Q980H3 - SULSO - GREMLIN Contacts

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Q980H3 - NADH dehydrogenase subunit D (NuoD)

UniProt:	Q980H3	Sequences: MTSQPQNEIQEQLLAATGMSVEFIPVQGELNVGPQHPGSGHMRIFVKLNGDIIEDVDLDVGYVHRAVEKLSENRNYMHLIPLVERPAILDSIHMNLGYIIAVEKILGVDVPERAQYLRSFAAEVNRIASHLYGLGILAIFLGHSTGFMWGFGDREVWVTILEALTGARVTNSYVIPGGVRKDITQEIKEMTIKAIAYQRKRLEDWKKIFFYNPSIRARLENVGVMSRENAIKWGAVGPNLRASGVYYDVRKIEPYGAYDKLDFEIPVYKEGDGLARGLVRLEEIEQSMRILEQIIKNIPEGNILSDRFFKQIPPIRLKKYWETYRRIVLPGYYASFRPPKGEAISRVEAGRGELAYYVVSDGSPKPYRLRMITPSYRLIYVFKELCKGSRYADLVSIYGSLDYFPPEADR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	410 (361)
Sequences:	4145 (2431)
Seq/√Len:	127.9

ECOLI - NUOCD HYCE HYFG MBHL MBHM
HALSA - Q9HRL9
SULSO - Q980H3 Q97ZA7

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
199_R	292_E	5.084	1.00
286_Q	289_R	4.228	1.00
69_K	72_E	3.987	1.00
270_E	275_A	3.415	1.00
226_S	229_N	3.378	1.00
342_E	359_V	3.282	1.00
361_D	367_Y	3.257	1.00
163_A	190_M	3.199	1.00
196_A	292_E	3.160	1.00
112_E	260_K	3.039	1.00
97_G	347_V	2.988	1.00
203_E	285_E	2.970	1.00
268_Y	275_A	2.921	1.00
105_I	343_A	2.870	1.00
268_Y	282_E	2.866	1.00
86_P	371_M	2.720	1.00
156_V	197_Y	2.716	1.00
120_F	294_I	2.680	1.00
192_I	296_K	2.669	1.00
101_A	358_V	2.537	1.00
225_M	235_A	2.466	1.00
47_K	55_D	2.412	1.00
71_S	79_L	2.338	1.00
385_L	401_L	2.331	1.00
124_V	157_W	2.284	1.00
257_A	261_L	2.275	1.00
117_L	179_V	2.262	1.00
342_E	357_Y	2.258	1.00
99_I	174_V	2.220	1.00
359_V	367_Y	2.211	1.00
282_E	286_Q	2.155	1.00
119_S	257_A	2.150	1.00
271_G	275_A	2.105	1.00
272_D	275_A	2.077	1.00
302_N	306_D	2.070	1.00
79_L	366_P	2.069	1.00
87_A	404_F	2.053	1.00
109_D	115_Q	2.048	1.00
264_E	286_Q	2.034	1.00
216_R	220_E	1.988	1.00
96_L	122_A	1.951	1.00
49_N	54_E	1.940	1.00
104_K	343_A	1.929	1.00
71_S	369_L	1.926	1.00
340_K	361_D	1.917	1.00
111_P	114_A	1.915	1.00
285_E	288_M	1.850	1.00
259_D	265_I	1.813	1.00
358_V	369_L	1.798	1.00
246_Y	251_K	1.780	1.00
46_V	56_V	1.762	1.00
188_K	192_I	1.739	1.00
112_E	116_Y	1.727	1.00
55_D	387_K	1.725	1.00
404_F	407_E	1.723	1.00
303_I	306_D	1.713	1.00
187_I	191_T	1.708	1.00
113_R	182_D	1.706	1.00
260_K	297_N	1.684	1.00
206_K	285_E	1.683	1.00
160_I	191_T	1.657	1.00
248_D	251_K	1.641	1.00
229_N	384_E	1.605	1.00
120_F	291_L	1.604	1.00
344_I	355_A	1.601	1.00
229_N	232_K	1.581	1.00
119_S	261_L	1.519	1.00
384_E	387_K	1.510	1.00
27_Q	47_K	1.509	1.00
103_E	118_R	1.502	1.00
280_R	283_E	1.501	1.00
238_P	241_R	1.500	1.00
110_V	115_Q	1.499	1.00
112_E	115_Q	1.491	1.00
192_I	295_I	1.485	1.00
192_I	292_E	1.479	1.00
205_W	212_N	1.477	1.00
254_P	259_D	1.473	1.00
301_G	306_D	1.472	1.00
196_A	199_R	1.457	1.00
101_A	343_A	1.448	1.00
218_R	223_G	1.442	1.00
193_K	197_Y	1.439	1.00
261_L	294_I	1.431	1.00
199_R	203_E	1.417	1.00
189_E	193_K	1.404	1.00
90_D	93_H	1.403	1.00
256_G	261_L	1.398	1.00
235_A	381_V	1.396	1.00
93_H	122_A	1.387	1.00
204_D	207_K	1.387	1.00
259_D	263_F	1.383	1.00
258_Y	261_L	1.382	1.00
46_V	394_L	1.371	1.00
44_I	56_V	1.367	1.00
156_V	159_T	1.356	1.00
356_Y	371_M	1.336	1.00
210_F	277_G	1.335	1.00
263_F	266_P	1.320	1.00
93_H	350_G	1.317	1.00
254_P	258_Y	1.306	1.00
184_T	187_I	1.305	1.00
216_R	274_L	1.293	1.00
246_Y	252_I	1.293	1.00
257_A	265_I	1.286	1.00
138_A	143_H	1.280	1.00
105_I	360_S	1.276	1.00
261_L	290_I	1.273	1.00
343_A	358_V	1.271	1.00
116_Y	299_P	1.262	1.00
199_R	288_M	1.262	1.00
97_G	356_Y	1.249	1.00
215_I	218_R	1.242	1.00
94_M	356_Y	1.239	1.00
254_P	261_L	1.231	1.00
275_A	279_V	1.231	1.00
194_A	198_Q	1.230	1.00
100_I	345_S	1.226	1.00
252_I	258_Y	1.224	0.99
228_E	232_K	1.218	0.99
167_A	170_T	1.213	0.99
373_T	407_E	1.210	0.99
247_Y	252_I	1.207	0.99
257_A	260_K	1.205	0.99
93_H	125_N	1.203	0.99
44_I	58_L	1.202	0.99
264_E	289_R	1.199	0.99
254_P	260_K	1.196	0.99
285_E	289_R	1.195	0.99
114_A	179_V	1.181	0.99
238_P	243_S	1.181	0.99
329_L	332_Y	1.180	0.99
329_L	333_Y	1.176	0.99
389_S	397_I	1.172	0.99
240_L	245_V	1.171	0.99
271_G	279_V	1.164	0.99
235_A	239_N	1.158	0.99
272_D	280_R	1.147	0.99
278_L	282_E	1.146	0.99
294_I	297_N	1.139	0.99
79_L	83_V	1.135	0.99
218_R	222_V	1.113	0.99
246_Y	265_I	1.113	0.99
383_K	387_K	1.107	0.99
224_V	227_R	1.102	0.99
127_I	284_I	1.095	0.99
208_I	212_N	1.092	0.99
71_S	83_V	1.088	0.99
190_M	193_K	1.086	0.99
218_R	221_N	1.084	0.99
207_K	211_Y	1.075	0.99
220_E	223_G	1.075	0.99
83_V	95_N	1.073	0.99
222_V	225_M	1.072	0.99
92_I	121_A	1.070	0.99
302_N	307_R	1.063	0.99
249_V	254_P	1.062	0.99
210_F	278_L	1.057	0.99
223_G	397_I	1.054	0.98
275_A	278_L	1.054	0.98
90_D	407_E	1.052	0.98
193_K	196_A	1.052	0.98
237_G	241_R	1.051	0.98
259_D	264_E	1.049	0.98
215_I	219_L	1.048	0.98
403_Y	407_E	1.044	0.98
119_S	294_I	1.035	0.98
373_T	376_Y	1.034	0.98
192_I	196_A	1.034	0.98
275_A	282_E	1.029	0.98
240_L	243_S	1.028	0.98
90_D	404_F	1.022	0.98
231_I	234_G	1.021	0.98
251_K	264_E	1.020	0.98
261_L	265_I	1.015	0.98
257_A	266_P	1.005	0.98
272_D	284_I	1.005	0.98
121_A	164_L	1.004	0.98
110_V	114_A	0.998	0.98
125_N	171_N	0.997	0.98
45_F	57_D	0.996	0.98
121_A	173_Y	0.995	0.98
282_E	285_E	0.993	0.98
286_Q	290_I	0.993	0.98
272_D	283_E	0.985	0.98
234_G	237_G	0.985	0.98
87_A	407_E	0.974	0.97
87_A	90_D	0.973	0.97
227_R	245_V	0.971	0.97
87_A	351_R	0.967	0.97
242_A	279_V	0.966	0.97
195_I	288_M	0.963	0.97
257_A	263_F	0.960	0.97
74_R	78_H	0.959	0.97
262_D	265_I	0.955	0.97
263_F	267_V	0.955	0.97
251_K	265_I	0.954	0.97
273_G	280_R	0.953	0.97
302_N	305_S	0.946	0.97
115_Q	256_G	0.944	0.97
128_A	132_Y	0.944	0.97
265_I	270_E	0.942	0.97
76_Y	360_S	0.939	0.97
249_V	255_Y	0.937	0.97
115_Q	119_S	0.926	0.97
204_D	208_I	0.925	0.97
72_E	368_R	0.925	0.97
116_Y	297_N	0.923	0.97
99_I	176_P	0.918	0.96
225_M	229_N	0.915	0.96
265_I	268_Y	0.914	0.96
96_L	100_I	0.914	0.96
301_G	304_L	0.910	0.96
53_I	394_L	0.898	0.96
56_V	386_C	0.895	0.96
205_W	217_A	0.894	0.96
263_F	269_K	0.893	0.96
292_E	296_K	0.893	0.96
116_Y	257_A	0.886	0.96
271_G	280_R	0.882	0.95
135_G	150_G	0.880	0.95
116_Y	260_K	0.879	0.95
272_D	279_V	0.875	0.95
356_Y	369_L	0.874	0.95
250_R	255_Y	0.871	0.95
188_K	298_I	0.871	0.95
251_K	254_P	0.869	0.95
349_A	354_L	0.868	0.95
195_I	199_R	0.867	0.95
188_K	295_I	0.867	0.95
256_G	259_D	0.863	0.95
197_Y	201_R	0.862	0.95
260_K	263_F	0.861	0.95
261_L	266_P	0.860	0.95
271_G	274_L	0.859	0.95
262_D	266_P	0.855	0.95
230_A	240_L	0.853	0.95
244_G	250_R	0.851	0.95
153_D	205_W	0.850	0.94
359_V	368_R	0.850	0.94
258_Y	263_F	0.849	0.94
116_Y	261_L	0.848	0.94
238_P	242_A	0.844	0.94
398_Y	403_Y	0.839	0.94
259_D	262_D	0.839	0.94
55_D	379_I	0.838	0.94
97_G	345_S	0.837	0.94
255_Y	259_D	0.834	0.94
261_L	264_E	0.834	0.94
281_L	285_E	0.833	0.94
346_R	353_E	0.831	0.94
127_I	131_L	0.830	0.94
186_E	189_E	0.830	0.94
200_K	203_E	0.830	0.94
86_P	356_Y	0.829	0.94
202_L	284_I	0.828	0.94
100_I	115_Q	0.825	0.94
258_Y	264_E	0.821	0.93
253_E	257_A	0.816	0.93
206_K	209_F	0.816	0.93
209_F	212_N	0.815	0.93
218_R	225_M	0.811	0.93
84_E	95_N	0.803	0.93
221_N	225_M	0.803	0.93
233_W	236_V	0.797	0.92
122_A	347_V	0.797	0.92
251_K	255_Y	0.795	0.92
139_I	144_S	0.795	0.92
205_W	208_I	0.794	0.92
244_G	249_V	0.791	0.92
277_G	281_L	0.791	0.92
351_R	402_D	0.789	0.92
257_A	264_E	0.788	0.92
252_I	261_L	0.786	0.92
255_Y	260_K	0.785	0.92
153_D	198_Q	0.785	0.92
304_L	307_R	0.784	0.92
35_Q	38_G	0.780	0.92
199_R	285_E	0.777	0.91
272_D	277_G	0.770	0.91
71_S	366_P	0.768	0.91
296_K	300_E	0.767	0.91
399_G	403_Y	0.764	0.91
52_I	390_R	0.763	0.91
222_V	226_S	0.761	0.91
263_F	293_Q	0.758	0.90
273_G	284_I	0.757	0.90
90_D	94_M	0.752	0.90
253_E	259_D	0.751	0.90
133_G	402_D	0.747	0.90
294_I	298_I	0.745	0.90
84_E	172_S	0.745	0.90
89_L	402_D	0.743	0.89
274_L	278_L	0.742	0.89
290_I	294_I	0.741	0.89
65_R	406_P	0.739	0.89
279_V	282_E	0.738	0.89
119_S	256_G	0.738	0.89
106_L	338_P	0.736	0.89
339_P	362_G	0.736	0.89
160_I	194_A	0.735	0.89
77_M	176_P	0.733	0.89
375_S	378_L	0.733	0.89
262_D	293_Q	0.731	0.89
351_R	403_Y	0.730	0.89
351_R	404_F	0.728	0.88
255_Y	266_P	0.727	0.88
297_N	300_E	0.725	0.88
90_D	402_D	0.725	0.88
273_G	277_G	0.724	0.88
263_F	268_Y	0.724	0.88
140_F	402_D	0.724	0.88
117_L	183_I	0.723	0.88
266_P	269_K	0.723	0.88
256_G	260_K	0.719	0.88
206_K	281_L	0.718	0.88
252_I	260_K	0.717	0.88
225_M	228_E	0.717	0.88
27_Q	49_N	0.714	0.88
255_Y	258_Y	0.707	0.87
303_I	307_R	0.705	0.87
291_L	295_I	0.704	0.87
227_R	231_I	0.702	0.87
330_P	333_Y	0.702	0.87
259_D	266_P	0.702	0.87
67_V	70_L	0.701	0.87
254_P	257_A	0.696	0.86
271_G	278_L	0.695	0.86
279_V	289_R	0.694	0.86
247_Y	256_G	0.692	0.86
129_S	132_Y	0.689	0.86
254_P	263_F	0.688	0.86
255_Y	265_I	0.686	0.85
284_I	287_S	0.686	0.85
239_N	401_L	0.685	0.85
206_K	210_F	0.684	0.85
250_R	254_P	0.684	0.85
282_E	289_R	0.683	0.85
137_L	399_G	0.683	0.85
266_P	282_E	0.682	0.85
204_D	212_N	0.680	0.85
386_C	397_I	0.679	0.85
38_G	42_M	0.679	0.85
149_W	152_G	0.677	0.85
370_R	373_T	0.675	0.84
258_Y	266_P	0.675	0.84
402_D	407_E	0.674	0.84
107_G	110_V	0.672	0.84
354_L	374_P	0.672	0.84
275_A	285_E	0.672	0.84
244_G	248_D	0.668	0.84
375_S	407_E	0.666	0.84
87_A	402_D	0.665	0.84
237_G	243_S	0.665	0.84
253_E	256_G	0.664	0.83
125_N	129_S	0.664	0.83
100_I	104_K	0.664	0.83
137_L	141_L	0.664	0.83
279_V	285_E	0.662	0.83
27_Q	54_E	0.661	0.83
105_I	341_G	0.658	0.83
234_G	238_P	0.658	0.83
123_E	126_R	0.657	0.83
94_M	97_G	0.656	0.83
129_S	351_R	0.655	0.83
275_A	286_Q	0.655	0.83
248_D	254_P	0.655	0.83
256_G	265_I	0.654	0.83
295_I	298_I	0.653	0.82
266_P	270_E	0.651	0.82
360_S	366_P	0.650	0.82
224_V	228_E	0.649	0.82
32_V	395_V	0.646	0.82
90_D	129_S	0.646	0.82
199_R	289_R	0.644	0.82
185_Q	188_K	0.644	0.82
264_E	267_V	0.643	0.81
219_L	273_G	0.642	0.81
337_R	341_G	0.641	0.81
234_G	241_R	0.640	0.81
166_G	348_E	0.640	0.81
334_A	337_R	0.639	0.81
275_A	281_L	0.637	0.81
128_A	157_W	0.636	0.81
53_I	389_S	0.635	0.81
301_G	305_S	0.633	0.80
80_I	99_I	0.633	0.80
51_D	218_R	0.633	0.80
258_Y	262_D	0.633	0.80
129_S	402_D	0.632	0.80
346_R	355_A	0.630	0.80
89_L	132_Y	0.628	0.80
247_Y	253_E	0.626	0.80
223_G	226_S	0.625	0.80
246_Y	250_R	0.624	0.80
250_R	258_Y	0.624	0.80
91_S	169_V	0.622	0.79
55_D	383_K	0.622	0.79
141_L	396_S	0.622	0.79
248_D	255_Y	0.621	0.79
190_M	194_A	0.619	0.79
138_A	146_G	0.619	0.79
226_S	230_A	0.618	0.79
381_V	385_L	0.618	0.79
221_N	224_V	0.615	0.79
221_N	226_S	0.615	0.79
391_Y	394_L	0.615	0.79
244_G	247_Y	0.614	0.78
104_K	345_S	0.613	0.78
89_L	404_F	0.613	0.78
301_G	307_R	0.612	0.78
273_G	396_S	0.612	0.78
128_A	158_V	0.611	0.78
244_G	252_I	0.610	0.78
213_P	218_R	0.609	0.78
236_V	241_R	0.609	0.78
218_R	237_G	0.609	0.78
244_G	255_Y	0.606	0.78
247_Y	254_P	0.603	0.77
92_I	165_T	0.601	0.77
64_H	69_K	0.597	0.76
252_I	259_D	0.596	0.76
231_I	236_V	0.596	0.76
128_A	161_L	0.595	0.76
254_P	265_I	0.595	0.76
253_E	258_Y	0.595	0.76
186_E	190_M	0.593	0.76
300_E	305_S	0.593	0.76
47_K	57_D	0.592	0.76
245_V	250_R	0.591	0.76
175_I	180_R	0.590	0.76
130_H	283_E	0.590	0.76
253_E	261_L	0.588	0.75
224_V	229_N	0.587	0.75
232_K	237_G	0.586	0.75
156_V	194_A	0.585	0.75
163_A	187_I	0.584	0.75
93_H	347_V	0.584	0.75
144_S	148_M	0.582	0.75
245_V	248_D	0.582	0.75
154_R	158_V	0.582	0.75
261_L	270_E	0.580	0.74
235_A	240_L	0.579	0.74
228_E	231_I	0.579	0.74
41_H	404_F	0.578	0.74
89_L	407_E	0.578	0.74
118_R	177_G	0.577	0.74
378_L	403_Y	0.575	0.74
330_P	334_A	0.573	0.74
290_I	293_Q	0.573	0.74
206_K	212_N	0.571	0.73
101_A	345_S	0.571	0.73
273_G	281_L	0.570	0.73
184_T	189_E	0.569	0.73
32_V	53_I	0.569	0.73
152_G	197_Y	0.569	0.73
264_E	269_K	0.569	0.73
165_T	170_T	0.569	0.73
89_L	125_N	0.568	0.73
241_R	244_G	0.567	0.73
121_A	179_V	0.567	0.73
288_M	292_E	0.566	0.73
283_E	287_S	0.566	0.73
81_P	172_S	0.565	0.72
92_I	125_N	0.563	0.72
281_L	289_R	0.563	0.72
229_N	233_W	0.562	0.72
271_G	283_E	0.562	0.72
134_L	205_W	0.560	0.72
114_A	118_R	0.558	0.72
90_D	350_G	0.554	0.71
398_Y	405_P	0.551	0.71
239_N	243_S	0.551	0.71
298_I	302_N	0.551	0.71
253_E	346_R	0.551	0.71
197_Y	200_K	0.550	0.70
120_F	227_R	0.550	0.70
160_I	187_I	0.549	0.70
234_G	240_L	0.548	0.70
200_K	204_D	0.548	0.70
253_E	265_I	0.546	0.70
264_E	268_Y	0.546	0.70
207_K	210_F	0.546	0.70
255_Y	263_F	0.546	0.70
195_I	292_E	0.546	0.70
337_R	340_K	0.544	0.70
44_I	394_L	0.544	0.70
208_I	214_S	0.544	0.70
41_H	87_A	0.544	0.70
295_I	299_P	0.543	0.70
271_G	285_E	0.542	0.69
259_D	268_Y	0.541	0.69
239_N	242_A	0.540	0.69
93_H	349_A	0.540	0.69
84_E	167_A	0.539	0.69
273_G	397_I	0.539	0.69
98_Y	369_L	0.538	0.69
272_D	281_L	0.538	0.69
32_V	39_S	0.537	0.69
100_I	256_G	0.537	0.69
231_I	245_V	0.533	0.68
30_L	48_L	0.532	0.68
32_V	394_L	0.532	0.68
259_D	269_K	0.531	0.68
32_V	46_V	0.531	0.68
198_Q	202_L	0.530	0.68
279_V	286_Q	0.529	0.68
158_V	168_R	0.528	0.67
230_A	233_W	0.527	0.67
275_A	280_R	0.526	0.67
256_G	263_F	0.524	0.67
79_L	98_Y	0.523	0.67
249_V	253_E	0.523	0.67
402_D	405_P	0.521	0.66
153_D	201_R	0.520	0.66
213_P	217_A	0.520	0.66
329_L	335_S	0.520	0.66
291_L	294_I	0.520	0.66
247_Y	250_R	0.518	0.66
74_R	79_L	0.517	0.66
212_N	218_R	0.516	0.66
230_A	243_S	0.516	0.66
196_A	288_M	0.515	0.65
260_K	264_E	0.515	0.65
95_N	170_T	0.514	0.65
283_E	289_R	0.514	0.65
366_P	369_L	0.513	0.65
192_I	195_I	0.511	0.65
244_G	258_Y	0.508	0.64
232_K	235_A	0.507	0.64
129_S	350_G	0.507	0.64
29_E	47_K	0.507	0.64
90_D	403_Y	0.506	0.64
385_L	397_I	0.506	0.64
121_A	171_N	0.505	0.64
278_L	281_L	0.504	0.64
45_F	59_D	0.504	0.64
102_V	358_V	0.504	0.64
220_E	274_L	0.503	0.64
262_D	269_K	0.501	0.63
225_M	230_A	0.501	0.63
341_G	360_S	0.500	0.63

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
3i9v4	1	0.9098	100	0.125	Contact Map
4kn9L	2	0.9073	100	0.241	Contact Map
4uqlQ	1	0.9439	100	0.243	Contact Map
4u9hL	1	0.9317	100	0.248	Contact Map
1e3dB	1	0.9463	100	0.253	Contact Map
3ze9B	1	0.9317	100	0.258	Contact Map
1yq9H	1	0.9293	100	0.262	Contact Map
4omfA	1	0.9146	100	0.264	Contact Map
4ue3L	2	0.961	100	0.27	Contact Map
3myrB	2	0.9317	100	0.277	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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