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 | |
|---|
| Homeodomain-like | Tetracyclin repressor-like, C-terminal domain | 110 | 6 |  |
| Acyl-CoA dehydrogenase NM domain-like | Acyl-CoA dehydrogenase C-terminal domain-like | 70 | 6 | |
| P-loop containing nucleoside triphosphate hydrolases | P-loop containing nucleoside triphosphate hydrolases | 42 | 16 | |
| GroES-like | NAD(P)-binding Rossmann-fold domains | 34 | 3 | |
| Thiolase-like | Thiolase-like | 31 | 3 | |
| "Winged helix" DNA-binding domain | Periplasmic binding protein-like II | 29 | 1 | |
| CheY-like | C-terminal effector domain of the bipartite response regulators | 26 | 2 | |
| ABC transporter transmembrane region | P-loop containing nucleoside triphosphate hydrolases | 22 | 3 | |
| Composite domain of metallo-dependent hydrolases | Metallo-dependent hydrolases | 22 | 5 | |
| NAD(P)-binding Rossmann-fold domains | Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 22 | 4 | |
| NAD(P)-binding Rossmann-fold domains | 6-phosphogluconate dehydrogenase C-terminal domain-like | 22 | 4 | |
| "Winged helix" DNA-binding domain | GntR ligand-binding domain-like | 22 | 1 | |
| "Winged helix" DNA-binding domain | GAF domain-like | 18 | 2 | |
| Sigma2 domain of RNA polymerase sigma factors | Sigma3 and sigma4 domains of RNA polymerase sigma factors | 18 | 5 | |
| CoA-dependent acyltransferases | CoA-dependent acyltransferases | 18 | 10 | |
| Thioesterase/thiol ester dehydrase-isomerase | Thioesterase/thiol ester dehydrase-isomerase | 17 | 1 | |
| FAD/NAD(P)-binding domain | FAD/NAD(P)-binding domain | 16 | 7 | |
| Homeodomain-like | Homeodomain-like | 15 | 9 | |
| Zn-dependent exopeptidases | Bacterial exopeptidase dimerisation domain | 14 | 1 | |
| FAD/NAD(P)-binding domain | Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | 14 | 4 | |
| "Winged helix" DNA-binding domain | Dimeric alpha+beta barrel | 14 | 6 | |
| PreATP-grasp domain | Glutathione synthetase ATP-binding domain-like | 13 | 7 | |
| FAD/NAD(P)-binding domain | FAD-linked reductases, C-terminal domain | 13 | 4 | |
| Riboflavin synthase domain-like | Ferredoxin reductase-like, C-terminal NADP-linked domain | 13 | 5 | |
| Homodimeric domain of signal transducing histidine kinase | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 13 | 3 | |
| Aminoacid dehydrogenase-like, N-terminal domain | NAD(P)-binding Rossmann-fold domains | 13 | 2 | |
| ACP-like | ACP-like | 12 | 11 | |
| RmlC-like cupins | Homeodomain-like | 12 | 5 | |
| Thiamin diphosphate-binding fold (THDP-binding) | Thiamin diphosphate-binding fold (THDP-binding) | 12 | 8 | |
| Multidrug resistance efflux transporter EmrE | Multidrug resistance efflux transporter EmrE | 12 | 2 | |
| Actin-like ATPase domain | Actin-like ATPase domain | 12 | 4 | |
| Acetyl-CoA synthetase-like | ACP-like | 12 | 11 | |
| ClpP/crotonase | ClpP/crotonase | 11 | 3 | |
| PreATP-grasp domain | Rudiment single hybrid motif | 11 | 5 | |
| FAD-binding/transporter-associated domain-like | FAD-linked oxidases, C-terminal domain | 11 | 2 | |
| Glutathione synthetase ATP-binding domain-like | Rudiment single hybrid motif | 11 | 5 | |
| FAD/NAD(P)-binding domain | FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 10 | 3 | |
| P-loop containing nucleoside triphosphate hydrolases | Translation proteins | 10 | 6 | |
| CoA-dependent acyltransferases | ACP-like | 10 | 9 | |
| Acetyl-CoA synthetase-like | Acetyl-CoA synthetase-like | 10 | 9 | |
| CoA-dependent acyltransferases | Acetyl-CoA synthetase-like | 10 | 9 | |
| ACP-like | alpha/beta-Hydrolases | 9 | 8 | |
| Multidrug efflux transporter AcrB transmembrane domain | Multidrug efflux transporter AcrB transmembrane domain | 9 | 2 | |
| Acetyl-CoA synthetase-like | alpha/beta-Hydrolases | 9 | 8 | |
| GroES-like | GroES-like | 9 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Single hybrid motif | 8 | 4 | |
| Calcium ATPase, transduction domain A | HAD-like | 8 | 3 | |
| Calcium ATPase, transduction domain A | Calcium ATPase, transmembrane domain M | 8 | 3 | |
| Rudiment single hybrid motif | Single hybrid motif | 8 | 4 | |
| PreATP-grasp domain | Single hybrid motif | 8 | 4 | |
| HAD-like | Calcium ATPase, transmembrane domain M | 8 | 3 | |
| Thiamin diphosphate-binding fold (THDP-binding) | TK C-terminal domain-like | 8 | 4 | |
| HAMP domain-like | Homodimeric domain of signal transducing histidine kinase | 8 | 2 | |
| lambda repressor-like DNA-binding domains | RmlC-like cupins | 8 | 2 | |
| HAMP domain-like | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 7 | 1 | |
| lambda repressor-like DNA-binding domains | Periplasmic binding protein-like I | 7 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | MOP-like | 7 | 1 | |
| Ferredoxin reductase-like, C-terminal NADP-linked domain | 2Fe-2S ferredoxin-like | 7 | 1 | |
| CoA-dependent acyltransferases | alpha/beta-Hydrolases | 7 | 6 | |
| Riboflavin synthase domain-like | 2Fe-2S ferredoxin-like | 7 | 1 | |
| Rhodanese/Cell cycle control phosphatase | Rhodanese/Cell cycle control phosphatase | 6 | 2 | |
| Cupredoxins | Cupredoxins | 6 | 4 | |
| Aldolase | post-HMGL domain-like | 6 | 4 | |
| Nucleotidylyl transferase | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 6 | 5 | |
| Adenine nucleotide alpha hydrolases-like | Adenine nucleotide alpha hydrolases-like | 6 | 1 | |
| Formate/glycerate dehydrogenase catalytic domain-like | NAD(P)-binding Rossmann-fold domains | 5 | 3 | |
| MurD-like peptide ligases, catalytic domain | MurD-like peptide ligases, peptide-binding domain | 5 | 5 | |
| Class I glutamine amidotransferase-like | Homeodomain-like | 5 | 1 | |
| ISP domain | Bet v1-like | 5 | 2 | |
| "Winged helix" DNA-binding domain | Chorismate lyase-like | 5 | 1 | |
| Acyl-CoA dehydrogenase C-terminal domain-like | Acyl-CoA dehydrogenase C-terminal domain-like | 5 | 2 | |
| Class II aaRS and biotin synthetases | Class II aaRS ABD-related | 5 | 3 | |
| P-loop containing nucleoside triphosphate hydrolases | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 5 | 2 | |
| TPR-like | C-terminal effector domain of the bipartite response regulators | 5 | 4 | |
| Dimeric alpha+beta barrel | Dimeric alpha+beta barrel | 5 | 4 | |
| Translation proteins | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 5 | 2 | |
| FMN-linked oxidoreductases | FAD/NAD(P)-binding domain | 5 | 2 | |
| Enolase N-terminal domain-like | Enolase C-terminal domain-like | 5 | 1 | |
| Double Clp-N motif | P-loop containing nucleoside triphosphate hydrolases | 4 | 2 | |
| Single hybrid motif | Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | 4 | 3 | |
| Phosphoglucomutase, first 3 domains | Phosphoglucomutase, first 3 domains | 4 | 2 | |
| PYP-like sensor domain (PAS domain) | Nucleotide cyclase | 4 | 1 | |
| "Winged helix" DNA-binding domain | PLP-dependent transferases | 4 | 1 | |
| N-terminal domain of MutM-like DNA repair proteins | S13-like H2TH domain | 4 | 1 | |
| Phosphoglucomutase, first 3 domains | Phosphoglucomutase, C-terminal domain | 4 | 2 | |
| Translation proteins | EF-G C-terminal domain-like | 4 | 3 | |
| Nucleotide cyclase | EAL domain-like | 4 | 1 | |
| Metallo-hydrolase/oxidoreductase | SCP-like | 4 | 1 | |
| FabD/lysophospholipase-like | Probable ACP-binding domain of malonyl-CoA ACP transacylase | 4 | 4 | |
| Sigma3 and sigma4 domains of RNA polymerase sigma factors | Sigma3 and sigma4 domains of RNA polymerase sigma factors | 4 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | EF-G C-terminal domain-like | 4 | 3 | |
| N-terminal domain of MutM-like DNA repair proteins | Glucocorticoid receptor-like (DNA-binding domain) | 4 | 1 | |
| Single hybrid motif | CoA-dependent acyltransferases | 4 | 3 | |
| S13-like H2TH domain | Glucocorticoid receptor-like (DNA-binding domain) | 4 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | C-terminal effector domain of the bipartite response regulators | 4 | 3 | |
| Formate dehydrogenase/DMSO reductase, domains 1-3 | ADC-like | 4 | 3 | |
| PYP-like sensor domain (PAS domain) | EAL domain-like | 4 | 1 | |
| Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | CoA-dependent acyltransferases | 4 | 3 | |
| PurM N-terminal domain-like | PurM C-terminal domain-like | 4 | 2 | |
| E set domains | (Trans)glycosidases | 4 | 4 | |
| DPP6 N-terminal domain-like | alpha/beta-Hydrolases | 4 | 2 | |
| Nucleic acid-binding proteins | Class II aaRS and biotin synthetases | 4 | 4 | |
| Acyl-CoA dehydrogenase NM domain-like | Acyl-CoA dehydrogenase NM domain-like | 4 | 1 | |
| FAD/NAD(P)-binding domain | Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain | 4 | 3 | |
| "Winged helix" DNA-binding domain | "Winged helix" DNA-binding domain | 4 | 4 | |
| Lysozyme-like | beta-lactamase/transpeptidase-like | 3 | 3 | |
| P-loop containing nucleoside triphosphate hydrolases | TPR-like | 3 | 2 | |
| MoeA N-terminal region -like | Molybdenum cofactor biosynthesis proteins | 3 | 2 | |
| Ribosomal protein S5 domain 2-like | GHMP Kinase, C-terminal domain | 3 | 1 | |
| Leukotriene A4 hydrolase N-terminal domain | Metalloproteases ("zincins"), catalytic domain | 3 | 2 | |
| PLP-binding barrel | Alanine racemase C-terminal domain-like | 3 | 2 | |
| Thiamin diphosphate-binding fold (THDP-binding) | DHS-like NAD/FAD-binding domain | 3 | 1 | |
| 6-phosphogluconate dehydrogenase C-terminal domain-like | UDP-glucose/GDP-mannose dehydrogenase C-terminal domain | 3 | 1 | |
| GAF domain-like | CheY-like | 3 | 2 | |
| ValRS/IleRS/LeuRS editing domain | Nucleotidylyl transferase | 3 | 3 | |
| P-loop containing nucleoside triphosphate hydrolases | Restriction endonuclease-like | 3 | 2 | |
| Cation efflux protein transmembrane domain-like | Cation efflux protein cytoplasmic domain-like | 3 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | Alpha subunit of glutamate synthase, C-terminal domain | 3 | 2 | |
| Globin-like | Riboflavin synthase domain-like | 3 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Ribosomal protein S5 domain 2-like | 3 | 3 | |
| PH0987 N-terminal domain-like | Cyclophilin-like | 3 | 2 | |
| alpha/beta-Hydrolases | Galactose-binding domain-like | 3 | 2 | |
| Thiolase-like | FabD/lysophospholipase-like | 3 | 3 | |
| CO dehydrogenase molybdoprotein N-domain-like | Molybdenum cofactor-binding domain | 3 | 2 | |
| Chaperone J-domain | HSP40/DnaJ peptide-binding domain | 3 | 3 | |
| Nucleic acid-binding proteins | RuvA domain 2-like | 3 | 3 | |
| P-loop containing nucleoside triphosphate hydrolases | post-AAA+ oligomerization domain-like | 3 | 3 | |
| Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain | 3 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | Class I glutamine amidotransferase-like | 3 | 2 | |
| HSP40/DnaJ peptide-binding domain | HSP40/DnaJ peptide-binding domain | 3 | 3 | |
| L30e-like | alpha/beta knot | 3 | 2 | |
| GAF domain-like | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 3 | 3 | |
| ACT-like | ACT-like | 3 | 3 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | Nucleic acid-binding proteins | 3 | 3 | |
| ValRS/IleRS/LeuRS editing domain | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 3 | 3 | |
| E set domains | Glycosyl hydrolase domain | 3 | 3 | |
| Nudix | "Winged helix" DNA-binding domain | 3 | 1 | |
| MFS general substrate transporter | MFS general substrate transporter | 3 | 2 | |
| Formyltransferase | FMT C-terminal domain-like | 3 | 2 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | FMN-linked oxidoreductases | 3 | 2 | |
| Trypsin-like serine proteases | PDZ domain-like | 3 | 2 | |
| NAD(P)-binding Rossmann-fold domains | UDP-glucose/GDP-mannose dehydrogenase C-terminal domain | 3 | 1 | |
| Glutamine synthetase, N-terminal domain | Glutamine synthetase/guanido kinase | 3 | 1 | |
| EF-G C-terminal domain-like | EF-G C-terminal domain-like | 3 | 2 | |
| "Winged helix" DNA-binding domain | Acyl-CoA N-acyltransferases (Nat) | 3 | 2 | |
| FMN-linked oxidoreductases | Alpha subunit of glutamate synthase, C-terminal domain | 3 | 2 | |
| Thiolase-like | Probable ACP-binding domain of malonyl-CoA ACP transacylase | 3 | 3 | |
| CBS-domain pair | FAD-binding/transporter-associated domain-like | 3 | 1 | |
| 2Fe-2S ferredoxin-like | CO dehydrogenase ISP C-domain like | 3 | 2 | |
| Nucleic acid-binding proteins | Nucleic acid-binding proteins | 3 | 3 | |
| (Trans)glycosidases | Glycosyl hydrolase domain | 3 | 3 | |
| Globin-like | Ferredoxin reductase-like, C-terminal NADP-linked domain | 3 | 1 | |
| Nucleic acid-binding proteins | Translation proteins SH3-like domain | 2 | 2 | |
| Nitrite/Sulfite reductase N-terminal domain-like | Nitrite/Sulfite reductase N-terminal domain-like | 2 | 2 | |
| Regulatory protein AraC | Homeodomain-like | 2 | 2 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | Ribosomal protein S5 domain 2-like | 2 | 2 | |
| Nucleotide-diphospho-sugar transferases | Trimeric LpxA-like enzymes | 2 | 1 | |
| Probable ACP-binding domain of malonyl-CoA ACP transacylase | NAD(P)-binding Rossmann-fold domains | 2 | 2 | |
| IlvD/EDD N-terminal domain-like | LeuD/IlvD-like | 2 | 1 | |
| Nucleotide-binding domain | Nucleotide-binding domain | 2 | 2 | |
| MetI-like | P-loop containing nucleoside triphosphate hydrolases | 2 | 2 | |
| Sensory domain-like | Sporulation response regulatory protein Spo0B | 2 | 2 | |
| tRNA-binding arm | Class II aaRS and biotin synthetases | 2 | 1 | |
| N-terminal domain of alpha and beta subunits of F1 ATP synthase | P-loop containing nucleoside triphosphate hydrolases | 2 | 2 | |
| Mechanosensitive channel protein MscS (YggB), transmembrane region | Mechanosensitive channel protein MscS (YggB), C-terminal domain | 2 | 1 | |
| ParB/Sulfiredoxin | KorB DNA-binding domain-like | 2 | 1 | |
| Sigma3 and sigma4 domains of RNA polymerase sigma factors | NTF2-like | 2 | 1 | |
| Sm-like ribonucleoproteins | Mechanosensitive channel protein MscS (YggB), C-terminal domain | 2 | 1 | |
| Nucleotide-binding domain | FAD-linked reductases, C-terminal domain | 2 | 2 | |
| Alpha-L RNA-binding motif | Pseudouridine synthase | 2 | 2 | |
| Phosphohistidine domain | Phosphoenolpyruvate/pyruvate domain | 2 | 1 | |
| DNA/RNA polymerases | Lesion bypass DNA polymerase (Y-family), little finger domain | 2 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Aldolase | 2 | 1 | |
| Methylated DNA-protein cysteine methyltransferase domain | Methylated DNA-protein cysteine methyltransferase, C-terminal domain | 2 | 2 | |
| Lysozyme-like | LysM domain | 2 | 1 | |
| GroEL equatorial domain-like | GroEL-intermediate domain like | 2 | 1 | |
| Succinyl-CoA synthetase domains | Glutathione synthetase ATP-binding domain-like | 2 | 2 | |
| CO dehydrogenase ISP C-domain like | Molybdenum cofactor-binding domain | 2 | 1 | |
| NAD(P)-binding Rossmann-fold domains | TrkA C-terminal domain-like | 2 | 1 | |
| Flavoproteins | Ferredoxin reductase-like, C-terminal NADP-linked domain | 2 | 2 | |
| post-HMGL domain-like | 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain | 2 | 2 | |
| Sensory domain-like | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 2 | 2 | |
| CheY-like | "Winged helix" DNA-binding domain | 2 | 1 | |
| Glutathione synthetase ATP-binding domain-like | post-HMGL domain-like | 2 | 1 | |
| RmlC-like cupins | RmlC-like cupins | 2 | 2 | |
| PYP-like sensor domain (PAS domain) | CheY-like | 2 | 1 | |
| Iron-dependent repressor protein, dimerization domain | C-terminal domain of transcriptional repressors | 2 | 1 | |
| Flavoproteins | Riboflavin synthase domain-like | 2 | 2 | |
| PreATP-grasp domain | post-HMGL domain-like | 2 | 1 | |
| CBS-domain pair | Inosine monophosphate dehydrogenase (IMPDH) | 2 | 1 | |
| ClpP/crotonase | NAD(P)-binding Rossmann-fold domains | 2 | 1 | |
| 4Fe-4S ferredoxins | Nucleotide-binding domain | 2 | 2 | |
| PYP-like sensor domain (PAS domain) | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 2 | 2 | |
| UROD/MetE-like | UROD/MetE-like | 2 | 1 | |
| Single hybrid motif | ClpP/crotonase | 2 | 2 | |
| Actin-like ATPase domain | Heat shock protein 70kD (HSP70), peptide-binding domain | 2 | 2 | |
| Thioesterase/thiol ester dehydrase-isomerase | NAD(P)-binding Rossmann-fold domains | 2 | 2 | |
| ACP-like | Probable ACP-binding domain of malonyl-CoA ACP transacylase | 2 | 2 | |
| Fe,Mn superoxide dismutase (SOD), N-terminal domain | Fe,Mn superoxide dismutase (SOD), C-terminal domain | 2 | 1 | |
| ThrRS/AlaRS common domain | Class II aaRS and biotin synthetases | 2 | 2 | |
| Quinoprotein alcohol dehydrogenase-like | Quinoprotein alcohol dehydrogenase-like | 2 | 2 | |
| Nucleotidyltransferase | ACT-like | 2 | 2 | |
| 2Fe-2S ferredoxin-like | Molybdenum cofactor-binding domain | 2 | 1 | |
| 2Fe-2S ferredoxin-like | CO dehydrogenase molybdoprotein N-domain-like | 2 | 1 | |
| Acyl-CoA N-acyltransferases (Nat) | Acyl-CoA N-acyltransferases (Nat) | 2 | 2 | |
| Thioesterase/thiol ester dehydrase-isomerase | Nucleic acid-binding proteins | 2 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | C-terminal domain of alpha and beta subunits of F1 ATP synthase | 2 | 2 | |
| Sporulation response regulatory protein Spo0B | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 2 | 2 | |
| PreATP-grasp domain | ClpP/crotonase | 2 | 2 | |
| Ribosomal protein S5 domain 2-like | Ribosomal protein S5 domain 2-like | 2 | 2 | |
| HD-domain/PDEase-like | ACT-like | 2 | 2 | |
| 2Fe-2S ferredoxin-like | alpha-helical ferredoxin | 2 | 1 | |
| Nicotinate/Quinolinate PRTase N-terminal domain-like | Nicotinate/Quinolinate PRTase C-terminal domain-like | 2 | 1 | |
| ACP-like | Thiolase-like | 2 | 2 | |
| Molybdenum cofactor biosynthesis proteins | MoeA C-terminal domain-like | 2 | 1 | |
| Thioesterase/thiol ester dehydrase-isomerase | Thiolase-like | 2 | 2 | |
| Probable ACP-binding domain of malonyl-CoA ACP transacylase | Thioesterase/thiol ester dehydrase-isomerase | 2 | 2 | |
| Ribosomal protein S5 domain 2-like | Ribonuclease PH domain 2-like | 2 | 2 | |
| Rudiment single hybrid motif | ClpP/crotonase | 2 | 2 | |
| NAD(P)-binding Rossmann-fold domains | LDH C-terminal domain-like | 2 | 1 | |
| Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain | Phosphoenolpyruvate/pyruvate domain | 2 | 1 | |
| PIN domain-like | 5' to 3' exonuclease, C-terminal subdomain | 2 | 2 | |
| "Winged helix" DNA-binding domain | C-terminal domain of transcriptional repressors | 2 | 1 | |
| Aldolase | 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain | 2 | 2 | |
| 6-phosphogluconate dehydrogenase C-terminal domain-like | 6-phosphogluconate dehydrogenase C-terminal domain-like | 2 | 1 | |
| "Winged helix" DNA-binding domain | Iron-dependent repressor protein, dimerization domain | 2 | 1 | |
| Peptidase/esterase 'gauge' domain | alpha/beta-Hydrolases | 2 | 1 | |
| MurCD N-terminal domain | MurD-like peptide ligases, peptide-binding domain | 2 | 2 | |
| DnaJ/Hsp40 cysteine-rich domain | HSP40/DnaJ peptide-binding domain | 2 | 2 | |
| FabD/lysophospholipase-like | NAD(P)-binding Rossmann-fold domains | 2 | 2 | |
| CO dehydrogenase ISP C-domain like | CO dehydrogenase molybdoprotein N-domain-like | 2 | 1 | |
| MurE/MurF N-terminal domain | MurD-like peptide ligases, peptide-binding domain | 2 | 2 | |
| Coiled-coil domain of nucleotide exchange factor GrpE | Head domain of nucleotide exchange factor GrpE | 2 | 1 | |
| Cobalamin (vitamin B12)-dependent enzymes | Cobalamin (vitamin B12)-binding domain | 2 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Succinyl-CoA synthetase domains | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | "Winged helix" DNA-binding domain | 2 | 2 | |
| Creatinase/prolidase N-terminal domain | Creatinase/aminopeptidase | 2 | 1 | |
| Aspartate/glutamate racemase | Aspartate/glutamate racemase | 2 | 1 | |
| lambda integrase-like, N-terminal domain | DNA breaking-rejoining enzymes | 2 | 1 | |
| DPP6 N-terminal domain-like | beta-lactamase/transpeptidase-like | 2 | 1 | |
| Galactose-binding domain-like | Galactose-binding domain-like | 2 | 2 | |
| Nitrite/Sulfite reductase N-terminal domain-like | Nitrite and sulphite reductase 4Fe-4S domain-like | 2 | 2 | |
| Rudiment single hybrid motif | Aldolase | 2 | 1 | |
| ACP-like | FabD/lysophospholipase-like | 2 | 2 | |
| GAF domain-like | GAF domain-like | 2 | 2 | |
| Putative DNA-binding domain | Antibiotic binding domain of TipA-like multidrug resistance regulators | 2 | 2 | |
| GroEL-intermediate domain like | GroEL apical domain-like | 2 | 1 | |
| alpha/beta-Hydrolases | beta-lactamase/transpeptidase-like | 2 | 1 | |
| MoeA N-terminal region -like | MoeA C-terminal domain-like | 2 | 1 | |
| "Winged helix" DNA-binding domain | LexA/Signal peptidase | 2 | 1 | |
| Aldolase | Single hybrid motif | 2 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Thiolase-like | 2 | 2 | |
| NAD(P)-binding Rossmann-fold domains | ACT-like | 2 | 2 | |
| HAMP domain-like | Nucleotide cyclase | 2 | 2 | |
| TPR-like | Sec-C motif | 2 | 1 | |
| MurE/MurF N-terminal domain | MurD-like peptide ligases, catalytic domain | 2 | 2 | |
| Periplasmic binding protein-like II | MetI-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 | 2 | |
| Rudiment single hybrid motif | post-HMGL domain-like | 2 | 1 | |
| GroEL equatorial domain-like | GroEL apical domain-like | 2 | 1 | |
| Phospholipase D/nuclease | Phospholipase D/nuclease | 2 | 2 | |
| Nucleic acid-binding proteins | P-loop containing nucleoside triphosphate hydrolases | 2 | 2 | |
| CorA soluble domain-like | Magnesium transport protein CorA, transmembrane region | 2 | 1 | |
| alpha-helical ferredoxin | Nucleotide-binding domain | 2 | 2 | |
| Sigma2 domain of RNA polymerase sigma factors | NTF2-like | 2 | 1 | |
| NTF2-like | beta-lactamase/transpeptidase-like | 2 | 1 | |
| GAF domain-like | C-terminal effector domain of the bipartite response regulators | 2 | 1 | |
| HD-domain/PDEase-like | Nucleotidyltransferase | 2 | 2 | |
| FabD/lysophospholipase-like | Thioesterase/thiol ester dehydrase-isomerase | 2 | 2 | |
| Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase | Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase | 2 | 1 | |
| "Winged helix" DNA-binding domain | Actin-like ATPase domain | 2 | 1 | |
| Glutathione synthetase ATP-binding domain-like | ClpP/crotonase | 2 | 2 | |
| PreATP-grasp domain | Aldolase | 2 | 1 | |
| Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain | Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain | 2 | 2 | |
| post-HMGL domain-like | Single hybrid motif | 2 | 1 | |
| Mechanosensitive channel protein MscS (YggB), transmembrane region | Sm-like ribonucleoproteins | 2 | 1 | |
| MurCD N-terminal domain | MurD-like peptide ligases, catalytic domain | 2 | 2 | |
| Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain | Phosphohistidine domain | 2 | 1 | |
| ClpP/crotonase | 6-phosphogluconate dehydrogenase C-terminal domain-like | 2 | 1 | |
| Chaperone J-domain | DnaJ/Hsp40 cysteine-rich domain | 2 | 2 | |
| Putative DNA-binding domain | Anticodon-binding domain of PheRS | 1 | 1 | |
| LuxS/MPP-like metallohydrolase | LuxS/MPP-like metallohydrolase | 1 | 1 | |
| PUA domain-like | alpha/beta knot | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Glutathione synthetase ATP-binding domain-like | 1 | 1 | |
| GAF domain-like | Nucleotide cyclase | 1 | 1 | |
| C-terminal UvrC-binding domain of UvrB | RuvA domain 2-like | 1 | 1 | |
| Carbamoyl phosphate synthetase, large subunit connection domain | Methylglyoxal synthase-like | 1 | 1 | |
| Fumarylacetoacetate hydrolase, FAH, N-terminal domain | FAH | 1 | 1 | |
| Nqo1 middle domain-like | Nqo1C-terminal domain-like | 1 | 1 | |
| Glutamyl tRNA-reductase catalytic, N-terminal domain | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Heme-dependent peroxidases | Heme-dependent peroxidases | 1 | 1 | |
| PRC-barrel domain | CBS-domain pair | 1 | 1 | |
| beta-Galactosidase/glucuronidase domain | beta-Galactosidase/glucuronidase domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| PGBD-like | Zn-dependent exopeptidases | 1 | 1 | |
| Ribosomal protein L7/12, oligomerisation (N-terminal) domain | ClpS-like | 1 | 1 | |
| Protein kinase-like (PK-like) | TPR-like | 1 | 1 | |
| EF-G C-terminal domain-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| Acyl-CoA N-acyltransferases (Nat) | Succinyl-CoA synthetase domains | 1 | 1 | |
| 5' to 3' exonuclease, C-terminal subdomain | DNA/RNA polymerases | 1 | 1 | |
| alpha/beta-Hydrolases | alpha/beta-Hydrolases | 1 | 1 | |
| HAD-like | Glycerol-3-phosphate (1)-acyltransferase | 1 | 1 | |
| CBS-domain pair | Nucleotidyltransferase | 1 | 1 | |
| 4Fe-4S ferredoxins | Formate dehydrogenase/DMSO reductase, domains 1-3 | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | MesJ substrate recognition domain-like | 1 | 1 | |
| MFS general substrate transporter | Carboxypeptidase regulatory domain-like | 1 | 1 | |
| Nucleic acid-binding proteins | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| Class II aaRS and biotin synthetases | GAD domain-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | TGS-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Signal peptide-binding domain | 1 | 1 | |
| Tex N-terminal region-like | RuvA domain 2-like | 1 | 1 | |
| Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | ACT-like | 1 | 1 | |
| Putative DNA-binding domain | Putative DNA-binding domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | PEP carboxykinase-like | 1 | 1 | |
| Tetrapyrrole methylase | Tetrapyrrole methylase | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | Argininosuccinate synthetase, C-terminal domain | 1 | 1 | |
| Prokaryotic type KH domain (KH-domain type II) | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| Cryptochrome/photolyase, N-terminal domain | Cryptochrome/photolyase FAD-binding domain | 1 | 1 | |
| PurM N-terminal domain-like | PurM N-terminal domain-like | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Carbamoyl phosphate synthetase, large subunit connection domain | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | HSP90 C-terminal domain | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Methylglyoxal synthase-like | 1 | 1 | |
| Periplasmic binding protein-like II | vWA-like | 1 | 1 | |
| Duplicated hybrid motif | LysM domain | 1 | 1 | |
| Actin-crosslinking proteins | Metallo-dependent hydrolases | 1 | 1 | |
| PIN domain-like | Ribonuclease H-like | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | GMP synthetase C-terminal dimerisation domain | 1 | 1 | |
| Homo-oligomeric flavin-containing Cys decarboxylases, HFCD | CoaB-like | 1 | 1 | |
| Nucleic acid-binding proteins | BRCT domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | FtsH protease domain-like | 1 | 1 | |
| Translation proteins | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| 2Fe-2S ferredoxin-like | Formate dehydrogenase/DMSO reductase, domains 1-3 | 1 | 1 | |
| lambda repressor-like DNA-binding domains | Tetracyclin repressor-like, C-terminal domain | 1 | 1 | |
| Eukaryotic type KH-domain (KH-domain type I) | Nucleic acid-binding proteins | 1 | 1 | |
| Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | 1 | 1 | |
| PIN domain-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Zinc beta-ribbon | Prokaryotic SH3-related domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Helical scaffold and wing domains of SecA | 1 | 1 | |
| Serine metabolism enzymes domain | ACT-like | 1 | 1 | |
| ABC transporter transmembrane region | ABC transporter transmembrane region | 1 | 1 | |
| Type II DNA topoisomerase | Acyl-CoA N-acyltransferases (Nat) | 1 | 1 | |
| Ribonuclease H-like | HRDC-like | 1 | 1 | |
| Metal cation-transporting ATPase, ATP-binding domain N | HAD-like | 1 | 1 | |
| PreATP-grasp domain | PreATP-grasp domain | 1 | 1 | |
| Probable ACP-binding domain of malonyl-CoA ACP transacylase | alpha/beta-Hydrolases | 1 | 1 | |
| Periplasmic binding protein-like II | GlnB-like | 1 | 1 | |
| Folate-binding domain | Aminomethyltransferase beta-barrel domain | 1 | 1 | |
| Class II aaRS and biotin synthetases | YbaK/ProRS associated domain | 1 | 1 | |
| 4Fe-4S ferredoxins | ADC-like | 1 | 1 | |
| PRC-barrel domain | MgtE N-terminal domain-like | 1 | 1 | |
| FabD/lysophospholipase-like | FabD/lysophospholipase-like | 1 | 1 | |
| Nucleic acid-binding proteins | Anticodon-binding domain of PheRS | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | ACT-like | 1 | 1 | |
| Duplicated hybrid motif | Cysteine proteinases | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | C-terminal UvrC-binding domain of UvrB | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | Type II DNA topoisomerase | 1 | 1 | |
| Penicillin binding protein dimerisation domain | beta-lactamase/transpeptidase-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Initiation factor IF2/eIF5b, domain 3 | 1 | 1 | |
| Molybdenum cofactor biosynthesis protein C, MoaC | Molybdenum cofactor biosynthesis proteins | 1 | 1 | |
| TGS-like | ACT-like | 1 | 1 | |
| Acyl-CoA N-acyltransferases (Nat) | Glutathione synthetase ATP-binding domain-like | 1 | 1 | |
| Carbamate kinase-like | PUA domain-like | 1 | 1 | |
| Single hybrid motif | Single hybrid motif | 1 | 1 | |
| Translation proteins | ThrRS/AlaRS common domain | 1 | 1 | |
| Carbamate kinase-like | ACT-like | 1 | 1 | |
| Cupredoxins | Integrin alpha N-terminal domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | HprK N-terminal domain-like | 1 | 1 | |
| Tex N-terminal region-like | Ribonuclease H-like | 1 | 1 | |
| beta-lactamase/transpeptidase-like | cAMP-binding domain-like | 1 | 1 | |
| Putative DNA-binding domain | DNA clamp | 1 | 1 | |
| TTHA1013/TTHA0281-like | Ribbon-helix-helix | 1 | 1 | |
| Homeodomain-like | SIS domain | 1 | 1 | |
| Radical SAM enzymes | Radical SAM enzymes | 1 | 1 | |
| PurM C-terminal domain-like | PurM C-terminal domain-like | 1 | 1 | |
| RNase III domain-like | dsRNA-binding domain-like | 1 | 1 | |
| Nucleotidylyl transferase | An anticodon-binding domain of class I aminoacyl-tRNA synthetases | 1 | 1 | |
| Metallo-dependent phosphatases | 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain | 1 | 1 | |
| Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | Translation proteins | 1 | 1 | |
| Ribonuclease H-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| YjeF N-terminal domain-like | Ribokinase-like | 1 | 1 | |
| Putative DNA-binding domain | lambda repressor-like DNA-binding domains | 1 | 1 | |
| Tryptophan synthase beta subunit-like PLP-dependent enzymes | CBS-domain pair | 1 | 1 | |
| RuvA domain 2-like | RuvA domain 2-like | 1 | 1 | |
| (Phosphotyrosine protein) phosphatases II | Macro domain-like | 1 | 1 | |
| PheT/TilS domain | Anticodon-binding domain of PheRS | 1 | 1 | |
| PIN domain-like | DNA/RNA polymerases | 1 | 1 | |
| Phosphoenolpyruvate/pyruvate domain | PK C-terminal domain-like | 1 | 1 | |
| Ribonuclease H-like | Nucleic acid-binding proteins | 1 | 1 | |
| Nucleotidyltransferase | Nucleotidyltransferase substrate binding subunit/domain | 1 | 1 | |
| Aromatic compound dioxygenase | Aromatic compound dioxygenase | 1 | 1 | |
| PK beta-barrel domain-like | Phosphoenolpyruvate/pyruvate domain | 1 | 1 | |
| FAD/NAD(P)-binding domain | Nitrite and sulphite reductase 4Fe-4S domain-like | 1 | 1 | |
| Probable ACP-binding domain of malonyl-CoA ACP transacylase | Inosine monophosphate dehydrogenase (IMPDH) | 1 | 1 | |
| Nucleotidylyl transferase | Alpha-L RNA-binding motif | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Homeodomain-like | 1 | 1 | |
| Nqo1 FMN-binding domain-like | Nqo1C-terminal domain-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | vWA-like | 1 | 1 | |
| HMA, heavy metal-associated domain | HAD-like | 1 | 1 | |
| Alpha-L RNA-binding motif | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | CBS-domain pair | 1 | 1 | |
| Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 1 | 1 | |
| ADC-like | Ferredoxin reductase-like, C-terminal NADP-linked domain | 1 | 1 | |
| PheT/TilS domain | Class II aaRS and biotin synthetases | 1 | 1 | |
| cAMP-binding domain-like | FAD/NAD(P)-binding domain | 1 | 1 | |
| Cytochrome c | Cytochrome c | 1 | 1 | |
| Rhomboid-like | Acyl-CoA N-acyltransferases (Nat) | 1 | 1 | |
| Eukaryotic type KH-domain (KH-domain type I) | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Actin-like ATPase domain | Heat shock protein 70kD (HSP70), C-terminal subdomain | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Glutathione synthetase ATP-binding domain-like | 1 | 1 | |
| Class II aaRS and biotin synthetases | Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | 1 | 1 | |
| RuvA domain 2-like | BRCT domain | 1 | 1 | |
| Formate dehydrogenase/DMSO reductase, domains 1-3 | Riboflavin synthase domain-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | TrpR-like | 1 | 1 | |
| Galactose-binding domain-like | (Trans)glycosidases | 1 | 1 | |
| HemD-like | C-terminal effector domain of the bipartite response regulators | 1 | 1 | |
| alpha-D-mannose-specific plant lectins | LysM domain | 1 | 1 | |
| ADP-ribosylglycohydrolase | Macro domain-like | 1 | 1 | |
| PPK N-terminal domain-like | Phospholipase D/nuclease | 1 | 1 | |
| Nucleotide-diphospho-sugar transferases | Molybdenum cofactor biosynthesis proteins | 1 | 1 | |
| Homeodomain-like | Probable bacterial effector-binding domain | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | HSP90 C-terminal domain | 1 | 1 | |
| Ribosomal protein L6 | Ribosomal protein L6 | 1 | 1 | |
| Ribonuclease PH domain 2-like | Nucleic acid-binding proteins | 1 | 1 | |
| Putative DNA-binding domain | Class II aaRS and biotin synthetases | 1 | 1 | |
| Composite domain of metallo-dependent hydrolases | Composite domain of metallo-dependent hydrolases | 1 | 1 | |
| GreA transcript cleavage protein, N-terminal domain | FKBP-like | 1 | 1 | |
| HMA, heavy metal-associated domain | Calcium ATPase, transduction domain A | 1 | 1 | |
| Glutamyl tRNA-reductase catalytic, N-terminal domain | Glutamyl tRNA-reductase dimerization domain | 1 | 1 | |
| Tex N-terminal region-like | Nucleic acid-binding proteins | 1 | 1 | |
| Alkaline phosphatase-like | Concanavalin A-like lectins/glucanases | 1 | 1 | |
| Homocysteine S-methyltransferase | Dihydropteroate synthetase-like | 1 | 1 | |
| Ribonuclease PH domain 2-like | Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | 1 | 1 | |
| Voltage-gated potassium channels | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| "Winged helix" DNA-binding domain | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| Nucleotidylyl transferase | Riboflavin kinase-like | 1 | 1 | |
| Acid phosphatase/Vanadium-dependent haloperoxidase | NAD kinase/diacylglycerol kinase-like | 1 | 1 | |
| YbaK/ProRS associated domain | Class II aaRS ABD-related | 1 | 1 | |
| "Winged helix" DNA-binding domain | C-terminal domain of arginine repressor | 1 | 1 | |
| Cytidine deaminase-like | Dihydrofolate reductase-like | 1 | 1 | |
| cAMP-binding domain-like | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | RecA protein, C-terminal domain | 1 | 1 | |
| HprK N-terminal domain-like | Isocitrate/Isopropylmalate dehydrogenase-like | 1 | 1 | |
| HAD-like | Six-hairpin glycosidases | 1 | 1 | |
| RBP11-like subunits of RNA polymerase | C-terminal domain of RNA polymerase alpha subunit | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | 1 | 1 | |
| Nucleotidylyl transferase | tRNA-binding arm | 1 | 1 | |
| PHP14-like | Phospholipase D/nuclease | 1 | 1 | |
| Cytochrome c oxidase subunit II-like, transmembrane region | Cupredoxins | 1 | 1 | |
| Dihydropteroate synthetase-like | Cobalamin (vitamin B12)-binding domain | 1 | 1 | |
| Nucleotide-diphospho-sugar transferases | MoeA N-terminal region -like | 1 | 1 | |
| PheT/TilS domain | Putative DNA-binding domain | 1 | 1 | |
| Ribonuclease H-like | GIY-YIG endonuclease | 1 | 1 | |
| CoA-transferase family III (CaiB/BaiF) | CoA-transferase family III (CaiB/BaiF) | 1 | 1 | |
| Formyltransferase | ClpP/crotonase | 1 | 1 | |
| Ribonuclease H-like | DNA/RNA polymerases | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Nucleic acid-binding proteins | 1 | 1 | |
| MFS general substrate transporter | Class II aaRS and biotin synthetases | 1 | 1 | |
| Thiolase-like | alpha/beta-Hydrolases | 1 | 1 | |
| FabD/lysophospholipase-like | alpha/beta-Hydrolases | 1 | 1 | |
| ValRS/IleRS/LeuRS editing domain | tRNA-binding arm | 1 | 1 | |
| "Winged helix" DNA-binding domain | SCP-like | 1 | 1 | |
| Nucleotidyltransferase substrate binding subunit/domain | Nucleotidyltransferase substrate binding subunit/domain | 1 | 1 | |
| TK C-terminal domain-like | Pyruvate-ferredoxin oxidoreductase, PFOR, domain III | 1 | 1 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | RuvA domain 2-like | 1 | 1 | |
| Methylglyoxal synthase-like | Cytidine deaminase-like | 1 | 1 | |
| FKBP-like | Triger factor/SurA peptide-binding domain-like | 1 | 1 | |
| Methionine synthase domain | Cobalamin (vitamin B12)-binding domain | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Type II DNA topoisomerase | 1 | 1 | |
| "Winged helix" DNA-binding domain | NagB/RpiA/CoA transferase-like | 1 | 1 | |
| Metallo-hydrolase/oxidoreductase | ISP domain | 1 | 1 | |
| Tetrapyrrole methylase | HemD-like | 1 | 1 | |
| Zinc beta-ribbon | DNA primase core | 1 | 1 | |
| Prokaryotic type KH domain (KH-domain type II) | Ribosomal protein S3 C-terminal domain | 1 | 1 | |
| Nucleic acid-binding proteins | Putative DNA-binding domain | 1 | 1 | |
| cAMP-binding domain-like | "Winged helix" DNA-binding domain | 1 | 1 | |
| Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | Nucleic acid-binding proteins | 1 | 1 | |
| GIY-YIG endonuclease | RuvA domain 2-like | 1 | 1 | |
| CofE-like | FMN-dependent nitroreductase-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Nucleotidyltransferase | 1 | 1 | |
| "Winged helix" DNA-binding domain | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | DNA ligase/mRNA capping enzyme, catalytic domain | 1 | 1 | |
| Nucleic acid-binding proteins | DNA helicase RuvA subunit, C-terminal domain | 1 | 1 | |
| DinB/YfiT-like putative metalloenzymes | C-type lectin-like | 1 | 1 | |
| FAD-binding/transporter-associated domain-like | Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain | 1 | 1 | |
| NHL repeat | Cadherin-like | 1 | 1 | |
| NusB-like | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| Cobalamin (vitamin B12)-binding domain | Methionine synthase activation domain-like | 1 | 1 | |
| NagB/RpiA/CoA transferase-like | 4Fe-4S ferredoxins | 1 | 1 | |
| beta-Galactosidase/glucuronidase domain | (Trans)glycosidases | 1 | 1 | |
| Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain | Pyrimidine nucleoside phosphorylase C-terminal domain | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | Adenine nucleotide alpha hydrolases-like | 1 | 1 | |
| Acyl-CoA N-acyltransferases (Nat) | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain | 1 | 1 | |
| Metallo-dependent phosphatases | DNA ligase/mRNA capping enzyme, catalytic domain | 1 | 1 | |
| Macro domain-like | Zn-dependent exopeptidases | 1 | 1 | |
| PEP carboxykinase N-terminal domain | PEP carboxykinase-like | 1 | 1 | |
| Nudix | Phosphoglycerate mutase-like | 1 | 1 | |
| 2Fe-2S ferredoxin-like | ADC-like | 1 | 1 | |
| Oxidoreductase molybdopterin-binding domain | E set domains | 1 | 1 | |
| Insert subdomain of RNA polymerase alpha subunit | RBP11-like subunits of RNA polymerase | 1 | 1 | |
| Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | Eukaryotic type KH-domain (KH-domain type I) | 1 | 1 | |
| PLP-dependent transferases | PLP-dependent transferases | 1 | 1 | |
| CoA-dependent acyltransferases | Thiamin diphosphate-binding fold (THDP-binding) | 1 | 1 | |
| Dihydropteroate synthetase-like | Methionine synthase domain | 1 | 1 | |
| Trigger factor ribosome-binding domain | FKBP-like | 1 | 1 | |
| Nqo1 FMN-binding domain-like | Nqo1 middle domain-like | 1 | 1 | |
| Glycoside hydrolase/deacetylase | Families 57/38 glycoside transferase middle domain | 1 | 1 | |
| Homocysteine S-methyltransferase | Methionine synthase activation domain-like | 1 | 1 | |
| ACT-like | HAD-like | 1 | 1 | |
| Rho N-terminal domain-like | Nucleic acid-binding proteins | 1 | 1 | |
| PreATP-grasp domain | Carbamoyl phosphate synthetase, large subunit connection domain | 1 | 1 | |
| Formate dehydrogenase/DMSO reductase, domains 1-3 | Ferredoxin reductase-like, C-terminal NADP-linked domain | 1 | 1 | |
| Acyl-CoA N-acyltransferases (Nat) | SCP-like | 1 | 1 | |
| S-adenosyl-L-methionine-dependent methyltransferases | Putative methyltransferase TM0872, insert domain | 1 | 1 | |
| ACP-like | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| MFS general substrate transporter | Nucleic acid-binding proteins | 1 | 1 | |
| Class II aaRS and biotin synthetases | Anticodon-binding domain of PheRS | 1 | 1 | |
| Metallo-hydrolase/oxidoreductase | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Putative DNA-binding domain | Probable bacterial effector-binding domain | 1 | 1 | |
| FMN-linked oxidoreductases | Nucleotide-binding domain | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Tetrapyrrole methylase | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | SIS domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Hypothetical protein YjiA, C-terminal domain | 1 | 1 | |
| Transcription factor NusA, N-terminal domain | Nucleic acid-binding proteins | 1 | 1 | |
| Phoshotransferase/anion transport protein | PTS system IIB component-like | 1 | 1 | |
| Nucleic acid-binding proteins | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| GIY-YIG endonuclease | C-terminal UvrC-binding domain of UvrB | 1 | 1 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | BRCT domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Quinoprotein alcohol dehydrogenase-like | 1 | 1 | |
| PPK N-terminal domain-like | PHP14-like | 1 | 1 | |
| Acetyl-CoA synthetase-like | Trimeric LpxA-like enzymes | 1 | 1 | |
| Obg GTP-binding protein N-terminal domain | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| YrdC/RibB | RibA-like | 1 | 1 | |
| Ribonuclease PH domain 2-like | Ribonuclease PH domain 2-like | 1 | 1 | |
| ADC-like | Flavoproteins | 1 | 1 | |
| DAK1/DegV-like | DhaL-like | 1 | 1 | |
| MFS general substrate transporter | HAMP domain-like | 1 | 1 | |
| CheY-like | FAD/NAD(P)-binding domain | 1 | 1 | |
| (Trans)glycosidases | Beta-D-glucan exohydrolase, C-terminal domain | 1 | 1 | |
| 2Fe-2S ferredoxin-like | 4Fe-4S ferredoxins | 1 | 1 | |
| Glucocorticoid receptor-like (DNA-binding domain) | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| E set domains | E set domains | 1 | 1 | |
| 5' to 3' exonuclease, C-terminal subdomain | Ribonuclease H-like | 1 | 1 | |
| Formate dehydrogenase/DMSO reductase, domains 1-3 | Flavoproteins | 1 | 1 | |
| Fe-S cluster assembly (FSCA) 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 | |
| alpha/beta-Hydrolases | AhpD-like | 1 | 1 | |
| Xylose isomerase-like | Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase | 1 | 1 | |
| NagB/RpiA/CoA transferase-like | NagB/RpiA/CoA transferase-like | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | Homodimeric domain of signal transducing histidine kinase | 1 | 1 | |
| YajQ-like | YajQ-like | 1 | 1 | |
| Putative DNA-binding domain | ARM repeat | 1 | 1 | |
| YojJ-like | RuvA domain 2-like | 1 | 1 | |
| FMT C-terminal domain-like | ClpP/crotonase | 1 | 1 | |
| Trimeric LpxA-like enzymes | Trimeric LpxA-like enzymes | 1 | 1 | |
| lambda repressor-like DNA-binding domains | lambda repressor-like DNA-binding domains | 1 | 1 | |
| Class I glutamine amidotransferase-like | GMP synthetase C-terminal dimerisation domain | 1 | 1 | |
| CarD-like | TRCF domain-like | 1 | 1 | |
| Pentapeptide repeat-like | Pentapeptide repeat-like | 1 | 1 | |
| Carboxypeptidase regulatory domain-like | Cna protein B-type domain | 1 | 1 | |
| lambda repressor-like DNA-binding domains | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| Nucleic acid-binding proteins | PheT/TilS domain | 1 | 1 | |
| "Winged helix" DNA-binding domain | Bet v1-like | 1 | 1 | |
| ALDH-like | Thioesterase/thiol ester dehydrase-isomerase | 1 | 1 | |
| Periplasmic binding protein-like II | Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Bet v1-like | 1 | 1 | |
| Acylphosphatase/BLUF domain-like | YrdC/RibB | 1 | 1 | |
| Inosine monophosphate dehydrogenase (IMPDH) | Thiolase-like | 1 | 1 | |
| Domain of the SRP/SRP receptor G-proteins | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | C-terminal effector domain of the bipartite response regulators | 1 | 1 | |
| R1 subunit of ribonucleotide reductase, N-terminal domain | PFL-like glycyl radical enzymes | 1 | 1 | |
| PK beta-barrel domain-like | PK C-terminal domain-like | 1 | 1 | |
| Trigger factor ribosome-binding domain | Triger factor/SurA peptide-binding domain-like | 1 | 1 | |
| NTF2-like | FAD/NAD(P)-binding domain | 1 | 1 | |
| ADP-ribosylglycohydrolase | (Phosphotyrosine protein) phosphatases II | 1 | 1 | |
| Translation proteins | Initiation factor IF2/eIF5b, domain 3 | 1 | 1 | |
| PDZ domain-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | TRCF domain-like | 1 | 1 | |
| Cyclophilin-like | Cyclophilin-like | 1 | 1 | |
| Homocysteine S-methyltransferase | Cobalamin (vitamin B12)-binding domain | 1 | 1 | |
| Insert subdomain of RNA polymerase alpha subunit | C-terminal domain of RNA polymerase alpha subunit | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Glutamyl tRNA-reductase dimerization domain | 1 | 1 | |
| Translation proteins | Translation proteins | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | DHS-like NAD/FAD-binding domain | 1 | 1 | |
| Tetrapyrrole methylase | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| Homeodomain-like | NagB/RpiA/CoA transferase-like | 1 | 1 | |
| Periplasmic binding protein-like II | ACT-like | 1 | 1 | |
| HMA, heavy metal-associated domain | Calcium ATPase, transmembrane domain M | 1 | 1 | |
| Aconitase iron-sulfur domain | LeuD/IlvD-like | 1 | 1 | |
| PA domain | Zn-dependent exopeptidases | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Serine metabolism enzymes domain | 1 | 1 | |
| S-adenosylmethionine synthetase | S-adenosylmethionine synthetase | 1 | 1 | |
| dsRNA-binding domain-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| Nucleotide-binding domain | FAD/NAD(P)-binding domain | 1 | 1 | |
| Thioredoxin-like | Six-hairpin glycosidases | 1 | 1 | |
| DNA clamp | DNA clamp | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | CarD-like | 1 | 1 | |
| E set domains | alpha/beta-Hydrolases | 1 | 1 | |
| Ribonuclease H-like | RuvA domain 2-like | 1 | 1 | |
| Translation proteins | PRC-barrel domain | 1 | 1 | |
| PreATP-grasp domain | Methylglyoxal synthase-like | 1 | 1 | |
| Pre-protein crosslinking domain of SecA | Helical scaffold and wing domains of SecA | 1 | 1 | |
| Sensory domain-like | PYP-like sensor domain (PAS domain) | 1 | 1 | |
| Obg GTP-binding protein N-terminal domain | Obg GTP-binding protein C-terminal domain | 1 | 1 | |
| PGBD-like | PGBD-like | 1 | 1 | |
| ADC-like | Riboflavin synthase domain-like | 1 | 1 | |
| FAD-binding/transporter-associated domain-like | CO dehydrogenase flavoprotein C-terminal domain-like | 1 | 1 | |
| NAD-binding domain of HMG-CoA reductase | Substrate-binding domain of HMG-CoA reductase | 1 | 1 | |
| FabD/lysophospholipase-like | Inosine monophosphate dehydrogenase (IMPDH) | 1 | 1 | |
| FAD/NAD(P)-binding domain | Nitrite/Sulfite reductase N-terminal domain-like | 1 | 1 | |
| Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain | Nucleotidylyl transferase | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Isocitrate/Isopropylmalate dehydrogenase-like | 1 | 1 | |
| Thioredoxin-like | GST C-terminal domain-like | 1 | 1 | |
| ThrRS/AlaRS common domain | Class II aaRS ABD-related | 1 | 1 | |
| HD-domain/PDEase-like | TGS-like | 1 | 1 | |
| Methionine synthase domain | Methionine synthase activation domain-like | 1 | 1 | |
| Aminopeptidase/glucanase lid domain | Zn-dependent exopeptidases | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 1 | 1 | |
| Thiamin diphosphate-binding fold (THDP-binding) | Pyruvate-ferredoxin oxidoreductase, PFOR, domain III | 1 | 1 | |
| Riboflavin synthase domain-like | Riboflavin synthase domain-like | 1 | 1 | |
| Nucleotidyltransferase | TGS-like | 1 | 1 | |
| PYP-like sensor domain (PAS domain) | Sporulation response regulatory protein Spo0B | 1 | 1 | |
| Formin homology 2 domain (FH2 domain) | Quinoprotein alcohol dehydrogenase-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Smc hinge domain | 1 | 1 | |
| PLP-binding barrel | Arginase/deacetylase | 1 | 1 | |
| Heme-dependent catalase-like | Class I glutamine amidotransferase-like | 1 | 1 | |
| Rho N-terminal domain-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Metal cation-transporting ATPase, ATP-binding domain N | Calcium ATPase, transmembrane domain M | 1 | 1 | |
| Formate/glycerate dehydrogenase catalytic domain-like | Serine metabolism enzymes domain | 1 | 1 | |
| Glutamine synthetase/guanido kinase | GatB/YqeY motif | 1 | 1 | |
| Tubulin nucleotide-binding domain-like | Tubulin C-terminal domain-like | 1 | 1 | |
| Homocysteine S-methyltransferase | Methionine synthase domain | 1 | 1 | |
| Nitrite and sulphite reductase 4Fe-4S domain-like | Nitrite and sulphite reductase 4Fe-4S domain-like | 1 | 1 | |
| MFS general substrate transporter | Nucleotide cyclase | 1 | 1 | |
| Putative DNA-binding domain | RmlC-like cupins | 1 | 1 | |
| Elongation factor Ts (EF-Ts), dimerisation domain | Elongation factor Ts (EF-Ts), dimerisation domain | 1 | 1 | |
| Ribonuclease H-like | Phosphoglycerate mutase-like | 1 | 1 | |
| L9 N-domain-like | Ribosomal protein L9 C-domain | 1 | 1 | |
| Type II DNA topoisomerase | GyrA/ParC C-terminal domain-like | 1 | 1 | |
| Protein kinase-like (PK-like) | LanC-like | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain | 1 | 1 | |
| Metallo-hydrolase/oxidoreductase | Rhodanese/Cell cycle control phosphatase | 1 | 1 | |
| Formate/glycerate dehydrogenase catalytic domain-like | ACT-like | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | PRTase-like | 1 | 1 | |
| Fe-S cluster assembly (FSCA) domain-like | ISP domain | 1 | 1 | |
| ACP-like | Trimeric LpxA-like enzymes | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Obg GTP-binding protein C-terminal domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | PRTase-like | 1 | 1 | |
| UBA-like | Elongation factor Ts (EF-Ts), dimerisation domain | 1 | 1 | |
| MFS general substrate transporter | Cna protein B-type domain | 1 | 1 | |
| Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 1 | 1 | |
| Class I glutamine amidotransferase-like | Adenine nucleotide alpha hydrolases-like | 1 | 1 | |
| Inosine monophosphate dehydrogenase (IMPDH) | Thioesterase/thiol ester dehydrase-isomerase | 1 | 1 | |
| Carbamoyl phosphate synthetase, small subunit N-terminal domain | Class I glutamine amidotransferase-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Metallo-dependent phosphatases | 1 | 1 | |
| Class II aaRS and biotin synthetases | Translation proteins | 1 | 1 | |
| Diaminopimelate epimerase-like | Diaminopimelate epimerase-like | 1 | 1 | |
| Succinyl-CoA synthetase domains | Succinyl-CoA synthetase domains | 1 | 1 | |
| Tetrahydrobiopterin biosynthesis enzymes-like | Tetrahydrobiopterin biosynthesis enzymes-like | 1 | 1 | |
| NTF2-like | NTF2-like | 1 | 1 | |
| ACT-like | Formyltransferase | 1 | 1 | |
| Nucleotidyltransferase | Poly A polymerase C-terminal region-like | 1 | 1 | |
| ACP-like | Thioesterase/thiol ester dehydrase-isomerase | 1 | 1 | |
| Transcription factor NusA, N-terminal domain | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| Dihydropteroate synthetase-like | Nitrite and sulphite reductase 4Fe-4S domain-like | 1 | 1 | |
| MgtE N-terminal domain-like | CBS-domain pair | 1 | 1 | |
| Nucleic acid-binding proteins | GAD domain-like | 1 | 1 | |
| Inosine monophosphate dehydrogenase (IMPDH) | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | HRDC-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Pre-protein crosslinking domain of SecA | 1 | 1 | |
| lambda repressor-like DNA-binding domains | Homeodomain-like | 1 | 1 | |
| TATA-box binding protein-like | DNA-glycosylase | 1 | 1 | |
| Galactose-binding domain-like | beta-Galactosidase/glucuronidase domain | 1 | 1 | |
| HIT-like | HIT-like | 1 | 1 | |
| Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain | Pyrimidine nucleoside phosphorylase C-terminal domain | 1 | 1 | |
| Pseudouridine synthase | PUA domain-like | 1 | 1 | |
| Nucleotidyltransferase | Nucleotidyltransferase | 1 | 1 | |
| Class I glutamine amidotransferase-like | ADC synthase | 1 | 1 | |
| N-utilization substance G protein NusG, N-terminal domain | Translation proteins SH3-like domain | 1 | 1 | |
| Heat shock protein 70kD (HSP70), peptide-binding domain | Heat shock protein 70kD (HSP70), C-terminal subdomain | 1 | 1 | |
| Ribonuclease H-like | BRCT domain | 1 | 1 | |
| Ribonuclease PH domain 2-like | Eukaryotic type KH-domain (KH-domain type I) | 1 | 1 | |
| Dihydropteroate synthetase-like | Methionine synthase activation domain-like | 1 | 1 | |
| Nucleic acid-binding proteins | ArfGap/RecO-like zinc finger | 1 | 1 | |
| N-terminal domain of DnaB helicase | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Sec-C motif | NTF2-like | 1 | 1 | |
| Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | ThrRS/AlaRS common domain | 1 | 1 | |
| Calcium ATPase, transduction domain A | Metal cation-transporting ATPase, ATP-binding domain N | 1 | 1 | |
| Ribosomal L11/L12e N-terminal domain | Ribosomal protein L11, C-terminal domain | 1 | 1 | |
| ADC-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| RuvA domain 2-like | DNA helicase RuvA subunit, C-terminal domain | 1 | 1 | |
| DNA polymerase beta, N-terminal domain-like | PHP domain-like | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Eukaryotic type KH-domain (KH-domain type I) | 1 | 1 | |
| Lysozyme-like | Cysteine proteinases | 1 | 1 | |
| Translation initiation factor IF3, N-terminal domain | Translation initiation factor IF3, C-terminal domain | 1 | 1 | |
