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Table 5 Homology search results within the four substrate families based on BLAST

From: Transferring functional annotations of membrane transporters on the basis of sequence similarity and sequence motifs

  Ec- At Ec- Sc Sc- At
1e-20 1e-16 1e-12 1e-8 1e-4 1e-20 1e-16 1e-12 1e-8 1e-4 1e-20 1e-16 1e-12 1e-8 1e-4
Precision [%] 71.6 72.9 66.1 56.8 37.8 57.7 44.1 38.5 39.3 34.9 95.5 79.8 69.9 62.2 37.0
Recall [%] 93.1 93.1 93.8 90.8 55.6 85.2 84.6 82.7 75.6 51.5 100.0 100.0 100.0 100.0 100.0
F-measure[%] 78.9 80.5 71.5 61.3 42.3 64.3 50.6 43.2 43.6 35.7 97.2 87.0 79.0 73.6 52.1
Unclassified [%] 90.3 86.1 79.2 72.2 8.3 65.3 56.9 52.8 51.4 1.4 45.7 44.3 37.1 27.1 1.4
  1. BLAST prediction results for the four created substrate families of metal ion, phosphate, sugar and amino acid transporters. The results were normalized by the size of the reference database (see text). Unlike the TC family prediction, a smaller fraction of transporters was correctly classified and many were misclassified.