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 | |
|---|
| beta-beta-alpha zinc fingers | beta-beta-alpha zinc fingers | 60 | 29 |  |
| P-loop containing nucleoside triphosphate hydrolases | P-loop containing nucleoside triphosphate hydrolases | 56 | 28 | |
| Actin-like ATPase domain | Actin-like ATPase domain | 29 | 10 | |
| ABC transporter transmembrane region | P-loop containing nucleoside triphosphate hydrolases | 24 | 11 | |
| Calcium ATPase, transduction domain A | Calcium ATPase, transmembrane domain M | 23 | 9 | |
| HAD-like | Calcium ATPase, transmembrane domain M | 22 | 9 | |
| GroES-like | NAD(P)-binding Rossmann-fold domains | 19 | 1 | |
| Calcium ATPase, transduction domain A | HAD-like | 17 | 6 | |
| EGF/Laminin | EGF/Laminin | 17 | 17 | |
| ARM repeat | ARM repeat | 17 | 10 | |
| FAD/NAD(P)-binding domain | FAD-linked reductases, C-terminal domain | 16 | 5 | |
| NAD(P)-binding Rossmann-fold domains | 6-phosphogluconate dehydrogenase C-terminal domain-like | 16 | 8 | |
| Cna protein B-type domain | Hypothetical protein PA1324 | 15 | 13 | |
| RNA-binding domain, RBD | RNA-binding domain, RBD | 15 | 9 | |
| L domain-like | L domain-like | 15 | 9 | |
| PDZ domain-like | PDZ domain-like | 15 | 5 | |
| Cna protein B-type domain | Cna protein B-type domain | 14 | 12 | |
| TPR-like | TPR-like | 14 | 9 | |
| Thioredoxin-like | Thioredoxin-like | 13 | 9 | |
| Riboflavin synthase domain-like | Ferredoxin reductase-like, C-terminal NADP-linked domain | 13 | 10 | |
| Metal cation-transporting ATPase, ATP-binding domain N | HAD-like | 13 | 5 | |
| EGF/Laminin | Growth factor receptor domain | 13 | 13 | |
| F-box domain | RNI-like | 12 | 6 | |
| Thioredoxin-like | GST C-terminal domain-like | 12 | 2 | |
| Acyl-CoA dehydrogenase NM domain-like | Acyl-CoA dehydrogenase C-terminal domain-like | 11 | 4 | |
| Metal cation-transporting ATPase, ATP-binding domain N | Calcium ATPase, transmembrane domain M | 11 | 4 | |
| Nucleotidylyl transferase | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 11 | 6 | |
| Cyclin-like | Cyclin-like | 11 | 7 | |
| NAD(P)-binding Rossmann-fold domains | Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 11 | 4 | |
| P-loop containing nucleoside triphosphate hydrolases | Translation proteins | 11 | 7 | |
| Calcium ATPase, transduction domain A | Metal cation-transporting ATPase, ATP-binding domain N | 10 | 3 | |
| Thiolase-like | Thiolase-like | 10 | 3 | |
| Actin-like ATPase domain | Heat shock protein 70kD (HSP70), peptide-binding domain | 10 | 4 | |
| GroEL-intermediate domain like | GroEL apical domain-like | 9 | 1 | |
| Glucocorticoid receptor-like (DNA-binding domain) | Glucocorticoid receptor-like (DNA-binding domain) | 9 | 6 | |
| GroEL equatorial domain-like | GroEL apical domain-like | 9 | 1 | |
| Carboxypeptidase regulatory domain-like | Cna protein B-type domain | 9 | 9 | |
| GroEL equatorial domain-like | GroEL-intermediate domain like | 9 | 1 | |
| Aminoacid dehydrogenase-like, N-terminal domain | NAD(P)-binding Rossmann-fold domains | 9 | 5 | |
| PreATP-grasp domain | Glutathione synthetase ATP-binding domain-like | 9 | 8 | |
| HIT/MYND zinc finger-like | beta-beta-alpha zinc fingers | 9 | 7 | |
| BRCT domain | BRCT domain | 8 | 6 | |
| ValRS/IleRS/LeuRS editing domain | Nucleotidylyl transferase | 8 | 5 | |
| FYVE/PHD zinc finger | FYVE/PHD zinc finger | 8 | 7 | |
| Hypothetical protein PA1324 | Hypothetical protein PA1324 | 8 | 7 | |
| Ankyrin repeat | Protein kinase-like (PK-like) | 8 | 3 | |
| Hypothetical protein PA1324 | Carboxypeptidase regulatory domain-like | 8 | 8 | |
| Thiamin diphosphate-binding fold (THDP-binding) | Thiamin diphosphate-binding fold (THDP-binding) | 8 | 5 | |
| ABC transporter transmembrane region | ABC transporter transmembrane region | 8 | 5 | |
| Ypt/Rab-GAP domain of gyp1p | Ypt/Rab-GAP domain of gyp1p | 8 | 5 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | Ribosomal protein S5 domain 2-like | 8 | 7 | |
| Metallo-dependent hydrolases | Composite domain of metallo-dependent hydrolases | 7 | 5 | |
| Ribonuclease H-like | DNA/RNA polymerases | 7 | 2 | |
| (Trans)glycosidases | Glycosyl hydrolase domain | 7 | 5 | |
| Actin-like ATPase domain | Heat shock protein 70kD (HSP70), C-terminal subdomain | 7 | 3 | |
| Heat shock protein 70kD (HSP70), peptide-binding domain | Heat shock protein 70kD (HSP70), C-terminal subdomain | 7 | 3 | |
| LuxS/MPP-like metallohydrolase | LuxS/MPP-like metallohydrolase | 7 | 5 | |
| Protein kinase-like (PK-like) | KA1-like | 7 | 2 | |
| Formate/glycerate dehydrogenase catalytic domain-like | NAD(P)-binding Rossmann-fold domains | 7 | 4 | |
| Metalloproteases ("zincins"), catalytic domain | EGF/Laminin | 7 | 7 | |
| C2 domain (Calcium/lipid-binding domain, CaLB) | C2 domain (Calcium/lipid-binding domain, CaLB) | 7 | 4 | |
| E set domains | E set domains | 7 | 5 | |
| Ribosomal protein S5 domain 2-like | GHMP Kinase, C-terminal domain | 7 | 3 | |
| F-box domain | Ankyrin repeat | 7 | 5 | |
| ValRS/IleRS/LeuRS editing domain | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 6 | 3 | |
| Metalloproteases ("zincins"), catalytic domain | Growth factor receptor domain | 6 | 6 | |
| Acetyl-CoA synthetase-like | ACP-like | 6 | 6 | |
| Nucleotidyltransferase | PAP/OAS1 substrate-binding domain | 6 | 6 | |
| Homeodomain-like | Homeodomain-like | 6 | 5 | |
| Glutathione synthetase ATP-binding domain-like | Rudiment single hybrid motif | 6 | 6 | |
| TSP-1 type 1 repeat | TSP-1 type 1 repeat | 6 | 6 | |
| Nucleic acid-binding proteins | P-loop containing nucleoside triphosphate hydrolases | 6 | 4 | |
| Starch-binding domain-like | Cna protein B-type domain | 6 | 6 | |
| FAD/NAD(P)-binding domain | FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 6 | 4 | |
| PH domain-like | Protein kinase-like (PK-like) | 6 | 5 | |
| FAS1 domain | FAS1 domain | 6 | 4 | |
| EF-hand | Protein kinase-like (PK-like) | 5 | 4 | |
| Translation proteins | EF-G C-terminal domain-like | 5 | 4 | |
| RNA-binding domain, RBD | Retrovirus zinc finger-like domains | 5 | 2 | |
| SH3-domain | SH3-domain | 5 | 5 | |
| Thioesterase/thiol ester dehydrase-isomerase | Thioesterase/thiol ester dehydrase-isomerase | 5 | 3 | |
| Ankyrin repeat | Ankyrin repeat | 5 | 5 | |
| Aconitase iron-sulfur domain | LeuD/IlvD-like | 5 | 3 | |
| WW domain | WW domain | 5 | 4 | |
| Mannose 6-phosphate receptor domain | Mannose 6-phosphate receptor domain | 5 | 3 | |
| Cullin homology domain | "Winged helix" DNA-binding domain | 5 | 3 | |
| C2 domain (Calcium/lipid-binding domain, CaLB) | vWA-like | 5 | 2 | |
| alpha/beta-Hydrolases | alpha/beta-Hydrolases | 5 | 3 | |
| EF-G C-terminal domain-like | EF-G C-terminal domain-like | 5 | 4 | |
| Leech antihemostatic proteins | Leech antihemostatic proteins | 5 | 5 | |
| Chaperone J-domain | DnaJ/Hsp40 cysteine-rich domain | 5 | 4 | |
| Nucleic acid-binding proteins | Class II aaRS and biotin synthetases | 5 | 2 | |
| HSP40/DnaJ peptide-binding domain | HSP40/DnaJ peptide-binding domain | 5 | 4 | |
| DnaJ/Hsp40 cysteine-rich domain | HSP40/DnaJ peptide-binding domain | 5 | 4 | |
| Cupredoxins | Cupredoxins | 5 | 3 | |
| "Winged helix" DNA-binding domain | "Winged helix" DNA-binding domain | 5 | 4 | |
| Nucleic acid-binding proteins | Nucleic acid-binding proteins | 5 | 5 | |
| Phospholipase D/nuclease | Phospholipase D/nuclease | 5 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | post-AAA+ oligomerization domain-like | 5 | 1 | |
| Single hybrid motif | CoA-dependent acyltransferases | 5 | 3 | |
| Thiamin diphosphate-binding fold (THDP-binding) | TK C-terminal domain-like | 5 | 4 | |
| Calponin-homology domain, CH-domain | Calponin-homology domain, CH-domain | 5 | 2 | |
| (Trans)glycosidases | E set domains | 5 | 4 | |
| Chaperone J-domain | HSP40/DnaJ peptide-binding domain | 5 | 4 | |
| Pectin lyase-like | Cna protein B-type domain | 5 | 4 | |
| P-loop containing nucleoside triphosphate hydrolases | TGS-like | 5 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Smc hinge domain | 5 | 4 | |
| Metallo-hydrolase/oxidoreductase | SCP-like | 5 | 3 | |
| Pectin lyase-like | Hypothetical protein PA1324 | 5 | 4 | |
| PH domain-like | EF-hand | 5 | 4 | |
| Cysteine-rich domain | Cysteine-rich domain | 5 | 5 | |
| P-loop containing nucleoside triphosphate hydrolases | "Winged helix" DNA-binding domain | 5 | 5 | |
| Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | CoA-dependent acyltransferases | 4 | 2 | |
| Ran binding protein zinc finger-like | Ran binding protein zinc finger-like | 4 | 4 | |
| Hypothetical protein PA1324 | Starch-binding domain-like | 4 | 4 | |
| HIT/MYND zinc finger-like | HIT/MYND zinc finger-like | 4 | 4 | |
| UDP-Glycosyltransferase/glycogen phosphorylase | Nucleotide-diphospho-sugar transferases | 4 | 2 | |
| Voltage-gated potassium channels | EF-hand | 4 | 3 | |
| Single hybrid motif | Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | 4 | 2 | |
| Ricin B-like lectins | TSP-1 type 1 repeat | 4 | 4 | |
| P-loop containing nucleoside triphosphate hydrolases | EF-G C-terminal domain-like | 4 | 3 | |
| Ribosomal protein S5 domain 2-like | Ribonuclease PH domain 2-like | 4 | 2 | |
| WD40 repeat-like | WD40 repeat-like | 4 | 3 | |
| Cullin repeat-like | Cullin homology domain | 4 | 2 | |
| Glutathione synthetase ATP-binding domain-like | Glutathione synthetase ATP-binding domain-like | 4 | 4 | |
| Leukotriene A4 hydrolase N-terminal domain | Metalloproteases ("zincins"), catalytic domain | 4 | 2 | |
| beta-sandwich domain of Sec23/24 | vWA-like | 4 | 4 | |
| Subtilisin-like | Galactose-binding domain-like | 4 | 2 | |
| PreATP-grasp domain | Single hybrid motif | 4 | 4 | |
| Clc chloride channel | CBS-domain pair | 4 | 3 | |
| beta-sandwich domain of Sec23/24 | Helical domain of Sec23/24 | 4 | 4 | |
| Class II aaRS and biotin synthetases | Class II aaRS ABD-related | 4 | 3 | |
| vWA-like | Helical domain of Sec23/24 | 4 | 4 | |
| Glutathione synthetase ATP-binding domain-like | Single hybrid motif | 4 | 4 | |
| PreATP-grasp domain | Rudiment single hybrid motif | 4 | 4 | |
| Heme-dependent peroxidases | Heme-dependent peroxidases | 4 | 1 | |
| RING/U-box | Cysteine proteinases | 4 | 3 | |
| Trimeric LpxA-like enzymes | Trimeric LpxA-like enzymes | 4 | 4 | |
| RCC1/BLIP-II | RCC1/BLIP-II | 4 | 1 | |
| Ankyrin repeat | RNI-like | 4 | 2 | |
| Ubiquitin-like | Ubiquitin-like | 4 | 4 | |
| Bromodomain | Bromodomain | 4 | 3 | |
| FAD/NAD(P)-binding domain | FAD/NAD(P)-binding domain | 4 | 4 | |
| PIN domain-like | 5' to 3' exonuclease, C-terminal subdomain | 4 | 3 | |
| P-loop containing nucleoside triphosphate hydrolases | Phosphoglycerate mutase-like | 4 | 2 | |
| beta-N-acetylhexosaminidase-like domain | (Trans)glycosidases | 4 | 3 | |
| HLH, helix-loop-helix DNA-binding domain | PYP-like sensor domain (PAS domain) | 4 | 1 | |
| "Winged helix" DNA-binding domain | E2F-DP heterodimerization region | 4 | 2 | |
| EF-hand | PLC-like phosphodiesterases | 4 | 4 | |
| Translation proteins | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 4 | 2 | |
| Flavoproteins | Riboflavin synthase domain-like | 4 | 4 | |
| Pectin lyase-like | Pectin lyase-like | 4 | 4 | |
| Multidrug resistance efflux transporter EmrE | Multidrug resistance efflux transporter EmrE | 4 | 3 | |
| MFS general substrate transporter | MFS general substrate transporter | 4 | 3 | |
| Ankyrin repeat | Glucocorticoid receptor-like (DNA-binding domain) | 4 | 4 | |
| EF-G C-terminal domain-like | Ribosomal protein S5 domain 2-like | 4 | 3 | |
| CRAL/TRIO N-terminal domain | CRAL/TRIO domain | 4 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 4 | 2 | |
| Carboxypeptidase regulatory domain-like | Carboxypeptidase regulatory domain-like | 3 | 3 | |
| beta-sandwich domain of Sec23/24 | Zn-finger domain of Sec23/24 | 3 | 3 | |
| Class II aaRS and biotin synthetases | Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | 3 | 3 | |
| Ribonuclease H-like | Ribonuclease H-like | 3 | 2 | |
| Protein kinase-like (PK-like) | Protein kinase-like (PK-like) | 3 | 3 | |
| EGF/Laminin | Protein kinase-like (PK-like) | 3 | 3 | |
| PLP-dependent transferases | PLP-dependent transferases | 3 | 2 | |
| Ribosomal protein S5 domain 2-like | HSP90 C-terminal domain | 3 | 3 | |
| TPR-like | Ankyrin repeat | 3 | 1 | |
| Translation proteins SH3-like domain | Nucleic acid-binding proteins | 3 | 3 | |
| 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 | 3 | |
| Translation proteins | ThrRS/AlaRS common domain | 3 | 3 | |
| CAD & PB1 domains | RING/U-box | 3 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | C-terminal domain of alpha and beta subunits of F1 ATP synthase | 3 | 3 | |
| Creatinase/prolidase N-terminal domain | Creatinase/aminopeptidase | 3 | 3 | |
| Metalloproteases ("zincins"), catalytic domain | Blood coagulation inhibitor (disintegrin) | 3 | 2 | |
| PDZ domain-like | BAR/IMD domain-like | 3 | 1 | |
| FKBP-like | TPR-like | 3 | 3 | |
| Helical domain of Sec23/24 | C-terminal, gelsolin-like domain of Sec23/24 | 3 | 3 | |
| CBS-domain pair | CBS-domain pair | 3 | 1 | |
| BAR/IMD domain-like | SH3-domain | 3 | 2 | |
| beta-sandwich domain of Sec23/24 | C-terminal, gelsolin-like domain of Sec23/24 | 3 | 3 | |
| Retrovirus zinc finger-like domains | Retrovirus zinc finger-like domains | 3 | 3 | |
| Flavoproteins | Ferredoxin reductase-like, C-terminal NADP-linked domain | 3 | 3 | |
| FAD-binding/transporter-associated domain-like | FAD-linked oxidases, C-terminal domain | 3 | 2 | |
| Concanavalin A-like lectins/glucanases | RING/U-box | 3 | 2 | |
| Nicotinate/Quinolinate PRTase N-terminal domain-like | Nicotinate/Quinolinate PRTase C-terminal domain-like | 3 | 2 | |
| Ribonuclease H-like | HRDC-like | 3 | 2 | |
| BAR/IMD domain-like | ArfGap/RecO-like zinc finger | 3 | 2 | |
| Translation proteins | Ribosomal protein S5 domain 2-like | 3 | 2 | |
| Metallo-dependent phosphatases | 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain | 3 | 2 | |
| t-snare proteins | SNARE fusion complex | 3 | 2 | |
| Pectin lyase-like | Protein kinase-like (PK-like) | 3 | 2 | |
| Zn-dependent exopeptidases | Bacterial exopeptidase dimerisation domain | 3 | 2 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | HSP90 C-terminal domain | 3 | 3 | |
| TPR-like | Chaperone J-domain | 3 | 3 | |
| FF domain | FF domain | 3 | 2 | |
| WW domain | FF domain | 3 | 2 | |
| BEACH domain | WD40 repeat-like | 3 | 2 | |
| Cullin repeat-like | "Winged helix" DNA-binding domain | 3 | 1 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | Nucleic acid-binding proteins | 3 | 3 | |
| Nucleotidylyl transferase | Nucleotidylyl transferase | 3 | 2 | |
| PH domain-like | PH domain-like | 3 | 2 | |
| L domain-like | PP2C-like | 3 | 2 | |
| EF-hand | C2 domain (Calcium/lipid-binding domain, CaLB) | 3 | 3 | |
| C2 domain (Calcium/lipid-binding domain, CaLB) | GTPase activation domain, GAP | 3 | 3 | |
| Clavaminate synthase-like | FYVE/PHD zinc finger | 3 | 1 | |
| DBL homology domain (DH-domain) | PH domain-like | 3 | 3 | |
| DNA repair protein MutS, domain I | DNA repair protein MutS, domain II | 3 | 3 | |
| P-loop containing nucleoside triphosphate hydrolases | FtsH protease domain-like | 3 | 3 | |
| Thioredoxin-like | Ubiquitin-like | 3 | 3 | |
| Nucleic acid-binding proteins | BAR/IMD domain-like | 3 | 1 | |
| Regulator of G-protein signaling, RGS | PYP-like sensor domain (PAS domain) | 3 | 2 | |
| ARM repeat | Clathrin adaptor appendage domain | 3 | 3 | |
| E set domains | Glycosyl hydrolase domain | 3 | 2 | |
| "Winged helix" DNA-binding domain | RNA-binding domain, RBD | 3 | 3 | |
| F1F0 ATP synthase subunit C | F1F0 ATP synthase subunit C | 3 | 2 | |
| CoA-dependent acyltransferases | CoA-dependent acyltransferases | 3 | 2 | |
| vWA-like | C-terminal, gelsolin-like domain of Sec23/24 | 3 | 3 | |
| 6-phosphogluconate dehydrogenase C-terminal domain-like | 6-phosphogluconate dehydrogenase C-terminal domain-like | 3 | 3 | |
| PH domain-like | BEACH domain | 3 | 2 | |
| tRNA-binding arm | Class II aaRS and biotin synthetases | 3 | 2 | |
| Rudiment single hybrid motif | Single hybrid motif | 3 | 3 | |
| SET domain | FYVE/PHD zinc finger | 3 | 3 | |
| EF-hand | EF-hand | 3 | 3 | |
| Actin depolymerizing proteins | Actin depolymerizing proteins | 3 | 2 | |
| Kazal-type serine protease inhibitors | Kazal-type serine protease inhibitors | 3 | 3 | |
| RING/U-box | WD40 repeat-like | 3 | 2 | |
| Zn-finger domain of Sec23/24 | vWA-like | 3 | 3 | |
| Voltage-gated potassium channels | E set domains | 3 | 1 | |
| (Trans)glycosidases | alpha-D-mannose-specific plant lectins | 3 | 3 | |
| P-loop containing nucleoside triphosphate hydrolases | Bromodomain | 3 | 3 | |
| P-loop containing nucleoside triphosphate hydrolases | Ribosomal protein S5 domain 2-like | 3 | 2 | |
| Zn-finger domain of Sec23/24 | Helical domain of Sec23/24 | 3 | 3 | |
| Phosphoglucomutase, first 3 domains | Phosphoglucomutase, first 3 domains | 3 | 2 | |
| CCCH zinc finger | RNA-binding domain, RBD | 3 | 2 | |
| (Trans)glycosidases | EGF/Laminin | 3 | 3 | |
| WD40 repeat-like | Quinoprotein alcohol dehydrogenase-like | 3 | 3 | |
| N-terminal domain of alpha and beta subunits of F1 ATP synthase | P-loop containing nucleoside triphosphate hydrolases | 3 | 3 | |
| SNARE-like | Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor | 3 | 2 | |
| SNARE-like | SNARE fusion complex | 3 | 2 | |
| DNA repair protein MutS, domain III | P-loop containing nucleoside triphosphate hydrolases | 3 | 2 | |
| Transducin (alpha subunit), insertion domain | P-loop containing nucleoside triphosphate hydrolases | 3 | 2 | |
| Clathrin adaptor appendage domain | Subdomain of clathrin and coatomer appendage domain | 3 | 3 | |
| (Trans)glycosidases | TSP-1 type 1 repeat | 3 | 3 | |
| ClpP/crotonase | ClpP/crotonase | 3 | 2 | |
| Nucleic acid-binding proteins | PDZ domain-like | 3 | 1 | |
| Zn-finger domain of Sec23/24 | C-terminal, gelsolin-like domain of Sec23/24 | 3 | 3 | |
| TPR-like | RNI-like | 3 | 1 | |
| Tubulin nucleotide-binding domain-like | Tubulin C-terminal domain-like | 3 | 2 | |
| ACT-like | ACT-like | 3 | 3 | |
| Creatinase/aminopeptidase | "Winged helix" DNA-binding domain | 3 | 2 | |
| PurM N-terminal domain-like | PurM C-terminal domain-like | 3 | 3 | |
| Phosphoglucomutase, first 3 domains | Phosphoglucomutase, C-terminal domain | 3 | 2 | |
| Metallo-hydrolase/oxidoreductase | Metallo-hydrolase/oxidoreductase | 3 | 3 | |
| Homeodomain-like | Glucocorticoid receptor-like (DNA-binding domain) | 3 | 2 | |
| RING/U-box | SH2 domain | 3 | 3 | |
| PreATP-grasp domain | PreATP-grasp domain | 2 | 2 | |
| Galactose mutarotase-like | (Trans)glycosidases | 2 | 2 | |
| TRAF domain-like | TRAF domain-like | 2 | 2 | |
| PH domain-like | SH3-domain | 2 | 2 | |
| N-terminal, heterodimerisation domain of RBP7 (RpoE) | Nucleic acid-binding proteins | 2 | 1 | |
| cAMP-binding domain-like | cAMP-binding domain-like | 2 | 2 | |
| Ankyrin repeat | SAM/Pointed domain | 2 | 2 | |
| Kelch motif | Kelch motif | 2 | 1 | |
| ARM repeat | P-loop containing nucleoside triphosphate hydrolases | 2 | 2 | |
| Phosphoenolpyruvate/pyruvate domain | PK C-terminal domain-like | 2 | 2 | |
| beta-beta-alpha zinc fingers | Homeodomain-like | 2 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Aminoacid dehydrogenase-like, N-terminal domain | 2 | 2 | |
| Regulator of G-protein signaling, RGS | PX domain | 2 | 2 | |
| Thiamin diphosphate-binding fold (THDP-binding) | DHS-like NAD/FAD-binding domain | 2 | 1 | |
| CoA-dependent acyltransferases | ACP-like | 2 | 2 | |
| Chromo domain-like | Chromo domain-like | 2 | 1 | |
| beta-N-acetylhexosaminidase-like domain | E set domains | 2 | 2 | |
| NAD(P)-binding Rossmann-fold domains | ACT-like | 2 | 2 | |
| DNA repair protein MutS, domain II | DNA repair protein MutS, domain III | 2 | 2 | |
| Carbamoyl phosphate synthetase, small subunit N-terminal domain | Class I glutamine amidotransferase-like | 2 | 2 | |
| WGR domain-like | ADP-ribosylation | 2 | 2 | |
| ACP-like | NAD(P)-binding Rossmann-fold domains | 2 | 2 | |
| Ankyrin repeat | Ribonuclease H-like | 2 | 2 | |
| EGF/Laminin | Lysozyme-like | 2 | 2 | |
| Pectin lyase-like | Starch-binding domain-like | 2 | 2 | |
| Glutamine synthetase, N-terminal domain | Glutamine synthetase/guanido kinase | 2 | 1 | |
| Cyclophilin-like | RNA-binding domain, RBD | 2 | 2 | |
| Cation efflux protein transmembrane domain-like | Cation efflux protein cytoplasmic domain-like | 2 | 2 | |
| Class I glutamine amidotransferase-like | Carbamoyl phosphate synthetase, large subunit connection domain | 2 | 2 | |
| PUA domain-like | Clavaminate synthase-like | 2 | 1 | |
| Formate/glycerate dehydrogenase catalytic domain-like | ACT-like | 2 | 2 | |
| Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | ThrRS/AlaRS common domain | 2 | 2 | |
| beta-beta-alpha zinc fingers | Glucocorticoid receptor-like (DNA-binding domain) | 2 | 1 | |
| WW domain | Hect, E3 ligase catalytic domain | 2 | 2 | |
| L domain-like | Nucleotide cyclase | 2 | 1 | |
| C2 domain (Calcium/lipid-binding domain, CaLB) | Hect, E3 ligase catalytic domain | 2 | 2 | |
| Glutathione synthetase ATP-binding domain-like | Carbamoyl phosphate synthetase, large subunit connection domain | 2 | 2 | |
| Glycoside hydrolase/deacetylase | Growth factor receptor domain | 2 | 2 | |
| Class I glutamine amidotransferase-like | Glutathione synthetase ATP-binding domain-like | 2 | 2 | |
| NAD(P)-binding Rossmann-fold domains | EF-hand | 2 | 2 | |
| WGR domain-like | Domain of poly(ADP-ribose) polymerase | 2 | 2 | |
| Cytochrome b5-like heme/steroid binding domain | FAD/NAD(P)-binding domain | 2 | 2 | |
| Chromo domain-like | P-loop containing nucleoside triphosphate hydrolases | 2 | 1 | |
| Chromo domain-like | Arginase/deacetylase | 2 | 1 | |
| L domain-like | PH domain-like | 2 | 1 | |
| F-box domain | WD40 repeat-like | 2 | 2 | |
| Trypsin-like serine proteases | PDZ domain-like | 2 | 2 | |
| Tropomyosin | Tropomyosin | 2 | 2 | |
| Translational machinery components | L30e-like | 2 | 2 | |
| Cysteine proteinases | DUSP-like | 2 | 2 | |
| RNA-binding domain, RBD | P-loop containing nucleoside triphosphate hydrolases | 2 | 2 | |
| Nucleotide-diphospho-sugar transferases | Nucleotide-diphospho-sugar transferases | 2 | 2 | |
| TPR-like | SMR domain-like | 2 | 2 | |
| Peptidase/esterase 'gauge' domain | alpha/beta-Hydrolases | 2 | 2 | |
| Class II aaRS and biotin synthetases | ThrRS/AlaRS common domain | 2 | 2 | |
| HAD-like | P-loop containing nucleoside triphosphate hydrolases | 2 | 1 | |
| NAD(P)-binding Rossmann-fold domains | LDH C-terminal domain-like | 2 | 1 | |
| ENTH/VHS domain | GAT-like domain | 2 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | DNA mismatch repair protein MutL | 2 | 1 | |
| Nitrite/Sulfite reductase N-terminal domain-like | Nitrite and sulphite reductase 4Fe-4S domain-like | 2 | 2 | |
| Starch-binding domain-like | Carboxypeptidase regulatory domain-like | 2 | 2 | |
| PA domain | RING/U-box | 2 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Sec63 N-terminal domain-like | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | PH domain-like | 2 | 2 | |
| HMG-box | HMG-box | 2 | 2 | |
| RNA-binding domain, RBD | PWI domain | 2 | 1 | |
| EF-hand | SH2 domain | 2 | 2 | |
| Leukotriene A4 hydrolase N-terminal domain | ARM repeat | 2 | 1 | |
| (Trans)glycosidases | Beta-D-glucan exohydrolase, C-terminal domain | 2 | 1 | |
| RNA-binding domain, RBD | PABC (PABP) domain | 2 | 1 | |
| Class II aaRS and biotin synthetases | Translation proteins | 2 | 2 | |
| Cysteine-rich domain | GTPase activation domain, GAP | 2 | 2 | |
| Concanavalin A-like lectins/glucanases | P-domain of calnexin/calreticulin | 2 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Phosphohistidine domain | 2 | 1 | |
| Metalloproteases ("zincins"), catalytic domain | ARM repeat | 2 | 1 | |
| Mitochondrial carrier | Mitochondrial carrier | 2 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | PLP-dependent transferases | 2 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | NAD(P)-binding Rossmann-fold domains | 2 | 2 | |
| FYVE/PHD zinc finger | WD40 repeat-like | 2 | 2 | |
| Carbohydrate-binding domain | beta-N-acetylhexosaminidase-like domain | 2 | 2 | |
| NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | 2 | 2 | |
| S15/NS1 RNA-binding domain | Nucleotidylyl transferase | 2 | 2 | |
| Voltage-gated potassium channels | Voltage-gated potassium channels | 2 | 1 | |
| Carbohydrate-binding domain | (Trans)glycosidases | 2 | 2 | |
| Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | Translation proteins | 2 | 2 | |
| Concanavalin A-like lectins/glucanases | Concanavalin A-like lectins/glucanases | 2 | 2 | |
| Sec63 N-terminal domain-like | Sec63 N-terminal domain-like | 2 | 2 | |
| Chromo domain-like | Methyl-accepting chemotaxis protein (MCP) signaling domain | 2 | 2 | |
| PriA/YqbF domain | GINS helical bundle-like | 2 | 2 | |
| Ubiquitin-like | AN1-like Zinc finger | 2 | 2 | |
| EGF/Laminin | alpha-D-mannose-specific plant lectins | 2 | 2 | |
| SET domain | RuBisCo LSMT C-terminal, substrate-binding domain | 2 | 2 | |
| Cysteine proteinases | Concanavalin A-like lectins/glucanases | 2 | 1 | |
| CCCH zinc finger | RING/U-box | 2 | 2 | |
| Zinc beta-ribbon | Cyclin-like | 2 | 2 | |
| Eukaryotic RPB5 N-terminal domain | RPB5-like RNA polymerase subunit | 2 | 1 | |
| MurD-like peptide ligases, catalytic domain | MurD-like peptide ligases, peptide-binding domain | 2 | 2 | |
| SH2 domain | SH3-domain | 2 | 2 | |
| Protein kinase-like (PK-like) | RING/U-box | 2 | 2 | |
| Bromodomain | RING/U-box | 2 | 2 | |
| PX domain | Protein kinase-like (PK-like) | 2 | 1 | |
| Coiled-coil domain of nucleotide exchange factor GrpE | Head domain of nucleotide exchange factor GrpE | 2 | 2 | |
| PAH2 domain | PAH2 domain | 2 | 2 | |
| EF-hand | SH3-domain | 2 | 2 | |
| Nucleotidylyl transferase | An anticodon-binding domain of class I aminoacyl-tRNA synthetases | 2 | 1 | |
| Starch-binding domain-like | Starch-binding domain-like | 2 | 2 | |
| (Trans)glycosidases | (Trans)glycosidases | 2 | 2 | |
| PH domain-like | Ankyrin repeat | 2 | 2 | |
| Periplasmic binding protein-like II | Periplasmic binding protein-like II | 2 | 1 | |
| PH domain-like | (Phosphotyrosine protein) phosphatases II | 2 | 2 | |
| Initiation factor IF2/eIF5b, domain 3 | Translation proteins | 2 | 1 | |
| RBP11-like subunits of RNA polymerase | Insert subdomain of RNA polymerase alpha subunit | 2 | 2 | |
| TSP-1 type 1 repeat | alpha-D-mannose-specific plant lectins | 2 | 2 | |
| L domain-like | RING/U-box | 2 | 1 | |
| E set domains | Cysteine proteinases | 2 | 1 | |
| F-box domain | L domain-like | 2 | 1 | |
| Ubiquitin-like | UBA-like | 2 | 2 | |
| Sec63 N-terminal domain-like | E set domains | 2 | 2 | |
| Carbamoyl phosphate synthetase, small subunit N-terminal domain | PreATP-grasp domain | 2 | 2 | |
| Trimeric LpxA-like enzymes | Protein kinase-like (PK-like) | 2 | 2 | |
| alpha-catenin/vinculin-like | alpha-catenin/vinculin-like | 2 | 2 | |
| Carbohydrate-binding domain | E set domains | 2 | 2 | |
| Bromodomain | TAZ domain | 2 | 2 | |
| TSP-1 type 1 repeat | EGF/Laminin | 2 | 2 | |
| Class I glutamine amidotransferase-like | PreATP-grasp domain | 2 | 2 | |
| GAF domain-like | Regulator of G-protein signaling, RGS | 2 | 2 | |
| Ribosomal L27 protein-like | Nucleic acid-binding proteins | 2 | 2 | |
| HMA, heavy metal-associated domain | Calcium ATPase, transmembrane domain M | 2 | 2 | |
| DNA clamp | DNA clamp | 2 | 1 | |
| Voltage-gated potassium channels | cAMP-binding domain-like | 2 | 2 | |
| PLP-binding barrel | Alanine racemase C-terminal domain-like | 2 | 2 | |
| Protein kinase-like (PK-like) | beta-beta-alpha zinc fingers | 2 | 1 | |
| Ribosomal protein S5 domain 2-like | DNA mismatch repair protein MutL | 2 | 1 | |
| RNA-binding domain, RBD | S-adenosyl-L-methionine-dependent methyltransferases | 2 | 1 | |
| NagB/RpiA/CoA transferase-like | NagB/RpiA/CoA transferase-like | 2 | 2 | |
| UBA-like | UBA-like | 2 | 2 | |
| Carbamoyl phosphate synthetase, small subunit N-terminal domain | Glutathione synthetase ATP-binding domain-like | 2 | 2 | |
| Cryptochrome/photolyase, N-terminal domain | Cryptochrome/photolyase FAD-binding domain | 2 | 2 | |
| Obg GTP-binding protein N-terminal domain | P-loop containing nucleoside triphosphate hydrolases | 2 | 2 | |
| NAD-binding domain of HMG-CoA reductase | Substrate-binding domain of HMG-CoA reductase | 2 | 1 | |
| DNA repair protein MutS, domain I | DNA repair protein MutS, domain III | 2 | 2 | |
| FKBP-like | Cyclophilin-like | 2 | 2 | |
| FabD/lysophospholipase-like | Probable ACP-binding domain of malonyl-CoA ACP transacylase | 2 | 2 | |
| Ribosomal L11/L12e N-terminal domain | Ribosomal protein L11, C-terminal domain | 2 | 1 | |
| ArfGap/RecO-like zinc finger | Ankyrin repeat | 2 | 2 | |
| RING/U-box | TAZ domain | 2 | 2 | |
| "Winged helix" DNA-binding domain | E set domains | 2 | 2 | |
| Translation initiation factor 2 beta, aIF2beta, N-terminal domain | Zinc-binding domain of translation initiation factor 2 beta | 2 | 2 | |
| Acyl-CoA N-acyltransferases (Nat) | Acyl-CoA N-acyltransferases (Nat) | 2 | 1 | |
| Zn-dependent exopeptidases | Zn-dependent exopeptidases | 2 | 2 | |
| PP2C-like | Nucleotide cyclase | 2 | 1 | |
| Ribosomal protein L6 | Ribosomal protein L6 | 2 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Initiation factor IF2/eIF5b, domain 3 | 2 | 1 | |
| RING/U-box | RING/U-box | 2 | 2 | |
| ARM repeat | Subdomain of clathrin and coatomer appendage domain | 2 | 2 | |
| PH domain-like | PLC-like phosphodiesterases | 2 | 2 | |
| Anthrax protective antigen | EGF/Laminin | 2 | 1 | |
| Eukaryotic type KH-domain (KH-domain type I) | Eukaryotic type KH-domain (KH-domain type I) | 2 | 2 | |
| HIT/MYND zinc finger-like | FYVE/PHD zinc finger | 2 | 2 | |
| alpha-helical ferredoxin | Nucleotide-binding domain | 2 | 2 | |
| "Winged helix" DNA-binding domain | Sec63 N-terminal domain-like | 2 | 2 | |
| HMA, heavy metal-associated domain | Calcium ATPase, transduction domain A | 2 | 2 | |
| DUSP-like | DUSP-like | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | vWA-like | 2 | 2 | |
| 6-phosphogluconate dehydrogenase C-terminal domain-like | UDP-glucose/GDP-mannose dehydrogenase C-terminal domain | 2 | 1 | |
| CoA-dependent acyltransferases | Acetyl-CoA synthetase-like | 2 | 2 | |
| Domain of poly(ADP-ribose) polymerase | ADP-ribosylation | 2 | 2 | |
| FAD/NAD(P)-binding domain | Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | 2 | 2 | |
| DNA/RNA polymerases | DNA/RNA polymerases | 2 | 2 | |
| Cysteine-rich domain | Protein kinase-like (PK-like) | 2 | 2 | |
| p53-like transcription factors | Ankyrin repeat | 2 | 2 | |
| Nucleotidyltransferase | Poly A polymerase C-terminal region-like | 2 | 2 | |
| cAMP-binding domain-like | NAD(P)-binding Rossmann-fold domains | 2 | 2 | |
| Chaperone J-domain | BRCT domain | 2 | 1 | |
| HMA, heavy metal-associated domain | HMA, heavy metal-associated domain | 2 | 2 | |
| PreATP-grasp domain | Carbamoyl phosphate synthetase, large subunit connection domain | 2 | 2 | |
| Acetyl-CoA synthetase-like | NAD(P)-binding Rossmann-fold domains | 2 | 2 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | Adenine nucleotide alpha hydrolases-like | 2 | 1 | |
| UDP-Glycosyltransferase/glycogen phosphorylase | UDP-Glycosyltransferase/glycogen phosphorylase | 2 | 2 | |
| Ricin B-like lectins | Ricin B-like lectins | 2 | 2 | |
| Phosphofructokinase | Phosphofructokinase | 2 | 1 | |
| Protein kinase-like (PK-like) | Bet v1-like | 2 | 2 | |
| NAD(P)-binding Rossmann-fold domains | UDP-glucose/GDP-mannose dehydrogenase C-terminal domain | 2 | 1 | |
| Carbamoyl phosphate synthetase, small subunit N-terminal domain | Carbamoyl phosphate synthetase, large subunit connection domain | 2 | 2 | |
| HIT/MYND zinc finger-like | SET domain | 2 | 2 | |
| Growth factor receptor domain | Growth factor receptor domain | 2 | 2 | |
| POZ domain | Pentapeptide repeat-like | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | E set domains | 2 | 2 | |
| S-adenosyl-L-methionine-dependent methyltransferases | S-adenosyl-L-methionine-dependent methyltransferases | 2 | 2 | |
| Thiolase-like | 4'-phosphopantetheinyl transferase | 1 | 1 | |
| CoA-dependent acyltransferases | alpha/beta-Hydrolases | 1 | 1 | |
| FAD/NAD(P)-binding domain | 4Fe-4S ferredoxins | 1 | 1 | |
| Nitric oxide (NO) synthase oxygenase domain | Riboflavin synthase domain-like | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | post-HMGL domain-like | 1 | 1 | |
| L domain-like | FYVE/PHD zinc finger | 1 | 1 | |
| EF-hand | Mitochondrial carrier | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | Nucleotidylyl transferase | 1 | 1 | |
| FAD/NAD(P)-binding domain | ISP domain | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | PurM C-terminal domain-like | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | YjgF-like | 1 | 1 | |
| S13-like H2TH domain | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| post-HMGL domain-like | Single hybrid motif | 1 | 1 | |
| TPR-like | SET domain | 1 | 1 | |
| EPT/RTPC-like | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| HLH, helix-loop-helix DNA-binding domain | Chondroitin AC/alginate lyase | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | PurM N-terminal domain-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | ArfGap/RecO-like zinc finger | 1 | 1 | |
| FAD/NAD(P)-binding domain | Nitrite/Sulfite reductase N-terminal domain-like | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Type II DNA topoisomerase | 1 | 1 | |
| Terpenoid synthases | Terpenoid synthases | 1 | 1 | |
| 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK | 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK | 1 | 1 | |
| Nucleotidyltransferase | PAP/Archaeal CCA-adding enzyme, C-terminal domain | 1 | 1 | |
| SET domain | SET domain | 1 | 1 | |
| Kelch motif | Galactose oxidase, central domain | 1 | 1 | |
| PreATP-grasp domain | PurM N-terminal domain-like | 1 | 1 | |
| Acyl-CoA N-acyltransferases (Nat) | Bromodomain | 1 | 1 | |
| C2 domain (Calcium/lipid-binding domain, CaLB) | E set domains | 1 | 1 | |
| Carbamate kinase-like | ACT-like | 1 | 1 | |
| Ubiquitin-like | HAD-like | 1 | 1 | |
| HIT-like | HIT-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | PRTase-like | 1 | 1 | |
| ATP-dependent DNA ligase DNA-binding domain | Nucleic acid-binding proteins | 1 | 1 | |
| N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 | Translational machinery components | 1 | 1 | |
| Ankyrin repeat | Domain of poly(ADP-ribose) polymerase | 1 | 1 | |
| Ubiquitin-like | EF-hand | 1 | 1 | |
| Class I glutamine amidotransferase-like | Ribulose-phoshate binding barrel | 1 | 1 | |
| SCP-like | FAD/NAD(P)-binding domain | 1 | 1 | |
| PLC-like phosphodiesterases | SH2 domain | 1 | 1 | |
| A middle domain of Talin 1 | I/LWEQ domain | 1 | 1 | |
| Rhodanese/Cell cycle control phosphatase | (Phosphotyrosine protein) phosphatases II | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | FMN-linked oxidoreductases | 1 | 1 | |
| Nucleotidylyl transferase | Ribosomal protein L25-like | 1 | 1 | |
| Nucleoporin domain | WD40 repeat-like | 1 | 1 | |
| Subtilisin-like | EGF/Laminin | 1 | 1 | |
| Homocysteine S-methyltransferase | Cobalamin (vitamin B12)-binding domain | 1 | 1 | |
| EGF/Laminin | 6-phosphogluconate dehydrogenase C-terminal domain-like | 1 | 1 | |
| Chaperone J-domain | HSC20 (HSCB), C-terminal oligomerisation domain | 1 | 1 | |
| Nqo1 FMN-binding domain-like | Nqo1 middle domain-like | 1 | 1 | |
| EF-hand | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain | Pyrimidine nucleoside phosphorylase C-terminal domain | 1 | 1 | |
| Ankyrin repeat | SH3-domain | 1 | 1 | |
| Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain | 1 | 1 | |
| FAD/NAD(P)-binding domain | Class I glutamine amidotransferase-like | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | FAD/NAD(P)-binding domain | 1 | 1 | |
| WWE domain | ADP-ribosylation | 1 | 1 | |
| Zinc hairpin stack | RING/U-box | 1 | 1 | |
| Rudiment single hybrid motif | ClpP/crotonase | 1 | 1 | |
| FYVE/PHD zinc finger | Concanavalin A-like lectins/glucanases | 1 | 1 | |
| Ferredoxin reductase-like, C-terminal NADP-linked domain | Ferredoxin reductase-like, C-terminal NADP-linked domain | 1 | 1 | |
| PH domain-like | Bet v1-like | 1 | 1 | |
| Activating enzymes of the ubiquitin-like proteins | Activating enzymes of the ubiquitin-like proteins | 1 | 1 | |
| Oxidoreductase molybdopterin-binding domain | Cytochrome b5-like heme/steroid binding domain | 1 | 1 | |
| ACT-like | Aromatic aminoacid monoxygenases, catalytic and oligomerization domains | 1 | 1 | |
| WWE domain | Domain of poly(ADP-ribose) polymerase | 1 | 1 | |
| TPR-like | Metallo-dependent phosphatases | 1 | 1 | |
| Thioesterase/thiol ester dehydrase-isomerase | 4'-phosphopantetheinyl transferase | 1 | 1 | |
| Class II aaRS and biotin synthetases | C-terminal domain of ProRS | 1 | 1 | |
| RING/U-box | vWA-like | 1 | 1 | |
| beta-N-acetylhexosaminidase-like domain | beta-N-acetylhexosaminidase-like domain | 1 | 1 | |
| CO dehydrogenase ISP C-domain like | CO dehydrogenase molybdoprotein N-domain-like | 1 | 1 | |
| Aldolase | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| CHY zinc finger-like | Zinc hairpin stack | 1 | 1 | |
| 2Fe-2S ferredoxin-like | alpha-helical ferredoxin | 1 | 1 | |
| UBC-like | Endosomal sorting complex assembly domain | 1 | 1 | |
| EF-hand | Tropomyosin | 1 | 1 | |
| Ribulose-phoshate binding barrel | Ribulose-phoshate binding barrel | 1 | 1 | |
| NTF2-like | RNA-binding domain, RBD | 1 | 1 | |
| Pectin lyase-like | Growth factor receptor domain | 1 | 1 | |
| TK C-terminal domain-like | Pyruvate-ferredoxin oxidoreductase, PFOR, domain III | 1 | 1 | |
| ADC-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Methionine synthase domain | Methionine synthase activation domain-like | 1 | 1 | |
| L domain-like | Actin depolymerizing proteins | 1 | 1 | |
| Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | S15/NS1 RNA-binding domain | 1 | 1 | |
| TPR-like | PIN domain-like | 1 | 1 | |
| Proton glutamate symport protein | Proton glutamate symport protein | 1 | 1 | |
| C-type lectin-like | EGF/Laminin | 1 | 1 | |
| TATA-box binding protein-like | TATA-box binding protein-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Myosin rod fragments | 1 | 1 | |
| 2Fe-2S ferredoxin-like | FAD-binding/transporter-associated domain-like | 1 | 1 | |
| Periplasmic binding protein-like I | Periplasmic binding protein-like I | 1 | 1 | |
| C2 domain (Calcium/lipid-binding domain, CaLB) | CCCH zinc finger | 1 | 1 | |
| Dom34/Pelota N-terminal domain-like | Translational machinery components | 1 | 1 | |
| "Winged helix" DNA-binding domain | Protein kinase-like (PK-like) | 1 | 1 | |
| WGR domain-like | WWE domain | 1 | 1 | |
| C-type lectin-like | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| Pyruvate-ferredoxin oxidoreductase, PFOR, domain III | Riboflavin synthase domain-like | 1 | 1 | |
| CCHHC domain | Acyl-CoA N-acyltransferases (Nat) | 1 | 1 | |
| Pectin lyase-like | Carboxypeptidase regulatory domain-like | 1 | 1 | |
| Dipeptidyl peptidase I (cathepsin C), exclusion domain | Cysteine proteinases | 1 | 1 | |
| Polo-box domain | Polo-box domain | 1 | 1 | |
| Globin-like | Riboflavin synthase domain-like | 1 | 1 | |
| Transcription factor IIA (TFIIA), alpha-helical domain | Transcription factor IIA (TFIIA), beta-barrel domain | 1 | 1 | |
| Chaperone J-domain | Chaperone J-domain | 1 | 1 | |
| PLC-like phosphodiesterases | SH3-domain | 1 | 1 | |
| Calponin-homology domain, CH-domain | Spectrin repeat | 1 | 1 | |
| FAD/NAD(P)-binding domain | Single hybrid motif | 1 | 1 | |
| L domain-like | WD40 repeat-like | 1 | 1 | |
| AN1-like Zinc finger | AN1-like Zinc finger | 1 | 1 | |
| C-terminal domain of adenylylcyclase associated protein | Sec-C motif | 1 | 1 | |
| Glycerol-3-phosphate (1)-acyltransferase | Glycerol-3-phosphate (1)-acyltransferase | 1 | 1 | |
| Dehydroquinate synthase-like | EPT/RTPC-like | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | 4'-phosphopantetheinyl transferase | 1 | 1 | |
| ClpP/crotonase | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Thioesterase/thiol ester dehydrase-isomerase | Thiolase-like | 1 | 1 | |
| Cyclophilin-like | TPR-like | 1 | 1 | |
| Cobalamin (vitamin B12)-dependent enzymes | Cobalamin (vitamin B12)-binding domain | 1 | 1 | |
| PH domain-like | HMG-box | 1 | 1 | |
| Glycoside hydrolase/deacetylase | EGF/Laminin | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | GMP synthetase C-terminal dimerisation domain | 1 | 1 | |
| FabD/lysophospholipase-like | FabD/lysophospholipase-like | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) | 1 | 1 | |
| MOSC N-terminal domain-like | MOSC N-terminal domain-like | 1 | 1 | |
| Dihydropteroate synthetase-like | Cobalamin (vitamin B12)-binding domain | 1 | 1 | |
| Urocanase | L-aspartase-like | 1 | 1 | |
| N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 | L30e-like | 1 | 1 | |
| Starch-binding domain-like | (Trans)glycosidases | 1 | 1 | |
| Ubiquitin-like | BAG domain | 1 | 1 | |
| EF-hand | NAD kinase/diacylglycerol kinase-like | 1 | 1 | |
| Class II aaRS and biotin synthetases | GAD domain-like | 1 | 1 | |
| beta-lactamase/transpeptidase-like | Ankyrin repeat | 1 | 1 | |
| Methionine synthase domain | Cobalamin (vitamin B12)-binding domain | 1 | 1 | |
| Quinoprotein alcohol dehydrogenase-like | Quinoprotein alcohol dehydrogenase-like | 1 | 1 | |
| PH domain-like | Oxysterol-binding protein-like | 1 | 1 | |
| Protein kinase-like (PK-like) | SAM/Pointed domain | 1 | 1 | |
| FMN-linked oxidoreductases | dsRNA-binding domain-like | 1 | 1 | |
| E set domains | Cytochrome b5-like heme/steroid binding domain | 1 | 1 | |
| ISP transmembrane anchor | ISP domain | 1 | 1 | |
| UBA-like | XPC-binding domain | 1 | 1 | |
| Class I glutamine amidotransferase-like | Aspartate/ornithine carbamoyltransferase | 1 | 1 | |
| Carbamate kinase-like | Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 1 | 1 | |
| PUA domain-like | eIF1-like | 1 | 1 | |
| Aldolase | Aminoacid dehydrogenase-like, N-terminal domain | 1 | 1 | |
| EF-hand | CorA soluble domain-like | 1 | 1 | |
| Inosine monophosphate dehydrogenase (IMPDH) | Thioesterase/thiol ester dehydrase-isomerase | 1 | 1 | |
| Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 | Zinc beta-ribbon | 1 | 1 | |
| Metallo-hydrolase/oxidoreductase | Rhodanese/Cell cycle control phosphatase | 1 | 1 | |
| PurS-like | PurM N-terminal domain-like | 1 | 1 | |
| Nitrite/Sulfite reductase N-terminal domain-like | ISP domain | 1 | 1 | |
| Carbamate kinase-like | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Glutamine synthetase/guanido kinase | GatB/YqeY motif | 1 | 1 | |
| SET domain | WW domain | 1 | 1 | |
| Methylated DNA-protein cysteine methyltransferase domain | Methylated DNA-protein cysteine methyltransferase, C-terminal domain | 1 | 1 | |
| HMA, heavy metal-associated domain | HAD-like | 1 | 1 | |
| C2 domain (Calcium/lipid-binding domain, CaLB) | Cysteine-rich domain | 1 | 1 | |
| FYVE/PHD zinc finger | HMG-box | 1 | 1 | |
| PLP-dependent transferases | MOSC N-terminal domain-like | 1 | 1 | |
| Tetrahydrobiopterin biosynthesis enzymes-like | Tetrahydrobiopterin biosynthesis enzymes-like | 1 | 1 | |
| 4'-phosphopantetheinyl transferase | 4'-phosphopantetheinyl transferase | 1 | 1 | |
| Nitric oxide (NO) synthase oxygenase domain | Flavoproteins | 1 | 1 | |
| Carbohydrate-binding domain | Carbohydrate-binding domain | 1 | 1 | |
| PAP/OAS1 substrate-binding domain | Retrovirus zinc finger-like domains | 1 | 1 | |
| TK C-terminal domain-like | Flavoproteins | 1 | 1 | |
| SNARE fusion complex | SNARE fusion complex | 1 | 1 | |
| PreATP-grasp domain | ClpP/crotonase | 1 | 1 | |
| GroEL apical domain-like | SAICAR synthase-like | 1 | 1 | |
| Tropomyosin | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| vWA-like | C-terminal domain of Ku80 | 1 | 1 | |
| DNase I-like | RNA-binding domain, RBD | 1 | 1 | |
| Nitrite and sulphite reductase 4Fe-4S domain-like | ISP domain | 1 | 1 | |
| Periplasmic binding protein-like II | GlnB-like | 1 | 1 | |
| Aldolase | Single hybrid motif | 1 | 1 | |
| Arp2/3 complex subunits | Arp2/3 complex subunits | 1 | 1 | |
| NagB/RpiA/CoA transferase-like | EF-hand | 1 | 1 | |
| EPT/RTPC-like | Aldolase | 1 | 1 | |
| TAZ domain | TAZ domain | 1 | 1 | |
| PreATP-grasp domain | PurM C-terminal domain-like | 1 | 1 | |
| Methyl-accepting chemotaxis protein (MCP) signaling domain | Methyl-accepting chemotaxis protein (MCP) signaling domain | 1 | 1 | |
| HAD-like | Protein kinase-like (PK-like) | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | FYVE/PHD zinc finger | 1 | 1 | |
| Nucleotide-binding domain | Nucleotide-binding domain | 1 | 1 | |
| Probable ACP-binding domain of malonyl-CoA ACP transacylase | 4'-phosphopantetheinyl transferase | 1 | 1 | |
| PreATP-grasp domain | Methylglyoxal synthase-like | 1 | 1 | |
| Acetyl-CoA synthetase-like | alpha/beta-Hydrolases | 1 | 1 | |
| FAD-binding/transporter-associated domain-like | CO dehydrogenase flavoprotein C-terminal domain-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Hypothetical protein YjiA, C-terminal domain | 1 | 1 | |
| TK C-terminal domain-like | Nitrite/Sulfite reductase N-terminal domain-like | 1 | 1 | |
| Class I glutamine amidotransferase-like | ADC synthase | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | DHS-like NAD/FAD-binding domain | 1 | 1 | |
| Inosine monophosphate dehydrogenase (IMPDH) | 4'-phosphopantetheinyl transferase | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| IlvD/EDD N-terminal domain-like | LeuD/IlvD-like | 1 | 1 | |
| Ankyrin repeat | SET domain | 1 | 1 | |
| alpha-catenin/vinculin-like | I/LWEQ domain | 1 | 1 | |
| S-adenosyl-L-methionine-dependent methyltransferases | Acyl-CoA N-acyltransferases (Nat) | 1 | 1 | |
| Pyruvate-ferredoxin oxidoreductase, PFOR, domain III | Ferredoxin reductase-like, C-terminal NADP-linked domain | 1 | 1 | |
| Dimerization-anchoring domain of cAMP-dependent PK regulatory subunit | cAMP-binding domain-like | 1 | 1 | |
| NSFL1 (p97 ATPase) cofactor p47, SEP domain | Ubiquitin-like | 1 | 1 | |
| Calponin-homology domain, CH-domain | DBL homology domain (DH-domain) | 1 | 1 | |
| Formate/glycerate dehydrogenase catalytic domain-like | Serine metabolism enzymes domain | 1 | 1 | |
| Zinc-binding domain of translation initiation factor 2 beta | ARM repeat | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Ankyrin repeat | 1 | 1 | |
| beta-sandwich domain of Sec23/24 | Protein kinase-like (PK-like) | 1 | 1 | |
| Thiamin diphosphate-binding fold (THDP-binding) | Flavoproteins | 1 | 1 | |
| ARM repeat | Hect, E3 ligase catalytic domain | 1 | 1 | |
| Inhibitor of apoptosis (IAP) repeat | Inhibitor of apoptosis (IAP) repeat | 1 | 1 | |
| Periplasmic binding protein-like II | Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain | 1 | 1 | |
| Homocysteine S-methyltransferase | Methionine synthase activation domain-like | 1 | 1 | |
| Thioredoxin-like | YccV-like | 1 | 1 | |
| beta-beta-alpha zinc fingers | SAM/Pointed domain | 1 | 1 | |
| PheT/TilS domain | Putative DNA-binding domain | 1 | 1 | |
| ARID-like | FYVE/PHD zinc finger | 1 | 1 | |
| WD40 repeat-like | Cyclophilin-like | 1 | 1 | |
| Starch-binding domain-like | Acyl-CoA N-acyltransferases (Nat) | 1 | 1 | |
| RNI-like | GAT-like domain | 1 | 1 | |
| HCP-like | HCP-like | 1 | 1 | |
| Indigoidine synthase A-like | Ribokinase-like | 1 | 1 | |
| CCCH zinc finger | CCCH zinc finger | 1 | 1 | |
| CorA soluble domain-like | Magnesium transport protein CorA, transmembrane region | 1 | 1 | |
| Class I glutamine amidotransferase-like | Methylglyoxal synthase-like | 1 | 1 | |
| Glycoside hydrolase/deacetylase | Galactose mutarotase-like | 1 | 1 | |
| PDZ domain-like | ClpP/crotonase | 1 | 1 | |
| CoA-dependent acyltransferases | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Chaperone J-domain | Sec63 N-terminal domain-like | 1 | 1 | |
| Elongation factor TFIIS domain 2 | Zinc beta-ribbon | 1 | 1 | |
| CO dehydrogenase molybdoprotein N-domain-like | Molybdenum cofactor-binding domain | 1 | 1 | |
| C2 domain (Calcium/lipid-binding domain, CaLB) | Protein kinase-like (PK-like) | 1 | 1 | |
| Pseudouridine synthase | PUA domain-like | 1 | 1 | |
| PX domain | SNARE fusion complex | 1 | 1 | |
| Flavoproteins | Prismane protein-like | 1 | 1 | |
| Purple acid phosphatase, N-terminal domain | Galactose-binding domain-like | 1 | 1 | |
| Rhodanese/Cell cycle control phosphatase | DsrEFH-like | 1 | 1 | |
| N-terminal domain of adenylylcyclase associated protein, CAP | C-terminal domain of adenylylcyclase associated protein | 1 | 1 | |
| FYVE/PHD zinc finger | "Winged helix" DNA-binding domain | 1 | 1 | |
| NagB/RpiA/CoA transferase-like | D-ribose-5-phosphate isomerase (RpiA), lid domain | 1 | 1 | |
| POZ domain | RNI-like | 1 | 1 | |
| Thiamin diphosphate-binding fold (THDP-binding) | Pyruvate-ferredoxin oxidoreductase, PFOR, domain III | 1 | 1 | |
| vWA-like | SPOC domain-like | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Metallo-dependent hydrolases | 1 | 1 | |
| C2 domain (Calcium/lipid-binding domain, CaLB) | UBA-like | 1 | 1 | |
| Class I glutamine amidotransferase-like | Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain | 1 | 1 | |
| Oxidoreductase molybdopterin-binding domain | FAD/NAD(P)-binding domain | 1 | 1 | |
| Cdc48 domain 2-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| "Winged helix" DNA-binding domain | SAICAR synthase-like | 1 | 1 | |
| EGF/Laminin | Trimeric LpxA-like enzymes | 1 | 1 | |
| PurM N-terminal domain-like | Class I glutamine amidotransferase-like | 1 | 1 | |
| Heme-dependent peroxidases | Notch domain | 1 | 1 | |
| RNI-like | RNI-like | 1 | 1 | |
| FYVE/PHD zinc finger | alpha/beta-Hydrolases | 1 | 1 | |
| Cysteine proteinases | UBA-like | 1 | 1 | |
| Nucleic acid-binding proteins | eIF2alpha middle domain-like | 1 | 1 | |
| RING/U-box | Cyclophilin-like | 1 | 1 | |
| Periplasmic binding protein-like II | FAD/NAD(P)-binding domain | 1 | 1 | |
| alpha-ketoacid dehydrogenase kinase, N-terminal domain | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 1 | 1 | |
| RNA-binding domain, RBD | Ran binding protein zinc finger-like | 1 | 1 | |
| ATP-dependent DNA ligase DNA-binding domain | DNA ligase/mRNA capping enzyme, catalytic domain | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | alpha-helical ferredoxin | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | PRTase-like | 1 | 1 | |
| alpha-D-mannose-specific plant lectins | alpha-D-mannose-specific plant lectins | 1 | 1 | |
| SWIB/MDM2 domain | eIF1-like | 1 | 1 | |
| alpha/beta-Hydrolases | UBC-like | 1 | 1 | |
| Tetrahydrobiopterin biosynthesis enzymes-like | 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK | 1 | 1 | |
| Plant lectins/antimicrobial peptides | (Trans)glycosidases | 1 | 1 | |
| Putative isomerase YbhE | ARM repeat | 1 | 1 | |
| Homeodomain-like | FYVE/PHD zinc finger | 1 | 1 | |
| Nqo1 middle domain-like | Nqo1C-terminal domain-like | 1 | 1 | |
| Single hybrid motif | ClpP/crotonase | 1 | 1 | |
| Class II aaRS ABD-related | C-terminal domain of ProRS | 1 | 1 | |
| Dihydropteroate synthetase-like | Dihydropteroate synthetase-like | 1 | 1 | |
| Spectrin repeat | Spectrin repeat | 1 | 1 | |
| POZ domain | F-box domain | 1 | 1 | |
| HprK N-terminal domain-like | Isocitrate/Isopropylmalate dehydrogenase-like | 1 | 1 | |
| Fibronectin type III | Hect, E3 ligase catalytic domain | 1 | 1 | |
| Tricorn protease domain 2 | alpha/beta-Hydrolases | 1 | 1 | |
| Flavoproteins | Radical SAM enzymes | 1 | 1 | |
| Ankyrin repeat | Pentein | 1 | 1 | |
| Myosin rod fragments | Myosin rod fragments | 1 | 1 | |
| "Winged helix" DNA-binding domain | GroEL apical domain-like | 1 | 1 | |
| Periplasmic binding protein-like II | ACT-like | 1 | 1 | |
| GST C-terminal domain-like | Nucleic acid-binding proteins | 1 | 1 | |
| FYVE/PHD zinc finger | CCHHC domain | 1 | 1 | |
| PurM C-terminal domain-like | PurM C-terminal domain-like | 1 | 1 | |
| Multidrug efflux transporter AcrB transmembrane domain | WD40 repeat-like | 1 | 1 | |
| RNA-binding domain, RBD | Tetrahydrobiopterin biosynthesis enzymes-like | 1 | 1 | |
| Thiamin diphosphate-binding fold (THDP-binding) | Nitrite and sulphite reductase 4Fe-4S domain-like | 1 | 1 | |
| Nucleotide-diphospho-sugar transferases | Trimeric LpxA-like enzymes | 1 | 1 | |
| Alpha subunit of glutamate synthase, C-terminal domain | alpha-helical ferredoxin | 1 | 1 | |
| Methylglyoxal synthase-like | Cytidine deaminase-like | 1 | 1 | |
| Acyl-CoA binding protein | Supernatant protein factor (SPF), C-terminal domain | 1 | 1 | |
| Radical SAM enzymes | Radical SAM enzymes | 1 | 1 | |
| Fibronectin type III | Thioredoxin-like | 1 | 1 | |
| Carbamoyl phosphate synthetase, small subunit N-terminal domain | Aspartate/ornithine carbamoyltransferase | 1 | 1 | |
| Inosine monophosphate dehydrogenase (IMPDH) | Thiolase-like | 1 | 1 | |
| TPR-like | HCP-like | 1 | 1 | |
| RNI-like | L domain-like | 1 | 1 | |
| Dehydroquinate synthase-like | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Pentein | Pentein | 1 | 1 | |
| SH2 domain | Protein kinase-like (PK-like) | 1 | 1 | |
| Clathrin heavy-chain terminal domain | ARM repeat | 1 | 1 | |
| S-adenosylmethionine synthetase | S-adenosylmethionine synthetase | 1 | 1 | |
| YrdC/RibB | HAD-like | 1 | 1 | |
| Rad51 N-terminal domain-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| DNA repair protein MutS, domain I | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| eIF2alpha middle domain-like | eIF-2-alpha, C-terminal domain | 1 | 1 | |
| alpha/beta-Hydrolases | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Nucleotidyltransferase | Retrovirus zinc finger-like domains | 1 | 1 | |
| PH domain-like | SH2 domain | 1 | 1 | |
| FYVE/PHD zinc finger | RNI-like | 1 | 1 | |
| Carbohydrate phosphatase | Protein kinase-like (PK-like) | 1 | 1 | |
| Aldolase | 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain | 1 | 1 | |
| BAR/IMD domain-like | DBL homology domain (DH-domain) | 1 | 1 | |
| FabD/lysophospholipase-like | Thioesterase/thiol ester dehydrase-isomerase | 1 | 1 | |
| Pre-PUA domain | PUA domain-like | 1 | 1 | |
| ARM repeat | HMA, heavy metal-associated domain | 1 | 1 | |
| Second domain of FERM | PH domain-like | 1 | 1 | |
| cAMP-binding domain-like | FabD/lysophospholipase-like | 1 | 1 | |
| I/LWEQ domain | I/LWEQ domain | 1 | 1 | |
| HisI-like | all-alpha NTP pyrophosphatases | 1 | 1 | |
| L domain-like | Ubiquitin-like | 1 | 1 | |
| Families 57/38 glycoside transferase middle domain | Galactose mutarotase-like | 1 | 1 | |
| SET domain | Bromodomain | 1 | 1 | |
| PP2C-like | PP2C-like | 1 | 1 | |
| Methylglyoxal synthase-like | Metallo-dependent hydrolases | 1 | 1 | |
| cAMP-binding domain-like | F-box domain | 1 | 1 | |
| Glycoside hydrolase/deacetylase | Families 57/38 glycoside transferase middle domain | 1 | 1 | |
| Metalloproteases ("zincins"), catalytic domain | 6-phosphogluconate dehydrogenase C-terminal domain-like | 1 | 1 | |
| Thiamin diphosphate-binding fold (THDP-binding) | Riboflavin synthase domain-like | 1 | 1 | |
| Tryptophan synthase beta subunit-like PLP-dependent enzymes | ACT-like | 1 | 1 | |
| PreATP-grasp domain | Aspartate/ornithine carbamoyltransferase | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Succinyl-CoA synthetase domains | 1 | 1 | |
| DNA/RNA polymerases | Lesion bypass DNA polymerase (Y-family), little finger domain | 1 | 1 | |
| PreATP-grasp domain | Aldolase | 1 | 1 | |
| PAP/OAS1 substrate-binding domain | PAP/Archaeal CCA-adding enzyme, C-terminal domain | 1 | 1 | |
| HAD-like | Acyl-CoA dehydrogenase NM domain-like | 1 | 1 | |
| RING/U-box | Ankyrin repeat | 1 | 1 | |
| CO dehydrogenase ISP C-domain like | FAD-binding/transporter-associated domain-like | 1 | 1 | |
| Cysteine-rich domain | Actin-like ATPase domain | 1 | 1 | |
| Thiamin diphosphate-binding fold (THDP-binding) | Ferredoxin reductase-like, C-terminal NADP-linked domain | 1 | 1 | |
| Urease, beta-subunit | Metallo-dependent hydrolases | 1 | 1 | |
| Cytochrome c | Cytochrome c1 subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase), transmembrane anchor | 1 | 1 | |
| Metallo-dependent hydrolases | Zn-dependent exopeptidases | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Aldolase | 1 | 1 | |
| BAR/IMD domain-like | GTPase activation domain, GAP | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | ClpP/crotonase | 1 | 1 | |
| Prokaryotic type KH domain (KH-domain type II) | Ribosomal protein S3 C-terminal domain | 1 | 1 | |
| Thiamin diphosphate-binding fold (THDP-binding) | Nitrite/Sulfite reductase N-terminal domain-like | 1 | 1 | |
| p53-like transcription factors | E set domains | 1 | 1 | |
| UBA-like | Elongation factor Ts (EF-Ts), dimerisation domain | 1 | 1 | |
| L9 N-domain-like | Ribosomal protein L9 C-domain | 1 | 1 | |
| FAD-binding/transporter-associated domain-like | CO dehydrogenase molybdoprotein N-domain-like | 1 | 1 | |
| Urease, beta-subunit | Composite domain of metallo-dependent hydrolases | 1 | 1 | |
| TrmE connector domain | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Phosphoglycerate mutase-like | BRCT domain | 1 | 1 | |
| WGR domain-like | WGR domain-like | 1 | 1 | |
| Ferredoxin reductase-like, C-terminal NADP-linked domain | Prismane protein-like | 1 | 1 | |
| FYVE/PHD zinc finger | Acyl-CoA N-acyltransferases (Nat) | 1 | 1 | |
| Ankyrin repeat | L domain-like | 1 | 1 | |
| beta-sandwich domain of Sec23/24 | SH2 domain | 1 | 1 | |
| FMN-linked oxidoreductases | Nucleotide-binding domain | 1 | 1 | |
| Aldolase | post-HMGL domain-like | 1 | 1 | |
| PLC-like phosphodiesterases | C2 domain (Calcium/lipid-binding domain, CaLB) | 1 | 1 | |
| Nitric oxide (NO) synthase oxygenase domain | Ferredoxin reductase-like, C-terminal NADP-linked domain | 1 | 1 | |
| Glucocorticoid receptor-like (DNA-binding domain) | AN1-like Zinc finger | 1 | 1 | |
| PurS-like | Class I glutamine amidotransferase-like | 1 | 1 | |
| Plant lectins/antimicrobial peptides | Chitinase insertion domain | 1 | 1 | |
| Apolipoprotein A-I | Apolipoprotein A-I | 1 | 1 | |
| Class II aaRS and biotin synthetases | Anticodon-binding domain of PheRS | 1 | 1 | |
| SAP domain | SAP domain | 1 | 1 | |
| Tetrahydrobiopterin biosynthesis enzymes-like | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Calponin-homology domain, CH-domain | EB1 dimerisation domain-like | 1 | 1 | |
| ADC-like | Cdc48 domain 2-like | 1 | 1 | |
| Nqo1 FMN-binding domain-like | Nqo1C-terminal domain-like | 1 | 1 | |
| PX domain | Cyclin-like | 1 | 1 | |
| Sec7 domain | PH domain-like | 1 | 1 | |
| Ankyrin repeat | RCC1/BLIP-II | 1 | 1 | |
| Dehydroquinate synthase-like | Aminoacid dehydrogenase-like, N-terminal domain | 1 | 1 | |
| ArfGap/RecO-like zinc finger | UBA-like | 1 | 1 | |
| SH3-domain | beta-sandwich domain of Sec23/24 | 1 | 1 | |
| Cytochrome b5-like heme/steroid binding domain | Ankyrin repeat | 1 | 1 | |
| HMG-box | DEK C-terminal domain | 1 | 1 | |
| R1 subunit of ribonucleotide reductase, N-terminal domain | PFL-like glycyl radical enzymes | 1 | 1 | |
| HAD-like | HAD-like | 1 | 1 | |
| Class I glutamine amidotransferase-like | Adenine nucleotide alpha hydrolases-like | 1 | 1 | |
| Probable ACP-binding domain of malonyl-CoA ACP transacylase | Thiolase-like | 1 | 1 | |
| VHL | VHL | 1 | 1 | |
| E set domains | FAD/NAD(P)-binding domain | 1 | 1 | |
| Protein kinase-like (PK-like) | Polo-box domain | 1 | 1 | |
| Galactose oxidase, central domain | Galactose oxidase, central domain | 1 | 1 | |
| mRNA decapping enzyme DcpS N-terminal domain | HIT-like | 1 | 1 | |
| PDZ domain-like | WW domain | 1 | 1 | |
| FLJ32549 domain-like | FLJ32549 C-terminal domain-like | 1 | 1 | |
| Pectin lyase-like | EGF/Laminin | 1 | 1 | |
| RNase III domain-like | dsRNA-binding domain-like | 1 | 1 | |
| beta-lactamase/transpeptidase-like | beta-lactamase/transpeptidase-like | 1 | 1 | |
| DNA repair protein MutS, domain II | DNA repair protein MutS, domain II | 1 | 1 | |
| Nucleic acid-binding proteins | eIF-2-alpha, C-terminal domain | 1 | 1 | |
| FMN-linked oxidoreductases | alpha-helical ferredoxin | 1 | 1 | |
| Saposin | Saposin | 1 | 1 | |
| UBA-like | NSFL1 (p97 ATPase) cofactor p47, SEP domain | 1 | 1 | |
| Aconitase iron-sulfur domain | Aconitase iron-sulfur domain | 1 | 1 | |
| CO dehydrogenase flavoprotein C-terminal domain-like | CO dehydrogenase molybdoprotein N-domain-like | 1 | 1 | |
| all-alpha NTP pyrophosphatases | ALDH-like | 1 | 1 | |
| alpha/beta-Hydrolases | Adenine nucleotide alpha hydrolases-like | 1 | 1 | |
| Zn-dependent exopeptidases | Carboxypeptidase regulatory domain-like | 1 | 1 | |
| Flavoproteins | Nitrite and sulphite reductase 4Fe-4S domain-like | 1 | 1 | |
| Nucleotidylyl transferase | Alpha-L RNA-binding motif | 1 | 1 | |
| Inosine monophosphate dehydrogenase (IMPDH) | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Rudiment single hybrid motif | Aldolase | 1 | 1 | |
| Ankyrin repeat | FYVE/PHD zinc finger | 1 | 1 | |
| ARM repeat | Formin homology 2 domain (FH2 domain) | 1 | 1 | |
| Class I glutamine amidotransferase-like | GMP synthetase C-terminal dimerisation domain | 1 | 1 | |
| RING/U-box | TRAF domain-like | 1 | 1 | |
| Actin-like ATPase domain | AF1104-like | 1 | 1 | |
| Growth factor receptor domain | Protein kinase-like (PK-like) | 1 | 1 | |
| Composite domain of metallo-dependent hydrolases | Composite domain of metallo-dependent hydrolases | 1 | 1 | |
| 2Fe-2S ferredoxin-like | Molybdenum cofactor-binding domain | 1 | 1 | |
| HLH, helix-loop-helix DNA-binding domain | CRAL/TRIO domain | 1 | 1 | |
| Rhomboid-like | UBA-like | 1 | 1 | |
| Riboflavin synthase domain-like | Prismane protein-like | 1 | 1 | |
| Macro domain-like | Zn-dependent exopeptidases | 1 | 1 | |
| RNA-binding domain, RBD | PAP/OAS1 substrate-binding domain | 1 | 1 | |
| RNA-binding domain, RBD | Nucleotidyltransferase | 1 | 1 | |
| MIT domain | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Restriction endonuclease-like | RuvA domain 2-like | 1 | 1 | |
| Carbamoyl phosphate synthetase, small subunit N-terminal domain | Methylglyoxal synthase-like | 1 | 1 | |
| Ankyrin repeat | Oxysterol-binding protein-like | 1 | 1 | |
| PreATP-grasp domain | Metallo-dependent hydrolases | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Serine metabolism enzymes domain | 1 | 1 | |
| Oxidoreductase molybdopterin-binding domain | E set domains | 1 | 1 | |
| RING/U-box | RNA-binding domain, RBD | 1 | 1 | |
| Nucleotide-binding domain | 4Fe-4S ferredoxins | 1 | 1 | |
| Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase | Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase | 1 | 1 | |
| PheT/TilS domain | Class II aaRS and biotin synthetases | 1 | 1 | |
| Carbamate kinase-like | PUA domain-like | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | SIS domain | 1 | 1 | |
| Single hybrid motif | Class II aaRS and biotin synthetases | 1 | 1 | |
| Fibronectin type III | CCCH zinc finger | 1 | 1 | |
| Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain | Pyrimidine nucleoside phosphorylase C-terminal domain | 1 | 1 | |
| Ankyrin repeat | WGR domain-like | 1 | 1 | |
| Ribosomal L27 protein-like | Eukaryotic type KH-domain (KH-domain type I) | 1 | 1 | |
| Nucleotide cyclase | Nucleotide cyclase | 1 | 1 | |
| Acyl-CoA N-acyltransferases (Nat) | Diaminopimelate epimerase-like | 1 | 1 | |
| TK C-terminal domain-like | Nitrite and sulphite reductase 4Fe-4S domain-like | 1 | 1 | |
| TK C-terminal domain-like | Riboflavin synthase domain-like | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | Alpha subunit of glutamate synthase, C-terminal domain | 1 | 1 | |
| PKD domain | PKD domain | 1 | 1 | |
| Class II aaRS and biotin synthetases | Class I glutamine amidotransferase-like | 1 | 1 | |
| PEP carboxykinase N-terminal domain | PEP carboxykinase-like | 1 | 1 | |
| Ankyrin repeat | ADP-ribosylation | 1 | 1 | |
| CoA-transferase family III (CaiB/BaiF) | CoA-transferase family III (CaiB/BaiF) | 1 | 1 | |
| Lissencephaly-1 protein (Lis-1, PAF-AH alpha) N-terminal domain | WD40 repeat-like | 1 | 1 | |
| LDL receptor-like module | Mannose 6-phosphate receptor domain | 1 | 1 | |
| Inosine monophosphate dehydrogenase (IMPDH) | Inosine monophosphate dehydrogenase (IMPDH) | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Aspartate/ornithine carbamoyltransferase | 1 | 1 | |
| Carbamoyl phosphate synthetase, large subunit connection domain | Metallo-dependent hydrolases | 1 | 1 | |
| EF-hand | RING/U-box | 1 | 1 | |
| CCCH zinc finger | Hect, E3 ligase catalytic domain | 1 | 1 | |
| Spectrin repeat | EF-hand | 1 | 1 | |
| Fe,Mn superoxide dismutase (SOD), N-terminal domain | Fe,Mn superoxide dismutase (SOD), C-terminal domain | 1 | 1 | |
| Homeodomain-like | RING/U-box | 1 | 1 | |
| "Winged helix" DNA-binding domain | FKBP-like | 1 | 1 | |
| CheY-like | CheY-like | 1 | 1 | |
| ARM repeat | Protein kinase-like (PK-like) | 1 | 1 | |
| Rhodanese/Cell cycle control phosphatase | Rhodanese/Cell cycle control phosphatase | 1 | 1 | |
| cAMP-binding domain-like | RNI-like | 1 | 1 | |
| FAD/NAD-linked reductases, dimerisation (C-terminal) domain | Rhodanese/Cell cycle control phosphatase | 1 | 1 | |
| 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK | Dihydropteroate synthetase-like | 1 | 1 | |
| alpha/beta-Hydrolases | Protein kinase-like (PK-like) | 1 | 1 | |
| Class I glutamine amidotransferase-like | Metallo-dependent hydrolases | 1 | 1 | |
| beta-sandwich domain of Sec23/24 | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| TAZ domain | Kix domain of CBP (creb binding protein) | 1 | 1 | |
| FAD/NAD(P)-binding domain | Class II aaRS and biotin synthetases | 1 | 1 | |
| CHY zinc finger-like | RING/U-box | 1 | 1 | |
| NTF2-like | FAD/NAD(P)-binding domain | 1 | 1 | |
| FYVE/PHD zinc finger | GroEL apical domain-like | 1 | 1 | |
| Riboflavin synthase domain-like | Riboflavin synthase domain-like | 1 | 1 | |
| UBC-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Translation initiation factor 2 beta, aIF2beta, N-terminal domain | ARM repeat | 1 | 1 | |
| Calponin-homology domain, CH-domain | EF-hand | 1 | 1 | |
| TK C-terminal domain-like | Ferredoxin reductase-like, C-terminal NADP-linked domain | 1 | 1 | |
| Protein kinase-like (PK-like) | Alkaline phosphatase-like | 1 | 1 | |
| PurS-like | PurM C-terminal domain-like | 1 | 1 | |
| PRP4-like | Functional domain of the splicing factor Prp18 | 1 | 1 | |
| Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain | Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | S13-like H2TH domain | 1 | 1 | |
| Dehydroquinate synthase-like | Aldolase | 1 | 1 | |
| Nucleic acid-binding proteins | BRCT domain | 1 | 1 | |
| Ribosomal protein L7/12, oligomerisation (N-terminal) domain | ClpS-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | HRDC-like | 1 | 1 | |
| Nucleic acid-binding proteins | Eukaryotic type KH-domain (KH-domain type I) | 1 | 1 | |
| Metallo-dependent hydrolases | Aspartate/ornithine carbamoyltransferase | 1 | 1 | |
| PH domain-like | ArfGap/RecO-like zinc finger | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | Type II DNA topoisomerase | 1 | 1 | |
| TolB, C-terminal domain | WD40 repeat-like | 1 | 1 | |
| Ankyrin repeat | Galactose-binding domain-like | 1 | 1 | |
| Ubiquitin-like | XPC-binding domain | 1 | 1 | |
| Diaminopimelate epimerase-like | Diaminopimelate epimerase-like | 1 | 1 | |
| RNA-binding domain, RBD | dsRNA-binding domain-like | 1 | 1 | |
| Regulator of G-protein signaling, RGS | Regulator of G-protein signaling, RGS | 1 | 1 | |
| WD40 repeat-like | Bromodomain | 1 | 1 | |
| Flavoproteins | Nitrite/Sulfite reductase N-terminal domain-like | 1 | 1 | |
| beta-Galactosidase/glucuronidase domain | (Trans)glycosidases | 1 | 1 | |
| PH domain-like | CRAL/TRIO N-terminal domain | 1 | 1 | |
| Duplicated hybrid motif | PLP-dependent transferases | 1 | 1 | |
| TPR-like | HSP20-like chaperones | 1 | 1 | |
| Homocysteine S-methyltransferase | Dihydropteroate synthetase-like | 1 | 1 | |
| Chromo domain-like | FYVE/PHD zinc finger | 1 | 1 | |
| PLC-like phosphodiesterases | PLC-like phosphodiesterases | 1 | 1 | |
| Concanavalin A-like lectins/glucanases | Growth factor receptor domain | 1 | 1 | |
| Radical SAM enzymes | Acyl-CoA N-acyltransferases (Nat) | 1 | 1 | |
| PH domain-like | CRAL/TRIO domain | 1 | 1 | |
| EPT/RTPC-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| RING/U-box | FYVE/PHD zinc finger | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | HAND domain of the nucleosome remodeling ATPase ISWI | 1 | 1 | |
| Cysteine-rich domain | SH2 domain | 1 | 1 | |
| PreATP-grasp domain | post-HMGL domain-like | 1 | 1 | |
| Regulator of G-protein signaling, RGS | Cysteine-rich domain | 1 | 1 | |
| Electron transport accessory proteins | Nitrile hydratase alpha chain | 1 | 1 | |
| Rudiment single hybrid motif | post-HMGL domain-like | 1 | 1 | |
| Hypothetical protein SAV1430 | Fe-S cluster assembly (FSCA) domain-like | 1 | 1 | |
| Nitrite/Sulfite reductase N-terminal domain-like | Nitrite/Sulfite reductase N-terminal domain-like | 1 | 1 | |
| FabD/lysophospholipase-like | Thiolase-like | 1 | 1 | |
| 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| 2Fe-2S ferredoxin-like | CO dehydrogenase molybdoprotein N-domain-like | 1 | 1 | |
| Chromo domain-like | Acyl-CoA N-acyltransferases (Nat) | 1 | 1 | |
| Glucocorticoid receptor-like (DNA-binding domain) | Putative DNA-binding domain | 1 | 1 | |
| "Helical backbone" metal receptor | Adenine nucleotide alpha hydrolases-like | 1 | 1 | |
| DNA repair protein MutS, domain II | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| CO dehydrogenase ISP C-domain like | CO dehydrogenase flavoprotein C-terminal domain-like | 1 | 1 | |
| cAMP-binding domain-like | Formate/glycerate dehydrogenase catalytic domain-like | 1 | 1 | |
| Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 | Elongation factor TFIIS domain 2 | 1 | 1 | |
| Rudiment single hybrid motif | PurM C-terminal domain-like | 1 | 1 | |
| RING/U-box | UBA-like | 1 | 1 | |
| PK beta-barrel domain-like | PK C-terminal domain-like | 1 | 1 | |
| Thioesterase/thiol ester dehydrase-isomerase | Bet v1-like | 1 | 1 | |
| Mitochondrial import receptor subunit Tom20 | SET domain | 1 | 1 | |
| Carbamoyl phosphate synthetase, large subunit connection domain | Methylglyoxal synthase-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Class I glutamine amidotransferase-like | 1 | 1 | |
| "Winged helix" DNA-binding domain | FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Retrovirus zinc finger-like domains | 1 | 1 | |
| EGF/Laminin | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| PUA domain-like | SWIB/MDM2 domain | 1 | 1 | |
| Heat shock protein 70kD (HSP70), peptide-binding domain | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| 4Fe-4S ferredoxins | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Metalloproteases ("zincins"), catalytic domain | (Trans)glycosidases | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | PUA domain-like | 1 | 1 | |
| Staphylococcal nuclease | Tudor/PWWP/MBT | 1 | 1 | |
| Ubiquitin-like | Acid proteases | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Methylglyoxal synthase-like | 1 | 1 | |
| Elongation factor Ts (EF-Ts), dimerisation domain | Elongation factor Ts (EF-Ts), dimerisation domain | 1 | 1 | |
| EF-hand | SAM/Pointed domain | 1 | 1 | |
| SMAD/FHA domain | BRCT domain | 1 | 1 | |
| Prokaryotic type I DNA topoisomerase | Retrovirus zinc finger-like domains | 1 | 1 | |
| Nucleic acid-binding proteins | TPR-like | 1 | 1 | |
| Tropomyosin | FYVE/PHD zinc finger | 1 | 1 | |
| Tryptophan synthase beta subunit-like PLP-dependent enzymes | CBS-domain pair | 1 | 1 | |
| SH3-domain | Protein kinase-like (PK-like) | 1 | 1 | |
| FabD/lysophospholipase-like | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Single hybrid motif | Class I glutamine amidotransferase-like | 1 | 1 | |
| 2Fe-2S ferredoxin-like | CO dehydrogenase ISP C-domain like | 1 | 1 | |
| "Winged helix" DNA-binding domain | Regulator of G-protein signaling, RGS | 1 | 1 | |
| HCP-like | HIT/MYND zinc finger-like | 1 | 1 | |
| FYVE/PHD zinc finger | ARM repeat | 1 | 1 | |
| Cystatin/monellin | Cystatin/monellin | 1 | 1 | |
| PH domain-like | Wiscott-Aldrich syndrome protein, WASP, C-terminal domain | 1 | 1 | |
| Dimeric alpha+beta barrel | Dimeric alpha+beta barrel | 1 | 1 | |
| ARID-like | ARM repeat | 1 | 1 | |
| FAD/NAD(P)-binding domain | Nitrite and sulphite reductase 4Fe-4S domain-like | 1 | 1 | |
| Carbamoyl phosphate synthetase, small subunit N-terminal domain | Metallo-dependent hydrolases | 1 | 1 | |
| ACP-like | alpha/beta-Hydrolases | 1 | 1 | |
| Acid proteases | UBA-like | 1 | 1 | |
| PurM N-terminal domain-like | PurM N-terminal domain-like | 1 | 1 | |
| ACT-like | Formyltransferase | 1 | 1 | |
| Alpha subunit of glutamate synthase, C-terminal domain | Nucleotide-binding domain | 1 | 1 | |
| PurM C-terminal domain-like | Class I glutamine amidotransferase-like | 1 | 1 | |
| Serine metabolism enzymes domain | ACT-like | 1 | 1 | |
| (Phosphotyrosine protein) phosphatases II | (Phosphotyrosine protein) phosphatases II | 1 | 1 | |
| Acetyl-CoA synthetase-like | Ankyrin repeat | 1 | 1 | |
| Ubiquitin-like | Zn-binding ribosomal proteins | 1 | 1 | |
| ARM repeat | Chaperone J-domain | 1 | 1 | |
| BRCT domain | DNA/RNA polymerases | 1 | 1 | |
| Ribulose-phoshate binding barrel | Tryptophan synthase beta subunit-like PLP-dependent enzymes | 1 | 1 | |
| TRAF domain-like | Cysteine proteinases | 1 | 1 | |
| Probable ACP-binding domain of malonyl-CoA ACP transacylase | Thioesterase/thiol ester dehydrase-isomerase | 1 | 1 | |
| FAD-binding/transporter-associated domain-like | Molybdenum cofactor-binding domain | 1 | 1 | |
| EPT/RTPC-like | Aminoacid dehydrogenase-like, N-terminal domain | 1 | 1 | |
| FabD/lysophospholipase-like | Inosine monophosphate dehydrogenase (IMPDH) | 1 | 1 | |
| 2Fe-2S ferredoxin-like | CO dehydrogenase flavoprotein C-terminal domain-like | 1 | 1 | |
| SMAD/FHA domain | Protein kinase-like (PK-like) | 1 | 1 | |
| Acetyl-CoA synthetase-like | Acetyl-CoA synthetase-like | 1 | 1 | |
| SMAD/FHA domain | "Winged helix" DNA-binding domain | 1 | 1 | |
| C2 domain (Calcium/lipid-binding domain, CaLB) | WW domain | 1 | 1 | |
| Activator of Hsp90 ATPase, Aha1 | Bet v1-like | 1 | 1 | |
| Fumarylacetoacetate hydrolase, FAH, N-terminal domain | FAH | 1 | 1 | |
| cAMP-binding domain-like | Aminoacid dehydrogenase-like, N-terminal domain | 1 | 1 | |
| ClpP/crotonase | 6-phosphogluconate dehydrogenase C-terminal domain-like | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Thiolase-like | 1 | 1 | |
| N-terminal domain of MutM-like DNA repair proteins | S13-like H2TH domain | 1 | 1 | |
| FYVE/PHD zinc finger | SAICAR synthase-like | 1 | 1 | |
| Trypsin-like serine proteases | EGF/Laminin | 1 | 1 | |
| EF-hand | Aminoacid dehydrogenase-like, N-terminal domain | 1 | 1 | |
| PDZ domain-like | PH domain-like | 1 | 1 | |
| FAD/NAD(P)-binding domain | Rhodanese/Cell cycle control phosphatase | 1 | 1 | |
| Metalloproteases ("zincins"), catalytic domain | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Putative DNA-binding domain | Class II aaRS and biotin synthetases | 1 | 1 | |
| Eukaryotic type KH-domain (KH-domain type I) | Retrovirus zinc finger-like domains | 1 | 1 | |
| HAD-like | 6-phosphogluconate dehydrogenase C-terminal domain-like | 1 | 1 | |
| Retrovirus zinc finger-like domains | RING/U-box | 1 | 1 | |
| HAD-like | Acyl-CoA dehydrogenase C-terminal domain-like | 1 | 1 | |
| (Trans)glycosidases | Chitinase insertion domain | 1 | 1 | |
| Aspartate/glutamate racemase | Aspartate/glutamate racemase | 1 | 1 | |
| Formyltransferase | FMT C-terminal domain-like | 1 | 1 | |
| L domain-like | Protein kinase-like (PK-like) | 1 | 1 | |
| PAZ domain | Ribonuclease H-like | 1 | 1 | |
| Clavaminate synthase-like | Clavaminate synthase-like | 1 | 1 | |
| Carbamoyl phosphate synthetase, large subunit connection domain | Aspartate/ornithine carbamoyltransferase | 1 | 1 | |
| Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain | Nucleotidylyl transferase | 1 | 1 | |
| Protein kinase-like (PK-like) | Acyl-CoA dehydrogenase NM domain-like | 1 | 1 | |
| SH3-domain | DBL homology domain (DH-domain) | 1 | 1 | |
| SH2 domain | SH2 domain | 1 | 1 | |
| Probable ACP-binding domain of malonyl-CoA ACP transacylase | Inosine monophosphate dehydrogenase (IMPDH) | 1 | 1 | |
| RNA-binding domain, RBD | DPP6 N-terminal domain-like | 1 | 1 | |
| Metallo-dependent phosphatases | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Globin-like | Ferredoxin reductase-like, C-terminal NADP-linked domain | 1 | 1 | |
| CO dehydrogenase ISP C-domain like | Molybdenum cofactor-binding domain | 1 | 1 | |
| FAD/NAD(P)-binding domain | Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain | 1 | 1 | |
| Homeodomain-like | TPR-like | 1 | 1 | |
| Cobalamin (vitamin B12)-binding domain | Methionine synthase activation domain-like | 1 | 1 | |
| FAD-linked oxidases, C-terminal domain | alpha-helical ferredoxin | 1 | 1 | |
| PUA domain-like | Nucleotidylyl transferase | 1 | 1 | |
| PLC-like phosphodiesterases | TSP-1 type 1 repeat | 1 | 1 | |
| UBC-like | UBA-like | 1 | 1 | |
| RmlC-like cupins | ADP-ribosylation | 1 | 1 | |
| FMN-linked oxidoreductases | Alpha subunit of glutamate synthase, C-terminal domain | 1 | 1 | |
| HAD-like | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| EF-hand | cAMP-binding domain-like | 1 | 1 | |
| SH2 domain | Regulator of G-protein signaling, RGS | 1 | 1 | |
| HAD-like | PDZ domain-like | 1 | 1 | |
| vWA-like | Protein kinase-like (PK-like) | 1 | 1 | |
| Smc hinge domain | Tropomyosin | 1 | 1 | |
| FAD-linked reductases, C-terminal domain | 4Fe-4S ferredoxins | 1 | 1 | |
| Zn2/Cys6 DNA-binding domain | PYP-like sensor domain (PAS domain) | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Aldolase | 1 | 1 | |
| HisI-like | ALDH-like | 1 | 1 | |
| Dihydropteroate synthetase-like | Methionine synthase domain | 1 | 1 | |
| HLH, helix-loop-helix DNA-binding domain | HLH, helix-loop-helix DNA-binding domain | 1 | 1 | |
| Chaperone J-domain | CSL zinc finger | 1 | 1 | |
| Thioesterase/thiol ester dehydrase-isomerase | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| GTPase activation domain, GAP | RGC domain-like | 1 | 1 | |
| Blood coagulation inhibitor (disintegrin) | (Trans)glycosidases | 1 | 1 | |
| dsRNA-binding domain-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| CRAL/TRIO domain | GTPase activation domain, GAP | 1 | 1 | |
| Rudiment single hybrid motif | N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) | 1 | 1 | |
| Probable ACP-binding domain of malonyl-CoA ACP transacylase | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Dihydropteroate synthetase-like | Methionine synthase activation domain-like | 1 | 1 | |
| Trypsin-like serine proteases | Trypsin-like serine proteases | 1 | 1 | |
| Cu,Zn superoxide dismutase-like | Cu,Zn superoxide dismutase-like | 1 | 1 | |
| HAD-like | Starch-binding domain-like | 1 | 1 | |
| RmlC-like cupins | RmlC-like cupins | 1 | 1 | |
| "Winged helix" DNA-binding domain | FAD/NAD(P)-binding domain | 1 | 1 | |
| Protein kinase-like (PK-like) | Acyl-CoA dehydrogenase C-terminal domain-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | RING/U-box | 1 | 1 | |
| Nitrite and sulphite reductase 4Fe-4S domain-like | Nitrite and sulphite reductase 4Fe-4S domain-like | 1 | 1 | |
| TPR-like | Adenine nucleotide alpha hydrolases-like | 1 | 1 | |
| Galactose mutarotase-like | Glycosyl hydrolase domain | 1 | 1 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | BRCT domain | 1 | 1 | |
| ARM repeat | Ubiquitin-like | 1 | 1 | |
| Thioredoxin-like | ERP29 C domain-like | 1 | 1 | |
| PUG domain-like | FYVE/PHD zinc finger | 1 | 1 | |
| SPOC domain-like | C-terminal domain of Ku80 | 1 | 1 | |
| Rudiment single hybrid motif | PurM N-terminal domain-like | 1 | 1 | |
| Enolase N-terminal domain-like | Enolase C-terminal domain-like | 1 | 1 | |
| CO dehydrogenase flavoprotein C-terminal domain-like | Molybdenum cofactor-binding domain | 1 | 1 | |
| POZ domain | Skp1 dimerisation domain-like | 1 | 1 | |
| WW domain | FKBP-like | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Succinyl-CoA synthetase domains | 1 | 1 | |
| L domain-like | NTF2-like | 1 | 1 | |
| Homocysteine S-methyltransferase | Methionine synthase domain | 1 | 1 | |
| PIN domain-like | Nucleic acid-binding proteins | 1 | 1 | |
| Staphylococcal nuclease | Staphylococcal nuclease | 1 | 1 | |
| PK beta-barrel domain-like | Phosphoenolpyruvate/pyruvate domain | 1 | 1 | |
| PYP-like sensor domain (PAS domain) | PYP-like sensor domain (PAS domain) | 1 | 1 | |
| Dehydroquinate synthase-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Dom34/Pelota N-terminal domain-like | L30e-like | 1 | 1 | |
| Kelch motif | EGF/Laminin | 1 | 1 | |
| B-box zinc-binding domain | NHL repeat | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | Nucleotide-binding domain | 1 | 1 | |
| DAK1/DegV-like | DhaL-like | 1 | 1 | |
| BRCT domain | Lesion bypass DNA polymerase (Y-family), little finger domain | 1 | 1 | |
| L30e-like | Supernatant protein factor (SPF), C-terminal domain | 1 | 1 | |
| alpha-D-mannose-specific plant lectins | Pectin lyase-like | 1 | 1 | |
| Terpenoid cyclases/Protein prenyltransferases | Terpenoid cyclases/Protein prenyltransferases | 1 | 1 | |
| Calponin-homology domain, CH-domain | PH domain-like | 1 | 1 | |
| C2 domain (Calcium/lipid-binding domain, CaLB) | Fibronectin type III | 1 | 1 | |
| Metallo-dependent phosphatases | EF-hand | 1 | 1 | |
| Glycerol-3-phosphate (1)-acyltransferase | EF-hand | 1 | 1 | |
| Neurotransmitter-gated ion-channel transmembrane pore | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | Argininosuccinate synthetase, C-terminal domain | 1 | 1 | |
| Lipocalins | FAS1 domain | 1 | 1 | |
| Methylglyoxal synthase-like | Aspartate/ornithine carbamoyltransferase | 1 | 1 | |
| alpha/beta knot | Nucleic acid-binding proteins | 1 | 1 | |
| Metallo-dependent hydrolases | Bacterial exopeptidase dimerisation domain | 1 | 1 | |
| alpha-helical ferredoxin | 4Fe-4S ferredoxins | 1 | 1 | |
| FabD/lysophospholipase-like | 4'-phosphopantetheinyl transferase | 1 | 1 | |
