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 | |
|---|
| Nucleotidylyl transferase | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 6 | 6 |  |
| Actin-like ATPase domain | Actin-like ATPase domain | 5 | 3 | |
| P-loop containing nucleoside triphosphate hydrolases | Translation proteins | 4 | 4 | |
| NAD(P)-binding Rossmann-fold domains | Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 4 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | P-loop containing nucleoside triphosphate hydrolases | 4 | 4 | |
| Nucleic acid-binding proteins | Class II aaRS and biotin synthetases | 4 | 3 | |
| Thiamin diphosphate-binding fold (THDP-binding) | Thiamin diphosphate-binding fold (THDP-binding) | 4 | 4 | |
| P-loop containing nucleoside triphosphate hydrolases | EF-G C-terminal domain-like | 3 | 3 | |
| EF-G C-terminal domain-like | EF-G C-terminal domain-like | 3 | 3 | |
| ValRS/IleRS/LeuRS editing domain | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 3 | 3 | |
| ValRS/IleRS/LeuRS editing domain | Nucleotidylyl transferase | 3 | 3 | |
| Alpha-L RNA-binding motif | Pseudouridine synthase | 3 | 1 | |
| Nucleic acid-binding proteins | Nucleic acid-binding proteins | 3 | 3 | |
| Nucleic acid-binding proteins | Translation proteins SH3-like domain | 2 | 2 | |
| Class II aaRS and biotin synthetases | Class II aaRS ABD-related | 2 | 2 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | Ribosomal protein S5 domain 2-like | 2 | 2 | |
| Actin-like ATPase domain | Heat shock protein 70kD (HSP70), peptide-binding domain | 2 | 2 | |
| Single hybrid motif | CoA-dependent acyltransferases | 2 | 2 | |
| Ribosomal protein S5 domain 2-like | Ribosomal protein S5 domain 2-like | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | post-AAA+ oligomerization domain-like | 2 | 1 | |
| Translation proteins | EF-G C-terminal domain-like | 2 | 2 | |
| tRNA-binding arm | Class II aaRS and biotin synthetases | 2 | 1 | |
| NAD(P)-binding Rossmann-fold domains | 6-phosphogluconate dehydrogenase C-terminal domain-like | 2 | 2 | |
| Class II aaRS and biotin synthetases | ThrRS/AlaRS common domain | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | Ribosomal protein S5 domain 2-like | 2 | 2 | |
| ACT-like | ACT-like | 2 | 2 | |
| Thiamin diphosphate-binding fold (THDP-binding) | TK C-terminal domain-like | 2 | 2 | |
| Sigma2 domain of RNA polymerase sigma factors | Sigma3 and sigma4 domains of RNA polymerase sigma factors | 2 | 2 | |
| PheT/TilS domain | Class II aaRS and biotin synthetases | 1 | 1 | |
| PUA domain-like | alpha/beta knot | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | GHMP Kinase, C-terminal domain | 1 | 1 | |
| L9 N-domain-like | Ribosomal protein L9 C-domain | 1 | 1 | |
| dsRNA-binding domain-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Carbamoyl phosphate synthetase, large subunit connection domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Initiation factor IF2/eIF5b, domain 3 | 1 | 1 | |
| DNA primase core | DNA primase DnaG, C-terminal domain | 1 | 1 | |
| HesB-like domain | Fe-S cluster assembly (FSCA) domain-like | 1 | 1 | |
| Ribonuclease PH domain 2-like | Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | 1 | 1 | |
| Ribonuclease PH domain 2-like | Ribonuclease PH domain 2-like | 1 | 1 | |
| Zinc beta-ribbon | DNA primase core | 1 | 1 | |
| ACT-like | Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 1 | 1 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | Nucleic acid-binding proteins | 1 | 1 | |
| Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | tRNA-binding arm | 1 | 1 | |
| Obg GTP-binding protein N-terminal domain | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Translation proteins | Initiation factor IF2/eIF5b, domain 3 | 1 | 1 | |
| Sm-like ribonucleoproteins | Mechanosensitive channel protein MscS (YggB), C-terminal domain | 1 | 1 | |
| Transcription factor NusA, N-terminal domain | Nucleic acid-binding proteins | 1 | 1 | |
| Cytochrome c oxidase subunit II-like, transmembrane region | Cupredoxins | 1 | 1 | |
| Chaperone J-domain | DnaJ/Hsp40 cysteine-rich domain | 1 | 1 | |
| Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | CoA-dependent acyltransferases | 1 | 1 | |
| Tubulin nucleotide-binding domain-like | Tubulin C-terminal domain-like | 1 | 1 | |
| Enolase N-terminal domain-like | Enolase C-terminal domain-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Helical scaffold and wing domains of SecA | 1 | 1 | |
| Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | ThrRS/AlaRS common domain | 1 | 1 | |
| N-terminal domain of DnaB helicase | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Nqo1 FMN-binding domain-like | Nqo1 middle domain-like | 1 | 1 | |
| Glucocorticoid receptor-like (DNA-binding domain) | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| 5' to 3' exonuclease, C-terminal subdomain | DNA/RNA polymerases | 1 | 1 | |
| DNA-glycosylase | Nudix | 1 | 1 | |
| RBP11-like subunits of RNA polymerase | C-terminal domain of RNA polymerase alpha subunit | 1 | 1 | |
| Ribonuclease H-like | DNA/RNA polymerases | 1 | 1 | |
| Chaperone J-domain | HSP40/DnaJ peptide-binding domain | 1 | 1 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | BRCT domain | 1 | 1 | |
| Putative DNA-binding domain | Anticodon-binding domain of PheRS | 1 | 1 | |
| Ribulose-phoshate binding barrel | Ribulose-phoshate binding barrel | 1 | 1 | |
| Diaminopimelate epimerase-like | Diaminopimelate epimerase-like | 1 | 1 | |
| Formyltransferase | FMT C-terminal domain-like | 1 | 1 | |
| PreATP-grasp domain | PreATP-grasp domain | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | HSP90 C-terminal domain | 1 | 1 | |
| Methionyl-tRNA synthetase (MetRS), Zn-domain | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | HSP90 C-terminal domain | 1 | 1 | |
| Periplasmic binding protein-like II | GlnB-like | 1 | 1 | |
| Ribosomal protein L6 | Ribosomal protein L6 | 1 | 1 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | RuvA domain 2-like | 1 | 1 | |
| PIN domain-like | Ribonuclease H-like | 1 | 1 | |
| S-adenosyl-L-methionine-dependent methyltransferases | Putative methyltransferase TM0872, insert domain | 1 | 1 | |
| PreATP-grasp domain | Methylglyoxal synthase-like | 1 | 1 | |
| Putative DNA-binding domain | Class II aaRS and biotin synthetases | 1 | 1 | |
| Nucleotidylyl transferase | tRNA-binding arm | 1 | 1 | |
| PheT/TilS domain | Anticodon-binding domain of PheRS | 1 | 1 | |
| Class II aaRS and biotin synthetases | Anticodon-binding domain of PheRS | 1 | 1 | |
| Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain | Nucleotidylyl transferase | 1 | 1 | |
| Type II DNA topoisomerase | GyrA/ParC C-terminal domain-like | 1 | 1 | |
| Transcription factor NusA, N-terminal domain | Rad51 N-terminal domain-like | 1 | 1 | |
| Pre-protein crosslinking domain of SecA | Helical scaffold and wing domains of SecA | 1 | 1 | |
| PIN domain-like | 5' to 3' exonuclease, C-terminal subdomain | 1 | 1 | |
| PUA domain-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| PUA domain-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Nqo5-like | HydB/Nqo4-like | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | Argininosuccinate synthetase, C-terminal domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | TGS-like | 1 | 1 | |
| Domain of the SRP/SRP receptor G-proteins | Signal peptide-binding domain | 1 | 1 | |
| Transcription factor NusA, N-terminal domain | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| Insert subdomain of RNA polymerase alpha subunit | C-terminal domain of RNA polymerase alpha subunit | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Methylglyoxal synthase-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 1 | 1 | |
| Translation proteins | ThrRS/AlaRS common domain | 1 | 1 | |
| ValRS/IleRS/LeuRS editing domain | tRNA-binding arm | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | TRCF domain-like | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Glutathione synthetase ATP-binding domain-like | 1 | 1 | |
| 2Fe-2S ferredoxin-like | 4Fe-4S ferredoxins | 1 | 1 | |
| Class II aaRS and biotin synthetases | Translation proteins | 1 | 1 | |
| Chorismate mutase II | Periplasmic binding protein-like II | 1 | 1 | |
| FliG | FliG | 1 | 1 | |
| PIN domain-like | DNA/RNA polymerases | 1 | 1 | |
| Nucleic acid-binding proteins | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Nucleic acid-binding proteins | Putative DNA-binding domain | 1 | 1 | |
| 5' to 3' exonuclease, C-terminal subdomain | Ribonuclease H-like | 1 | 1 | |
| Nudix | YggX-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Pre-protein crosslinking domain of SecA | 1 | 1 | |
| Putative DNA-binding domain | PheT/TilS domain | 1 | 1 | |
| Class II aaRS and biotin synthetases | Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | 1 | 1 | |
| Sigma3 and sigma4 domains of RNA polymerase sigma factors | Sigma3 and sigma4 domains of RNA polymerase sigma factors | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | FtsH protease domain-like | 1 | 1 | |
| GroEL-intermediate domain like | GroEL apical domain-like | 1 | 1 | |
| UROD/MetE-like | UROD/MetE-like | 1 | 1 | |
| Aminoacid dehydrogenase-like, N-terminal domain | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| FAD/NAD(P)-binding domain | FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 1 | 1 | |
| GroEL equatorial domain-like | GroEL apical domain-like | 1 | 1 | |
| GroEL equatorial domain-like | GroEL-intermediate domain like | 1 | 1 | |
| Mechanosensitive channel protein MscS (YggB), transmembrane region | Sm-like ribonucleoproteins | 1 | 1 | |
| HSP40/DnaJ peptide-binding domain | HSP40/DnaJ peptide-binding domain | 1 | 1 | |
| ClpP/crotonase | ClpP/crotonase | 1 | 1 | |
| HisI-like | all-alpha NTP pyrophosphatases | 1 | 1 | |
| Nucleic acid-binding proteins | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| 6-phosphogluconate dehydrogenase C-terminal domain-like | 6-phosphogluconate dehydrogenase C-terminal domain-like | 1 | 1 | |
| Nqo1 middle domain-like | Nqo1C-terminal domain-like | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | MesJ substrate recognition domain-like | 1 | 1 | |
| Mechanosensitive channel protein MscS (YggB), transmembrane region | Mechanosensitive channel protein MscS (YggB), C-terminal domain | 1 | 1 | |
| Macro domain-like | Zn-dependent exopeptidases | 1 | 1 | |
| Phosphoenolpyruvate/pyruvate domain | PK C-terminal domain-like | 1 | 1 | |
| Nucleotidylyl transferase | Ribosomal protein L25-like | 1 | 1 | |
| DNA clamp | DNA clamp | 1 | 1 | |
| Nucleotidylyl transferase | An anticodon-binding domain of class I aminoacyl-tRNA synthetases | 1 | 1 | |
| Thiamin diphosphate-binding fold (THDP-binding) | DHS-like NAD/FAD-binding domain | 1 | 1 | |
| Carbamoyl phosphate synthetase, small subunit N-terminal domain | Class I glutamine amidotransferase-like | 1 | 1 | |
| Ribonuclease PH domain 2-like | Eukaryotic type KH-domain (KH-domain type I) | 1 | 1 | |
| Prokaryotic type KH domain (KH-domain type II) | Rad51 N-terminal domain-like | 1 | 1 | |
| Nucleic acid-binding proteins | BRCT domain | 1 | 1 | |
| HAD-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| PK beta-barrel domain-like | PK C-terminal domain-like | 1 | 1 | |
| Riboflavin synthase domain-like | Ferredoxin reductase-like, C-terminal NADP-linked domain | 1 | 1 | |
| Rho N-terminal domain-like | Nucleic acid-binding proteins | 1 | 1 | |
| Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | Eukaryotic type KH-domain (KH-domain type I) | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | Type II DNA topoisomerase | 1 | 1 | |
| GreA transcript cleavage protein, N-terminal domain | FKBP-like | 1 | 1 | |
| UBA-like | Elongation factor Ts (EF-Ts), dimerisation domain | 1 | 1 | |
| Nqo1 FMN-binding domain-like | Nqo1C-terminal domain-like | 1 | 1 | |
| Translation proteins | Translation proteins | 1 | 1 | |
| Class II aaRS and biotin synthetases | GAD domain-like | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Type II DNA topoisomerase | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Signal peptide-binding domain | 1 | 1 | |
| RNase III domain-like | dsRNA-binding domain-like | 1 | 1 | |
| Nucleic acid-binding proteins | Anticodon-binding domain of PheRS | 1 | 1 | |
| PreATP-grasp domain | Glutathione synthetase ATP-binding domain-like | 1 | 1 | |
| Ribosomal L11/L12e N-terminal domain | Ribosomal protein L11, C-terminal domain | 1 | 1 | |
| PK beta-barrel domain-like | Phosphoenolpyruvate/pyruvate domain | 1 | 1 | |
| PreATP-grasp domain | Carbamoyl phosphate synthetase, large subunit connection domain | 1 | 1 | |
| Putative DNA-binding domain | Putative DNA-binding domain | 1 | 1 | |
| Nucleic acid-binding proteins | Rad51 N-terminal domain-like | 1 | 1 | |
| Surface presentation of antigens (SPOA) | Surface presentation of antigens (SPOA) | 1 | 1 | |
| Zn-dependent exopeptidases | Bacterial exopeptidase dimerisation domain | 1 | 1 | |
| CarD-like | TRCF domain-like | 1 | 1 | |
| Nucleic acid-binding proteins | RuvA domain 2-like | 1 | 1 | |
| Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain | Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain | 1 | 1 | |
| Carbamate kinase-like | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Thiolase-like | Thiolase-like | 1 | 1 | |
| Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | Nucleic acid-binding proteins | 1 | 1 | |
| EF-G C-terminal domain-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| RuvA domain 2-like | BRCT domain | 1 | 1 | |
| Translation proteins | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 1 | 1 | |
| Carbamoyl phosphate synthetase, large subunit connection domain | Methylglyoxal synthase-like | 1 | 1 | |
| Carbamate kinase-like | Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 1 | 1 | |
| Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | Translation proteins | 1 | 1 | |
| 2Fe-2S ferredoxin-like | Formate dehydrogenase/DMSO reductase, domains 1-3 | 1 | 1 | |
| ThrRS/AlaRS common domain | Class II aaRS ABD-related | 1 | 1 | |
| 4Fe-4S ferredoxins | Formate dehydrogenase/DMSO reductase, domains 1-3 | 1 | 1 | |
| Rho N-terminal domain-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Zinc beta-ribbon | DNA primase DnaG, C-terminal domain | 1 | 1 | |
| Translation proteins | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| Translation proteins | PRC-barrel domain | 1 | 1 | |
| Eukaryotic type KH-domain (KH-domain type I) | Nucleic acid-binding proteins | 1 | 1 | |
| Prokaryotic type KH domain (KH-domain type II) | Ribosomal protein S3 C-terminal domain | 1 | 1 | |
| FabD/lysophospholipase-like | Probable ACP-binding domain of malonyl-CoA ACP transacylase | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Nucleic acid-binding proteins | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Restriction endonuclease-like | 1 | 1 | |
| Nucleotidyltransferase | Poly A polymerase C-terminal region-like | 1 | 1 | |
| Ribonuclease PH domain 2-like | Nucleic acid-binding proteins | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | TrpR-like | 1 | 1 | |
| IlvD/EDD N-terminal domain-like | LeuD/IlvD-like | 1 | 1 | |
| DnaK suppressor protein DksA, alpha-hairpin domain | Glucocorticoid receptor-like (DNA-binding domain) | 1 | 1 | |
| Methionyl-tRNA synthetase (MetRS), Zn-domain | Nucleotidylyl transferase | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Ribonuclease PH domain 2-like | 1 | 1 | |
| Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 1 | 1 | |
| ACT-like | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Prokaryotic type KH domain (KH-domain type II) | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| CarD-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| NagB/RpiA/CoA transferase-like | D-ribose-5-phosphate isomerase (RpiA), lid domain | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Eukaryotic type KH-domain (KH-domain type I) | 1 | 1 | |
| Coiled-coil domain of nucleotide exchange factor GrpE | Head domain of nucleotide exchange factor GrpE | 1 | 1 | |
| Rad51 N-terminal domain-like | Rad51 N-terminal domain-like | 1 | 1 | |
| N-utilization substance G protein NusG, N-terminal domain | Translation proteins SH3-like domain | 1 | 1 | |
| Nucleic acid-binding proteins | PheT/TilS domain | 1 | 1 | |
| Insert subdomain of RNA polymerase alpha subunit | RBP11-like subunits of RNA polymerase | 1 | 1 | |
| DnaJ/Hsp40 cysteine-rich domain | HSP40/DnaJ peptide-binding domain | 1 | 1 | |
| Carbamate kinase-like | ACT-like | 1 | 1 | |
| PLP-binding barrel | Alanine racemase C-terminal domain-like | 1 | 1 | |
| Chaperone J-domain | HSC20 (HSCB), C-terminal oligomerisation domain | 1 | 1 | |
| Nucleic acid-binding proteins | GAD domain-like | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | 1 | 1 | |
| Ribosomal protein L7/12, oligomerisation (N-terminal) domain | ClpS-like | 1 | 1 | |
| Domain of the SRP/SRP receptor G-proteins | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Single hybrid motif | Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | 1 | 1 | |
| Translation initiation factor IF3, N-terminal domain | Translation initiation factor IF3, C-terminal domain | 1 | 1 | |
| DNA-glycosylase | YggX-like | 1 | 1 | |
| Nucleotidylyl transferase | Alpha-L RNA-binding motif | 1 | 1 | |
