All pairs of domain combinations at the superfamily level are listed here.
The identification of domain pairs does not account for the possibility of non-contiguous domains. Inserted, or interlaced, domains are seen as having a simple pair ordering.
The links below permit the addition or removal of specific sets of domain combination pairs.
Change the list of genome two-letter codes in the 'Include genomes' box to include domain-pairs from those genomes.
Change the list of genomes in the 'Exclude genomes' box to exclude domain-pairs from those genomes.
List of all two-letter genome codes.
| Superfamily (N) | Superfamily (C) | Number of occurrances | Number unique | |
|---|
| P-loop containing nucleoside triphosphate hydrolases | P-loop containing nucleoside triphosphate hydrolases | 99 | 27 |  |
| Actin-like ATPase domain | Actin-like ATPase domain | 36 | 10 | |
| GroES-like | NAD(P)-binding Rossmann-fold domains | 21 | 2 | |
| Calcium ATPase, transduction domain A | HAD-like | 16 | 6 | |
| Calcium ATPase, transduction domain A | Calcium ATPase, transmembrane domain M | 16 | 6 | |
| HAD-like | Calcium ATPase, transmembrane domain M | 16 | 6 | |
| RNA-binding domain, RBD | RNA-binding domain, RBD | 14 | 8 | |
| P-loop containing nucleoside triphosphate hydrolases | Translation proteins | 14 | 10 | |
| Actin-like ATPase domain | Heat shock protein 70kD (HSP70), peptide-binding domain | 13 | 4 | |
| ABC transporter transmembrane region | P-loop containing nucleoside triphosphate hydrolases | 12 | 7 | |
| NAD(P)-binding Rossmann-fold domains | Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 11 | 4 | |
| Homeodomain-like | Homeodomain-like | 10 | 6 | |
| Cyclin-like | Cyclin-like | 10 | 5 | |
| Riboflavin synthase domain-like | Ferredoxin reductase-like, C-terminal NADP-linked domain | 10 | 7 | |
| GroEL equatorial domain-like | GroEL apical domain-like | 10 | 2 | |
| NAD(P)-binding Rossmann-fold domains | 6-phosphogluconate dehydrogenase C-terminal domain-like | 10 | 3 | |
| PreATP-grasp domain | Glutathione synthetase ATP-binding domain-like | 10 | 9 | |
| Thiamin diphosphate-binding fold (THDP-binding) | Thiamin diphosphate-binding fold (THDP-binding) | 10 | 3 | |
| Heat shock protein 70kD (HSP70), peptide-binding domain | Heat shock protein 70kD (HSP70), C-terminal subdomain | 9 | 2 | |
| (Trans)glycosidases | Glycosyl hydrolase domain | 9 | 4 | |
| GroEL equatorial domain-like | GroEL-intermediate domain like | 9 | 1 | |
| Nucleotidylyl transferase | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 9 | 7 | |
| Protein kinase-like (PK-like) | ARM repeat | 9 | 8 | |
| GroEL-intermediate domain like | GroEL apical domain-like | 9 | 1 | |
| Actin-like ATPase domain | Heat shock protein 70kD (HSP70), C-terminal subdomain | 9 | 2 | |
| Ribonuclease H-like | DNA/RNA polymerases | 8 | 4 | |
| Ypt/Rab-GAP domain of gyp1p | Ypt/Rab-GAP domain of gyp1p | 8 | 4 | |
| Aminoacid dehydrogenase-like, N-terminal domain | NAD(P)-binding Rossmann-fold domains | 8 | 5 | |
| FAD/NAD(P)-binding domain | FAD/NAD(P)-binding domain | 8 | 5 | |
| TPR-like | TPR-like | 8 | 6 | |
| Thioredoxin-like | Glutathione S-transferase (GST), C-terminal domain | 8 | 5 | |
| LuxS/MPP-like metallohydrolase | LuxS/MPP-like metallohydrolase | 8 | 5 | |
| Homing endonucleases | Homing endonucleases | 8 | 8 | |
| Class II aaRS and biotin synthetases | Class II aaRS ABD-related | 7 | 6 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | Ribosomal protein S5 domain 2-like | 7 | 4 | |
| Formate/glycerate dehydrogenase catalytic domain-like | NAD(P)-binding Rossmann-fold domains | 7 | 3 | |
| Thiamin diphosphate-binding fold (THDP-binding) | DHS-like NAD/FAD-binding domain | 7 | 1 | |
| PreATP-grasp domain | Rudiment single hybrid motif | 7 | 6 | |
| Translation proteins | EF-G C-terminal domain-like | 7 | 6 | |
| Metal cation-transporting ATPase, ATP-binding domain N | Calcium ATPase, transmembrane domain M | 7 | 2 | |
| EF-G C-terminal domain-like | EF-G C-terminal domain-like | 7 | 6 | |
| Nucleic acid-binding proteins | P-loop containing nucleoside triphosphate hydrolases | 7 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | EF-G C-terminal domain-like | 7 | 6 | |
| Glutathione synthetase ATP-binding domain-like | Rudiment single hybrid motif | 7 | 6 | |
| Calcium ATPase, transduction domain A | Metal cation-transporting ATPase, ATP-binding domain N | 7 | 2 | |
| Metal cation-transporting ATPase, ATP-binding domain N | HAD-like | 7 | 2 | |
| DNA repair protein MutS, domain III | P-loop containing nucleoside triphosphate hydrolases | 6 | 6 | |
| Nucleic acid-binding proteins | Class II aaRS and biotin synthetases | 6 | 3 | |
| P-loop containing nucleoside triphosphate hydrolases | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 6 | 3 | |
| P-loop containing nucleoside triphosphate hydrolases | Ribosomal protein S5 domain 2-like | 6 | 5 | |
| Chaperone J-domain | HSP40/DnaJ peptide-binding domain | 6 | 6 | |
| FAD/NAD(P)-binding domain | FAD-linked reductases, C-terminal domain | 6 | 4 | |
| Nucleic acid-binding proteins | Translation proteins SH3-like domain | 5 | 3 | |
| Leukotriene A4 hydrolase N-terminal domain | Metalloproteases ("zincins"), catalytic domain | 5 | 3 | |
| Rudiment single hybrid motif | Single hybrid motif | 5 | 4 | |
| Bromodomain | Bromodomain | 5 | 3 | |
| vWA-like | C-terminal, gelsolin-like domain of Sec23/24 | 5 | 4 | |
| EF-G C-terminal domain-like | Ribosomal protein S5 domain 2-like | 5 | 4 | |
| Chaperone J-domain | DnaJ/Hsp40 cysteine-rich domain | 5 | 5 | |
| Translation proteins | Ribosomal protein S5 domain 2-like | 5 | 4 | |
| ValRS/IleRS/LeuRS editing domain | Nucleotidylyl transferase | 5 | 3 | |
| Enolase N-terminal domain-like | Enolase C-terminal domain-like | 5 | 1 | |
| CBS-domain | CBS-domain | 5 | 2 | |
| CRAL/TRIO N-terminal domain | CRAL/TRIO domain | 5 | 2 | |
| Glutathione synthetase ATP-binding domain-like | Single hybrid motif | 5 | 4 | |
| DnaJ/Hsp40 cysteine-rich domain | HSP40/DnaJ peptide-binding domain | 5 | 5 | |
| PIN domain-like | 5' to 3' exonuclease, C-terminal subdomain | 5 | 4 | |
| Thioredoxin-like | Thioredoxin-like | 5 | 3 | |
| PreATP-grasp domain | Single hybrid motif | 5 | 4 | |
| Translation proteins | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 5 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | DNA polymerase III clamp loader subunits, C-terminal domain | 5 | 2 | |
| Ribosomal protein S5 domain 2-like | GHMP Kinase, C-terminal domain | 5 | 3 | |
| PA domain | Zn-dependent exopeptidases | 4 | 2 | |
| beta-sandwich domain of Sec23/24 | Helical domain of Sec23/24 | 4 | 3 | |
| FAD/NAD(P)-binding domain | Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | 4 | 2 | |
| Thiamin diphosphate-binding fold (THDP-binding) | TK C-terminal domain-like | 4 | 3 | |
| vWA-like | Helical domain of Sec23/24 | 4 | 3 | |
| Aldolase | post-HMGL domain-like | 4 | 3 | |
| P-loop containing nucleoside triphosphate hydrolases | Smc hinge domain | 4 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | RING/U-box | 4 | 1 | |
| Helical domain of Sec23/24 | C-terminal, gelsolin-like domain of Sec23/24 | 4 | 3 | |
| beta-sandwich domain of Sec23/24 | C-terminal, gelsolin-like domain of Sec23/24 | 4 | 3 | |
| C2 domain (Calcium/lipid-binding domain, CaLB) | C2 domain (Calcium/lipid-binding domain, CaLB) | 4 | 3 | |
| Zn2/Cys6 DNA-binding domain | Leucine zipper domain | 4 | 2 | |
| beta-sandwich domain of Sec23/24 | Zn-finger domain of Sec23/24 | 4 | 3 | |
| Zn-finger domain of Sec23/24 | vWA-like | 4 | 3 | |
| Phosphoglucomutase, first 3 domains | Phosphoglucomutase, C-terminal domain | 4 | 3 | |
| Tubulin nucleotide-binding domain-like | Tubulin C-terminal domain-like | 4 | 2 | |
| ValRS/IleRS/LeuRS editing domain | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 4 | 2 | |
| ARM repeat | P-loop containing nucleoside triphosphate hydrolases | 4 | 2 | |
| Zn-finger domain of Sec23/24 | Helical domain of Sec23/24 | 4 | 3 | |
| beta-sandwich domain of Sec23/24 | vWA-like | 4 | 3 | |
| CoA-dependent acyltransferases | CoA-dependent acyltransferases | 4 | 3 | |
| Aconitase iron-sulfur domain | LeuD/IlvD-like | 4 | 2 | |
| ARM repeat | ARM repeat | 4 | 3 | |
| CBS-domain | Inosine monophosphate dehydrogenase (IMPDH) | 4 | 1 | |
| SNARE-like | Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor | 4 | 3 | |
| Thiolase-like | Thiolase-like | 4 | 3 | |
| Phosphoglucomutase, first 3 domains | Phosphoglucomutase, first 3 domains | 4 | 3 | |
| Zn-finger domain of Sec23/24 | C-terminal, gelsolin-like domain of Sec23/24 | 4 | 3 | |
| ENTH/VHS domain | GAT-like domain | 4 | 2 | |
| Transmembrane di-heme cytochromes | Homing endonucleases | 3 | 3 | |
| Retrovirus zinc finger-like domains | Acid proteases | 3 | 1 | |
| SMAD/FHA domain | Protein kinase-like (PK-like) | 3 | 2 | |
| PH domain-like | Oxysterol-binding protein-like | 3 | 2 | |
| DNA repair protein MutS, domain I | P-loop containing nucleoside triphosphate hydrolases | 3 | 3 | |
| NAD(P)-binding Rossmann-fold domains | P-loop containing nucleoside triphosphate hydrolases | 3 | 2 | |
| Acid proteases | DNA/RNA polymerases | 3 | 1 | |
| F-box domain | WD40 repeat-like | 3 | 3 | |
| DNA repair protein MutS, domain II | P-loop containing nucleoside triphosphate hydrolases | 3 | 3 | |
| Cullin homology domain | "Winged helix" DNA-binding domain | 3 | 2 | |
| Retrovirus zinc finger-like domains | Ribonuclease H-like | 3 | 1 | |
| Aminoacid dehydrogenase-like, N-terminal domain | P-loop containing nucleoside triphosphate hydrolases | 3 | 2 | |
| Leucine zipper domain | YAP1 redox domain | 3 | 2 | |
| POZ domain | POZ domain | 3 | 3 | |
| Ribosomal protein L6 | Ribosomal protein L6 | 3 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | Adenine nucleotide alpha hydrolases-like | 3 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | FtsH protease domain-like | 3 | 1 | |
| "Winged helix" DNA-binding domain | "Winged helix" DNA-binding domain | 3 | 1 | |
| Nucleotidyltransferase | PAP/OAS1 substrate-binding domain | 3 | 2 | |
| Sialidases | Oligoxyloglucan reducing end-specific cellobiohydrolase | 3 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | C-terminal domain of alpha and beta subunits of F1 ATP synthase | 3 | 2 | |
| HSP40/DnaJ peptide-binding domain | HSP40/DnaJ peptide-binding domain | 3 | 3 | |
| Rhodanese/Cell cycle control phosphatase | Cysteine proteinases | 3 | 2 | |
| Acid proteases | Ribonuclease H-like | 3 | 1 | |
| Thioesterase/thiol ester dehydrase-isomerase | Thioesterase/thiol ester dehydrase-isomerase | 3 | 3 | |
| Eukaryotic type KH-domain (KH-domain type I) | Eukaryotic type KH-domain (KH-domain type I) | 3 | 3 | |
| Ubiquitin-like | UBA-like | 3 | 3 | |
| C2H2 and C2HC zinc fingers | C2H2 and C2HC zinc fingers | 3 | 3 | |
| SH3-domain | SH3-domain | 3 | 3 | |
| MurD-like peptide ligases, catalytic domain | MurD-like peptide ligases, peptide-binding domain | 3 | 2 | |
| EF-hand | EF-hand | 3 | 3 | |
| Cupredoxins | Cupredoxins | 3 | 2 | |
| DNA repair protein MutS, domain II | DNA repair protein MutS, domain III | 3 | 3 | |
| UDP-Glycosyltransferase/glycogen phosphorylase | HAD-like | 3 | 2 | |
| NAD(P)-binding Rossmann-fold domains | LDH C-terminal domain-like | 3 | 1 | |
| C2 domain (Calcium/lipid-binding domain, CaLB) | Protein kinase-like (PK-like) | 3 | 3 | |
| DNA repair protein MutS, domain I | DNA repair protein MutS, domain III | 3 | 3 | |
| Protease propeptides/inhibitors | Subtilisin-like | 3 | 2 | |
| PA domain | Transferrin receptor-like dimerisation domain | 3 | 1 | |
| Zn-dependent exopeptidases | Transferrin receptor-like dimerisation domain | 3 | 1 | |
| N-terminal domain of alpha and beta subunits of F1 ATP synthase | P-loop containing nucleoside triphosphate hydrolases | 3 | 2 | |
| Cytochrome c oxidase subunit I-like | Homing endonucleases | 3 | 3 | |
| FYVE/PHD zinc finger | FYVE/PHD zinc finger | 3 | 2 | |
| Ribokinase-like | Heme oxygenase-like | 3 | 1 | |
| Retrovirus zinc finger-like domains | DNA/RNA polymerases | 3 | 1 | |
| CorA soluble domain-like | Magnesium transport protein CorA, transmembrane region | 3 | 2 | |
| N-terminal domain of alpha and beta subunits of F1 ATP synthase | C-terminal domain of alpha and beta subunits of F1 ATP synthase | 3 | 2 | |
| Multidrug resistance efflux transporter EmrE | Multidrug resistance efflux transporter EmrE | 3 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Phosphoglycerate mutase-like | 3 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | TGS-like | 3 | 1 | |
| Cdc48 domain 2-like | P-loop containing nucleoside triphosphate hydrolases | 3 | 3 | |
| FAD-binding domain | FAD-linked oxidases, C-terminal domain | 3 | 1 | |
| SMAD/FHA domain | "Winged helix" DNA-binding domain | 3 | 3 | |
| FAD/NAD(P)-binding domain | FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 3 | 2 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | Nucleic acid-binding proteins | 3 | 3 | |
| Ribosomal L11/L12e N-terminal domain | Ribosomal protein L11, C-terminal domain | 3 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Bromodomain | 3 | 3 | |
| ARM repeat | Clathrin adaptor appendage domain | 3 | 3 | |
| Class I glutamine amidotransferase-like | Ribulose-phoshate binding barrel | 2 | 1 | |
| Translation proteins | Initiation factor IF2/eIF5b, domain 3 | 2 | 2 | |
| HMA, heavy metal-associated domain | Calcium ATPase, transmembrane domain M | 2 | 2 | |
| Cyclophilin-like | TPR-like | 2 | 1 | |
| Ribosomal protein S5 domain 2-like | DNA mismatch repair protein MutL | 2 | 1 | |
| Carbamoyl phosphate synthetase, large subunit connection domain | Methylglyoxal synthase-like | 2 | 2 | |
| GAT-like domain | Clathrin adaptor appendage domain | 2 | 1 | |
| WW domain | FF domain | 2 | 2 | |
| PRTase-like | PRTase-like | 2 | 2 | |
| RNA-binding domain, RBD | ARM repeat | 2 | 1 | |
| Rudiment single hybrid motif | post-HMGL domain-like | 2 | 1 | |
| Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain | Nucleotidylyl transferase | 2 | 2 | |
| E set domains | Ankyrin repeat | 2 | 1 | |
| Eukaryotic initiation factor 4f subunit eIF4g, eIF4e-binding domain | ARM repeat | 2 | 1 | |
| Transducin (alpha subunit), insertion domain | P-loop containing nucleoside triphosphate hydrolases | 2 | 1 | |
| ARM repeat | FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) | 2 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Carbamoyl phosphate synthetase, large subunit connection domain | 2 | 2 | |
| DNA/RNA polymerases | Cytochrome c oxidase subunit I-like | 2 | 2 | |
| Nucleic acid-binding proteins | Nucleic acid-binding proteins | 2 | 2 | |
| Insert subdomain of RNA polymerase alpha subunit | RBP11-like subunits of RNA polymerase | 2 | 2 | |
| WD40 repeat-like | RING/U-box | 2 | 2 | |
| PreATP-grasp domain | Methylglyoxal synthase-like | 2 | 2 | |
| alpha-ketoacid dehydrogenase kinase, N-terminal domain | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 2 | 2 | |
| Glutathione synthetase ATP-binding domain-like | Aldolase | 2 | 1 | |
| Aldolase | 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | Homeodomain-like | 2 | 1 | |
| Single hybrid motif | CoA-dependent acyltransferases | 2 | 2 | |
| Hedgehog/intein (Hint) domain | Homing endonucleases | 2 | 2 | |
| Fe,Mn superoxide dismutase (SOD), N-terminal domain | Fe,Mn superoxide dismutase (SOD), C-terminal domain | 2 | 2 | |
| Glutathione synthetase ATP-binding domain-like | Glutathione synthetase ATP-binding domain-like | 2 | 2 | |
| dsRNA-binding domain-like | Ribosomal protein S5 domain 2-like | 2 | 1 | |
| SNARE fusion complex | SNARE fusion complex | 2 | 1 | |
| S-adenosylmethionine synthetase | S-adenosylmethionine synthetase | 2 | 1 | |
| DNA-binding domain of Mlu1-box binding protein MBP1 | Ankyrin repeat | 2 | 1 | |
| ACT-like | ACT-like | 2 | 2 | |
| Carbamoyl phosphate synthetase, small subunit N-terminal domain | Class I glutamine amidotransferase-like | 2 | 2 | |
| Cullin repeat-like | Cullin homology domain | 2 | 1 | |
| PreATP-grasp domain | ClpP/crotonase | 2 | 2 | |
| DPP6 N-terminal domain-like | alpha/beta-Hydrolases | 2 | 1 | |
| Carbamate kinase-like | PUA domain-like | 2 | 1 | |
| BRCT domain | BRCT domain | 2 | 2 | |
| Translation initiation factor 2 beta, aIF2beta, N-terminal domain | Zinc-binding domain of translation initiation factor 2 beta | 2 | 2 | |
| DNA/RNA polymerases | Lesion bypass DNA polymerase (Y-family), little finger domain | 2 | 2 | |
| FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) | Protein kinase-like (PK-like) | 2 | 1 | |
| ClpP/crotonase | ClpP/crotonase | 2 | 2 | |
| SAM/Pointed domain | PH domain-like | 2 | 1 | |
| Phosphoenolpyruvate/pyruvate domain | PK C-terminal domain-like | 2 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | HAND domain of the nucleosome remodeling ATPase ISWI | 2 | 1 | |
| Flavoproteins | Ferredoxin reductase-like, C-terminal NADP-linked domain | 2 | 2 | |
| Glutathione synthetase ATP-binding domain-like | post-HMGL domain-like | 2 | 1 | |
| Methylglyoxal synthase-like | Cytidine deaminase-like | 2 | 1 | |
| DNA repair protein MutS, domain I | DNA repair protein MutS, domain II | 2 | 2 | |
| cAMP-binding domain-like | cAMP-binding domain-like | 2 | 2 | |
| FAD/NAD(P)-binding domain | Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain | 2 | 1 | |
| Phosphofructokinase | Phosphofructokinase | 2 | 2 | |
| RING/U-box | RING/U-box | 2 | 2 | |
| DAK1/DegV-like | Citrobacter dihydroxyacetone kinase extra ATP-binding domain | 2 | 1 | |
| TPR-like | HCP-like | 2 | 2 | |
| HAND domain of the nucleosome remodeling ATPase ISWI | Homeodomain-like | 2 | 1 | |
| Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain | 2 | 1 | |
| Clathrin adaptor appendage domain | Subdomain of clathrin and coatomer appendage domain | 2 | 2 | |
| L domain-like | L domain-like | 2 | 1 | |
| PreATP-grasp domain | PreATP-grasp domain | 2 | 2 | |
| Glutathione synthetase ATP-binding domain-like | ClpP/crotonase | 2 | 2 | |
| PreATP-grasp domain | Aldolase | 2 | 1 | |
| N-terminal, heterodimerisation domain of RBP7 (RpoE) | Nucleic acid-binding proteins | 2 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | SH3-domain | 2 | 1 | |
| PurM N-terminal domain-like | PurM C-terminal domain-like | 2 | 2 | |
| Glutathione synthetase ATP-binding domain-like | Methylglyoxal synthase-like | 2 | 2 | |
| R1 subunit of ribonucleotide reductase, N-terminal domain | PFL-like glycyl radical enzymes | 2 | 2 | |
| NAD(P)-binding Rossmann-fold domains | ACT-like | 2 | 1 | |
| Creatinase/prolidase N-terminal domain | Creatinase/aminopeptidase | 2 | 2 | |
| post-HMGL domain-like | Single hybrid motif | 2 | 1 | |
| Ankyrin repeat | Oxysterol-binding protein-like | 2 | 1 | |
| SH3-domain | SAM/Pointed domain | 2 | 1 | |
| Ankyrin repeat | PH domain-like | 2 | 1 | |
| ARM repeat | WD40 repeat-like | 2 | 2 | |
| vWA-like | SPOC domain-like | 2 | 1 | |
| Zinc beta-ribbon | Cyclin-like | 2 | 2 | |
| Nucleotidylyl transferase | Ribosomal protein L25-like | 2 | 2 | |
| SMAD/FHA domain | RING/U-box | 2 | 1 | |
| mRNA decapping enzyme DcpS N-terminal domain | HIT-like | 2 | 2 | |
| SET domain | FYVE/PHD zinc finger | 2 | 2 | |
| Clavaminate synthase-like | C2H2 and C2HC zinc fingers | 2 | 2 | |
| NAD-binding domain of HMG-CoA reductase | Substrate-binding domain of HMG-CoA reductase | 2 | 2 | |
| HMA, heavy metal-associated domain | Calcium ATPase, transduction domain A | 2 | 2 | |
| Ankyrin repeat | PLC-like phosphodiesterases | 2 | 1 | |
| ARM repeat | Hect, E3 ligase catalytic domain | 2 | 1 | |
| Cullin repeat-like | "Winged helix" DNA-binding domain | 2 | 1 | |
| CCCH zinc finger | CCCH zinc finger | 2 | 1 | |
| t-snare proteins | SNARE fusion complex | 2 | 2 | |
| PK beta-barrel domain-like | Phosphoenolpyruvate/pyruvate domain | 2 | 1 | |
| Cap-Gly domain | Ubiquitin-like | 2 | 2 | |
| Rad51 N-terminal domain-like | P-loop containing nucleoside triphosphate hydrolases | 2 | 2 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | HSP90 C-terminal domain | 2 | 1 | |
| Aldolase | Single hybrid motif | 2 | 1 | |
| SH3-domain | PH domain-like | 2 | 1 | |
| SNARE-like | SNARE fusion complex | 2 | 1 | |
| ARM repeat | Subdomain of clathrin and coatomer appendage domain | 2 | 2 | |
| PUA domain-like | P-loop containing nucleoside triphosphate hydrolases | 2 | 2 | |
| HMA, heavy metal-associated domain | HAD-like | 2 | 2 | |
| Rudiment single hybrid motif | ClpP/crotonase | 2 | 2 | |
| Formate/glycerate dehydrogenase catalytic domain-like | ACT-like | 2 | 1 | |
| Thioredoxin-like | eEF1-gamma domain | 2 | 1 | |
| Ubiquitin-like | Ubiquitin-like | 2 | 2 | |
| ADC-like | P-loop containing nucleoside triphosphate hydrolases | 2 | 2 | |
| HMG-box | HMG-box | 2 | 2 | |
| Aminopeptidase/glucanase lid domain | Zn-dependent exopeptidases | 2 | 1 | |
| Domain of the SRP/SRP receptor G-proteins | P-loop containing nucleoside triphosphate hydrolases | 2 | 2 | |
| PH domain-like | Protein kinase-like (PK-like) | 2 | 2 | |
| Protein kinase-like (PK-like) | Kinase associated domain 1, KA1 | 2 | 1 | |
| ADC-like | Cdc48 domain 2-like | 2 | 2 | |
| Ribosomal protein S5 domain 2-like | Ribonuclease PH domain 2-like | 2 | 1 | |
| WW domain | WW domain | 2 | 2 | |
| Nicotinate/Quinolinate PRTase N-terminal domain-like | Nicotinate/Quinolinate PRTase C-terminal domain-like | 2 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | DNA mismatch repair protein MutL | 2 | 1 | |
| PreATP-grasp domain | Carbamoyl phosphate synthetase, large subunit connection domain | 2 | 2 | |
| Ribosomal protein S5 domain 2-like | HSP90 C-terminal domain | 2 | 1 | |
| ARM repeat | Formin homology 2 domain (FH2 domain) | 2 | 2 | |
| Flavoproteins | Riboflavin synthase domain-like | 2 | 2 | |
| UBC-like | UBA-like | 2 | 2 | |
| "Winged helix" DNA-binding domain | DBL homology domain (DH-domain) | 2 | 1 | |
| FYVE/PHD zinc finger | Clavaminate synthase-like | 2 | 2 | |
| Multiheme cytochromes | GTPase activation domain, GAP | 2 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Initiation factor IF2/eIF5b, domain 3 | 2 | 2 | |
| PreATP-grasp domain | post-HMGL domain-like | 2 | 1 | |
| Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 2 | 2 | |
| PK beta-barrel domain-like | PK C-terminal domain-like | 2 | 1 | |
| Transcription factor IIA (TFIIA), alpha-helical domain | Transcription factor IIA (TFIIA), beta-barrel domain | 2 | 2 | |
| Zn2/Cys6 DNA-binding domain | PYP-like sensor domain (PAS domain) | 2 | 1 | |
| post-HMGL domain-like | 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | Class I glutamine amidotransferase-like | 2 | 1 | |
| RNase III domain-like | dsRNA-binding domain-like | 2 | 1 | |
| ENTH/VHS domain | Clathrin adaptor appendage domain | 2 | 1 | |
| Rudiment single hybrid motif | Aldolase | 2 | 1 | |
| Glutathione S-transferase (GST), C-terminal domain | eEF1-gamma domain | 2 | 1 | |
| tRNA-binding arm | Class II aaRS and biotin synthetases | 2 | 1 | |
| Single hybrid motif | ClpP/crotonase | 2 | 2 | |
| Class II aaRS and biotin synthetases | ThrRS/AlaRS common domain | 2 | 2 | |
| PH domain-like | EF-hand | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| Nucleic acid-binding proteins | "Winged helix" DNA-binding domain | 1 | 1 | |
| Acetyl-CoA synthetase-like | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Actin depolymerizing proteins | Actin depolymerizing proteins | 1 | 1 | |
| lambda integrase-like, N-terminal domain | DNA breaking-rejoining enzymes | 1 | 1 | |
| PurS-like | Class I glutamine amidotransferase-like | 1 | 1 | |
| Thiamin diphosphate-binding fold (THDP-binding) | Sulfite reductase, domains 1 and 3 | 1 | 1 | |
| PH domain-like | WD40 repeat-like | 1 | 1 | |
| Homodimeric domain of signal transducing histidine kinase | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 1 | 1 | |
| Galactose-binding domain-like | Galactose-binding domain-like | 1 | 1 | |
| HisI-like | all-alpha NTP pyrophosphatases | 1 | 1 | |
| Double Clp-N motif | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| L domain-like | PP2C-like | 1 | 1 | |
| Class II aaRS ABD-related | C-terminal domain of ProRS | 1 | 1 | |
| eIF2alpha middle domain-like | eIF-2-alpha, C-terminal domain | 1 | 1 | |
| CoA-dependent acyltransferases | Acetyl-CoA synthetase-like | 1 | 1 | |
| Carbamoyl phosphate synthetase, large subunit connection domain | Aspartate/ornithine carbamoyltransferase | 1 | 1 | |
| Acid proteases | UBA-like | 1 | 1 | |
| Voltage-gated potassium channels | Voltage-gated potassium channels | 1 | 1 | |
| PX domain | BAR/IMD domain-like | 1 | 1 | |
| Rudiment single hybrid motif | PurM C-terminal domain-like | 1 | 1 | |
| Carbamate kinase-like | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | PurM C-terminal domain-like | 1 | 1 | |
| UBC-like | Class II aaRS and biotin synthetases | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | Argininosuccinate synthetase, C-terminal domain | 1 | 1 | |
| PH domain-like | C2 domain (Calcium/lipid-binding domain, CaLB) | 1 | 1 | |
| UBA-like | TPR-like | 1 | 1 | |
| 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK | Dihydropteroate synthetase-like | 1 | 1 | |
| GroEL apical domain-like | SAICAR synthase-like | 1 | 1 | |
| Chaperone J-domain | HSC20 (HSCB), C-terminal oligomerisation domain | 1 | 1 | |
| TATA-box binding protein-like | TATA-box binding protein-like | 1 | 1 | |
| PH domain-like | Cullin repeat-like | 1 | 1 | |
| PLP-dependent transferases | PLP-dependent transferases | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | HRDC-like | 1 | 1 | |
| TRAF domain-like | Cysteine proteinases | 1 | 1 | |
| TK C-terminal domain-like | Sulfite reductase, domains 1 and 3 | 1 | 1 | |
| PH domain-like | BSD domain-like | 1 | 1 | |
| Dehydroquinate synthase-like | Aldolase | 1 | 1 | |
| Arabinanase/levansucrase/invertase | Concanavalin A-like lectins/glucanases | 1 | 1 | |
| Metalloproteases ("zincins"), catalytic domain | ARM repeat | 1 | 1 | |
| Cap-Gly domain | RNI-like | 1 | 1 | |
| Cryptochrome/photolyase, N-terminal domain | Cryptochrome/photolyase FAD-binding domain | 1 | 1 | |
| Thiolase-like | 4'-phosphopantetheinyl transferase | 1 | 1 | |
| FYVE/PHD zinc finger | GroEL apical domain-like | 1 | 1 | |
| ISP transmembrane anchor | ISP domain | 1 | 1 | |
| EF-hand | PLC-like phosphodiesterases | 1 | 1 | |
| Activating enzymes of the ubiquitin-like proteins | Activating enzymes of the ubiquitin-like proteins | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | CheY-like | 1 | 1 | |
| Protein kinase-like (PK-like) | WD40 repeat-like | 1 | 1 | |
| NSFL1 (p97 ATPase) cofactor p47, SEP domain | Ubiquitin-like | 1 | 1 | |
| Class I glutamine amidotransferase-like | Glutathione synthetase ATP-binding domain-like | 1 | 1 | |
| TK C-terminal domain-like | Pyruvate-ferredoxin oxidoreductase, PFOR, domain III | 1 | 1 | |
| Retrovirus zinc finger-like domains | Retrovirus zinc finger-like domains | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Cysteine proteinases | 1 | 1 | |
| Ribonuclease H-like | HRDC-like | 1 | 1 | |
| Pyruvate-ferredoxin oxidoreductase, PFOR, domain III | Ferredoxin reductase-like, C-terminal NADP-linked domain | 1 | 1 | |
| ARM repeat | RING/U-box | 1 | 1 | |
| Glucocorticoid receptor-like (DNA-binding domain) | Glucocorticoid receptor-like (DNA-binding domain) | 1 | 1 | |
| Methionyl-tRNA synthetase (MetRS), Zn-domain | Nucleotidylyl transferase | 1 | 1 | |
| WD40 repeat-like | Quinoprotein alcohol dehydrogenase-like | 1 | 1 | |
| RNA-binding domain, RBD | PABC (PABP) domain | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | Nucleotide-binding domain | 1 | 1 | |
| TK C-terminal domain-like | Riboflavin synthase domain-like | 1 | 1 | |
| Rap30/74 interaction domains | "Winged helix" DNA-binding domain | 1 | 1 | |
| Coiled-coil domain of nucleotide exchange factor GrpE | Head domain of nucleotide exchange factor GrpE | 1 | 1 | |
| Zinc beta-ribbon | Zinc beta-ribbon | 1 | 1 | |
| YjgF-like | YjgF-like | 1 | 1 | |
| BAR/IMD domain-like | SH3-domain | 1 | 1 | |
| Ribosomal protein L7/12, oligomerisation (N-terminal) domain | ClpS-like | 1 | 1 | |
| SWIB/MDM2 domain | eIF1-like | 1 | 1 | |
| Translation proteins | Translation proteins | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Signal peptide-binding domain | 1 | 1 | |
| SAM/Pointed domain | Protein kinase-like (PK-like) | 1 | 1 | |
| Chromo domain-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| WD40 repeat-like | Zn-dependent exopeptidases | 1 | 1 | |
| MIT domain | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| RING/U-box | YVTN repeat-like/Quinoprotein amine dehydrogenase | 1 | 1 | |
| Creatinase/aminopeptidase | "Winged helix" DNA-binding domain | 1 | 1 | |
| Alpha subunit of glutamate synthase, C-terminal domain | alpha-helical ferredoxin | 1 | 1 | |
| Homing endonucleases | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Sec7 domain | ARM repeat | 1 | 1 | |
| Metallo-hydrolase/oxidoreductase | Sterol carrier protein, SCP | 1 | 1 | |
| UBC-like | Endosomal sorting complex assembly domain | 1 | 1 | |
| Protein kinase-like (PK-like) | CheY-like | 1 | 1 | |
| Pseudouridine synthase | PUA domain-like | 1 | 1 | |
| HAD-like | BRCT domain | 1 | 1 | |
| UBA-like | Chaperone J-domain | 1 | 1 | |
| SH3-domain | CAD & PB1 domains | 1 | 1 | |
| Siroheme synthase middle domains-like | Tetrapyrrole methylase | 1 | 1 | |
| Galactose mutarotase-like | (Trans)glycosidases | 1 | 1 | |
| FabD/lysophospholipase-like | 4'-phosphopantetheinyl transferase | 1 | 1 | |
| Retrovirus zinc finger-like domains | Clathrin adaptor appendage domain | 1 | 1 | |
| VPS9 domain | Pseudo ankyrin repeat-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Aldolase | 1 | 1 | |
| PurM C-terminal domain-like | Class I glutamine amidotransferase-like | 1 | 1 | |
| PurS-like | PurM C-terminal domain-like | 1 | 1 | |
| Protein kinase-like (PK-like) | Class II aaRS and biotin synthetases | 1 | 1 | |
| Class II aaRS and biotin synthetases | C-terminal domain of ProRS | 1 | 1 | |
| PurM N-terminal domain-like | PurM N-terminal domain-like | 1 | 1 | |
| Quinoprotein alcohol dehydrogenase-like | Protein kinase-like (PK-like) | 1 | 1 | |
| Class I glutamine amidotransferase-like | Methylglyoxal synthase-like | 1 | 1 | |
| Supernatant protein factor (SPF), C-terminal domain | PH domain-like | 1 | 1 | |
| Aldolase | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| N-terminal domain of alpha and beta subunits of F1 ATP synthase | Hedgehog/intein (Hint) domain | 1 | 1 | |
| Glutathione S-transferase (GST), C-terminal domain | Ribosomal protein L25-like | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | alpha-helical ferredoxin | 1 | 1 | |
| Clc chloride channel | CBS-domain | 1 | 1 | |
| Ras GEF | Ras GEF | 1 | 1 | |
| EPT/RTPC-like | Aminoacid dehydrogenase-like, N-terminal domain | 1 | 1 | |
| YbaK/ProRS associated domain | Class II aaRS and biotin synthetases | 1 | 1 | |
| FGAM synthase PurL, linker domain | Class I glutamine amidotransferase-like | 1 | 1 | |
| TPR-like | HSP20-like chaperones | 1 | 1 | |
| E set domains | Glycosyl hydrolase domain | 1 | 1 | |
| TPR-like | RNI-like | 1 | 1 | |
| DBL homology domain (DH-domain) | CAD & PB1 domains | 1 | 1 | |
| FabD/lysophospholipase-like | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Calponin-homology domain, CH-domain | GTPase activation domain, GAP | 1 | 1 | |
| alpha-helical ferredoxin | FAD/NAD(P)-binding domain | 1 | 1 | |
| WWE domain | alpha/beta-Hydrolases | 1 | 1 | |
| FMN-linked oxidoreductases | FAD/NAD(P)-binding domain | 1 | 1 | |
| Pseudouridine synthase | Cytidine deaminase-like | 1 | 1 | |
| Aldolase | Aminoacid dehydrogenase-like, N-terminal domain | 1 | 1 | |
| SET domain | WW domain | 1 | 1 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | BRCT domain | 1 | 1 | |
| Nucleic acid-binding proteins | TPR-like | 1 | 1 | |
| BRCT domain | DNA/RNA polymerases | 1 | 1 | |
| POZ domain | Skp1 dimerisation domain-like | 1 | 1 | |
| Domain of the SRP/SRP receptor G-proteins | Signal peptide-binding domain | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Aspartate/ornithine carbamoyltransferase | 1 | 1 | |
| Glutathione S-transferase (GST), C-terminal domain | Nucleotidylyl transferase | 1 | 1 | |
| EGF/Laminin | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Cysteine-rich domain | Cysteine-rich domain | 1 | 1 | |
| ATP-dependent DNA ligase DNA-binding domain | Nucleic acid-binding proteins | 1 | 1 | |
| Carbamoyl phosphate synthetase, small subunit N-terminal domain | Metallo-dependent hydrolases | 1 | 1 | |
| Clathrin heavy-chain terminal domain | ARM repeat | 1 | 1 | |
| L domain-like | Nucleotide cyclase | 1 | 1 | |
| Glucocorticoid receptor-like (DNA-binding domain) | GTPase activation domain, GAP | 1 | 1 | |
| Translation initiation factor 2 beta, aIF2beta, N-terminal domain | ARM repeat | 1 | 1 | |
| Class I glutamine amidotransferase-like | Carbamoyl phosphate synthetase, large subunit connection domain | 1 | 1 | |
| BAH domain | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| ATP-dependent DNA ligase DNA-binding domain | DNA ligase/mRNA capping enzyme, catalytic domain | 1 | 1 | |
| F1F0 ATP synthase subunit C | F1F0 ATP synthase subunit C | 1 | 1 | |
| WD40 repeat-like | Cysteine proteinases | 1 | 1 | |
| Rudiment single hybrid motif | N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) | 1 | 1 | |
| Carbamoyl phosphate synthetase, small subunit N-terminal domain | PreATP-grasp domain | 1 | 1 | |
| PUA domain-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| SurE-like | Glutathione synthetase ATP-binding domain-like | 1 | 1 | |
| Acyl-CoA dehydrogenase NM domain-like | Acyl-CoA dehydrogenase C-terminal domain-like | 1 | 1 | |
| Methylglyoxal synthase-like | Aspartate/ornithine carbamoyltransferase | 1 | 1 | |
| Class II aaRS and biotin synthetases | Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | 1 | 1 | |
| Flavoproteins | Radical SAM enzymes | 1 | 1 | |
| PX domain | SNARE fusion complex | 1 | 1 | |
| L domain-like | DNase I-like | 1 | 1 | |
| Rhodanese/Cell cycle control phosphatase | (Phosphotyrosine protein) phosphatases II | 1 | 1 | |
| SH3-domain | Cysteine proteinases | 1 | 1 | |
| alpha-helical ferredoxin | Nucleotide-binding domain | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | Type II DNA topoisomerase | 1 | 1 | |
| Carbamoyl phosphate synthetase, large subunit connection domain | Metallo-dependent hydrolases | 1 | 1 | |
| Eukaryotic RPB5 N-terminal domain | RPB5-like RNA polymerase subunit | 1 | 1 | |
| HR1 repeat | C2 domain (Calcium/lipid-binding domain, CaLB) | 1 | 1 | |
| Globin-like | Riboflavin synthase domain-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Hypothetical protein YjiA, C-terminal domain | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | DHS-like NAD/FAD-binding domain | 1 | 1 | |
| Dehydroquinate synthase-like | EPT/RTPC-like | 1 | 1 | |
| Nucleotide-diphospho-sugar transferases | ARM repeat | 1 | 1 | |
| Endosomal sorting complex assembly domain | VPS28 C-terminal domain-like | 1 | 1 | |
| Carbamoyl phosphate synthetase, small subunit N-terminal domain | Carbamoyl phosphate synthetase, large subunit connection domain | 1 | 1 | |
| Tetrahydrobiopterin biosynthesis enzymes-like | Tetrahydrobiopterin biosynthesis enzymes-like | 1 | 1 | |
| RNA-binding domain, RBD | Ran BP2/NZF zinc finger-like | 1 | 1 | |
| Actin depolymerizing proteins | SH3-domain | 1 | 1 | |
| Activator of Hsp90 ATPase, Aha1 | Bet v1-like | 1 | 1 | |
| SAP domain | RING/U-box | 1 | 1 | |
| Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase | Phosphofructokinase | 1 | 1 | |
| PreATP-grasp domain | Metallo-dependent hydrolases | 1 | 1 | |
| Tetrahydrobiopterin biosynthesis enzymes-like | Dihydropteroate synthetase-like | 1 | 1 | |
| Periplasmic binding protein-like II | GlnB-like | 1 | 1 | |
| ENTH/VHS domain | I/LWEQ domain | 1 | 1 | |
| Galactose mutarotase-like | Glycosyl hydrolase domain | 1 | 1 | |
| Rhodanese/Cell cycle control phosphatase | Rhodanese/Cell cycle control phosphatase | 1 | 1 | |
| EPT/RTPC-like | Aldolase | 1 | 1 | |
| Homodimeric domain of signal transducing histidine kinase | CheY-like | 1 | 1 | |
| Sulfite reductase, domains 1 and 3 | Sulfite reductase, domains 1 and 3 | 1 | 1 | |
| DNA polymerase beta, N-terminal domain-like | Nucleotidyltransferase | 1 | 1 | |
| UROD/MetE-like | UROD/MetE-like | 1 | 1 | |
| Eukaryotic type KH-domain (KH-domain type I) | Retrovirus zinc finger-like domains | 1 | 1 | |
| Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 | Zinc beta-ribbon | 1 | 1 | |
| N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 | L30e-like | 1 | 1 | |
| "Winged helix" DNA-binding domain | Regulator of G-protein signaling, RGS | 1 | 1 | |
| Metallo-hydrolase/oxidoreductase | Metallo-hydrolase/oxidoreductase | 1 | 1 | |
| UBC-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| 4'-phosphopantetheinyl transferase | 4'-phosphopantetheinyl transferase | 1 | 1 | |
| Ran BP2/NZF zinc finger-like | Ran BP2/NZF zinc finger-like | 1 | 1 | |
| FGAM synthase PurL, linker domain | PurM C-terminal domain-like | 1 | 1 | |
| Restriction endonuclease-like | RuvA domain 2-like | 1 | 1 | |
| PH domain-like | "Winged helix" DNA-binding domain | 1 | 1 | |
| PP2C-like | Nucleotide cyclase | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Succinyl-CoA synthetase domains | 1 | 1 | |
| Arp2/3 complex subunits | Arp2/3 complex subunits | 1 | 1 | |
| PAP/OAS1 substrate-binding domain | PAP/Archaeal CCA-adding enzyme, C-terminal domain | 1 | 1 | |
| Thiamin phosphate synthase | Ribokinase-like | 1 | 1 | |
| Supernatant protein factor (SPF), C-terminal domain | Oxysterol-binding protein-like | 1 | 1 | |
| Subtilisin-like | Galactose-binding domain-like | 1 | 1 | |
| Glutamine synthetase/guanido kinase | GatB/YqeY motif | 1 | 1 | |
| Globin-like | Ferredoxin reductase-like, C-terminal NADP-linked domain | 1 | 1 | |
| PUA domain-like | SWIB/MDM2 domain | 1 | 1 | |
| Carbamoyl phosphate synthetase, small subunit N-terminal domain | Aspartate/ornithine carbamoyltransferase | 1 | 1 | |
| Ubiquitin-like | Cysteine proteinases | 1 | 1 | |
| Dcp2 domain-like | Nudix | 1 | 1 | |
| TGS-like | Class II aaRS ABD-related | 1 | 1 | |
| E set domains | (Trans)glycosidases | 1 | 1 | |
| Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | ThrRS/AlaRS common domain | 1 | 1 | |
| Chromo domain-like | Acyl-CoA N-acyltransferases (Nat) | 1 | 1 | |
| Surp module (SWAP domain) | Surp module (SWAP domain) | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Microbial and mitochondrial ADK, insert "zinc finger" domain | 1 | 1 | |
| Hypothetical protein SAV1430 | Fe-S cluster assembly (FSCA) domain-like | 1 | 1 | |
| Flavoproteins | Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 | 1 | 1 | |
| L9 N-domain-like | L9 N-domain-like | 1 | 1 | |
| Protein kinase-like (PK-like) | Polo-box domain | 1 | 1 | |
| FYSH domain | Hypothetical protein AF0491, middle domain | 1 | 1 | |
| Chaperone J-domain | C2H2 and C2HC zinc fingers | 1 | 1 | |
| L domain-like | UBA-like | 1 | 1 | |
| Nucleotide-binding domain | FAD/NAD(P)-binding domain | 1 | 1 | |
| WW domain | Hect, E3 ligase catalytic domain | 1 | 1 | |
| "Winged helix" DNA-binding domain | RNA-binding domain, RBD | 1 | 1 | |
| Alpha subunit of glutamate synthase, C-terminal domain | FAD/NAD(P)-binding domain | 1 | 1 | |
| CoA-dependent acyltransferases | ACP-like | 1 | 1 | |
| FYVE/PHD zinc finger | SAICAR synthase-like | 1 | 1 | |
| FF domain | FF domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | vWA-like | 1 | 1 | |
| L domain-like | NTF2-like | 1 | 1 | |
| HIT-like | HIT-like | 1 | 1 | |
| FabD/lysophospholipase-like | Thioesterase/thiol ester dehydrase-isomerase | 1 | 1 | |
| UBA-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Thiamin pyrophosphokinase, catalytic domain | Thiamin pyrophosphokinase, substrate-binding domain | 1 | 1 | |
| EF-hand | UBA-like | 1 | 1 | |
| RNA-binding domain, RBD | Class II aaRS ABD-related | 1 | 1 | |
| Methylglyoxal synthase-like | Metallo-dependent hydrolases | 1 | 1 | |
| BRCT domain | Homeodomain-like | 1 | 1 | |
| Tetrahydrobiopterin biosynthesis enzymes-like | 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK | 1 | 1 | |
| ENTH/VHS domain | FYVE/PHD zinc finger | 1 | 1 | |
| Hedgehog/intein (Hint) domain | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| BRCT domain | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| ENTH/VHS domain | SH3-domain | 1 | 1 | |
| Nucleotidylyl transferase | An anticodon-binding domain of class I aminoacyl-tRNA synthetases | 1 | 1 | |
| PurS-like | PurM N-terminal domain-like | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) | 1 | 1 | |
| Class I glutamine amidotransferase-like | Metallo-dependent hydrolases | 1 | 1 | |
| Pre-PUA domain | PUA domain-like | 1 | 1 | |
| Acyl-CoA dehydrogenase C-terminal domain-like | Acyl-CoA dehydrogenase C-terminal domain-like | 1 | 1 | |
| Zn-dependent exopeptidases | Bacterial exopeptidase dimerisation domain | 1 | 1 | |
| BEACH domain | WD40 repeat-like | 1 | 1 | |
| N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 | Translational machinery components | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | YjgF-like | 1 | 1 | |
| vWA-like | Cysteine-rich domain | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Thioesterase/thiol ester dehydrase-isomerase | 1 | 1 | |
| PH domain-like | UDP-Glycosyltransferase/glycogen phosphorylase | 1 | 1 | |
| Ankyrin repeat | POZ domain | 1 | 1 | |
| Chaperone J-domain | CSL zinc finger | 1 | 1 | |
| Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 | Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 | 1 | 1 | |
| C2 domain (Calcium/lipid-binding domain, CaLB) | Hect, E3 ligase catalytic domain | 1 | 1 | |
| Cysteine proteinases | UBA-like | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Metallo-dependent hydrolases | 1 | 1 | |
| Nucleic acid-binding proteins | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | PRTase-like | 1 | 1 | |
| HisI-like | ALDH-like | 1 | 1 | |
| FAD/NAD(P)-binding domain | 4Fe-4S ferredoxins | 1 | 1 | |
| PurS-like | FGAM synthase PurL, linker domain | 1 | 1 | |
| Carbamoyl phosphate synthetase, small subunit N-terminal domain | Methylglyoxal synthase-like | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Siroheme synthase middle domains-like | 1 | 1 | |
| Rudiment single hybrid motif | PurM N-terminal domain-like | 1 | 1 | |
| L30e-like | alpha/beta knot | 1 | 1 | |
| Translational machinery components | L30e-like | 1 | 1 | |
| Eukaryotic type KH-domain (KH-domain type I) | Clathrin adaptor appendage domain | 1 | 1 | |
| RNI-like | Ubiquitin-like | 1 | 1 | |
| UBA-like | UBA-like | 1 | 1 | |
| EPT/RTPC-like | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Ribulose-phoshate binding barrel | Tryptophan synthase beta subunit-like PLP-dependent enzymes | 1 | 1 | |
| NagB/RpiA/CoA transferase-like | NagB/RpiA/CoA transferase-like | 1 | 1 | |
| ENTH/VHS domain | RNA-binding domain, RBD | 1 | 1 | |
| Dehydroquinate synthase-like | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| TPR-like | Chaperone J-domain | 1 | 1 | |
| Amidase signature (AS) enzymes | Rudiment single hybrid motif | 1 | 1 | |
| PH domain-like | Phospholipase D/nuclease | 1 | 1 | |
| FYVE/PHD zinc finger | Rabenosyn-5 Rab-binding domain-like | 1 | 1 | |
| HMA, heavy metal-associated domain | Cu,Zn superoxide dismutase-like | 1 | 1 | |
| ARID-like | FYVE/PHD zinc finger | 1 | 1 | |
| TATA-box binding protein-like | DNA-glycosylase | 1 | 1 | |
| Ypt/Rab-GAP domain of gyp1p | EF-hand | 1 | 1 | |
| FYVE/PHD zinc finger | Elongation factor TFIIS domain 2 | 1 | 1 | |
| L9 N-domain-like | Ribonuclease H-like | 1 | 1 | |
| all-alpha NTP pyrophosphatases | ALDH-like | 1 | 1 | |
| TK C-terminal domain-like | Ferredoxin reductase-like, C-terminal NADP-linked domain | 1 | 1 | |
| "Winged helix" DNA-binding domain | GTPase activation domain, GAP | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | SIS domain | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Succinyl-CoA synthetase domains | 1 | 1 | |
| Carbon-nitrogen hydrolase | Adenine nucleotide alpha hydrolases-like | 1 | 1 | |
| SAM/Pointed domain | Ubiquitin-like | 1 | 1 | |
| Single hybrid motif | Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | 1 | 1 | |
| C2 domain (Calcium/lipid-binding domain, CaLB) | ARM repeat | 1 | 1 | |
| DUSP-like | Cysteine proteinases | 1 | 1 | |
| Nucleotidylyl transferase | Nucleotidylyl transferase | 1 | 1 | |
| Carbamate kinase-like | Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 1 | 1 | |
| Nucleotidylyl transferase | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| WD40 repeat-like | Ribonuclease H-like | 1 | 1 | |
| Calponin-homology domain, CH-domain | EB1 dimerisation domain-like | 1 | 1 | |
| Acyl-CoA N-acyltransferases (Nat) | Acyl-CoA N-acyltransferases (Nat) | 1 | 1 | |
| Folate-binding domain | Aminomethyltransferase beta-barrel domain | 1 | 1 | |
| N-terminal domain of alpha and beta subunits of F1 ATP synthase | Homing endonucleases | 1 | 1 | |
| HR1 repeat | Protein kinase-like (PK-like) | 1 | 1 | |
| Class I glutamine amidotransferase-like | Aspartate/ornithine carbamoyltransferase | 1 | 1 | |
| DNA clamp | DNA clamp | 1 | 1 | |
| FGAM synthase PurL, linker domain | PurM N-terminal domain-like | 1 | 1 | |
| Tryptophan synthase beta subunit-like PLP-dependent enzymes | ACT-like | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Thiolase-like | 1 | 1 | |
| Glutamine synthetase, N-terminal domain | Glutamine synthetase/guanido kinase | 1 | 1 | |
| Fibronectin type III | BRCT domain | 1 | 1 | |
| YbaK/ProRS associated domain | C-terminal domain of ProRS | 1 | 1 | |
| Quinoprotein alcohol dehydrogenase-like | YVTN repeat-like/Quinoprotein amine dehydrogenase | 1 | 1 | |
| (Trans)glycosidases | Chitinase insertion domain | 1 | 1 | |
| ThrRS/AlaRS common domain | Class II aaRS ABD-related | 1 | 1 | |
| FMN-linked oxidoreductases | alpha-helical ferredoxin | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Prismane protein-like | 1 | 1 | |
| Nucleotidyltransferase | PAP/Archaeal CCA-adding enzyme, C-terminal domain | 1 | 1 | |
| YbaK/ProRS associated domain | Class II aaRS ABD-related | 1 | 1 | |
| Acyl-CoA N-acyltransferases (Nat) | Bromodomain | 1 | 1 | |
| WD40 repeat-like | C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase | 1 | 1 | |
| Cadherin-like | Cadherin-like | 1 | 1 | |
| Leukotriene A4 hydrolase N-terminal domain | ARM repeat | 1 | 1 | |
| NTF2-like | UBA-like | 1 | 1 | |
| PAH2 domain | PAH2 domain | 1 | 1 | |
| Thiamin diphosphate-binding fold (THDP-binding) | Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 | 1 | 1 | |
| PUA domain-like | eIF1-like | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | 4'-phosphopantetheinyl transferase | 1 | 1 | |
| Flavoproteins | Sulfite reductase, domains 1 and 3 | 1 | 1 | |
| SMAD/FHA domain | SMAD/FHA domain | 1 | 1 | |
| Protein kinase-like (PK-like) | Protein kinase-like (PK-like) | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | PRTase-like | 1 | 1 | |
| PreATP-grasp domain | N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) | 1 | 1 | |
| RING/U-box | RNA-binding domain, RBD | 1 | 1 | |
| TK C-terminal domain-like | Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 | 1 | 1 | |
| TGS-like | ThrRS/AlaRS common domain | 1 | 1 | |
| WW domain | FKBP-like | 1 | 1 | |
| FMN-linked oxidoreductases | Alpha subunit of glutamate synthase, C-terminal domain | 1 | 1 | |
| SH3-domain | PX domain | 1 | 1 | |
| TK C-terminal domain-like | Flavoproteins | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | EF-hand | 1 | 1 | |
| Putative DNA-binding domain | Class II aaRS and biotin synthetases | 1 | 1 | |
| Cytochrome c | Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor | 1 | 1 | |
| UBC-like | Protein kinase-like (PK-like) | 1 | 1 | |
| Amidase signature (AS) enzymes | Single hybrid motif | 1 | 1 | |
| Class I glutamine amidotransferase-like | PreATP-grasp domain | 1 | 1 | |
| TPR-like | Metallo-dependent phosphatases | 1 | 1 | |
| ArfGap/RecO-like zinc finger | UBA-like | 1 | 1 | |
| Cytochrome b5-like heme/steroid binding domain | FMN-linked oxidoreductases | 1 | 1 | |
| EF-hand | Mitochondrial carrier | 1 | 1 | |
| Acetyl-CoA synthetase-like | ACP-like | 1 | 1 | |
| CoA-dependent acyltransferases | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Nucleic acid-binding proteins | eIF2alpha middle domain-like | 1 | 1 | |
| Tryptophan synthase beta subunit-like PLP-dependent enzymes | CBS-domain | 1 | 1 | |
| Class II aaRS and biotin synthetases | Anticodon-binding domain of PheRS | 1 | 1 | |
| Prokaryotic type KH domain (KH-domain type II) | Ribosomal protein S3 C-terminal domain | 1 | 1 | |
| CCCH zinc finger | RING/U-box | 1 | 1 | |
| Metallo-dependent hydrolases | Aspartate/ornithine carbamoyltransferase | 1 | 1 | |
| FabD/lysophospholipase-like | Thiolase-like | 1 | 1 | |
| Trypsin-like serine proteases | PDZ domain-like | 1 | 1 | |
| UBA-like | XPC-binding domain | 1 | 1 | |
| Cysteine-rich domain | Protein kinase-like (PK-like) | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | PurM N-terminal domain-like | 1 | 1 | |
| DNA polymerase beta, N-terminal domain-like | Restriction endonuclease-like | 1 | 1 | |
| (Trans)glycosidases | Six-hairpin glycosidases | 1 | 1 | |
| N-terminal domain of adenylylcyclase associated protein, CAP | C-terminal domain of adenylylcyclase associated protein | 1 | 1 | |
| FMN-binding split barrel | UbiD C-terminal domain-like | 1 | 1 | |
| PH domain-like | (Phosphotyrosine protein) phosphatases II | 1 | 1 | |
| C2 domain (Calcium/lipid-binding domain, CaLB) | WW domain | 1 | 1 | |
| Ubiquitin-like | XPC-binding domain | 1 | 1 | |
| Nucleotidyltransferase | Poly A polymerase C-terminal region-like | 1 | 1 | |
| Phospholipase D/nuclease | Phospholipase D/nuclease | 1 | 1 | |
| TGS-like | Class II aaRS and biotin synthetases | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Galactose mutarotase-like | 1 | 1 | |
| BRCT domain | DNA polymerase III clamp loader subunits, C-terminal domain | 1 | 1 | |
| PurM N-terminal domain-like | Class I glutamine amidotransferase-like | 1 | 1 | |
| Zinc-binding domain of translation initiation factor 2 beta | ARM repeat | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | Alpha subunit of glutamate synthase, C-terminal domain | 1 | 1 | |
| Chromo domain-like | Chromo domain-like | 1 | 1 | |
| PreATP-grasp domain | PurM C-terminal domain-like | 1 | 1 | |
| Nucleic acid-binding proteins | BRCT domain | 1 | 1 | |
| EF-hand | C2 domain (Calcium/lipid-binding domain, CaLB) | 1 | 1 | |
| Elongation factor TFIIS domain 2 | Zinc beta-ribbon | 1 | 1 | |
| PreATP-grasp domain | Aspartate/ornithine carbamoyltransferase | 1 | 1 | |
| Amidase signature (AS) enzymes | Glutathione synthetase ATP-binding domain-like | 1 | 1 | |
| Nucleic acid-binding proteins | eIF-2-alpha, C-terminal domain | 1 | 1 | |
| SH3-domain | Ras GEF | 1 | 1 | |
| PLP-binding barrel | Alanine racemase C-terminal domain-like | 1 | 1 | |
| PreATP-grasp domain | PurM N-terminal domain-like | 1 | 1 | |
| Eukaryotic DNA topoisomerase I, N-terminal DNA-binding fragment | DNA breaking-rejoining enzymes | 1 | 1 | |
| SNARE-like | Domain of the SRP/SRP receptor G-proteins | 1 | 1 | |
| Pyruvate-ferredoxin oxidoreductase, PFOR, domain III | Riboflavin synthase domain-like | 1 | 1 | |
| Inhibitor of apoptosis (IAP) repeat | Inhibitor of apoptosis (IAP) repeat | 1 | 1 | |
| FAS1 domain | FAS1 domain | 1 | 1 | |
| Cytochrome c oxidase subunit II-like, transmembrane region | Cupredoxins | 1 | 1 | |
| Multidrug efflux transporter AcrB transmembrane domain | Multidrug efflux transporter AcrB transmembrane domain | 1 | 1 | |
| Trypsin-like serine proteases | Trypsin-like serine proteases | 1 | 1 | |
| PLC-like phosphodiesterases | C2 domain (Calcium/lipid-binding domain, CaLB) | 1 | 1 | |
| WD40 repeat-like | Peptidase/esterase 'gauge' domain | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | FAD/NAD(P)-binding domain | 1 | 1 | |
| Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 | Elongation factor TFIIS domain 2 | 1 | 1 | |
| Transmembrane di-heme cytochromes | a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) | 1 | 1 | |
| HMA, heavy metal-associated domain | HMA, heavy metal-associated domain | 1 | 1 | |
| Class I glutamine amidotransferase-like | Adenine nucleotide alpha hydrolases-like | 1 | 1 | |
| HR1 repeat | Cysteine-rich domain | 1 | 1 | |
| C2 domain (Calcium/lipid-binding domain, CaLB) | Cysteine-rich domain | 1 | 1 | |
| Class I glutamine amidotransferase-like | Class II aaRS and biotin synthetases | 1 | 1 | |
| EPT/RTPC-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Dehydroquinate synthase-like | Aminoacid dehydrogenase-like, N-terminal domain | 1 | 1 | |
| Concanavalin A-like lectins/glucanases | P-domain of calnexin/calreticulin | 1 | 1 | |
| Radical SAM enzymes | Acyl-CoA N-acyltransferases (Nat) | 1 | 1 | |
| 4Fe-4S ferredoxins | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Nucleotidylyl transferase | Alpha-L RNA-binding motif | 1 | 1 | |
| NagB/RpiA/CoA transferase-like | D-ribose-5-phosphate isomerase (RpiA), lid domain | 1 | 1 | |
| PEP carboxykinase N-terminal domain | PEP carboxykinase-like | 1 | 1 | |
| Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | CoA-dependent acyltransferases | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Type II DNA topoisomerase | 1 | 1 | |
| "Winged helix" DNA-binding domain | CheY-like | 1 | 1 | |
| WD40 repeat-like | Calcium-dependent phosphotriesterase | 1 | 1 | |
| RNA-binding domain, RBD | DPP6 N-terminal domain-like | 1 | 1 | |
| SNARE-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | FMN-linked oxidoreductases | 1 | 1 | |
| Class I glutamine amidotransferase-like | ADC synthase | 1 | 1 | |
| UBC-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| Cysteine proteinases | Ribonuclease H-like | 1 | 1 | |
| FYVE/PHD zinc finger | RING/U-box | 1 | 1 | |
| Alpha subunit of glutamate synthase, C-terminal domain | Nucleotide-binding domain | 1 | 1 | |
| Dehydroquinate synthase-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| PurM C-terminal domain-like | PurM C-terminal domain-like | 1 | 1 | |
| PH domain-like | BEACH domain | 1 | 1 | |
| Sulfite reductase, domains 1 and 3 | Sulfite reductase hemoprotein (SiRHP), domains 2 and 4 | 1 | 1 | |
| Hedgehog/intein (Hint) domain | C-terminal domain of alpha and beta subunits of F1 ATP synthase | 1 | 1 | |
| Periplasmic binding protein-like II | Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain | 1 | 1 | |
| FAD-linked reductases, C-terminal domain | 4Fe-4S ferredoxins | 1 | 1 | |
| "Winged helix" DNA-binding domain | Protein kinase-like (PK-like) | 1 | 1 | |
| ORC1-binding domain | ORC1-binding domain | 1 | 1 | |
| F-box domain | RCC1/BLIP-II | 1 | 1 | |
| Ras GEF | GTPase activation domain, GAP | 1 | 1 | |
| Thiamin diphosphate-binding fold (THDP-binding) | Flavoproteins | 1 | 1 | |
| PH domain-like | GTPase activation domain, GAP | 1 | 1 | |
| Amidase signature (AS) enzymes | PreATP-grasp domain | 1 | 1 | |
| PH domain-like | PLC-like phosphodiesterases | 1 | 1 | |
| VPS9 domain | UBA-like | 1 | 1 | |
| 2Fe-2S ferredoxin-like | alpha-helical ferredoxin | 1 | 1 | |
| Riboflavin synthase domain-like | Riboflavin synthase domain-like | 1 | 1 | |
| Obg GTP-binding protein N-terminal domain | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| BRCT domain | Lesion bypass DNA polymerase (Y-family), little finger domain | 1 | 1 | |
| FMN-linked oxidoreductases | Nucleotide-binding domain | 1 | 1 | |
| (Phosphotyrosine protein) phosphatases II | (Phosphotyrosine protein) phosphatases II | 1 | 1 | |
| PX domain | CAD & PB1 domains | 1 | 1 | |
| Carbamate kinase-like | ACT-like | 1 | 1 | |
| Glycoside hydrolase/deacetylase | Galactose mutarotase-like | 1 | 1 | |
| Acetyl-CoA synthetase-like | Acetyl-CoA synthetase-like | 1 | 1 | |
| Metallo-dependent hydrolases | Composite domain of metallo-dependent hydrolases | 1 | 1 | |
| cAMP-binding domain-like | FabD/lysophospholipase-like | 1 | 1 | |
| Homing endonucleases | C-terminal domain of alpha and beta subunits of F1 ATP synthase | 1 | 1 | |
| ACP-like | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| PUA domain-like | Nucleotidylyl transferase | 1 | 1 | |
| Carbamoyl phosphate synthetase, small subunit N-terminal domain | Glutathione synthetase ATP-binding domain-like | 1 | 1 | |
| EF-hand | Calponin-homology domain, CH-domain | 1 | 1 | |
| Methionyl-tRNA synthetase (MetRS), Zn-domain | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 1 | 1 | |
| S-adenosyl-L-methionine-dependent methyltransferases | Galactose oxidase, central domain | 1 | 1 | |
| IlvD/EDD N-terminal domain-like | LeuD/IlvD-like | 1 | 1 | |
