TraH - PFAM28P - GREMLIN Contacts

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TraH - Conjugative relaxosome accessory transposon protein

PFAM:	PF06122	Sequences: MDDFFNAMSNVTGPGAYQGQTRGYYTGGSLSARTPVKNIQLVSIQPPSIKAGCGGIDLFLGSFSFINADQLVQLLRNIASNAPGYAFQLALKTLCPQCANIMKELQALAQKLNQMNINSCEAAQALVGGLAPAKTDAASQKICAAIGTSSGLFSDWAAARQGCGTGGQADSTLAKADSDPALKDCPAEVPDNGNLVWKALKKNGFLSGDDELAELIMSLVGTVIVDKPGADGSGPVTVRYIPPLATNEDLLKALLEGGTAKVVYKCDDGTDTDKCLNPTVTISANKGLRARVRTLLDSIVDKIRNDTALTAEEKAFLNSTPLPVYKILNVAAAYGPGLADSLIEQLAEVIALDLAYQYLSD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	361 (356)
Sequences:	1282 (1035)
Seq/√Len:	54.9
META:	0.754

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
95_C	98_C	11.472	1.00
302_K	313_E	8.619	1.00
107_A	111_K	3.723	1.00
92_K	99_A	3.668	1.00
123_A	127_V	3.238	1.00
267_D	278_P	3.232	1.00
298_S	313_E	3.173	1.00
85_Y	98_C	3.122	1.00
267_D	277_N	3.116	1.00
99_A	103_K	3.078	1.00
290_A	294_T	2.982	1.00
224_I	241_I	2.890	1.00
310_T	313_E	2.762	1.00
196_V	220_V	2.702	1.00
311_A	314_K	2.523	1.00
66_I	105_L	2.504	1.00
295_L	316_F	2.500	1.00
201_K	213_A	2.482	1.00
194_N	197_W	2.443	1.00
67_N	70_Q	2.427	1.00
295_L	313_E	2.426	1.00
218_S	244_L	2.406	1.00
71_L	84_G	2.343	1.00
147_G	153_F	2.304	1.00
88_Q	99_A	2.303	1.00
299_I	309_L	2.242	1.00
77_N	81_N	2.148	1.00
286_K	294_T	2.137	1.00
68_A	71_L	2.114	1.00
71_L	105_L	2.109	1.00
88_Q	103_K	2.100	1.00
196_V	200_L	2.093	1.00
81_N	84_G	2.087	1.00
92_K	100_N	2.057	1.00
217_M	222_T	2.032	1.00
303_I	328_L	2.029	1.00
92_K	96_P	2.012	1.00
88_Q	102_M	1.980	1.00
74_L	109_A	1.973	1.00
118_N	121_E	1.966	1.00
143_C	163_C	1.964	1.00
298_S	302_K	1.945	1.00
303_I	325_Y	1.886	1.00
49_I	58_L	1.884	0.99
52_G	56_I	1.883	0.99
92_K	97_Q	1.827	0.99
106_Q	110_Q	1.824	0.99
151_G	155_D	1.745	0.99
321_P	353_D	1.735	0.99
244_L	264_Y	1.722	0.99
155_D	158_A	1.712	0.99
111_K	114_Q	1.700	0.99
81_N	127_V	1.675	0.99
268_D	271_D	1.673	0.99
119_S	123_A	1.670	0.99
94_L	98_C	1.656	0.99
92_K	101_I	1.647	0.99
266_C	275_C	1.644	0.99
289_R	348_E	1.619	0.98
16_A	25_Y	1.608	0.98
39_I	74_L	1.590	0.98
293_R	344_E	1.585	0.98
92_K	103_K	1.569	0.98
51_A	84_G	1.568	0.98
85_Y	95_C	1.560	0.98
98_C	105_L	1.544	0.98
194_N	217_M	1.544	0.98
113_N	116_N	1.536	0.98
100_N	104_E	1.536	0.98
64_S	155_D	1.528	0.98
81_N	123_A	1.527	0.98
69_D	72_V	1.523	0.98
83_P	123_A	1.521	0.98
85_Y	105_L	1.500	0.97
197_W	217_M	1.489	0.97
131_A	134_K	1.486	0.97
217_M	278_P	1.483	0.97
19_G	24_Y	1.479	0.97
67_N	83_P	1.478	0.97
71_L	75_L	1.453	0.97
256_E	289_R	1.451	0.97
91_L	99_A	1.446	0.97
74_L	106_Q	1.444	0.97
193_G	198_K	1.443	0.97
36_V	118_N	1.439	0.97
346_L	350_I	1.431	0.97
20_Q	23_G	1.421	0.96
295_L	298_S	1.410	0.96
155_D	159_A	1.377	0.96
25_Y	326_K	1.356	0.95
241_I	264_Y	1.354	0.95
252_K	256_E	1.350	0.95
194_N	222_T	1.341	0.95
72_V	87_F	1.340	0.95
75_L	88_Q	1.326	0.95
84_G	88_Q	1.323	0.95
70_Q	73_Q	1.320	0.95
44_I	62_S	1.317	0.95
37_K	77_N	1.306	0.94
271_D	274_K	1.303	0.94
11_V	30_L	1.285	0.94
89_L	127_V	1.282	0.94
268_D	278_P	1.278	0.94
201_K	210_D	1.269	0.93
222_T	241_I	1.266	0.93
118_N	122_A	1.264	0.93
302_K	307_T	1.261	0.93
169_A	173_L	1.253	0.93
91_L	102_M	1.253	0.93
18_Q	21_T	1.252	0.93
75_L	87_F	1.252	0.93
84_G	105_L	1.251	0.93
255_L	355_A	1.235	0.92
298_S	310_T	1.232	0.92
241_I	278_P	1.231	0.92
293_R	297_D	1.221	0.92
89_L	98_C	1.210	0.92
257_G	287_G	1.208	0.92
158_A	162_G	1.198	0.91
326_K	330_V	1.198	0.91
38_N	118_N	1.195	0.91
70_Q	106_Q	1.191	0.91
197_W	200_L	1.186	0.91
33_R	57_D	1.182	0.91
58_L	65_F	1.176	0.90
314_K	325_Y	1.162	0.90
268_D	277_N	1.160	0.90
198_K	201_K	1.160	0.90
117_I	121_E	1.151	0.89
267_D	271_D	1.143	0.89
62_S	109_A	1.136	0.89
74_L	78_I	1.134	0.89
316_F	350_I	1.133	0.89
135_T	139_S	1.130	0.89
194_N	266_C	1.110	0.88
197_W	214_E	1.110	0.88
268_D	274_K	1.109	0.88
141_K	261_K	1.105	0.87
85_Y	89_L	1.092	0.87
258_G	263_V	1.089	0.87
14_P	28_G	1.085	0.86
98_C	101_I	1.084	0.86
291_R	295_L	1.063	0.85
47_P	61_G	1.060	0.85
48_S	59_F	1.059	0.85
88_Q	104_E	1.052	0.85
79_A	95_C	1.051	0.85
322_L	327_I	1.048	0.84
231_D	234_G	1.034	0.84
173_L	176_A	1.028	0.83
316_F	319_S	1.026	0.83
16_A	23_G	1.025	0.83
224_I	276_L	1.019	0.83
210_D	262_V	1.018	0.83
18_Q	22_R	1.017	0.83
206_L	209_D	1.011	0.82
112_L	116_N	1.009	0.82
68_A	72_V	1.008	0.82
73_Q	321_P	1.003	0.82
65_F	110_Q	0.995	0.81
302_K	309_L	0.991	0.81
21_T	24_Y	0.991	0.81
299_I	313_E	0.990	0.81
79_A	102_M	0.989	0.81
76_R	80_S	0.985	0.81
68_A	209_D	0.985	0.81
249_D	252_K	0.982	0.80
69_D	73_Q	0.977	0.80
81_N	119_S	0.974	0.80
66_I	70_Q	0.969	0.79
343_I	347_A	0.967	0.79
87_F	94_L	0.964	0.79
122_A	125_A	0.960	0.79
44_I	109_A	0.957	0.79
63_F	90_A	0.957	0.79
5_F	10_N	0.956	0.79
342_L	346_L	0.955	0.78
172_T	176_A	0.951	0.78
197_W	266_C	0.943	0.78
71_L	79_A	0.941	0.77
171_S	175_K	0.939	0.77
326_K	329_N	0.937	0.77
295_L	299_I	0.935	0.77
267_D	272_T	0.935	0.77
217_M	266_C	0.930	0.77
93_T	99_A	0.928	0.76
59_F	86_A	0.927	0.76
62_S	112_L	0.924	0.76
45_Q	48_S	0.919	0.76
74_L	119_S	0.919	0.76
242_P	259_T	0.916	0.76
60_L	63_F	0.914	0.75
6_N	27_G	0.913	0.75
65_F	84_G	0.912	0.75
93_T	97_Q	0.910	0.75
117_I	122_A	0.909	0.75
353_D	357_Q	0.908	0.75
40_Q	46_P	0.906	0.75
268_D	273_D	0.905	0.75
131_A	136_D	0.902	0.74
29_S	33_R	0.897	0.74
104_E	108_L	0.888	0.73
73_Q	76_R	0.888	0.73
209_D	212_L	0.887	0.73
79_A	83_P	0.886	0.73
121_E	125_A	0.886	0.73
95_C	99_A	0.880	0.73
79_A	296_L	0.879	0.72
20_Q	24_Y	0.878	0.72
145_A	308_A	0.869	0.72
141_K	145_A	0.865	0.71
197_W	213_A	0.863	0.71
298_S	342_L	0.859	0.71
87_F	90_A	0.858	0.71
282_I	285_N	0.858	0.71
219_L	359_L	0.857	0.71
300_V	339_A	0.857	0.71
170_D	173_L	0.855	0.70
95_C	105_L	0.855	0.70
49_I	76_R	0.850	0.70
339_A	343_I	0.850	0.70
22_R	39_I	0.849	0.70
309_L	313_E	0.849	0.70
259_T	307_T	0.847	0.70
38_N	41_L	0.845	0.69
2_D	6_N	0.840	0.69
153_F	162_G	0.840	0.69
136_D	139_S	0.834	0.68
73_Q	81_N	0.830	0.68
291_R	312_E	0.830	0.68
287_G	290_A	0.829	0.68
51_A	81_N	0.829	0.68
138_A	142_I	0.825	0.68
324_V	350_I	0.822	0.67
180_P	183_K	0.821	0.67
147_G	151_G	0.819	0.67
169_A	174_A	0.819	0.67
88_Q	91_L	0.817	0.67
209_D	292_V	0.815	0.67
295_L	312_E	0.812	0.66
74_L	117_I	0.812	0.66
290_A	293_R	0.810	0.66
222_T	276_L	0.809	0.66
228_P	239_R	0.807	0.66
15_G	19_G	0.803	0.66
27_G	345_Q	0.802	0.65
80_S	86_A	0.802	0.65
141_K	144_A	0.801	0.65
218_S	266_C	0.801	0.65
11_V	291_R	0.787	0.64
65_F	106_Q	0.787	0.64
148_T	159_A	0.786	0.64
303_I	329_N	0.785	0.64
15_G	26_T	0.784	0.64
102_M	306_D	0.784	0.64
171_S	174_A	0.783	0.64
54_G	65_F	0.778	0.63
286_K	307_T	0.777	0.63
67_N	162_G	0.776	0.63
183_K	259_T	0.776	0.63
76_R	85_Y	0.775	0.63
24_Y	62_S	0.773	0.63
103_K	107_A	0.772	0.62
332_A	349_V	0.771	0.62
99_A	105_L	0.770	0.62
118_N	147_G	0.770	0.62
299_I	317_L	0.769	0.62
226_D	229_G	0.767	0.62
123_A	128_G	0.765	0.62
31_S	57_D	0.765	0.62
16_A	29_S	0.763	0.62
85_Y	101_I	0.760	0.61
309_L	314_K	0.760	0.61
196_V	217_M	0.758	0.61
229_G	234_G	0.758	0.61
172_T	175_K	0.756	0.61
84_G	119_S	0.756	0.61
65_F	82_A	0.756	0.61
77_N	100_N	0.754	0.61
131_A	142_I	0.753	0.61
58_L	326_K	0.752	0.60
161_Q	165_T	0.749	0.60
95_C	102_M	0.747	0.60
2_D	5_F	0.746	0.60
77_N	95_C	0.738	0.59
106_Q	109_A	0.737	0.59
51_A	103_K	0.737	0.59
88_Q	92_K	0.737	0.59
212_L	220_V	0.732	0.58
14_P	26_T	0.731	0.58
75_L	79_A	0.731	0.58
66_I	79_A	0.730	0.58
130_L	227_K	0.727	0.58
87_F	91_L	0.726	0.58
197_W	222_T	0.726	0.58
344_E	347_A	0.725	0.58
316_F	320_T	0.725	0.58
83_P	291_R	0.725	0.58
94_L	97_Q	0.724	0.57
88_Q	106_Q	0.723	0.57
352_L	356_Y	0.722	0.57
52_G	63_F	0.721	0.57
239_R	242_P	0.717	0.57
156_W	160_R	0.716	0.57
57_D	113_N	0.716	0.57
62_S	65_F	0.714	0.56
43_S	62_S	0.714	0.56
12_T	15_G	0.714	0.56
259_T	311_A	0.714	0.56
264_Y	278_P	0.713	0.56
51_A	55_G	0.712	0.56
302_K	310_T	0.711	0.56
210_D	272_T	0.710	0.56
138_A	141_K	0.709	0.56
39_I	119_S	0.709	0.56
268_D	276_L	0.708	0.56
125_A	137_A	0.708	0.56
74_L	112_L	0.706	0.56
25_Y	75_L	0.706	0.56
214_E	222_T	0.704	0.55
162_G	165_T	0.704	0.55
6_N	331_A	0.702	0.55
66_I	217_M	0.702	0.55
97_Q	104_E	0.699	0.55
261_K	309_L	0.696	0.55
10_N	31_S	0.695	0.54
121_E	124_Q	0.694	0.54
46_P	95_C	0.693	0.54
15_G	24_Y	0.692	0.54
127_V	332_A	0.691	0.54
322_L	326_K	0.690	0.54
224_I	266_C	0.690	0.54
102_M	128_G	0.688	0.54
123_A	126_L	0.688	0.54
62_S	72_V	0.686	0.53
102_M	199_A	0.686	0.53
200_L	203_N	0.685	0.53
91_L	104_E	0.682	0.53
45_Q	59_F	0.680	0.53
4_F	15_G	0.678	0.53
85_Y	123_A	0.676	0.52
109_A	116_N	0.675	0.52
53_C	61_G	0.673	0.52
41_L	44_I	0.672	0.52
18_Q	298_S	0.672	0.52
97_Q	101_I	0.667	0.51
11_V	14_P	0.665	0.51
62_S	322_L	0.663	0.51
53_C	56_I	0.662	0.51
194_N	200_L	0.662	0.51
19_G	26_T	0.661	0.51
222_T	266_C	0.661	0.51
8_M	11_V	0.661	0.51
25_Y	330_V	0.661	0.51
182_L	219_L	0.659	0.51
147_G	167_G	0.659	0.51
320_T	350_I	0.658	0.50
265_K	268_D	0.657	0.50
20_Q	317_L	0.654	0.50
31_S	37_K	0.654	0.50
136_D	142_I	0.654	0.50
16_A	20_Q	0.653	0.50
66_I	83_P	0.652	0.50
47_P	53_C	0.650	0.50
20_Q	323_P	0.649	0.49
258_G	281_T	0.646	0.49
156_W	163_C	0.646	0.49
79_A	99_A	0.641	0.49
97_Q	100_N	0.640	0.49
189_V	192_N	0.639	0.48
121_E	151_G	0.637	0.48
214_E	217_M	0.635	0.48
94_L	109_A	0.632	0.48
25_Y	292_V	0.631	0.48
217_M	224_I	0.629	0.47
21_T	94_L	0.624	0.47
66_I	266_C	0.624	0.47
214_E	218_S	0.623	0.47
299_I	328_L	0.620	0.46
63_F	82_A	0.620	0.46
174_A	191_D	0.618	0.46
41_L	117_I	0.617	0.46
227_K	231_D	0.615	0.46
327_I	349_V	0.613	0.46
79_A	108_L	0.613	0.46
203_N	332_A	0.612	0.46
46_P	98_C	0.611	0.45
58_L	327_I	0.610	0.45
118_N	212_L	0.609	0.45
108_L	112_L	0.609	0.45
39_I	59_F	0.609	0.45
7_A	34_T	0.609	0.45
11_V	259_T	0.608	0.45
100_N	351_A	0.608	0.45
36_V	110_Q	0.607	0.45
59_F	275_C	0.606	0.45
186_P	190_P	0.605	0.45
325_Y	330_V	0.604	0.45
112_L	115_M	0.602	0.44
64_S	142_I	0.601	0.44
15_G	18_Q	0.601	0.44
100_N	105_L	0.600	0.44
74_L	118_N	0.597	0.44
229_G	271_D	0.596	0.44
147_G	150_S	0.596	0.44
80_S	138_A	0.595	0.44
69_D	91_L	0.592	0.43
293_R	347_A	0.591	0.43
11_V	29_S	0.589	0.43
144_A	148_T	0.589	0.43
70_Q	218_S	0.587	0.43
288_L	355_A	0.587	0.43
95_C	101_I	0.585	0.43
76_R	339_A	0.585	0.43
337_G	341_S	0.585	0.43
70_Q	76_R	0.584	0.43
16_A	30_L	0.583	0.42
84_G	123_A	0.582	0.42
20_Q	320_T	0.582	0.42
80_S	331_A	0.582	0.42
194_N	224_I	0.581	0.42
218_S	222_T	0.579	0.42
299_I	316_F	0.579	0.42
240_Y	243_P	0.579	0.42
153_F	331_A	0.577	0.42
206_L	216_I	0.577	0.42
9_S	32_A	0.576	0.42
200_L	206_L	0.575	0.42
94_L	310_T	0.575	0.42
85_Y	127_V	0.574	0.42
58_L	71_L	0.573	0.41
159_A	163_C	0.572	0.41
31_S	34_T	0.572	0.41
30_L	148_T	0.567	0.41
288_L	358_Y	0.566	0.41
239_R	359_L	0.565	0.41
192_N	296_L	0.565	0.41
94_L	101_I	0.562	0.40
192_N	251_L	0.561	0.40
45_Q	95_C	0.558	0.40
39_I	117_I	0.558	0.40
17_Y	20_Q	0.558	0.40
193_G	196_V	0.558	0.40
132_P	140_Q	0.558	0.40
204_G	314_K	0.557	0.40
194_N	275_C	0.557	0.40
67_N	341_S	0.557	0.40
201_K	273_D	0.556	0.40
292_V	350_I	0.554	0.39
295_L	310_T	0.554	0.39
134_K	143_C	0.553	0.39
292_V	354_L	0.553	0.39
214_E	266_C	0.552	0.39
32_A	355_A	0.551	0.39
146_I	201_K	0.551	0.39
92_K	157_A	0.550	0.39
163_C	224_I	0.549	0.39
62_S	113_N	0.549	0.39
106_Q	358_Y	0.549	0.39
230_A	340_D	0.548	0.39
67_N	102_M	0.547	0.39
222_T	278_P	0.547	0.39
116_N	160_R	0.547	0.39
88_Q	108_L	0.546	0.39
300_V	343_I	0.546	0.39
70_Q	194_N	0.546	0.39
296_L	350_I	0.545	0.39
32_A	145_A	0.544	0.38
132_P	136_D	0.544	0.38
93_T	100_N	0.544	0.38
324_V	331_A	0.543	0.38
65_F	102_M	0.541	0.38
49_I	162_G	0.540	0.38
123_A	306_D	0.540	0.38
104_E	107_A	0.540	0.38
316_F	354_L	0.540	0.38
7_A	80_S	0.540	0.38
106_Q	113_N	0.539	0.38
160_R	163_C	0.539	0.38
19_G	73_Q	0.537	0.38
20_Q	65_F	0.537	0.38
115_M	328_L	0.537	0.38
213_A	217_M	0.536	0.38
78_I	85_Y	0.535	0.38
194_N	218_S	0.535	0.38
30_L	150_S	0.534	0.37
216_I	220_V	0.533	0.37
356_Y	360_S	0.533	0.37
169_A	172_T	0.532	0.37
139_S	143_C	0.532	0.37
154_S	158_A	0.531	0.37
268_D	272_T	0.529	0.37
135_T	143_C	0.529	0.37
124_Q	298_S	0.527	0.37
129_G	132_P	0.527	0.37
80_S	317_L	0.527	0.37
327_I	331_A	0.527	0.37
17_Y	349_V	0.527	0.37
162_G	173_L	0.526	0.37
52_G	55_G	0.526	0.37
281_T	284_A	0.526	0.37
241_I	245_A	0.525	0.37
330_V	342_L	0.523	0.36
67_N	202_K	0.523	0.36
75_L	126_L	0.523	0.36
159_A	236_V	0.522	0.36
229_G	232_G	0.520	0.36
42_V	112_L	0.518	0.36
108_L	111_K	0.517	0.36
189_V	193_G	0.516	0.36
196_V	218_S	0.515	0.36
331_A	343_I	0.515	0.36
67_N	115_M	0.513	0.35
289_R	292_V	0.513	0.35
314_K	318_N	0.512	0.35
74_L	193_G	0.509	0.35
46_P	80_S	0.509	0.35
31_S	35_P	0.509	0.35
95_C	100_N	0.509	0.35
220_V	250_L	0.507	0.35
22_R	64_S	0.507	0.35
183_K	216_I	0.507	0.35
329_N	334_Y	0.506	0.35
31_S	292_V	0.505	0.35
182_L	185_C	0.505	0.35
354_L	357_Q	0.505	0.35
8_M	14_P	0.504	0.34
306_D	314_K	0.504	0.34
41_L	74_L	0.503	0.34
151_G	291_R	0.503	0.34
140_Q	149_S	0.503	0.34
282_I	287_G	0.502	0.34
79_A	146_I	0.501	0.34
194_N	198_K	0.500	0.34

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
3b34A	1	0.3352	20	0.966	Contact Map
1whsA	2	0.3102	18.7	0.966	Contact Map
4x2uA	1	0.3352	13.7	0.968	Contact Map
4qhpA	1	0.3352	12.5	0.969	Contact Map
1vk4A	1	0.2548	11.2	0.97	Contact Map
1vm7A	2	0.277	9.2	0.971	Contact Map
4gm6A	5	0.277	6.8	0.973	Contact Map
3pl2A	2	0.2465	6.4	0.973	Contact Map
3jywF	1	0.2022	6.1	0.973	Contact Map
4grhA	1	0.2188	5.6	0.973	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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