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Table 10 Comparison between our structural alphabet (used in SA-FAST) and those of Yang & Tung (used in 3D-BLAST) and de Brevern et al. (converted by PBE-T, a facility associated with PBE-align) for describing motifs found by MEME within the EGF family

From: Protein structure search and local structure characterization

   Our SA Yang & Tung's de Brevern et al.'s
Sub-domain Type A B C A B C A B C
EGF proteins No.a Hitsb Covc Hits Cov Hits Cov Hits Cov Hits Cov Hits Cov Hits Cov Hits Cov Hits Cov
Type 1 24 23 95.8 22 91.7 23 95.8 11 45.8 21 87.5 19 79.2 18 75.0 14 58.3 18 75.0
Type 2 74 73 98.6 71 95.9 74 100.0 62 83.8 73 98.6 60 81.1 68 91.9 62 83.8 70 94.6
Type 3 117 116 99.1 106 90.6 61 52.1 54 46.2 102 87.2 25 21.4 109 93.2 112 95.7 48 41.0
Others 12 12 100.0 11 91.7 11 91.7 9 75.0 11 91.7 9 75.0 12 100.0 11 91.7 9 75.0
All 227 224 98.6 210 92.5 169 74.4 136 59.9 207 91.2 113 49.8 207 91.2 199 87.7 145 63.9
  1. aThe number of EGF proteins of a specific type, bA hit for a sub-domain occurred when more than half of the sub-domain residues were contained in a given motif. We present the number of hits of different types, cCov(Coverage) was defined as the ratio of the number of hits to the number of EGF proteins, e.g., if No. = 24 and Hits = 22, then Cov = 22/24 = 91.7%.