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Table 2 Protein domain hierarchies generated automatically either from a single curated alignment or from non-aligned sequences

From: Automated hierarchical classification of protein domain subfamilies based on functionally-divergent residue signatures

identifier Protein superfamily name # seqs # nodes amcBPPS LLR Run time§
Started from curated alignments:     
cd00075 Histidine kinase-like ATPase c 87,258 95(62) 518062 119.27
cd00130 PAS 50,200 117(115) 416375 103.95
cd00174 SH3 13,890 44(35) 26971 3.83
cd00590 RRM 107,488 63(56) 557782 63.75
cd01427 HAD-like hydrolases 41,818 85(73) 324699 59.77
cd02440 AdoMet_MTases 150,872 112(99) 1417985 250.27
cd04301 NAT-SF 43,486 71 244420 23.30
cl02566 SET (pfam00856) 8,946 21 54230 2.58
cl10444 P-loop GTPases 198,624 115 (109) 3826672 464.67
none AAA + ATPases 84,695 86(85) 1779227 173.73
Started from unaligned sequences:     
none α,β- hydrolase fold 50,811 109(104) 752259 139.82
none Helicases 86,287 117 (111) 1935380 342.10
  1. For these non-CDD curated alignments were used as input.
  2. § The time (in minutes) is for Steps 2 and 3 of the algorithm only.
  3. Unaligned sequences were aligned using the multiple alignment procedures cited in Methods to generate an input alignment for the amcBPPS program.