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 | |
|---|
| Carboxypeptidase regulatory domain-like | Porins | 86 | 6 |  |
| Starch-binding domain-like | Porins | 45 | 4 | |
| Sigma2 domain of RNA polymerase sigma factors | Sigma3 and sigma4 domains of RNA polymerase sigma factors | 31 | 4 | |
| Homodimeric domain of signal transducing histidine kinase | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 29 | 14 | |
| (Trans)glycosidases | Glycosyl hydrolase domain | 25 | 11 | |
| Galactose-binding domain-like | (Trans)glycosidases | 25 | 14 | |
| "Winged helix" DNA-binding domain | Periplasmic binding protein-like II | 24 | 1 | |
| Homeodomain-like | Homeodomain-like | 24 | 4 | |
| Homeodomain-like | Tetracyclin repressor-like, C-terminal domain | 24 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 21 | 4 | |
| P-loop containing nucleoside triphosphate hydrolases | P-loop containing nucleoside triphosphate hydrolases | 21 | 14 | |
| TPR-like | TPR-like | 20 | 11 | |
| beta-Galactosidase/glucuronidase domain | (Trans)glycosidases | 17 | 8 | |
| Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains | Multidrug efflux transporter AcrB transmembrane domain | 17 | 4 | |
| Galactose-binding domain-like | beta-Galactosidase/glucuronidase domain | 17 | 8 | |
| Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains | Multidrug efflux transporter AcrB transmembrane domain | 17 | 4 | |
| Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains | Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains | 17 | 4 | |
| Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains | Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains | 17 | 4 | |
| Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains | Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains | 17 | 4 | |
| Multidrug efflux transporter AcrB transmembrane domain | Multidrug efflux transporter AcrB transmembrane domain | 17 | 4 | |
| Composite domain of metallo-dependent hydrolases | Metallo-dependent hydrolases | 16 | 4 | |
| NAD(P)-binding Rossmann-fold domains | 6-phosphogluconate dehydrogenase C-terminal domain-like | 15 | 3 | |
| GroES-like | NAD(P)-binding Rossmann-fold domains | 15 | 1 | |
| lambda repressor-like DNA-binding domains | Periplasmic binding protein-like I | 14 | 1 | |
| Actin-like ATPase domain | Actin-like ATPase domain | 14 | 6 | |
| CheY-like | C-terminal effector domain of the bipartite response regulators | 14 | 1 | |
| CoA-dependent acyltransferases | CoA-dependent acyltransferases | 13 | 7 | |
| (Trans)glycosidases | Beta-D-glucan exohydrolase, C-terminal domain | 12 | 3 | |
| Protease propeptides/inhibitors | Subtilisin-like | 11 | 2 | |
| PYP-like sensor domain (PAS domain) | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 11 | 8 | |
| Thiamin diphosphate-binding fold (THDP-binding) | Thiamin diphosphate-binding fold (THDP-binding) | 11 | 4 | |
| PYP-like sensor domain (PAS domain) | Homodimeric domain of signal transducing histidine kinase | 11 | 8 | |
| C-terminal effector domain of the bipartite response regulators | TPR-like | 10 | 3 | |
| DPP6 N-terminal domain-like | alpha/beta-Hydrolases | 9 | 2 | |
| Zn-dependent exopeptidases | Bacterial exopeptidase dimerisation domain | 8 | 1 | |
| HAMP domain-like | Homodimeric domain of signal transducing histidine kinase | 8 | 2 | |
| HAMP domain-like | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 8 | 2 | |
| Acetyl-CoA synthetase-like | ACP-like | 8 | 8 | |
| P-loop containing nucleoside triphosphate hydrolases | Translation proteins | 7 | 5 | |
| PreATP-grasp domain | Glutathione synthetase ATP-binding domain-like | 7 | 5 | |
| Cupredoxins | Cupredoxins | 7 | 3 | |
| ABC transporter transmembrane region | P-loop containing nucleoside triphosphate hydrolases | 7 | 2 | |
| Calcium-dependent phosphotriesterase | Calcium-dependent phosphotriesterase | 7 | 3 | |
| E set domains | (Trans)glycosidases | 6 | 3 | |
| Acetyl-CoA synthetase-like | CoA-dependent acyltransferases | 6 | 6 | |
| Galactose-binding domain-like | Galactose-binding domain-like | 6 | 5 | |
| ACP-like | CoA-dependent acyltransferases | 6 | 6 | |
| "Winged helix" DNA-binding domain | NagB/RpiA/CoA transferase-like | 6 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Homeodomain-like | 6 | 5 | |
| "Winged helix" DNA-binding domain | GntR ligand-binding domain-like | 6 | 2 | |
| Thiolase-like | Thiolase-like | 6 | 2 | |
| MurD-like peptide ligases, catalytic domain | MurD-like peptide ligases, peptide-binding domain | 6 | 3 | |
| Multidrug resistance efflux transporter EmrE | Multidrug resistance efflux transporter EmrE | 6 | 1 | |
| Nucleotidylyl transferase | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 6 | 6 | |
| Nucleic acid-binding proteins | Nucleic acid-binding proteins | 6 | 5 | |
| HlyD-like secretion proteins | HlyD-like secretion proteins | 6 | 3 | |
| Phage tail proteins | gp5 N-terminal domain-like | 5 | 3 | |
| beta-Galactosidase/glucuronidase domain | beta-Galactosidase/glucuronidase domain | 5 | 3 | |
| Tricorn protease N-terminal domain | DPP6 N-terminal domain-like | 5 | 4 | |
| Calcium-dependent phosphotriesterase | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 5 | 2 | |
| Formate/glycerate dehydrogenase catalytic domain-like | NAD(P)-binding Rossmann-fold domains | 5 | 2 | |
| Thiamin diphosphate-binding fold (THDP-binding) | DHS-like NAD/FAD-binding domain | 5 | 1 | |
| PurM N-terminal domain-like | PurM C-terminal domain-like | 5 | 2 | |
| beta-N-acetylhexosaminidase-like domain | (Trans)glycosidases | 5 | 1 | |
| ACP-like | ACP-like | 5 | 5 | |
| cAMP-binding domain-like | "Winged helix" DNA-binding domain | 5 | 2 | |
| FAD/NAD(P)-binding domain | FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 5 | 2 | |
| Enolase N-terminal domain-like | Enolase C-terminal domain-like | 5 | 2 | |
| FAD/NAD(P)-binding domain | FAD-linked reductases, C-terminal domain | 5 | 2 | |
| "Winged helix" DNA-binding domain | GAF domain-like | 4 | 1 | |
| Class I glutamine amidotransferase-like | Homeodomain-like | 4 | 2 | |
| Phage tail proteins | Phage fibre proteins | 4 | 2 | |
| Ribosomal protein S5 domain 2-like | P-loop containing nucleoside triphosphate hydrolases | 4 | 3 | |
| PDZ domain-like | ClpP/crotonase | 4 | 4 | |
| Calcium-dependent phosphotriesterase | NHL repeat | 4 | 2 | |
| Thiamin diphosphate-binding fold (THDP-binding) | TK C-terminal domain-like | 4 | 2 | |
| Triger factor/SurA peptide-binding domain-like | FKBP-like | 4 | 4 | |
| gp5 N-terminal domain-like | Phage fibre proteins | 4 | 2 | |
| (Trans)glycosidases | Anthrax protective antigen | 4 | 1 | |
| Aminoacid dehydrogenase-like, N-terminal domain | NAD(P)-binding Rossmann-fold domains | 4 | 3 | |
| Galactose-binding domain-like | Glycosyl hydrolase domain | 4 | 3 | |
| CheY-like | Homodimeric domain of signal transducing histidine kinase | 4 | 4 | |
| C-terminal effector domain of the bipartite response regulators | DPP6 N-terminal domain-like | 4 | 4 | |
| Acetyl-CoA synthetase-like | Acetyl-CoA synthetase-like | 4 | 4 | |
| LuxS/MPP-like metallohydrolase | LuxS/MPP-like metallohydrolase | 4 | 3 | |
| Leukotriene A4 hydrolase N-terminal domain | Metalloproteases ("zincins"), catalytic domain | 4 | 3 | |
| Glutathione synthetase ATP-binding domain-like | Rudiment single hybrid motif | 4 | 2 | |
| CheY-like | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 4 | 4 | |
| Galactose mutarotase-like | Glycosyl hydrolase domain | 4 | 1 | |
| PYP-like sensor domain (PAS domain) | PYP-like sensor domain (PAS domain) | 4 | 4 | |
| Protein kinase-like (PK-like) | TPR-like | 4 | 4 | |
| "Winged helix" DNA-binding domain | Dimeric alpha+beta barrel | 4 | 1 | |
| Ribosomal protein S5 domain 2-like | GHMP Kinase, C-terminal domain | 4 | 2 | |
| PreATP-grasp domain | Rudiment single hybrid motif | 4 | 2 | |
| Beta-D-glucan exohydrolase, C-terminal domain | Anthrax protective antigen | 4 | 1 | |
| Glycoside hydrolase/deacetylase | Families 57/38 glycoside transferase middle domain | 4 | 3 | |
| Methylated DNA-protein cysteine methyltransferase domain | Methylated DNA-protein cysteine methyltransferase, C-terminal domain | 4 | 3 | |
| Double Clp-N motif | P-loop containing nucleoside triphosphate hydrolases | 4 | 2 | |
| E set domains | Glycosyl hydrolase domain | 4 | 2 | |
| Galactose mutarotase-like | (Trans)glycosidases | 4 | 1 | |
| MurCD N-terminal domain | MurD-like peptide ligases, peptide-binding domain | 3 | 1 | |
| CoA-dependent acyltransferases | alpha/beta-Hydrolases | 3 | 3 | |
| Calcium ATPase, transduction domain A | Calcium ATPase, transmembrane domain M | 3 | 3 | |
| Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase | Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase | 3 | 2 | |
| Homeodomain-like | Ribonuclease H-like | 3 | 1 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | Nucleic acid-binding proteins | 3 | 3 | |
| Nucleic acid-binding proteins | RuvA domain 2-like | 3 | 3 | |
| Glycoside hydrolase/deacetylase | Galactose mutarotase-like | 3 | 2 | |
| FAD-binding/transporter-associated domain-like | FAD-linked oxidases, C-terminal domain | 3 | 1 | |
| 4Fe-4S ferredoxins | Formate dehydrogenase/DMSO reductase, domains 1-3 | 3 | 3 | |
| EF-G C-terminal domain-like | EF-G C-terminal domain-like | 3 | 2 | |
| MurCD N-terminal domain | MurD-like peptide ligases, catalytic domain | 3 | 1 | |
| CheY-like | P-loop containing nucleoside triphosphate hydrolases | 3 | 2 | |
| HAD-like | Calcium ATPase, transmembrane domain M | 3 | 3 | |
| FAD-linked oxidases, C-terminal domain | alpha-helical ferredoxin | 3 | 1 | |
| 6-phosphogluconate dehydrogenase C-terminal domain-like | UDP-glucose/GDP-mannose dehydrogenase C-terminal domain | 3 | 1 | |
| Families 57/38 glycoside transferase middle domain | Galactose mutarotase-like | 3 | 2 | |
| Nitrite and sulphite reductase 4Fe-4S domain-like | Nitrite and sulphite reductase 4Fe-4S domain-like | 3 | 1 | |
| ParB/Sulfiredoxin | KorB DNA-binding domain-like | 3 | 1 | |
| FabD/lysophospholipase-like | Probable ACP-binding domain of malonyl-CoA ACP transacylase | 3 | 2 | |
| Translation proteins | EF-G C-terminal domain-like | 3 | 2 | |
| NAD(P)-binding Rossmann-fold domains | UDP-glucose/GDP-mannose dehydrogenase C-terminal domain | 3 | 1 | |
| DNA repair protein MutS, domain III | P-loop containing nucleoside triphosphate hydrolases | 3 | 3 | |
| Ribosomal protein S5 domain 2-like | Ribosomal protein S5 domain 2-like | 3 | 2 | |
| "Winged helix" DNA-binding domain | Chorismate lyase-like | 3 | 1 | |
| FAD-binding/transporter-associated domain-like | alpha-helical ferredoxin | 3 | 1 | |
| NHL repeat | NHL repeat | 3 | 3 | |
| "Winged helix" DNA-binding domain | Actin-like ATPase domain | 3 | 1 | |
| Fibronectin type III | Galactose-binding domain-like | 3 | 3 | |
| GAF domain-like | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 3 | 3 | |
| Cobalamin (vitamin B12)-binding domain | Radical SAM enzymes | 3 | 1 | |
| Nitrite/Sulfite reductase N-terminal domain-like | Nitrite/Sulfite reductase N-terminal domain-like | 3 | 1 | |
| Acyl-CoA dehydrogenase NM domain-like | Acyl-CoA dehydrogenase C-terminal domain-like | 3 | 1 | |
| Nucleic acid-binding proteins | Translation proteins SH3-like domain | 3 | 2 | |
| Acetyl-CoA synthetase-like | alpha/beta-Hydrolases | 3 | 3 | |
| Class II aaRS and biotin synthetases | Class II aaRS ABD-related | 3 | 3 | |
| PDZ domain-like | PDZ domain-like | 3 | 3 | |
| Translation proteins | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 3 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | post-AAA+ oligomerization domain-like | 3 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | Class I glutamine amidotransferase-like | 3 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 3 | 2 | |
| cAMP-binding domain-like | FAD/NAD(P)-binding domain | 3 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | EF-G C-terminal domain-like | 3 | 2 | |
| GAF domain-like | Homodimeric domain of signal transducing histidine kinase | 3 | 3 | |
| Fibronectin type III | Fibronectin type III | 3 | 3 | |
| Phosphoglucomutase, first 3 domains | Phosphoglucomutase, C-terminal domain | 3 | 3 | |
| Nitrite/Sulfite reductase N-terminal domain-like | Nitrite and sulphite reductase 4Fe-4S domain-like | 3 | 1 | |
| Phosphoglucomutase, first 3 domains | Phosphoglucomutase, first 3 domains | 3 | 3 | |
| Nucleic acid-binding proteins | Class II aaRS and biotin synthetases | 3 | 2 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | Ribosomal protein S5 domain 2-like | 3 | 3 | |
| GreA transcript cleavage protein, N-terminal domain | FKBP-like | 3 | 1 | |
| ValRS/IleRS/LeuRS editing domain | Nucleotidylyl transferase | 3 | 3 | |
| ValRS/IleRS/LeuRS editing domain | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 3 | 3 | |
| ACP-like | alpha/beta-Hydrolases | 3 | 3 | |
| CheY-like | Homeodomain-like | 3 | 2 | |
| E set domains | E set domains | 3 | 3 | |
| Calcium ATPase, transduction domain A | HAD-like | 3 | 3 | |
| Carbohydrate binding domain | (Trans)glycosidases | 2 | 2 | |
| "Winged helix" DNA-binding domain | PLP-dependent transferases | 2 | 1 | |
| Nucleotidyltransferase | ACT-like | 2 | 2 | |
| ACT-like | ACT-like | 2 | 2 | |
| Creatinase/prolidase N-terminal domain | Creatinase/aminopeptidase | 2 | 1 | |
| Formate dehydrogenase/DMSO reductase, domains 1-3 | ADC-like | 2 | 2 | |
| Cytochrome c oxidase subunit II-like, transmembrane region | Cytochrome c | 2 | 1 | |
| PUA domain-like | Ribosomal protein S5 domain 2-like | 2 | 1 | |
| "Winged helix" DNA-binding domain | "Winged helix" DNA-binding domain | 2 | 2 | |
| Concanavalin A-like lectins/glucanases | Ricin B-like lectins | 2 | 1 | |
| Tricorn protease N-terminal domain | ClpP/crotonase | 2 | 2 | |
| PLP-binding barrel | Alanine racemase C-terminal domain-like | 2 | 2 | |
| NAD(P)-binding Rossmann-fold domains | ACT-like | 2 | 2 | |
| Ada DNA repair protein, N-terminal domain (N-Ada 10) | Homeodomain-like | 2 | 2 | |
| Concanavalin A-like lectins/glucanases | Galactose-binding domain-like | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | ARM repeat | 2 | 2 | |
| Pectin lyase-like | Fibronectin type III | 2 | 2 | |
| CO dehydrogenase molybdoprotein N-domain-like | Molybdenum cofactor-binding domain | 2 | 1 | |
| Clc chloride channel | CBS-domain pair | 2 | 1 | |
| Ricin B-like lectins | (Trans)glycosidases | 2 | 2 | |
| 2Fe-2S ferredoxin-like | CO dehydrogenase ISP C-domain like | 2 | 1 | |
| MurE/MurF N-terminal domain | MurD-like peptide ligases, peptide-binding domain | 2 | 1 | |
| Nucleic acid-binding proteins | P-loop containing nucleoside triphosphate hydrolases | 2 | 2 | |
| Actin-like ATPase domain | Heat shock protein 70kD (HSP70), peptide-binding domain | 2 | 2 | |
| Cupredoxins | Cytochrome c | 2 | 1 | |
| CheY-like | CheY-like | 2 | 2 | |
| CheY-like | PYP-like sensor domain (PAS domain) | 2 | 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 | 2 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | "Winged helix" DNA-binding domain | 2 | 2 | |
| Lysozyme-like | beta-lactamase/transpeptidase-like | 2 | 2 | |
| Metal cation-transporting ATPase, ATP-binding domain N | HAD-like | 2 | 2 | |
| ACP-like | NAD(P)-binding Rossmann-fold domains | 2 | 2 | |
| Penicillin binding protein dimerisation domain | beta-lactamase/transpeptidase-like | 2 | 2 | |
| MetI-like | MetI-like | 2 | 1 | |
| N-terminal domain of MutM-like DNA repair proteins | S13-like H2TH domain | 2 | 2 | |
| TPR-like | Carbohydrate-binding domain | 2 | 1 | |
| Arabinanase/levansucrase/invertase | Concanavalin A-like lectins/glucanases | 2 | 1 | |
| Cadherin-like | Cadherin-like | 2 | 2 | |
| 2Fe-2S ferredoxin-like | Formate dehydrogenase/DMSO reductase, domains 1-3 | 2 | 2 | |
| Ribosomal protein S5 domain 2-like | Ribonuclease PH domain 2-like | 2 | 2 | |
| Galactose-binding domain-like | Six-hairpin glycosidases | 2 | 2 | |
| E set domains | Pectin lyase-like | 2 | 2 | |
| L30e-like | alpha/beta knot | 2 | 1 | |
| DPP6 N-terminal domain-like | DPP6 N-terminal domain-like | 2 | 2 | |
| Cytochrome c oxidase subunit II-like, transmembrane region | Cupredoxins | 2 | 1 | |
| FAD/NAD(P)-binding domain | Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain | 2 | 1 | |
| Cation efflux protein transmembrane domain-like | Cation efflux protein cytoplasmic domain-like | 2 | 2 | |
| FAD-binding/transporter-associated domain-like | CO dehydrogenase flavoprotein C-terminal domain-like | 2 | 1 | |
| Acetyl-CoA synthetase-like | Thiolase-like | 2 | 2 | |
| Phage tail proteins | Phage tail proteins | 2 | 1 | |
| Ada DNA repair protein, N-terminal domain (N-Ada 10) | Methylated DNA-protein cysteine methyltransferase domain | 2 | 2 | |
| HD-domain/PDEase-like | ACT-like | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | C-terminal domain of alpha and beta subunits of F1 ATP synthase | 2 | 1 | |
| Heat shock protein 70kD (HSP70), peptide-binding domain | Heat shock protein 70kD (HSP70), C-terminal subdomain | 2 | 2 | |
| HSP40/DnaJ peptide-binding domain | HSP40/DnaJ peptide-binding domain | 2 | 2 | |
| Alpha-L RNA-binding motif | Pseudouridine synthase | 2 | 2 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 2 | 2 | |
| Nitrous oxide reductase, N-terminal domain | Alkaline phosphatase-like | 2 | 2 | |
| Chaperone J-domain | HSP40/DnaJ peptide-binding domain | 2 | 2 | |
| NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | 2 | 2 | |
| Nucleotidyltransferase | HD-domain/PDEase-like | 2 | 2 | |
| Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain | Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain | 2 | 2 | |
| N-terminal domain of alpha and beta subunits of F1 ATP synthase | P-loop containing nucleoside triphosphate hydrolases | 2 | 1 | |
| MFS general substrate transporter | MFS general substrate transporter | 2 | 2 | |
| Actin-like ATPase domain | Heat shock protein 70kD (HSP70), C-terminal subdomain | 2 | 2 | |
| FAD/NAD(P)-binding domain | Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | 2 | 1 | |
| Regulatory protein AraC | Homeodomain-like | 2 | 1 | |
| Calcium-dependent phosphotriesterase | Cadherin-like | 2 | 2 | |
| Acetyl-CoA synthetase-like | NAD(P)-binding Rossmann-fold domains | 2 | 2 | |
| Phospholipase D/nuclease | Phospholipase D/nuclease | 2 | 2 | |
| Metal cation-transporting ATPase, ATP-binding domain N | Calcium ATPase, transmembrane domain M | 2 | 2 | |
| tRNA-binding arm | Class II aaRS and biotin synthetases | 2 | 1 | |
| (Trans)glycosidases | Class I glutamine amidotransferase-like | 2 | 2 | |
| FucI/AraA N-terminal and middle domains | FucI/AraA C-terminal domain-like | 2 | 1 | |
| Homeodomain-like | Methylated DNA-protein cysteine methyltransferase, C-terminal domain | 2 | 2 | |
| Calcium ATPase, transduction domain A | Metal cation-transporting ATPase, ATP-binding domain N | 2 | 2 | |
| Tricorn protease N-terminal domain | PDZ domain-like | 2 | 2 | |
| N-terminal domain of MutM-like DNA repair proteins | Glucocorticoid receptor-like (DNA-binding domain) | 2 | 2 | |
| "Winged helix" DNA-binding domain | C-terminal domain of arginine repressor | 2 | 1 | |
| PA domain | Zn-dependent exopeptidases | 2 | 2 | |
| ISP domain | Bet v1-like | 2 | 1 | |
| Trypsin-like serine proteases | PDZ domain-like | 2 | 2 | |
| Concanavalin A-like lectins/glucanases | Fibronectin type III | 2 | 2 | |
| Glucocorticoid receptor-like (DNA-binding domain) | P-loop containing nucleoside triphosphate hydrolases | 2 | 2 | |
| Carboxypeptidase regulatory domain-like | TPR-like | 2 | 2 | |
| Homeodomain-like | Methylated DNA-protein cysteine methyltransferase domain | 2 | 2 | |
| DnaJ/Hsp40 cysteine-rich domain | HSP40/DnaJ peptide-binding domain | 2 | 2 | |
| Nucleotide-diphospho-sugar transferases | Trimeric LpxA-like enzymes | 2 | 1 | |
| Chaperone J-domain | DnaJ/Hsp40 cysteine-rich domain | 2 | 2 | |
| alpha/beta-Hydrolases | Galactose-binding domain-like | 2 | 2 | |
| ACP-like | Thiolase-like | 2 | 2 | |
| Translation proteins | ThrRS/AlaRS common domain | 2 | 2 | |
| Thiolase-like | NAD(P)-binding Rossmann-fold domains | 2 | 2 | |
| Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain | 2 | 1 | |
| RmlC-like cupins | Homeodomain-like | 2 | 2 | |
| Ada DNA repair protein, N-terminal domain (N-Ada 10) | Methylated DNA-protein cysteine methyltransferase, C-terminal domain | 2 | 2 | |
| CBS-domain pair | FAD-binding/transporter-associated domain-like | 2 | 1 | |
| C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase | Alkaline phosphatase-like | 2 | 2 | |
| Peptidase/esterase 'gauge' domain | alpha/beta-Hydrolases | 2 | 1 | |
| Nucleotidyltransferase | Poly A polymerase C-terminal region-like | 2 | 2 | |
| PYP-like sensor domain (PAS domain) | GAF domain-like | 2 | 2 | |
| Cupredoxins | Carboxypeptidase regulatory domain-like | 2 | 2 | |
| ThrRS/AlaRS common domain | Class II aaRS and biotin synthetases | 2 | 2 | |
| MurE/MurF N-terminal domain | MurD-like peptide ligases, catalytic domain | 2 | 1 | |
| S13-like H2TH domain | Glucocorticoid receptor-like (DNA-binding domain) | 2 | 2 | |
| PUA domain-like | P-loop containing nucleoside triphosphate hydrolases | 2 | 1 | |
| "Winged helix" DNA-binding domain | Periplasmic binding protein-like I | 2 | 1 | |
| Integrin alpha N-terminal domain | Integrin alpha N-terminal domain | 2 | 2 | |
| Cytochrome c | Cytochrome c | 2 | 2 | |
| Nicotinate/Quinolinate PRTase N-terminal domain-like | Nicotinate/Quinolinate PRTase C-terminal domain-like | 2 | 1 | |
| 2Fe-2S ferredoxin-like | 4Fe-4S ferredoxins | 2 | 2 | |
| IlvD/EDD N-terminal domain-like | LeuD/IlvD-like | 2 | 1 | |
| Riboflavin synthase domain-like | Ferredoxin reductase-like, C-terminal NADP-linked domain | 2 | 2 | |
| Tetrapyrrole methylase | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| PIN domain-like | DNA/RNA polymerases | 1 | 1 | |
| Thioredoxin-like | Thioredoxin-like | 1 | 1 | |
| Aldolase | AFP III-like domain | 1 | 1 | |
| Single hybrid motif | Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | 1 | 1 | |
| DNA repair protein MutS, domain II | DNA repair protein MutS, domain III | 1 | 1 | |
| MgtE N-terminal domain-like | CBS-domain pair | 1 | 1 | |
| ClpP/crotonase | ClpP/crotonase | 1 | 1 | |
| DNA-binding domain of intron-encoded endonucleases | DNA-binding domain of intron-encoded endonucleases | 1 | 1 | |
| Nucleic acid-binding proteins | HD-domain/PDEase-like | 1 | 1 | |
| ATP-dependent DNA ligase DNA-binding domain | DNA ligase/mRNA capping enzyme, catalytic domain | 1 | 1 | |
| Quinoprotein alcohol dehydrogenase-like | Fibronectin type III | 1 | 1 | |
| Tex N-terminal region-like | Ribonuclease H-like | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Nucleic acid-binding proteins | 1 | 1 | |
| Transmembrane di-heme cytochromes | Cytochrome c | 1 | 1 | |
| Chemotaxis receptor methyltransferase CheR, N-terminal domain | PYP-like sensor domain (PAS domain) | 1 | 1 | |
| 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain | Alkaline phosphatase-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Initiation factor IF2/eIF5b, domain 3 | 1 | 1 | |
| PGBD-like | L,D-transpeptidase catalytic domain-like | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | HSP90 C-terminal domain | 1 | 1 | |
| Ribonuclease PH domain 2-like | Nucleic acid-binding proteins | 1 | 1 | |
| 2Fe-2S ferredoxin-like | alpha-helical ferredoxin | 1 | 1 | |
| Cyclophilin-like | Single hybrid motif | 1 | 1 | |
| Nucleotidylyl transferase | Nucleic acid-binding proteins | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | HRDC-like | 1 | 1 | |
| PA domain | Transferrin receptor-like dimerisation domain | 1 | 1 | |
| YjeF N-terminal domain-like | Ribokinase-like | 1 | 1 | |
| beta-Galactosidase/glucuronidase domain | Immunoglobulin | 1 | 1 | |
| (Trans)glycosidases | Protein kinase-like (PK-like) | 1 | 1 | |
| PLP-dependent transferases | Ornithine decarboxylase C-terminal domain | 1 | 1 | |
| Thiolase-like | Probable ACP-binding domain of malonyl-CoA ACP transacylase | 1 | 1 | |
| Cryptochrome/photolyase, N-terminal domain | Cryptochrome/photolyase FAD-binding domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Helical scaffold and wing domains of SecA | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Hypothetical protein YjiA, C-terminal domain | 1 | 1 | |
| Lysozyme-like | LysM domain | 1 | 1 | |
| ACT-like | Formyltransferase | 1 | 1 | |
| DNA repair protein MutS, domain II | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Integrin alpha N-terminal domain | NHL repeat | 1 | 1 | |
| Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | ThrRS/AlaRS common domain | 1 | 1 | |
| TROVE domain-like | vWA-like | 1 | 1 | |
| Class II aaRS and biotin synthetases | YbaK/ProRS associated domain | 1 | 1 | |
| Periplasmic binding protein-like II | Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain | 1 | 1 | |
| FMN-binding split barrel | FMN-binding split barrel | 1 | 1 | |
| Alkaline phosphatase-like | Concanavalin A-like lectins/glucanases | 1 | 1 | |
| Sigma2 domain of RNA polymerase sigma factors | NTF2-like | 1 | 1 | |
| S-adenosyl-L-methionine-dependent methyltransferases | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | HSP90 C-terminal domain | 1 | 1 | |
| Trigger factor ribosome-binding domain | FKBP-like | 1 | 1 | |
| CBS-domain pair | Inosine monophosphate dehydrogenase (IMPDH) | 1 | 1 | |
| FGAM synthase PurL, linker domain | PurM N-terminal domain-like | 1 | 1 | |
| Concanavalin A-like lectins/glucanases | Cadherin-like | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Methylglyoxal synthase-like | 1 | 1 | |
| TGS-like | ThrRS/AlaRS common domain | 1 | 1 | |
| Homo-oligomeric flavin-containing Cys decarboxylases, HFCD | CoaB-like | 1 | 1 | |
| Pectin lyase-like | (Trans)glycosidases | 1 | 1 | |
| Folate-binding domain | Aminomethyltransferase beta-barrel domain | 1 | 1 | |
| Galactose-binding domain-like | Immunoglobulin | 1 | 1 | |
| RuvA domain 2-like | DNA helicase RuvA subunit, C-terminal domain | 1 | 1 | |
| Fibronectin type III | Type I dockerin domain | 1 | 1 | |
| GIY-YIG endonuclease | RuvA domain 2-like | 1 | 1 | |
| Respiratory nitrate reductase 1 gamma chain | alpha-helical ferredoxin | 1 | 1 | |
| HAD-like | UDP-Glycosyltransferase/glycogen phosphorylase | 1 | 1 | |
| Quinoprotein alcohol dehydrogenase-like | Ricin B-like lectins | 1 | 1 | |
| Actin-like ATPase domain | HD-domain/PDEase-like | 1 | 1 | |
| Tex N-terminal region-like | Nucleic acid-binding proteins | 1 | 1 | |
| UBA-like | Elongation factor Ts (EF-Ts), dimerisation domain | 1 | 1 | |
| PPK N-terminal domain-like | PHP14-like | 1 | 1 | |
| all-alpha NTP pyrophosphatases | all-alpha NTP pyrophosphatases | 1 | 1 | |
| Sigma3 and sigma4 domains of RNA polymerase sigma factors | NTF2-like | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Single hybrid motif | 1 | 1 | |
| RuvA domain 2-like | BRCT domain | 1 | 1 | |
| Putative DNA-binding domain | Class II aaRS and biotin synthetases | 1 | 1 | |
| TIMP-like | Starch-binding domain-like | 1 | 1 | |
| SIS domain | CBS-domain pair | 1 | 1 | |
| "Winged helix" DNA-binding domain | LexA/Signal peptidase | 1 | 1 | |
| TGS-like | Class II aaRS ABD-related | 1 | 1 | |
| PheT/TilS domain | Class II aaRS and biotin synthetases | 1 | 1 | |
| PYP-like sensor domain (PAS domain) | Homeodomain-like | 1 | 1 | |
| NagB/RpiA/CoA transferase-like | alpha-helical ferredoxin | 1 | 1 | |
| Ribonuclease PH domain 2-like | Eukaryotic type KH-domain (KH-domain type I) | 1 | 1 | |
| ACP-like | Glycerol-3-phosphate (1)-acyltransferase | 1 | 1 | |
| DPP6 N-terminal domain-like | 3-carboxy-cis,cis-mucoante lactonizing enzyme | 1 | 1 | |
| HIT-like | HIT-like | 1 | 1 | |
| Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | tRNA-binding arm | 1 | 1 | |
| Arabinanase/levansucrase/invertase | Galactose-binding domain-like | 1 | 1 | |
| Cysteine proteinases | TPR-like | 1 | 1 | |
| C-terminal effector domain of the bipartite response regulators | YVTN repeat-like/Quinoprotein amine dehydrogenase | 1 | 1 | |
| CheY-like | Nucleotide cyclase | 1 | 1 | |
| CheY-like | FAD/NAD(P)-binding domain | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Type II DNA topoisomerase | 1 | 1 | |
| Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 1 | 1 | |
| Methylesterase CheB, C-terminal domain | PYP-like sensor domain (PAS domain) | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | MesJ substrate recognition domain-like | 1 | 1 | |
| MoeA N-terminal region -like | Molybdenum cofactor biosynthesis proteins | 1 | 1 | |
| DNA clamp | DNA clamp | 1 | 1 | |
| Thiolase-like | FabD/lysophospholipase-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Pre-protein crosslinking domain of SecA | 1 | 1 | |
| Putative DNA-binding domain | MOP-like | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | Alpha subunit of glutamate synthase, C-terminal domain | 1 | 1 | |
| Chemotaxis receptor methyltransferase CheR, N-terminal domain | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 1 | 1 | |
| Fibronectin type III | (Trans)glycosidases | 1 | 1 | |
| Sm-like ribonucleoproteins | Mechanosensitive channel protein MscS (YggB), C-terminal domain | 1 | 1 | |
| 4Fe-4S ferredoxins | ADC-like | 1 | 1 | |
| TolB, N-terminal domain | Tricorn protease N-terminal domain | 1 | 1 | |
| S-adenosylmethionine synthetase | S-adenosylmethionine synthetase | 1 | 1 | |
| Single hybrid motif | Single hybrid motif | 1 | 1 | |
| Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | Translation proteins | 1 | 1 | |
| Tetrapyrrole methylase | Tetrapyrrole methylase | 1 | 1 | |
| Translation proteins | Translation proteins | 1 | 1 | |
| Nucleotidylyl transferase | Riboflavin kinase-like | 1 | 1 | |
| DNA repair protein MutS, domain I | DNA repair protein MutS, domain III | 1 | 1 | |
| GIY-YIG endonuclease | C-terminal UvrC-binding domain of UvrB | 1 | 1 | |
| (Trans)glycosidases | Nucleotide-diphospho-sugar transferases | 1 | 1 | |
| DinB/YfiT-like putative metalloenzymes | C-type lectin-like | 1 | 1 | |
| GAF domain-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Quinoprotein alcohol dehydrogenase-like | Tricorn protease domain 2 | 1 | 1 | |
| Carbon-nitrogen hydrolase | Adenine nucleotide alpha hydrolases-like | 1 | 1 | |
| DPP6 N-terminal domain-like | PDZ domain-like | 1 | 1 | |
| Probable ACP-binding domain of malonyl-CoA ACP transacylase | CoA-dependent acyltransferases | 1 | 1 | |
| Methylesterase CheB, C-terminal domain | Homodimeric domain of signal transducing histidine kinase | 1 | 1 | |
| HemD-like | CheY-like | 1 | 1 | |
| Rudiment single hybrid motif | Cyclophilin-like | 1 | 1 | |
| CarD-like | TRCF domain-like | 1 | 1 | |
| Quinoprotein alcohol dehydrogenase-like | Concanavalin A-like lectins/glucanases | 1 | 1 | |
| C-terminal effector domain of the bipartite response regulators | 3-carboxy-cis,cis-mucoante lactonizing enzyme | 1 | 1 | |
| C-terminal effector domain of the bipartite response regulators | Tricorn protease N-terminal domain | 1 | 1 | |
| Glutamyl tRNA-reductase catalytic, N-terminal domain | Glutamyl tRNA-reductase dimerization domain | 1 | 1 | |
| Galactose-binding domain-like | SGNH hydrolase | 1 | 1 | |
| ADC synthase | D-aminoacid aminotransferase-like PLP-dependent enzymes | 1 | 1 | |
| LmbE-like | Class I glutamine amidotransferase-like | 1 | 1 | |
| FabD/lysophospholipase-like | Acetyl-CoA synthetase-like | 1 | 1 | |
| Macro domain-like | Zn-dependent exopeptidases | 1 | 1 | |
| Galactose oxidase, central domain | YVTN repeat-like/Quinoprotein amine dehydrogenase | 1 | 1 | |
| Dihydropteroate synthetase-like | Cobalamin (vitamin B12)-binding domain | 1 | 1 | |
| Glycosyl hydrolase domain | Protein kinase-like (PK-like) | 1 | 1 | |
| Eukaryotic type KH-domain (KH-domain type I) | Nucleic acid-binding proteins | 1 | 1 | |
| PurM C-terminal domain-like | PurM C-terminal domain-like | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Eukaryotic type KH-domain (KH-domain type I) | 1 | 1 | |
| Prokaryotic type KH domain (KH-domain type II) | Rad51 N-terminal domain-like | 1 | 1 | |
| Cyclophilin-like | Cyclophilin-like | 1 | 1 | |
| DPP6 N-terminal domain-like | ClpP/crotonase | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | DNA mismatch repair protein MutL | 1 | 1 | |
| Rhodanese/Cell cycle control phosphatase | Rhodanese/Cell cycle control phosphatase | 1 | 1 | |
| Sialidases | Sialidases | 1 | 1 | |
| RuvA domain 2-like | RuvA domain 2-like | 1 | 1 | |
| Transcription factor NusA, N-terminal domain | Nucleic acid-binding proteins | 1 | 1 | |
| Methionine synthase domain | Cobalamin (vitamin B12)-binding domain | 1 | 1 | |
| Concanavalin A-like lectins/glucanases | beta-Galactosidase/glucuronidase domain | 1 | 1 | |
| Alpha-L RNA-binding motif | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| Zinc beta-ribbon | Zinc beta-ribbon | 1 | 1 | |
| N-utilization substance G protein NusG, N-terminal domain | Translation proteins SH3-like domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Signal peptide-binding domain | 1 | 1 | |
| Dimeric alpha+beta barrel | Dimeric alpha+beta barrel | 1 | 1 | |
| PreATP-grasp domain | Methylglyoxal synthase-like | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Serine metabolism enzymes domain | 1 | 1 | |
| Class II aaRS and biotin synthetases | Anticodon-binding domain of PheRS | 1 | 1 | |
| E set domains | C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase | 1 | 1 | |
| N-terminal domain of DnaB helicase | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| PKD domain | Six-hairpin glycosidases | 1 | 1 | |
| PUA domain-like | alpha/beta knot | 1 | 1 | |
| Obg GTP-binding protein N-terminal domain | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Fibronectin type III | Cadherin-like | 1 | 1 | |
| beta-lactamase/transpeptidase-like | Penicillin-binding protein 2x (pbp-2x), c-terminal domain | 1 | 1 | |
| PreATP-grasp domain | Cyclophilin-like | 1 | 1 | |
| alpha-helical ferredoxin | Nucleotide-binding domain | 1 | 1 | |
| FabD/lysophospholipase-like | FabD/lysophospholipase-like | 1 | 1 | |
| Glutamyl tRNA-reductase catalytic, N-terminal domain | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Mechanosensitive channel protein MscS (YggB), transmembrane region | Sm-like ribonucleoproteins | 1 | 1 | |
| HRDC-like | HRDC-like | 1 | 1 | |
| Formate/glycerate dehydrogenase catalytic domain-like | ACT-like | 1 | 1 | |
| DNA repair protein MutS, domain I | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Nucleotidylyl transferase | Alpha-L RNA-binding motif | 1 | 1 | |
| SGNH hydrolase | SGNH hydrolase | 1 | 1 | |
| Molybdenum cofactor biosynthesis proteins | MoeA C-terminal domain-like | 1 | 1 | |
| ALDH-like | ALDH-like | 1 | 1 | |
| Glutamine synthetase, N-terminal domain | Glutamine synthetase/guanido kinase | 1 | 1 | |
| PreATP-grasp domain | PH0987 N-terminal domain-like | 1 | 1 | |
| C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase | DPP6 N-terminal domain-like | 1 | 1 | |
| Class II aaRS and biotin synthetases | Translation proteins | 1 | 1 | |
| Chemotaxis receptor methyltransferase CheR, N-terminal domain | Homodimeric domain of signal transducing histidine kinase | 1 | 1 | |
| NusB-like | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| DNA methylase specificity domain | DNA methylase specificity domain | 1 | 1 | |
| Dihydropteroate synthetase-like | Methionine synthase activation domain-like | 1 | 1 | |
| dsRNA-binding domain-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| L9 N-domain-like | Ribosomal protein L9 C-domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | TGS-like | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | SIS domain | 1 | 1 | |
| Nucleic acid-binding proteins | Rad51 N-terminal domain-like | 1 | 1 | |
| Cyclophilin-like | PH0987 N-terminal domain-like | 1 | 1 | |
| Tex N-terminal region-like | RuvA domain 2-like | 1 | 1 | |
| Ribosomal protein L7/12, oligomerisation (N-terminal) domain | ClpS-like | 1 | 1 | |
| Zn-dependent exopeptidases | Transferrin receptor-like dimerisation domain | 1 | 1 | |
| YhbC-like, N-terminal domain | YhbC-like, C-terminal domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Probable GTPase Der, C-terminal domain | 1 | 1 | |
| Metallo-dependent phosphatases | DNA ligase/mRNA capping enzyme, catalytic domain | 1 | 1 | |
| "Winged helix" DNA-binding domain | Iron-dependent repressor protein, dimerization domain | 1 | 1 | |
| Quinoprotein alcohol dehydrogenase-like | Type I dockerin domain | 1 | 1 | |
| PHP14-like | Phospholipase D/nuclease | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | TRCF domain-like | 1 | 1 | |
| Ricin B-like lectins | Pectin lyase-like | 1 | 1 | |
| ISP domain | FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | Adenine nucleotide alpha hydrolases-like | 1 | 1 | |
| FMN-linked oxidoreductases | 4Fe-4S ferredoxins | 1 | 1 | |
| Ribonuclease H-like | RuvA domain 2-like | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | DHS-like NAD/FAD-binding domain | 1 | 1 | |
| Quinoprotein alcohol dehydrogenase-like | Cadherin-like | 1 | 1 | |
| FMN-linked oxidoreductases | Alpha subunit of glutamate synthase, C-terminal domain | 1 | 1 | |
| TIMP-like | Cna protein B-type domain | 1 | 1 | |
| LysM domain | LysM domain | 1 | 1 | |
| Nucleic acid-binding proteins | BRCT domain | 1 | 1 | |
| PEP carboxykinase N-terminal domain | PEP carboxykinase-like | 1 | 1 | |
| DNA topoisomerase I domain | DNA breaking-rejoining enzymes | 1 | 1 | |
| Phosphoenolpyruvate/pyruvate domain | PK C-terminal domain-like | 1 | 1 | |
| Ricin B-like lectins | Ricin B-like lectins | 1 | 1 | |
| Insert subdomain of RNA polymerase alpha subunit | C-terminal domain of RNA polymerase alpha subunit | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain | 1 | 1 | |
| Class II aaRS and biotin synthetases | Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | 1 | 1 | |
| PPK N-terminal domain-like | Phospholipase D/nuclease | 1 | 1 | |
| Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain | Nucleotidylyl transferase | 1 | 1 | |
| EF-G C-terminal domain-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| Thiolase-like | CoA-dependent acyltransferases | 1 | 1 | |
| FAD-binding/transporter-associated domain-like | Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain | 1 | 1 | |
| Formyltransferase | FMT C-terminal domain-like | 1 | 1 | |
| cAMP-binding domain-like | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 1 | 1 | |
| HemD-like | GAF domain-like | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | Type II DNA topoisomerase | 1 | 1 | |
| Glutamine synthetase/guanido kinase | GatB/YqeY motif | 1 | 1 | |
| Fucose-specific lectin | Fucose-specific lectin | 1 | 1 | |
| TGS-like | ACT-like | 1 | 1 | |
| Galactose oxidase, central domain | DPP6 N-terminal domain-like | 1 | 1 | |
| Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain | Pyrimidine nucleoside phosphorylase C-terminal domain | 1 | 1 | |
| Six-hairpin glycosidases | SGNH hydrolase | 1 | 1 | |
| Penicillin binding protein dimerisation domain | Penicillin-binding protein 2x (pbp-2x), c-terminal domain | 1 | 1 | |
| Sialidases | Oligoxyloglucan reducing end-specific cellobiohydrolase | 1 | 1 | |
| Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | Eukaryotic type KH-domain (KH-domain type I) | 1 | 1 | |
| RmlC-like cupins | Rhodanese/Cell cycle control phosphatase | 1 | 1 | |
| Acetyl-CoA synthetase-like | Glycerol-3-phosphate (1)-acyltransferase | 1 | 1 | |
| Carbamoyl phosphate synthetase, small subunit N-terminal domain | Class I glutamine amidotransferase-like | 1 | 1 | |
| PurM N-terminal domain-like | PurM N-terminal domain-like | 1 | 1 | |
| HAMP domain-like | PYP-like sensor domain (PAS domain) | 1 | 1 | |
| E set domains | DPP6 N-terminal domain-like | 1 | 1 | |
| Methylesterase CheB, C-terminal domain | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| Formate/glycerate dehydrogenase catalytic domain-like | Serine metabolism enzymes domain | 1 | 1 | |
| Concanavalin A-like lectins/glucanases | (Trans)glycosidases | 1 | 1 | |
| FMN-binding split barrel | UbiD C-terminal domain-like | 1 | 1 | |
| Galactose-binding domain-like | PKD domain | 1 | 1 | |
| PurS-like | PurM N-terminal domain-like | 1 | 1 | |
| Rho N-terminal domain-like | Nucleic acid-binding proteins | 1 | 1 | |
| Aldolase | Aminoacid dehydrogenase-like, N-terminal domain | 1 | 1 | |
| PK beta-barrel domain-like | PK C-terminal domain-like | 1 | 1 | |
| (Trans)glycosidases | Chitinase insertion domain | 1 | 1 | |
| YVTN repeat-like/Quinoprotein amine dehydrogenase | C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase | 1 | 1 | |
| EspE N-terminal domain-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Sigma3 and sigma4 domains of RNA polymerase sigma factors | Sigma3 and sigma4 domains of RNA polymerase sigma factors | 1 | 1 | |
| Mechanosensitive channel protein MscS (YggB), transmembrane region | Mechanosensitive channel protein MscS (YggB), C-terminal domain | 1 | 1 | |
| Metalloproteases ("zincins"), catalytic domain | TPR-like | 1 | 1 | |
| FGAM synthase PurL, linker domain | PurM C-terminal domain-like | 1 | 1 | |
| FabD/lysophospholipase-like | ACP-like | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | CoA-dependent acyltransferases | 1 | 1 | |
| Tricorn protease N-terminal domain | Alkaline phosphatase-like | 1 | 1 | |
| ThrRS/AlaRS common domain | Class II aaRS ABD-related | 1 | 1 | |
| Calcium-dependent phosphotriesterase | Concanavalin A-like lectins/glucanases | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | LDH C-terminal domain-like | 1 | 1 | |
| RNase III domain-like | dsRNA-binding domain-like | 1 | 1 | |
| NagB/RpiA/CoA transferase-like | NagB/RpiA/CoA transferase-like | 1 | 1 | |
| (Trans)glycosidases | Glycoside hydrolase/deacetylase | 1 | 1 | |
| Calcium-dependent phosphotriesterase | Thermostable phytase (3-phytase) | 1 | 1 | |
| Aldolase | Aldolase | 1 | 1 | |
| Nucleotide-diphospho-sugar transferases | Nucleotide-diphospho-sugar transferases | 1 | 1 | |
| DNA polymerase beta, N-terminal domain-like | PHP domain-like | 1 | 1 | |
| Ribonuclease PH domain 2-like | Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | 1 | 1 | |
| PurS-like | Class I glutamine amidotransferase-like | 1 | 1 | |
| lambda repressor-like DNA-binding domains | LexA/Signal peptidase | 1 | 1 | |
| Putative DNA-binding domain | Anticodon-binding domain of PheRS | 1 | 1 | |
| Nucleic acid-binding proteins | ArfGap/RecO-like zinc finger | 1 | 1 | |
| Fe,Mn superoxide dismutase (SOD), N-terminal domain | Fe,Mn superoxide dismutase (SOD), C-terminal domain | 1 | 1 | |
| S-adenosyl-L-methionine-dependent methyltransferases | Homodimeric domain of signal transducing histidine kinase | 1 | 1 | |
| Galactose-binding domain-like | Cadherin-like | 1 | 1 | |
| YrdC/RibB | RibA-like | 1 | 1 | |
| FAD/NAD(P)-binding domain | HI0933 insert domain-like | 1 | 1 | |
| Periplasmic binding protein-like II | GlnB-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Metallo-dependent phosphatases | 1 | 1 | |
| YbaK/ProRS associated domain | Class II aaRS ABD-related | 1 | 1 | |
| PK beta-barrel domain-like | Phosphoenolpyruvate/pyruvate domain | 1 | 1 | |
| PreATP-grasp domain | Carbamoyl phosphate synthetase, large subunit connection domain | 1 | 1 | |
| YVTN repeat-like/Quinoprotein amine dehydrogenase | Alkaline phosphatase-like | 1 | 1 | |
| Carboxypeptidase regulatory domain-like | Starch-binding domain-like | 1 | 1 | |
| Six-hairpin glycosidases | Class I glutamine amidotransferase-like | 1 | 1 | |
| ValRS/IleRS/LeuRS editing domain | tRNA-binding arm | 1 | 1 | |
| Riboflavin synthase domain-like | Riboflavin synthase domain-like | 1 | 1 | |
| Molybdenum cofactor biosynthesis proteins | CinA-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | TrpR-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Restriction endonuclease-like | 1 | 1 | |
| Origin of replication-binding domain, RBD-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| E set domains | Six-hairpin glycosidases | 1 | 1 | |
| DPP6 N-terminal domain-like | YVTN repeat-like/Quinoprotein amine dehydrogenase | 1 | 1 | |
| Dihydropteroate synthetase-like | Methionine synthase domain | 1 | 1 | |
| Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain | 1 | 1 | |
| PurS-like | FGAM synthase PurL, linker domain | 1 | 1 | |
| Chemotaxis receptor methyltransferase CheR, N-terminal domain | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| PheT/TilS domain | Anticodon-binding domain of PheRS | 1 | 1 | |
| PIN domain-like | Ribonuclease H-like | 1 | 1 | |
| DNA-glycosylase | Nudix | 1 | 1 | |
| PH0987 N-terminal domain-like | Single hybrid motif | 1 | 1 | |
| Translation initiation factor IF3, N-terminal domain | Translation initiation factor IF3, C-terminal domain | 1 | 1 | |
| GAF domain-like | CheY-like | 1 | 1 | |
| 5' to 3' exonuclease, C-terminal subdomain | DNA/RNA polymerases | 1 | 1 | |
| Nucleotidyltransferase | TGS-like | 1 | 1 | |
| Prokaryotic type I DNA topoisomerase | Zinc beta-ribbon | 1 | 1 | |
| GAF domain-like | Homeodomain-like | 1 | 1 | |
| Cytidine deaminase-like | Dihydrofolate reductase-like | 1 | 1 | |
| Nucleotide-diphospho-sugar transferases | Guanosine diphospho-D-mannose pyrophosphorylase/mannose-6-phosphate isomerase linker domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | vWA-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | RecA protein, C-terminal domain | 1 | 1 | |
| PurS-like | PurM C-terminal domain-like | 1 | 1 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | BRCT domain | 1 | 1 | |
| Invasin/intimin cell-adhesion fragments | YWTD domain | 1 | 1 | |
| Probable ACP-binding domain of malonyl-CoA ACP transacylase | Acetyl-CoA synthetase-like | 1 | 1 | |
| lambda repressor-like DNA-binding domains | Cyanase C-terminal domain | 1 | 1 | |
| Ribosomal L11/L12e N-terminal domain | Ribosomal protein L11, C-terminal domain | 1 | 1 | |
| Chondroitin AC/alginate lyase | Hyaluronate lyase-like, C-terminal domain | 1 | 1 | |
| S-adenosyl-L-methionine-dependent methyltransferases | Putative methyltransferase TM0872, insert domain | 1 | 1 | |
| Ribonuclease H-like | DNA/RNA polymerases | 1 | 1 | |
| Formiminotransferase domain of formiminotransferase-cyclodeaminase. | Formiminotransferase domain of formiminotransferase-cyclodeaminase. | 1 | 1 | |
| Type I dockerin domain | Cadherin-like | 1 | 1 | |
| Concanavalin A-like lectins/glucanases | Type I dockerin domain | 1 | 1 | |
| Nqo1 FMN-binding domain-like | Nqo1 middle domain-like | 1 | 1 | |
| Insert subdomain of RNA polymerase alpha subunit | RBP11-like subunits of RNA polymerase | 1 | 1 | |
| GroEL equatorial domain-like | GroEL-intermediate domain like | 1 | 1 | |
| Rudiment single hybrid motif | Single hybrid motif | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | Argininosuccinate synthetase, C-terminal domain | 1 | 1 | |
| Thymidylate synthase-complementing protein Thy1 | Thymidylate synthase-complementing protein Thy1 | 1 | 1 | |
| Carbamate kinase-like | ACT-like | 1 | 1 | |
| Ribokinase-like | Nucleotidylyl transferase | 1 | 1 | |
| Triger factor/SurA peptide-binding domain-like | Triger factor/SurA peptide-binding domain-like | 1 | 1 | |
| Protein kinase-like (PK-like) | Carboxypeptidase regulatory domain-like | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | Histidine-containing phosphotransfer domain, HPT domain | 1 | 1 | |
| Chondroitin AC/alginate lyase | Galactose mutarotase-like | 1 | 1 | |
| Class I glutamine amidotransferase-like | GMP synthetase C-terminal dimerisation domain | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Cyclophilin-like | 1 | 1 | |
| Terpenoid cyclases/Protein prenyltransferases | Terpenoid cyclases/Protein prenyltransferases | 1 | 1 | |
| Zn-dependent exopeptidases | Fibronectin type III | 1 | 1 | |
| Nqo1 FMN-binding domain-like | Nqo1C-terminal domain-like | 1 | 1 | |
| DNA repair protein MutS, domain I | DNA repair protein MutS, domain II | 1 | 1 | |
| Zinc beta-ribbon | DNA primase core | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Smc hinge domain | 1 | 1 | |
| S-adenosyl-L-methionine-dependent methyltransferases | PYP-like sensor domain (PAS domain) | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | PRTase-like | 1 | 1 | |
| Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | CoA-dependent acyltransferases | 1 | 1 | |
| Type II DNA topoisomerase | GyrA/ParC C-terminal domain-like | 1 | 1 | |
| Cation efflux protein cytoplasmic domain-like | Cation efflux protein cytoplasmic domain-like | 1 | 1 | |
| Translation proteins | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| Nucleotidylyl transferase | tRNA-binding arm | 1 | 1 | |
| 2Fe-2S ferredoxin-like | ADC-like | 1 | 1 | |
| alpha/beta-Hydrolases | alpha/beta-Hydrolases | 1 | 1 | |
| Nucleic acid-binding proteins | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| TGS-like | Class II aaRS and biotin synthetases | 1 | 1 | |
| Nucleotidyltransferase | PHP domain-like | 1 | 1 | |
| Single hybrid motif | CoA-dependent acyltransferases | 1 | 1 | |
| Serine metabolism enzymes domain | ACT-like | 1 | 1 | |
| Coiled-coil domain of nucleotide exchange factor GrpE | Head domain of nucleotide exchange factor GrpE | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Succinyl-CoA synthetase domains | 1 | 1 | |
| FGAM synthase PurL, linker domain | Class I glutamine amidotransferase-like | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Succinyl-CoA synthetase domains | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| TPR-like | Thioredoxin-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | C-terminal UvrC-binding domain of UvrB | 1 | 1 | |
| Ribosomal protein L6 | Ribosomal protein L6 | 1 | 1 | |
| ACP-like | Probable ACP-binding domain of malonyl-CoA ACP transacylase | 1 | 1 | |
| PreATP-grasp domain | Single hybrid motif | 1 | 1 | |
| YWTD domain | Soluble quinoprotein glucose dehydrogenase | 1 | 1 | |
| Porins | Porins | 1 | 1 | |
| RBP11-like subunits of RNA polymerase | C-terminal domain of RNA polymerase alpha subunit | 1 | 1 | |
| MoeA N-terminal region -like | MoeA C-terminal domain-like | 1 | 1 | |
| PIN domain-like | 5' to 3' exonuclease, C-terminal subdomain | 1 | 1 | |
| Tricorn protease N-terminal domain | Tricorn protease N-terminal domain | 1 | 1 | |
| Immunoglobulin | Immunoglobulin | 1 | 1 | |
| Periplasmic binding protein-like II | ACT-like | 1 | 1 | |
| PreATP-grasp domain | PreATP-grasp domain | 1 | 1 | |
| Single hybrid motif | HlyD-like secretion proteins | 1 | 1 | |
| Methionine synthase domain | Methionine synthase activation domain-like | 1 | 1 | |
| YajQ-like | YajQ-like | 1 | 1 | |
| MoaD/ThiS | Molybdopterin synthase subunit MoaE | 1 | 1 | |
| Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | Nucleic acid-binding proteins | 1 | 1 | |
| E set domains | alpha/beta-Hydrolases | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | DNA mismatch repair protein MutL | 1 | 1 | |
| Pentein | PLP-dependent transferases | 1 | 1 | |
| Methylesterase CheB, C-terminal domain | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 1 | 1 | |
| ARM repeat | ARM repeat | 1 | 1 | |
| Ribonuclease H-like | Nucleic acid-binding proteins | 1 | 1 | |
| Galactose mutarotase-like | Hyaluronate lyase-like, C-terminal domain | 1 | 1 | |
| DNA/RNA polymerases | Lesion bypass DNA polymerase (Y-family), little finger domain | 1 | 1 | |
| Class I glutamine amidotransferase-like | LD-carboxypeptidase A C-terminal domain-like | 1 | 1 | |
| Tetrahydrobiopterin biosynthesis enzymes-like | Tetrahydrobiopterin biosynthesis enzymes-like | 1 | 1 | |
| Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | Nucleic acid-binding proteins | 1 | 1 | |
| Aconitase iron-sulfur domain | LeuD/IlvD-like | 1 | 1 | |
| CBS-domain pair | Nucleotide-diphospho-sugar transferases | 1 | 1 | |
| PUA domain-like | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| Pectin lyase-like | Calcium-dependent phosphotriesterase | 1 | 1 | |
| C-terminal effector domain of the bipartite response regulators | Galactose oxidase, central domain | 1 | 1 | |
| Aldolase | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Barwin-like endoglucanases | Sporulation related repeat | 1 | 1 | |
| Terpenoid cyclases/Protein prenyltransferases | Ankyrin repeat | 1 | 1 | |
| PLC-like phosphodiesterases | ARM repeat | 1 | 1 | |
| Chondroitin AC/alginate lyase | Pectin lyase-like | 1 | 1 | |
| ATP-dependent DNA ligase DNA-binding domain | Nucleic acid-binding proteins | 1 | 1 | |
| Homocysteine S-methyltransferase | FAD-linked oxidoreductase | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | PH0987 N-terminal domain-like | 1 | 1 | |
| (Trans)glycosidases | PKD domain | 1 | 1 | |
| GIY-YIG endonuclease | DNA-binding domain of intron-encoded endonucleases | 1 | 1 | |
| Lamin A/C globular tail domain | DNase I-like | 1 | 1 | |
| Pre-protein crosslinking domain of SecA | Helical scaffold and wing domains of SecA | 1 | 1 | |
| Domain of the SRP/SRP receptor G-proteins | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | FMN-linked oxidoreductases | 1 | 1 | |
| Rudiment single hybrid motif | PH0987 N-terminal domain-like | 1 | 1 | |
| E set domains | Nitrous oxide reductase, N-terminal domain | 1 | 1 | |
| SGNH hydrolase | alpha-D-mannose-specific plant lectins | 1 | 1 | |
| Glycoside hydrolase/deacetylase | Nucleotide-diphospho-sugar transferases | 1 | 1 | |
| Carbohydrate binding domain | Fibronectin type III | 1 | 1 | |
| Carbamoyl phosphate synthetase, large subunit connection domain | Methylglyoxal synthase-like | 1 | 1 | |
| Phage fibre proteins | Phage fibre proteins | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | GMP synthetase C-terminal dimerisation domain | 1 | 1 | |
| FabD/lysophospholipase-like | CoA-dependent acyltransferases | 1 | 1 | |
| Quinoprotein alcohol dehydrogenase-like | Galactose-binding domain-like | 1 | 1 | |
| CheY-like | Histidine-containing phosphotransfer domain, HPT domain | 1 | 1 | |
| HD-domain/PDEase-like | TGS-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | CarD-like | 1 | 1 | |
| Diaminopimelate epimerase-like | Diaminopimelate epimerase-like | 1 | 1 | |
| PurM C-terminal domain-like | Class I glutamine amidotransferase-like | 1 | 1 | |
| PurM N-terminal domain-like | Class I glutamine amidotransferase-like | 1 | 1 | |
| Transcription factor NusA, N-terminal domain | Rad51 N-terminal domain-like | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Glutamyl tRNA-reductase dimerization domain | 1 | 1 | |
| ISP domain | FAD/NAD(P)-binding domain | 1 | 1 | |
| Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain | Pyrimidine nucleoside phosphorylase C-terminal domain | 1 | 1 | |
| Nucleotide-diphospho-sugar transferases | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| Nucleotidylyl transferase | An anticodon-binding domain of class I aminoacyl-tRNA synthetases | 1 | 1 | |
| NagB/RpiA/CoA transferase-like | D-ribose-5-phosphate isomerase (RpiA), lid domain | 1 | 1 | |
| Acid proteases | PDZ domain-like | 1 | 1 | |
| Nqo1 middle domain-like | Nqo1C-terminal domain-like | 1 | 1 | |
| Tricorn protease N-terminal domain | C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase | 1 | 1 | |
| FabD/lysophospholipase-like | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Cna protein B-type domain | Starch-binding domain-like | 1 | 1 | |
| Type I dockerin domain | Galactose-binding domain-like | 1 | 1 | |
| Flavoproteins | Ferredoxin reductase-like, C-terminal NADP-linked domain | 1 | 1 | |
| Galactose-binding domain-like | Ricin B-like lectins | 1 | 1 | |
| NHL repeat | YWTD domain | 1 | 1 | |
| DNA polymerase beta, N-terminal domain-like | Nucleotidyltransferase | 1 | 1 | |
| Putative DNA-binding domain | PheT/TilS domain | 1 | 1 | |
| Ribonuclease PH domain 2-like | Ribonuclease PH domain 2-like | 1 | 1 | |
| Methylesterase CheB, C-terminal domain | Chemotaxis receptor methyltransferase CheR, N-terminal domain | 1 | 1 | |
| Transcription factor NusA, N-terminal domain | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| Myosin rod fragments | TPR-like | 1 | 1 | |
| GAF domain-like | GAF domain-like | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Siroheme synthase middle domains-like | 1 | 1 | |
| 5' to 3' exonuclease, C-terminal subdomain | Ribonuclease H-like | 1 | 1 | |
| Acylphosphatase/BLUF domain-like | YrdC/RibB | 1 | 1 | |
| FAD/NAD(P)-binding domain | FAD/NAD(P)-binding domain | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Glutathione synthetase ATP-binding domain-like | 1 | 1 | |
| Fumarylacetoacetate hydrolase, FAH, N-terminal domain | FAH | 1 | 1 | |
| Leukotriene A4 hydrolase N-terminal domain | TPR-like | 1 | 1 | |
| Class I glutamine amidotransferase-like | Adenine nucleotide alpha hydrolases-like | 1 | 1 | |
| GroEL equatorial domain-like | GroEL apical domain-like | 1 | 1 | |
| (Trans)glycosidases | Cadherin-like | 1 | 1 | |
| Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | ACT-like | 1 | 1 | |
| Thioredoxin-like | Six-hairpin glycosidases | 1 | 1 | |
| Ricin B-like lectins | Cadherin-like | 1 | 1 | |
| Aspartate/glutamate racemase | Aspartate/glutamate racemase | 1 | 1 | |
| Fibronectin type III | Ricin B-like lectins | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Carbamoyl phosphate synthetase, large subunit connection domain | 1 | 1 | |
| Pectin lyase-like | NHL repeat | 1 | 1 | |
| Putative DNA-binding domain | Putative DNA-binding domain | 1 | 1 | |
| Tubulin nucleotide-binding domain-like | Tubulin C-terminal domain-like | 1 | 1 | |
| Homodimeric domain of signal transducing histidine kinase | Histidine-containing phosphotransfer domain, HPT domain | 1 | 1 | |
| Cobalamin (vitamin B12)-binding domain | Methionine synthase activation domain-like | 1 | 1 | |
| Multiheme cytochromes | TPR-like | 1 | 1 | |
| Class II aaRS and biotin synthetases | C-terminal domain of transcriptional repressors | 1 | 1 | |
| Heme-dependent peroxidases | Heme-dependent peroxidases | 1 | 1 | |
| Rho N-terminal domain-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | DNA ligase/mRNA capping enzyme, catalytic domain | 1 | 1 | |
| GroEL-intermediate domain like | GroEL apical domain-like | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | PP2C-like | 1 | 1 | |
| Integrin alpha N-terminal domain | Pectin lyase-like | 1 | 1 | |
| Flavoproteins | Riboflavin synthase domain-like | 1 | 1 | |
| C-terminal UvrC-binding domain of UvrB | RuvA domain 2-like | 1 | 1 | |
| AraD/HMP-PK domain-like | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| (Trans)glycosidases | Immunoglobulin | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | FtsH protease domain-like | 1 | 1 | |
| PYP-like sensor domain (PAS domain) | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Nucleic acid-binding proteins | DNA helicase RuvA subunit, C-terminal domain | 1 | 1 | |
| Prokaryotic type KH domain (KH-domain type II) | Ribosomal protein S3 C-terminal domain | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | 1 | 1 | |
| Methylglyoxal synthase-like | Cytidine deaminase-like | 1 | 1 | |
| Trigger factor ribosome-binding domain | Triger factor/SurA peptide-binding domain-like | 1 | 1 | |
| Bacterial muramidases | Lysozyme-like | 1 | 1 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | RuvA domain 2-like | 1 | 1 | |
| Galactose mutarotase-like | Six-hairpin glycosidases | 1 | 1 | |
| Translation proteins | Initiation factor IF2/eIF5b, domain 3 | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Probable ACP-binding domain of malonyl-CoA ACP transacylase | 1 | 1 | |
| Prokaryotic type KH domain (KH-domain type II) | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| Starch-binding domain-like | Galactose-binding domain-like | 1 | 1 | |
