Domain combination pairs in Sludge/US, Phrap Assembly

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

1057 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
Homodimeric domain of signal transducing histidine kinase	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	157	40
P-loop containing nucleoside triphosphate hydrolases	P-loop containing nucleoside triphosphate hydrolases	120	25
Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains	Multidrug efflux transporter AcrB transmembrane domain	77	23
PYP-like sensor domain (PAS domain)	PYP-like sensor domain (PAS domain)	75	44
Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains	Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains	74	31
CheY-like	C-terminal effector domain of the bipartite response regulators	68	2
NAD(P)-binding Rossmann-fold domains	6-phosphogluconate dehydrogenase C-terminal domain-like	65	7
Actin-like ATPase domain	Actin-like ATPase domain	64	6
beta-Roll	beta-Roll	60	26
"Winged helix" DNA-binding domain	Periplasmic binding protein-like II	60	1
PYP-like sensor domain (PAS domain)	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	58	25
Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains	Multidrug efflux transporter AcrB transmembrane domain	57	23
Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains	Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains	57	19
PYP-like sensor domain (PAS domain)	Homodimeric domain of signal transducing histidine kinase	56	26
PYP-like sensor domain (PAS domain)	Nucleotide cyclase	54	24
Nucleotide cyclase	EAL domain-like	52	20
Acyl-CoA dehydrogenase NM domain-like	Acyl-CoA dehydrogenase C-terminal domain-like	51	4
Sigma2 domain of RNA polymerase sigma factors	Sigma3 and sigma4 domains of RNA polymerase sigma factors	49	5
PreATP-grasp domain	Glutathione synthetase ATP-binding domain-like	48	6
NAD(P)-binding Rossmann-fold domains	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	48	7
Calcium ATPase, transduction domain A	Calcium ATPase, transmembrane domain M	47	20
ABC transporter transmembrane region	P-loop containing nucleoside triphosphate hydrolases	47	2
Metallo-dependent hydrolases	Composite domain of metallo-dependent hydrolases	44	5
GroES-like	NAD(P)-binding Rossmann-fold domains	42	6
Thioredoxin-like	GST C-terminal domain-like	41	3
Multidrug resistance efflux transporter EmrE	Multidrug resistance efflux transporter EmrE	37	3
Nucleotidylyl transferase	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	36	12
MurD-like peptide ligases, catalytic domain	MurD-like peptide ligases, peptide-binding domain	36	8
P-loop containing nucleoside triphosphate hydrolases	Homeodomain-like	36	6
Formate/glycerate dehydrogenase catalytic domain-like	NAD(P)-binding Rossmann-fold domains	35	6
ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	CheY-like	35	22
TPR-like	TPR-like	35	13
P-loop containing nucleoside triphosphate hydrolases	Translation proteins	34	12
Thiolase-like	Thiolase-like	33	2
Thiamin diphosphate-binding fold (THDP-binding)	TK C-terminal domain-like	32	8
Calcium ATPase, transmembrane domain M	HAD-like	32	20
Thiamin diphosphate-binding fold (THDP-binding)	Thiamin diphosphate-binding fold (THDP-binding)	31	10
PYP-like sensor domain (PAS domain)	EAL domain-like	29	13
ValRS/IleRS/LeuRS editing domain	Nucleotidylyl transferase	28	9
ACT-like	ACT-like	28	10
Riboflavin synthase domain-like	Ferredoxin reductase-like, C-terminal NADP-linked domain	28	10
CheY-like	P-loop containing nucleoside triphosphate hydrolases	27	3
Multidrug efflux transporter AcrB transmembrane domain	Multidrug efflux transporter AcrB transmembrane domain	26	11
Cytochrome c	Cytochrome c	26	5
PYP-like sensor domain (PAS domain)	CheY-like	24	17
Aminoacid dehydrogenase-like, N-terminal domain	NAD(P)-binding Rossmann-fold domains	23	5
PurM N-terminal domain-like	PurM C-terminal domain-like	23	8
Zn-dependent exopeptidases	Bacterial exopeptidase dimerisation domain	23	4
P-loop containing nucleoside triphosphate hydrolases	MOP-like	23	2
(Trans)glycosidases	Glycosyl hydrolase domain	23	10
Phospholipase D/nuclease	Phospholipase D/nuclease	22	5
CheY-like	Nucleotide cyclase	22	13
Glutathione synthetase ATP-binding domain-like	Rudiment single hybrid motif	22	4
Homodimeric domain of signal transducing histidine kinase	CheY-like	22	17
Alpha-L RNA-binding motif	Pseudouridine synthase	21	1
Calcium ATPase, transduction domain A	HAD-like	21	14
P-loop containing nucleoside triphosphate hydrolases	Ribosomal protein S5 domain 2-like	21	7
Nucleic acid-binding proteins	Nucleic acid-binding proteins	21	10
Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains	Multidrug efflux transporter AcrB TolC docking domain; DN and DC subdomains	21	6
Carboxypeptidase regulatory domain-like	Porins	20	4
CheY-like	Homeodomain-like	20	4
Calcium ATPase, transmembrane domain M	Metal cation-transporting ATPase, ATP-binding domain N	19	10
Cation efflux protein transmembrane domain-like	Cation efflux protein cytoplasmic domain-like	19	3
GAF domain-like	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	18	9
CBS-domain pair	FAD-binding/transporter-associated domain-like	18	2
FAD/NAD(P)-binding domain	FAD/NAD(P)-binding domain	18	6
Homeodomain-like	Ribonuclease H-like	17	3
PLP-binding barrel	Alanine racemase C-terminal domain-like	17	6
Translation proteins	EF-G C-terminal domain-like	17	9
6-phosphogluconate dehydrogenase C-terminal domain-like	UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	17	2
Nucleic acid-binding proteins	RuvA domain 2-like	17	9
ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	Ribosomal protein S5 domain 2-like	17	6
GAF domain-like	Homodimeric domain of signal transducing histidine kinase	17	11
FAD-binding/transporter-associated domain-like	FAD-linked oxidases, C-terminal domain	17	5
Ribosomal protein S5 domain 2-like	Ribonuclease PH domain 2-like	17	7
P-loop containing nucleoside triphosphate hydrolases	C-terminal domain of alpha and beta subunits of F1 ATP synthase	16	2
FAD/NAD(P)-binding domain	FAD-linked reductases, C-terminal domain	16	5
HAMP domain-like	Homodimeric domain of signal transducing histidine kinase	16	9
cAMP-binding domain-like	"Winged helix" DNA-binding domain	16	3
FAD/NAD(P)-binding domain	FAD/NAD-linked reductases, dimerisation (C-terminal) domain	16	6
EF-G C-terminal domain-like	EF-G C-terminal domain-like	16	8
FAD/NAD(P)-binding domain	Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain	16	5
LuxS/MPP-like metallohydrolase	LuxS/MPP-like metallohydrolase	16	3
Enolase N-terminal domain-like	Enolase C-terminal domain-like	16	1
MurCD N-terminal domain	MurD-like peptide ligases, catalytic domain	15	2
P-loop containing nucleoside triphosphate hydrolases	EF-G C-terminal domain-like	15	8
DHS-like NAD/FAD-binding domain	Thiamin diphosphate-binding fold (THDP-binding)	15	3
HMA, heavy metal-associated domain	Calcium ATPase, transduction domain A	15	8
Formate dehydrogenase/DMSO reductase, domains 1-3	ADC-like	15	3
Double Clp-N motif	P-loop containing nucleoside triphosphate hydrolases	15	4
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Adenine nucleotide alpha hydrolases-like	15	2
E set domains	(Trans)glycosidases	15	9
Translation proteins	EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	15	4
"Winged helix" DNA-binding domain	GntR ligand-binding domain-like	15	1
Sm-like ribonucleoproteins	Mechanosensitive channel protein MscS (YggB), C-terminal domain	15	7
DNA methylase specificity domain	DNA methylase specificity domain	15	4
NAD(P)-binding Rossmann-fold domains	UDP-glucose/GDP-mannose dehydrogenase C-terminal domain	14	1
ParB/Sulfiredoxin	KorB DNA-binding domain-like	14	3
"Winged helix" DNA-binding domain	GAF domain-like	14	1
Nitrite/Sulfite reductase N-terminal domain-like	Nitrite and sulphite reductase 4Fe-4S domain-like	14	6
PYP-like sensor domain (PAS domain)	GAF domain-like	14	11
HAMP domain-like	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	14	8
PKD domain	PKD domain	14	13
Calcium ATPase, transduction domain A	Metal cation-transporting ATPase, ATP-binding domain N	14	6
Mechanosensitive channel protein MscS (YggB), transmembrane region	Sm-like ribonucleoproteins	14	5
Metal cation-transporting ATPase, ATP-binding domain N	HAD-like	14	8
EF-G C-terminal domain-like	Ribosomal protein S5 domain 2-like	14	6
EspE N-terminal domain-like	P-loop containing nucleoside triphosphate hydrolases	13	6
Triger factor/SurA peptide-binding domain-like	FKBP-like	13	7
CorA soluble domain-like	Magnesium transport protein CorA, transmembrane region	13	3
Class II aaRS and biotin synthetases	Class II aaRS ABD-related	13	4
N-terminal domain of alpha and beta subunits of F1 ATP synthase	P-loop containing nucleoside triphosphate hydrolases	13	2
PreATP-grasp domain	Rudiment single hybrid motif	13	2
ClpP/crotonase	ClpP/crotonase	13	2
Class II aaRS and biotin synthetases	ThrRS/AlaRS common domain	13	6
Phosphohistidine domain	Phosphoenolpyruvate/pyruvate domain	13	9
Actin-like ATPase domain	Heat shock protein 70kD (HSP70), peptide-binding domain	13	7
P-loop containing nucleoside triphosphate hydrolases	"Winged helix" DNA-binding domain	13	4
Riboflavin synthase domain-like	2Fe-2S ferredoxin-like	13	8
Pre-protein crosslinking domain of SecA	P-loop containing nucleoside triphosphate hydrolases	12	5
"Winged helix" DNA-binding domain	Dimeric alpha+beta barrel	12	1
PDZ domain-like	ClpP/crotonase	12	3
Homeodomain-like	Tetracyclin repressor-like, C-terminal domain	12	1
CheY-like	Histidine-containing phosphotransfer domain, HPT domain	12	9
Sigma3 and sigma4 domains of RNA polymerase sigma factors	Sigma3 and sigma4 domains of RNA polymerase sigma factors	12	4
Phosphoglucomutase, first 3 domains	Phosphoglucomutase, first 3 domains	12	4
NAD(P)-binding Rossmann-fold domains	ACT-like	12	8
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	CoA-dependent acyltransferases	12	5
ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	Histidine-containing phosphotransfer domain, HPT domain	12	9
MurCD N-terminal domain	MurD-like peptide ligases, peptide-binding domain	11	1
Homeodomain-like	Homeodomain-like	11	7
Trypsin-like serine proteases	PDZ domain-like	11	5
Translation proteins SH3-like domain	Nucleic acid-binding proteins	11	3
HSP40/DnaJ peptide-binding domain	HSP40/DnaJ peptide-binding domain	11	5
Phosphoglucomutase, first 3 domains	Phosphoglucomutase, C-terminal domain	11	3
Ribosomal protein S5 domain 2-like	Ribosomal protein S5 domain 2-like	11	5
Chemotaxis receptor methyltransferase CheR, N-terminal domain	S-adenosyl-L-methionine-dependent methyltransferases	11	4
CheY-like	CheY-like	11	6
Nucleotide-diphospho-sugar transferases	Trimeric LpxA-like enzymes	11	1
Nucleotidyltransferase	Nucleotidyltransferase substrate binding subunit/domain	11	9
Tubulin nucleotide-binding domain-like	Tubulin C-terminal domain-like	11	2
Ferredoxin reductase-like, C-terminal NADP-linked domain	2Fe-2S ferredoxin-like	11	7
Chaperone J-domain	HSP40/DnaJ peptide-binding domain	11	5
CheY-like	EAL domain-like	11	7
Methionine synthase domain	Cobalamin (vitamin B12)-binding domain	10	5
HMA, heavy metal-associated domain	Calcium ATPase, transmembrane domain M	10	6
alpha-helical ferredoxin	Nucleotide-binding domain	10	7
DnaJ/Hsp40 cysteine-rich domain	HSP40/DnaJ peptide-binding domain	10	5
P-loop containing nucleoside triphosphate hydrolases	Class I glutamine amidotransferase-like	10	2
DNA ligase/mRNA capping enzyme, catalytic domain	Nucleic acid-binding proteins	10	5
MurE/MurF N-terminal domain	MurD-like peptide ligases, catalytic domain	10	3
Thioesterase/thiol ester dehydrase-isomerase	Thioesterase/thiol ester dehydrase-isomerase	10	2
HD-domain/PDEase-like	CheY-like	10	2
Ribosomal protein S5 domain 2-like	GHMP Kinase, C-terminal domain	10	1
2Fe-2S ferredoxin-like	CO dehydrogenase ISP C-domain like	10	3
Ribonuclease PH domain 2-like	Eukaryotic type KH-domain (KH-domain type I)	10	5
Cupredoxins	Cupredoxins	10	6
HlyD-like secretion proteins	HlyD-like secretion proteins	10	4
Nucleic acid-binding proteins	P-loop containing nucleoside triphosphate hydrolases	10	6
Succinate dehydrogenase/fumarate reductase flavoprotein, catalytic domain	Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain	10	3
FAD/NAD(P)-binding domain	Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain	10	3
Lysozyme-like	beta-lactamase/transpeptidase-like	10	5
Nucleic acid-binding proteins	Class II aaRS and biotin synthetases	9	4
Homodimeric domain of signal transducing histidine kinase	Histidine-containing phosphotransfer domain, HPT domain	9	7
Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain	Nucleotidylyl transferase	9	3
PDZ domain-like	PDZ domain-like	9	4
NAD(P)-binding Rossmann-fold domains	NAD(P)-binding Rossmann-fold domains	9	7
Methylated DNA-protein cysteine methyltransferase domain	Methylated DNA-protein cysteine methyltransferase, C-terminal domain	9	3
Nqo1 middle domain-like	Nqo1C-terminal domain-like	9	4
Aspartate/glutamate racemase	Aspartate/glutamate racemase	9	3
GroEL equatorial domain-like	GroEL apical domain-like	9	4
6-phosphogluconate dehydrogenase C-terminal domain-like	6-phosphogluconate dehydrogenase C-terminal domain-like	9	4
LeuD/IlvD-like	Aconitase iron-sulfur domain	9	2
NAD(P)-binding Rossmann-fold domains	Succinyl-CoA synthetase domains	9	2
Cadherin-like	Cadherin-like	9	9
Nucleotidyltransferase	Poly A polymerase C-terminal region-like	9	2
Cytochrome c	C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase	9	2
P-loop containing nucleoside triphosphate hydrolases	EF-Tu/eEF-1alpha/eIF2-gamma C-terminal domain	9	2
NAD(P)-binding Rossmann-fold domains	TrkA C-terminal domain-like	9	5
Nqo1 FMN-binding domain-like	Nqo1 middle domain-like	9	3
ValRS/IleRS/LeuRS editing domain	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	9	4
Actin-like ATPase domain	HD-domain/PDEase-like	9	2
ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	CheW-like	9	7
CalX-like	CalX-like	9	5
PK beta-barrel domain-like	Phosphoenolpyruvate/pyruvate domain	9	3
N-terminal domain of alpha and beta subunits of F1 ATP synthase	C-terminal domain of alpha and beta subunits of F1 ATP synthase	8	1
HMA, heavy metal-associated domain	HAD-like	8	5
Carbon-nitrogen hydrolase	Adenine nucleotide alpha hydrolases-like	8	2
Single hybrid motif	CoA-dependent acyltransferases	8	3
Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain	Phosphohistidine domain	8	4
Single hybrid motif	Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex	8	3
Type II DNA topoisomerase	GyrA/ParC C-terminal domain-like	8	1
HD-domain/PDEase-like	Nucleotidyltransferase	8	5
Dihydropteroate synthetase-like	Methionine synthase domain	8	3
NagB/RpiA/CoA transferase-like	NagB/RpiA/CoA transferase-like	8	2
P-loop containing nucleoside triphosphate hydrolases	post-AAA+ oligomerization domain-like	8	2
CBS-domain pair	Inosine monophosphate dehydrogenase (IMPDH)	8	2
Mechanosensitive channel protein MscS (YggB), transmembrane region	Mechanosensitive channel protein MscS (YggB), C-terminal domain	8	2
Translation proteins	ThrRS/AlaRS common domain	8	5
E set domains	Glycosyl hydrolase domain	8	5
Dihydropteroate synthetase-like	Cobalamin (vitamin B12)-binding domain	8	3
DNA repair protein MutS, domain III	P-loop containing nucleoside triphosphate hydrolases	8	6
Eukaryotic type KH-domain (KH-domain type I)	Nucleic acid-binding proteins	8	4
Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain	Phosphoenolpyruvate/pyruvate domain	8	4
DPP6 N-terminal domain-like	alpha/beta-Hydrolases	8	2
Succinyl-CoA synthetase domains	Glutathione synthetase ATP-binding domain-like	8	3
L9 N-domain-like	Ribosomal protein L9 C-domain	8	1
Glutathione synthetase ATP-binding domain-like	MurD-like peptide ligases, catalytic domain	8	5
S-adenosylmethionine synthetase	S-adenosylmethionine synthetase	8	2
Ribosomal protein S5 domain 2-like	Type II DNA topoisomerase	8	4
Starch-binding domain-like	Porins	7	3
tRNA-binding arm	Class II aaRS and biotin synthetases	7	1
FMN-linked oxidoreductases	Nucleotide-binding domain	7	2
Nicotinate/Quinolinate PRTase N-terminal domain-like	Nicotinate/Quinolinate PRTase C-terminal domain-like	7	1
HD-domain/PDEase-like	ACT-like	7	5
HD-domain/PDEase-like	GAF domain-like	7	5
Ribosomal protein S5 domain 2-like	Eukaryotic type KH-domain (KH-domain type I)	7	4
Cobalamin (vitamin B12)-binding domain	Methionine synthase activation domain-like	7	4
Ribonuclease H-like	DNA/RNA polymerases	7	2
Translation proteins	Ribosomal protein S5 domain 2-like	7	4
L30e-like	alpha/beta knot	7	2
P-loop containing nucleoside triphosphate hydrolases	Signal peptide-binding domain	7	2
Fe,Mn superoxide dismutase (SOD), N-terminal domain	Fe,Mn superoxide dismutase (SOD), C-terminal domain	7	1
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	Nucleic acid-binding proteins	7	3
Glutathione synthetase ATP-binding domain-like	Carbamoyl phosphate synthetase, large subunit connection domain	7	4
Voltage-gated potassium channels	NAD(P)-binding Rossmann-fold domains	7	3
C-terminal effector domain of the bipartite response regulators	TPR-like	7	6
PEP carboxykinase N-terminal domain	PEP carboxykinase-like	7	1
RuvA domain 2-like	RuvA domain 2-like	7	5
Chaperone J-domain	DnaJ/Hsp40 cysteine-rich domain	7	3
Ribonuclease PH domain 2-like	Nucleic acid-binding proteins	7	3
"Winged helix" DNA-binding domain	"Winged helix" DNA-binding domain	7	2
Heat shock protein 70kD (HSP70), peptide-binding domain	Heat shock protein 70kD (HSP70), C-terminal subdomain	7	3
Adenine nucleotide alpha hydrolases-like	Argininosuccinate synthetase, C-terminal domain	7	1
WD40 repeat-like	WD40 repeat-like	7	6
Translation initiation factor IF3, N-terminal domain	Translation initiation factor IF3, C-terminal domain	7	1
P-loop containing nucleoside triphosphate hydrolases	Hypothetical protein YjiA, C-terminal domain	7	2
PIN domain-like	5' to 3' exonuclease, C-terminal subdomain	7	3
E set domains	E set domains	7	5
Penicillin binding protein dimerisation domain	beta-lactamase/transpeptidase-like	7	2
Adenine nucleotide alpha hydrolases-like	GMP synthetase C-terminal dimerisation domain	7	2
Thiamin diphosphate-binding fold (THDP-binding)	Pyruvate-ferredoxin oxidoreductase, PFOR, domain III	7	5
Leukotriene A4 hydrolase N-terminal domain	Metalloproteases ("zincins"), catalytic domain	7	3
DnaK suppressor protein DksA, alpha-hairpin domain	Glucocorticoid receptor-like (DNA-binding domain)	7	1
CheW-like	CheY-like	7	4
Epsilon subunit of F1F0-ATP synthase N-terminal domain	Epsilon subunit of F1F0-ATP synthase C-terminal domain	7	1
Carbamate kinase-like	ACT-like	7	4
Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain	Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	7	2
YrdC/RibB	RibA-like	7	1
Nucleotidylyl transferase	An anticodon-binding domain of class I aminoacyl-tRNA synthetases	7	1
Putative methyltransferase TM0872, insert domain	S-adenosyl-L-methionine-dependent methyltransferases	7	2
TGS-like	ThrRS/AlaRS common domain	6	2
P-loop containing nucleoside triphosphate hydrolases	TGS-like	6	1
HCP-like	Lysozyme-like	6	2
ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	Type II DNA topoisomerase	6	2
Actin-like ATPase domain	Heat shock protein 70kD (HSP70), C-terminal subdomain	6	2
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	SIS domain	6	1
Nucleic acid-binding proteins	S-adenosyl-L-methionine-dependent methyltransferases	6	2
Nucleotide cyclase	SMAD/FHA domain	6	1
Methionyl-tRNA synthetase (MetRS), Zn-domain	Nucleotidylyl transferase	6	3
Fe-S cluster assembly (FSCA) domain-like	P-loop containing nucleoside triphosphate hydrolases	6	1
GreA transcript cleavage protein, N-terminal domain	FKBP-like	6	1
P-loop containing nucleoside triphosphate hydrolases	Prokaryotic type KH domain (KH-domain type II)	6	1
Zinc beta-ribbon	DNA primase core	6	3
TGS-like	Class II aaRS and biotin synthetases	6	2
HAMP domain-like	PYP-like sensor domain (PAS domain)	6	5
Class II aaRS and biotin synthetases	Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)	6	3
Nucleotidyltransferase	ACT-like	6	4
DNA ligase/mRNA capping enzyme, catalytic domain	RuvA domain 2-like	6	4
RNase III domain-like	dsRNA-binding domain-like	6	1
P-loop containing nucleoside triphosphate hydrolases	TPR-like	6	6
NAD(P)-binding Rossmann-fold domains	LDH C-terminal domain-like	6	1
DNA clamp	DNA clamp	6	2
N-terminal domain of DnaB helicase	P-loop containing nucleoside triphosphate hydrolases	6	2
Cobalamin (vitamin B12)-binding domain	Cobalamin (vitamin B12)-dependent enzymes	6	2
Sensory domain-like	Homodimeric domain of signal transducing histidine kinase	6	5
P-loop containing nucleoside triphosphate hydrolases	FtsH protease domain-like	6	2
"Winged helix" DNA-binding domain	LexA/Signal peptidase	6	1
HprK N-terminal domain-like	PEP carboxykinase-like	6	1
DNA-glycosylase	Nudix	6	1
Formyltransferase	FMT C-terminal domain-like	6	2
TGS-like	ACT-like	6	4
P-loop containing nucleoside triphosphate hydrolases	Helical scaffold and wing domains of SecA	6	4
Nqo1 FMN-binding domain-like	alpha-helical ferredoxin	6	3
Class II aaRS and biotin synthetases	Anticodon-binding domain of PheRS	6	4
SpoIIaa-like	cAMP-binding domain-like	6	2
CBS-domain pair	MgtE membrane domain-like	6	2
MurE/MurF N-terminal domain	MurD-like peptide ligases, peptide-binding domain	6	2
NAD(P)-binding Rossmann-fold domains	Isocitrate/Isopropylmalate dehydrogenase-like	6	2
Putative DNA-binding domain	Class II aaRS and biotin synthetases	6	6
DNA repair protein MutS, domain II	DNA repair protein MutS, domain III	5	5
HI0933 insert domain-like	FAD/NAD(P)-binding domain	5	2
FAD-linked oxidases, C-terminal domain	alpha-helical ferredoxin	5	4
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain	5	2
"Winged helix" DNA-binding domain	PLP-dependent transferases	5	1
Carbamoyl phosphate synthetase, large subunit connection domain	PreATP-grasp domain	5	4
beta-Roll	Cadherin-like	5	5
IlvD/EDD N-terminal domain-like	LeuD/IlvD-like	5	1
R1 subunit of ribonucleotide reductase, N-terminal domain	PFL-like glycyl radical enzymes	5	2
P-loop containing nucleoside triphosphate hydrolases	Glucocorticoid receptor-like (DNA-binding domain)	5	3
Thioredoxin-like	FAD/NAD(P)-binding domain	5	2
Succinyl-CoA synthetase domains	Succinyl-CoA synthetase domains	5	2
Nucleotidyltransferase	TGS-like	5	4
Translation proteins	Initiation factor IF2/eIF5b, domain 3	5	4
lambda integrase-like, N-terminal domain	DNA breaking-rejoining enzymes	5	1
Ribonuclease H-like	RuvA domain 2-like	5	3
Formate/glycerate dehydrogenase catalytic domain-like	ACT-like	5	2
Subtilisin-like	Galactose-binding domain-like	5	4
P-loop containing nucleoside triphosphate hydrolases	C-terminal UvrC-binding domain of UvrB	5	3
Glutamine synthetase/guanido kinase	GatB/YqeY motif	5	2
Protein kinase-like (PK-like)	cAMP-binding domain-like	5	2
Nucleic acid-binding proteins	PheT/TilS domain	5	5
Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	ACT-like	5	4
FAD-binding/transporter-associated domain-like	Uridine diphospho-N-Acetylenolpyruvylglucosamine reductase, MurB, C-terminal domain	5	1
Thioredoxin-like	Thioredoxin-like	5	2
Nitrous oxide reductase, N-terminal domain	Cupredoxins	5	3
Periplasmic binding protein-like II	ACT-like	5	2
CheY-like	Methylesterase CheB, C-terminal domain	5	1
Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)	Translation proteins	5	4
FKBP-like	FKBP-like	5	3
Methionine synthase domain	Methionine synthase activation domain-like	5	3
beta-N-acetylhexosaminidase-like domain	(Trans)glycosidases	5	3
P-loop containing nucleoside triphosphate hydrolases	Restriction endonuclease-like	5	4
Metallo-dependent phosphatases	5'-nucleotidase (syn. UDP-sugar hydrolase), C-terminal domain	5	2
P-loop containing nucleoside triphosphate hydrolases	RecA protein, C-terminal domain	5	1
Hsp33 domain	HSP33 redox switch-like	5	1
HAMP domain-like	Nucleotide cyclase	5	4
Carbamate kinase-like	PUA domain-like	5	1
Folate-binding domain	Aminomethyltransferase beta-barrel domain	5	2
Nqo1 FMN-binding domain-like	Nqo1C-terminal domain-like	5	2
LysM domain	LysM domain	5	5
Homo-oligomeric flavin-containing Cys decarboxylases, HFCD	CoaB-like	5	1
PLP-dependent transferases	PLP-dependent transferases	5	2
Glutamine synthetase, N-terminal domain	Glutamine synthetase/guanido kinase	5	1
RuBisCO, large subunit, small (N-terminal) domain	RuBisCo, C-terminal domain	5	1
NusB-like	S-adenosyl-L-methionine-dependent methyltransferases	5	1
Hypothetical protein PA1324	Hypothetical protein PA1324	5	5
5' to 3' exonuclease, C-terminal subdomain	Ribonuclease H-like	5	3
EAL domain-like	HD-domain/PDEase-like	5	1
Sec-C motif	TPR-like	5	5
Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS)	ThrRS/AlaRS common domain	5	4
MoeA N-terminal region -like	Molybdenum cofactor biosynthesis proteins	5	2
YajQ-like	YajQ-like	5	1
FabD/lysophospholipase-like	Probable ACP-binding domain of malonyl-CoA ACP transacylase	5	1
Thioesterase/thiol ester dehydrase-isomerase	Isocitrate/Isopropylmalate dehydrogenase-like	5	1
PheT/TilS domain	Putative DNA-binding domain	5	5
Ribosomal protein S5 domain 2-like	DNA mismatch repair protein MutL	5	2
Ribosomal protein L7/12, oligomerisation (N-terminal) domain	ClpS-like	5	1
Periplasmic binding protein-like II	Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain	5	1
Aldolase	2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain	5	2
Trigger factor ribosome-binding domain	FKBP-like	5	3
Adenine nucleotide alpha hydrolases-like	DHS-like NAD/FAD-binding domain	5	1
Molybdenum cofactor biosynthesis proteins	MoeA C-terminal domain-like	5	2
Pseudouridine synthase	PUA domain-like	4	1
GAF domain-like	P-loop containing nucleoside triphosphate hydrolases	4	4
Transmembrane di-heme cytochromes	4Fe-4S ferredoxins	4	2
PHP14-like	Phospholipase D/nuclease	4	3
alpha/beta-Hydrolases	beta-Roll	4	4
PIN domain-like	Ribonuclease H-like	4	2
P-loop containing nucleoside triphosphate hydrolases	TRCF domain-like	4	3
RuvA domain 2-like	DNA helicase RuvA subunit, C-terminal domain	4	1
Adenine nucleotide alpha hydrolases-like	Adenine nucleotide alpha hydrolases-like	4	1
2Fe-2S ferredoxin-like	4Fe-4S ferredoxins	4	2
P-loop containing nucleoside triphosphate hydrolases	HRDC-like	4	2
Protein kinase-like (PK-like)	Protein kinase-like (PK-like)	4	3
GroEL equatorial domain-like	GroEL-intermediate domain like	4	2
ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	DNA mismatch repair protein MutL	4	1
GroEL-intermediate domain like	GroEL apical domain-like	4	2
RuvA domain 2-like	BRCT domain	4	2
Cytidine deaminase-like	Dihydrofolate reductase-like	4	1
NAD(P)-binding Rossmann-fold domains	Glutamyl tRNA-reductase dimerization domain	4	1
PheT/TilS domain	Class II aaRS and biotin synthetases	4	4
Molybdenum cofactor-binding domain	Molybdenum cofactor-binding domain	4	1
(Trans)glycosidases	Galactose-binding domain-like	4	3
Riboflavin synthase domain-like	Riboflavin synthase domain-like	4	1
TrmE connector domain	P-loop containing nucleoside triphosphate hydrolases	4	2
Zn-dependent exopeptidases	PA domain	4	2
HD-domain/PDEase-like	Nucleotide cyclase	4	2
TolB, N-terminal domain	Tricorn protease N-terminal domain	4	1
FMN-binding split barrel	UbiD C-terminal domain-like	4	2
Ribosomal protein S5 domain 2-like	Nucleic acid-binding proteins	4	2
Homodimeric domain of signal transducing histidine kinase	CheW-like	4	3
Cytochrome c oxidase subunit II-like, transmembrane region	Cupredoxins	4	3
Prokaryotic type KH domain (KH-domain type II)	Ribosomal protein S3 C-terminal domain	4	2
Rho N-terminal domain-like	Nucleic acid-binding proteins	4	4
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	FMN-linked oxidoreductases	4	2
PUA domain-like	P-loop containing nucleoside triphosphate hydrolases	4	3
Class II aaRS and biotin synthetases	GAD domain-like	4	3
PYP-like sensor domain (PAS domain)	Hemerythrin-like	4	2
PPK N-terminal domain-like	PHP14-like	4	3
6-phosphogluconate dehydrogenase C-terminal domain-like	ClpP/crotonase	4	3
4Fe-4S ferredoxins	Formate dehydrogenase/DMSO reductase, domains 1-3	4	2
Transmembrane di-heme cytochromes	a domain/subunit of cytochrome bc1 complex (Ubiquinol-cytochrome c reductase)	4	2
Rhodanese/Cell cycle control phosphatase	Rhodanese/Cell cycle control phosphatase	4	1
Rudiment single hybrid motif	Single hybrid motif	4	2
GIY-YIG endonuclease	C-terminal UvrC-binding domain of UvrB	4	2
Ribonuclease H-like	Nucleic acid-binding proteins	4	2
Ribosomal protein S5 domain 2-like	HSP90 C-terminal domain	4	2
Bacterial muramidases	Lysozyme-like	4	1
DNA repair protein MutS, domain I	DNA repair protein MutS, domain II	4	4
Ribosomal protein L6	Ribosomal protein L6	4	1
FMN-linked oxidoreductases	Alpha subunit of glutamate synthase, C-terminal domain	4	2
Tex N-terminal region-like	Ribonuclease H-like	4	3
PH0987 N-terminal domain-like	Cyclophilin-like	4	1
Bacterial fluorinating enzyme, N-terminal domain	Bacterial fluorinating enzyme, C-terminal domain	4	1
Nqo5-like	HydB/Nqo4-like	4	1
lambda repressor-like DNA-binding domains	Periplasmic binding protein-like I	4	1
TPR-like	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	4	2
RBP11-like subunits of RNA polymerase	Insert subdomain of RNA polymerase alpha subunit	4	3
Nucleotidylyl transferase	Ribosomal protein L25-like	4	1
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	PRTase-like	4	1
GAF domain-like	Nucleotide cyclase	4	4
Sensory domain-like	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	4	4
NAD(P)-binding Rossmann-fold domains	CBS-domain pair	4	2
Elongation factor Ts (EF-Ts), dimerisation domain	Elongation factor Ts (EF-Ts), dimerisation domain	4	2
Class II aaRS and biotin synthetases	C-terminal domain of transcriptional repressors	4	1
"Winged helix" DNA-binding domain	NagB/RpiA/CoA transferase-like	4	1
Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	tRNA-binding arm	4	3
RBP11-like subunits of RNA polymerase	C-terminal domain of RNA polymerase alpha subunit	4	3
Chorismate mutase II	Periplasmic binding protein-like II	4	2
beta-lactamase/transpeptidase-like	Penicillin-binding protein associated domain	4	1
Aminoacid dehydrogenase-like, N-terminal domain	Isocitrate/Isopropylmalate dehydrogenase-like	4	1
Glutathione synthetase ATP-binding domain-like	Phosphohistidine domain	4	4
"Winged helix" DNA-binding domain	HRDC-like	4	3
P-loop containing nucleoside triphosphate hydrolases	CarD-like	4	3
Homeodomain-like	TATA-box binding protein-like	4	3
Resolvase-like	Homeodomain-like	4	1
2Fe-2S ferredoxin-like	alpha-helical ferredoxin	4	1
Carbamoyl phosphate synthetase, small subunit N-terminal domain	Class I glutamine amidotransferase-like	4	1
Glutamyl tRNA-reductase catalytic, N-terminal domain	Glutamyl tRNA-reductase dimerization domain	4	1
HD-domain/PDEase-like	TGS-like	4	3
TrkA C-terminal domain-like	TrkA C-terminal domain-like	4	2
FAD/NAD(P)-binding domain	4Fe-4S ferredoxins	4	2
Nucleic acid-binding proteins	BRCT domain	4	2
Spermadhesin, CUB domain	Fibronectin type III	4	4
Alkaline phosphatase-like	2,3-Bisphosphoglycerate-independent phosphoglycerate mutase, substrate-binding domain	4	3
Glutamyl tRNA-reductase catalytic, N-terminal domain	NAD(P)-binding Rossmann-fold domains	4	1
Thioredoxin-like	Six-hairpin glycosidases	4	3
DsbC/DsbG N-terminal domain-like	Thioredoxin-like	4	3
C-terminal UvrC-binding domain of UvrB	RuvA domain 2-like	4	3
YegP-like	YegP-like	4	1
Dihydropteroate synthetase-like	Methionine synthase activation domain-like	4	2
DNA ligase/mRNA capping enzyme, catalytic domain	BRCT domain	4	2
Nucleic acid-binding proteins	DNA helicase RuvA subunit, C-terminal domain	4	1
Nucleotidylyl transferase	Alpha-L RNA-binding motif	4	1
Glutathione synthetase ATP-binding domain-like	Acyl-CoA N-acyltransferases (Nat)	4	2
Pre-protein crosslinking domain of SecA	Helical scaffold and wing domains of SecA	4	2
PLP-dependent transferases	Ornithine decarboxylase C-terminal domain	4	2
Nucleotide cyclase	Hemerythrin-like	4	3
CO dehydrogenase ISP C-domain like	FAD-binding/transporter-associated domain-like	4	3
Urease metallochaperone UreE, N-terminal domain	Urease metallochaperone UreE, C-terminal domain	4	2
Methylglyoxal synthase-like	Cytidine deaminase-like	4	1
PUA domain-like	alpha/beta knot	4	2
PreATP-grasp domain	Single hybrid motif	3	1
lambda repressor-like DNA-binding domains	LexA/Signal peptidase	3	1
Macro domain-like	Zn-dependent exopeptidases	3	1
PurS-like	PurM C-terminal domain-like	3	3
Single hybrid motif	Single hybrid motif	3	2
Aconitase B, N-terminal domain	LeuD/IlvD-like	3	3
FAD-binding/transporter-associated domain-like	alpha-helical ferredoxin	3	3
Class I glutamine amidotransferase-like	GMP synthetase C-terminal dimerisation domain	3	1
HMA, heavy metal-associated domain	HMA, heavy metal-associated domain	3	3
TATA-box binding protein-like	DNA-glycosylase	3	2
GAF domain-like	EAL domain-like	3	3
N-terminal domain of MutM-like DNA repair proteins	S13-like H2TH domain	3	1
PurM N-terminal domain-like	Class I glutamine amidotransferase-like	3	3
FGAM synthase PurL, linker domain	PurM C-terminal domain-like	3	3
TK C-terminal domain-like	Pyruvate-ferredoxin oxidoreductase, PFOR, domain III	3	3
YgfB-like	Sec-C motif	3	1
PUA domain-like	Ribosomal protein S5 domain 2-like	3	2
Cobalamin (vitamin B12)-binding domain	P-loop containing nucleoside triphosphate hydrolases	3	2
Histidine-containing phosphotransfer domain, HPT domain	Histidine-containing phosphotransfer domain, HPT domain	3	3
Homeodomain-like	DNA-glycosylase	3	2
Lysozyme-like	LysM domain	3	2
Glutathione synthetase ATP-binding domain-like	MurD-like peptide ligases, peptide-binding domain	3	3
alpha/beta-Hydrolases	S-adenosyl-L-methionine-dependent methyltransferases	3	1
TGS-like	Class II aaRS ABD-related	3	1
Obg GTP-binding protein N-terminal domain	P-loop containing nucleoside triphosphate hydrolases	3	1
Class I glutamine amidotransferase-like	Adenine nucleotide alpha hydrolases-like	3	1
Nucleotidylyl transferase	tRNA-binding arm	3	2
DNA repair protein MutS, domain II	P-loop containing nucleoside triphosphate hydrolases	3	3
PUA domain-like	S-adenosyl-L-methionine-dependent methyltransferases	3	1
Nudix	Thiamin phosphate synthase	3	1
FGAM synthase PurL, linker domain	PurM N-terminal domain-like	3	3
Voltage-gated potassium channels	TrkA C-terminal domain-like	3	1
beta-Galactosidase/glucuronidase domain	(Trans)glycosidases	3	2
Ribonuclease PH domain 2-like	Ribonuclease PH domain 2-like	3	2
Diaminopimelate epimerase-like	Diaminopimelate epimerase-like	3	1
Trypsin-like serine proteases	TPR-like	3	2
Methylesterase CheB, C-terminal domain	Chemotaxis receptor methyltransferase CheR, N-terminal domain	3	2
RuvA domain 2-like	JAB1/MPN domain	3	1
Class II aaRS and biotin synthetases	Translation proteins	3	2
FMN-linked oxidoreductases	FAD/NAD(P)-binding domain	3	2
Rho N-terminal domain-like	P-loop containing nucleoside triphosphate hydrolases	3	3
PhoU-like	Phosphotyrosine protein phosphatases I	3	1
NAD(P)-binding Rossmann-fold domains	Glutathione synthetase ATP-binding domain-like	3	1
Sm-like ribonucleoproteins	cAMP-binding domain-like	3	2
4Fe-4S ferredoxins	4Fe-4S ferredoxins	3	1
Calcium-dependent phosphotriesterase	Calcium-dependent phosphotriesterase	3	3
Peptidase/esterase 'gauge' domain	alpha/beta-Hydrolases	3	1
Nucleic acid-binding proteins	Putative DNA-binding domain	3	3
Toll/Interleukin receptor TIR domain	P-loop containing nucleoside triphosphate hydrolases	3	3
ACT-like	Formyltransferase	3	1
Creatinase/prolidase N-terminal domain	Creatinase/aminopeptidase	3	1
NAD(P)-binding Rossmann-fold domains	Acyl-CoA N-acyltransferases (Nat)	3	1
MFS general substrate transporter	Glycerol-3-phosphate (1)-acyltransferase	3	1
Trigger factor ribosome-binding domain	Triger factor/SurA peptide-binding domain-like	3	1
UBA-like	Elongation factor Ts (EF-Ts), dimerisation domain	3	1
Insert subdomain of RNA polymerase alpha subunit	C-terminal domain of RNA polymerase alpha subunit	3	2
ThrRS/AlaRS common domain	Class II aaRS ABD-related	3	1
Ada DNA repair protein, N-terminal domain (N-Ada 10)	Homeodomain-like	3	2
N-terminal domain of MutM-like DNA repair proteins	Glucocorticoid receptor-like (DNA-binding domain)	3	1
S13-like H2TH domain	Glucocorticoid receptor-like (DNA-binding domain)	3	1
Tex N-terminal region-like	RuvA domain 2-like	3	2
Ada DNA repair protein, N-terminal domain (N-Ada 10)	TATA-box binding protein-like	3	2
Succinyl-CoA synthetase domains	Acyl-CoA N-acyltransferases (Nat)	3	1
PurS-like	PurM N-terminal domain-like	3	3
Chaperone J-domain	HSC20 (HSCB), C-terminal oligomerisation domain	3	1
P-loop containing nucleoside triphosphate hydrolases	C-type lectin-like	3	3
Glutathione synthetase ATP-binding domain-like	Single hybrid motif	3	1
Cryptochrome/photolyase, N-terminal domain	Cryptochrome/photolyase FAD-binding domain	3	1
Glutathione synthetase ATP-binding domain-like	Glutathione synthetase ATP-binding domain-like	3	2
(Trans)glycosidases	(Trans)glycosidases	3	2
EreA/ChaN-like	PDZ domain-like	3	1
DNA repair protein MutS, domain I	DNA repair protein MutS, domain III	3	3
PurS-like	FGAM synthase PurL, linker domain	3	3
Phosphofructokinase	Phosphofructokinase	3	1
NagB/RpiA/CoA transferase-like	alpha-helical ferredoxin	3	2
Phospholipase D/nuclease	SMAD/FHA domain	3	2
HD-domain/PDEase-like	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	3	1
PurM N-terminal domain-like	PurM N-terminal domain-like	3	3
HD-domain/PDEase-like	HD-domain/PDEase-like	3	2
MOP-like	MOP-like	3	1
alpha-helical ferredoxin	alpha-helical ferredoxin	3	3
N-terminal domain of bifunctional PutA protein	FAD-linked oxidoreductase	3	2
Heme-dependent peroxidases	Heme-dependent peroxidases	3	1
ACP-like	Acetyl-CoA synthetase-like	3	3
PurM C-terminal domain-like	Class I glutamine amidotransferase-like	3	3
Nucleotide-binding domain	FAD/NAD(P)-binding domain	3	2
Class II aaRS and biotin synthetases	YbaK/ProRS associated domain	3	2
FAD-linked reductases, C-terminal domain	4Fe-4S ferredoxins	3	1
alpha-helical ferredoxin	4Fe-4S ferredoxins	3	3
Methylesterase CheB, C-terminal domain	S-adenosyl-L-methionine-dependent methyltransferases	3	2
Histidine-containing phosphotransfer domain, HPT domain	CheW-like	3	2
ADC synthase	D-aminoacid aminotransferase-like PLP-dependent enzymes	3	1
P-loop containing nucleoside triphosphate hydrolases	Smc hinge domain	3	3
NagB/RpiA/CoA transferase-like	D-ribose-5-phosphate isomerase (RpiA), lid domain	3	1
YjeF N-terminal domain-like	Ribokinase-like	3	1
Translation proteins	Translation proteins	3	2
2Fe-2S ferredoxin-like	Formate dehydrogenase/DMSO reductase, domains 1-3	3	1
Galactose-binding domain-like	beta-Galactosidase/glucuronidase domain	3	2
Nitrite and sulphite reductase 4Fe-4S domain-like	Nitrite and sulphite reductase 4Fe-4S domain-like	3	2
alpha/beta-Hydrolases	alpha/beta-Hydrolases	3	3
Ribosomal L11/L12e N-terminal domain	Ribosomal protein L11, C-terminal domain	3	1
Tryptophan synthase beta subunit-like PLP-dependent enzymes	ACT-like	3	1
NAD(P)-binding Rossmann-fold domains	1-deoxy-D-xylulose-5-phosphate reductoisomerase, C-terminal domain	3	1
Glutathione synthetase ATP-binding domain-like	Methylglyoxal synthase-like	3	2
Arginyl-tRNA synthetase (ArgRS), N-terminal 'additional' domain	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	3	1
Multiheme cytochromes	TPR-like	3	1
Mechanosensitive channel protein MscS (YggB), C-terminal domain	cAMP-binding domain-like	3	2
PreATP-grasp domain	PreATP-grasp domain	3	2
MgtE N-terminal domain-like	CBS-domain pair	3	2
Nucleotidylyl transferase	Riboflavin kinase-like	3	1
DNA primase core	DNA primase DnaG, C-terminal domain	3	2
Coiled-coil domain of nucleotide exchange factor GrpE	Head domain of nucleotide exchange factor GrpE	3	1
GroES-like	GroES-like	3	1
Nucleic acid-binding proteins	Prokaryotic type KH domain (KH-domain type II)	3	2
Aldehyde ferredoxin oxidoreductase, N-terminal domain	Aldehyde ferredoxin oxidoreductase, C-terminal domains	3	1
Lysozyme-like	PGBD-like	3	3
Glutathione synthetase ATP-binding domain-like	Phosphoenolpyruvate/pyruvate domain	3	3
Pectin lyase-like	Pectin lyase-like	3	2
Transmembrane di-heme cytochromes	2Fe-2S ferredoxin-like	3	3
NAD(P)-binding Rossmann-fold domains	ClpP/crotonase	3	2
Putative DNA-binding domain	Anticodon-binding domain of PheRS	3	3
alpha-helical ferredoxin	FAD/NAD(P)-binding domain	3	3
Adenine nucleotide alpha hydrolases-like	GAF domain-like	3	2
HAMP domain-like	CheY-like	3	3
Adenine nucleotide alpha hydrolases-like	Homodimeric domain of signal transducing histidine kinase	3	2
MoeA N-terminal region -like	MoeA C-terminal domain-like	3	1
Transcription factor NusA, N-terminal domain	Nucleic acid-binding proteins	3	2
FMT C-terminal domain-like	ClpP/crotonase	3	2
Single hybrid motif	Thiolase-like	2	2
Pentapeptide repeat-like	Pentapeptide repeat-like	2	1
TPR-like	Homodimeric domain of signal transducing histidine kinase	2	1
Calcium-dependent phosphotriesterase	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	2	2
Nucleic acid-binding proteins	Rad51 N-terminal domain-like	2	1
post-HMGL domain-like	2-isopropylmalate synthase LeuA, allosteric (dimerisation) domain	2	2
PYP-like sensor domain (PAS domain)	Histidine-containing phosphotransfer domain, HPT domain	2	2
RuvA domain 2-like	P-loop containing nucleoside triphosphate hydrolases	2	1
PheT/TilS domain	Anticodon-binding domain of PheRS	2	2
Aldolase	Chorismate mutase II	2	1
Sensory domain-like	CheY-like	2	2
Nitrite/Sulfite reductase N-terminal domain-like	Nitrite/Sulfite reductase N-terminal domain-like	2	1
Thioredoxin-like	Nqo1 FMN-binding domain-like	2	2
Transcription factor NusA, N-terminal domain	Rad51 N-terminal domain-like	2	1
PIN domain-like	DNA/RNA polymerases	2	1
Hemerythrin-like	Homodimeric domain of signal transducing histidine kinase	2	1
Phase 1 flagellin	Phase 1 flagellin	2	1
all-alpha NTP pyrophosphatases	all-alpha NTP pyrophosphatases	2	1
DNA repair protein MutS, domain I	P-loop containing nucleoside triphosphate hydrolases	2	2
4'-phosphopantetheinyl transferase	4'-phosphopantetheinyl transferase	2	1
Quinoprotein alcohol dehydrogenase-like	Calcium-dependent phosphotriesterase	2	2
FAD/NAD(P)-binding domain	Rhodanese/Cell cycle control phosphatase	2	1
alpha/beta-Hydrolases	Cadherin-like	2	2
dsRNA-binding domain-like	Ribosomal protein S5 domain 2-like	2	1
beta-lactamase/transpeptidase-like	Penicillin-binding protein 2x (pbp-2x), c-terminal domain	2	2
HisI-like	all-alpha NTP pyrophosphatases	2	1
PGBD-like	L,D-transpeptidase catalytic domain-like	2	1
Methyl-accepting chemotaxis protein (MCP) signaling domain	Hemerythrin-like	2	1
GroES-like	CBS-domain pair	2	1
TPR-like	DPP6 N-terminal domain-like	2	1
Thiamin diphosphate-binding fold (THDP-binding)	4Fe-4S ferredoxins	2	2
SMAD/FHA domain	SMAD/FHA domain	2	2
Integrin alpha N-terminal domain	beta-Roll	2	2
P-loop containing nucleoside triphosphate hydrolases	Initiation factor IF2/eIF5b, domain 3	2	2
Phosphohistidine domain	Acyl-CoA N-acyltransferases (Nat)	2	2
gp5 N-terminal domain-like	Phage fibre proteins	2	1
Phosphoenolpyruvate/pyruvate domain	Acyl-CoA N-acyltransferases (Nat)	2	2
TK C-terminal domain-like	Thiolase-like	2	2
HCP-like	Trypsin-like serine proteases	2	2
Carbamate kinase-like	NAD(P)-binding Rossmann-fold domains	2	2
MgtE N-terminal domain-like	MgtE membrane domain-like	2	1
Class I glutamine amidotransferase-like	LD-carboxypeptidase A C-terminal domain-like	2	1
Sensory domain-like	PYP-like sensor domain (PAS domain)	2	2
Cytochrome c	Rhodanese/Cell cycle control phosphatase	2	2
N-utilization substance G protein NusG, N-terminal domain	Translation proteins SH3-like domain	2	1
TPR-like	UDP-Glycosyltransferase/glycogen phosphorylase	2	1
GIY-YIG endonuclease	RuvA domain 2-like	2	1
N-terminal domain of bifunctional PutA protein	ALDH-like	2	1
PIN domain-like	PLP-dependent transferases	2	1
Rad51 N-terminal domain-like	Rad51 N-terminal domain-like	2	1
YVTN repeat-like/Quinoprotein amine dehydrogenase	Caspase-like	2	2
Caspase-like	Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	2	1
Aldolase	post-HMGL domain-like	2	2
RuvA domain 2-like	MCP/YpsA-like	2	2
DNA/RNA polymerases	Lesion bypass DNA polymerase (Y-family), little finger domain	2	1
Translation proteins	PRC-barrel domain	2	1
PreATP-grasp domain	Methylglyoxal synthase-like	2	1
Tetrapyrrole methylase	S-adenosyl-L-methionine-dependent methyltransferases	2	1
Adenine nucleotide alpha hydrolases-like	PheT/TilS domain	2	1
Nucleotidyltransferase substrate binding subunit/domain	ACT-like	2	1
Tryptophan synthase beta subunit-like PLP-dependent enzymes	CBS-domain pair	2	1
ValRS/IleRS/LeuRS editing domain	tRNA-binding arm	2	1
FMN-binding split barrel	Riboflavin synthase domain-like	2	2
Methionyl-tRNA synthetase (MetRS), Zn-domain	Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases	2	2
"Winged helix" DNA-binding domain	Chorismate lyase-like	2	1
GAF domain-like	EspE N-terminal domain-like	2	2
Fic-like	"Winged helix" DNA-binding domain	2	1
Barwin-like endoglucanases	Sporulation related repeat	2	1
Zn-dependent exopeptidases	PDZ domain-like	2	2
Nucleotidyltransferase substrate binding subunit/domain	Nucleotidyltransferase substrate binding subunit/domain	2	2
Transcription factor NusA, N-terminal domain	Prokaryotic type KH domain (KH-domain type II)	2	1
DinB/YfiT-like putative metalloenzymes	C-type lectin-like	2	2
PYP-like sensor domain (PAS domain)	Homeodomain-like	2	1
Toll/Interleukin receptor TIR domain	S-adenosyl-L-methionine-dependent methyltransferases	2	1
Rhodanese/Cell cycle control phosphatase	Activating enzymes of the ubiquitin-like proteins	2	1
P-loop containing nucleoside triphosphate hydrolases	Cobalamin (vitamin B12)-dependent enzymes	2	2
Nucleotide-binding domain	FAD-linked reductases, C-terminal domain	2	2
Nucleotidyltransferase	PAP/OAS1 substrate-binding domain	2	1
Protein kinase-like (PK-like)	P-loop containing nucleoside triphosphate hydrolases	2	1
PIN domain-like	P-loop containing nucleoside triphosphate hydrolases	2	1
FAD/NAD(P)-binding domain	PurM N-terminal domain-like	2	2
Domain of the SRP/SRP receptor G-proteins	P-loop containing nucleoside triphosphate hydrolases	2	2
Acylphosphatase/BLUF domain-like	YrdC/RibB	2	2
MgtE N-terminal domain-like	CorA soluble domain-like	2	2
Hemerythrin-like	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	2	1
"Winged helix" DNA-binding domain	Phosphotyrosine protein phosphatases I	2	1
Acyl-CoA N-acyltransferases (Nat)	beta-carbonic anhydrase, cab	2	1
Nucleotidylyl transferase	Nucleic acid-binding proteins	2	2
MesJ substrate recognition domain-like	PheT/TilS domain	2	1
MurD-like peptide ligases, peptide-binding domain	PLP-binding barrel	2	2
(Trans)glycosidases	Beta-D-glucan exohydrolase, C-terminal domain	2	2
Cytochrome c oxidase subunit II-like, transmembrane region	Cytochrome c	2	1
Nucleoside phosphorylase/phosphoribosyltransferase catalytic domain	Pyrimidine nucleoside phosphorylase C-terminal domain	2	2
Homocysteine S-methyltransferase	Dihydropteroate synthetase-like	2	2
OMPA-like	OmpA-like	2	1
MFS general substrate transporter	MFS general substrate transporter	2	1
2Fe-2S ferredoxin-like	FAD/NAD(P)-binding domain	2	2
Carbamate kinase-like	Acyl-CoA N-acyltransferases (Nat)	2	1
P-loop containing nucleoside triphosphate hydrolases	Ankyrin repeat	2	2
Ribonuclease PH domain 2-like	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3	2	2
Prokaryotic type KH domain (KH-domain type II)	Rad51 N-terminal domain-like	2	1
Nucleic acid-binding proteins	GAD domain-like	2	1
Adenine nucleotide alpha hydrolases-like	MesJ substrate recognition domain-like	2	1
HCP-like	HCP-like	2	2
FAD-linked oxidoreductase	ALDH-like	2	1
FAD/NAD(P)-binding domain	Nitrite/Sulfite reductase N-terminal domain-like	2	2
PYP-like sensor domain (PAS domain)	P-loop containing nucleoside triphosphate hydrolases	2	1
Single hybrid motif	FAD/NAD(P)-binding domain	2	2
Nucleotidyltransferase	Nucleotidyltransferase	2	2
NAD(P)-binding Rossmann-fold domains	RmlC-like cupins	2	1
P-loop containing nucleoside triphosphate hydrolases	WD40 repeat-like	2	2
TPR-like	HCP-like	2	2
Nucleotide-binding domain	4Fe-4S ferredoxins	2	2
Phosphoenolpyruvate/pyruvate domain	PK C-terminal domain-like	2	1
ACT-like	PLP-binding barrel	2	2
Nucleotide-diphospho-sugar transferases	RmlC-like cupins	2	1
Hemerythrin-like	CheY-like	2	1
MurD-like peptide ligases, peptide-binding domain	Alanine racemase C-terminal domain-like	2	2
HAMP domain-like	EAL domain-like	2	2
Class I glutamine amidotransferase-like	Homeodomain-like	2	1
Sensory domain-like	Methyl-accepting chemotaxis protein (MCP) signaling domain	2	1
RmlC-like cupins	RmlC-like cupins	2	1
"Winged helix" DNA-binding domain	Nucleotidyltransferase	2	1
Ribosomal protein S5 domain 2-like	Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3	2	2
SufE/NifU	Fe-S cluster assembly (FSCA) domain-like	2	1
Phosphoglycerate mutase-like	Nudix	2	1
Tex N-terminal region-like	Nucleic acid-binding proteins	2	1
Zinc beta-ribbon	DNA primase DnaG, C-terminal domain	2	1
Nucleotidyltransferase substrate binding subunit/domain	HD-domain/PDEase-like	2	1
Adenine nucleotide alpha hydrolases-like	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	2	1
YbaK/ProRS associated domain	Class II aaRS ABD-related	2	1
PK beta-barrel domain-like	PK C-terminal domain-like	2	1
MetI-like	MetI-like	2	1
PPK N-terminal domain-like	Phospholipase D/nuclease	2	2
GAF domain-like	HlyD-like secretion proteins	2	1
Class II aaRS ABD-related	C-terminal domain of ProRS	2	2
ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	GntR ligand-binding domain-like	2	1
Cupredoxins	Cytochrome c	2	1
S-adenosyl-L-methionine-dependent methyltransferases	NAD(P)-binding Rossmann-fold domains	2	2
P-loop containing nucleoside triphosphate hydrolases	TrpR-like	2	1
Quinoprotein alcohol dehydrogenase-like	Caspase-like	2	2
CheC-like	Surface presentation of antigens (SPOA)	2	1
Carbamoyl phosphate synthetase, large subunit connection domain	Methylglyoxal synthase-like	2	1
Chorismate mutase II	ACT-like	2	1
Prokaryotic type KH domain (KH-domain type II)	Prokaryotic type KH domain (KH-domain type II)	2	1
TK C-terminal domain-like	Single hybrid motif	2	2
Acetyl-CoA synthetase-like	Glycerol-3-phosphate (1)-acyltransferase	2	2
TSP type-3 repeat	OmpA-like	2	2
beta-Roll	CalX-like	2	2
Ada DNA repair protein, N-terminal domain (N-Ada 10)	DNA-glycosylase	2	1
WD40 repeat-like	YVTN repeat-like/Quinoprotein amine dehydrogenase	2	2
PYP-like sensor domain (PAS domain)	GntR ligand-binding domain-like	2	1
P-loop containing nucleoside triphosphate hydrolases	C-terminal effector domain of the bipartite response regulators	2	2
YhbC-like, N-terminal domain	YhbC-like, C-terminal domain	2	1
5' to 3' exonuclease, C-terminal subdomain	DNA/RNA polymerases	2	1
Protein kinase-like (PK-like)	HD-domain/PDEase-like	2	2
PurM C-terminal domain-like	PurM C-terminal domain-like	2	2
CarD-like	TRCF domain-like	2	2
DPP6 N-terminal domain-like	Caspase-like	2	2
Toll/Interleukin receptor TIR domain	C-type lectin-like	2	2
Metalloproteases ("zincins"), catalytic domain	CalX-like	2	2
CoA-transferase family III (CaiB/BaiF)	CoA-transferase family III (CaiB/BaiF)	2	1
ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	HSP90 C-terminal domain	2	1
FAD/NAD-linked reductases, dimerisation (C-terminal) domain	Rhodanese/Cell cycle control phosphatase	2	1
Periplasmic binding protein-like II	PYP-like sensor domain (PAS domain)	1	1
2Fe-2S ferredoxin-like	CO dehydrogenase molybdoprotein N-domain-like	1	1
Acetyl-CoA synthetase-like	Trimeric LpxA-like enzymes	1	1
Nucleoside phosphorylase/phosphoribosyltransferase N-terminal domain	Pyrimidine nucleoside phosphorylase C-terminal domain	1	1
Trimeric LpxA-like enzymes	Trimeric LpxA-like enzymes	1	1
Chemotaxis receptor methyltransferase CheR, N-terminal domain	PYP-like sensor domain (PAS domain)	1	1
Quinoprotein alcohol dehydrogenase-like	CheY-like	1	1
Homocysteine S-methyltransferase	Methionine synthase domain	1	1
ISP domain	Bet v1-like	1	1
Thioredoxin-like	TPR-like	1	1
UROD/MetE-like	UROD/MetE-like	1	1
HCP-like	CheW-like	1	1
"Winged helix" DNA-binding domain	S-adenosyl-L-methionine-dependent methyltransferases	1	1
Urease, beta-subunit	Metallo-dependent hydrolases	1	1
SpoIIaa-like	SpoIIaa-like	1	1
Globin-like	Cobalamin (vitamin B12)-binding domain	1	1
FAD/NAD(P)-binding domain	PurM C-terminal domain-like	1	1
SGNH hydrolase	beta-N-acetylhexosaminidase-like domain	1	1
Class II aaRS and biotin synthetases	SufE/NifU	1	1
N-terminal nucleophile aminohydrolases (Ntn hydrolases)	Alpha subunit of glutamate synthase, C-terminal domain	1	1
Immunoglobulin	Immunoglobulin	1	1
Homocysteine S-methyltransferase	Cobalamin (vitamin B12)-binding domain	1	1
CoA-dependent acyltransferases	CoA-dependent acyltransferases	1	1
C-terminal effector domain of the bipartite response regulators	TolB, N-terminal domain	1	1
WD40 repeat-like	Caspase-like	1	1
(Trans)glycosidases	Protein kinase-like (PK-like)	1	1
Galactose-binding domain-like	beta-Roll	1	1
Formyltransferase	ClpP/crotonase	1	1
YefM-like	RelE-like	1	1
UDP-Glycosyltransferase/glycogen phosphorylase	HAD-like	1	1
Restriction endonuclease-like	Pentapeptide repeat-like	1	1
NagB/RpiA/CoA transferase-like	LmbE-like	1	1
PRTase-like	PRTase-like	1	1
Protein kinase-like (PK-like)	Adenine nucleotide alpha hydrolases-like	1	1
ParB/Sulfiredoxin	S-adenosyl-L-methionine-dependent methyltransferases	1	1
S-adenosyl-L-methionine-dependent methyltransferases	LexA/Signal peptidase	1	1
Putative DNA-binding domain	P-loop containing nucleoside triphosphate hydrolases	1	1
Purple acid phosphatase, N-terminal domain	Metallo-dependent phosphatases	1	1
P-loop containing nucleoside triphosphate hydrolases	LexA/Signal peptidase	1	1
His-Me finger endonucleases	DNA-binding domain	1	1
Cation efflux protein transmembrane domain-like	Cation efflux protein transmembrane domain-like	1	1
P-loop containing nucleoside triphosphate hydrolases	Nucleotide-diphospho-sugar transferases	1	1
Acyl-CoA N-acyltransferases (Nat)	Acyl-CoA N-acyltransferases (Nat)	1	1
Nucleic acid-binding proteins	Anticodon-binding domain of PheRS	1	1
Inosine monophosphate dehydrogenase (IMPDH)	Inosine monophosphate dehydrogenase (IMPDH)	1	1
MgtE N-terminal domain-like	Magnesium transport protein CorA, transmembrane region	1	1
PP2C-like	Protein kinase-like (PK-like)	1	1
KorB DNA-binding domain-like	C-terminal domain of transcriptional repressors	1	1
AhpD-like	AhpD-like	1	1
PKD domain	Anthrax protective antigen	1	1
Homocysteine S-methyltransferase	Methionine synthase activation domain-like	1	1
Chaperone J-domain	Trypsin-like serine proteases	1	1
Chaperone J-domain	P-loop containing nucleoside triphosphate hydrolases	1	1
Thiamin diphosphate-binding fold (THDP-binding)	Single hybrid motif	1	1
Kelch motif	Galactose oxidase, central domain	1	1
Methyl-accepting chemotaxis protein (MCP) signaling domain	PilZ domain-like	1	1
Ribonuclease H-like	P-loop containing nucleoside triphosphate hydrolases	1	1
EspE N-terminal domain-like	EspE N-terminal domain-like	1	1
Caspase-like	HCP-like	1	1
GroES-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	1	1
DPP6 N-terminal domain-like	Quinoprotein alcohol dehydrogenase-like	1	1
Metalloproteases ("zincins"), catalytic domain	Hemopexin-like domain	1	1
His-Me finger endonucleases	Fibronectin type III	1	1
lambda repressor-like DNA-binding domains	YrdC/RibB	1	1
Caspase-like	C-type lectin-like	1	1
ADC-like	P-loop containing nucleoside triphosphate hydrolases	1	1
Trypsin-like serine proteases	Bacterial muramidases	1	1
Eukaryotic type KH-domain (KH-domain type I)	HD-domain/PDEase-like	1	1
Porins	OMPA-like	1	1
Phoshotransferase/anion transport protein	Phosphohistidine domain	1	1
Cysteine proteinases	UDP-Glycosyltransferase/glycogen phosphorylase	1	1
LysM domain	Duplicated hybrid motif	1	1
Formyltransferase	Glycoside hydrolase/deacetylase	1	1
Phoshotransferase/anion transport protein	Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain	1	1
Integrin alpha N-terminal domain	Integrin alpha N-terminal domain	1	1
FMN-binding split barrel	GAF domain-like	1	1
Thioredoxin-like	NHL repeat	1	1
PYP-like sensor domain (PAS domain)	Methyl-accepting chemotaxis protein (MCP) signaling domain	1	1
E set domains	FabD/lysophospholipase-like	1	1
DPP6 N-terminal domain-like	DPP6 N-terminal domain-like	1	1
Pectin lyase-like	Caspase-like	1	1
ACP-like	Trimeric LpxA-like enzymes	1	1
Putative DNA-binding domain	Cobalamin (vitamin B12)-binding domain	1	1
Starch-binding domain-like	(Trans)glycosidases	1	1
Nucleotide-diphospho-sugar transferases	UDP-Glycosyltransferase/glycogen phosphorylase	1	1
HMA, heavy metal-associated domain	Porins	1	1
Calcium-dependent phosphotriesterase	NHL repeat	1	1
Homeodomain-like	Methylated DNA-protein cysteine methyltransferase, C-terminal domain	1	1
Aconitase B, N-terminal domain	Aconitase iron-sulfur domain	1	1
Resolvase-like	Putative DNA-binding domain	1	1
EPT/RTPC-like	EPT/RTPC-like	1	1
Subtilisin-like	Fibronectin type III	1	1
Methylesterase CheB, C-terminal domain	EAL domain-like	1	1
Porins	Porins	1	1
Leukotriene A4 hydrolase N-terminal domain	ARM repeat	1	1
Nucleotide-binding domain	Nucleotide-binding domain	1	1
Hypothetical protein PA1324	Bacterial adhesins	1	1
Metalloproteases ("zincins"), catalytic domain	Oligoxyloglucan reducing end-specific cellobiohydrolase	1	1
MurE/MurF N-terminal domain	PLP-binding barrel	1	1
Calcium-dependent phosphotriesterase	CheY-like	1	1
RmlC-like cupins	Homeodomain-like	1	1
Protein kinase-like (PK-like)	TPR-like	1	1
N-acetylmuramoyl-L-alanine amidase-like	PGBD-like	1	1
Metalloproteases ("zincins"), catalytic domain	PDZ domain-like	1	1
Galactose mutarotase-like	(Trans)glycosidases	1	1
CBS-domain pair	Nucleotide-diphospho-sugar transferases	1	1
TPR-like	NTF2-like	1	1
ARM repeat	S-adenosyl-L-methionine-dependent methyltransferases	1	1
FAD/NAD(P)-binding domain	Nitrite and sulphite reductase 4Fe-4S domain-like	1	1
Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	TolA/TonB C-terminal domain	1	1
EPT/RTPC-like	P-loop containing nucleoside triphosphate hydrolases	1	1
Periplasmic binding protein-like II	GAF domain-like	1	1
Hedgehog/intein (Hint) domain	P-loop containing nucleoside triphosphate hydrolases	1	1
Periplasmic binding protein-like II	Nucleotide cyclase	1	1
Calcium-dependent phosphotriesterase	Homodimeric domain of signal transducing histidine kinase	1	1
Radical SAM enzymes	Nitrogenase accessory factor-like	1	1
FliG	FliG	1	1
Activating enzymes of the ubiquitin-like proteins	JAB1/MPN domain	1	1
ACP-like	Glycerol-3-phosphate (1)-acyltransferase	1	1
TTHA1013/TTHA0281-like	Ribbon-helix-helix	1	1
Metallo-hydrolase/oxidoreductase	Flavoproteins	1	1
CheY-like	"Winged helix" DNA-binding domain	1	1
Hypothetical protein SAV1430	Fe-S cluster assembly (FSCA) domain-like	1	1
Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain	Acyl-CoA N-acyltransferases (Nat)	1	1
Lysozyme-like	Trypsin-like serine proteases	1	1
P-loop containing nucleoside triphosphate hydrolases	Quinoprotein alcohol dehydrogenase-like	1	1
HAMP domain-like	Histidine-containing phosphotransfer domain, HPT domain	1	1
S-adenosyl-L-methionine-dependent methyltransferases	Nucleotide cyclase	1	1
GAF domain-like	Homeodomain-like	1	1
Homeodomain-like	Methylated DNA-protein cysteine methyltransferase domain	1	1
CO dehydrogenase molybdoprotein N-domain-like	Molybdenum cofactor-binding domain	1	1
ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	HCP-like	1	1
Homing endonucleases	P-loop containing nucleoside triphosphate hydrolases	1	1
ThiG-like	S-adenosyl-L-methionine-dependent methyltransferases	1	1
Respiratory nitrate reductase 1 gamma chain	alpha-helical ferredoxin	1	1
DPP6 N-terminal domain-like	WD40 repeat-like	1	1
Thioredoxin-like	PurM N-terminal domain-like	1	1
MurE/MurF N-terminal domain	Alanine racemase C-terminal domain-like	1	1
Putative DNA-binding domain	Translation proteins	1	1
Periplasmic binding protein-like II	Periplasmic binding protein-like II	1	1
Bacterial adhesins	Bacterial adhesins	1	1
Quinoprotein alcohol dehydrogenase-like	WD40 repeat-like	1	1
Periplasmic binding protein-like II	OmpA-like	1	1
Hcp1-like	gpW/gp25-like	1	1
Galactose mutarotase-like	Galactose mutarotase-like	1	1
Thioredoxin-like	PurM C-terminal domain-like	1	1
6-phosphogluconate dehydrogenase C-terminal domain-like	ACT-like	1	1
ParB/Sulfiredoxin	C-terminal domain of transcriptional repressors	1	1
Phoshotransferase/anion transport protein	HPr-like	1	1
MurD-like peptide ligases, catalytic domain	Alanine racemase C-terminal domain-like	1	1
beta-Galactosidase/glucuronidase domain	beta-Galactosidase/glucuronidase domain	1	1
Thiol:disulfide interchange protein DsbD, N-terminal domain (DsbD-alpha)	Thioredoxin-like	1	1
dsRNA-binding domain-like	Ribosomal protein L30p/L7e	1	1
Nucleotidylyl transferase	YegP-like	1	1
Pentapeptide repeat-like	WD40 repeat-like	1	1
HesB-like domain	Rhodanese/Cell cycle control phosphatase	1	1
Ribbon-helix-helix	ACT-like	1	1
L,D-transpeptidase catalytic domain-like	NTF2-like	1	1
ACT-like	Alanine racemase C-terminal domain-like	1	1
Lysozyme-like	N-acetylmuramoyl-L-alanine amidase-like	1	1
TSP type-3 repeat	TSP type-3 repeat	1	1
Quinoprotein alcohol dehydrogenase-like	Homodimeric domain of signal transducing histidine kinase	1	1
Carbamate kinase-like	Alanine racemase C-terminal domain-like	1	1
TPR-like	TolB, N-terminal domain	1	1
P-loop containing nucleoside triphosphate hydrolases	Pentapeptide repeat-like	1	1
Thioredoxin-like	FGAM synthase PurL, linker domain	1	1
HPr-like	Phosphoenolpyruvate/pyruvate domain	1	1
Phoshotransferase/anion transport protein	Phosphoenolpyruvate/pyruvate domain	1	1
FAD-linked oxidases, C-terminal domain	FAD-linked oxidases, C-terminal domain	1	1
Subtilisin-like	beta-Roll	1	1
Ferritin-like	Calcium ATPase, transmembrane domain M	1	1
lambda repressor-like DNA-binding domains	RmlC-like cupins	1	1
Putative DNA-binding domain	Initiation factor IF2/eIF5b, domain 3	1	1
Quinoprotein alcohol dehydrogenase-like	NHL repeat	1	1
S-adenosyl-L-methionine-dependent methyltransferases	P-loop containing nucleoside triphosphate hydrolases	1	1
Ferritin-like	Calcium ATPase, transduction domain A	1	1
PurS-like	Class I glutamine amidotransferase-like	1	1
Nucleotide-diphospho-sugar transferases	Guanosine diphospho-D-mannose pyrophosphorylase/mannose-6-phosphate isomerase linker domain	1	1
Phospholipase D/nuclease	P-loop containing nucleoside triphosphate hydrolases	1	1
Receptor-binding domain of short tail fibre protein gp12	Receptor-binding domain of short tail fibre protein gp12	1	1
GAF domain-like	C-terminal effector domain of the bipartite response regulators	1	1
TPR-like	SirA-like	1	1
alpha/beta-Hydrolases	Caspase-like	1	1
alpha/beta-Hydrolases	Galactose-binding domain-like	1	1
Protein kinase-like (PK-like)	GAF domain-like	1	1
Composite domain of metallo-dependent hydrolases	Composite domain of metallo-dependent hydrolases	1	1
PA domain	Metalloproteases ("zincins"), catalytic domain	1	1
MFS general substrate transporter	S-adenosyl-L-methionine-dependent methyltransferases	1	1
Cytochrome c oxidase subunit I-like	Cytochrome c	1	1
Oligoxyloglucan reducing end-specific cellobiohydrolase	Immunoglobulin	1	1
Class II aaRS and biotin synthetases	C-terminal domain of ProRS	1	1
Ferritin-like	HAD-like	1	1
FGAM synthase PurL, linker domain	Class I glutamine amidotransferase-like	1	1
Carbamate kinase-like	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	1	1
Nudix	Metallo-hydrolase/oxidoreductase	1	1
RCC1/BLIP-II	beta-Roll	1	1
DsbC/DsbG N-terminal domain-like	FGAM synthase PurL, linker domain	1	1
Chemotaxis receptor methyltransferase CheR, N-terminal domain	Nucleotide cyclase	1	1
ARM repeat	Nucleotide cyclase	1	1
Metallo-hydrolase/oxidoreductase	Rhodanese/Cell cycle control phosphatase	1	1
Transmembrane di-heme cytochromes	Ferredoxin reductase-like, C-terminal NADP-linked domain	1	1
Terpenoid cyclases/Protein prenyltransferases	Terpenoid cyclases/Protein prenyltransferases	1	1
Thioredoxin-like	Nqo1 middle domain-like	1	1
Chemotaxis receptor methyltransferase CheR, N-terminal domain	EAL domain-like	1	1
(Trans)glycosidases	CBD9-like	1	1
Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	Histone H3 K4-specific methyltransferase SET7/9 N-terminal domain	1	1
Fibronectin type III	Collagen-binding domain	1	1
Pectin lyase-like	Concanavalin A-like lectins/glucanases	1	1
FMN-binding split barrel	2Fe-2S ferredoxin-like	1	1
Toll/Interleukin receptor TIR domain	alpha/beta-Hydrolases	1	1
Metalloproteases ("zincins"), catalytic domain	beta-Roll	1	1
Thioredoxin-like	PurS-like	1	1
DsbC/DsbG N-terminal domain-like	PurM N-terminal domain-like	1	1
Trypsin-like serine proteases	Trypsin-like serine proteases	1	1
Domain of the SRP/SRP receptor G-proteins	Signal peptide-binding domain	1	1
Quinoprotein alcohol dehydrogenase-like	Nucleotide cyclase	1	1
CYTH-like phosphatases	beta-lactamase/transpeptidase-like	1	1
Restriction endonuclease-like	Zinc beta-ribbon	1	1
Metalloproteases ("zincins"), catalytic domain	ARM repeat	1	1
SGNH hydrolase	(Trans)glycosidases	1	1
DsbC/DsbG N-terminal domain-like	PurM C-terminal domain-like	1	1
FAS1 domain	FAS1 domain	1	1
MurD-like peptide ligases, catalytic domain	PLP-binding barrel	1	1
Methylesterase CheB, C-terminal domain	PYP-like sensor domain (PAS domain)	1	1
TPR-like	Clavaminate synthase-like	1	1
HAMP domain-like	GAF domain-like	1	1
Methylesterase CheB, C-terminal domain	Nucleotide cyclase	1	1
Glycosyl hydrolase domain	Protein kinase-like (PK-like)	1	1
S-adenosyl-L-methionine-dependent methyltransferases	EAL domain-like	1	1
Nucleic acid-binding proteins	TPR-like	1	1
Ribonuclease H-like	GIY-YIG endonuclease	1	1
Siroheme synthase middle domains-like	Tetrapyrrole methylase	1	1
Ankyrin repeat	Ankyrin repeat	1	1
CheY-like	cAMP-binding domain-like	1	1
FMN-binding split barrel	Ferredoxin reductase-like, C-terminal NADP-linked domain	1	1
P-loop containing nucleoside triphosphate hydrolases	Sec-C motif	1	1
CO dehydrogenase ISP C-domain like	CO dehydrogenase flavoprotein C-terminal domain-like	1	1
HPr-like	Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain	1	1
ALDH-like	ALDH-like	1	1
PRC-barrel domain	alpha/beta knot	1	1
GAF domain-like	GAF domain-like	1	1
Porins	Periplasmic binding protein-like II	1	1
Urease, beta-subunit	Composite domain of metallo-dependent hydrolases	1	1
CO dehydrogenase ISP C-domain like	CO dehydrogenase molybdoprotein N-domain-like	1	1
Fibronectin type III	Cadherin-like	1	1
Adhesin YadA, collagen-binding domain	Adhesin YadA, collagen-binding domain	1	1
Restriction endonuclease-like	WGR domain-like	1	1
Galactose-binding domain-like	Fibronectin type III	1	1
DNA/RNA polymerases	C-type lectin-like	1	1
HD-domain/PDEase-like	P-loop containing nucleoside triphosphate hydrolases	1	1
E set domains	Six-hairpin glycosidases	1	1
EAL domain-like	CBS-domain pair	1	1
Ribokinase-like	N-(deoxy)ribosyltransferase-like	1	1
S-adenosyl-L-methionine-dependent methyltransferases	PYP-like sensor domain (PAS domain)	1	1
Subtilisin-like	Formin homology 2 domain (FH2 domain)	1	1
Homeodomain-like	SIS domain	1	1
2Fe-2S ferredoxin-like	FAD-binding/transporter-associated domain-like	1	1
Cysteine proteinases	alpha/beta-Hydrolases	1	1
HPr-like	Phosphohistidine domain	1	1
DsbC/DsbG N-terminal domain-like	PurS-like	1	1
Clc chloride channel	CBS-domain pair	1	1
P-loop containing nucleoside triphosphate hydrolases	UDP-Glycosyltransferase/glycogen phosphorylase	1	1
Calcium-dependent phosphotriesterase	Nucleotide cyclase	1	1
IVS-encoded protein-like	YjgF-like	1	1
Quinoprotein alcohol dehydrogenase-like	ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase	1	1
CheY-like	TPR-like	1	1
Histidine-containing phosphotransfer domain, HPT domain	HD-domain/PDEase-like	1	1
Alkaline phosphatase-like	Alkaline phosphatase-like	1	1
SGNH hydrolase	Autotransporter	1	1
Hedgehog/intein (Hint) domain	Homing endonucleases	1	1
Nucleotide-diphospho-sugar transferases	HAD-like	1	1
Zn-dependent exopeptidases	Class I glutamine amidotransferase-like	1	1
Phage tail proteins	gp5 N-terminal domain-like	1	1
S-adenosyl-L-methionine-dependent methyltransferases	S-adenosyl-L-methionine-dependent methyltransferases	1	1
Cdc48 domain 2-like	P-loop containing nucleoside triphosphate hydrolases	1	1
Thiamin diphosphate-binding fold (THDP-binding)	Thiolase-like	1	1
EPT/RTPC-like	RNA 3'-terminal phosphate cyclase, RPTC, insert domain	1	1
ADC-like	Cdc48 domain 2-like	1	1
OMPA-like	TSP type-3 repeat	1	1
Concanavalin A-like lectins/glucanases	Concanavalin A-like lectins/glucanases	1	1
SMAD/FHA domain	EAL domain-like	1	1
Trimeric LpxA-like enzymes	lambda repressor-like DNA-binding domains	1	1
PTS system IIB component-like	PTS system IIB component-like	1	1
Homodimeric domain of signal transducing histidine kinase	HCP-like	1	1
Carbamate kinase-like	PLP-binding barrel	1	1
P-loop containing nucleoside triphosphate hydrolases	Cell division protein MinE topological specificity domain	1	1
Single hybrid motif	FAD/NAD-linked reductases, dimerisation (C-terminal) domain	1	1
ISP domain	ISP domain	1	1
Carboxypeptidase regulatory domain-like	vWA-like	1	1
Sensory domain-like	Histidine-containing phosphotransfer domain, HPT domain	1	1
PYP-like sensor domain (PAS domain)	Ribonuclease H-like	1	1
cAMP-binding domain-like	CBS-domain pair	1	1
DHS-like NAD/FAD-binding domain	Trypsin-like serine proteases	1	1
Carbohydrate-binding domain	CalX-like	1	1
HMA, heavy metal-associated domain	FAD/NAD(P)-binding domain	1	1
Protein kinase-like (PK-like)	C-terminal domain of RNA polymerase alpha subunit	1	1
Methionyl-tRNA synthetase (MetRS), Zn-domain	Nucleic acid-binding proteins	1	1
Periplasmic binding protein-like II	EAL domain-like	1	1
FAD-binding/transporter-associated domain-like	CO dehydrogenase flavoprotein C-terminal domain-like	1	1
P-loop containing nucleoside triphosphate hydrolases	CBS-domain pair	1	1
CBS-domain pair	Nucleotide cyclase	1	1
Periplasmic binding protein-like II	GlnB-like	1	1
YVTN repeat-like/Quinoprotein amine dehydrogenase	beta-Roll	1	1
Aminopeptidase/glucanase lid domain	Zn-dependent exopeptidases	1	1
HMA, heavy metal-associated domain	Homeodomain-like	1	1
HAD-like	Ribosomal protein S5 domain 2-like	1	1
Thioredoxin-like	Nqo1C-terminal domain-like	1	1
Nqo1C-terminal domain-like	Nqo1C-terminal domain-like	1	1
Transmembrane di-heme cytochromes	Riboflavin synthase domain-like	1	1
Molybdenum cofactor biosynthesis protein C, MoaC	Molybdenum cofactor biosynthesis proteins	1	1
Quinoprotein alcohol dehydrogenase-like	Quinoprotein alcohol dehydrogenase-like	1	1
Outer membrane efflux proteins (OEP)	NTF2-like	1	1