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 | |
|---|
| Nucleotidylyl transferase | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 6 | 5 |  |
| NAD(P)-binding Rossmann-fold domains | Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 6 | 4 | |
| Actin-like ATPase domain | Actin-like ATPase domain | 5 | 2 | |
| MurD-like peptide ligases, catalytic domain | MurD-like peptide ligases, peptide-binding domain | 5 | 3 | |
| Thiamin diphosphate-binding fold (THDP-binding) | Thiamin diphosphate-binding fold (THDP-binding) | 5 | 4 | |
| P-loop containing nucleoside triphosphate hydrolases | P-loop containing nucleoside triphosphate hydrolases | 5 | 5 | |
| NAD(P)-binding Rossmann-fold domains | 6-phosphogluconate dehydrogenase C-terminal domain-like | 4 | 4 | |
| Nucleic acid-binding proteins | Class II aaRS and biotin synthetases | 4 | 3 | |
| P-loop containing nucleoside triphosphate hydrolases | Translation proteins | 4 | 4 | |
| Class II aaRS and biotin synthetases | Class II aaRS ABD-related | 3 | 2 | |
| ValRS/IleRS/LeuRS editing domain | Nucleotidylyl transferase | 3 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | post-AAA+ oligomerization domain-like | 3 | 2 | |
| PreATP-grasp domain | Glutathione synthetase ATP-binding domain-like | 3 | 3 | |
| Thiamin diphosphate-binding fold (THDP-binding) | TK C-terminal domain-like | 3 | 2 | |
| ValRS/IleRS/LeuRS editing domain | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 3 | 2 | |
| Ribosomal protein S5 domain 2-like | Ribosomal protein S5 domain 2-like | 3 | 3 | |
| P-loop containing nucleoside triphosphate hydrolases | EF-G C-terminal domain-like | 2 | 2 | |
| Single hybrid motif | Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | 2 | 1 | |
| N-terminal domain of alpha and beta subunits of F1 ATP synthase | P-loop containing nucleoside triphosphate hydrolases | 2 | 1 | |
| EF-G C-terminal domain-like | EF-G C-terminal domain-like | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | C-terminal domain of alpha and beta subunits of F1 ATP synthase | 2 | 1 | |
| CBS-domain pair | FAD-binding/transporter-associated domain-like | 2 | 1 | |
| Nucleic acid-binding proteins | Translation proteins SH3-like domain | 2 | 2 | |
| Riboflavin synthase domain-like | Ferredoxin reductase-like, C-terminal NADP-linked domain | 2 | 2 | |
| MurCD N-terminal domain | MurD-like peptide ligases, catalytic domain | 2 | 1 | |
| MurE/MurF N-terminal domain | MurD-like peptide ligases, peptide-binding domain | 2 | 1 | |
| Single hybrid motif | CoA-dependent acyltransferases | 2 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Restriction endonuclease-like | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | Ribosomal protein S5 domain 2-like | 2 | 2 | |
| Alpha-L RNA-binding motif | Pseudouridine synthase | 2 | 1 | |
| Aminoacid dehydrogenase-like, N-terminal domain | NAD(P)-binding Rossmann-fold domains | 2 | 1 | |
| PDZ domain-like | PDZ domain-like | 2 | 2 | |
| Translation proteins | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 2 | 2 | |
| Ribosomal protein S5 domain 2-like | GHMP Kinase, C-terminal domain | 2 | 1 | |
| Penicillin binding protein dimerisation domain | beta-lactamase/transpeptidase-like | 2 | 1 | |
| Phosphoglucomutase, first 3 domains | Phosphoglucomutase, C-terminal domain | 2 | 2 | |
| Sigma2 domain of RNA polymerase sigma factors | Sigma3 and sigma4 domains of RNA polymerase sigma factors | 2 | 2 | |
| MurCD N-terminal domain | MurD-like peptide ligases, peptide-binding domain | 2 | 1 | |
| Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex | CoA-dependent acyltransferases | 2 | 1 | |
| tRNA-binding arm | Class II aaRS and biotin synthetases | 2 | 1 | |
| Composite domain of metallo-dependent hydrolases | Metallo-dependent hydrolases | 2 | 2 | |
| P-loop containing nucleoside triphosphate hydrolases | EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain | 2 | 2 | |
| Domain of the SRP/SRP receptor G-proteins | P-loop containing nucleoside triphosphate hydrolases | 2 | 2 | |
| Nucleic acid-binding proteins | Nucleic acid-binding proteins | 2 | 2 | |
| Glucocorticoid receptor-like (DNA-binding domain) | P-loop containing nucleoside triphosphate hydrolases | 2 | 2 | |
| Phospholipase D/nuclease | Phospholipase D/nuclease | 2 | 2 | |
| MurE/MurF N-terminal domain | MurD-like peptide ligases, catalytic domain | 2 | 1 | |
| Phosphoglucomutase, first 3 domains | Phosphoglucomutase, first 3 domains | 2 | 2 | |
| N-terminal domain of alpha and beta subunits of F1 ATP synthase | C-terminal domain of alpha and beta subunits of F1 ATP synthase | 2 | 1 | |
| Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain | 1 | 1 | |
| Nitrite and sulphite reductase 4Fe-4S domain-like | Nitrite and sulphite reductase 4Fe-4S domain-like | 1 | 1 | |
| L30e-like | alpha/beta knot | 1 | 1 | |
| Triger factor/SurA peptide-binding domain-like | FKBP-like | 1 | 1 | |
| Ribonuclease PH domain 2-like | Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | 1 | 1 | |
| 6-phosphogluconate dehydrogenase C-terminal domain-like | 6-phosphogluconate dehydrogenase C-terminal domain-like | 1 | 1 | |
| Translation proteins | EF-G C-terminal domain-like | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | PheT/TilS domain | 1 | 1 | |
| PUA domain-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain | Phosphoenolpyruvate/pyruvate domain | 1 | 1 | |
| PreATP-grasp domain | Carbamoyl phosphate synthetase, large subunit connection domain | 1 | 1 | |
| 2Fe-2S ferredoxin-like | alpha-helical ferredoxin | 1 | 1 | |
| Nucleic acid-binding proteins | Rad51 N-terminal domain-like | 1 | 1 | |
| Folate-binding domain | Aminomethyltransferase beta-barrel domain | 1 | 1 | |
| PLP-binding barrel | Alanine racemase C-terminal domain-like | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Methylglyoxal synthase-like | 1 | 1 | |
| Carbamoyl phosphate synthetase, large subunit connection domain | Methylglyoxal synthase-like | 1 | 1 | |
| Putative DNA-binding domain | Anticodon-binding domain of PheRS | 1 | 1 | |
| PreATP-grasp domain | Methylglyoxal synthase-like | 1 | 1 | |
| dsRNA-binding domain-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| 2Fe-2S ferredoxin-like | Formate dehydrogenase/DMSO reductase, domains 1-3 | 1 | 1 | |
| FKBP-like | FKBP-like | 1 | 1 | |
| Transcription factor NusA, N-terminal domain | Nucleic acid-binding proteins | 1 | 1 | |
| Glutamine synthetase, N-terminal domain | Glutamine synthetase/guanido kinase | 1 | 1 | |
| Chorismate mutase II | 6-phosphogluconate dehydrogenase C-terminal domain-like | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Rudiment single hybrid motif | 1 | 1 | |
| PIN domain-like | DNA/RNA polymerases | 1 | 1 | |
| L9 N-domain-like | Ribosomal protein L9 C-domain | 1 | 1 | |
| Translation initiation factor IF3, N-terminal domain | Translation initiation factor IF3, C-terminal domain | 1 | 1 | |
| PreATP-grasp domain | PreATP-grasp domain | 1 | 1 | |
| Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain | Phosphohistidine domain | 1 | 1 | |
| Nucleotide-diphospho-sugar transferases | Trimeric LpxA-like enzymes | 1 | 1 | |
| Nucleotidylyl transferase | Alpha-L RNA-binding motif | 1 | 1 | |
| Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | Translation proteins | 1 | 1 | |
| PheT/TilS domain | Putative DNA-binding domain | 1 | 1 | |
| Siroheme synthase middle domains-like | Tetrapyrrole methylase | 1 | 1 | |
| Ribosomal L11/L12e N-terminal domain | Ribosomal protein L11, C-terminal domain | 1 | 1 | |
| Translation proteins | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| Periplasmic binding protein-like II | Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain | 1 | 1 | |
| PK beta-barrel domain-like | PK C-terminal domain-like | 1 | 1 | |
| Aldolase | 2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain | 1 | 1 | |
| S-adenosylmethionine synthetase | S-adenosylmethionine synthetase | 1 | 1 | |
| Thiolase-like | Thiolase-like | 1 | 1 | |
| PheT/TilS domain | Anticodon-binding domain of PheRS | 1 | 1 | |
| Nqo1 middle domain-like | Nqo1C-terminal domain-like | 1 | 1 | |
| Nucleic acid-binding proteins | GAD domain-like | 1 | 1 | |
| Sigma3 and sigma4 domains of RNA polymerase sigma factors | Sigma3 and sigma4 domains of RNA polymerase sigma factors | 1 | 1 | |
| S-adenosyl-L-methionine-dependent methyltransferases | Putative methyltransferase TM0872, insert domain | 1 | 1 | |
| Class II aaRS and biotin synthetases | SufE/NifU | 1 | 1 | |
| Epsilon subunit of F1F0-ATP synthase N-terminal domain | Epsilon subunit of F1F0-ATP synthase C-terminal domain | 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 | |
| Flavoproteins | Riboflavin synthase domain-like | 1 | 1 | |
| RNase III domain-like | dsRNA-binding domain-like | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Succinyl-CoA synthetase domains | 1 | 1 | |
| 4Fe-4S ferredoxins | Formate dehydrogenase/DMSO reductase, domains 1-3 | 1 | 1 | |
| Carbamate kinase-like | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| PUA domain-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| Chaperone J-domain | DnaJ/Hsp40 cysteine-rich domain | 1 | 1 | |
| Ribosomal protein L6 | Ribosomal protein L6 | 1 | 1 | |
| Class II aaRS and biotin synthetases | Anticodon-binding domain of PheRS | 1 | 1 | |
| DNA clamp | DNA clamp | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | 1 | 1 | |
| Nucleic acid-binding proteins | Anticodon-binding domain of PheRS | 1 | 1 | |
| Multidrug resistance efflux transporter EmrE | Multidrug resistance efflux transporter EmrE | 1 | 1 | |
| Nqo1 FMN-binding domain-like | Nqo1 middle domain-like | 1 | 1 | |
| Flavoproteins | Ferredoxin reductase-like, C-terminal NADP-linked domain | 1 | 1 | |
| THUMP domain-like | Adenine nucleotide alpha hydrolases-like | 1 | 1 | |
| Tryptophan synthase beta subunit-like PLP-dependent enzymes | ACT-like | 1 | 1 | |
| Nucleotidyltransferase | Poly A polymerase C-terminal region-like | 1 | 1 | |
| DnaK suppressor protein DksA, alpha-hairpin domain | Glucocorticoid receptor-like (DNA-binding domain) | 1 | 1 | |
| Phosphohistidine domain | Phosphoenolpyruvate/pyruvate domain | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | GMP synthetase C-terminal dimerisation domain | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Succinyl-CoA synthetase domains | 1 | 1 | |
| Lysozyme-like | beta-lactamase/transpeptidase-like | 1 | 1 | |
| Nucleotidylyl transferase | An anticodon-binding domain of class I aminoacyl-tRNA synthetases | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Initiation factor IF2/eIF5b, domain 3 | 1 | 1 | |
| Rho N-terminal domain-like | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Transcription factor NusA, N-terminal domain | Rad51 N-terminal domain-like | 1 | 1 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | Nucleic acid-binding proteins | 1 | 1 | |
| DNA primase core | DNA primase DnaG, C-terminal domain | 1 | 1 | |
| Putative DNA-binding domain | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Obg GTP-binding protein N-terminal domain | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Trypsin-like serine proteases | PDZ domain-like | 1 | 1 | |
| Macro domain-like | Zn-dependent exopeptidases | 1 | 1 | |
| Sm-like ribonucleoproteins | Mechanosensitive channel protein MscS (YggB), C-terminal domain | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | MesJ substrate recognition domain-like | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | TGS-like | 1 | 1 | |
| Band 7/SPFH domain | Band 7/SPFH domain | 1 | 1 | |
| HesB-like domain | Fe-S cluster assembly (FSCA) domain-like | 1 | 1 | |
| Periplasmic binding protein-like II | GlnB-like | 1 | 1 | |
| Class II aaRS and biotin synthetases | Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | 1 | 1 | |
| GroEL-intermediate domain like | GroEL apical domain-like | 1 | 1 | |
| Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | Eukaryotic type KH-domain (KH-domain type I) | 1 | 1 | |
| GroEL equatorial domain-like | GroEL-intermediate domain like | 1 | 1 | |
| Phosphoenolpyruvate/pyruvate domain | PK C-terminal domain-like | 1 | 1 | |
| Carbamate kinase-like | ACT-like | 1 | 1 | |
| "Winged helix" DNA-binding domain | Periplasmic binding protein-like II | 1 | 1 | |
| PIN domain-like | Ribonuclease H-like | 1 | 1 | |
| Domain of the SRP/SRP receptor G-proteins | Signal peptide-binding domain | 1 | 1 | |
| Chorismate mutase II | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Adenine nucleotide alpha hydrolases-like | Rhodanese/Cell cycle control phosphatase | 1 | 1 | |
| Thiamin diphosphate-binding fold (THDP-binding) | DHS-like NAD/FAD-binding domain | 1 | 1 | |
| Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain | Nucleotidylyl transferase | 1 | 1 | |
| Class II aaRS and biotin synthetases | GAD domain-like | 1 | 1 | |
| Rho N-terminal domain-like | Nucleic acid-binding proteins | 1 | 1 | |
| Enolase N-terminal domain-like | Enolase C-terminal domain-like | 1 | 1 | |
| PIN domain-like | 5' to 3' exonuclease, C-terminal subdomain | 1 | 1 | |
| Diaminopimelate epimerase-like | Diaminopimelate epimerase-like | 1 | 1 | |
| ACT-like | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| Tubulin nucleotide-binding domain-like | Tubulin C-terminal domain-like | 1 | 1 | |
| Nucleic acid-binding proteins | PheT/TilS domain | 1 | 1 | |
| EF-G C-terminal domain-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| Prokaryotic type KH domain (KH-domain type II) | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| HisI-like | all-alpha NTP pyrophosphatases | 1 | 1 | |
| Insert subdomain of RNA polymerase alpha subunit | C-terminal domain of RNA polymerase alpha subunit | 1 | 1 | |
| Carbamoyl phosphate synthetase, small subunit N-terminal domain | Class I glutamine amidotransferase-like | 1 | 1 | |
| Zinc beta-ribbon | DNA primase core | 1 | 1 | |
| Ribulose-phoshate binding barrel | Ribulose-phoshate binding barrel | 1 | 1 | |
| Carbamate kinase-like | Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| Nucleic acid-binding proteins | Putative DNA-binding domain | 1 | 1 | |
| Coiled-coil domain of nucleotide exchange factor GrpE | Head domain of nucleotide exchange factor GrpE | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Glutathione synthetase ATP-binding domain-like | 1 | 1 | |
| GroEL equatorial domain-like | GroEL apical domain-like | 1 | 1 | |
| HSP40/DnaJ peptide-binding domain | HSP40/DnaJ peptide-binding domain | 1 | 1 | |
| Nucleotidylyl transferase | Ribosomal protein L25-like | 1 | 1 | |
| Methylglyoxal synthase-like | Cytidine deaminase-like | 1 | 1 | |
| Eukaryotic type KH-domain (KH-domain type I) | Nucleic acid-binding proteins | 1 | 1 | |
| Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) | ThrRS/AlaRS common domain | 1 | 1 | |
| Insert subdomain of RNA polymerase alpha subunit | RBP11-like subunits of RNA polymerase | 1 | 1 | |
| Ribosomal protein L7/12, oligomerisation (N-terminal) domain | ClpS-like | 1 | 1 | |
| Actin-like ATPase domain | Heat shock protein 70kD (HSP70), peptide-binding domain | 1 | 1 | |
| ACT-like | ACT-like | 1 | 1 | |
| ClpP/crotonase | ClpP/crotonase | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Helical scaffold and wing domains of SecA | 1 | 1 | |
| Ribonuclease PH domain 2-like | Ribonuclease PH domain 2-like | 1 | 1 | |
| Putative DNA-binding domain | Initiation factor IF2/eIF5b, domain 3 | 1 | 1 | |
| Ribonuclease PH domain 2-like | Eukaryotic type KH-domain (KH-domain type I) | 1 | 1 | |
| GreA transcript cleavage protein, N-terminal domain | FKBP-like | 1 | 1 | |
| FabD/lysophospholipase-like | Probable ACP-binding domain of malonyl-CoA ACP transacylase | 1 | 1 | |
| FAD/NAD(P)-binding domain | FAD/NAD-linked reductases, dimerisation (C-terminal) domain | 1 | 1 | |
| DnaJ/Hsp40 cysteine-rich domain | HSP40/DnaJ peptide-binding domain | 1 | 1 | |
| Carbon-nitrogen hydrolase | ABC transporter transmembrane region | 1 | 1 | |
| Glutathione synthetase ATP-binding domain-like | Carbamoyl phosphate synthetase, large subunit connection domain | 1 | 1 | |
| PK beta-barrel domain-like | Phosphoenolpyruvate/pyruvate domain | 1 | 1 | |
| Class II aaRS and biotin synthetases | Translation proteins | 1 | 1 | |
| Mechanosensitive channel protein MscS (YggB), transmembrane region | Mechanosensitive channel protein MscS (YggB), C-terminal domain | 1 | 1 | |
| N-terminal domain of DnaB helicase | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| Type II DNA topoisomerase | GyrA/ParC C-terminal domain-like | 1 | 1 | |
| Prokaryotic type KH domain (KH-domain type II) | Ribosomal protein S3 C-terminal domain | 1 | 1 | |
| THUMP domain-like | Rhodanese/Cell cycle control phosphatase | 1 | 1 | |
| PheT/TilS domain | Class II aaRS and biotin synthetases | 1 | 1 | |
| 5' to 3' exonuclease, C-terminal subdomain | Ribonuclease H-like | 1 | 1 | |
| Nitrite/Sulfite reductase N-terminal domain-like | Nitrite and sulphite reductase 4Fe-4S domain-like | 1 | 1 | |
| DNA ligase/mRNA capping enzyme, catalytic domain | RuvA domain 2-like | 1 | 1 | |
| FAD/NAD(P)-binding domain | Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain | 1 | 1 | |
| Ribonuclease PH domain 2-like | Nucleic acid-binding proteins | 1 | 1 | |
| Formate/glycerate dehydrogenase catalytic domain-like | NAD(P)-binding Rossmann-fold domains | 1 | 1 | |
| TolB, N-terminal domain | Tricorn protease N-terminal domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Pre-protein crosslinking domain of SecA | 1 | 1 | |
| N-utilization substance G protein NusG, N-terminal domain | Translation proteins SH3-like domain | 1 | 1 | |
| Transcription factor NusA, N-terminal domain | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| IlvD/EDD N-terminal domain-like | LeuD/IlvD-like | 1 | 1 | |
| Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Type II DNA topoisomerase | 1 | 1 | |
| Cytochrome c oxidase subunit II-like, transmembrane region | Cupredoxins | 1 | 1 | |
| Class II aaRS and biotin synthetases | ThrRS/AlaRS common domain | 1 | 1 | |
| Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 | Nucleic acid-binding proteins | 1 | 1 | |
| Methionyl-tRNA synthetase (MetRS), Zn-domain | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 1 | 1 | |
| Mechanosensitive channel protein MscS (YggB), transmembrane region | Sm-like ribonucleoproteins | 1 | 1 | |
| R1 subunit of ribonucleotide reductase, N-terminal domain | PFL-like glycyl radical enzymes | 1 | 1 | |
| ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase | Type II DNA topoisomerase | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Nucleic acid-binding proteins | 1 | 1 | |
| Pre-protein crosslinking domain of SecA | Helical scaffold and wing domains of SecA | 1 | 1 | |
| UBA-like | Elongation factor Ts (EF-Ts), dimerisation domain | 1 | 1 | |
| CorA soluble domain-like | Magnesium transport protein CorA, transmembrane region | 1 | 1 | |
| MesJ substrate recognition domain-like | PheT/TilS domain | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | FtsH protease domain-like | 1 | 1 | |
| Double Clp-N motif | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| PreATP-grasp domain | Rudiment single hybrid motif | 1 | 1 | |
| FMN-binding split barrel | UbiD C-terminal domain-like | 1 | 1 | |
| Composite domain of metallo-dependent hydrolases | Composite domain of metallo-dependent hydrolases | 1 | 1 | |
| Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Ribonuclease PH domain 2-like | 1 | 1 | |
| 2Fe-2S ferredoxin-like | 4Fe-4S ferredoxins | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Signal peptide-binding domain | 1 | 1 | |
| Chaperone J-domain | HSP40/DnaJ peptide-binding domain | 1 | 1 | |
| Nqo5-like | HydB/Nqo4-like | 1 | 1 | |
| Formyltransferase | FMT C-terminal domain-like | 1 | 1 | |
| HAD-like | Ribosomal protein S5 domain 2-like | 1 | 1 | |
| 5' to 3' exonuclease, C-terminal subdomain | DNA/RNA polymerases | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Tetrapyrrole methylase | 1 | 1 | |
| FAD-binding/transporter-associated domain-like | Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain | 1 | 1 | |
| Nucleic acid-binding proteins | RuvA domain 2-like | 1 | 1 | |
| Methionyl-tRNA synthetase (MetRS), Zn-domain | Nucleotidylyl transferase | 1 | 1 | |
| Zinc beta-ribbon | DNA primase DnaG, C-terminal domain | 1 | 1 | |
| Ribosomal protein S5 domain 2-like | Eukaryotic type KH-domain (KH-domain type I) | 1 | 1 | |
| FAD/NAD(P)-binding domain | Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain | 1 | 1 | |
| NAD(P)-binding Rossmann-fold domains | Siroheme synthase middle domains-like | 1 | 1 | |
| Zn-dependent exopeptidases | Bacterial exopeptidase dimerisation domain | 1 | 1 | |
| Putative DNA-binding domain | Translation proteins | 1 | 1 | |
| Rad51 N-terminal domain-like | Rad51 N-terminal domain-like | 1 | 1 | |
| Nucleotidylyl transferase | Riboflavin kinase-like | 1 | 1 | |
| Ribokinase-like | Nucleotidylyl transferase | 1 | 1 | |
| HD-domain/PDEase-like | Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases | 1 | 1 | |
| CBS-domain pair | Inosine monophosphate dehydrogenase (IMPDH) | 1 | 1 | |
| Translation proteins | Initiation factor IF2/eIF5b, domain 3 | 1 | 1 | |
| Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain | Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain | 1 | 1 | |
| ACT-like | Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain | 1 | 1 | |
| Translation proteins | Translation proteins | 1 | 1 | |
| Fe,Mn superoxide dismutase (SOD), N-terminal domain | Fe,Mn superoxide dismutase (SOD), C-terminal domain | 1 | 1 | |
| ABC transporter transmembrane region | P-loop containing nucleoside triphosphate hydrolases | 1 | 1 | |
| UROD/MetE-like | UROD/MetE-like | 1 | 1 | |
| PTS system fructose IIA component-like | PTS IIb component | 1 | 1 | |
| Nitrite/Sulfite reductase N-terminal domain-like | Nitrite/Sulfite reductase N-terminal domain-like | 1 | 1 | |
| Ribonuclease H-like | DNA/RNA polymerases | 1 | 1 | |
| P-loop containing nucleoside triphosphate hydrolases | Class I glutamine amidotransferase-like | 1 | 1 | |
| Cytidine deaminase-like | Dihydrofolate reductase-like | 1 | 1 | |
| Class I glutamine amidotransferase-like | Adenine nucleotide alpha hydrolases-like | 1 | 1 | |
| Class I glutamine amidotransferase-like | GMP synthetase C-terminal dimerisation domain | 1 | 1 | |
| Riboflavin synthase domain-like | Riboflavin synthase domain-like | 1 | 1 | |
| Prokaryotic type KH domain (KH-domain type II) | Rad51 N-terminal domain-like | 1 | 1 | |
| Translation proteins | ThrRS/AlaRS common domain | 1 | 1 | |
| Nqo1 FMN-binding domain-like | Nqo1C-terminal domain-like | 1 | 1 | |
| Nucleic acid-binding proteins | Prokaryotic type KH domain (KH-domain type II) | 1 | 1 | |
| Putative DNA-binding domain | Class II aaRS and biotin synthetases | 1 | 1 | |
| Translation proteins | PRC-barrel domain | 1 | 1 | |
| RBP11-like subunits of RNA polymerase | C-terminal domain of RNA polymerase alpha subunit | 1 | 1 | |
