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 | 9 | 5 |  |
| Nucleotidylyl transferase | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 6 | 5 | |
| Actin-like ATPase domain | Actin-like ATPase domain | 4 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | Translation proteins | 4 | 4 | |
| Nucleic acid-binding proteins | Class II aaRS and biotin synthetases | 4 | 3 | |
| Class II aaRS and biotin synthetases | Class II aaRS ABD-related | 4 | 3 | |
| ValRS/IleRS/LeuRS editing domain | Nucleotidylyl transferase | 3 | 3 | |
| P-loop containing nucleoside triphosphate hydrolases | C-terminal domain of alpha and beta subunits of F1 ATP synthase | 3 | 1 | |
| HAD-like | Calcium ATPase, transmembrane domain M | 3 | 2 | |
| ValRS/IleRS/LeuRS editing domain | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 3 | 3 | |
| N-terminal domain of alpha and beta subunits of F1 ATP synthase | P-loop containing nucleoside triphosphate hydrolases | 3 | 1 | |
| FAD/NAD(P)-binding domain | FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 3 | 2 | |
| N-terminal domain of alpha and beta subunits of F1 ATP synthase | C-terminal domain of alpha and beta subunits of F1 ATP synthase | 3 | 1 | |
| Calcium ATPase, transduction domain A | Calcium ATPase, transmembrane domain M | 3 | 2 | |
| Alpha-L RNA-binding motif | Pseudouridine synthase | 3 | 1 | |
| EF-G C-terminal domain-like | EF-G C-terminal domain-like | 3 | 3 | |
| Calcium ATPase, transduction domain A | HAD-like | 3 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | EF-G C-terminal domain-like | 3 | 3 | |
| Thiamin diphosphate-binding fold (THDP-binding) | TK C-terminal domain-like | 2 | 2 | |
| Type II DNA topoisomerase | GyrA/ParC C-terminal domain-like | 2 | 2 | |
| Metal cation-transporting ATPase, ATP-binding domain N | Calcium ATPase, transmembrane domain M | 2 | 1 | |
| tRNA-binding arm | Class II aaRS and biotin synthetases | 2 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | Ribosomal protein S5 domain 2-like | 2 | 1 | |
| PIN domain-like | 5' to 3' exonuclease, C-terminal subdomain | 2 | 2 | |
| Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain | Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain | 2 | 1 | |
| MetI-like | MetI-like | 2 | 2 | |
| L30e-like | alpha/beta knot | 2 | 1 | |
| Class II aaRS and biotin synthetases | ThrRS/AlaRS common domain | 2 | 2 | |
| Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain | Pyrimidine nucleoside phosphorylase C-terminal domain | 2 | 1 | |
| Translation proteins | EF-G C-terminal domain-like | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | post-AAA+ oligomerization domain-like | 2 | 1 | |
| Metal cation-transporting ATPase, ATP-binding domain N | HAD-like | 2 | 1 | |
| Calcium ATPase, transduction domain A | Metal cation-transporting ATPase, ATP-binding domain N | 2 | 1 | |
| Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain | Pyrimidine nucleoside phosphorylase C-terminal domain | 2 | 1 | |
| Nucleic acid-binding proteins | Nucleic acid-binding proteins | 2 | 2 | |
| Homeodomain-like | SIS domain | 2 | 1 | |
| Class II aaRS and biotin synthetases | SufE/NifU | 2 | 1 | |
| Domain of the SRP/SRP receptor G-proteins | P-loop containing nucleoside triphosphate hydrolases | 2 | 2 | |
| Nucleic acid-binding proteins | RuvA domain 2-like | 2 | 2 | |
| Ribosomal protein S5 domain 2-like | Type II DNA topoisomerase | 2 | 1 | |
| Nucleic acid-binding proteins | Translation proteins SH3-like domain | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | Ribosomal protein S5 domain 2-like | 2 | 2 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | Type II DNA topoisomerase | 2 | 1 | |
| Nucleic acid-binding proteins | HD-domain/PDEase-like | 2 | 1 | |
| S-adenosyl-L-methionine-dependent methyltransferases | Putative methyltransferase TM0872, insert domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | RecA protein, C-terminal domain | 1 | 1 | |
| Thiamin diphosphate-binding fold (THDP-binding) | Thiamin diphosphate-binding fold (THDP-binding) | 1 | 1 | |
| Nucleotidylyl transferase | Alpha-L RNA-binding motif | 1 | 1 | |
| Class II aaRS and biotin synthetases | C-terminal domain of ProRS | 1 | 1 | |
| THUMP domain-like | Adenine nucleotide alpha hydrolases-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| (Trans)glycosidases | Glycosyl hydrolase domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Obg GTP-binding protein C-terminal domain | 1 | 1 | |
| GIY-YIG endonuclease | C-terminal UvrC-binding domain of UvrB | 1 | 1 | |
| Nucleic acid-binding proteins | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| 5' to 3' exonuclease, C-terminal subdomain | Ribonuclease H-like | 1 | 1 | |
| Insert subdomain of RNA polymerase alpha subunit | C-terminal domain of RNA polymerase alpha subunit | 1 | 1 | |
| HSP40/DnaJ peptide-binding domain | HSP40/DnaJ peptide-binding domain | 1 | 1 | |
| N-terminal domain of MutM-like DNA repair proteins | S13-like H2TH domain | 1 | 1 | |
| ValRS/IleRS/LeuRS editing domain | tRNA-binding arm | 1 | 1 | |
| Translation proteins | PRC-barrel domain | 1 | 1 | |
| Ribosomal L11/L12e N-terminal domain | Ribosomal protein L11, C-terminal domain | 1 | 1 | |
| PUA domain-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain | Phosphoenolpyruvate/pyruvate domain | 1 | 1 | |
| Trigger factor ribosome-binding domain | FKBP-like | 1 | 1 | |
| GIY-YIG endonuclease | RuvA domain 2-like | 1 | 1 | |
| Phosphoglucomutase, first 3 domains | Phosphoglucomutase, C-terminal domain | 1 | 1 | |
| S-adenosylmethionine synthetase | S-adenosylmethionine synthetase | 1 | 1 | |
| Class II aaRS and biotin synthetases | Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | 1 | 1 | |
| Enolase N-terminal domain-like | Enolase C-terminal domain-like | 1 | 1 | |
| PheT/TilS domain | Putative DNA-binding domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Glucocorticoid receptor-like (DNA-binding domain) | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 1 | 1 | |
| Ribosomal protein L6 | Ribosomal protein L6 | 1 | 1 | |
| Creatinase/prolidase N-terminal domain | Creatinase/aminopeptidase | 1 | 1 | |
| PheT/TilS domain | Anticodon-binding domain of PheRS | 1 | 1 | |
| Nucleotidyltransferase | TGS-like | 1 | 1 | |
| Class II aaRS ABD-related | C-terminal domain of ProRS | 1 | 1 | |
| Class II aaRS and biotin synthetases | Translation proteins | 1 | 1 | |
| 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain | Alkaline phosphatase-like | 1 | 1 | |
| Nucleotidylyl transferase | An anticodon-binding domain of class I aminoacyl-tRNA synthetases | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | "Winged helix" DNA-binding domain | 1 | 1 | |
| Translation proteins | ThrRS/AlaRS common domain | 1 | 1 | |
| Translation proteins | Initiation factor IF2/eIF5b, domain 3 | 1 | 1 | |
| EF-G C-terminal domain-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| GreA transcript cleavage protein, N-terminal domain | FKBP-like | 1 | 1 | |
| Translation initiation factor IF3, N-terminal domain | Translation initiation factor IF3, C-terminal domain | 1 | 1 | |
| FKBP-like | Triger factor/SurA peptide-binding domain-like | 1 | 1 | |
| ThrRS/AlaRS common domain | Class II aaRS ABD-related | 1 | 1 | |
| Sigma3 and sigma4 domains of RNA polymerase sigma factors | Sigma3 and sigma4 domains of RNA polymerase sigma factors | 1 | 1 | |
| MgtE N-terminal domain-like | MgtE membrane domain-like | 1 | 1 | |
| PK beta-barrel domain-like | Phosphoenolpyruvate/pyruvate domain | 1 | 1 | |
| Zinc beta-ribbon | DNA primase core | 1 | 1 | |
| UBA-like | Elongation factor Ts (EF-Ts), dimerisation domain | 1 | 1 | |
| YhbC-like, N-terminal domain | YhbC-like, C-terminal domain | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | 6-phosphogluconate dehydrogenase C-terminal domain-like | 1 | 1 | |
| Phoshotransferase/anion transport protein | PTS system IIB component-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Helical scaffold and wing domains of SecA | 1 | 1 | |
| Ribosomal protein L7/12, oligomerisation (N-terminal) domain | ClpS-like | 1 | 1 | |
| DNA clamp | DNA clamp | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | C-terminal UvrC-binding domain of UvrB | 1 | 1 | |
| RNase III domain-like | dsRNA-binding domain-like | 1 | 1 | |
| RBP11-like subunits of RNA polymerase | C-terminal domain of RNA polymerase alpha subunit | 1 | 1 | |
| Thiamin pyrophosphokinase, catalytic domain | Thiamin pyrophosphokinase, substrate-binding domain | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 1 | 1 | |
| DnaJ/Hsp40 cysteine-rich domain | HSP40/DnaJ peptide-binding domain | 1 | 1 | |
| Pre-protein crosslinking domain of SecA | Helical scaffold and wing domains of SecA | 1 | 1 | |
| TGS-like | Class II aaRS ABD-related | 1 | 1 | |
| Nicotinate/Quinolinate PRTase N-terminal domain-like | Nicotinate/Quinolinate PRTase C-terminal domain-like | 1 | 1 | |
| PK beta-barrel domain-like | PK C-terminal domain-like | 1 | 1 | |
| Single hybrid motif | FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 1 | 1 | |
| Putative DNA-binding domain | Class II aaRS and biotin synthetases | 1 | 1 | |
| Nucleic acid-binding proteins | BRCT domain | 1 | 1 | |
| MetI-like | Periplasmic binding protein-like II | 1 | 1 | |
| R1 subunit of ribonucleotide reductase, N-terminal domain | PFL-like glycyl radical enzymes | 1 | 1 | |
| Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain | Phosphohistidine domain | 1 | 1 | |
| Ribonuclease H-like | DNA/RNA polymerases | 1 | 1 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | BRCT domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | FtsH protease domain-like | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | LDH C-terminal domain-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Initiation factor IF2/eIF5b, domain 3 | 1 | 1 | |
| "Winged helix" DNA-binding domain | GAF domain-like | 1 | 1 | |
| Phosphoenolpyruvate/pyruvate domain | PK C-terminal domain-like | 1 | 1 | |
| Domain of the SRP/SRP receptor G-proteins | Signal peptide-binding domain | 1 | 1 | |
| PIN domain-like | Ribonuclease H-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 | |
| Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain | Nucleotidylyl transferase | 1 | 1 | |
| Chaperone J-domain | DnaJ/Hsp40 cysteine-rich domain | 1 | 1 | |
| Putative DNA-binding domain | Anticodon-binding domain of PheRS | 1 | 1 | |
| Nucleotidylyl transferase | tRNA-binding arm | 1 | 1 | |
| PIN domain-like | DNA/RNA polymerases | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Smc hinge domain | 1 | 1 | |
| TGS-like | ThrRS/AlaRS common domain | 1 | 1 | |
| N-terminal domain of DnaB helicase | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Galactose mutarotase-like | Glycosyl hydrolase domain | 1 | 1 | |
| Coiled-coil domain of nucleotide exchange factor GrpE | Head domain of nucleotide exchange factor GrpE | 1 | 1 | |
| Transcription factor NusA, N-terminal domain | Nucleic acid-binding proteins | 1 | 1 | |
| Nucleotidylyl transferase | HD-domain/PDEase-like | 1 | 1 | |
| Phosphoglucomutase, first 3 domains | Phosphoglucomutase, first 3 domains | 1 | 1 | |
| Single hybrid motif | FAD/NAD(P)-binding domain | 1 | 1 | |
| Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | Translation proteins | 1 | 1 | |
| Galactose mutarotase-like | (Trans)glycosidases | 1 | 1 | |
| ABC transporter transmembrane region | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Nucleic acid-binding proteins | Putative DNA-binding domain | 1 | 1 | |
| TGS-like | ACT-like | 1 | 1 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | Nucleic acid-binding proteins | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | MOP-like | 1 | 1 | |
| 5' to 3' exonuclease, C-terminal subdomain | DNA/RNA polymerases | 1 | 1 | |
| CBS-domain pair | MgtE membrane domain-like | 1 | 1 | |
| NusB-like | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| "Winged helix" DNA-binding domain | "Winged helix" DNA-binding domain | 1 | 1 | |
| Hsp33 domain | HSP33 redox switch-like | 1 | 1 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | RuvA domain 2-like | 1 | 1 | |
| Nucleic acid-binding proteins | Anticodon-binding domain of PheRS | 1 | 1 | |
| Nucleic acid-binding proteins | ArfGap/RecO-like zinc finger | 1 | 1 | |
| Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | ThrRS/AlaRS common domain | 1 | 1 | |
| Obg GTP-binding protein N-terminal domain | Obg GTP-binding protein C-terminal domain | 1 | 1 | |
| Aminoacid dehydrogenase-like, N-terminal domain | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| HprK N-terminal domain-like | PEP carboxykinase-like | 1 | 1 | |
| L9 N-domain-like | Ribosomal protein L9 C-domain | 1 | 1 | |
| Chaperone J-domain | HSP40/DnaJ peptide-binding domain | 1 | 1 | |
| Class II aaRS and biotin synthetases | Anticodon-binding domain of PheRS | 1 | 1 | |
| PheT/TilS domain | Class II aaRS and biotin synthetases | 1 | 1 | |
| N-utilization substance G protein NusG, N-terminal domain | Translation proteins SH3-like domain | 1 | 1 | |
| HD-domain/PDEase-like | TGS-like | 1 | 1 | |
| Elongation factor Ts (EF-Ts), dimerisation domain | Elongation factor Ts (EF-Ts), dimerisation domain | 1 | 1 | |
| Nucleic acid-binding proteins | PheT/TilS domain | 1 | 1 | |
| RuvA domain 2-like | BRCT domain | 1 | 1 | |
| Translation proteins | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| Prokaryotic type KH domain (KH-domain type II) | Ribosomal protein S3 C-terminal domain | 1 | 1 | |
| Zn-dependent exopeptidases | Bacterial exopeptidase dimerisation domain | 1 | 1 | |
| Tubulin nucleotide-binding domain-like | Tubulin C-terminal domain-like | 1 | 1 | |
| Transcription factor NusA, N-terminal domain | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| Formyltransferase | FMT C-terminal domain-like | 1 | 1 | |
| Prokaryotic type KH domain (KH-domain type II) | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| C-terminal UvrC-binding domain of UvrB | RuvA domain 2-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | TGS-like | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | TrkA C-terminal domain-like | 1 | 1 | |
| Nucleic acid-binding proteins | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| PUA domain-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Signal peptide-binding domain | 1 | 1 | |
| N-terminal domain of MutM-like DNA repair proteins | Glucocorticoid receptor-like (DNA-binding domain) | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | TrpR-like | 1 | 1 | |
| Phosphohistidine domain | Phosphoenolpyruvate/pyruvate domain | 1 | 1 | |
| TGS-like | Class II aaRS and biotin synthetases | 1 | 1 | |
| Actin-like ATPase domain | Heat shock protein 70kD (HSP70), peptide-binding domain | 1 | 1 | |
| Nucleotidyltransferase | ACT-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Pre-protein crosslinking domain of SecA | 1 | 1 | |
| Glutamine synthetase/guanido kinase | GatB/YqeY motif | 1 | 1 | |
| Insert subdomain of RNA polymerase alpha subunit | RBP11-like subunits of RNA polymerase | 1 | 1 | |
| HD-domain/PDEase-like | Nucleotidyltransferase | 1 | 1 | |
| Translation proteins | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 1 | 1 | |
| Formate/glycerate dehydrogenase catalytic domain-like | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Obg GTP-binding protein N-terminal domain | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Trigger factor ribosome-binding domain | Triger factor/SurA peptide-binding domain-like | 1 | 1 | |
| dsRNA-binding domain-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| DNA/RNA polymerases | Lesion bypass DNA polymerase (Y-family), little finger domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Class I glutamine amidotransferase-like | 1 | 1 | |
| Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | tRNA-binding arm | 1 | 1 | |
| Peptide methionine sulfoxide reductase | Mss4-like | 1 | 1 | |
| Translation proteins | Translation proteins | 1 | 1 | |
| MurD-like peptide ligases, catalytic domain | MurD-like peptide ligases, peptide-binding domain | 1 | 1 | |
| Nucleic acid-binding proteins | GAD domain-like | 1 | 1 | |
| Sigma2 domain of RNA polymerase sigma factors | Sigma3 and sigma4 domains of RNA polymerase sigma factors | 1 | 1 | |
| L9 N-domain-like | Ribonuclease H-like | 1 | 1 | |
| S13-like H2TH domain | Glucocorticoid receptor-like (DNA-binding domain) | 1 | 1 | |
| Eukaryotic type KH-domain (KH-domain type I) | HD-domain/PDEase-like | 1 | 1 | |
| Class II aaRS and biotin synthetases | GAD domain-like | 1 | 1 | |
| Phospholipase D/nuclease | Phospholipase D/nuclease | 1 | 1 | |
| MgtE N-terminal domain-like | CBS-domain pair | 1 | 1 | |
| FAD/NAD(P)-binding domain | FAD-linked reductases, C-terminal domain | 1 | 1 | |
| HD-domain/PDEase-like | ACT-like | 1 | 1 | |
