Table 2.
Domains lacking known structures found with merged profile
| Superfamily/fold | New domain | Merged profile | HMMer | PSI-BLAST |
| Similarities found with SMART profiles | ||||
| 4-helical cytokines | DAGKa | CSF2/IL2 (SF) | — | 0.003 |
| knottins | ChtBD2a | PTI/EGF (F) | 1.5e-11 | — |
| P-loop ATPases | MCM | AAA/ART (SF) | 5.9e-11 | — |
| winged 3-α bundle | HTH_DEOR | HTH_ARSR/HSF (SF) | — | 0.003 |
| HTH_ICLR | ETS/HTH_CRP (SF) | 6.9e-07 | 2.0e-04 | |
| Similarities found with PFAM profiles | ||||
| Crotonase | DUF114 | CLP_protease/ECH (SF) | 0.27 | 1.0e-05 |
| DUF107 | CLP_protease/ECH (SF) | 0.047 | 6.0e-08 | |
| Cys-knot | DAN | TGF-β/Cys_knot (SF) | 0.029 | — |
| FAD/NAD binding | GIDA | pyr_redox/GDI (SF) | (0.023) | 1.0e-05 |
| Thi4 | GMC_oxred/FAD_binding_3 (SF) | 0.007 | 5.0e-05 | |
| FMO-like | pyr_redox/Monooxygenase (SF) | (0.074) | 9.0e-07 | |
| Phytoene_dh | pyr_redox/Monooxygenase (SF) | 0.011 | 5.0e-06 | |
| DAOa | GDI/FAD_binding_3 (SF) | (0.064) | 1.0e-04 | |
| Glu synth ATP binding | DUF201 | CPSase_L_chain/Dala_Dala_ligas (SF) | — | 2.0e-07 |
| Immunoglobulin-like | K1 | Neocarzinostat/ig (F) | 0.21 | — |
| λ-repressor | Sigma54_factors | lacl/pou (SF) | 0.001 | — |
| Transposase_12 | lacl/pou (SF) | 0.17 | — | |
| P-loop ATPases | bac_dnaA | arf/UvrD-helicase (SF) | — | 0.002 |
| FeoB | GTP_EFTU/arf (SF) | 0.17 | — | |
| CoaE | Adenylatekinase/SRP54 (SF) | — | 1.0e-03 | |
| MMR_HSR1 | recA/arf (SF) | (0.013) | 6.0e-06 | |
| CobA_CobO_BtuR | recA/UvrD-helicase (SF) | — | 1.0e-03 | |
| ATP-bind | PRK/SRP54 (SF) | — | 1.0e-04 | |
| PLP-dependent | GDC-P | Cys_Met_Meta_PP/aminotran_2 (SF) | — | 5.0e-06 |
| pyridoxal_deC | Cys_Met_Meta_PP/SHMT (SF) | — | 2.0e-05 | |
| Phosphatase | Phosphodiest | alk_phosphatase/Sulfatase (SF) | — | 1.0e-03 |
| Rossmann-like | NAD_Gly3P_dh | llvC/3HCDH (SF) | — | 2.0e-06 |
| Acetylald_DH | GFO_IDH_MocA/DapB (SF) | 0.17 | — | |
| DAOa | 3HCDH/adh_short_C2 (SF) | — | 0.002 | |
| Polysacc_synt_2 | Epimerase/adh_short_C2 (SF) | (5.5e-10) | 2.0e-22 | |
| Octopine_DH_N | GFO_IDH_MocA/3HCDH (SF) | 0.12 | — | |
| PDH | llvC/3HCDH (SF) | (0.078) | 1.0e-07 | |
| Isoflavone_redu | THF_DHG_CYH/3β_HSD (SF) | (0.013) | 4.0e-04 | |
| Homoserine_dh | GFO_IDH_MocA/3HCDH (SF) | 0.3 | — | |
| ODC_Mu_crystall | llvC/3β_HSD (SF) | — | 4.0e-04 | |
| DUF108 | GFO_IDH_MocA/DapB (SF) | (0.005) | 5.0e-05 | |
| P5CR | llvC/3HCDH (SF) | (0.160) | 0.003 | |
| Snake-toxins | PLA2_inh | Activin_recp/UPAR_LY6 (SF) | 0.099 | — |
| TIM-barrel | UPF0034 | oxidored_FMN/FMN_dh (SF) | — | 2.0e-07 |
| Glyco_hydro_70 | Glyco_hydro_10/α-amylase (SF) | 0.035 | — | |
| Glyco_hydro_39 | Glyco_hydro_1/cellulose (SF) | 0.085 | — | |
| NPD | IMPDH_C/IMPDH_N (F) | (0.058) | 2.0e-07 | |
| Thioredoxin-like | SCO1-SenC | AhpC-TSA/thiored (SF) | — | 0.003 |
| Zincins | Fragilysin | Reprolysin/Peptidase_M10 (SF) | — | 0.003 |
| α/β hydrolases | Thioesterase | Lipase_3/abhydrolase (SF) | 1.3e-04 | (1.0e-03) |
| Ndr | Peptidase_S9/abhydrolase (SF) | 0.023 | — | |
| Lipase_2 | Peptidase_S9/abhydrolase (SF) | (0.18) | 0.003 | |
| Methyltransferase | PCMT | Methyltransf_3/RrnaAD (SF) | — | 7.0e-09 |
| UPF0020 | DNA_methylase/RrnaAD (SF) | — | 4.0e-05 | |
| Nol1_Nop2_Sun | Methyltransf_3/RrnaAD (SF) | — | 1.0e-05 | |
| Met_10 | PARP_regulatory/Methyltransf_3 (SF) | — | 2.0e-05 | |
| Spermine_synth | Methyltransf_3/RrnaAD (SF) | — | 3.0e-04 | |
| Methyltransf_2 | CheR/Methyltransf_3 (SF) | — | 4.0e-04 | |
| Methyltransf_4 | Methyltransf_3/RrnaAD (SF) | — | 3.0e-05 | |
| Ubie_methyltran | Methyltransf_3/RrnaAD (SF) | (0.005) | 5.0e-05 | |
| Winged 3-α bundle | TFIIE_α | HTH_5/IRF (SF) | 0.27 | — |
a Proteins with similarities in structure lying in different SCOP folds (not included in the total).