TnpPred: A Web Service for the Robust Prediction of Prokaryotic Transposases

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	Cutoff^1	HMM	Selectivity	Sensitivity	Cutoff^1
		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
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
3	IS1380	—	—	—	—	ORF1*	100.0%	100.0%	2.3𝐸−224
4	IS200/IS605	Transposase_17	100.0%	100.0%	3.9𝐸−21	ORF1*	100.0%	100.0%	4.2𝐸−79
		—	—	—	—	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
6	IS256	Transposase_mut*	100.0%	100.0%	8.7𝐸−01	ORF1	99.4%	98.8%	3.1𝐸−55
		—	—	—	—	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
8	IS30	—	—	—	—	ORF1*	100.0%	100.0%	1.7𝐸−127
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
10	IS481	Mu-transpos_C	67.7%	54.0%	6.7𝐸+04	ORF1*	99.9%	100.0%	4.0𝐸−84
	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
12	IS6	—	—	—	—	ORF1*	100.0%	100.0%	4.1𝐸−65
13	IS630	Transposase_14	52.8%	68.2%	9.8𝐸+04	ORF1*	98.4%	97.7%	2.7𝐸−93
		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
15	IS91	Transposase_32	100.0%	100.0%	7.9𝐸−16	ORF1*	100.0%	100.0%	4.1𝐸−216
16	IS982	—	—	—	—	ORF1*	99.3%	99.2%	3.5𝐸−102
17	ISAs1	—	—	—	—	ORF1*	100.0%	100.0%	4.1𝐸−205
18	ISL3	Transposase_12	100.0%	99.0%	4.7𝐸−31	ORF1*	100.0%	99.0%	5.0𝐸−95
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.