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 | |
|---|
| Homodimeric domain of signal transducing histidine kinase | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 43 | 23 |  |
| PYP-like sensor domain (PAS domain) | GAF domain-like | 32 | 29 | |
| PYP-like sensor domain (PAS domain) | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 30 | 21 | |
| PYP-like sensor domain (PAS domain) | PYP-like sensor domain (PAS domain) | 27 | 23 | |
| PYP-like sensor domain (PAS domain) | Homodimeric domain of signal transducing histidine kinase | 26 | 17 | |
| NAD(P)-binding Rossmann-fold domains | Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 24 | 2 | |
| GroES-like | NAD(P)-binding Rossmann-fold domains | 23 | 2 | |
| "Winged helix" DNA-binding domain | GAF domain-like | 23 | 3 | |
| Thiolase-like | Thiolase-like | 21 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | "Winged helix" DNA-binding domain | 21 | 5 | |
| NAD(P)-binding Rossmann-fold domains | 6-phosphogluconate dehydrogenase C-terminal domain-like | 19 | 4 | |
| GAF domain-like | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 19 | 17 | |
| Acyl-CoA dehydrogenase NM domain-like | Acyl-CoA dehydrogenase C-terminal domain-like | 18 | 2 | |
| GAF domain-like | Homodimeric domain of signal transducing histidine kinase | 16 | 14 | |
| Enolase N-terminal domain-like | Enolase C-terminal domain-like | 14 | 1 | |
| GAF domain-like | GAF domain-like | 13 | 13 | |
| Aminoacid dehydrogenase-like, N-terminal domain | NAD(P)-binding Rossmann-fold domains | 12 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | P-loop containing nucleoside triphosphate hydrolases | 12 | 7 | |
| Adenine nucleotide alpha hydrolases-like | Adenine nucleotide alpha hydrolases-like | 11 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | MOP-like | 11 | 2 | |
| Composite domain of metallo-dependent hydrolases | Metallo-dependent hydrolases | 11 | 3 | |
| Multidrug resistance efflux transporter EmrE | Multidrug resistance efflux transporter EmrE | 10 | 3 | |
| Formate dehydrogenase/DMSO reductase, domains 1-3 | ADC-like | 9 | 4 | |
| FAD/NAD(P)-binding domain | FAD-linked reductases, C-terminal domain | 9 | 3 | |
| NAD(P)-binding Rossmann-fold domains | TrkA C-terminal domain-like | 9 | 4 | |
| Aldehyde ferredoxin oxidoreductase, N-terminal domain | Aldehyde ferredoxin oxidoreductase, C-terminal domains | 8 | 1 | |
| Thiamin diphosphate-binding fold (THDP-binding) | Thiamin diphosphate-binding fold (THDP-binding) | 8 | 2 | |
| Galactose-binding domain-like | (Trans)glycosidases | 8 | 7 | |
| TrkA C-terminal domain-like | TrkA C-terminal domain-like | 8 | 4 | |
| "Winged helix" DNA-binding domain | Dimeric alpha+beta barrel | 8 | 1 | |
| Quinoprotein alcohol dehydrogenase-like | Quinoprotein alcohol dehydrogenase-like | 8 | 3 | |
| Cupredoxins | Cupredoxins | 7 | 4 | |
| Nucleotidylyl transferase | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 7 | 6 | |
| (Trans)glycosidases | Glycosyl hydrolase domain | 7 | 6 | |
| Formate/glycerate dehydrogenase catalytic domain-like | NAD(P)-binding Rossmann-fold domains | 7 | 2 | |
| Thiamin diphosphate-binding fold (THDP-binding) | DHS-like NAD/FAD-binding domain | 7 | 1 | |
| Zn-dependent exopeptidases | Bacterial exopeptidase dimerisation domain | 7 | 1 | |
| beta-Galactosidase/glucuronidase domain | (Trans)glycosidases | 6 | 5 | |
| Cyclin-like | Cyclin-like | 6 | 1 | |
| Galactose-binding domain-like | beta-Galactosidase/glucuronidase domain | 6 | 5 | |
| Periplasmic binding protein-like II | Periplasmic binding protein-like II | 6 | 2 | |
| FAD/NAD(P)-binding domain | FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 6 | 2 | |
| Calcium ATPase, transduction domain A | HAD-like | 6 | 5 | |
| Thiamin diphosphate-binding fold (THDP-binding) | TK C-terminal domain-like | 6 | 3 | |
| PurM N-terminal domain-like | PurM C-terminal domain-like | 6 | 2 | |
| Creatinase/prolidase N-terminal domain | Creatinase/aminopeptidase | 6 | 1 | |
| Zinc beta-ribbon | Cyclin-like | 6 | 1 | |
| CheY-like | GAF domain-like | 6 | 6 | |
| Sm-like ribonucleoproteins | Mechanosensitive channel protein MscS (YggB), C-terminal domain | 5 | 5 | |
| FAD/NAD(P)-binding domain | FAD/NAD(P)-binding domain | 5 | 3 | |
| PYP-like sensor domain (PAS domain) | Sigma3 and sigma4 domains of RNA polymerase sigma factors | 5 | 4 | |
| PreATP-grasp domain | Glutathione synthetase ATP-binding domain-like | 5 | 4 | |
| HAD-like | Calcium ATPase, transmembrane domain M | 5 | 4 | |
| FAD/NAD(P)-binding domain | Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | 5 | 4 | |
| Calcium ATPase, transduction domain A | Calcium ATPase, transmembrane domain M | 5 | 4 | |
| Folate-binding domain | Aminomethyltransferase beta-barrel domain | 5 | 2 | |
| GAF domain-like | Sigma3 and sigma4 domains of RNA polymerase sigma factors | 5 | 4 | |
| Rhodanese/Cell cycle control phosphatase | Metallo-hydrolase/oxidoreductase | 5 | 1 | |
| Phosphohistidine domain | Phosphoenolpyruvate/pyruvate domain | 5 | 3 | |
| Homeodomain-like | Tetracyclin repressor-like, C-terminal domain | 5 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | Translation proteins | 5 | 4 | |
| "Winged helix" DNA-binding domain | "Winged helix" DNA-binding domain | 5 | 3 | |
| Nucleic acid-binding proteins | Nucleic acid-binding proteins | 5 | 5 | |
| FAD-binding/transporter-associated domain-like | FAD-linked oxidases, C-terminal domain | 5 | 3 | |
| HMA, heavy metal-associated domain | Calcium ATPase, transduction domain A | 5 | 4 | |
| HMA, heavy metal-associated domain | HAD-like | 5 | 4 | |
| NAD(P)-binding Rossmann-fold domains | LDH C-terminal domain-like | 5 | 1 | |
| NAD(P)-binding Rossmann-fold domains | NAD(P)-binding Rossmann-fold domains | 5 | 2 | |
| 2Fe-2S ferredoxin-like | 4Fe-4S ferredoxins | 4 | 2 | |
| Nitrite/Sulfite reductase N-terminal domain-like | Nitrite/Sulfite reductase N-terminal domain-like | 4 | 2 | |
| HMA, heavy metal-associated domain | Calcium ATPase, transmembrane domain M | 4 | 3 | |
| Ribbon-helix-helix | ACT-like | 4 | 1 | |
| Phosphoglucomutase, first 3 domains | Phosphoglucomutase, C-terminal domain | 4 | 1 | |
| Phosphoglucomutase, first 3 domains | Phosphoglucomutase, first 3 domains | 4 | 1 | |
| CBS-domain pair | FAD-binding/transporter-associated domain-like | 4 | 1 | |
| 6-phosphogluconate dehydrogenase C-terminal domain-like | UDP-glucose/GDP-mannose dehydrogenase C-terminal domain | 4 | 2 | |
| Nqo1 FMN-binding domain-like | Nqo1C-terminal domain-like | 4 | 1 | |
| Nucleotide-diphospho-sugar transferases | Trimeric LpxA-like enzymes | 4 | 1 | |
| Multidrug efflux transporter AcrB transmembrane domain | Multidrug efflux transporter AcrB transmembrane domain | 4 | 2 | |
| ValRS/IleRS/LeuRS editing domain | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 4 | 3 | |
| Nitrite and sulphite reductase 4Fe-4S domain-like | Nitrite and sulphite reductase 4Fe-4S domain-like | 4 | 2 | |
| ValRS/IleRS/LeuRS editing domain | Nucleotidylyl transferase | 4 | 3 | |
| Translation proteins | ThrRS/AlaRS common domain | 4 | 3 | |
| CheY-like | PYP-like sensor domain (PAS domain) | 4 | 4 | |
| Voltage-gated potassium channels | NAD(P)-binding Rossmann-fold domains | 4 | 2 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | SIS domain | 4 | 1 | |
| Class II aaRS and biotin synthetases | Class II aaRS ABD-related | 4 | 4 | |
| NAD(P)-binding Rossmann-fold domains | UDP-glucose/GDP-mannose dehydrogenase C-terminal domain | 4 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | Hypothetical protein YjiA, C-terminal domain | 4 | 2 | |
| "Winged helix" DNA-binding domain | TrmB C-terminal domain-like | 4 | 3 | |
| Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase | Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase | 4 | 1 | |
| Nitrite/Sulfite reductase N-terminal domain-like | Nitrite and sulphite reductase 4Fe-4S domain-like | 4 | 2 | |
| Arabinanase/levansucrase/invertase | Concanavalin A-like lectins/glucanases | 4 | 4 | |
| GroEL equatorial domain-like | GroEL-intermediate domain like | 3 | 1 | |
| Thioesterase/thiol ester dehydrase-isomerase | Thioesterase/thiol ester dehydrase-isomerase | 3 | 2 | |
| Mechanosensitive channel protein MscS (YggB), transmembrane region | Mechanosensitive channel protein MscS (YggB), C-terminal domain | 3 | 3 | |
| Voltage-gated potassium channels | TrkA C-terminal domain-like | 3 | 1 | |
| ADC-like | Cdc48 domain 2-like | 3 | 1 | |
| Mechanosensitive channel protein MscS (YggB), transmembrane region | Sm-like ribonucleoproteins | 3 | 3 | |
| Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain | 3 | 3 | |
| ISP domain | Bet v1-like | 3 | 1 | |
| Cation efflux protein transmembrane domain-like | Cation efflux protein cytoplasmic domain-like | 3 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Phosphohistidine domain | 3 | 1 | |
| MoeA N-terminal region -like | Molybdenum cofactor biosynthesis proteins | 3 | 3 | |
| Ribosomal protein S5 domain 2-like | GHMP Kinase, C-terminal domain | 3 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 3 | 2 | |
| Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain | Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain | 3 | 1 | |
| Cdc48 domain 2-like | P-loop containing nucleoside triphosphate hydrolases | 3 | 1 | |
| Pectin lyase-like | Ricin B-like lectins | 3 | 3 | |
| Translational machinery components | L30e-like | 3 | 2 | |
| PreATP-grasp domain | Rudiment single hybrid motif | 3 | 2 | |
| 4Fe-4S ferredoxins | ADC-like | 3 | 1 | |
| FAD-linked oxidases, C-terminal domain | alpha-helical ferredoxin | 3 | 2 | |
| Adenine nucleotide alpha hydrolases-like | DHS-like NAD/FAD-binding domain | 3 | 1 | |
| Translation proteins | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 3 | 2 | |
| 6-phosphogluconate dehydrogenase C-terminal domain-like | ClpP/crotonase | 3 | 1 | |
| beta-Galactosidase/glucuronidase domain | beta-Galactosidase/glucuronidase domain | 3 | 3 | |
| P-loop containing nucleoside triphosphate hydrolases | Class I glutamine amidotransferase-like | 3 | 1 | |
| Arabinanase/levansucrase/invertase | Ricin B-like lectins | 3 | 2 | |
| Rhodanese/Cell cycle control phosphatase | Rhodanese/Cell cycle control phosphatase | 3 | 2 | |
| Concanavalin A-like lectins/glucanases | Concanavalin A-like lectins/glucanases | 3 | 3 | |
| Thiolase-like | Nucleic acid-binding proteins | 3 | 1 | |
| 2Fe-2S ferredoxin-like | Formate dehydrogenase/DMSO reductase, domains 1-3 | 3 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Phosphoenolpyruvate/pyruvate domain | 3 | 1 | |
| Tryptophan synthase beta subunit-like PLP-dependent enzymes | ACT-like | 3 | 1 | |
| FAD-binding/transporter-associated domain-like | alpha-helical ferredoxin | 3 | 2 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | Adenine nucleotide alpha hydrolases-like | 3 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | Ribosomal protein S5 domain 2-like | 3 | 3 | |
| GroEL-intermediate domain like | GroEL apical domain-like | 3 | 1 | |
| NAD(P)-binding Rossmann-fold domains | ClpP/crotonase | 3 | 1 | |
| GroEL equatorial domain-like | GroEL apical domain-like | 3 | 1 | |
| 4Fe-4S ferredoxins | Formate dehydrogenase/DMSO reductase, domains 1-3 | 3 | 1 | |
| FAD/NAD(P)-binding domain | Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain | 3 | 3 | |
| ADC-like | P-loop containing nucleoside triphosphate hydrolases | 3 | 1 | |
| 6-phosphogluconate dehydrogenase C-terminal domain-like | 6-phosphogluconate dehydrogenase C-terminal domain-like | 3 | 1 | |
| 2Fe-2S ferredoxin-like | ADC-like | 3 | 1 | |
| ABC transporter transmembrane region | P-loop containing nucleoside triphosphate hydrolases | 3 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | TGS-like | 3 | 1 | |
| (Trans)glycosidases | Galactose mutarotase-like | 3 | 3 | |
| CheY-like | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 3 | 3 | |
| Glutathione synthetase ATP-binding domain-like | Rudiment single hybrid motif | 3 | 2 | |
| FMN-binding split barrel | UbiD C-terminal domain-like | 2 | 2 | |
| Nucleic acid-binding proteins | DHH phosphoesterases | 2 | 2 | |
| Thioredoxin-like | Six-hairpin glycosidases | 2 | 2 | |
| CBS-domain pair | CBS-domain pair | 2 | 2 | |
| ACT-like | ACT-like | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | Restriction endonuclease-like | 2 | 2 | |
| tRNA-guanine transglycosylase | Pre-PUA domain | 2 | 2 | |
| Translation proteins SH3-like domain | Nucleic acid-binding proteins | 2 | 2 | |
| FAD-linked reductases, C-terminal domain | Folate-binding domain | 2 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Sec63 N-terminal domain-like | 2 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Tropomyosin | 2 | 2 | |
| N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 | Translational machinery components | 2 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Succinyl-CoA synthetase domains | 2 | 2 | |
| (Trans)glycosidases | Beta-D-glucan exohydrolase, C-terminal domain | 2 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | post-AAA+ oligomerization domain-like | 2 | 1 | |
| PA domain | Zn-dependent exopeptidases | 2 | 1 | |
| Heme-dependent peroxidases | Heme-dependent peroxidases | 2 | 1 | |
| "Winged helix" DNA-binding domain | TrkA C-terminal domain-like | 2 | 1 | |
| PDZ domain-like | PDZ domain-like | 2 | 2 | |
| PEP carboxykinase N-terminal domain | PEP carboxykinase-like | 2 | 1 | |
| Trypsin-like serine proteases | PDZ domain-like | 2 | 1 | |
| Nicotinate/Quinolinate PRTase N-terminal domain-like | Nicotinate/Quinolinate PRTase C-terminal domain-like | 2 | 1 | |
| Actin-like ATPase domain | Actin-like ATPase domain | 2 | 2 | |
| EF-G C-terminal domain-like | Ribosomal protein S5 domain 2-like | 2 | 2 | |
| Glutamine synthetase/guanido kinase | GatB/YqeY motif | 2 | 2 | |
| Glutathione synthetase ATP-binding domain-like | Succinyl-CoA synthetase domains | 2 | 2 | |
| "Winged helix" DNA-binding domain | C-terminal domain of transcriptional repressors | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | C-terminal domain of alpha and beta subunits of F1 ATP synthase | 2 | 2 | |
| DNA repair protein MutS, domain I | DNA repair protein MutS, domain III | 2 | 2 | |
| Phospholipase D/nuclease | Phospholipase D/nuclease | 2 | 2 | |
| N-terminal domain of eukaryotic peptide chain release factor subunit 1, ERF1 | L30e-like | 2 | 1 | |
| NAD(P)-binding Rossmann-fold domains | DHH phosphoesterases | 2 | 1 | |
| Aconitase iron-sulfur domain | LeuD/IlvD-like | 2 | 2 | |
| DNA repair protein MutS, domain III | P-loop containing nucleoside triphosphate hydrolases | 2 | 2 | |
| Oxidoreductase molybdopterin-binding domain | E set domains | 2 | 2 | |
| ACT-like | Formyltransferase | 2 | 2 | |
| Galactose-binding domain-like | Galactose mutarotase-like | 2 | 2 | |
| Tubulin nucleotide-binding domain-like | Tubulin C-terminal domain-like | 2 | 1 | |
| Pyruvate-ferredoxin oxidoreductase, PFOR, domain III | Thiamin diphosphate-binding fold (THDP-binding) | 2 | 1 | |
| FMN-dependent nitroreductase-like | FMN-dependent nitroreductase-like | 2 | 2 | |
| beta-Galactosidase/glucuronidase domain | Galactose mutarotase-like | 2 | 2 | |
| Restriction endonuclease-like | RuvA domain 2-like | 2 | 2 | |
| CO dehydrogenase molybdoprotein N-domain-like | Molybdenum cofactor-binding domain | 2 | 1 | |
| DPP6 N-terminal domain-like | alpha/beta-Hydrolases | 2 | 1 | |
| Pre-PUA domain | PUA domain-like | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | Ribosomal protein S5 domain 2-like | 2 | 2 | |
| CheY-like | Homodimeric domain of signal transducing histidine kinase | 2 | 2 | |
| Dimeric alpha+beta barrel | Dimeric alpha+beta barrel | 2 | 2 | |
| Aminoacid dehydrogenase-like, N-terminal domain | Isocitrate/Isopropylmalate dehydrogenase-like | 2 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Rad51 N-terminal domain-like | 2 | 2 | |
| ClpP/crotonase | ClpP/crotonase | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | RuvA domain 2-like | 2 | 2 | |
| Nqo1 FMN-binding domain-like | Nqo1 middle domain-like | 2 | 1 | |
| NagB/RpiA/CoA transferase-like | alpha-helical ferredoxin | 2 | 1 | |
| DNA repair protein MutS, domain I | P-loop containing nucleoside triphosphate hydrolases | 2 | 2 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | Nucleic acid-binding proteins | 2 | 2 | |
| Pyruvate-ferredoxin oxidoreductase, PFOR, domain III | TK C-terminal domain-like | 2 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | vWA-like | 2 | 1 | |
| DNA repair protein MutS, domain II | DNA repair protein MutS, domain III | 2 | 2 | |
| FAD/NAD(P)-binding domain | Aminomethyltransferase beta-barrel domain | 2 | 1 | |
| HAMP domain-like | Methyl-accepting chemotaxis protein (MCP) signaling domain | 2 | 2 | |
| Single hybrid motif | CoA-dependent acyltransferases | 2 | 2 | |
| "Winged helix" DNA-binding domain | Class II aaRS and biotin synthetases | 2 | 2 | |
| DNA repair protein MutS, domain II | P-loop containing nucleoside triphosphate hydrolases | 2 | 2 | |
| NAD kinase/diacylglycerol kinase-like | Carbohydrate phosphatase | 2 | 1 | |
| HMA, heavy metal-associated domain | HMA, heavy metal-associated domain | 2 | 1 | |
| MurD-like peptide ligases, catalytic domain | MurD-like peptide ligases, peptide-binding domain | 2 | 1 | |
| Nqo5-like | HydB/Nqo4-like | 2 | 1 | |
| Fe-S cluster assembly (FSCA) domain-like | P-loop containing nucleoside triphosphate hydrolases | 2 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Isocitrate/Isopropylmalate dehydrogenase-like | 2 | 1 | |
| "Winged helix" DNA-binding domain | PYP-like sensor domain (PAS domain) | 2 | 2 | |
| "Winged helix" DNA-binding domain | S-adenosyl-L-methionine-dependent methyltransferases | 2 | 1 | |
| MoeA N-terminal region -like | MoeA C-terminal domain-like | 2 | 2 | |
| Molybdenum cofactor biosynthesis proteins | MoeA C-terminal domain-like | 2 | 2 | |
| Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | CoA-dependent acyltransferases | 2 | 2 | |
| lambda repressor-like DNA-binding domains | AraD/HMP-PK domain-like | 2 | 1 | |
| DNA repair protein MutS, domain I | DNA repair protein MutS, domain II | 2 | 2 | |
| Respiratory nitrate reductase 1 gamma chain | alpha-helical ferredoxin | 2 | 1 | |
| Glutamine synthetase, N-terminal domain | Glutamine synthetase/guanido kinase | 2 | 1 | |
| GroES-like | GroES-like | 2 | 1 | |
| Domain of the SRP/SRP receptor G-proteins | P-loop containing nucleoside triphosphate hydrolases | 2 | 2 | |
| FMN-linked oxidoreductases | FAD/NAD(P)-binding domain | 2 | 1 | |
| MurD-like peptide ligases, peptide-binding domain | Dihydropteroate synthetase-like | 2 | 1 | |
| "Winged helix" DNA-binding domain | Phospholipase D/nuclease | 2 | 2 | |
| 2Fe-2S ferredoxin-like | CO dehydrogenase ISP C-domain like | 2 | 1 | |
| Fe,Mn superoxide dismutase (SOD), N-terminal domain | Fe,Mn superoxide dismutase (SOD), C-terminal domain | 2 | 2 | |
| FAD/NAD(P)-binding domain | Folate-binding domain | 2 | 1 | |
| Cytochrome c oxidase subunit I-like | Cytochrome c oxidase subunit III-like | 2 | 1 | |
| Single hybrid motif | Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | 2 | 2 | |
| MurD-like peptide ligases, catalytic domain | Dihydropteroate synthetase-like | 2 | 1 | |
| Class II aaRS and biotin synthetases | ThrRS/AlaRS common domain | 2 | 2 | |
| FAD-linked reductases, C-terminal domain | Aminomethyltransferase beta-barrel domain | 2 | 1 | |
| "Winged helix" DNA-binding domain | Sec63 N-terminal domain-like | 2 | 1 | |
| (Trans)glycosidases | Chitinase insertion domain | 1 | 1 | |
| Class I glutamine amidotransferase-like | Glycosyl hydrolase domain | 1 | 1 | |
| Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 1 | 1 | |
| Fibronectin type III | CBD9-like | 1 | 1 | |
| FAD/NAD(P)-binding domain | ISP domain | 1 | 1 | |
| Carbamate kinase-like | ACT-like | 1 | 1 | |
| YegP-like | YegP-like | 1 | 1 | |
| Homo-oligomeric flavin-containing Cys decarboxylases, HFCD | CoaB-like | 1 | 1 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | BRCT domain | 1 | 1 | |
| Integrin alpha N-terminal domain | 3-carboxy-cis,cis-mucoante lactonizing enzyme | 1 | 1 | |
| tRNA-guanine transglycosylase | Uracil-DNA glycosylase-like | 1 | 1 | |
| 2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain | Alkaline phosphatase-like | 1 | 1 | |
| 4Fe-4S ferredoxins | 4Fe-4S ferredoxins | 1 | 1 | |
| N-terminal domain of alpha and beta subunits of F1 ATP synthase | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Acyl-CoA N-acyltransferases (Nat) | SCP-like | 1 | 1 | |
| Domain of the SRP/SRP receptor G-proteins | Signal peptide-binding domain | 1 | 1 | |
| PK beta-barrel domain-like | PK C-terminal domain-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Mitotic arrest deficient-like 1, Mad1 | 1 | 1 | |
| "Winged helix" DNA-binding domain | Iron-dependent repressor protein, dimerization domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Acyl-CoA N-acyltransferases (Nat) | 1 | 1 | |
| Heme-dependent catalase-like | Class I glutamine amidotransferase-like | 1 | 1 | |
| Aminopeptidase/glucanase lid domain | Zn-dependent exopeptidases | 1 | 1 | |
| Glutamine synthetase/guanido kinase | GAD domain-like | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | CheW-like | 1 | 1 | |
| dsRNA-binding domain-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| "Winged helix" DNA-binding domain | Protein kinase-like (PK-like) | 1 | 1 | |
| Chelatase | Thioredoxin-like | 1 | 1 | |
| Rudiment single hybrid motif | Single hybrid motif | 1 | 1 | |
| Eukaryotic type KH-domain (KH-domain type I) | Eukaryotic type KH-domain (KH-domain type I) | 1 | 1 | |
| Radical SAM enzymes | Acyl-CoA N-acyltransferases (Nat) | 1 | 1 | |
| HAMP domain-like | Homodimeric domain of signal transducing histidine kinase | 1 | 1 | |
| Formate/glycerate dehydrogenase catalytic domain-like | ACT-like | 1 | 1 | |
| Six-hairpin glycosidases | Six-hairpin glycosidases | 1 | 1 | |
| Subtilisin-like | Carboxypeptidase regulatory domain-like | 1 | 1 | |
| PK beta-barrel domain-like | Phosphohistidine domain | 1 | 1 | |
| PPK N-terminal domain-like | PHP14-like | 1 | 1 | |
| "Winged helix" DNA-binding domain | Nucleotidyltransferase | 1 | 1 | |
| Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | ThrRS/AlaRS common domain | 1 | 1 | |
| "Winged helix" DNA-binding domain | Restriction endonuclease-like | 1 | 1 | |
| PK beta-barrel domain-like | Phosphoenolpyruvate/pyruvate domain | 1 | 1 | |
| Translation proteins | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Carbamoyl phosphate synthetase, large subunit connection domain | 1 | 1 | |
| Chaperone J-domain | DnaJ/Hsp40 cysteine-rich domain | 1 | 1 | |
| Radical SAM enzymes | PsbU/PolX domain-like | 1 | 1 | |
| Nucleotidyltransferase | PAP/OAS1 substrate-binding domain | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| PreATP-grasp domain | Single hybrid motif | 1 | 1 | |
| Concanavalin A-like lectins/glucanases | Ricin B-like lectins | 1 | 1 | |
| eIF2alpha middle domain-like | eIF-2-alpha, C-terminal domain | 1 | 1 | |
| DNA/RNA polymerases | Lesion bypass DNA polymerase (Y-family), little finger domain | 1 | 1 | |
| Putative DNA-binding domain | Class II aaRS and biotin synthetases | 1 | 1 | |
| Uracil-DNA glycosylase-like | Pre-PUA domain | 1 | 1 | |
| 2Fe-2S ferredoxin-like | alpha-helical ferredoxin | 1 | 1 | |
| PhoU-like | TrkA C-terminal domain-like | 1 | 1 | |
| Actin-like ATPase domain | Protein kinase-like (PK-like) | 1 | 1 | |
| Translation initiation factor 2 beta, aIF2beta, N-terminal domain | Nucleic acid-binding proteins | 1 | 1 | |
| IlvD/EDD N-terminal domain-like | LeuD/IlvD-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Microbial and mitochondrial ADK, insert "zinc finger" domain | 1 | 1 | |
| Nucleic acid-binding proteins | Class II aaRS and biotin synthetases | 1 | 1 | |
| Histone-fold | Histone-fold | 1 | 1 | |
| PIN domain-like | 5' to 3' exonuclease, C-terminal subdomain | 1 | 1 | |
| Ribosomal L11/L12e N-terminal domain | Ribosomal protein L11, C-terminal domain | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Glutathione synthetase ATP-binding domain-like | 1 | 1 | |
| Sensory domain-like | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 1 | 1 | |
| Sec63 N-terminal domain-like | PHP domain-like | 1 | 1 | |
| (Trans)glycosidases | CBD9-like | 1 | 1 | |
| Histidine-containing phosphotransfer domain, HPT domain | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 1 | 1 | |
| tRNA-binding arm | Class II aaRS and biotin synthetases | 1 | 1 | |
| Succinyl-CoA synthetase domains | Succinyl-CoA synthetase domains | 1 | 1 | |
| Pseudouridine synthase | PUA domain-like | 1 | 1 | |
| tRNA-guanine transglycosylase | PUA domain-like | 1 | 1 | |
| Initiation factor IF2/eIF5b, domain 3 | Translation proteins | 1 | 1 | |
| PK C-terminal domain-like | Phosphohistidine domain | 1 | 1 | |
| Homodimeric domain of signal transducing histidine kinase | CheW-like | 1 | 1 | |
| PIN domain-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | DNA mismatch repair protein MutL | 1 | 1 | |
| PLP-binding barrel | Alanine racemase C-terminal domain-like | 1 | 1 | |
| YjeF N-terminal domain-like | Ribokinase-like | 1 | 1 | |
| HAMP domain-like | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 1 | 1 | |
| PreATP-grasp domain | Carbamoyl phosphate synthetase, large subunit connection domain | 1 | 1 | |
| Nucleic acid-binding proteins | eIF-2-alpha, C-terminal domain | 1 | 1 | |
| CBS-domain pair | MgtE membrane domain-like | 1 | 1 | |
| Phosphoenolpyruvate/pyruvate domain | PK C-terminal domain-like | 1 | 1 | |
| Nucleic acid-binding proteins | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| NagB/RpiA/CoA transferase-like | D-ribose-5-phosphate isomerase (RpiA), lid domain | 1 | 1 | |
| TATA-box binding protein-like | DNA-glycosylase | 1 | 1 | |
| MgtE N-terminal domain-like | CBS-domain pair | 1 | 1 | |
| Prokaryotic type KH domain (KH-domain type II) | Ribosomal protein S3 C-terminal domain | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Type II DNA topoisomerase | 1 | 1 | |
| Nucleotidyltransferase | PHP domain-like | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | ACT-like | 1 | 1 | |
| Class II aaRS and biotin synthetases | C-terminal domain of ProRS | 1 | 1 | |
| TATA-box binding protein-like | TATA-box binding protein-like | 1 | 1 | |
| CBS-domain pair | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain | Phosphohistidine domain | 1 | 1 | |
| "Winged helix" DNA-binding domain | Riboflavin kinase-like | 1 | 1 | |
| S-adenosyl-L-methionine-dependent methyltransferases | Nucleic acid-binding proteins | 1 | 1 | |
| Rad51 N-terminal domain-like | Ribonuclease H-like | 1 | 1 | |
| Aldolase | 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain | 1 | 1 | |
| Class II aaRS ABD-related | C-terminal domain of ProRS | 1 | 1 | |
| tRNA-intron endonuclease N-terminal domain-like | tRNA-intron endonuclease N-terminal domain-like | 1 | 1 | |
| Methionyl-tRNA synthetase (MetRS), Zn-domain | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 1 | 1 | |
| Translation proteins | EF-G C-terminal domain-like | 1 | 1 | |
| Prokaryotic type KH domain (KH-domain type II) | Metallo-hydrolase/oxidoreductase | 1 | 1 | |
| CbiG N-terminal domain-like | CobE/GbiG C-terminal domain-like | 1 | 1 | |
| Phospholipase D/nuclease | TrmB C-terminal domain-like | 1 | 1 | |
| Nudix | NagB/RpiA/CoA transferase-like | 1 | 1 | |
| PKD domain | (Trans)glycosidases | 1 | 1 | |
| (Trans)glycosidases | Class I glutamine amidotransferase-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Bacterial hemolysins | 1 | 1 | |
| S-adenosyl-L-methionine-dependent methyltransferases | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| Prokaryotic type KH domain (KH-domain type II) | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| Rhodanese/Cell cycle control phosphatase | Nitrite/Sulfite reductase N-terminal domain-like | 1 | 1 | |
| Thymidylate synthase/dCMP hydroxymethylase | Thymidylate synthase/dCMP hydroxymethylase | 1 | 1 | |
| GIY-YIG endonuclease | RuvA domain 2-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Signal peptide-binding domain | 1 | 1 | |
| beta-Galactosidase/glucuronidase domain | Concanavalin A-like lectins/glucanases | 1 | 1 | |
| Riboflavin synthase domain-like | Riboflavin synthase domain-like | 1 | 1 | |
| C-terminal UvrC-binding domain of UvrB | RuvA domain 2-like | 1 | 1 | |
| Dom34/Pelota N-terminal domain-like | Translational machinery components | 1 | 1 | |
| MgtE N-terminal domain-like | MgtE membrane domain-like | 1 | 1 | |
| Carboxypeptidase regulatory domain-like | Invasin/intimin cell-adhesion fragments | 1 | 1 | |
| Translation initiation factor 2 beta, aIF2beta, N-terminal domain | Zinc-binding domain of translation initiation factor 2 beta | 1 | 1 | |
| Nucleic acid-binding proteins | BRCT domain | 1 | 1 | |
| Subtilisin-like | PKD domain | 1 | 1 | |
| CBS-domain pair | Thioesterase/thiol ester dehydrase-isomerase | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | CBS-domain pair | 1 | 1 | |
| ATP-dependent DNA ligase DNA-binding domain | Nucleic acid-binding proteins | 1 | 1 | |
| Thioredoxin-like | FAD/NAD(P)-binding domain | 1 | 1 | |
| ThrRS/AlaRS common domain | Class II aaRS ABD-related | 1 | 1 | |
| Class II aaRS and biotin synthetases | Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | 1 | 1 | |
| PIN domain-like | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| CBS-domain pair | Ribosome binding protein Y (YfiA homologue) | 1 | 1 | |
| Creatinase/aminopeptidase | "Winged helix" DNA-binding domain | 1 | 1 | |
| Hypothetical protein AF0491, middle domain | EF-G C-terminal domain-like | 1 | 1 | |
| HSP40/DnaJ peptide-binding domain | HSP40/DnaJ peptide-binding domain | 1 | 1 | |
| DnaJ/Hsp40 cysteine-rich domain | Pseudouridine synthase | 1 | 1 | |
| Glutamyl tRNA-reductase catalytic, N-terminal domain | Glutamyl tRNA-reductase dimerization domain | 1 | 1 | |
| FabD/lysophospholipase-like | Probable ACP-binding domain of malonyl-CoA ACP transacylase | 1 | 1 | |
| PKD domain | Carbohydrate binding domain | 1 | 1 | |
| Diaminopimelate epimerase-like | Diaminopimelate epimerase-like | 1 | 1 | |
| Iron-dependent repressor protein, dimerization domain | C-terminal domain of transcriptional repressors | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | C-terminal UvrC-binding domain of UvrB | 1 | 1 | |
| Galactose-binding domain-like | Concanavalin A-like lectins/glucanases | 1 | 1 | |
| ARM repeat | Quinoprotein alcohol dehydrogenase-like | 1 | 1 | |
| Concanavalin A-like lectins/glucanases | Galactose mutarotase-like | 1 | 1 | |
| GIY-YIG endonuclease | C-terminal UvrC-binding domain of UvrB | 1 | 1 | |
| PurM C-terminal domain-like | PurM C-terminal domain-like | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | Alpha subunit of glutamate synthase, C-terminal domain | 1 | 1 | |
| PAP/OAS1 substrate-binding domain | PAP/Archaeal CCA-adding enzyme, C-terminal domain | 1 | 1 | |
| Ribosomal protein L6 | Ribosomal protein L6 | 1 | 1 | |
| Formyltransferase | Cytidine deaminase-like | 1 | 1 | |
| TGS-like | ThrRS/AlaRS common domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | EF-G C-terminal domain-like | 1 | 1 | |
| MoeA C-terminal domain-like | Periplasmic binding protein-like II | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | GMP synthetase C-terminal dimerisation domain | 1 | 1 | |
| Periplasmic binding protein-like II | GlnB-like | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | Type II DNA topoisomerase | 1 | 1 | |
| Periplasmic binding protein-like II | ACT-like | 1 | 1 | |
| EF-G C-terminal domain-like | EF-G C-terminal domain-like | 1 | 1 | |
| Galactose mutarotase-like | Galactose mutarotase-like | 1 | 1 | |
| Thioredoxin-like | GST C-terminal domain-like | 1 | 1 | |
| "Winged helix" DNA-binding domain | Ribokinase-like | 1 | 1 | |
| CBS-domain pair | ParB/Sulfiredoxin | 1 | 1 | |
| Carbohydrate binding domain | (Trans)glycosidases | 1 | 1 | |
| Serine metabolism enzymes domain | ACT-like | 1 | 1 | |
| Bacterial fluorinating enzyme, N-terminal domain | Bacterial fluorinating enzyme, C-terminal domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Initiation factor IF2/eIF5b, domain 3 | 1 | 1 | |
| RuvA domain 2-like | BRCT domain | 1 | 1 | |
| Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | Nucleic acid-binding proteins | 1 | 1 | |
| PhoU-like | PhoU-like | 1 | 1 | |
| Glutamyl tRNA-reductase catalytic, N-terminal domain | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| PurM N-terminal domain-like | PurM N-terminal domain-like | 1 | 1 | |
| CBS-domain pair | Inosine monophosphate dehydrogenase (IMPDH) | 1 | 1 | |
| Putative DNA-binding domain | Putative DNA-binding domain | 1 | 1 | |
| Coiled-coil domain of nucleotide exchange factor GrpE | Head domain of nucleotide exchange factor GrpE | 1 | 1 | |
| Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | Translation proteins | 1 | 1 | |
| (Trans)glycosidases | Fibronectin type III | 1 | 1 | |
| Galactose mutarotase-like | Glycosyl hydrolase domain | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Single hybrid motif | 1 | 1 | |
| THUMP domain-like | Adenine nucleotide alpha hydrolases-like | 1 | 1 | |
| PPK N-terminal domain-like | Phospholipase D/nuclease | 1 | 1 | |
| DNA breaking-rejoining enzymes | GAF domain-like | 1 | 1 | |
| UDP-Glycosyltransferase/glycogen phosphorylase | UDP-Glycosyltransferase/glycogen phosphorylase | 1 | 1 | |
| TGS-like | Class II aaRS ABD-related | 1 | 1 | |
| Insert subdomain of RNA polymerase alpha subunit | RBP11-like subunits of RNA polymerase | 1 | 1 | |
| Ribonuclease H-like | DNA/RNA polymerases | 1 | 1 | |
| MFS general substrate transporter | MFS general substrate transporter | 1 | 1 | |
| "Winged helix" DNA-binding domain | FAD/NAD(P)-binding domain | 1 | 1 | |
| (Trans)glycosidases | Concanavalin A-like lectins/glucanases | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Glutamyl tRNA-reductase dimerization domain | 1 | 1 | |
| Carbohydrate binding domain | Chitinase insertion domain | 1 | 1 | |
| AN1-like Zinc finger | Rhomboid-like | 1 | 1 | |
| Pentapeptide repeat-like | Voltage-gated potassium channels | 1 | 1 | |
| lambda repressor-like DNA-binding domains | CBS-domain pair | 1 | 1 | |
| GatD N-terminal domain-like | Glutaminase/Asparaginase | 1 | 1 | |
| Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain | Phosphoenolpyruvate/pyruvate domain | 1 | 1 | |
| Periplasmic binding protein-like II | Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain | 1 | 1 | |
| Ribokinase-like | AraD/HMP-PK domain-like | 1 | 1 | |
| Chaperone J-domain | HSP40/DnaJ peptide-binding domain | 1 | 1 | |
| NAD-binding domain of HMG-CoA reductase | Substrate-binding domain of HMG-CoA reductase | 1 | 1 | |
| tRNA-intron endonuclease catalytic domain-like | tRNA-intron endonuclease catalytic domain-like | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Acid proteases | 1 | 1 | |
| tRNA-intron endonuclease N-terminal domain-like | tRNA-intron endonuclease catalytic domain-like | 1 | 1 | |
| Nucleotide-diphospho-sugar transferases | S-adenosyl-L-methionine-dependent methyltransferases | 1 | 1 | |
| Cupredoxins | Integrin alpha N-terminal domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | ARM repeat | 1 | 1 | |
| Histidine-containing phosphotransfer domain, HPT domain | Homodimeric domain of signal transducing histidine kinase | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | HprK N-terminal domain-like | 1 | 1 | |
| ATP-dependent DNA ligase DNA-binding domain | DNA ligase/mRNA capping enzyme, catalytic domain | 1 | 1 | |
| FMN-linked oxidoreductases | Alpha subunit of glutamate synthase, C-terminal domain | 1 | 1 | |
| CheY-like | Methylesterase CheB, C-terminal domain | 1 | 1 | |
| Periplasmic binding protein-like I | Periplasmic binding protein-like I | 1 | 1 | |
| FYSH domain | EF-G C-terminal domain-like | 1 | 1 | |
| TrmB C-terminal domain-like | Ribokinase-like | 1 | 1 | |
| ARM repeat | ARM repeat | 1 | 1 | |
| FYSH domain | Hypothetical protein AF0491, middle domain | 1 | 1 | |
| Mitotic arrest deficient-like 1, Mad1 | "Winged helix" DNA-binding domain | 1 | 1 | |
| Rad51 N-terminal domain-like | Ribosomal protein L32e | 1 | 1 | |
| TGS-like | Class II aaRS and biotin synthetases | 1 | 1 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | RuvA domain 2-like | 1 | 1 | |
| Methionyl-tRNA synthetase (MetRS), Zn-domain | Nucleic acid-binding proteins | 1 | 1 | |
| Nucleotidylyl transferase | Ribosomal protein L25-like | 1 | 1 | |
| Carboxypeptidase regulatory domain-like | Carboxypeptidase regulatory domain-like | 1 | 1 | |
| MetI-like | MetI-like | 1 | 1 | |
| Rhodanese/Cell cycle control phosphatase | Nitrite and sulphite reductase 4Fe-4S domain-like | 1 | 1 | |
| NTF2-like | FAD-binding/transporter-associated domain-like | 1 | 1 | |
| Riboflavin synthase domain-like | Ferredoxin reductase-like, C-terminal NADP-linked domain | 1 | 1 | |
| DnaJ/Hsp40 cysteine-rich domain | HSP40/DnaJ peptide-binding domain | 1 | 1 | |
| Aspartate carbamoyltransferase, Regulatory-chain, N-terminal domain | Aspartate carbamoyltransferase, Regulatory-chain, C-terminal domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Rad50 coiled-coil Zn hook | 1 | 1 | |
| GAD domain-like | GatB/YqeY motif | 1 | 1 | |
| Formate/glycerate dehydrogenase catalytic domain-like | Serine metabolism enzymes domain | 1 | 1 | |
| DNA polymerase beta, N-terminal domain-like | Nucleotidyltransferase | 1 | 1 | |
| "Winged helix" DNA-binding domain | NagB/RpiA/CoA transferase-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Smc hinge domain | 1 | 1 | |
| EPT/RTPC-like | RNA 3'-terminal phosphate cyclase, RPTC, insert domain | 1 | 1 | |
| Metallo-dependent phosphatases | 5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain | 1 | 1 | |
| Cupredoxins | Soluble quinoprotein glucose dehydrogenase | 1 | 1 | |
| Methionyl-tRNA synthetase (MetRS), Zn-domain | Nucleotidylyl transferase | 1 | 1 | |
| Subtilisin-like | Invasin/intimin cell-adhesion fragments | 1 | 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 | 1 | 1 | |
| Histidine-containing phosphotransfer domain, HPT domain | CheW-like | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | DNA mismatch repair protein MutL | 1 | 1 | |
| alpha/beta-Hydrolases | Rad51 N-terminal domain-like | 1 | 1 | |
| Nucleotidylyl transferase | An anticodon-binding domain of class I aminoacyl-tRNA synthetases | 1 | 1 | |
| DNA clamp | DNA clamp | 1 | 1 | |
| Arabinanase/levansucrase/invertase | Arabinanase/levansucrase/invertase | 1 | 1 | |
| Ferritin-like | Ferritin-like | 1 | 1 | |
| DNA polymerase beta, N-terminal domain-like | PHP domain-like | 1 | 1 | |
| Pectin lyase-like | Pectin lyase-like | 1 | 1 | |
| Carbamoyl phosphate synthetase, small subunit N-terminal domain | Class I glutamine amidotransferase-like | 1 | 1 | |
| Zinc-binding domain of translation initiation factor 2 beta | Nucleic acid-binding proteins | 1 | 1 | |
| Nucleotidyltransferase | PAP/Archaeal CCA-adding enzyme, C-terminal domain | 1 | 1 | |
| Cytochrome c oxidase subunit II-like, transmembrane region | Cupredoxins | 1 | 1 | |
| Galactose-binding domain-like | CBD9-like | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Glutathione synthetase ATP-binding domain-like | 1 | 1 | |
| Cytochrome c oxidase subunit I-like | Cytochrome c oxidase subunit I-like | 1 | 1 | |
| N-terminal, heterodimerisation domain of RBP7 (RpoE) | Nucleic acid-binding proteins | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| Starch-binding domain-like | Starch-binding domain-like | 1 | 1 | |
| Actin-like ATPase domain | Heat shock protein 70kD (HSP70), peptide-binding domain | 1 | 1 | |
| "Winged helix" DNA-binding domain | MOP-like | 1 | 1 | |
| Chemotaxis receptor methyltransferase CheR, N-terminal domain | S-adenosyl-L-methionine-dependent methyltransferases | 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 | |
| MOSC N-terminal domain-like | PK beta-barrel domain-like | 1 | 1 | |
| Class II aaRS and biotin synthetases | Translation proteins | 1 | 1 | |
| Uracil-DNA glycosylase-like | PUA domain-like | 1 | 1 | |
| Molybdenum cofactor biosynthesis proteins | Periplasmic binding protein-like II | 1 | 1 | |
| PKD domain | Chitinase insertion domain | 1 | 1 | |
| 4Fe-4S ferredoxins | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Nucleic acid-binding proteins | eIF2alpha middle domain-like | 1 | 1 | |
| Sec63 N-terminal domain-like | Nucleotidyltransferase | 1 | 1 | |
| MoeA N-terminal region -like | Periplasmic binding protein-like II | 1 | 1 | |
| Dom34/Pelota N-terminal domain-like | L30e-like | 1 | 1 | |
| Nucleotidylyl transferase | Nucleic acid-binding proteins | 1 | 1 | |
| Nucleic acid-binding proteins | RuvA domain 2-like | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | PRTase-like | 1 | 1 | |
| PHP14-like | Phospholipase D/nuclease | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | Argininosuccinate synthetase, C-terminal domain | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Serine metabolism enzymes domain | 1 | 1 | |
| CheC-like | CheC-like | 1 | 1 | |
| DNA breaking-rejoining enzymes | PYP-like sensor domain (PAS domain) | 1 | 1 | |
| Ammonium transporter | GlnB-like | 1 | 1 | |
| Smc hinge domain | Tropomyosin | 1 | 1 | |
| Class II aaRS and biotin synthetases | C-terminal domain of transcriptional repressors | 1 | 1 | |
| DNA polymerase beta, N-terminal domain-like | Sec63 N-terminal domain-like | 1 | 1 | |
| "Winged helix" DNA-binding domain | Periplasmic binding protein-like II | 1 | 1 | |
| Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain | Nucleotidylyl transferase | 1 | 1 | |
| Type II DNA topoisomerase | GyrA/ParC C-terminal domain-like | 1 | 1 | |
| PreATP-grasp domain | PreATP-grasp domain | 1 | 1 | |
| N-terminal nucleophile aminohydrolases (Ntn hydrolases) | FMN-linked oxidoreductases | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Siroheme synthase middle domains-like | 1 | 1 | |
| Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | 1 | 1 | |
