DDE_Tnp_1_7 - PFAM28P - GREMLIN Contacts

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DDE_Tnp_1_7 - Transposase IS4

PFAM:	PF13843	Sequences: TPLDFFELFFDDELIELIVEETNRYAAQKRKWKPTTVEELKAFLGLLILMGLVKLPSLRDYWSTDPLLGTPFFSKVMSRNRFELILRFLHFSDNSTRPPEYDKLAKIRPLLDHLNENFQKLYTPGENLSIDESMVPFKGRLSFKQYIPNKPIKFGIKIWVLCDSSTGYVYNFEVYTGKDTDGELEPELGLGGRVVLRLTEPLLGKGHHVYMDNFFTSPPLAEELLKKGIYACGTVRKNRKGLPKELKKKLKRGESDFRRKGDLLAVKWKDKKVVLLLSTAHSDETVERKRRRGKKVVPKPEIVKDYNKHMGGVDRSDQLRSYYSISRKTSKKWYKKLFFHLLDIAVVNAY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	350 (346)
Sequences:	2468 (2187)
Seq/√Len:	117.6
META:	0.655

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
102_D	108_R	4.509	1.00
21_E	24_R	4.459	1.00
35_T	85_I	4.286	1.00
115_N	171_N	3.958	1.00
173_E	197_R	3.834	1.00
221_A	231_A	3.814	1.00
213_N	236_R	3.654	1.00
211_M	231_A	3.590	1.00
39_E	81_R	3.417	1.00
170_Y	202_L	2.830	1.00
46_L	77_M	2.827	1.00
199_T	209_V	2.789	1.00
128_L	161_L	2.607	1.00
59_R	83_E	2.459	1.00
48_I	346_V	2.457	1.00
43_F	86_L	2.407	1.00
7_E	41_K	2.362	1.00
16_E	37_V	2.334	1.00
114_L	118_F	2.272	1.00
135_V	158_I	2.184	1.00
35_T	40_L	2.166	1.00
216_T	233_G	2.165	1.00
196_L	223_E	2.163	1.00
204_G	227_K	2.161	1.00
128_L	202_L	2.161	1.00
169_V	316_S	2.129	1.00
104_L	174_V	2.067	1.00
15_I	41_K	2.057	1.00
50_M	61_Y	2.048	1.00
46_L	73_F	2.026	1.00
11_D	117_N	2.014	1.00
91_F	334_Y	1.995	1.00
119_Q	171_N	1.993	1.00
276_L	303_V	1.989	1.00
211_M	221_A	1.920	1.00
47_L	82_F	1.900	1.00
127_N	309_H	1.828	1.00
281_H	305_D	1.814	1.00
223_E	226_K	1.814	1.00
93_D	96_T	1.789	1.00
19_V	40_L	1.781	1.00
19_V	37_V	1.767	1.00
126_E	208_H	1.757	1.00
251_K	254_E	1.750	1.00
159_W	214_F	1.728	1.00
208_H	232_C	1.697	1.00
18_I	40_L	1.694	1.00
288_R	292_R	1.686	1.00
18_I	91_F	1.676	1.00
163_D	166_T	1.675	1.00
16_E	20_E	1.666	1.00
135_V	337_L	1.662	1.00
216_T	277_L	1.636	1.00
141_L	156_I	1.618	1.00
162_C	313_V	1.616	1.00
203_L	229_I	1.615	1.00
160_V	169_V	1.610	1.00
35_T	39_E	1.589	1.00
103_K	142_S	1.588	1.00
69_G	74_S	1.585	1.00
289_K	292_R	1.585	1.00
221_A	279_T	1.584	1.00
125_G	163_D	1.575	1.00
192_G	223_E	1.573	1.00
15_I	19_V	1.572	1.00
278_S	281_H	1.554	1.00
15_I	40_L	1.537	1.00
6_F	10_F	1.536	1.00
288_R	291_R	1.518	1.00
211_M	216_T	1.518	1.00
53_V	70_T	1.511	1.00
208_H	280_A	1.501	1.00
191_G	194_V	1.497	1.00
15_I	37_V	1.489	1.00
216_T	221_A	1.474	1.00
171_N	201_P	1.470	1.00
18_I	89_L	1.466	1.00
37_V	41_K	1.461	1.00
146_Y	153_K	1.454	1.00
43_F	85_I	1.449	1.00
159_W	194_V	1.445	1.00
221_A	277_L	1.428	1.00
123_T	207_H	1.420	1.00
27_A	34_P	1.415	1.00
134_M	152_I	1.405	1.00
28_Q	94_N	1.399	1.00
26_A	32_W	1.390	1.00
216_T	231_A	1.389	1.00
269_K	273_V	1.387	1.00
114_L	345_A	1.375	1.00
210_Y	309_H	1.372	1.00
29_K	88_F	1.368	1.00
25_Y	90_H	1.363	1.00
159_W	215_F	1.362	1.00
332_K	335_K	1.356	1.00
129_S	164_S	1.344	1.00
122_Y	163_D	1.333	1.00
169_V	344_I	1.329	1.00
127_N	210_Y	1.325	1.00
230_Y	280_A	1.322	1.00
133_S	160_V	1.316	1.00
24_R	28_Q	1.305	1.00
235_V	265_A	1.297	1.00
15_I	44_L	1.296	1.00
115_N	172_F	1.288	1.00
158_I	337_L	1.287	1.00
210_Y	232_C	1.284	1.00
325_I	343_D	1.284	1.00
17_L	21_E	1.278	0.99
301_E	305_D	1.276	0.99
125_G	207_H	1.274	0.99
307_N	310_M	1.267	0.99
276_L	302_I	1.267	0.99
128_L	170_Y	1.261	0.99
146_Y	154_F	1.256	0.99
14_L	110_L	1.246	0.99
19_V	35_T	1.245	0.99
111_L	172_F	1.244	0.99
213_N	234_T	1.231	0.99
12_D	41_K	1.212	0.99
250_L	254_E	1.211	0.99
235_V	242_L	1.210	0.99
199_T	203_L	1.206	0.99
134_M	147_I	1.194	0.99
189_G	192_G	1.191	0.99
108_R	112_D	1.189	0.99
17_L	113_H	1.187	0.99
274_V	278_S	1.185	0.99
162_C	169_V	1.182	0.99
48_I	342_L	1.181	0.99
117_N	120_K	1.176	0.99
129_S	312_G	1.173	0.99
318_Q	322_Y	1.172	0.99
218_P	235_V	1.146	0.99
91_F	110_L	1.144	0.99
55_L	70_T	1.136	0.99
80_N	83_E	1.124	0.99
289_K	293_G	1.114	0.99
138_K	154_F	1.113	0.99
92_S	109_P	1.110	0.99
131_D	213_N	1.106	0.99
90_H	94_N	1.104	0.99
225_L	230_Y	1.098	0.98
222_E	260_K	1.094	0.98
3_L	7_E	1.090	0.98
129_S	310_M	1.090	0.98
90_H	106_K	1.087	0.98
56_P	60_D	1.086	0.98
79_R	83_E	1.086	0.98
42_A	76_V	1.084	0.98
128_L	207_H	1.081	0.98
204_G	228_G	1.079	0.98
92_S	105_A	1.079	0.98
6_F	48_I	1.074	0.98
158_I	174_V	1.072	0.98
288_R	293_G	1.071	0.98
265_A	277_L	1.069	0.98
7_E	12_D	1.069	0.98
116_E	120_K	1.061	0.98
46_L	76_V	1.059	0.98
119_Q	201_P	1.048	0.98
267_K	275_L	1.046	0.98
192_G	219_P	1.043	0.98
192_G	196_L	1.040	0.98
319_L	347_V	1.038	0.98
267_K	273_V	1.036	0.98
45_G	76_V	1.035	0.98
44_L	342_L	1.033	0.98
225_L	262_D	1.033	0.98
264_L	302_I	1.032	0.98
35_T	81_R	1.030	0.98
209_V	229_I	1.026	0.98
60_D	63_S	1.026	0.98
315_R	318_Q	1.025	0.98
14_L	113_H	1.024	0.98
191_G	214_F	1.020	0.98
134_M	155_G	1.016	0.97
266_V	302_I	1.010	0.97
218_P	263_L	1.006	0.97
130_I	195_V	1.005	0.97
191_G	215_F	1.005	0.97
113_H	117_N	1.003	0.97
118_F	345_A	0.999	0.97
145_Q	175_Y	0.998	0.97
124_P	170_Y	0.998	0.97
316_S	344_I	0.998	0.97
290_R	293_G	0.995	0.97
161_L	171_N	0.995	0.97
338_F	342_L	0.994	0.97
84_L	87_R	0.993	0.97
118_F	168_Y	0.992	0.97
21_E	94_N	0.985	0.97
320_R	340_H	0.984	0.97
24_R	93_D	0.979	0.97
125_G	166_T	0.978	0.97
203_L	227_K	0.975	0.97
162_C	316_S	0.969	0.97
222_E	263_L	0.960	0.96
242_L	265_A	0.958	0.96
94_N	106_K	0.954	0.96
127_N	208_H	0.951	0.96
63_S	68_L	0.948	0.96
22_T	35_T	0.948	0.96
224_L	231_A	0.948	0.96
124_P	128_L	0.947	0.96
223_E	227_K	0.944	0.96
49_L	73_F	0.943	0.96
220_L	224_L	0.941	0.96
57_S	60_D	0.937	0.96
205_K	229_I	0.920	0.95
138_K	153_K	0.920	0.95
52_L	56_P	0.919	0.95
188_L	192_G	0.916	0.95
271_K	274_V	0.915	0.95
190_L	194_V	0.912	0.95
147_I	153_K	0.911	0.95
40_L	43_F	0.911	0.95
250_L	269_K	0.903	0.95
114_L	341_L	0.902	0.95
190_L	214_F	0.897	0.95
96_T	105_A	0.895	0.95
193_R	197_R	0.882	0.94
340_H	344_I	0.880	0.94
21_E	93_D	0.876	0.94
232_C	280_A	0.876	0.94
137_F	141_L	0.876	0.94
173_E	193_R	0.873	0.94
164_S	312_G	0.873	0.94
97_R	105_A	0.870	0.94
285_T	289_K	0.867	0.94
285_T	292_R	0.865	0.94
255_S	266_V	0.857	0.93
134_M	151_P	0.855	0.93
300_P	303_V	0.855	0.93
8_L	121_L	0.852	0.93
81_R	85_I	0.847	0.93
208_H	230_Y	0.845	0.93
136_P	152_I	0.845	0.93
40_L	44_L	0.843	0.93
158_I	215_F	0.838	0.93
232_C	281_H	0.838	0.93
29_K	87_R	0.834	0.92
130_I	209_V	0.828	0.92
274_V	279_T	0.826	0.92
316_S	320_R	0.825	0.92
130_I	198_L	0.823	0.92
299_K	304_K	0.823	0.92
346_V	349_A	0.820	0.92
232_C	305_D	0.819	0.92
12_D	37_V	0.815	0.92
130_I	161_L	0.815	0.92
195_V	220_L	0.808	0.91
135_V	340_H	0.806	0.91
307_N	314_D	0.802	0.91
12_D	16_E	0.801	0.91
21_E	28_Q	0.799	0.91
286_V	289_K	0.799	0.91
286_V	293_G	0.796	0.91
146_Y	234_T	0.795	0.91
345_A	349_A	0.794	0.90
147_I	155_G	0.791	0.90
211_M	277_L	0.791	0.90
316_S	347_V	0.788	0.90
310_M	314_D	0.782	0.90
58_L	83_E	0.780	0.90
14_L	18_I	0.779	0.90
26_A	88_F	0.777	0.89
235_V	277_L	0.773	0.89
159_W	190_L	0.773	0.89
188_L	196_L	0.769	0.89
129_S	311_G	0.768	0.89
207_H	229_I	0.764	0.89
210_Y	305_D	0.761	0.89
132_E	314_D	0.760	0.88
169_V	348_N	0.760	0.88
53_V	73_F	0.760	0.88
110_L	338_F	0.760	0.88
84_L	88_F	0.759	0.88
304_K	308_K	0.758	0.88
62_W	77_M	0.755	0.88
25_Y	28_Q	0.752	0.88
159_W	175_Y	0.750	0.88
221_A	225_L	0.747	0.88
92_S	97_R	0.746	0.88
20_E	24_R	0.746	0.88
189_G	193_R	0.745	0.87
314_D	317_D	0.743	0.87
144_K	154_F	0.741	0.87
190_L	193_R	0.741	0.87
25_Y	94_N	0.738	0.87
197_R	200_E	0.738	0.87
143_F	156_I	0.737	0.87
147_I	214_F	0.736	0.87
117_N	121_L	0.736	0.87
44_L	338_F	0.735	0.87
255_S	258_R	0.734	0.87
252_R	255_S	0.732	0.87
21_E	90_H	0.731	0.86
130_I	199_T	0.728	0.86
118_F	171_N	0.728	0.86
275_L	278_S	0.725	0.86
196_L	227_K	0.724	0.86
133_S	340_H	0.723	0.86
324_S	327_R	0.723	0.86
19_V	23_N	0.722	0.86
287_E	291_R	0.721	0.86
167_G	315_R	0.720	0.86
311_G	315_R	0.719	0.86
89_L	338_F	0.716	0.85
131_D	314_D	0.716	0.85
36_T	85_I	0.716	0.85
212_D	234_T	0.713	0.85
28_Q	93_D	0.713	0.85
104_L	108_R	0.712	0.85
106_K	334_Y	0.711	0.85
124_P	202_L	0.710	0.85
118_F	348_N	0.709	0.85
139_G	144_K	0.708	0.85
253_G	268_W	0.706	0.84
69_G	75_K	0.699	0.84
287_E	292_R	0.699	0.84
310_M	313_V	0.697	0.84
42_A	45_G	0.696	0.84
122_Y	166_T	0.695	0.84
234_T	314_D	0.695	0.84
8_L	124_P	0.694	0.83
163_D	167_G	0.692	0.83
17_L	20_E	0.692	0.83
21_E	25_Y	0.691	0.83
138_K	146_Y	0.689	0.83
71_P	75_K	0.689	0.83
25_Y	106_K	0.688	0.83
157_K	175_Y	0.683	0.83
121_L	168_Y	0.682	0.82
12_D	19_V	0.680	0.82
134_M	149_N	0.680	0.82
307_N	311_G	0.677	0.82
257_F	264_L	0.677	0.82
28_Q	95_S	0.673	0.82
259_R	264_L	0.672	0.81
115_N	118_F	0.671	0.81
32_W	84_L	0.670	0.81
244_K	247_K	0.669	0.81
111_L	115_N	0.668	0.81
70_T	74_S	0.667	0.81
188_L	193_R	0.667	0.81
58_L	86_L	0.666	0.81
130_I	194_V	0.666	0.81
219_P	241_G	0.665	0.81
277_L	281_H	0.665	0.81
23_N	32_W	0.663	0.81
91_F	338_F	0.663	0.81
132_E	234_T	0.662	0.81
156_I	337_L	0.662	0.81
210_Y	281_H	0.661	0.80
199_T	229_I	0.658	0.80
212_D	314_D	0.658	0.80
115_N	119_Q	0.657	0.80
11_D	14_L	0.656	0.80
161_L	209_V	0.656	0.80
266_V	270_D	0.654	0.80
18_I	338_F	0.654	0.80
245_E	258_R	0.652	0.80
70_T	73_F	0.652	0.80
268_W	274_V	0.651	0.79
156_I	174_V	0.651	0.79
225_L	279_T	0.650	0.79
159_W	191_G	0.650	0.79
169_V	172_F	0.648	0.79
311_G	318_Q	0.648	0.79
128_L	199_T	0.648	0.79
287_E	293_G	0.644	0.79
59_R	79_R	0.644	0.79
126_E	206_G	0.640	0.78
285_T	288_R	0.638	0.78
132_E	150_K	0.637	0.78
104_L	143_F	0.636	0.78
286_V	291_R	0.636	0.78
222_E	226_K	0.635	0.78
35_T	43_F	0.633	0.77
305_D	309_H	0.629	0.77
310_M	317_D	0.629	0.77
4_D	7_E	0.629	0.77
125_G	165_S	0.629	0.77
312_G	323_Y	0.626	0.77
203_L	206_G	0.623	0.76
131_D	212_D	0.621	0.76
141_L	144_K	0.620	0.76
275_L	279_T	0.619	0.76
109_P	112_D	0.619	0.76
246_L	256_D	0.619	0.76
40_L	85_I	0.618	0.76
33_K	36_T	0.617	0.76
234_T	239_R	0.615	0.75
257_F	266_V	0.614	0.75
286_V	290_R	0.613	0.75
20_E	27_A	0.609	0.75
263_L	277_L	0.609	0.75
26_A	84_L	0.606	0.74
62_W	79_R	0.605	0.74
194_V	198_L	0.603	0.74
124_P	207_H	0.603	0.74
23_N	39_E	0.603	0.74
203_L	207_H	0.602	0.74
328_K	331_K	0.601	0.74
11_D	16_E	0.600	0.74
206_G	230_Y	0.600	0.74
284_E	292_R	0.593	0.73
253_G	256_D	0.589	0.72
11_D	113_H	0.588	0.72
93_D	105_A	0.588	0.72
111_L	174_V	0.587	0.72
10_F	15_I	0.586	0.72
148_P	153_K	0.585	0.72
9_F	117_N	0.583	0.72
325_I	342_L	0.582	0.71
313_V	317_D	0.582	0.71
192_G	217_S	0.581	0.71
131_D	234_T	0.580	0.71
174_V	337_L	0.577	0.71
287_E	290_R	0.577	0.71
274_V	281_H	0.576	0.71
169_V	347_V	0.575	0.71
131_D	150_K	0.573	0.70
112_D	116_E	0.573	0.70
38_E	41_K	0.571	0.70
52_L	55_L	0.570	0.70
339_F	343_D	0.568	0.70
221_A	263_L	0.568	0.70
291_R	294_K	0.566	0.69
270_D	274_V	0.565	0.69
133_S	169_V	0.565	0.69
106_K	332_K	0.564	0.69
324_S	343_D	0.564	0.69
23_N	33_K	0.564	0.69
305_D	308_K	0.561	0.69
56_P	70_T	0.561	0.69
114_L	342_L	0.560	0.69
122_Y	170_Y	0.560	0.69
145_Q	157_K	0.557	0.68
62_W	80_N	0.557	0.68
122_Y	125_G	0.557	0.68
118_F	121_L	0.556	0.68
254_E	258_R	0.555	0.68
51_G	323_Y	0.552	0.67
306_Y	310_M	0.552	0.67
320_R	343_D	0.552	0.67
266_V	276_L	0.552	0.67
326_S	336_K	0.551	0.67
20_E	45_G	0.551	0.67
131_D	151_P	0.550	0.67
171_N	202_L	0.550	0.67
85_I	89_L	0.549	0.67
204_G	229_I	0.548	0.67
143_F	215_F	0.547	0.67
303_V	307_N	0.546	0.67
128_L	209_V	0.545	0.66
218_P	242_L	0.545	0.66
30_R	34_P	0.545	0.66
320_R	344_I	0.544	0.66
24_R	94_N	0.544	0.66
253_G	257_F	0.543	0.66
80_N	84_L	0.542	0.66
285_T	290_R	0.542	0.66
155_G	314_D	0.542	0.66
81_R	243_P	0.541	0.66
335_K	339_F	0.539	0.66
210_Y	280_A	0.539	0.66
134_M	157_K	0.539	0.66
160_V	344_I	0.538	0.65
320_R	347_V	0.538	0.65
316_S	340_H	0.535	0.65
23_N	35_T	0.534	0.65
144_K	148_P	0.533	0.65
131_D	155_G	0.533	0.65
257_F	260_K	0.531	0.64
175_Y	213_N	0.531	0.64
9_F	118_F	0.530	0.64
134_M	154_F	0.529	0.64
200_E	203_L	0.529	0.64
16_E	19_V	0.528	0.64
242_L	246_L	0.528	0.64
252_R	256_D	0.527	0.64
56_P	61_Y	0.527	0.64
19_V	85_I	0.527	0.64
45_G	72_F	0.526	0.64
104_L	176_T	0.526	0.64
14_L	117_N	0.525	0.64
55_L	61_Y	0.524	0.63
151_P	312_G	0.522	0.63
159_W	173_E	0.522	0.63
39_E	85_I	0.522	0.63
196_L	203_L	0.521	0.63
103_K	159_W	0.520	0.63
112_D	155_G	0.520	0.63
217_S	239_R	0.519	0.63
250_L	256_D	0.519	0.63
199_T	224_L	0.519	0.63
274_V	277_L	0.518	0.63
149_N	154_F	0.517	0.62
222_E	262_D	0.517	0.62
278_S	302_I	0.516	0.62
15_I	110_L	0.515	0.62
265_A	268_W	0.514	0.62
306_Y	313_V	0.509	0.61
49_L	52_L	0.509	0.61
146_Y	272_K	0.509	0.61
230_Y	281_H	0.509	0.61
132_E	213_N	0.507	0.61
213_N	314_D	0.507	0.61
107_I	172_F	0.506	0.61
98_P	101_Y	0.505	0.61
103_K	179_D	0.504	0.60
311_G	314_D	0.504	0.60
58_L	79_R	0.503	0.60
145_Q	214_F	0.502	0.60
19_V	36_T	0.502	0.60
72_F	76_V	0.501	0.60
32_W	35_T	0.500	0.60

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
1musA	2	0.7943	55	0.954	Contact Map
4mq3A	1	0.3629	5.5	0.972	Contact Map
3j25A	1	0.2943	4.8	0.973	Contact Map
3l3uA	2	0.4257	4.6	0.973	Contact Map
4cf8A	2	0.4086	4.3	0.973	Contact Map
2jxcB	1	0.0429	4.1	0.974	Contact Map
1c6vA	4	0.42	3.8	0.974	Contact Map
1cxqA	2	0.4	3.8	0.974	Contact Map
2cqkA	1	0.2886	3.3	0.975	Contact Map
4wv4B	1	0.1857	3.2	0.975	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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