SUPERFAMILY 1.75 HMM library and genome assignments server

Domain combination pairs in Candidatus Riesia pediculicola USDA

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.

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Domain combination pairs

213 domain combination pairs.
Click on a column heading to sort that column, or the 'View' button to see domain architetures for that domain pair combination.

Superfamily (N) Superfamily (C) Number of occurrances Number unique
Actin-like ATPase domain Actin-like ATPase domain 82
Nucleotidylyl transferase Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 66
MurD-like peptide ligases, catalytic domain MurD-like peptide ligases, peptide-binding domain 53
Thiamin diphosphate-binding fold (THDP-binding) Thiamin diphosphate-binding fold (THDP-binding) 43
Aminoacid dehydrogenase-like, N-terminal domain NAD(P)-binding Rossmann-fold domains 42
P-loop containing nucleoside triphosphate hydrolases Translation proteins 44
Sigma2 domain of RNA polymerase sigma factors Sigma3 and sigma4 domains of RNA polymerase sigma factors 42
Nucleic acid-binding proteins Class II aaRS and biotin synthetases 43
NAD(P)-binding Rossmann-fold domains Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain 42
PreATP-grasp domain Glutathione synthetase ATP-binding domain-like 42
ValRS/IleRS/LeuRS editing domain Nucleotidylyl transferase 33
P-loop containing nucleoside triphosphate hydrolases post-AAA+ oligomerization domain-like 31
ValRS/IleRS/LeuRS editing domain Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 33
Thiamin diphosphate-binding fold (THDP-binding) TK C-terminal domain-like 32
Class II aaRS and biotin synthetases Class II aaRS ABD-related 32
Zinc beta-ribbon DNA primase core 21
P-loop containing nucleoside triphosphate hydrolases EF-G C-terminal domain-like 22
PreATP-grasp domain Rudiment single hybrid motif 21
Single hybrid motif CoA-dependent acyltransferases 22
Translation proteins SH3-like domain Nucleic acid-binding proteins 22
Glutathione synthetase ATP-binding domain-like Rudiment single hybrid motif 21
Phospholipase D/nuclease Phospholipase D/nuclease 21
MurCD N-terminal domain MurD-like peptide ligases, catalytic domain 21
Domain of the SRP/SRP receptor G-proteins P-loop containing nucleoside triphosphate hydrolases 22
MurE/MurF N-terminal domain MurD-like peptide ligases, peptide-binding domain 21
Sigma3 and sigma4 domains of RNA polymerase sigma factors Sigma3 and sigma4 domains of RNA polymerase sigma factors 21
MurCD N-terminal domain MurD-like peptide ligases, peptide-binding domain 21
CBS-domain pair FAD-binding/transporter-associated domain-like 21
Nucleotidyltransferase Poly A polymerase C-terminal region-like 21
MurE/MurF N-terminal domain MurD-like peptide ligases, catalytic domain 21
Translation proteins EF-G C-terminal domain-like 22
ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase Ribosomal protein S5 domain 2-like 22
Penicillin binding protein dimerisation domain beta-lactamase/transpeptidase-like 21
Nucleic acid-binding proteins P-loop containing nucleoside triphosphate hydrolases 22
P-loop containing nucleoside triphosphate hydrolases Ribosomal protein S5 domain 2-like 22
Formate/glycerate dehydrogenase catalytic domain-like NAD(P)-binding Rossmann-fold domains 22
Ribokinase-like Nucleotidylyl transferase 21
Zinc beta-ribbon DNA primase DnaG, C-terminal domain 21
EF-G C-terminal domain-like EF-G C-terminal domain-like 22
DNA primase core DNA primase DnaG, C-terminal domain 21
Nucleic acid-binding proteins Nucleic acid-binding proteins 22
NAD(P)-binding Rossmann-fold domains 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain 11
GroEL equatorial domain-like GroEL apical domain-like 11
Class I glutamine amidotransferase-like GMP synthetase C-terminal dimerisation domain 11
Nucleotidylyl transferase Riboflavin kinase-like 11
PUA domain-like P-loop containing nucleoside triphosphate hydrolases 11
2Fe-2S ferredoxin-like alpha-helical ferredoxin 11
Actin-like ATPase domain Heat shock protein 70kD (HSP70), C-terminal subdomain 11
Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 Nucleic acid-binding proteins 11
FMN-binding split barrel UbiD C-terminal domain-like 11
Ribosomal protein S5 domain 2-like Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 11
Trypsin-like serine proteases PDZ domain-like 11
Nucleic acid-binding proteins Anticodon-binding domain of PheRS 11
P-loop containing nucleoside triphosphate hydrolases Helical scaffold and wing domains of SecA 11
NAD(P)-binding Rossmann-fold domains 6-phosphogluconate dehydrogenase C-terminal domain-like 11
Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 11
P-loop containing nucleoside triphosphate hydrolases EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain 11
ValRS/IleRS/LeuRS editing domain tRNA-binding arm 11
Prokaryotic type KH domain (KH-domain type II) Ribosomal protein S3 C-terminal domain 11
Cytochrome c oxidase subunit II-like, transmembrane region Cupredoxins 11
Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain 11
S-adenosyl-L-methionine-dependent methyltransferases Putative methyltransferase TM0872, insert domain 11
Ribosomal protein L7/12, oligomerisation (N-terminal) domain ClpS-like 11
Rho N-terminal domain-like P-loop containing nucleoside triphosphate hydrolases 11
Nucleic acid-binding proteins PheT/TilS domain 11
Nucleic acid-binding proteins RuvA domain 2-like 11
Ribonuclease PH domain 2-like Eukaryotic type KH-domain (KH-domain type I) 11
Zn-dependent exopeptidases Bacterial exopeptidase dimerisation domain 11
Nucleotidylyl transferase Ribosomal protein L25-like 11
tRNA-binding arm Class II aaRS and biotin synthetases 11
Insert subdomain of RNA polymerase alpha subunit RBP11-like subunits of RNA polymerase 11
Phosphoglucomutase, first 3 domains Phosphoglucomutase, C-terminal domain 11
Heat shock protein 70kD (HSP70), peptide-binding domain Heat shock protein 70kD (HSP70), C-terminal subdomain 11
P-loop containing nucleoside triphosphate hydrolases RecA protein, C-terminal domain 11
Ribonuclease PH domain 2-like Ribonuclease PH domain 2-like 11
Band 7/SPFH domain Band 7/SPFH domain 11
DnaJ/Hsp40 cysteine-rich domain HSP40/DnaJ peptide-binding domain 11
Translation proteins Initiation factor IF2/eIF5b, domain 3 11
Folate-binding domain P-loop containing nucleoside triphosphate hydrolases 11
Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain Phosphohistidine domain 11
Formyltransferase FMT C-terminal domain-like 11
Chaperone J-domain DnaJ/Hsp40 cysteine-rich domain 11
Glucocorticoid receptor-like (DNA-binding domain) P-loop containing nucleoside triphosphate hydrolases 11
Class II aaRS and biotin synthetases Anticodon-binding domain of PheRS 11
P-loop containing nucleoside triphosphate hydrolases MOP-like 11
Translation proteins Translation proteins 11
Nucleic acid-binding proteins Putative DNA-binding domain 11
Coiled-coil domain of nucleotide exchange factor GrpE Head domain of nucleotide exchange factor GrpE 11
N-utilization substance G protein NusG, N-terminal domain Translation proteins SH3-like domain 11
ClpP/crotonase ClpP/crotonase 11
Nucleic acid-binding proteins GAD domain-like 11
DNA ligase/mRNA capping enzyme, catalytic domain Nucleic acid-binding proteins 11
ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase HSP90 C-terminal domain 11
DNA-glycosylase Nudix 11
L9 N-domain-like Ribosomal protein L9 C-domain 11
Transcription factor NusA, N-terminal domain Prokaryotic type KH domain (KH-domain type II) 11
Class II aaRS and biotin synthetases Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) 11
NAD(P)-binding Rossmann-fold domains Succinyl-CoA synthetase domains 11
Fe,Mn superoxide dismutase (SOD), N-terminal domain Fe,Mn superoxide dismutase (SOD), C-terminal domain 11
Phosphoglucomutase, first 3 domains Phosphoglucomutase, first 3 domains 11
Ribosomal protein S5 domain 2-like GHMP Kinase, C-terminal domain 11
Translation proteins Ribosomal protein S5 domain 2-like 11
ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase Type II DNA topoisomerase 11
Glutathione synthetase ATP-binding domain-like Succinyl-CoA synthetase domains 11
Aminoacid dehydrogenase-like, N-terminal domain Isocitrate/Isopropylmalate dehydrogenase-like 11
Rho N-terminal domain-like Nucleic acid-binding proteins 11
Ribonuclease PH domain 2-like Nucleic acid-binding proteins 11
Nucleotidylyl transferase An anticodon-binding domain of class I aminoacyl-tRNA synthetases 11
N-terminal domain of DnaB helicase P-loop containing nucleoside triphosphate hydrolases 11
NAD(P)-binding Rossmann-fold domains NAD(P)-binding Rossmann-fold domains 11
TrmE connector domain P-loop containing nucleoside triphosphate hydrolases 11
PUA domain-like Ribosomal protein S5 domain 2-like 11
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex CoA-dependent acyltransferases 11
Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 Eukaryotic type KH-domain (KH-domain type I) 11
Aspartate/glutamate racemase Aspartate/glutamate racemase 11
EF-G C-terminal domain-like Ribosomal protein S5 domain 2-like 11
Cytidine deaminase-like Dihydrofolate reductase-like 11
GreA transcript cleavage protein, N-terminal domain FKBP-like 11
Carbon-nitrogen hydrolase Adenine nucleotide alpha hydrolases-like 11
Diaminopimelate epimerase-like Diaminopimelate epimerase-like 11
Transcription factor NusA, N-terminal domain Nucleic acid-binding proteins 11
PheT/TilS domain Class II aaRS and biotin synthetases 11
Riboflavin synthase domain-like Riboflavin synthase domain-like 11
FAD/NAD(P)-binding domain FAD/NAD-linked reductases, dimerisation (C-terminal) domain 11
Nucleotidylyl transferase Alpha-L RNA-binding motif 11
MesJ substrate recognition domain-like PheT/TilS domain 11
Homo-oligomeric flavin-containing Cys decarboxylases, HFCD CoaB-like 11
RBP11-like subunits of RNA polymerase C-terminal domain of RNA polymerase alpha subunit 11
NagB/RpiA/CoA transferase-like D-ribose-5-phosphate isomerase (RpiA), lid domain 11
PTS system fructose IIA component-like PTS IIb component 11
Thiolase-like Thiolase-like 11
Obg GTP-binding protein N-terminal domain P-loop containing nucleoside triphosphate hydrolases 11
FAD/NAD(P)-binding domain FAD/NAD(P)-binding domain 11
Domain of the SRP/SRP receptor G-proteins Signal peptide-binding domain 11
L30e-like alpha/beta knot 11
Adenine nucleotide alpha hydrolases-like PheT/TilS domain 11
Ribosomal L11/L12e N-terminal domain Ribosomal protein L11, C-terminal domain 11
PK beta-barrel domain-like PK C-terminal domain-like 11
Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain Nucleotidylyl transferase 11
P-loop containing nucleoside triphosphate hydrolases Signal peptide-binding domain 11
Methionyl-tRNA synthetase (MetRS), Zn-domain Nucleotidylyl transferase 11
Adenine nucleotide alpha hydrolases-like GMP synthetase C-terminal dimerisation domain 11
P-loop containing nucleoside triphosphate hydrolases FtsH protease domain-like 11
Nicotinate/Quinolinate PRTase N-terminal domain-like Nicotinate/Quinolinate PRTase C-terminal domain-like 11
TerB-like Chaperone J-domain 11
HSP40/DnaJ peptide-binding domain HSP40/DnaJ peptide-binding domain 11
PLP-binding barrel Alanine racemase C-terminal domain-like 11
PheT/TilS domain Anticodon-binding domain of PheRS 11
Ribosomal protein S5 domain 2-like Type II DNA topoisomerase 11
R1 subunit of ribonucleotide reductase, N-terminal domain PFL-like glycyl radical enzymes 11
Putative DNA-binding domain Anticodon-binding domain of PheRS 11
Ribosomal protein L6 Ribosomal protein L6 11
Nucleotide-diphospho-sugar transferases Trimeric LpxA-like enzymes 11
PheT/TilS domain Putative DNA-binding domain 11
Enolase N-terminal domain-like Enolase C-terminal domain-like 11
Chaperone J-domain HSP40/DnaJ peptide-binding domain 11
Adenine nucleotide alpha hydrolases-like MesJ substrate recognition domain-like 11
GroEL equatorial domain-like GroEL-intermediate domain like 11
NAD(P)-binding Rossmann-fold domains TrkA C-terminal domain-like 11
Alpha-L RNA-binding motif Pseudouridine synthase 11
Putative DNA-binding domain Class II aaRS and biotin synthetases 11
UBA-like Elongation factor Ts (EF-Ts), dimerisation domain 11
Eukaryotic type KH-domain (KH-domain type I) Nucleic acid-binding proteins 11
Translation proteins EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain 11
Type II DNA topoisomerase GyrA/ParC C-terminal domain-like 11
Ribonuclease PH domain 2-like Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 11
Class I glutamine amidotransferase-like Adenine nucleotide alpha hydrolases-like 11
Ribosomal protein S5 domain 2-like HSP90 C-terminal domain 11
P-loop containing nucleoside triphosphate hydrolases Class I glutamine amidotransferase-like 11
DNA clamp DNA clamp 11
Ribosomal protein S5 domain 2-like Ribosomal protein S5 domain 2-like 11
Ribosomal protein S5 domain 2-like Nucleic acid-binding proteins 11
P-loop containing nucleoside triphosphate hydrolases Pre-protein crosslinking domain of SecA 11
FAD-binding/transporter-associated domain-like Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain 11
Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain Phosphoenolpyruvate/pyruvate domain 11
Class II aaRS and biotin synthetases GAD domain-like 11
Phosphoenolpyruvate/pyruvate domain PK C-terminal domain-like 11
Actin-like ATPase domain Heat shock protein 70kD (HSP70), peptide-binding domain 11
Nucleic acid-binding proteins Prokaryotic type KH domain (KH-domain type II) 11
MetI-like MetI-like 11
Folate-binding domain TrmE connector domain 11
Ribosomal protein S5 domain 2-like Ribonuclease PH domain 2-like 11
S-adenosylmethionine synthetase S-adenosylmethionine synthetase 11
Pre-protein crosslinking domain of SecA Helical scaffold and wing domains of SecA 11
Dihydropteroate synthetase-like Nitrite and sulphite reductase 4Fe-4S domain-like 11
Macro domain-like Zn-dependent exopeptidases 11
N-terminal nucleophile aminohydrolases (Ntn hydrolases) SIS domain 11
Tubulin nucleotide-binding domain-like Tubulin C-terminal domain-like 11
NAD(P)-binding Rossmann-fold domains Isocitrate/Isopropylmalate dehydrogenase-like 11
Single hybrid motif Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex 11
FAD/NAD(P)-binding domain Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain 11
DnaK suppressor protein DksA, alpha-hairpin domain Glucocorticoid receptor-like (DNA-binding domain) 11
P-loop containing nucleoside triphosphate hydrolases Initiation factor IF2/eIF5b, domain 3 11
PDZ domain-like PDZ domain-like 11
DNA ligase/mRNA capping enzyme, catalytic domain RuvA domain 2-like 11
P-loop containing nucleoside triphosphate hydrolases P-loop containing nucleoside triphosphate hydrolases 11
Prokaryotic type KH domain (KH-domain type II) Prokaryotic type KH domain (KH-domain type II) 11
FAD/NAD(P)-binding domain Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain 11
Triger factor/SurA peptide-binding domain-like FKBP-like 11
RNase III domain-like dsRNA-binding domain-like 11
Phosphohistidine domain Phosphoenolpyruvate/pyruvate domain 11
Insert subdomain of RNA polymerase alpha subunit C-terminal domain of RNA polymerase alpha subunit 11
dsRNA-binding domain-like Ribosomal protein S5 domain 2-like 11
Riboflavin synthase domain-like Ferredoxin reductase-like, C-terminal NADP-linked domain 11
Nucleotidylyl transferase tRNA-binding arm 11
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases tRNA-binding arm 11
GroEL-intermediate domain like GroEL apical domain-like 11
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain 1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain 11
Ribosomal protein S5 domain 2-like Eukaryotic type KH-domain (KH-domain type I) 11
Methionyl-tRNA synthetase (MetRS), Zn-domain Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases 11
FabD/lysophospholipase-like Probable ACP-binding domain of malonyl-CoA ACP transacylase 11
Translation initiation factor IF3, N-terminal domain Translation initiation factor IF3, C-terminal domain 11
PK beta-barrel domain-like Phosphoenolpyruvate/pyruvate domain 11

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