Table 1.
A comparison of the selectivities, sensitivities, and cutoff e-values derived from TnpPred versus the corresponding Pfam HMM profiles for 19 IS families.
| IS family | Pfam | TnpPred | |||||||
|---|---|---|---|---|---|---|---|---|---|
| HMM | Selectivity | Sensitivity | Cutoff1 | HMM | Selectivity | Sensitivity | Cutoff1 | ||
| Transposase_27 | 96.4% | 83.2% | 1.2E + 04 | Combined* | 100.0% | 95.4% | 2.0E − 06 | ||
| 1 | IS1 | — | — | — | — | ORF1* | 99.9% | 100.0% | 32E − 34 |
| — | — | — | — | ORF2* | 99.4% | 100.0% | 3.9E − 40 | ||
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| |||||||||
| 2 | IS110 | Transposase_9 | 95.3% | 94.2% | 7.0E + 03 | ORF1* | 100.0% | 100.0% | 1.3E − 63 |
| Transposase_20 | 100.0% | 99.1% | 1.2E − 06 | ||||||
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| |||||||||
| 3 | IS1380 | — | — | — | — | ORF1* | 100.0% | 100.0% | 2.3E − 224 |
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| |||||||||
| 4 | IS200/IS605 | Transposase_17 | 100.0% | 100.0% | 3.9E − 21 | ORF1* | 100.0% | 100.0% | 4.2E − 79 |
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| |||||||||
| — | — | — | — | Combined* | 93.9% | 96.0% | l.8E − 09 | ||
| 5 | IS21 | — | — | — | — | ORF1* | 100.0% | 93.7% | 84E − 10 |
| IstB_N | 72.8% | 79.3% | 6.7E + 04 | ORF2* | 100.0% | 100.0% | 2.0E − 06 | ||
| IstB | 76.6% | 79.5% | 2.6E + 04 | 100.0% | 100.0% | 2.0E − 06 | |||
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| 6 | IS256 | Transposase_mut* | 100.0% | 100.0% | 8.7E − 01 | ORF1 | 99.4% | 98.8% | 3.1E − 55 |
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| |||||||||
| — | — | — | — | Combined* | 99.5% | 81.8% | 2.7E + 02 | ||
| IS3_IS150 | — | — | — | — | ORF1* | 90.3% | 69.7% | 5.4E + 03 | |
| — | — | — | — | ORF2 | 100.0% | 100.0% | 2.4E − 114 | ||
| Transposase_8 | 80.1% | 78.8% | 2.5E + 04 | Combined* | 100.0% | 100.0% | 5.7E − 06 | ||
| IS3_IS2 | — | — | — | — | ORF1* | 100.0% | 90.0% | 1.2E − 83 | |
| — | — | — | — | ORF2* | 100.0% | 100.0% | 1.3E − 223 | ||
| — | — | — | — | Combined* | 98.6% | 89.6% | 3.3E + 02 | ||
| 7 | IS3_IS3 | — | — | — | — | ORF1* | 93.6% | 76.5% | 2.5E − 11 |
| — | — | — | — | ORF2* | 100.0% | 100.0% | 7.9E − 140 | ||
| — | — | — | — | Combined* | 99.9% | 100.0% | 3.9E − 04 | ||
| IS3_IS407 | — | — | — | — | ORF1* | 99.7% | 95.8% | 3.0E − 44 | |
| — | — | — | — | ORF2* | 100.0% | 100.0% | 3.5E − 135 | ||
| — | — | — | — | Combined* | 100.0% | 91.4% | 5.4E − 98 | ||
| IS3_IS51 | — | — | — | — | ORF1* | 87.4% | 74.3% | 5.5E − 24 | |
| — | — | — | — | ORF2 | 100.0% | 100.0% | 8.1E − 205 | ||
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| |||||||||
| 8 | IS30 | — | — | — | — | ORF1* | 100.0% | 100.0% | 1.7E − 127 |
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| |||||||||
| 9 | IS4 | Transposase_11 | 99.0% | 96.0% | 9.5E + 02 | ORF1* | 100.0% | 96.1% | 1.3E − 01 |
| Transposase_Tn5 | 51.8% | 58.9% | 1.1E + 05 | ||||||
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| |||||||||
| 10 | IS481 | Mu-transpos_C | 67.7% | 54.0% | 6.7E + 04 | ORF1* | 99.9% | 100.0% | 4.0E − 84 |
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| |||||||||
| IS5_IS1031 | — | — | — | — | ORF1* | 100.0% | 100.0% | 1.2E − 162 | |
| IS5_IS427 | — | — | — | — | Combined* | 99.7% | 97.7% | 6.7E − 11 | |
| 11 | IS5_IS5 | Transposase_33 | 54.6% | 60.4% | 1.1E + 05 | ORF1* | 100.0% | 100.0% | 4.2E − 48 |
| IS5_IS903 | — | — | — | — | ORF1* | 100.0% | 100.0% | 7.3E − 155 | |
| IS5_ISH1 | — | — | — | — | ORF1* | 100.0% | 100.0% | 1.5E − 216 | |
| IS5_ISL2 | — | — | — | ORF1* | 100.0% | 100.0% | 2.6E − 129 | ||
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| 12 | IS6 | — | — | — | — | ORF1* | 100.0% | 100.0% | 4.1E − 65 |
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| 13 | IS630 | Transposase_14 | 52.8% | 68.2% | 9.8E + 04 | ORF1* | 98.4% | 97.7% | 2.7E − 93 |
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| Transposase_34 | 89.9% | 73.1% | 2.4E − 35 | Combined | 85.6% | 79.0% | 1.5E + 04 | ||
| 14 | IS66 | — | — | — | — | ORF1* | 97.8% | 82.6% | 1.4E − 32 |
| — | — | — | — | ORF2* | 94.0% | 88.4% | 3.4E + 02 | ||
| — | — | — | — | ORF3* | 100.0% | 88.8% | 1.7E − 299 | ||
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| 15 | IS91 | Transposase_32 | 100.0% | 100.0% | 7.9E − 16 | ORF1* | 100.0% | 100.0% | 4.1E − 216 |
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| 16 | IS982 | — | — | — | — | ORF1* | 99.3% | 99.2% | 3.5E − 102 |
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| 17 | ISAs1 | — | — | — | — | ORF1* | 100.0% | 100.0% | 4.1E − 205 |
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| 18 | ISL3 | Transposase_12 | 100.0% | 99.0% | 4.7E − 31 | ORF1* | 100.0% | 99.0% | 5.0E − 95 |
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| 19 | Tn3 | Transposase_7* | 100.0% | 63.3% | 1.7E − 156 | ORF1* | 94.8% | 68.3% | 0.0E + 00 |
1Cutoff e-values are derived from ROC charts for each model (Supplementary File 1); *indicates the HMM that was selected for incorporation into the TnpPred web service.