Table 1.

Sum up of protein domain features and main results

Pfam_IDMeffClassPDB IDPrecisiondRMSD, ÅN/Ng
Thioredoxin4,388α/β1RQM0.751.9/2.26362
HTH_312,901α3F520.691.3/1.96449
Sigma70_r28,008α1OR70.741.0/1.96853
RRM_17,076α/β1G2E0.801.2/2.07150
Trans_Reg_C6,458α1ODD0.552.1/3.17665
cNMP_binding7,539α/β3FHI0.891.6/2.18172
CMD1,488α3D7I0.392.4/3.88561
HxlR1,674α3DF80.482.2/2.68777
fn38,862β1BQU0.582.1/2.98857
Cadherin6,219β2O720.692.5/3.19066
OmpA4,081α/β1OAP0.631.8/2.49678
Response_reg36,372α/β1KGS0.702.5/3.111199
PAS3,350α/β2GJ30.583.6/7.311280
Peptidase_M232,975β3NYY0.712.7/3.511282
TrkA_N2,630α/β3FWZ0.732.1/3.0116100
ADH_zinc_N5,932α/β1A710.662.9/3.611999
Ras2,528α/β5P210.732.7/3.3160144
Trypsin4,703β3TGI0.782.8/4.0216167
  • Each of the 18 protein domains analyzed in this work is marked by its Pfam identifier (Pfam_ID), and the domains are ordered by size. Shown in columns from left to right are (i) the number of effective sequences in the corresponding family MSA (Meff); (ii) the fold class according to CATH classification (54) (Class), (iii) the PDB identifier for the representative structure of the family; (iv) the precision for the top N predictions, where N denotes the number of amino acids in the corresponding protein structure; (v) the dRMSD to the native conformations of the best (on the left) and minimum energy (on the right) sampled structure. The dRMSD are calculated from the coordinates of the Cα atoms corresponding to positions with less than 5% gaps in the (reweighted) MSA; (vi) the number of amino acids in the structure (N) and the number of positions with less than 5% gaps (Ng, as a subscript) that were included in the dRMSD calculation.