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Table 6 HMMER search results within the four chosen substrate families

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 [%] 51.4 58.3 69.1 66.0 57.7 85.2 77.0 72.7 71.3 70.3 99.3 90.4 76.3 71.7 59.9
Recall [%] 51.4 58.3 100.0 93.5 88.7 83.8 82.4 82.3 78.4 74.6 96.2 95.3 93.4 90.1 86.0
F-measure[%] 51.4 58.3 75.9 70.3 61.9 81.9 75.5 73.3 71.1 69.0 97.2 91.4 78.6 75.4 68.2
Unclassified [%] 93.1 88.9 83.3 79.2 65.3 69.4 61.1 55.6 51.4 47.2 45.7 44.3 41.4 34.3 17.1
  1. HMMER prediction results for substrate families. The results were normalized by the size of the reference database (see text). HMMER gave a slightly higher prediction accuracy than BLAST in the Ec-Sc analysis.