YBDG - ECOLI - GREMLIN Contacts

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YBDG - Miniconductance mechanosensitive channel YbdG

UniProt:	P0AAT4	Sequences: MQDLISQVEDLAGIEIDHTTSMVMIFGIIFLTAVVVHIILHWVVLRTFEKRAIASSRLWLQIITQNKLFHRLAFTLQGIIVNIQAVFWLQKGTEAADILTTCAQLWIMMYALLSVFSLLDVILNLAQKFPAASQLPLKGIFQGIKLIGAILVGILMISLLIGQSPAILISGLGAMAAVLMLVFKDPILGLVAGIQLSANDMLKLGDWLEMPKYGADGAVIDIGLTTVKVRNWDNTITTIPTWSLVSDSFKNWSGMSASGGRRIKRSISIDVTSIRFLDEDEMQRLNKAHLLKPYLTSRHQEINEWNRQQGSTESVLNLRRMTNIGTFRAYLNEYLRNHPRIRKDMTLMVRQLAPGDNGLPLEIYAFTNTVVWLEYESIQADIFDHIFAIVEEFGLRLHQSPTGNDIRSLAGAFKQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12620
Length:	415 (332)
Sequences:	1230 (954)
Seq/√Len:	52.4

ECOLI - YBDG

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
274_I	324_I	7.855	1.00
277_L	281_E	4.717	1.00
167_I	170_S	4.582	1.00
55_S	60_L	4.132	1.00
112_L	152_V	4.008	1.00
236_I	254_G	3.629	1.00
332_N	336_R	3.531	1.00
200_D	203_K	3.450	1.00
275_R	281_E	3.413	1.00
140_I	193_G	3.410	1.00
209_E	250_K	3.233	1.00
220_I	230_R	2.888	1.00
186_P	225_T	2.785	1.00
278_D	281_E	2.591	1.00
37_H	74_F	2.581	1.00
157_I	168_L	2.442	1.00
301_E	306_N	2.403	1.00
201_M	238_T	2.348	1.00
201_M	228_K	2.339	1.00
212_K	247_D	2.302	1.00
285_L	295_L	2.258	1.00
209_E	232_W	2.252	1.00
277_L	282_M	2.222	1.00
216_D	264_K	2.150	1.00
342_R	345_M	2.134	1.00
165_P	170_S	2.118	1.00
317_N	325_G	2.098	1.00
286_N	296_T	2.020	1.00
277_L	285_L	1.971	1.00
230_R	234_N	1.953	1.00
231_N	235_T	1.944	1.00
300_Q	303_N	1.916	0.99
281_E	285_L	1.879	0.99
203_K	253_S	1.858	0.99
136_P	142_Q	1.828	0.99
320_R	323_N	1.823	0.99
174_A	178_V	1.819	0.99
211_P	214_G	1.816	0.99
322_T	325_G	1.788	0.99
341_I	347_L	1.766	0.99
135_L	200_D	1.749	0.99
43_V	47_T	1.742	0.99
303_N	307_R	1.736	0.99
218_A	234_N	1.716	0.99
36_V	41_H	1.713	0.99
343_K	347_L	1.708	0.99
78_G	106_W	1.672	0.99
116_F	149_A	1.647	0.98
199_N	225_T	1.627	0.98
184_K	188_L	1.621	0.98
184_K	242_W	1.597	0.98
319_R	325_G	1.595	0.98
300_Q	304_E	1.594	0.98
35_V	39_I	1.588	0.98
215_A	237_T	1.585	0.98
108_M	159_L	1.585	0.98
239_I	248_S	1.570	0.98
139_G	176_A	1.568	0.98
321_M	326_T	1.560	0.98
37_H	41_H	1.554	0.98
176_A	200_D	1.541	0.97
29_I	88_W	1.528	0.97
216_D	232_W	1.525	0.97
59_W	125_L	1.523	0.97
120_D	145_K	1.522	0.97
306_N	317_N	1.479	0.97
269_I	278_D	1.475	0.97
286_N	299_H	1.454	0.96
329_A	333_E	1.448	0.96
154_I	165_P	1.433	0.96
55_S	61_Q	1.425	0.96
326_T	329_A	1.421	0.96
271_V	353_A	1.408	0.96
225_T	249_F	1.408	0.96
108_M	155_L	1.407	0.96
204_L	234_N	1.401	0.96
170_S	209_E	1.399	0.96
195_Q	232_W	1.373	0.95
52_A	55_S	1.369	0.95
174_A	177_A	1.362	0.95
323_N	327_F	1.359	0.95
195_Q	227_V	1.358	0.95
154_I	164_S	1.353	0.95
321_M	325_G	1.349	0.95
132_A	137_L	1.329	0.94
82_N	100_T	1.324	0.94
223_G	241_T	1.324	0.94
218_A	232_W	1.313	0.94
32_T	76_L	1.282	0.93
217_G	229_V	1.280	0.93
161_I	164_S	1.278	0.93
298_R	301_E	1.269	0.93
201_M	244_L	1.269	0.93
333_E	337_N	1.264	0.92
154_I	172_L	1.236	0.91
181_L	187_I	1.233	0.91
189_G	225_T	1.229	0.91
208_L	244_L	1.224	0.91
155_L	165_P	1.212	0.91
232_W	252_W	1.211	0.91
339_P	344_D	1.208	0.91
306_N	325_G	1.207	0.90
138_K	223_G	1.205	0.90
278_D	282_M	1.204	0.90
140_I	143_G	1.202	0.90
132_A	171_G	1.193	0.90
133_S	292_K	1.190	0.90
275_R	278_D	1.187	0.90
202_L	244_L	1.182	0.90
267_I	331_L	1.178	0.89
74_F	106_W	1.174	0.89
202_L	249_F	1.174	0.89
306_N	319_R	1.171	0.89
112_L	153_G	1.166	0.89
288_A	317_N	1.165	0.89
100_T	168_L	1.165	0.89
21_S	25_I	1.159	0.89
336_R	343_K	1.155	0.88
283_Q	287_K	1.153	0.88
230_R	236_I	1.149	0.88
320_R	325_G	1.148	0.88
196_L	201_M	1.144	0.88
243_S	247_D	1.139	0.88
241_T	245_V	1.137	0.88
313_E	318_L	1.132	0.87
105_L	156_M	1.131	0.87
130_P	137_L	1.130	0.87
283_Q	286_N	1.124	0.87
227_V	249_F	1.121	0.87
29_I	84_Q	1.121	0.87
291_L	294_Y	1.121	0.87
221_D	239_I	1.113	0.87
207_W	261_R	1.110	0.86
136_P	143_G	1.109	0.86
227_V	241_T	1.107	0.86
174_A	179_L	1.099	0.86
42_W	76_L	1.097	0.86
336_R	347_L	1.095	0.86
170_S	223_G	1.093	0.86
180_M	193_G	1.085	0.85
81_V	103_A	1.083	0.85
234_N	254_G	1.082	0.85
280_D	283_Q	1.078	0.85
147_I	151_L	1.068	0.84
135_L	193_G	1.068	0.84
50_K	54_A	1.068	0.84
37_H	40_L	1.066	0.84
224_L	262_R	1.051	0.83
220_I	236_I	1.047	0.83
39_I	292_K	1.045	0.83
234_N	258_S	1.044	0.83
38_I	42_W	1.037	0.82
126_A	132_A	1.034	0.82
111_A	151_L	1.031	0.82
231_N	261_R	1.030	0.82
184_K	196_L	1.022	0.81
193_G	299_H	1.017	0.81
116_F	196_L	1.010	0.81
65_Q	124_N	1.008	0.81
79_I	94_E	1.006	0.80
135_L	197_S	1.005	0.80
302_I	326_T	1.003	0.80
302_I	306_N	1.001	0.80
137_L	141_F	1.000	0.80
134_Q	147_I	0.996	0.80
89_L	225_T	0.996	0.80
151_L	155_L	0.993	0.79
298_R	302_I	0.988	0.79
324_I	331_L	0.987	0.79
118_L	122_I	0.984	0.79
63_I	68_L	0.983	0.79
36_V	76_L	0.980	0.79
120_D	141_F	0.979	0.79
68_L	121_V	0.970	0.78
111_A	150_I	0.968	0.78
221_D	228_K	0.962	0.77
28_I	43_V	0.960	0.77
293_P	297_S	0.953	0.77
76_L	80_I	0.951	0.76
140_I	225_T	0.948	0.76
30_F	49_E	0.944	0.76
183_F	273_S	0.937	0.75
192_A	195_Q	0.932	0.75
217_G	328_R	0.931	0.75
195_Q	225_T	0.929	0.75
158_S	271_V	0.926	0.75
189_G	242_W	0.925	0.74
301_E	305_W	0.924	0.74
77_Q	143_G	0.918	0.74
327_F	331_L	0.917	0.74
202_L	245_V	0.917	0.74
202_L	331_L	0.917	0.74
245_V	248_S	0.916	0.74
258_S	345_M	0.915	0.74
144_I	333_E	0.913	0.73
25_I	28_I	0.912	0.73
157_I	161_I	0.910	0.73
135_L	140_I	0.909	0.73
85_A	88_W	0.908	0.73
266_S	271_V	0.902	0.73
48_F	110_Y	0.896	0.72
333_E	336_R	0.894	0.72
177_A	183_F	0.887	0.71
196_L	331_L	0.884	0.71
161_I	166_A	0.884	0.71
36_V	279_E	0.882	0.71
212_K	243_S	0.882	0.71
230_R	254_G	0.882	0.71
143_G	146_L	0.880	0.71
144_I	297_S	0.879	0.71
138_K	221_D	0.878	0.71
268_S	271_V	0.873	0.70
338_H	341_I	0.870	0.70
190_L	197_S	0.869	0.70
201_M	245_V	0.864	0.69
200_D	223_G	0.862	0.69
295_L	326_T	0.855	0.68
137_L	143_G	0.854	0.68
193_G	241_T	0.854	0.68
249_F	252_W	0.852	0.68
28_I	46_R	0.851	0.68
140_I	200_D	0.848	0.68
36_V	70_H	0.845	0.68
290_L	294_Y	0.845	0.68
155_L	158_S	0.841	0.67
281_E	284_R	0.837	0.67
39_I	202_L	0.837	0.67
231_N	262_R	0.831	0.66
72_L	284_R	0.826	0.66
45_L	72_L	0.822	0.65
127_Q	162_G	0.822	0.65
193_G	270_D	0.821	0.65
186_P	190_L	0.820	0.65
304_E	307_R	0.817	0.65
94_E	99_L	0.816	0.65
124_N	284_R	0.815	0.65
67_K	70_H	0.815	0.65
237_T	247_D	0.815	0.65
317_N	321_M	0.812	0.64
195_Q	249_F	0.807	0.64
215_A	243_S	0.806	0.64
320_R	333_E	0.805	0.64
172_L	185_D	0.805	0.64
54_A	57_R	0.800	0.63
51_R	110_Y	0.800	0.63
233_D	252_W	0.798	0.63
216_D	235_T	0.796	0.63
69_F	78_G	0.794	0.63
304_E	308_Q	0.794	0.63
180_M	241_T	0.793	0.63
245_V	250_K	0.792	0.63
22_M	28_I	0.790	0.62
27_G	39_I	0.789	0.62
280_D	316_L	0.789	0.62
79_I	83_I	0.786	0.62
301_E	317_N	0.784	0.62
169_I	239_I	0.782	0.62
157_I	160_L	0.782	0.62
261_R	264_K	0.777	0.61
332_N	335_L	0.775	0.61
43_V	56_S	0.771	0.60
36_V	99_L	0.769	0.60
176_A	203_K	0.768	0.60
109_M	169_I	0.767	0.60
278_D	286_N	0.767	0.60
158_S	165_P	0.766	0.60
189_G	223_G	0.766	0.60
189_G	245_V	0.765	0.60
331_L	348_M	0.763	0.60
96_A	99_L	0.763	0.60
320_R	327_F	0.762	0.60
181_L	188_L	0.761	0.59
200_D	225_T	0.760	0.59
327_F	330_Y	0.758	0.59
318_L	324_I	0.754	0.59
101_T	162_G	0.754	0.59
35_V	109_M	0.753	0.59
302_I	340_R	0.750	0.58
284_R	287_K	0.750	0.58
94_E	151_L	0.748	0.58
201_M	243_S	0.748	0.58
234_N	346_T	0.744	0.58
85_A	96_A	0.743	0.58
329_A	332_N	0.742	0.57
308_Q	311_S	0.742	0.57
180_M	187_I	0.740	0.57
32_T	297_S	0.739	0.57
146_L	218_A	0.738	0.57
23_V	122_I	0.738	0.57
123_L	271_V	0.736	0.57
122_I	299_H	0.735	0.57
262_R	330_Y	0.734	0.57
212_K	343_K	0.733	0.57
192_A	252_W	0.732	0.56
314_S	319_R	0.730	0.56
35_V	161_I	0.729	0.56
57_R	60_L	0.724	0.56
101_T	245_V	0.721	0.55
317_N	326_T	0.720	0.55
52_A	64_T	0.719	0.55
211_P	221_D	0.717	0.55
323_N	334_Y	0.717	0.55
142_Q	227_V	0.709	0.54
29_I	81_V	0.709	0.54
201_M	226_T	0.706	0.54
330_Y	334_Y	0.706	0.54
305_W	318_L	0.705	0.54
151_L	214_G	0.705	0.54
207_W	252_W	0.704	0.54
185_D	261_R	0.704	0.54
139_G	168_L	0.703	0.53
193_G	225_T	0.703	0.53
133_S	136_P	0.703	0.53
331_L	334_Y	0.702	0.53
43_V	332_N	0.700	0.53
288_A	316_L	0.700	0.53
176_A	184_K	0.698	0.53
339_P	343_K	0.697	0.53
146_L	179_L	0.697	0.53
75_T	110_Y	0.696	0.53
96_A	267_I	0.696	0.53
186_P	241_T	0.692	0.52
88_W	115_V	0.688	0.52
233_D	264_K	0.688	0.52
223_G	326_T	0.688	0.52
231_N	328_R	0.686	0.52
340_R	344_D	0.686	0.52
71_R	117_S	0.685	0.52
169_I	204_L	0.684	0.51
102_C	113_L	0.683	0.51
323_N	326_T	0.682	0.51
172_L	244_L	0.682	0.51
294_Y	298_R	0.676	0.51
346_T	351_Q	0.676	0.51
345_M	348_M	0.673	0.50
189_G	201_M	0.672	0.50
60_L	63_I	0.669	0.50
317_N	329_A	0.665	0.49
193_G	217_G	0.663	0.49
46_R	54_A	0.661	0.49
118_L	347_L	0.661	0.49
282_M	321_M	0.659	0.49
57_R	61_Q	0.657	0.49
182_V	253_S	0.656	0.49
32_T	38_I	0.656	0.49
281_E	291_L	0.654	0.48
30_F	83_I	0.653	0.48
233_D	261_R	0.653	0.48
78_G	175_M	0.652	0.48
142_Q	183_F	0.651	0.48
48_F	51_R	0.649	0.48
32_T	97_D	0.647	0.48
300_Q	309_Q	0.642	0.47
177_A	323_N	0.642	0.47
287_K	311_S	0.641	0.47
156_M	159_L	0.641	0.47
187_I	190_L	0.640	0.47
274_I	278_D	0.640	0.47
165_P	171_G	0.638	0.47
258_S	342_R	0.637	0.47
260_G	345_M	0.635	0.46
78_G	127_Q	0.634	0.46
215_A	249_F	0.634	0.46
196_L	271_V	0.629	0.46
153_G	173_G	0.629	0.46
224_L	263_I	0.628	0.46
158_S	161_I	0.625	0.45
158_S	169_I	0.625	0.45
274_I	289_H	0.623	0.45
150_I	172_L	0.619	0.45
228_K	238_T	0.617	0.44
189_G	243_S	0.617	0.44
30_F	55_S	0.615	0.44
116_F	145_K	0.613	0.44
263_I	322_T	0.612	0.44
263_I	341_I	0.610	0.44
56_S	125_L	0.609	0.44
44_V	55_S	0.606	0.43
28_I	129_F	0.604	0.43
289_H	292_K	0.604	0.43
74_F	246_S	0.604	0.43
113_L	222_I	0.603	0.43
193_G	196_L	0.597	0.42
24_M	56_S	0.596	0.42
41_H	74_F	0.596	0.42
242_W	246_S	0.596	0.42
50_K	76_L	0.594	0.42
120_D	238_T	0.594	0.42
23_V	27_G	0.593	0.42
112_L	148_G	0.593	0.42
207_W	231_N	0.592	0.42
30_F	62_I	0.592	0.42
192_A	245_V	0.590	0.42
81_V	107_I	0.590	0.42
207_W	233_D	0.589	0.42
192_A	249_F	0.587	0.41
24_M	28_I	0.586	0.41
35_V	42_W	0.586	0.41
165_P	176_A	0.586	0.41
260_G	265_R	0.585	0.41
107_I	111_A	0.585	0.41
131_A	193_G	0.583	0.41
197_S	346_T	0.579	0.41
24_M	32_T	0.578	0.40
20_T	35_V	0.576	0.40
174_A	193_G	0.576	0.40
275_R	332_N	0.575	0.40
54_A	61_Q	0.574	0.40
137_L	140_I	0.574	0.40
39_I	59_W	0.572	0.40
192_A	232_W	0.572	0.40
195_Q	252_W	0.572	0.40
347_L	353_A	0.571	0.40
196_L	223_G	0.570	0.40
164_S	170_S	0.569	0.40
161_I	167_I	0.568	0.39
200_D	253_S	0.568	0.39
142_Q	191_V	0.568	0.39
161_I	168_L	0.568	0.39
269_I	352_L	0.566	0.39
60_L	149_A	0.566	0.39
189_G	238_T	0.566	0.39
63_I	149_A	0.565	0.39
31_L	59_W	0.564	0.39
135_L	142_Q	0.564	0.39
216_D	231_N	0.562	0.39
59_W	69_F	0.561	0.39
303_N	316_L	0.561	0.39
50_K	115_V	0.561	0.39
190_L	302_I	0.561	0.39
119_L	133_S	0.560	0.39
294_Y	326_T	0.559	0.39
174_A	183_F	0.558	0.38
41_H	45_L	0.557	0.38
98_I	144_I	0.557	0.38
167_I	184_K	0.557	0.38
167_I	345_M	0.557	0.38
47_T	81_V	0.554	0.38
65_Q	68_L	0.551	0.38
282_M	296_T	0.548	0.37
108_M	190_L	0.544	0.37
84_Q	91_K	0.542	0.37
37_H	110_Y	0.542	0.37
126_A	137_L	0.541	0.37
285_L	290_L	0.540	0.37
155_L	159_L	0.540	0.37
103_A	147_I	0.539	0.37
43_V	81_V	0.538	0.36
25_I	71_R	0.538	0.36
114_S	223_G	0.537	0.36
53_I	147_I	0.537	0.36
36_V	81_V	0.537	0.36
51_R	55_S	0.537	0.36
262_R	265_R	0.534	0.36
89_L	189_G	0.533	0.36
159_L	245_V	0.533	0.36
177_A	241_T	0.532	0.36
53_I	148_G	0.532	0.36
180_M	184_K	0.531	0.36
294_Y	319_R	0.530	0.36
216_D	250_K	0.530	0.36
179_L	239_I	0.530	0.36
295_L	317_N	0.529	0.36
36_V	80_I	0.528	0.36
182_V	225_T	0.528	0.36
58_L	61_Q	0.527	0.35
207_W	216_D	0.525	0.35
317_N	327_F	0.525	0.35
205_G	219_V	0.524	0.35
199_N	228_K	0.524	0.35
97_D	101_T	0.523	0.35
46_R	144_I	0.521	0.35
289_H	318_L	0.520	0.35
334_Y	338_H	0.518	0.35
208_L	219_V	0.517	0.34
74_F	77_Q	0.517	0.34
21_S	81_V	0.515	0.34
111_A	280_D	0.514	0.34
201_M	247_D	0.514	0.34
59_W	62_I	0.513	0.34
147_I	267_I	0.513	0.34
59_W	196_L	0.512	0.34
28_I	31_L	0.512	0.34
52_A	60_L	0.510	0.34
135_L	139_G	0.510	0.34
24_M	31_L	0.509	0.34
283_Q	300_Q	0.508	0.34
177_A	235_T	0.508	0.34
294_Y	325_G	0.507	0.34
58_L	269_I	0.504	0.33
51_R	78_G	0.503	0.33
253_S	327_F	0.503	0.33
53_I	108_M	0.502	0.33
186_P	200_D	0.502	0.33
88_W	267_I	0.502	0.33
35_V	147_I	0.501	0.33
59_W	129_F	0.500	0.33
275_R	284_R	0.500	0.33

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
5ajiA	3	0.6337	100	0.613	Contact Map
3udcA	3	0.6241	100	0.614	Contact Map
4hw9A	3	0.6096	100	0.62	Contact Map
3mlqE	1	0.0964	63.9	0.963	Contact Map
4l5gA	1	0.3349	46.8	0.967	Contact Map
2lt1A	1	0.1542	30.3	0.97	Contact Map
2lt4A	1	0.1494	25.4	0.971	Contact Map
4kbmB	1	0.3301	20.2	0.972	Contact Map
3udfA	2	0.1012	19.3	0.973	Contact Map
2lwjA	1	0.3422	14.3	0.974	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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