Table 2. Potential pairings for Pfam families at fold and superfamily level
SCOP fold	N	Pfam family	SCOP fold	N	Pfam family	SCOP fold	N	Pfam family
TIM beta/alpha-barrel	38	TGT, MM_CoA_mutase, UPF0001, PI-PLC-Y, DAHP_synth_1, F_bP_aldolase, ALAD, Glyco_hydro_14, PI-PLC-X, IGPS, oxidored_FMN, QRPTase, enolase, MR_MLE, chitinase_2, DHDPS, DHPS, bac_luciferase, Glu_synthase, IMPDH_N, Glyco_hydro_1, Glyco_hydro_10, FMN_dh, Glyco_hydro_17, IMPDH_C glycolytic_enzy, aldo_ket_red, AP_endonuclease2, PRAI, Ala_racemase, Transaldolase, RuBisCO_large, Xylose_isom, cellulase, TIM, alpha-amylase, Glyco_hydro_2, PEP-utilizers	DNA/RNA-binding 3-helical bundle	17	HTH_5, Methyltransf_1, HTH_2, Fork_head, ARID, myb_DNA-binding, trans_reg_C, HSF_DNA-bind, linker_histone, Arg_repressor, LexA_DNA_bind, PAX, IRF, recombinase, Ets, homeobox	Ferredoxin-like	17	Ribosomal_S6, HPPK, ACT, Thr_dehydrat_C, Translat_reg, FTR, guanylate_cyc, EF1BD, E2_C, PyrI, HMA, NDK, P-II, Ribosomal_L30, rrm, fer4, Acylphosphatase
			Immunoglobulin-like beta-sandwich	14	MSP_domain, Transglutamin_C, PKD, arrestin, Filamin, pili_assembly, Neocarzinostat, oxidored_molyb, Tissue_fac, TIG, sodcu, fn3, RHD, ig	Knottins (small inhibitors, toxins, lectins)	13	wap, Colipase, Hirudin, Furin-like, Gamma-thionin, CBD_1, squash, Bowman-Birk_leg, chitin_binding, toxin_3, toxin_2, EGF, Arthro_defensin
			OB-fold	12	Ribosomal_S17, SNase, SSB, ATP-synt_a-c, Enterotoxin_B, TIMP, S1, Pyrophosphatase, Stap_Strp_toxin, eIF-5a, Aspartyl_tRNA_N, CSD	Common fold of diphtheria toxin/transcription factors/cytochrome f	10	STAT, Fimbrial, CBD_2, Cohesin, T-box, A2M, Diphtheria_tox, P53, RHD, Apocytochrome_F
Ribonuclease H-like motif	8	Creatinase_N, actin, HSP70, rnaseH, hexokinase, DNA_pol_B, integrase,3_5_exonuclease	Flavodoxin-like	8	DHquinase_II, ligase-CoA, Cutinase, flavodoxin, AlaDH_PNT, AdoHcyase, response_reg, 2-Hacid_DH	beta-Grasp (ubiquitin-like)	7	IgG_binding_B, IF3, RA, ubiquitin, Stap_Strp_toxin, fer2, gln-synt
Phosphorylase/hydrolase-like	6	Pept_tRNA_hydro, Peptidase_M17, Mtap_PNP, Peptidase_M20, Peptidase_C15, Zn_carbOpept	Rubredoxin-like	5	Desulfoferrodox, COX5B, TFIIS, rubredoxin, PyrI	SH3-like barrel	5	CcdB, Peptidase_S24, SH3, eIF-5a, integrase
alpha-alpha superhelix	5	14-3-3, PPTA, Sec7, AspPc, Armadillo_seg	beta-Trefoil	4	interleukin-1, Ricin_B_lectin, FGF, Kunitz_legume	Double-stranded beta-helix	4	PMI_typeI, Seedstore_7s, Fe_Asc_oxidored, cNMP_binding
Prealbumin-like	4	VHL, Dioxygenase, Transthyretin, CBD_4	Toxins' membrane translocation domains	4	Bcl-2, endotoxin, Diphtheria_tox, Colicin	Long alpha-hairpin	3	DnaJ, GreA_GreB, sodfe
Barrel-sandwich hybrid	4	GCV_H, PTS_EIIA_1, biotin_lipoyl, CPSase_L_chain	ATP-grasp	4	CPSase_sm_chain, Aconitase_C, cpn60_TCP1, PEP-utilizers	Acyl carrier protein-like	3	Colicin_Pyocin, pp-binding, gag_p24
Four-helical up-and-down bundle	3	Hemerythrin, TMV_coat, Cytochrome_C_2	Beta-clip	3	Antifreeze, Urease-beta, dUTPase	PNGase F-like	2	Adeno_hexon, Cu2_monooxygen
Multiheme cytochromes	2	2-Hacid_DH, Molydop_binding

SCOP superfamily	N	Pfam family	SCOP superfamily	N	Pfam family	SCOP superfamily	N	Pfam family
P-loop containing nucleotide triphosphate hydrolases	20	PRK, TK_herpes, ABC_tran, Guanylate_kin, Sulfotransfer, adenylatekinase, recA, AAA, GTP_EFTU, kinesin, G-alpha, arf, ras, fer4_NifH, SRP54, myosin_head, UvrD-helicase, IQ, Adenylsucc_synt, ATP-synt_ab,	NAD(P)-binding Rossmann-fold domains	17	THF_DHG_CYH, IlvC, Semialdhyde_dh, 6PGD, GFO_IDH_MocA, adh_zinc, GLFV_dehydrog, DapB, gpdh, ldh, 3HCDH, malic, adh_short, Epimerase, 3Beta_HSD, adh_short_C2, 2-Hacid_DH	4-helical cytokines	10	LIF_OSM, IL4, GM_CSF, EPO_TPO, IL2, interferon, hormone, IFN-gamma, IL10, IL-6
Membrane all-alpha	9	MscL, photoRC, COX1, COX2, COX3, ATP-synt_C, cytochrome_b_C, Ba_rodopsin, cytochrome_b_N	ConA-like lectins/glucanases	8	Glyco_hydro_12, Glyco_hydro_16, pentaxin, Glyco_hydro_7, Gal-bind_lectin, Glyco_hydro_11, lectin_legB, lectin_legA	Glycosyltransferases	8	Glyco_hydro_14, chitinase_2, Glyco_hydro_10, Glyco_hydro_17, Glyco_hydro_1, cellulase, alpha-amylase, Glyco_hydro_2
PLP-dependent transferases	8	OKR_DC_1, Cys_Met_Meta_PP, aminotran_1, aminotran_2, SHMT, aminotran_3, aminotran_5, Beta_elim_lyase	Periplasmic binding protein-like II	8	PstS, lig_chan, SBP_bac_5, SBP_bac_3, Sulphate_bind, Porphobil_deam, transferrin, SBP_bacterial_1	Winged helix DNA-binding domain	8	HTH_5, Fork_head, trans_reg_C, HSF_DNA-bind, linker_histone, Arg_repressor, LexA_DNA_bind, IRF, Ets
alpha/beta-Hydrolases	7	serine_carbpept, Lipase_3, DLH, Peptidase_S9, lipase, COesterase, abhydrolase	Viral coat and capsid proteins	7	Bromo_CP, Peptidase_A6, Polyoma_coat, Parvo_coat, Viral_coat, Tymo_coat, rhv	Nucleic acid-binding proteins	7	Ribosomal_S17, SSB, CSD, S1, eIF-5a, ATP-synt_A-c, Aspartyl_tRNA_N
Thioredoxin-like	7	Calsequestrin, GSHPx, DSBA, thiored, glutaredoxin, GST, AhpC-TSA	FAD/NAD(P)-binding domain	6	CHOD, GMC_oxred, pyr_redox, GDI, FAD_binding_3, Monooxygenase	S-adenosyl-L-methionine-dependent methyltransferases	6	PARP_regulatory, N6_N4_Mtase, CheR, Methyltransf_3, DNA_methylase, RrnaAD
Aldolase	6	DAHP_synth_1, ALAD, F_bP_aldolase, Transaldolase, DHDPS, glycolytic_enzy	Metalloproteases ("zincins"), catalytic domain	6	Peptidase_M27, Peptidase_M8, Reprolysin, Peptidase_M4, Peptidase_M10, Astacin	Immunoglobulin	6	arrestin, Filamin, oxidored_molyb, TIG, RHD, ig
Membrane all-alpha	5	COX2, Cu-oxidase, copper-bind, COX1, COX3	Nucleotidylyl transferase	5	tRNA-synt_1d, tRNA-synt_1b, tRNA-synt_1c, Cytidylyltransf, tRNA-synt_1	Homeodomain-like	5	HTH_2, myb_DNA-binding, PAX, recombinase, homeobox
Cystine-knot cytokines	5	hormone6, TGF-beta, NGF, PDGF, Cys_knot	Cyclin-like	4	RB_A, RB_B, cyclin, transcript_fac2	Lysozyme-like	4	Phage_lysozyme, Glyco_hydro_46, SLT, lys
Glutathione synthetase ATP-binding domain-like	4	GARS, Dala_Dala_ligas, CPSase_L_chain, PPDK_N_term	DHS-like NAD/FAD-binding domain	4	DS, ETF_alpha, TPP_enzymes, ETF_beta	ATPase domain of HSP9	4	signal, HSP90, DNA_topoisoII, DNA_mis_repair
Galactose-binding domain-like	4	XRCC1_N, EPH_lbd, Glyco_hydro_2, endotoxin	p53-like transcription factors	4	STAT, T-box, P53, RHD	DNA/RNA polymerases	4	RNA_dep_RNA_pol, rvt, DNA_pol_B, DNA_pol_A
PH domain-like	4	Ran_BP1, PID, WH1, PH	Scorpion toxin-like	4	Gamma-thionin, toxin_3, toxin_2, Arthro_defensin	(Phosphotyrosine protein) phosphatases II	3	Rhodanese, DSPc, Y_phosphatase
Ferritin-like	4	FA_desaturase, ribonuc_red, ferritin, Bactriofer	DNA/RNA polymerases	4	rnaseH, DNA_pol_B, integrase, 3_5_exonuclease	NAD(P)-binding Rossmann-fold domains	3	THF_DHG_CYH, malic, GLFV_dehydrog
Zn-dependent exopeptidases	3	Peptidase_M17, Peptidase_M20, Zn_carbOpept	lambda repressor-like DNA-binding domains	3	lacI, HTH_3, pou	Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin	3	Seedstore_2S, tryp_alpha_amyl, LTP
DEATH domain	3	DED, CARD, death	P-loop containing nucleotide triphosphate hydrolases	3	G-alpha, arf, ras	Thiolase-like	3	ketoacyl-synt, thiolase, Chal_stil_synt
Six-hairpin glycosyltransferases	3	Glyco_hydro_8, Glyco_hydro_15, Glyco_hydro_9	N-terminal nucleophile aminohydrolases (Ntn hydrolases)	3	Penicil_amidase, proteasome, GATase_2	FAD/NAD(P)-binding domain	3	CHOD, GDI, GMC_oxred
MHC antigen-recognition domain	3	MHC_I, MHC_II_alpha, MHC_II_beta	Cysteine proteinases	3	Peptidase_C5, UCH, Peptidase_C1	FKBP-like	3	Rotamase, GreA_GreB, FKBP
ADP-ribosylation	3	Enterotoxin_A, Diphtheria_tox, PARP	Tetrahydrobiopterin biosynthesis enzymes-like	3	GTP_cyclohydroI, PTPS, Uricase	Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain	3	G6PD, Semialdhyde_dh, gpdh
Class II aaRS and biotin synthetases	3	tRNA-synt_2b, tRNA-synt_2d, tRNA-synt_2	beta-Lactamase/D-ala carboxypeptidase	3	Transpeptidase, Peptidase_S11, beta-lactamase	FMN-linked oxidoreductases	3	oxidored_FMN, FMN_dh, Glu_synthase
ETFP adenine nucleotide-binding domain-like	3	Usp, ETF_alpha, ETF_beta	Glutathione synthetase ATP-binding domain-like	3	CPSase_L_chain, Dala_Dala_ligas, GARS	Thiamin diphosphate-binding fold (THDP-binding)	3	POR_N, TPP_enzymes, transketolase
Actin-like ATPase domain	3	actin, HSP70, hexokinase	Glucocorticoid receptor-like (DNA-binding domain)	3	zf-C4, LIM, GATA	Defensin-like	3	Defensin_beta, defensins, toxin_4
Inosine monophosphate dehydrogenase (IMPDH)	3	aldo_ket_red, IMPDH_C, IMPDH_N	S15/NS	2	Flu_NS1, Ribosomal_S15	Phosphatase/sulphatase	2	alk_phosphatase, Sulfatase
Histone-fold	2	CBFD_NFYB_HMF, histone	CoA-dependent acyltransferases	2	2-oxoacid_dh, CAT	Phosphoglycerate mutase-like	2	acid_phosphat, PGAM
Terpenoid synthases	2	polyprenyl_synt, Terpene_synth	GTPase activation domain, GAP	2	RhoGAP, RasGAP	Di-copper centre-containing domain	2	hemocyanin, tyrosinase
NAD(P)-binding Rossmann-fold domains	2	IlvC, 3HCDH	PapD-like	2	MSP_domain, pili_assembly	Ribosomal protein S	2	Ribonuclease_P, Ribosomal_S5
Rubredoxin-like	2	COX5B, rubredoxin	Arginase/deacetylase	2	Hist_deacetyl, arginase	Snake toxin-like	3	UPAR_LY6, toxin, Activin_recp
DNA clamp	2	DNA_pol3_beta, PCNA	Fibronectin type III	2	Tissue_fac, fn3	HIT-like	2	GalP_UDP_transf, HIT
Segmented RNA-genome viruses' proteins	2	Hemagglutinin, Orbi_VP7	Bacterial enterotoxins	2	Enterotoxin_B, Stap_Strp_toxin	Ferredoxin reductase-like, FAD-linked (N-terminal) domain	2	Pyridox_oxidase, Cyt_reductase
C-type lectin-like	2	lectin_c, Xlink	SAICAR synthase-like	2	SAICAR_synt, PIP5K	GroES-like	2	cpn10, adh_zinc
Carbohydrate-binding domain	2	CBD_2, Cohesin	2Fe-2S ferredoxin-related	2	fer2, fer4	DNA breaking-rejoining enzymes	2	Topoisomerase_I, Phage_integrase
TNF-like	2	TNF, C1q	Cytokine	2	interleukin-1, FGF	Acid proteases	2	rvp, asp
dsRNA-binding domain-like	2	dsrm, Ribosomal_S5	Trypsin-like serine proteases	3	Flavi_helicase, trypsin, Alpha_core	Enolase C-terminal domain-like	2	enolase, MR_MLE
Pectin lyase-like	2	pec_lyase, Glyco_hydro_28	Single hybrid motif	2	GCV_H, biotin_lipoyl	Tautomerase/MIF	2	Tautomerase, MIF
Actin depolymerizing proteins	2	cofilin_ADF, Gelsolin	Ribulose-phoshate binding barrel	2	IGPS, PRAI	Prokaryotic type I DNA topoisomerase	2	Toprim, Topoisom_bac
Phosphatidylinositol-specific phospholipase C	2	PI-PLC-Y, PI-PLC-X	Xylose Isomarase-like	2	AP_endonucleaase, Xylose_isom	Porins	2	Gram-ve_porins, TonB_boxC
ClpP/crotonase	2	CLP_protease, ECH	Kringle-like	2	fn2, kringle	Sugar phosphatases	2	inositol_P, FBPase
Caspase-like	2	ICE_p20, ICE_p10	Globin-like	2	Phycobilisome, globin	POZ domain	2	BTB, Skp1
Regulatory domain in Amino acid metabolism	2	ACT, Thr_dehydrat_C	Barwin-like endoglucanases	2	2-Hacid_DH, Barwin	Metallo dependent phosphatases	2	5_nucleotidase, STphosphatase
Dnase I-like	2	AP_endonucleas1, DNase-I	Periplasmic binding protein-like I	2	ANF_receptor, Peripla_BP_like	Alanine racemase like C-term domain	2	Ala_racemase, UPF0001
Bet v1-like	2	Ring_hydroxyl_A, Bet_v_I