| 60 | 50 | 20 | 5 | SCOP 52540 | P-loop containing nucleoside triphosphate hydrolases |
| 18 | 18 | 8 | 1 | SCOP 50249 | Nucleic acid-binding proteins |
| 15 | 14 | 5 | 0 | SCOP 50978 | WD40 repeat-like |
| 12 | 12 | 1 | 1 | SCOP 56235 | N-terminal nucleophile aminohydrolases (Ntn hydrolases) |
| 11 | 10 | 3 | 1 | SCOP 48592 | GroEL equatorial domain-like |
| 10 | 10 | 4 | 1 | SCOP 50104 | Translation proteins SH3-like domain |
| 10 | 10 | 3 | 2 | SCOP 52029 | GroEL apical domain-like |
| 9 | 9 | 6 | 3 | SCOP 54211 | Ribosomal protein S5 domain 2-like |
| 9 | 9 | 3 | 2 | SCOP 64484 | beta and beta-prime subunits of DNA dependent RNA-polymerase |
| 9 | 9 | 2 | 0 | SCOP 54849 | GroEL-intermediate domain like |
| 8 | 8 | 1 | 0 | SCOP 50182 | Sm-like ribonucleoproteins |
| 8 | 7 | 5 | 2 | SCOP 50447 | Translation proteins |
| 7 | 7 | 3 | 1 | SCOP 56112 | Protein kinase-like (PK-like) |
| 7 | 4 | 3 | 0 | SCOP 54928 | RNA-binding domain, RBD |
| 6 | 6 | 2 | 0 | SCOP 57829 | Zn-binding ribosomal proteins |
| 6 | 3 | 3 | 1 | SCOP 47954 | Cyclin-like |
| 5 | 5 | 3 | 2 | SCOP 53137 | Translational machinery components |
| 5 | 5 | 1 | 1 | SCOP 47113 | Histone-fold |
| 5 | 5 | 3 | 0 | SCOP 55257 | RBP11-like subunits of RNA polymerase |
| 4 | 4 | 1 | 1 | SCOP 54189 | Ribosomal proteins S24e, L23 and L15e |
| 4 | 2 | 1 | 1 | SCOP 53067 | Actin-like ATPase domain |
| 4 | 4 | 2 | 0 | SCOP 48452 | TPR-like |
| 4 | 4 | 3 | 1 | SCOP 55315 | L30e-like |
| 4 | 4 | 1 | 1 | SCOP 52490 | Tubulin nucleotide-binding domain-like |
| 4 | 4 | 1 | 1 | SCOP 55307 | Tubulin C-terminal domain-like |
| 4 | 2 | 1 | 1 | SCOP 56053 | Ribosomal protein L6 |
| 3 | 3 | 3 | 0 | SCOP 46785 | "Winged helix" DNA-binding domain |
| 3 | 3 | 2 | 2 | SCOP 53335 | S-adenosyl-L-methionine-dependent methyltransferases |
| 3 | 3 | 3 | 1 | SCOP 48371 | ARM repeat |
| 3 | 3 | 1 | 1 | SCOP 54495 | UBC-like |
| 3 | 3 | 2 | 0 | SCOP 55729 | Acyl-CoA N-acyltransferases (Nat) |
| 3 | 3 | 3 | 0 | SCOP 57850 | RING/U-box |
| 3 | 3 | 3 | 0 | SCOP 57783 | Zinc beta-ribbon |
| 3 | 3 | 2 | 1 | SCOP 56553 | Insert subdomain of RNA polymerase alpha subunit |
| 2 | 2 | 1 | 1 | SCOP 56808 | Ribosomal protein L1 |
| 2 | 2 | 1 | 1 | SCOP 47973 | Ribosomal protein S7 |
| 2 | 2 | 2 | 0 | SCOP 51735 | NAD(P)-binding Rossmann-fold domains |
| 2 | 2 | 1 | 1 | SCOP 54999 | Ribosomal protein S10 |
| 2 | 2 | 1 | 1 | SCOP 52166 | Ribosomal protein L4 |
| 2 | 2 | 2 | 1 | SCOP 54570 | Ribosomal protein S19 |
| 2 | 2 | 1 | 0 | SCOP 54843 | Ribosomal protein L22 |
| 2 | 2 | 1 | 2 | SCOP 54686 | Ribosomal protein L16p/L10e |
| 2 | 2 | 1 | 1 | SCOP 50193 | Ribosomal protein L14 |
| 2 | 2 | 1 | 1 | SCOP 55282 | RL5-like |
| 2 | 2 | 2 | 0 | SCOP 57716 | Glucocorticoid receptor-like (DNA-binding domain) |
| 2 | 2 | 1 | 1 | SCOP 56047 | Ribosomal protein S8 |
| 2 | 2 | 1 | 0 | SCOP 52080 | Ribosomal proteins L15p and L18e |
| 2 | 1 | 1 | 2 | SCOP 52518 | Thiamin diphosphate-binding fold (THDP-binding) |
| 2 | 2 | 2 | 2 | SCOP 53098 | Ribonuclease H-like |
| 2 | 2 | 1 | 1 | SCOP 55174 | Alpha-L RNA-binding motif |
| 2 | 2 | 2 | 1 | SCOP 52161 | Ribosomal protein L13 |
| 2 | 2 | 1 | 0 | SCOP 47060 | S15/NS1 RNA-binding domain |
| 2 | 2 | 2 | 1 | SCOP 54862 | 4Fe-4S ferredoxins |
| 2 | 2 | 1 | 1 | SCOP 52313 | Ribosomal protein S2 |
| 2 | 2 | 1 | 1 | SCOP 52096 | ClpP/crotonase |
| 2 | 1 | 1 | 0 | SCOP 46689 | Homeodomain-like |
| 2 | 2 | 1 | 0 | SCOP 53032 | tRNA-intron endonuclease catalytic domain-like |
| 2 | 2 | 1 | 0 | SCOP 63562 | RPB6/omega subunit-like |
| 2 | 2 | 1 | 1 | SCOP 101960 | Stabilizer of iron transporter SufD |
| 2 | 2 | 1 | 1 | SCOP 81558 | Photosystem I subunits PsaA/PsaB |
| 2 | 2 | 1 | 1 | SCOP 81483 | Bacterial photosystem II reaction centre, L and M subunits |
| 2 | 2 | 1 | 1 | SCOP 161077 | Photosystem II antenna protein-like |
| 2 | 2 | 1 | 1 | SCOP 161045 | Cytochrome b559 subunits |
| 2 | 2 | 1 | 0 | SCOP 103511 | Chlorophyll a-b binding protein |
| 2 | 2 | 2 | 0 | SCOP 52954 | Class II aaRS ABD-related |
| 2 | 2 | 1 | 1 | SCOP 52172 | CheY-like |
| 2 | 2 | 2 | 2 | SCOP 55874 | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase |
| 2 | 2 | 2 | 0 | SCOP 88697 | PUA domain-like |
| 2 | 1 | 1 | 0 | SCOP 88659 | Sigma3 and sigma4 domains of RNA polymerase sigma factors |
| 2 | 2 | 1 | 0 | SCOP 54814 | Prokaryotic type KH domain (KH-domain type II) |
| 2 | 1 | 1 | 0 | SCOP 55021 | ACT-like |
| 2 | 2 | 2 | 0 | SCOP 82199 | SET domain |
| 2 | 2 | 1 | 1 | SCOP 89124 | Nop domain |
| 2 | 2 | 1 | 1 | SCOP 50465 | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain |
| 2 | 1 | 1 | 1 | SCOP 55979 | DNA clamp |
| 2 | 2 | 1 | 1 | SCOP 46906 | Ribosomal protein L11, C-terminal domain |
| 2 | 1 | 1 | 1 | SCOP 54980 | EF-G C-terminal domain-like |
| 2 | 2 | 1 | 1 | SCOP 54821 | Ribosomal protein S3 C-terminal domain |
| 2 | 2 | 2 | 1 | SCOP 56719 | Type II DNA topoisomerase |
| 2 | 2 | 1 | 1 | SCOP 100920 | Heat shock protein 70kD (HSP70), peptide-binding domain |
| 2 | 1 | 1 | 1 | SCOP 55945 | TATA-box binding protein-like |
| 2 | 2 | 1 | 0 | SCOP 54768 | dsRNA-binding domain-like |
| 2 | 2 | 1 | 0 | SCOP 100934 | Heat shock protein 70kD (HSP70), C-terminal subdomain |
| 2 | 2 | 1 | 1 | SCOP 50615 | N-terminal domain of alpha and beta subunits of F1 ATP synthase |
| 2 | 2 | 1 | 1 | SCOP 54747 | Ribosomal L11/L12e N-terminal domain |
| 2 | 2 | 1 | 1 | SCOP 47917 | C-terminal domain of alpha and beta subunits of F1 ATP synthase |
| 2 | 2 | 1 | 0 | SCOP 50784 | Transcription factor IIA (TFIIA), beta-barrel domain |
| 1 | 1 | 1 | 0 | SCOP 56731 | DNA primase core |
| 1 | 1 | 1 | 0 | SCOP 46911 | Ribosomal protein S18 |
| 1 | 1 | 1 | 0 | SCOP 51905 | FAD/NAD(P)-binding domain |
| 1 | 1 | 1 | 0 | SCOP 52833 | Thioredoxin-like |
| 1 | 1 | 1 | 0 | SCOP 103491 | Preprotein translocase SecY subunit |
| 1 | 1 | 1 | 0 | SCOP 57840 | Ribosomal protein L36 |
| 1 | 1 | 1 | 1 | SCOP 46946 | S13-like H2TH domain |
| 1 | 1 | 1 | 0 | SCOP 143034 | L35p-like |
| 1 | 1 | 1 | 1 | SCOP 74731 | Ribosomal protein L20 |
| 1 | 1 | 1 | 1 | SCOP 56300 | Metallo-dependent phosphatases |
| 1 | 1 | 1 | 0 | SCOP 141091 | L21p-like |
| 1 | 1 | 1 | 0 | SCOP 110324 | Ribosomal L27 protein-like |
| 1 | 1 | 1 | 0 | SCOP 143800 | L28p-like |
| 1 | 1 | 1 | 0 | SCOP 47336 | ACP-like |
| 1 | 1 | 1 | 1 | SCOP 47729 | IHF-like DNA-binding proteins |
| 1 | 1 | 1 | 0 | SCOP 160369 | Ribosomal protein L10-like |
| 1 | 1 | 1 | 0 | SCOP 46992 | Ribosomal protein S20 |
| 1 | 1 | 1 | 0 | SCOP 81333 | F1F0 ATP synthase subunit C |
| 1 | 1 | 1 | 0 | SCOP 53850 | Periplasmic binding protein-like II |
| 1 | 1 | 1 | 0 | SCOP 54565 | Ribosomal protein S16 |
| 1 | 1 | 1 | 1 | SCOP 55681 | Class II aaRS and biotin synthetases |
| 1 | 1 | 1 | 1 | SCOP 54292 | 2Fe-2S ferredoxin-like |
| 1 | 1 | 1 | 0 | SCOP 55205 | EPT/RTPC-like |
| 1 | 1 | 1 | 0 | SCOP 55229 | Cell division protein MinE topological specificity domain |
| 1 | 1 | 1 | 0 | SCOP 55129 | Ribosomal protein L30p/L7e |
| 1 | 1 | 1 | 0 | SCOP 46561 | Ribosomal protein L29 (L29p) |
| 1 | 1 | 1 | 0 | SCOP 54995 | Ribosomal protein S6 |
| 1 | 1 | 1 | 0 | SCOP 48140 | Ribosomal protein L19 (L19e) |
| 1 | 1 | 1 | 0 | SCOP 52042 | Ribosomal protein L32e |
| 1 | 1 | 1 | 1 | SCOP 48613 | Heme oxygenase-like |
| 1 | 1 | 1 | 0 | SCOP 110296 | Oligoxyloglucan reducing end-specific cellobiohydrolase |
| 1 | 1 | 1 | 0 | SCOP 81296 | E set domains |
| 1 | 1 | 1 | 0 | SCOP 54575 | Ribosomal protein L31e |
| 1 | 1 | 1 | 0 | SCOP 88723 | PIN domain-like |
| 1 | 1 | 1 | 1 | SCOP 54534 | FKBP-like |
| 1 | 1 | 1 | 1 | SCOP 46626 | Cytochrome c |
| 1 | 1 | 1 | 0 | SCOP 48239 | Terpenoid cyclases/Protein prenyltransferases |
| 1 | 1 | 1 | 0 | SCOP 63393 | RNA polymerase subunits |
| 1 | 1 | 1 | 0 | SCOP 47819 | HRDC-like |
| 1 | 1 | 1 | 0 | SCOP 49899 | Concanavalin A-like lectins/glucanases |
| 1 | 1 | 1 | 0 | SCOP 55159 | eIF1-like |
| 1 | 1 | 1 | 0 | SCOP 55418 | eIF4e-like |
| 1 | 1 | 1 | 1 | SCOP 46924 | RNA polymerase subunit RPB10 |
| 1 | 1 | 1 | 1 | SCOP 52768 | Arginase/deacetylase |
| 1 | 1 | 1 | 1 | SCOP 55909 | Pentein |
| 1 | 1 | 1 | 1 | SCOP 81342 | Transmembrane di-heme cytochromes |
| 1 | 1 | 1 | 1 | SCOP 57662 | Ferredoxin thioredoxin reductase (FTR), catalytic beta chain |
| 1 | 1 | 1 | 1 | SCOP 81648 | a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) |
| 1 | 1 | 1 | 0 | SCOP 103446 | PetG subunit of the cytochrome b6f complex |
| 1 | 1 | 1 | 0 | SCOP 103451 | PetN subunit of the cytochrome b6f complex |
| 1 | 1 | 1 | 1 | SCOP 46458 | Globin-like |
| 1 | 1 | 1 | 1 | SCOP 64234 | Photosystem I subunit PsaD |
| 1 | 1 | 1 | 0 | SCOP 50090 | Electron transport accessory proteins |
| 1 | 1 | 1 | 1 | SCOP 81536 | Subunit III of photosystem I reaction centre, PsaF |
| 1 | 1 | 1 | 0 | SCOP 81540 | Subunit VIII of photosystem I reaction centre, PsaI |
| 1 | 1 | 1 | 0 | SCOP 81544 | Subunit IX of photosystem I reaction centre, PsaJ |
| 1 | 1 | 1 | 0 | SCOP 81563 | Photosystem I reaction center subunit X, PsaK |
| 1 | 1 | 1 | 1 | SCOP 81568 | Photosystem I reaction center subunit XI, PsaL |
| 1 | 1 | 1 | 0 | SCOP 81548 | Subunit XII of photosystem I reaction centre, PsaM |
| 1 | 1 | 1 | 0 | SCOP 161025 | Photosystem II 10 kDa phosphoprotein PsbH |
| 1 | 1 | 1 | 0 | SCOP 161041 | Photosystem II reaction center protein I, PsbI |
| 1 | 1 | 1 | 0 | SCOP 161021 | Photosystem II reaction center protein J, PsbJ |
| 1 | 1 | 1 | 0 | SCOP 161037 | Photosystem II reaction center protein K, PsbK |
| 1 | 1 | 1 | 0 | SCOP 161017 | Photosystem II reaction center protein L, PsbL |
| 1 | 1 | 1 | 0 | SCOP 161029 | Photosystem II reaction center protein T, PsbT |
| 1 | 1 | 1 | 0 | SCOP 161055 | PsbZ-like |
| 1 | 1 | 1 | 1 | SCOP 55239 | RuBisCO, small subunit |
| 1 | 1 | 1 | 0 | SCOP 101546 | ASF1-like |
| 1 | 1 | 1 | 0 | SCOP 144091 | Rhomboid-like |
| 1 | 1 | 1 | 0 | SCOP 102405 | MCP/YpsA-like |
| 1 | 1 | 1 | 0 | SCOP 52091 | SpoIIaa-like |
| 1 | 1 | 1 | 0 | SCOP 102712 | JAB1/MPN domain |
| 1 | 1 | 1 | 1 | SCOP 88946 | Sigma2 domain of RNA polymerase sigma factors |
| 1 | 1 | 1 | 0 | SCOP 50692 | ADC-like |
| 1 | 1 | 1 | 1 | SCOP 52467 | DHS-like NAD/FAD-binding domain |
| 1 | 1 | 1 | 0 | SCOP 54736 | ClpS-like |
| 1 | 1 | 1 | 0 | SCOP 52425 | Cryptochrome/photolyase, N-terminal domain |
| 1 | 1 | 1 | 1 | SCOP 57802 | Rubredoxin-like |
| 1 | 1 | 1 | 0 | SCOP 69322 | Tricorn protease domain 2 |
| 1 | 1 | 1 | 0 | SCOP 82171 | DPP6 N-terminal domain-like |
| 1 | 1 | 1 | 0 | SCOP 56091 | DNA ligase/mRNA capping enzyme, catalytic domain |
| 1 | 1 | 1 | 0 | SCOP 55287 | RPB5-like RNA polymerase subunit |
| 1 | 1 | 1 | 0 | SCOP 116820 | Rps17e-like |
| 1 | 1 | 1 | 0 | SCOP 160374 | RplX-like |
| 1 | 1 | 1 | 0 | SCOP 48024 | N-terminal domain of DnaB helicase |
| 1 | 1 | 1 | 0 | SCOP 50156 | PDZ domain-like |
| 1 | 1 | 1 | 0 | SCOP 51246 | Rudiment single hybrid motif |
| 1 | 1 | 1 | 0 | SCOP 81923 | Double Clp-N motif |
| 1 | 1 | 1 | 0 | SCOP 81336 | F1F0 ATP synthase subunit A |
| 1 | 1 | 1 | 0 | SCOP 47789 | C-terminal domain of RNA polymerase alpha subunit |
| 1 | 1 | 1 | 0 | SCOP 51344 | Epsilon subunit of F1F0-ATP synthase N-terminal domain |
| 1 | 1 | 1 | 1 | SCOP 140990 | FtsH protease domain-like |
| 1 | 1 | 1 | 0 | SCOP 51294 | Hedgehog/intein (Hint) domain |
| 1 | 1 | 1 | 0 | SCOP 54791 | Eukaryotic type KH-domain (KH-domain type I) |
| 1 | 1 | 1 | 1 | SCOP 101904 | GyrA/ParC C-terminal domain-like |
| 1 | 1 | 1 | 0 | SCOP 48300 | Ribosomal protein L7/12, oligomerisation (N-terminal) domain |
| 1 | 1 | 1 | 0 | SCOP 46934 | UBA-like |
| 1 | 1 | 1 | 0 | SCOP 75689 | Zinc-binding domain of translation initiation factor 2 beta |
| 1 | 1 | 1 | 0 | SCOP 100966 | Translation initiation factor 2 beta, aIF2beta, N-terminal domain |
| 1 | 1 | 1 | 0 | SCOP 47794 | Rad51 N-terminal domain-like |
| 1 | 1 | 1 | 0 | SCOP 158702 | Sec63 N-terminal domain-like |
| 1 | 1 | 1 | 0 | SCOP 47928 | N-terminal domain of the delta subunit of the F1F0-ATP synthase |
| 1 | 1 | 1 | 0 | SCOP 158573 | GINS helical bundle-like |
| 1 | 1 | 1 | 1 | SCOP 55481 | N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 |
| 1 | 1 | 1 | 0 | SCOP 88798 | N-terminal, heterodimerisation domain of RBP7 (RpoE) |
| 1 | 1 | 1 | 1 | SCOP 54713 | Elongation factor Ts (EF-Ts), dimerisation domain |
| 1 | 1 | 1 | 0 | SCOP 110942 | HSP90 C-terminal domain |
| 1 | 1 | 1 | 1 | SCOP 51649 | RuBisCo, C-terminal domain |
| 1 | 1 | 1 | 1 | SCOP 54966 | RuBisCO, large subunit, small (N-terminal) domain |
| 1 | 1 | 1 | 0 | SCOP 110993 | eIF-2-alpha, C-terminal domain |
| 1 | 1 | 1 | 0 | SCOP 75553 | Smc hinge domain |
| 1 | 1 | 1 | 0 | SCOP 53036 | Eukaryotic RPB5 N-terminal domain |
| 1 | 1 | 1 | 1 | SCOP 81886 | Helical scaffold and wing domains of SecA |
| 1 | 1 | 1 | 0 | SCOP 88802 | Pre-PUA domain |
| 1 | 1 | 1 | 0 | SCOP 52156 | Initiation factor IF2/eIF5b, domain 3 |
| 1 | 1 | 1 | 1 | SCOP 54585 | Cdc48 domain 2-like |
| 1 | 1 | 1 | 1 | SCOP 49441 | Cytochrome f, large domain |
| 1 | 1 | 1 | 0 | SCOP 103431 | Cytochrome f subunit of the cytochrome b6f complex, transmembrane anchor |
| 1 | 1 | 1 | 1 | SCOP 81767 | Pre-protein crosslinking domain of SecA |
