cas_Csy2   CRISPR-associated protein (Cas_Csy2) 5uz9 B:10-316 rna 3.40
  Cas_Csy3   CRISPR-associated protein (Cas_Csy3) 5uz9 G:27-356 rna 3.40
  Cas_Csy4   CRISPR-associated protein (Cas_Csy4) 2xlk A:4-187 hybrid 1.80
  Cas_CT1975   CT1975-like protein 5h9f E:5-358 hybrid 2.45
  Cauli_VI   Caulimovirus viroplasmin 3bsu A:27-70 hybrid 2.10
  CBFB_NFYA   CCAAT-binding transcription factor (CBF-B/NF-YA) subunit B 4g92 A:232-288 dna 1.80
  CBFD_NFYB_HMF   Histone-like transcription factor (CBF/NF-Y) and archaeal histone 4g92 C:85-149 dna 1.80
  Cdc6_C   CDC6, C terminal winged helix domain 2v1u A:308-388 dna 3.10
  Cdd1   Pathogenicity locus 3osn A:230-283 dna 1.90
  CENP-B_N   CENP-B N-terminal DNA-binding domain 1hlv A:2-56 dna 2.50
  CENP-S   CENP-S protein 4ne1 n:17-92 dna 6.50
  CENP-T_C   Centromere kinetochore component CENP-T histone fold 1kx5 F:17-98 dna 1.94
  CENP-X   CENP-S associating Centromere protein X 4ne1 p:12-81 dna 6.50
  Circo_capsid   Circovirus capsid protein 5j37 D:42-242 dna 2.30
  Cir_N   N-terminal domain of CBF1 interacting co-repressor CIR 5gmk G:11-42 rna 3.40
  CLP1_P   mRNA cleavage and polyadenylation factor CLP1 P-loop 4ohy A:121-307 rna 2.00
  cNMP_binding   Cyclic nucleotide-binding domain 1zrf A:20-109 dna 2.10
  COE1_DBD   Transcription factor COE1 DNA-binding domain 3mln A:35-240 dna 2.40
  Como_LCP   Large coat protein 1pgl 2:1-370 rna 2.80
  CPL   CPL (NUC119) domain 4wzw A:434-574 dna 2.95
  CR6_interact   Growth arrest and DNA-damage-inducible proteins-interacting protein 1 3j7y q:25-152 rna 3.40
  Cren7   Chromatin protein Cren7 3kxt A:5-59 dna 1.60
  CRISPR_assoc   CRISPR associated protein 2y8y A:1-211 rna 1.44
  CRISPR_Cas6   CRISPR-associated endoribonuclease Cas6 4c8y A:120-234 hybrid 1.80
  CRISPR_Cse1   CRISPR-associated protein Cse1 (CRISPR_cse1) 5h9f A:2-461 hybrid 2.45
  CRISPR_Cse2   CRISPR-associated protein Cse2 (CRISPR_cse2) 5h9f C:21-152 hybrid 2.45
  Cro   Cro 6cro A:2-60 dna 3.00
  Crp   Bacterial regulatory proteins, crp family 1zrf B:165-196 dna 2.10
  CSD   'Cold-shock' DNA-binding domain 2hax B:2-66 dna 1.29
  CsrA   Global regulator protein family 4kji B:3-66 rna 3.20
  CtsR   Firmicute transcriptional repressor of class III stress genes (CtsR) 3h0d A:2-150 dna 2.40
  Cucumo_2B   Cucumovirus protein 2B 2zi0 B:7-57 rna 2.82
  CUT   CUT domain 2o4a A:370-445 dna 1.75
  Cwf_Cwc_15   Cwf15/Cwc15 cell cycle control protein 5gmk S:4-133 rna 3.40
  Cyclin_N   Cyclin, N-terminal domain 2w2h B:10-149 rna 3.25
  Cytotoxic   Cytotoxic 2xfz Y:10-93 rna 3.20
  C_LFY_FLO   DNA Binding Domain (C-terminal) Leafy/Floricaula 4bhk B:189-346 dna 2.32
  DALR_1   DALR anticodon binding domain 2zue A:507-629 rna 2.00
  DALR_2   DALR domain 1u0b B:341-402 rna 2.30
  DAP3   Mitochondrial ribosomal death-associated protein 3 5aj3 g:98-393 rna 3.60
  DbpA   DbpA RNA binding domain 3moj B:405-476 rna 2.90
  DcpS_C   Scavenger mRNA decapping enzyme C-term binding 4ndh B:167-278 dna 1.85
  DDE_Tnp_1   Transposase DDE domain 1mus A:124-362 dna 1.90
  DdrB   DdrB-like protein 4noe C:3-134 dna 2.20
  DEAD   DEAD/DEAH box helicase 3pey A:116-281 rna 1.40
  Denso_VP4   Capsid protein VP4 4mgu A:23-417 dna 3.50
  DHH   DHH family 5f56 A:73-217 dna 2.30
  DHHA1   DHHA1 domain 5f56 A:300-421 dna 2.30
  DIM1   Mitosis protein DIM1 5gap D:5-137 rna 3.60
  Dimer_Tnp_Tn5   Transposase Tn5 dimerisation domain 1mus A:358-470 dna 1.90
  DKCLD   DKCLD (NUC011) domain 3hax A:12-66 rna 2.11
  DM   DM DNA binding domain 4yj0 C:72-118 dna 3.81
  Dna2   DNA replication factor Dna2 5ean A:72-283 dna 2.36
  DnaB_C   DnaB-like helicase C terminal domain 4esv B:185-440 dna 3.20
  DNA_alkylation   DNA alkylation repair enzyme 5cl8 A:8-221 dna 1.38
  DNA_binding_1   6-O-methylguanine DNA methyltransferase, DNA binding domain 3gx4 X:5-87 dna 2.70
  DNA_gyraseB_C   DNA gyrase B subunit, carboxyl terminus 5iwi B:544-634 dna 1.98
  DNA_ligase_aden   NAD-dependent DNA ligase adenylation domain 4glx A:3-318 dna 1.90
  DNA_ligase_A_C   ATP dependent DNA ligase C terminal region 3l2p A:617-727 dna 3.00
  DNA_ligase_A_M   ATP dependent DNA ligase domain 2q2t A:6-188 dna 2.30
  DNA_ligase_A_N   DNA ligase N terminus 1x9n A:288-464 dna 3.00
  DNA_ligase_OB   NAD-dependent DNA ligase OB-fold domain 4glx A:321-399 dna 1.90
  DNA_ligase_OB_2   DNA ligase OB-like domain 2q2t A:225-293 dna 2.30
  DNA_ligase_ZBD   NAD-dependent DNA ligase C4 zinc finger domain 4glx A:407-434 dna 1.90
  DNA_methylase   C-5 cytosine-specific DNA methylase 5ciy A:12-320 dna 1.59
  DNA_photolyase   DNA photolyase 1tez C:5-169 dna 1.80
  DNA_pol3_alpha   Bacterial DNA polymerase III alpha subunit 3f2b A:831-1256 dna 2.39
  DNA_pol3_beta   DNA polymerase III beta subunit, N-terminal domain 3bep A:1-120 dna 1.92
  DNA_pol3_beta_2   DNA polymerase III beta subunit, central domain 3bep B:129-243 dna 1.92
  DNA_pol3_delta2   DNA polymerase III, delta subunit 3glg E:8-167 dna 3.25
  DNA_pol3_delt_C   Processivity clamp loader gamma complex DNA pol III C-term 3glg F:214-333 dna 3.25
  DNA_pol_A   DNA polymerase family A 4yfu A:497-874 dna 1.50
  DNA_pol_A_exo1   3'-5' exonuclease 2kfz A:330-517 dna 2.03
  DNA_pol_B   DNA polymerase family B 3qex A:350-791 dna 1.73
  DNA_pol_B_2   DNA polymerase type B, organellar and viral 2py5 B:49-477 dna 1.60
  DNA_pol_B_exo1   DNA polymerase family B, exonuclease domain 3qex A:19-293 dna 1.73
  DNA_pol_B_palm   DNA polymerase beta palm 4lzg A:290-424 dna 1.60
  DNA_pol_B_thumb   DNA polymerase beta thumb 4lzg A:430-493 dna 1.60
  DNA_pol_lambd_f   Fingers domain of DNA polymerase lambda 4lzg A:238-287 dna 1.60
  DNA_primase_lrg   Eukaryotic and archaeal DNA primase, large subunit 5f0q A:270-448 hybrid 2.21
  DNA_primase_S   DNA primase small subunit 5l2x A:113-327 dna 2.20
  DNA_processg_A   DNA recombination-mediator protein A 4ljr B:6-205 dna 1.80
  DNA_topoisoIV   DNA gyrase/topoisomerase IV, subunit A 5iwi A:33-474 dna 1.98
  DpnI   Dam-replacing family 4esj B:1-253 dna 2.05
  DSHCT   DSHCT (NUC185) domain 2xgj A:898-1068 rna 2.90
  dsrm   Double-stranded RNA binding motif 2nug A:152-217 rna 1.70
  DUF1115   Protein of unknown function (DUF1115) 4yhw A:340-467 rna 3.25
  DUF1713   Mitochondrial domain of unknown function (DUF1713) 5aj3 n:128-159 rna 3.60
  DUF1743   Domain of unknown function (DUF1743) 3amt A:139-252 rna 2.90
  DUF2258   Uncharacterized protein conserved in archaea (DUF2258) 4pso I:4-81 dna 2.90
  DUF331   Domain of unknown function 5u4j w:9-46 rna 3.70
  DUF3378   Domain of unknown function (DUF3378) 4py5 A:1-66 hybrid 2.10
  DUF3578   Domain of unknown function (DUF3578) 3ssc B:3-136 dna 2.10
  DUF3591   Protein of unknown function (DUF3591) 5fur G:609-1103 dna 8.50
  DUF4152   Protein of unknown function (DUF4152) 4yoy A:1-225 dna 1.95
  DUF445   Protein of unknown function (DUF445) 4lln C:6-139 dna 2.84
  DUF4496   Domain of unknown function (DUF4496) 4yew C:6-79 dna 2.68
  DUF4918   Domain of unknown function (DUF4918) 1oe4 A:64-226 dna 2.00
  DUF5323   Family of unknown function (DUF5323) 5mmi 7:48-93 rna 3.25
  DUF5328   Family of unknown function (DUF5328) 4z7k A:67-217 hybrid 3.00
  DUF5467   Family of unknown function (DUF5467) 5gae g:82-254 rna 3.33
  DUF572   Family of unknown function (DUF572) 5gmk F:2-116 rna 3.40
  Dus   Dihydrouridine synthase (Dus) 3b0u X:7-312 rna 1.95
  E2F_TDP   E2F/DP family winged-helix DNA-binding domain 1cf7 A:18-82 dna 2.60
  EAL   EAL domain 4afy A:444-678 rna 2.01
  EBV-NA1   Epstein Barr virus nuclear antigen-1, DNA-binding domain 1b3t A:461-606 dna 2.20
  Eco57I   Eco57I restriction-modification methylase 2ih2 D:97-213 dna 1.61
  EcoRI   Restriction endonuclease EcoRI 1cl8 D:17-273 dna 1.80
  EcoRII-C   EcoRII C terminal 3bm3 B:64-183 dna 1.70
  EcoRII-N   Restriction endonuclease EcoRII, N-terminal 3hqf A:14-167 dna 2.51
  EFG_C   Elongation factor G C-terminus 5anb K:979-1066 rna 4.10
  EFG_II   Elongation Factor G, domain II 4juw Y:404-478 rna 2.86
  EFG_IV   Elongation factor G, domain IV 4kiy V:486-609 rna 2.90
  EFP_N   Elongation factor P (EF-P) KOW-like domain 3huy V:3-60 rna 3.10
  eIF-1a   Translation initiation factor 1A / IF-1 1hr0 W:7-70 rna 3.20
  eIF-3c_N   Eukaryotic translation initiation factor 3 subunit 8 N-terminus 4uer c:251-640 rna 6.47
  eIF-5_eIF-2B   Domain found in IF2B/IF5 5jb3 8:15-133 rna 5.34
  eIF-6   eIF-6 family 2x7n B:4-204 rna 11.80
  eIF2A   Eukaryotic translation initiation factor eIF2A 4uer b:458-685 rna 6.47
  eIF2_C   Initiation factor eIF2 gamma, C terminal 3qsy A:327-413 rna 3.20
  EIF_2_alpha   Eukaryotic translation initiation factor 2 alpha subunit 3qsy B:176-236 rna 3.20
  Elong-fact-P_C   Elongation factor P, C-terminal 3huy V:126-183 rna 3.10
  EMG1   EMG1/NEP1 methyltransferase 3oin B:43-246 rna 1.90
  Endonuc-BglII   Restriction endonuclease BglII 1dfm B:10-171 dna 1.50
  Endonuc-BsobI   Restriction endonuclease BsobI 1dc1 B:7-323 dna 1.70
  Endonuc-dimeris   T4 recombination endonuclease VII, dimerisation 2qnf B:104-157 dna 3.00
  Endonuc-EcoRV   Restriction endonuclease EcoRV 1sx5 A:10-241 dna 1.50
  Endonuc-FokI_C   Restriction endonuclease FokI, C terminal 1fok A:387-576 dna 2.80
  Endonuc-HincII   Restriction endonuclease HincII 2gig A:11-257 dna 1.83
  Endonuc-MspI   Restriction endonuclease MspI 1sa3 B:16-262 dna 1.95
  Endonuc-PvuII   Restriction endonuclease PvuII 3pvi A:4-157 dna 1.59
  Endonuclease_1   Endonuclease I 1oup A:23-228 dna 2.30
  Endonuclease_5   Endonuclease V 4b20 A:21-215 dna 2.75
  Endonuclease_7   Recombination endonuclease VII 3gox A:102-187 dna 1.50
  Endonuclease_NS   DNA/RNA non-specific endonuclease 5gkp B:65-293 dna 2.30
  Endonuc_BglI   Restriction endonuclease BglI 1dmu C:2-299 dna 2.20
  EnY2   Transcription factor e(y)2 4zux k:9-89 dna 3.82
  ERCC3_RAD25_C   ERCC3/RAD25/XPB C-terminal helicase 5fmf 1:535-784 dna 6.00
  ERCC4   ERCC4 domain 2bgw B:23-143 dna 2.80
  eRF1_1   eRF1 domain 1 5a8l Q:18-140 rna 3.80
  eRF1_2   eRF1 domain 2 5a8l Q:145-277 rna 3.80
  eRF1_3   eRF1 domain 3 5a8l Q:280-417 rna 3.80
  Ets   Ets-domain 1bc8 C:6-85 dna 1.93
  EVE   EVE domain 5j3e B:55-219 dna 2.60
  Exc   Excisionase-like protein 1rh6 B:1-52 dna 1.70
  Exonuc_X-T_C   Exonuclease C-terminal 4jrp B:212-473 dna 1.95
  EXOSC1   Exosome component EXOSC1/CSL4 5k36 I:132-191 rna 3.10
  Exo_endo_phos   Endonuclease/Exonuclease/phosphatase family 5ht2 A:127-359 dna 1.43
  FAD_binding_7   FAD binding domain of DNA photolyase 1tez A:280-470 dna 1.80
  Fapy_DNA_glyco   Formamidopyrimidine-DNA glycosylase N-terminal domain 1k3x A:1-106 dna 1.25
  FDX-ACB   Ferredoxin-fold anticodon binding domain 3tup A:322-414 rna 3.05
  FemAB   FemAB family 4ii9 A:233-333 rna 1.66
  Fer4_16   4Fe-4S double cluster binding domain 5d0a B:187-250 rna 2.10
  Fe_dep_repress   Iron dependent repressor, N-terminal DNA binding domain 2isz D:3-62 dna 2.40
  Fibrillarin   Fibrillarin 5gip P:6-231 rna 3.13
  Filo_VP35   Filoviridae VP35 3l25 A:218-340 rna 2.00
  Flavi_DEAD   Flavivirus DEAD domain 5mfx A:184-331 rna 1.60
  Flexi_CP   Viral coat protein 5fn1 A:49-188 rna 3.90
  Flp_C   Recombinase Flp protein 1flo B:137-379 dna 2.65
  Flp_N   Recombinase Flp protein N-terminus 1flo B:44-128 dna 2.65
  Flu_NS1   Influenza non-structural protein (NS1) 2zko A:1-70 rna 1.70
  Flu_PA   Influenza RNA-dependent RNA polymerase subunit PA 5m3h A:21-710 rna 2.50
  Flu_PB1   Influenza RNA-dependent RNA polymerase subunit PB1 5m3h B:1-742 rna 2.50
  Flu_PB2   Influenza RNA-dependent RNA polymerase subunit PB2 5m3h C:1-742 rna 2.50
  FokI_C   Restriction endonuclease FokI, catalytic domain 1fok A:148-288 dna 2.80
  FokI_N   Restriction endonuclease FokI, recognition domain 1fok A:6-141 dna 2.80
  Forkhead   Forkhead domain 3l2c A:98-177 dna 1.87
  Formyl_trans_C   Formyl transferase, C-terminal domain 2fmt B:206-304 rna 2.80
  Formyl_trans_N   Formyl transferase 2fmt A:4-183 rna 2.80
  FtsJ   FtsJ-like methyltransferase 5dto A:54-224 rna 2.60
  Ftsk_gamma   Ftsk gamma domain 2ve9 B:747-806 dna 1.90
  FUR   Ferric uptake regulator family 4mtd A:19-140 dna 2.50
  G10   G10 protein 5gmk T:1-155 rna 3.40
  GAD   GAD domain 1c0a A:307-406 rna 2.40
  Gal4_dimer   Gal4-like dimerisation domain 3coq A:50-96 dna 2.40
  GATA   GATA zinc finger 4hc9 A:264-298 dna 1.60
  GatB_N   GatB/GatE catalytic domain 3kfu F:4-281 rna 3.00
  GatB_Yqey   GatB domain 3kfu F:319-603 rna 3.00
  Gcd10p   Gcd10p family 5ccb B:19-365 rna 2.00
  GCD14   tRNA methyltransferase complex GCD14 subunit 5cd1 A:64-264 rna 3.60
  GCD14_N   tRNA methyltransferase complex GCD14 subunit N-term 5cd1 D:8-58 rna 3.60
  GCM   GCM motif protein 1odh A:30-167 dna 2.85
  GerE   Bacterial regulatory proteins, luxR family 1l3l D:172-228 dna 1.66
  GntR   Bacterial regulatory proteins, gntR family 4u0y C:11-74 dna 1.91
  gp45-slide_C   gp45 sliding clamp, C terminal 3u5z F:7115-7222 dna 3.50
  Gti1_Pac2   Gti1/Pac2 family 4qtj A:9-203 dna 2.10
  GTP-bdg_M   GTP-binding GTPase Middle Region 5ady 6:114-192 rna 4.50
  GTP1_OBG   GTP1/OBG 4csu 9:4-158 rna 5.50
  GTP_EFTU   Elongation factor Tu GTP binding domain 1b23 P:9-212 rna 2.60
  GTP_EFTU_D2   Elongation factor Tu domain 2 3avx A:509-578 rna 2.41
  GTP_EFTU_D3   Elongation factor Tu C-terminal domain 1b23 P:309-404 rna 2.60
  GTP_EFTU_D4   Elongation factor Tu domain 4 4byx V:461-546 rna 6.60
  H2TH   Formamidopyrimidine-DNA glycosylase H2TH domain 1k3x A:125-223 dna 1.25
  HA2   Helicase associated domain (HA2) 5aor A:836-951 rna 2.08
  HABP4_PAI-RBP1   Hyaluronan / mRNA binding family 4ujp i:87-176 rna 2.80
  HAT   HAT (Half-A-TPR) repeat 5mqf O:256-288 rna 5.90
  HBB   Helical and beta-bridge domain 5h8w A:236-427 dna 2.20
  HD   HD domain 4x9e B:66-182 rna 3.10
  HEAT_2   HEAT repeats 5d0a B:295-373 rna 2.10
  Helicase_C   Helicase conserved C-terminal domain 3pey A:316-431 rna 1.40
  Helicase_C_2   Helicase C-terminal domain 5h8w A:440-598 dna 2.20
  Herpes_alk_exo   Herpesvirus alkaline exonuclease 3pov A:27-478 dna 2.50
  Hfq   Hfq protein 5sze A:8-71 rna 1.50
  HGTP_anticodon   Anticodon binding domain 4yye B:349-457 rna 2.30
  HHH   Helix-hairpin-helix motif 1orn A:100-129 dna 1.70
  HhH-GPD   HhH-GPD superfamily base excision DNA repair protein 4ofa A:461-571 dna 1.55
  HHH_2   Helix-hairpin-helix motif 4glx A:510-573 dna 1.90
  HHH_4   Helix-hairpin-helix containing domain 3gpl A:184-242 dna 2.50
  HHH_5   Helix-hairpin-helix domain 4glx A:445-502 dna 1.90
  HHH_6   Helix-hairpin-helix motif 3f2b A:1356-1441 dna 2.39
  HHH_8   Helix-hairpin-helix domain 4lzg A:153-218 dna 1.60
  HigB-like_toxin   RelE-like toxin of type II toxin-antitoxin system HigB 4yy3 Y:3-92 rna 3.60
  HIN   HIN-200/IF120x domain 4l5r C:58-223 dna 1.87
  HipA_C   HipA-like C-terminal domain 4pu3 A:145-391 dna 3.39
  HIRAN   HIRAN domain 4s0n B:60-155 dna 1.50
  Histone   Core histone H2A/H2B/H3/H4 1kx5 A:1-131 dna 1.94
  Histone_H2A_C   C-terminus of histone H2A 1kx5 C:91-125 dna 1.94
  HIT   HIT domain 3spd D:44-156 dna 1.91
  Hjc   Archaeal holliday junction resolvase (hjc) 2wiw B:7-99 dna 1.80
  HLH   Helix-loop-helix DNA-binding domain 1nkp E:704-754 dna 1.80
  HMG_box   HMG (high mobility group) box 4y60 C:3-71 dna 1.75
  HMG_box_2   HMG-box domain 4qr9 B:5-77 dna 2.00
  HNF-1_N   Hepatocyte nuclear factor 1 (HNF-1), N terminus 1ic8 A:87-168 dna 2.60
  HNH_3   HNH endonuclease 1u3e M:53-98 dna 2.92
  HNH_4   HNH endonuclease 5fq5 B:821-872 hybrid 2.14
  Homeobox   Homeobox domain 3rkq B:139-193 dna 1.70
  Homeobox_KN   Homeobox KN domain 4xrm B:290-329 dna 1.60
  Hom_end   Homing endonuclease 1lwt A:302-413 dna 3.20
  Hom_end_hint   Hom_end-associated Hint 1lwt A:1-453 dna 3.20
  HPD   Homeo-prospero domain 1xpx A:1247-1400 dna 2.80
  HRDC   HRDC domain 5c0y B:438-505 rna 2.10
  HSF_DNA-bind   HSF-type DNA-binding 5hdn A:18-118 dna 1.68
  HTH_1   Bacterial regulatory helix-turn-helix protein, lysR family 4iht C:3-62 dna 3.00
  HTH_18   Helix-turn-helix domain 1bl0 A:33-112 dna 2.30
  HTH_19   Helix-turn-helix domain 4jcy A:3-70 dna 1.80
  HTH_24   Winged helix-turn-helix DNA-binding 5f7q L:13-59 dna 2.40
  HTH_27   Winged helix DNA-binding domain 3gfi A:37-102 dna 2.10
  HTH_3   Helix-turn-helix 2r1j R:10-64 dna 1.53
  HTH_31   Helix-turn-helix domain 4pu3 D:28-95 dna 3.39
  HTH_5   Bacterial regulatory protein, arsR family 4on0 C:28-74 dna 3.00
  HTH_7   Helix-turn-helix domain of resolvase 1jko C:139-183 dna 2.24
  HTH_8   Bacterial regulatory protein, Fis family 5ds9 B:54-95 dna 2.56
  HTH_AsnC-type   AsnC-type helix-turn-helix domain 2e1c A:25-66 dna 2.10
  HTH_Crp_2   Crp-like helix-turn-helix domain 4i2o A:159-230 dna 1.77
  HTH_IclR   IclR helix-turn-helix domain 2xro A:16-67 dna 3.40
  HTH_Tnp_Tc3_1   Tc3 transposase 1tc3 C:203-252 dna 2.45
  HTH_Tnp_Tc5   Tc5 transposase DNA-binding domain 1hlv A:74-131 dna 2.50
  HutP   HutP 1wpu B:9-146 rna 1.48
  HxlR   HxlR-like helix-turn-helix 4hqe B:14-107 dna 2.30
  IBD   Transcription-initiator DNA-binding domain IBD 1pp7 U:6-112 dna 2.45
  IF-2   Translation-initiation factor 2 5lmv a:358-463 rna 4.90
  IF3_C   Translation initiation factor IF-3, C-terminal domain 5lmn X:83-168 rna 3.55
  IF3_N   Translation initiation factor IF-3, N-terminal domain 5lmn X:7-76 rna 3.55
  Ig_3   Immunoglobulin domain 3s59 A:23-103 dna 2.80
  IL6   Interleukin-6/G-CSF/MGF family 4ni7 A:16-184 dna 2.40
  Img2   Mitochondrial large subunit ribosomal protein (Img2) 3j7y g:82-166 rna 3.40
  IMS   impB/mucB/samB family 5kfz A:12-228 dna 1.44
  IMS_C   impB/mucB/samB family C-terminal domain 5kfz A:309-432 dna 1.44
  IMS_HHH   IMS family HHH motif 4tqr A:168-199 dna 1.58
  IncA   IncA protein 1nkp E:705-783 dna 1.80
  Integrase_Zn   Integrase Zinc binding domain 5ejk A:5-42 dna 3.80
  Intron_maturas2   Type II intron maturase 5g2x C:381-544 rna 3.80
  IN_DBD_C   Integrase DNA binding domain 5ejk D:224-267 dna 3.80
  IPPT   IPP transferase 3foz B:45-293 rna 2.50
  IRF   Interferon regulatory factor transcription factor 4hly B:5-108 dna 1.48
  Isy1   Isy1-like splicing family 5gmk H:2-96 rna 3.40
  KH_1   KH domain 2p2r A:289-353 dna 1.60
  KH_2   KH domain 3iev A:209-288 rna 1.90
  KH_5   NusA-like KH domain 2asb A:214-282 rna 1.50
  KH_dom-like   KH-domain-like of EngA bacterial GTPase enzymes, C-terminal 3j8g X:378-458 rna 5.00
  KilA-N   KilA-N domain 4ux5 B:30-110 dna 2.40
  KORA   TrfB plasmid transcriptional repressor 2w7n A:5-88 dna 1.85
  KorB   KorB domain 1r71 B:166-252 dna 2.20
  KOW   KOW motif 1vq8 T:44-75 hybrid 2.20
  KTI12   Chromatin associated protein KTI12 3add B:2-233 rna 2.40
  Ku   Ku70/Ku80 beta-barrel domain 1jey A:263-467 dna 2.50
  Ku_C   Ku70/Ku80 C-terminal arm 1jey B:476-545 dna 2.50
  Ku_N   Ku70/Ku80 N-terminal alpha/beta domain 1jey B:9-244 dna 2.50
  L51_S25_CI-B8   Mitochondrial ribosomal protein L51 / S25 / CI-B8 domain 3j7y b:43-95 rna 3.40
  La   La domain 2voo B:17-74 rna 1.80
  LacI   Bacterial regulatory proteins, lacI family 1qpz A:3-48 dna 2.50
  Lactamase_B   Metallo-beta-lactamase superfamily 4xww B:27-215 rna 1.70
  Lactamase_B_2   Beta-lactamase superfamily domain 5hab B:63-192 rna 2.30
  LAG1-DNAbind   LAG1, DNA binding 3iag C:74-204 dna 2.00
  LAGLIDADG_1   LAGLIDADG endonuclease 1t9i A:13-104 dna 1.60
  LAGLIDADG_2   LAGLIDADG DNA endonuclease family 3c0w A:34-208 dna 2.20
  LAGLIDADG_3   LAGLIDADG-like domain 2vs7 D:11-95 dna 2.05
  Ldh_1_C   lactate/malate dehydrogenase, alpha/beta C-terminal domain 5hru A:152-315 dna 1.71
  Ldh_1_N   lactate/malate dehydrogenase, NAD binding domain 5hru A:5-149 dna 1.71
  Lectin_legB   Legume lectin domain 4tzd D:1-127 dna 3.20
  LepA_C   GTP-binding protein LepA C-terminus 4qjt y:496-602 rna 2.90
  Levi_coat   Levivirus coat protein 2bu1 A:2-128 rna 2.20
  LexA_DNA_bind   LexA DNA binding domain 3jso A:2-65 dna 2.29
  Linker_histone   linker histone H1 and H5 family 4qlc U:25-96 dna 3.50
  LRR_4   Leucine Rich repeats (2 copies) 4z0c D:198-244 rna 2.30
  LRR_8   Leucine rich repeat 3wpc B:619-665 dna 1.60
  LRR_9   Leucine-rich repeat 1a9n A:2-163 rna 2.38
  LSM   LSM domain 4m7d D:14-83 rna 2.60
  LUC7   LUC7 N_terminus 4rb7 T:9-102 rna 2.40
  Lys   C-type lysozyme/alpha-lactalbumin family 4m4o A:1-127 rna 2.00
  LytTR   LytTr DNA-binding domain 3bs1 A:149-238 dna 1.60
  MA3   MA3 domain 5lj5 H:291-398 rna 3.80
  Mab-21   Mab-21 protein 4o6a B:200-495 dna 1.86
  Macro   Macro domain 3gpq A:20-125 rna 2.00
  MafB19-deam   MafB19-like deaminase 2b3j C:1-149 rna 2.00
  MarR   MarR family 4aik A:29-88 dna 1.85
  MarR_2   MarR family 5fb2 A:27-88 dna 1.80
  MazE_antitoxin   Antidote-toxin recognition MazE, bacterial antitoxin 3zvk H:7-47 dna 2.50
  MBD   Methyl-CpG binding domain 3vxv A:71-135 dna 2.00
  MCM   MCM2/3/5 family 5v8f 4:505-834 dna 3.90
  MCM_OB   MCM OB domain 4pog H:103-231 dna 3.20
  Med12-LCEWAV   Eukaryotic Mediator 12 subunit domain 5mmj t:72-175 rna 3.65
  MerR_1   MerR HTH family regulatory protein 4wls B:2-69 dna 2.11
  Metallophos   Calcineurin-like phosphoesterase 4pei C:7-234 rna 1.95
  Methylase_S   Type I restriction modification DNA specificity domain 2y7h A:7-191 dna 18.00
  MethyltransfD12   D12 class N6 adenine-specific DNA methyltransferase 2g1p B:10-262 dna 1.89
  Methyltransf_31   Methyltransferase domain 3htx A:711-885 rna 3.10
  Methyltransf_4   Putative methyltransferase 4ox9 Y:25-107 rna 3.80
  MetJ   Met Apo-repressor, MetJ 1mjo B:2-98 dna 2.10
  Met_10   Met-10+ like-protein 2zzm A:95-289 rna 2.65
  MH1   MH1 domain 1ozj A:31-131 dna 2.40
  Microvir_J   Microvirus J protein 2bpa 3:2-37 dna 3.00
  MMR_HSR1   50S ribosome-binding GTPase 3r9w A:5-124 rna 2.05
  MobA_MobL   MobA/MobL family 4ht4 A:17-195 dna 2.91
  Mob_Pre   Plasmid recombination enzyme 4lvi A:2-194 dna 1.90
  MogR_DNAbind   DNA binding domain of the motility gene repressor (MogR) 3fdq A:9-143 dna 1.75
  MotCF   Bacteriophage T4 MotA, C-terminal 5jlt B:106-208 dna 2.96
  MqsA_antitoxin   Antitoxin component of bacterial toxin-antitoxin system, MqsA 3o9x B:1-131 dna 2.10
  MRP   Mitochondrial RNA binding protein MRP 2gje D:27-167 rna 3.37
  MRP-63   Mitochondrial ribosome protein 63 3j7y o:13-101 rna 3.40
  MRP-L27   Mitochondrial ribosomal protein L27 3j7y 9:15-135 rna 3.40
  MRP-L28   Mitochondrial ribosomal protein L28 3j7y 8:63-119 rna 3.40
  MRP-L47   Mitochondrial 39-S ribosomal protein L47 (MRP-L47) 3j7y Y:64-149 rna 3.40
  MRP-L51   Mitochondrial ribosomal subunit 3j7y i:38-126 rna 3.40
  MRP-S23   Mitochondrial ribosomal protein S23 5aj3 b:2-130 rna 3.60
  MRP-S24   Mitochondrial ribosome subunit S24 5aj3 C:36-167 rna 3.60
  MRP-S26   Mitochondrial ribosome subunit S26 5aj3 d:28-197 rna 3.60
  MRP-S27   Mitochondrial 28S ribosomal protein S27 3jd5 e:37-401 rna 7.00
  MRP-S28   Mitochondrial ribosomal subunit protein 5aj3 k:143-285 rna 3.60
  MRP-S32   Mitochondrial 28S ribosomal protein S32 3j7y a:104-142 rna 3.40
  MRP-S33   Mitochondrial ribosomal subunit S27 5aj3 i:6-96 rna 3.60
  MRP-S34   Mitochondrial 28S ribosomal protein S34 5aj3 j:61-187 rna 3.60
  MRP-S35   Mitochondrial ribosomal protein MRP-S35 5aj3 f:78-176 rna 3.60
  MRP_L53   39S ribosomal protein L53/MRP-L53 3j7y k:20-71 rna 3.40
  MSL2-CXC   CXC domain of E3 ubiquitin-protein ligase MSL2 4rkh E:519-569 dna 2.00
  mTERF   mTERF 3mva O:76-389 dna 2.20
  MutH   DNA mismatch repair enzyme MutH 2aor B:59-157 dna 2.00
  MutS_I   MutS domain I 1wb9 B:14-123 dna 2.10
  MutS_III   MutS domain III 1wb9 B:272-559 dna 2.10
  MutS_IV   MutS family domain IV 1wb9 B:428-519 dna 2.10
  MvaI_BcnI   MvaI/BcnI restriction endonuclease family 2odi A:10-231 dna 1.45
  Myb_Cef   pre-mRNA splicing factor component 5gap G:221-366 rna 3.60
  Myb_DNA-binding   Myb-like DNA-binding domain 3sjm A:447-495 dna 1.35
  Myb_DNA-bind_5   Myb/SANT-like DNA-binding domain 5cqq B:53-128 dna 3.10
  Myb_DNA-bind_6   Myb-like DNA-binding domain 3ted A:1175-1246 dna 2.00
  N36   36-mer N-terminal peptide of the N protein (N36) 5lm7 N:2-36 rna 3.35
  N6_Mtase   N-6 DNA Methylase 4xqk A:840-1190 dna 2.70
  N6_N4_Mtase   DNA methylase 4zcf B:117-479 dna 2.60
  NaeI   Restriction endonuclease NaeI 1iaw B:16-307 dna 2.40
  NAM   No apical meristem (NAM) protein 3swp D:15-139 dna 4.11
  NARP1   NMDA receptor-regulated protein 1 5udi A:217-326 rna 1.58
  NDC10_II   Centromere DNA-binding protein complex CBF3 subunit, domain 2 3sqi A:110-343 dna 2.82
  NDT80_PhoG   NDT80 / PhoG like DNA-binding family 1mnn A:105-334 dna 1.40
  Neil1-DNA_bind   Endonuclease VIII-like 1, DNA bind 5itu B:238-290 dna 2.41
  NGF   Nerve growth factor family 4zbn A:11-114 dna 2.45
  NgoMIV_restric   NgoMIV restriction enzyme 1fiu A:12-286 dna 1.60
  NHL   NHL repeat 4zlr B:957-985 rna 2.30
  NikR_C   NikR C terminal nickel binding domain 2hzv B:53-129 dna 3.10
  Nop   snoRNA binding domain, fibrillarin 2ozb E:99-330 rna 2.60
  Nop10p   Nucleolar RNA-binding protein, Nop10p family 3hax C:3-52 rna 2.11
  NotI   Restriction endonuclease NotI 3c25 A:17-263 dna 2.50
  NTP_transf_2   Nucleotidyltransferase domain 5hrb A:13-136 dna 1.70
  NucS   Endonuclease NucS 5gke B:27-240 dna 2.40
  NUDIX   NUDIX domain 4s2x A:7-148 rna 1.50
  NUDIX_2   Nucleotide hydrolase 3mdi A:35-222 rna 2.07
  NUDIX_4   NUDIX domain 3fsp A:240-354 dna 2.20
  NUMOD4   NUMOD4 motif 1u3e M:1-45 dna 2.92
  NusB   NusB family 3r2c A:5-132 rna 1.90
  NusG   Transcription termination factor nusG 5ms0 F:7-112 hybrid 9.80
  OAS1_C   2'-5'-oligoadenylate synthetase 1, domain 2, C-terminus 4rwn A:163-348 rna 2.00
  OB_NTP_bind   Oligonucleotide/oligosaccharide-binding (OB)-fold 5aor B:1001-1082 rna 2.08
  OGG_N   8-oxoguanine DNA glycosylase, N-terminal domain 3ih7 A:25-141 dna 3.10
  Omega_Repress   Omega Transcriptional Repressor 2bnw B:19-71 dna 2.45
  ORC2   Origin recognition complex subunit 2 5udb B:268-608 dna 3.90
  ORC4_C   Origin recognition complex (ORC) subunit 4 C-terminus 5v8f D:286-517 dna 3.90
  ORC5_C   Origin recognition complex (ORC) subunit 5 C-terminus 5v8f E:187-474 dna 3.90
  P22_Cro   DNA-binding transcriptional regulator Cro 3qws B:2-63 dna 2.10
  P53   P53 DNA-binding domain 4ibu A:96-289 dna 1.70
  PAP_assoc   Cid1 family poly A polymerase 4nku A:267-336 rna 1.94
  PAP_central   Poly(A) polymerase central domain 2q66 A:8-351 rna 1.80
  PAP_RNA-bind   Poly(A) polymerase predicted RNA binding domain 2q66 A:353-529 rna 1.80
  Paramyxo_ncap   Paramyxovirus nucleocapsid protein 4xjn H:12-400 rna 3.11
  ParB   ParB family 3vwb A:182-246 dna 2.42
  ParE_toxin   ParE toxin of type II toxin-antitoxin system, parDE 3kiq y:5-85 rna 3.30
  PARP_regulatory   Poly A polymerase regulatory subunit 1av6 A:5-296 rna 2.80
  Parvo_coat   Parvovirus coat protein VP2 3ra4 A:220-712 dna 2.70
  PAS   PAS fold 4zpk B:85-201 dna 3.60
  PAX   'Paired box' domain 1k78 A:19-140 dna 2.25
  PAZ   PAZ domain 4z4d A:231-365 rna 1.60
  PC4   Transcriptional Coactivator p15 (PC4) 2c62 B:64-116 dna 1.74
  PCNA_C   Proliferating cell nuclear antigen, C-terminal domain 5l7c A:127-254 dna 2.82
  PCNA_N   Proliferating cell nuclear antigen, N-terminal domain 5l7c A:1-125 dna 2.82
  PCRF   PCRF domain 3f1e X:35-221 rna 3.00
  PD-C2-AF1   POU domain, class 2, associating factor 1 1cqt J:800-822 dna 3.20
  PDCD9   Mitochondrial 28S ribosomal protein S30 (PDCD9) 3j7y s:41-429 rna 3.40
  PDDEXK_1   PD-(D/E)XK nuclease superfamily 4cei B:789-1131 dna 2.80
  PDDEXK_5   PD-(D/E)XK endonuclease 2ost B:2-148 dna 3.10
  PemK_toxin   PemK-like, MazF-like toxin of type II toxin-antitoxin system 5dlo A:2-109 dna 1.40
  Penicillinase_R   Penicillinase repressor 1xsd D:8-122 dna 2.70
  Peptidase_A21   Peptidase family A21 2qqp F:557-623 rna 3.80
  Peptidase_A6   Peptidase A6 family 4ftb C:55-363 rna 2.70
  Peptidase_S48   Peptidase family S48 4izz A:54-202 dna 2.50
  Pept_tRNA_hydro   Peptidyl-tRNA hydrolase 3vjr A:8-192 rna 2.40
  Phage_CII   Bacteriophage CII protein 1zs4 C:4-82 dna 1.70
  Phage_clamp_A   Bacteriophage clamp loader A subunit 3u60 A:37-173 dna 3.34
  Phage_coat   Phage PP7 coat protein 2qux E:1-127 rna 2.44
  Phage_endo_I   Phage endonuclease I 2pfj A:17-145 dna 3.10
  Phage_F   Capsid protein (F protein) 2bpa 1:184-424 dna 3.00
  Phage_integrase   Phage integrase family 1xo0 H:138-330 dna 2.00
  Phage_int_SAM_1   Phage integrase, N-terminal SAM-like domain 1p7d B:80-158 dna 2.95
  Phage_int_SAM_4   Phage integrase, N-terminal SAM-like domain 1xo0 A:26-102 dna 2.00
  Phage_mat-A   Phage maturation protein 5tc1 M:3-393 rna 3.60
  Phage_NinH   Phage NinH protein 5ds9 A:60-96 dna 2.56
  PhdYeFM_antitox   Antitoxin Phd_YefM, type II toxin-antitoxin system 4zm0 B:1-55 dna 3.17
  Phe_tRNA-synt_N   Aminoacyl tRNA synthetase class II, N-terminal domain 2iy5 A:15-81 rna 3.10
  Phi-29_GP16_7   Bacteriophage phi-29 early protein GP16.7 2c5r F:66-128 dna 2.90
  Phi-29_GP4   Phi-29-like late genes activator (early protein GP4) 2fio A:2-124 dna 2.70
  Phosphodiest   Type I phosphodiesterase / nucleotide pyrophosphatase 5hrt A:165-477 dna 2.00
  PIF1   PIF1-like helicase 5fhd B:5-272 dna 2.00
  Piwi   Piwi domain 4z4d A:517-818 rna 1.60
  Pkinase   Protein kinase domain 3uzt A:191-453 rna 3.51
  Pneumo_ncap   Pneumovirus nucleocapsid protein 2wj8 T:2-375 rna 3.29
  PNK3P   Polynucleotide kinase 3 phosphatase 3u7f B:165-327 dna 1.80
  PolC_DP2   DNA polymerase II large subunit DP2 3hax C:3-50 rna 2.11
  PolyA_pol   Poly A polymerase head domain 1vfg B:13-139 rna 2.80
  PolyA_pol_RNAbd   Probable RNA and SrmB- binding site of polymerase A 1vfg B:164-227 rna 2.80
  Polyketide_cyc2   Polyketide cyclase / dehydrase and lipid transport 2gje A:99-218 rna 3.37
  Polyoma_lg_T_C   Polyomavirus large T antigen C-terminus 4gdf E:265-627 dna 2.80
  POT1   Telomeric single stranded DNA binding POT1/CDC13 1xjv A:11-141 dna 1.73
  POT1PC   ssDNA-binding domain of telomere protection protein 4hik A:7-141 dna 1.64
  Pou   Pou domain - N-terminal to homeobox domain 1e3o C:4-75 dna 1.90
  Pox_polyA_pol   Poxvirus poly(A) polymerase nucleotidyltransferase domain 3erc C:131-279 hybrid 3.21
  Pox_polyA_pol_C   Poxvirus poly(A) polymerase C-terminal domain 3er8 D:282-479 hybrid 3.18
  Pox_polyA_pol_N   Poxvirus poly(A) polymerase N-terminal domain 3er9 B:12-117 rna 2.06
  PPR   PPR repeat 4oe1 A:246-276 rna 2.80
  PPR_1   PPR repeat 5i9f A:45-78 rna 2.19
  PPR_2   PPR repeat family 5i9f A:224-273 rna 2.19
  PPR_3   Pentatricopeptide repeat domain 4m59 A:267-332 rna 2.46
  PPV_E1_C   Papillomavirus helicase 1ksy C:166-303 dna 3.05
  PPV_E2_C   E2 (early) protein, C terminal 2bop A:328-406 dna 1.70
  PQQ_2   PQQ-like domain 3vh0 A:161-344 dna 2.90
  PriCT_1   Primase C terminal 1 (PriCT-1) 3vw4 A:171-238 dna 2.70
  PRO8NT   PRO8NT (NUC069), PrP8 N-terminal domain 5gmk A:131-282 rna 3.40
  PROCN   PROCN (NUC071) domain 5gmk A:470-874 rna 3.40
  Pro_isomerase   Cyclophilin type peptidyl-prolyl cis-trans isomerase/CLD 5mqf o:143-299 rna 5.90
  Prp18   Prp18 domain 5mps a:114-223 rna 3.85
  Prp19   Prp19/Pso4-like 5gmk p:62-139 rna 3.40
  PRP3   pre-mRNA processing factor 3 (PRP3) 5gap G:152-318 rna 3.60
  Prp31_C   Prp31 C terminal domain 5gap F:350-455 rna 3.60
  PRP8_domainIV   PRP8 domain IV core 5gmk A:1824-2061 rna 3.40
  PseudoU_synth_1   tRNA pseudouridine synthase 2nqp C:15-112 rna 3.50
  PseudoU_synth_2   RNA pseudouridylate synthase 4lgt A:68-202 rna 1.30
  PspA_IM30   PspA/IM30 family 5t01 A:271-313 dna 1.89
  PUA   PUA domain 1r3e A:239-315 rna 2.10
  PUF   Pumilio-family RNA binding repeat 5kla A:1219-1253 rna 1.14
  PurA   PurA ssDNA and RNA-binding protein 5fgp A:41-183 dna 2.00
  Pur_DNA_glyco   Methylpurine-DNA glycosylase (MPG) 1ewn A:89-283 dna 2.10
  Put_DNA-bind_N   Putative DNA-binding protein N-terminus 3ikt B:2-50 dna 2.26
  Pyr_excise   Pyrimidine dimer DNA glycosylase 2fcc A:2-136 dna 2.30
  R-HINP1I   R.HinP1I restriction endonuclease 2fl3 A:41-245 dna 2.39
  Rad4   Rad4 transglutaminase-like domain 2qsh A:284-426 dna 2.81
  Rad51   Rad51 5h1b B:84-336 dna 4.40
  Radical_SAM   Radical SAM superfamily 5hr7 A:119-299 rna 2.40
  RAG1   Recombination-activation protein 1 (RAG1), recombinase 3jbx C:480-1029 dna 3.40
  RAG2   Recombination activating protein 2 3jby B:51-351 dna 3.70
  RAI1   RAI1 like PD-(D/E)XK nuclease 4j7m A:235-302 rna 1.70
  RAMPs   RAMP superfamily 3x1l H:102-338 hybrid 2.10
  Rap1-DNA-bind   Rap1, DNA-binding 1ign B:448-592 dna 2.25
  Ras   Ras family 3a6p H:12-170 rna 2.92
  RbpA   RNA polymerase-binding protein 5vi8 J:26-106 dna 2.76
  RCC1   Regulator of chromosome condensation (RCC1) repeat 3mvd L:196-255 dna 2.90
  RdRP_1   RNA dependent RNA polymerase 3bso A:20-485 rna 1.74
  RdRP_3   Viral RNA dependent RNA polymerase 4wtl A:3-514 rna 2.00
  RdRP_4   Viral RNA-directed RNA-polymerase 2r7w A:100-748 rna 2.60
  RdRP_5   Reovirus RNA-dependent RNA polymerase lambda 3 1n35 A:2-1263 rna 2.50
  RecA   recA bacterial DNA recombination protein 3cmw C:2008-2269 dna 2.80
  RecG_wedge   RecG wedge domain 1gm5 A:116-280 dna 3.24
  Recombinase   Recombinase 4kis C:171-254 dna 3.20
  RecQ_Zn_bind   RecQ zinc-binding 4o3m A:995-1067 dna 2.30
  RecR   RecR protein 4v19 5:98-131 rna 3.40
  RecU   Recombination protein U 5fdk D:31-194 dna 3.21
  RepA_N   Replication initiator protein A (RepA) N-terminus 5kbj G:14-89 dna 3.09
  REPA_OB_2   Replication protein A OB domain 1jmc A:305-402 dna 2.40
  RepB_primase   RepB DNA-primase from phage plasmid 3h25 A:10-198 dna 2.70
  Rep_3   Initiator Replication protein 1rep C:15-242 dna 2.60
  Rep_fac-A_C   Replication factor-A C terminal domain 4gnx C:470-615 dna 2.80
  Rep_N   Rep protein catalytic domain like 1uut B:4-189 dna 2.00
  ResIII   Type III restriction enzyme, res subunit 5jaj A:2-172 rna 1.50
  Resolvase   Resolvase, N terminal domain 1gdt A:3-139 dna 3.00
  RestrictionMunI   Type II restriction enzyme MunI 1d02 A:6-197 dna 1.70
  REV   REV protein (anti-repression trans-activator protein) 4pmi C:13-64 rna 3.20
  RE_Eco29kI   Eco29kI restriction endonuclease 3mx4 E:41-208 dna 2.50
  RE_EcoO109I   Type II restriction endonuclease EcoO109I 1wte A:16-230 dna 1.90
  RE_HindIII   HindIII restriction endonuclease 2e52 C:3-292 dna 2.00
  RE_NgoFVII   NgoFVII restriction endonuclease 4rd5 B:185-302 dna 2.70
  RE_R_Pab1   R.Pab1 restriction endonuclease 5iff A:114-222 dna 1.90
  RF-1   RF-1 domain 3f1g X:229-338 rna 3.00
  RF3_C   Class II release factor RF3, C-terminal domain 3sfs W:387-515 rna 3.20
  RFX_DNA_binding   RFX DNA-binding domain 1dp7 P:1-76 dna 1.50
  Rhabdo_ncap   Rhabdovirus nucleocapsid protein 2gic J:10-405 rna 2.92
  RHD_dimer   Rel homology dimerisation domain 1a3q A:229-327 dna 2.10
  RHD_DNA_bind   Rel homology DNA-binding domain 1a3q A:40-220 dna 2.10
  RHH_1   Ribbon-helix-helix protein, copG family 1b01 G:4-41 dna 2.56
  Rho_RNA_bind   Rho termination factor, RNA-binding domain 2a8v A:51-118 rna 2.40
  Ribonuclease   ribonuclease 1brn M:20-108 dna 1.76
  Ribonuclease_3   Ribonuclease III domain 5t16 I:238-331 rna 2.78
  Ribonuclease_P   Ribonuclease P 3q1q A:6-116 rna 3.80
  Ribonuclease_T2   Ribonuclease T2 family 2z70 A:13-218 dna 1.70
  Ribonucleas_3_3   Ribonuclease-III-like 2nug A:17-138 rna 1.70
  Ribosomal_L1   Ribosomal protein L1p/L10e family 4qvi A:28-220 rna 1.90
  Ribosomal_L10   Ribosomal protein L10 4hub G:11-109 rna 2.40
  Ribosomal_L11   Ribosomal protein L11, RNA binding domain 1vq8 I:72-139 hybrid 2.20
  Ribosomal_L11_N   Ribosomal protein L11, N-terminal domain 1mms A:9-66 rna 2.57
  Ribosomal_L12   Ribosomal protein L7/L12 C-terminal domain 4kd9 e:60-122 rna 3.50
  Ribosomal_L12_N   Ribosomal protein L7/L12 dimerisation domain 1yl3 I:2-54 rna 5.50
  Ribosomal_L13   Ribosomal protein L13 1vqo J:10-114 rna 2.20
  Ribosomal_L13e   Ribosomal protein L13e 4ujq N:8-175 rna 2.80
  Ribosomal_L14   Ribosomal protein L14p/L23e 1vq8 K:12-132 hybrid 2.20
  Ribosomal_L14e   Ribosomal protein L14 4ujq O:54-128 rna 2.80
  Ribosomal_L15e   Ribosomal L15 1vq8 M:3-190 hybrid 2.20
  Ribosomal_L16   Ribosomal protein L16p/L10e 1vqo H:9-164 rna 2.20
  Ribosomal_L17   Ribosomal protein L17 4rb6 R:20-117 rna 2.40
  Ribosomal_L18   Ribosomal protein 60S L18 and 50S L18e 1vqo O:1-115 rna 2.20
  Ribosomal_L18A   Ribosomal proteins 50S-L18Ae/60S-L20/60S-L18A 4a19 X:18-141 rna 3.52
  Ribosomal_L18p   Ribosomal L18 of archaea, bacteria, mitoch. and chloroplast 4rb8 S:3-112 rna 2.40
  Ribosomal_L18_c   Ribosomal L18 C-terminal region 4ujq G:192-289 rna 2.80
  Ribosomal_L19   Ribosomal protein L19 4rb8 T:5-115 rna 2.40
  Ribosomal_L19e   Ribosomal protein L19e 1vqo P:2-143 rna 2.20
  Ribosomal_L2   Ribosomal Proteins L2, RNA binding domain 1vqo A:10-82 rna 2.20
  Ribosomal_L20   Ribosomal protein L20 4rb8 U:3-109 rna 2.40
  Ribosomal_L21e   Ribosomal protein L21e 1vq8 Q:2-94 hybrid 2.20
  Ribosomal_L21p   Ribosomal prokaryotic L21 protein 4rb6 V:1-99 rna 2.40
  Ribosomal_L22   Ribosomal protein L22p/L17e 1vqo R:16-148 rna 2.20
  Ribosomal_L22e   Ribosomal L22e protein family 4a19 M:12-111 rna 3.52
  Ribosomal_L23   Ribosomal protein L23 1vq8 S:3-76 hybrid 2.20
  Ribosomal_L23eN   Ribosomal protein L23, N-terminal domain 4a1c R:30-58 rna 3.52
  ribosomal_L24   Ribosomal proteins 50S L24/mitochondrial 39S L24 4rb6 Y:42-106 rna 2.40
  Ribosomal_L24e   Ribosomal protein L24e 1vqo U:4-56 rna 2.20
  Ribosomal_L25p   Ribosomal L25p family 1dfu P:4-91 rna 1.80
  Ribosomal_L26   Ribosomal proteins L26 eukaryotic, L24P archaeal 1vq8 T:1-115 hybrid 2.20
  Ribosomal_L27   Ribosomal L27 protein 4rb6 0:2-81 rna 2.40
  Ribosomal_L27A   Ribosomal proteins 50S-L15, 50S-L18e, 60S-L27A 1vqo L:24-142 rna 2.20
  Ribosomal_L27e   Ribosomal L27e protein family 4a1b N:52-144 rna 3.52
  Ribosomal_L28   Ribosomal L28 family 4rb6 1:3-68 rna 2.40
  Ribosomal_L28e   Ribosomal L28e protein family 4a19 O:4-117 rna 3.52
  Ribosomal_L29   Ribosomal L29 protein 1vqo V:6-62 rna 2.20
  Ribosomal_L29e   Ribosomal L29e protein family 4a1b T:3-42 rna 3.52
  Ribosomal_L2_C   Ribosomal Proteins L2, C-terminal domain 1vqo A:89-224 rna 2.20
  Ribosomal_L3   Ribosomal protein L3 1vq8 B:1-337 hybrid 2.20
  Ribosomal_L30   Ribosomal protein L30p/L7e 1vq8 W:2-52 hybrid 2.20
  Ribosomal_L30_N   Ribosomal L30 N-terminal domain 4ujs Q:22-79 rna 2.80
  Ribosomal_L31   Ribosomal protein L31 4rb6 4:1-64 rna 2.40
  Ribosomal_L31e   Ribosomal protein L31e 1vqo X:8-84 rna 2.20
  Ribosomal_L32e   Ribosomal protein L32 1vq8 Y:125-230 hybrid 2.20
  Ribosomal_L32p   Ribosomal L32p protein family 4rb8 5:5-60 rna 2.40
  Ribosomal_L33   Ribosomal protein L33 4rb8 6:7-53 rna 2.40
  Ribosomal_L34   Ribosomal protein L34 4rb8 7:1-44 rna 2.40
  Ribosomal_L34e   Ribosomal protein L34e 4a19 L:2-96 rna 3.52
  Ribosomal_L35Ae   Ribosomal protein L35Ae 4a19 H:14-107 rna 3.52
  Ribosomal_L35p   Ribosomal protein L35 4rb6 8:2-62 rna 2.40
  Ribosomal_L36   Ribosomal protein L36 4rb8 9:1-37 rna 2.40
  Ribosomal_L36e   Ribosomal protein L36e 4a1b Q:2-103 rna 3.52
  Ribosomal_L37ae   Ribosomal L37ae protein family 1vqo Z:10-82 rna 2.20
  Ribosomal_L37e   Ribosomal protein L37e 1vq8 1:2-55 hybrid 2.20
  Ribosomal_L38e   Ribosomal L38e protein family 4a19 P:2-77 rna 3.52
  Ribosomal_L39   Ribosomal L39 protein 1vqo 2:7-48 rna 2.20
  Ribosomal_L4   Ribosomal protein L4/L1 family 1vq8 C:16-246 hybrid 2.20
  Ribosomal_L40e   Ribosomal L40e family 5an9 H:1-50 rna 3.30
  Ribosomal_L41   Ribosomal protein L41 3jam h:1-25 rna 3.46
  Ribosomal_L44   Ribosomal protein L44 1vq8 3:16-91 hybrid 2.20
  Ribosomal_L5   Ribosomal protein L5 1vq8 D:11-64 hybrid 2.20
  Ribosomal_L50   Ribosomal subunit 39S 3j7y h:60-155 rna 3.40
  Ribosomal_L5e   Ribosomal large subunit proteins 60S L5, and 50S L18 1vqo N:4-99 rna 2.20
  Ribosomal_L5_C   ribosomal L5P family C-terminus 1vq8 D:68-152 hybrid 2.20
  Ribosomal_L6   Ribosomal protein L6 1vqo E:91-165 rna 2.20
  Ribosomal_L6e   Ribosomal protein L6e 4ujq H:107-176 rna 2.80
  Ribosomal_L7Ae   Ribosomal protein L7Ae/L30e/S12e/Gadd45 family 1sds C:12-106 rna 1.80
  Ribosomal_L9_C   Ribosomal protein L9, C-terminal domain 5gag H:63-148 rna 3.80
  Ribosomal_L9_N   Ribosomal protein L9, N-terminal domain 4rb6 I:1-47 rna 2.40
  Ribosomal_S10   Ribosomal protein S10p/S20e 3r2d J:7-50 rna 2.20
  Ribosomal_S11   Ribosomal protein S11 4rb7 K:17-126 rna 2.40
  Ribosomal_S13   Ribosomal protein S13/S18 4rb5 M:3-109 rna 2.40
  Ribosomal_S13_N   Ribosomal S13/S15 N-terminal domain 4ujr r:2-60 rna 2.80
  Ribosomal_S14   Ribosomal protein S14p/S29e 4rb5 N:9-60 rna 2.40
  Ribosomal_S15   Ribosomal protein S15 4rb7 O:8-88 rna 2.40
  Ribosomal_S16   Ribosomal protein S16 4rb5 P:8-67 rna 2.40
  Ribosomal_S17   Ribosomal protein S17 4rb7 Q:8-75 rna 2.40
  Ribosomal_S17e   Ribosomal S17 4ujp S:2-122 rna 2.80
  Ribosomal_S17_N   Ribosomal_S17 N-terminal 4ujr p:8-71 rna 2.80
  Ribosomal_S18   Ribosomal protein S18 4rb5 R:30-79 rna 2.40
  Ribosomal_S19   Ribosomal protein S19 4rb5 S:3-83 rna 2.40
  Ribosomal_S19e   Ribosomal protein S19e 4ujp U:5-142 rna 2.80
  Ribosomal_S2   Ribosomal protein S2 4rb5 B:10-225 rna 2.40
  Ribosomal_S20p   Ribosomal protein S20 4rb7 T:8-89 rna 2.40
  Ribosomal_S21   Ribosomal protein S21 4tp8 U:4-54 rna 2.80
  Ribosomal_S21e   Ribosomal protein S21e 4ujr z:1-80 rna 2.80
  Ribosomal_S24e   Ribosomal protein S24e 4ujr 2:24-102 rna 2.80
  Ribosomal_S25   S25 ribosomal protein 4ujr 3:37-104 rna 2.80
  Ribosomal_S26e   Ribosomal protein S26e 4ujp b:2-98 rna 2.80
  Ribosomal_S27   Ribosomal protein S27a 4ujp g:102-147 rna 2.80
  Ribosomal_S27e   Ribosomal protein S27 4ujp c:28-82 rna 2.80
  Ribosomal_S28e   Ribosomal protein S28e 4ujp d:5-66 rna 2.80
  Ribosomal_S30   Ribosomal protein S30 4ujp f:3-61 rna 2.80
  Ribosomal_S30AE   Sigma 54 modulation protein / S30EA ribosomal protein 3v2e Y:3-93 rna 2.70
  Ribosomal_S3Ae   Ribosomal S3Ae family 4ujr f:20-221 rna 2.80
  Ribosomal_S3_C   Ribosomal protein S3, C-terminal domain 4rb5 C:120-202 rna 2.40
  Ribosomal_S4   Ribosomal protein S4/S9 N-terminal domain 4rb7 D:3-98 rna 2.40
  Ribosomal_S4e   Ribosomal family S4e 4ujp F:95-169 rna 2.80
  Ribosomal_S5   Ribosomal protein S5, N-terminal domain 4rb5 E:6-70 rna 2.40
  Ribosomal_S5_C   Ribosomal protein S5, C-terminal domain 4rb7 E:81-152 rna 2.40
  Ribosomal_S6   Ribosomal protein S6 4rb7 F:3-92 rna 2.40
  Ribosomal_S6e   Ribosomal protein S6e 4ujp H:1-126 rna 2.80
  Ribosomal_S7   Ribosomal protein S7p/S5e 4rb7 G:2-149 rna 2.40
  Ribosomal_S7e   Ribosomal protein S7e 4ujr l:5-187 rna 2.80
  Ribosomal_S8   Ribosomal protein S8 4rb7 H:4-138 rna 2.40
  Ribosomal_S8e   Ribosomal protein S8e 4ujp J:2-184 rna 2.80
  Ribosomal_S9   Ribosomal protein S9/S16 4rb5 I:8-128 rna 2.40
  Ribosomal_TL5_C   Ribosomal protein TL5, C-terminal domain 4rb8 Z:95-174 rna 2.40
  Ribosom_S12_S23   Ribosomal protein S12/S23 4rb7 L:15-126 rna 2.40
  Ribos_L4_asso_C   60S ribosomal protein L4 C-terminal domain 4ujs N:272-348 rna 2.80
  RIG-I_C-RD   C-terminal domain of RIG-I 5jaj A:550-665 rna 1.50
  RIP   Ribosome inactivating protein 3rtj A:16-219 rna 3.00
  RLI   Possible Fer4-like domain in RNase L inhibitor, RLI 5ll6 h:6-37 rna 3.90
  RMF   Ribosome modulation factor 3v22 V:3-53 rna 3.00
  RMMBL   Zn-dependent metallo-hydrolase RNA specificity domain 4xww B:366-435 rna 1.70
  RnaseA   Pancreatic ribonuclease 1oj8 A:2-99 dna 1.70
  RNaseH_C   T4 RNase H, C terminal 2ihn A:183-305 dna 3.00
  RNase_E_G   Ribonuclease E/G family 5f6c A:121-392 rna 3.00
  RNase_H   RNase H 4htu B:68-187 dna 1.49
  RNase_HII   Ribonuclease HII 3o3f A:15-188 hybrid 2.00
  RNase_H_2   RNase_H superfamily 3u3y B:83-224 dna 2.28
  RNase_PH   3' exoribonuclease family, domain 1 2jea J:27-156 rna 2.33
  RNase_PH_C   3' exoribonuclease family, domain 2 2jea E:159-224 rna 2.33
  RNase_T   Exonuclease 3v9w A:20-194 dna 1.70
  RNA_ligase   RNA ligase 2hvr A:28-227 hybrid 2.45
  RNA_pol   DNA-dependent RNA polymerase 1msw D:450-883 hybrid 2.10
  RNA_pol_A_CTD   Bacterial RNA polymerase, alpha chain C terminal domain 5tw1 T:251-303 dna 2.76
  RNA_pol_I_TF   RNA polymerase I specific initiation factor 5n61 R:173-406 hybrid 3.40
  RNA_pol_Rpb1_1   RNA polymerase Rpb1, domain 1 2o5i N:2-618 hybrid 2.50
  RNA_pol_Rpb1_2   RNA polymerase Rpb1, domain 2 2o5i N:620-765 hybrid 2.50
  RNA_pol_Rpb1_4   RNA polymerase Rpb1, domain 4 4bxx A:693-800 hybrid 3.28
  RNA_pol_Rpb1_5   RNA polymerase Rpb1, domain 5 2o5i D:1064-1258 hybrid 2.50
  RNA_pol_Rpb2_1   RNA polymerase beta subunit 4oin C:17-380 dna 2.80
  RNA_pol_Rpb2_2   RNA polymerase Rpb2, domain 2 4oin C:142-334 dna 2.80
  RNA_pol_Rpb2_3   RNA polymerase Rpb2, domain 3 2o5i M:393-461 hybrid 2.50
  RNA_pol_Rpb2_6   RNA polymerase Rpb2, domain 6 2o5i C:596-1026 hybrid 2.50
  RNA_pol_Rpb2_7   RNA polymerase Rpb2, domain 7 2o5i M:1028-1104 hybrid 2.50
  RNA_pol_Rpb5_N   RNA polymerase Rpb5, N-terminal domain 3m4o E:6-100 hybrid 3.57
  RNA_replicase_B   RNA replicase, beta-chain 3avx A:717-1264 rna 2.41
  RNB   RNB domain 2vnu D:531-863 rna 2.30
  Rotavirus_VP1   Rotavirus VP1 C-terminal domain 2r7w A:778-1088 rna 2.60
  Rota_NSP3   Rotavirus non-structural protein NSP3 1knz C:7-163 rna 2.45
  RPOL_N   DNA-directed RNA polymerase N-terminal 1msw D:227-325 hybrid 2.10
  Rpp20   Rpp20 subunit of nuclear RNase MRP and P 3iab B:28-136 rna 2.70
  RPS31   Ribosomal protein S31e 5mmj x:55-94 rna 3.65
  RQC   RQC domain 3aaf B:956-1061 dna 1.90
  RRF   Ribosome recycling factor 2qbg 6:21-184 rna 3.30
  Rrf2   Transcriptional regulator 4hf1 B:1-83 dna 2.22
  RRM_1   RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 2xs2 A:42-109 rna 1.35
  RRM_3   RNA binding motif 4erd B:379-531 rna 2.59
  RRM_4   RNA recognition motif of the spliceosomal PrP8 5gmk A:1059-1150 rna 3.40
  RRM_5   RNA recognition motif. (a.k.a. RRM, RBD, or RNP domain) 5gmk a:29-110 rna 3.40
  RRM_occluded   Occluded RNA-recognition motif 4n0t A:311-393 rna 1.70
  RrnaAD   Ribosomal RNA adenine dimethylase 3ftf A:1-245 rna 2.80
  Rrp44_CSD1   Rrp44-like cold shock domain 2vnu D:252-387 rna 2.30
  RS4NT   RS4NT (NUC023) domain 4ujp F:3-39 rna 2.80
  RsgA_GTPase   RsgA GTPase 5uz4 Z:100-276 rna 5.80
  RTC   RNA 3'-terminal phosphate cyclase 4o8j B:8-325 rna 2.04
  RTP   Replication terminator protein 2efw B:8-122 dna 2.50
  Runt   Runt domain 4l18 A:53-191 dna 2.30
  RusA   Endodeoxyribonuclease RusA 2h8c C:9-115 dna 3.10
  RuvA_C   RuvA, C-terminal domain 1c7y j:158-203 dna 3.10
  RuvC   Crossover junction endodeoxyribonuclease RuvC 4ld0 A:3-154 dna 3.75
  rve   Integrase core domain 5frm A:118-231 dna 2.58
  RVT_1   Reverse transcriptase (RNA-dependent DNA polymerase) 4xpc A:94-273 dna 1.68
  RVT_3   Reverse transcriptase-like 4h8k A:7-134 hybrid 2.30
  RVT_connect   Reverse transcriptase connection domain 5d3g D:318-419 dna 2.30
  RVT_thumb   Reverse transcriptase thumb domain 5d3g A:241-304 dna 2.30
  S1   S1 RNA binding domain 2ix1 A:557-636 rna 2.74
  S10_plectin   Plectin/S10 domain 4ujr o:3-95 rna 2.80
  S4   S4 domain 4lgt D:3-56 rna 1.30
  SAD_SRA   SAD/SRA domain 3fde B:422-590 dna 1.41
  SAM_2   SAM domain (Sterile alpha motif) 2f8k A:448-510 rna 2.00
  SAP   SAP domain 4qoz B:76-110 rna 2.30
  SASP   Small, acid-soluble spore proteins, alpha/beta type 2z3x C:2-56 dna 2.10
  SBDS   Shwachman-Bodian-Diamond syndrome (SBDS) protein 5anb J:14-101 rna 4.10
  SBDS_C   SBDS protein C-terminal domain 5an9 J:107-225 rna 3.30
  Sec63   Sec63 Brl domain 5gao B:1846-2159 rna 3.60
  SecY   SecY translocase 5gae g:76-417 rna 3.33
  SelB-wing_2   Elongation factor SelB, winged helix 2uwm B:448-504 rna 2.31
  SelB-wing_3   Elongation factor SelB, winged helix 2pjp A:558-605 rna 2.30
  SepSecS   O-phosphoseryl-tRNA(Sec) selenium transferase, SepSecS 4zdo A:61-459 rna 2.65
  SeqA   SeqA protein C-terminal domain 1j3e A:5-115 dna 2.50
  Seryl_tRNA_N   Seryl-tRNA synthetase N-terminal domain 1ser B:501-605 rna 2.90
  Sgf11   Sgf11 (transcriptional regulation protein) 4zux l:67-95 dna 3.82
  She2p   RNA binding protein She2p 5m0i C:17-223 rna 2.41
  Sigma54_DBD   Sigma-54, DNA binding domain 5ui5 V:244-397 dna 3.40
  Sigma70_r1_2   Sigma-70 factor, region 1.2 3ugo A:94-127 dna 2.10
  Sigma70_r2   Sigma-70 region 2 4lup C:25-92 dna 1.20
  Sigma70_r3   Sigma-70 region 3 5tw1 F:312-389 dna 2.76
  Sigma70_r4   Sigma-70, region 4 1ais B:1254-1294 dna 2.10
  Sigma70_r4_2   Sigma-70, region 4 2h27 A:128-181 dna 2.30
  SKIP_SNW   SKIP/SNW domain 5gmk P:88-247 rna 3.40
  SLBP_RNA_bind   Histone RNA hairpin-binding protein RNA-binding domain 4qoz C:130-199 rna 2.30
  Slu7   Pre-mRNA splicing Prp18-interacting factor 5mps c:166-226 rna 3.85
  SmpB   SmpB protein 2czj A:4-123 rna 3.01
  SNF2_N   SNF2 family N-terminal domain 1z63 A:453-720 dna 3.00
  Spo0A_C   Sporulation initiation factor Spo0A C terminal 1lq1 D:157-260 dna 2.30
  SRF-TF   SRF-type transcription factor (DNA-binding and dimerisation domain) 1egw C:10-57 dna 1.50
  SRP-alpha_N   Signal recognition particle, alpha subunit, N-terminal 2go5 1:27-130 rna 7.40
  SRP14   Signal recognition particle 14kD protein 5aox E:4-94 rna 2.04
  SRP19   SRP19 protein 1jid A:17-115 rna 1.80
  SRP54   SRP54-type protein, GTPase domain 4c7o B:99-300 rna 2.60
  SRP54_N   SRP54-type protein, helical bundle domain 3ndb B:5-82 rna 3.00
  SRP68   RNA-binding signal recognition particle 68 5m73 C:75-254 rna 3.40
  SRP72   SRP72 RNA-binding domain 5m73 H:557-588 rna 3.40
  SRP9-21   Signal recognition particle 9 kDa protein (SRP9) 1e8o C:5-73 rna 3.20
  SRP_SPB   Signal peptide binding domain 1hq1 A:9-79 rna 1.52
  SSB   Single-strand binding protein family 3ulp D:82-191 dna 2.10
  STAT_bind   STAT protein, DNA binding domain 1bg1 D:321-573 dna 2.25
  SUI1   Translation initiation factor SUI1 3jam j:23-99 rna 3.46
  Sulf_coat_C   Sulfolobus virus coat protein C terminal 3j9x F:59-127 dna 3.80
  SYF2   SYF2 splicing factor 5gmk I:93-210 rna 3.40
  T-box   T-box 1h6f A:105-285 dna 1.70
  T4-Gluco-transf   Bacteriophage T4 beta-glucosyltransferase 1m5r B:1-38 dna 1.80
  TAL_effector   TAL effector repeat 3v6t A:663-695 dna 1.85
  Tap-RNA_bind   Tap, RNA-binding 3rw6 B:117-198 rna 2.30
  Taq-exonuc   Taq polymerase, exonuclease 4bwj A:294-420 dna 1.55
  TaqI_C   TaqI-like C-terminal specificity domain 2ih2 A:290-405 dna 1.61
  Tat   Transactivating regulatory protein (Tat) 5l1z D:2-49 rna 5.90
  TatD_DNase   TatD related DNase 4pe8 A:2-257 dna 2.89
  Tau95   RNA polymerase III transcription factor (TF)IIIC subunit 5fyw R:99-350 dna 4.35
  Taxilin   Myosin-like coiled-coil protein 1h88 B:272-336 dna 2.80
  TBP   Transcription factor TFIID (or TATA-binding protein, TBP) 1ytb A:64-146 dna 1.80
  TCR   Tesmin/TSO1-like CXC domain, cysteine-rich domain 5fd3 A:582-633 dna 2.42
  TEA   TEA/ATTS domain family 5gzb A:42-129 dna 2.70
  TEBP_beta   Telomere-binding protein beta subunit (TEBP beta) 1jb7 B:9-224 dna 1.86
  Telomerase_RBD   Telomerase ribonucleoprotein complex - RNA binding domain 5c9h B:375-503 rna 3.00
  Telomere_res   Telomere resolvase 4f43 A:144-410 dna 2.35
  Tenui_N   Tenuivirus/Phlebovirus nucleocapsid protein 4csf X:5-229 rna 2.60
  Ter   DNA replication terminus site-binding protein (Ter protein) 2i06 A:9-306 dna 2.20
  TetR_N   Bacterial regulatory proteins, tetR family 5haw A:13-60 dna 1.89
  Tet_JBP   Oxygenase domain of the 2OGFeDO superfamily 5deu A:1842-1905 dna 1.80
  Tfb5   Transcription factor TFIIH complex subunit Tfb5 5fmf X:2-64 dna 6.00
  TFIIA   Transcription factor IIA, alpha/beta subunit 1nh2 C:231-285 dna 1.90
  TFIIB   Transcription factor TFIIB repeat 1ais B:1212-1282 dna 2.10
  TFIIE_alpha   TFIIE alpha subunit 5iyb Q:16-123 dna 3.90
  TFIIF_alpha   Transcription initiation factor IIF, alpha subunit (TFIIF-alpha) 5iya S:52-180 dna 5.40
  TFIIF_beta   Transcription initiation factor IIF, beta subunit 5iyb T:95-238 dna 3.90
  TFIIS_C   Transcription factor S-II (TFIIS) 3po3 S:269-307 hybrid 3.30
  TF_Zn_Ribbon   TFIIB zinc-binding 4bbs M:22-66 hybrid 3.60
  TGT   Queuine tRNA-ribosyltransferase 1q2r C:139-377 rna 2.90
  TGT_C1   C1 domain of tRNA-guanine transglycosylase dimerisation 1j2b B:361-430 rna 3.30
  TGT_C2   Patch-forming domain C2 of tRNA-guanine transglycosylase 1j2b A:438-506 rna 3.30
  ThaI   Restriction endonuclease ThaI 3ndh A:14-215 dna 1.30
  THAP   THAP domain 3kde C:2-76 dna 1.74
  Thg1   tRNAHis guanylyltransferase 5axm B:5-119 rna 2.21
  Thg1C   Thg1 C terminal domain 5axm A:121-234 rna 2.21
  ThiI   Thiamine biosynthesis protein (ThiI) 4kr6 B:172-369 rna 2.85
  Thioredoxin   Thioredoxin 1t8e B:3-106 dna 2.54
  Thrombin_light   Thrombin light chain 5do4 L:5-36 rna 1.86
  THUMP   THUMP domain 4kr6 A:25-162 rna 2.85
  Thx   30S ribosomal protein Thx 4rb5 U:2-24 rna 2.40
  TilS   TilS substrate binding domain 3a2k A:256-325 rna 3.65
  TilS_C   TilS substrate C-terminal domain 3a2k A:384-457 rna 3.65
  Tim44   Tim44-like domain 3j7y d:118-266 rna 3.40
  TMV_coat   Virus coat protein (TMV like) 2tmv P:1-145 rna 2.90
  Tna_leader   Tryptophanase operon leader peptide 4uy8 7:5-24 rna 3.80
  Tnp_DNA_bind   Transposase DNA-binding 1mus A:11-69 dna 1.90
  TNV_CP   Satellite tobacco necrosis virus coat protein 3s4g A:12-195 rna 6.00
  TolA_bind_tri   TolA binding protein trimerisation 5i50 A:29-90 dna 2.70
  Tombus_P19   Tombusvirus P19 core protein 1r9f F:25-148 rna 1.85
  Topoisom_bac   DNA topoisomerase 1mw8 X:156-565 dna 1.90
  Topoisom_I   Eukaryotic DNA topoisomerase I, catalytic core 2h7g X:75-294 dna 1.90
  Topoisom_I_N   Eukaryotic DNA topoisomerase I, DNA binding fragment 1a31 A:215-429 dna 2.10
  Topo_C_assoc   C-terminal topoisomerase domain 1k4t A:695-765 dna 2.10
  Topo_Zn_Ribbon   Topoisomerase I zinc-ribbon-like 4rul A:818-862 dna 2.90
  Toprim   Toprim domain 1mw8 X:4-142 dna 1.90
  TOPRIM_C   C-terminal associated domain of TOPRIM 3qx3 B:589-727 dna 2.16
  Toprim_N   DNA primase catalytic core, N-terminal domain 3b39 B:126-252 dna 2.35
  Torus   Torus domain 5gmk R:4-114 rna 3.40
  Tospo_nucleocap   Tospovirus nucleocapsid protein 5ip3 A:4-246 dna 3.00
  Tower   Tower 1mje A:2752-2792 dna 3.50
  ToxN_toxin   Toxin ToxN, type III toxin-antitoxin system 2xdb A:1-160 rna 2.55
  TPR_15   Tetratricopeptide repeat 4hor A:221-289 rna 1.86
  TPR_19   Tetratricopeptide repeat 5udi A:319-372 rna 1.58
  TRAM   TRAM domain 2bh2 A:15-67 rna 2.15
  Translin   Translin family 5jrc C:6-183 rna 1.90
  Transposase_1   Transposase (partial DDE domain) 4u7b B:161-240 dna 3.09
  Trans_reg_C   Transcriptional regulatory protein, C terminal 5ed4 A:169-243 dna 2.40
  Tra_M   TraM protein, DNA-binding 4qpq C:2-53 dna 3.11
  Trigger_N   Bacterial trigger factor protein (TF) 2d3o 1:10-109 rna 3.35
  TrmB   Sugar-specific transcriptional regulator TrmB 5bpd D:10-78 dna 2.40
  tRNA-synt_1   tRNA synthetases class I (I, L, M and V) 4arc A:409-573 rna 2.00
  tRNA-synt_1b   tRNA synthetases class I (W and Y) 1j1u D:24-300 rna 1.95
  tRNA-synt_1c   tRNA synthetases class I (E and Q), catalytic domain 1n78 B:1-312 rna 2.10
  tRNA-synt_1c_C   tRNA synthetases class I (E and Q), anti-codon binding domain 1qtq A:339-527 rna 2.25
  tRNA-synt_1d   tRNA synthetases class I (R) 2zue A:99-358 rna 2.00
  tRNA-synt_1e   tRNA synthetases class I (C) catalytic domain 1u0b B:14-314 rna 2.30
  tRNA-synt_1g   tRNA synthetases class I (M) 2csx B:122-359 rna 2.70
  tRNA-synt_1_2   Leucyl-tRNA synthetase, Domain 2 4arc A:221-404 rna 2.00
  tRNA-synt_2   tRNA synthetases class II (D, K and N) 1c0a A:117-558 rna 2.40
  tRNA-synt_2b   tRNA synthetase class II core domain (G, H, P, S and T) 4yye A:114-337 rna 2.30
  tRNA-synt_2c   tRNA synthetases class II (A) 3wqy A:64-592 rna 3.30
  tRNA-synt_2d   tRNA synthetases class II core domain (F) 3tup A:183-307 rna 3.05
  tRNA_anti-codon   OB-fold nucleic acid binding domain 4oww B:22-105 dna 2.30
  tRNA_int_endo   tRNA intron endonuclease, catalytic C-terminal domain 2gjw D:219-302 rna 2.85
  tRNA_m1G_MT   tRNA (Guanine-1)-methyltransferase 4yvj B:22-221 rna 2.90
  tRNA_Me_trans   tRNA methyl transferase 2der A:6-360 rna 3.10
  tRNA_NucTran2_2   tRNA nucleotidyltransferase domain 2 putative 5hc9 B:362-421 rna 2.90
  tRNA_NucTransf2   tRNA nucleotidyltransferase, second domain 3ovb A:146-255 rna 1.95
  tRNA_SAD   Threonyl and Alanyl tRNA synthetase second additional domain 1qf6 A:171-219 rna 2.90
  tRNA_U5-meth_tr   tRNA (Uracil-5-)-methyltransferase 2bh2 A:95-432 rna 2.15
  TROVE   TROVE domain 1yvp A:16-369 rna 2.20
  TrpBP   Tryptophan RNA-binding attenuator protein 1gtf V:5-73 rna 1.75
  Trp_repressor   Trp repressor protein 1tro C:17-104 dna 1.90
  TruB-C_2   Pseudouridine synthase II TruB, C-terminal 1k8w A:252-309 rna 1.85
  TruB_C_2   tRNA pseudouridylate synthase B C-terminal domain 3hax A:184-251 rna 2.11
  TruB_N   TruB family pseudouridylate synthase (N terminal domain) 1k8w A:33-180 rna 1.85
  TrwC   TrwC relaxase 1omh A:3-288 dna 1.95
  Trypsin   Trypsin 4lz1 H:16-238 dna 1.65
  Tudor-knot   RNA binding activity-knot of a chromodomain 3oa6 A:11-74 dna 2.35
  Tymo_coat   Tymovirus coat protein 1ddl A:8-177 rna 2.70
  Type2_restr_D3   Type-2 restriction enzyme D3 domain 1fok A:296-363 dna 2.80
  Tyr-DNA_phospho   Tyrosyl-DNA phosphodiesterase 1rff B:165-582 dna 1.70
  T_Ag_DNA_bind   Origin of replication binding protein 2itl B:136-229 dna 1.65
  U-box   U-box domain 5gmk r:1-85 rna 3.40
  U1snRNP70_N   U1 small nuclear ribonucleoprotein of 70kDa MW N terminal 4pkd B:77-159 rna 2.50
  U5_2-snRNA_bdg   U5-snRNA binding site 2 of PrP8 5gmk A:1282-1415 rna 3.40
  U6-snRNA_bdg   U6-snRNA interacting domain of PrP8 5gmk A:1577-1672 rna 3.40
  ubiquitin   Ubiquitin family 4zux m:3-74 dna 3.82
  UCH   Ubiquitin carboxyl-terminal hydrolase 4zux j:137-465 dna 3.82
  UDG   Uracil DNA glycosylase superfamily 4uqm A:68-230 dna 1.35
  UQ_con   Ubiquitin-conjugating enzyme 4r8p L:205-342 dna 3.28
  UvdE   UV-endonuclease UvdE 4gle A:3-259 dna 2.70
  UvrD-helicase   UvrD/REP helicase N-terminal domain 2is6 A:10-272 dna 2.20
  UvrD_C   UvrD-like helicase C-terminal domain 2is6 B:277-617 dna 2.20
  UvrD_C_2   UvrD-like helicase C-terminal domain 5fhd A:354-398 dna 2.00
  V-set   Immunoglobulin V-set domain 4z8f H:8-112 dna 1.75
  Val_tRNA-synt_C   Valyl tRNA synthetase tRNA binding arm 1ivs A:797-862 rna 2.90
  Viral_coat   Viral coat protein (S domain) 4fy5 j:54-237 rna 2.90
  Viral_helicase1   Viral (Superfamily 1) RNA helicase 4n0o A:154-390 dna 2.65
  VirDNA-topo-I_N   Viral DNA topoisomerase I, N-terminal 2h7g X:4-61 dna 1.90
  VP40   Matrix protein VP40 1h2c A:69-192 rna 1.60
  VRR_NUC   VRR-NUC domain 4ri8 A:893-1008 dna 2.90
  Vsr   DNA mismatch endonuclease Vsr 1cw0 A:2-75 dna 2.30
  VWA   von Willebrand factor type A domain 3hxo A:514-689 dna 2.40
  WD40   WD domain, G-beta repeat 5gxh A:629-668 rna 1.80
  WGR   WGR domain 4dqy C:553-633 dna 3.25
  Whirly   Whirly transcription factor 3n1i A:63-198 dna 2.20
  XPA_C   XPA protein C-terminus 5a3d B:223-273 dna 1.80
  XPG_I   XPG I-region 1rxw A:139-235 dna 2.00
  XPG_N   XPG N-terminal domain 1rxw A:7-101 dna 2.00
  Xpo1   Exportin 1-like protein 3icq U:101-253 rna 3.20
  XRN_N   XRN 5'-3' exonuclease N-terminus 2y35 A:1-226 dna 3.20
  Y1_Tnp   Transposase IS200 like 2vjv B:14-130 dna 1.90
  YoeB_toxin   YoeB-like toxin of bacterial type II toxin-antitoxin system 4byb Y:5-84 rna 3.35
  YqaJ   YqaJ-like viral recombinase domain 3sm4 C:23-168 dna 1.88
  YTH   YT521-B-like domain 5eim A:350-477 rna 1.54
  z-alpha   Adenosine deaminase z-alpha domain 3eyi A:105-162 dna 1.45
  ZapB   Cell division protein ZapB 5t01 B:267-312 dna 1.89
  zf-C2H2   Zinc finger, C2H2 type 4m9v F:139-161 dna 0.97
  zf-C2HE   C2HE / C2H2 / C2HC zinc-binding finger 4ndh A:283-340 dna 1.85
  zf-C4   Zinc finger, C4 type (two domains) 3g9m A:438-507 dna 1.61
  zf-C4_Topoisom   Topoisomerase DNA binding C4 zinc finger 4rul A:708-745 dna 2.90
  zf-CCCH   Zinc finger C-x8-C-x5-C-x3-H type (and similar) 3d2s B:180-206 rna 1.70
  zf-CCCH_2   RNA-binding, Nab2-type zinc finger 5l2l E:457-474 rna 1.55
  zf-CCHC   Zinc knuckle 5udz A:137-154 rna 2.00
  zf-CXXC   CXXC zinc finger domain 5exh C:52-89 dna 1.30
  zf-Di19   Drought induced 19 protein (Di19), zinc-binding 2drp D:109-165 dna 2.80
  zf-FPG_IleRS   Zinc finger found in FPG and IleRS 1k3x A:234-262 dna 1.25
  zf-H2C2_2   Zinc-finger double domain 4x9j A:121-146 dna 1.41
  zf-His_Me_endon   Zinc-binding loop region of homing endonuclease 1a73 B:65-150 dna 1.80
  zf-nanos   Nanos RNA binding domain 5kl1 B:319-372 rna 3.70
  zf-PARP   Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region 3od8 F:12-89 dna 2.40
  zf-RanBP   Zn-finger in Ran binding protein and others 3g9y A:67-94 rna 1.40
  zf-U1   U1 zinc finger 4pjo L:2-38 rna 3.30
  zf-UBP   Zn-finger in ubiquitin-hydrolases and other protein 4zux e:46-108 dna 3.82
  zinc_ribbon_2   zinc-ribbon domain 3j44 g:16-39 rna 9.00
  Zn-ribbon_8   Zinc ribbon domain 2i13 B:105-146 dna 1.96
  Zn_clus   Fungal Zn(2)-Cys(6) binuclear cluster domain 3coq A:9-47 dna 2.40
  Zn_ribbon_recom   Recombinase zinc beta ribbon domain 4kis A:267-333 dna 3.20
© NPIDB team 2003 - 2017

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