TnpPred: A Web Service for the Robust Prediction of Prokaryotic Transposases
Table 1
A comparison of the selectivities, sensitivities, and cutoff -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%
Combined*
100.0%
95.4%
1
IS1
—
—
—
—
ORF1*
99.9%
100.0%
—
—
—
—
ORF2*
99.4%
100.0%
2
IS110
Transposase_9
95.3%
94.2%
ORF1*
100.0%
100.0%
Transposase_20
100.0%
99.1%
3
IS1380
—
—
—
—
ORF1*
100.0%
100.0%
4
IS200/IS605
Transposase_17
100.0%
100.0%
ORF1*
100.0%
100.0%
—
—
—
—
Combined*
93.9%
96.0%
5
IS21
—
—
—
—
ORF1*
100.0%
93.7%
IstB_N
72.8%
79.3%
ORF2*
100.0%
100.0%
IstB
76.6%
79.5%
100.0%
100.0%
6
IS256
Transposase_mut*
100.0%
100.0%
ORF1
99.4%
98.8%
—
—
—
—
Combined*
99.5%
81.8%
IS3_IS150
—
—
—
—
ORF1*
90.3%
69.7%
—
—
—
—
ORF2
100.0%
100.0%
Transposase_8
80.1%
78.8%
Combined*
100.0%
100.0%
IS3_IS2
—
—
—
—
ORF1*
100.0%
90.0%
—
—
—
—
ORF2*
100.0%
100.0%
—
—
—
—
Combined*
98.6%
89.6%
7
IS3_IS3
—
—
—
—
ORF1*
93.6%
76.5%
—
—
—
—
ORF2*
100.0%
100.0%
—
—
—
—
Combined*
99.9%
100.0%
IS3_IS407
—
—
—
—
ORF1*
99.7%
95.8%
—
—
—
—
ORF2*
100.0%
100.0%
—
—
—
—
Combined*
100.0%
91.4%
IS3_IS51
—
—
—
—
ORF1*
87.4%
74.3%
—
—
—
—
ORF2
100.0%
100.0%
8
IS30
—
—
—
—
ORF1*
100.0%
100.0%
9
IS4
Transposase_11
99.0%
96.0%
ORF1*
100.0%
96.1%
Transposase_Tn5
51.8%
58.9%
10
IS481
Mu-transpos_C
67.7%
54.0%
ORF1*
99.9%
100.0%
IS5_IS1031
—
—
—
—
ORF1*
100.0%
100.0%
IS5_IS427
—
—
—
—
Combined*
99.7%
97.7%
11
IS5_IS5
Transposase_33
54.6%
60.4%
ORF1*
100.0%
100.0%
IS5_IS903
—
—
—
—
ORF1*
100.0%
100.0%
IS5_ISH1
—
—
—
—
ORF1*
100.0%
100.0%
IS5_ISL2
—
—
—
ORF1*
100.0%
100.0%
12
IS6
—
—
—
—
ORF1*
100.0%
100.0%
13
IS630
Transposase_14
52.8%
68.2%
ORF1*
98.4%
97.7%
Transposase_34
89.9%
73.1%
Combined
85.6%
79.0%
14
IS66
—
—
—
—
ORF1*
97.8%
82.6%
—
—
—
—
ORF2*
94.0%
88.4%
—
—
—
—
ORF3*
100.0%
88.8%
15
IS91
Transposase_32
100.0%
100.0%
ORF1*
100.0%
100.0%
16
IS982
—
—
—
—
ORF1*
99.3%
99.2%
17
ISAs1
—
—
—
—
ORF1*
100.0%
100.0%
18
ISL3
Transposase_12
100.0%
99.0%
ORF1*
100.0%
99.0%
19
Tn3
Transposase_7*
100.0%
63.3%
ORF1*
94.8%
68.3%
1Cutoff -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.