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 | 9 |  |
| Nucleotidylyl transferase | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 6 | 6 | |
| NAD(P)-binding Rossmann-fold domains | Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 5 | 3 | |
| Nucleic acid-binding proteins | Nucleic acid-binding proteins | 4 | 3 | |
| P-loop containing nucleoside triphosphate hydrolases | Translation proteins | 4 | 4 | |
| MurD-like peptide ligases, catalytic domain | MurD-like peptide ligases, peptide-binding domain | 4 | 3 | |
| Thiamin diphosphate-binding fold (THDP-binding) | TK C-terminal domain-like | 4 | 3 | |
| Thiamin diphosphate-binding fold (THDP-binding) | Thiamin diphosphate-binding fold (THDP-binding) | 4 | 3 | |
| Phospholipase D/nuclease | Phospholipase D/nuclease | 4 | 2 | |
| Translation proteins SH3-like domain | Nucleic acid-binding proteins | 3 | 2 | |
| Single hybrid motif | CoA-dependent acyltransferases | 3 | 3 | |
| Aminoacid dehydrogenase-like, N-terminal domain | NAD(P)-binding Rossmann-fold domains | 3 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | Ribosomal protein S5 domain 2-like | 3 | 3 | |
| GroEL equatorial domain-like | GroEL apical domain-like | 3 | 2 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | Ribosomal protein S5 domain 2-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 | |
| Class II aaRS and biotin synthetases | Class II aaRS ABD-related | 3 | 3 | |
| Nucleic acid-binding proteins | Class II aaRS and biotin synthetases | 3 | 3 | |
| Class II aaRS and biotin synthetases | ThrRS/AlaRS common domain | 3 | 2 | |
| CBS-domain pair | FAD-binding/transporter-associated domain-like | 3 | 1 | |
| Riboflavin synthase domain-like | Ferredoxin reductase-like, C-terminal NADP-linked domain | 3 | 2 | |
| Nucleic acid-binding proteins | RuvA domain 2-like | 2 | 2 | |
| Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | CoA-dependent acyltransferases | 2 | 2 | |
| Translation proteins | ThrRS/AlaRS common domain | 2 | 1 | |
| FAD/NAD(P)-binding domain | FAD-linked reductases, C-terminal domain | 2 | 1 | |
| MurE/MurF N-terminal domain | MurD-like peptide ligases, catalytic domain | 2 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | CarD-like | 2 | 1 | |
| CarD-like | TRCF domain-like | 2 | 1 | |
| Ribosomal protein S5 domain 2-like | Type II DNA topoisomerase | 2 | 2 | |
| Alpha-L RNA-binding motif | Pseudouridine synthase | 2 | 1 | |
| Actin-like ATPase domain | Actin-like ATPase domain | 2 | 2 | |
| MurCD N-terminal domain | MurD-like peptide ligases, peptide-binding domain | 2 | 2 | |
| NAD(P)-binding Rossmann-fold domains | 6-phosphogluconate dehydrogenase C-terminal domain-like | 2 | 2 | |
| E set domains | (Trans)glycosidases | 2 | 2 | |
| Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | Translation proteins | 2 | 1 | |
| Single hybrid motif | Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | 2 | 2 | |
| EF-G C-terminal domain-like | EF-G C-terminal domain-like | 2 | 2 | |
| Translation proteins | EF-G C-terminal domain-like | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | post-AAA+ oligomerization domain-like | 2 | 2 | |
| MurCD N-terminal domain | MurD-like peptide ligases, catalytic domain | 2 | 2 | |
| Sigma2 domain of RNA polymerase sigma factors | Sigma3 and sigma4 domains of RNA polymerase sigma factors | 2 | 2 | |
| Class II aaRS and biotin synthetases | Translation proteins | 2 | 1 | |
| PreATP-grasp domain | Glutathione synthetase ATP-binding domain-like | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | EF-G C-terminal domain-like | 2 | 2 | |
| Double Clp-N motif | P-loop containing nucleoside triphosphate hydrolases | 2 | 1 | |
| Domain of the SRP/SRP receptor G-proteins | P-loop containing nucleoside triphosphate hydrolases | 2 | 2 | |
| tRNA-binding arm | Class II aaRS and biotin synthetases | 2 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | Type II DNA topoisomerase | 2 | 2 | |
| Sigma3 and sigma4 domains of RNA polymerase sigma factors | Sigma3 and sigma4 domains of RNA polymerase sigma factors | 2 | 2 | |
| Penicillin binding protein dimerisation domain | beta-lactamase/transpeptidase-like | 2 | 2 | |
| LuxS/MPP-like metallohydrolase | LuxS/MPP-like metallohydrolase | 2 | 2 | |
| Phosphoglucomutase, first 3 domains | Phosphoglucomutase, C-terminal domain | 2 | 2 | |
| MurE/MurF N-terminal domain | MurD-like peptide ligases, peptide-binding domain | 2 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | TrpR-like | 2 | 1 | |
| Phosphoglucomutase, first 3 domains | Phosphoglucomutase, first 3 domains | 2 | 2 | |
| Ribosomal protein S5 domain 2-like | Ribosomal protein S5 domain 2-like | 2 | 2 | |
| Class II aaRS and biotin synthetases | Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | 2 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | TRCF domain-like | 2 | 1 | |
| 2Fe-2S ferredoxin-like | Ferredoxin reductase-like, C-terminal NADP-linked domain | 2 | 1 | |
| Nucleotidyltransferase | Poly A polymerase C-terminal region-like | 2 | 1 | |
| Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain | Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | Restriction endonuclease-like | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | "Winged helix" DNA-binding domain | 2 | 2 | |
| Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | ThrRS/AlaRS common domain | 2 | 1 | |
| 2Fe-2S ferredoxin-like | Riboflavin synthase domain-like | 2 | 1 | |
| Prokaryotic type KH domain (KH-domain type II) | Ribosomal protein S3 C-terminal domain | 1 | 1 | |
| FAD/NAD(P)-binding domain | FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 1 | 1 | |
| Zinc beta-ribbon | SWIB/MDM2 domain | 1 | 1 | |
| PheT/TilS domain | Anticodon-binding domain of PheRS | 1 | 1 | |
| Protein kinase-like (PK-like) | C-type lectin-like | 1 | 1 | |
| Glutamine synthetase/guanido kinase | GatB/YqeY motif | 1 | 1 | |
| Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain | 1 | 1 | |
| PYP-like sensor domain (PAS domain) | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 1 | 1 | |
| MgtE N-terminal domain-like | CBS-domain pair | 1 | 1 | |
| DNA repair protein MutS, domain III | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Chaperone J-domain | DnaJ/Hsp40 cysteine-rich domain | 1 | 1 | |
| 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase, HPPK | Dihydropteroate synthetase-like | 1 | 1 | |
| dsRNA-binding domain-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| RNase III domain-like | dsRNA-binding domain-like | 1 | 1 | |
| Insert subdomain of RNA polymerase alpha subunit | C-terminal domain of RNA polymerase alpha subunit | 1 | 1 | |
| lambda integrase-like, N-terminal domain | DNA breaking-rejoining enzymes | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Rubredoxin-like | 1 | 1 | |
| Fe,Mn superoxide dismutase (SOD), N-terminal domain | Fe,Mn superoxide dismutase (SOD), C-terminal domain | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain | 1 | 1 | |
| Class II aaRS and biotin synthetases | Anticodon-binding domain of PheRS | 1 | 1 | |
| GIY-YIG endonuclease | C-terminal UvrC-binding domain of UvrB | 1 | 1 | |
| Prokaryotic type KH domain (KH-domain type II) | Rad51 N-terminal domain-like | 1 | 1 | |
| Thiolase-like | Thiolase-like | 1 | 1 | |
| PIN domain-like | Ribonuclease H-like | 1 | 1 | |
| Ribonuclease PH domain 2-like | Ribonuclease PH domain 2-like | 1 | 1 | |
| ABC transporter involved in vitamin B12 uptake, BtuC | Iron-dependent repressor protein, dimerization domain | 1 | 1 | |
| Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain | Phosphoenolpyruvate/pyruvate domain | 1 | 1 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | RuvA domain 2-like | 1 | 1 | |
| Ribosomal L11/L12e N-terminal domain | Ribosomal protein L11, C-terminal domain | 1 | 1 | |
| FabD/lysophospholipase-like | Probable ACP-binding domain of malonyl-CoA ACP transacylase | 1 | 1 | |
| Enolase N-terminal domain-like | Enolase C-terminal domain-like | 1 | 1 | |
| Putative DNA-binding domain | Class II aaRS and biotin synthetases | 1 | 1 | |
| (Trans)glycosidases | Glycosyl hydrolase domain | 1 | 1 | |
| Rho N-terminal domain-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| YrdC/RibB | RibA-like | 1 | 1 | |
| RBP11-like subunits of RNA polymerase | C-terminal domain of RNA polymerase alpha subunit | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | DNA mismatch repair protein MutL | 1 | 1 | |
| Ribosomal protein L7/12, oligomerisation (N-terminal) domain | ClpS-like | 1 | 1 | |
| Thioredoxin-like | Six-hairpin glycosidases | 1 | 1 | |
| FAD-binding/transporter-associated domain-like | Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain | 1 | 1 | |
| Class II aaRS and biotin synthetases | GAD domain-like | 1 | 1 | |
| PDZ domain-like | PDZ domain-like | 1 | 1 | |
| Transcription factor NusA, N-terminal domain | Nucleic acid-binding proteins | 1 | 1 | |
| Homodimeric domain of signal transducing histidine kinase | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 1 | 1 | |
| E set domains | Glycosyl hydrolase domain | 1 | 1 | |
| MurD-like peptide ligases, peptide-binding domain | Glutathione synthetase ATP-binding domain-like | 1 | 1 | |
| Ribonuclease H-like | DNA/RNA polymerases | 1 | 1 | |
| Zinc beta-ribbon | DNA primase core | 1 | 1 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | BRCT domain | 1 | 1 | |
| Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | Nucleic acid-binding proteins | 1 | 1 | |
| HSP40/DnaJ peptide-binding domain | HSP40/DnaJ peptide-binding domain | 1 | 1 | |
| FMN-binding split barrel | UbiD C-terminal domain-like | 1 | 1 | |
| Translation proteins | Translation proteins | 1 | 1 | |
| Heat shock protein 70kD (HSP70), peptide-binding domain | Heat shock protein 70kD (HSP70), C-terminal subdomain | 1 | 1 | |
| UBA-like | Elongation factor Ts (EF-Ts), dimerisation domain | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Ribonuclease PH domain 2-like | 1 | 1 | |
| RuvA domain 2-like | BRCT domain | 1 | 1 | |
| MgtE N-terminal domain-like | MgtE membrane domain-like | 1 | 1 | |
| Phosphoenolpyruvate/pyruvate domain | PK C-terminal domain-like | 1 | 1 | |
| Transcription factor NusA, N-terminal domain | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| Nucleic acid-binding proteins | ArfGap/RecO-like zinc finger | 1 | 1 | |
| Calcium ATPase, transduction domain A | HAD-like | 1 | 1 | |
| CheY-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Putative DNA-binding domain | Anticodon-binding domain of PheRS | 1 | 1 | |
| DnaK suppressor protein DksA, alpha-hairpin domain | Glucocorticoid receptor-like (DNA-binding domain) | 1 | 1 | |
| F1F0 ATP synthase subunit C | F1F0 ATP synthase subunit C | 1 | 1 | |
| Nucleic acid-binding proteins | BRCT domain | 1 | 1 | |
| Nucleic acid-binding proteins | Anticodon-binding domain of PheRS | 1 | 1 | |
| GroEL-intermediate domain like | GroEL apical domain-like | 1 | 1 | |
| Prokaryotic type KH domain (KH-domain type II) | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | RecA protein, C-terminal domain | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | SIS domain | 1 | 1 | |
| "Winged helix" DNA-binding domain | GAF domain-like | 1 | 1 | |
| Nucleic acid-binding proteins | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Ribosomal protein L6 | Ribosomal protein L6 | 1 | 1 | |
| SMAD/FHA domain | SMAD/FHA domain | 1 | 1 | |
| EF-G C-terminal domain-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| ABC transporter transmembrane region | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Creatinase/prolidase N-terminal domain | Creatinase/aminopeptidase | 1 | 1 | |
| UbiD C-terminal domain-like | UbiD C-terminal domain-like | 1 | 1 | |
| Multidrug efflux transporter AcrB transmembrane domain | Multidrug efflux transporter AcrB transmembrane domain | 1 | 1 | |
| PEP carboxykinase N-terminal domain | PEP carboxykinase-like | 1 | 1 | |
| PK beta-barrel domain-like | PK C-terminal domain-like | 1 | 1 | |
| Nucleic acid-binding proteins | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| Eukaryotic type KH-domain (KH-domain type I) | Nucleic acid-binding proteins | 1 | 1 | |
| Class II aaRS and biotin synthetases | YbaK/ProRS associated domain | 1 | 1 | |
| L30e-like | alpha/beta knot | 1 | 1 | |
| SufE/NifU | Fe-S cluster assembly (FSCA) domain-like | 1 | 1 | |
| Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain | Nucleotidylyl transferase | 1 | 1 | |
| MurCD N-terminal domain | PreATP-grasp domain | 1 | 1 | |
| Formyltransferase | FMT C-terminal domain-like | 1 | 1 | |
| Aldolase | Aminoacid dehydrogenase-like, N-terminal domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Class I glutamine amidotransferase-like | 1 | 1 | |
| DNA repair protein MutS, domain II | DNA repair protein MutS, domain III | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Eukaryotic type KH-domain (KH-domain type I) | 1 | 1 | |
| Diaminopimelate epimerase-like | Diaminopimelate epimerase-like | 1 | 1 | |
| CBS-domain pair | MgtE membrane domain-like | 1 | 1 | |
| Glucocorticoid receptor-like (DNA-binding domain) | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Prokaryotic type I DNA topoisomerase | SWIB/MDM2 domain | 1 | 1 | |
| Nucleic acid-binding proteins | Putative DNA-binding domain | 1 | 1 | |
| Riboflavin synthase domain-like | Riboflavin synthase domain-like | 1 | 1 | |
| PIN domain-like | DNA/RNA polymerases | 1 | 1 | |
| Chaperone J-domain | HSP40/DnaJ peptide-binding domain | 1 | 1 | |
| S-adenosyl-L-methionine-dependent methyltransferases | Putative methyltransferase TM0872, insert domain | 1 | 1 | |
| Nucleotide-diphospho-sugar transferases | Trimeric LpxA-like enzymes | 1 | 1 | |
| Translation proteins | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| alpha/beta knot | Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase | 1 | 1 | |
| beta-lactamase/transpeptidase-like | beta-lactamase/transpeptidase-like | 1 | 1 | |
| Cytidine deaminase-like | Dihydrofolate reductase-like | 1 | 1 | |
| Nucleotidylyl transferase | tRNA-binding arm | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | LDH C-terminal domain-like | 1 | 1 | |
| N-terminal domain of DnaB helicase | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| PheT/TilS domain | Class II aaRS and biotin synthetases | 1 | 1 | |
| Cadherin-like | Cadherin-like | 1 | 1 | |
| MurD-like peptide ligases, peptide-binding domain | PreATP-grasp domain | 1 | 1 | |
| DNA repair protein MutS, domain II | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| PHP domain-like | RuvA domain 2-like | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Rudiment single hybrid motif | 1 | 1 | |
| Rho N-terminal domain-like | Nucleic acid-binding proteins | 1 | 1 | |
| LysM domain | LysM domain | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Succinyl-CoA synthetase domains | 1 | 1 | |
| RuvA domain 2-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| N-utilization substance G protein NusG, N-terminal domain | Translation proteins SH3-like domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | TGS-like | 1 | 1 | |
| MetI-like | Periplasmic binding protein-like II | 1 | 1 | |
| TPR-like | TPR-like | 1 | 1 | |
| Sec-C motif | Creatinase/aminopeptidase | 1 | 1 | |
| FAD/NAD(P)-binding domain | Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | 1 | 1 | |
| Domain of the SRP/SRP receptor G-proteins | Signal peptide-binding domain | 1 | 1 | |
| PUA domain-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| Actin-like ATPase domain | Heat shock protein 70kD (HSP70), peptide-binding domain | 1 | 1 | |
| Homeodomain-like | Tetracyclin repressor-like, C-terminal 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 | |
| Translation proteins | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 1 | 1 | |
| DNA repair protein MutS, domain I | DNA repair protein MutS, domain II | 1 | 1 | |
| E set domains | E set domains | 1 | 1 | |
| Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain | Phosphohistidine domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Signal peptide-binding domain | 1 | 1 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | Nucleic acid-binding proteins | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | DNA mismatch repair protein MutL | 1 | 1 | |
| NagB/RpiA/CoA transferase-like | D-ribose-5-phosphate isomerase (RpiA), lid domain | 1 | 1 | |
| 2Fe-2S ferredoxin-like | alpha-helical ferredoxin | 1 | 1 | |
| MurD-like peptide ligases, catalytic domain | Glutathione synthetase ATP-binding domain-like | 1 | 1 | |
| MFS general substrate transporter | ARM repeat | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 1 | 1 | |
| Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain | 1 | 1 | |
| Translation proteins | Initiation factor IF2/eIF5b, domain 3 | 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 | |
| CheY-like | C-terminal effector domain of the bipartite response regulators | 1 | 1 | |
| DnaJ/Hsp40 cysteine-rich domain | HSP40/DnaJ peptide-binding domain | 1 | 1 | |
| Thymidylate synthase-complementing protein Thy1 | Thymidylate synthase-complementing protein Thy1 | 1 | 1 | |
| Multidrug resistance efflux transporter EmrE | Multidrug resistance efflux transporter EmrE | 1 | 1 | |
| Nucleotidylyl transferase | Alpha-L RNA-binding motif | 1 | 1 | |
| Ribonuclease PH domain 2-like | Nucleic acid-binding proteins | 1 | 1 | |
| MurCD N-terminal domain | Glutathione synthetase ATP-binding domain-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Helical scaffold and wing domains of SecA | 1 | 1 | |
| ThrRS/AlaRS common domain | Class II aaRS ABD-related | 1 | 1 | |
| Pectin lyase-like | Autotransporter | 1 | 1 | |
| FAD/NAD(P)-binding domain | Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain | 1 | 1 | |
| GreA transcript cleavage protein, N-terminal domain | FKBP-like | 1 | 1 | |
| YbaK/ProRS associated domain | Class II aaRS ABD-related | 1 | 1 | |
| Prokaryotic type I DNA topoisomerase | Zinc beta-ribbon | 1 | 1 | |
| Trigger factor ribosome-binding domain | Triger factor/SurA peptide-binding domain-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Initiation factor IF2/eIF5b, domain 3 | 1 | 1 | |
| PUA domain-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Probable GTPase Der, C-terminal domain | 1 | 1 | |
| ValRS/IleRS/LeuRS editing domain | tRNA-binding arm | 1 | 1 | |
| Methionyl-tRNA synthetase (MetRS), Zn-domain | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 1 | 1 | |
| Type II DNA topoisomerase | GyrA/ParC C-terminal domain-like | 1 | 1 | |
| Pre-protein crosslinking domain of SecA | Helical scaffold and wing domains of SecA | 1 | 1 | |
| DNA repair protein MutS, domain I | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| R1 subunit of ribonucleotide reductase, N-terminal domain | PFL-like glycyl radical enzymes | 1 | 1 | |
| Coiled-coil domain of nucleotide exchange factor GrpE | Head domain of nucleotide exchange factor GrpE | 1 | 1 | |
| Nucleic acid-binding proteins | PheT/TilS domain | 1 | 1 | |
| 5' to 3' exonuclease, C-terminal subdomain | Ribonuclease H-like | 1 | 1 | |
| Translation initiation factor IF3, N-terminal domain | Translation initiation factor IF3, C-terminal domain | 1 | 1 | |
| DNA-glycosylase | Nudix | 1 | 1 | |
| Methionyl-tRNA synthetase (MetRS), Zn-domain | Nucleotidylyl transferase | 1 | 1 | |
| GroEL equatorial domain-like | GroEL-intermediate domain like | 1 | 1 | |
| Putative DNA-binding domain | Phoshotransferase/anion transport protein | 1 | 1 | |
| Nucleotidylyl transferase | Riboflavin kinase-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | FtsH protease domain-like | 1 | 1 | |
| Nucleic acid-binding proteins | Rad51 N-terminal domain-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | C-terminal UvrC-binding domain of UvrB | 1 | 1 | |
| Obg GTP-binding protein N-terminal domain | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Pre-protein crosslinking domain of SecA | 1 | 1 | |
| Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Succinyl-CoA synthetase domains | 1 | 1 | |
| 5' to 3' exonuclease, C-terminal subdomain | DNA/RNA polymerases | 1 | 1 | |
| Actin-like ATPase domain | Heat shock protein 70kD (HSP70), C-terminal subdomain | 1 | 1 | |
| PIN domain-like | 5' to 3' exonuclease, C-terminal subdomain | 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 | |
| PIN domain-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | tRNA-binding arm | 1 | 1 | |
| Phosphohistidine domain | Phosphoenolpyruvate/pyruvate domain | 1 | 1 | |
| PYP-like sensor domain (PAS domain) | Homodimeric domain of signal transducing histidine kinase | 1 | 1 | |
| Transcription factor NusA, N-terminal domain | Rad51 N-terminal domain-like | 1 | 1 | |
| PreATP-grasp domain | Rudiment single hybrid motif | 1 | 1 | |
| PheT/TilS domain | Putative DNA-binding domain | 1 | 1 | |
| PDZ domain-like | ClpP/crotonase | 1 | 1 | |
| Aldolase | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| MurD-like peptide ligases, catalytic domain | PreATP-grasp domain | 1 | 1 | |
| Trypsin-like serine proteases | PDZ domain-like | 1 | 1 | |
| Calcium ATPase, transduction domain A | Calcium ATPase, transmembrane domain M | 1 | 1 | |
| PK beta-barrel domain-like | Phosphoenolpyruvate/pyruvate domain | 1 | 1 | |
| DNA repair protein MutS, domain I | DNA repair protein MutS, domain III | 1 | 1 | |
| Calcium ATPase, transmembrane domain M | HAD-like | 1 | 1 | |
| Insert subdomain of RNA polymerase alpha subunit | RBP11-like subunits of RNA polymerase | 1 | 1 | |
| EspE N-terminal domain-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| C-terminal UvrC-binding domain of UvrB | RuvA domain 2-like | 1 | 1 | |
| Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | Eukaryotic type KH-domain (KH-domain type I) | 1 | 1 | |
| Ribonuclease PH domain 2-like | Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Nucleic acid-binding proteins | 1 | 1 | |
| DNA clamp | DNA clamp | 1 | 1 | |
| GIY-YIG endonuclease | RuvA domain 2-like | 1 | 1 | |
| Macro domain-like | Zn-dependent exopeptidases | 1 | 1 | |
| Invasin/intimin cell-adhesion fragments | Cadherin-like | 1 | 1 | |
| Ribonuclease PH domain 2-like | Eukaryotic type KH-domain (KH-domain type I) | 1 | 1 | |
| Nucleotidylyl transferase | An anticodon-binding domain of class I aminoacyl-tRNA synthetases | 1 | 1 | |
