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 | |
|---|
| Homodimeric domain of signal transducing histidine kinase | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 128 | 69 |  |
| PYP-like sensor domain (PAS domain) | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 95 | 59 | |
| PYP-like sensor domain (PAS domain) | Homodimeric domain of signal transducing histidine kinase | 84 | 53 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | CheY-like | 68 | 45 | |
| PYP-like sensor domain (PAS domain) | PYP-like sensor domain (PAS domain) | 66 | 48 | |
| Homodimeric domain of signal transducing histidine kinase | CheY-like | 62 | 42 | |
| PYP-like sensor domain (PAS domain) | CheY-like | 57 | 41 | |
| P-loop containing nucleoside triphosphate hydrolases | Homeodomain-like | 32 | 10 | |
| P-loop containing nucleoside triphosphate hydrolases | P-loop containing nucleoside triphosphate hydrolases | 22 | 12 | |
| Homodimeric domain of signal transducing histidine kinase | Histidine-containing phosphotransfer domain, HPT domain | 19 | 16 | |
| PYP-like sensor domain (PAS domain) | Methyl-accepting chemotaxis protein (MCP) signaling domain | 19 | 4 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | Histidine-containing phosphotransfer domain, HPT domain | 19 | 16 | |
| CheY-like | P-loop containing nucleoside triphosphate hydrolases | 18 | 3 | |
| HAMP domain-like | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 17 | 8 | |
| CheY-like | Histidine-containing phosphotransfer domain, HPT domain | 16 | 14 | |
| CheY-like | Homeodomain-like | 16 | 1 | |
| HAMP domain-like | Homodimeric domain of signal transducing histidine kinase | 16 | 7 | |
| PYP-like sensor domain (PAS domain) | Nucleotide cyclase | 16 | 11 | |
| GAF domain-like | PYP-like sensor domain (PAS domain) | 15 | 13 | |
| GAF domain-like | Homodimeric domain of signal transducing histidine kinase | 14 | 12 | |
| CheY-like | HD-domain/PDEase-like | 14 | 4 | |
| GAF domain-like | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 14 | 12 | |
| GAF domain-like | CheY-like | 11 | 9 | |
| Actin-like ATPase domain | Actin-like ATPase domain | 11 | 3 | |
| Formate dehydrogenase/DMSO reductase, domains 1-3 | ADC-like | 11 | 3 | |
| CheY-like | CheY-like | 11 | 9 | |
| PYP-like sensor domain (PAS domain) | P-loop containing nucleoside triphosphate hydrolases | 10 | 6 | |
| P-loop containing nucleoside triphosphate hydrolases | Translation proteins | 10 | 6 | |
| Multidrug resistance efflux transporter EmrE | Multidrug resistance efflux transporter EmrE | 10 | 3 | |
| CheY-like | Nucleotide cyclase | 10 | 7 | |
| Sensory domain-like | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 10 | 9 | |
| HAMP domain-like | PYP-like sensor domain (PAS domain) | 10 | 7 | |
| Sensory domain-like | Methyl-accepting chemotaxis protein (MCP) signaling domain | 10 | 6 | |
| NAD(P)-binding Rossmann-fold domains | Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 10 | 4 | |
| PYP-like sensor domain (PAS domain) | Histidine-containing phosphotransfer domain, HPT domain | 9 | 9 | |
| P-loop containing nucleoside triphosphate hydrolases | Ribosomal protein S5 domain 2-like | 9 | 6 | |
| CheY-like | C-terminal effector domain of the bipartite response regulators | 9 | 1 | |
| Sensory domain-like | Homodimeric domain of signal transducing histidine kinase | 9 | 8 | |
| Homeodomain-like | Tetracyclin repressor-like, C-terminal domain | 9 | 1 | |
| Sensory domain-like | PYP-like sensor domain (PAS domain) | 9 | 8 | |
| Multidrug efflux transporter AcrB transmembrane domain | Multidrug efflux transporter AcrB transmembrane domain | 8 | 3 | |
| NAD(P)-binding Rossmann-fold domains | 6-phosphogluconate dehydrogenase C-terminal domain-like | 8 | 3 | |
| Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains | Multidrug efflux transporter AcrB transmembrane domain | 8 | 3 | |
| Sigma2 domain of RNA polymerase sigma factors | Sigma3 and sigma4 domains of RNA polymerase sigma factors | 8 | 3 | |
| Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains | Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains | 8 | 3 | |
| Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains | Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains | 8 | 3 | |
| TPR-like | TPR-like | 8 | 7 | |
| ABC transporter transmembrane region | P-loop containing nucleoside triphosphate hydrolases | 8 | 3 | |
| Thiamin diphosphate-binding fold (THDP-binding) | Thiamin diphosphate-binding fold (THDP-binding) | 8 | 4 | |
| Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains | Multidrug efflux transporter AcrB transmembrane domain | 8 | 3 | |
| Chemotaxis receptor methyltransferase CheR, N-terminal domain | S-adenosyl-L-methionine-dependent methyltransferases | 8 | 7 | |
| Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains | Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains | 8 | 3 | |
| PYP-like sensor domain (PAS domain) | Homeodomain-like | 7 | 5 | |
| Calcium ATPase, transduction domain A | HAD-like | 7 | 5 | |
| Homeodomain-like | Homeodomain-like | 7 | 5 | |
| Nucleotide cyclase | EAL domain-like | 7 | 6 | |
| CheW-like | CheY-like | 7 | 2 | |
| "Winged helix" DNA-binding domain | Periplasmic binding protein-like II | 7 | 1 | |
| Nucleotidylyl transferase | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 7 | 7 | |
| Nucleotide-diphospho-sugar transferases | UDP-Glycosyltransferase/glycogen phosphorylase | 6 | 5 | |
| Aldehyde ferredoxin oxidoreductase, N-terminal domain | Aldehyde ferredoxin oxidoreductase, C-terminal domains | 6 | 2 | |
| Thiamin diphosphate-binding fold (THDP-binding) | TK C-terminal domain-like | 6 | 3 | |
| HAD-like | Calcium ATPase, transmembrane domain M | 6 | 4 | |
| Methylesterase CheB, C-terminal domain | S-adenosyl-L-methionine-dependent methyltransferases | 6 | 6 | |
| S-adenosyl-L-methionine-dependent methyltransferases | PYP-like sensor domain (PAS domain) | 6 | 6 | |
| Calcium ATPase, transduction domain A | Calcium ATPase, transmembrane domain M | 6 | 4 | |
| Periplasmic binding protein-like II | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 6 | 5 | |
| Translation proteins | EF-G C-terminal domain-like | 6 | 3 | |
| Composite domain of metallo-dependent hydrolases | Metallo-dependent hydrolases | 6 | 4 | |
| Methylesterase CheB, C-terminal domain | Chemotaxis receptor methyltransferase CheR, N-terminal domain | 6 | 6 | |
| P-loop containing nucleoside triphosphate hydrolases | EF-G C-terminal domain-like | 6 | 3 | |
| PreATP-grasp domain | Glutathione synthetase ATP-binding domain-like | 6 | 4 | |
| Periplasmic binding protein-like II | PYP-like sensor domain (PAS domain) | 5 | 4 | |
| CheY-like | TPR-like | 5 | 2 | |
| PYP-like sensor domain (PAS domain) | EAL domain-like | 5 | 5 | |
| Methylesterase CheB, C-terminal domain | PYP-like sensor domain (PAS domain) | 5 | 5 | |
| LysM domain | LysM domain | 5 | 5 | |
| FAD/NAD(P)-binding domain | Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | 5 | 2 | |
| Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain | 5 | 2 | |
| Periplasmic binding protein-like II | Homodimeric domain of signal transducing histidine kinase | 5 | 4 | |
| Homodimeric domain of signal transducing histidine kinase | CheW-like | 5 | 4 | |
| 4Fe-4S ferredoxins | Fe-only hydrogenase | 5 | 4 | |
| Sm-like ribonucleoproteins | Mechanosensitive channel protein MscS (YggB), C-terminal domain | 5 | 3 | |
| EF-G C-terminal domain-like | EF-G C-terminal domain-like | 5 | 2 | |
| Glutathione synthetase ATP-binding domain-like | Phosphohistidine domain | 5 | 4 | |
| FAD/NAD(P)-binding domain | Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain | 5 | 2 | |
| Histidine-containing phosphotransfer domain, HPT domain | CheW-like | 5 | 4 | |
| GAF domain-like | Homeodomain-like | 5 | 2 | |
| MurD-like peptide ligases, catalytic domain | MurD-like peptide ligases, peptide-binding domain | 5 | 3 | |
| GAF domain-like | P-loop containing nucleoside triphosphate hydrolases | 5 | 2 | |
| FAD-binding/transporter-associated domain-like | FAD-linked oxidases, C-terminal domain | 5 | 4 | |
| Sensory domain-like | Nucleotide cyclase | 5 | 2 | |
| PurM N-terminal domain-like | PurM C-terminal domain-like | 5 | 2 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | CheW-like | 5 | 4 | |
| FAD/NAD(P)-binding domain | FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 5 | 2 | |
| CheY-like | Methylesterase CheB, C-terminal domain | 5 | 4 | |
| Chemotaxis receptor methyltransferase CheR, N-terminal domain | PYP-like sensor domain (PAS domain) | 5 | 5 | |
| FMN-binding split barrel | UbiD C-terminal domain-like | 4 | 3 | |
| Nucleic acid-binding proteins | Class II aaRS and biotin synthetases | 4 | 3 | |
| HAMP domain-like | CheY-like | 4 | 4 | |
| CBS-domain pair | CBS-domain pair | 4 | 4 | |
| cAMP-binding domain-like | "Winged helix" DNA-binding domain | 4 | 1 | |
| Thiamin diphosphate-binding fold (THDP-binding) | DHS-like NAD/FAD-binding domain | 4 | 1 | |
| FAD/NAD(P)-binding domain | 4Fe-4S ferredoxins | 4 | 3 | |
| Aminoacid dehydrogenase-like, N-terminal domain | NAD(P)-binding Rossmann-fold domains | 4 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | Class I glutamine amidotransferase-like | 4 | 2 | |
| Sensory domain-like | CheY-like | 4 | 4 | |
| Mechanosensitive channel protein MscS (YggB), transmembrane region | Mechanosensitive channel protein MscS (YggB), C-terminal domain | 4 | 2 | |
| Mechanosensitive channel protein MscS (YggB), transmembrane region | Sm-like ribonucleoproteins | 4 | 2 | |
| NAD(P)-binding Rossmann-fold domains | TrkA C-terminal domain-like | 4 | 4 | |
| Sensory domain-like | Sensory domain-like | 4 | 2 | |
| HAMP domain-like | Methyl-accepting chemotaxis protein (MCP) signaling domain | 4 | 2 | |
| Nucleic acid-binding proteins | Nucleic acid-binding proteins | 4 | 4 | |
| P-loop containing nucleoside triphosphate hydrolases | "Winged helix" DNA-binding domain | 4 | 4 | |
| (Trans)glycosidases | Glycosyl hydrolase domain | 3 | 3 | |
| Nitrite/Sulfite reductase N-terminal domain-like | Nitrite and sulphite reductase 4Fe-4S domain-like | 3 | 2 | |
| HAMP domain-like | PP2C-like | 3 | 1 | |
| Translation proteins | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 3 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 3 | 2 | |
| Riboflavin synthase domain-like | Ferredoxin reductase-like, C-terminal NADP-linked domain | 3 | 2 | |
| Glutathione synthetase ATP-binding domain-like | NAD(P)-binding Rossmann-fold domains | 3 | 3 | |
| DNA breaking-rejoining enzymes | MOP-like | 3 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | Ribosomal protein S5 domain 2-like | 3 | 3 | |
| Nitrite and sulphite reductase 4Fe-4S domain-like | 4Fe-4S ferredoxins | 3 | 2 | |
| Phosphoglucomutase, first 3 domains | Phosphoglucomutase, first 3 domains | 3 | 2 | |
| 2Fe-2S ferredoxin-like | 4Fe-4S ferredoxins | 3 | 3 | |
| Prim-pol domain | P-loop containing nucleoside triphosphate hydrolases | 3 | 2 | |
| Formate/glycerate dehydrogenase catalytic domain-like | NAD(P)-binding Rossmann-fold domains | 3 | 1 | |
| Succinyl-CoA synthetase domains | Succinyl-CoA synthetase domains | 3 | 3 | |
| PreATP-grasp domain | Rudiment single hybrid motif | 3 | 2 | |
| LuxS/MPP-like metallohydrolase | LuxS/MPP-like metallohydrolase | 3 | 2 | |
| Phosphohistidine domain | Phosphoenolpyruvate/pyruvate domain | 3 | 3 | |
| RuvA domain 2-like | P-loop containing nucleoside triphosphate hydrolases | 3 | 2 | |
| ACT-like | ACT-like | 3 | 2 | |
| FKBP-like | Triger factor/SurA peptide-binding domain-like | 3 | 2 | |
| CheY-like | PP2C-like | 3 | 1 | |
| PLP-binding barrel | Alanine racemase C-terminal domain-like | 3 | 1 | |
| S-adenosyl-L-methionine-dependent methyltransferases | Homodimeric domain of signal transducing histidine kinase | 3 | 3 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | Adenine nucleotide alpha hydrolases-like | 3 | 1 | |
| PUA domain-like | P-loop containing nucleoside triphosphate hydrolases | 3 | 2 | |
| Nqo1 FMN-binding domain-like | Nqo1 middle domain-like | 3 | 3 | |
| Translation proteins | Ribosomal protein S5 domain 2-like | 3 | 1 | |
| Methylesterase CheB, C-terminal domain | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 3 | 3 | |
| Chemotaxis receptor methyltransferase CheR, N-terminal domain | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 3 | 3 | |
| Glutathione synthetase ATP-binding domain-like | Rudiment single hybrid motif | 3 | 2 | |
| GroES-like | NAD(P)-binding Rossmann-fold domains | 3 | 1 | |
| lambda repressor-like DNA-binding domains | LexA/Signal peptidase | 3 | 1 | |
| Chemotaxis receptor methyltransferase CheR, N-terminal domain | CheY-like | 3 | 3 | |
| Nucleic acid-binding proteins | RuvA domain 2-like | 3 | 3 | |
| ValRS/IleRS/LeuRS editing domain | Nucleotidylyl transferase | 3 | 3 | |
| Alpha-L RNA-binding motif | Pseudouridine synthase | 3 | 2 | |
| Nqo1 middle domain-like | Nqo1C-terminal domain-like | 3 | 3 | |
| 4Fe-4S ferredoxins | FMN-dependent nitroreductase-like | 3 | 1 | |
| S-adenosyl-L-methionine-dependent methyltransferases | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 3 | 3 | |
| Voltage-gated potassium channels | NAD(P)-binding Rossmann-fold domains | 3 | 3 | |
| ValRS/IleRS/LeuRS editing domain | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 3 | 3 | |
| EF-G C-terminal domain-like | Ribosomal protein S5 domain 2-like | 3 | 1 | |
| S-adenosyl-L-methionine-dependent methyltransferases | CheY-like | 3 | 3 | |
| PDZ domain-like | PDZ domain-like | 3 | 2 | |
| Periplasmic binding protein-like II | Nucleotide cyclase | 3 | 2 | |
| Glutathione synthetase ATP-binding domain-like | Succinyl-CoA synthetase domains | 3 | 3 | |
| Succinyl-CoA synthetase domains | NAD(P)-binding Rossmann-fold domains | 3 | 3 | |
| Class II aaRS and biotin synthetases | Class II aaRS ABD-related | 3 | 3 | |
| Nqo1 FMN-binding domain-like | Nqo1C-terminal domain-like | 3 | 3 | |
| Cation efflux protein transmembrane domain-like | Cation efflux protein cytoplasmic domain-like | 3 | 1 | |
| Resolvase-like | Homeodomain-like | 3 | 1 | |
| Chemotaxis receptor methyltransferase CheR, N-terminal domain | Homodimeric domain of signal transducing histidine kinase | 3 | 3 | |
| MOP-like | MOP-like | 3 | 1 | |
| Methylesterase CheB, C-terminal domain | Homodimeric domain of signal transducing histidine kinase | 3 | 3 | |
| Phosphoglucomutase, first 3 domains | Phosphoglucomutase, C-terminal domain | 3 | 2 | |
| Chaperone J-domain | HSP40/DnaJ peptide-binding domain | 3 | 3 | |
| CBS-domain pair | Nucleotide cyclase | 2 | 1 | |
| TTHA1013/TTHA0281-like | Ribbon-helix-helix | 2 | 1 | |
| FAD/NAD(P)-binding domain | Rhodanese/Cell cycle control phosphatase | 2 | 1 | |
| MoeA N-terminal region -like | MoeA C-terminal domain-like | 2 | 2 | |
| Nitrite/Sulfite reductase N-terminal domain-like | 4Fe-4S ferredoxins | 2 | 1 | |
| 2Fe-2S ferredoxin-like | Fe-only hydrogenase | 2 | 2 | |
| E set domains | Glycosyl hydrolase domain | 2 | 2 | |
| Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain | Phosphoenolpyruvate/pyruvate domain | 2 | 2 | |
| EAL domain-like | HD-domain/PDEase-like | 2 | 1 | |
| S-adenosyl-L-methionine-dependent methyltransferases | S-adenosyl-L-methionine-dependent methyltransferases | 2 | 2 | |
| GAF domain-like | Nucleotide cyclase | 2 | 2 | |
| DnaJ/Hsp40 cysteine-rich domain | HSP40/DnaJ peptide-binding domain | 2 | 2 | |
| MurE/MurF N-terminal domain | MurD-like peptide ligases, peptide-binding domain | 2 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | post-AAA+ oligomerization domain-like | 2 | 2 | |
| MurCD N-terminal domain | MurD-like peptide ligases, catalytic domain | 2 | 1 | |
| 6-phosphogluconate dehydrogenase C-terminal domain-like | UDP-glucose/GDP-mannose dehydrogenase C-terminal domain | 2 | 1 | |
| Adenine nucleotide alpha hydrolases-like | Adenine nucleotide alpha hydrolases-like | 2 | 1 | |
| CBS-domain pair | PYP-like sensor domain (PAS domain) | 2 | 2 | |
| Lysozyme-like | beta-lactamase/transpeptidase-like | 2 | 2 | |
| lambda repressor-like DNA-binding domains | RmlC-like cupins | 2 | 1 | |
| PDZ domain-like | Nitrogenase accessory factor-like | 2 | 2 | |
| Methyl-accepting chemotaxis protein (MCP) signaling domain | Hemerythrin-like | 2 | 2 | |
| HD-domain/PDEase-like | Nucleotidyltransferase | 2 | 2 | |
| Regulatory protein AraC | Homeodomain-like | 2 | 1 | |
| HMA, heavy metal-associated domain | Calcium ATPase, transduction domain A | 2 | 2 | |
| Creatinase/prolidase N-terminal domain | Creatinase/aminopeptidase | 2 | 1 | |
| 2Fe-2S ferredoxin-like | alpha-helical ferredoxin | 2 | 1 | |
| Ribosomal protein S5 domain 2-like | GHMP Kinase, C-terminal domain | 2 | 1 | |
| FAD-binding/transporter-associated domain-like | Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain | 2 | 1 | |
| GAF domain-like | GAF domain-like | 2 | 2 | |
| PYP-like sensor domain (PAS domain) | HD-domain/PDEase-like | 2 | 2 | |
| Voltage-gated potassium channels | TrkA C-terminal domain-like | 2 | 2 | |
| Aspartate/glutamate racemase | Aspartate/glutamate racemase | 2 | 1 | |
| Nicotinate/Quinolinate PRTase N-terminal domain-like | Nicotinate/Quinolinate PRTase C-terminal domain-like | 2 | 2 | |
| NAD(P)-binding Rossmann-fold domains | UDP-glucose/GDP-mannose dehydrogenase C-terminal domain | 2 | 1 | |
| Trypsin-like serine proteases | PDZ domain-like | 2 | 1 | |
| Periplasmic binding protein-like II | CheY-like | 2 | 2 | |
| Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain | Phosphohistidine domain | 2 | 2 | |
| HAMP domain-like | Histidine-containing phosphotransfer domain, HPT domain | 2 | 2 | |
| Nqo5-like | HydB/Nqo4-like | 2 | 2 | |
| SGNH hydrolase | LysM domain | 2 | 2 | |
| HMA, heavy metal-associated domain | Calcium ATPase, transmembrane domain M | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | C-terminal domain of alpha and beta subunits of F1 ATP synthase | 2 | 1 | |
| EAL domain-like | CBS-domain pair | 2 | 1 | |
| Penicillin binding protein dimerisation domain | beta-lactamase/transpeptidase-like | 2 | 2 | |
| S-adenosyl-L-methionine-dependent methyltransferases | UDP-Glycosyltransferase/glycogen phosphorylase | 2 | 2 | |
| N-terminal domain of DnaB helicase | P-loop containing nucleoside triphosphate hydrolases | 2 | 2 | |
| NagB/RpiA/CoA transferase-like | alpha-helical ferredoxin | 2 | 1 | |
| MurCD N-terminal domain | MurD-like peptide ligases, peptide-binding domain | 2 | 1 | |
| Aldolase | AFP III-like domain | 2 | 1 | |
| EF-hand | LysM domain | 2 | 2 | |
| PhoU-like | Protein kinase-like (PK-like) | 2 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | FtsH protease domain-like | 2 | 2 | |
| Thioredoxin-like | 4Fe-4S ferredoxins | 2 | 2 | |
| PUA domain-like | Nucleotidylyl transferase | 2 | 2 | |
| HMA, heavy metal-associated domain | HAD-like | 2 | 2 | |
| CBS-domain pair | FAD-binding/transporter-associated domain-like | 2 | 1 | |
| CBS-domain pair | Homodimeric domain of signal transducing histidine kinase | 2 | 2 | |
| Epsilon subunit of F1F0-ATP synthase N-terminal domain | Epsilon subunit of F1F0-ATP synthase C-terminal domain | 2 | 1 | |
| DnaK suppressor protein DksA, alpha-hairpin domain | Glucocorticoid receptor-like (DNA-binding domain) | 2 | 1 | |
| MurE/MurF N-terminal domain | MurD-like peptide ligases, catalytic domain | 2 | 1 | |
| 2Fe-2S ferredoxin-like | CO dehydrogenase ISP C-domain like | 2 | 2 | |
| Aldolase | 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain | 2 | 1 | |
| FAD/NAD(P)-binding domain | FAD/NAD(P)-binding domain | 2 | 2 | |
| Nqo1 middle domain-like | 4Fe-4S ferredoxins | 2 | 2 | |
| Ribosomal protein S5 domain 2-like | Ribosomal protein S5 domain 2-like | 2 | 2 | |
| PHP domain-like | P-loop containing nucleoside triphosphate hydrolases | 2 | 1 | |
| Ferritin-like | Rubredoxin-like | 2 | 1 | |
| Nqo1C-terminal domain-like | 4Fe-4S ferredoxins | 2 | 2 | |
| Nucleic acid-binding proteins | Translation proteins SH3-like domain | 2 | 2 | |
| CheY-like | EAL domain-like | 2 | 2 | |
| Double Clp-N motif | P-loop containing nucleoside triphosphate hydrolases | 2 | 1 | |
| Molybdenum cofactor biosynthesis proteins | MoeA C-terminal domain-like | 2 | 2 | |
| CBS-domain pair | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 2 | 2 | |
| "Winged helix" DNA-binding domain | GAF domain-like | 2 | 1 | |
| CO dehydrogenase molybdoprotein N-domain-like | Molybdenum cofactor-binding domain | 2 | 2 | |
| tRNA-binding arm | Class II aaRS and biotin synthetases | 2 | 1 | |
| Nucleotidyltransferase | Poly A polymerase C-terminal region-like | 2 | 2 | |
| HSP40/DnaJ peptide-binding domain | HSP40/DnaJ peptide-binding domain | 2 | 2 | |
| DNA repair protein MutS, domain III | P-loop containing nucleoside triphosphate hydrolases | 2 | 2 | |
| Nqo1 FMN-binding domain-like | 4Fe-4S ferredoxins | 2 | 2 | |
| Composite domain of metallo-dependent hydrolases | Composite domain of metallo-dependent hydrolases | 2 | 1 | |
| Sensory domain-like | Histidine-containing phosphotransfer domain, HPT domain | 2 | 2 | |
| Class II aaRS and biotin synthetases | ThrRS/AlaRS common domain | 2 | 2 | |
| MoeA N-terminal region -like | Molybdenum cofactor biosynthesis proteins | 2 | 2 | |
| lambda repressor-like DNA-binding domains | PYP-like sensor domain (PAS domain) | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | HprK N-terminal domain-like | 2 | 2 | |
| CBS-domain pair | CheY-like | 2 | 2 | |
| N-terminal domain of alpha and beta subunits of F1 ATP synthase | P-loop containing nucleoside triphosphate hydrolases | 2 | 1 | |
| FAD/NAD-linked reductases, dimerisation (C-terminal) domain | Rhodanese/Cell cycle control phosphatase | 2 | 1 | |
| Nucleotidyltransferase | ACT-like | 2 | 2 | |
| PUA domain-like | Ribosomal protein S5 domain 2-like | 2 | 1 | |
| 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 | |
| HlyD-like secretion proteins | HlyD-like secretion proteins | 2 | 2 | |
| Chaperone J-domain | DnaJ/Hsp40 cysteine-rich domain | 2 | 2 | |
| EspE N-terminal domain-like | P-loop containing nucleoside triphosphate hydrolases | 2 | 2 | |
| CorA soluble domain-like | Magnesium transport protein CorA, transmembrane region | 2 | 1 | |
| HD-domain/PDEase-like | ACT-like | 2 | 2 | |
| GAF domain-like | Histidine-containing phosphotransfer domain, HPT domain | 2 | 2 | |
| Staphylococcal nuclease | Ada DNA repair protein, N-terminal domain (N-Ada 10) | 2 | 1 | |
| alpha-helical ferredoxin | Nucleotide-binding domain | 2 | 2 | |
| Sigma3 and sigma4 domains of RNA polymerase sigma factors | Sigma3 and sigma4 domains of RNA polymerase sigma factors | 2 | 2 | |
| Zn-dependent exopeptidases | Bacterial exopeptidase dimerisation domain | 2 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | TrpR-like | 2 | 1 | |
| E set domains | (Trans)glycosidases | 2 | 2 | |
| NAD(P)-linked oxidoreductase | alpha-helical ferredoxin | 2 | 1 | |
| Metallo-hydrolase/oxidoreductase | Flavoproteins | 2 | 1 | |
| lambda repressor-like DNA-binding domains | Histidine-containing phosphotransfer domain, HPT domain | 1 | 1 | |
| Hedgehog/intein (Hint) domain | Homing endonucleases | 1 | 1 | |
| Peptide methionine sulfoxide reductase | Mss4-like | 1 | 1 | |
| PIN domain-like | DNA/RNA polymerases | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Glutathione synthetase ATP-binding domain-like | 1 | 1 | |
| Ribosomal protein L7/12, oligomerisation (N-terminal) domain | ClpS-like | 1 | 1 | |
| ACT-like | 4Fe-4S ferredoxins | 1 | 1 | |
| TK C-terminal domain-like | Pyruvate-ferredoxin oxidoreductase, PFOR, domain III | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain | 1 | 1 | |
| Galactose-binding domain-like | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Acyl-CoA N-acyltransferases (Nat) | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | GAF domain-like | 1 | 1 | |
| MoeA N-terminal region -like | Periplasmic binding protein-like II | 1 | 1 | |
| Metal cation-transporting ATPase, ATP-binding domain N | HAD-like | 1 | 1 | |
| Oligoxyloglucan reducing end-specific cellobiohydrolase | Oligoxyloglucan reducing end-specific cellobiohydrolase | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | TGS-like | 1 | 1 | |
| Homing endonucleases | PFL-like glycyl radical enzymes | 1 | 1 | |
| cAMP-binding domain-like | FliG | 1 | 1 | |
| IlvD/EDD N-terminal domain-like | LeuD/IlvD-like | 1 | 1 | |
| Nucleotidylyl transferase | Alpha-L RNA-binding motif | 1 | 1 | |
| Nucleotidylyl transferase | Riboflavin kinase-like | 1 | 1 | |
| Tex N-terminal region-like | Nucleic acid-binding proteins | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Pentapeptide repeat-like | 1 | 1 | |
| TPR-like | Zn-dependent exopeptidases | 1 | 1 | |
| Homo-oligomeric flavin-containing Cys decarboxylases, HFCD | CoaB-like | 1 | 1 | |
| MoeA C-terminal domain-like | Periplasmic binding protein-like II | 1 | 1 | |
| C-terminal UvrC-binding domain of UvrB | RuvA domain 2-like | 1 | 1 | |
| ADC synthase | D-aminoacid aminotransferase-like PLP-dependent enzymes | 1 | 1 | |
| Chorismate mutase II | ACT-like | 1 | 1 | |
| ACT-like | Homeodomain-like | 1 | 1 | |
| PLP-dependent transferases | Class I glutamine amidotransferase-like | 1 | 1 | |
| DNA repair protein MutS, domain I | DNA repair protein MutS, domain III | 1 | 1 | |
| N-terminal domain of MutM-like DNA repair proteins | S13-like H2TH domain | 1 | 1 | |
| S-adenosyl-L-methionine-dependent methyltransferases | Putative methyltransferase TM0872, insert domain | 1 | 1 | |
| HD-domain/PDEase-like | TGS-like | 1 | 1 | |
| Tetrapyrrole methylase | HemD-like | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Nucleic acid-binding proteins | 1 | 1 | |
| Tropomyosin | OmpA-like | 1 | 1 | |
| CBS-domain pair | Poly A polymerase C-terminal region-like | 1 | 1 | |
| Ribonuclease PH domain 2-like | Eukaryotic type KH-domain (KH-domain type I) | 1 | 1 | |
| Ribosomal protein L6 | Ribosomal protein L6 | 1 | 1 | |
| Iron-dependent repressor protein, dimerization domain | C-terminal domain of transcriptional repressors | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | SMR domain-like | 1 | 1 | |
| PilZ domain-like | PilZ domain-like | 1 | 1 | |
| Phosphoenolpyruvate/pyruvate domain | PK C-terminal domain-like | 1 | 1 | |
| Acetyl-CoA synthetase-like | Trimeric LpxA-like enzymes | 1 | 1 | |
| 2Fe-2S ferredoxin-like | Formate dehydrogenase/DMSO reductase, domains 1-3 | 1 | 1 | |
| alpha-helical ferredoxin | alpha-helical ferredoxin | 1 | 1 | |
| lambda repressor-like DNA-binding domains | Homodimeric domain of signal transducing histidine kinase | 1 | 1 | |
| Nucleic acid-binding proteins | GAD domain-like | 1 | 1 | |
| PHP domain-like | UDP-Glycosyltransferase/glycogen phosphorylase | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Carbamoyl phosphate synthetase, large subunit connection domain | 1 | 1 | |
| Tex N-terminal region-like | Ribonuclease H-like | 1 | 1 | |
| Glycerol-3-phosphate (1)-acyltransferase | Acyl-CoA N-acyltransferases (Nat) | 1 | 1 | |
| Translation initiation factor IF3, N-terminal domain | Translation initiation factor IF3, C-terminal domain | 1 | 1 | |
| ClpP/crotonase | NfeD domain-like | 1 | 1 | |
| EspE N-terminal domain-like | CheW-like | 1 | 1 | |
| GAF domain-like | HD-domain/PDEase-like | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | DHS-like NAD/FAD-binding domain | 1 | 1 | |
| Alkaline phosphatase-like | Alkaline phosphatase-like | 1 | 1 | |
| Folate-binding domain | Aminomethyltransferase beta-barrel domain | 1 | 1 | |
| Glutamyl tRNA-reductase catalytic, N-terminal domain | Glutamyl tRNA-reductase dimerization domain | 1 | 1 | |
| CO dehydrogenase ISP C-domain like | CO dehydrogenase molybdoprotein N-domain-like | 1 | 1 | |
| Nucleotide cyclase | Hemerythrin-like | 1 | 1 | |
| Carbamate kinase-like | PUA domain-like | 1 | 1 | |
| Rubredoxin-like | Superoxide reductase-like | 1 | 1 | |
| HD-domain/PDEase-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Calcium-dependent phosphotriesterase | Homodimeric domain of signal transducing histidine kinase | 1 | 1 | |
| Carbamoyl phosphate synthetase, small subunit N-terminal domain | Class I glutamine amidotransferase-like | 1 | 1 | |
| Translation proteins | "Winged helix" DNA-binding domain | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Rhodanese/Cell cycle control phosphatase | 1 | 1 | |
| ACT-like | HAD-like | 1 | 1 | |
| Acetyl-CoA synthetase-like | ACP-like | 1 | 1 | |
| MFS general substrate transporter | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | ACT-like | 1 | 1 | |
| Methyl-accepting chemotaxis protein (MCP) signaling domain | Ligand-binding domain in the NO signalling and Golgi transport | 1 | 1 | |
| Homocysteine S-methyltransferase | Methionine synthase domain | 1 | 1 | |
| Nucleotide-diphospho-sugar transferases | IpsF-like | 1 | 1 | |
| PurM C-terminal domain-like | PurM C-terminal domain-like | 1 | 1 | |
| PTS system fructose IIA component-like | HPr-like | 1 | 1 | |
| Nucleic acid-binding proteins | PheT/TilS domain | 1 | 1 | |
| DHH phosphoesterases | Nucleotidyltransferase | 1 | 1 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | BRCT domain | 1 | 1 | |
| Translation proteins | PRC-barrel domain | 1 | 1 | |
| Ribonuclease PH domain 2-like | Nucleic acid-binding proteins | 1 | 1 | |
| Class II aaRS and biotin synthetases | Anticodon-binding domain of PheRS | 1 | 1 | |
| Mechanosensitive channel protein MscS (YggB), C-terminal domain | cAMP-binding domain-like | 1 | 1 | |
| PUA domain-like | alpha/beta knot | 1 | 1 | |
| Tetrapyrrole methylase | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| Histidine-containing phosphotransfer domain, HPT domain | EspE N-terminal domain-like | 1 | 1 | |
| RmlC-like cupins | Homeodomain-like | 1 | 1 | |
| TPR-like | Lysozyme-like | 1 | 1 | |
| CheY-like | SpoIIaa-like | 1 | 1 | |
| Aconitase iron-sulfur domain | LeuD/IlvD-like | 1 | 1 | |
| DNA repair protein MutS, domain II | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Helical scaffold and wing domains of SecA | 1 | 1 | |
| (Trans)glycosidases | Nucleotide-diphospho-sugar transferases | 1 | 1 | |
| Class I glutamine amidotransferase-like | GMP synthetase C-terminal dimerisation domain | 1 | 1 | |
| Bacterial fluorinating enzyme, N-terminal domain | Bacterial fluorinating enzyme, C-terminal domain | 1 | 1 | |
| Eukaryotic type KH-domain (KH-domain type I) | Nucleic acid-binding proteins | 1 | 1 | |
| YVTN repeat-like/Quinoprotein amine dehydrogenase | Caspase-like | 1 | 1 | |
| Phospholipase D/nuclease | Phospholipase D/nuclease | 1 | 1 | |
| GroEL equatorial domain-like | GroEL apical domain-like | 1 | 1 | |
| Aminopeptidase/glucanase lid domain | Zn-dependent exopeptidases | 1 | 1 | |
| lambda repressor-like DNA-binding domains | CheY-like | 1 | 1 | |
| 4Fe-4S ferredoxins | FMN-linked oxidoreductases | 1 | 1 | |
| YrdC/RibB | RibA-like | 1 | 1 | |
| ACP-like | Trimeric LpxA-like enzymes | 1 | 1 | |
| Transcription factor NusA, N-terminal domain | Nucleic acid-binding proteins | 1 | 1 | |
| Obg GTP-binding protein N-terminal domain | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Actin-like ATPase domain | Heat shock protein 70kD (HSP70), peptide-binding domain | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | Argininosuccinate synthetase, C-terminal domain | 1 | 1 | |
| ThrRS/AlaRS common domain | Class II aaRS ABD-related | 1 | 1 | |
| "Winged helix" DNA-binding domain | GntR ligand-binding domain-like | 1 | 1 | |
| Rudiment single hybrid motif | Aldolase | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Eukaryotic type KH-domain (KH-domain type I) | 1 | 1 | |
| Cytidine deaminase-like | Dihydrofolate reductase-like | 1 | 1 | |
| RuvA domain 2-like | RuvA domain 2-like | 1 | 1 | |
| Radical SAM enzymes | Nitrogenase accessory factor-like | 1 | 1 | |
| Thioredoxin-like | FAD/NAD(P)-binding domain | 1 | 1 | |
| ClpP/crotonase | ClpP/crotonase | 1 | 1 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | Nucleic acid-binding proteins | 1 | 1 | |
| Trigger factor ribosome-binding domain | FKBP-like | 1 | 1 | |
| Thioredoxin-like | Nqo1 middle domain-like | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | HRDC-like | 1 | 1 | |
| Tryptophan synthase beta subunit-like PLP-dependent enzymes | ACT-like | 1 | 1 | |
| PreATP-grasp domain | Methylglyoxal synthase-like | 1 | 1 | |
| Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain | Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain | 1 | 1 | |
| Glucocorticoid receptor-like (DNA-binding domain) | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| DNA/RNA polymerases | Lesion bypass DNA polymerase (Y-family), little finger domain | 1 | 1 | |
| Acyl-CoA dehydrogenase NM domain-like | Acyl-CoA dehydrogenase C-terminal domain-like | 1 | 1 | |
| alpha-helical ferredoxin | Respiratory nitrate reductase 1 gamma chain | 1 | 1 | |
| Glutamine synthetase, N-terminal domain | Glutamine synthetase/guanido kinase | 1 | 1 | |
| Rudiment single hybrid motif | Single hybrid motif | 1 | 1 | |
| Nucleotidylyl transferase | Nucleic acid-binding proteins | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | Homodimeric domain of signal transducing histidine kinase | 1 | 1 | |
| HMA, heavy metal-associated domain | HMA, heavy metal-associated domain | 1 | 1 | |
| FAD-linked oxidoreductase | ALDH-like | 1 | 1 | |
| EspE N-terminal domain-like | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 1 | 1 | |
| Putative DNA-binding domain | Anticodon-binding domain of PheRS | 1 | 1 | |
| Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | Translation proteins | 1 | 1 | |
| Quinoprotein alcohol dehydrogenase-like | CheY-like | 1 | 1 | |
| Nucleotide-diphospho-sugar transferases | RmlC-like cupins | 1 | 1 | |
| Glutamine synthetase/guanido kinase | GatB/YqeY motif | 1 | 1 | |
| Trigger factor ribosome-binding domain | Triger factor/SurA peptide-binding domain-like | 1 | 1 | |
| Thioredoxin-like | Six-hairpin glycosidases | 1 | 1 | |
| lambda repressor-like DNA-binding domains | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 1 | 1 | |
| Ribosomal L11/L12e N-terminal domain | Ribosomal protein L11, C-terminal domain | 1 | 1 | |
| Histidine-containing phosphotransfer domain, HPT domain | Histidine-containing phosphotransfer domain, HPT domain | 1 | 1 | |
| WD40 repeat-like | YVTN repeat-like/Quinoprotein amine dehydrogenase | 1 | 1 | |
| Nucleic acid-binding proteins | Putative DNA-binding domain | 1 | 1 | |
| Class II aaRS and biotin synthetases | GAD domain-like | 1 | 1 | |
| EF-hand | TPR-like | 1 | 1 | |
| Nucleic acid-binding proteins | Anticodon-binding domain of PheRS | 1 | 1 | |
| FAD-binding/transporter-associated domain-like | 4Fe-4S ferredoxins | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | DNA mismatch repair protein MutL | 1 | 1 | |
| (Phosphotyrosine protein) phosphatases II | Autotransporter | 1 | 1 | |
| DNA repair protein MutS, domain II | DNA repair protein MutS, domain III | 1 | 1 | |
| Dihydropteroate synthetase-like | Cobalamin (vitamin B12)-binding domain | 1 | 1 | |
| Nucleic acid-binding proteins | ArfGap/RecO-like zinc finger | 1 | 1 | |
| Cupredoxins | Cupredoxins | 1 | 1 | |
| Prokaryotic type KH domain (KH-domain type II) | Ribosomal protein S3 C-terminal domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | CarD-like | 1 | 1 | |
| FwdE-like | Molybdenum cofactor biosynthesis proteins | 1 | 1 | |
| GroEL-intermediate domain like | GroEL apical domain-like | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | GMP synthetase C-terminal dimerisation domain | 1 | 1 | |
| Molybdenum cofactor biosynthesis proteins | Periplasmic binding protein-like II | 1 | 1 | |
| GIY-YIG endonuclease | C-terminal UvrC-binding domain of UvrB | 1 | 1 | |
| N-utilization substance G protein NusG, N-terminal domain | Translation proteins SH3-like domain | 1 | 1 | |
| PTS system fructose IIA component-like | Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain | 1 | 1 | |
| Class I glutamine amidotransferase-like | Homeodomain-like | 1 | 1 | |
| "Winged helix" DNA-binding domain | PLP-dependent transferases | 1 | 1 | |
| HydA/Nqo6-like | Nqo5-like | 1 | 1 | |
| PUA domain-like | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| Quinoprotein alcohol dehydrogenase-like | PYP-like sensor domain (PAS domain) | 1 | 1 | |
| RuvA domain 2-like | BRCT domain | 1 | 1 | |
| Heat shock protein 70kD (HSP70), peptide-binding domain | Heat shock protein 70kD (HSP70), C-terminal subdomain | 1 | 1 | |
| vWA-like | TPR-like | 1 | 1 | |
| FAD/NAD(P)-binding domain | Radical SAM enzymes | 1 | 1 | |
| PTS system fructose IIA component-like | Phosphohistidine domain | 1 | 1 | |
| Insert subdomain of RNA polymerase alpha subunit | C-terminal domain of RNA polymerase alpha subunit | 1 | 1 | |
| Class I glutamine amidotransferase-like | Adenine nucleotide alpha hydrolases-like | 1 | 1 | |
| Rho N-terminal domain-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| GreA transcript cleavage protein, N-terminal domain | FKBP-like | 1 | 1 | |
| Ribonuclease PH domain 2-like | Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | 1 | 1 | |
| Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | Nucleic acid-binding proteins | 1 | 1 | |
| Translation proteins | Initiation factor IF2/eIF5b, domain 3 | 1 | 1 | |
| Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 1 | 1 | |
| Nucleic acid-binding proteins | HD-domain/PDEase-like | 1 | 1 | |
| Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain | Nucleotidylyl transferase | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Methylglyoxal synthase-like | 1 | 1 | |
| Zinc beta-ribbon | Zinc beta-ribbon | 1 | 1 | |
| Nucleic acid-binding proteins | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| Carbamoyl phosphate synthetase, large subunit connection domain | Methylglyoxal synthase-like | 1 | 1 | |
| Nucleotidylyl transferase | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| S13-like H2TH domain | Glucocorticoid receptor-like (DNA-binding domain) | 1 | 1 | |
| CbiG N-terminal domain-like | CobE/GbiG C-terminal domain-like | 1 | 1 | |
| beta-lactamase/transpeptidase-like | Penicillin-binding protein 2x (pbp-2x), c-terminal domain | 1 | 1 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | RuvA domain 2-like | 1 | 1 | |
| Nucleic acid-binding proteins | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| S-adenosylmethionine synthetase | S-adenosylmethionine synthetase | 1 | 1 | |
| FAD-linked oxidases, C-terminal domain | FAD-linked oxidases, C-terminal domain | 1 | 1 | |
| Rho N-terminal domain-like | Nucleic acid-binding proteins | 1 | 1 | |
| EspE N-terminal domain-like | Homodimeric domain of signal transducing histidine kinase | 1 | 1 | |
| Cryptochrome/photolyase, N-terminal domain | Cryptochrome/photolyase FAD-binding domain | 1 | 1 | |
| CarD-like | TRCF domain-like | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | SpoIIaa-like | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Bet v1-like | 1 | 1 | |
| Periplasmic binding protein-like II | GlnB-like | 1 | 1 | |
| Pectin lyase-like | Glycoside hydrolase/deacetylase | 1 | 1 | |
| Pectin lyase-like | Autotransporter | 1 | 1 | |
| ACT-like | PYP-like sensor domain (PAS domain) | 1 | 1 | |
| Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | ACT-like | 1 | 1 | |
| Bacterial muramidases | Lysozyme-like | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Concanavalin A-like lectins/glucanases | 1 | 1 | |
| Sm-like ribonucleoproteins | cAMP-binding domain-like | 1 | 1 | |
| ParB/Sulfiredoxin | KorB DNA-binding domain-like | 1 | 1 | |
| Radical SAM enzymes | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| FAD-binding/transporter-associated domain-like | alpha-helical ferredoxin | 1 | 1 | |
| Quinoprotein alcohol dehydrogenase-like | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 1 | 1 | |
| WD40 repeat-like | Caspase-like | 1 | 1 | |
| FabD/lysophospholipase-like | Probable ACP-binding domain of malonyl-CoA ACP transacylase | 1 | 1 | |
| dsRNA-binding domain-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| YjeF N-terminal domain-like | Ribokinase-like | 1 | 1 | |
| Methyl-accepting chemotaxis protein (MCP) signaling domain | Methyl-accepting chemotaxis protein (MCP) signaling domain | 1 | 1 | |
| Thiamin diphosphate-binding fold (THDP-binding) | 4Fe-4S ferredoxins | 1 | 1 | |
| Metal cation-transporting ATPase, ATP-binding domain N | Calcium ATPase, transmembrane domain M | 1 | 1 | |
| Diaminopimelate epimerase-like | Diaminopimelate epimerase-like | 1 | 1 | |
| FliG | FliG | 1 | 1 | |
| Rhodanese/Cell cycle control phosphatase | Ferritin-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Signal peptide-binding domain | 1 | 1 | |
| CBS-domain pair | ACT-like | 1 | 1 | |
| Quinoprotein alcohol dehydrogenase-like | Homodimeric domain of signal transducing histidine kinase | 1 | 1 | |
| 2Fe-2S ferredoxin-like | Thioredoxin-like | 1 | 1 | |
| vWA-like | OmpA-like | 1 | 1 | |
| Acyl-CoA N-acyltransferases (Nat) | Acyl-CoA N-acyltransferases (Nat) | 1 | 1 | |
| Nucleotidyltransferase | TGS-like | 1 | 1 | |
| Cytochrome c | Multiheme cytochromes | 1 | 1 | |
| Fumarylacetoacetate hydrolase, FAH, N-terminal domain | FAH | 1 | 1 | |
| Phase 1 flagellin | Phase 1 flagellin | 1 | 1 | |
| PreATP-grasp domain | Single hybrid motif | 1 | 1 | |
| Translation proteins | ThrRS/AlaRS common domain | 1 | 1 | |
| CheC-like | Surface presentation of antigens (SPOA) | 1 | 1 | |
| Fe-only hydrogenase | Thioredoxin-like | 1 | 1 | |
| Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | Nucleic acid-binding proteins | 1 | 1 | |
| 2Fe-2S ferredoxin-like | Molybdenum cofactor-binding domain | 1 | 1 | |
| PK beta-barrel domain-like | Phosphoenolpyruvate/pyruvate domain | 1 | 1 | |
| Calcium-dependent phosphotriesterase | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 1 | 1 | |
| ARM repeat | ARM repeat | 1 | 1 | |
| L9 N-domain-like | Ribosomal protein L9 C-domain | 1 | 1 | |
| DHH phosphoesterases | Poly A polymerase C-terminal region-like | 1 | 1 | |
| Putative DNA-binding domain | mu transposase, C-terminal domain | 1 | 1 | |
| Pseudouridine synthase | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| PIN domain-like | 5' to 3' exonuclease, C-terminal subdomain | 1 | 1 | |
| Lysozyme-like | LysM domain | 1 | 1 | |
| Alpha-L RNA-binding motif | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Phosphohistidine domain | Concanavalin A-like lectins/glucanases | 1 | 1 | |
| S-adenosyl-L-methionine-dependent methyltransferases | GAF domain-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | RecA protein, C-terminal domain | 1 | 1 | |
| S-adenosyl-L-methionine-dependent methyltransferases | Nucleotide-diphospho-sugar transferases | 1 | 1 | |
| DNA repair protein MutS, domain I | DNA repair protein MutS, domain II | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | HSP90 C-terminal domain | 1 | 1 | |
| HPr-like | Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain | 1 | 1 | |
| Pectin lyase-like | Pectin lyase-like | 1 | 1 | |
| ValRS/IleRS/LeuRS editing domain | tRNA-binding arm | 1 | 1 | |
| 4'-phosphopantetheinyl transferase | 4'-phosphopantetheinyl transferase | 1 | 1 | |
| Barwin-like endoglucanases | Sporulation related repeat | 1 | 1 | |
| EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | "Winged helix" DNA-binding domain | 1 | 1 | |
| Penicillin binding protein dimerisation domain | Penicillin-binding protein 2x (pbp-2x), c-terminal domain | 1 | 1 | |
| Class II aaRS and biotin synthetases | YbaK/ProRS associated domain | 1 | 1 | |
| Tex N-terminal region-like | RuvA domain 2-like | 1 | 1 | |
| Periplasmic binding protein-like II | Voltage-gated potassium channels | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Glutamyl tRNA-reductase dimerization domain | 1 | 1 | |
| Quinoprotein alcohol dehydrogenase-like | Calcium-dependent phosphotriesterase | 1 | 1 | |
| Alpha subunit of glutamate synthase, C-terminal domain | FAD/NAD(P)-binding domain | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Phosphoenolpyruvate/pyruvate domain | 1 | 1 | |
| Sensory domain-like | HAMP domain-like | 1 | 1 | |
| Tryptophan synthase beta subunit-like PLP-dependent enzymes | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 1 | 1 | |
| lambda repressor-like DNA-binding domains | GAF domain-like | 1 | 1 | |
| Folate-binding domain | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| GAF domain-like | PP2C-like | 1 | 1 | |
| HCP-like | Trypsin-like serine proteases | 1 | 1 | |
| UBA-like | Elongation factor Ts (EF-Ts), dimerisation domain | 1 | 1 | |
| Riboflavin synthase domain-like | Riboflavin synthase domain-like | 1 | 1 | |
| PK beta-barrel domain-like | PK C-terminal domain-like | 1 | 1 | |
| Chemotaxis receptor methyltransferase CheR, N-terminal domain | GAF domain-like | 1 | 1 | |
| DNA repair protein MutS, domain I | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| DNA-glycosylase | Nudix | 1 | 1 | |
| DNA methylase specificity domain | DNA methylase specificity domain | 1 | 1 | |
| Carbamate kinase-like | ACT-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| PreATP-grasp domain | PreATP-grasp domain | 1 | 1 | |
| HPr-like | Phosphohistidine domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | DNA/RNA polymerases | 1 | 1 | |
| Flavoproteins | Flavoproteins | 1 | 1 | |
| "Winged helix" DNA-binding domain | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| UDP-Glycosyltransferase/glycogen phosphorylase | UDP-Glycosyltransferase/glycogen phosphorylase | 1 | 1 | |
| PreATP-grasp domain | Carbamoyl phosphate synthetase, large subunit connection domain | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | 1 | 1 | |
| Terpenoid cyclases/Protein prenyltransferases | Terpenoid cyclases/Protein prenyltransferases | 1 | 1 | |
| PTS system fructose IIA component-like | Phosphoenolpyruvate/pyruvate domain | 1 | 1 | |
| EreA/ChaN-like | PDZ domain-like | 1 | 1 | |
| TGS-like | ACT-like | 1 | 1 | |
| Class II aaRS and biotin synthetases | Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | 1 | 1 | |
| Metallo-dependent phosphatases | 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain | 1 | 1 | |
| Formyltransferase | FMT C-terminal domain-like | 1 | 1 | |
| Glutamyl tRNA-reductase catalytic, N-terminal domain | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | HSP90 C-terminal domain | 1 | 1 | |
| Cytochrome c oxidase subunit II-like, transmembrane region | Cupredoxins | 1 | 1 | |
| ACT-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| N-terminal domain of MutM-like DNA repair proteins | Glucocorticoid receptor-like (DNA-binding domain) | 1 | 1 | |
| Ribonuclease PH domain 2-like | Ribonuclease PH domain 2-like | 1 | 1 | |
| FAD/NAD(P)-binding domain | HI0933 insert domain-like | 1 | 1 | |
| Pre-protein crosslinking domain of SecA | Helical scaffold and wing domains of SecA | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Acyl-CoA N-acyltransferases (Nat) | 1 | 1 | |
| Nucleic acid-binding proteins | BRCT domain | 1 | 1 | |
| PGBD-like | Lysozyme-like | 1 | 1 | |
| YhbC-like, N-terminal domain | YhbC-like, C-terminal domain | 1 | 1 | |
| Nucleic acid-binding proteins | DNA helicase RuvA subunit, C-terminal domain | 1 | 1 | |
| NusB-like | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| LysM domain | Sm-like ribonucleoproteins | 1 | 1 | |
| DHH phosphoesterases | CBS-domain pair | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | Type II DNA topoisomerase | 1 | 1 | |
| GlnB-like | CBS-domain pair | 1 | 1 | |
| Tryptophan synthase beta subunit-like PLP-dependent enzymes | Nucleotidylyl transferase | 1 | 1 | |
| Eukaryotic type KH-domain (KH-domain type I) | HD-domain/PDEase-like | 1 | 1 | |
| Homocysteine S-methyltransferase | Cobalamin (vitamin B12)-binding domain | 1 | 1 | |
| Phase 1 flagellin | 3-carboxy-cis,cis-mucoante lactonizing enzyme | 1 | 1 | |
| YbaK/ProRS associated domain | Class II aaRS ABD-related | 1 | 1 | |
| PYP-like sensor domain (PAS domain) | PP2C-like | 1 | 1 | |
| Succinyl-CoA synthetase domains | Acyl-CoA N-acyltransferases (Nat) | 1 | 1 | |
| Putative DNA-binding domain | Class II aaRS and biotin synthetases | 1 | 1 | |
| Sensory domain-like | GAF domain-like | 1 | 1 | |
| Carbon-nitrogen hydrolase | Adenine nucleotide alpha hydrolases-like | 1 | 1 | |
| Type II DNA topoisomerase | GyrA/ParC C-terminal domain-like | 1 | 1 | |
| PreATP-grasp domain | post-HMGL domain-like | 1 | 1 | |
| Enolase N-terminal domain-like | Enolase C-terminal domain-like | 1 | 1 | |
| Tubulin nucleotide-binding domain-like | Tubulin C-terminal domain-like | 1 | 1 | |
| ACT-like | Formyltransferase | 1 | 1 | |
| HAMP domain-like | Nucleotide cyclase | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Phosphoglycerate mutase-like | 1 | 1 | |
| 2Fe-2S ferredoxin-like | CO dehydrogenase molybdoprotein N-domain-like | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | DNA mismatch repair protein MutL | 1 | 1 | |
| RuvA domain 2-like | DNA helicase RuvA subunit, C-terminal domain | 1 | 1 | |
| Thiamin diphosphate-binding fold (THDP-binding) | Pyruvate-ferredoxin oxidoreductase, PFOR, domain III | 1 | 1 | |
| 2Fe-2S ferredoxin-like | ADC-like | 1 | 1 | |
| CBS-domain pair | Histidine-containing phosphotransfer domain, HPT domain | 1 | 1 | |
| "Winged helix" DNA-binding domain | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| 4Fe-4S ferredoxins | ADC-like | 1 | 1 | |
| Fe,Mn superoxide dismutase (SOD), N-terminal domain | Fe,Mn superoxide dismutase (SOD), C-terminal domain | 1 | 1 | |
| Calcium ATPase, transduction domain A | Metal cation-transporting ATPase, ATP-binding domain N | 1 | 1 | |
| Ribonuclease H-like | Nucleic acid-binding proteins | 1 | 1 | |
| post-HMGL domain-like | Single hybrid motif | 1 | 1 | |
| Clc chloride channel | CBS-domain pair | 1 | 1 | |
| Methylesterase CheB, C-terminal domain | GAF domain-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | C-terminal UvrC-binding domain of UvrB | 1 | 1 | |
| Calcium-dependent phosphotriesterase | PYP-like sensor domain (PAS domain) | 1 | 1 | |
| Trimeric LpxA-like enzymes | Trimeric LpxA-like enzymes | 1 | 1 | |
| PEP carboxykinase N-terminal domain | PEP carboxykinase-like | 1 | 1 | |
| cAMP-binding domain-like | CBS-domain pair | 1 | 1 | |
| PIN domain-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Prokaryotic type KH domain (KH-domain type II) | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| Transcription factor NusA, N-terminal domain | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| Hedgehog/intein (Hint) domain | PFL-like glycyl radical enzymes | 1 | 1 | |
| Putative DNA-binding domain | Ribonuclease H-like | 1 | 1 | |
| Zinc beta-ribbon | DNA primase core | 1 | 1 | |
| "Winged helix" DNA-binding domain | "Winged helix" DNA-binding domain | 1 | 1 | |
| TPR-like | OMPA-like | 1 | 1 | |
| DNA clamp | DNA clamp | 1 | 1 | |
| Aldolase | Single hybrid motif | 1 | 1 | |
| LysM domain | TPR-like | 1 | 1 | |
| Trypsin-like serine proteases | Multiheme cytochromes | 1 | 1 | |
| Class II aaRS and biotin synthetases | SufE/NifU | 1 | 1 | |
| 4Fe-4S ferredoxins | 4Fe-4S ferredoxins | 1 | 1 | |
| Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | ThrRS/AlaRS common domain | 1 | 1 | |
| PYP-like sensor domain (PAS domain) | Ligand-binding domain in the NO signalling and Golgi transport | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Ribonuclease PH domain 2-like | 1 | 1 | |
| FAD-linked reductases, C-terminal domain | 4Fe-4S ferredoxins | 1 | 1 | |
| SirA-like | DsrEFH-like | 1 | 1 | |
| PheT/TilS domain | Class II aaRS and biotin synthetases | 1 | 1 | |
| Periplasmic binding protein-like II | Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain | 1 | 1 | |
| Coiled-coil domain of nucleotide exchange factor GrpE | Head domain of nucleotide exchange factor GrpE | 1 | 1 | |
| PLP-dependent transferases | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Actin-like ATPase domain | Heat shock protein 70kD (HSP70), C-terminal subdomain | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | SIS domain | 1 | 1 | |
| "Winged helix" DNA-binding domain | HRDC-like | 1 | 1 | |
| PDZ domain-like | ClpP/crotonase | 1 | 1 | |
| Thioredoxin-like | Nqo1C-terminal domain-like | 1 | 1 | |
| SufE/NifU | Fe-S cluster assembly (FSCA) domain-like | 1 | 1 | |
| Homeodomain-like | Probable bacterial effector-binding domain | 1 | 1 | |
| Nucleotidylyl transferase | An anticodon-binding domain of class I aminoacyl-tRNA synthetases | 1 | 1 | |
| Ribonuclease H-like | mu transposase, C-terminal domain | 1 | 1 | |
| MgtE N-terminal domain-like | CBS-domain pair | 1 | 1 | |
| Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | tRNA-binding arm | 1 | 1 | |
| Dihydropteroate synthetase-like | Nitrite and sulphite reductase 4Fe-4S domain-like | 1 | 1 | |
| 4Fe-4S ferredoxins | Radical SAM enzymes | 1 | 1 | |
| Calcium-dependent phosphotriesterase | CheY-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Hypothetical protein YjiA, C-terminal domain | 1 | 1 | |
| Nucleotide-diphospho-sugar transferases | HD-domain/PDEase-like | 1 | 1 | |
| NTF2-like | Sec-C motif | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Ribonuclease H-like | 1 | 1 | |
| Dihydropteroate synthetase-like | Methionine synthase domain | 1 | 1 | |
| lambda integrase-like, N-terminal domain | DNA breaking-rejoining enzymes | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | TRCF domain-like | 1 | 1 | |
| Thioredoxin-like | Thioredoxin-like | 1 | 1 | |
| Insert subdomain of RNA polymerase alpha subunit | RBP11-like subunits of RNA polymerase | 1 | 1 | |
| Sec-C motif | TPR-like | 1 | 1 | |
| Pyruvate-ferredoxin oxidoreductase, PFOR, domain III | 4Fe-4S ferredoxins | 1 | 1 | |
| NagB/RpiA/CoA transferase-like | D-ribose-5-phosphate isomerase (RpiA), lid domain | 1 | 1 | |
| Nucleotide-diphospho-sugar transferases | Trimeric LpxA-like enzymes | 1 | 1 | |
| Alpha subunit of glutamate synthase, C-terminal domain | 4Fe-4S ferredoxins | 1 | 1 | |
| Periplasmic binding protein-like II | ACT-like | 1 | 1 | |
| Ribbon-helix-helix | ACT-like | 1 | 1 | |
| FAD/NAD(P)-binding domain | Nucleotide-binding domain | 1 | 1 | |
| 4Fe-4S ferredoxins | Formate dehydrogenase/DMSO reductase, domains 1-3 | 1 | 1 | |
| PHP domain-like | AF1531-like | 1 | 1 | |
| Nucleic acid-binding proteins | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| Ribonuclease H-like | RuvA domain 2-like | 1 | 1 | |
| 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain | Alkaline phosphatase-like | 1 | 1 | |
| Rudiment single hybrid motif | post-HMGL domain-like | 1 | 1 | |
| TrkA C-terminal domain-like | TrkA C-terminal domain-like | 1 | 1 | |
| PheT/TilS domain | Anticodon-binding domain of PheRS | 1 | 1 | |
| TK C-terminal domain-like | 4Fe-4S ferredoxins | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Pre-protein crosslinking domain of SecA | 1 | 1 | |
| 4Fe-4S ferredoxins | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| 5' to 3' exonuclease, C-terminal subdomain | DNA/RNA polymerases | 1 | 1 | |
| all-alpha NTP pyrophosphatases | all-alpha NTP pyrophosphatases | 1 | 1 | |
| Nudix | Nudix | 1 | 1 | |
| Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain | 1 | 1 | |
| PreATP-grasp domain | Aldolase | 1 | 1 | |
| ACP-like | Acyl-CoA N-acyltransferases (Nat) | 1 | 1 | |
| Methionine synthase domain | Cobalamin (vitamin B12)-binding domain | 1 | 1 | |
| GroEL equatorial domain-like | GroEL-intermediate domain like | 1 | 1 | |
| FAD-linked oxidases, C-terminal domain | alpha-helical ferredoxin | 1 | 1 | |
| DPP6 N-terminal domain-like | alpha/beta-Hydrolases | 1 | 1 | |
| R1 subunit of ribonucleotide reductase, N-terminal domain | Homing endonucleases | 1 | 1 | |
| Inosine monophosphate dehydrogenase (IMPDH) | Inosine monophosphate dehydrogenase (IMPDH) | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Type II DNA topoisomerase | 1 | 1 | |
| CheY-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| Translation proteins | Translation proteins | 1 | 1 | |
| Pheromone-binding domain of LuxR-like quorum-sensing transcription factors | C-terminal effector domain of the bipartite response regulators | 1 | 1 | |
| RBP11-like subunits of RNA polymerase | C-terminal domain of RNA polymerase alpha subunit | 1 | 1 | |
| Phosphohistidine domain | Rhodanese/Cell cycle control phosphatase | 1 | 1 | |
| Homocysteine S-methyltransferase | Dihydropteroate synthetase-like | 1 | 1 | |
| Bacterial muramidases | TPR-like | 1 | 1 | |
| NTF2-like | NTF2-like | 1 | 1 | |
| R1 subunit of ribonucleotide reductase, N-terminal domain | Hedgehog/intein (Hint) domain | 1 | 1 | |
| PYP-like sensor domain (PAS domain) | Hemerythrin-like | 1 | 1 | |
| Globin-like | Nucleotide cyclase | 1 | 1 | |
| PheT/TilS domain | Putative DNA-binding domain | 1 | 1 | |
| FAD/NAD(P)-binding domain | FAD-linked reductases, C-terminal domain | 1 | 1 | |
| 4Fe-4S ferredoxins | HydA/Nqo6-like | 1 | 1 | |
| GIY-YIG endonuclease | RuvA domain 2-like | 1 | 1 | |
| DNA repair protein MutS, domain III | SMR domain-like | 1 | 1 | |
| FAD-binding/transporter-associated domain-like | CO dehydrogenase flavoprotein C-terminal domain-like | 1 | 1 | |
| Nucleotidylyl transferase | tRNA-binding arm | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Single hybrid motif | 1 | 1 | |
| Prokaryotic type I DNA topoisomerase | Zinc beta-ribbon | 1 | 1 | |
| Pentapeptide repeat-like | Pentapeptide repeat-like | 1 | 1 | |
| L,D-transpeptidase catalytic domain-like | NTF2-like | 1 | 1 | |
| Aldolase | post-HMGL domain-like | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | post-HMGL domain-like | 1 | 1 | |
| Periplasmic binding protein-like II | Periplasmic binding protein-like II | 1 | 1 | |
| HPr-like | Phosphoenolpyruvate/pyruvate domain | 1 | 1 | |
| Acylphosphatase/BLUF domain-like | YrdC/RibB | 1 | 1 | |
| CBS-domain pair | Nucleotidyltransferase | 1 | 1 | |
| Class II aaRS and biotin synthetases | Translation proteins | 1 | 1 | |
| RNase III domain-like | dsRNA-binding domain-like | 1 | 1 | |
| Radical SAM enzymes | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Aldolase | 1 | 1 | |
| TPR-like | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| Thioredoxin-like | Nqo1 FMN-binding domain-like | 1 | 1 | |
| HCP-like | HCP-like | 1 | 1 | |
| Domain of the SRP/SRP receptor G-proteins | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Nucleic acid-binding proteins | beta-lactamase/transpeptidase-like | 1 | 1 | |
| "Winged helix" DNA-binding domain | Dimeric alpha+beta barrel | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Siroheme synthase middle domains-like | 1 | 1 | |
| Nucleotide cyclase | TPR-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Initiation factor IF2/eIF5b, domain 3 | 1 | 1 | |
| HydA/Nqo6-like | HydB/Nqo4-like | 1 | 1 | |
| CO dehydrogenase ISP C-domain like | Molybdenum cofactor-binding domain | 1 | 1 | |
| Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | Eukaryotic type KH-domain (KH-domain type I) | 1 | 1 | |
| FAD-linked oxidases, C-terminal domain | 4Fe-4S ferredoxins | 1 | 1 | |
| Lysozyme-like | Nucleic acid-binding proteins | 1 | 1 | |
| PurM N-terminal domain-like | PurM N-terminal domain-like | 1 | 1 | |
| Thiolase-like | Thiolase-like | 1 | 1 | |
| Chorismate mutase II | Periplasmic binding protein-like II | 1 | 1 | |
| Concanavalin A-like lectins/glucanases | Rhodanese/Cell cycle control phosphatase | 1 | 1 | |
| TolB, N-terminal domain | Tricorn protease N-terminal domain | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | PRTase-like | 1 | 1 | |
| R1 subunit of ribonucleotide reductase, N-terminal domain | PFL-like glycyl radical enzymes | 1 | 1 | |
| Nucleotidylyl transferase | Ribosomal protein L25-like | 1 | 1 | |
