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 |  |
| Actin-like ATPase domain | Actin-like ATPase domain | 7 | 4 | |
| NAD(P)-binding Rossmann-fold domains | Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 7 | 3 | |
| Nucleotidylyl transferase | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 6 | 6 | |
| P-loop containing nucleoside triphosphate hydrolases | Translation proteins | 5 | 4 | |
| NAD(P)-binding Rossmann-fold domains | 6-phosphogluconate dehydrogenase C-terminal domain-like | 5 | 1 | |
| Glutathione synthetase ATP-binding domain-like | PreATP-grasp domain | 5 | 4 | |
| MurD-like peptide ligases, catalytic domain | MurD-like peptide ligases, peptide-binding domain | 5 | 3 | |
| PLP-binding barrel | Alanine racemase C-terminal domain-like | 4 | 2 | |
| Thiamin diphosphate-binding fold (THDP-binding) | TK C-terminal domain-like | 4 | 2 | |
| CheW-like | CheY-like | 4 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | Ribosomal protein S5 domain 2-like | 4 | 4 | |
| Homodimeric domain of signal transducing histidine kinase | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 4 | 3 | |
| CheY-like | C-terminal effector domain of the bipartite response regulators | 3 | 1 | |
| HMA, heavy metal-associated domain | HAD-like | 3 | 3 | |
| HCP-like | HCP-like | 3 | 2 | |
| HMA, heavy metal-associated domain | Calcium ATPase, transduction domain A | 3 | 3 | |
| Calcium ATPase, transduction domain A | Calcium ATPase, transmembrane domain M | 3 | 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 | 3 | 2 | |
| Calcium ATPase, transmembrane domain M | HAD-like | 3 | 3 | |
| P-loop containing nucleoside triphosphate hydrolases | EF-G C-terminal domain-like | 3 | 2 | |
| Translation proteins | EF-G C-terminal domain-like | 3 | 2 | |
| Class II aaRS and biotin synthetases | Class II aaRS ABD-related | 3 | 3 | |
| ValRS/IleRS/LeuRS editing domain | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 3 | 3 | |
| ABC transporter transmembrane region | P-loop containing nucleoside triphosphate hydrolases | 3 | 1 | |
| Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains | Multidrug efflux transporter AcrB transmembrane domain | 3 | 2 | |
| Cytochrome c | Cytochrome c | 3 | 2 | |
| Aminoacid dehydrogenase-like, N-terminal domain | NAD(P)-binding Rossmann-fold domains | 3 | 1 | |
| Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains | Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains | 3 | 2 | |
| Metallo-dependent hydrolases | Composite domain of metallo-dependent hydrolases | 3 | 3 | |
| Nucleic acid-binding proteins | Class II aaRS and biotin synthetases | 3 | 3 | |
| ValRS/IleRS/LeuRS editing domain | Nucleotidylyl transferase | 3 | 3 | |
| Formate/glycerate dehydrogenase catalytic domain-like | NAD(P)-binding Rossmann-fold domains | 3 | 2 | |
| Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains | Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains | 3 | 2 | |
| Calcium ATPase, transduction domain A | HAD-like | 3 | 3 | |
| Multidrug efflux transporter AcrB transmembrane domain | Multidrug efflux transporter AcrB transmembrane domain | 3 | 2 | |
| HMA, heavy metal-associated domain | Calcium ATPase, transmembrane domain M | 3 | 3 | |
| EF-G C-terminal domain-like | EF-G C-terminal domain-like | 3 | 2 | |
| Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains | Multidrug efflux transporter AcrB transmembrane domain | 3 | 2 | |
| PreATP-grasp domain | Rudiment single hybrid motif | 2 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | Ribosomal protein S5 domain 2-like | 2 | 2 | |
| Phosphoglucomutase, first 3 domains | Phosphoglucomutase, first 3 domains | 2 | 1 | |
| NAD(P)-binding Rossmann-fold domains | ACT-like | 2 | 2 | |
| Sigma3 and sigma4 domains of RNA polymerase sigma factors | Sigma3 and sigma4 domains of RNA polymerase sigma factors | 2 | 2 | |
| Alpha-L RNA-binding motif | Pseudouridine synthase | 2 | 1 | |
| tRNA-binding arm | Class II aaRS and biotin synthetases | 2 | 1 | |
| Mechanosensitive channel protein MscS (YggB), transmembrane region | Mechanosensitive channel protein MscS (YggB), C-terminal domain | 2 | 2 | |
| PIN domain-like | 5' to 3' exonuclease, C-terminal subdomain | 2 | 2 | |
| Phosphoglucomutase, first 3 domains | Phosphoglucomutase, C-terminal domain | 2 | 1 | |
| CheC-like | Surface presentation of antigens (SPOA) | 2 | 2 | |
| Sm-like ribonucleoproteins | Mechanosensitive channel protein MscS (YggB), C-terminal domain | 2 | 2 | |
| Penicillin binding protein dimerisation domain | beta-lactamase/transpeptidase-like | 2 | 1 | |
| Nucleic acid-binding proteins | RuvA domain 2-like | 2 | 2 | |
| N-terminal domain of alpha and beta subunits of F1 ATP synthase | P-loop containing nucleoside triphosphate hydrolases | 2 | 1 | |
| Chaperone J-domain | HSP40/DnaJ peptide-binding domain | 2 | 2 | |
| Nucleic acid-binding proteins | Translation proteins SH3-like domain | 2 | 2 | |
| LuxS/MPP-like metallohydrolase | LuxS/MPP-like metallohydrolase | 2 | 1 | |
| Ribosomal protein S5 domain 2-like | GHMP Kinase, C-terminal domain | 2 | 1 | |
| ThrRS/AlaRS common domain | Class II aaRS and biotin synthetases | 2 | 2 | |
| PDZ domain-like | PDZ domain-like | 2 | 2 | |
| Double Clp-N motif | P-loop containing nucleoside triphosphate hydrolases | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | FtsH protease domain-like | 2 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | C-terminal domain of alpha and beta subunits of F1 ATP synthase | 2 | 1 | |
| FKBP-like | Triger factor/SurA peptide-binding domain-like | 2 | 2 | |
| Glutathione synthetase ATP-binding domain-like | Rudiment single hybrid motif | 2 | 1 | |
| Nucleotidylyl transferase | An anticodon-binding domain of class I aminoacyl-tRNA synthetases | 2 | 1 | |
| Thiolase-like | Thiolase-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 | |
| Nucleic acid-binding proteins | Nucleic acid-binding proteins | 2 | 2 | |
| Thiamin diphosphate-binding fold (THDP-binding) | Thiamin diphosphate-binding fold (THDP-binding) | 2 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | "Winged helix" DNA-binding domain | 2 | 2 | |
| Ribosomal protein S5 domain 2-like | Ribosomal protein S5 domain 2-like | 2 | 2 | |
| TPR-like | TPR-like | 2 | 1 | |
| Phospholipase D/nuclease | Phospholipase D/nuclease | 2 | 2 | |
| Mechanosensitive channel protein MscS (YggB), transmembrane region | Sm-like ribonucleoproteins | 2 | 2 | |
| Sigma2 domain of RNA polymerase sigma factors | Sigma3 and sigma4 domains of RNA polymerase sigma factors | 2 | 2 | |
| DNA methylase specificity domain | DNA methylase specificity domain | 2 | 1 | |
| HSP40/DnaJ peptide-binding domain | HSP40/DnaJ peptide-binding domain | 2 | 2 | |
| FAD-binding/transporter-associated domain-like | FAD-linked oxidases, C-terminal domain | 2 | 2 | |
| Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | Nucleic acid-binding proteins | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Ribonuclease PH domain 2-like | 1 | 1 | |
| HAMP domain-like | Homodimeric domain of signal transducing histidine kinase | 1 | 1 | |
| ADC synthase | D-aminoacid aminotransferase-like PLP-dependent enzymes | 1 | 1 | |
| PIN domain-like | Ribonuclease H-like | 1 | 1 | |
| Creatinase/prolidase N-terminal domain | Creatinase/aminopeptidase | 1 | 1 | |
| L,D-transpeptidase catalytic domain-like | NTF2-like | 1 | 1 | |
| Ribulose-phoshate binding barrel | Ribulose-phoshate binding barrel | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | TRCF domain-like | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | GMP synthetase C-terminal dimerisation domain | 1 | 1 | |
| Diaminopimelate epimerase-like | Diaminopimelate epimerase-like | 1 | 1 | |
| Glutamine synthetase, N-terminal domain | Glutamine synthetase/guanido kinase | 1 | 1 | |
| Chaperone J-domain | DnaJ/Hsp40 cysteine-rich domain | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Glutathione synthetase ATP-binding domain-like | 1 | 1 | |
| PUA domain-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| DNA repair protein MutS, domain III | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Aspartate/glutamate racemase | Aspartate/glutamate racemase | 1 | 1 | |
| Ribokinase-like | Nucleotidylyl transferase | 1 | 1 | |
| Nucleic acid-binding proteins | BRCT domain | 1 | 1 | |
| Carbamoyl phosphate synthetase, large subunit connection domain | Methylglyoxal synthase-like | 1 | 1 | |
| Periplasmic binding protein-like II | Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain | 1 | 1 | |
| Fe-S cluster assembly (FSCA) domain-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | ACT-like | 1 | 1 | |
| Nucleic acid-binding proteins | GAD domain-like | 1 | 1 | |
| Nucleotide-diphospho-sugar transferases | Trimeric LpxA-like enzymes | 1 | 1 | |
| UBA-like | Elongation factor Ts (EF-Ts), dimerisation domain | 1 | 1 | |
| C-terminal UvrC-binding domain of UvrB | RuvA domain 2-like | 1 | 1 | |
| Trigger factor ribosome-binding domain | FKBP-like | 1 | 1 | |
| Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain | 1 | 1 | |
| Carbamate kinase-like | ACT-like | 1 | 1 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | Nucleic acid-binding proteins | 1 | 1 | |
| Zinc beta-ribbon | Prokaryotic SH3-related domain | 1 | 1 | |
| ACT-like | Formyltransferase | 1 | 1 | |
| Glutamyl tRNA-reductase catalytic, N-terminal domain | Glutamyl tRNA-reductase dimerization domain | 1 | 1 | |
| S-adenosyl-L-methionine-dependent methyltransferases | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| N-utilization substance G protein NusG, N-terminal domain | Translation proteins SH3-like domain | 1 | 1 | |
| PreATP-grasp domain | Carbamoyl phosphate synthetase, large subunit connection domain | 1 | 1 | |
| Putative DNA-binding domain | Anticodon-binding domain of PheRS | 1 | 1 | |
| Aldolase | AFP III-like domain | 1 | 1 | |
| Formate/glycerate dehydrogenase catalytic domain-like | ACT-like | 1 | 1 | |
| Enolase N-terminal domain-like | Enolase C-terminal domain-like | 1 | 1 | |
| Nucleotidylyl transferase | tRNA-binding arm | 1 | 1 | |
| Zinc beta-ribbon | Zinc beta-ribbon | 1 | 1 | |
| Flagellar hook protein flgE | Flagellar hook protein flgE | 1 | 1 | |
| ParB/Sulfiredoxin | KorB DNA-binding domain-like | 1 | 1 | |
| Translation proteins | Translation proteins | 1 | 1 | |
| Multidrug resistance efflux transporter EmrE | Multidrug resistance efflux transporter EmrE | 1 | 1 | |
| Class II aaRS and biotin synthetases | GAD domain-like | 1 | 1 | |
| R1 subunit of ribonucleotide reductase, N-terminal domain | PFL-like glycyl radical enzymes | 1 | 1 | |
| Zinc beta-ribbon | DNA primase core | 1 | 1 | |
| dsRNA-binding domain-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| Prokaryotic type I DNA topoisomerase | Zinc beta-ribbon | 1 | 1 | |
| Translation initiation factor IF3, N-terminal domain | Translation initiation factor IF3, C-terminal domain | 1 | 1 | |
| FAD-linked oxidoreductase | ALDH-like | 1 | 1 | |
| beta and beta-prime subunits of DNA dependent RNA-polymerase | beta and beta-prime subunits of DNA dependent RNA-polymerase | 1 | 1 | |
| Restriction endonuclease-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| IlvD/EDD N-terminal domain-like | LeuD/IlvD-like | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Methylglyoxal synthase-like | 1 | 1 | |
| CarD-like | TRCF domain-like | 1 | 1 | |
| Insert subdomain of RNA polymerase alpha subunit | RBP11-like subunits of RNA polymerase | 1 | 1 | |
| Obg GTP-binding protein N-terminal domain | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Domain of the SRP/SRP receptor G-proteins | Signal peptide-binding domain | 1 | 1 | |
| GroES-like | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | ACT-like | 1 | 1 | |
| Putative DNA-binding domain | Class II aaRS and biotin synthetases | 1 | 1 | |
| Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | Translation proteins | 1 | 1 | |
| FAD/NAD(P)-binding domain | Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Carbamoyl phosphate synthetase, large subunit connection domain | 1 | 1 | |
| Nicotinate/Quinolinate PRTase N-terminal domain-like | Nicotinate/Quinolinate PRTase C-terminal domain-like | 1 | 1 | |
| Nucleotidyltransferase | TGS-like | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | CheW-like | 1 | 1 | |
| Heat shock protein 70kD (HSP70), peptide-binding domain | Heat shock protein 70kD (HSP70), C-terminal subdomain | 1 | 1 | |
| Nucleotidylyl transferase | Riboflavin kinase-like | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Type II DNA topoisomerase | 1 | 1 | |
| Class II aaRS and biotin synthetases | Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | 1 | 1 | |
| Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | Nucleic acid-binding proteins | 1 | 1 | |
| Rho N-terminal domain-like | Nucleic acid-binding proteins | 1 | 1 | |
| Coiled-coil domain of nucleotide exchange factor GrpE | Head domain of nucleotide exchange factor GrpE | 1 | 1 | |
| HD-domain/PDEase-like | Nucleotidyltransferase | 1 | 1 | |
| Domain of the SRP/SRP receptor G-proteins | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| PurM N-terminal domain-like | PurM C-terminal domain-like | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | 1 | 1 | |
| Urease metallochaperone UreE, N-terminal domain | Urease metallochaperone UreE, C-terminal domain | 1 | 1 | |
| Methylated DNA-protein cysteine methyltransferase domain | Methylated DNA-protein cysteine methyltransferase, C-terminal domain | 1 | 1 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | BRCT domain | 1 | 1 | |
| GIY-YIG endonuclease | C-terminal UvrC-binding domain of UvrB | 1 | 1 | |
| PDZ domain-like | ClpP/crotonase | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | TrkA C-terminal domain-like | 1 | 1 | |
| Glutamyl tRNA-reductase catalytic, N-terminal domain | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Homodimeric domain of signal transducing histidine kinase | CheY-like | 1 | 1 | |
| Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain | Nucleotidylyl transferase | 1 | 1 | |
| 4Fe-4S ferredoxins | Formate dehydrogenase/DMSO reductase, domains 1-3 | 1 | 1 | |
| Translation proteins | ThrRS/AlaRS common domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | RecA protein, C-terminal domain | 1 | 1 | |
| Alpha-L RNA-binding motif | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| PUA domain-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Histidine-containing phosphotransfer domain, HPT domain | Homodimeric domain of signal transducing histidine kinase | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Signal peptide-binding domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | SMR domain-like | 1 | 1 | |
| FAD/NAD(P)-binding domain | Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain | 1 | 1 | |
| PreATP-grasp domain | Methylglyoxal synthase-like | 1 | 1 | |
| Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain | 1 | 1 | |
| YjeF N-terminal domain-like | Ribokinase-like | 1 | 1 | |
| Ribonuclease PH domain 2-like | Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | 1 | 1 | |
| Homodimeric domain of signal transducing histidine kinase | CheW-like | 1 | 1 | |
| 5' to 3' exonuclease, C-terminal subdomain | DNA/RNA polymerases | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Glutamyl tRNA-reductase dimerization domain | 1 | 1 | |
| Transcription factor NusA, N-terminal domain | Nucleic acid-binding proteins | 1 | 1 | |
| 2Fe-2S ferredoxin-like | Formate dehydrogenase/DMSO reductase, domains 1-3 | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Pre-protein crosslinking domain of SecA | 1 | 1 | |
| Urease, gamma-subunit | Urease, beta-subunit | 1 | 1 | |
| Nucleic acid-binding proteins | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| FabD/lysophospholipase-like | Probable ACP-binding domain of malonyl-CoA ACP transacylase | 1 | 1 | |
| S-adenosyl-L-methionine-dependent methyltransferases | Putative methyltransferase TM0872, insert domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | TrpR-like | 1 | 1 | |
| S-adenosyl-L-methionine-dependent methyltransferases | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 1 | 1 | |
| Ribonuclease PH domain 2-like | Ribonuclease PH domain 2-like | 1 | 1 | |
| Pre-protein crosslinking domain of SecA | Helical scaffold and wing domains of SecA | 1 | 1 | |
| Macro domain-like | Zn-dependent exopeptidases | 1 | 1 | |
| Aconitase B, N-terminal domain | Aconitase iron-sulfur domain | 1 | 1 | |
| Formate/glycerate dehydrogenase catalytic domain-like | Serine metabolism enzymes domain | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | CheY-like | 1 | 1 | |
| Zn-dependent exopeptidases | Bacterial exopeptidase dimerisation domain | 1 | 1 | |
| GroEL equatorial domain-like | GroEL equatorial domain-like | 1 | 1 | |
| Ribosomal protein L6 | Ribosomal protein L6 | 1 | 1 | |
| Tubulin nucleotide-binding domain-like | Tubulin C-terminal domain-like | 1 | 1 | |
| Histidine-containing phosphotransfer domain, HPT domain | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 1 | 1 | |
| Lysozyme-like | beta-lactamase/transpeptidase-like | 1 | 1 | |
| PHP domain-like | AF1531-like | 1 | 1 | |
| Eukaryotic type KH-domain (KH-domain type I) | HD-domain/PDEase-like | 1 | 1 | |
| Transcription factor NusA, N-terminal domain | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| MurCD N-terminal domain | MurD-like peptide ligases, catalytic domain | 1 | 1 | |
| Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | ThrRS/AlaRS common domain | 1 | 1 | |
| Cytidine deaminase-like | Dihydrofolate reductase-like | 1 | 1 | |
| Class II aaRS and biotin synthetases | YbaK/ProRS associated domain | 1 | 1 | |
| Actin-like ATPase domain | Heat shock protein 70kD (HSP70), peptide-binding domain | 1 | 1 | |
| CBS-domain pair | FAD-binding/transporter-associated domain-like | 1 | 1 | |
| Nucleotidyltransferase | Poly A polymerase C-terminal region-like | 1 | 1 | |
| Calcium ATPase, transmembrane domain M | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Translation proteins | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| Phosphohistidine domain | Phosphoenolpyruvate/pyruvate domain | 1 | 1 | |
| Outer membrane efflux proteins (OEP) | HlyD-like secretion proteins | 1 | 1 | |
| Composite domain of metallo-dependent hydrolases | Composite domain of metallo-dependent hydrolases | 1 | 1 | |
| DNA repair protein MutS, domain III | SMR domain-like | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Eukaryotic type KH-domain (KH-domain type I) | 1 | 1 | |
| Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | Eukaryotic type KH-domain (KH-domain type I) | 1 | 1 | |
| Nucleotide-diphospho-sugar transferases | IpsF-like | 1 | 1 | |
| GIY-YIG endonuclease | RuvA domain 2-like | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | SIS domain | 1 | 1 | |
| Histidine-containing phosphotransfer domain, HPT domain | CheY-like | 1 | 1 | |
| Class I glutamine amidotransferase-like | GMP synthetase C-terminal dimerisation domain | 1 | 1 | |
| Ribonuclease PH domain 2-like | Nucleic acid-binding proteins | 1 | 1 | |
| PPK N-terminal domain-like | PHP14-like | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | Type II DNA topoisomerase | 1 | 1 | |
| YbaK/ProRS associated domain | Class II aaRS ABD-related | 1 | 1 | |
| Translation proteins | PRC-barrel domain | 1 | 1 | |
| Translation proteins | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 1 | 1 | |
| Nucleotide-diphospho-sugar transferases | RmlC-like cupins | 1 | 1 | |
| 2Fe-2S ferredoxin-like | alpha-helical ferredoxin | 1 | 1 | |
| Insert subdomain of RNA polymerase alpha subunit | C-terminal domain of RNA polymerase alpha subunit | 1 | 1 | |
| Formyltransferase | FMT C-terminal domain-like | 1 | 1 | |
| Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain | Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain | 1 | 1 | |
| Carbamoyl phosphate synthetase, small subunit N-terminal domain | Class I glutamine amidotransferase-like | 1 | 1 | |
| RuvA domain 2-like | DNA helicase RuvA subunit, C-terminal domain | 1 | 1 | |
| Class II aaRS and biotin synthetases | Translation proteins | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Class I glutamine amidotransferase-like | 1 | 1 | |
| Acyl-CoA N-acyltransferases (Nat) | Acyl-CoA N-acyltransferases (Nat) | 1 | 1 | |
| CorA soluble domain-like | Magnesium transport protein CorA, transmembrane region | 1 | 1 | |
| HAMP domain-like | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 1 | 1 | |
| Ribonuclease H-like | DNA/RNA polymerases | 1 | 1 | |
| Aconitase B, N-terminal domain | LeuD/IlvD-like | 1 | 1 | |
| Metallo-dependent phosphatases | 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain | 1 | 1 | |
| Ribbon-helix-helix | ACT-like | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Phosphohistidine domain | 1 | 1 | |
| FAD-binding/transporter-associated domain-like | Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain | 1 | 1 | |
| Voltage-gated potassium channels | TrkA C-terminal domain-like | 1 | 1 | |
| Ribosomal protein L7/12, oligomerisation (N-terminal) domain | ClpS-like | 1 | 1 | |
| L30e-like | alpha/beta knot | 1 | 1 | |
| EF-G C-terminal domain-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | TGS-like | 1 | 1 | |
| NagB/RpiA/CoA transferase-like | alpha-helical ferredoxin | 1 | 1 | |
| Class I glutamine amidotransferase-like | Adenine nucleotide alpha hydrolases-like | 1 | 1 | |
| Bacterial fluorinating enzyme, N-terminal domain | Bacterial fluorinating enzyme, C-terminal domain | 1 | 1 | |
| Rho N-terminal domain-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Eukaryotic type KH-domain (KH-domain type I) | Nucleic acid-binding proteins | 1 | 1 | |
| GreA transcript cleavage protein, N-terminal domain | FKBP-like | 1 | 1 | |
| UbiD C-terminal domain-like | UbiD C-terminal domain-like | 1 | 1 | |
| PreATP-grasp domain | PreATP-grasp domain | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain | 1 | 1 | |
| Prokaryotic type KH domain (KH-domain type II) | Ribosomal protein S3 C-terminal domain | 1 | 1 | |
| DeoB insert domain-like | Alkaline phosphatase-like | 1 | 1 | |
| Transmembrane di-heme cytochromes | a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase) | 1 | 1 | |
| Enolase C-terminal domain-like | Nitrite and sulphite reductase 4Fe-4S domain-like | 1 | 1 | |
| RuvA domain 2-like | BRCT domain | 1 | 1 | |
| CBS-domain pair | Inosine monophosphate dehydrogenase (IMPDH) | 1 | 1 | |
| Histidine-containing phosphotransfer domain, HPT domain | CheW-like | 1 | 1 | |
| Voltage-gated potassium channels | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Nucleotidylyl transferase | Nucleic acid-binding proteins | 1 | 1 | |
| TolB, N-terminal domain | Tricorn protease N-terminal domain | 1 | 1 | |
| Actin-like ATPase domain | HD-domain/PDEase-like | 1 | 1 | |
| PPK N-terminal domain-like | Phospholipase D/nuclease | 1 | 1 | |
| Nucleotidylyl transferase | Alpha-L RNA-binding motif | 1 | 1 | |
| Trypsin-like serine proteases | PDZ domain-like | 1 | 1 | |
| Homo-oligomeric flavin-containing Cys decarboxylases, HFCD | CoaB-like | 1 | 1 | |
| Glutamine synthetase/guanido kinase | GatB/YqeY motif | 1 | 1 | |
| DNA clamp | DNA clamp | 1 | 1 | |
| 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain | Alkaline phosphatase-like | 1 | 1 | |
| Actin-like ATPase domain | Heat shock protein 70kD (HSP70), C-terminal subdomain | 1 | 1 | |
| MetI-like | Periplasmic binding protein-like II | 1 | 1 | |
| ValRS/IleRS/LeuRS editing domain | tRNA-binding arm | 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 | |
| DnaJ/Hsp40 cysteine-rich domain | HSP40/DnaJ peptide-binding domain | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Phosphoenolpyruvate/pyruvate domain | 1 | 1 | |
| FAD-linked oxidases, C-terminal domain | alpha-helical ferredoxin | 1 | 1 | |
| RBP11-like subunits of RNA polymerase | C-terminal domain of RNA polymerase alpha subunit | 1 | 1 | |
| ACT-like | ACT-like | 1 | 1 | |
| Trigger factor ribosome-binding domain | Triger factor/SurA peptide-binding domain-like | 1 | 1 | |
| Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | tRNA-binding arm | 1 | 1 | |
| Serine metabolism enzymes domain | ACT-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 | |
| SufE/NifU | Fe-S cluster assembly (FSCA) domain-like | 1 | 1 | |
| FliG | FliG | 1 | 1 | |
| Fe,Mn superoxide dismutase (SOD), N-terminal domain | Fe,Mn superoxide dismutase (SOD), C-terminal domain | 1 | 1 | |
| N-terminal domain of DnaB helicase | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Nucleic acid-binding proteins | 1 | 1 | |
| MurCD N-terminal domain | MurD-like peptide ligases, peptide-binding domain | 1 | 1 | |
| Formate dehydrogenase/DMSO reductase, domains 1-3 | ADC-like | 1 | 1 | |
| Nucleic acid-binding proteins | Anticodon-binding domain of PheRS | 1 | 1 | |
| Nucleic acid-binding proteins | Putative DNA-binding domain | 1 | 1 | |
| PHP14-like | Phospholipase D/nuclease | 1 | 1 | |
| CheY-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| L9 N-domain-like | Ribosomal protein L9 C-domain | 1 | 1 | |
| 2Fe-2S ferredoxin-like | 4Fe-4S ferredoxins | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | CarD-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | post-AAA+ oligomerization domain-like | 1 | 1 | |
| Nucleic acid-binding proteins | DNA helicase RuvA subunit, C-terminal domain | 1 | 1 | |
| LeuD/IlvD-like | Aconitase iron-sulfur domain | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | HSP90 C-terminal domain | 1 | 1 | |
| ThrRS/AlaRS common domain | Class II aaRS ABD-related | 1 | 1 | |
| 5' to 3' exonuclease, C-terminal subdomain | Ribonuclease H-like | 1 | 1 | |
| Barwin-like endoglucanases | Sporulation related repeat | 1 | 1 | |
| Translation proteins | Initiation factor IF2/eIF5b, domain 3 | 1 | 1 | |
| GroEL equatorial domain-like | GroEL apical domain-like | 1 | 1 | |
| Class II aaRS and biotin synthetases | Anticodon-binding domain of PheRS | 1 | 1 | |
| YrdC/RibB | RibA-like | 1 | 1 | |
| FMN-binding split barrel | UbiD C-terminal domain-like | 1 | 1 | |
| Nucleic acid-binding proteins | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| PHP domain-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| HD-domain/PDEase-like | TGS-like | 1 | 1 | |
| Lysozyme-like | LysM domain | 1 | 1 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | RuvA domain 2-like | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | HSP90 C-terminal domain | 1 | 1 | |
| MoeA N-terminal region -like | Molybdenum cofactor biosynthesis proteins | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Hypothetical protein YjiA, C-terminal domain | 1 | 1 | |
| FMN-binding split barrel | FMN-binding split barrel | 1 | 1 | |
| Peptide methionine sulfoxide reductase | Mss4-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| Fibronectin type III | Fibronectin type III | 1 | 1 | |
| FAD-binding/transporter-associated domain-like | alpha-helical ferredoxin | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Initiation factor IF2/eIF5b, domain 3 | 1 | 1 | |
| Ribonuclease PH domain 2-like | Eukaryotic type KH-domain (KH-domain type I) | 1 | 1 | |
| PIN domain-like | DNA/RNA polymerases | 1 | 1 | |
| S-adenosylmethionine synthetase | S-adenosylmethionine synthetase | 1 | 1 | |
| Ribosomal L11/L12e N-terminal domain | Ribosomal protein L11, C-terminal domain | 1 | 1 | |
| Riboflavin synthase domain-like | Riboflavin synthase domain-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Helical scaffold and wing domains of SecA | 1 | 1 | |
| Type II DNA topoisomerase | GyrA/ParC C-terminal domain-like | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Serine metabolism enzymes domain | 1 | 1 | |
| Acylphosphatase/BLUF domain-like | YrdC/RibB | 1 | 1 | |
