All pairs of domain combinations at the superfamily level are listed here.
The identification of domain pairs does not account for the possibility of non-contiguous domains. Inserted, or interlaced, domains are seen as having a simple pair ordering.
The links below permit the addition or removal of specific sets of domain combination pairs.
Change the list of genome two-letter codes in the 'Include genomes' box to include domain-pairs from those genomes.
Change the list of genomes in the 'Exclude genomes' box to exclude domain-pairs from those genomes.
List of all two-letter genome codes.
| Superfamily (N) | Superfamily (C) | Number of occurrances | Number unique | |
|---|
| P-loop containing nucleoside triphosphate hydrolases | P-loop containing nucleoside triphosphate hydrolases | 14 | 10 |  |
| Hedgehog/intein (Hint) domain | Homing endonucleases | 11 | 11 | |
| Thiamin diphosphate-binding fold (THDP-binding) | TK C-terminal domain-like | 11 | 3 | |
| "Winged helix" DNA-binding domain | P-loop containing nucleoside triphosphate hydrolases | 10 | 6 | |
| "Winged helix" DNA-binding domain | Dimeric alpha+beta barrel | 9 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 8 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Hedgehog/intein (Hint) domain | 7 | 7 | |
| P-loop containing nucleoside triphosphate hydrolases | Homing endonucleases | 7 | 7 | |
| P-loop containing nucleoside triphosphate hydrolases | MOP-like | 7 | 1 | |
| PurM N-terminal domain-like | PurM C-terminal domain-like | 6 | 2 | |
| NAD(P)-binding Rossmann-fold domains | Succinyl-CoA synthetase domains | 6 | 2 | |
| Nucleotidylyl transferase | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 6 | 5 | |
| Metallo-dependent hydrolases | Composite domain of metallo-dependent hydrolases | 5 | 3 | |
| Succinyl-CoA synthetase domains | Succinyl-CoA synthetase domains | 5 | 1 | |
| Putative DNA-binding domain | Resolvase-like | 5 | 1 | |
| Multidrug resistance efflux transporter EmrE | Multidrug resistance efflux transporter EmrE | 5 | 2 | |
| Riboflavin synthase domain-like | Ferredoxin reductase-like, C-terminal NADP-linked domain | 5 | 2 | |
| PreATP-grasp domain | Glutathione synthetase ATP-binding domain-like | 5 | 2 | |
| Zn-dependent exopeptidases | Bacterial exopeptidase dimerisation domain | 5 | 1 | |
| FAD/NAD(P)-binding domain | FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 4 | 3 | |
| Aldehyde ferredoxin oxidoreductase, N-terminal domain | Aldehyde ferredoxin oxidoreductase, C-terminal domains | 4 | 2 | |
| Creatinase/prolidase N-terminal domain | Creatinase/aminopeptidase | 4 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Restriction endonuclease-like | 4 | 3 | |
| Phosphoglucomutase, first 3 domains | Phosphoglucomutase, first 3 domains | 4 | 2 | |
| Formate/glycerate dehydrogenase catalytic domain-like | NAD(P)-binding Rossmann-fold domains | 4 | 1 | |
| Class II aaRS and biotin synthetases | Class II aaRS ABD-related | 4 | 4 | |
| P-loop containing nucleoside triphosphate hydrolases | Translation proteins | 4 | 3 | |
| Homing endonucleases | Homing endonucleases | 4 | 4 | |
| NAD(P)-binding Rossmann-fold domains | 6-phosphogluconate dehydrogenase C-terminal domain-like | 4 | 2 | |
| Aminopeptidase/glucanase lid domain | Zn-dependent exopeptidases | 3 | 1 | |
| ValRS/IleRS/LeuRS editing domain | Nucleotidylyl transferase | 3 | 2 | |
| Nucleotide-diphospho-sugar transferases | Trimeric LpxA-like enzymes | 3 | 1 | |
| TK C-terminal domain-like | 4Fe-4S ferredoxins | 3 | 1 | |
| alpha-helical ferredoxin | Nucleotide-binding domain | 3 | 3 | |
| 4Fe-4S ferredoxins | P-loop containing nucleoside triphosphate hydrolases | 3 | 2 | |
| Phosphoglucomutase, first 3 domains | Phosphoglucomutase, C-terminal domain | 3 | 1 | |
| Thiamin diphosphate-binding fold (THDP-binding) | 4Fe-4S ferredoxins | 3 | 1 | |
| Translation proteins | ThrRS/AlaRS common domain | 3 | 3 | |
| ValRS/IleRS/LeuRS editing domain | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 3 | 2 | |
| Hedgehog/intein (Hint) domain | Hedgehog/intein (Hint) domain | 3 | 3 | |
| Formate dehydrogenase/DMSO reductase, domains 1-3 | ADC-like | 3 | 1 | |
| Ribosomal protein S5 domain 2-like | GHMP Kinase, C-terminal domain | 3 | 1 | |
| FAD/NAD(P)-binding domain | FAD-linked reductases, C-terminal domain | 3 | 1 | |
| "Winged helix" DNA-binding domain | TrmB C-terminal domain-like | 3 | 2 | |
| MetI-like | MetI-like | 3 | 2 | |
| Aminoacid dehydrogenase-like, N-terminal domain | NAD(P)-binding Rossmann-fold domains | 3 | 1 | |
| Thiamin diphosphate-binding fold (THDP-binding) | Thiamin diphosphate-binding fold (THDP-binding) | 3 | 1 | |
| ABC transporter transmembrane region | P-loop containing nucleoside triphosphate hydrolases | 3 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Class I glutamine amidotransferase-like | 2 | 1 | |
| DPP6 N-terminal domain-like | alpha/beta-Hydrolases | 2 | 1 | |
| Terpenoid cyclases/Protein prenyltransferases | Terpenoid cyclases/Protein prenyltransferases | 2 | 2 | |
| tRNA-guanine transglycosylase | PUA domain-like | 2 | 2 | |
| "Winged helix" DNA-binding domain | Restriction endonuclease-like | 2 | 1 | |
| Domain of the SRP/SRP receptor G-proteins | P-loop containing nucleoside triphosphate hydrolases | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | Acyl-CoA N-acyltransferases (Nat) | 2 | 2 | |
| Tubulin nucleotide-binding domain-like | Tubulin C-terminal domain-like | 2 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | C-terminal domain of alpha and beta subunits of F1 ATP synthase | 2 | 2 | |
| MoeA N-terminal region -like | MoeA C-terminal domain-like | 2 | 1 | |
| PhoU-like | TrkA C-terminal domain-like | 2 | 1 | |
| HMA, heavy metal-associated domain | Calcium ATPase, transmembrane domain M | 2 | 2 | |
| Enolase N-terminal domain-like | Enolase C-terminal domain-like | 2 | 1 | |
| ADC-like | Cdc48 domain 2-like | 2 | 1 | |
| Nucleic acid-binding proteins | Class II aaRS and biotin synthetases | 2 | 1 | |
| CBS-domain pair | CBS-domain pair | 2 | 2 | |
| NAD(P)-binding Rossmann-fold domains | UDP-glucose/GDP-mannose dehydrogenase C-terminal domain | 2 | 1 | |
| Nucleic acid-binding proteins | Nucleic acid-binding proteins | 2 | 2 | |
| Nicotinate/Quinolinate PRTase N-terminal domain-like | Nicotinate/Quinolinate PRTase C-terminal domain-like | 2 | 1 | |
| "Winged helix" DNA-binding domain | "Winged helix" DNA-binding 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 | 2 | |
| tRNA-guanine transglycosylase | Pre-PUA domain | 2 | 2 | |
| Sm-like ribonucleoproteins | Mechanosensitive channel protein MscS (YggB), C-terminal domain | 2 | 2 | |
| Translational machinery components | L30e-like | 2 | 2 | |
| PreATP-grasp domain | Rudiment single hybrid motif | 2 | 1 | |
| Glycoside hydrolase/deacetylase | Families 57/38 glycoside transferase middle domain | 2 | 2 | |
| Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain | Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | TGS-like | 2 | 2 | |
| Nucleic acid-binding proteins | P-loop containing nucleoside triphosphate hydrolases | 2 | 2 | |
| Cation efflux protein transmembrane domain-like | Cation efflux protein cytoplasmic domain-like | 2 | 1 | |
| Mechanosensitive channel protein MscS (YggB), transmembrane region | Sm-like ribonucleoproteins | 2 | 2 | |
| PUA domain-like | S-adenosyl-L-methionine-dependent methyltransferases | 2 | 2 | |
| Thiolase-like | Thiolase-like | 2 | 1 | |
| Cyclin-like | Cyclin-like | 2 | 1 | |
| THUMP domain-like | Adenine nucleotide alpha hydrolases-like | 2 | 1 | |
| Zinc beta-ribbon | Cyclin-like | 2 | 1 | |
| Ribosomal L27 protein-like | Nucleic acid-binding proteins | 2 | 2 | |
| THUMP domain-like | S-adenosyl-L-methionine-dependent methyltransferases | 2 | 1 | |
| Aspartate/glutamate racemase | Aspartate/glutamate racemase | 2 | 1 | |
| HMA, heavy metal-associated domain | HAD-like | 2 | 2 | |
| Translation proteins | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 2 | 1 | |
| Calcium ATPase, transduction domain A | HAD-like | 2 | 2 | |
| Calcium ATPase, transduction domain A | Calcium ATPase, transmembrane domain M | 2 | 2 | |
| ADC-like | P-loop containing nucleoside triphosphate hydrolases | 2 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Rudiment single hybrid motif | 2 | 1 | |
| HMA, heavy metal-associated domain | Calcium ATPase, transduction domain A | 2 | 2 | |
| Mechanosensitive channel protein MscS (YggB), transmembrane region | Mechanosensitive channel protein MscS (YggB), C-terminal domain | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 2 | 1 | |
| Cdc48 domain 2-like | P-loop containing nucleoside triphosphate hydrolases | 2 | 1 | |
| Molybdenum cofactor biosynthesis proteins | MoeA C-terminal domain-like | 2 | 1 | |
| Ribosomal protein S5 domain 2-like | Ribonuclease PH domain 2-like | 2 | 1 | |
| Metallo-hydrolase/oxidoreductase | Flavoproteins | 2 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Ribosomal protein S5 domain 2-like | 2 | 2 | |
| Pre-PUA domain | PUA domain-like | 2 | 2 | |
| MoeA N-terminal region -like | Molybdenum cofactor biosynthesis proteins | 2 | 1 | |
| Ribosomal protein S5 domain 2-like | EF-G C-terminal domain-like | 2 | 2 | |
| HAD-like | Calcium ATPase, transmembrane domain M | 2 | 2 | |
| "Winged helix" DNA-binding domain | Class II aaRS and biotin synthetases | 2 | 2 | |
| Translation proteins SH3-like domain | Nucleic acid-binding proteins | 2 | 2 | |
| "Winged helix" DNA-binding domain | Sec63 N-terminal domain-like | 1 | 1 | |
| Ribosomal L11/L12e N-terminal domain | Ribosomal protein L11, C-terminal domain | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | CheW-like | 1 | 1 | |
| PIN domain-like | 5' to 3' exonuclease, C-terminal subdomain | 1 | 1 | |
| N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 | L30e-like | 1 | 1 | |
| Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | ThrRS/AlaRS common domain | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | PRTase-like | 1 | 1 | |
| Class II aaRS and biotin synthetases | C-terminal domain of transcriptional repressors | 1 | 1 | |
| Prokaryotic type I DNA topoisomerase | Hedgehog/intein (Hint) domain | 1 | 1 | |
| CBS-domain pair | Inosine monophosphate dehydrogenase (IMPDH) | 1 | 1 | |
| FAD/NAD(P)-binding domain | Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain | 1 | 1 | |
| Homing endonucleases | post-AAA+ oligomerization domain-like | 1 | 1 | |
| EPT/RTPC-like | RNA 3'-terminal phosphate cyclase, RPTC, insert domain | 1 | 1 | |
| CheY-binding domain of CheA | Homodimeric domain of signal transducing histidine kinase | 1 | 1 | |
| LEA14-like | LEA14-like | 1 | 1 | |
| Nucleotidylyl transferase | Nucleic acid-binding proteins | 1 | 1 | |
| Nucleic acid-binding proteins | alpha/beta knot | 1 | 1 | |
| Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain | 1 | 1 | |
| GroES-like | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| ClpP/crotonase | ClpP/crotonase | 1 | 1 | |
| Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain | Pyrimidine nucleoside phosphorylase C-terminal domain | 1 | 1 | |
| Histidine-containing phosphotransfer domain, HPT domain | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 1 | 1 | |
| Ribosomal protein L6 | Ribosomal protein L6 | 1 | 1 | |
| Ferritin-like | Major capsid protein gp5 | 1 | 1 | |
| Hedgehog/intein (Hint) domain | lambda repressor-like DNA-binding domains | 1 | 1 | |
| Nqo1 FMN-binding domain-like | Nqo1C-terminal domain-like | 1 | 1 | |
| Families 57/38 glycoside transferase middle domain | Rad51 N-terminal domain-like | 1 | 1 | |
| all-alpha NTP pyrophosphatases | YbaK/ProRS associated domain | 1 | 1 | |
| Thioredoxin-like | 4Fe-4S ferredoxins | 1 | 1 | |
| ATP-dependent DNA ligase DNA-binding domain | DNA ligase/mRNA capping enzyme, catalytic domain | 1 | 1 | |
| Hedgehog/intein (Hint) domain | "Winged helix" DNA-binding domain | 1 | 1 | |
| Aldolase | Single hybrid motif | 1 | 1 | |
| Class II aaRS and biotin synthetases | Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | 1 | 1 | |
| Aldolase | post-HMGL domain-like | 1 | 1 | |
| MalF N-terminal region-like | MetI-like | 1 | 1 | |
| N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 | Translational machinery components | 1 | 1 | |
| Nucleotidyltransferase | PAP/Archaeal CCA-adding enzyme, C-terminal domain | 1 | 1 | |
| Cobalamin (vitamin B12)-binding domain | Radical SAM enzymes | 1 | 1 | |
| Putative DNA-binding domain | Class II aaRS and biotin synthetases | 1 | 1 | |
| Acylphosphatase/BLUF domain-like | Actin-like ATPase domain | 1 | 1 | |
| YrdC/RibB | Actin-like ATPase domain | 1 | 1 | |
| Prokaryotic type KH domain (KH-domain type II) | Metallo-hydrolase/oxidoreductase | 1 | 1 | |
| Glutamine synthetase, N-terminal domain | Glutamine synthetase/guanido kinase | 1 | 1 | |
| SirA-like | SP0561-like | 1 | 1 | |
| Creatinase/aminopeptidase | "Winged helix" DNA-binding domain | 1 | 1 | |
| CorA soluble domain-like | Magnesium transport protein CorA, transmembrane region | 1 | 1 | |
| Sensory domain-like | Methyl-accepting chemotaxis protein (MCP) signaling domain | 1 | 1 | |
| Nucleic acid-binding proteins | Hedgehog/intein (Hint) domain | 1 | 1 | |
| Pentapeptide repeat-like | Voltage-gated potassium channels | 1 | 1 | |
| MgtE membrane domain-like | MgtE membrane domain-like | 1 | 1 | |
| Homodimeric domain of signal transducing histidine kinase | CheW-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Smc hinge domain | 1 | 1 | |
| Nqo1 middle domain-like | 4Fe-4S ferredoxins | 1 | 1 | |
| NusB-like | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| HD-domain/PDEase-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| CheY-binding domain of CheA | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 1 | 1 | |
| Histidine-containing phosphotransfer domain, HPT domain | Homodimeric domain of signal transducing histidine kinase | 1 | 1 | |
| Dom34/Pelota N-terminal domain-like | Translational machinery components | 1 | 1 | |
| YrdC/RibB | RibA-like | 1 | 1 | |
| Cytidine deaminase-like | Dihydrofolate reductase-like | 1 | 1 | |
| Methylated DNA-protein cysteine methyltransferase domain | Methylated DNA-protein cysteine methyltransferase, C-terminal domain | 1 | 1 | |
| alpha-helical ferredoxin | 4Fe-4S ferredoxins | 1 | 1 | |
| Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain | Nucleotidylyl transferase | 1 | 1 | |
| Ribulose-phoshate binding barrel | SIS domain | 1 | 1 | |
| PK beta-barrel domain-like | Phosphoenolpyruvate/pyruvate domain | 1 | 1 | |
| Hedgehog/intein (Hint) domain | post-AAA+ oligomerization domain-like | 1 | 1 | |
| R1 subunit of ribonucleotide reductase, N-terminal domain | Homing endonucleases | 1 | 1 | |
| Uracil-DNA glycosylase-like | Pre-PUA domain | 1 | 1 | |
| Homing endonucleases | lambda repressor-like DNA-binding domains | 1 | 1 | |
| EF-G C-terminal domain-like | EF-G C-terminal domain-like | 1 | 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 | 1 | 1 | |
| Phospholipase D/nuclease | TrmB C-terminal domain-like | 1 | 1 | |
| GroEL-intermediate domain like | GroEL apical domain-like | 1 | 1 | |
| E set domains | (Trans)glycosidases | 1 | 1 | |
| Zinc beta-ribbon | Zinc beta-ribbon | 1 | 1 | |
| eIF2alpha middle domain-like | eIF-2-alpha, C-terminal domain | 1 | 1 | |
| PUA domain-like | 4Fe-4S ferredoxins | 1 | 1 | |
| DNA/RNA polymerases | Homing endonucleases | 1 | 1 | |
| Multidrug efflux transporter AcrB transmembrane domain | Multidrug efflux transporter AcrB transmembrane domain | 1 | 1 | |
| Homing endonucleases | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| FMN-binding split barrel | UbiD C-terminal domain-like | 1 | 1 | |
| lambda repressor-like DNA-binding domains | CBS-domain pair | 1 | 1 | |
| lambda repressor-like DNA-binding domains | post-AAA+ oligomerization domain-like | 1 | 1 | |
| Prokaryotic type I DNA topoisomerase | Homing endonucleases | 1 | 1 | |
| Glycoside hydrolase/deacetylase | Rad51 N-terminal domain-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Tropomyosin | 1 | 1 | |
| PIN domain-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| EPT/RTPC-like | EPT/RTPC-like | 1 | 1 | |
| CPE0013-like | Formate dehydrogenase/DMSO reductase, domains 1-3 | 1 | 1 | |
| Histidine-containing phosphotransfer domain, HPT domain | CheY-binding domain of CheA | 1 | 1 | |
| Integrin alpha N-terminal domain | PKD domain | 1 | 1 | |
| "Winged helix" DNA-binding domain | post-AAA+ oligomerization domain-like | 1 | 1 | |
| E set domains | E set domains | 1 | 1 | |
| GAD domain-like | GatB/YqeY motif | 1 | 1 | |
| Homing endonucleases | PFL-like glycyl radical enzymes | 1 | 1 | |
| Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | Translation proteins | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | 4Fe-4S ferredoxins | 1 | 1 | |
| Homing endonucleases | C-terminal domain of alpha and beta subunits of F1 ATP synthase | 1 | 1 | |
| Class II aaRS and biotin synthetases | Translation proteins | 1 | 1 | |
| Nucleotide-binding domain | 4Fe-4S ferredoxins | 1 | 1 | |
| tRNA-intron endonuclease N-terminal domain-like | tRNA-intron endonuclease catalytic domain-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| tRNA-binding arm | Class II aaRS and biotin synthetases | 1 | 1 | |
| R1 subunit of ribonucleotide reductase, N-terminal domain | PFL-like glycyl radical enzymes | 1 | 1 | |
| CheY-like | Methylesterase CheB, C-terminal domain | 1 | 1 | |
| Hedgehog/intein (Hint) domain | Radical SAM enzymes | 1 | 1 | |
| Periplasmic binding protein-like II | Periplasmic binding protein-like II | 1 | 1 | |
| 2Fe-2S ferredoxin-like | FAD/NAD(P)-binding domain | 1 | 1 | |
| Restriction endonuclease-like | RuvA domain 2-like | 1 | 1 | |
| Nqo1 FMN-binding domain-like | 4Fe-4S ferredoxins | 1 | 1 | |
| NAD-binding domain of HMG-CoA reductase | Substrate-binding domain of HMG-CoA reductase | 1 | 1 | |
| CheY-binding domain of CheA | CheW-like | 1 | 1 | |
| Rad51 N-terminal domain-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Glucocorticoid receptor-like (DNA-binding domain) | 1 | 1 | |
| Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | CoA-dependent acyltransferases | 1 | 1 | |
| Nqo1 middle domain-like | Nqo1C-terminal domain-like | 1 | 1 | |
| Insert subdomain of RNA polymerase alpha subunit | RBP11-like subunits of RNA polymerase | 1 | 1 | |
| Nucleotide-diphospho-sugar transferases | RmlC-like cupins | 1 | 1 | |
| Bacterial fluorinating enzyme, N-terminal domain | Bacterial fluorinating enzyme, C-terminal domain | 1 | 1 | |
| Glycoside hydrolase/deacetylase | CBD9-like | 1 | 1 | |
| THUMP domain-like | alpha/beta knot | 1 | 1 | |
| Nucleic acid-binding proteins | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| Folate-binding domain | Aminomethyltransferase beta-barrel domain | 1 | 1 | |
| Rad51 N-terminal domain-like | Homing endonucleases | 1 | 1 | |
| "Winged helix" DNA-binding domain | Riboflavin kinase-like | 1 | 1 | |
| Hedgehog/intein (Hint) domain | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| Prokaryotic type KH domain (KH-domain type II) | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| "Winged helix" DNA-binding domain | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| Hedgehog/intein (Hint) domain | C-terminal domain of alpha and beta subunits of F1 ATP synthase | 1 | 1 | |
| ADC-like | Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain | 1 | 1 | |
| Ribonuclease H-like | Hedgehog/intein (Hint) domain | 1 | 1 | |
| Alkaline phosphatase-like | Type I dockerin domain | 1 | 1 | |
| Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain | Pyrimidine nucleoside phosphorylase C-terminal domain | 1 | 1 | |
| Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain | Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain | 1 | 1 | |
| DNA/RNA polymerases | Hedgehog/intein (Hint) domain | 1 | 1 | |
| Homing endonucleases | "Winged helix" DNA-binding domain | 1 | 1 | |
| GroEL equatorial domain-like | GroEL apical domain-like | 1 | 1 | |
| Class II aaRS and biotin synthetases | ThrRS/AlaRS common domain | 1 | 1 | |
| Translation proteins | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| Homing endonucleases | Radical SAM enzymes | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Phosphoenolpyruvate/pyruvate domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | RuvA domain 2-like | 1 | 1 | |
| PIN domain-like | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| 2Fe-2S ferredoxin-like | alpha-helical ferredoxin | 1 | 1 | |
| Nqo1C-terminal domain-like | 4Fe-4S ferredoxins | 1 | 1 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | Nucleic acid-binding proteins | 1 | 1 | |
| Methionyl-tRNA synthetase (MetRS), Zn-domain | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 1 | 1 | |
| "Winged helix" DNA-binding domain | GAD domain-like | 1 | 1 | |
| PA domain | Zn-dependent exopeptidases | 1 | 1 | |
| PK beta-barrel domain-like | PK C-terminal domain-like | 1 | 1 | |
| lambda repressor-like DNA-binding domains | AraD/HMP-PK domain-like | 1 | 1 | |
| Thioredoxin-like | Nqo1 middle domain-like | 1 | 1 | |
| Pyruvate-ferredoxin oxidoreductase, PFOR, domain III | Thiamin diphosphate-binding fold (THDP-binding) | 1 | 1 | |
| Smc hinge domain | Tropomyosin | 1 | 1 | |
| Prokaryotic type I DNA topoisomerase | Zinc beta-ribbon | 1 | 1 | |
| DNA clamp | DNA clamp | 1 | 1 | |
| post-HMGL domain-like | Single hybrid motif | 1 | 1 | |
| RuBisCO, large subunit, small (N-terminal) domain | RuBisCo, C-terminal domain | 1 | 1 | |
| ClpP/crotonase | NfeD domain-like | 1 | 1 | |
| HMA, heavy metal-associated domain | HMA, heavy metal-associated domain | 1 | 1 | |
| tRNA-guanine transglycosylase | Uracil-DNA glycosylase-like | 1 | 1 | |
| dsRNA-binding domain-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| Homing endonucleases | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Signal peptide-binding domain | 1 | 1 | |
| CheY-binding domain of CheA | CheY-binding domain of CheA | 1 | 1 | |
| PIN domain-like | Homing endonucleases | 1 | 1 | |
| 2Fe-2S ferredoxin-like | Formate dehydrogenase/DMSO reductase, domains 1-3 | 1 | 1 | |
| HAD-like | Nucleotide-diphospho-sugar transferases | 1 | 1 | |
| Riboflavin synthase domain-like | Riboflavin synthase domain-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | lambda repressor-like DNA-binding domains | 1 | 1 | |
| Nqo5-like | HydB/Nqo4-like | 1 | 1 | |
| Tryptophan synthase beta subunit-like PLP-dependent enzymes | "Winged helix" DNA-binding domain | 1 | 1 | |
| Nucleic acid-binding proteins | eIF2alpha middle domain-like | 1 | 1 | |
| TPR-like | TPR-like | 1 | 1 | |
| Metallo-dependent phosphatases | Metallo-dependent phosphatases | 1 | 1 | |
| Glutamine synthetase/guanido kinase | GatB/YqeY motif | 1 | 1 | |
| Thioredoxin-like | Thioredoxin-like | 1 | 1 | |
| Rad51 N-terminal domain-like | Hedgehog/intein (Hint) domain | 1 | 1 | |
| Radical SAM enzymes | Acyl-CoA N-acyltransferases (Nat) | 1 | 1 | |
| PH0987 N-terminal domain-like | Cyclophilin-like | 1 | 1 | |
| DNA/RNA polymerases | DNA/RNA polymerases | 1 | 1 | |
| Ribokinase-like | AraD/HMP-PK domain-like | 1 | 1 | |
| Pyruvate-ferredoxin oxidoreductase, PFOR, domain III | TK C-terminal domain-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | EF-G C-terminal domain-like | 1 | 1 | |
| Nucleotide-binding domain | Formate dehydrogenase/DMSO reductase, domains 1-3 | 1 | 1 | |
| PurM C-terminal domain-like | PurM C-terminal domain-like | 1 | 1 | |
| Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | Nucleic acid-binding proteins | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Phosphohistidine domain | 1 | 1 | |
| NagB/RpiA/CoA transferase-like | D-ribose-5-phosphate isomerase (RpiA), lid domain | 1 | 1 | |
| Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 1 | 1 | |
| YjeF N-terminal domain-like | Ribokinase-like | 1 | 1 | |
| Methionyl-tRNA synthetase (MetRS), Zn-domain | Nucleic acid-binding proteins | 1 | 1 | |
| Acylphosphatase/BLUF domain-like | YrdC/RibB | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | TPR-like | 1 | 1 | |
| Histidine-containing phosphotransfer domain, HPT domain | CheW-like | 1 | 1 | |
| Peptidase/esterase 'gauge' domain | alpha/beta-Hydrolases | 1 | 1 | |
| Thioredoxin-like | Nqo1 FMN-binding domain-like | 1 | 1 | |
| FAD/NAD(P)-binding domain | FAD/NAD(P)-binding domain | 1 | 1 | |
| HIT-like | HIT-like | 1 | 1 | |
| S-adenosyl-L-methionine-dependent methyltransferases | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| 2Fe-2S ferredoxin-like | 4Fe-4S ferredoxins | 1 | 1 | |
| Glycoside hydrolase/deacetylase | Galactose mutarotase-like | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | SIS domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Sec63 N-terminal domain-like | 1 | 1 | |
| Nucleotidylyl transferase | Ribosomal protein L25-like | 1 | 1 | |
| Restriction endonuclease-like | BT0923-like | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | TrkA C-terminal domain-like | 1 | 1 | |
| Eukaryotic type KH-domain (KH-domain type I) | Eukaryotic type KH-domain (KH-domain type I) | 1 | 1 | |
| PIN domain-like | Hedgehog/intein (Hint) domain | 1 | 1 | |
| R1 subunit of ribonucleotide reductase, N-terminal domain | Hedgehog/intein (Hint) domain | 1 | 1 | |
| Nucleotidyltransferase | PAP/OAS1 substrate-binding domain | 1 | 1 | |
| "Winged helix" DNA-binding domain | Iron-dependent repressor protein, dimerization domain | 1 | 1 | |
| N-terminal domain of alpha and beta subunits of F1 ATP synthase | Hedgehog/intein (Hint) domain | 1 | 1 | |
| Putative DNA-binding domain | Putative DNA-binding domain | 1 | 1 | |
| Initiation factor IF2/eIF5b, domain 3 | Translation proteins | 1 | 1 | |
| "Winged helix" DNA-binding domain | Phospholipase D/nuclease | 1 | 1 | |
| Ribbon-helix-helix | ACT-like | 1 | 1 | |
| "Winged helix" DNA-binding domain | TPR-like | 1 | 1 | |
| N-terminal, heterodimerisation domain of RBP7 (RpoE) | Nucleic acid-binding proteins | 1 | 1 | |
| Nucleic acid-binding proteins | Homing endonucleases | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | CBS-domain pair | 1 | 1 | |
| Hedgehog/intein (Hint) domain | PFL-like glycyl radical enzymes | 1 | 1 | |
| Uracil-DNA glycosylase-like | PUA domain-like | 1 | 1 | |
| Nucleotidylyl transferase | An anticodon-binding domain of class I aminoacyl-tRNA synthetases | 1 | 1 | |
| Glutamine synthetase/guanido kinase | GAD domain-like | 1 | 1 | |
| DnaJ/Hsp40 cysteine-rich domain | DHH phosphoesterases | 1 | 1 | |
| 4Fe-4S ferredoxins | Formate dehydrogenase/DMSO reductase, domains 1-3 | 1 | 1 | |
| 4Fe-4S ferredoxins | 4Fe-4S ferredoxins | 1 | 1 | |
| Phosphohistidine domain | Phosphoenolpyruvate/pyruvate domain | 1 | 1 | |
| PurM N-terminal domain-like | PurM N-terminal domain-like | 1 | 1 | |
| Methionyl-tRNA synthetase (MetRS), Zn-domain | Nucleotidylyl transferase | 1 | 1 | |
| PKD domain | PKD domain | 1 | 1 | |
| "Winged helix" DNA-binding domain | Protein kinase-like (PK-like) | 1 | 1 | |
| Class II aaRS ABD-related | C-terminal domain of ProRS | 1 | 1 | |
| PEP carboxykinase N-terminal domain | PEP carboxykinase-like | 1 | 1 | |
| lambda repressor-like DNA-binding domains | PRTase-like | 1 | 1 | |
| PAP/OAS1 substrate-binding domain | PAP/Archaeal CCA-adding enzyme, C-terminal domain | 1 | 1 | |
| Nucleic acid-binding proteins | Eukaryotic type KH-domain (KH-domain type I) | 1 | 1 | |
| DnaJ/Hsp40 cysteine-rich domain | Nucleic acid-binding proteins | 1 | 1 | |
| Homo-oligomeric flavin-containing Cys decarboxylases, HFCD | CoaB-like | 1 | 1 | |
| Dom34/Pelota N-terminal domain-like | L30e-like | 1 | 1 | |
| Nucleic acid-binding proteins | eIF-2-alpha, C-terminal domain | 1 | 1 | |
| FAD/NAD(P)-binding domain | Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | 1 | 1 | |
| Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 1 | 1 | |
| GatD N-terminal domain-like | Glutaminase/Asparaginase | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | DHH phosphoesterases | 1 | 1 | |
| Prokaryotic type KH domain (KH-domain type II) | Ribosomal protein S3 C-terminal domain | 1 | 1 | |
| ADC-like | Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain | 1 | 1 | |
| Domain of the SRP/SRP receptor G-proteins | Signal peptide-binding domain | 1 | 1 | |
| GroEL equatorial domain-like | GroEL-intermediate domain like | 1 | 1 | |
| N-terminal domain of alpha and beta subunits of F1 ATP synthase | Homing endonucleases | 1 | 1 | |
| Families 57/38 glycoside transferase middle domain | Galactose mutarotase-like | 1 | 1 | |
| 2Fe-2S ferredoxin-like | Nucleotide-binding domain | 1 | 1 | |
| Pseudouridine synthase | PUA domain-like | 1 | 1 | |
| Translation initiation factor 2 beta, aIF2beta, N-terminal domain | Zinc-binding domain of translation initiation factor 2 beta | 1 | 1 | |
| Ferritin-like | Rubredoxin-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Initiation factor IF2/eIF5b, domain 3 | 1 | 1 | |
| Ribosomal L27 protein-like | Eukaryotic type KH-domain (KH-domain type I) | 1 | 1 | |
| Hedgehog/intein (Hint) domain | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| Translation proteins | EF-G C-terminal domain-like | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | Adenine nucleotide alpha hydrolases-like | 1 | 1 | |
| F1F0 ATP synthase subunit C | F1F0 ATP synthase subunit C | 1 | 1 | |
| Ribonuclease H-like | Homing endonucleases | 1 | 1 | |
| alpha-helical ferredoxin | Formate dehydrogenase/DMSO reductase, domains 1-3 | 1 | 1 | |
| Clc chloride channel | CBS-domain pair | 1 | 1 | |
| Phosphoenolpyruvate/pyruvate domain | PK C-terminal domain-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Prokaryotic type I DNA topoisomerase | 1 | 1 | |
| lambda repressor-like DNA-binding domains | "Winged helix" DNA-binding domain | 1 | 1 | |
| Ribonuclease H-like | DNA/RNA polymerases | 1 | 1 | |
| PUA domain-like | Adenine nucleotide alpha hydrolases-like | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | GMP synthetase C-terminal dimerisation domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | post-AAA+ oligomerization domain-like | 1 | 1 | |
| N-terminal domain of alpha and beta subunits of F1 ATP synthase | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Nucleotide-binding domain | Nucleotide-binding domain | 1 | 1 | |
| Homodimeric domain of signal transducing histidine kinase | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 1 | 1 | |
| TATA-box binding protein-like | TATA-box binding protein-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Rad50 coiled-coil Zn hook | 1 | 1 | |
| Nqo1 FMN-binding domain-like | Nqo1 middle domain-like | 1 | 1 | |
| ADC-like | Pyrimidine nucleoside phosphorylase C-terminal domain | 1 | 1 | |
| Thioredoxin-like | Nqo1C-terminal domain-like | 1 | 1 | |
| Class II aaRS and biotin synthetases | C-terminal domain of ProRS | 1 | 1 | |
| ATP-dependent DNA ligase DNA-binding domain | Nucleic acid-binding proteins | 1 | 1 | |
| Chemotaxis receptor methyltransferase CheR, N-terminal domain | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| Nucleic acid-binding proteins | DHH phosphoesterases | 1 | 1 | |
